@article {pmid31637799, year = {2019}, author = {Dedysh, SN and Henke, P and Ivanova, AA and Kulichevskaya, IS and Philippov, DA and Meier-Kolthoff, JP and Göker, M and Huang, S and Overmann, J}, title = {100-year-old enigma solved: identification, genomic characterization and biogeography of the yet uncultured Planctomyces bekefii.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14838}, pmid = {31637799}, issn = {1462-2920}, abstract = {The first representative of the phylum Planctomycetes, Planctomyces bekefii, was described nearly one century ago. This morphologically conspicuous freshwater bacterium is a rare example of as-yet-uncultivated prokaryotes with validly published names and unknown identity. We report the results of molecular identification of this elusive bacterium, which was detected in an eutrophic boreal lake in Northern Russia. By using high-performance cell sorting, P. bekefii-like cell rosettes were selectively enriched from lake water. The retrieved 16S rRNA gene sequence was nearly identical to those in dozens of metagenomes assembled from freshwater lakes during cyanobacterial blooms and was phylogenetically placed within a large group of environmental sequences originating from various freshwater habitats worldwide. In contrast, 16S rRNA gene sequence similarity to all currently described members of the order Planctomycetales was only 83-92%. The metagenome assembled for P. bekefii reached 43% genome coverage and showed the potential for degradation of peptides, pectins, and sulfated polysaccharides. Tracing the seasonal dynamics of P. bekefii by Illumina paired-end sequencing of 16S rRNA gene fragments and by fluorescence in situ hybridization revealed that these bacteria only transiently surpass the detection limit, with a characteristic population peak of up to 104 cells ml-1 following cyanobacterial blooms. This article is protected by copyright. All rights reserved.}, }
@article {pmid31637492, year = {2019}, author = {Zhu, X and Wang, J and De Belie, N and Boon, N}, title = {Complementing urea hydrolysis and nitrate reduction for improved microbially induced calcium carbonate precipitation.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-019-10128-2}, pmid = {31637492}, issn = {1432-0614}, support = {File No. 201706140108//Distinguished International Students Scholarship/ ; reference code: 01SC4918//Universiteit Gent/ ; }, abstract = {Microbial-induced CaCO3 precipitation has been widely applied in bacterial-based self-healing concrete. However, the limited biogenetic CaCO3 production by bacteria after they were introduced into the incompatible concrete matrix is a major challenge of this technology. In the present study, the potential of combining two metabolic pathways, urea hydrolysis and nitrate reduction, simultaneously in one bacteria strain for improving the bacterial CaCO3 yield has been investigated. One bacterial strain, Ralstonia eutropha H16, which has the highest Ca2+ tolerance and is capable of performing both urea hydrolysis and nitrate reduction in combined media was selected among three bacterial candidates based on the enzymatic examinations. Results showed that H16 does not need oxygen for urea hydrolysis and urease activity was determined primarily by cell concentration. However, the additional urea in the combined medium slowed down the nitrate reduction rate to 7 days until full NO3- decomposition. Moreover, the nitrate reduction of H16 was significantly restricted by an increased Ca2+ ion concentration in the media. Nevertheless, the overall CaCO3 precipitation yield can be improved by 20 to 30% after optimization through the combination of two metabolic pathways. The highest total CaCO3 precipitation yield achieved in an orthogonal experiment was 14 g/L. It can be concluded that Ralstonia eutropha H16 is a suitable bacterium for simultaneous activation of urea hydrolysis and nitrate reduction for improving the CaCO3 precipitation and it can be studied later, on activation of multiple metabolic pathways in bacteria-based self-healing concrete.}, }
@article {pmid31637468, year = {2019}, author = {de Roos, B and Aura, AM and Bronze, M and Cassidy, A and Conesa, MG and Gibney, ER and Greyling, A and Kaput, J and Kerem, Z and Knežević, N and Kroon, P and Landberg, R and Manach, C and Milenkovic, D and Rodriguez-Mateos, A and Tomás-Barberán, FA and van de Wiele, T and Morand, C}, title = {Targeting the delivery of dietary plant bioactives to those who would benefit most: from science to practical applications.}, journal = {European journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00394-019-02075-5}, pmid = {31637468}, issn = {1436-6215}, support = {FA 1403//European Cooperation in Science and Technology/ ; }, abstract = {BACKGROUND: A healthy diet and optimal lifestyle choices are amongst the most important actions for the prevention of cardiometabolic diseases. Despite this, it appears difficult to convince consumers to select more nutritious foods. Furthermore, the development and production of healthier foods do not always lead to economic profits for the agro-food sector. Most dietary recommendations for the general population represent a &quot;one-size-fits-all approach&quot; which does not necessarily ensure that everyone has adequate exposure to health-promoting constituents of foods. Indeed, we now know that individuals show a high variability in responses when exposed to specific nutrients, foods, or diets.<br><br>PURPOSE: This review aims to highlight our current understanding of inter-individual variability in response to dietary bioactives, based on the integration of findings of the COST Action POSITIVe. We also evaluate opportunities for translation of scientific knowledge on inter-individual variability in response to dietary bioactives, once it becomes available, into practical applications for stakeholders, such as the agro-food industry. The potential impact from such applications will form an important impetus for the food industry to develop and market new high quality and healthy foods for specific groups of consumers in the future. This may contribute to a decrease in the burden of diet-related chronic diseases.}, }
@article {pmid31635887, year = {2019}, author = {Čanković, M and Žučko, J and Radić, ID and Janeković, I and Petrić, I and Ciglenečki, I and Collins, G}, title = {Microbial diversity and long-term geochemical trends in the euxinic zone of a marine, meromictic lake.}, journal = {Systematic and applied microbiology}, volume = {}, number = {}, pages = {126016}, doi = {10.1016/j.syapm.2019.126016}, pmid = {31635887}, issn = {1618-0984}, abstract = {Hypoxic and anoxic niches of meromictic lakes are important sites for studying the microbial ecology of conditions resembling ancient Earth. The expansion and increasing global distribution of such environments also means that information about them serves to understand future phenomena. In this study, a long-term chemical dataset (1996-2015) was explored together with seasonal (in 2015) information on the diversity and abundance of bacterial and archaeal communities residing in the chemocline, monimolimnion and surface sediment of the marine meromictic Rogoznica Lake. The results of quantitative PCR assays, and high-throughput sequencing, targeting 16S rRNA genes and transcripts, revealed a clear vertical structure of the microbial community with Gammaproteobacteria (Halochromatium) and cyanobacteria (Synechococcus spp.) dominating the chemocline, Deltaproteobacteria and Bacteroidetes dominating the monimolimnion, and significantly more abundant archaeal populations in the surface sediment, most of which affiliated to Nanoarchaeota. Seasonal changes in the community structure and abundance were not pronounced. Diversity in Rogoznica Lake was found to be high, presumably as a consequence of stable environmental conditions accompanied by high dissolved carbon and nutrient concentrations. Long-term data indicated that Rogoznica Lake exhibited climate changes that could alter its physico-chemical features and, consequently, induce structural and physiological changes within its microbial community.}, }
@article {pmid31633390, year = {2019}, author = {Baker, JL and He, X and Shi, W}, title = {Precision Reengineering of the Oral Microbiome for Caries Management.}, journal = {Advances in dental research}, volume = {30}, number = {2}, pages = {34-39}, doi = {10.1177/0022034519877386}, pmid = {31633390}, issn = {1544-0737}, abstract = {Technological advancements have revolutionized our understanding of the complexity and importance of the human microbiome. This progress has also emphasized the need for precision therapeutics, as it has underscored the dilemmas, such as dysbiosis and increasing antibiotic resistance, associated with current, broad-spectrum treatment modalities. Dental caries remains the most common chronic disease worldwide, accompanied by a tremendous financial and social burden, despite widespread and efficacious fluoride and hygienic regimens. Over the past several decades, various precision approaches to combat dental caries, including vaccines, probiotics, and antimicrobial compounds, have been pursued. Despite the distinct overall conceptual strengths of each approach, for various reasons, there are currently no approved precision antibiotic therapeutics to prevent dental caries. Specifically targeted antimicrobial peptides (STAMPs) are synthetic molecules that combine the antibiotic moiety of a traditional antimicrobial peptide with a targeting domain to provide specificity against a particular organism. Conjoining the killing domain from the antimicrobial, novispirin G10, and a targeting domain derived from the Streptococcus mutans pheromone, CSP, the STAMP C16G2 was designed to provide targeted killing of S. mutans, widely considered the keystone species in dental caries pathogenesis. C16G2 was able to selectively eliminate S. mutans from complex ecosystems while leaving closely related, yet health-associated, oral species unharmed. This remodeling of the dental plaque community is expected to have significant advantages compared to conventional broad-spectrum mouthwashes, as the intact, surviving community is apt to prevent reinfection by pathogens. Following successful phase I clinical trials that evaluated the safety and basic microbiology of C16G2 treatments, the phase II trials of several C16G2 formulations are currently in progress. C16G2 represents an exciting advance in precision therapeutics, and the STAMP platform provides vast opportunities for both the development of additional therapeutics and the overall study of microbial ecology.}, }
@article {pmid31633060, year = {2019}, author = {Krych, Ł and Castro-Mejía, JL and Forero-Junco, LM and Moesby, DN and Mikkelsen, MB and Rasmussen, MA and Sykulski, M and Nielsen, DS}, title = {DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {369}, doi = {10.1038/s42003-019-0617-x}, pmid = {31633060}, issn = {2399-3642}, abstract = {Despite the massive developments within culture-independent methods for detection of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. Yet, the problem of rapid, accurate and inexpensive identification of bacterial isolates down to species/strain level remains unresolved. We have developed a new method for bacterial DNA enrichment and tagmentation allowing fast (<24 h) and cost-effective species level identification and strain level differentiation using the MinION portable sequencing platform (ON-rep-seq). DNA library preparation for 96 isolates takes less than 5 h and ensures highly reproducible distribution of reads that can be used to generate strain level specific read length counts profiles (LCp). We have developed a pipeline that by correcting reads error within peaks of LCp generates a set of high quality (>99%) consensus reads. Whereas, the information from high quality reads is used to retrieve species level taxonomy, comparison of LCp allows for strain level differentiation.}, }
@article {pmid31632370, year = {2019}, author = {Mendes, LW and de Chaves, MG and Fonseca, MC and Mendes, R and Raaijmakers, JM and Tsai, SM}, title = {Resistance Breeding of Common Bean Shapes the Physiology of the Rhizosphere Microbiome.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2252}, doi = {10.3389/fmicb.2019.02252}, pmid = {31632370}, issn = {1664-302X}, abstract = {The taxonomically diverse rhizosphere microbiome contributes to plant nutrition, growth and health, including protection against soil-borne pathogens. We previously showed that breeding for Fusarium-resistance in common bean changed the rhizosphere microbiome composition and functioning. Here, we assessed the impact of Fusarium-resistance breeding in common bean on microbiome physiology. Combined with metatranscriptome data, community-level physiological profiling by Biolog EcoPlate analyses revealed that the rhizosphere microbiome of the Fusarium-resistant accession was distinctly different from that of the Fusarium-susceptible accession, with higher consumption of amino acids and amines, higher metabolism of xylanase and sialidase, and higher expression of genes associated with nitrogen, phosphorus and iron metabolism. The resistome analysis indicates higher expression of soxR, which is involved in protecting bacteria against oxidative stress induced by a pathogen invasion. These results further support our hypothesis that breeding for resistance has unintentionally shaped the assembly and activity of the rhizobacterial community toward a higher abundance of specific rhizosphere competent bacterial taxa that can provide complementary protection against fungal root infections.}, }
@article {pmid31630686, year = {2019}, author = {Kavagutti, VS and Andrei, AŞ and Mehrshad, M and Salcher, MM and Ghai, R}, title = {Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {135}, doi = {10.1186/s40168-019-0752-0}, pmid = {31630686}, issn = {2049-2618}, support = {17-04828S//Grantová Agentura České Republiky/ ; 17-04828S//Grantová Agentura České Republiky/ ; 17-04828S//Grantová Agentura České Republiky/ ; GAJU 158/2016/P//The Grant Agency of the Faculty of Science, University of South Bohemia/ ; MSM200961801//Akademie Věd České Republiky/ ; L200961651//Akademie Věd České Republiky/ ; CZ.02.1.01/0.0/0.0/16_025/0007417//ERDF/ESF/ ; }, abstract = {The persistent inertia in the ability to culture environmentally abundant microbes from aquatic ecosystems represents an obstacle in disentangling the complex web of ecological interactions spun by a diverse assortment of participants (pro- and eukaryotes and their viruses). In aquatic microbial communities, the numerically most abundant actors, the viruses, remain the most elusive, and especially in freshwaters their identities and ecology remain unknown. Here, using ultra-deep metagenomic sequencing from pelagic freshwater habitats, we recovered complete genomes of > 2000 phages, including small &quot;miniphages&quot; and large &quot;megaphages&quot; infecting iconic freshwater prokaryotic lineages. For instance, abundant freshwater Actinobacteria support infection by a very broad size range of phages (13-200 Kb). We describe many phages encoding genes that likely afford protection to their host from reactive oxygen species (ROS) in the aquatic environment and in the oxidative burst in protist phagolysosomes (phage-mediated ROS defense). Spatiotemporal abundance analyses of phage genomes revealed evanescence as the primary dynamic in upper water layers, where they displayed short-lived existences. In contrast, persistence was characteristic for the deeper layers where many identical phage genomes were recovered repeatedly. Phage and host abundances corresponded closely, with distinct populations displaying preferential distributions in different seasons and depths, closely mimicking overall stratification and mixis.}, }
@article {pmid31589437, year = {2019}, author = {Syrpas, M and Bukauskaitė, J and Ramanauskienė, K and Karosienė, JR and Majienė, D and Bašinskienė, L and Venskutonis, PR}, title = {Ultrasound-Assisted Extraction and Assessment of Biological Activity of Phycobiliprotein-Rich Aqueous Extracts from Wild Cyanobacteria (Aphanizomenon flos-aquae).}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.9b05483}, pmid = {31589437}, issn = {1520-5118}, abstract = {Cyanobacteria are photosynthetic microorganisms that are considered as an important source of bioactive metabolites, among which phycobiliproteins (PBPs) are a class of water-soluble macromolecules of cyanobacteria with a wide range of applications. Massive proliferation of cyanobacteria can lead to excessive surface water blooms, of which removal, as a management measure, should be prioritized. In this study, the utilization of wild cyanobacteria biomass (Aphanizomenon flos-aquae) for extraction of phycobiliproteins is reported. Extraction of phycobiliproteins by conventional methods, such as homogenization, freeze-thaw cycles, and solid-liquid extraction, were optimized prior to ultrasound-assisted extraction. Standardization of ultrasonication for different parameters, such as ultrasonication amplitude (38, 114, and 190 μm) and ultrasonication time (1, 5.5, and 10 min), was carried out using a central composite design and response surface methodology for each of the primary techniques. A substantial increase on the individual and total phycobiliprotein yields was observed after ultrasonic treatment. The highest total PBP yield (115.37 mg/g of dry weight) was observed with samples treated with a homogenizer (30 min, 30 °C, and 1 cycle) combined with ultrasound treatment (8.7 min at 179 μm). Moreover, in vitro antioxidant capacity was observed for the obtained extracts in the Folin-Ciocalteu and ABTS* + assays. In addition, a cytotoxic effect against C6 glioma cells was observed for A. flos-aquae PBPs. Conclusively, wild cyanobacteria could be considered as an alternative feedstock for recovery of PBPs.}, }
@article {pmid31518408, year = {2019}, author = {Bugge Harder, C and Nyrop Albers, C and Rosendahl, S and Aamand, J and Ellegaard-Jensen, L and Ekelund, F}, title = {Successional trophic complexity and biogeographical structure of eukaryotic communities in waterworks' rapid sand filters.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {11}, pages = {}, doi = {10.1093/femsec/fiz148}, pmid = {31518408}, issn = {1574-6941}, abstract = {As groundwater-fed waterworks clean their raw inlet water with sand filters, a variety of pro- and eukaryotic microbial communities develop on these filters. While several studies have targeted the prokaryotic sand filter communities, little is known about the eukaryotic communities, despite the obvious need for knowledge of microorganisms that get in contact with human drinking water. With a new general eukaryotic primer set (18S, V1-V3 region), we performed FLX-454 sequencing of material from 21 waterworks' sand filters varying in age (3-40 years) and geographical location on a 250 km east-west axis in Denmark, and put the data in context of their previously published prokaryotic communities. We find that filters vary highly in trophic complexity depending on age, from simple systems with bacteria and protozoa (3-6 years) to complex, mature systems with nematodes, rotifers and turbellarians as apex predators (40 years). Unlike the bacterial communities, the eukaryotic communities display a clear distance-decay relationship that predominates over environmental variations, indicating that the underlying aquifers feeding the filters harbor distinct eukaryotic communities with limited dispersal in between. Our findings have implications for waterworks' filter management, and offer a window down to the largely unexplored eukaryotic microbiology of groundwater aquifers.}, }
@article {pmid31624348, year = {2019}, author = {Gwak, JH and Jung, MY and Hong, H and Kim, JG and Quan, ZX and Reinfelder, JR and Spasov, E and Neufeld, JD and Wagner, M and Rhee, SK}, title = {Archaeal nitrification is constrained by copper complexation with organic matter in municipal wastewater treatment plants.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0538-1}, pmid = {31624348}, issn = {1751-7370}, support = {NRF-2015R1A4A1041869//National Research Foundation of Korea (NRF)/ ; NRF-2015M3D3A1A01064881//National Research Foundation of Korea (NRF)/ ; }, abstract = {Consistent with the observation that ammonia-oxidizing bacteria (AOB) outnumber ammonia-oxidizing archaea (AOA) in many eutrophic ecosystems globally, AOB typically dominate activated sludge aeration basins from municipal wastewater treatment plants (WWTPs). In this study, we demonstrate that the growth of AOA strains inoculated into sterile-filtered wastewater was inhibited significantly, in contrast to uninhibited growth of a reference AOB strain. In order to identify possible mechanisms underlying AOA-specific inhibition, we show that complex mixtures of organic compounds, such as yeast extract, were highly inhibitory to all AOA strains but not to the AOB strain. By testing individual organic compounds, we reveal strong inhibitory effects of organic compounds with high metal complexation potentials implying that the inhibitory mechanism for AOA can be explained by the reduced bioavailability of an essential metal. Our results further demonstrate that the inhibitory effect on AOA can be alleviated by copper supplementation, which we observed for pure AOA cultures in a defined medium and for AOA inoculated into nitrifying sludge. Our study offers a novel mechanistic explanation for the relatively low abundance of AOA in most WWTPs and provides a basis for modulating the composition of nitrifying communities in both engineered systems and naturally occurring environments.}, }
@article {pmid31624166, year = {2019}, author = {Schultz, J and Kallies, R and Nunes da Rocha, U and Rosado, AS}, title = {Draft Genome Sequence of Geobacillus sp. Strain LEMMJ02, a Thermophile Isolated from Deception Island, an Active Volcano in Antarctica.}, journal = {Microbiology resource announcements}, volume = {8}, number = {42}, pages = {}, doi = {10.1128/MRA.00920-19}, pmid = {31624166}, issn = {2576-098X}, abstract = {The thermophilic Geobacillus sp. strain LEMMJ02 was isolated from Fumarole Bay sediment on Deception Island, an active Antarctic volcano. Here, we report the draft genome of LEMMJ02, which consists of 3,160,938 bp with 52.8% GC content and 3,523 protein-coding genes.}, }
@article {pmid31623889, year = {2019}, author = {Christiaens, MER and De Paepe, J and Ilgrande, C and De Vrieze, J and Barys, J and Teirlinck, P and Meerbergen, K and Lievens, B and Boon, N and Clauwaert, P and Vlaeminck, SE}, title = {Urine nitrification with a synthetic microbial community.}, journal = {Systematic and applied microbiology}, volume = {}, number = {}, pages = {126021}, doi = {10.1016/j.syapm.2019.126021}, pmid = {31623889}, issn = {1618-0984}, abstract = {During long-term extra-terrestrial missions, food is limited and waste is generated. By recycling valuable nutrients from this waste via regenerative life support systems, food can be produced in space. Astronauts' urine can, for instance, be nitrified by micro-organisms into a liquid nitrate fertilizer for plant growth in space. Due to stringent conditions in space, microbial communities need to be be defined (gnotobiotic); therefore, synthetic rather than mixed microbial communities are preferred. For urine nitrification, synthetic communities face challenges, such as from salinity, ureolysis, and organics. In this study, a synthetic microbial community containing an AOB (Nitrosomonas europaea), NOB (Nitrobacter winogradskyi), and three ureolytic heterotrophs (Pseudomonas fluorescens, Acidovorax delafieldii, and Delftia acidovorans) was compiled and evaluated for these challenges. In reactor 1, salt adaptation of the ammonium-fed AOB and NOB co-culture was possible up to 45mScm-1, which resembled undiluted nitrified urine, while maintaining a 44±10mgNH4+-NL-1d-1 removal rate. In reactor 2, the nitrifiers and ureolytic heterotrophs were fed with urine and achieved a 15±6mg NO3--NL-1d-1 production rate for 1% and 10% synthetic and fresh real urine, respectively. Batch activity tests with this community using fresh real urine even reached 29±3mgNL-1d-1. Organics removal in the reactor (69±15%) should be optimized to generate a nitrate fertilizer for future space applications.}, }
@article {pmid31623169, year = {2019}, author = {García-Mantrana, I and Calatayud, M and Romo-Vaquero, M and Espín, JC and Selma, MV and Collado, MC}, title = {Urolithin Metabotypes Can Determine the Modulation of Gut Microbiota in Healthy Individuals by Tracking Walnuts Consumption over Three Days.}, journal = {Nutrients}, volume = {11}, number = {10}, pages = {}, doi = {10.3390/nu11102483}, pmid = {31623169}, issn = {2072-6643}, support = {RTI2018-097982-B-I00//Spanish Ministry of Science, Innovation and Universities (MICINN)/ ; ERC starting grant, n° 639226/ERC_/European Research Council/International ; }, abstract = {Walnuts are rich in polyphenols ellagitannins, modulate gut microbiota (GM), and exert health benefits after long-term consumption. The metabolism of ellagitannins to urolithins via GM depends on urolithin metabotypes (UM-A, -B, or -0), which have been reported to predict host responsiveness to a polyphenol-rich intervention. This study aims to assess whether UMs were associated with differential GM modulation after short-term walnut consumption. In this study, 27 healthy individuals consumed 33 g of peeled raw walnuts over three days. GM profiling was determined using 16S rRNA illumina sequencing and specific real-time quantitative polymerase chain reactions (qPCRs), as well as microbial activity using short-chain fatty acids analysis in stool samples. UMs stratification of volunteers was assessed using ultra performance liquid chromatography-electro spray ionization-quadrupole time of flight-mass spectrometry (UPLC-ESI-QTOF-MS) analysis of urolithins in urine samples. The gut microbiota associated with UM-B was more sensitive to the walnut intervention. Blautia, Bifidobacterium, and members of the Coriobacteriaceae family, including Gordonibacter, increased exclusively in UM-B subjects, while some members of the Lachnospiraceae family decreased in UM-A individuals. Coprococcus and Collinsella increased in both UMs and higher acetate and propionate production resulted after walnuts intake. Our results show that walnuts consumption after only three days modulates GM in a urolithin metabotype-depending manner and increases the production of short-chain fatty acids (SCFA).}, }
@article {pmid31622236, year = {2019}, author = {Cho, GY and Whang, KS}, title = {Aliifodinibius saliphilus sp. nov., a moderately halophilic bacterium isolated from sediment of a crystallizing pond of a saltern.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1099/ijsem.0.003765}, pmid = {31622236}, issn = {1466-5034}, abstract = {Two Gram-stain-negative, moderately halophilic bacteria, designated strains ECH52T and KHM46, were isolated from the sediment of a grey saltern located in Sinui island at Shinan, Korea. The isolates were aerobic, non-motile, short rods and grew at 15-45 °C (optimum, 37 °C), at pH 6.0-10.0 (optimum, pH 8.0) and with 3-25 % (w/v) NaCl (optimum, 10 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains ECH52T and KHM46 belonged to the genus Aliifodinibius in the family Balneolaceae with sequence similarities of 94.3-98.6 % and showed the highest sequence similarity to Aliifodinibius halophilus 2W32T (98.6 %), A. sediminis YIM J21T (94.7%), A. salicampi KHM44T (94.6 %) and A. roseus YIM D15T (94.3 %). The DNA G+C content of the genomic DNA of strain ECH52T was 40.8 mol%. The predominant isoprenoid quinone was menaquinone-7 (MK-7) and the major cellular fatty acids were iso-C17 : 1ω9c, iso-C15 : 0, and C16 : 1ω7c and/or iso-C15 : 0 2-OH. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified glycolipids and four unidentified lipids. Based on the phylogenetic, phenotypic and chemotaxonomic data, strains ECH52T and KHM46 are considered to represent a novel species of the genus Aliifodinibius, for which the name Aliifodinibiussaliphilus sp. nov. is proposed. The type strain is ECH52T (=KACC 19126T=NBRC 112664T).}, }
@article {pmid31444200, year = {2019}, author = {Campa, MF and Techtmann, SM and Ladd, MP and Yan, J and Patterson, M and Garcia de Matos Amaral, A and Carter, KE and Ulrich, N and Grant, CJ and Hettich, RL and Lamendella, R and Hazen, TC}, title = {Surface Water Microbial Community Response to the Biocide 2,2-Dibromo-3-Nitrilopropionamide, Used in Unconventional Oil and Gas Extraction.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {21}, pages = {}, doi = {10.1128/AEM.01336-19}, pmid = {31444200}, issn = {1098-5336}, abstract = {Production of unconventional oil and gas continues to rise, but the effects of high-density hydraulic fracturing (HF) activity near aquatic ecosystems are not fully understood. A commonly used biocide in HF, 2,2-dibromo-3-nitrilopropionamide (DBNPA), was studied in microcosms of HF-impacted (HF+) versus HF-unimpacted (HF-) surface water streams to (i) compare the microbial community response, (ii) investigate DBNPA degradation products based on past HF exposure, and (iii) compare the microbial community response differences and similarities between the HF biocides DBNPA and glutaraldehyde. The microbial community responded to DBNPA differently in HF-impacted versus HF-unimpacted microcosms in terms of the number of 16S rRNA gene copies quantified, alpha and beta diversity, and differential abundance analyses of microbial community composition through time. The differences in microbial community changes affected degradation dynamics. HF-impacted microbial communities were more sensitive to DBNPA, causing the biocide and by-products of the degradation to persist for longer than in HF-unimpacted microcosms. A total of 17 DBNPA by-products were detected, many of them not widely known as DBNPA by-products. Many of the brominated by-products detected that are believed to be uncharacterized may pose environmental and health impacts. Similar taxa were able to tolerate glutaraldehyde and DBNPA; however, DBNPA was not as effective for microbial control, as indicated by a smaller overall decrease of 16S rRNA gene copies/ml after exposure to the biocide, and a more diverse set of taxa was able to tolerate it. These findings suggest that past HF activity in streams can affect the microbial community response to environmental perturbation such as that caused by the biocide DBNPA.IMPORTANCE Unconventional oil and gas activity can affect pH, total organic carbon, and microbial communities in surface water, altering their ability to respond to new environmental and/or anthropogenic perturbations. These findings demonstrate that 2,2-dibromo-3-nitrilopropionamide (DBNPA), a common hydraulic fracturing (HF) biocide, affects microbial communities differently as a consequence of past HF exposure, persisting longer in HF-impacted (HF+) waters. These findings also demonstrate that DBNPA has low efficacy in environmental microbial communities regardless of HF impact. These findings are of interest, as understanding microbial responses is key for formulating remediation strategies in unconventional oil and gas (UOG)-impacted environments. Moreover, some DBNPA degradation by-products are even more toxic and recalcitrant than DBNPA itself, and this work identifies novel brominated degradation by-products formed.}, }
@article {pmid31402530, year = {2019}, author = {Onnis-Hayden, A and Srinivasan, V and Tooker, NB and Li, G and Wang, D and Barnard, JL and Bott, C and Dombrowski, P and Schauer, P and Menniti, A and Shaw, A and Stinson, B and Stevens, G and Dunlap, P and Takács, I and McQuarrie, J and Phillips, H and Lambrecht, A and Analla, H and Russell, A and Gu, AZ}, title = {Survey of full-scale sidestream enhanced biological phosphorus removal (S2EBPR) systems and comparison with conventional EBPRs in North America: Process stability, kinetics, and microbial populations.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {}, number = {}, pages = {}, doi = {10.1002/wer.1198}, pmid = {31402530}, issn = {1554-7531}, support = {U1R13//Water Environment &amp; Reuse Foundation/ ; //Hampton Roads Sanitation District/ ; //Woodard &amp; Curran, Inc./ ; }, abstract = {Sidestream EBPR (S2EBPR) is an emerging alternative process to address common challenges in EBPR related to weak wastewater influent and may improve EBPR process stability. A systematic evaluation and comparison of the process performance and microbial community structure was conducted between conventional and S2EBPR facilities in North America. The statistical analysis suggested higher performance stability in S2EBPR than conventional EBPR, although possible bias associated with other plant-specific factors might have affected the comparison. Variations in stoichiometric values related to EBPR activity and discrepancies between the observed values and current model predictions suggested a varying degree of metabolic versatility of PAOs in S2EBPR systems that warrant further investigation. Microbial community analysis using various techniques suggested comparable known candidate PAO relative abundances in S2EBPR and conventional EBPR systems, whereas the relative abundance of known candidate GAOs seemed to be consistently lower in S2EBPR facilities than conventional EBPR facilities. 16S rRNA gene sequencing analysis revealed differences in the community phylogenetic fingerprints between S2EBPR and conventional facilities and indicated statistically higher microbial diversity index values in S2EBPR facilities than those in conventional EBPRs. PRACTITIONER POINTS: Sidestream EBPR (S2EBPR) can be implemented with varying and flexible configurations, and they offer advantages over conventional configurations for addressing the common challenges in EBPR related to weak wastewater influent and may improve EBPR process stability. Survey of S2EBPR plants in North America suggested statistically more stable phosphorus removal performance in S2EBPR plants than conventional EBPRs, although possible bias might affect the comparison due to other plant-specific factors. The EBPR kinetics and stoichiometry of the S2EBPR facilities seemed to vary and are associated with metabolic versatility of PAOs in S2EBPR systems that warrant further investigation. The abundance of known candidate PAOs in S2EBPR plants was similar to those in conventional EBPRs, and the abundance of known candidate GAOs was generally lower in S2EBPR than conventional EBPR facilities. Further finer-resolution analysis of PAOs and GAOs, as well as identification of other unknown PAOs and GAOs, is needed. Microbial diversity is higher in S2EBPR facilities compared with conventional ones, implying that S2EBPR microbial communities could show better resilience to perturbations due to potential functional redundancy.}, }
@article {pmid31615877, year = {2019}, author = {Deng, J and Auchtung, JM and Konstantinidis, KT and Brettar, I and Höfle, MG and Tiedje, JM}, title = {Genomic Variations Underlying Speciation and Niche Specialization of Shewanella baltica.}, journal = {mSystems}, volume = {4}, number = {5}, pages = {}, doi = {10.1128/mSystems.00560-19}, pmid = {31615877}, issn = {2379-5077}, abstract = {Shewanella baltica was the dominant culturable nitrate-reducing bacterium in the eutrophic and strongly stratified Baltic Sea in the 1980s, where it primarily inhabited the oxic-anoxic transition zone. The genomic structures of 46 of these isolates were investigated through comparative genomic hybridization (CGH), which revealed a gradient of genomic similarity, ranging from 65% to as high as 99%. The core genome of the S. baltica species was enriched in anaerobic respiration-associated genes. Auxiliary genes, most of which locate within a few genomic islands (GIs), were nonuniformly distributed among the isolates. Specifically, hypothetical and mobile genetic element (MGE)-associated genes dominated intraclade gene content differences, whereas gain/loss of functional genes drove gene content differences among less related strains. Among the major S. baltica clades, gene signatures related to specific redox-driven and spatial niches within the water column were identified. For instance, genes involved in anaerobic respiration of sulfur compounds may provide key adaptive advantages for clade A strains in anoxic waters where sulfur-containing electron acceptors are present. Genes involved in cell motility, in particular, a secondary flagellar biosynthesis system, may be associated with the free-living lifestyle by clade E strains. Collectively, this study revealed characteristics of genome variations present in the water column and active speciation of S. baltica strains, driven by niche partitioning and horizontal gene transfer (HGT).IMPORTANCE Speciation in nature is a fundamental process driving the formation of the vast microbial diversity on Earth. In the central Baltic Sea, the long-term stratification of water led to formation of a large-scale vertical redoxcline that provided a gradient of environmental niches with respect to the availability of electron acceptors and donors. The region was home to Shewanella baltica populations, which composed the dominant culturable nitrate-reducing bacteria, particularly in the oxic-anoxic transition zone. Using the collection of S. baltica isolates as a model system, genomic variations showed contrasting gene-sharing patterns within versus among S. baltica clades and revealed genomic signatures of S. baltica clades related to redox niche specialization as well as particle association. This study provides important insights into genomic mechanisms underlying bacterial speciation within this unique natural redoxcline.}, }
@article {pmid31613739, year = {2019}, author = {Dumolin, C and Peeters, C and Ehsani, E and Tahon, G and De Canck, E and Cnockaert, M and Boon, N and Vandamme, P}, title = {Achromobacter veterisilvae sp. nov., from a mixed hydrogen-oxidizing bacteria enrichment reactor for microbial protein production.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1099/ijsem.0.003786}, pmid = {31613739}, issn = {1466-5034}, abstract = {Strain LMG 30378T was isolated from a hydrogen-oxidizing bacteria enrichment reactor inoculated with forest soil. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Achromobacter. Multilocus sequence analysis combined with sequence analysis of a 765 bp nrdA gene fragment both showed Achromobacter agilis LMG 3411T and Achromobacter denitrificans LMG 1231T to be the closest-related neighbours to strain LMG 30378T. Genome sequence analysis revealed a draft genome of 6.81 Mb with a G+C content of 67.2 mol%. In silico DNA-DNA hybridization with A. denitrificans LMG 1231T and A. agilis LMG 3411T showed 42.7 and 42.5% similarity, respectively, confirming that strain LMG 30378T represented a novel Achromobacter species. Phenotypic and metabolic characterization revealed acid phosphatase activity and the absence of phosphoamidase activity as distinctive features. The draft genome composes all necessary metabolic components to fix carbon dioxide and to oxidize molecular hydrogen, suggesting that strain LMG 30378T is a key organism in the enrichment reactor. Together, these data demonstrate that strain LMG 30378T represents a novel species of the genus Achromobacter, for which the name Achromobacter veterisilvae sp. nov. is proposed. The type strain is LMG 30378T (=CCUG 71558T).}, }
@article {pmid31612608, year = {2019}, author = {Seto, M and Iwasa, Y}, title = {The fitness of chemotrophs increases when their catabolic by-products are consumed by other species.}, journal = {Ecology letters}, volume = {}, number = {}, pages = {}, doi = {10.1111/ele.13397}, pmid = {31612608}, issn = {1461-0248}, support = {19K06853//Japan Society for the Promotion of Science Grant-in-Aid for Scientific Research (C)/ ; }, abstract = {Chemotrophic microorganisms synthesise biomass by utilising energy obtained from a set of chemical reactions that convert resources to by-products, forming catabolic interactions. The amount of energy obtained per catabolic reaction decreases with the abundance of the by-product named as the 'abundant resource premium'. Consider two species, Species 1 and 2, Species 1 obtains energy from a reaction that converts resource A to by-product B. Species 2 then utilises B as its resource, extracting energy from a reaction that converts B to C. Thus, the presence of Species 2 reduces the abundance of B, which improves the fitness of Species 1 by increasing the energy acquisition per reaction of A to B. We discuss the population dynamic implication of this effect and its importance in expanding a realised niche, boosting material flow through the ecosystem and providing mutualistic interactions among species linked by the material flow. Introducing thermodynamics into population ecology could offer us fundamental ecological insights into understanding the ecology of chemotrophic microorganisms dominating the subsurface realm.}, }
@article {pmid31612601, year = {2019}, author = {Simonsen, AK and Barrett, LG and Thrall, PH and Prober, SM}, title = {Novel model-based clustering reveals ecologically differentiated bacterial genomes across a large climate gradient.}, journal = {Ecology letters}, volume = {}, number = {}, pages = {}, doi = {10.1111/ele.13389}, pmid = {31612601}, issn = {1461-0248}, support = {//OCE Postdoctoral Fellowship, Australian Research Council/ ; }, abstract = {A pervasive challenge in microbial ecology is understanding the genetic level where ecological units can be differentiated. Ecological differentiation often occurs at fine genomic levels, yet it is unclear how to utilise ecological information to define ecotypes given the breadth of environmental variation among microbial taxa. Here, we present an analytical framework that infers clusters along genome-based microbial phylogenies according to shared environmental responses. The advantage of our approach is the ability to identify genomic clusters that best fit complex environmental information whilst characterising cluster niches through model predictions. We apply our method to determine climate-associated ecotypes in populations of nitrogen-fixing symbionts using whole genomes, explicitly sampled to detect climate differentiation across a heterogeneous landscape. Although soil and plant host characteristics strongly influence distribution patterns of inferred ecotypes, our flexible statistical method enabled us to identify climate-associated genomic clusters using environmental data, providing solid support for ecological specialisation in soil symbionts.}, }
@article {pmid31612432, year = {2019}, author = {Rattes de Almeida Couto, C and Catharine de Assis Leite, D and Jurelevicius, D and van Elsas, JD and Seldin, L}, title = {Chemical and biological dispersants differently affect the bacterial communities of uncontaminated and oil-contaminated marine water.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, doi = {10.1007/s42770-019-00153-8}, pmid = {31612432}, issn = {1678-4405}, support = {01//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; -//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; }, abstract = {The use of dispersants in marine environments is a common practice worldwide for oil spill remediation. While the effects of chemical dispersants have been extensively studied, those of biosurfactants, mainly surfactin that is considered one of the most effective surfactants produced by bacteria, have been less considered. We constructed microcosms containing marine water collected from Grumari beach (W_GB, Brazil) and from Schiermonnikoog beach (W_SI, The Netherlands) with the addition of oil (WO), Ultrasperse II plus oil (WOS), surfactin plus oil (WOB), and both dispersants (WS or WB) individually. In these treatments, the composition of bacterial communities and their predictive biodegradation potential were determined over time. High-throughput sequencing of the rrs gene encoding bacterial 16S rRNA revealed that Bacteroidetes (Flavobacteria class) and Proteobacteria (mainly Gammaproteobacteria and Alphaproteobacteria classes) were the most abundant phyla found among the W_GB and W_SI microbiomes, and the relative abundance of the bacterial types in the different microcosms varied based on the treatment applied. Non-metrical multidimensional scaling (NMDS) revealed a clear clustering based on the addition of oil and on the dispersant type added to the GB or SI microcosms, i.e., WB and WOB were separated from WS and WOS in both marine ecosystems studied. The potential presence of diverse enzymes involved in oil degradation was indicated by predictive bacterial metagenome reconstruction. The abundance of predicted genes for degradation of petroleum hydrocarbons increased more in surfactin-treated microcosms than those treated with Ultrasperse II, mainly in the marine water samples from Grumari beach.}, }
@article {pmid31612324, year = {2019}, author = {Norte, AC and Lopes de Carvalho, I and Núncio, MS and Araújo, PM and Matthysen, E and Albino Ramos, J and Sprong, H and Heylen, D}, title = {Getting under the birds' skin: tissue tropism of Borrelia burgdorferi s.l. in naturally and experimentally infected avian hosts.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01442-3}, pmid = {31612324}, issn = {1432-184X}, support = {MARE - UID/MAR/04292/2013//Fundação para a Ciência e a Tecnologia/ ; SFRH/BPD/108197/2015//Fundação para a Ciência e Tecnologia/ ; na//Portuguese National Institute of Health Doutor Ricardo Jorge/ ; Marie 544 Sklodowska-Curie Actions, Individual Global Fellowship, project n° 545 799609//European Union - Horizon2020/ ; G0.049.10//Fund for Scientific Research - Flanders/ ; na//Bill and Melinda Gates Foundation/ ; }, abstract = {Wild birds are frequently exposed to the zoonotic tick-borne bacteria Borrelia burgdorferi sensu lato (s.l.), and some bird species act as reservoirs for some Borrelia genospecies. Studying the tropism of Borrelia in the host, how it is sequestered in different organs, and whether it is maintained in circulation and/or in the host's skin is important to understand pathogenicity, infectivity to vector ticks and reservoir competency.We evaluated tissue dissemination of Borrelia in blackbirds (Turdus merula) and great tits (Parus major), naturally and experimentally infected with Borrelia genospecies from enzootic foci. We collected both minimally invasive biological samples (feathers, skin biopsies and blood) and skin, joint, brain and visceral tissues from necropsied birds. Infectiousness of the host was evaluated through xenodiagnoses and infection rates in fed and moulted ticks. Skin biopsies were the most reliable method for assessing avian hosts' Borrelia infectiousness, which was supported by the agreement of infection status results obtained from the analysis of chin and lore skin samples from necropsied birds and of their xenodiagnostic ticks, including a significant correlation between the estimated concentration of Borrelia genome copies in the skin and the Borrelia infection rate in the xenodiagnostic ticks. This confirms a dermatropism of Borrelia garinii, B. valaisiana and B. turdi in its avian hosts. However, time elapsed from exposure to Borrelia and interaction between host species and Borrelia genospecies may affect the reliability of skin biopsies. The blood was not useful to assess infectiousness of birds, even during the period of expected maximum spirochetaemia. From the tissues sampled (foot joint, liver, spleen, heart, kidney, gut and brain), Borrelia was detected only in the gut, which could be related with infection mode, genospecies competition, genospecies-specific seasonality and/or excretion processes.}, }
@article {pmid31611655, year = {2019}, author = {Jiao, S and Yang, Y and Xu, Y and Zhang, J and Lu, Y}, title = {Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0522-9}, pmid = {31611655}, issn = {1751-7370}, abstract = {Revealing the linkages between community assembly and species coexistence, which is crucial for the understanding of ecosystem diversity and functioning, is a fundamental but rarely investigated subject in microbial ecology. Here we examined archaeal, bacterial, and fungal community assembly in adjacent pairs of maize (water-unsaturated) and rice (water-saturated) fields across different habitats and regions throughout Eastern China. The high-throughput sequencing dataset was analyzed by variation partitioning, null model, and neutral community model analyses. We demonstrated that microbial community assembly was governed more by species sorting than by dispersal limitation in maize fields, and to a lesser extent in rice fields. The relative importance of species sorting in maize soils was greater at low latitudes than at high latitudes, while rice soils exhibited an opposite trend. Microbial co-occurrence associations tended to be higher when communities were primarily driven by dispersal limitation relative to species sorting. There were greater community dissimilarities between maize and rice soils in low-latitude regions, which was consistent with the higher proportion of negative edges in the correlation networks. The results indicate that a balance between species sorting and dispersal limitation mediates species coexistence in soil microbiomes. This study enhances our understanding of contemporary coexistence theory in microbial ecosystems.}, }
@article {pmid31611646, year = {2019}, author = {Ansorge, R and Romano, S and Sayavedra, L and Porras, MÁG and Kupczok, A and Tegetmeyer, HE and Dubilier, N and Petersen, J}, title = {Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-019-0572-9}, pmid = {31611646}, issn = {2058-5276}, support = {Grant GBMF3811//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; Grant GBMF3811//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; Grant GBMF3811//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; CRC 1182//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Genetic diversity of closely related free-living microorganisms is widespread and underpins ecosystem functioning, but most evolutionary theories predict that it destabilizes intimate mutualisms. Accordingly, strain diversity is assumed to be highly restricted in intracellular bacteria associated with animals. Here, we sequenced metagenomes and metatranscriptomes of 18 Bathymodiolus mussel individuals from four species, covering their known distribution range at deep-sea hydrothermal vents in the Atlantic. We show that as many as 16 strains of intracellular, sulfur-oxidizing symbionts coexist in individual Bathymodiolus mussels. Co-occurring symbiont strains differed extensively in key functions, such as the use of energy and nutrient sources, electron acceptors and viral defence mechanisms. Most strain-specific genes were expressed, highlighting their potential to affect fitness. We show that fine-scale diversity is pervasive in Bathymodiolus sulfur-oxidizing symbionts, and hypothesize that it may be widespread in low-cost symbioses where the environment, rather than the host, feeds the symbionts.}, }
@article {pmid31608034, year = {2019}, author = {Cai, Y and Cao, Y and Tang, C}, title = {Evidence for the Primary Role of Phytoplankton on Nitrogen Cycle in a Subtropical Reservoir: Reflected by the Stable Isotope Ratios of Particulate Nitrogen and Total Dissolved Nitrogen.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2202}, doi = {10.3389/fmicb.2019.02202}, pmid = {31608034}, issn = {1664-302X}, abstract = {Knowledge about the primary factor controlling stable isotope ratios of particulate nitrogen (δ15NPN) and total dissolved nitrogen (δ15NTDN) in a subtropical reservoir can improve the understanding of regional and global nitrogen cycles. Taking Lianhe Reservoir as a representative subtropical reservoir, we studied the spatial and temporal distributions of δ15NPN andδ15NTDN and their relationships with the surrounding physicochemical factors and phytoplankton. The results showed that variations in δ15NPN and δ15NTDN followed seasonal thermal cycles. The values of δ15NTDN were inversely proportional to those of δ15NPN. PCA showed that phytoplankton cell density and pH were the primary drivers of the variation of δ15NPN (45.2%). The primary factors influencing δ15NTDN were Chl a and phytoplankton cell density, which both indicated phytoplankton biomass. We also determined that the dominant species was Microcystis densa during the thermal stratification period and Staurodesmus aristiferus during the mixing period. Laboratory experiments showed that δ15NPN values in both M. densa (from 19.5 to 14.6‰) and S. aristiferus (from 19.4 to 16.0 ‰) media decreased significantly as the algal cells grew. Furthermore, the δ15NTDN values increased from 4.9 to 7.9‰ and from 4.7 to 6.9‰ in M. densa and S. aristiferus media, respectively, when the δ15NPN values decreased. These experimental results were consistent with field investigation results and indicated that variations in δ15NPN and δ15NTDN were mainly controlled by phytoplankton cell density, especially the cell density of the dominant species, in both the thermal stratification and mixing periods. The results also suggested that cell density, not phytoplankton species, was the key factor regulating the distribution of nitrogen stable isotopes. These results together indicated that phytoplankton cell density is the primary factor in the regulation of nitrogen stable isotope composition and that its influence is greater than that of other physical and chemical factors. This study provided detailed information supporting the primary role of phytoplankton in the nitrogen geochemical cycle and improved the understanding of biochemical processes in natural subtropical reservoirs.}, }
@article {pmid31605197, year = {2019}, author = {Hess, AL and Benítez-Páez, A and Blædel, T and Larsen, LH and Iglesias, JR and Madera, C and Sanz, Y and Larsen, TM and , }, title = {The effect of inulin and resistant maltodextrin on weight loss during energy restriction: a randomised, placebo-controlled, double-blinded intervention.}, journal = {European journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00394-019-02099-x}, pmid = {31605197}, issn = {1436-6215}, support = {613979//Seventh Framework Programme/ ; }, abstract = {PURPOSE: The objective of this study was to investigate the additive effects of combining energy restriction with dietary fibres on change in body weight and gut microbiota composition.<br><br>METHODS: The study was a 12-week randomised, placebo-controlled, double-blinded, parallel intervention trial. A total of 116 overweight or obese participants were assigned randomly either to 10 g inulin plus 10 g resistant maltodextrin or to 20 g of placebo supplementation through 400 mL of milk a day, while on a - 500 kcal/day energy restricted diet.<br><br>RESULTS: Altogether, 86 participants completed the intervention. There were no significant differences in weight loss or body composition between the groups. The fibre supplement reduced systolic (5.35 ± 2.4 mmHg, p = 0.043) and diastolic (2.82 ± 1.3 mmHg, p = 0.047) blood pressure to a larger extent than placebo. Furthermore, a larger decrease in serum insulin was observed in the placebo group compared to the fibre group (- 26.0 ± 9.2 pmol/L, p = 0.006). The intake of fibre induced changes in the composition of gut microbiota resulting in higher abundances of Parabacteroides and Bifidobacteria, compared to placebo. The effects on blood pressure and glucose metabolism were mainly observed in women, and could be attributed to a higher gut microbiota diversity after intervention. Finally, the fibre group experienced a higher degree of gastrointestinal symptoms, which attenuated over time.<br><br>CONCLUSIONS: Supplementation of inulin and resistant maltodextrin did not provide an additional weight loss during an energy-restricted diet, but reduced both systolic and diastolic blood pressure. Furthermore, the fibre supplement did stimulate the growth of potentially beneficial bacteria genera.<br><br>CLINICAL TRIAL REGISTRY: The study was registered at http://www.clinicaltrials.gov , NCT03135041.}, }
@article {pmid31600966, year = {2019}, author = {Lin, X and Gao, D and Lu, K and Li, X}, title = {Bacterial Community Shifts Driven by Nitrogen Pollution in River Sediments of a Highly Urbanized City.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {20}, pages = {}, doi = {10.3390/ijerph16203794}, pmid = {31600966}, issn = {1660-4601}, support = {No. YRWEF201804//Key Laboratory of Yangtze River Water Environment, Ministry of Education (Tongji University), China/ ; Grant No. 41701548//the National Natural Science Foundation of China/ ; No. 2019M653151//China Postdoctoral Science Foundation/ ; }, abstract = {Effects of nitrogen pollution on bacterial community shifts in river sediments remain barely understood. Here, we investigated the bacterial communities in sediments of urban and suburban rivers in a highly urbanized city, Shanghai. Sediment nitrate (NO3-) and ammonia (NH4+) were highly accumulated in urban river. Operation Taxonomic Units (OTUs), Abundance-based Coverage Estimators (ACEs) and Chao 1 estimator in urban rivers were slightly lower than those in suburban rivers, while Shannon and Simpson indices were higher in urban rivers than those in suburban rivers. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant bacterial phylum communities, accounting for 68.5-84.9% of all communities. In particular, the relative abundances of Firmicutes and Nitrospirae were significantly higher in suburban rivers than in urban rivers, while relative abundances of Bacteroidetes, Verrucomicrobia, and Spirochaetes were significantly lower in suburban rivers than in urban rivers. NH4+ was significantly and negatively correlated with abundances of Firmicutes, Nitrospirae, and Actinobacteria. Importantly, the significant and negative effects of sediment NH4+ on bacterial richness and diversity suggested that nitrogen pollution likely contribute to the decrease in the bacterial richness and diversity. The results highlight that nitrogen enrichment could drive the shifts of bacterial abundance and diversity in the urban river sediments where are strongly influenced by human activities under the rapid urbanization stress.}, }
@article {pmid31599931, year = {2019}, author = {Cavaco, MA and Louis St, VL and Engel, K and Pierre St, KA and Schiff, SL and Stibal, M and Neufeld, JD}, title = {Freshwater microbial community diversity in a rapidly changing high arctic watershed.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiz161}, pmid = {31599931}, issn = {1574-6941}, abstract = {Current models predict increases in High Arctic temperatures and precipitation that will have profound impacts on the Arctic hydrological cycle, including enhanced glacial melt and thawing of active layer soils. However, it remains uncertain how these changes will impact the structure of downstream resident freshwater microbial communities and ensuing microbially-driven freshwater ecosystem services. Using the Lake Hazen watershed (Nunavut, Canada; 82°N, 71°W) as a sentinel system, we related microbial community composition, (16S rRNA gene sequencing), to physicochemical parameters (e.g. dissolved oxygen, nutrients) over an annual hydrological cycle in three freshwater compartments within the watershed: 1) glacial rivers; 2) active layer thaw-fed streams and waterbodies, and; 3) Lake Hazen, into which 1) and 2) drain. Microbial communities throughout these freshwater compartments were strongly interconnected, hydrologically, and often correlated with the presence of melt-sourced chemicals (e.g. dissolved inorganic carbon) as the melt season progressed. Within Lake Hazen itself, water column microbial profiles were generally stable over spring and summer, despite fluctuating lake physicochemistry, indicating that microbial communities and the potential ecosystem services they provide therein may be resilient to environmental change. This work helps to establish a baseline understanding of how microbial communities and the ecosystem services they provide in Arctic watersheds might respond to future climate change.}, }
@article {pmid31598761, year = {2019}, author = {Brunel, C and Beifen, Y and Pouteau, R and Li, J and van Kleunen, M}, title = {Responses of Rhizospheric Microbial Communities of Native and Alien Plant Species to Cuscuta Parasitism.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01438-z}, pmid = {31598761}, issn = {1432-184X}, support = {2016YFC1201100//Chinese National Key Research and Development Program/ ; 15-2//International Science and Technology Cooperation Programme/ ; 30800133//National Natural Science Foundation of China/ ; }, abstract = {Parasitic plants have major impacts on host fitness. In the case of species of the holoparasitic Cuscuta genus, these impacts were shown to be particularly strong in some invasive alien plants, which has raised interest in the underlying mechanism. We hypothesized that Cuscuta parasitization may exert strong influence in shaping the diversity patterns in the host rhizosphere microbiome and that this may vary between native (coevolved) and alien (non-coevolved) plants. Here, we report on a field study exploring the effect of parasitization by Cuscuta australis on the rhizosphere microbiota (16S and ITS rDNA) of four plant species sharing and three plant species not sharing the parasite's native range. Despite a predominant role of the host species in shaping the rhizosphere microbiota, the role of host origin and of parasitization still appeared important in structuring microbial communities and their associated functions. Bacterial communities were more strongly influenced than fungi by the native range of the host plant, while fungi were slightly more affected than bacteria by parasitization. About 7% of bacterial phylotypes and 11% of fungal phylotypes were sensitive to Cuscuta parasitization. Parasitization also reduced the abundance of arbuscular mycorrhizal fungi by ca. 18% and of several genes related to plant growth promoting functions (e.g., nitrogen metabolism and quorum sensing). Both fungi and bacteria differentially responded to host parasitization depending on host origin, and the extent of these shifts suggests that they may have more dramatic consequences for alien than for native plants.}, }
@article {pmid31598755, year = {2019}, author = {Sodhi, KK and Kumar, M and Balan, B and Dhaulaniya, AS and Singh, DK}, title = {Isolation and characterization of amoxicillin-resistant bacteria and amoxicillin-induced alteration in its protein profiling and RNA yield.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-019-01737-6}, pmid = {31598755}, issn = {1432-072X}, support = {(NASF/CA-6030/2017-18)//Indian Council of Agricultural Research/ ; }, abstract = {Amoxicillin-resistant bacteria were isolated using selective enrichment procedure. The morphological, biochemical and molecular characterization based on 16S rRNA gene sequencing and phylogenetic analysis of the bacterial strain WA5 confirmed that the strain belongs to the genus Stenotrophomonas. The bacteria were named as Stenotrophomonas sp. strain WA5 (MK110499). Substantial growth was seen in M9 minimal media supplemented with 5 mg L-1 of amoxicillin as a sole source of carbon and energy. RNA yield was also observed to be decreased in the presence of amoxicillin. Amoxicillin (5 mg L-1)-induced alteration is seen on bacterial protein profile and unique polypeptide bands were seen to be induced in the presence of amoxicillin, the bands were subjected to trypsin digestion, and LC-MS/MS analysis showed that the bands belong to the family of DNA-dependent RNA polymerase subunit β (rpoC). Plasmid DNA isolation indicated the presence of antibiotic-resistant genes being harboured by the plasmid.}, }
@article {pmid31598633, year = {2019}, author = {Baruzzo, G and Patuzzi, I and Di Camillo, B}, title = {SPARSim Single Cell: a count data simulator for scRNA-seq data.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btz752}, pmid = {31598633}, issn = {1367-4811}, abstract = {MOTIVATION: Single cell RNA-seq (scRNA-seq) count data shows many differences compared to bulk RNA-seq count data, making the application of many RNA-seq preprocessing/analysis methods not straightforward or even inappropriate.For this reason, the development of new methods for handling scRNA-seq count data is currently one of the most active research field in bioinformatics. To help the development of such new methods, the availability of simulated data could play a pivotal role. However, only few scRNA-seq count data simulators are available, often showing poor or not demonstrated similarity with real data.<br><br>RESULTS: In this article we present SPARSim, a scRNA-seq count data simulator based on a Gamma-Multivariate Hypergeometric model. We demonstrate that SPARSim allows to generate count data that resemble real data in terms of count intensity, variability and sparsity, performing comparably or better than one of the most used scRNA-seq simulator, Splat. In particular, SPARSim simulated count matrices well resemble the distribution of zeros across different expression intensities observed in real count data.<br><br>AVAILABILITY: SPARSim R package is freely available at http://sysbiobig.dei.unipd.it/?q=SPARSim and at https://gitlab.com/sysbiobig/sparsim.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid31595680, year = {2019}, author = {Wepking, C and Badgley, B and Barrett, JE and Knowlton, KF and Lucas, JM and Minick, KJ and Ray, PP and Shawver, SE and Strickland, MS}, title = {Prolonged exposure to manure from livestock-administered antibiotics decreases ecosystem carbon-use efficiency and alters nitrogen cycling.}, journal = {Ecology letters}, volume = {}, number = {}, pages = {}, doi = {10.1111/ele.13390}, pmid = {31595680}, issn = {1461-0248}, support = {1832888//NSF/ ; 2013-67019-21363//USDA-NIFA/ ; }, abstract = {Microbial communities drive soil ecosystem function but are also susceptible to environmental disturbances. We investigated whether exposure to manure sourced from cattle either administered or not administered antibiotics affected microbially mediated terrestrial ecosystem function. We quantified changes in microbial community composition via amplicon sequencing, and terrestrial elemental cycling via a stable isotope pulse-chase. Exposure to manure from antibiotic-treated cattle caused: (i) changes in microbial community structure; and (ii) alterations in elemental cycling throughout the terrestrial system. This exposure caused changes in fungal : bacterial ratios, as well as changes in bacterial community structure. Additionally, exposure to manure from cattle treated with pirlimycin resulted in an approximate two-fold increase in ecosystem respiration of recently fixed-carbon, and a greater proportion of recently added nitrogen in plant and soil pools compared to the control manure. Manure from antibiotic-treated cattle therefore affects terrestrial ecosystem function via the soil microbiome, causing decreased ecosystem carbon use efficiency, and altered nitrogen cycling.}, }
@article {pmid31595328, year = {2019}, author = {Li, F and Li, P and Hua, H and Hou, M and Wang, F}, title = {Diversity, Tissue Localization, and Infection Pattern of Bacterial Symbionts of the White-Backed Planthopper, Sogatella furcifera (Hemiptera: Delphacidae).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01433-4}, pmid = {31595328}, issn = {1432-184X}, support = {2018YFD0200300//National Key R&amp;D Project of China/ ; 31371951//National Natural Science Foundation of China/ ; }, abstract = {The white-backed planthopper (WBPH), Sogatella furcifera (Horváth), is a destructive pest of rice. Bacterial symbionts play an important role in insect hosts, especially hemipteran hosts. This study was designed to examine the bacterial symbionts of the WBPH using 16S rDNA high-throughput sequencing. A total of 63 and 177 operational taxonomic units (OTUs) were identified in females and males of three WBPH populations, respectively. These OTUs included bacteria of 75 genera from 11 phyla, where Wolbachia, Cardinium, and Asaia were the dominant genera, accounting for over 97.99% of all the symbiotic bacteria. Fluorescence in situ hybridization detected Wolbachia, Cardinium, and Asaia in the salivary glands, guts, testes, and eggs of the WBPH, indicating the potential for both horizontal and vertical transmission. Moreover, the infection pattern of the three dominant bacterial symbionts was detected in six WBPH populations. The frequencies of Wolbachia infection of females and Cardinium infection of both sexes were over 96.7%. Wolbachia infection of males ranged between 46.7 and 63.3%, which was significantly lower than that observed for females. Asaia infection of both sexes varied substantially among the populations. These results indicate that the complex host-symbiotic bacteria interaction is influenced by host sex and geographical origin and potentially by the transmission modes of the symbionts.}, }
@article {pmid31595008, year = {2019}, author = {Soffe, R and Bernach, M and Remus-Emsermann, MNP and Nock, V}, title = {Replicating Arabidopsis Model Leaf Surfaces for Phyllosphere Microbiology.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {14420}, doi = {10.1038/s41598-019-50983-7}, pmid = {31595008}, issn = {2045-2322}, abstract = {Artificial surfaces are commonly used in place of leaves in phyllosphere microbiology to study microbial behaviour on plant leaf surfaces. These surfaces enable a reductionist approach to be undertaken, to enable individual environmental factors influencing microorganisms to be studied. Commonly used artificial surfaces include nutrient agar, isolated leaf cuticles, and reconstituted leaf waxes. Recently, replica surfaces mimicking the complex topography of leaf surfaces for phyllosphere microbiology studies are appearing in literature. Replica leaf surfaces have been produced in agar, epoxy, polystyrene, and polydimethylsiloxane (PDMS). However, none of these protocols are suitable for replicating fragile leaves such as of the model plant Arabidopsis thaliana. This is of importance, as A. thaliana is a model system for molecular plant genetics, molecular plant biology, and microbial ecology. To overcome this limitation, we introduce a versatile replication protocol for replicating fragile leaf surfaces into PDMS. Here we demonstrate the capacity of our replication process using optical microscopy, atomic force microscopy (AFM), and contact angle measurements to compare living and PDMS replica A. thaliana leaf surfaces. To highlight the use of our replica leaf surfaces for phyllosphere microbiology, we visualise bacteria on the replica leaf surfaces in comparison to living leaf surfaces.}, }
@article {pmid31593911, year = {2019}, author = {Prévoteau, A and Carvajal-Arroyo, JM and Ganigué, R and Rabaey, K}, title = {Microbial electrosynthesis from CO2: forever a promise?.}, journal = {Current opinion in biotechnology}, volume = {62}, number = {}, pages = {48-57}, doi = {10.1016/j.copbio.2019.08.014}, pmid = {31593911}, issn = {1879-0429}, abstract = {Microbial electrosynthesis (MES) is an electrochemical process used to drive microbial metabolism for bio-production, such as the reduction of CO2 into industrially relevant organic products as an alternative to current fossil-fuel-derived commodities. After a decade of research on MES from CO2, figures of merit have increased significantly but are plateauing yet far from those expected to allow competitiveness for synthesis of commodity chemicals. Here we discuss the substantial technological shortcomings still associated with MES and evoke possible ways to mitigate them. It appears particularly challenging to obtain both relevant production rates (driven by high current densities) and energy conversion efficiency (i.e. low cell voltage) in microbial-compatible electrolytes. More competitive processes could arise by decoupling effective abiotic electroreductions (e.g. CO2 to CO or ethanol; H2 evolution) with subsequent fermentation processes.}, }
@article {pmid31591493, year = {2019}, author = {Ben Maamar, S and Hu, J and Hartmann, EM}, title = {Implications of indoor microbial ecology and evolution on antibiotic resistance.}, journal = {Journal of exposure science &amp; environmental epidemiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41370-019-0171-0}, pmid = {31591493}, issn = {1559-064X}, abstract = {The indoor environment is an important source of microbial exposures for its human occupants. While we naturally want to favor positive health outcomes, built environment design and operation may counter-intuitively favor negative health outcomes, particularly with regard to antibiotic resistance. Indoor environments contain microbes from both human and non-human origins, providing a unique venue for microbial interactions, including horizontal gene transfer. Furthermore, stressors present in the built environment could favor the exchange of genetic material in general and the retention of antibiotic resistance genes in particular. Intrinsic and acquired antibiotic resistance both pose a potential threat to human health; these phenomena need to be considered and controlled separately. The presence of both environmental and human-associated microbes, along with their associated antibiotic resistance genes, in the face of stressors, including antimicrobial chemicals, creates a unique opportunity for the undesirable spread of antibiotic resistance. In this review, we summarize studies and findings related to various interactions between human-associated bacteria, environmental bacteria, and built environment conditions, and particularly their relation to antibiotic resistance, aiming to guide &quot;healthy&quot; building design.}, }
@article {pmid31590609, year = {2019}, author = {Diaz, PI and Valm, AM}, title = {Microbial Interactions in Oral Communities Mediate Emergent Biofilm Properties.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {22034519880157}, doi = {10.1177/0022034519880157}, pmid = {31590609}, issn = {1544-0591}, abstract = {Oral microbial communities are extraordinarily complex in taxonomic composition and comprise interdependent biological systems. The bacteria, archaea, fungi, and viruses that thrive within these communities engage in extensive cell-cell interactions, which are both beneficial and antagonistic. Direct physical interactions among individual cells mediate large-scale architectural biofilm arrangements and provide spatial proximity for chemical communication and metabolic cooperation. In this review, we summarize recent work in identifying specific molecular components that mediate cell-cell interactions and describe metabolic interactions, such as cross-feeding and exchange of electron acceptors and small molecules, that modify the growth and virulence of individual species. We argue, however, that although pairwise interaction models have provided useful information, complex community-like systems are needed to study the properties of oral communities. The networks of multiple synergistic and antagonistic interactions within oral biofilms give rise to the emergent properties of persistence, stability, and long-range spatial structure, with these properties mediating the dysbiotic transitions from health to oral diseases. A better understanding of the fundamental properties of interspecies networks will lead to the development of effective strategies to manipulate oral communities.}, }
@article {pmid31588957, year = {2019}, author = {Le, D and Nguyen, P and Nguyen, D and Dierckens, K and Boon, N and Lacoere, T and Kerckhof, FM and De Vrieze, J and Vadstein, O and Bossier, P}, title = {Gut Microbiota of Migrating Wild Rabbit Fish (Siganus guttatus) Larvae Have Low Spatial and Temporal Variability.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01436-1}, pmid = {31588957}, issn = {1432-184X}, support = {ZIUS2015AP026//VLIR-IUC/ ; }, abstract = {We investigated the gut microbiota of rabbit fish larvae at three locations in Vietnam (ThuanAn-northern, QuangNam-intermediate, BinhDinh-southern sampling site) over a three-year period. In the wild, the first food for rabbit fish larvae remains unknown, while the juveniles and adults are herbivores, forming schools near the coasts, lagoons, and river mouths, and feeding mainly on filamentous algae. This is the first study on the gut microbiota of the wild fish larvae and with a large number of individuals analyzed spatially and temporally. The Clostridiales order was the most predominant in the gut, and location-by-location alpha diversity showed significant differences in Chao-1, Hill number 1, and evenness. Analysis of beta diversity indicated that the location, not year, had an effect on the composition of the microbiota. In 2014, the gut microbiota of fish from QuangNam was different from that in BinhDinh; in 2015, the gut microbiota was different for all locations; and, in 2016, the gut microbiota in ThuanAn was different from that in the other locations. There was a time-dependent trend in the north-south axis for the gut microbiota, which is considered to be tentative awaiting larger datasets. We found limited variation in the gut microbiota geographically and in time and strong indications for a core microbiome. Five and fifteen OTUs were found in 100 and 99% of the individuals, respectively. This suggests that at this life stage the gut microbiota is under strong selection due to a combination of fish-microbe and microbe-microbe interactions.}, }
@article {pmid31587650, year = {2019}, author = {Sebastián, M and Gasol, JM}, title = {Visualization is crucial for understanding microbial processes in the ocean.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1786}, pages = {20190083}, doi = {10.1098/rstb.2019.0083}, pmid = {31587650}, issn = {1471-2970}, abstract = {Recent developments in community and single-cell genomic approaches have provided an unprecedented amount of information on the ecology of microbes in the aquatic environment. However, linkages between each specific microbe's identity and their in situ level of activity (be it growth, division or just metabolic activity) are much more scarce. The ultimate goal of marine microbial ecology is to understand how the environment determines the types of different microbes in nature, their function, morphology and cell-to-cell interactions and to do so we should gather three levels of information, the genomic (including identity), the functional (activity or growth), and the morphological, and for as many individual cells as possible. We present a brief overview of methodologies applied to address single-cell activity in marine prokaryotes, together with a discussion of the difficulties in identifying and categorizing activity and growth. We then provide and discuss some examples showing how visualization has been pivotal for challenging established paradigms and for understanding the role of microbes in the environment, unveiling processes and interactions that otherwise would have been overlooked. We conclude by stating that more effort should be directed towards integrating visualization in future approaches if we want to gain a comprehensive insight into how microbes contribute to the functioning of ecosystems. This article is part of a discussion meeting issue 'Single cell ecology'.}, }
@article {pmid31585384, year = {2019}, author = {Wang, D and Tooker, NB and Srinivasan, V and Li, G and Fernandez, LA and Schauer, P and Menniti, A and Maher, C and Bott, CB and Dombrowski, P and Barnard, JL and Onnis-Hayden, A and Gu, AZ}, title = {Side-stream enhanced biological phosphorus removal (S2EBPR) process improves system performance - A full-scale comparative study.}, journal = {Water research}, volume = {167}, number = {}, pages = {115109}, doi = {10.1016/j.watres.2019.115109}, pmid = {31585384}, issn = {1879-2448}, abstract = {To address the common challenges in enhanced biological phosphorus removal (EBPR) related to stability and unfavorable influent carbon to phosphorus ratio, a side-stream EBPR (S2EBPR) process that involves a side-stream anaerobic biological sludge hydrolysis and fermentation reactor was proposed as an emerging alternative. In this study, a full-scale pilot testing was performed with side-by-side operation of a conventional anaerobic-anoxic-aerobic (A2O) process versus a S2EBPR process. A comparison of the performance, activity and microbial community between the two configurations was performed. The results demonstrated that, with the same influent wastewater characteristics, S2EBPR configuration showed improved P removal performance and stability than the conventional A2O configuration, especially when the mixers in the side-stream anaerobic reactor were operated intermittently. Mass balance analysis illustrated that both denitrification and EBPR were enhanced in S2EBPR configuration, where return activated sludge was diverted into the anaerobic zone to promote fermentation and enrichment of polyphosphate accumulating organisms (PAOs), and the influent was bypassed to the anoxic zone for enhancing denitrification. A relatively higher PAO activity and total PAO abundance were observed in S2EBPR than in A2O configuration, accompanied by a higher degree of dependence on glycolysis pathway than tricarboxylic acid cycle. No significant difference in the relative abundances of putative PAOs, including Ca. Accumulibacter and Tetrasphaera, were observed between the two configurations. However, higher microbial community diversity indices were observed in S2EBPR configuration than in conventional one. In addition, consistently lower relative abundance of known glycogen accumulating organisms (GAOs) was observed in S2EBPR system. Extended anaerobic retention time and conditions that generate continuous and more complex volatile fatty acids in the side-stream anaerobic reactor of S2EBPR process likely give more competitive advantage for PAOs over GAOs. PAOs exhibited sustained EBPR activity and delayed decay under extended anaerobic condition, likely due to their versatile metabolic pathways depending on the availability and utilization of multiple intracellular polymers. This study provided new insights into the effects of implementing side-stream EBPR configuration on microbial populations, EBPR activity profiles and resulted system performance.}, }
@article {pmid31584168, year = {2020}, author = {Browne, PD and Kot, W and Jørgensen, TS and Hansen, LH}, title = {The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2075}, number = {}, pages = {253-264}, doi = {10.1007/978-1-4939-9877-7_18}, pmid = {31584168}, issn = {1940-6029}, abstract = {Isolation, sequencing, and analysis of circular genetic elements bring new insights to mobile genetic elements related to microbial ecology. One method used to study circular plasmids, viruses, and other elements is called the mobilome method. The mobilome method presented here is an unamplified mobilome approach allowing fast isolation of circular DNA elements from a variety of samples followed by directly building unamplified Illumina-compatible sequencing libraries using enzymatic tagging and fragmentation. Several methods for bioinformatic analysis of mobilome data are also suggested.}, }
@article {pmid31582458, year = {2019}, author = {Schultz, J and Kallies, R and Nunes da Rocha, U and Rosado, AS}, title = {Draft Genome Sequence of Brevibacillus sp. Strain LEMMJ03, Isolated from an Antarctic Volcano.}, journal = {Microbiology resource announcements}, volume = {8}, number = {40}, pages = {}, doi = {10.1128/MRA.00921-19}, pmid = {31582458}, issn = {2576-098X}, abstract = {Here, we announce the draft genome sequence of Brevibacillus sp. strain LEMMJ03, isolated from Whalers Bay sediment (Deception Island, Antarctica). In total, 4,500 coding sequences (CDS), among those 102 coding for tRNAs and 5 for noncoding RNAs (ncRNAs), were predicted from the 4.64-Mb genome. Predicted functions were for bacteriocin and degradation of aromatic compounds.}, }
@article {pmid31580006, year = {2019}, author = {Li, X and Garbeva, P and Liu, X and Klein Gunnewiek, PJ and Clocchiatti, A and Hundscheid, MP and Wang, X and de Boer, W}, title = {Volatile-mediated antagonism of soil bacterial communities against fungi.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14808}, pmid = {31580006}, issn = {1462-2920}, abstract = {Competition is a major type of interaction between fungi and bacteria in soil and is also an important factor in suppression of plant diseases caused by soil-borne fungal pathogens. There is increasing attention for the possible role of volatiles in competitive interactions between bacteria and fungi. However, knowledge on the actual role of bacterial volatiles in interactions with fungi within soil microbial communities is lacking. Here, we examined colonization of sterile agricultural soils by fungi and bacteria from non-sterile soil inoculums during exposure to volatiles emitted by soil-derived bacterial communities. We found that colonisation of soil by fungi was negatively affected by exposure to volatiles emitted by bacterial communities whereas that of bacteria was barely changed. Furthermore, there were strong effects of bacterial community volatiles on the assembly of fungal soil colonizers. Identification of volatile composition produced by bacterial communities revealed several compounds with known fungistatic activity. Our results are the first to reveal a collective volatile-mediated antagonism of soil bacteria against fungi. Given the better exploration abilities of filamentous fungi in unsaturated soils, this may be an important strategy for bacteria to defend occupied nutrient patches against invading fungi. Another implication of our research is that bacterial volatiles in soil atmospheres can have a major contribution to soil fungistasis. This article is protected by copyright. All rights reserved.}, }
@article {pmid31579614, year = {2019}, author = {Benucci, GMN and Longley, R and Zhang, P and Zhao, Q and Bonito, G and Yu, F}, title = {Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e7744}, doi = {10.7717/peerj.7744}, pmid = {31579614}, issn = {2167-8359}, abstract = {Morels (Morchella spp.) are iconic edible mushrooms with a long history of human consumption. Some microbial taxa are hypothesized to be important in triggering the formation of morel primordia and development of fruiting bodies, thus, there is interest in the microbial ecology of these fungi. To identify and compare fungal and prokaryotic communities in soils where Morchella sextelata is cultivated in outdoor greenhouses, ITS and 16S rDNA high throughput amplicon sequencing and microbiome analyses were performed. Pedobacter, Pseudomonas, Stenotrophomonas, and Flavobacterium were found to comprise the core microbiome of M. sextelata ascocarps. These bacterial taxa were also abundant in the soil beneath growing fruiting bodies. A total of 29 bacterial taxa were found to be statistically associated to Morchella fruiting bodies. Bacterial community network analysis revealed high modularity with some 16S rDNA operational taxonomic unit clusters living in specialized fungal niches (e.g., pileus, stipe). Other fungi dominating the soil mycobiome beneath morels included Morchella, Phialophora, and Mortierella. This research informs understanding of microbial indicators and potential facilitators of Morchella ecology and fruiting body production.}, }
@article {pmid31578554, year = {2019}, author = {An, SQ and Potnis, N and Dow, M and Vorhölter, FJ and He, YQ and Becker, A and Teper, D and Li, Y and Wang, N and Bleris, L and Tang, JL}, title = {Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuz024}, pmid = {31578554}, issn = {1574-6976}, abstract = {Xanthomonas is a well-studied genus of bacterial plant pathogens whose members cause a variety of diseases in economically important crops worldwide. Genomic and functional studies of these phytopathogens have provided significant understanding of microbial-host interactions, bacterial virulence and host adaptation mechanisms including microbial ecology and epidemiology. In addition, several strains of Xanthomonas are important as producers of the extracellular polysaccharide, xanthan, used in the food and pharmaceutical industries. This polymer has also been implicated in several phases of the bacterial disease cycle. In this review, we summarise the current knowledge on the infection strategies and regulatory networks controlling virulence and adaptation mechanisms from Xanthomonas species and discuss the novel opportunities that this body of work has provided for disease control and plant health.}, }
@article {pmid31575762, year = {2019}, author = {Brewer, TE and Aronson, EL and Arogyaswamy, K and Billings, SA and Botthoff, JK and Campbell, AN and Dove, NC and Fairbanks, D and Gallery, RE and Hart, SC and Kaye, J and King, G and Logan, G and Lohse, KA and Maltz, MR and Mayorga, E and O'Neill, C and Owens, SM and Packman, A and Pett-Ridge, J and Plante, AF and Richter, DD and Silver, WL and Yang, WH and Fierer, N}, title = {Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons.}, journal = {mBio}, volume = {10}, number = {5}, pages = {}, doi = {10.1128/mBio.01318-19}, pmid = {31575762}, issn = {2150-7511}, abstract = {While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.}, }
@article {pmid31574348, year = {2019}, author = {Carney, RL and Labbate, M and Siboni, N and Tagg, KA and Mitrovic, SM and Seymour, JR}, title = {Urban beaches are environmental hotspots for antibiotic resistance following rainfall.}, journal = {Water research}, volume = {167}, number = {}, pages = {115081}, doi = {10.1016/j.watres.2019.115081}, pmid = {31574348}, issn = {1879-2448}, abstract = {To reveal the occurrence and mechanisms for dispersal of antibiotic resistance (AbR) among the microbial assemblages inhabiting impacted coastal environments, we performed a weekly, two-year duration time-series study at two urban beaches between 2014 and 2016. We combined quantitative PCR and multiplex PCR/reverse line blot techniques to track patterns in the occurrence of 31 AbR genes, including genes that confer resistance to antibiotics that are critically important antimicrobials for human medicine. Patterns in the abundance of these genes were linked to specific microbial groups and environmental parameters by coupling qPCR and 16S rRNA amplicon sequencing data with network analysis. Up to 100-fold increases in the abundance of several AbR genes, including genes conferring resistance to quinolones, trimethoprim, sulfonamides, tetracycline, vancomycin and carbapenems, occurred following storm-water and modelled wet-weather sewer overflow events. The abundance of AbR genes strongly and significantly correlated with several potentially pathogenic bacterial OTUs regularly associated with wastewater infrastructure, such as Arcobacter, Acinetobacter, Aeromonas and Cloacibacterium. These high-resolution observations provide clear links between storm-water discharge and sewer overflow events and the occurrence of AbR in the coastal microbial assemblages inhabiting urban beaches, highlighting a direct mechanism for potentially significant AbR exposure risks to humans.}, }
@article {pmid31572496, year = {2019}, author = {Mondo, SJ and Jiménez, DJ and Hector, RE and Lipzen, A and Yan, M and LaButti, K and Barry, K and van Elsas, JD and Grigoriev, IV and Nichols, NN}, title = {Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery.}, journal = {Biotechnology for biofuels}, volume = {12}, number = {}, pages = {229}, doi = {10.1186/s13068-019-1569-6}, pmid = {31572496}, issn = {1754-6834}, abstract = {Background: Particular species of the genus Coniochaeta (Sordariomycetes) exhibit great potential for bioabatement of furanic compounds and have been identified as an underexplored source of novel lignocellulolytic enzymes, especially Coniochaeta ligniaria. However, there is a lack of information about their genomic features and metabolic capabilities. Here, we report the first in-depth genome/transcriptome survey of a Coniochaeta species (strain 2T2.1).<br><br>Results: The genome of Coniochaeta sp. strain 2T2.1 has a size of 74.53 Mbp and contains 24,735 protein-encoding genes. Interestingly, we detected a genome expansion event, resulting ~ 98% of the assembly being duplicated with 91.9% average nucleotide identity between the duplicated regions. The lack of gene loss, as well as the high divergence and strong genome-wide signatures of purifying selection between copies indicates that this is likely a recent duplication, which arose through hybridization between two related Coniochaeta-like species (allopolyploidization). Phylogenomic analysis revealed that 2T2.1 is related Coniochaeta sp. PMI546 and Lecythophora sp. AK0013, which both occur endophytically. Based on carbohydrate-active enzyme (CAZy) annotation, we observed that even after in silico removal of its duplicated content, the 2T2.1 genome contains exceptional lignocellulolytic machinery. Moreover, transcriptomic data reveal the overexpression of proteins affiliated to CAZy families GH11, GH10 (endoxylanases), CE5, CE1 (xylan esterases), GH62, GH51 (α-l-arabinofuranosidases), GH12, GH7 (cellulases), and AA9 (lytic polysaccharide monoxygenases) when the fungus was grown on wheat straw compared with glucose as the sole carbon source.<br><br>Conclusions: We provide data that suggest that a recent hybridization between the genomes of related species may have given rise to Coniochaeta sp. 2T2.1. Moreover, our results reveal that the degradation of arabinoxylan, xyloglucan and cellulose are key metabolic processes in strain 2T2.1 growing on wheat straw. Different genes for key lignocellulolytic enzymes were identified, which can be starting points for production, characterization and/or supplementation of enzyme cocktails used in saccharification of agricultural residues. Our findings represent first steps that enable a better understanding of the reticulate evolution and &quot;eco-enzymology&quot; of lignocellulolytic Coniochaeta species.}, }
@article {pmid31572347, year = {2019}, author = {Dagher, DJ and de la Providencia, IE and Pitre, FE and St-Arnaud, M and Hijri, M}, title = {Plant Identity Shaped Rhizospheric Microbial Communities More Strongly Than Bacterial Bioaugmentation in Petroleum Hydrocarbon-Polluted Sediments.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2144}, doi = {10.3389/fmicb.2019.02144}, pmid = {31572347}, issn = {1664-302X}, abstract = {Manipulating the plant-root microbiota has the potential to reduce plant stress and promote their growth and production in harsh conditions. Community composition and activity of plant-roots microbiota can be either beneficial or deleterious to plant health. Shifting this equilibrium could then strongly affect plant productivity in anthropized areas. In this study, we tested whether repeated bioaugmentation with Proteobacteria influenced plant productivity and the microbial communities associated with the rhizosphere of four plant species growing in sediments contaminated with petroleum hydrocarbons (PHCs). A mesocosm experiment was performed in randomized block design with two factors: (1) presence or absence of four plants species collected from a sedimentation basin of a former petrochemical plant, and (2) bioaugmentation or not with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over 4 months. MiSeq amplicon sequencing, targeting the bacterial 16S rRNA gene and the fungal ITS, was used to assess microbial community structures of sediments from planted or unplanted microcosms. Our results showed that while bioaugmentation caused a significant shift in microbial communities, presence of plant and their species identity had a stronger influence on the structure of the microbiome in PHCs contaminated sediments. The outcome of this study provides knowledge on the diversity and behavior of rhizosphere microbes associated with indigenous plants following repeated bioaugmentation, underlining the importance of plant selection in order to facilitate their efficient management, in order to accelerate processes of land reclamation.}, }
@article {pmid31572346, year = {2019}, author = {Schweitzer-Natan, O and Ofek-Lalzar, M and Sher, D and Sukenik, A}, title = {Particle-Associated Microbial Community in a Subtropical Lake During Thermal Mixing and Phytoplankton Succession.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2142}, doi = {10.3389/fmicb.2019.02142}, pmid = {31572346}, issn = {1664-302X}, abstract = {Ecosystem dynamics in monomictic lakes are characterized by seasonal thermal mixing and stratification. These physical processes bring about seasonal variations in nutrients and organic matter fluxes, affecting the biogeochemical processes that occur in the water column. Physical and chemical dynamics are generally reflected in seasonal structural changes in the phytoplankton and bacterio-plankton community. In this study, we analyzed, using 16S rRNA amplicon sequencing, the structure of the bacterial community associated with large particles (>20 μm) in Lake Kinneret (Sea of Galilee, Israel), and its associations to phytoplankton populations. The study was carried out during late winter and early spring, a highly dynamic period in terms of thermal mixing, nutrient availability, and shifts in phytoplankton composition. Structural changes in the bacterioplankton population corresponded with limnological variations in the lake. In terms of the entire heterotrophic community, the structural patterns of particle-associated bacteria were mainly correlated with abiotic factors such as pH, ammonia, water temperature and nitrate. However, analysis of microbial taxon-specific correlations with phytoplankton species revealed a strong potential link between specific bacterial populations and the presence of different phytoplankton species, such as the cyanobacterium Microcystis, as well as the dinoflagellates Peridinium and Peridiniopsis. We found that Brevundimonas, a common freshwater genus, and Bdellovibrio, a well-known Gram-negative bacteria predator, were positively associated to Microcystis, suggesting a potentially important role of these three taxa in the microbial ecology of the lake. Our results show that the dynamics of environmental abiotic conditions, rather than specific phytoplankton assemblages, are the main factors positively correlated with changes in the community structure as a whole. Nevertheless, some specific bacteria may interact and be linked with specific phytoplankton, which may potentially control the dynamic patterns of the microbial community.}, }
@article {pmid31572315, year = {2019}, author = {Shin, GY and Schachterle, JK and Shyntum, DY and Moleleki, LN and Coutinho, TA and Sundin, GW}, title = {Functional Characterization of a Global Virulence Regulator Hfq and Identification of Hfq-Dependent sRNAs in the Plant Pathogen Pantoea ananatis.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2075}, doi = {10.3389/fmicb.2019.02075}, pmid = {31572315}, issn = {1664-302X}, abstract = {To successfully infect plant hosts, the collective regulation of virulence factors in a bacterial pathogen is crucial. Hfq is an RNA chaperone protein that facilitates the small RNA (sRNA) regulation of global gene expression at the post-transcriptional level. In this study, the functional role of Hfq in a broad host range phytopathogen Pantoea ananatis was determined. Inactivation of the hfq gene in P. ananatis LMG 2665T resulted in the loss of pathogenicity and motility. In addition, there was a significant reduction of quorum sensing signal molecule acyl-homoserine lactone (AHL) production and biofilm formation. Differential sRNA expression analysis between the hfq mutant and wild-type strains of P. ananatis revealed 276 sRNAs affected in their abundance by the loss of hfq at low (OD600 = 0.2) and high cell (OD600 = 0.6) densities. Further analysis identified 25 Hfq-dependent sRNAs, all showing a predicted Rho-independent terminator of transcription and mapping within intergenic regions of the P. ananatis genome. These included known sRNAs such as ArcZ, FnrS, GlmZ, RprA, RyeB, RyhB, RyhB2, Spot42, and SsrA, and 16 novel P. ananatis sRNAs. The current study demonstrated that Hfq is an important component of the collective regulation of virulence factors and sets a foundation for understanding Hfq-sRNA mediated regulation in the phytopathogen P. ananatis.}, }
@article {pmid31566612, year = {2019}, author = {Šimek, K and Sirova, D}, title = {Fluorescently Labeled Bacteria as a Tracer to Reveal Novel Pathways of Organic Carbon Flow in Aquatic Ecosystems.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {151}, pages = {}, doi = {10.3791/59903}, pmid = {31566612}, issn = {1940-087X}, abstract = {Elucidating trophic interactions, such as predation and its effects, is a frequent task for many researchers in ecology. The study of microbial communities has many limitations, and determining a predator, prey, and predatory rates is often difficult. Presented here is an optimized method based on the addition of fluorescently labelled prey as a tracer, which allows for reliable quantitation of the grazing rates in aquatic predatory eukaryotes and estimation of nutrient transfer to higher trophic levels.}, }
@article {pmid31565058, year = {2019}, author = {Ahmed, EH and Hassan, HM and El-Sherbiny, NM and Soliman, AMA}, title = {Bacteriological Monitoring of Inanimate Surfaces and Equipment in Some Referral Hospitals in Assiut City, Egypt.}, journal = {International journal of microbiology}, volume = {2019}, number = {}, pages = {5907507}, doi = {10.1155/2019/5907507}, pmid = {31565058}, issn = {1687-918X}, abstract = {Hospital-acquired infections represent a serious public health problem in all countries. It is clear that monitoring of the hospital environment is an essential element in the control and a part of the policy for preventing nosocomial infections. It allows a better understanding of the microbial ecology for the purpose of conducting preventive and corrective actions. The aims of this work were to determine the percentage of bacterial contamination of environmental samples and to identify potential nosocomial pathogens isolated from environments of seven referral hospitals from 2009 to 2015. By using the swab technique, 12863 samples were collected. Qualitative and quantitative cultures were performed. The organisms were primarily identified by colony morphology, microscopy of Gram stain, and standard biochemical tests. 25.6% of total samples showed contamination (93% was monomicrobial and 7.0% was polymicrobial). The predominant species was coagulase-negative staphylococcus (CNS) (32%), followed by methicillin-resistant S. aureus (MRSA) (26%) and then K. pneumonia (10.6%). The percentage of contamination varied among the covered hospitals and according to the year of monitoring with highly statistically significant difference (p value < 0.001). Direct contact with environmental surfaces or equipment transmits the majority of nosocomial infection. Major nosocomial pathogens have been identified. Hospital managers and healthcare bodies must be aware of the reality of the concept of environmental bacterial tanks and the need for respect of biocleaning procedures and choice of biocleaning tools.}, }
@article {pmid31563048, year = {2019}, author = {Villegas-Plazas, M and Sanabria, J and Junca, H}, title = {A composite taxonomical and functional framework of microbiomes under acid mine drainage bioremediation systems.}, journal = {Journal of environmental management}, volume = {251}, number = {}, pages = {109581}, doi = {10.1016/j.jenvman.2019.109581}, pmid = {31563048}, issn = {1095-8630}, abstract = {Mining-industry is one of the most important activities in the economic development of many countries and produces highly significant alterations on the environment, mainly due to the release of a strong acidic metal-rich wastewater called acid mine drainage (AMD). Consequently, the establishment of multiple wastewater treatment strategies remains as a fundamental challenge in AMD research. Bioremediation, as a constantly-evolving multidisciplinary endeavor had been complemented during the last decades by novel tools of increasingly higher resolution such as those based on omics approaches, which are providing detailed insights into the ecology, evolution and mechanisms of microbial communities acting in bioremediation processes. This review specifically addresses, reanalyzes and reexamines in a composite comparative manner, the available sequence information and associated metadata available in public databases about AMD impacted microbial communities; summarizing our understanding of its composition and functions, and proposing potential genetic enhancements for improved bioremediation strategies. 16 S rRNA gene-targeted sequencing data from 9 studies previously published including AMD systems reported and studied around the world, were collected and reanalyzed to compare and identify the core and most abundant genera in four distinct AMD ecosystems: surface biofilm, water, impacted soils/sediments and bioreactor microbiomes. We determined that the microbial communities of bioreactors were the most diverse in bacterial types detected. The metabolic pathways predicted strongly suggest the key role of syntrophic communities with denitrification, methanogenesis, manganese, sulfate and iron reduction. The perspectives to explore the dynamics of engineering systems by high-throughput sequencing and biochemical techniques are discussed and foreseen application of synthetic biology and omics exploration on improved AMD biotransformation are proposed.}, }
@article {pmid31562384, year = {2019}, author = {Assié, A and Leisch, N and Meier, DV and Gruber-Vodicka, H and Tegetmeyer, HE and Meyerdierks, A and Kleiner, M and Hinzke, T and Joye, S and Saxton, M and Dubilier, N and Petersen, JM}, title = {Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria).}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0508-7}, pmid = {31562384}, issn = {1751-7370}, support = {0801741//National Science Foundation (NSF)/ ; GBMF3811//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; }, abstract = {Most autotrophs use the Calvin-Benson-Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts (&quot;Candidatus Thiobarba&quot;) of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that &quot;Ca. Thiobarba&quot; switched from the rTCA cycle to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated &quot;Ca. Thiobarba&quot;. Direct stable isotope fingerprinting showed that &quot;Ca. Thiobarba&quot; has typical CBB signatures, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment.}, }
@article {pmid31559142, year = {2019}, author = {Zheng, P and Li, Y and Wu, J and Zhang, H and Huang, Y and Tan, X and Pan, J and Duan, J and Liang, W and Yin, B and Deng, F and Perry, SW and Wong, ML and Licinio, J and Wei, H and Yu, G and Xie, P}, title = {Perturbed Microbial Ecology in Myasthenia Gravis: Evidence from the Gut Microbiome and Fecal Metabolome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {6}, number = {18}, pages = {1901441}, doi = {10.1002/advs.201901441}, pmid = {31559142}, issn = {2198-3844}, abstract = {Myasthenia gravis (MG) is a devastating acquired autoimmune disease. Emerging evidence indicates that the gut microbiome plays a key role in maintaining immune system homeostasis. This work reports that MG is characterized by decreased α-phylogenetic diversity, and significantly disturbed gut microbiome and fecal metabolome. The altered gut microbial composition is associated with fecal metabolome changes, with 38.75% of altered bacterial operational taxonomic units showing significant correlations with a range of metabolite biomarkers. Some microbes are particularly linked with MG severity. Moreover, a combination of microbial makers and their correlated metabolites enable discriminating MG from healthy controls (HCs) with 100% accuracy. To investigate whether disturbed gut mcirobiome might contribute to the onset of MG, germ-free (GF) mice are initially colonized with MG microbiota (MMb) or healthy microbiota (HMb), and then immunized in a classic mouse model of MG. The MMb mice demonstrate substantially impaired locomotion ability compared with the HMb mice. This effect could be reversed by cocolonizing GF mice with both MMb and HMb. The MMb mice also exhibit similar disturbances of fecal metabolic pathways as found in MG. Together these data demonstrate disturbances in microbiome composition and activity that are likely to be relevant to the pathogenesis of MG.}, }
@article {pmid31557953, year = {2019}, author = {Zhang, Z and Mocanu, V and Cai, C and Dang, J and Slater, L and Deehan, EC and Walter, J and Madsen, KL}, title = {Impact of Fecal Microbiota Transplantation on Obesity and Metabolic Syndrome-A Systematic Review.}, journal = {Nutrients}, volume = {11}, number = {10}, pages = {}, doi = {10.3390/nu11102291}, pmid = {31557953}, issn = {2072-6643}, support = {./CAPMC/CIHR/Canada ; }, abstract = {Fecal microbiota transplantation (FMT) is a gut microbial-modulation strategy that has been investigated for the treatment of a variety of human diseases, including obesity-associated metabolic disorders. This study appraises current literature and provides an overview of the effectiveness and limitations of FMT as a potential therapeutic strategy for obesity and metabolic syndrome (MS). Five electronic databases and two gray literature sources were searched up to 10 December 2018. All interventional and observational studies that contained information on the relevant population (adult patients with obesity and MS), intervention (receiving allogeneic FMT) and outcomes (metabolic parameters) were eligible. From 1096 unique citations, three randomized placebo-controlled studies (76 patients with obesity and MS, body mass index = 34.8 ± 4.1 kg/m2, fasting plasma glucose = 5.8 ± 0.7 mmol/L) were included for review. Studies reported mixed results with regards to improvement in metabolic parameters. Two studies reported improved peripheral insulin sensitivity (rate of glucose disappearance, RD) at 6 weeks in patients receiving donor FMT versus patients receiving the placebo control. In addition, one study observed lower HbA1c levels in FMT patients at 6 weeks. No differences in fasting plasma glucose, hepatic insulin sensitivity, body mass index (BMI), or cholesterol markers were observed between two groups across all included studies. While promising, the influence of FMT on long-term clinical endpoints needs to be further explored. Future studies are also required to better understand the mechanisms through which changes in gut microbial ecology and engraftment of microbiota affect metabolic outcomes for patients with obesity and MS. In addition, further research is needed to better define the optimal fecal microbial preparation, dosing, and method of delivery.}, }
@article {pmid31557655, year = {2019}, author = {Wang, Y and Lin, Z and He, L and Huang, W and Zhou, J and He, Q}, title = {Simultaneous partial nitrification, anammox and denitrification (SNAD) process for nitrogen and refractory organic compounds removal from mature landfill leachate: Performance and metagenome-based microbial ecology.}, journal = {Bioresource technology}, volume = {294}, number = {}, pages = {122166}, doi = {10.1016/j.biortech.2019.122166}, pmid = {31557655}, issn = {1873-2976}, abstract = {In this study, a simultaneous partial nitrification, Anammox and denitrification (SNAD) bioreactor was constructed for mature landfill leachate treatment, which exhibited favorable NH4+-N (98.9-99.9%), TN (90.7-94.9%) and bio-refractory organic compounds (46.2-67.7%) removal efficiencies. Stoichiometric analysis demonstrated that the synergy of ammonium-oxidizing bacteria and Anammox bacteria dominated TN removal (96.1-97.2%). NO3--N produced in Anammox could be further reduced through (partial) denitrification and dissimilatory nitrate reduction to ammonium (DNRA). The results highlighted that humic-like and their intermediates might serve as the electron donor for these (partial) denitrifiers and DNRA bacteria to remove NO3--N, and could be effectively removed from mature landfill leachate in SNAD bioreactor. Metagenomic characterization further demonstrated that phyla Chloroflexi, Chlorobi and genera Nitrosomonas, Ignavibacterium and Aminiphilus might be responsible for such humic-like degradation. Overall, this work offers new insights into the metagenome-based bioinformatic roles for the previously understudied microorganisms in SNAD bioreactor for mature landfill leachate treatment.}, }
@article {pmid31556187, year = {2019}, author = {Tang, HC and Sieo, CC and Abdullah, N and Chong, CW and Gan, HM and Mohd Asrore, MS and Yong, CY and Omar, AR and Ho, YW}, title = {Effects of supplementing freeze-dried Mitsuokella jalaludinii phytase on the growth performance and gut microbial diversity of broiler chickens.}, journal = {Journal of animal physiology and animal nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpn.13208}, pmid = {31556187}, issn = {1439-0396}, support = {06-01-04-SF1376//eScience Fund/ ; }, abstract = {Inclusion of phytase in animal feedstuff is a common practice to enhance nutrients availability. However, little is known about the effects of phytase supplementation on the microbial ecology of the gastrointestinal tract. In this study, freeze-dried Mitsuokella jalaludinii phytase (MJ) was evaluated in a feeding trial with broilers fed a low available phosphorus (aP) diet. A total of 180 male broiler chicks (day-old Cobb) were assigned into three dietary treatments: Control fed with 0.4% (w/w) of available phosphorus (aP); Group T1 fed low aP [0.2% (w/w)] supplemented with MJ; and T2 fed low aP and deactivated MJ. The source of readily available P, dicalcium phosphate (DCP), was removed from low aP diet, whereby additional limestone was provided to replace the amount of Ca normally found in DCP. For each treatment, 4 replicate pens were used, where each pen consisted of 15 animals. The animals' energy intake and caecal bacterial community were monitored weekly for up to 3 weeks. The apparent metabolizable energy (AME) and apparent digestibility of dry matter (ADDM) of broilers fed with different diets were determined. In addition, the caecal microbial diversities of broilers were assessed using high-throughput next-generation sequencing targeting the V3-V4 region of bacterial 16S rRNA. The results showed that broilers fed with T1 diet have better feed conversion ratio (FCR) when compared to the Control (p < .05) and T2 diets (p < .05), demonstrating the efficiency of MJ as a supplement to low aP diet. Nevertheless, MJ did not significantly affect the microbial population and diversity in broilers' caeca, which mainly consists of members from Bacteroidetes, Firmicutes, and Proteobacteria. Regardless, significant variations in the caecal bacterial composition were observed over time, probably due to succession as the broilers aged. This is the first reported study on the effect of MJ on the microbial diversity of broiler's caeca.}, }
@article {pmid31555253, year = {2019}, author = {Sarkar, A and Morita, D and Ghosh, A and Chowdhury, G and Mukhopadhyay, AK and Okamoto, K and Ramamurthy, T}, title = {Altered Integrative and Conjugative Elements (ICEs) in Recent Vibrio cholerae O1 Isolated From Cholera Cases, Kolkata, India.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2072}, doi = {10.3389/fmicb.2019.02072}, pmid = {31555253}, issn = {1664-302X}, abstract = {The self-transferring integrative and conjugative elements (ICEs) are large genomic segments carrying several bacterial adaptive functions including antimicrobial resistance (AMR). SXT/R391 family is one of the ICEs extensively studied in cholera-causing pathogen Vibrio cholerae. The genetic characteristics of ICE-SXT/R391 in V. cholerae are dynamic and region-specific. These ICEs in V. cholerae are strongly correlated with resistance to several antibiotics such as tetracycline, streptomycin and trimethoprim-sulfamethoxazole. We screened V. cholerae O1 strains isolated from cholera patients in Kolkata, India from 2008 to 2015 for antibiotic susceptibility and the presence of ICEs, and subsequently sequenced their conserved genes. Resistance to tetracycline, streptomycin and trimethoprim-sulfamethoxazole was detected in strains isolated during 2008-2010 and 2014-2015. The genes encoding resistance to tetracycline (tetA), trimethoprim-sulfamethoxazole (dfrA1 and sul2), streptomycin (strAB), and chloramphenicol (floR) were detected in the ICEs of these strains. There was a decrease in overall drug resistance in V. cholerae associated with the ICEs in 2011. DNA sequence analysis also showed that AMR in these strains was conferred mainly by two types of ICEs, i.e., ICETET (comprising tetA, strAB, sul2, and dfrA1) and ICEGEN (floR, strAB, sul2, and dfrA1). Based on the genetic structure, Kolkata strains of V. cholerae O1 had distinct genetic traits different from the ICEs reported in other cholera endemic regions. Transfer of AMR was confirmed by conjugation with sodium azide resistant Escherichia coli J53. In addition to the acquired resistance to streptomycin and trimethoprim-sulfamethoxazole, the conjugally transferred (CT) E. coli J53 with ICE showed higher resistance to chloramphenicol and tetracycline than the donor V. cholerae. Pulsed-field gel electrophoresis (PFGE) based clonal analysis revealed that the V. cholerae strains could be grouped based on their ICEs and AMR patterns. Our findings demonstrate the epidemiological importance of ICEs and their role in the emergence of multidrug resistance (MDR) in El Tor vibrios.}, }
@article {pmid31555238, year = {2019}, author = {Pires, ES and Hardoim, CCP and Miranda, KR and Secco, DA and Lobo, LA and de Carvalho, DP and Han, J and Borchers, CH and Ferreira, RBR and Salles, JF and Domingues, RMCP and Antunes, LCM}, title = {The Gut Microbiome and Metabolome of Two Riparian Communities in the Amazon.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2003}, doi = {10.3389/fmicb.2019.02003}, pmid = {31555238}, issn = {1664-302X}, abstract = {During the last decades it has become increasingly clear that the microbes that live on and in humans are critical for health. The communities they form, termed microbiomes, are involved in fundamental processes such as the maturation and constant regulation of the immune system. Additionally, they constitute a strong defense barrier to invading pathogens, and are also intricately linked to nutrition. The parameters that affect the establishment and maintenance of these microbial communities are diverse, and include the genetic background, mode of birth, nutrition, hygiene, and host lifestyle in general. Here, we describe the characterization of the gut microbiome of individuals living in the Amazon, and the comparison of these microbial communities to those found in individuals from an urban, industrialized setting. Our results showed striking differences in microbial communities from these two types of populations. Additionally, we used high-throughput metabolomics to study the chemical ecology of the gut environment and found significant metabolic changes between the two populations. Although we cannot point out a single cause for the microbial and metabolic changes observed between Amazonian and urban individuals, they are likely to include dietary differences as well as diverse patterns of environmental exposure. To our knowledge, this is the first description of gut microbial and metabolic profiles in Amazonian populations, and it provides a starting point for thorough characterizations of the impact of individual environmental conditions on the human microbiome and metabolome.}, }
@article {pmid31554820, year = {2019}, author = {Riva, A and Kuzyk, O and Forsberg, E and Siuzdak, G and Pfann, C and Herbold, C and Daims, H and Loy, A and Warth, B and Berry, D}, title = {A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4366}, doi = {10.1038/s41467-019-12413-0}, pmid = {31554820}, issn = {2041-1723}, support = {P26127-B20//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; I 2320-B22//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; J-3808//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; }, abstract = {Compartmentalization of the gut microbiota is thought to be important to system function, but the extent of spatial organization in the gut ecosystem remains poorly understood. Here, we profile the murine colonic microbiota along longitudinal and lateral axes using laser capture microdissection. We found fine-scale spatial structuring of the microbiota marked by gradients in composition and diversity along the length of the colon. Privation of fiber reduces the diversity of the microbiota and disrupts longitudinal and lateral gradients in microbiota composition. Both mucus-adjacent and luminal communities are influenced by the absence of dietary fiber, with the loss of a characteristic distal colon microbiota and a reduction in the mucosa-adjacent community, concomitant with depletion of the mucus layer. These results indicate that diet has not only global but also local effects on the composition of the gut microbiota, which may affect function and resilience differently depending on location.}, }
@article {pmid31554088, year = {2019}, author = {Vissenaekens, H and Grootaert, C and Rajkovic, A and De Schutter, K and Raes, K and Smagghe, G and Van de Wiele, T and Van Camp, J}, title = {Cell line-dependent increase in cellular quercetin accumulation upon stress induced by valinomycin and lipopolysaccharide, but not by TNF-α.}, journal = {Food research international (Ottawa, Ont.)}, volume = {125}, number = {}, pages = {108596}, doi = {10.1016/j.foodres.2019.108596}, pmid = {31554088}, issn = {1873-7145}, abstract = {As the interface between the luminal and internal environment, the intestinal epithelium is strongly exposed to food-related, host-related and microbial stress. Furthermore, the endothelial stress response plays an important role in vascular disease development, which may be improved upon consumption of dietary bioactives such as polyphenols. The impact of the latter, however, is largely individual-dependent and effects are, in most cases, only observed under mild diseased conditions. Here, it is hypothesized that the individual's stressor levels may contribute to this variable response. To this end, the impact of the stressors (i) valinomycin (as model for cereulide, food-related microbial metabolite), (ii) TNF-α (host-related) and (iii) lipopolysaccharide (gram-negative bacterial cell related) on flavonoid accumulation was investigated in several intestinal and endothelial cell lines. Flow cytometry, confocal microscopy and an in-house developed, robust and high-throughput spectrofluorometric method, showed that quercetin accumulated in all tested cell lines in a dose-dependent manner. Upon stress induced by valinomycin and to a lesser extent by lipopolysaccharide, but not by TNF-α, an increased quercetin accumulation was observed in proliferating intestinal and endothelial cells and not in differentiated intestinal or quiescent endothelial cells. Therefore, flavonoid accumulation may be a potential cellular stress response mechanism which strongly depends on the applied stressor, flavonoid, cell line and even growth conditions. This opens perspectives for further understanding the mechanisms by which cellular stress may shape the individual's response to bioactive compounds.}, }
@article {pmid31553939, year = {2019}, author = {Zhang, Y and Shen, Z and Zhang, F and Yu, Y and Li, J and Lin, X}, title = {Taxonomy and phylogeny of Pseudovorticella littoralis sp. n. and P. alani sp. n. (Ciliophora: Peritrichia) from coastal waters of southern China.}, journal = {European journal of protistology}, volume = {71}, number = {}, pages = {125635}, doi = {10.1016/j.ejop.2019.125635}, pmid = {31553939}, issn = {1618-0429}, abstract = {The morphology, infraciliature, and silverline system of two peritrich ciliates, Pseudovorticella littoralis sp. n. and P. alani sp. n., isolated from coastal waters of southern China, were investigated based on both living and silver-stained specimens. Pseudovorticella littoralis sp. n. is characterized by the following combination of characters: cell inverted cone-shaped; contractile vacuole ventral; J-shaped macronucleus; infundibular polykinety 3 with two kinetosome rows of equal length; 19-26 silverlines from peristome to trochal band and 5-14 from trochal band to scopula. Pseudovorticella alani sp. n. is characterized by: cell inverted bell-shaped; contractile vacuole ventral; J-shaped macronucleus recurved almost forming a loop; infundibular polykinety 3 with three kinetosome rows, outer two rows longer than inner one; 48-61 silverlines between peristome and aboral trochal band, and 12-20 between aboral trochal band and scopula. The SSU rDNA sequences of both new species are reported and their genetic distances with congeners and phylogenetic relationships are investigated. Pseudovorticella and Epicarchesium cluster into two subclades with low support values. One subclade contains nearly all the available sequences of Pseudovorticella and Epicarchesium. Another one contains P. monilata and E. pectinatum. This calls on the need of a generic re-classification of Pseudovorticella and Epicarchesium based on more morphological and molecular data.}, }
@article {pmid31553931, year = {2019}, author = {Subirats, J and Di Cesare, A and Varela Della Giustina, S and Fiorentino, A and Eckert, EM and Rodriguez-Mozaz, S and Borrego, CM and Corno, G}, title = {High-quality treated wastewater causes remarkable changes in natural microbial communities and intI1 gene abundance.}, journal = {Water research}, volume = {167}, number = {}, pages = {114895}, doi = {10.1016/j.watres.2019.114895}, pmid = {31553931}, issn = {1879-2448}, abstract = {We carry out a mesocosms experiment to assess the impact of high-quality treated wastewater intended for agricultural reuse (HQWR) on freshwater bacteria seldom exposed to anthropogenic pollution. Effects were assessed by comparing the abundance and composition of bacterial communities as well as their resistance profile under control (source water from an unpolluted lake) and treatment conditions (source water mixed 1:1 with HQWR, with and without 5 μg L-1 of cefotaxime). We investigated the effect of the different conditions on the abundance of genes encoding resistance to β-lactams and carbapenems (blaTEM, blaCTX-M, blaOXA, and blaKPC), fluoroquinolones (qnrS), tetracyclines (tetA), sulfonamides (sul2), macrolides (ermB), arsenic and cadmium (arsB and czcA, respectively), and on the gene encoding the Class 1 integron integrase (intI1). Bacterial communities exposed to HQWR showed a significant higher abundance of tetA, arsB, czcA, and intI1 genes, whereas those exposed to Cefotaxime-amended HQWR did not. Genes conferring resistance to carbapenems, β-lactams, fluoroquinolones, and macrolides were below detection limit in all treatments. Besides, the higher availability of nutrients under treatment conditions favored bacterial growth in comparison to those exposed to control conditions. Particularly, Acinetobacter spp. and Pseudomonas spp. were significantly enriched after 22 days of treatment exposure. The presence of cefotaxime (a third generation cephalosporine) in the feeding medium caused an enrichment of bacterial communities in sequences affiliated to Acinetobacter thus suggesting that these resistant forms may possess resistance genes other than those studied here (blaCTX-M, blaOXA, and blaKPC). Although derived from a mesocosm experiment in continuous cultures, our results call attention to the need of refined regulations regarding the use of reclaimed water in agriculture since even high-quality treated wastewater may lead to undesired effects on receiving bacterial communities in terms of composition and dissemination of antibiotic resistance genes.}, }
@article {pmid31553930, year = {2019}, author = {Regnery, J and Parrhysius, P and Schulz, RS and Möhlenkamp, C and Buchmeier, G and Reifferscheid, G and Brinke, M}, title = {Wastewater-borne exposure of limnic fish to anticoagulant rodenticides.}, journal = {Water research}, volume = {167}, number = {}, pages = {115090}, doi = {10.1016/j.watres.2019.115090}, pmid = {31553930}, issn = {1879-2448}, abstract = {The recent emergence of second-generation anticoagulant rodenticides (AR) in the aquatic environment emphasizes the relevance and impact of aquatic exposure pathways during rodent control. Pest control in municipal sewer systems of urban and suburban areas is thought to be an important emission pathway for AR to reach wastewater and municipal wastewater treatment plants (WWTP), respectively. To circumstantiate that AR will enter streams via effluent discharges and bioaccumulate in aquatic organisms despite very low predicted environmental emissions, we conducted a retrospective biological monitoring of fish tissue samples from different WWTP fish monitoring ponds exclusively fed by municipal effluents in Bavaria, Germany. At the same time, information about rodent control in associated sewer systems was collected by telephone survey to assess relationships between sewer baiting and rodenticide residues in fish. In addition, mussel and fish tissue samples from several Bavarian surface waters with different effluent impact were analyzed to evaluate the prevalence of anticoagulants in indigenous aquatic organisms. Hepatic AR residues were detected at 12 out of 25 WWTP sampling sites in the low μg/kg range, thereof six sites with one or more second-generation AR (i.e., brodifacoum, difenacoum, bromadiolone). 14 of 18 surveyed sites confirmed sewer baiting with AR and detected hepatic residues matched the reported active ingredients used for sewer baiting at six sites. Furthermore, second-generation AR were detected in more than 80% of fish liver samples from investigated Bavarian streams. Highest total hepatic AR concentrations in these fish were 9.1 and 8.5 μg/kg wet weight, respectively and were observed at two riverine sampling sites characterized by close proximity to upstream WWTP outfalls. No anticoagulant residues were found in fish liver samples from two lakes without known influences of effluent discharges. The findings of our study clearly show incomplete removal of anticoagulants during conventional wastewater treatment and confirm exposure of aquatic organisms via municipal effluents. Based on the demonstrated temporal and spatial coherence between sewer baiting and hepatic AR residues in effluent-exposed fish, sewer baiting in combined sewer systems contributes to the release of active ingredients into the aquatic environment.}, }
@article {pmid31552450, year = {2019}, author = {Wagner, AO and Praeg, N and Illmer, P}, title = {Spiking a Silty-Sand Reference Soil with Bacterial DNA: Limits and Pitfalls in the Discrimination of Live and Dead Cells When Applying Ethidium Monoazide (EMA) Treatment.}, journal = {Current microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00284-019-01772-y}, pmid = {31552450}, issn = {1432-0991}, support = {P 22815//Austrian Science Fund/ ; }, abstract = {In the present study, EMA (ethidium monoazide) treatment was applied to a silty-sand reference soil prior to DNA extraction to enable a differentiation between dead and living cells. For this purpose, a reference soil was spiked with Listeria monocytogenes cells or cell equivalents, respectively. With the purpose of evaluating optimum treatment conditions, different EMA concentrations have been tested. However, the results remained largely inconclusive. Furthermore, varied dark incubation periods allowing EMA to penetrate dead cells did not allow the selective removal of DNA from membrane-compromised cells in downstream analyses. In contrast to undiluted soil, an effect of EMA treatment during DNA extraction could be observed when using a 1:10 dilution of the reference soil; however, the effect has not been sufficiently selective to act on heat-treated cells only. Although the application of EMA to soil requires further evaluation, the procedure harbors future potential for improving DNA-based approaches in microbial ecology studies.}, }
@article {pmid31551063, year = {2019}, author = {Keiser, CN and Hammer, TJ and Pruitt, JN}, title = {Social spider webs harbour largely consistent bacterial communities across broad spatial scales.}, journal = {Biology letters}, volume = {15}, number = {9}, pages = {20190436}, doi = {10.1098/rsbl.2019.0436}, pmid = {31551063}, issn = {1744-957X}, abstract = {Social animals that live in domiciles constructed from biomaterials may facilitate microbial growth. Spider webs are one of the most conspicuous biomaterials in nature, yet almost nothing is known about the potential for webs to harbour microbes, even in social spiders that live in dense, long-term aggregations. Here, we tested whether the dominant bacteria present in social spider webs vary across sampling localities and whether the more permanent retreat web harbours compositionally distinct microbes from the more ephemeral capture webs in the desert social spider, Stegodyphus dumicola. We also sampled spider cuticles and prey items in a subset of colonies. We found that spider colonies across large spatial scales harboured similar web-associated bacterial communities. We also found substantial overlap in bacterial community composition between spider cuticle, prey and web samples. These data suggest that social spider webs can harbour characteristic microbial communities and potentially facilitate microbial transmission among individuals, and this study serves as the first step towards understanding the microbial ecology of these peculiar animal societies.}, }
@article {pmid31550548, year = {2019}, author = {De Vrieze, J and Verbeeck, K and Pikaar, I and Boere, J and Van Wijk, A and Rabaey, K and Verstraete, W}, title = {The hydrogen gas bio-based economy and the production of renewable building block chemicals, food and energy.}, journal = {New biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.nbt.2019.09.004}, pmid = {31550548}, issn = {1876-4347}, abstract = {The carrying capacity of the planet is being exceeded and there is an urgent need to bring forward revolutionary approaches, particularly in terms of energy supply, carbon emissions and nitrogen inputs into the biosphere. Hydrogen gas, generated by means of renewable energy through water electrolysis, can be a platform molecule to drive the future bioeconomy and electrification in the 21st century. The potential to use hydrogen gas in microbial metabolic processes is highly versatile, and this opens a broad range of opportunities for novel biotechnological developments and applications. A first approach concerns the central role of hydrogen gas in the production of bio-based building block chemicals using the methane route, thus, bypassing the inherent low economic value of methane towards higher-value products. Secondly, hydrogen gas can serve as a key carbon-neutral source to produce third-generation proteins, i.e. microbial protein for food applications, whilst simultaneously enabling carbon capture and nutrient recovery, directly at their point of emission. Combining both approaches to deal with the intermittent nature of renewable energy sources maximises the ability for efficient use of renewable resources.}, }
@article {pmid31550268, year = {2019}, author = {Mahjoubi, M and Aliyu, H and Cappello, S and Naifer, M and Souissi, Y and Cowan, DA and Cherif, A}, title = {The genome of Alcaligenes aquatilis strain BU33N: Insights into hydrocarbon degradation capacity.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0221574}, doi = {10.1371/journal.pone.0221574}, pmid = {31550268}, issn = {1932-6203}, abstract = {Environmental contamination with hydrocarbons though natural and anthropogenic activities is a serious threat to biodiversity and human health. Microbial bioremediation is considered as the effective means of treating such contamination. This study describes a biosurfactant producing bacterium capable of utilizing crude oil and various hydrocarbons as the sole carbon source. Strain BU33N was isolated from hydrocarbon polluted sediments from the Bizerte coast (northern Tunisia) and was identified as Alcaligenes aquatilis on the basis of 16S rRNA gene sequence analysis. When grown on crude oil and phenanthrene as sole carbon and energy sources, isolate BU33N was able to degrade ~86%, ~56% and 70% of TERHc, n-alkanes and phenanthrene, respectively. The draft genome sequence of the A. aquatilis strain BU33N was assembled into one scaffold of 3,838,299 bp (G+C content of 56.1%). Annotation of the BU33N genome resulted in 3,506 protein-coding genes and 56 rRNA genes. A large repertoire of genes related to the metabolism of aromatic compounds including genes encoding enzymes involved in the complete degradation of benzoate were identified. Also genes associated with resistance to heavy metals such as copper tolerance and cobalt-zinc-cadmium resistance were identified in BU33N. This work provides insight into the genomic basis of biodegradation capabilities and bioremediation/detoxification potential of A. aquatilis BU33N.}, }
@article {pmid31548611, year = {2019}, author = {Soares-Castro, P and Araújo-Rodrigues, H and Godoy-Vitorino, F and Ferreira, M and Covelo, P and López, A and Vingada, J and Eira, C and Santos, PM}, title = {Microbiota fingerprints within the oral cavity of cetaceans as indicators for population biomonitoring.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13679}, doi = {10.1038/s41598-019-50139-7}, pmid = {31548611}, issn = {2045-2322}, abstract = {The composition of mammalian microbiota has been related with the host health status. In this study, we assessed the oral microbiome of 3 cetacean species most commonly found stranded in Iberian Atlantic waters (Delphinus delphis, Stenella coeruleoalba and Phocoena phocoena), using 16S rDNA-amplicon metabarcoding. All oral microbiomes were dominated by Proteobacteria, Firmicutes, Bacteroidetes and Fusobacteria bacteria, which were also predominant in the oral cavity of Tursiops truncatus. A Constrained Canonical Analysis (CCA) showed that the major factors shaping the composition of 38 oral microbiomes (p-value < 0.05) were: (i) animal species and (ii) age class, segregating adults and juveniles. The correlation analysis also grouped the microbiomes by animal stranding location and health status. Similar discriminatory patterns were detected using the data from a previous study on Tursiops truncatus, indicating that this correlation approach may facilitate data comparisons between different studies on several cetacean species. This study identified a total of 15 bacterial genera and 27 OTUs discriminating between the observed CCA groups, which can be further explored as microbiota fingerprints to develop (i) specific diagnostic assays for cetacean population conservation and (ii) bio-monitoring approaches to assess the health of marine ecosystems from the Iberian Atlantic basin, using cetaceans as bioindicators.}, }
@article {pmid31548387, year = {2019}, author = {Petersen, J and Vollmers, J and Ringel, V and Brinkmann, H and Ellebrandt-Sperling, C and Spröer, C and Howat, AM and Murrell, JC and Kaster, AK}, title = {A marine plasmid hitchhiking vast phylogenetic and geographic distances.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1905878116}, pmid = {31548387}, issn = {1091-6490}, abstract = {Horizontal gene transfer (HGT) plays an important role in bacterial evolution and serves as a driving force for bacterial diversity and versatility. HGT events often involve mobile genetic elements like plasmids, which can promote their own dissemination by associating with adaptive traits in the gene pool of the so-called mobilome. Novel traits that evolve through HGT can therefore lead to the exploitation of new ecological niches, prompting an adaptive radiation of bacterial species. In this study, we present phylogenetic, biogeographic, and functional analyses of a previously unrecognized RepL-type plasmid found in diverse members of the marine Roseobacter group across the globe. Noteworthy, 100% identical plasmids were detected in phylogenetically and geographically distant bacteria, revealing a so-far overlooked, but environmentally highly relevant vector for HGT. The genomic and functional characterization of this plasmid showed a completely conserved backbone dedicated to replication, stability, and mobilization as well as an interchangeable gene cassette with highly diverse, but recurring motifs. The majority of the latter appear to be involved in mechanisms coping with toxins and/or pollutants in the marine environment. Furthermore, we provide experimental evidence that the plasmid has the potential to be transmitted across bacterial orders, thereby increasing our understanding of evolution and microbial niche adaptation in the environment.}, }
@article {pmid31547186, year = {2019}, author = {Messal, M and Slippers, B and Naidoo, S and Bezuidt, O and Kemler, M}, title = {Active Fungal Communities in Asymptomatic Eucalyptus grandis Stems Differ between a Susceptible and Resistant Clone.}, journal = {Microorganisms}, volume = {7}, number = {10}, pages = {}, doi = {10.3390/microorganisms7100375}, pmid = {31547186}, issn = {2076-2607}, abstract = {Fungi represent a common and diverse part of the microbial communities that associate with plants. They also commonly colonise various plant parts asymptomatically. The molecular mechanisms of these interactions are, however, poorly understood. In this study we use transcriptomic data from Eucalyptus grandis, to demonstrate that RNA-seq data are a neglected source of information to study fungal-host interactions, by exploring the fungal transcripts they inevitably contain. We identified fungal transcripts from E. grandis data based on their sequence dissimilarity to the E. grandis genome and predicted biological functions. Taxonomic classifications identified, amongst other fungi, many well-known pathogenic fungal taxa in the asymptomatic tissue of E. grandis. The comparison of a clone of E. grandis resistant to Chrysoporthe austroafricana with a susceptible clone revealed a significant difference in the number of fungal transcripts, while the number of fungal taxa was not substantially affected. Classifications of transcripts based on their respective biological functions showed that the fungal communities of the two E. grandis clones associate with fundamental biological processes, with some notable differences. To shield the greater host defence machinery in the resistant E. grandis clone, fungi produce more secondary metabolites, whereas the environment for fungi associated with the susceptible E. grandis clone is more conducive for building fungal cellular structures and biomass growth. Secreted proteins included carbohydrate active enzymes that potentially are involved in fungal-plant and fungal-microbe interactions. While plant transcriptome datasets cannot replace the need for designed experiments to probe plant-microbe interactions at a molecular level, they clearly hold potential to add to the understanding of the diversity of plant-microbe interactions.}, }
@article {pmid31547035, year = {2019}, author = {Wang, J and Sun, Y and Tao, D and Wang, S and Li, C and Zheng, F and Wu, Z}, title = {Reduction of Escherichia coli O157:H7, Listeria monocytogenes, and Naturally Present Microbe Counts on Lettuce using an Acid Mixture of Acetic and Lactic Acid.}, journal = {Microorganisms}, volume = {7}, number = {10}, pages = {}, doi = {10.3390/microorganisms7100373}, pmid = {31547035}, issn = {2076-2607}, abstract = {Lactic acid (LA) and acetic acid (AA) are independently used to disinfect fresh leaf vegetables. LA has a higher efficacy but costs more than AA. Herein, we compared the disinfection efficacy of LA, AA, and their mixture on lettuce to determine whether the cheaper acid mixture shows similar or more efficacy than LA. Quality analysis indicated that the acid mixture and individual acids did not cause additional loss of instrument color and polyphenolic content compared with that of the control; however, visible defects were observed at AA concentrations exceeding 0.8%. Analysis of Escherichia coli O157:H7, Listeria monocytogenes, and naturally present microbes (aerobic mesophilic and psychrotrophic bacteria, coliforms, molds, and yeasts) showed that the acid mixture led to the highest reduction in microbial count during storage. 16S rRNA sequencing was further employed to understand the effects of the acid mixture and individual acids on lettuce microbial ecology. During storage, the acid mixture and individual acids significantly decreased the abundance of Massilia spp. and Alkanindiges spp. but there was a marked increase in Escherichia-Shigella abundance (LA: 0.003-58.82%; AA: 0.01-55.34%; acid mixture: undetected to 50.71%; control: 0.007-33.09%), indicating that acid disinfection altered the microbial ecology to stimulate Escherichia-Shigella growth. These results enhance our understanding of the relationship between lettuce disinfection and ecological changes.}, }
@article {pmid31546184, year = {2019}, author = {Pietro-Souza, W and de Campos Pereira, F and Mello, IS and Stachack, FFF and Terezo, AJ and Cunha, CND and White, JF and Li, H and Soares, MA}, title = {Mercury resistance and bioremediation mediated by endophytic fungi.}, journal = {Chemosphere}, volume = {240}, number = {}, pages = {124874}, doi = {10.1016/j.chemosphere.2019.124874}, pmid = {31546184}, issn = {1879-1298}, abstract = {The present study proposes the use of endophytic fungi for mercury bioremediation in in vitro and host-associated systems. We examined mercury resistance in 32 strains of endophytic fungi grown in culture medium supplemented with toxic metal concentrations. The residual mercury concentrations were quantified after mycelial growth. Aspergillus sp. A31, Curvularia geniculata P1, Lindgomycetaceae P87, and Westerdykella sp. P71 were selected and further tested for mercury bioremediation and bioaccumulation in vitro, as well as for growth promotion of Aeschynomene fluminensis and Zea mays in the presence or absence of the metal. Aspergillus sp. A31, C. geniculata P1, Lindgomycetaceae P87 and Westerdykella sp. P71 removed up to 100% of mercury from the culture medium in a species-dependent manner and they promoted A. fluminensis and Z. mays growth in substrates containing mercury or not (Dunnett's test, p < 0.05). Lindgomycetaceae P87 and C. geniculata P1 are dark septate endophytic fungi that endophytically colonize root cells of their host plants. The increase of host biomass correlated with the reduction of soil mercury concentration due to the metal bioaccumulation in host tissues and its possible volatilization. The soil mercury concentration was decreased by 7.69% and 57.14% in A. fluminensis plants inoculated with Lindgomycetaceae P87 + Aspergillus sp. A31 and Lindgomycetaceae P87, respectively (Dunnet's test, p < 0.05). The resistance mechanisms of mercury volatilization and bioaccumulation in plant tissues mediated by these endophytic fungi can contribute to bioremediation programs. The biochemical and genetic mechanisms involved in bioaccumulation and volatilization need to be elucidated in the future.}, }
@article {pmid31546029, year = {2019}, author = {Pikaar, I and Flugen, M and Lin, HW and Salehin, S and Li, J and Donose, BC and Dennis, PG and Bethke, L and Johnson, I and Rabaey, K and Yuan, Z}, title = {Full-scale investigation of in-situ iron and alkalinity generation for efficient sulfide control.}, journal = {Water research}, volume = {167}, number = {}, pages = {115032}, doi = {10.1016/j.watres.2019.115032}, pmid = {31546029}, issn = {1879-2448}, abstract = {Hydrogen sulfide induced corrosion of concrete sewer pipes is a major issue for wastewater utilities globally. One of the most commonly used methods to combat hydrogen sulfide is the addition of ferric chloride. While a reliable and effective method, ferric chloride is acidic causing OH&amp;S concerns as well as alkalinity consumption in sewage. This study investigates, under full-scale field conditions, an alternative method for sulfide control by in-situ electrochemical generation of iron ions using sacrificial iron electrodes. This method concomitantly produces alkalinity through cathodic OH- generation, rather than consumption. The gaseous hydrogen sulfide concentrations at the discharge wet well of a real-life rising main (length: ∼1 km in, diameter: 150 mm) decreased from 173 ppm to 43 ppm (90 percentile of peak values), when a current of 0.86 A/m3 of sewage was applied. The 90 percentile peak H2S value was further reduced to 6.6 ppm when the applied current was increased to 1.14 A/m3 sewage. Moreover, methane generation was almost completely inhibited from 25.3 ± 1.46 mg COD/L to 0.06 ± 0.04 mg COD/L. The overall cell voltage remained constant throughout the experimental period clearly showing the stability of the process. Detailed characterization of the down-stream sewer pipe biofilm revealed the complexity of the iron chemistry as the in-situ produced iron ions undergo transformation into a variety of iron species. Overall, this study demonstrates that in-situ generation of iron and alkalinity is an effective alternative method for hydrogen sulfide control in sewers.}, }
@article {pmid31545283, year = {2019}, author = {Huang, X and Chen, W and Yan, C and Yang, R and Chen, Q and Xu, H and Huang, Y}, title = {Gypenosides improve the intestinal microbiota of non-alcoholic fatty liver in mice and alleviate its progression.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {118}, number = {}, pages = {109258}, doi = {10.1016/j.biopha.2019.109258}, pmid = {31545283}, issn = {1950-6007}, abstract = {Gypenosides (GP) are a type of traditional Chinese medicine (TCM) extracted from plants and commonly applied for treatment of metabolic diseases. This study aims to explore the effects of GP extracts on alleviating non-alcoholic fatty liver disease (NAFLD). In this experiment, C57BL/6 J mice were randomly assigned into normal diet control (ND), HFHC (high-fat and high-cholesterol) and HFHC + GP (GP) groups. Mice in HFHC group were fed HFHC diet combined with fructose drinking water for 12 weeks to induce the animal model of NAFLD, followed by ordinary drinking water until the end of the experiment. In the HFHC + GP group, mice were fed HFHC diet combined with fructose drinking water for 12 weeks, followed by GP-containing drinking water till the end. Mouse body weight was measured weekly. After animal procedures, mouse liver and serum samples were collected. It is shown that GP administration reduced body weight, enhanced the sensitivity to insulin resistance (IR) and decreased serum levels of ALT, AST and TG in NAFLD mice. In addition, GP treatment alleviated steatohepatitis, and downregulated ACC1, PPARγ, CD36, APOC3 and MTTP levels in mice fed with HFHC diet. Furthermore, GP treatment markedly improved intestinal microbiota, and reduced relative abundance ratio of Firmicutes / Bacteroidetes in the feces of NAFLD mice. Our results suggested that GP alleviated NAFLD in mice through improving intestinal microbiota.}, }
@article {pmid31543873, year = {2019}, author = {Alviz-Gazitua, P and Fuentes-Alburquenque, S and Rojas, LA and Turner, RJ and Guiliani, N and Seeger, M}, title = {Corrigendum: The Response of Cupriavidus metallidurans CH34 to Cadmium Involves Inhibition of the Initiation of Biofilm Formation, Decrease in Intracellular c-di-GMP Levels, and a Novel Metal Regulated Phosphodiesterase.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2014}, doi = {10.3389/fmicb.2019.02014}, pmid = {31543873}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2019.01499.].}, }
@article {pmid31541814, year = {2019}, author = {Petrin, S and Patuzzi, I and Di Cesare, A and Tiengo, A and Sette, G and Biancotto, G and Corno, G and Drigo, M and Losasso, C and Cibin, V}, title = {Evaluation and quantification of antimicrobial residues and antimicrobial resistance genes in two Italian swine farms.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {255}, number = {Pt 1}, pages = {113183}, doi = {10.1016/j.envpol.2019.113183}, pmid = {31541814}, issn = {1873-6424}, abstract = {Antimicrobial resistance genes (ARGs) are considered emerging environmental pollutants, posing potential risks for human and animal health: the misuse of antimicrobials in food-producing animals could favour the maintenance and spread of resistances in bacteria. The occurrence of ARGs in Italian swine farming - which has specific characteristics - was investigated in order to explore resistance spread dynamics. Two farrow-to-finish pig farms were longitudinally monitored: faecal samples from animals and environmental samples were collected. DNA was extracted and tetA, ermB, qnrS and mcr1 ARGs were analysed by qPCR for their ability to confer resistance to highly or critically important antimicrobials (CIAs). Moreover, 16SrDNA gene was analysed to assess bacterial abundance. ermB and tetA genes were found in animal samples and manure samples. On the contrary, mcr1 was exclusively found in weaners, while qnrS occurred in all animal categories but sows and finishers. Among the analysed genes, ermB and tetA showed the highest absolute and relative abundances. Our results indicate that ermB and tetA ARGs are widely disseminated in the explored farms, suggesting efficient maintenance among bacteria and persistence in the environment. Interestingly, the presence of qnrS and mcr1, limited to just a few animal categories, highlights inefficient dissemination of these genes in the farm environment, in particular for mcr1, a stable plasmid gene conferring resistance to the last-resort antimicrobial, colistin. Paying close attention only to the finishing phase would have hampered the discovery of resistances to CIAs at farm level, which we instead identified thanks to an intensive longitudinal monitoring programme.}, }
@article {pmid31539855, year = {2019}, author = {Santos-Clotas, E and Cabrera-Codony, A and Boada, E and Gich, F and Muñoz, R and Martín, MJ}, title = {Efficient removal of siloxanes and volatile organic compounds from sewage biogas by an anoxic biotrickling filter supplemented with activated carbon.}, journal = {Bioresource technology}, volume = {294}, number = {}, pages = {122136}, doi = {10.1016/j.biortech.2019.122136}, pmid = {31539855}, issn = {1873-2976}, abstract = {The removal of siloxanes (D4 and D5) and volatile organic contaminants (hexane, toluene and limonene) typically found in sewage biogas was investigated in a lab-scale biotrickling filter (BTF) packed with lava rock under anoxic conditions. Complete removal efficiencies for toluene and limonene were recorded at all empty bed residence time (EBRT) tested. The influence of EBRT was remarkable on the abatement of D5, whose removal decreased from 37% at 14.5 min to 16% at 4 min, while the removal of D4 and hexane remained below 16%. The packing material was supplemented with 20% of activated carbon aiming at increasing the mass transfer of the most hydrophobic pollutants. This strategy supported high removal efficiencies of 43 and 45% for hexane and D5 at the lowest EBRT. CO2 and silica were identified as mineralization products along with the presence of metabolites in the trickling solution such as dimethylsilanediol, 2-carene and α-terpinene.}, }
@article {pmid31538807, year = {2019}, author = {Tomar, SL}, title = {Oral Health Effects of Tobacco Products: Science and Regulatory Policy.}, journal = {Advances in dental research}, volume = {30}, number = {1}, pages = {2-3}, doi = {10.1177/0022034519872481}, pmid = {31538807}, issn = {1544-0737}, }
@article {pmid31536878, year = {2019}, author = {Lambrecht, E and Van Coillie, E and Van Meervenne, E and Boon, N and Heyndrickx, M and Van de Wiele, T}, title = {Commensal E. coli rapidly transfer antibiotic resistance genes to human intestinal microbiota in the Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME).}, journal = {International journal of food microbiology}, volume = {311}, number = {}, pages = {108357}, doi = {10.1016/j.ijfoodmicro.2019.108357}, pmid = {31536878}, issn = {1879-3460}, abstract = {Food-producing animals are indicated as a reservoir of antibiotic resistance genes and a potential vector for transmission of plasmid-encoded antibiotic resistance genes by conjugation to the human intestinal microbiota. In this study, transfer of an antibiotic resistance plasmid from a commensal E. coli originating from a broiler chicken towards the human intestinal microbiota was assessed by using a Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME). This in vitro model mimics the human intestinal ecosystem and received a single dose of 109E. coli MB6212, which harbors a plasmid known to confer resistance towards several antibiotics including tetracycline, sulfamethoxazole and cefotaxime. Since the degree of stress imposed by stomach pH and bile acids vary with the consumed meal size, the effect of meal size on E. coli donor survival and on plasmid transfer towards lumen and mucosal coliforms and anaerobes was determined. The administered commensal E. coli strain survived stomach acid and bile salt stress and was able to grow in the colon environment during the timeframe of the experiment (72 h). Transfer of antibiotic resistance was observed rapidly since cultivable transconjugant coliforms and anaerobes were already detected in the lumen and mucosa after 2 h in the simulated proximal colon. The presence of the resistance plasmid in the transconjugants was confirmed by PCR. Differences in meal size and adapted digestion had neither a detectable impact on antibiotic resistance transfer, nor on the survival of the E. coli donor strain, nor on short chain fatty acid profiles. The median number of resistant indigenous coliforms in the lumen of the inoculated colon vessels was 5.00 × 105 cfu/ml [min - max: 3.47 × 104-3.70 × 108 cfu/ml], and on the mucosa 1.44 × 107 cfu/g [min-max: 4.00 × 103-4.00 × 108 cfu/g]. Exact quantification of the anaerobic transconjugants was difficult, as (intrinsic) resistant anaerobic background microbiota were present. QPCR data supported the observation of plasmid transfer in the simulated colon. Moreover, inoculation of E. coli MB6212 had no significant impact on the microbial diversity in the lumen as determined by 16 S ribosomal gene based next generation sequencing on lumen samples. This study demonstrates that a commensal, antibiotic resistant E. coli strain present in food can transfer its antibiotic resistance plasmid relatively quickly to intestinal microbiota in the M-SHIME. The spread and persistence of antibiotic resistance genes and resistant bacteria in our intestinal system is an alarming scenario which might present clinical challenges, since it implies a potential reservoir for dissemination to pathogenic bacteria.}, }
@article {pmid31535335, year = {2019}, author = {Contador, CA and Veas-Castillo, L and Tapia, E and Antipán, M and Miranda, N and Ruiz-Tagle, B and García-Araya, J and Andrews, BA and Marin, M and Dorador, C and Asenjo, JA}, title = {Atacama Database: a platform of the microbiome of the Atacama Desert.}, journal = {Antonie van Leeuwenhoek}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10482-019-01328-x}, pmid = {31535335}, issn = {1572-9699}, support = {FB0001//Comisión Nacional de Investigación Científica y Tecnológica/ ; }, abstract = {The Atacama Desert is one of the oldest and driest places on Earth. In the last decade, microbial richness and diversity has been acknowledged as an important biological resource of this region. Owing to the value of the microbial diversity apparent in potential biotechnology applications and conservation purposes, it is necessary to catalogue these microbial communities to promote research activities and help to preserve the wide range of ecological niches of the Atacama region. A prototype Atacama Database has been designed and it provides a description of the rich microbial diversity of the Atacama Desert, and helps to visualise available literature resources. Data has been collected, curated, and organised into several categories to generate a single record for each organism in the database that covers classification, isolation metadata, morphology, physiology, genome and metabolism information. The current version of Atacama Database contains 2302 microorganisms and includes cultured and uncultured organisms retrieved from different environments within the desert between 1984 and 2016. These organisms are distributed in bacterial, archaeal or eukaryotic domains, along with those that are unclassified taxonomically. The initial prototype of the Atacama Database includes a basic search and taxonomic and advanced search tools to allow identification and comparison of microbial populations, and space distribution within this biome. A geolocation search was implemented to visualise the microbial diversity of the ecological niches defined by sectors and extract general information of the sampling sites. This effort will aid understanding of the microbial ecology of the desert, microbial population dynamics, seasonal behaviour, impact of climate change over time, and reveal further biotechnological applications of these microorganisms. The Atacama Database is freely available at: https://www.atacamadb.cl .}, }
@article {pmid31534146, year = {2019}, author = {Harkes, P and Suleiman, AKA and van den Elsen, SJJ and de Haan, JJ and Holterman, M and Kuramae, EE and Helder, J}, title = {Conventional and organic soil management as divergent drivers of resident and active fractions of major soil food web constituents.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13521}, doi = {10.1038/s41598-019-49854-y}, pmid = {31534146}, issn = {2045-2322}, support = {870.15.021//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 870.15.021//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; }, abstract = {Conventional agricultural production systems, typified by large inputs of mineral fertilizers and pesticides, reduce soil biodiversity and may negatively affect ecosystem services such as carbon fixation, nutrient cycling and disease suppressiveness. Organic soil management is thought to contribute to a more diverse and stable soil food web, but data detailing this effect are sparse and fragmented. We set out to map both the resident (rDNA) and the active (rRNA) fractions of bacterial, fungal, protozoan and metazoan communities under various soil management regimes in two distinct soil types with barley as the main crop. Contrasts between resident and active communities explained 22%, 14%, 21% and 25% of the variance within the bacterial, fungal, protozoan, and metazoan communities. As the active fractions of organismal groups define the actual ecological functioning of soils, our findings underline the relevance of characterizing both resident and active pools. All four major organismal groups were affected by soil management (p < 0.01), and most taxa showed both an increased presence and an enlarged activity under the organic regime. Hence, a prolonged organic soil management not only impacts the primary decomposers, bacteria and fungi, but also major representatives of the next trophic level, protists and metazoa.}, }
@article {pmid31533344, year = {2019}, author = {Zwart, MP and Ali, G and Strien, EAV and Schijlen, EGWM and Wang, M and Werf, WV and Vlak, JM}, title = {Identification of Loci Associated with Enhanced Virulence in Spodoptera litura Nucleopolyhedrovirus Isolates Using Deep Sequencing.}, journal = {Viruses}, volume = {11}, number = {9}, pages = {}, doi = {10.3390/v11090872}, pmid = {31533344}, issn = {1999-4915}, support = {CF7554/2011//Netherlands Organization for International Cooperation in Higher Education/ ; }, abstract = {Spodoptera litura is an emerging pest insect in cotton and arable crops in Central Asia. To explore the possibility of using baculoviruses as biological control agents instead of chemical pesticides, in a previous study we characterized a number of S. litura nucleopolyhedrovirus (SpltNPV) isolates from Pakistan. We found significant differences in speed of kill, an important property of a biological control agent. Here we set out to understand the genetic basis of these differences in speed of kill, by comparing the genome of the fast-killing SpltNPV-Pak-TAX1 isolate with that of the slow-killing SpltNPV-Pak-BNG isolate. These two isolates and the SpltNPV-G2 reference strain from China were deep sequenced with Illumina. As expected, the two Pakistani isolates were closely related with >99% sequence identity, whereas the Chinese isolate was more distantly related. We identified two loci that may be associated with the fast action of the SpltNPV-Pak-TAX1 isolate. First, an analysis of rates of synonymous and non-synonymous mutations identified neutral to positive selection on open reading frame (ORF) 122, encoding a viral fibroblast growth factor (vFGF) that is known to affect virulence in other baculoviruses. Second, the homologous repeat region hr17, a putative enhancer of transcription and origin of replication, is absent in SpltNPV-Pak-TAX1 suggesting it may also affect virulence. Additionally, we found there is little genetic variation within both Pakistani isolates, and we identified four genes under positive selection in both isolates that may have played a role in adaptation of SpltNPV to conditions in Central Asia. Our results contribute to the understanding of the enhanced activity of SpltNPV-Pak-TAX1, and may help to select better SpltNPV isolates for the control of S. litura in Pakistan and elsewhere.}, }
@article {pmid31528722, year = {2019}, author = {Tiwari, UP and Singh, AK and Jha, R}, title = {Fermentation characteristics of resistant starch, arabinoxylan, and β-glucan and their effects on the gut microbial ecology of pigs: A review.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {5}, number = {3}, pages = {217-226}, doi = {10.1016/j.aninu.2019.04.003}, pmid = {31528722}, issn = {2405-6383}, abstract = {Dietary fibers (DF) contain an abundant amount of energy, although the mammalian genome does not encode most of the enzymes required to degrade them. However, a mutual dependence is developed between the host and symbiotic microbes, which has the potential to extract the energy present in these DF. Dietary fibers escape digestion in the foregut and are fermented in the hindgut, producing short-chain fatty acids (SCFA) that alter the microbial ecology in the gastrointestinal tract (GIT) of pigs. Most of the carbohydrates are fermented in the proximal part, allowing protein fermentation in the distal part, resulting in colonic diseases. The structures of resistant starch (RS), arabinoxylan (AX), and β-glucan (βG) are complex; hence, makes their way into the hindgut where these are fermented and provide energy substrates for the colonic epithelial cells. Different microbes have different preferences of binding to different substrates. The RS, AX and βG act as a unique substrate for the microbes and modify the relative composition of the gut microbial community. The granule dimension and surface area of each substrate are different, which influences the penetration capacity of microbes. Arabinose and xylan are 2 different hemicelluloses, but arabinose is substituted on the xylan backbone and occurs in the form of AX. Fermentation of xylan produces butyrate primarily in the small intestine, whereas arabinose produces butyrate in the large intestine. Types of RS and forms of βG also exert beneficial effects by producing different metabolites and modulating the intestinal microbiota. Therefore, it is important to have information of different types of RS, AX and βG and their roles in microbial modulation to get the optimum benefits of fiber fermentation in the gut. This review provides relevant information on the similarities and differences that exist in the way RS, AX, and βG are fermented, and their positive and negative effects on SCFA production and gut microbial ecology of pigs. These insights will help nutritionists to develop dietary strategies that can modulate specific SCFA production and promote beneficial microbiota in the GIT of swine.}, }
@article {pmid31527408, year = {2019}, author = {Connor, R and Brister, R and Buchmann, JP and Deboutte, W and Edwards, R and Martí-Carreras, J and Tisza, M and Zalunin, V and Andrade-Martínez, J and Cantu, A and D'Amour, M and Efremov, A and Fleischmann, L and Forero-Junco, L and Garmaeva, S and Giluso, M and Glickman, C and Henderson, M and Kellman, B and Kristensen, D and Leubsdorf, C and Levi, K and Levi, S and Pakala, S and Peddu, V and Ponsero, A and Ribeiro, E and Roy, F and Rutter, L and Saha, S and Shakya, M and Shean, R and Miller, M and Tully, B and Turkington, C and Youens-Clark, K and Vanmechelen, B and Busby, B}, title = {NCBI's Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements.}, journal = {Genes}, volume = {10}, number = {9}, pages = {}, doi = {10.3390/genes10090714}, pmid = {31527408}, issn = {2073-4425}, support = {Intramural Research Program//U.S. National Library of Medicine/ ; 721367//HONOURs Marie-Sklodowska-Curie training network/ ; }, abstract = {A wealth of viral data sits untapped in publicly available metagenomic data sets when it might be extracted to create a usable index for the virological research community. We hypothesized that work of this complexity and scale could be done in a hackathon setting. Ten teams comprised of over 40 participants from six countries, assembled to create a crowd-sourced set of analysis and processing pipelines for a complex biological data set in a three-day event on the San Diego State University campus starting 9 January 2019. Prior to the hackathon, 141,676 metagenomic data sets from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) were pre-assembled into contiguous assemblies (contigs) by NCBI staff. During the hackathon, a subset consisting of 2953 SRA data sets (approximately 55 million contigs) was selected, which were further filtered for a minimal length of 1 kb. This resulted in 4.2 million (Mio) contigs, which were aligned using BLAST against all known virus genomes, phylogenetically clustered and assigned metadata. Out of the 4.2 Mio contigs, 360,000 contigs were labeled with domains and an additional subset containing 4400 contigs was screened for virus or virus-like genes. The work yielded valuable insights into both SRA data and the cloud infrastructure required to support such efforts, revealing analysis bottlenecks and possible workarounds thereof. Mainly: (i) Conservative assemblies of SRA data improves initial analysis steps; (ii) existing bioinformatic software with weak multithreading/multicore support can be elevated by wrapper scripts to use all cores within a computing node; (iii) redesigning existing bioinformatic algorithms for a cloud infrastructure to facilitate its use for a wider audience; and (iv) a cloud infrastructure allows a diverse group of researchers to collaborate effectively. The scientific findings will be extended during a follow-up event. Here, we present the applied workflows, initial results, and lessons learned from the hackathon.}, }
@article {pmid31526457, year = {2019}, author = {de Los Santos Villalobos, S and Robles, RI and Parra Cota, FI and Larsen, J and Lozano, P and Tiedje, JM}, title = {Bacillus cabrialesii sp. nov., an endophytic plant growth promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) in the Yaqui Valley, Mexico.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1099/ijsem.0.003711}, pmid = {31526457}, issn = {1466-5034}, abstract = {Strain TE3T, an endophytic plant growth promoting bacterium, was isolated from wheat (Triticumturgidum subsp. durum) sampled in the Yaqui Valley, Mexico. Biochemical, phenotypic and genotypic approaches were used to clarify the taxonomic affiliation of this strain. Based on analysis of its full-length 16S rRNA gene, strain TE3T was assigned to the genus Bacillus (similarity ≥98.7 %). This finding was supported by morphological and metabolic characteristics, such as rod shape, strictly aerobic metabolism, spore formation, Gram-positive staining, catalase-positive activity, reduction of nitrate to nitrite, starch and casein hydrolysis, growth in presence of lysozyme and 2 % NaCl, citrate utilization, growth pH from 6.0 to 8.0, and acid and indole production from glucose and tryptophan, respectively. The whole-genome phylogenetic relationship showed that TE3T formed an individual clade with Bacillus tequilensis KCTC 13622T, distant from that generated by all Bacillus subtilis subspecies. The maximum values for average nucleotide identity and in silico DNA-DNA hybridization were 93.85 and 54.30 %, respectively, related to Bacillus subtilissubsp. inaquosorum KCTC 13429T. Analysis of its fatty acid content showed the ability of strain TE3T to bio-synthetize fatty acids that are not present in closely related Bacillus species, such as C12 : 0, C12 : 0 2OH, C12 : 0 3OH, C17 : 0, iso-C17 : 0 3OH and C18 : 1ω9c. These results provide evidence that strain TE3T is a novel species of the genus Bacillus, for which the name Bacilluscabrialesii sp. nov. is proposed. The type strain of Bacilluscabrialesii is TE3T (CM-CNRG TB54T=CCStamb A1T).}, }
@article {pmid31523442, year = {2019}, author = {Koga, Y and Ohtsu, T and Kimura, K and Asami, Y}, title = {Probiotic L. gasseri strain (LG21) for the upper gastrointestinal tract acting through improvement of indigenous microbiota.}, journal = {BMJ open gastroenterology}, volume = {6}, number = {1}, pages = {e000314}, doi = {10.1136/bmjgast-2019-000314}, pmid = {31523442}, issn = {2054-4774}, abstract = {Objective: To describe probiotics including a Lactobacillus gasseri strain LG21 used for the upper gastrointestinal tract, which are considered to act through improvement of indigenous microbiota inhabiting there.<br><br>Background and design: Because the early definition of probiotics emphasized their effects on improving the intestinal microbial ecology, their effects on the intestinal tract and its immunity have been considered common general benefits associated with probiotics. This conclusion was also based on a body of successful clinical trials whose endpoints were the prevention or treatment of intestinal diseases. In contrast to intestinal microbiota, our understanding of the role of gastric microbiota in human health and physiology remains poor, as the bacterial load in the stomach is considered too small to exert a significant effect due to the highly acidic environment of the human stomach. Therefore, the intervention using probiotics in the stomach is still limited at present.Results:In this article using representative 38 quoted articles, we first describe the gastric microbiota, as the indigenous microbiota in the stomach is thought to be significantly involved in the pathophysiology of this organ, since probiotics exert their beneficial effects through improving the resident microbiota. We then review the present status and future prospects of probiotics for the treatment of upper gastrointestinal diseases by quoting representative published articles, including our basic and clinical data.<br><br>Conclusions: Probiotics have been demonstrated to suppress Helicobacter pylori in the stomach, and are also expected to improve functional dyspepsia through the correction of dysbiotic gastric microbiota.}, }
@article {pmid31483625, year = {2019}, author = {Cruz, H and Law, YY and Guest, JS and Rabaey, K and Batstone, D and Laycock, B and Verstraete, W and Pikaar, I}, title = {Mainstream Ammonium Recovery to Advance Sustainable Urban Wastewater Management.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.9b00603}, pmid = {31483625}, issn = {1520-5851}, abstract = {Throughout the 20th century, the prevailing approach toward nitrogen management in municipal wastewater treatment was to remove ammonium by transforming it into dinitrogen (N2) using biological processes such as conventional activated sludge. While this has been a very successful strategy for safeguarding human health and protecting aquatic ecosystems, the conversion of ammonium into its elemental form is incompatible with the developing circular economy of the 21st century. Equally important, the activated sludge process and other emerging ammonium removal pathways have several environmental and technological limitations. Here, we assess that the theoretical energy embedded in ammonium in domestic wastewater represents roughly 38-48% of the embedded chemical energy available in the whole of the discharged bodily waste. The current routes for ammonium removal not only neglect the energy embedded in ammonium, but they can also produce N2O, a very strong greenhouse gas, with such emissions comprising the equivalent of 14-26% of the overall carbon footprint of wastewater treatment plants. N2O emissions often exceed the carbon emissions related to the electricity consumption for the process requirements of WWTPs. Considering these limitations, there is a need to develop alternative ammonium management approaches that center around recovery of ammonium from domestic wastewater rather than deal with its &quot;destruction&quot; into elemental dinitrogen. Current ammonium recovery techniques are applicable only at orders of magnitude above domestic wastewater strength, and so new techniques based on physicochemical adsorption are of particular interest. A new pathway is proposed that allows for mainstream ammonium recovery from wastewater based on physicochemical adsorption through development of polymer-based adsorbents. Provided adequate adsorbents corresponding to characteristics outlined in this paper are designed and brought to industrial production, this adsorption-based approach opens perspectives for mainstream continuous adsorption coupled with side-stream recovery of ammonium with minimal chemical requirements. This proposed pathway can bring forward an effective resource-oriented approach to upgrade the fate of ammonium in urban water management without generating hidden externalized environmental costs.}, }
@article {pmid31520875, year = {2019}, author = {Wichmann, S and Ardern, Z}, title = {Optimality in the standard genetic code is robust with respect to comparison code sets.}, journal = {Bio Systems}, volume = {185}, number = {}, pages = {104023}, doi = {10.1016/j.biosystems.2019.104023}, pmid = {31520875}, issn = {1872-8324}, abstract = {The genetic code and its evolution have been studied by many different approaches. One approach is to compare the properties of the standard genetic code (SGC) to theoretical alternative codes in order to determine how optimal it is and from this infer whether or not it is likely that it has undergone a selective evolutionary process. Many different properties have been studied in this way in the literature. Less focus has been put on the alternative code sets which are used as a comparison to the standard code. Each implicitly represents an evolutionary hypothesis and the sets used differ greatly across the literature. Here we determine the influence of the comparison set on the results of the optimality calculation by using codes based upon different sub-structures of the SGC. With these results we can generalize the results to different evolutionary hypotheses. We find that the SGC's optimality is very robust, as no code set with no optimised properties is found. We therefore conclude that the optimality of the SGC is a robust feature across all evolutionary hypotheses. Our results provide important information for any future studies on the evolution of the standard genetic code. We also studied properties of the SGC concerning overlapping genes, which have recently been found to be more widespread than often believed. Although our results are not conclusive yet we find additional intriguing structures in the SGC that need explanation.}, }
@article {pmid31517286, year = {2019}, author = {Duysburgh, C and Van den Abbeele, P and Krishnan, K and Bayne, TF and Marzorati, M}, title = {A synbiotic concept containing spore-forming Bacillus strains and a prebiotic fiber blend consistently enhanced metabolic activity by modulation of the gut microbiome in vitro.}, journal = {International journal of pharmaceutics: X}, volume = {1}, number = {}, pages = {100021}, doi = {10.1016/j.ijpx.2019.100021}, pmid = {31517286}, issn = {2590-1567}, abstract = {A standardized in vitro simulation of the human gastrointestinal tract (M-SHIME®) was used to assess the effect of repeated daily administration of a synbiotic formulation, containing five spore-forming Bacillus strains and a prebiotic fiber blend, on the microbial activity and composition of three simulated human subjects. Firstly, while confirming recent findings, deeper phylogenetic insight was obtained in the resident M-SHIME® microbiota, demonstrating that the model maintains a diverse and representative, colon region-specific luminal and mucosal microbial community. Supplementation of the synbiotic concept increased microbial diversity in the distal colon areas, whereas specific enhancement of Bacillaceae levels was observed in the ascending colon suggesting a successful engraftment of the Bacillus spores, which probably resulted in a stimulatory effect on, among others, Bifidobacteriaceae, Lactobacillaceae, Prevotellaceae, Tannerellaceae and Faecalibacterium prausnitzii contributing directly or indirectly to stimulation of acetate, propionate and butyrate production. When compared with a previous study investigating the Bacillus strains, the generated data suggest a synergistic effect on the intestinal microbiota for the synbiotic formulation. Given the fact that the probiotic strains have been shown to impact post-prandial metabolic endotoxemia in human individuals, it might be interesting to further investigate the efficacy of the synbiotic concept in protecting against obesity-related disorders.}, }
@article {pmid31515652, year = {2019}, author = {Lee, HJ and Shin, SY and Whang, KS}, title = {Paenibacillus pinistramenti sp. nov., isolated from pine litter.}, journal = {Antonie van Leeuwenhoek}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10482-019-01325-0}, pmid = {31515652}, issn = {1572-9699}, abstract = {A Gram-stain-positive bacterium, designated strain ASL46T, was isolated from litter layer of a pine forest located in Anmyondo, Korea. Strain ASL46T was found to be an aerobic, motile, endospore-forming rod which can grow at 20-45 °C (optimum, 37 °C), at pH 6.0-11.0 (optimum, pH 7.0) and at salinities of 0-2% (w/v) NaCl (optimum, 1% NaCl). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain ASL46T belongs to the genus Paenibacillus, showing highest sequence similarity to P. yonginensis DCY84T (98.3%), P. physcomitrella XBT (97.4%) and P. faecis CIP 101062T (96.6%). The average nucleotide identity (ANI) and DNA-DNA relatedness between the strain ASL46T and P. physcomitrella XBT and P. yonginensis DCY84T yielded ANI values of 84.6 and 84.5% and DNA-DNA relatedness of 11.7 ± 0.7 and 10.9 ± 0.2%, respectively. The DNA G+C content of the genomic DNA of strain ASL46T was 52.1 mol%. The predominant isoprenoid quinone was identified as menaquinone-7 and the major cellular fatty acids were determined to be anteiso-C15:0, C16:0 and iso-C16:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five unidentified aminophospholipids, an unidentified phospholipid and an unidentified glycolipid. The whole-cell sugar was found to be ribose and cell wall peptidoglycan contained meso-diaminopimelic acid. On the basis of phylogenetic analyses, and phenotypic and chemotaxonomic characteristics, strain ASL46T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus pinistramenti sp. nov. is proposed. The type strain is ASL46T (= KACC 18701T = NBRC 111876T).}, }
@article {pmid31488068, year = {2019}, author = {Pereira-Flores, E and Glöckner, FO and Fernandez-Guerra, A}, title = {Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data.}, journal = {BMC bioinformatics}, volume = {20}, number = {1}, pages = {453}, doi = {10.1186/s12859-019-3031-y}, pmid = {31488068}, issn = {1471-2105}, support = {57129354//Deutscher Akademischer Austauschdienst/ ; POS_EXT_2012_1_10105//Agencia Nacional de Investigación e Innovación/ ; 634486//Horizon 2020 Framework Programme/ ; }, abstract = {BACKGROUND: Metagenomics caused a quantum leap in microbial ecology. However, the inherent size and complexity of metagenomic data limit its interpretation. The quantification of metagenomic traits in metagenomic analysis workflows has the potential to improve the exploitation of metagenomic data. Metagenomic traits are organisms' characteristics linked to their performance. They are measured at the genomic level taking a random sample of individuals in a community. As such, these traits provide valuable information to uncover microorganisms' ecological patterns. The Average Genome Size (AGS) and the 16S rRNA gene Average Copy Number (ACN) are two highly informative metagenomic traits that reflect microorganisms' ecological strategies as well as the environmental conditions they inhabit.<br><br>RESULTS: Here, we present the ags.sh and acn.sh tools, which analytically derive the AGS and ACN metagenomic traits. These tools represent an advance on previous approaches to compute the AGS and ACN traits. Benchmarking shows that ags.sh is up to 11 times faster than state-of-the-art tools dedicated to the estimation AGS. Both ags.sh and acn.sh show comparable or higher accuracy than existing tools used to estimate these traits. To exemplify the applicability of both tools, we analyzed the 139 prokaryotic metagenomes of TARA Oceans and revealed the ecological strategies associated with different water layers.<br><br>CONCLUSION: We took advantage of recent advances in gene annotation to develop the ags.sh and acn.sh tools to combine easy tool usage with fast and accurate performance. Our tools compute the AGS and ACN metagenomic traits on unassembled metagenomes and allow researchers to improve their metagenomic data analysis to gain deeper insights into microorganisms' ecology. The ags.sh and acn.sh tools are publicly available using Docker container technology at https://github.com/pereiramemo/AGS-and-ACN-tools .}, }
@article {pmid31512011, year = {2019}, author = {Sekhohola-Dlamini, L and Tekere, M}, title = {Microbiology of municipal solid waste landfills: a review of microbial dynamics and ecological influences in waste bioprocessing.}, journal = {Biodegradation}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10532-019-09890-x}, pmid = {31512011}, issn = {1572-9729}, abstract = {Municipal solid waste landfills are widely used as a waste management tool and landfill microbiology is at the core of waste degradation in these ecosystems. This review investigates the microbiology of municipal solid waste landfills, focusing on the current state of knowledge pertaining to microbial diversity and functions facilitating in situ waste bioprocessing, as well as ecological factors influencing microbial dynamics in landfills. Bioprocessing of waste in municipal landfills emanates from substrate metabolism and co-metabolism by several syntrophic microorganisms, resulting in partial transformation of complex substrates into simpler polymeric compounds and complete mineralisation into inorganic salts, water and gases including the biofuel gas methane. The substrate decomposition is characterised by evolution and interactions of different bacterial, archaeal and fungal groups due to prevailing biotic and abiotic conditions in the landfills, allowing for hydrolytic, fermentative, acetogenic and methanogenic processes to occur. Application of metagenomics studies based on high throughput Next Generation Sequencing technique has advanced research on profiling of the microbial communities in municipal solid waste landfills. However, functional diversity and bioprocess dynamics, as well as key factors influencing the in situ bioprocesses involved in landfill waste degradation; the very elements that are key in determining the efficiency of municipal landfills as tools of waste management, remain ambiguous. Such gaps also hinder progressive understanding of fundamentals that underlie technology development based on waste biodegradation, and exploration of municipal waste as a bioresource.}, }
@article {pmid31511911, year = {2019}, author = {Wang, L and Han, M and Li, X and Ginawi, A and Ning, K and Yan, Y}, title = {Niche and Neutrality Work Differently in Microbial Communities in Fluidic and Non-fluidic Ecosystems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01439-y}, pmid = {31511911}, issn = {1432-184X}, abstract = {This data-intensive study investigated the delicate balance of niche and neutrality underlying microbial communities in freshwater ecosystems through comprehensive application of high-throughput sequencing, species abundance distribution (SAD), and the neutral community model (NCM), combined with species diversity and phylogenetic measures, which unite the traditional and microbial ecology. On the genus level, 45.10% and 41.18% of the water samples could be explained by the log-normal and Volkov model respectively, among which 31.37% could fit both models. Meanwhile, 55.56% of the sediment samples could be depicted by the log-normal model, and Volkov-fitted samples comprised only 13.33%. Besides, operational taxonomic units (OTUs) from water samples fit Sloan's neutral model significantly better than those in sediment. Therefore, it was concluded that deterministic processes played a great role in both water and sediment ecosystems, whereas neutrality was much more involved in water assemblages than in non-fluidic sediment ecosystems. Secondly, log-normal fitted samples had lower phylogenetic species variability (PSV) than Volkov-fitted ones, indicating that niche-based communities were more phylogenetically clustered than neutrally assembled counterparts. Additionally, further testing showed that the relative richness of rare species was vital to SAD modeling, either niche-based or neutral, and communities containing fewer rare species were more easily captured by theoretical SAD models.}, }
@article {pmid31511558, year = {2019}, author = {Makarchuk, S and Braz, VC and Araújo, NAM and Ciric, L and Volpe, G}, title = {Enhanced propagation of motile bacteria on surfaces due to forward scattering.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4110}, doi = {10.1038/s41467-019-12010-1}, pmid = {31511558}, issn = {2041-1723}, support = {204240/Z/16/Z//Wellcome Trust (Wellcome)/ ; }, abstract = {How motile bacteria move near a surface is a problem of fundamental biophysical interest and is key to the emergence of several phenomena of biological, ecological and medical relevance, including biofilm formation. Solid boundaries can strongly influence a cell's propulsion mechanism, thus leading many flagellated bacteria to describe long circular trajectories stably entrapped by the surface. Experimental studies on near-surface bacterial motility have, however, neglected the fact that real environments have typical microstructures varying on the scale of the cells' motion. Here, we show that micro-obstacles influence the propagation of peritrichously flagellated bacteria on a flat surface in a non-monotonic way. Instead of hindering it, an optimal, relatively low obstacle density can significantly enhance cells' propagation on surfaces due to individual forward-scattering events. This finding provides insight on the emerging dynamics of chiral active matter in complex environments and inspires possible routes to control microbial ecology in natural habitats.}, }
@article {pmid31507553, year = {2019}, author = {Durán-Viseras, A and Andrei, AS and Ghai, R and Sánchez-Porro, C and Ventosa, A}, title = {New Halonotius Species Provide Genomics-Based Insights Into Cobalamin Synthesis in Haloarchaea.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1928}, doi = {10.3389/fmicb.2019.01928}, pmid = {31507553}, issn = {1664-302X}, abstract = {Hypersaline aquatic and terrestrial ecosystems display a cosmopolitan distribution. These environments teem with microbes and harbor a plethora of prokaryotic lineages that evaded ecological characterization due to the prior inability to cultivate them or to access their genomic information. In order to close the current knowledge gap, we performed two sampling and isolation campaigns in the saline soils of the Odiel Saltmarshes and the salterns of Isla Cristina (Huelva, Spain). From the isolated haloarchaeal strains subjected to high-throughput phylogenetic screening, two were chosen (F15BT and F9-27T) for physiological and genomic characterization due of their relatedness to the genus Halonotius. Comparative genomic analyses were carried out between the isolated strains and the genomes of previously described species Halonotius pteroides CECT 7525T, Halonotius aquaticus F13-13T and environmentaly recovered metagenome-assembled representatives of the genus Halonotius. The topology of the phylogenomic tree showed agreement with the phylogenetic ones based on 16S rRNA and rpoB' genes, and together with average amino acid and nucleotide identities suggested the two strains as novel species within the genus. We propose the names Halonotius terrestris sp. nov. (type strain F15BT = CECT 9688T = CCM 8954T) and Halonotius roseus sp. nov. (type strain F9-27T = CECT 9745T = CCM 8956T) for these strains. Comparative genomic analyses within the genus highlighted a typical salt-in signature, characterized by acidic proteomes with low isoelectric points, and indicated heterotrophic aerobic lifestyles. Genome-scale metabolic reconstructions revealed that the newly proposed species encode all the necessary enzymatic reactions involved in cobalamin (vitamin B12) biosynthesis. Based on the worldwide distribution of the genus and its abundance in hypersaline habitats we postulate that its members perform a critical function by being able to provide &quot;expensive&quot; commodities (i.e., vitamin B12) to the halophilic microbial communities at large.}, }
@article {pmid31507541, year = {2019}, author = {Bates, KA and Shelton, JMG and Mercier, VL and Hopkins, KP and Harrison, XA and Petrovan, SO and Fisher, MC}, title = {Captivity and Infection by the Fungal Pathogen Batrachochytrium salamandrivorans Perturb the Amphibian Skin Microbiome.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1834}, doi = {10.3389/fmicb.2019.01834}, pmid = {31507541}, issn = {1664-302X}, abstract = {The emerging fungal pathogen, Batrachochytrium salamandrivorans (Bsal) is responsible for the catastrophic decline of European salamanders and poses a threat to amphibians globally. The amphibian skin microbiome can influence disease outcome for several host-pathogen systems, yet little is known of its role in Bsal infection. In addition, many experimental in-vivo amphibian disease studies to date have relied on specimens that have been kept in captivity for long periods without considering the influence of environment on the microbiome and how this may impact the host response to pathogen exposure. We characterized the impact of captivity and exposure to Bsal on the skin bacterial and fungal communities of two co-occurring European newt species, the smooth newt, Lissotriton vulgaris and the great-crested newt, Triturus cristatus. We show that captivity led to significant losses in bacterial and fungal diversity of amphibian skin, which may be indicative of a decline in microbe-mediated protection. We further demonstrate that in both L. vulgaris and T. cristatus, Bsal infection was associated with changes in the composition of skin bacterial communities with possible negative consequences to host health. Our findings advance current understanding of the role of host-associated microbiota in Bsal infection and highlight important considerations for ex-situ amphibian conservation programmes.}, }
@article {pmid31506821, year = {2019}, author = {Callejas, C and Fernández, A and Passeggi, M and Wenzel, J and Bovio, P and Borzacconi, L and Etchebehere, C}, title = {Microbiota adaptation after an alkaline pH perturbation in a full-scale UASB anaerobic reactor treating dairy wastewater.}, journal = {Bioprocess and biosystems engineering}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00449-019-02198-3}, pmid = {31506821}, issn = {1615-7605}, abstract = {The aim of this study was to understand how the microbial community adapted to changes, including a pH perturbation, occurring during the start-up and operation processes in a full-scale methanogenic UASB reactor designed to treat dairy wastewater. The reactor performance, prokaryotic community, and lipid degradation capacity were monitored over a 9-month period. The methanogenic community was studied by mcrA/mrtA gene copy-number quantification and methanogenic activity tests. A diverse prokaryotic community characterized the seeding sludge as assessed by sequencing the V4 region of the 16S rRNA gene. As the feeding began, the bacterial community was dominated by Firmicutes, Synergistetes, and Proteobacteria phyla. After an accidental pH increase that affected the microbial community structure, a sharp increase in the relative abundance of Clostridia and a decrease in the mcrA/mrtA gene copy number and methanogenic activity were observed. After a recovery period, the microbial population regained diversity and methanogenic activity. Alkaline shocks are likely to happen in dairy wastewater treatment because of the caustic soda usage. In this work, the plasticity of the prokaryotic community was key to surviving changes to the external environment and supporting biogas production in the reactor.}, }
@article {pmid31506760, year = {2019}, author = {Lamei, S and Stephan, JG and Nilson, B and Sieuwerts, S and Riesbeck, K and de Miranda, JR and Forsgren, E}, title = {Feeding Honeybee Colonies with Honeybee-Specific Lactic Acid Bacteria (Hbs-LAB) Does Not Affect Colony-Level Hbs-LAB Composition or Paenibacillus larvae Spore Levels, Although American Foulbrood Affected Colonies Harbor a More Diverse Hbs-LAB Community.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01434-3}, pmid = {31506760}, issn = {1432-184X}, support = {222-2013-423//Svenska Forskningsrådet Formas/ ; }, abstract = {The main current methods for controlling American Foulbrood (AFB) in honeybees, caused by the bacterial pathogen Paenibacillus larvae, are enforced incineration or prophylactic antibiotic treatment, neither of which is fully satisfactory. This has led to an increased interest in the natural relationships between the pathogenic and mutualistic microorganisms of the honeybee microbiome, in particular, the antagonistic effects of Honeybee-Specific Lactic Acid Bacteria (hbs-LAB) against P. larvae. We investigated whether supplemental administration of these bacteria affected P. larvae infection at colony level over an entire flowering season. Over the season, the supplements affected neither colony-level hbs-LAB composition nor naturally subclinical or clinical P. larvae spore levels. The composition of hbs-LAB in colonies was, however, more diverse in apiaries with a history of clinical AFB, although this was also unrelated to P. larvae spore levels. During the experiments, we also showed that qPCR could detect a wider range of hbs-LAB, with higher specificity and sensitivity than mass spectrometry. Honeybee colonies are complex super-organisms where social immune defenses, natural homeostatic mechanisms, and microbiome diversity and function play a major role in disease resistance. This means that observations made at the individual bee level cannot be simply extrapolated to infer similar effects at colony level. Although individual laboratory larval assays have clearly demonstrated the antagonistic effects of hbs-LAB on P. larvae infection, the results from the experiments presented here indicate that direct conversion of such practice to colony-level administration of live hbs-LAB is not effective.}, }
@article {pmid31506516, year = {2019}, author = {Bridier, A and Le Grandois, P and Moreau, MH and Prénom, C and Le Roux, A and Feurer, C and Soumet, C}, title = {Impact of cleaning and disinfection procedures on microbial ecology and Salmonella antimicrobial resistance in a pig slaughterhouse.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12947}, doi = {10.1038/s41598-019-49464-8}, pmid = {31506516}, issn = {2045-2322}, abstract = {To guarantee food safety, a better deciphering of ecology and adaptation strategies of bacterial pathogens such as Salmonella in food environments is crucial. The role of food processing conditions such as cleaning and disinfection procedures on antimicrobial resistance emergence should especially be investigated. In this work, the prevalence and antimicrobial resistance of Salmonella and the microbial ecology of associated surfaces communities were investigated in a pig slaughterhouse before and after cleaning and disinfection procedures. Salmonella were detected in 67% of samples and isolates characterization revealed the presence of 15 PFGE-patterns belonging to five serotypes: S.4,5,12:i:-, Rissen, Typhimurium, Infantis and Derby. Resistance to ampicillin, sulfamethoxazole, tetracycline and/or chloramphenicol was detected depending on serotypes. 16S rRNA-based bacterial diversity analyses showed that Salmonella surface associated communities were highly dominated by the Moraxellaceae family with a clear site-specific composition suggesting a persistent colonization of the pig slaughterhouse. Cleaning and disinfection procedures did not lead to a modification of Salmonella susceptibility to antimicrobials in this short-term study but they tended to significantly reduce bacterial diversity and favored some genera such as Rothia and Psychrobacter. Such data participate to the construction of a comprehensive view of Salmonella ecology and antimicrobial resistance emergence in food environments in relation with cleaning and disinfection procedures.}, }
@article {pmid31506265, year = {2019}, author = {Zhang, CJ and Pan, J and Duan, CH and Wang, YM and Liu, Y and Sun, J and Zhou, HC and Song, X and Li, M}, title = {Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes.}, journal = {mSystems}, volume = {4}, number = {5}, pages = {}, doi = {10.1128/mSystems.00442-19}, pmid = {31506265}, issn = {2379-5077}, abstract = {Mangroves, as a blue carbon reservoir, provide an environment for a variety of microorganisms. Mangroves lie in special locations connecting coastal and estuarine areas and experience fluctuating conditions, which are expected to intensify with climate change, creating a need to better understand the relative roles of stochastic and deterministic processes in shaping microbial community assembly. Here, a study of microbial communities inhabiting mangrove sediments across southeastern China, spanning mangroves in six nature reserves, was conducted. We performed high-throughput DNA sequencing of these samples and compared them with data of 1,370 sediment samples collected from the Earth Microbiome Project (EMP) to compare the microbial diversity of mangroves with that of other biomes. Our results showed that prokaryotic alpha diversity in mangroves was significantly higher than that in other biomes and that microbial beta diversity generally clustered according to biome types. The core operational taxonomic units (OTUs) in mangroves were mostly assigned to Gammaproteobacteria, Deltaproteobacteria, Chloroflexi, and Euryarchaeota The majority of beta nearest-taxon index values were higher than 2, indicating that community assembly in mangroves was better explained through a deterministic process than through a stochastic process. Mean annual precipitation (MAP) and total organic carbon (TOC) were main deterministic factors explaining variation in the microbial community. This study fills a gap in addressing the unique microbial diversity of mangrove ecosystems and their microbial community assembly mechanisms.IMPORTANCE Understanding the underlying mechanisms of microbial community assembly patterns is a vital issue in microbial ecology. Mangroves, as an important and special ecosystem, provide a unique environment for examining the relative importance of stochastic and deterministic processes. We made the first global-scale comparison and found that microbial diversity was significantly different in mangrove sediments compared to that of other biomes. Furthermore, our results suggest that a deterministic process is more important in shaping microbial community assembly in mangroves.}, }
@article {pmid31506264, year = {2019}, author = {Dumolin, C and Aerts, M and Verheyde, B and Schellaert, S and Vandamme, T and Van der Jeugt, F and De Canck, E and Cnockaert, M and Wieme, AD and Cleenwerck, I and Peiren, J and Dawyndt, P and Vandamme, P and Carlier, A}, title = {Introducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry Data.}, journal = {mSystems}, volume = {4}, number = {5}, pages = {}, doi = {10.1128/mSystems.00437-19}, pmid = {31506264}, issn = {2379-5077}, abstract = {The isolation of microorganisms from microbial community samples often yields a large number of conspecific isolates. Increasing the diversity covered by an isolate collection entails the implementation of methods and protocols to minimize the number of redundant isolates. Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry methods are ideally suited to this dereplication problem because of their low cost and high throughput. However, the available software tools are cumbersome and rely either on the prior development of reference databases or on global similarity analyses, which are inconvenient and offer low taxonomic resolution. We introduce SPeDE, a user-friendly spectral data analysis tool for the dereplication of MALDI-TOF mass spectra. Rather than relying on global similarity approaches to classify spectra, SPeDE determines the number of unique spectral features by a mix of global and local peak comparisons. This approach allows the identification of a set of nonredundant spectra linked to operational isolation units. We evaluated SPeDE on a data set of 5,228 spectra representing 167 bacterial strains belonging to 132 genera across six phyla and on a data set of 312 spectra of 78 strains measured before and after lyophilization and subculturing. SPeDE was able to dereplicate with high efficiency by identifying redundant spectra while retrieving reference spectra for all strains in a sample. SPeDE can identify distinguishing features between spectra, and its performance exceeds that of established methods in speed and precision. SPeDE is open source under the MIT license and is available from https://github.com/LM-UGent/SPeDEIMPORTANCE Estimation of the operational isolation units present in a MALDI-TOF mass spectral data set involves an essential dereplication step to identify redundant spectra in a rapid manner and without sacrificing biological resolution. We describe SPeDE, a new algorithm which facilitates culture-dependent clinical or environmental studies. SPeDE enables the rapid analysis and dereplication of isolates, a critical feature when long-term storage of cultures is limited or not feasible. We show that SPeDE can efficiently identify sets of similar spectra at the level of the species or strain, exceeding the taxonomic resolution of other methods. The high-throughput capacity, speed, and low cost of MALDI-TOF mass spectrometry and SPeDE dereplication over traditional gene marker-based sequencing approaches should facilitate adoption of the culturomics approach to bacterial isolation campaigns.}, }
@article {pmid31506260, year = {2019}, author = {Rubbens, P and Schmidt, ML and Props, R and Biddanda, BA and Boon, N and Waegeman, W and Denef, VJ}, title = {Randomized Lasso Links Microbial Taxa with Aquatic Functional Groups Inferred from Flow Cytometry.}, journal = {mSystems}, volume = {4}, number = {5}, pages = {}, doi = {10.1128/mSystems.00093-19}, pmid = {31506260}, issn = {2379-5077}, abstract = {High-nucleic-acid (HNA) and low-nucleic-acid (LNA) bacteria are two operational groups identified by flow cytometry (FCM) in aquatic systems. A number of reports have shown that HNA cell density correlates strongly with heterotrophic production, while LNA cell density does not. However, which taxa are specifically associated with these groups, and by extension, productivity has remained elusive. Here, we addressed this knowledge gap by using a machine learning-based variable selection approach that integrated FCM and 16S rRNA gene sequencing data collected from 14 freshwater lakes spanning a broad range in physicochemical conditions. There was a strong association between bacterial heterotrophic production and HNA absolute cell abundances (R2 = 0.65), but not with the more abundant LNA cells. This solidifies findings, mainly from marine systems, that HNA and LNA bacteria could be considered separate functional groups, the former contributing a disproportionately large share of carbon cycling. Taxa selected by the models could predict HNA and LNA absolute cell abundances at all taxonomic levels. Selected operational taxonomic units (OTUs) ranged from low to high relative abundance and were mostly lake system specific (89.5% to 99.2%). A subset of selected OTUs was associated with both LNA and HNA groups (12.5% to 33.3%), suggesting either phenotypic plasticity or within-OTU genetic and physiological heterogeneity. These findings may lead to the identification of system-specific putative ecological indicators for heterotrophic productivity. Generally, our approach allows for the association of OTUs with specific functional groups in diverse ecosystems in order to improve our understanding of (microbial) biodiversity-ecosystem functioning relationships.IMPORTANCE A major goal in microbial ecology is to understand how microbial community structure influences ecosystem functioning. Various methods to directly associate bacterial taxa to functional groups in the environment are being developed. In this study, we applied machine learning methods to relate taxonomic data obtained from marker gene surveys to functional groups identified by flow cytometry. This allowed us to identify the taxa that are associated with heterotrophic productivity in freshwater lakes and indicated that the key contributors were highly system specific, regularly rare members of the community, and that some could possibly switch between being low and high contributors. Our approach provides a promising framework to identify taxa that contribute to ecosystem functioning and can be further developed to explore microbial contributions beyond heterotrophic production.}, }
@article {pmid31504446, year = {2019}, author = {Blackwell, N and Perkins, W and Palumbo-Roe, B and Bearcock, J and Lloyd, JR and Edwards, A}, title = {Seasonal blooms of neutrophilic Betaproteobacterial Fe(II) oxidizers and Chlorobi in iron-rich coal mine drainage sediments.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiz140}, pmid = {31504446}, issn = {1574-6941}, abstract = {Waters draining from flooded and abandoned coal mines in the South Wales Coalfield (SWC), are substantial sources of pollution to the environment characterized by circumneutral pH and elevated dissolved iron concentrations (>1 mg L-1). The discharged Fe precipitates to form Fe(III) (oxyhydr)oxides which sustain microbial communities. However, while several studies have investigated the geochemistry of mine drainage in the SWC, less is known about the microbial ecology of the sites presenting a gap in our understanding of biogeochemical cycling and pollutant turnover. This study investigated the biogeochemistry of the Ynysarwed mine adit in the SWC. Samples were collected from nine locations within sediment at the mine entrance from the upper and lower layers three times over one year for geochemical and bacterial 16S rRNA gene sequence analysis. During winter, members of the Betaproteobacteria bloomed in relative abundance (>40%) including the microaerophilic Fe(II)-oxidizing genus Gallionella. A concomitant decrease in Chlorobi-associated bacteria occurred, although by summer the community composition resembled that observed in the previous autumn. Here, we provide the first insights into the microbial ecology and seasonal dynamics of bacterial communities of Fe(III)-rich deposits in the SWC and demonstrate that neutrophilic Fe(II)-oxidizing bacteria are important and dynamic members of these communities.}, }
@article {pmid31499451, year = {2019}, author = {Chen, S and Smith, AL}, title = {Performance and microbial ecology of methane-driven microbial fuel cells at temperatures ranging from 25 to 5 °C.}, journal = {Water research}, volume = {166}, number = {}, pages = {115036}, doi = {10.1016/j.watres.2019.115036}, pmid = {31499451}, issn = {1879-2448}, abstract = {The effluent of mainstream anaerobic processes is saturated with dissolved methane, representing a lost energy source and potent greenhouse gas emission if left unmanaged. This study investigated the impact of operational temperature on methane-driven microbial fuel cells (MFCs) designed for continuous operation to mitigate dissolved methane emissions in anaerobic effluents. Two bench-scale, single-chamber MFCs were operated sequentially at 25, 20, 15, 10 and 5 °C. Voltage production from both MFCs ranged from approximately 0.463 to 0.512 V over 1 kΩ resistance at temperatures ≥15 °C, but abruptly dropped as temperature decreased to 10 and 5 °C, averaging just 0.156 and 0.190 V for the replicate systems. Dissolved methane removal efficiency remained relatively stable across all operational temperatures, ranging from 53.0% to 63.6%. High-throughput sequencing of 16S rRNA genes and reverse transcription quantitative polymerase chain reaction indicated distinct distribution of methanotrophs (e.g., Methylomonas) and exoelectrogens (e.g., Geobacter) on the cathode and anode, respectively. Spearman's rank correlation suggested that an indirect interaction between methanotrophs and exoelectrogens via fermentative bacteria (e.g., Acetobacterium) may play a role in system function. Notably, diversity of the anode microbial community was positively correlated with both voltage production and Coulombic efficiency, suggesting overall diversity, as opposed to abundance or activity of exoelectrogens, was the primary factor governing performance at varying temperatures.}, }
@article {pmid31497590, year = {2019}, author = {Ramamurthy, T and Mutreja, A and Weill, FX and Das, B and Ghosh, A and Nair, GB}, title = {Corrigendum: Revisiting the Global Epidemiology of Cholera in Conjunction With the Genomics of Vibrio cholerae.}, journal = {Frontiers in public health}, volume = {7}, number = {}, pages = {237}, doi = {10.3389/fpubh.2019.00237}, pmid = {31497590}, issn = {2296-2565}, abstract = {[This corrects the article DOI: 10.3389/fpubh.2019.00203.].}, }
@article {pmid31494089, year = {2019}, author = {Hsu, RH and Clark, RL and Tan, JW and Ahn, JC and Gupta, S and Romero, PA and Venturelli, OS}, title = {Microbial Interaction Network Inference in Microfluidic Droplets.}, journal = {Cell systems}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cels.2019.06.008}, pmid = {31494089}, issn = {2405-4720}, abstract = {Microbial interactions are major drivers of microbial community dynamics and functions but remain challenging to identify because of limitations in parallel culturing and absolute abundance quantification of community members across environments and replicates. To this end, we developed Microbial Interaction Network Inference in microdroplets (MINI-Drop). Fluorescence microscopy coupled to computer vision techniques were used to rapidly determine the absolute abundance of each strain in hundreds to thousands of droplets per condition. We showed that MINI-Drop could accurately infer pairwise and higher-order interactions in synthetic consortia. We developed a stochastic model of community assembly to provide insight into the heterogeneity in community states across droplets. Finally, we elucidated the complex web of interactions linking antibiotics and different species in a synthetic consortium. In sum, we demonstrated a robust and generalizable method to infer microbial interaction networks by random encapsulation of sub-communities into microfluidic droplets.}, }
@article {pmid31493988, year = {2019}, author = {Calatayud, M and Koren, O and Collado, MC}, title = {Maternal Microbiome and Metabolic Health Program Microbiome Development and Health of the Offspring.}, journal = {Trends in endocrinology and metabolism: TEM}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tem.2019.07.021}, pmid = {31493988}, issn = {1879-3061}, abstract = {Maternal nutritional, metabolic, and physiological states, as well as exposure to various environmental factors during conception, gestation, and lactation, have a fundamental role in the health programming of the offspring. Therefore, alterations affecting the maternal microbiota might indirectly influence fetal development. In addition, such alterations could be transmitted to the progeny at different stages of infant development (e.g., preconception, prenatal, or postnatal), thereby favoring the development of an altered microbiota in the neonate. Microbial changes of this kind have been linked to an increased risk of non-communicable diseases (NCDs), including obesity and metabolic syndrome, allergy-related problems, and diabetes. In this review, we summarize the relevance of the maternal microbiota to fetal-neonatal health programming, with a focus on maternal nutritional and metabolic states.}, }
@article {pmid31492977, year = {2019}, author = {Expósito, JR and Coello, AJ and Barreno, E and Casano, LM and Catalá, M}, title = {Endogenous NO Is Involved in Dissimilar Responses to Rehydration and Pb(NO3)2 in Ramalina farinacea Thalli and Its Isolated Phycobionts.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01427-2}, pmid = {31492977}, issn = {1432-184X}, support = {PROMETEOIII /2017/039 GVA//Generalitat Valenciana/ ; CGL2016-79158-P//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; CGL2016-40058-P//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; }, abstract = {Lichens undergo desiccation/rehydration cycles and are permeable to heavy metals, which induce free radicals. Nitrogen monoxide (NO) regulates important cellular functions, but the research on lichen NO is still very scarce. In Ramalina farinacea thalli, NO seems to be involved in the peroxidative damage caused by air pollution, antioxidant defence and regulation of lipid peroxidation and photosynthesis. Our hypothesis is that NO also has a critical role during the rehydration and in the responses to lead of its isolated phycobionts (Trebouxia sp. TR9 and Trebouxia jamesii). Therefore, we studied the intracellular reactive oxygen species (ROS) production, lipid peroxidation and chlorophyll autofluorescence during rehydration of thalli and isolated microalgae in the presence of a NO scavenger and Pb(NO3)2. During rehydration, NO scavenging modulates free radical release and chlorophyll autofluorescence but not lipid peroxidation in both thalli and phycobionts. Pb(NO3)2 reduced free radical release (hormetic effect) both in the whole thallus and in microalgae. However, only in TR9, the ROS production, chlorophyll autofluorescence and lipid peroxidation were dependent on NO. In conclusion, Pb hormetic effect seems to depend on NO solely in TR9, while is doubtful for T. jamesii and the whole thalli.}, }
@article {pmid31489900, year = {2019}, author = {Jaswal, R and Pathak, A and Chauhan, A}, title = {Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils.}, journal = {Microorganisms}, volume = {7}, number = {9}, pages = {}, doi = {10.3390/microorganisms7090324}, pmid = {31489900}, issn = {2076-2607}, support = {DE-AC09-08SR22470//Savannah River National Laboratory/ ; }, abstract = {Despite significant technological advancements in the field of microbial ecology, cultivation and subsequent isolation of the vast majority of environmental microorganisms continues to pose challenges. Isolation of the environmental microbiomes is prerequisite to better understand a myriad of ecosystem services they provide, such as bioremediation of contaminants. Towards this end, in this culturomics study, we evaluated the colonization of soil bacterial and fungal communities within diffusion chambers (DC) and microbial traps (MT) established using uraniferous soils collected from a historically contaminated soil from Aiken, USA. Microbial assemblages were compared between the DC and MT relative to the native soils using amplicon based metagenomic and bioinformatic analysis. The overall rationale of this study is that DC and MT growth chambers provide the optimum conditions under which desired microbiota, identified in a previous study to serve as the &quot;core&quot; microbiomes, will proliferate, leading to their successful isolation. Specifically, the core microbiomes consisted of assemblages of bacteria (Burkholderia spp.) and fungi (Penicillium spp.), respectively. The findings from this study further supported previous data such that the abundance and diversity of the desired &quot;core&quot; microbiomes significantly increased as a function of enrichments over three consecutive generations of DC and MT, respectively. Metagenomic analysis of the DC/MT generations also revealed that enrichment and stable populations of the desired &quot;core&quot; bacterial and fungal microbiomes develop within the first 20 days of incubation and the practice of subsequent transfers for second and third generations, as is standard in previous studies, may be unnecessary. As a cost and time cutting measure, this study recommends running the DC/MT chambers for only a 20-day time period, as opposed to previous studies, which were run for months. In summation, it was concluded that, using the diffusion chamber-based enrichment techniques, growth of desired microbiota possessing environmentally relevant functions can be achieved in a much shorter time frame than has been previously shown.}, }
@article {pmid31487597, year = {2019}, author = {Griffero, L and Alcántara-Durán, J and Alonso, C and Rodríguez-Gallego, L and Moreno-González, D and García-Reyes, JF and Molina-Díaz, A and Pérez-Parada, A}, title = {Basin-scale monitoring and risk assessment of emerging contaminants in South American Atlantic coastal lagoons.}, journal = {The Science of the total environment}, volume = {697}, number = {}, pages = {134058}, doi = {10.1016/j.scitotenv.2019.134058}, pmid = {31487597}, issn = {1879-1026}, abstract = {Emerging contaminants (ECs) such as pharmaceuticals, personal care products, drugs of abuse and polar pesticides are under particular attention due to their high consumption, frequent detection in the environment and reported ecotoxicological risk. This study investigates the occurrence and distribution of multiclass of ECs in surface waters at basin scale of two Atlantic coastal lagoons of Uruguay, South America. For this purpose, a target screening approach covering up to 362 compounds was employed using nanoflow liquid chromatography - high resolution mass spectrometry (nanoLC/HRMS). 56 compounds were identified including five banned pesticides in the European Union: atrazine, carbendazim, chlorpyrifos ethyl, diazinon, and ethion. Pharmaceuticals, hormones and drugs of abuse showed maximum detection frequencies and concentrations downstream cities. The highest occurrence of pesticides was found in lagoons and streams with neighboring agricultural activity. ECs were also found in coastal sea. Environmental risk assessment revealed that the hormones 17α-ethinylestradiol and 17-β-estradiol showed the highest risk to aquatic organisms in these basins. This study represents the first basin- scale monitoring of ECs in superficial waters encompassing streams, lagoons, and coastal seas in Uruguay, South America.}, }
@article {pmid31487593, year = {2019}, author = {Field, HR and Whitaker, AH and Henson, JA and Duckworth, OW}, title = {Sorption of copper and phosphate to diverse biogenic iron (oxyhydr)oxide deposits.}, journal = {The Science of the total environment}, volume = {697}, number = {}, pages = {134111}, doi = {10.1016/j.scitotenv.2019.134111}, pmid = {31487593}, issn = {1879-1026}, abstract = {Iron (Fe) transformations partially control the biogeochemical cycling of biologically and environmentally important elements, such as carbon (C), nitrogen (N), phosphorus (P), and trace metals. In marine and freshwater environments, iron oxidizing bacteria commonly promote the oxidation of ferrous iron (Fe(II)) at circumneutral oxic-anoxic interfaces, resulting in the formation of mineral-organic composites known as biogenic Fe(III) (oxyhydr)oxides (BIOS). Previous studies have examined the microbial ecology, composition, morphology, and sorption reactivity of BIOS. However, a broad survey of BIOS properties and sorption reactivity is lacking. To further explore these relationships, this study utilized X-ray absorption spectroscopy (XAS) to characterize the Fe mineral species, acid digestions and elemental analysis to determine composition, Brunauer-Emmett-Teller (BET) analysis to measure specific surface area, and copper (Cu) and phosphorus (P) adsorption experiments at concentrations designed to measure maximum sorption to evaluate reactivity of BIOS samples collected in lakes and streams of the North Carolina Piedmont. Sample composition varied widely, with Fe and C content ranging from 6.3 to 34% and 3.4-13%, respectively. XAS spectra were best fit with 42-100% poorly crystalline Fe (oxyhydr)oxides, with the remainder composed of crystalline Fe minerals and organic complexes. On a sorbent mass basis, Cu and P sorption varied by a factor of two and 15, respectively. Regression analyses reveal interrelationships between physicochemical properties, and suggest that differences in P binding are driven by sorption to Fe(III) (oxyhydr)oxide surfaces. In total, results suggest that the physical and chemical characteristics of organic and Fe(III) (oxyhydr)oxide phases in BIOS interplay to control the sorption of solutes, and thus influence nutrient and contaminant cycling in soil and natural waters.}, }
@article {pmid31486865, year = {2019}, author = {Hernández-Del Amo, E and Ramió-Pujol, S and Gich, F and Trias, R and Bañeras, L}, title = {Changes in the Potential Activity of Nitrite Reducers and the Microbial Community Structure After Sediment Dredging and Plant Removal in the Empuriabrava FWS-CW.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01425-4}, pmid = {31486865}, issn = {1432-184X}, support = {IF-UDG2013//Universitat de Girona/ ; (MPCUdG2016/121//Universitat de Girona/ ; CGL2009-08338/BOS//Ministerio de Educación, Cultura y Deporte/ ; 2017SGR-548//Agència de Gestió d'Ajuts Universitaris i de Recerca/ ; }, abstract = {In constructed wetlands (CW), denitrification usually accounts for > 60% of nitrogen removal and is supposedly affected by wetland management practices, such as dredging (and plant removal). These practices cause an impact in sediment properties and microbial communities living therein. We have quantified the effects of a sediment dredging event on dissimilatory nitrite reduction by analysing the structure and activities of the microbial community before and after the event. Potential rates for nitrate reduction to ammonia and denitrification were in accordance with changes in the physicochemical conditions. Denitrification was the predominant pathway for nitrite removal (> 60%) and eventually led to the complete removal of nitrate. On the contrary, dissimilatory nitrite reduction to ammonia (DNRA) increased from 5 to 18% after the dredging event. Both actual activities and abundances of 16S rRNA, nirK and nirS significantly decreased after sediment dredging. However, genetic potential for denitrification (qnirS + qnirK/q16S rRNA) remained unchanged. Analyses of the 16S rRNA gene sequences revealed the importance of vegetation in shaping microbial community structures, selecting specific phylotypes potentially contributing to the nitrogen cycle. Overall, we confirmed that sediment dredging and vegetation removal exerted a measurable effect on the microbial community, but not on potential nitrite + nitrate removal rates. According to redundancy analysis, nitrate concentration and pH were the main variables affecting sediment microbial communities in the Empuriabrava CWs. Our results highlight a high recovery of the functionality of an ecosystem service after a severe intervention and point to metabolic redundancy of denitrifiers. We are confident these results will be taken into account in future management strategies in CWs.}, }
@article {pmid31482748, year = {2019}, author = {Arias-Borrego, A and Callejón-Leblic, B and Calatayud, M and Gómez-Ariza, JL and Collado, MC and García-Barrera, T}, title = {Insights into cancer and neurodegenerative diseases through selenoproteins and the connection with gut microbiota - current analytical methodologies.}, journal = {Expert review of proteomics}, volume = {}, number = {}, pages = {}, doi = {10.1080/14789450.2019.1664292}, pmid = {31482748}, issn = {1744-8387}, abstract = {Introduction: Selenium plays many key roles in health especially in connection with cancer and neurodegenerative diseases, among others. However, it needs to be appreciated that the essentiality or toxicity action of selenium depends on both, a narrow range of concentration and the chemical specie involved. In this context, human selenoproteins are essential biomolecules against these disorders, mainly due to its antioxidant action. To this end, analytical methodologies may allow identifying and quantifying individual selenospecies in human biofluids and tissues. Areas covered: This review explores the role of selenoproteins in medicine, with special emphasis in cancer and neurodegenerative diseases, considering the possible link with gut microbiota, and analytical techniques and procedures recently developed for the absolute quantification of selenoproteins and selenometabolites in human biofluids and tissues. Expert opinion: The beneficial role of selenium in human health has been extensively studied and reviewed. However, several challenges remain unsolved as discussed in this article: (i) speciation of selenium (especially selenoproteins) in cancer and neurodegenerative disease patients; (ii) supplementation of selenium in humans using functional foods and nutraceuticals; (iii) the link between selenium and selenoproteins expression and the gut microbiota and (iv) analytical methods and pitfalls for the absolute quantification of selenoproteins and selenometabolites.}, }
@article {pmid31482287, year = {2019}, author = {Veach, AM and Zeglin, LH}, title = {Historical Drought Affects Microbial Population Dynamics and Activity During Soil Drying and Re-Wet.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01432-5}, pmid = {31482287}, issn = {1432-184X}, support = {EPS-0903806//Kansas NSF-EPSCoR First Award/ ; }, abstract = {A history of drought exposure promoted by variable precipitation regimes can select for drought-tolerant soil microbial taxa, but the mechanisms of survival and death of microbial populations through the selective stresses of soil drying and re-wet are not well understood. We subjected soils collected from a 15-year field drought experiment (&quot;Altered&quot; precipitation history with extended dry periods, versus the &quot;Ambient&quot; field control) to a laboratory drying/re-wetting experiment, to learn whether selective population survival, death, or maintenance of protein synthesis potential and microbial respiration through variable soil water conditions was affected by field drought legacy. Microbial community composition, as measured by Illumina MiSeq sequencing of the 16S rRNA and 16S rRNA gene, shifted with laboratory drying/re-wet and field drought treatments. In Ambient soils, there was a higher proportion of reduced OTU abundance (indicative of mortality) during re-wet, whereas Altered soils had a greater proportion of stable OTU populations that did not change in abundance (indicative of survival) through drying/re-wet. Altered soils also had a lower proportion of rRNA:rRNA genes (lower protein synthesis potential) during dry-down, a greater weighted mean rRNA operon number (potential growth rate and r-selection) which was associated with higher abundance of Firmicutes (order Bacillales), and lower average microbial respiration rates. These data demonstrate that soils with a weaker historical drought legacy exhibit a higher prevalence of microbial water-stress mortality and differential survival and death at OTU levels following short-term dryingand re-wetting, concurrent with higher carbon loss potential. This work provides novel insight into the mechanisms and consequences of soil microbial changes resulting from extended drought conditions.}, }
@article {pmid31482282, year = {2019}, author = {Ehsani, E and Dumolin, C and Arends, JBA and Kerckhof, FM and Hu, X and Vandamme, P and Boon, N}, title = {Enriched hydrogen-oxidizing microbiomes show a high diversity of co-existing hydrogen-oxidizing bacteria.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-019-10082-z}, pmid = {31482282}, issn = {1432-0614}, support = {Geconcerteerde Onderzoeksactie (GOA) of Ghent University (BOF15/GOA/006)//Universiteit Gent/ ; Geconcerteerde Onderzoeksactie (GOA) of Ghent University (BOF15/GOA/006)//Universiteit Gent/ ; }, abstract = {While numerous reports exist on the axenic culturing of different hydrogen-oxidizing bacteria (HOB), knowledge about the enrichment of microbial communities growing on hydrogen, oxygen, and carbon dioxide as sole carbon and energy sources remains negligible. We want to elucidate if in such enrichments, most enriched populations are HOBs or heterotrophic organisms. In the present study, bacteria enriched from a soil sample and grown over 5 transfers using a continuous supply of hydrogen, oxygen, and carbon dioxide to obtain an enriched autotrophic hydrogen-oxidizing microbiome. The success of the enrichment was evaluated by monitoring ammonium consumption and biomass concentration for 120 days. The shift in the microbial composition of the original soil inoculum and all transfers was observed based on 16S rRNA amplicon sequencing. The hydrogen-oxidizing facultative chemolithoautotroph Hydrogenophaga electricum was isolated and found to be one of the abundant species in most transfers. Moreover, Achromobacter was isolated both under heterotrophic and autotrophic conditions, which was characterized as a hydrogen-oxidizing bacterium. The HOB enrichment condition constructed in this study provided an environment for HOB to develop and conquer in all transfers. In conclusion, we showed that enrichments on hydrogen, oxygen, and carbon dioxide as sole carbon and energy sources contain a diverse mixture of HOB and heterotrophs that resulted in a collection of culturable isolates. These isolates can be useful for further investigation for industrial applications.}, }
@article {pmid31482007, year = {2019}, author = {Keshvardoust, P and Huron, VAA and Clemson, M and Constancias, F and Barraud, N and Rice, SA}, title = {Biofilm formation inhibition and dispersal of multi-species communities containing ammonia-oxidising bacteria.}, journal = {NPJ biofilms and microbiomes}, volume = {5}, number = {}, pages = {22}, doi = {10.1038/s41522-019-0095-4}, pmid = {31482007}, issn = {2055-5008}, abstract = {Despite considerable research, the biofilm-forming capabilities of Nitrosomonas europaea are poorly understood for both mono and mixed-species communities. This study combined biofilm assays and molecular techniques to demonstrate that N. europaea makes very little biofilm on its own, and relies on the activity of associated heterotrophic bacteria to establish a biofilm. However, N. europaea has a vital role in the proliferation of mixed-species communities under carbon-limited conditions, such as in drinking water distribution systems, through the provision of organic carbon via ammonia oxidation. Results show that the addition of nitrification inhibitors to mixed-species nitrifying cultures under carbon-limited conditions disrupted biofilm formation and caused the dispersal of pre-formed biofilms. This dispersal effect was not observed when an organic carbon source, glucose, was included in the medium. Interestingly, inhibition of nitrification activity of these mixed-species biofilms in the presence of added glucose resulted in increased total biofilm formation compared to controls without the addition of nitrification inhibitors, or with only glucose added. This suggests that active AOB partially suppress or limit the overall growth of the heterotrophic bacteria. The experimental model developed here provides evidence that ammonia-oxidising bacteria (AOB) are involved in both the formation and maintenance of multi-species biofilm communities. The results demonstrate that the activity of the AOB not only support the growth and biofilm formation of heterotrophic bacteria by providing organic carbon, but also restrict and limit total biomass in mixed community systems.}, }
@article {pmid31475212, year = {2019}, author = {Godoy-Vitorino, F}, title = {Human microbial ecology and the rising new medicine.}, journal = {Annals of translational medicine}, volume = {7}, number = {14}, pages = {342}, doi = {10.21037/atm.2019.06.56}, pmid = {31475212}, issn = {2305-5839}, abstract = {The first life forms on earth were Prokaryotic, and the evolution of all Eukaryotic life occurred with the help of bacteria. Animal-associated microbiota also includes members of the archaea, fungi, protists, and viruses. The genomes of this host-associated microbial life are called the microbiome. Across the mammalian tree, microbiomes guarantee the development of immunity, physiology, and resistance to pathogens. In humans, all surfaces and cavities are colonized by a microbiome, maintained by a careful balance between the host response and its colonizers-thus humans are considered now supraorganisms. These microbiomes supply essential ecosystem services that benefit health through homeostasis, and the loss of the indigenous microbiota leads to dysbiosis, which can have significant consequences to disease. This educational review aims to describe the importance of human microbial ecology, explain the ecological terms applied to the study of the human microbiome, developments within the cutting-edge microbiome field, and implications to diagnostic and treatment.}, }
@article {pmid31469487, year = {2019}, author = {Overholt, WA and Schwing, P and Raz, KM and Hastings, D and Hollander, DJ and Kostka, JE}, title = {The core seafloor microbiome in the Gulf of Mexico is remarkably consistent and shows evidence of recovery from disturbance caused by major oil spills.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14794}, pmid = {31469487}, issn = {1462-2920}, abstract = {The microbial ecology of oligotrophic deep ocean sediments is understudied relative to their shallow counterparts, and this lack of understanding hampers our ability to predict responses to current and future perturbations. The Gulf of Mexico has experienced two of the largest accidental marine oil spills, the 1979 Ixtoc-1 blowout and the 2010 Deepwater Horizon (DWH) discharge. Here, microbial communities were characterized for 29 sites across multiple years in >700 samples. The composition of the seafloor microbiome was broadly consistent across the region and was well approximated by the overlying water depth and depth within the sediment column, while geographic distance played a limited role. Biogeographical distributions were employed to generate predictive models for over 4000 OTU that leverage easy-to-obtain geospatial variables which are linked to measured sedimentary oxygen profiles. Depth stratification and putative niche diversification are evidenced by the distribution of taxa that mediate the microbial nitrogen cycle. Further, these results demonstrate that sediments impacted by the DWH spill had returned to near baseline conditions after two years. The distributions of benthic microorganisms in the Gulf can be constrained, and moreover deviations from these predictions may pinpoint impacted sites and aid in future response efforts or long-term stability studies. This article is protected by copyright. All rights reserved.}, }
@article {pmid31466158, year = {2019}, author = {Zhang, L and Shen, Z and Fang, W and Gao, G}, title = {Composition of bacterial communities in municipal wastewater treatment plant.}, journal = {The Science of the total environment}, volume = {689}, number = {}, pages = {1181-1191}, doi = {10.1016/j.scitotenv.2019.06.432}, pmid = {31466158}, issn = {1879-1026}, abstract = {Efforts to understand the environmental and biological factors that influence the dynamics of microbial communities have received substantial attention in microbial ecology. In this study, Illumina MiSeq high-throughput sequencing technology was used to examine the microbial community structure of activated sludge in municipal wastewater treatment systems (Chuzhou city, China). Overall, Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were the most dominant phyla in the five activated sludge samples. However, the community structure of nitrifying bacteria was relatively simple, and diversity was low; only AOB (Nitrosomonas) and NOB (Nitrospira) were detected. The dominant bacteria in the anaerobic sludge, anoxic sludge and oxic sludge were the same, and each bacterial species was relatively uniform, with differences only in proportions. Redundancy analysis indicated that pH, TP and COD were strong environmental factors influencing the bacterial community distribution. PICRUSt was used to describe the metabolic and functional abilities of the activated sludge bacterial communities. The results emphasized the vast genetic diversity of these organisms, which are involved in various essential processes such as amino acid transport and metabolism, energy production and conversion, cell wall/membrane/envelope/biogenesis, signal transduction mechanisms, and carbohydrate transport and metabolism. Activated sludge of municipal wastewater treatment systems can be ranked in the following order based on the 16S rRNA gene copy numbers of the detected phylotypes: S1 > S2 > S4 > S5 > S3. This study provides basic data and a theoretical analysis of the optimal design and operation in wastewater treatment plants.}, }
@article {pmid31466157, year = {2019}, author = {Xu, M and Stedtfeld, RD and Wang, F and Hashsham, SA and Song, Y and Chuang, Y and Fan, J and Li, H and Jiang, X and Tiedje, JM}, title = {Composting increased persistence of manure-borne antibiotic resistance genes in soils with different fertilization history.}, journal = {The Science of the total environment}, volume = {689}, number = {}, pages = {1172-1180}, doi = {10.1016/j.scitotenv.2019.06.376}, pmid = {31466157}, issn = {1879-1026}, abstract = {Different long-term fertilization regimes may change indigenous microorganism diversity in the arable soil and thus might influence the persistence and transmission of manure-born antibiotic resistance genes (ARGs). Different manure origins and composting techniques might affect the fate of introduced ARGs in farmland. A four-month microcosm experiment was performed using two soils, which originated from the same field and applied with the same chemical fertilizer or swine manure for 26 years, to investigate the dynamics of ARGs in soil amended with manure or compost from the farm and an agro-technology company. High throughput qPCR and sequencing were applied to quantify ARGs using 144 primer sets and microorganism in soil. Fertilization history had little effect on dynamics of manure-borne ARGs in soil regardless of manure origin or composting. Very different half-lives of ARGs and mobile genetic elements from farm manure and commercial manure were observed in both soils. Composting decreased abundance of most ARGs in manure, but increased the persistence of manure-introduced ARGs in soil irrespective of fertilization history, especially for those from farm manure. These findings help understanding the fate of ARGs in manured soil and may inform techniques to mitigate ARGs transmission.}, }
@article {pmid31463982, year = {2019}, author = {Elghandour, MMY and Khusro, A and Adegbeye, MJ and Tan, Z and Abu Hafsa, SH and Greiner, R and Ugbogu, EA and Anele, UY and Salem, AZM}, title = {Dynamic role of single-celled fungi in ruminal microbial ecology and activities.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.14427}, pmid = {31463982}, issn = {1365-2672}, abstract = {In ruminants, high fermentation capacity is necessary to develop more efficient ruminant production systems. Greater level of production depends on the ability of the microbial ecosystem to convert organic matter into precursors of milk and meat. This has led to increased interest by animal nutritionists, biochemists and microbiologists in evaluating different strategies to manipulate the rumen biota to improve animal performance, production efficiency and animal health. One of such strategies is the use of natural feed additives such as single-celled fungi yeast. The main objectives of using yeasts as natural additives in ruminant diets include; a) to prevent rumen microflora disorders, b) to improve and sustain higher production of milk and meat, c) to reduce rumen acidosis and bloat which adversely affect animal health and performance, d) to decrease the risk of ruminant-associated human pathogens, e) to reduce the excretion of nitrogenous-based compounds, carbon dioxide and methane. Yeast, a natural feed additive, has the potential to enhance feed degradation by increasing the concentration of volatile fatty acids during fermentation processes. In addition, microbial growth in the rumen is enhanced in the presence of yeast leading to the delivery of a greater amount of microbial protein to the duodenum and high nitrogen retention. Single-celled fungi yeast has demonstrated its ability to increase fiber digestibility and lower fecal output of organic matter due to improved digestion of organic matter, which subsequently improves animal productivity. Yeast also has the ability to alter the fermentation process in the rumen in a way that reduces methane formation. Furthermore, yeast inclusion in ruminant diets has been reported to decrease toxins absorption such as mycotoxins and promote epithelial cell integrity. This review article provides information on the impact of single-celled fungi yeast as a feed supplement on ruminal microbiota and its function to improve the health and productive longevity of ruminants. This article is protected by copyright. All rights reserved.}, }
@article {pmid31463664, year = {2019}, author = {Erni-Cassola, G and Wright, RJ and Gibson, MI and Christie-Oleza, JA}, title = {Early Colonization of Weathered Polyethylene by Distinct Bacteria in Marine Coastal Seawater.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01424-5}, pmid = {31463664}, issn = {1432-184X}, support = {NE/K009044/1//Natural Environment Research Council/ ; NE/S005501/1//Natural Environment Research Council/ ; CENTA//Natural Environment Research Council/ ; BB/M01116X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Plastic debris in aquatic environments is rapidly colonized by a diverse community of microorganisms, often referred to as the &quot;Plastisphere.&quot; Given that common plastics are derived from fossil fuels, one would expect that Plastispheres should be enriched with obligate hydrocarbon-degrading bacteria (OHCB). So far, though, different polymer types do not seem to exert a strong effect on determining the composition of the Plastisphere, and putative biodegrading bacteria are only found as rare taxa within these biofilms. Here, we show through 16S rRNA gene sequencing that the enrichment of a prominent OHCB member on weathered and non-weathered polyethylene only occurred at early stages of colonization (i.e., after 2 days of incubation in coastal marine water; 5.8% and 3.7% of relative abundance, respectively, vs. 0.6% on glass controls). As biofilms matured, these bacteria decreased in relative abundance on all materials (< 0.3% after 9 days). Apart from OHCB, weathered polyethylene strongly enriched for other distinct organisms during early stages of colonization, such as a specific member of the Roseobacter group and a member of the genus Aestuariibacter (median 26.9% and 1.8% of the community, respectively), possibly as a consequence of the availability of short-oxidized chains generated from weathering. Our results demonstrate that Plastispheres can vary in accordance with the weathering state of the material and that very early colonizing communities are enriched with taxa that can potentially degrade hydrocarbons. Given the lack of persistent enrichment and overall community convergence between materials over time, common non-hydrolysable polymers might not serve as an important source of carbon for mature Plastispheres once the labile substrates generated from weathering have been depleted.}, }
@article {pmid31463663, year = {2019}, author = {Baselga-Cervera, B and García-Balboa, C and Díaz-Alejo, HM and Costas, E and López-Rodas, V}, title = {Rapid Colonization of Uranium Mining-Impacted Waters, the Biodiversity of Successful Lineages of Phytoplankton Extremophiles.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01431-6}, pmid = {31463663}, issn = {1432-184X}, support = {CTM-2013-44366-R.//Spanish Secretaría de Estado, Investigación, Desarrollo e Innovación/ ; BES-2014-067580.//Secretaría de Estado, Investigación, Desarrollo e Innovación/ ; }, abstract = {Anthropogenic extreme environments are emphasized as interesting sites for the study of evolutionary pathways, biodiversity, and extremophile bioprospection. Organisms that grow under these conditions are usually regarded as extremophiles; however, the extreme novelty of these environments may have favor adaptive radiations of facultative extremophiles. At the Iberian Peninsula, uranium mining operations have rendered highly polluted extreme environments in multiple locations. In this study, we examined the phytoplankton diversity, community structure, and possible determining factors in separate uranium mining-impacted waters. Some of these human-induced extreme environments may be able to sustain indigenous facultative extremophile phytoplankton species, as well as alleged obligate extremophiles. Therefore, we investigated the adaptation capacity of three laboratory strains, two Chlamydomonas reinhardtii and a Dictyosphaerium chlorelloides, to uranium-polluted waters. The biodiversity among the sampled waters was very low, and despite presenting unique taxonomic records, ecological patterns can be identified. The microalgae adaptation experiments indicated a gradient of ecological novelty and different phenomena of adaptation, from acclimation in some waters to non-adaptation in the harshest anthropogenic environment. Certainly, phytoplankton extremophiles might have been often overlooked, and the ability to flourish in extreme environments might be a functional feature in some neutrophilic species. Evolutionary biology and microbial biodiversity can benefit the study of recently evolved systems such as uranium-polluted waters. Moreover, anthropogenic extremophiles can be harnessed for industrial applications.}, }
@article {pmid31462415, year = {2019}, author = {McGonigle, JM and Bernau, JA and Bowen, BB and Brazelton, WJ}, title = {Robust Archaeal and Bacterial Communities Inhabit Shallow Subsurface Sediments of the Bonneville Salt Flats.}, journal = {mSphere}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSphere.00378-19}, pmid = {31462415}, issn = {2379-5042}, abstract = {We report the first census of natural microbial communities of the Bonneville Salt Flats (BSF), a perennial salt pan at the Utah-Nevada border. Environmental DNA sequencing of archaeal and bacterial 16S rRNA genes was conducted on samples from multiple evaporite sediment layers collected from the upper 30 cm of the surface salt crust. Our results show that at the time of sampling (September 2016), BSF hosted a robust microbial community dominated by diverse halobacteria and Salinibacter species. Sequences identical to Geitlerinema sp. strain PCC 9228, an anoxygenic cyanobacterium that uses sulfide as the electron donor for photosynthesis, are also abundant in many samples. We identified taxonomic groups enriched in each layer of the salt crust sediment and revealed that the upper gypsum sediment layer found immediately under the uppermost surface halite contains a robust microbial community. In these sediments, we found an increased presence of Thermoplasmatales, Hadesarchaeota, Nanoarchaeaeota, Acetothermia, Desulfovermiculus, Halanaerobiales, Bacteroidetes, and Rhodovibrio This study provides insight into the diversity, spatial heterogeneity, and geologic context of a surprisingly complex microbial ecosystem within this macroscopically sterile landscape.IMPORTANCE Pleistocene Lake Bonneville, which covered a third of Utah, desiccated approximately 13,000 years ago, leaving behind the Bonneville Salt Flats (BSF) in the Utah West Desert. The potash salts that saturate BSF basin are extracted and sold as an additive for agricultural fertilizers. The salt crust is a well-known recreational and economic commodity, but the biological interactions with the salt crust have not been studied. This study is the first geospatial analysis of microbially diverse populations at this site using cultivation-independent environmental DNA sequencing methods. Identification of the microbes present within this unique, dynamic, and valued sedimentary evaporite environment is an important step toward understanding the potential consequences of perturbations to the microbial ecology on the surrounding landscape and ecosystem.}, }
@article {pmid31456784, year = {2019}, author = {Gogulancea, V and González-Cabaleiro, R and Li, B and Taniguchi, D and Jayathilake, PG and Chen, J and Wilkinson, D and Swailes, D and McGough, AS and Zuliani, P and Ofiteru, ID and Curtis, TP}, title = {Individual Based Model Links Thermodynamics, Chemical Speciation and Environmental Conditions to Microbial Growth.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1871}, doi = {10.3389/fmicb.2019.01871}, pmid = {31456784}, issn = {1664-302X}, abstract = {Individual based Models (IbM) must transition from research tools to engineering tools. To make the transition we must aspire to develop large, three dimensional and physically and biologically credible models. Biological credibility can be promoted by grounding, as far as possible, the biology in thermodynamics. Thermodynamic principles are known to have predictive power in microbial ecology. However, this in turn requires a model that incorporates pH and chemical speciation. Physical credibility implies plausible mechanics and a connection with the wider environment. Here, we propose a step toward that ideal by presenting an individual based model connecting thermodynamics, pH and chemical speciation and environmental conditions to microbial growth for 5·105 individuals. We have showcased the model in two scenarios: a two functional group nitrification model and a three functional group anaerobic community. In the former, pH and connection to the environment had an important effect on the outcomes simulated. Whilst in the latter pH was less important but the spatial arrangements and community productivity (that is, methane production) were highly dependent on thermodynamic and reactor coupling. We conclude that if IbM are to attain their potential as tools to evaluate the emergent properties of engineered biological systems it will be necessary to combine the chemical, physical, mechanical and biological along the lines we have proposed. We have still fallen short of our ideals because we cannot (yet) calculate specific uptake rates and must develop the capacity for longer runs in larger models. However, we believe such advances are attainable. Ideally in a common, fast and modular platform. For future innovations in IbM will only be of use if they can be coupled with all the previous advances.}, }
@article {pmid31455798, year = {2019}, author = {Park, CH and Lee, JG and Lee, AR and Eun, CS and Han, DS}, title = {Network construction of gastric microbiome and organization of microbial modules associated with gastric carcinogenesis.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12444}, doi = {10.1038/s41598-019-48925-4}, pmid = {31455798}, issn = {2045-2322}, support = {NRF-2017R1C1B5015928//National Research Foundation of Korea (NRF)/ ; }, abstract = {In addition to Helicobacter pylori infection, nitrosating/nitrate-reducing bacteria and type IV secretion system (T4SS) protein gene-contributing bacteria have been proposed as potential causes of gastric cancer development. However, bacterial modules related with gastric carcinogenesis have not been clarified. In this study, we analyzed gastric microbiome using the gastric mucosal samples obtained from the Hanyang University Gastric Microbiome Cohort by 16S rRNA gene sequencing. Weighted correlation network analysis was performed to construct a microbiome network and to identify microbial modules associated with gastric carcinogenesis. At the family level, 420 bacterial taxa were identified in the gastric microbiome of 83 participants. Through network analysis, 18 microbial modules were organized. Among them, two modules-pink and brown-were positively correlated with a higher-risk of gastric cancer development such as intestinal metaplasia with no current H. pylori infection (correlation coefficient [γ]: pink module, 0.31 [P = 0.004], brown module, 0.26 [P = 0.02]). At the family level, twenty-two and thirty-two bacterial taxa belonged to the pink and brown modules, respectively. They included nitrosating/nitrate-reducing bacteria, T4SS protein gene-contributing bacteria, and various other bacteria, including Gordoniaceae, Tsukamurellaceae, Prevotellaceae, Cellulomonadaceae, Methylococcaceae, and Procabacteriaceae. The blue module, which included H. pylori, was correlated negatively with intestinal metaplasia (γ = -0.49 [P < 0.001]). In conclusion, intragastric bacterial taxa associated with gastric carcinogenesis can be classified by network analysis. Microbial modules may provide an integrative view of the microbial ecology relevant to precancerous lesions in the stomach.}, }
@article {pmid31454177, year = {2019}, author = {Goulart, MC and Cueva-Yesquén, LG and Hidalgo Martinez, KJ and Attili-Angelis, D and Fantinatti-Garboggini, F}, title = {Comparison of specific endophytic bacterial communities in different developmental stages of Passiflora incarnata using culture-dependent and culture-independent analysis.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e896}, doi = {10.1002/mbo3.896}, pmid = {31454177}, issn = {2045-8827}, support = {141298/2017-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 15/02395-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, abstract = {Plants and endophytic microorganisms have coevolved unique relationships over many generations. Plants show a specific physiological status in each developmental stage, which may determine the occurrence and dominance of specific endophytic populations with a predetermined ecological role. This study aimed to compare and determine the structure and composition of cultivable and uncultivable bacterial endophytic communities in vegetative and reproductive stages (RS) of Passiflora incarnata. To that end, the endophytic communities were assessed by plating and Illumina-based 16S rRNA gene amplicon sequencing. Two hundred and four cultivable bacterial strains were successfully isolated. From the plant's RS, the isolated strains were identified mainly as belonging to the genera Sphingomonas, Curtobacterium, and Methylobacterium, whereas Bacillus was the dominant genus isolated from the vegetative stage (VS). From a total of 133,399 sequences obtained from Illumina-based sequencing, a subset of 25,092 was classified in operational taxonomy units (OTUs). Four hundred and sixteen OTUs were obtained from the VS and 66 from the RS. In the VS, the most abundant families were Pseudoalteromonadaceae and Alicyclobacillaceae, while in the RS, Enterobacteriaceae and Bacillaceae were the most abundant families. The exclusive abundance of specific bacterial populations for each developmental stage suggests that plants may modulate bacterial endophytic community structure in response to different physiological statuses occurring at the different plant developmental stages.}, }
@article {pmid31451772, year = {2019}, author = {Adam, PS and Borrel, G and Gribaldo, S}, title = {An archaeal origin of the Wood-Ljungdahl H4MPT branch and the emergence of bacterial methylotrophy.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-019-0534-2}, pmid = {31451772}, issn = {2058-5276}, support = {ANR-16-CE02-0005-01//Agence Nationale de la Recherche (French National Research Agency)/ ; }, abstract = {The tetrahydromethanopterin (H4MPT) methyl branch of the Wood-Ljungdahl pathway is shared by archaeal and bacterial metabolisms that greatly contribute to the global carbon budget and greenhouse gas fluxes: methanogenesis and methylotrophy, including methanotrophy1-3. It has been proposed that the H4MPT branch dates back to the last universal common ancestor4-6. Interestingly, it has been identified in numerous recently sequenced and mostly uncultured non-methanogenic and non-methylotrophic archaeal and bacterial lineages, where its function remains unclear5,7. Here, we have examined the distribution and phylogeny of the enzymes involved in the H4MPT branch and the biosynthesis of its cofactors in over 6,400 archaeal and bacterial genomes. We find that a full Wood-Ljungdahl H4MPT pathway is widespread in Archaea and is likely ancestral to this domain, whereas this is not the case for Bacteria. Moreover, the inclusion of recently sequenced lineages leads to an important shortening of the branch separating Archaea and Bacteria with respect to previous phylogenies of the H4MPT branch. Finally, the genes for the pathway are colocalized in many of the recently sequenced archaeal lineages, similar to bacteria. Together, these results weaken the last universal common ancestor hypothesis and rather favour an origin of the H4MPT branch in Archaea and its subsequent transfer to Bacteria. We propose a scenario for its potential initial role in the first bacterial recipients and its evolution up to the emergence of aerobic methylotrophy. Finally, we discuss how an ancient horizontal transfer not only triggered the emergence of key metabolic processes but also important transitions in Earth's history.}, }
@article {pmid31451346, year = {2019}, author = {Voulgari-Kokota, A and McFrederick, QS and Steffan-Dewenter, I and Keller, A}, title = {Drivers, Diversity, and Functions of the Solitary-Bee Microbiota.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2019.07.011}, pmid = {31451346}, issn = {1878-4380}, abstract = {Accumulating reports of global bee declines have drawn much attention to the bee microbiota and its importance. Most research has focused on social bees, while solitary species have received scant attention despite their enormous biodiversity, ecological importance, and agroeconomic value. We review insights from several recent studies on diversity, function, and drivers of the solitary-bee microbiota, and compare these factors with those relevant to the social-bee microbiota. Despite basic similarities, the social-bee model, with host-specific core microbiota and social transmission, is not representative of the vast majority of bee species. The solitary-bee microbiota exhibits greater variability and biodiversity, with a strong impact of environmental acquisition routes. Our synthesis identifies outstanding questions that will build understanding of these interactions, responses to environmental threats, and consequences for health.}, }
@article {pmid31450207, year = {2019}, author = {He, Q and Song, J and Zhang, W and Gao, S and Wang, H and Yu, J}, title = {Enhanced simultaneous nitrification, denitrification and phosphorus removal through mixed carbon source by aerobic granular sludge.}, journal = {Journal of hazardous materials}, volume = {382}, number = {}, pages = {121043}, doi = {10.1016/j.jhazmat.2019.121043}, pmid = {31450207}, issn = {1873-3336}, abstract = {Aerobic granular sludge-based simultaneous nitrification, denitrification and phosphorus removal (SNDPR) systems were configured for the treatment of low-strength municipal wastewater. Granular characteristics, process performance, and the corresponding microbial ecology dynamics were comprehensively explored with sodium acetate and succinate as mixed carbon source. Results revealed that aerobic granules kept structural and functional resilience, while mixed carbon source largely altered and balanced the growth and competition of phosphorus/glycogen accumulating organisms (PAOs/GAOs). Appropriate ratio of mixed carbon source was vital for superb physiochemical behaviors and reliable removal performance by aerobic granules. Therefore, the aerobic granular SNDPR system could achieve deep-level nutrients removal through enhancing the anaerobic carbon uptake rate and strengthening the carbon usage efficiency. The present work could add some guiding sight into the application of aerobic granular SNDPR system for wastewater treatment.}, }
@article {pmid31449563, year = {2019}, author = {Kim, JG and Gwak, JH and Jung, MY and An, SU and Hyun, JH and Kang, S and Rhee, SK}, title = {Distinct temporal dynamics of planktonic archaeal and bacterial assemblages in the bays of the Yellow Sea.}, journal = {PloS one}, volume = {14}, number = {8}, pages = {e0221408}, doi = {10.1371/journal.pone.0221408}, pmid = {31449563}, issn = {1932-6203}, abstract = {The Yellow Sea features unique characteristics due to strong tides and nutrient-enriched freshwater outflows from China and Korea. The coupling of archaeal and bacterial assemblages associated with environmental factors at two bay areas in the Yellow Sea was investigated. Temporal variations of the archaeal and bacterial assemblages were shown to be greater than the spatial variations based on an analysis of the 16S rRNA gene sequences. Distinct temporal dynamics of both planktonic archaeal and bacterial assemblages was associated with temperature, NO2-, and chlorophyll a ([chl-a]) concentrations in the bays of the Yellow Sea. The [chl-a] was the prime predictor of bacterial abundance, and some taxa were clearly correlated with [chl-a]. Bacteroidetes and Alpha-proteobacteria dominated at high [chl-a] stations while Gamma-proteobacteria (esp. SAR86 clade) and Actinobacteria (Candidatus Actinomarina clade) were abundant at low [chl-a] stations. The archaeal abundance was comparable with the bacterial abundance in most of the October samples. Co-dominance of Marine Group II (MGII) and Candidatus Nitrosopumilus suggests that the assimilation of organic nitrogen by MGII could be coupled with nitrification by ammonia-oxidizing archaea. The distinct temporal dynamics of the archaeal and bacterial assemblages might be attributable to the strong tides and the inflow of nutrient-rich freshwater.}, }
@article {pmid31448388, year = {2019}, author = {Rojas, EC and Sapkota, R and Jensen, B and Jørgensen, HJL and Henriksson, T and Jørgensen, LN and Nicolaisen, M and Collinge, DB}, title = {Fusarium Head Blight Modifies Fungal Endophytic Communities During Infection of Wheat Spikes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01426-3}, pmid = {31448388}, issn = {1432-184X}, support = {674964//H2020 Marie Skłodowska-Curie Actions/ ; }, abstract = {Fusarium head blight (FHB) is a devastating disease of wheat heads. It is caused by several species from the genus Fusarium. Several endophytic fungi also colonize wheat spikes asymptomatically. Pathogenic and commensal fungi share and compete for the same niche and thereby influence plant performance. Understanding the natural dynamics of the fungal community and how the pre-established species react to pathogen attack can provide useful information on the disease biology and the potential use of some of these endophytic organisms in disease control strategies. Fungal community composition was assessed during anthesis as well as during FHB attack in wheat spikes during 2016 and 2017 in two locations. Community metabarcoding revealed that endophyte communities are dominated by basidiomycete yeasts before anthesis and shift towards a more opportunistic ascomycete-rich community during kernel development. These dynamics are interrupted when Fusarium spp. colonize wheat spikes. The Fusarium pathogens appear to exclude other fungi from floral tissues as they are associated with a reduction in community diversity, especially in the kernel which they colonize rapidly. Similarly, the presence of several endophytes was negatively correlated with Fusarium spp. and linked with spikes that stayed healthy despite exposure to the pathogen. These endophytes belonged to the genera Cladosporium, Itersonillia and Holtermanniella. These findings support the hypothesis that some naturally occurring endophytes could outcompete or prevent FHB and represent a source of potential biological control agents in wheat.}, }
@article {pmid31448296, year = {2019}, author = {Rothrock, MJ and Locatelli, A and Feye, KM and Caudill, AJ and Guard, J and Hiett, K and Ricke, SC}, title = {A Microbiomic Analysis of a Pasture-Raised Broiler Flock Elucidates Foodborne Pathogen Ecology Along the Farm-To-Fork Continuum.}, journal = {Frontiers in veterinary science}, volume = {6}, number = {}, pages = {260}, doi = {10.3389/fvets.2019.00260}, pmid = {31448296}, issn = {2297-1769}, abstract = {While conventionally grown poultry continues to dominate the U. S. poultry industry, there is an increasing demand for locally-grown, &quot;all natural&quot; alternatives. The use of next generation sequencing allows for not only the gross (e.g., community structure) but also fine-scale (e.g., taxa abundances) examination of these complex microbial communities. This data provides a better understanding of how a pasture flock's microbiome changes throughout the production life cycle and how that change in microbial ecology changes foodborne pathogens in alternative poultry production systems. In order to understand this ecology better, pooled broiler samples were taken during the entire flock life cycle, from pre-hatch gastrointestinal samples (N = 12) to fecal samples from the brood (N = 5), and pasture (N = 10) periods. Additional samples were taken during processing, including skin and feather rinsates (N = 12), ceca (N = 12), and whole carcass rinses (N = 12), and finally whole carcasss rinsates of final products (N = 3). Genomic DNA was extracted, 16S rDNA microbiome sequencing was conducted (Illumina MiSeq), and microbiomes were analyzed and compared using QIIME 1.9.1 to determine how microbiomes shifted throughout production continuum, as well as what environmental factors may be influencing these shifts. Significant microbiome shifts occurred during the life cycle of the pasture broiler flock, with the brood and pasture fecal samples and cecal samples being very distinct from the other pre-hatch, processing, and final product samples. Throughout these varied microbiomes, there was a stable core microbiome containing 13 taxa. Within this core microbiome, five taxa represented known foodborne pathogens (Salmonella, Campylobacter) or potential/emerging pathogens (Pseudomonas, Enterococcus, Acinetobacter) whose relative abundances varied throughout the farm-to-fork continuum, although all were more prevalent in the fecal samples. Additionally, of the 25 physiochemical and nutrient variables measured from the fecal samples, the carbon to nitrogen ratio was one of the most significant variables to warrant further investigations because it impacted both general fecal microbial ecology and Campylobacter and Enterococcus taxa within the core fecal microbiomes. These findings demonstrate the need for further longitudinal, farm-to-fork studies to understand the ecology of the microbial ecology of pasture production flocks to improve animal, environmental, and public health.}, }
@article {pmid31446647, year = {2019}, author = {Lemos, LN and Medeiros, JD and Dini-Andreote, F and Fernandes, GR and Varani, AM and Oliveira, G and Pylro, VS}, title = {Genomic signatures and co-occurrence patterns of the ultra-small Saccharimonadia (CPR/Patescibacteria phylum) suggest a symbiotic lifestyle.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15208}, pmid = {31446647}, issn = {1365-294X}, abstract = {The size of bacterial genomes is often associated with organismal metabolic capabilities determining ecological breadth and lifestyle. The recently proposed Candidate Phyla Radiation (CPR)/Patescibacteria encompasses mostly unculturable bacterial taxa with relatively small genome sizes with potential to co-metabolism interdependencies. Up to date, little is known about the ecology and evolution of CPR, particularly with respect to how they might interact with other taxa. Here, we reconstructed two novel genomes (namely, Candidatus Saccharibacter sossegus and Candidatus Chaer renensis) of taxa belonging to the class Saccharimonadia within the CPR/Patescibacteria using metagenomes obtained from Acid Mine Drainage (AMD). By testing the hypothesis of genome streamlining or symbiotic lifestyle, our results revealed clear signatures of gene losses in these genomes, such as those associated with de novo biosynthesis of essential amino acids, nucleotide, fatty acids, and cofactors. In addition, co-occurrence analysis provided evidence supporting potential symbioses of these organisms with Hydrotalea sp. in the AMD system. Taken together, our findings provide a better understanding of the ecology and evolution of CPR/Patescibacteria and highlight the importance of genome-reconstruction for studying metabolic interdependencies between unculturable Saccharimonadia representatives. This article is protected by copyright. All rights reserved.}, }
@article {pmid31446448, year = {2019}, author = {Wise, BR and Roane, TM and Mosier, AC}, title = {Community Composition of Nitrite Reductase Gene Sequences in an Acid Mine Drainage Environment.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01420-9}, pmid = {31446448}, issn = {1432-184X}, abstract = {Denitrifying microbial communities play a central role in the nitrogen cycle, contribute to greenhouse gas production, and provide ecosystem services through the mitigation of nitrogen pollution. The impacts of human-induced acid mine drainage (AMD) and naturally occurring acid rock drainage (ARD), both characterized by low pH and high metal concentrations, on denitrifying microbial communities is not well understood. This study examined denitrifying microbes within sediments impacted by acidic and metal-rich AMD or ARD in the Iron Springs Mining District (10 sites across four regions over four time points) located in Southwest Colorado, USA. Denitrification functional gene sequences (nirS and nirK coding for nitrite reductase) had a high number of observed OTUs (260 for nirS and 253 for nirK) and were observed at sites with pH as low as 3.5 and metals > 2 mg/L (including aluminum, iron, manganese, strontium, and zinc). A majority of the nirK and nirS OTUs (> 60%) were present in only one sampling region. Approximately 8% of the nirK and nirS OTUs had a more cosmopolitan distribution with presence in three or more regions. Phylogenetically related OTUs were found across sites with very different chemistry. The overall community structure for nirK and nirS genes was correlated to conductivity and calcium (respectively), which may suggest that conductivity may play an important role in shaping the distribution of nirK- and nirS-type denitrifiers. Overall, these findings improve upon our understanding of the potential for denitrification within an ecosystem impacted by AMD or ARD and provide a foundation for future research to understand the rates and physiology of denitrifying organisms in these systems.}, }
@article {pmid31444524, year = {2019}, author = {Zhang, G and Bai, J and Zhao, Q and Jia, J and Wang, W and Wang, X}, title = {Bacterial Succession in Salt Marsh Soils Along a Short-term Invasion Chronosequence of Spartina alterniflora in the Yellow River Estuary, China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01430-7}, pmid = {31444524}, issn = {1432-184X}, support = {2017YFC0505906//National Key R &amp; D Program of China/ ; 310430001//Fundamental Research Funds for the Central Universities/ ; }, abstract = {As an exotic plant species, Spartina alterniflora seriously threatens native ecosystem function in Chinese coastal regions. Unveiling the dynamics of soil bacteria community during its invasion is essential for a better understanding of related biogeochemical processes, while the shift in soil bacterial community over invasive time remains unclear. A short-term chronosequence was identified to assess the impacts of Spartina alterniflora invasion on soil nutrients and bacterial community composition and structure (using 16S rRNA gene high-throughput sequencing) over the time of invasion (i.e., (1) at least 10 years, (2) nearly 5 years, (3) less than 2 years, and (4) in native salt marshes or 0 years) in the Yellow River Estuary. The results exhibited an orderly change in the soil physicochemical properties and bacterial community composition over the invasion time. Soil pH showed a significant decrease with the accumulation of soil organic matter (SOM), whereas soil nutrients such as soil dissolved organic carbon (DOC), total nitrogen (TN), nitrate (NO3-), ammonium (NH4+), K+, and Mg2+ were generally increased with the age of the invasion. The number of operational taxonomic units (OTUs, 97% similarity level) exhibited a decreasing trend, which suggested a decline in bacterial diversity with the invasion age. The dominant groups at the phylum level were Proteobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, and Gemmatimonadetes (the sum of relative abundance was > 70% across all samples). The relative abundances of Chloroflexi and Gemmatimonadetes steadily decreased, while the abundance of Bacteroidetes significantly increased with the plant invasion. The distribution pattern of the soil bacteria was clearly separated according to the principal coordinate analysis (PCoA) and canonical correspondence analysis (CCA) in native and invaded salt marshes. The variation in the soil bacterial community was tightly associated with the soil physicochemical properties (Mantel test, P < 0.05). Variance partitioning analysis (VPA) showed that plant traits explained 4.95% of the bacterial community variation, and soil variables explained approximately 26.96% of the variation. Network analysis also revealed that plant invasion strengthens the interaction among soil bacterial communities. Overall, our findings highlight the bacterial community succession during the Spartina alterniflora invasion in coastal salt marsh soils, which can provide insight regarding the association between soil development and invasive plant.}, }
@article {pmid31443509, year = {2019}, author = {Hernández-Arriaga, A and Baumann, A and Witte, OW and Frahm, C and Bergheim, I and Camarinha-Silva, A}, title = {Changes in Oral Microbial Ecology of C57BL/6 Mice at Different Ages Associated with Sampling Methodology.}, journal = {Microorganisms}, volume = {7}, number = {9}, pages = {}, doi = {10.3390/microorganisms7090283}, pmid = {31443509}, issn = {2076-2607}, support = {CA 1708/1-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {The mouth is an important niche for bacterial colonization. Previous research used mouth microbiota to predict diseases like colon cancer and inflammatory bowel disease (IBD). It is still unclear how the sampling methodology influences microbial characterization. Our aim was to determine if the sampling methods, e.g., cotton swab or tissue biopsy, and the age influence the oral microbial composition of mice. Microbial DNA was extracted using a commercial kit and characterized targeting the 16s rRNA gene from mouth swabs and tissue biopsies from 2 and 15 months old C57BL/6 male mice kept in the same SPF facility. Our results show statistical different microbial community of the different ages, type of sampling, and the two fixed factors age x type of sample (p-value <0.05). At the genus level, we identified that the genera Actinobacillus, Neisseria, Staphylococcus, and Streptococcus either increase or decrease in abundance depending on sampling and age. Additionally, the abundance of Streptococcusdanieliae, Moraxellaosloensis, and some unclassified Streptococcus was affected by the sampling method. While swab and tissue biopsies both identified the common colonizers of oral microbiota, cotton swabbing is a low-cost and practical method, validating the use of the swab as the preferred oral sampling approach.}, }
@article {pmid31441243, year = {2019}, author = {Smessaert, J and Van Geel, M and Verreth, C and Crauwels, S and Honnay, O and Keulemans, W and Lievens, B}, title = {Temporal and spatial variation in bacterial communities of &quot;Jonagold&quot; apple (Malus x domestica Borkh.) and &quot;Conference&quot; pear (Pyrus communis L.) floral nectar.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e918}, doi = {10.1002/mbo3.918}, pmid = {31441243}, issn = {2045-8827}, support = {VLAIO: project LA 150888//Agentschap voor Innovatie door Wetenschap en Technologie/ ; //Flanders Innovation and Entrepreneurship/ ; }, abstract = {Production of many agricultural crops and fruits strongly depends on pollinators. For instance, pome fruits such as apple and pear are highly dependent on pollination for fruit set, fruit quality, and yield. Nectar is often inhabited by microbes, most often yeasts and bacteria, which may change nectar quality and therefore also affect plant-pollinator interactions. Here, we used high-throughput 16S ribosomal RNA gene amplicon sequencing to investigate the temporal and spatial variation in bacterial communities in floral nectar of apple and pear. We sampled 15 apple (Malus x domestica Borkh.) and 15 pear (Pyrus communis L.) orchards distributed over the eastern part of Belgium over a timespan of seven days. Nectar bacterial community composition differed strongly among fruit species. Nectar of pear was dominated by Actinobacteria, followed by Proteobacteria and Firmicutes. Apple nectar was strongly enriched in Bacteroidetes, a phylum which until now has been found to be rarely associated with floral nectar. Nectar was dominated by only a few bacterial species, with Brevibacterium (Actinobacteria) and Undibacterium (Proteobacteria) as the most abundant bacteria in pear and apple nectar, respectively. Bacterial richness and diversity were found to fluctuate during flowering, likely due to changing environmental conditions. Additionally, spatial structure in nectar bacterial community composition was found in apple orchards, while this was not the case for pear. Differences in nectar bacterial communities between apple and pear nectar may differently affect the chemical and nutritional composition of the nectar, influencing pollinator attraction and visitation, and thus pollination efficacy in general.}, }
@article {pmid31438955, year = {2019}, author = {Vavourakis, CD and Mehrshad, M and Balkema, C and van Hall, R and Andrei, AŞ and Ghai, R and Sorokin, DY and Muyzer, G}, title = {Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {69}, doi = {10.1186/s12915-019-0688-7}, pmid = {31438955}, issn = {1741-7007}, support = {322551/ERC_/European Research Council/International ; 322551/ERC_/European Research Council/International ; 322551/ERC_/European Research Council/International ; L200961651//Czech Academy of Sciences/ ; MSM200961801//Czech Academy of Sciences/ ; 17-04828S//Grant Agency of the Czech Republic/ ; 17-04828S//Grant Agency of the Czech Republic/ ; 24002002//SYAM-Gravitation Program/ ; RFBR 19-04-00401//Russian Foundation for Basic Research/ ; }, abstract = {BACKGROUND: The planetary sulfur cycle is a complex web of chemical reactions that can be microbial-mediated or can occur spontaneously in the environment, depending on the temperature and pH. Inorganic sulfur compounds can serve as energy sources for specialized prokaryotes and are important substrates for microbial growth in general. Here, we investigate dissimilatory sulfur cycling in the brine and sediments of a southwestern Siberian soda lake characterized by an extremely high pH and salinity, combining meta-omics analyses of its uniquely adapted highly diverse prokaryote communities with biogeochemical profiling to identify key microbial players and expand our understanding of sulfur cycling under haloalkaline conditions.<br><br>RESULTS: Peak microbial activity was found in the top 4 cm of the sediments, a layer with a steep drop in oxygen concentration and redox potential. The majority of sulfur was present as sulfate or iron sulfide. Thiosulfate was readily oxidized by microbes in the presence of oxygen, but oxidation was partially inhibited by light. We obtained 1032 metagenome-assembled genomes, including novel population genomes of characterized colorless sulfur-oxidizing bacteria (SOB), anoxygenic purple sulfur bacteria, heterotrophic SOB, and highly active lithoautotrophic sulfate reducers. Surprisingly, we discovered the potential for nitrogen fixation in a new genus of colorless SOB, carbon fixation in a new species of phototrophic Gemmatimonadetes, and elemental sulfur/sulfite reduction in the &quot;Candidatus Woesearchaeota.&quot; Polysulfide/thiosulfate and tetrathionate reductases were actively transcribed by various (facultative) anaerobes.<br><br>CONCLUSIONS: The recovery of over 200 genomes that encoded enzymes capable of catalyzing key reactions in the inorganic sulfur cycle indicates complete cycling between sulfate and sulfide at moderately hypersaline and extreme alkaline conditions. Our results suggest that more taxonomic groups are involved in sulfur dissimilation than previously assumed.}, }
@article {pmid31435691, year = {2019}, author = {Damjanovic, K and Menéndez, P and Blackall, LL and van Oppen, MJH}, title = {Early Life Stages of a Common Broadcast Spawning Coral Associate with Specific Bacterial Communities Despite Lack of Internalized Bacteria.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01428-1}, pmid = {31435691}, issn = {1432-184X}, support = {DP160101468//Australian Research Council/ ; Holsworth Wildlife Endowment//Ecological Society of Australia/ ; }, abstract = {Coral-associated bacteria are critical for the well-being of their host and may play essential roles during ontogeny, as suggested by the vertical transmission of some bacteria in brooding corals. Bacterial acquisition patterns in broadcast spawners remain uncertain, as 16S rRNA gene metabarcoding of coral early life stages suggests the presence of bacterial communities, which have not been detected by microscopic examinations. Here, we combined 16S rRNA gene metabarcoding with fluorescence in situ hybridization (FISH) microscopy to analyze bacterial assemblages in Acropora tenuis egg-sperm bundles, embryos, and larvae following a spawning event. Metabarcoding results indicated that A. tenuis offspring ≤ 4-day-old were associated with diverse and dynamic bacterial microbiomes, dominated by Rhodobacteraceae, Alteromonadaceae, and Oceanospirillaceae. While FISH analyses confirmed the lack of internalized bacteria in A. tenuis offspring, metabarcoding showed that even the earliest life stages examined (egg-sperm bundles and two-cell stages) were associated with a diverse bacterial community, suggesting the bacteria were confined to the mucus layer. These results can be explained by vertical transmission of certain taxa (mainly Endozoicomonas) in the mucus surrounding the gametes within bundles, or by horizontal bacterial transmission through the release of bacteria by spawning adults into the water column.}, }
@article {pmid31435492, year = {2019}, author = {Onywera, H and Williamson, AL and Mbulawa, ZZA and Coetzee, D and Meiring, TL}, title = {Factors associated with the composition and diversity of the cervical microbiota of reproductive-age Black South African women: a retrospective cross-sectional study.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e7488}, doi = {10.7717/peerj.7488}, pmid = {31435492}, issn = {2167-8359}, abstract = {Background: Lactobacillus spp. are common bacteria in the cervical and vaginal microbiota (CVM) and are thought to represent a &quot;healthy&quot; cervicovaginal state. Several studies have found an independent association between ethnicity/race and cervical and vaginal microbiota (CVM) composition. Women of sub-Saharan African descent appear to be significantly more likely to have non-Lactobacillus-dominated CVM compared to women of European descent. The factors contributing to these differences remain to be fully elucidated. The CVM of Black South African women and factors influencing their CVM remain understudied. In this study, we characterized the cervical microbiota of reproductive-age South African women and assessed the associations of these microbiota with participants' metadata.<br><br>Methods: The cervical microbiota from cervical DNA of 62 reproductive-age women were profiled by Ion Torrent sequencing the V4 hypervariable region of the bacterial 16S ribosomal RNA (rRNA) gene and analyzed with the Quantitative Insights Into Microbial Ecology (QIIME), UPARSE, and metagenomeSeq tools. Associations between cervical microbiota and participants' metadata were assessed using GraphPad Prism, R packages and an in-house script.<br><br>Results: The cervical microbiota clustered into three distinct community state types (CSTs): Lactobacillus iners-dominated cervical microbiota (CST I (38.7%, 24/62)), unclassified Lactobacillus-dominated cervical microbiota (CST II (4.8%, 3/62)), and diverse cervical microbiota (CST III (56.5%, 35/62)) with an array of heterogeneous bacteria, predominantly the bacterial vaginosis (BV)-associated Gardnerella, Prevotella, Sneathia, and Shuttleworthia. CST III was associated with BV (p = 0.001). Women in CST I were more likely to be on hormonal contraception, especially progestin-based, compared to women in CST III (odds ratio: 5.2 (95% CI [1.6-17.2]); p = 0.005). Women on hormonal contraception had a significantly lower alpha (Shannon indices: 0.9 (0.2-1.9) versus 2.3 (0.6-2.3); p = 0.025) and beta (permutational multivariate analysis of variance (PERMANOVA) pseudo-F statistic =4.31, p = 0.019) diversity compared to non-users. There was no significant difference in the alpha (Shannon indices: 1.0 (0.3-2.2) versus 1.9 (0.3-2.2); p = 0.483) and beta (PERMANOVA pseudo-F statistic = 0.89, p = 0.373) diversity in women with versus without human papillomavirus infection.<br><br>Conclusions: The majority of Black women in our study had non-Lactobacillus-dominated cervical microbiota. Additional studies are needed to examine whether such microbiota represent abnormal, intermediate or variant states of health. Lastly, the association of hormonal contraception with L. iners dominance requires further in-depth research to confirm this association, determine its biological mechanism and whether it has a beneficial effect on the cervicovaginal health.}, }
@article {pmid31434790, year = {2019}, author = {Weiner, BG and Posfai, A and Wingreen, NS}, title = {Spatial ecology of territorial populations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {36}, pages = {17874-17879}, doi = {10.1073/pnas.1911570116}, pmid = {31434790}, issn = {1091-6490}, abstract = {Many ecosystems, from vegetation to biofilms, are composed of territorial populations that compete for both nutrients and physical space. What are the implications of such spatial organization for biodiversity? To address this question, we developed and analyzed a model of territorial resource competition. In the model, all species obey trade-offs inspired by biophysical constraints on metabolism; the species occupy nonoverlapping territories, while nutrients diffuse in space. We find that the nutrient diffusion time is an important control parameter for both biodiversity and the timescale of population dynamics. Interestingly, fast nutrient diffusion allows the populations of some species to fluctuate to zero, leading to extinctions. Moreover, territorial competition spontaneously gives rise to both multistability and the Allee effect (in which a minimum population is required for survival), so that small perturbations can have major ecological effects. While the assumption of trade-offs allows for the coexistence of more species than the number of nutrients-thus violating the principle of competitive exclusion-overall biodiversity is curbed by the domination of &quot;oligotroph&quot; species. Importantly, in contrast to well-mixed models, spatial structure renders diversity robust to inequalities in metabolic trade-offs. Our results suggest that territorial ecosystems can display high biodiversity and rich dynamics simply due to competition for resources in a spatial community.}, }
@article {pmid31432245, year = {2019}, author = {Sun, Y and Liu, Y and Pan, J and Wang, F and Li, M}, title = {Perspectives on Cultivation Strategies of Archaea.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01422-7}, pmid = {31432245}, issn = {1432-184X}, support = {31622002//NSFC/ ; 91851105//NSFC/ ; }, abstract = {Archaea have been recognized as a major domain of life since the 1970s and occupy a key position in the tree of life. Recent advances in culture-independent approaches have greatly accelerated the research son Archaea. However, many hypotheses concerning the diversity, physiology, and evolution of archaea are waiting to be confirmed by culture-base experiments. Consequently, archaeal isolates are in great demand. On the other hand, traditional approaches of archaeal cultivation are rarely successful and require urgent improvement. Here, we review the current practices and applicable microbial cultivation techniques, to inform on potential strategies that could improve archaeal cultivation in the future. We first summarize the current knowledge on archaeal diversity, with an emphasis on cultivated and uncultivated lineages pertinent to future research. Possible causes for the low success rate of the current cultivation practices are then discussed to propose future improvements. Finally, innovative insights for archaeal cultivation are described, including (1) medium refinement for selective cultivation based on the genetic and transcriptional information; (2) consideration of the up-to-date archaeal culturing skills; and (3) application of multiple cultivation techniques, such as co-culture, direct interspecies electron transfer (DIET), single-cell isolation, high-throughput culturing (HTC), and simulation of the natural habitat. Improved cultivation efforts should allow successful isolation of as yet uncultured archaea, contributing to the much-needed physiological investigation of archaea.}, }
@article {pmid31432244, year = {2019}, author = {Nasser, NA and Gregory, BRB and Steele, RE and Patterson, RT and Galloway, JM}, title = {Behind the Organic Veil: Assessing the Impact of Chemical Deflocculation on Organic Content Reduction and Lacustrine Arcellinida (Testate Amoebae) Analysis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01429-0}, pmid = {31432244}, issn = {1432-184X}, abstract = {Arcellinida (testate lobose amoebae) are widely used as bio-indicators of lacustrine environmental change. Too much obscuring organic material in a gridded wet Petri dish preparation makes it difficult to observe all specimens present and slows quantification as the organic material has to be carefully worked through with a dissection probe. Chemical deflocculation using soda ash (Na2CO3·H2O), potassium hydroxide (KOH), or sodium hexametaphosphate ((NaPO3)6) has previously been shown to disaggregate and reduce organic content in lake sediments, but to date, no attempt has been made to comparatively evaluate the efficiency of these deflocculants in disaggregating organic content and their impact on Arcellinida analysis in lacustrine sediments. Here, we assess the effectiveness of soda ash, potassium hydroxide, and sodium hexametaphosphate treatments on removing organic content and the impact of those digestions on Arcellinida preservation in 126 sample aliquots subdivided from three sediment samples (YK-20, YK-25, and YK-57) collected from three lakes near Yellowknife, Northwest Territories, Canada. Following treatment, cluster analysis and Bray-Curtis dissimilarity matrix (BCDM) were utilized to determine whether treatments resulted in dissolution-driven changes in Arcellinida assemblage composition. Observed Arcellinida tests in aliquots increased drastically after treatment of organic-rich samples (47.5-452.7% in organic-rich aliquots and by 14.8% in aliquots with less organic matter). The BCDM results revealed that treatment with 5% KOH resulted in the highest reduction in observed organic content without significantly affecting Arcellinida assemblage structure, while soda ash and sodium hexametaphosphate treatments resulted in marginal organic matter reduction and caused severe damage to the arcellinidan tests.}, }
@article {pmid31431510, year = {2019}, author = {Taroni, JN}, title = {Making Workshops Work: Insights from EDAMAME.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSystems.00467-19}, pmid = {31431510}, issn = {2379-5077}, abstract = {Microbiology, like many areas of life science research, is increasingly data-intensive. As such, bioinformatics and data science skills have become essential to leverage microbiome sequencing data for discovery. Short intensive courses have sprung up as formal computational training opportunities at individual institutions fail to meet demands. In this issue, Shade et al. (A. Shade, T. K. Dunivin, J. Choi, T. K. Teal, et al., mSystems 4:e00297-19, 2019, https://doi.org/10.1128/mSystems.00297-19) share their experience and approach in executing the annual, weeklong Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology (EDAMAME) workshop from 2014 to 2018. EDAMAME introduced learners to general scientific computing concepts and domain-specific data analysis approaches. Workshop learners self-reported appreciable gains in understanding and ability. This report on the EDAMAME workshop strategy and lessons learned will help others in the life sciences to plan, execute, and assess short hands-on computing-intensive courses that support research in a particular domain.}, }
@article {pmid31431509, year = {2019}, author = {Shade, A and Dunivin, TK and Choi, J and Teal, TK and Howe, AC}, title = {Strategies for Building Computing Skills To Support Microbiome Analysis: a Five-Year Perspective from the EDAMAME Workshop.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSystems.00297-19}, pmid = {31431509}, issn = {2379-5077}, support = {R25 GM115335/GM/NIGMS NIH HHS/United States ; }, abstract = {Here, we report our educational approach and learner evaluations of the first 5 years of the Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology (EDAMAME) workshop, held annually at Michigan State University's Kellogg Biological Station from 2014 to 2018. We hope this information will be useful for others who want to organize computing-intensive workshops and will encourage quantitative skill development among microbiologists.IMPORTANCE High-throughput sequencing and related statistical and bioinformatic analyses have become routine in microbiology in the past decade, but there are few formal training opportunities to develop these skills. A weeklong workshop can offer sufficient time for novices to become introduced to best computing practices and common workflows in sequence analysis. We report our experiences in executing such a workshop targeted to professional learners (graduate students, postdoctoral scientists, faculty, and research staff).}, }
@article {pmid31431508, year = {2019}, author = {Sun, Z and Huang, S and Zhu, P and Yue, F and Zhao, H and Yang, M and Niu, Y and Jing, G and Su, X and Li, H and Callewaert, C and Knight, R and Liu, J and Smith, E and Wei, K and Xu, J}, title = {A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSystems.00293-19}, pmid = {31431508}, issn = {2379-5077}, abstract = {A quantitative and objective indicator for skin health via the microbiome is of great interest for personalized skin care, but differences among skin sites and across human populations can make this goal challenging. A three-city (two Chinese and one American) comparison of skin microbiota from atopic dermatitis (AD) and healthy pediatric cohorts revealed that, although city has the greatest effect size (the skin microbiome can predict the originated city with near 100% accuracy), a microbial index of skin health (MiSH) based on 25 bacterial genera can diagnose AD with 83 to ∼95% accuracy within each city and 86.4% accuracy across cities (area under the concentration-time curve [AUC], 0.90). Moreover, nonlesional skin sites across the bodies of AD-active children (which include shank, arm, popliteal fossa, elbow, antecubital fossa, knee, neck, and axilla) harbor a distinct but lesional state-like microbiome that features relative enrichment of Staphylococcus aureus over healthy individuals, confirming the extension of microbiome dysbiosis across body surface in AD patients. Intriguingly, pretreatment MiSH classifies children with identical AD clinical symptoms into two host types with distinct microbial diversity and treatment effects of corticosteroid therapy. These findings suggest that MiSH has the potential to diagnose AD, assess risk-prone state of skin, and predict treatment response in children across human populations.IMPORTANCE MiSH, which is based on the skin microbiome, can quantitatively assess pediatric skin health across cohorts from distinct countries over large geographic distances. Moreover, the index can identify a risk-prone skin state and compare treatment effect in children, suggesting applications in diagnosis and patient stratification.}, }
@article {pmid31429989, year = {2019}, author = {Velazquez, S and Griffiths, W and Dietz, L and Horve, P and Nunez, S and Hu, J and Shen, J and Fretz, M and Bi, C and Xu, Y and Van Den Wymelenberg, KG and Hartmann, EM and Ishaq, SL}, title = {From one species to another: A review on the interaction of chemistry and microbiology in relation to cleaning in the built environment.}, journal = {Indoor air}, volume = {}, number = {}, pages = {}, doi = {10.1111/ina.12596}, pmid = {31429989}, issn = {1600-0668}, abstract = {Since the advent of soap, personal hygiene practices have revolved around removal, sterilization, and disinfection - both of visible soil and microscopic organisms - for a myriad of cultural, aesthetic, or health-related reasons. Cleaning methods and products vary widely in their recommended use, effectiveness, risk to users or building occupants, environmental sustainability, and ecological impact. Advancements in science and technology have facilitated in-depth analyses of the indoor microbiome and studies in this field suggest that the traditional &quot;scorched-earth cleaning&quot; mentality - that surfaces must be completely sterilized and prevent microbial establishment - may contribute to long-term human health consequences. Moreover, the materials, products, activities, and microbial communities indoors all contribute to, or remove, chemical species to the indoor environment. This review examines the effects of cleaning with respect to the interaction of chemistry, indoor microbiology, and human health. PRACTICAL IMPLICATIONS: Simple interventions, such as hand washing, can dramatically improve health and reduce infectious disease. Chemical intervention, while effective, may encourage the development of microbial resistance over time if not implemented properly. Microbial communities adapt, reassemble, and persist, and recent theory in microbial ecology suggests that curating microbial communities may be more sustainable than perpetually attempting to remove them. This article is protected by copyright. All rights reserved.}, }
@article {pmid31428833, year = {2019}, author = {Tang, Y and Dai, T and Su, Z and Hasegawa, K and Tian, J and Chen, L and Wen, D}, title = {A Tripartite Microbial-Environment Network Indicates How Crucial Microbes Influence the Microbial Community Ecology.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01421-8}, pmid = {31428833}, issn = {1432-184X}, support = {51678003//National Natural Science Foundation of China/ ; 51678334//National Natural Science Foundation of China/ ; }, abstract = {Current technologies could identify the abundance and functions of specific microbes, and evaluate their individual effects on microbial ecology. However, these microbes interact with each other, as well as environmental factors, in the form of complex network. Determination of their combined ecological influences remains a challenge. In this study, we developed a tripartite microbial-environment network (TMEN) analysis method that integrates microbial abundance, metabolic function, and environmental data as a tripartite network to investigate the combined ecological effects of microbes. Applying TMEN to analyzing the microbial-environment community structure in the sediments of Hangzhou Bay, one of the most seriously polluted coastal areas in China, we found that microbes were well-organized into 4 bacterial communities and 9 archaeal communities. The total organic carbon, sulfate, chemical oxygen demand, salinity, and nitrogen-related indexes were detected as crucial environmental factors in the microbial-environmental network. With close interactions with these environmental factors, Nitrospirales and Methanimicrococcu were identified as hub microbes with connection advantage. Our TMEN method could close the gap between lack of efficient statistical and computational approaches and the booming of large-scale microbial genomic and environmental data. Based on TMEN, we discovered a potential microbial ecological mechanism that crucial species with significant influence on the microbial community ecology would possess one or two of the community advantages for enhancing their ecological status and essentiality, including abundance advantage and connection advantage.}, }
@article {pmid31420342, year = {2019}, author = {In 't Zandt, MH and Kip, N and Frank, J and Jansen, S and van Veen, JA and Jetten, MSM and Welte, CU}, title = {High abundance of Methanobacteriales and Syntrophobacterales may help to prevent corrosion of metal sheet piles.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.01369-19}, pmid = {31420342}, issn = {1098-5336}, abstract = {Iron sheet piles are widely used in flood protection, dike construction and river bank reinforcement. Their corrosion leads to gradual deterioration and often makes replacement necessary. Natural deposit layers on these sheet piles can prevent degradation and significantly increase their lifespan. However, little is known about the mechanisms of natural protective layer formation. Here, we studied the microbial diversity of corrosion-protective deposit layers on iron sheet piles at the Gouderak pumping station in Zuid-Holland, the Netherlands. Deposit layers, surrounding sediment and top sediment samples were analyzed for soil physicochemical parameters, microbial diversity and metabolic potential. Methanogens appeared to be enriched 18-fold in the deposit layers. After sequencing, metagenome assembly and binning, we obtained four near-complete draft genomes of microorganisms (Methanobacteriales, two Coriobacteriales and Syntrophobacterales) that were highly enriched in the deposit layers, strongly indicating a potential role in corrosion protection. Coriobacteriales and Syntrophobacterales could be part of a microbial foodweb degrading organic matter to supply methanogenic substrates. Methane-producing Methanobacteriales could metabolize iron which may initially lead to mild corrosion but potentially stimulates the formation of a carbonate-rich protective deposit layer in the long term. In addition, Methanobacteriales and Coriobacteriales have the potential to interact with metal surfaces via direct interspecies or extracellular electron transfer. In conclusion, our study provides valuable insights into microbial populations involved in iron corrosion protection and potentially enables the development of novel strategies for in-situ screening of iron sheet piles in order to reduce risks and develop more sustainable replacement practices.Importance Iron sheet piles are widely used to reinforce dikes and river banks. Damage due to iron corrosion poses a significant safety risk and has major economical impacts. Different groups of microorganisms are known to either stimulate or inhibit the corrosion process. Recently, natural corrosion-protective deposit layers were found on sheet piles. Analyses of the microbial composition indicated a potential role for methane-producing archaea. However, the full metabolic potential of the microbial communities within these protective layers has not been determined. The significance of this work lies in the reconstruction of the microbial food web of natural corrosion-protective layers isolated from non-corroding metal sheet piles. With this work, we provide insights into the microbiological mechanisms that potentially promote corrosion protection in freshwater ecosystems. Our findings could support the development of screening protocols to assess the integrity of iron sheet piles to decide whether replacement is required.}, }
@article {pmid31420340, year = {2019}, author = {Bale, NJ and Palatinszky, M and Rijpstra, WIC and Herbold, CW and Wagner, M and Sinninghe Damsté, JS}, title = {The membrane lipid composition of the moderately thermophilic ammonia-oxidizing archaeon Ca. Nitrosotenuis uzonensis at different growth temperatures.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.01332-19}, pmid = {31420340}, issn = {1098-5336}, abstract = {Ca. Nitrosotenuis uzonensis is the only cultured moderately thermophilic member of the thaumarchaeotal order Nitrosopumilales (NP) that contains many mesophilic marine strains. We examined its membrane lipid composition at different growth temperatures (37, 46 and 50 °C). Its lipids were all membrane-spanning glycerol dialkyl glycerol tetraethers (GDGTs), with 0 to 4 cyclopentane moieties. Crenarchaeol (cren), the characteristic thaumarchaeotal GDGT, and its isomer (cren') were present in high abundance (30-70 %). The GDGT polar headgroups were mono-, di- and trihexoses and hexose/phosphohexose. The ratio of glycolipid to phospholipid GDGTs was highest in the cultures grown at 50 °C. With increasing growth temperature, the relative contribution of cren and cren' increased, while GDGT-0 to GDGT-4 (including isomers) decreased. TEX86 (tetraether index of tetraethers consisting of 86 carbons)-derived temperatures were much lower than the actual growth temperatures, further demonstrating that TEX86 does not accurately reflect the membrane lipid adaptation of thermophilic Thaumarchaeota. As temperature increased, specific GDGTs changed relative to their isomers, possibly representing temperature adaption-induced changes in cyclopentane ring stereochemistry. Comparison of a wide range of thaumarcheotal core lipid compositions revealed the Ca. N. uzonensis cultures clustered separately from other members of the NP order and the Nitrososphaerales (NS) order. While phylogeny generally seems to have a strong influence on GDGT distribution, our analysis of Ca. Nitrosotenuis uzonensis demonstrates that its terrestrial, higher temperature niche has led to a lipid composition that clearly differentiates it from other NP members and that this difference is mostly driven by its high cren' content.Importance For Thaumarchaeota the ratio of their Glycerol Dialkyl Glycerol Tetraether (GDGT) lipids depends on growth temperature, a premise that forms the basis of the widely applied TEX86 paleotemperature proxy. A thorough understanding of which GDGTs are produced by which Thaumarchaeota and what the effect of temperature is on their GDGT composition is essential for constraining the TEX86 proxy. Ca. Nitrosotenuis uzonensis is a moderately thermophilic Thaumarchaeote enriched from a thermal spring, setting it apart in its environmental niche from the other marine mesophilic members of its order. Indeed, we found that the GDGT composition of Ca. N. uzonensis cultures was distinct from other members of its order and was more similar to other thermophilic, terrestrial Thaumarchaeota. This suggests that while phylogeny has a strong influence on GDGT distribution, the environmental niche that a Thaumarchaeote inhabits also shapes its GDGT composition.}, }
@article {pmid31418250, year = {2019}, author = {Jiang, Y and Xu, ZW and Wang, RZ and Li, H and Zhang, YG}, title = {[Effects of long-term fertilization and water addition on soil properties and plant community characteristics in a semiarid grassland.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {30}, number = {7}, pages = {2470-2480}, doi = {10.13287/j.1001-9332.201907.034}, pmid = {31418250}, issn = {1001-9332}, mesh = {*Agriculture ; China ; Ecosystem ; *Fertilizers ; *Grassland ; Nitrogen ; Plants ; *Soil ; Water ; }, abstract = {We summarized the effects of fertilization and water addition on some soil properties and plant community characteristics in a long-term field experiment established in 2005 in a degraded grassland in Duolun, Inner Mongolia, China. The results showed that nitrogen (N) addition resulted in surface soil acidification and decreased acid buffering capacity, increased the availability of carbon (C), N, phosphorus (P), sulfur (S) and DTPA-extractable iron (Fe), manganese (Mn), and copper (Cu) contents, depleted the sum of base cations calcium (Ca), magnesium (Mg), potassium (K) and sodium (Na), decreased the diversity of soil microbial community. Nitrogen addition enhanced the uptake of N, P, S, K, Mn, Cu and Zn by plants, while inhibited plant Fe uptake, but with no effect on the uptake of Ca or Mg. Nitrogen addition increased aboveground net primary productivity (ANPP) but declined plant species diversity and community stability. Phosphorus addition alone increased total P and Olsen-P contents and fungal abundance in the surface soil, and improved N, P and S uptake by leaves, but had no significant influence on other soil basic chemical properties, ANPP, and plant species diversity. Water addition could improve the resistance of plant community, but its contribution to ANPP was limited by soil N availa-bility. Water addition could buffer soil acidification and the decline of microbial and plant diversity induced by N addition. Under the treatments of N and water addition or P and water addition, the diversity and function of soil microorganisms were affected by plant community structure and function. Long-term controlled field experiments were useful for understanding ecosystem structure and functions of grasslands. However, to uncover the underlying mechanisms in grassland ecosystem ecology, single-site experiments should be incorporated with multiple-site controlled field experiments in different regions. More attentions should be paid to the linkage of above- and below-ground ecological processes.}, }
@article {pmid31415965, year = {2019}, author = {Deng, Y and Ruan, Y and Ma, B and Timmons, MB and Lu, H and Xu, X and Zhao, H and Yin, X}, title = {Multi-omics analysis reveals niche and fitness differences in typical denitrification microbial aggregations.}, journal = {Environment international}, volume = {132}, number = {}, pages = {105085}, doi = {10.1016/j.envint.2019.105085}, pmid = {31415965}, issn = {1873-6750}, abstract = {Suspended floc and fixed biofilm are two commonly applied strategies for heterotrophic denitrification in wastewater treatment. These two strategies use different carbon sources and reside within different ecological niches for microbial aggregation, which were hypothesized to show distinct microbial structures and metabolic fitness. We surveyed three floc reactors and three biofilm reactors for denitrification and determined if there were distinct microbial aggregations. Multiple molecular omics approaches were used to determine the microbial community composition, co-occurrence network and metabolic pathways. Proteobacteria was the dominating and most active phylum among all samples. Carbon source played an important role in shaping the microbial community composition while the distribution of functional protein was largely influenced by salinity. We found that the topological network features had different ecological patterns and that the microorganisms in the biofilm reactors had more nodes but less interactions than those in floc reactors. The large niche differences in the biofilm reactors explained the observed high microbial diversity, functional redundancy and resulting high system stability. We also observed a lower proportion of denitrifiers and higher resistance to oxygen and salinity perturbation in the biofilm reactors than the floc reactors. Our findings support our hypothesis that niche differences caused a distinct microbial structure and increased microbial ecology distribution, which has the potential to improve system efficiency and stability.}, }
@article {pmid31412927, year = {2019}, author = {Pérez-Jaramillo, JE and de Hollander, M and Ramírez, CA and Mendes, R and Raaijmakers, JM and Carrión, VJ}, title = {Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {114}, doi = {10.1186/s40168-019-0727-1}, pmid = {31412927}, issn = {2049-2618}, support = {568-2012-15517825//Departamento Administrativo de Ciencia, Tecnología e Innovación/ ; Back to the Roots program//Stichting voor de Technische Wetenschappen/ ; Back to the Roots program//Stichting voor de Technische Wetenschappen/ ; 443112/2014-2//CNPq Brazil/ ; }, abstract = {BACKGROUND: Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood.<br><br>RESULTS: Here, we investigated if the transition from a native to an agricultural soil affected rhizobacterial community assembly of wild and modern common bean (Phaseolus vulgaris) and if this led to a depletion of rhizobacterial diversity. The impact of the bean genotype on rhizobacterial assembly was more prominent in the agricultural soil than in the native soil. Although only 113 operational taxonomic units (OTUs) out of a total of 15,925 were shared by all eight bean accessions grown in native and agricultural soils, this core microbiome represented a large fraction (25.9%) of all sequence reads. More OTUs were exclusively found in the rhizosphere of common bean in the agricultural soil as compared to the native soil and in the rhizosphere of modern bean accessions as compared to wild accessions. Co-occurrence analyses further showed a reduction in complexity of the interactions in the bean rhizosphere microbiome in the agricultural soil as compared to the native soil.<br><br>CONCLUSIONS: Collectively, these results suggest that habitat expansion of common bean from its native soil environment to an agricultural context had an unexpected overall positive effect on rhizobacterial diversity and led to a stronger bean genotype-dependent effect on rhizosphere microbiome assembly.}, }
@article {pmid31409850, year = {2019}, author = {Posada-Perlaza, CE and Ramírez-Rojas, A and Porras, P and Adu-Oppong, B and Botero-Coy, AM and Hernández, F and Anzola, JM and Díaz, L and Dantas, G and Reyes, A and Zambrano, MM}, title = {Bogotá River anthropogenic contamination alters microbial communities and promotes spread of antibiotic resistance genes.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11764}, doi = {10.1038/s41598-019-48200-6}, pmid = {31409850}, issn = {2045-2322}, abstract = {The increase in antibiotic resistant bacteria has raised global concern regarding the future effectiveness of antibiotics. Human activities that influence microbial communities and environmental resistomes can generate additional risks to human health. In this work, we characterized aquatic microbial communities and their resistomes in samples collected at three sites along the Bogotá River and from wastewaters at three city hospitals, and investigated community profiles and antibiotic resistance genes (ARGs) as a function of anthropogenic contamination. The presence of antibiotics and other commonly used drugs increased in locations highly impacted by human activities, while the diverse microbial communities varied among sites and sampling times, separating upstream river samples from more contaminated hospital and river samples. Clinically relevant antibiotic resistant pathogens and ARGs were more abundant in contaminated water samples. Tracking of resistant determinants to upstream river waters and city sources suggested that human activities foster the spread of ARGs, some of which were co-localized with mobile genetic elements in assembled metagenomic contigs. Human contamination of this water ecosystem changed both community structure and environmental resistomes that can pose a risk to human health.}, }
@article {pmid31409661, year = {2019}, author = {Small, CM and Currey, M and Beck, EA and Bassham, S and Cresko, WA}, title = {Highly Reproducible 16S Sequencing Facilitates Measurement of Host Genetic Influences on the Stickleback Gut Microbiome.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSystems.00331-19}, pmid = {31409661}, issn = {2379-5077}, support = {F32 GM122419/GM/NIGMS NIH HHS/United States ; P50 GM098911/GM/NIGMS NIH HHS/United States ; R24 RR032670/RR/NCRR NIH HHS/United States ; }, abstract = {Multicellular organisms interact with resident microbes in important ways, and a better understanding of host-microbe interactions is aided by tools such as high-throughput 16S sequencing. However, rigorous evaluation of the veracity of these tools in a different context from which they were developed has often lagged behind. Our goal was to perform one such critical test by examining how variation in tissue preparation and DNA isolation could affect inferences about gut microbiome variation between two genetically divergent lines of threespine stickleback fish maintained in the same laboratory environment. Using careful experimental design and intensive sampling of individuals, we addressed technical and biological sources of variation in 16S-based estimates of microbial diversity. After employing a two-tiered bead beating approach that comprised tissue homogenization followed by microbial lysis in subsamples, we found an extremely minor effect of DNA isolation protocol relative to among-host microbial diversity differences. Abundance estimates for rare operational taxonomic units (OTUs), however, showed much lower reproducibility. Gut microbiome composition was highly variable across fish-even among cohoused siblings-relative to technical replicates, but a subtle effect of host genotype (stickleback line) was nevertheless detected for some microbial taxa.IMPORTANCE Our findings demonstrate the importance of appropriately quantifying biological and technical variance components when attempting to understand major influences on high-throughput microbiome data. Our focus was on understanding among-host (biological) variance in community metrics and its magnitude in relation to within-host (technical) variance, because meaningful comparisons among individuals are necessary in addressing major questions in host-microbe ecology and evolution, such as heritability of the microbiome. Our study design and insights should provide a useful example for others desiring to quantify microbiome variation at biological levels in the face of various technical factors in a variety of systems.}, }
@article {pmid31407303, year = {2019}, author = {Kröber, E and Eyice, Ö}, title = {Profiling of Active Microorganisms by Stable Isotope Probing-Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2046}, number = {}, pages = {151-161}, doi = {10.1007/978-1-4939-9721-3_12}, pmid = {31407303}, issn = {1940-6029}, abstract = {Stable isotope probing (SIP) provides researchers a culture-independent method to retrieve nucleic acids from active microbial populations performing a specific metabolic activity in complex ecosystems. In recent years, the use of the SIP method in microbial ecology studies has been accelerated. This is partly due to the advances in sequencing and bioinformatics tools, which enable fast and reliable analysis of DNA and RNA from the SIP experiments. One of these sequencing tools, metagenomics, has contributed significantly to the body of knowledge by providing data not only on taxonomy but also on the key functional genes in specific metabolic pathways and their relative abundances. In this chapter, we provide a general background on the application of the SIP-metagenomics approach in microbial ecology and a workflow for the analysis of metagenomic datasets using the most up-to-date bioinformatics tools.}, }
@article {pmid31407302, year = {2019}, author = {Finley, BK and Hayer, M and Mau, RL and Purcell, AM and Koch, BJ and van Gestel, NC and Schwartz, E and Hungate, BA}, title = {Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2046}, number = {}, pages = {137-149}, doi = {10.1007/978-1-4939-9721-3_11}, pmid = {31407302}, issn = {1940-6029}, abstract = {Quantitative stable isotope probing (qSIP) measures rates of taxon-specific element assimilation in intact microbial communities, utilizing substrates labeled with a heavy isotope.The laboratory protocol for qSIP is nearly identical to that for conventional stable isotope probing, with two key additions: (1) in qSIP, qPCR measurements are conducted on each density fraction recovered after isopycnic separation, and (2) in qSIP, multiple density fractions are sequenced spanning the entire range of densities over which nucleic acids were recovered. qSIP goes beyond identifying taxa assimilating a substrate, as it also allows for measuring that assimilation for each taxon within a given microbial community. Here, we describe an analysis process necessary to determine atom fraction excess of a heavy stable isotope added to an environmental sample for a given taxon's DNA.}, }
@article {pmid31407297, year = {2019}, author = {Mayali, X and Weber, PK and Nuccio, E and Lietard, J and Somoza, M and Blazewicz, SJ and Pett-Ridge, J}, title = {Chip-SIP: Stable Isotope Probing Analyzed with rRNA-Targeted Microarrays and NanoSIMS.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2046}, number = {}, pages = {71-87}, doi = {10.1007/978-1-4939-9721-3_6}, pmid = {31407297}, issn = {1940-6029}, abstract = {Chip-SIP is a stable isotope probing (SIP) method for linking microbial identity and function in mixed communities and is capable of analyzing multiple isotopes (13C, 15N, and 18O) simultaneously. This method uses a high-density microarray to separate taxon-specific 16S (or 18S) rRNA genes and a high sensitivity magnetic sector secondary ion mass spectrometer (SIMS) to determine the relative isotope incorporation of the rRNA at each probe location. Using a maskless array synthesizer (MAS), we synthesize multiple unique sequences to target hundreds of taxa at the ribosomal operational taxonomic unit (OTU) level on an array surface, and then analyze it with a NanoSIMS 50, using its high-spatial resolution imaging capability to generate isotope ratios for individual probes. The Chip-SIP method has been used in diverse systems, including surface marine and estuarine water, rhizosphere, and peat soils, to quantify taxon-specific relative incorporation of different substrates in complex microbial communities. Depending on the hypothesis and experimental design, Chip-SIP allows the user to compare the same community incorporating different substrates, different communities incorporating the same substrate(s), or quantify how a community responds to treatment effects, such as temperature or nutrient concentrations.}, }
@article {pmid31407296, year = {2019}, author = {Taubert, M}, title = {SIP-Metaproteomics: Linking Microbial Taxonomy, Function, and Activity.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2046}, number = {}, pages = {57-69}, doi = {10.1007/978-1-4939-9721-3_5}, pmid = {31407296}, issn = {1940-6029}, abstract = {Stable isotope probing combined with metaproteomics enables the detection and characterization of active key species in microbial populations under near-natural conditions, which greatly helps to understand the metabolic functions of complex microbial communities. This is achieved by providing growth substrates labeled with heavy isotopes such as 13C, which will be assimilated into microbial biomass. After subsequent extraction of proteins and proteolytic cleavage into peptides, the heavy isotope enrichment can be detected by high-resolution mass spectrometric analysis, and linked to the functional and taxonomic characterization of these biomarkers. Here we provide protocols for obtaining isotopically labeled proteins and for downstream SIP-metaproteomics analysis.}, }
@article {pmid31407294, year = {2019}, author = {Ghori, NU and Moreira-Grez, B and Vuong, P and Waite, I and Morald, T and Wise, M and Whiteley, AS}, title = {RNA Stable Isotope Probing (RNA-SIP).}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2046}, number = {}, pages = {31-44}, doi = {10.1007/978-1-4939-9721-3_3}, pmid = {31407294}, issn = {1940-6029}, abstract = {Stable isotope probing is a combined molecular and isotopic technique used to probe the identity and function of uncultivated microorganisms within environmental samples. Employing stable isotopes of common elements such as carbon and nitrogen, RNA-SIP exploits an increase in the buoyant density of RNA caused by the active metabolism and incorporation of heavier mass isotopes into the RNA after cellular utilization of labeled substrates pulsed into the community. Labeled RNAs are subsequently separated from unlabeled RNAs by density gradient centrifugation followed by identification of the RNAs by sequencing. Therefore, RNA stable isotope probing is a culture-independent technique that provides simultaneous information about microbiome community, composition and function. This chapter presents the detailed protocol for performing an RNA-SIP experiment, including the formation, ultracentrifugation, and fractional analyses of stable isotope-labeled RNAs extracted from environmental samples.}, }
@article {pmid31407021, year = {2019}, author = {Bockoven, AA and Bondy, EC and Flores, MJ and Kelly, SE and Ravenscraft, AM and Hunter, MS}, title = {What Goes Up Might Come Down: the Spectacular Spread of an Endosymbiont Is Followed by Its Decline a Decade Later.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01417-4}, pmid = {31407021}, issn = {1432-184X}, support = {DEB-1020460//Division of Environmental Biology/ ; IOS-1256905//Division of Integrative Organismal Systems/ ; }, abstract = {Facultative, intracellular bacterial symbionts of arthropods may dramatically affect host biology and reproduction. The length of these symbiont-host associations may be thousands to millions of years, and while symbiont loss is predicted, there have been very few observations of a decline of symbiont infection rates. In a population of the sweet potato whitefly species (Bemisia tabaci MEAM1) in Arizona, USA, we documented the frequency decline of a strain of Rickettsia in the Rickettsia bellii clade from near-fixation in 2011 to 36% of whiteflies infected in 2017. In previous studies, Rickettsia had been shown to increase from 1 to 97% from 2000 to 2006 and remained at high frequency for at least five years. At that time, Rickettsia infection was associated with both fitness benefits and female bias. In the current study, we established matrilines of whiteflies from the field (2016, Rickettsia infection frequency = 58%) and studied (a) Rickettsia vertical transmission, (b) fitness and sex ratios associated with Rickettsia infection, (c) symbiont titer, and (d) bacterial communities within whiteflies. The vertical transmission rate was high, approximately 98%. Rickettsia infection in the matrilines was not associated with fitness benefits or sex ratio bias and appeared to be slightly costly, as more Rickettsia-infected individuals produced non-hatching eggs. Overall, the titer of Rickettsia in the matrilines was lower in 2016 than in the whiteflies collected in 2011, but the titer distribution appeared bimodal, with high- and low-titer lines, and constancy of the average titer within lines over three generations. We found neither association between Rickettsia titer and fitness benefits or sex ratio bias nor evidence that Rickettsia was replaced by another secondary symbiont. The change in the interaction between symbiont and host in 2016 whiteflies may explain the drop in symbiont frequency we observed.}, }
@article {pmid31399723, year = {2019}, author = {Bolyen, E and Rideout, JR and Dillon, MR and Bokulich, NA and Abnet, CC and Al-Ghalith, GA and Alexander, H and Alm, EJ and Arumugam, M and Asnicar, F and Bai, Y and Bisanz, JE and Bittinger, K and Brejnrod, A and Brislawn, CJ and Brown, CT and Callahan, BJ and Caraballo-Rodríguez, AM and Chase, J and Cope, EK and Da Silva, R and Diener, C and Dorrestein, PC and Douglas, GM and Durall, DM and Duvallet, C and Edwardson, CF and Ernst, M and Estaki, M and Fouquier, J and Gauglitz, JM and Gibbons, SM and Gibson, DL and Gonzalez, A and Gorlick, K and Guo, J and Hillmann, B and Holmes, S and Holste, H and Huttenhower, C and Huttley, GA and Janssen, S and Jarmusch, AK and Jiang, L and Kaehler, BD and Kang, KB and Keefe, CR and Keim, P and Kelley, ST and Knights, D and Koester, I and Kosciolek, T and Kreps, J and Langille, MGI and Lee, J and Ley, R and Liu, YX and Loftfield, E and Lozupone, C and Maher, M and Marotz, C and Martin, BD and McDonald, D and McIver, LJ and Melnik, AV and Metcalf, JL and Morgan, SC and Morton, JT and Naimey, AT and Navas-Molina, JA and Nothias, LF and Orchanian, SB and Pearson, T and Peoples, SL and Petras, D and Preuss, ML and Pruesse, E and Rasmussen, LB and Rivers, A and Robeson, MS and Rosenthal, P and Segata, N and Shaffer, M and Shiffer, A and Sinha, R and Song, SJ and Spear, JR and Swafford, AD and Thompson, LR and Torres, PJ and Trinh, P and Tripathi, A and Turnbaugh, PJ and Ul-Hasan, S and van der Hooft, JJJ and Vargas, F and Vázquez-Baeza, Y and Vogtmann, E and von Hippel, M and Walters, W and Wan, Y and Wang, M and Warren, J and Weber, KC and Williamson, CHD and Willis, AD and Xu, ZZ and Zaneveld, JR and Zhang, Y and Zhu, Q and Knight, R and Caporaso, JG}, title = {Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.}, journal = {Nature biotechnology}, volume = {37}, number = {9}, pages = {1091}, doi = {10.1038/s41587-019-0252-6}, pmid = {31399723}, issn = {1546-1696}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid31399193, year = {2019}, author = {Xu, X and Zhu, X and Wang, C and Li, Y and Fan, C and Kao, X}, title = {microRNA-650 promotes inflammation induced apoptosis of intestinal epithelioid cells by targeting NLRP6.}, journal = {Biochemical and biophysical research communications}, volume = {517}, number = {4}, pages = {551-556}, doi = {10.1016/j.bbrc.2019.06.077}, pmid = {31399193}, issn = {1090-2104}, abstract = {Ulcerative colitis (UC), a serious threat to public health, is one of the main forms of inflammatory bowel disease, whereas the molecular mechanisms underlying ulcerative colitis induced by inflammation still remain elusive. NPLR6 gene is previously shown to regulate intestinal homeostasis and regulate the colonic microbial ecology. Here, we report that microRNA-650 (miR-650) plays an important role in the pathogenesis of UC as an upstream regulator of NPLR6 gene. MiR-650 is proved overexpressed in the inflamed mucosa of patients with ulcerative colitis and the DSS induced colitis model mice by qRT-PCR. Over-expression of miR-650 leads to increased apoptosis of Caco-2 and IEC-6 cells, and the DSS-induced mice aggravation, while knock-down of miR-650 shows opposite effects. Through constructing luciferase reporter genes containing 3'-untranslated regions of NLRP6, we further demonstrate that miR-650 inhibits NLRP6 through binding to its 3'-untranslated regions. Overexpression of NLRP6 in Caco-2 and IEC-6 cells suppress the increase apoptosis induced by miR-650 overexpression. Overall, the findings of this study indicate the role of miR-650 in ulcerative colitis, which provides a new target for therapeutic treatment.}, }
@article {pmid31398879, year = {2019}, author = {Hassan, Z and Sultana, M and Khan, SI and Braster, M and Röling, WFM and Westerhoff, HV}, title = {Ample Arsenite Bio-Oxidation Activity in Bangladesh Drinking Water Wells: A Bonanza for Bioremediation?.}, journal = {Microorganisms}, volume = {7}, number = {8}, pages = {}, doi = {10.3390/microorganisms7080246}, pmid = {31398879}, issn = {2076-2607}, support = {W01.65.324.00/project 4//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NFRADEV-4-2014-2015 #654248//Corbel: EU-H2020/ ; EU-H2020 MSCA-ITN-2014-ETN: Marie Skłodowska-Curie Innovative Training Networks (ITN-ETN) #642691, BBSRC China: BB/J020060/1//Epipredict/ ; }, abstract = {Millions of people worldwide are at risk of arsenic poisoning from their drinking water. In Bangladesh the problem extends to rural drinking water wells, where non-biological solutions are not feasible. In serial enrichment cultures of water from various Bangladesh drinking water wells, we found transfer-persistent arsenite oxidation activity under four conditions (aerobic/anaerobic; heterotrophic/autotrophic). This suggests that biological decontamination may help ameliorate the problem. The enriched microbial communities were phylogenetically at least as diverse as the unenriched communities: they contained a bonanza of 16S rRNA gene sequences. These related to Hydrogenophaga, Acinetobacter, Dechloromonas, Comamonas, and Rhizobium/Agrobacterium species. In addition, the enriched microbiomes contained genes highly similar to the arsenite oxidase (aioA) gene of chemolithoautotrophic (e.g., Paracoccus sp. SY) and heterotrophic arsenite-oxidizing strains. The enriched cultures also contained aioA phylotypes not detected in the previous survey of uncultivated samples from the same wells. Anaerobic enrichments disclosed a wider diversity of arsenite oxidizing aioA phylotypes than did aerobic enrichments. The cultivatable chemolithoautotrophic and heterotrophic arsenite oxidizers are of great interest for future in or ex-situ arsenic bioremediation technologies for the detoxification of drinking water by oxidizing arsenite to arsenate that should then precipitates with iron oxides. The microbial activities required for such a technology seem present, amplifiable, diverse and hence robust.}, }
@article {pmid31398339, year = {2019}, author = {Arevalo, P and VanInsberghe, D and Elsherbini, J and Gore, J and Polz, MF}, title = {A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations.}, journal = {Cell}, volume = {178}, number = {4}, pages = {820-834.e14}, doi = {10.1016/j.cell.2019.06.033}, pmid = {31398339}, issn = {1097-4172}, abstract = {Delineating ecologically meaningful populations among microbes is important for identifying their roles in environmental and host-associated microbiomes. Here, we introduce a metric of recent gene flow, which when applied to co-existing microbes, identifies congruent genetic and ecological units separated by strong gene flow discontinuities from their next of kin. We then develop a pipeline to identify genome regions within these units that show differential adaptation and allow mapping of populations onto environmental variables or host associations. Using this reverse ecology approach, we show that the human commensal bacterium Ruminococcus gnavus breaks up into sharply delineated populations that show different associations with health and disease. Defining populations by recent gene flow in this way will facilitate the analysis of bacterial and archaeal genomes using ecological and evolutionary theory developed for plants and animals, thus allowing for testing unifying principles across all biology.}, }
@article {pmid31397240, year = {2019}, author = {Lv, Y and Qin, X and Jia, H and Chen, S and Sun, W and Wang, X}, title = {The Association between Gut Microbiota Composition and Body Mass Index in Chinese Male College Students, as Analyzed by Next-generation Sequencing.}, journal = {The British journal of nutrition}, volume = {}, number = {}, pages = {1-17}, doi = {10.1017/S0007114519001909}, pmid = {31397240}, issn = {1475-2662}, abstract = {Altered gut microbial ecology contributes to the development of metabolic diseases including obesity. However, studies based on different populations have generated conflicting results due to diet, environment, methodologies, etc. The aim of our study was to explore the association between gut microbiota and Body Mass Index (BMI) in Chinese college students. 16S next-generation sequencing (NGS) was used to test the gut microbiota of 9 lean, 9 overweight/obesity, and 10 normal-weight male college students. The differences of gut microbiota distribution among three groups were compared, and the relationship between the richness, diversity, composition of gut microbiota and BMI were analyzed. The predominant phyla Bacteroidetes and Firmicutes were further confirmed by real-time PCR. Metagenomic biomarker discovery was conducted by Linear discriminant analysis (LDA) Effect Size (LEfSe). NGS revealed that gut microbiota composition was different among three groups, but there was no difference in the abundance ratio of Firmicutes/ Bacteroidetes. Several bacterial taxa were in linear relationship with BMI (positive relationship: uncultured bacterium (Bacteroides genus); negative relationship: Porphyromonadaceae, Acidaminococcaceae, Rikenellaceae, Desulfovibrionaceae, Blautia, Anaerotruncus, Parabacteroides, Alistipes). Moreover, gut microbiota diversity decreased with the increase of BMI. And LEfSe analyze indicated that Blautia, Anaerotruncus and its uncultured species were significantly enriched in the lean group (LDA score≥3), Parasuterella and its uncultured species were significantly enriched in the overweight/obese groups(LDA score≥3). In general, gut microbiota composition and microbial diversity were associated with BMI in Chinese male college students. Our results might enrich the understanding between gut microbiota and obesity.}, }
@article {pmid31396501, year = {2019}, author = {Ramamurthy, T and Mutreja, A and Weill, FX and Das, B and Ghosh, A and Nair, GB}, title = {Revisiting the Global Epidemiology of Cholera in Conjuction With the Genomics of Vibrio cholerae.}, journal = {Frontiers in public health}, volume = {7}, number = {}, pages = {203}, doi = {10.3389/fpubh.2019.00203}, pmid = {31396501}, issn = {2296-2565}, abstract = {Toxigenic Vibrio cholerae is responsible for 1.4 to 4.3 million cases with about 21,000-143,000 deaths per year. Dominance of O1 and O139 serogroups, classical and El tor biotypes, alterations in CTX phages and the pathogenicity Islands are some of the major features of V. cholerae isolates that are responsible for cholera epidemics. Whole-genome sequencing (WGS) based analyses of single-nucleotide polymorphisms (SNPs) and other infrequent genetic variants provide a robust phylogenetic framework. Recent studies on the global transmission of pandemic V. cholerae O1 strains have shown the existence of eight different phyletic lineages. In these, the classical and El Tor biotype strains were separated as two distinctly evolved lineages. The frequency of SNP accumulation and the temporal and geographical distribution supports the perception that the seventh cholera pandemic (7CP) has spread from the Bay of Bengal region in three independent but overlapping waves. The 2010 Haitian outbreak shared a common ancestor with South-Asian wave-3 strains. In West Africa and East/Southern Africa, cholera epidemics are caused by single expanded lineage, which has been introduced several times since 1970. The Latin American epidemics that occurred in 1991 and 2010 were the result of introductions of two 7CP sublineages. Sublineages representing wave-3 have caused huge outbreaks in Haiti and Yemen. The Ogawa-Inaba serotype switchover in several cholera epidemics are believed to be due to the involvement of certain selection mechanism(s) rather than due to random events. V. cholerae O139 serogroup is phylogenetically related to the 7CP El Tor, and almost all these isolates belonged to the multilocus sequence type-69. Additional phenotypic and genotypic information have been generated to understand the pathogenicity of classical and El Tor vibrios. Presence of integrative conjugative elements (ICE) with antibiotic resistance gene cassettes, clustered regularly interspaced short palindromic repeats-associated protein system and ctxAB promoter based ToxRS expression of cholera toxin (CT) separates classical and El Tor biotypes. With the availability of WGS information, several important applications including, molecular typing, antimicrobial resistance, new diagnostics, and vaccination strategies could be generated.}, }
@article {pmid31396176, year = {2019}, author = {Fernández-Martínez, MÁ and Dos Santos Severino, R and Moreno-Paz, M and Gallardo-Carreño, I and Blanco, Y and Warren-Rhodes, K and García-Villadangos, M and Ruiz-Bermejo, M and Barberán, A and Wettergreen, D and Cabrol, N and Parro, V}, title = {Prokaryotic Community Structure and Metabolisms in Shallow Subsurface of Atacama Desert Playas and Alluvial Fans After Heavy Rains: Repairing and Preparing for Next Dry Period.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1641}, doi = {10.3389/fmicb.2019.01641}, pmid = {31396176}, issn = {1664-302X}, abstract = {The Atacama Desert, the oldest and driest desert on Earth, displays significant rains only once per decade. To investigate how microbial communities take advantage of these sporadic wet events, we carried out a geomicrobiological study a few days after a heavy rain event in 2015. Different physicochemical and microbial community analyses were conducted on samples collected from playas and an alluvial fan from surface, 10, 20, 50, and 80 cm depth. Gravimetric moisture content peaks were measured in 10 and 20 cm depth samples (from 1.65 to 4.1% w/w maximum values) while, in general, main anions such as chloride, nitrate, and sulfate concentrations increased with depth, with maximum values of 13-1,125; 168-10,109; and 9,904-30,952 ppm, respectively. Small organic anions such as formate and acetate had maximum concentrations from 2.61 to 3.44 ppm and 6.73 to 28.75 ppm, respectively. Microbial diversity inferred from DNA analysis showed Actinobacteria and Alphaproteobacteria as the most abundant and widespread bacterial taxa among the samples, followed by Chloroflexi and Firmicutes at specific sites. Archaea were mainly dominated by Nitrososphaerales, Methanobacteria, with the detection of other groups such as Halobacteria. Metaproteomics showed a high and even distribution of proteins involved in primary metabolic processes such as energy production and biosynthetic pathways, and a limited but remarkable presence of proteins related to resistance to environmental stressors such as radiation, oxidation, or desiccation. The results indicated that extra humidity in the system allows the microbial community to repair, and prepare for the upcoming hyperarid period. Additionally, it supplies biomarkers to the medium whose preservation potential could be high under strong desiccation conditions and relevant for planetary exploration.}, }
@article {pmid31395953, year = {2019}, author = {Cardini, U and Bartoli, M and Lücker, S and Mooshammer, M and Polzin, J and Lee, RW and Micić, V and Hofmann, T and Weber, M and Petersen, JM}, title = {Chemosymbiotic bivalves contribute to the nitrogen budget of seagrass ecosystems.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0486-9}, pmid = {31395953}, issn = {1751-7370}, support = {VRG14-021//Vienna Science and Technology Fund (Wiener Wissenschafts-, Forschungs- und Technologiefonds)/ ; VRG14-021//Vienna Science and Technology Fund (Wiener Wissenschafts-, Forschungs- und Technologiefonds)/ ; 09.3.3-LMT-K-712-01-0069//Lietuvos Mokslo Taryba (Research Council of Lithuania)/ ; 09.3.3-LMT-K-712-01-0069//Lietuvos Mokslo Taryba (Research Council of Lithuania)/ ; }, abstract = {In many seagrass sediments, lucinid bivalves and their sulfur-oxidizing symbionts are thought to underpin key ecosystem functions, but little is known about their role in nutrient cycles, particularly nitrogen. We used natural stable isotopes, elemental analyses, and stable isotope probing to study the ecological stoichiometry of a lucinid symbiosis in spring and fall. Chemoautotrophy appeared to dominate in fall, when chemoautotrophic carbon fixation rates were up to one order of magnitude higher as compared with the spring, suggesting a flexible nutritional mutualism. In fall, an isotope pool dilution experiment revealed carbon limitation of the symbiosis and ammonium excretion rates up to tenfold higher compared with fluxes reported for nonsymbiotic marine bivalves. These results provide evidence that lucinid bivalves can contribute substantial amounts of ammonium to the ecosystem. Given the preference of seagrasses for this nitrogen source, lucinid bivalves' contribution may boost productivity of these important blue carbon ecosystems.}, }
@article {pmid31393934, year = {2019}, author = {Barone, M and Turroni, S and Rampelli, S and Soverini, M and D'Amico, F and Biagi, E and Brigidi, P and Troiani, E and Candela, M}, title = {Gut microbiome response to a modern Paleolithic diet in a Western lifestyle context.}, journal = {PloS one}, volume = {14}, number = {8}, pages = {e0220619}, doi = {10.1371/journal.pone.0220619}, pmid = {31393934}, issn = {1932-6203}, abstract = {The modern Paleolithic diet (MPD), featured by the consumption of vegetables, fruit, nuts, seeds, eggs, fish and lean meat, while excluding grains, dairy products, salt and refined sugar, has gained substantial public attention in recent years because of its potential multiple health benefits. However, to date little is known about the actual impact of this dietary pattern on the gut microbiome (GM) and its implications for human health. In the current scenario where Western diets, low in fiber while rich in industrialized and processed foods, are considered one of the leading causes of maladaptive GM changes along human evolution, likely contributing to the increasing incidence of chronic non-communicable diseases, we hypothesize that the MPD could modulate the Western GM towards a more &quot;ancestral&quot; configuration. In an attempt to shed light on this, here we profiled the GM structure of urban Italian subjects adhering to the MPD, and compared data with other urban Italians following a Mediterranean Diet (MD), as well as worldwide traditional hunter-gatherer populations from previous publications. Notwithstanding a strong geography effect on the GM structure, our results show an unexpectedly high degree of biodiversity in MPD subjects, which well approximates that of traditional populations. The GM of MPD individuals also shows some peculiarities, including a high relative abundance of bile-tolerant and fat-loving microorganisms. The consumption of plant-based foods-albeit with the exclusion of grains and pulses-along with the minimization of the intake of processed foods, both hallmarks of the MPD, could therefore contribute to partially rewild the GM but caution should be taken in adhering to this dietary pattern in the long term.}, }
@article {pmid31392355, year = {2019}, author = {Gray, L and Kernaghan, G}, title = {Fungal Succession During the Decomposition of Ectomycorrhizal Fine Roots.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01418-3}, pmid = {31392355}, issn = {1432-184X}, support = {rgpin-2015-04323//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Ectomycorrhizal (ECM) fine roots account for a substantial proportion of forest production and their decomposition releases large amounts of nutrients to the soil ecosystem. However, little is known about the fungi involved in ECM decomposition, including assemblages of fungal saprotrophs, endophytes, and the ECM fungi themselves. To follow fungal succession during the degradation of senescing fine roots, understory seedlings of Abies balsamea and Picea rubens at two sites in the Acadian forest of Nova Scotia were either severed at the root collar or left as controls. Root systems were collected sequentially over two growing seasons and assessed for fine root loss and ECM mantle integrity. ECM were identified by ITS-PCR and grouped into broad morphological categories. Fungal communities colonizing the senescing fine roots were also monitored by systematically constructing clone libraries over the course of the experiment. ECM with cottony, weakly pigmented mantles (e.g., Cortinarius) degraded within the first year. Those with cottony, but intensely pigmented mantles (Piloderma), and smooth mantles with weak pigmentation (Russulaceae) degraded more slowly. Smooth, melanized ECM (Cenococcum and Tomentella) generally maintained integrity over the course of the experiment. Rates of fine root loss and changes in ECM mantle integrity were positively correlated with soil temperature. ECM DNA was detected throughout the experiment, and was not replaced by that of saprotrophic species during the two seasons sampled. However, fungal root endophytes (e.g., Helotiaceae) initially increased in abundance and then decreased as mantles degraded, suggesting a possible role in ECM decomposition.}, }
@article {pmid31391302, year = {2019}, author = {Ning, D and Deng, Y and Tiedje, JM and Zhou, J}, title = {A general framework for quantitatively assessing ecological stochasticity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {34}, pages = {16892-16898}, doi = {10.1073/pnas.1904623116}, pmid = {31391302}, issn = {1091-6490}, abstract = {Understanding the community assembly mechanisms controlling biodiversity patterns is a central issue in ecology. Although it is generally accepted that both deterministic and stochastic processes play important roles in community assembly, quantifying their relative importance is challenging. Here we propose a general mathematical framework to quantify ecological stochasticity under different situations in which deterministic factors drive the communities more similar or dissimilar than null expectation. An index, normalized stochasticity ratio (NST), was developed with 50% as the boundary point between more deterministic (<50%) and more stochastic (>50%) assembly. NST was tested with simulated communities by considering abiotic filtering, competition, environmental noise, and spatial scales. All tested approaches showed limited performance at large spatial scales or under very high environmental noise. However, in all of the other simulated scenarios, NST showed high accuracy (0.90 to 1.00) and precision (0.91 to 0.99), with averages of 0.37 higher accuracy (0.1 to 0.7) and 0.33 higher precision (0.0 to 1.8) than previous approaches. NST was also applied to estimate stochasticity in the succession of a groundwater microbial community in response to organic carbon (vegetable oil) injection. Our results showed that community assembly was shifted from more deterministic (NST = 21%) to more stochastic (NST = 70%) right after organic carbon input. As the vegetable oil was consumed, the community gradually returned to be more deterministic (NST = 27%). In addition, our results demonstrated that null model algorithms and community similarity metrics had strong effects on quantifying ecological stochasticity.}, }
@article {pmid31388702, year = {2019}, author = {Moss, JA and Henriksson, NL and Pakulski, JD and Snyder, RA and Jeffrey, WH}, title = {Oceanic Microplankton Do Not Adhere to the Latitudinal Diversity Gradient.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01413-8}, pmid = {31388702}, issn = {1432-184X}, abstract = {A latitudinal biodiversity gradient has captivated ecologists for years, and has become a widely recognized pattern in biogeography, manifest as an increase in biodiversity from the poles to the tropics. Oceanographers have attempted to discern whether these distribution patterns are shared with marine biota, and a lively debate has emerged concerning the global distribution of microbes. Limitations in sampling resolution for such large-scale assessments have often prohibited definitive conclusions. We evaluated microbial planktonic communities along a ~ 15,400-km Pacific Ocean transect with DNA from samples acquired every 2 degrees of latitude within a 3-month period between late August and early November 2003. Next-generation sequencing targeting the Bacteria, Archaea, and Eukarya yielded ~ 10.8 million high-quality sequences. Beta-analysis revealed geographic patterns of microbial communities, primarily the Bacteria and Archaea domains. None of the domains exhibited a unimodal pattern of alpha-diversity with respect to latitude. Bacteria communities increased in richness from Arctic to Antarctic waters, whereas Archaea and Eukarya communities showed no latitudinal or polar trends. Based on our analyses, environmental factors related to latitude thought to influence various macrofauna may not define microplankton diversity patterns of richness in the global ocean.}, }
@article {pmid31387934, year = {2019}, author = {Ziels, RM and Nobu, MK and Sousa, DZ}, title = {Elucidating Syntrophic Butyrate-Degrading Populations in Anaerobic Digesters Using Stable-Isotope-Informed Genome-Resolved Metagenomics.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSystems.00159-19}, pmid = {31387934}, issn = {2379-5077}, abstract = {Linking the genomic content of uncultivated microbes to their metabolic functions remains a critical challenge in microbial ecology. Resolving this challenge has implications for improving our management of key microbial interactions in biotechnologies such as anaerobic digestion, which relies on slow-growing syntrophic and methanogenic communities to produce renewable methane from organic waste. In this study, we combined DNA stable-isotope probing (SIP) with genome-centric metagenomics to recover the genomes of populations enriched in 13C after growing on [13C]butyrate. Differential abundance analysis of recovered genomic bins across the SIP metagenomes identified two metagenome-assembled genomes (MAGs) that were significantly enriched in heavy [13C]DNA. Phylogenomic analysis assigned one MAG to the genus Syntrophomonas and the other MAG to the genus Methanothrix. Metabolic reconstruction of the annotated genomes showed that the Syntrophomonas genome encoded all the enzymes for beta-oxidizing butyrate, as well as several mechanisms for interspecies electron transfer via electron transfer flavoproteins, hydrogenases, and formate dehydrogenases. The Syntrophomonas genome shared low average nucleotide identity (<95%) with any cultured representative species, indicating that it is a novel species that plays a significant role in syntrophic butyrate degradation within anaerobic digesters. The Methanothrix genome contained the complete pathway for acetoclastic methanogenesis, indicating that it was enriched in 13C from syntrophic acetate transfer. This study demonstrates the potential of stable-isotope-informed genome-resolved metagenomics to identify in situ interspecies metabolic cooperation within syntrophic consortia important to anaerobic waste treatment as well as global carbon cycling.IMPORTANCE Predicting the metabolic potential and ecophysiology of mixed microbial communities remains a major challenge, especially for slow-growing anaerobes that are difficult to isolate. Unraveling the in situ metabolic activities of uncultured species may enable a more descriptive framework to model substrate transformations by microbiomes, which has broad implications for advancing the fields of biotechnology, global biogeochemistry, and human health. Here, we investigated the in situ function of mixed microbiomes by combining stable-isotope probing with metagenomics to identify the genomes of active syntrophic populations converting butyrate, a C4 fatty acid, into methane within anaerobic digesters. This approach thus moves beyond the mere presence of metabolic genes to resolve &quot;who is doing what&quot; by obtaining confirmatory assimilation of the labeled substrate into the DNA signature. Our findings provide a framework to further link the genomic identities of uncultured microbes with their ecological function within microbiomes driving many important biotechnological and global processes.}, }
@article {pmid31387904, year = {2019}, author = {Su, X and Jing, G and McDonald, D and Wang, H and Wang, Z and Gonzalez, A and Sun, Z and Huang, S and Navas, J and Knight, R and Xu, J}, title = {Reply to Sun et al., &quot;Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy&quot;.}, journal = {mBio}, volume = {10}, number = {4}, pages = {}, doi = {10.1128/mBio.01234-19}, pmid = {31387904}, issn = {2150-7511}, }
@article {pmid31384980, year = {2019}, author = {Siddiqee, MH and Henry, R and Deletic, A and Bulach, DM and Coleman, RA and McCarthy, DT}, title = {Salmonella from a Microtidal Estuary Are Capable of Invading Human Intestinal Cell Lines.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01419-2}, pmid = {31384980}, issn = {1432-184X}, support = {LP120100718//Australian Research Council/ ; LP120100718//Melbourne Water/ ; }, abstract = {Faecal contamination poses health risks for the recreational users of urban estuaries. However, our understanding of the potential pathogenicity of faecal microbes in these environments is limited. To this end, a study was conducted to understand the spatial and seasonal distribution of Salmonella in water and sediments of the Yarra River estuary, Melbourne, Australia. Among 210 samples in total, culturable Salmonella were recovered from 27%, 17%, and 19% of water, bank, and bed sediment samples, respectively. The combined detection increased from 15% in winter to 32% in summer (p < 0.05) indicating seasonal variation as potential part of public health risk assessments. Further, pathogenic potential of the Salmonella isolates was characterised via the quantification of attachment and invasion capacity using human epithelial colorectal cell line Caco-2 on a subset of isolates (n = 62). While all of these isolates could attach and invade Caco-2 cells, 52% and 13% of these showed greater attachment and invasiveness, respectively, than the corresponding mean values for S. Typhimurium ATCC14028 control. Isolates from winter were on average more invasive (seven out of eight isolates with the highest invasiveness recovered from the colder sampling period) than the isolates from summer, and Salmonella collected during summer showed lower invasion (p < 0.05) compared with the control. Similar low invasion compared with the same control was observed for isolates recovered from bank sediment (p < 0.05). While the higher prevalence in summer may imply higher risks during these peak recreational periods, it is essential that this information is used in combination with quantitative microbial risk assessments to fully understand the health risks posed by Salmonella in microtidal estuaries.}, }
@article {pmid31384013, year = {2019}, author = {Hale, L and Feng, W and Yin, H and Guo, X and Zhou, X and Bracho, R and Pegoraro, E and Penton, CR and Wu, L and Cole, J and Konstantinidis, KT and Luo, Y and Tiedje, JM and Schuur, EAG and Zhou, J}, title = {Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbon.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0485-x}, pmid = {31384013}, issn = {1751-7370}, support = {DESC0010715//U.S. Department of Energy (DOE)/ ; }, abstract = {The susceptibility of soil organic carbon (SOC) in tundra to microbial decomposition under warmer climate scenarios potentially threatens a massive positive feedback to climate change, but the underlying mechanisms of stable SOC decomposition remain elusive. Herein, Alaskan tundra soils from three depths (a fibric O horizon with litter and course roots, an O horizon with decomposing litter and roots, and a mineral-organic mix, laying just above the permafrost) were incubated. Resulting respiration data were assimilated into a 3-pool model to derive decomposition kinetic parameters for fast, slow, and passive SOC pools. Bacterial, archaeal, and fungal taxa and microbial functional genes were profiled throughout the 3-year incubation. Correlation analyses and a Random Forest approach revealed associations between model parameters and microbial community profiles, taxa, and traits. There were more associations between the microbial community data and the SOC decomposition parameters of slow and passive SOC pools than those of the fast SOC pool. Also, microbial community profiles were better predictors of model parameters in deeper soils, which had higher mineral contents and relatively greater quantities of old SOC than in surface soils. Overall, our analyses revealed the functional potential of microbial communities to decompose tundra SOC through a suite of specialized genes and taxa. These results portray divergent strategies by which microbial communities access SOC pools across varying depths, lending mechanistic insights into the vulnerability of what is considered stable SOC in tundra regions.}, }
@article {pmid31383901, year = {2019}, author = {Andrade-Martínez, JS and Moreno-Gallego, JL and Reyes, A}, title = {Defining a Core Genome for the Herpesvirales and Exploring their Evolutionary Relationship with the Caudovirales.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11342}, doi = {10.1038/s41598-019-47742-z}, pmid = {31383901}, issn = {2045-2322}, abstract = {The order Herpesvirales encompasses a wide variety of important and broadly distributed human pathogens. During the last decades, similarities in the viral cycle and the structure of some of their proteins with those of the order Caudovirales, the tailed bacterial viruses, have brought speculation regarding the existence of an evolutionary relationship between these clades. To evaluate such hypothesis, we used over 600 Herpesvirales and 2000 Caudovirales complete genomes to search for the presence or absence of clusters of orthologous protein domains and constructed a dendrogram based on their compositional similarities. The results obtained strongly suggest an evolutionary relationship between the two orders. Furthermore, they allowed to propose a core genome for the Herpesvirales, composed of 4 proteins, including the ATPase subunit of the DNA-packaging terminase, the only protein with previously verified conservation. Accordingly, a phylogenetic tree constructed with sequences derived from the clusters associated to these proteins grouped the Herpesvirales strains accordingly to the established families and subfamilies. Overall, this work provides results supporting the hypothesis that the two orders are evolutionarily related and contributes to the understanding of the history of the Herpesvirales.}, }
@article {pmid31379798, year = {2019}, author = {Vigneron, A and Lovejoy, C and Cruaud, P and Kalenitchenko, D and Culley, A and Vincent, WF}, title = {Contrasting Winter Versus Summer Microbial Communities and Metabolic Functions in a Permafrost Thaw Lake.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1656}, doi = {10.3389/fmicb.2019.01656}, pmid = {31379798}, issn = {1664-302X}, abstract = {Permafrost thawing results in the formation of thermokarst lakes, which are biogeochemical hotspots in northern landscapes and strong emitters of greenhouse gasses to the atmosphere. Most studies of thermokarst lakes have been in summer, despite the predominance of winter and ice-cover over much of the year, and the microbial ecology of these waters under ice remains poorly understood. Here we first compared the summer versus winter microbiomes of a subarctic thermokarst lake using DNA- and RNA-based 16S rRNA amplicon sequencing and qPCR. We then applied comparative metagenomics and used genomic bin reconstruction to compare the two seasons for changes in potential metabolic functions in the thermokarst lake microbiome. In summer, the microbial community was dominated by Actinobacteria and Betaproteobacteria, with phototrophic and aerobic pathways consistent with the utilization of labile and photodegraded substrates. The microbial community was strikingly different in winter, with dominance of methanogens, Planctomycetes, Chloroflexi and Deltaproteobacteria, along with various taxa of the Patescibacteria/Candidate Phyla Radiation (Parcubacteria, Microgenomates, Omnitrophica, Aminicenantes). The latter group was underestimated or absent in the amplicon survey, but accounted for about a third of the metagenomic reads. The winter lineages were associated with multiple reductive metabolic processes, fermentations and pathways for the mobilization and degradation of complex organic matter, along with a strong potential for syntrophy or cross-feeding. The results imply that the summer community represents a transient stage of the annual cycle, and that carbon dioxide and methane production continue through the prolonged season of ice cover via a taxonomically distinct winter community and diverse mechanisms of permafrost carbon transformation.}, }
@article {pmid31379789, year = {2019}, author = {Osorio, H and Mettert, E and Kiley, P and Dopson, M and Jedlicki, E and Holmes, DS}, title = {Identification and Unusual Properties of the Master Regulator FNR in the Extreme Acidophile Acidithiobacillus ferrooxidans.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1642}, doi = {10.3389/fmicb.2019.01642}, pmid = {31379789}, issn = {1664-302X}, abstract = {The ability to conserve energy in the presence or absence of oxygen provides a metabolic versatility that confers an advantage in natural ecosystems. The switch between alternative electron transport systems is controlled by the fumarate nitrate reduction transcription factor (FNR) that senses oxygen via an oxygen-sensitive [4Fe-4S]2+ iron-sulfur cluster. Under O2 limiting conditions, FNR plays a key role in allowing bacteria to transition from aerobic to anaerobic lifestyles. This is thought to occur via transcriptional activation of genes involved in anaerobic respiratory pathways and by repression of genes involved in aerobic energy production. The Proteobacterium Acidithiobacillus ferrooxidans is a model species for extremely acidophilic microorganisms that are capable of aerobic and anaerobic growth on elemental sulfur coupled to oxygen and ferric iron reduction, respectively. In this study, an FNR-like protein (FNRAF) was discovered in At. ferrooxidans that exhibits a primary amino acid sequence and major motifs and domains characteristic of the FNR family of proteins, including an effector binding domain with at least three of the four cysteines known to coordinate an [4Fe-4S]2+ center, a dimerization domain, and a DNA binding domain. Western blotting with antibodies against Escherichia coli FNR (FNREC) recognized FNRAF. FNRAF was able to drive expression from the FNR-responsive E. coli promoter PnarG, suggesting that it is functionally active as an FNR-like protein. Upon air exposure, FNRAF demonstrated an unusual lack of sensitivity to oxygen compared to the archetypal FNREC. Comparison of the primary amino acid sequence of FNRAF with that of other natural and mutated FNRs, including FNREC, coupled with an analysis of the predicted tertiary structure of FNRAF using the crystal structure of the related FNR from Aliivibrio fisheri as a template revealed a number of amino acid changes that could potentially stabilize FNRAF in the presence of oxygen. These include a truncated N terminus and amino acid changes both around the putative Fe-S cluster coordinating cysteines and also in the dimer interface. Increased O2 stability could allow At. ferrooxidans to survive in environments with fluctuating O2 concentrations, providing an evolutionary advantage in natural, and engineered environments where oxygen gradients shape the bacterial community.}, }
@article {pmid31379773, year = {2019}, author = {Gupta, VVSR and Bramley, RGV and Greenfield, P and Yu, J and Herderich, MJ}, title = {Vineyard Soil Microbiome Composition Related to Rotundone Concentration in Australian Cool Climate 'Peppery' Shiraz Grapes.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1607}, doi = {10.3389/fmicb.2019.01607}, pmid = {31379773}, issn = {1664-302X}, abstract = {Soil microbial communities have an integral association with plants and play an important role in shaping plant nutrition, health, crop productivity and product quality. The influence of bacteria and fungi on wine fermentation is well known. However, little is known about the role of soil microbes, other than microbial pathogens, on grape composition or their role in vintage or site (terroir) impacts on grape composition. In this study, we used an amplicon sequencing approach to investigate the potential relationships between soil microbes and inherent spatial variation in grape metabolite composition - specifically, the concentration of the 'impact aroma compound' rotundone in Shiraz grapes (Vitis vinifera L.) grown in a 6.1 ha vineyard in the Grampians region of Victoria, Australia. Previous work had demonstrated temporal stability in patterns of within-vineyard spatial variation in rotundone concentration, enabling identification of defined 'zones' of inherently 'low' or 'high' concentration of this grape metabolite. 16S rRNA and ITS region-amplicon sequencing analysis of microbial communities in the surface soils collected from these zones indicated marked differences between zones in the genetic diversity and composition of the soil bacterial and fungal microbiome. Soils in the High rotundone zone exhibited higher diversity of bacteria, but lower diversity of fungi, compared to the soils in the Low rotundone zone. In addition, the network analysis of the microbial community in the High rotundone zone soils appeared well structured, especially with respect to the bacterial community, compared to that in the Low rotundone zone soils. The key differences in the microbial community structure between the rotundone zones are obvious for taxa/groups of both bacteria and fungi, particularly for bacteria belonging to Acidobacteria-GP4 and GP7, Rhizobiales, Gaiellaceae, Alphaproteobacteria and the Nectriaceae and Tremellaceae families of fungi. Although mulching in some parts of the vineyard caused changes in bacterial and fungal composition and overall microbial catabolic diversity and activity, its effects did not mask the rotundone zone-based variation. This finding of a systematic rotundone zone-based variation in soil microbiomes suggests an opportunity to bring together understanding of microbial ecology, plant biochemistry, and viticultural management for improved management of grape metabolism, composition and wine flavor.}, }
@article {pmid31377832, year = {2019}, author = {Frankel-Bricker, J and Song, MJ and Benner, MJ and Schaack, S}, title = {Variation in the Microbiota Associated with Daphnia magna Across Genotypes, Populations, and Temperature.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01412-9}, pmid = {31377832}, issn = {1432-184X}, support = {MCB-1150213//National Science Foundation/ ; none//M.J. Murdock Charitable Trust/ ; }, abstract = {Studies of how the microbiome varies among individuals, populations, and abiotic conditions are critical for understanding this key component of an organism's biology and ecology. In the case of Daphnia, aquatic microcrustaceans widely used in population/community ecology and environmental science studies, understanding factors that influence microbiome shifts among individuals is useful for both basic and applied research contexts. In this study, we assess differences in the microbiome among genotypes of D. magna collected from three regions along a large latitudinal gradient (Finland, Germany, and Israel). After being reared in the lab for many years, we sought to characterize any differences in genotype- or population-specific microbial communities, and to assess whether the microbiota varied among temperatures. Our study is similar to a recent comparison of the microbial communities among D. magna genotypes raised in different temperatures published by Sullam et al. (Microb Ecol 76(2):506-517, 2017), and as such represents one of the first examples of a reproducible result in microbiome research. Like the previous study, we find evidence for a strong effect of temperature on the microbiome of D. magna, although across a much smaller temperature range representing potential near-future climates. In addition, we find evidence that the microbiomes of D. magna genotypes from different regions are distinct, even years after being brought into the laboratory. Finally, our results highlight a potentially common finding in the expanding area of microbiome research-differences among treatments are not necessarily observed in the most abundant taxonomic groups. This highlights the importance of considering sampling scheme and depth of coverage when characterizing the microbiome, as different experimental designs can significantly impact taxon-specific results, even when large-scale effects are reproduced.}, }
@article {pmid31376000, year = {2019}, author = {Cowan, DA and Hopkins, DW and Jones, BE and Maggs-Kölling, G and Majewska, R and Ramond, JB}, title = {Microbiomics of Namib Desert habitats.}, journal = {Extremophiles : life under extreme conditions}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00792-019-01122-7}, pmid = {31376000}, issn = {1433-4909}, abstract = {The Namib Desert is one of the world's only truly coastal desert ecosystem. Until the end of the 1st decade of the twenty-first century, very little was known of the microbiology of this southwestern African desert, with the few reported studies being based solely on culture-dependent approaches. However, from 2010, an intense research program was undertaken by researchers from the University of the Western Cape Institute for Microbial Biotechnology and Metagenomics, and subsequently the University of Pretoria Centre for Microbial Ecology and Genomics, and their collaborators, led to a more detailed understanding of the ecology of the indigenous microbial communities in many Namib Desert biotopes. Namib Desert soils and the associated specialized niche communities are inhabited by a wide array of prokaryotic, lower eukaryotic and virus/phage taxa. These communities are highly heterogeneous on both small and large spatial scales, with community composition impacted by a range of macro- and micro-environmental factors, from water regime to soil particle size. Community functionality is also surprisingly non-homogeneous, with some taxa retaining functionality even under hyper-arid soil conditions, and with subtle changes in gene expression and phylotype abundances even on diel timescales. Despite the growing understanding of the structure and function of Namib Desert microbiomes, there remain enormous gaps in our knowledge. We have yet to quantify many of the processes in these soil communities, from regional nutrient cycling to community growth rates. Despite the progress that has been made, we still have little knowledge of either the role of phages in microbial community dynamics or inter-species interactions. Furthermore, the intense research efforts of the past decade have highlighted the immense scope for future microbiological research in this dynamic, enigmatic and charismatic region of Africa.}, }
@article {pmid31375480, year = {2019}, author = {Lawley, B and Otal, A and Moloney-Geany, K and Diana, A and Houghton, L and Heath, AM and Taylor, RW and Tannock, GW}, title = {Comparison of the development of the fecal microbiota of Indonesian and New Zealand children during the first year of life reveals differences in bifidobacterial taxa and microbiota complexity at 12 months.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.01105-19}, pmid = {31375480}, issn = {1098-5336}, abstract = {The biological succession that occurs in the gut of infants inhabiting Western countries during the first year of life is broadly predictable in terms of the increasing complexity of microbiota composition. Less information is available about microbiotas in Asian countries where environmental, nutritional and cultural influences may differentially affect the composition and development of the microbial community. We compared the fecal microbiotas of Indonesian (n = 204) and New Zealand (NZ; n = 74) infants aged 6-7 months and 12 months. Comparisons were made by analysis of 16S rRNA gene sequences, and associated derivation of community diversity metrics, relative abundances of bacterial families, detection of enterotypes, and co-occurrence correlation networks. Abundances of Bifidobacterium longum subspecies infantis and longum were made by quantitative PCR. All observations supported the view that the Indonesian and NZ infant microbiotas developed in complexity over time, but the changes were much greater in NZ infants. B. longum subsp. infantis dominated the microbiota of Indonesian children whereas subsp. longum was dominant in NZ children. Network analysis showed that the niche model (trophic adaptation results in preferential colonization) of microbiota assemblage was supported in Indonesian infants, whereas the neutral (stochastic) model was supported by the development of the microbiota of NZ infants. The results of the study show that the development of the fecal microbiota is not the same for infants in all countries and points to the necessity of obtaining a better understanding of the factors that control the colonization of the gut in early life.Importance This study addresses the microbiology of a natural ecosystem (the infant bowel) associated with children in a rural setting in Indonesia and an urban environment in New Zealand. Analysis of DNA sequences generated from the microbial community (microbiota) in the feces of the infants during the first year of life showed marked differences in the composition and complexity of the bacterial collections. The differences were most likely due to differences in the prevalence and duration of breastfeeding of infants in the two countries. These kinds of studies are essential in developing concepts of microbial ecology that relate to the influence of nutrition and environment on the development of the gut microbiota and in determining the long-term effects of microbiological events in early life on human health and well-being.}, }
@article {pmid31374443, year = {2019}, author = {Zhu, YG and Zhao, Y and Zhu, D and Gillings, M and Penuelas, J and Ok, YS and Capon, A and Banwart, S}, title = {Soil biota, antimicrobial resistance and planetary health.}, journal = {Environment international}, volume = {131}, number = {}, pages = {105059}, doi = {10.1016/j.envint.2019.105059}, pmid = {31374443}, issn = {1873-6750}, abstract = {The concept of planetary health acknowledges the links between ecosystems, biodiversity and human health and well-being. Soil, the critical component of the interconnected ecosystem, is the most biodiverse habitat on Earth, and soil microbiomes play a major role in human health and well-being through ecosystem services such as nutrient cycling, pollutant remediation and synthesis of bioactive compounds such as antimicrobials. Soil is also a natural source of antimicrobial resistance, which is often termed intrinsic resistance. However, increasing use and misuse of antimicrobials in humans and animals in recent decades has increased both the diversity and prevalence of antimicrobial resistance in soils, particularly in areas affected by human and animal wastes, such as organic manures and reclaimed wastewater, and also by air transmission. Antimicrobials and antimicrobial resistance are two sides of the sword, while antimicrobials are essential in health care; globally, antimicrobial resistance is jeopardizing the effectiveness of antimicrobial drugs, thus threatening human health. Soil is a crucial pathway through which humans are exposed to antimicrobial resistance determinants, including those harbored by human pathogens. In this review, we use the nexus of antimicrobials and antimicrobial resistance as a focus to discuss the role of soil in planetary health and illustrate the impacts of soil microbiomes on human health and well-being. This review examines the sources and dynamics of antimicrobial resistance in soils and uses the perspective of planetary health to track the movement of antimicrobial-resistance genes between environmental compartments, including soil, water, food and air.}, }
@article {pmid31374141, year = {2019}, author = {Jakob, F and Quintero, Y and Musacchio, A and Estrada-de Los Santos, P and Hernández, L and Vogel, RF}, title = {Acetic acid bacteria encode two levansucrase types of different ecological relationship.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14768}, pmid = {31374141}, issn = {1462-2920}, support = {2816IP001//German Federal Ministry of Food and Agriculture (BMEL) through the Federal Office of Agriculture and Food (BLE)/ ; }, abstract = {Acetic acid bacteria (AAB) are associated with plants and insects. Determinants for the targeting and occupation of these widely different environments are unknown. However, most of these natural habitats share plant-derived sucrose, which can be metabolized by some AAB via polyfructose building levansucrases (LS) known to be involved in biofilm formation. Here, we propose two LS types (T) encoded by AAB as determinants for habitat selection, which emerged from vertical (T1) and horizontal (T2) lines of evolution and differ in their genetic organization, structural features and secretion mechanism, as well as their occurrence in proteobacteria. T1-LS are secreted by plant-pathogenic α- and γ-proteobacteria, while T2-LS genes are common in diazotrophic, plant-growth-promoting α-, β- and γ-proteobacteria. This knowledge may be exploited for a better understanding of microbial ecology, plant health and biofilm formation by sucrase-secreting proteobacteria in eukaryotic hosts.}, }
@article {pmid31373372, year = {2019}, author = {Brink, LR and Matazel, K and Piccolo, BD and Bowlin, AK and Chintapalli, SV and Shankar, K and Yeruva, L}, title = {Neonatal Diet Impacts Bioregional Microbiota Composition in Piglets Fed Human Breast Milk or Infant Formula.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1093/jn/nxz170}, pmid = {31373372}, issn = {1541-6100}, abstract = {BACKGROUND: Early infant diet influences postnatal gut microbial development, which in turn can modulate the developing immune system.<br><br>OBJECTIVES: The aim of this study was to characterize diet-specific bioregional microbiota differences in piglets fed either human breast milk (HM) or infant formula.<br><br>METHODS: Male piglets (White Dutch Landrace Duroc) were raised on HM or cow milk formula (MF) from postnatal day (PND) 2 to PND 21 and weaned to an ad libitum diet until PND 51. Piglets were euthanized on either PND 21 or PND 51, and the gastrointestinal contents were collected for 16s RNA sequencing. Data were analyzed using the Quantitative Insight into Microbial Ecology. Diversity measurements (Chao1 and Shannon) and the Wald test were used to determine relative abundance.<br><br>RESULTS: At PND 21, the ileal luminal region of HM-fed piglets showed lower Chao1 operational taxonomic unit diversity, while Shannon diversity was lower in cecal, proximal colon (PC), and distal colon (DC) luminal regions, relative to MF-fed piglets. In addition, at PND 51, the HM-fed piglets had lower genera diversity within the jejunum, ileum, PC, and DC luminal regions, relative to MF-fed piglets. At PND 21, Turicibacter was 4- to 5-fold lower in the HM-fed piglets' ileal, cecal, PC, and DC luminal regions, relative to the MF-fed piglets. Campylobacter is 3- to 6-fold higher in HM-fed piglets duodenal, ileal, cecal, PC, and DC luminal regions, in comparison to MF-fed piglets. Furthermore, the large intestine (cecum, PC, and rectum) luminal region of HM-fed piglets showed 4- to 7-fold higher genera that belong to class Bacteroidia, in comparison to MF-fed piglets at PND 21. In addition, at PND 51 distal colon lumen of HM-fed piglets showed 1.5-fold higher genera from class Bacteroidia than the MF-fed piglets.<br><br>CONCLUSIONS: In the large intestinal regions (cecum, PC, and rectum), MF diet alters microbiota composition, relative to HM diet, with sustained effects after weaning from the neonatal diet. These microbiota changes could impact immune system and health outcomes later in life.}, }
@article {pmid31372752, year = {2019}, author = {Mosina, NL and Schubert, WD and Cowan, DA}, title = {Characterization and homology modelling of a novel multi-modular and multi-functional Paenibacillus mucilaginosus glycoside hydrolase.}, journal = {Extremophiles : life under extreme conditions}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00792-019-01121-8}, pmid = {31372752}, issn = {1433-4909}, abstract = {Glycoside hydrolases, particularly cellulases, xylanases and mannanases, are essential for the depolymerisation of lignocellulosic substrates in various industrial bio-processes. In the present study, a novel glycoside hydrolase from Paenibacillus mucilaginosus (PmGH) was expressed in E. coli, purified and characterised. Functional analysis indicated that PmGH is a 130 kDa thermophilic multi-modular and multi-functional enzyme, comprising a GH5, a GH6 and two CBM3 domains and exhibiting cellulase, mannanase and xylanase activities. The enzyme displayed optimum hydrolytic activities at pH 6 and 60 °C and moderate thermostability. Homology modelling of the full-length protein highlighted the structural and functional novelty of native PmGH, with no close structural homologs identified. However, homology modelling of the individual GH5, GH6 and the two CBM3 domains yielded excellent models based on related structures from the Protein Data Bank. The catalytic GH5 and GH6 domains displayed a (β/α)8 and a distorted seven stranded (β/α) fold, respectively. The distinct homology at the domain level but low homology of the full-length protein suggests that this protein evolved by exogenous gene acquisition and recombination.}, }
@article {pmid31372686, year = {2019}, author = {Bonner, MTL and Allen, DE and Brackin, R and Smith, TE and Lewis, T and Shoo, LP and Schmidt, S}, title = {Tropical Rainforest Restoration Plantations Are Slow to Restore the Soil Biological and Organic Carbon Characteristics of Old Growth Rainforest.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01414-7}, pmid = {31372686}, issn = {1432-184X}, support = {Soil Carbon Research Program (SCaRP)//Commonwealth Scientific and Industrial Research Organisation/ ; Student Research Award//Ecological Society of Australia/ ; Australian Postgraduate Award//Australian Federal Government/ ; }, abstract = {Widespread and continuing losses of tropical old-growth forests imperil global biodiversity and alter global carbon (C) cycling. Soil organic carbon (SOC) typically declines with land use change from old-growth forest, but the underlying mechanisms are poorly understood. Ecological restoration plantations offer an established means of restoring aboveground biomass, structure and diversity of forests, but their capacity to recover the soil microbial community and SOC is unknown due to limited empirical data and consensus on the mechanisms of SOC formation. Here, we examine soil microbial community response and SOC in tropical rainforest restoration plantings, comparing them with the original old-growth forest and the previous land use (pasture). Two decades post-reforestation, we found a statistically significant but small increase in SOC in the fast-turnover particulate C fraction. Although the δ13C signature of the more stable humic organic C (HOC) fraction indicated a significant compositional turnover in reforested soils, from C4 pasture-derived C to C3 forest-derived C, this did not translate to HOC gains compared with the pasture baseline. Matched old-growth rainforest soils had significantly higher concentrations of HOC than pasture and reforested soils, and soil microbial enzyme efficiency and the ratio of gram-positive to gram-negative bacteria followed the same pattern. Restoration plantings had unique soil microbial composition and function, distinct from baseline pasture but not converging on target old growth rainforest within the examined timeframe. Our results suggest that tropical reforestation efforts could benefit from management interventions beyond re-establishing tree cover to realize the ambition of early recovery of soil microbial communities and stable SOC.}, }
@article {pmid31372685, year = {2019}, author = {Cania, B and Vestergaard, G and Kublik, S and Köhne, JM and Fischer, T and Albert, A and Winkler, B and Schloter, M and Schulz, S}, title = {Biological Soil Crusts from Different Soil Substrates Harbor Distinct Bacterial Groups with the Potential to Produce Exopolysaccharides and Lipopolysaccharides.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01415-6}, pmid = {31372685}, issn = {1432-184X}, support = {SCHU 2907/4-1//Deutsche Forschungsgemeinschaft/ ; TRR 38/2 2011 B04//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Biological soil crusts (biocrusts) play an important role in improving soil stability and resistance to erosion by promoting aggregation of soil particles. During initial development, biocrusts are dominated by bacteria. Some bacterial members of the biocrusts can contribute to the formation of soil aggregates by producing exopolysaccharides and lipopolysaccharides that act as &quot;glue&quot; for soil particles. However, little is known about the dynamics of &quot;soil glue&quot; producers during the initial development of biocrusts. We hypothesized that different types of initial biocrusts harbor distinct producers of adhesive polysaccharides. To investigate this, we performed a microcosm experiment, cultivating biocrusts on two soil substrates. High-throughput shotgun sequencing was used to obtain metagenomic information on microbiomes of bulk soils from the beginning of the experiment, and biocrusts sampled after 4 and 10 months of incubation. We discovered that the relative abundance of genes involved in the biosynthesis of exopolysaccharides and lipopolysaccharides increased in biocrusts compared with bulk soils. At the same time, communities of potential &quot;soil glue&quot; producers that were highly similar in bulk soils underwent differentiation once biocrusts started to develop. In the bulk soils, the investigated genes were harbored mainly by Betaproteobacteria, whereas in the biocrusts, the major potential producers of adhesive polysaccharides were, aside from Alphaproteobacteria, either Cyanobacteria or Chloroflexi and Acidobacteria. Overall, our results indicate that the potential to form exopolysaccharides and lipopolysaccharides is an important bacterial trait for initial biocrusts and is maintained despite the shifts in bacterial community composition during biocrust development.}, }
@article {pmid31372543, year = {2019}, author = {Ayala-Usma, DA and Lozano-Gutiérrez, RE and González Arango, C}, title = {Wood anatomy of two species of the genus Chrysochlamys (Clusiaceae: Clusioideae: Clusieae) from the northern Andes of Colombia.}, journal = {Heliyon}, volume = {5}, number = {7}, pages = {e02078}, doi = {10.1016/j.heliyon.2019.e02078}, pmid = {31372543}, issn = {2405-8440}, abstract = {Chrysochlamys is a genus of neotropical angiosperms distributed in wet and riparian forests from Bolivia to Mexico in altitudes from near sea-level to close to 3000 m. The wood anatomy of two species of the genus was investigated. Branches of mature stems were collected in a secondary wet forest in Colombian Northern Andes. Slides were obtained and visualized using light microscopy. Gelatinous fiber bands were found and described in C. colombiana and C. dependens. There was a higher amount of septate fibers in the latter. Average ray height and pigment deposit content in ray cells was greater in C. colombiana relative to C. dependens, but rays were commonly wider in the second one. The diversity of vessel-ray pit shapes in C. dependens is greater than in C. colombiana. In both cases rays are considered to be paedomorphic type I. Scanty to absent axial and apotracheal parenchyma was found for both species. We discuss the similarities and differences of the two species in order to establish diagnostic wood features. Also we include brief notes in comparative anatomy with other members of the Clusieaceae family, emphasizing in the incongruences found with previous reports for the genus. This is the first descriptive work in wood anatomy of C. colombiana and C. dependens.}, }
@article {pmid31371535, year = {2019}, author = {Hausmann, B and Vandieken, V and Pjevac, P and Schreck, K and Herbold, CW and Loy, A}, title = {Draft Genome Sequence of Desulfosporosinus fructosivorans Strain 63.6FT, Isolated from Marine Sediment in the Baltic Sea.}, journal = {Microbiology resource announcements}, volume = {8}, number = {31}, pages = {}, doi = {10.1128/MRA.00427-19}, pmid = {31371535}, issn = {2576-098X}, abstract = {Desulfosporosinus fructosivorans strain 63.6FT is a strictly anaerobic, spore-forming, sulfate-reducing bacterium isolated from marine sediment in the Baltic Sea. Here, we report the draft genome sequence of D. fructosivorans 63.6FT.}, }
@article {pmid31368886, year = {2019}, author = {Wuyts, S and Allonsius, CN and Wittouck, S and Thys, S and Lievens, B and Weckx, S and De Vuyst, L and Sarah, L}, title = {Comparative genome analysis of Lactobacillus mudanjiangensis, an understudied member of the Lactobacillus plantarum group.}, journal = {Microbial genomics}, volume = {}, number = {}, pages = {}, doi = {10.1099/mgen.0.000286}, pmid = {31368886}, issn = {2057-5858}, abstract = {The genus Lactobacillus is known to be extremely diverse and consists of different phylogenetic groups that show a diversity that is roughly equal to the expected diversity of a typical bacterial genus. One of the most prominent phylogenetic groups within this genus is the Lactobacillus plantarum group, which contains the understudied Lactobacillus mudanjiangensis species. Before this study, only one L. mudanjiangensis strain, DSM 28402T, had been described, but without whole-genome analysis. In this study, three strains classified as L. mudanjiangensis were isolated from three different carrot juice fermentations and their whole-genome sequence was determined, together with the genome sequence of the type strain. The genomes of all four strains were compared with publicly available L. plantarum group genome sequences. This analysis showed that L. mudanjiangensis harboured the second largest genome size and gene count of the whole L. plantarum group. In addition, all members of this species showed the presence of a gene coding for a cellulose-degrading enzyme. Finally, three of the four L. mudanjiangensis strains studied showed the presence of pili on scanning electron microscopy (SEM) images, which were linked to conjugative gene regions, coded on a plasmid in at least two of the strains studied.}, }
@article {pmid31368488, year = {2019}, author = {Sapriel, G and Brosch, R}, title = {Shared pathogenomic patterns characterize a new phylotype, revealing transition towards host-adaptation long before speciation of Mycobacterium tuberculosis.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evz162}, pmid = {31368488}, issn = {1759-6653}, abstract = {Tuberculosis remains one of the deadliest infectious diseases of humanity. To better understand the evolutionary history of host-adaptation of tubercle bacilli (MTB), we sought for mycobacterial species that were more closely related to MTB than the previously used comparator species Mycobacterium marinum and Mycobacterium kansasii. Our phylogenomic approach revealed some recently sequenced opportunistic mycobacterial pathogens i.e. Mycobacterium decipiens, Mycobacterium lacus, Mycobacterium riyadhense, and Mycobacterium shinjukuense - that constitute a common clade with MTB, hereafter called MTB-associated phylotype (MTBAP), from which MTB have emerged. Multivariate and clustering analyses of genomic functional content revealed that the MTBAP lineage forms a clearly distinct cluster of species that share common genomic characteristics, such as loss of core genes, shift in dN/dS ratios, and massive expansion of toxin-antitoxin systems. Consistently, analysis of predicted horizontal gene transfer regions suggests that putative functions acquired by MTBAP members were markedly associated with changes in microbial ecology, e.g. adaption to intracellular stress resistance. Our study thus considerably deepens our view on MTB evolutionary history, unveiling a decisive shift that promoted conversion to host-adaptation among ancestral founders of the MTBAP lineage long before M. tuberculosis has adapted to the human host.}, }
@article {pmid31366993, year = {2019}, author = {Kiersztyn, B and Chróst, R and Kaliński, T and Siuda, W and Bukowska, A and Kowalczyk, G and Grabowska, K}, title = {Structural and functional microbial diversity along a eutrophication gradient of interconnected lakes undergoing anthropopressure.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11144}, doi = {10.1038/s41598-019-47577-8}, pmid = {31366993}, issn = {2045-2322}, support = {2015/17/B/NZ9/01552//Narodowe Centrum Nauki (National Science Centre)/ ; 2015/17/B/NZ9/01552//Narodowe Centrum Nauki (National Science Centre)/ ; 2015/17/B/NZ9/01552//Narodowe Centrum Nauki (National Science Centre)/ ; 2015/17/B/NZ9/01552//Narodowe Centrum Nauki (National Science Centre)/ ; 2015/17/B/NZ9/01552//Narodowe Centrum Nauki (National Science Centre)/ ; }, abstract = {We present the results of an analysis of the 16S rRNA-based taxonomical structure of bacteria together with an analysis of carbon source utilization ability using EcoPlate (Biolog, USA) metabolic fingerprinting assessment against the backdrop of physicochemical parameters in fifteen interconnected lakes. The lakes exhibit a wide spectrum of trophic gradients and undergo different intensities of anthropopressure. Sequences of V3-V4 16S rRNA genes binned by taxonomic assignment to family indicated that bacterial communities in the highly eutrophicated lakes were distinctly different from the bacterial communities in the meso-eutrophic lakes (ANOSIM r = 0.99, p = 0.0002) and were characterized by higher richness and more diverse taxonomical structure. Representatives of the Actinobacteria, Proteobacteria, Cyanobacteria, Planctomycetes, Verrucomicrobia, Bacteroides phyla predominated. In most cases their relative abundance was significantly correlated with lake trophic state. We found no similar clear relationship of community-level physiological profiling with lake trophic state. However, we found some significant links between the taxonomic and metabolic structure of the microbes in the studied lakes (Mantel's correlation r = 0.22, p = 0.006). The carbon source utilization ability of the studied microorganisms was affected not only by the taxonomic groups present in the lakes but also by various characteristics like a high PO43- concentration inhibiting the utilization of phosphorylated carbon.}, }
@article {pmid31366952, year = {2019}, author = {Otte, JM and Blackwell, N and Ruser, R and Kappler, A and Kleindienst, S and Schmidt, C}, title = {N2O formation by nitrite-induced (chemo)denitrification in coastal marine sediment.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {10691}, doi = {10.1038/s41598-019-47172-x}, pmid = {31366952}, issn = {2045-2322}, support = {307320-MICROFOX//EC | European Research Council (ERC)/ ; 307320-MICROFOX//EC | European Research Council (ERC)/ ; 307320-MICROFOX//EC | European Research Council (ERC)/ ; }, abstract = {Nitrous oxide (N2O) is a potent greenhouse gas that also contributes to stratospheric ozone depletion. Besides microbial denitrification, abiotic nitrite reduction by Fe(II) (chemodenitrification) has the potential to be an important source of N2O. Here, using microcosms, we quantified N2O formation in coastal marine sediments under typical summer temperatures. Comparison between gamma-radiated and microbially-active microcosm experiments revealed that at least 15-25% of total N2O formation was caused by chemodenitrification, whereas 75-85% of total N2O was potentially produced by microbial N-transformation processes. An increase in (chemo)denitrification-based N2O formation and associated Fe(II) oxidation caused an upregulation of N2O reductase (typical nosZ) genes and a distinct community shift to potential Fe(III)-reducers (Arcobacter), Fe(II)-oxidizers (Sulfurimonas), and nitrate/nitrite-reducing microorganisms (Marinobacter). Our study suggests that chemodenitrification contributes substantially to N2O formation from marine sediments and significantly influences the N- and Fe-cycling microbial community.}, }
@article {pmid31366612, year = {2019}, author = {McBain, AJ and O'Neill, CA and Amezquita, A and Price, LJ and Faust, K and Tett, A and Segata, N and Swann, JR and Smith, AM and Murphy, B and Hoptroff, M and James, G and Reddy, Y and Dasgupta, A and Ross, T and Chapple, IL and Wade, WG and Fernandez-Piquer, J}, title = {Consumer Safety Considerations of Skin and Oral Microbiome Perturbation.}, journal = {Clinical microbiology reviews}, volume = {32}, number = {4}, pages = {}, doi = {10.1128/CMR.00051-19}, pmid = {31366612}, issn = {1098-6618}, abstract = {SUMMARYMicrobiomes associated with human skin and the oral cavity are uniquely exposed to personal care regimes. Changes in the composition and activities of the microbial communities in these environments can be utilized to promote consumer health benefits, for example, by reducing the numbers, composition, or activities of microbes implicated in conditions such as acne, axillary odor, dandruff, and oral diseases. It is, however, important to ensure that innovative approaches for microbiome manipulation do not unsafely disrupt the microbiome or compromise health, and where major changes in the composition or activities of the microbiome may occur, these require evaluation to ensure that critical biological functions are unaffected. This article is based on a 2-day workshop held at SEAC Unilever, Sharnbrook, United Kingdom, involving 31 specialists in microbial risk assessment, skin and oral microbiome research, microbial ecology, bioinformatics, mathematical modeling, and immunology. The first day focused on understanding the potential implications of skin and oral microbiome perturbation, while approaches to characterize those perturbations were discussed during the second day. This article discusses the factors that the panel recommends be considered for personal care products that target the microbiomes of the skin and the oral cavity.}, }
@article {pmid31365541, year = {2019}, author = {Yao, Y and Carretero-Paulet, L and Van de Peer, Y}, title = {Using digital organisms to study the evolutionary consequences of whole genome duplication and polyploidy.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0220257}, doi = {10.1371/journal.pone.0220257}, pmid = {31365541}, issn = {1932-6203}, abstract = {The potential role of whole genome duplication (WGD) in evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary 'dead end', there is growing evidence that the long-term establishment of polyploidy might be linked to environmental change, stressful conditions, or periods of extinction. However, despite much research, the mechanistic underpinnings of why and how polyploids might be able to outcompete non-polyploids at times of environmental upheaval remain indefinable. Here, we improved our recently developed bio-inspired framework, combining an artificial genome with an agent-based system, to form a population of so-called Digital Organisms (DOs), to examine the impact of WGD on evolution under different environmental scenarios mimicking extinction events of varying strength and frequency. We found that, under stable environments, DOs with non-duplicated genomes formed the majority, if not all, of the population, whereas the numbers of DOs with duplicated genomes increased under dramatically challenging environments. After tracking the evolutionary trajectories of individual genomes in terms of sequence and encoded gene regulatory networks (GRNs), we propose that duplicated GRNs might provide polyploids with better chances to acquire the drastic changes necessary to adapt to challenging conditions, thus endowing DOs with increased adaptive potential under extinction events. In contrast, under stable environments, random mutations might easily render the GRN less well adapted to such environments, a phenomenon that is exacerbated in duplicated, more complex GRNs. We believe that our results provide some additional insights into how genome duplication and polyploidy might help organisms to compete for novel niches and survive ecological turmoil, and confirm the usefulness of our computational simulation in studying the role of WGD in evolution and adaptation, helping to overcome some of the traditional limitations of evolution experiments with model organisms.}, }
@article {pmid31364812, year = {2019}, author = {Boll, M and Geiger, R and Junghare, M and Schink, B}, title = {Microbial degradation of phthalates: biochemistry and environmental implications.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.12787}, pmid = {31364812}, issn = {1758-2229}, support = {//University of Konstanz/ ; BO 1565/16-1//German research council/ ; }, abstract = {The environmentally relevant xenobiotic esters of phthalic acid (PA), isophthalic acid (IPA) and terephthalic acid (TPA) are produced on a million ton scale annually and are predominantly used as plastic polymers or plasticizers. Degradation by microorganisms is considered as the most effective means of their elimination from the environment and proceeds via hydrolysis to the corresponding PA isomers and alcohols under oxic and anoxic conditions. Further degradation of PA, IPA and TPA differs fundamentally between anaerobic and aerobic microorganisms. The latter introduce hydroxyl functionalities by dioxygenases to facilitate subsequent decarboxylation by either aromatizing dehydrogenases or cofactor-free decarboxylases. In contrast, anaerobic bacteria activate the PA isomers to the respective thioesters using CoA ligases or CoA transferases followed by decarboxylation to the central intermediate benzoyl-CoA. Decarboxylases acting on the three PA CoA thioesters belong to the UbiD enzyme family that harbour a prenylated flavin mononucleotide (FMN) cofactor to achieve the mechanistically challenging decarboxylation. Capture of the extremely instable PA-CoA intermediate is accomplished by a massive overproduction of phthaloyl-CoA decarboxylase and a balanced production of PA-CoA forming/decarboxylating enzymes. The strategy of anaerobic phthalate degradation probably represents a snapshot of an ongoing evolution of a xenobiotic degradation pathway via a short-lived reaction intermediate.}, }
@article {pmid31363029, year = {2019}, author = {Richardson, M and Gottel, N and Gilbert, JA and Lax, S}, title = {Microbial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial Signatures.}, journal = {mBio}, volume = {10}, number = {4}, pages = {}, doi = {10.1128/mBio.01054-19}, pmid = {31363029}, issn = {2150-7511}, abstract = {The microbiota of the built environment is an amalgamation of both human and environmental sources. While human sources have been examined within single-family households or in public environments, it is unclear what effect a large number of cohabitating people have on the microbial communities of their shared environment. We sampled the public and private spaces of a college dormitory, disentangling individual microbial signatures and their impact on the microbiota of common spaces. We compared multiple methods for marker gene sequence clustering and found that minimum entropy decomposition (MED) was best able to distinguish between the microbial signatures of different individuals and was able to uncover more discriminative taxa across all taxonomic groups. Further, weighted UniFrac- and random forest-based graph analyses uncovered two distinct spheres of hand- or shoe-associated samples. Using graph-based clustering, we identified spheres of interaction and found that connection between these clusters was enriched for hands, implicating them as a primary means of transmission. In contrast, shoe-associated samples were found to be freely interacting, with individual shoes more connected to each other than to the floors they interact with. Individual interactions were highly dynamic, with groups of samples originating from individuals clustering freely with samples from other individuals, while all floor and shoe samples consistently clustered together.IMPORTANCE Humans leave behind a microbial trail, regardless of intention. This may allow for the identification of individuals based on the &quot;microbial signatures&quot; they shed in built environments. In a shared living environment, these trails intersect, and through interaction with common surfaces may become homogenized, potentially confounding our ability to link individuals to their associated microbiota. We sought to understand the factors that influence the mixing of individual signatures and how best to process sequencing data to best tease apart these signatures.}, }
@article {pmid31363014, year = {2019}, author = {Chevrette, MG and Bratburd, JR and Currie, CR and Stubbendieck, RM}, title = {Experimental Microbiomes: Models Not to Scale.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSystems.00175-19}, pmid = {31363014}, issn = {2379-5077}, support = {T15 LM007359/LM/NLM NIH HHS/United States ; T32 AI055397/AI/NIAID NIH HHS/United States ; T32 GM008505/GM/NIGMS NIH HHS/United States ; U19 TW009872/TW/FIC NIH HHS/United States ; }, abstract = {Low-cost, high-throughput nucleic acid sequencing ushered the field of microbial ecology into a new era in which the microbial composition of nearly every conceivable environment on the planet is under examination. However, static &quot;screenshots&quot; derived from sequence-only approaches belie the underlying complexity of the microbe-microbe and microbe-host interactions occurring within these systems. Reductionist experimental models are essential to identify the microbes involved in interactions and to characterize the molecular mechanisms that manifest as complex host and environmental phenomena. Herein, we focus on three models (Bacillus-Streptomyces, Aliivibrio fischeri-Hawaiian bobtail squid, and gnotobiotic mice) at various levels of taxonomic complexity and experimental control used to gain molecular insight into microbe-mediated interactions. We argue that when studying microbial communities, it is crucial to consider the scope of questions that experimental systems are suited to address, especially for researchers beginning new projects. Therefore, we highlight practical applications, limitations, and tradeoffs inherent to each model.}, }
@article {pmid31361544, year = {2019}, author = {Cerdó, T and Diéguez, E and Campoy, C}, title = {Early nutrition and gut microbiome: interrelationship between bacterial metabolism, immune system, brain structure and neurodevelopment.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpendo.00188.2019}, pmid = {31361544}, issn = {1522-1555}, abstract = {Disturbances of diet during pregnancy and early postnatal life may impact colonization of gut microbiota during early life, which could influence infant health, leading to potential long-lasting consequences later in life. This is a non-systematic review that explores the recent scientific literature to provide a general perspective of this broad topic. Several studies have shown that gut microbiota composition is related to changes in metabolism, energy balance and immune system disturbances, through interaction between microbiota metabolites and host receptors by the gut-brain axis. Moreover, recent clinical studies suggest that an intestinal dysbiosis in gut microbiota may result in cognitive disorders and behavioral problems. Furthermore, recent research in the field of brain imaging focused on the study of the relationship between gut microbial ecology and large-scale brain networks, which will help to decipher the influence of the microbiome on brain function and potentially will serve to identify multiple mediators of the gut-brain axis. Thus, knowledge about optimal nutrition by modulating gut microbiota-brain axis activity, will allow a better understanding of the molecular mechanisms involved in the crosstalk between gut microbiota and the developing brain during critical windows. In addition, this knowledge will open new avenues for developing novel microbiota-modulating based diet interventions during pregnancy and early life to prevent metabolic disorders, as well as neurodevelopmental deficits and brain functional disorders.}, }
@article {pmid31359073, year = {2019}, author = {Cellini, A and Donati, I and Fiorentini, L and Vandelle, E and Polverari, A and Venturi, V and Buriani, G and Vanneste, JL and Spinelli, F}, title = {N-Acyl Homoserine Lactones and Lux Solos Regulate Social Behaviour and Virulence of Pseudomonas syringae pv. actinidiae.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01416-5}, pmid = {31359073}, issn = {1432-184X}, support = {613678//FP7-KBBE/ ; }, abstract = {The phyllosphere is a complex environment where microbes communicate through signalling molecules in a system, generally known as quorum sensing (QS). One of the most common QS systems in Gram-negative proteobacteria is based on the production of N-acyl homoserine lactones (AHLs) by a LuxI synthase and their perception by a LuxR sensor. Pseudomonas syringae pv. actinidiae (Psa), the aetiological agent of the bacterial canker of kiwifruit, colonises plant phyllosphere before penetrating via wounds and natural openings. Since Psa genome encodes three LuxR solos without a cognate LuxI, this bacterium may perceive diffusible signals, but it cannot produce AHLs, displaying a non-canonical QS system. The elucidation of the mechanisms underlying the perception of environmental cues in the phyllosphere by this pathogen and their influence on the onset of pathogenesis are of crucial importance for a long-lasting and sustainable management of the bacterial canker of kiwifruit. Here, we report the ability of Psa to sense its own population density and the presence of surrounding bacteria. Moreover, we show that Psa can perceive AHLs, indicating that AHL-producing neighbouring bacteria may regulate Psa virulence in the host. Our results suggest that the ecological environment is important in determining Psa fitness and pathogenic potential. This opens new perspectives in the use of more advanced biochemical and microbiological tools for the control of bacterial canker of kiwifruit.}, }
@article {pmid31357043, year = {2019}, author = {Cagnetta, C and Saerens, B and Meerburg, FA and Decru, SO and Broeders, E and Menkveld, W and Vandekerckhove, TGL and De Vrieze, J and Vlaeminck, SE and Verliefde, ARD and De Gusseme, B and Weemaes, M and Rabaey, K}, title = {High-rate activated sludge systems combined with dissolved air flotation enable effective organics removal and recovery.}, journal = {Bioresource technology}, volume = {291}, number = {}, pages = {121833}, doi = {10.1016/j.biortech.2019.121833}, pmid = {31357043}, issn = {1873-2976}, mesh = {Biofuels ; Flocculation ; *Sewage ; Waste Disposal, Fluid ; }, abstract = {High-rate activated sludge (HRAS) systems typically generate diluted sludge which requires further thickening prior to anaerobic digestion (AD), besides the need to add considerable coagulant and flocculant for the solids separation. As an alternative to conventional gravitational settling, a dissolved air flotation (DAF) unit was coupled to a HRAS system or a high-rate contact stabilization (HiCS) system. The HRAS-DAF system allowed up to 78% removal of the influent solids, and the HiCS-DAF 67%. Both were within the range of values typically obtained for HRAS-settler systems, albeit at a lower chemical requirement. The separated sludge had a high concentration of up to 47 g COD L-1, suppressing the need of further thickening before AD. Methanation tests showed a biogas yield of up to 68% on a COD basis. The use of a DAF separation system can thus enable direct organics removal at high sludge concentration and with low chemical needs.}, }
@article {pmid31355925, year = {2019}, author = {Shao, D and Vogtmann, E and Liu, A and Qin, J and Chen, W and Abnet, CC and Wei, W}, title = {Microbial characterization of esophageal squamous cell carcinoma and gastric cardia adenocarcinoma from a high-risk region of China.}, journal = {Cancer}, volume = {}, number = {}, pages = {}, doi = {10.1002/cncr.32403}, pmid = {31355925}, issn = {1097-0142}, support = {2016YFC0901400//National Key Research and Development Program of precision medicine, China/ ; 2016-I2M-3-001//Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences (CIFMS)/ ; 31570116//National Natural Science Foundation of China/ ; //Intramural Research Program of the National Cancer Institute of the National Institutes of Health/ ; }, abstract = {BACKGROUND: Little is known about the microbiota and upper gastrointestinal tumors. Esophageal squamous cell carcinoma (ESCC) and gastric cardia adenocarcinoma (GCA) occur in adjacent organs, co-occur geographically, and share many risk factors despite being of different tissue types.<br><br>METHODS: This study characterized the microbial communities of paired tumor and nontumor samples from 67 patients with ESCC and 36 patients with GCA in Henan, China. DNA was extracted with the MoBio PowerSoil kit. The V4 region of the 16S ribosomal RNA gene was sequenced with MiniSeq and was processed with Quantitative Insights Into Microbial Ecology 1. The linear discriminant analysis effect size method was used to identify differentially abundant microbes, the Wilcoxon rank-sum test was used to test α diversity differences, and permutational multivariate analysis of variance was used to test for differences in β diversity.<br><br>RESULTS: The microbial environments of ESCC and GCA tissues were all composed primarily of Firmicutes, Bacteroidetes, and Proteobacteria. ESCC tumor tissues contained more Fusobacterium (3.2% vs 1.3%) and less Streptococcus (12.0% vs 30.2%) than nontumor tissues. GCA nontumor tissues had a greater abundance of Helicobacter (60.5% vs 11.8%), which may have been linked to the lower α diversity (58.0 vs 102.5; P = .0012) in comparison with tumor tissues. A comparison of ESCC and GCA nontumor tissues showed that the microbial composition (P = .0040) and the α diversity (87.0 vs 58.0; P = .00052) were significantly different. No significant differences were detected for α diversity within ESCC and GCA tumor tissues.<br><br>CONCLUSIONS: This study showed differences in the microbial compositions of paired ESCC and GCA tumor and nontumor tissues and differences by organ site. Large-scale, prospective cohort studies are needed to confirm these findings.}, }
@article {pmid31354777, year = {2019}, author = {Del Frari, G and Gobbi, A and Aggerbeck, MR and Oliveira, H and Hansen, LH and Ferreira, RB}, title = {Characterization of the Wood Mycobiome of Vitis vinifera in a Vineyard Affected by Esca. Spatial Distribution of Fungal Communities and Their Putative Relation With Leaf Symptoms.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {910}, doi = {10.3389/fpls.2019.00910}, pmid = {31354777}, issn = {1664-462X}, abstract = {Esca is a disease complex belonging to the grapevine trunk diseases cluster. It comprises five syndromes, three main fungal pathogenic agents and several symptoms, both internal (i.e., affecting woody tissue) and external (e.g., affecting leaves and bunches). The etiology and epidemiology of this disease complex remain, in part, unclear. Some of the points that are still under discussion concern the sudden rise in disease incidence, the simultaneous presence of multiple wood pathogens in affected grapevines, the causal agents and the discontinuity in time of leaf symptoms manifestation. The standard approach to the study of esca has been mostly through culture-dependent studies, yet, leaving many questions unanswered. In this study, we used Illumina® next-generation amplicon sequencing to investigate the mycobiome of grapevines wood in a vineyard with history of esca. We characterized the wood mycobiome composition, investigated the spatial dynamics of the fungal communities in different areas of the stem and in canes, and assessed the putative link between mycobiome and leaf symptoms. An unprecedented diversity of fungi is presented (289 taxa), including five genera reported for the first time in association with grapevines wood (Debaryomyces, Trematosphaeria, Biatriospora, Lopadostoma, and Malassezia) and numerous hitherto unreported species. Esca-associated fungi Phaeomoniella chlamydospora and Fomitiporia sp. dominate the fungal community, and numerous other fungi associated with wood syndromes are also encountered (e.g., Eutypa spp., Inonotus hispidus). The spatial analysis revealed differences in diversity, evenness and taxa abundances, the unique presence of certain fungi in specific areas of the plants, and tissue specificity. Lastly, the mycobiome composition of the woody tissue in proximity to leaves manifesting 'tiger stripes' symptoms of esca, as well as in leaf-symptomatic canes, was highly similar to that of plants not exhibiting any leaf symptomatology. This observation supports the current understanding that leaf symptoms are not directly linked with the fungal communities in the wood. This work builds to the understanding of the microbial ecology of the grapevines wood, offering insights and a critical view on the current knowledge of the etiology of esca.}, }
@article {pmid31354673, year = {2019}, author = {Chen, C and He, R and Cheng, Z and Han, M and Zha, Y and Yang, P and Yao, Q and Zhou, H and Zhong, C and Ning, K}, title = {The Seasonal Dynamics and the Influence of Human Activities on Campus Outdoor Microbial Communities.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1579}, doi = {10.3389/fmicb.2019.01579}, pmid = {31354673}, issn = {1664-302X}, abstract = {Large-scale campus resembles a small &quot;semi-open community,&quot; harboring disturbances from the exchanges of people and vehicles, wherein stressors such as temperature and population density differ among the ground surfaces of functional partitions. Therefore, it represents a special ecological niche for the study on microbial ecology in the process of urbanization. In this study, we investigated outdoor microbial communities in four campuses in Wuhan, China. We obtained 284 samples from 55 sampling sites over six seasons, as well as their matching climatic and environmental records. The structure of campus outdoor microbial communities which influenced by multiple climatic factors featured seasonality. The dispersal influence of human activities on microbial communities also contributed to this seasonal pattern non-negligibly. However, despite the microbial composition alteration in response to multiple stressors, the overall predicted function of campus outdoor microbial communities remained stable across campuses. The spatial-temporal dynamic patterns on campus outdoor microbial communities and its predicted functions have bridged the gap between microbial and macro-level ecosystems, and provided hints toward a better understanding of the effects of climatic factors and human activities on campus micro-environments.}, }
@article {pmid31347068, year = {2019}, author = {Mihăşan, M and Babii, C and Aslebagh, R and Channaveerappa, D and Dupree, EJ and Darie, CC}, title = {Exploration of Nicotine Metabolism in Paenarthrobacter nicotinovorans pAO1 by Microbial Proteomics.}, journal = {Advances in experimental medicine and biology}, volume = {1140}, number = {}, pages = {515-529}, doi = {10.1007/978-3-030-15950-4_30}, pmid = {31347068}, issn = {0065-2598}, abstract = {Proteomics, or the large-scale study of proteins, is a post-genomics field that, together with transcriptomics and metabolomics, has moved the study of bacteria to a new era based on system-wide understanding of bacterial metabolic and regulatory networks. The study of bacterial proteins or microbial proteomics has found a wide array of applications in many fields of microbiology, from food, clinical, and industrial microbiology to microbial ecology and physiology. The current chapter makes a brief technical introduction into the available approaches for the large-scale study of bacterial proteins using mass-spectrometry. Furthermore, the advantages and disadvantages of using bacteria for proteomics studies are indicated as well as several example studies where MS-based bacterial proteomics had a fundamental role in deciphering the scientific question. Finally, the proteomics study of nicotine catabolism in Paenarthrobacter nicotinovorans pAO1 using nanoLC-MS/MS is given as an in-depth example for possible applications of microbial proteomics.The nicotine degradation pathway functioning in Paenarthrobacter nicotinovorans is encoded by the catabolic megaplasmid pAO1 that contains about 40 nicotine-related genes making out the nic-gens cluster. Despite the promising biotechnological potential for the production of green-chemicals, only half of the nic-genes have been experimentally linked to nicotine. In an attempt to systematically identify all the proteins involved in nicotine degradation, a gel-based proteomics approach was used to identify a total of 801 proteins when Paenarthrobacter nicotinovorans was grown on three carbon sources: citrate, nicotine and nicotine and citrate. The differences in protein abundance showed that the bacterium is able to switch between deamination and demethylation in the lower nicotine pathway based on the available C source. Several pAO1 putative genes including a hypothetical polyketide cyclase have been shown to have a nicotine-dependent expression and we hypothesize that the polyketide cyclase would hydrolyze the N1-C6 bond from the pyridine ring with the formation of alpha-keto-glutaramate. Two chromosomal proteins, a malate dehydrogenase, and a D-3-phosphoglycerate dehydrogenase were shown to be strongly upregulated when nicotine was the sole carbon source and could be related to the production of the alpha-keto-glutaramate by the polyketide cyclase.}, }
@article {pmid31346687, year = {2019}, author = {Jha, PN and Gomaa, AB and Yanni, YG and El-Saadany, AY and Stedtfeld, TM and Stedtfeld, RD and Gantner, S and Chai, B and Cole, J and Hashsham, SA and Dazzo, FB}, title = {Alterations in the Endophyte-Enriched Root-Associated Microbiome of Rice Receiving Growth-Promoting Treatments of Urea Fertilizer and Rhizobium Biofertilizer.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01406-7}, pmid = {31346687}, issn = {1432-184X}, support = {INT 0211267//National Science Foundation/ ; BIO10-001-011 Contract #303//US-Eqypt Science &amp; Technology Joint Fund/ ; 3852 [58-3148-1-140//US-Egypt Scientific and Technology Joint Fund/ ; DE-FG02-99ER62848//US Dept. of Energy/ ; F-5 20/2013[IC}//University Grants Commission (IN)/ ; MICLO 2346//Michigan State University / Hatch (US)/ ; }, abstract = {We examined the bacterial endophyte-enriched root-associated microbiome within rice (Oryza sativa) 55 days after growth in soil with and without urea fertilizer and/or biofertilization with a growth-promotive bacterial strain (Rhizobium leguminosarum bv. trifolii E11). After treatment to deplete rhizosphere/rhizoplane communities, washed roots were macerated and their endophyte-enriched communities were analyzed by 16S ribosomal DNA 454 amplicon pyrosequencing. This analysis clustered 99,990 valid sequence reads into 1105 operational taxonomic units (OTUs) with 97% sequence identity, 133 of which represented a consolidated core assemblage representing 12.04% of the fully detected OTU richness. Taxonomic affiliations indicated Proteobacteria as the most abundant phylum (especially α- and γ-Proteobacteria classes), followed by Firmicutes, Bacteroidetes, Verrucomicrobia, Actinobacteria, and several other phyla. Dominant genera included Rheinheimera, unclassified Rhodospirillaceae, Pseudomonas, Asticcacaulis, Sphingomonas, and Rhizobium. Several OTUs had close taxonomic affiliation to genera of diazotrophic rhizobacteria, including Rhizobium, unclassified Rhizobiales, Azospirillum, Azoarcus, unclassified Rhizobiaceae, Bradyrhizobium, Azonexus, Mesorhizobium, Devosia, Azovibrio, Azospira, Azomonas, and Azotobacter. The endophyte-enriched microbiome was restructured within roots receiving growth-promoting treatments. Compared to the untreated control, endophyte-enriched communities receiving urea and/or biofertilizer treatments were significantly reduced in OTU richness and relative read abundances. Several unique OTUs were enriched in each of the treatment communities. These alterations in structure of root-associated communities suggest dynamic interactions in the host plant microbiome, some of which may influence the well-documented positive synergistic impact of rhizobial biofertilizer inoculation plus low doses of urea-N fertilizer on growth promotion of rice, considered as one of the world's most important food crops.}, }
@article {pmid31342100, year = {2019}, author = {Long, XE and Yao, H}, title = {Phosphorus Input Alters the Assembly of Rice (Oryza sativa L.) Root-Associated Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01407-6}, pmid = {31342100}, issn = {1432-184X}, support = {41525002//National Natural Science Foundation of China (CN)/ ; 41773079//National Natural Science Foundation of China/ ; XDB15020303//Strategic Priority Research Program of Chinese Academy of Sciences/ ; }, abstract = {Rice root-associated microbial community play an important role in plant nutrient acquisition, biomass production, and stress tolerance. Herein, root-associated community assembly was investigated under different phosphate input levels in phosphorus (P)-deficient paddy soil. Rice was grown in a long-term P-depleted paddy soil with 0 (P0), 50 (PL), or 200 (PH) mg P2O5 kg-1 application. DNA from root endophytes was isolated after 46 days, and PCR amplicons from archaea, bacteria, and fungi were sequenced by an Illumina Miseq PE300 platform, respectively. P application had no significant effect on rice root endophytic archaea, which were dominated by ammonia-oxidizing Candidatus Nitrososphaera. By contrast, rice root endophytic community structure of the bacteria and fungi was affected by soil P. Low P input increased endophytic bacterial diversity, whereas high P input increased rhizosphere fungi diversity. Bacillus and Pleosporales, associated with phosphate solubilization and P uptake, dominated in P0 and PH treatments, and Pseudomonas were more abundant in the PL treatment than in the P0 and PH treatments. Co-occurrence network analysis revealed a close interaction between endophytic bacteria and fungi. Soil P application affected both the rice root endosphere and soil rhizosphere microbial community and interaction between rice root endophytic bacteria, and fungi, especially species related to P cycling.}, }
@article {pmid31341288, year = {2019}, author = {Bolyen, E and Rideout, JR and Dillon, MR and Bokulich, NA and Abnet, CC and Al-Ghalith, GA and Alexander, H and Alm, EJ and Arumugam, M and Asnicar, F and Bai, Y and Bisanz, JE and Bittinger, K and Brejnrod, A and Brislawn, CJ and Brown, CT and Callahan, BJ and Caraballo-Rodríguez, AM and Chase, J and Cope, EK and Da Silva, R and Diener, C and Dorrestein, PC and Douglas, GM and Durall, DM and Duvallet, C and Edwardson, CF and Ernst, M and Estaki, M and Fouquier, J and Gauglitz, JM and Gibbons, SM and Gibson, DL and Gonzalez, A and Gorlick, K and Guo, J and Hillmann, B and Holmes, S and Holste, H and Huttenhower, C and Huttley, GA and Janssen, S and Jarmusch, AK and Jiang, L and Kaehler, BD and Kang, KB and Keefe, CR and Keim, P and Kelley, ST and Knights, D and Koester, I and Kosciolek, T and Kreps, J and Langille, MGI and Lee, J and Ley, R and Liu, YX and Loftfield, E and Lozupone, C and Maher, M and Marotz, C and Martin, BD and McDonald, D and McIver, LJ and Melnik, AV and Metcalf, JL and Morgan, SC and Morton, JT and Naimey, AT and Navas-Molina, JA and Nothias, LF and Orchanian, SB and Pearson, T and Peoples, SL and Petras, D and Preuss, ML and Pruesse, E and Rasmussen, LB and Rivers, A and Robeson, MS and Rosenthal, P and Segata, N and Shaffer, M and Shiffer, A and Sinha, R and Song, SJ and Spear, JR and Swafford, AD and Thompson, LR and Torres, PJ and Trinh, P and Tripathi, A and Turnbaugh, PJ and Ul-Hasan, S and van der Hooft, JJJ and Vargas, F and Vázquez-Baeza, Y and Vogtmann, E and von Hippel, M and Walters, W and Wan, Y and Wang, M and Warren, J and Weber, KC and Williamson, CHD and Willis, AD and Xu, ZZ and Zaneveld, JR and Zhang, Y and Zhu, Q and Knight, R and Caporaso, JG}, title = {Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.}, journal = {Nature biotechnology}, volume = {37}, number = {8}, pages = {852-857}, doi = {10.1038/s41587-019-0209-9}, pmid = {31341288}, issn = {1546-1696}, support = {U54CA143925//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U54MD012388//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 1565057//National Science Foundation (NSF)/ ; 1565100//National Science Foundation (NSF)/ ; U54CA143925//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; U54MD012388//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; }, }
@article {pmid31339480, year = {2019}, author = {Lee, JC and Whang, KS}, title = {Aquibacillus sediminis sp. nov., a moderately halophilic bacterium isolated from saltern soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1099/ijsem.0.003599}, pmid = {31339480}, issn = {1466-5034}, abstract = {A Gram-stain-positive, moderately halophilic bacterium, designated strain BH258T, was isolated from solar saltern sediment sampled at Shinan in the Republic of Korea. Cells of strain BH258T were found to be strictly aerobic, motile, endospore-forming rods which could grow at 15-45 °C (optimum, 35 °C), at pH 5.5-9.0 (pH 7.0) and at salinities of 0.5-20 % (w/v) NaCl (7-10%). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BH258T belongs to the genus Aquibacillus, showing highest sequence similarity to Aquibacillus koreensis BH30097T (96.1 %), Aquibacillus albus YIM 93624T (95.9 %), Aquibacillus halophilus B6BT (95.6 %) and Aquibacillus salifodinae WSY08-1T (95.1 %). The predominant isoprenoid quinone was identified as menaquinone-7, and the cell-wall peptidoglycan was found to contain meso-diaminopimelic acid as the diagnostic diamino acid. The major fatty acids were identified as anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C15 : 0. The major polar lipids were identified as phosphatidylglycerol, diphosphatidylglycerol and three unidentified phospholipids. The DNA G+C content of this novel isolate was determined to be 37.35 mol%. On the basis of the results of phylogenetic, phenotypic and chemotaxonomic analyses in this study, strain BH258T is considered to represent a novel species of the genus Aquibacillus, for which the name Aquibacillus sediminis sp. nov. is proposed. The type strain is BH258T (=KACC 18680T=NBRC 111875T).}, }
@article {pmid31338843, year = {2019}, author = {Vincent, Q and Chartin, C and Krüger, I and Van Wesemael, B and Carnol, M}, title = {CARBIOSOL: Biological indicators of soil quality and organic carbon in grasslands and croplands in Wallonia, Belgium.}, journal = {Ecology}, volume = {}, number = {}, pages = {e02843}, doi = {10.1002/ecy.2843}, pmid = {31338843}, issn = {1939-9170}, abstract = {The protection of agricultural soil quality is critical to environmental sustainability and requires relevant indicators. Total soil organic carbon (SOC) is of importance for soil quality but its slow dynamic and inherent variability do not allow early detection of changes. The project CARBIOSOL provides a data set from agricultural soils in Wallonia (Southern Belgium), of total SOC, SOC fractions and biological indicators, selected for their relevance as indicators of soil quality. Two land uses (sampled in 2013), five agricultural regions (2015), seasonal variability in croplands (2016) and four management types (2017) were studied. Soil organic carbon content (total, stable fine fraction <20 μm, labile coarse fraction >20 μm), cold and hot water extractable carbon and nitrogen contents, total nitrogen, pHKCl , pHH2O , potential respiration, microbial biomass carbon and nitrogen, net nitrogen mineralization, metabolic potential of soil bacteria, earthworm density and biomass, and two ecophysiological quotients (metabolic and microbial quotient) were measured for a total of 415 samples. The present data set provides an important contribution for establishing a reference system of soil quality in Wallonia and eventually for large-scale studies through its integration into a global database. Moreover, the present data set could be used to support the interpretation of measurements of fractions of SOC and biological indicators by soil analyses laboratories, which will be useful for farmers and decision makers to evaluate the effect of different management practices. Information contained in this publication or product may be reproduced, in part or in whole, and by any means for personal or public non-commercial uses, without charge or further permission, unless otherwise specified. Users are required to exercise due diligence in ensuring the accuracy of the material reproduced, indicate the complete title of the material produced and refer to this publication (including author names), indicate that the reproduction is a copy/uses official work financed by the SPW-DGO3. Commercial reproduction and distribution is prohibited, except with written permission from SPW-DGO3 and publication authors.}, }
@article {pmid31338076, year = {2019}, author = {Alviz-Gazitua, P and Fuentes-Alburquenque, S and Rojas, LA and Turner, RJ and Guiliani, N and Seeger, M}, title = {The Response of Cupriavidus metallidurans CH34 to Cadmium Involves Inhibition of the Initiation of Biofilm Formation, Decrease in Intracellular c-di-GMP Levels, and a Novel Metal Regulated Phosphodiesterase.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1499}, doi = {10.3389/fmicb.2019.01499}, pmid = {31338076}, issn = {1664-302X}, abstract = {Cadmium is a highly toxic heavy metal for biological systems. Cupriavidus metallidurans CH34 is a model strain to study heavy metal resistance and bioremediation as it is able to deal with high heavy metal concentrations. Biofilm formation by bacteria is mediated by the second messenger bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP). The aim of this study was to characterize the response of C. metallidurans CH34 planktonic and biofilm cells to cadmium including their c-di-GMP regulatory pathway. Inhibition of the initiation of biofilm formation and EPS production by C. metallidurans CH34 correlates with increased concentration of cadmium. Planktonic and biofilm cells showed similar tolerance to cadmium. During exposure to cadmium an acute decrease of c-di-GMP levels in planktonic and biofilm cells was observed. Transcription analysis by RT-qPCR showed that cadmium exposure to planktonic and biofilm cells induced the expression of the urf2 gene and the mercuric reductase encoding merA gene, which belong to the Tn501/Tn21 mer operon. After exposure to cadmium, the cadA gene involved in cadmium resistance was equally upregulated in both lifestyles. Bioinformatic analysis and complementation assays indicated that the protein encoded by the urf2 gene is a functional phosphodiesterase (PDE) involved in the c-di-GMP metabolism. We propose to rename the urf2 gene as mrp gene for metal regulated PDE. An increase of the second messenger c-di-GMP content by the heterologous expression of the constitutively active diguanylate cyclase PleD correlated with an increase in biofilm formation and cadmium susceptibility. These results indicate that the response to cadmium in C. metallidurans CH34 inhibits the initiation of biofilm lifestyle and involves a decrease in c-di-GMP levels and a novel metal regulated PDE.}, }
@article {pmid31337729, year = {2019}, author = {Rath, KM and Maheshwari, A and Rousk, J}, title = {Linking Microbial Community Structure to Trait Distributions and Functions Using Salinity as an Environmental Filter.}, journal = {mBio}, volume = {10}, number = {4}, pages = {}, doi = {10.1128/mBio.01607-19}, pmid = {31337729}, issn = {2150-7511}, abstract = {The structure and function of microbial communities vary along environmental gradients; however, interlinking the two has been challenging. In this study, salinity was used as an environmental filter to study how it could shape trait distributions, community structures, and the resulting functions of soil microbes. The environmental filter was applied by salinizing nonsaline soil (0 to 22 mg NaCl g-1). Our targeted community trait distribution (salt tolerance) was determined with dose-response relationships between bacterial growth and salinity. The bacterial community structure responses were resolved with Illumina 16S rRNA gene amplicon sequencing, and the microbial functions determined were respiration and bacterial and fungal growth. Salt exposure quickly resulted in filtered trait distributions, and stronger filters resulted in larger shifts. The filtered trait distributions correlated well with community composition differences, suggesting that trait distribution shifts were driven at least partly by species turnover. While salt exposure decreased respiration, microbial growth responses appeared to be characterized by competitive interactions. Fungal growth was highest when bacterial growth was inhibited by the highest salinity, and it was lowest when the bacterial growth rate peaked at intermediate salt levels. These findings corroborated a higher potential for fungal salt tolerance than bacterial salt tolerance for communities derived from a nonsaline soil. In conclusion, by using salt as an environmental filter, we could interlink the targeted trait distribution with both the community structure and resulting functions of soil microbes.IMPORTANCE Understanding the role of ecological communities in maintaining multiple ecosystem processes is a central challenge in ecology. Soil microbial communities perform vital ecosystem functions, such as the decomposition of organic matter to provide plant nutrition. However, despite the functional importance of soil microorganisms, attribution of ecosystem function to particular constituents of the microbial community has been impeded by a lack of information linking microbial processes to community composition and structure. Here, we apply a conceptual framework to determine how microbial communities influence ecosystem processes, by applying a &quot;top-down&quot; trait-based approach. By determining the dependence of microbial processes on environmental factors (e.g., the tolerance to salinity), we can define the aggregate response trait distribution of the community, which then can be linked to the community structure and the resulting function performed by the microbial community.}, }
@article {pmid31336252, year = {2019}, author = {Shen, Y and Stedtfeld, RD and Guo, X and Bhalsod, GD and Jeon, S and Tiedje, JM and Li, H and Zhang, W}, title = {Pharmaceutical exposure changed antibiotic resistance genes and bacterial communities in soil-surface- and overhead-irrigated greenhouse lettuce.}, journal = {Environment international}, volume = {131}, number = {}, pages = {105031}, doi = {10.1016/j.envint.2019.105031}, pmid = {31336252}, issn = {1873-6750}, abstract = {New classes of emerging contaminants such as pharmaceuticals, antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs) have received increasing attention due to rapid increases of their abundance in agroecosystems. As food consumption is a direct exposure pathway of pharmaceuticals, ARB, and ARGs to humans, it is important to understand changes of bacterial communities and ARG profiles in food crops produced with contaminated soils and waters. This study examined the level and type of ARGs and bacterial community composition in soil, and lettuce shoots and roots under soil-surface or overhead irrigation with pharmaceuticals-contaminated water, using high throughput qPCR and 16S rRNA amplicon sequencing techniques, respectively. In total 52 ARG subtypes were detected in the soil, lettuce shoot and root samples, with mobile genetic elements (MGEs), and macrolide-lincosamide-streptogramin B (MLSB) and multidrug resistance (MDR) genes as dominant types. The overall abundance and diversity of ARGs and bacteria associated with lettuce shoots under soil-surface irrigation were lower than those under overhead irrigation, indicating soil-surface irrigation may have lower risks of producing food crops with high abundance of ARGs. ARG profiles and bacterial communities were sensitive to pharmaceutical exposure, but no consistent patterns of changes were observed. MGE intl1 was consistently more abundant with pharmaceutical exposure than in the absence of pharmaceuticals. Pharmaceutical exposure enriched Proteobacteria (specifically Methylophilaceae) and decreased bacterial alpha diversity. Finally, there were significant interplays among bacteria community, antibiotic concentrations, and ARG abundance possibly involving hotspots including Sphingomonadaceae, Pirellulaceae, and Chitinophagaceae, MGEs (intl1 and tnpA_1) and MDR genes (mexF and oprJ).}, }
@article {pmid31333629, year = {2019}, author = {Yuan, H and Mei, R and Liao, J and Liu, WT}, title = {Nexus of Stochastic and Deterministic Processes on Microbial Community Assembly in Biological Systems.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1536}, doi = {10.3389/fmicb.2019.01536}, pmid = {31333629}, issn = {1664-302X}, abstract = {Microbial community assembly in engineered biological systems is often simultaneously influenced by stochastic and deterministic processes, and the nexus of these two mechanisms remains to be further investigated. Here, three lab-scale activated sludge reactors were seeded with identical inoculum and operated in parallel under eight different sludge retention time (SRT) by sequentially reducing the SRT from 15 days to 1 day. Using 16S rRNA gene amplicon sequencing data, the microbial populations at the start-up (15-day SRT) and SRT-driven (≤10-day SRT) phases were observed to be noticeably different. Clustering results demonstrated ecological succession at the start-up phase with no consistent successional steps among the three reactors, suggesting that stochastic processes played an important role in the community assembly during primary succession. At the SRT-driven phase, the three reactors shared 31 core operational taxonomic units (OTUs). Putative primary acetate utilizers and secondary metabolizers were proposed based on K-means clustering, network and synchrony analysis. The shared core populations accounted for 65% of the total abundance, indicating that the microbial communities at the SRT-driven phase were shaped predominantly by deterministic processes. Sloan's Neutral model and a null model analysis were performed to disentangle and quantify the relative influence of stochastic and deterministic processes on community assembly. The increased estimated migration rate in the neutral community model and the higher percentage of stochasticity in the null model implied that stochastic community assembly was intensified by strong deterministic factors. This was confirmed by the significantly different α- and β-diversity indices at SRTs shorter than 2 days and the observation that over half of the core OTUs were unshared or unsynchronized. Overall, this study provided quantitative insights into the nexus of stochastic and deterministic processes on microbial community assembly in a biological process.}, }
@article {pmid31330399, year = {2019}, author = {Lippens, C and De Vrieze, J}, title = {Exploiting the unwanted: Sulphate reduction enables phosphate recovery from energy-rich sludge during anaerobic digestion.}, journal = {Water research}, volume = {163}, number = {}, pages = {114859}, doi = {10.1016/j.watres.2019.114859}, pmid = {31330399}, issn = {1879-2448}, abstract = {Anaerobic digestion is shifting from a single-purpose technology for renewable energy recovery from organic waste streams to a process for integrated resource recovery. The valorisation of high-rate energy- and phosphorus-rich sludge creates the opportunity for their combined recovery. This phosphate is present in a precipitated form in the sludge, and its release into the liquid phase is an important issue before recovery can be achieved. The objective of this research was to exploit the &quot;unwanted&quot; sulphate reduction process for the release of phosphate into the liquid phase during anaerobic digestion, thus, making it available for recovery. Two different treatments were considered, i.e., a control digester and a digester to which sulphate was added, each operated in triplicate for a period of 119 days. The control digester showed stable methane production at 628 ± 103 mL CH4 L-1 d-1, with a feedstock COD (chemical oxygen demand) conversion efficiency of 89.5 ± 14.6%. In contrast, the digester with sulphate addition showed a 29.9 ± 15.3% decrease in methane production, reaching an &quot;inhibited steady state&quot;, but phosphate release into the liquid phase increased to 58.7 ± 12.9% of total P, a factor 4.5 higher than the control digester. This inhibited steady state coincided with a clear shift from a Methanosaetaceae to a Methanosarcinaceae dominated methanogenic community. Overall, the sulphate reduction process allows phosphate release during the anaerobic digestion process, yet, at the cost of a reduced methane production rate.}, }
@article {pmid31329319, year = {2019}, author = {Onnis-Hayden, A and Majed, N and Li, Y and Rahman, SM and Drury, D and Risso, L and Gu, AZ}, title = {Impact of Solid Residence Time (SRT) on Functionally Relevant Microbial Populations and Performance in Full-scale Enhanced Biological Phosphorus Removal (EBPR) Systems.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {}, number = {}, pages = {}, doi = {10.1002/wer.1185}, pmid = {31329319}, issn = {1554-7531}, abstract = {Investigations of the impact of solid residence time (SRT) on microbial ecology and performance of Enhanced Biological Phosphorus process (EBPR) in full-scale systems has been scarce due to the challenges in isolating and examining the SRT from other complex plant-specific factors. This study performed a comprehensive evaluation of the influence of SRT on polyphosphate accumulating organisms (PAOs) and Glycogen Accumulating Organisms (GAOs) dynamics and on P removal performance at Clark County Water Reclamation District Facility in Las Vegas, US. Five parallel treatment trains with separated clarifiers were operated with five different SRTs ranging from 6 to 40 days. Microbial community analysis using multiple molecular and Raman techniques suggested that the relative abundances and diversity of PAOs and GAOs in EBPR systems is highly affected by the SRT. The resultant EBPR system stability and performance can be potentially controlled and optimized by manipulating the system SRT, and shorter SRT (<10 days) seems to be preferred. This article is protected by copyright. All rights reserved.}, }
@article {pmid31328364, year = {2019}, author = {Colangelo-Lillis, J and Pelikan, C and Herbold, CW and Altshuler, I and Loy, A and Whyte, LG and Wing, BA}, title = {Diversity decoupled from sulfur isotope fractionation in a sulfate-reducing microbial community.}, journal = {Geobiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gbi.12356}, pmid = {31328364}, issn = {1472-4669}, support = {NSERC CREATE 371308-09//Canadian Astrobiology Training Program/ ; OCE- 0939564//Center for Dark Energy Biosphere Investigations (C-DEBI)/ ; 294343//European Research Council Advanced Grant Nitrification Reloaded/ ; P25111-B22//Austrian Science Fund/ ; RGPIN-2014-06626//NSERC Discovery grants/ ; RGPNS 305490-2012//NSERC Discovery grants/ ; //University of Colorado Boulder/ ; }, abstract = {The extent of fractionation of sulfur isotopes by sulfate-reducing microbes is dictated by genomic and environmental factors. A greater understanding of species-specific fractionations may better inform interpretation of sulfur isotopes preserved in the rock record. To examine whether gene diversity influences net isotopic fractionation in situ, we assessed environmental chemistry, sulfate reduction rates, diversity of putative sulfur-metabolizing organisms by 16S rRNA and dissimilatory sulfite reductase (dsrB) gene amplicon sequencing, and net fractionation of sulfur isotopes along a sediment transect of a hypersaline Arctic spring. In situ sulfate reduction rates yielded minimum cell-specific sulfate reduction rates < 0.3 × 10-15 moles cell-1 day-1 . Neither 16S rRNA nor dsrB diversity indices correlated with relatively constant (38‰-45‰) net isotope fractionation (ε34 Ssulfide-sulfate). Measured ε34 S values could be reproduced in a mechanistic fractionation model if 1%-2% of the microbial community (10%-60% of Deltaproteobacteria) were engaged in sulfate respiration, indicating heterogeneous respiratory activity within sulfate-reducing populations. This model indicated enzymatic kinetic diversity of Apr was more likely to correlate with sulfur fractionation than DsrB. We propose that, above a threshold Shannon diversity value of 0.8 for dsrB, the influence of the specific composition of the microbial community responsible for generating an isotope signal is overprinted by the control exerted by environmental variables on microbial physiology.}, }
@article {pmid31325575, year = {2019}, author = {Kumar, KV and Pal, A and Bai, P and Kour, A and E, S and P, R and Kausar, A and Chatterjee, M and Prasad, G and Balayan, S and Dutta, P and Wijesekera, K}, title = {Co-aggregation of bacterial flora isolated from the human skin surface.}, journal = {Microbial pathogenesis}, volume = {135}, number = {}, pages = {103630}, doi = {10.1016/j.micpath.2019.103630}, pmid = {31325575}, issn = {1096-1208}, abstract = {Human hands play a prominent role in the intra and interpersonal transmission of microbes that constantly connect one's microbiome to other individuals and the environment. Along with beneficial bacteria, an individual may harbor pathogenic organisms which may get transferred to others. Thus, understanding the transmission mechanism and interaction among microbiota is crucial in preventing infection. In the present study, the ability of skin microbes, isolated from different individuals, to physically interact (coaggregate) intergenically was assessed. The bacterial flora from the hands (palm area) of similar age group students was isolated. The predominant isolates were selected and identified using 16s rRNA gene sequencing. Further, these isolates were subjected to visual coaggregation assay. A total of 27 bacteria were isolated from the human skin (palm area-fingers) of 10 individuals. These isolates belong to seven bacterial genera and 10 different species. Among 123 combinational visual coaggregation positive reactions; 53.66% showed a reaction score of +1, while 32.52%, 11.38% and 2.44% showed a score of +2, +3, and +4 respectively. Among 27 isolates, Staphylococcus haemolyticus had highest coaggregation partners of 17 followed by Acinetobacter spp. and Pseudomonas spp. with 15 partners each. The present study is the first report demonstrating the coaggregation potential of microbiota harboring the skin surface of the human hand. The study indicates that few microbes have high potential to influence coaggregation among distinct genera isolated from the skin. However, further studies are needed to understand the ability of these bacteria to coaggregate, their influence in interpersonal transmission and shaping of microbial ecology of the host skin.}, }
@article {pmid31324234, year = {2019}, author = {Ling, S and Hui, L}, title = {Evaluation of the complexity of indoor air in hospital wards based on PM2.5, real-time PCR, adenosine triphosphate bioluminescence assay, microbial culture and mass spectrometry.}, journal = {BMC infectious diseases}, volume = {19}, number = {1}, pages = {646}, doi = {10.1186/s12879-019-4249-z}, pmid = {31324234}, issn = {1471-2334}, support = {2018J12SN084//Scientific and Technological Innovation of Dalian/ ; }, abstract = {BACKGROUND: The aim of this study was to establish a set of assessment methods suitable for evaluating the complex indoor environment of hospital wards and to ascertain the composition of bacteria and microbial ecology of hospital wards.<br><br>METHODS: Colony-forming units (CFUs), PM2.5 detection, real-time PCR, and adenosine triphosphate (ATP) bioluminescence assay were employed to evaluate the complexity of indoor air in 18 wards of nine departments in a hospital and two student dormitories in a university. Subsequently, the microbial samples were quantified and identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS).<br><br>RESULTS: Although the studied indices were relatively independent, the PM2.5 content was correlated with bacterial CFUs determined by passive sedimentation method, bacterial and fungal counts measured by real-time PCR, and ATP bioluminescence assay. The composition of microorganisms in the air of hospital wards differed from that in the air of student dormitories. The dominant genera in hospital wards were Staphylococcus (39.4%), Micrococcus (21.9%), Corynebacterium (11.7%), Kocuria (4.4%), Bacillus (2.9%), Streptococcus (1.6%), Moraxella (1.6%), and Enterococcus (1.3%), and the microbial ecology differed between Respiration Dept. III and other hospital departments. Additionally, 11.1 and 27.3% of bacteria in hospital wards and student dormitories were not identified, respectively.<br><br>CONCLUSIONS: Assessment of environmental quality of hospital wards should be based on comprehensive analysis with multiple indicators. There may be imbalances in the microbial diversity in the hospital wards, therefore, monitoring of the environmental quality of hospitals is important in the prevention of nosocomial infections.}, }
@article {pmid31323513, year = {2019}, author = {Zamorano-López, N and Borrás, L and Giménez, JB and Seco, A and Aguado, D}, title = {Acclimatised rumen culture for raw microalgae conversion into biogas: Linking microbial community structure and operational parameters in anaerobic membrane bioreactors (AnMBR).}, journal = {Bioresource technology}, volume = {290}, number = {}, pages = {121787}, doi = {10.1016/j.biortech.2019.121787}, pmid = {31323513}, issn = {1873-2976}, abstract = {Ruminal fluid was inoculated in an Anaerobic Membrane Reactor (AnMBR) to produce biogas from raw Scenedesmus. This work explores the microbial ecology of the system during stable operation at different solids retention times (SRT). The 16S rRNA amplicon analysis revealed that the acclimatised community was mainly composed of Anaerolineaceae, Spirochaetaceae, Lentimicrobiaceae and Cloacimonetes fermentative and hydrolytic members. During the highest biodegradability achieved in the AnMBR (62%) the dominant microorganisms were Fervidobacterium and Methanosaeta. Different microbial community clusters were observed at different SRT conditions. Interestingly, syntrophic bacteria Gelria and Smithella were enhanced after increasing 2-fold the organic loading rate, suggesting their importance in continuous systems producing biogas from raw microalgae.}, }
@article {pmid31321764, year = {2019}, author = {Xie, M and An, F and Wu, J and Liu, Y and Shi, H and Wu, R}, title = {Meta-omics reveal microbial assortments and key enzymes in bean sauce mash, a traditional fermented soybean product.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.9932}, pmid = {31321764}, issn = {1097-0010}, support = {31470538//Natural Science Foundation of China/ ; 31471713//Natural Science Foundation of China/ ; RC170212//Shenyang Youth Science and Technology Innovation Talent Project/ ; 17-189-9-00//Liaoning BaiQianWan Talents Program Project, Shenyang Science and Technology Project/ ; XLYC1807040//LiaoNing Revitalization Talents Program/ ; }, abstract = {BACKGROUND: Dajiang is fermented based on the metabolism of microbial communities in bean sauce mash, a traditional fermented soybean product in China. The current study first investigated the metaproteome of bean sauce mash. This was followed by an analysis of its biological functions and its microbial community to reveal information about strains and about the expressed proteins to better understand the roles of the microbiota in bean sauce mash.<br><br>RESULTS: The metaproteomic results demonstrated that a total of 1415 microbial protein clusters were expressed mainly by members of the Penicillium and Rhizopus genera and were classified into 100 cellular components, 238 biological processes, and 220 molecular function categories by gene ontology (GO) annotation. Enzymes associated with glycolysis metabolic pathways were also identified. These can provide the energy required for microbial fermentation. Illumina MiSeq sequencing technology results showed that the microorganism communities of bean sauce mash exhibited a high level of diversity. Microbiological analysis demonstrated that the Penicillium, Mucor, Fusarium, Aspergillus, and Rhizopus fungi, and Lactobacillus, Enterococcus, Fructobacillus, Staphylococcus, Carnobacterium genera were predominant 22 samples.<br><br>CONCLUSION: The profiles and insights in the current study are important for research on bean sauce mash and related products in terms of their food microbial ecology. The information obtained from this study will help the development of stable sufu starter cultures with unique sensory qualities. © 2019 Society of Chemical Industry.}, }
@article {pmid31320430, year = {2019}, author = {Hausmann, B and Pjevac, P and Huemer, M and Herbold, CW and Pester, M and Loy, A}, title = {Draft Genome Sequence of Desulfosporosinus sp. Strain Sb-LF, Isolated from an Acidic Peatland in Germany.}, journal = {Microbiology resource announcements}, volume = {8}, number = {29}, pages = {}, doi = {10.1128/MRA.00428-19}, pmid = {31320430}, issn = {2576-098X}, abstract = {Desulfosporosinus sp. strain Sb-LF was isolated from an acidic peatland in Bavaria, Germany. Here, we report the draft genome sequence of the sulfate-reducing and lactate-utilizing strain Sb-LF.}, }
@article {pmid31316095, year = {2019}, author = {Mailloux, BJ and Kim, C and Kichuk, T and Nguyen, K and Precht, C and Wang, S and Jewell, TNM and Karaoz, U and Brodie, EL and Williams, KH and Beller, HR and Buchholz, BA}, title = {Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {10370}, doi = {10.1038/s41598-019-46663-1}, pmid = {31316095}, issn = {2045-2322}, support = {S10RR029668//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; S10RR027303//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; P42 ES010349/ES/NIEHS NIH HHS/United States ; DE-SC0006796//DOE | SC | Biological and Environmental Research (BER)/ ; 1521258//National Science Foundation (NSF)/ ; S10 RR029668/RR/NCRR NIH HHS/United States ; S10 RR027303/RR/NCRR NIH HHS/United States ; P41 GM103483/GM/NIGMS NIH HHS/United States ; AC52-07NA27344//DOE | LDRD | Lawrence Livermore National Laboratory (LLNL)/ ; P41GM103483//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; P42-ES010349//U.S. Department of Health &amp; Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; }, abstract = {Determining the carbon sources for active microbial populations in the subsurface is a challenging but highly informative component of subsurface microbial ecology. This work developed a method to provide ecological insights into groundwater microbial communities by characterizing community RNA through its radiocarbon and ribosomal RNA (rRNA) signatures. RNA was chosen as the biomolecule of interest because rRNA constitutes the majority of RNA in prokaryotes, represents recently active organisms, and yields detailed taxonomic information. The method was applied to a groundwater filter collected from a shallow alluvial aquifer in Colorado. RNA was extracted, radiometrically dated, and the 16S rRNA was analyzed by RNA-Seq. The RNA had a radiocarbon signature (Δ14C) of -193.4 ± 5.6‰. Comparison of the RNA radiocarbon signature to those of potential carbon pools in the aquifer indicated that at least 51% of the RNA was derived from autotrophy, in close agreement with the RNA-Seq data, which documented the prevalence of autotrophic taxa, such as Thiobacillus and Gallionellaceae. Overall, this hybrid method for RNA analysis provided cultivation-independent information on the in-situ carbon sources of active subsurface microbes and reinforced the importance of autotrophy and the preferential utilization of dissolved over sedimentary organic matter in alluvial aquifers.}, }
@article {pmid31314939, year = {2019}, author = {Ranchou-Peyruse, M and Auguet, JC and Mazière, C and Restrepo-Ortiz, CX and Guignard, M and Dequidt, D and Chiquet, P and Cézac, P and Ranchou-Peyruse, A}, title = {Geological gas-storage shapes deep life.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14745}, pmid = {31314939}, issn = {1462-2920}, support = {//Storengy and Teréga/ ; }, abstract = {Around the world, several dozen deep sedimentary aquifers are being used for storage of natural gas. Ad hoc studies of the microbial ecology of some of them have suggested that sulfate reducing and methanogenic microorganisms play a key role in how these aquifers' communities function. Here, we investigate the influence of gas storage on these two metabolic groups by using high-throughput sequencing and show the importance of sulfate-reducing Desulfotomaculum and a new monophyletic methanogenic group. Aquifer microbial diversity was significantly related to the geological level. The distance to the stored natural gas affects the ratio of sulfate-reducing Firmicutes to deltaproteobacteria. In only one aquifer, the methanogenic archaea dominate the sulfate-reducers. This aquifer was used to store town gas (containing at least 50% H2) around 50 years ago. The observed decrease of sulfates in this aquifer could be related to stimulation of subsurface sulfate-reducers. These results suggest that the composition of the microbial communities is impacted by decades old transient gas storage activity. The tremendous stability of these gas-impacted deep subsurface microbial ecosystems suggests that in situ biotic methanation projects in geological reservoirs may be sustainable over time.}, }
@article {pmid31314103, year = {2019}, author = {Stres, B and Kronegger, L}, title = {Shift in the paradigm towards next-generation microbiology.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnz159}, pmid = {31314103}, issn = {1574-6968}, abstract = {In this work, the position of contemporary microbiology is considered from the perspective of scientific success, and a list of historical points and lessons learned from the fields of medical microbiology, microbial ecology and systems biology are presented. In addition, patterns in the development of top-down research topics that emerged over time as well as overlapping ideas and personnel, which are the first signs of trans-domain research activities in the fields of metagenomics, metaproteomics, metatranscriptomics and metabolomics, are explored through analysis of the publication networks of 28.654 papers using the computer programme Pajek. The current state of affairs is defined, and the need for meta-analyses to leverage publication biases in the field of microbiology is put forward as a very important emerging field of microbiology, especially since microbiology is progressively dealing with multiscale systems. Consequently, the need for cross-fertilisation with other fields/disciplines instead of 'more microbiology' is needed to advance the field of microbiology as such. The reader is directed to consider how novel technologies, the introduction of big data approaches and artificial intelligence have transformed microbiology into a multi-scale field and initiated a shift away from its history of mostly manual work and towards a largely technology-, data- and statistics-driven discipline that is often coupled with automation and modelling.}, }
@article {pmid31314089, year = {2019}, author = {Paterson, JS and Smith, RJ and McKerral, JC and Dann, LM and Launer, E and Goonan, P and Kleinig, T and Fuhrman, JA and Mitchell, JG}, title = {A hydrocarbon-contaminated aquifer reveals a Piggyback-the-Persistent viral strategy.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {8}, pages = {}, doi = {10.1093/femsec/fiz116}, pmid = {31314089}, issn = {1574-6941}, abstract = {Subsurface environments hold the largest reservoir of microbes in the biosphere. They play essential roles in transforming nutrients, degrading contaminants and recycling organic matter. Here, we propose a previously unrecognised fundamental microbial process that influences aquifer bioremediation dynamics and that applies to all microbial communities. In contrast to previous models, our proposed Piggyback-the-Persistent (PtP) mechanism occurs when viruses become more dominated by those exhibiting temperate rather than lytic lifestyles driven by persistent chemicals (in our case chlorinated-hydrocarbon pollutants) that provide long-term carbon sources and that refocus the aquifer carbon cycle, thus altering the microbial community. In this ultra-oligotrophic system, the virus:microbial ratio (VMR) ranges from below the detection limit of 0.0001 to 0.6, well below the common aquatic range of 3-10. Shortest-average-path network analysis revealed VMR and trichlorethene (TCE) as nodes through which ecosystem information and biomass most efficiently pass. Novel network rearrangement revealed a hierarchy of Kill-the-Winner (KtW), Piggyback-the-Winner (PtW) and PtP nodes. We propose that KtW, PtW and PtP occur simultaneously as competing strategies, with their relative importance depending on conditions at a particular time and location with unusual nutrient sources, such as TCE, appearing to contribute to a shift in this balance between viral mechanisms.}, }
@article {pmid31313962, year = {2019}, author = {Moye, ZD and Woolston, J and Abbeele, PVD and Duysburgh, C and Verstrepen, L and DAS, CR and Marzorati, M and Sulakvelidze, A}, title = {A Bacteriophage Cocktail Eliminates Salmonella Typhimurium from the Human Colonic Microbiome while Preserving Cytokine Signaling and Preventing Attachment to and Invasion of Human Cells by Salmonella In Vitro.}, journal = {Journal of food protection}, volume = {82}, number = {8}, pages = {1336-1349}, doi = {10.4315/0362-028X.JFP-18-587}, pmid = {31313962}, issn = {1944-9097}, abstract = {Nontyphoidal Salmonella strains continue to be a major cause of foodborne illness globally. One intriguing approach to reducing the risk of salmonellosis is the direct ingestion of phages targeting Salmonella to enhance natural gut resilience and provide protection during foodborne disease outbreaks. We evaluated the ability of a prophylactically administered bacteriophage cocktail, the foodborne outbreak pill (FOP) targeting Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella, to resolve a Salmonella infection in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME), a simulated gut platform populated by the human intestinal microbiome of healthy donors. The FOP preparation eliminated Salmonella enterica serovar Typhimurium from the colon compartment of the SHIME platform but health-associated metabolites, such as short-chain fatty acids and lactate, remained stable or increased in a donor-dependent manner. In studies of human intestinal cells, pretreatment of Salmonella Typhimurium with the FOP cocktail preserved lipopolysaccharide-stimulated signaling in a Caco-2-THP-1 Transwell system and prevented destruction of the Caco-2 monolayer by Salmonella. Adhesion and invasion of intestinal epithelial cells by Salmonella-a critical factor in Salmonella pathogenesis-was blunted when the bacteria were incubated with the FOP preparation before addition to the monolayer. The FOP phage cocktail was effective for (i) eliminating Salmonella from a simulated human gut without disturbing the indigenous microbiota and (ii) reducing the risk of invasion by Salmonella into the intestinal epithelia. These results suggest that the FOP preparation may be of value for reducing the risk of salmonellosis in humans, e.g., during foodborne disease outbreaks.}, }
@article {pmid31312870, year = {2019}, author = {Shih, JL and Selph, KE and Wall, CB and Wallsgrove, NJ and Lesser, MP and Popp, BN}, title = {Trophic Ecology of the Tropical Pacific Sponge Mycale grandis Inferred from Amino Acid Compound-Specific Isotopic Analyses.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01410-x}, pmid = {31312870}, issn = {1432-184X}, support = {NA14OAR4170071//Hawai'i Sea Grant, University of Hawai'i/ ; }, abstract = {Many sponges host abundant and active microbial communities that may play a role in the uptake of dissolved organic matter (DOM) by the sponge holobiont, although the mechanism of DOM uptake and metabolism is uncertain. Bulk and compound-specific isotopic analysis of whole sponge, isolated sponge cells, and isolated symbiotic microbial cells of the shallow water tropical Pacific sponge Mycale grandis were used to elucidate the trophic relationships between the host sponge and its associated microbial community. δ15N and δ13C values of amino acids in M. grandis isolated sponge cells are not different from those of its bacterial symbionts. Consequently, there is no difference in trophic position of the sponge and its symbiotic microbes indicating that M. grandis sponge cell isolates do not display amino acid isotopic characteristics typical of metazoan feeding. Furthermore, both the isolated microbial and sponge cell fractions were characterized by a similarly high ΣV value-a measure of bacterial-re-synthesis of organic matter calculated from the sum of variance among individual δ15N values of trophic amino acids. These high ΣV values observed in the sponge suggest that M. grandis is not reliant on translocated photosynthate from photosymbionts or feeding on water column picoplankton, but obtains nutrition through the uptake of amino acids of bacterial origin. Our results suggest that direct assimilation of bacterially synthesized amino acids from its symbionts, either in a manner similar to translocation observed in the coral holobiont or through phagotrophic feeding, is an important if not primary pathway of amino acid acquisition for M. grandis.}, }
@article {pmid31309868, year = {2019}, author = {Pantoja-Feliciano, IG and Soares, JW and Doherty, LA and Karl, JP and McClung, HL and Armstrong, NJ and Branck, TA and Arcidiacono, S}, title = {Acute stressor alters inter-species microbial competition for resistant starch-supplemented medium.}, journal = {Gut microbes}, volume = {10}, number = {4}, pages = {439-446}, doi = {10.1080/19490976.2018.1554962}, pmid = {31309868}, issn = {1949-0984}, abstract = {Gut microbiome community dynamics are maintained by complex microbe-microbe and microbe-host interactions, which can be disturbed by stress. In vivo studies on the dynamics and manipulation of those interactions are costly and slow, but can be accelerated using in vitro fermentation. Herein, in vitro fermentation was used to determine how an acute stressor, a sudden change in diet, impacts inter-bacterial species competition for resistant starch-supplemented medium (RSM). Fermentation vessels were seeded with fecal samples collected from 10 individuals consuming a habitual diet or U.S. military rations for 21 days. Lactobacillus spp. growth in response to RSM was attenuated following ration consumption, whereas growth of Ruminococcus bromii was enhanced. These differences were not evident in the pre-fermentation samples. Findings demonstrate how incorporating in vitro fermentation into clinical studies can increase understanding of stress-induced changes in nutrient-microbiome dynamics, and suggest that sudden changes in diet may impact inter-species competition for substrates.}, }
@article {pmid31304521, year = {2019}, author = {Migliara, G and Di Paolo, C and Barbato, D and Baccolini, V and Salerno, C and Nardi, A and Alessandri, F and Giordano, A and Tufi, D and Marinelli, L and Cottarelli, A and De Giusti, M and Marzuillo, C and De Vito, C and Antonelli, G and Venditti, M and Tellan, G and Ranieri, MV and Villari, P}, title = {Multimodal surveillance of healthcare associated infections in an intensive care unit of a large teaching hospital.}, journal = {Annali di igiene : medicina preventiva e di comunita}, volume = {31}, number = {5}, pages = {399-413}, doi = {10.7416/ai.2019.2302}, pmid = {31304521}, issn = {1120-9135}, abstract = {BACKGROUND: Healthcare-associated infections (HAIs), or nosocomial infections, represent a significant burden in terms of mortality, morbidity, length of stay and costs for patients hospitalized in intensive care units (ICUs). Surveillance systems are recommended by national and international institutions to gather data on HAIs in order to develop and evaluate interventions that reduce the risk of HAIs.<br><br>STUDY DESIGN: ere we describe the methodology and the results of the surveillance system implemented in the ICU of the Policlinico Umberto I, a large teaching hospital in Rome, from April 2016 to October 2018.<br><br>METHODS: The multimodal infection surveillance system integrates four different approaches: i) active surveillance of inpatients; ii) environmental microbiological surveillance; iii) surveillance of isolated microorganisms; and iv) behavioral surveillance of healthcare personnel. Data were collected on catheter-related bloodstream infections, ventilation-associated pneumonia, catheter-associated urinary tract infections and primary bloodstream infections that developed in patients after 48 h in the ICU. For environmental surveillance 14 points were selected for sampling (i.e. bed edges, medication carts, PC keyboards, sink faucets). The system of active surveillance of HAIs also included surveillance of microorganisms, consisting of the molecular genotyping of bacterial isolates by pulsed-field gel electrophoresis (PFGE). From 1 November 2016, monitoring of compliance with guidelines for hand hygiene (HH) and proper glove or gown use by healthcare personnel was included in the surveillance system. After the first six months (baseline phase), a multimodal intervention to improve adherence to guidelines by healthcare personnel was conducted with the ICU staff.<br><br>RESULTS: Overall, 773 patients were included in the active surveillance. The overall incidence rate of device-related HAIs was 14.1 (95% CI: 12.2-16.3) per 1000 patient-days. The monthly device-related HAI incident rate showed a decreasing trend over time, with peaks of incidence becoming progressively lower. The most common bacterial isolates were Klebsiella pneumoniae (20.7%), Acinetobacter baumannii (17.2%), Pseudomonas aeruginosa (13.4%) and Staphylococcus aureus (5.4%). Acinetobacter baumannii and Klebsiella pneumoniae showed the highest proportion of isolates with a multidrug-resistant profile. A total of 819 environmental samples were collected, from which 305 bacterial isolates were retrieved. The most frequent bacterial isolates were Acinetobacter baumannii (27.2%), Staphylococcus aureus (12.1%), Enterococcus faecalis (11.1%), Klebsiella pneumoniae (5.2%) and Pseudomonas aeruginosa (4.7%). All Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae environmental isolates were at least multidrug-resistant. Genotyping showed a limited number of major PFGE patterns for both clinical and environmental isolates of Klebsiella pneumoniae and Acinetobacter baumannii. Behavioral compliance rates significantly improved from baseline to post-intervention phase.<br><br>CONCLUSIONS: By integrating information gathered from active surveillance, environmental microbiological surveillance, surveillance of bacterial isolates and behavioral surveillance of healthcare personnel, the multimodal infection surveillance system returned a precise and detailed view of the infectious risk and microbial ecology of the ICU.}, }
@article {pmid31303186, year = {2019}, author = {Garcia-Mazcorro, JF and Ishaq, SL and Rodriguez-Herrera, MV and Garcia-Hernandez, CA and Kawas, JR and Nagaraja, TG}, title = {Review: Are there indigenous Saccharomyces in the digestive tract of livestock animal species? Implications for health, nutrition and productivity traits.}, journal = {Animal : an international journal of animal bioscience}, volume = {}, number = {}, pages = {1-9}, doi = {10.1017/S1751731119001599}, pmid = {31303186}, issn = {1751-732X}, abstract = {All livestock animal species harbour complex microbial communities throughout their digestive tract that support vital biochemical processes, thus sustaining health and productivity. In part as a consequence of the strong and ancient alliance between the host and its associated microbes, the gut microbiota is also closely related to productivity traits such as feed efficiency. This phenomenon can help researchers and producers develop new and more effective microbiome-based interventions using probiotics, also known as direct-fed microbials (DFMs), in Animal Science. Here, we focus on one type of such beneficial microorganisms, the yeast Saccharomyces. Saccharomyces is one of the most widely used microorganisms as a DFM in livestock operations. Numerous studies have investigated the effects of dietary supplementation with different species, strains and doses of Saccharomyces (mostly Saccharomyces cerevisiae) on gut microbial ecology, health, nutrition and productivity traits of several livestock species. However, the possible existence of Saccharomyces which are indigenous to the animals' digestive tract has received little attention and has never been the subject of a review. We for the first time provide a comprehensive review, with the objective of shedding light into the possible existence of indigenous Saccharomyces of the digestive tract of livestock. Saccharomyces cerevisiae is a nomadic yeast able to survive in a broad range of environments including soil, grass and silages. Therefore, it is very likely that cattle and other animals have been in direct contact with this and other types of Saccharomyces throughout their entire existence. However, to date, the majority of animal scientists seem to agree that the presence of Saccharomyces in any section of the gut only reflects dietary contamination; in other words, these are foreign organisms that are only transiently present in the gut. Importantly, this belief (i.e. that Saccharomyces come solely from the diet) is often not well grounded and does not necessarily hold for all the many other groups of microbes in the gut. In addition to summarizing the current body of literature involving Saccharomyces in the digestive tract, we discuss whether the beneficial effects associated with the consumption of Saccharomyces may be related to its foreign origin, though this concept may not necessarily satisfy the theories that have been proposed to explain probiotic efficacy in vivo. This novel review may prove useful for biomedical scientists and others wishing to improve health and productivity using Saccharomyces and other beneficial microorganisms.}, }
@article {pmid31303107, year = {2019}, author = {Houldcroft, CJ and Rifkin, RF and Underdown, SJ}, title = {Human biology and ancient DNA: exploring disease, domestication and movement.}, journal = {Annals of human biology}, volume = {46}, number = {2}, pages = {95-98}, doi = {10.1080/03014460.2019.1629536}, pmid = {31303107}, issn = {1464-5033}, }
@article {pmid31300838, year = {2019}, author = {White, JA and Styer, A and Rosenwald, LC and Curry, MM and Welch, KD and Athey, KJ and Chapman, EG}, title = {Endosymbiotic Bacteria Are Prevalent and Diverse in Agricultural Spiders.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01411-w}, pmid = {31300838}, issn = {1432-184X}, support = {0224651//U.S. Department of Agriculture/ ; 148-502-16-377//Kentucky Science and Engineering Foundation/ ; 148-502-10-261//Kentucky Science and Engineering Foundation/ ; }, abstract = {Maternally inherited bacterial endosymbionts are common in arthropods, but their distribution and prevalence are poorly characterized in many host taxa. Initial surveys have suggested that vertically transmitted symbionts may be particularly common in spiders (Araneae). Here, we used diagnostic PCR and high-throughput sequencing to evaluate symbiont infection in 267 individual spiders representing 14 species (3 families) of agricultural spiders. We found 27 operational taxonomic units (OTUs) that are likely endosymbiotic, including multiple strains of Wolbachia, Rickettsia, and Cardinium, which are all vertically transmitted and frequently associated with reproductive manipulation of arthropod hosts. Additional strains included Rickettsiella, Spiroplasma, Rhabdochlamydia, and a novel Rickettsiales, all of which could range from pathogenic to mutualistic in their effects upon their hosts. Seventy percent of spider species had individuals that tested positive for one or more endosymbiotic OTUs, and specimens frequently contained multiple symbiotic strain types. The most symbiont-rich species, Idionella rugosa, had eight endosymbiotic OTUs, with as many as five present in the same specimen. Individual specimens within infected spider species had a variety of symbiotypes, differing from one another in the presence or absence of symbiotic strains. Our sample included both starved and unstarved specimens, and dominant bacterial OTUs were consistent per host species, regardless of feeding status. We conclude that spiders contain a remarkably diverse symbiotic microbiota. Spiders would be an informative group for investigating endosymbiont population dynamics in time and space, and unstarved specimens collected for other purposes (e.g., food web studies) could be used, with caution, for such investigations.}, }
@article {pmid31299565, year = {2019}, author = {Mahon, BM and Brehony, C and Cahill, N and McGrath, E and O'Connor, L and Varley, A and Cormican, M and Ryan, S and Hickey, P and Keane, S and Mulligan, M and Ruane, B and Jolley, KA and Maiden, MC and Brisse, S and Morris, D}, title = {Detection of OXA-48-like-producing Enterobacterales in Irish recreational water.}, journal = {The Science of the total environment}, volume = {690}, number = {}, pages = {1-6}, doi = {10.1016/j.scitotenv.2019.06.480}, pmid = {31299565}, issn = {1879-1026}, abstract = {The rapid dissemination of carbapenemase-producing Enterobacterales (CPE) is a major public health concern. The role that the aquatic environment plays in this dissemination is underexplored. This study aimed to examine seawater as a reservoir for CPE. Seawater sampling took place at a bathing site throughout the 2017 bathing season. Each 30 L sample (n = 6) was filtered using the CapE filtration system. Wastewater samples (200 mL) (pre-treatment (n = 3) and post-treatment (n = 3)) were obtained from a nearby secondary wastewater treatment plant, during the same time period. All samples were examined for CPE. Whole genome sequencing of confirmed CPE was carried out using Illumina sequencing. Isolate genomes were hosted in corresponding BIGSdb databases and analyses were performed using multiple web-based tools. CPE was detected in 2/6 seawater samples. It was not detected in any wastewater samples. OXA-48-like-producing ST131 Escherichia coli (Ec_BM707) was isolated from a seawater sample collected in May 2017 and OXA-48-like-producing ST101 Klebsiella pneumoniae (Kp_BM758) was isolated from a seawater sample collected in August 2017. The genomes of the environmental isolates were compared to a collection of previously described Irish clinical OXA-48-like-producing Enterobacterales (n = 105). Ec_BM707 and Kp_BM758 harboured blaOXA-48 on similar mobile genetic elements to those identified in the clinical collection (pOXA-48 fragment in Ec_BM707 and IncL(pOXA-48) plasmid in Kp_BM758). Genetic similarities were observed between Ec_BM707 and several of the clinical ST131 E. coli, with allele matches at up to 98.2% of 2513 core genome multilocus sequence type (cgMLST) loci. In contrast, Kp_BM758 and the 34 clinical K. pneumoniae were genetically distant. The source of the CPE at this site was not identified. The detection of OXA-48-like-producing ST131 E. coli and OXA-48-like-producing ST101 K. pneumoniae in Irish recreational water is a concern. The potential for contamination of the aquatic environment to contribute to dissemination of CPE in Europe warrants further study.}, }
@article {pmid31299167, year = {2019}, author = {Mayali, X}, title = {NanoSIMS: Microscale Quantification of Biogeochemical Activity with Large-Scale Impacts.}, journal = {Annual review of marine science}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-marine-010419-010714}, pmid = {31299167}, issn = {1941-0611}, abstract = {One major objective of aquatic microbial ecology is to understand the distribution of microbial populations over space and time and in response to environmental factors. Perhaps more importantly, it is crucial to quantify how those microbial cells affect biogeochemical processes of interest, such as primary production, nitrogen cycling, or the breakdown of pollutants. One valuable approach to link microbial identity to activity is to carry out incubations with stable-isotope-labeled substrates and then quantify the isotope incorporation by individual microbial cells using nanoscale secondary ion mass spectrometry (NanoSIMS). This review summarizes recent efforts in this field, highlights novel methods, describes studies investigating rare metabolisms as well as widespread microbial activity, and hopes to provide a framework to increase the use and capabilities of NanoSIMS for microbial biogeochemical studies in the future. Expected final online publication date for the Annual Review of Marine Science Volume 12 is January 3, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid31299137, year = {2019}, author = {Pjevac, P and Dyksma, S and Goldhammer, T and Mujakić, I and Koblížek, M and Mußmann, M and Amann, R and Orlić, S}, title = {In situ abundance and carbon fixation activity of distinct anoxygenic phototrophs in the stratified seawater lake Rogoznica.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14739}, pmid = {31299137}, issn = {1462-2920}, support = {//Croatian Science Foundation/ ; }, abstract = {Sulphide-driven anoxygenic photosynthesis is an ancient microbial metabolism that contributes significantly to inorganic carbon fixation in stratified, sulphidic water bodies. Methods commonly applied to quantify inorganic carbon fixation by anoxygenic phototrophs, however, cannot resolve the contributions of distinct microbial populations to the overall process. We implemented a straightforward workflow, consisting of radioisotope labelling and flow cytometric cell sorting based on the distinct autofluorescence of bacterial photopigments, to discriminate and quantify contributions of co-occurring anoxygenic phototrophic populations to in situ inorganic carbon fixation in environmental samples. This allowed us to assign 89.3% ± 7.6% of daytime inorganic carbon fixation by anoxygenic phototrophs in Lake Rogoznica (Croatia) to an abundant chemocline-dwelling population of green sulphur bacteria (dominated by Chlorobium phaeobacteroides), whereas the co-occurring purple sulphur bacteria (Halochromatium sp.) contributed only 1.8% ± 1.4%. Furthermore, we obtained two metagenome assembled genomes of green sulphur bacteria and one of a purple sulphur bacterium which provides the first genomic insights into the genus Halochromatium, confirming its high metabolic flexibility and physiological potential for mixo- and heterotrophic growth.}, }
@article {pmid31297747, year = {2019}, author = {Costa, FS and Macedo, MWFS and Araújo, ACM and Rodrigues, CA and Kuramae, EE and de Barros Alcanfor, SK and Pessoa-Filho, M and Barreto, CC}, title = {Assessing nickel tolerance of bacteria isolated from serpentine soils.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {50}, number = {3}, pages = {705-713}, doi = {10.1007/s42770-019-00111-4}, pmid = {31297747}, issn = {1678-4405}, abstract = {Serpentine soils present unique characteristics such as a low Ca/Mg ratio, low concentration of nutrients, and a high concentration of heavy metals, especially nickel. Soil bacterial isolates from an ultramafic complex located in the tropical savanna known as the Brazilian Cerrado were studied. Nickel-tolerant bacteria were obtained, and their ability to remove nickel from a culture medium was assessed. Bacterial isolates presented higher tolerance to nickel salts than previously reported for bacteria obtained from serpentine environments in other regions of the world. In addition, the quantification of nickel in cell pellets indicated that at least four isolates may adsorb soluble forms of nickel. It is expected that information gathered in this study will support future efforts to exploit serpentine soil bacteria for biotechnological processes involving nickel decontamination from environmental samples.}, }
@article {pmid31296406, year = {2019}, author = {Lajoie, G and Kembel, SW}, title = {Making the Most of Trait-Based Approaches for Microbial Ecology.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2019.06.003}, pmid = {31296406}, issn = {1878-4380}, abstract = {There is an increasing interest in applying trait-based approaches to microbial ecology, but the question of how and why to do it is still lagging behind. By anchoring our discussion of these questions in a framework derived from epistemology, we broaden the scope of trait-based approaches to microbial ecology from one oriented mostly around explanation towards one inclusive of the predictive and integrative potential of these approaches. We use case studies from macro-organismal ecology to concretely show how these goals for knowledge development can be fulfilled and propose clear directions, adapted to the biological reality of microbes, to make the most of recent advancements in the measurement of microbial phenotypes and traits.}, }
@article {pmid31295324, year = {2019}, author = {Defoirdt, T}, title = {Amino acid-derived quorum sensing molecules controlling the virulence of vibrios (and beyond).}, journal = {PLoS pathogens}, volume = {15}, number = {7}, pages = {e1007815}, doi = {10.1371/journal.ppat.1007815}, pmid = {31295324}, issn = {1553-7374}, }
@article {pmid31294971, year = {2019}, author = {Han, P and Yu, Y and Zhou, L and Tian, Z and Li, Z and Hou, L and Liu, M and Wu, Q and Wagner, M and Men, Y}, title = {Specific Micropollutant Biotransformation Pattern by the Comammox Bacterium Nitrospira inopinata.}, journal = {Environmental science &amp; technology}, volume = {53}, number = {15}, pages = {8695-8705}, doi = {10.1021/acs.est.9b01037}, pmid = {31294971}, issn = {1520-5851}, abstract = {The recently discovered complete ammonia-oxidizing (comammox) bacteria occur in various environments, including wastewater treatment plants. To better understand their role in micropollutant biotransformation in comparison with ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), we investigated the biotransformation capability of Nitrospira inopinata (the only comammox isolate) for 17 micropollutants. Asulam, fenhexamid, mianserin, and ranitidine were biotransformed by N. inopinata, Nitrososphaera gargensis (AOA), and Nitrosomonas nitrosa Nm90 (AOB). More distinctively, carbendazim, a benzimidazole fungicide, was exclusively biotransformed by N. inopinata. The biotransformation of carbendazim only occurred when N. inopinata was supplied with ammonia but not nitrite as the energy source. The exclusive biotransformation of carbendazim by N. inopinata was likely enabled by an enhanced substrate promiscuity of its unique AMO and its much higher substrate (for ammonia) affinity compared with the other two ammonia oxidizers. One major plausible transformation product (TP) of carbendazim is a hydroxylated form at the aromatic ring, which is consistent with the function of AMO. These findings provide fundamental knowledge on the micropollutant degradation potential of a comammox bacterium to better understand the fate of micropollutants in nitrifying environments.}, }
@article {pmid31293665, year = {2019}, author = {Martín-Sánchez, L and Singh, KS and Avalos, M and van Wezel, GP and Dickschat, JS and Garbeva, P}, title = {Phylogenomic analyses and distribution of terpene synthases among Streptomyces.}, journal = {Beilstein journal of organic chemistry}, volume = {15}, number = {}, pages = {1181-1193}, doi = {10.3762/bjoc.15.115}, pmid = {31293665}, issn = {1860-5397}, abstract = {Terpene synthases are widely distributed among microorganisms and have been mainly studied in members of the genus Streptomyces. However, little is known about the distribution and evolution of the genes for terpene synthases. Here, we performed whole-genome based phylogenetic analysis of Streptomyces species, and compared the distribution of terpene synthase genes among them. Overall, our study revealed that ten major types of terpene synthases are present within the genus Streptomyces, namely those for geosmin, 2-methylisoborneol, epi-isozizaene, 7-epi-α-eudesmol, epi-cubenol, caryolan-1-ol, cyclooctat-9-en-7-ol, isoafricanol, pentalenene and α-amorphene. The Streptomyces species divide in three phylogenetic groups based on their whole genomes for which the distribution of the ten terpene synthases was analysed. Geosmin synthases were the most widely distributed and were found to be evolutionary positively selected. Other terpene synthases were found to be specific for one of the three clades or a subclade within the genus Streptomyces. A phylogenetic analysis of the most widely distributed classes of Streptomyces terpene synthases in comparison to the phylogenomic analysis of this genus is discussed.}, }
@article {pmid31292537, year = {2019}, author = {Salcher, MM and Schaefle, D and Kaspar, M and Neuenschwander, SM and Ghai, R}, title = {Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0471-3}, pmid = {31292537}, issn = {1751-7370}, support = {19-23469S//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 17-04828S//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 310030E-160603/1//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 310030_185108//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, abstract = {The most abundant aquatic microbes are small in cell and genome size. Genome-streamlining theory predicts gene loss caused by evolutionary selection driven by environmental factors, favouring superior competitors for limiting resources. However, evolutionary histories of such abundant, genome-streamlined microbes remain largely unknown. Here we reconstruct the series of steps in the evolution of some of the most abundant genome-streamlined microbes in freshwaters (&quot;Ca. Methylopumilus&quot;) and oceans (marine lineage OM43). A broad genomic spectrum is visible in the family Methylophilaceae (Betaproteobacteria), from sediment microbes with medium-sized genomes (2-3 Mbp genome size), an occasionally blooming pelagic intermediate (1.7 Mbp), and the most reduced pelagic forms (1.3 Mbp). We show that a habitat transition from freshwater sediment to the relatively oligotrophic pelagial was accompanied by progressive gene loss and adaptive gains. Gene loss has mainly affected functions not necessarily required or advantageous in the pelagial or is encoded by redundant pathways. Likewise, we identified genes providing adaptations to oligotrophic conditions that have been transmitted horizontally from pelagic freshwater microbes. Remarkably, the secondary transition from the pelagial of lakes to the oceans required only slight modifications, i.e., adaptations to higher salinity, gained via horizontal gene transfer from indigenous microbes. Our study provides first genomic evidence of genome reduction taking place during habitat transitions. In this regard, the family Methylophilaceae is an exceptional model for tracing the evolutionary history of genome streamlining as such a collection of evolutionarily related microbes from different habitats is rare in the microbial world.}, }
@article {pmid31292259, year = {2019}, author = {Chuang, JS and Frentz, Z and Leibler, S}, title = {Homeorhesis and ecological succession quantified in synthetic microbial ecosystems.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {30}, pages = {14852-14861}, doi = {10.1073/pnas.1901055116}, pmid = {31292259}, issn = {1091-6490}, abstract = {The dynamics of ecological change following a major perturbation, known as succession, are influenced by random processes. Direct quantitation of the degree of contingency in succession requires chronological study of replicate ecosystems. We previously found that population dynamics in carefully controlled, replicated synthetic microbial ecosystems were strongly deterministic over several months. Here, we present simplified, two-species microbial ecosystems consisting of algae and ciliates, imaged in toto at single-cell resolution with fluorescence microscopy over a period of 1 to 2 weeks. To directly study succession in these ecosystems, we deliberately varied the initial cell abundances over replicates and quantified the ensuing dynamics. The distribution of abundance trajectories rapidly converged to a nearly deterministic path, with small fluctuations, despite variations in initial conditions, environmental perturbations, and intrinsic noise, indicative of homeorhesis. Homeorhesis was also observed for certain phenotypic variables, such as partitioning of the ciliates into distinct size classes and clumping of the algae. Although the mechanism of homeorhesis observed in these synthetic ecosystems remains to be elucidated, it is clear that it must emerge from the ways each species controls its own internal states, with respect to a diverse set of environmental conditions and ecological interactions.}, }
@article {pmid31292233, year = {2019}, author = {Moeller, AH and Gomes-Neto, JC and Mantz, S and Kittana, H and Segura Munoz, RR and Schmaltz, RJ and Ramer-Tait, AE and Nachman, MW}, title = {Experimental Evidence for Adaptation to Species-Specific Gut Microbiota in House Mice.}, journal = {mSphere}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSphere.00387-19}, pmid = {31292233}, issn = {2379-5042}, support = {R01 GM074245/GM/NIGMS NIH HHS/United States ; R01 GM127468/GM/NIGMS NIH HHS/United States ; }, abstract = {The gut microbial communities of mammals have codiversified with host species, and changes in the gut microbiota can have profound effects on host fitness. Therefore, the gut microbiota may drive adaptation in mammalian species, but this possibility is underexplored. Here, we show that the gut microbiota has codiversified with mice in the genus Mus over the past ∼6 million years, and we present experimental evidence that the gut microbiota has driven adaptive evolution of the house mouse, Mus musculusdomesticus Phylogenetic analyses of metagenome-assembled bacterial genomic sequences revealed that gut bacterial lineages have been retained within and diversified alongside Mus species over evolutionary time. Transplantation of gut microbiotas from various Mus species into germfree M. m. domesticus showed that foreign gut microbiotas slowed growth rate and upregulated macrophage inflammatory protein in hosts. These results suggest adaptation by M. m. domesticus to its gut microbiota since it diverged from other Mus species.IMPORTANCE The communities of bacteria that reside within mammalian guts are deeply integrated with their hosts, but the impact of this gut microbiota on mammalian evolution remains poorly understood. Experimental transplantation of the gut microbiota between mouse species revealed that foreign gut microbiotas lowered the host growth rate and upregulated the expression of an immunomodulating cytokine. In addition, foreign gut microbiotas increased host liver sizes and attenuated sex-specific differences in host muscle and fat content. These results suggest that the house mouse has adapted to its species-specific gut microbiota.}, }
@article {pmid31289346, year = {2019}, author = {Schmidt, R and Ulanova, D and Wick, LY and Bode, HB and Garbeva, P}, title = {Microbe-driven chemical ecology: past, present and future.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0469-x}, pmid = {31289346}, issn = {1751-7370}, abstract = {In recent years, research in the field of Microbial Ecology has revealed the tremendous diversity and complexity of microbial communities across different ecosystems. Microbes play a major role in ecosystem functioning and contribute to the health and fitness of higher organisms. Scientists are now facing many technological and methodological challenges in analyzing these complex natural microbial communities. The advances in analytical and omics techniques have shown that microbial communities are largely shaped by chemical interaction networks mediated by specialized (water-soluble and volatile) metabolites. However, studies concerning microbial chemical interactions need to consider biotic and abiotic factors on multidimensional levels, which require the development of new tools and approaches mimicking natural microbial habitats. In this review, we describe environmental factors affecting the production and transport of specialized metabolites. We evaluate their ecological functions and discuss approaches to address future challenges in microbial chemical ecology (MCE). We aim to emphasize that future developments in the field of MCE will need to include holistic studies involving organisms at all levels and to consider mechanisms underlying the interactions between viruses, micro-, and macro-organisms in their natural environments.}, }
@article {pmid31289280, year = {2019}, author = {De Tender, C and Mesuere, B and Van der Jeugt, F and Haegeman, A and Ruttink, T and Vandecasteele, B and Dawyndt, P and Debode, J and Kuramae, EE}, title = {Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9890}, doi = {10.1038/s41598-019-46106-x}, pmid = {31289280}, issn = {2045-2322}, abstract = {Chitin is a valuable peat substrate amendment by increasing lettuce growth and reducing the survival of the zoonotic pathogen Salmonella enterica on lettuce leaves. The production of chitin-catabolic enzymes (chitinases) play a crucial role and are mediated through the microbial community. A higher abundance of plant-growth promoting microorganisms and genera involved in N and chitin metabolism are present in a chitin-enriched substrate. In this study, we hypothesize that chitin addition to peat substrate stimulates the microbial chitinase production. The degradation of chitin leads to nutrient release and the production of small chitin oligomers that are related to plant growth promotion and activation of the plant's defense response. First a shotgun metagenomics approach was used to decipher the potential rhizosphere microbial functions then the nutritional content of the peat substrate was measured. Our results show that chitin addition increases chitin-catabolic enzymes, bacterial ammonium oxidizing and siderophore genes. Lettuce growth promotion can be explained by a cascade degradation of chitin to N-acetylglucosamine and eventually ammonium. The occurrence of increased ammonium oxidizing bacteria, Nitrosospira, and amoA genes results in an elevated concentration of plant-available nitrate. In addition, the increase in chitinase and siderophore genes may have stimulated the plant's systemic resistance.}, }
@article {pmid31286860, year = {2019}, author = {Meola, M and Rifa, E and Shani, N and Delbès, C and Berthoud, H and Chassard, C}, title = {DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {560}, doi = {10.1186/s12864-019-5914-8}, pmid = {31286860}, issn = {1471-2164}, abstract = {BACKGROUND: Reads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation of 16S reads, particularly at species rank, is still challenging due to the short size of read sequences and differently curated classification databases. The close phylogenetic relationship between species encountered in dairy products, however, makes it crucial to annotate species accurately to achieve sufficient phylogenetic resolution for further downstream ecological studies or for food diagnostics. Curated databases dedicated to the environment of interest are expected to improve the accuracy and resolution of taxonomy annotation.<br><br>RESULTS: We provide a manually curated database composed of 10'290 full-length 16S rRNA gene sequences from prokaryotes tailored for dairy products analysis (https://github.com/marcomeola/DAIRYdb). The performance of the DAIRYdb was compared with the universal databases Silva, LTP, RDP and Greengenes. The DAIRYdb significantly outperformed all other databases independently of the classification algorithm by enabling higher accurate taxonomy annotation down to the species rank. The DAIRYdb accurately annotates over 90% of the sequences of either single or paired hypervariable regions automatically. The manually curated DAIRYdb strongly improves taxonomic annotation accuracy for microbiome studies in dairy environments. The DAIRYdb is a practical solution that enables automatization of this key step, thus facilitating the routine application of NGS microbiome analyses for microbial ecology studies and diagnostics in dairy products.}, }
@article {pmid31286170, year = {2019}, author = {Puentes-Téllez, PE and Salles, JF}, title = {Dynamics of Abundant and Rare Bacteria During Degradation of Lignocellulose from Sugarcane Biomass.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01403-w}, pmid = {31286170}, issn = {1432-184X}, support = {729004006//FAPESP-NWO/ ; }, abstract = {Microorganisms play a crucial role in lignocellulosic degradation. Many enriched microbial communities have demonstrated to reach functional and structural stability with effective degrading capacities of industrial interest. These microbial communities are typically composed by only few dominant species and a high number of usually overlooked rare species. Here, we used two sources of lignocellulose (sugarcane bagasse and straw) in order to obtain lignocellulose-degrading bacteria through an enriched process, followed the selective trajectory of both abundant and rare bacterial communities by 16S rRNA gene amplification and analyzed the outcomes of selection in terms of capacities and specialization. We verified the importance of pre-selection by using two sources of microbial inoculum: soil samples from a sugarcane field with history of straw addition (St15) and control samples, from the same field, without amendments (St0). We found similitudes in terms of stabilization between the abundant and rare fractions. We also found positive correlations of both abundant and rare taxa (like Caulobacteraceae and Alcaligenaceae) and the degradation of lignocellulosic fractions. Differences in the inocula's initial diversity rapidly decreased during the enrichment resulting in comparable richness levels at the end of the process; however, the legacy of the St15 inoculum and its specialization positively influenced the degradation capacities of the community. Analysis of specialization of the final communities revealed increased straw degradation capacity in the communities enriched in bagasse, which could be potentially used as a strategy for improving lignocellulose waste degradation on the sugarcane fields. This work highlights the importance of including the rare fraction of bacterial communities during investigations involving the screening and assessment of effective degrading communities.}, }
@article {pmid31286169, year = {2019}, author = {Cutler, NA and Arróniz-Crespo, M and Street, LE and Jones, DL and Chaput, DL and DeLuca, TH}, title = {Correction to: Long-Term Recovery of Microbial Communities in the Boreal Bryosphere Following Fire Disturbance.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01408-5}, pmid = {31286169}, issn = {1432-184X}, abstract = {The original version of this article contained an error in the Molecular Analysis subsection of the Methods.}, }
@article {pmid31285347, year = {2019}, author = {Johnston, ER and Hatt, JK and He, Z and Wu, L and Guo, X and Luo, Y and Schuur, EAG and Tiedje, JM and Zhou, J and Konstantinidis, KT}, title = {Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {30}, pages = {15096-15105}, doi = {10.1073/pnas.1901307116}, pmid = {31285347}, issn = {1091-6490}, abstract = {Northern-latitude tundra soils harbor substantial carbon (C) stocks that are highly susceptible to microbial degradation with rising global temperatures. Understanding the magnitude and direction (e.g., C release or sequestration) of the microbial responses to warming is necessary to accurately model climate change. In this study, Alaskan tundra soils were subjected to experimental in situ warming by ∼1.1 °C above ambient temperature, and the microbial communities were evaluated using metagenomics after 4.5 years, at 2 depths: 15 to 25 cm (active layer at outset of the experiment) and 45 to 55 cm (transition zone at the permafrost/active layer boundary at the outset of the experiment). In contrast to small or insignificant shifts after 1.5 years of warming, 4.5 years of warming resulted in significant changes to the abundances of functional traits and the corresponding taxa relative to control plots (no warming), and microbial shifts differed qualitatively between the two soil depths. At 15 to 25 cm, increased abundances of carbohydrate utilization genes were observed that correlated with (increased) measured ecosystem carbon respiration. At the 45- to 55-cm layer, increased methanogenesis potential was observed, which corresponded with a 3-fold increase in abundance of a single archaeal clade of the Methanosarcinales order, increased annual thaw duration (45.3 vs. 79.3 days), and increased CH4 emissions. Collectively, these data demonstrate that the microbial responses to warming in tundra soil are rapid and markedly different between the 2 critical soil layers evaluated, and identify potential biomarkers for the corresponding microbial processes that could be important in modeling.}, }
@article {pmid31285337, year = {2019}, author = {Greenlon, A and Chang, PL and Damtew, ZM and Muleta, A and Carrasquilla-Garcia, N and Kim, D and Nguyen, HP and Suryawanshi, V and Krieg, CP and Yadav, SK and Patel, JS and Mukherjee, A and Udupa, S and Benjelloun, I and Thami-Alami, I and Yasin, M and Patil, B and Singh, S and Sarma, BK and von Wettberg, EJB and Kahraman, A and Bukun, B and Assefa, F and Tesfaye, K and Fikre, A and Cook, DR}, title = {Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {30}, pages = {15200-15209}, doi = {10.1073/pnas.1900056116}, pmid = {31285337}, issn = {1091-6490}, abstract = {Although microorganisms are known to dominate Earth's biospheres and drive biogeochemical cycling, little is known about the geographic distributions of microbial populations or the environmental factors that pattern those distributions. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea, generating 1,027 draft whole-genome sequences at the level of bacterial populations, including 14 high-quality PacBio genomes from a phylogenetically representative subset. We find that diverse Mesorhizobium taxa perform symbiosis with chickpea and have largely overlapping global distributions. However, sampled locations cluster based on the phylogenetic diversity of Mesorhizobium populations, and diversity clusters correspond to edaphic and environmental factors, primarily soil type and latitude. Despite long-standing evolutionary divergence and geographic isolation, the diverse taxa observed to nodulate chickpea share a set of integrative conjugative elements (ICEs) that encode the major functions of the symbiosis. This symbiosis ICE takes 2 forms in the bacterial chromosome-tripartite and monopartite-with tripartite ICEs confined to a broadly distributed superspecies clade. The pairwise evolutionary relatedness of these elements is controlled as much by geographic distance as by the evolutionary relatedness of the background genome. In contrast, diversity in the broader gene content of Mesorhizobium genomes follows a tight linear relationship with core genome phylogenetic distance, with little detectable effect of geography. These results illustrate how geography and demography can operate differentially on the evolution of bacterial genomes and offer useful insights for the development of improved technologies for sustainable agriculture.}, }
@article {pmid31285190, year = {2019}, author = {Wörner, S and Pester, M}, title = {Microbial Succession of Anaerobic Chitin Degradation in Freshwater Sediments.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {18}, pages = {}, doi = {10.1128/AEM.00963-19}, pmid = {31285190}, issn = {1098-5336}, abstract = {Chitin is massively produced by freshwater plankton species as a structural element of their exoskeleton or cell wall. At the same time, chitin does not accumulate in the predominantly anoxic sediments, underlining its importance as carbon and nitrogen sources for sedimentary microorganisms. We studied chitin degradation in littoral sediment of Lake Constance, Central Europe's third largest lake. Turnover of the chitin analog methyl-umbelliferyl-N,N-diacetylchitobioside (MUF-DC) was highest in the upper oxic sediment layer, with 5.4 nmol MUF-DC h-1 (g sediment [dry weight])-1 In the underlying anoxic sediment layers, chitin hydrolysis decreased with depth from 1.1 to 0.08 nmol MUF-DC h-1 (g sediment [dry weight])-1 Bacteria involved in chitin degradation were identified by 16S rRNA (gene) amplicon sequencing of anoxic microcosms incubated in the presence of chitin compared to microcosms amended either with N-acetylglucosamine as the monomer of chitin or no substrate. Chitin degradation was driven by a succession of bacteria responding specifically to chitin only. The early phase (0 to 9 days) was dominated by Chitinivibrio spp. (Fibrobacteres). The intermediate phase (9 to 21 days) was characterized by a higher diversity of chitin responders, including, besides Chitinivibrio spp., also members of the phyla Bacteroidetes, Proteobacteria, Spirochaetes, and Chloroflexi In the late phase (21 to 43 days), the Chitinivibrio populations broke down with a parallel strong increase of Ruminiclostridium spp. (formerly Clostridium cluster III, Firmicutes), which became the dominating chitin responders. Our study provides quantitative insights into anaerobic chitin degradation in lake sediments and linked this to a model of microbial succession associated with this activity.IMPORTANCE Chitin is the most abundant biopolymer in aquatic environments, with a direct impact on the carbon and nitrogen cycles. Despite its massive production as a structural element of crustaceans, insects, or algae, it does not accumulate in sediments. Little is known about its turnover in predominantly anoxic freshwater sediments and the responsible microorganisms. We proved that chitin is readily degraded under anoxic conditions and linked this to a succession of the members of the responsible microbial community over a 43-day period. While Fibrobacteres and Firmicutes members were driving the early and late phases of chitin degradation, respectively, a more diverse community was involved in chitin degradation in the intermediate phase. Entirely different microorganisms responded toward the chitin monomer N-acetylglucosamine, which underscores that soluble monomers are poor and misleading substrates to study polymer-utilizing microorganisms. Our study provides quantitative insights into the microbial ecology driving anaerobic chitin degradation in freshwater sediments.}, }
@article {pmid31284214, year = {2019}, author = {Lorenz, C and Roscher, L and Meyer, MS and Hildebrandt, L and Prume, J and Löder, MGJ and Primpke, S and Gerdts, G}, title = {Spatial distribution of microplastics in sediments and surface waters of the southern North Sea.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {252}, number = {Pt B}, pages = {1719-1729}, doi = {10.1016/j.envpol.2019.06.093}, pmid = {31284214}, issn = {1873-6424}, abstract = {Microplastic pollution within the marine environment is of pressing concern globally. Accordingly, spatial monitoring of microplastic concentrations, composition and size distribution may help to identify sources and entry pathways, and hence allow initiating focused mitigation. Spatial distribution patterns of microplastics were investigated in two compartments of the southern North Sea by collecting sublittoral sediment and surface water samples from 24 stations. Large microplastics (500-5000 μm) were detected visually and identified using attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy. The remaining sample was digested enzymatically, concentrated onto filters and analyzed for small microplastics (11-500 μm) using Focal Plane Array (FPA) FTIR imaging. Microplastics were detected in all samples with concentrations ranging between 2.8 and 1188.8 particles kg-1 for sediments and 0.1-245.4 particles m-3 for surface waters. On average 98% of microplastics were <100 μm in sediments and 86% in surface waters. The most prevalent polymer types in both compartments were polypropylene, acrylates/polyurethane/varnish, and polyamide. However, polymer composition differed significantly between sediment and surface water samples as well as between the Frisian Islands and the English Channel sites. These results show that microplastics are not evenly distributed, in neither location nor size, which is illuminating regarding the development of monitoring protocols.}, }
@article {pmid31283892, year = {2019}, author = {Philip, N and Leishman, SJ and Bandara, HMHN and Healey, DL and Walsh, LJ}, title = {Randomized Controlled Study to Evaluate Microbial Ecological Effects of CPP-ACP and Cranberry on Dental Plaque.}, journal = {JDR clinical and translational research}, volume = {}, number = {}, pages = {2380084419859871}, doi = {10.1177/2380084419859871}, pmid = {31283892}, issn = {2380-0852}, abstract = {INTRODUCTION: Ecological approaches to dental caries prevention play a key role in attaining long-term control over the disease and maintaining a symbiotic oral microbiome.<br><br>OBJECTIVES: This study aimed to investigate the microbial ecological effects of 2 interventional dentifrices: a casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) dentifrice and the same dentifrice supplemented with a polyphenol-rich cranberry extract.<br><br>METHODS: The interventional toothpastes were compared with each other and with an active control fluoride dentifrice in a double-blinded randomized controlled trial. Real-time quantitative polymerase chain reaction (qPCR) analysis was used to determine changes in the bacterial loads of 14 key bacterial species (8 caries associated and 6 health associated) in the dental plaque of trial participants after they used the dentifrices for 5 to 6 wk.<br><br>RESULTS: From the baseline to the recall visit, significant differences were observed between the treatment groups in the bacterial loads of 2 caries-associated bacterial species (Streptococcus mutans [P < 0.001] and Veillonella parvula [P < 0.001]) and 3 health-associated bacterial species (Corynebacterium durum [P = 0.008], Neisseria flavescens [P = 0.005], and Streptococcus sanguinis [P < 0.001]). Compared to the fluoride control dentifrice, the CPP-ACP dentifrice demonstrated significant differences for S. mutans (P = 0.032), C. durum (P = 0.007), and S. sanguinis (P < 0.001), while combination CPP-ACP-cranberry dentifrice showed significant differences for S. mutans (P < 0.001), V. parvula (P < 0.001), N. flavescens (P = 0.003), and S. sanguinis (P < 0.001). However, no significant differences were observed in the bacterial load comparisons between the CPP-ACP and combination dentifrices for any of the targeted bacterial species (P > 0.05).<br><br>CONCLUSIONS: Overall, the results indicate that dentifrices containing CPP-ACP and polyphenol-rich cranberry extracts can influence a species-level shift in the ecology of the oral microbiome, resulting in a microbial community less associated with dental caries (Australian New Zealand Clinical Trial Registry ANZCTR 12618000095268).<br><br>KNOWLEDGE TRANSFER STATEMENT: The results of this randomized controlled trial indicate that dentifrices containing casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) and polyphenol-rich cranberry extracts were able to beneficially modulate the microbial ecology of dental plaque in a group of high caries-risk patients. This could contribute toward lowering the risk of developing new caries lesions, an important goal sought by patients, clinicians, and policy makers.}, }
@article {pmid31280333, year = {2019}, author = {Ghosh, A and Bhadury, P}, title = {Vibrio chemaguriensis sp. nov., from Sundarbans, Bay of Bengal.}, journal = {Current microbiology}, volume = {76}, number = {10}, pages = {1118-1127}, doi = {10.1007/s00284-019-01731-7}, pmid = {31280333}, issn = {1432-0991}, abstract = {A new species of Vibrio (annotated as SBOTS_Iso1) was isolated in August 2014 from the Stn1 located in Chemaguri creek of Sundarbans mangrove ecoregion and taxonomically characterized using a polyphasic approach. Phenotypic analysis including biochemical tests and growth across a wide range of salinities indicated the typical estuarine characteristics of this new species. The bacterium was Gram negative, rod-shaped, oxidase and catalase negative and grows in the presence of NaCl. FAME analysis indicated 31.7% of the cellular fatty acids to be made up of 16:1 ω7c/16:1 ω6c. Amplification and sequencing of 16S rRNA and multilocus sequence analysis of four loci (2040 bp; rpoA, topA, mreB, pyrH) and additional sequence data of ftsZ, atpD, ompW and rpoB genes showed this isolate to be a member of Harveyi clade of the genus Vibrio. The closest phylogenetic neighbour was Vibrio alginolyticus ATCC 17749T with 96.8% similarity. Whole-genome sequence data indicates the presence of ~ 5 Mbp genome. GGDC, orthoANIu and AAI indicated 45%, 92% and 0.962 identity respectively with genome of Vibrio alginolyticus ATCC 17749T. The isolate SBOTS_Iso1 has been named Vibrio chemaguriensis sp. nov. on the name of the site from where it was first isolated.}, }
@article {pmid31280331, year = {2019}, author = {Chen, H and Li, C and Liu, T and Chen, S and Xiao, H}, title = {A Metagenomic Study of Intestinal Microbial Diversity in Relation to Feeding Habits of Surface and Cave-Dwelling Sinocyclocheilus Species.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01409-4}, pmid = {31280331}, issn = {1432-184X}, support = {31560111//National Natural Science Foundation of China/ ; }, abstract = {Light is completely absent in cave habitats, causing a shortage or lack of autochthonous photosynthesis. Thus, understanding the mechanisms underlying the ability of organisms to adapt to the unique cave habitat is of great interest. We used high-throughput sequencing of the 16S ribosomal RNA gene of intestinal microorganisms from 11 Sinocyclocheilus (Cypriniformes: Cyprinidae) species, to explore the characteristics of intestinal microorganisms and the adaptive mechanisms of Sinocyclocheilus cavefish and surface fish. We found that the α-diversity and richness of the intestinal microbiome were much higher in cavefish than in surface fish. Principal coordinate analysis showed that cavefish and surface fish formed three clusters because of different dominant gut microorganisms which are generated by different habitats. Based on PICRUSt-predicted functions, harmful substance degradation pathways were much more common in cavefish intestinal microorganisms than in those from surface fish. The intestinal microbiota of surface fish group 1 had a higher capacity for carbohydrate metabolism, whereas protein and amino acid metabolism and digestive pathways were more abundant in microorganisms from the cavefish group and surface fish group 2. Combined analysis of the intestinal microbial composition and functional predictions further revealed the structures and functions of intestinal microbial communities in Sinocyclocheilus cave and surface species. Moreover, based on their habits and intestinal microbial composition and intestinal microbial functional predictions, we inferred that the three fish groups were all omnivorous; however, surface fish group 1 preferred feeding on plants, while surface fish group 2 and cavefish preferred meat. This study improves our understanding of mechanisms of adaptation in cave habitats and may contribute to the protection of these habitats from water pollution.}, }
@article {pmid31279253, year = {2019}, author = {Gros, M and Marti, E and Balcázar, JL and Boy-Roura, M and Busquets, A and Colón, J and Sànchez-Melsió, A and Lekunberri, I and Borrego, CM and Ponsá, S and Petrovic, M}, title = {Fate of pharmaceuticals and antibiotic resistance genes in a full-scale on-farm livestock waste treatment plant.}, journal = {Journal of hazardous materials}, volume = {378}, number = {}, pages = {120716}, doi = {10.1016/j.jhazmat.2019.05.109}, pmid = {31279253}, issn = {1873-3336}, abstract = {This study investigated, for the first time, the distribution and fate of 28 multiple-class veterinary pharmaceuticals and antibiotics (PhACs), and their corresponding antibiotic resistance genes (ARGs), in a full-scale on-farm livestock waste treatment plant. The plant relies on several technologies, including: anaerobic digestion (AD), solid-liquid separation, and two stages reverse osmosis (RO) of the liquid digestate. Tetracycline, fluoroquinolone, lincosamide and pleuromutilin antibiotics, together with anti-helmintic (flubendazole) and anti-inflammatory (flunixin) drugs were the most frequently detected compounds in livestock waste and in slaughterhouse sludge. This last fraction is used as co-substrate in the AD process and showed to be an important input source of PhACs and ARGs. In terms of treatment performance, AD exhibited moderate to low PhACs and ARGs reduction, while a large fraction (<50%) of the PhACs present in the digestate were distributed onto the solid fraction, after solid-liquid separation. Both solid and liquid digestates had relatively high copy numbers of ARGs. Finally, RO showed high rejection percentages for all PhACs (<90%), with concentrations in the low ng L-1 range in permeates, for most target PhACs. Nevertheless, moderate copy numbers of ARGs were detected in permeates.}, }
@article {pmid31275291, year = {2019}, author = {Lukumbuzya, M and Schmid, M and Pjevac, P and Daims, H}, title = {A Multicolor Fluorescence in situ Hybridization Approach Using an Extended Set of Fluorophores to Visualize Microorganisms.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1383}, doi = {10.3389/fmicb.2019.01383}, pmid = {31275291}, issn = {1664-302X}, abstract = {Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes is a key method for the detection of (uncultured) microorganisms in environmental and medical samples. A major limitation of standard FISH protocols, however, is the small number of phylogenetically distinct target organisms that can be detected simultaneously. In this study, we introduce a multicolor FISH approach that uses eight fluorophores with distinct spectral properties, which can unambiguously be distinguished by confocal laser scanning microscopy combined with white light laser technology. Hybridization of rRNA-targeted DNA oligonucleotide probes, which were mono-labeled with these fluorophores, to Escherichia coli cultures confirmed that the fluorophores did not affect probe melting behavior. Application of the new multicolor FISH method enabled the differentiation of seven (potentially up to eight) phylogenetically distinct microbial populations in an artificial community of mixed pure cultures (five bacteria, one archaeon, and one yeast strain) and in activated sludge from a full-scale wastewater treatment plant. In contrast to previously published multicolor FISH approaches, this method does not rely on combinatorial labeling of the same microorganisms with different fluorophores, which is prone to biases. Furthermore, images acquired by this method do not require elaborate post-processing prior to analysis. We also demonstrate that the newly developed multicolor FISH method is compatible with an improved cell fixation protocol for FISH targeting Gram-negative bacterial populations. This fixation approach uses agarose embedding during formaldehyde fixation to better preserve the three-dimensional structure of spatially complex samples such as biofilms and activated sludge flocs. The new multicolor FISH approach should be highly suitable for studying structural and functional aspects of microbial communities in virtually all types of samples that can be analyzed by conventional FISH methods.}, }
@article {pmid31273405, year = {2019}, author = {Kerfahi, D and Ogwu, MC and Ariunzaya, D and Balt, A and Davaasuren, D and Enkhmandal, O and Purevsuren, T and Batbaatar, A and Tibbett, M and Undrakhbold, S and Boldgiv, B and Adams, JM}, title = {Metal-Tolerant Fungal Communities Are Delineated by High Zinc, Lead, and Copper Concentrations in Metalliferous Gobi Desert Soils.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01405-8}, pmid = {31273405}, issn = {1432-184X}, support = {NRF 2013-031400//National Research Foundation/ ; }, abstract = {The soil fungal ecology of the southern Gobi region of Mongolia has been little studied. We utilized the ITS1 region from soil DNA to study possible influences soil metal concentrations on soil fungal community variation. In the sample network, a distinctive fungal community was closely associated with high zinc (Zn), lead (Pb), and copper (Cu) concentrations. The pattern of occurrence suggests that high metal concentrations are natural and not a product of mining activities. The metal-associated fungal community differs little from the &quot;normal&quot; community in its major OTUs, and in terms of major fungal guilds and taxa, and its distinctiveness depends on a combination of many less common OTUs. The fungal community in the sites with high metal concentrations is no less diverse than that in areas with normal background levels. Overall, these findings raise interesting questions of the evolutionary origin and functional characteristics of this apparently &quot;metal-tolerant&quot; community, and of the associated soil biota in general. It is possible that rehabilitation of metal-contaminated mined soils from spoil heaps could benefit from the incorporation of fungi derived from these areas.}, }
@article {pmid31272871, year = {2019}, author = {Pant, A and Das, B and Bhadra, RK}, title = {CTX phage of Vibrio cholerae: Genomics and applications.}, journal = {Vaccine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.vaccine.2019.06.034}, pmid = {31272871}, issn = {1873-2518}, abstract = {The bipartite genome of Vibrio cholerae is divided into two circular non-homologous chromosomes, which harbor several genetic elements like phages, plasmids, transposons, integrative conjugative elements, and pathogenic islands that encode functions responsible for disease development, antimicrobial resistance, and subsistence in hostile environments. These elements are highly heterogeneous, mobile in nature, and encode their own mobility functions or exploit host-encoded enzymes for intra- and inter-cellular movements. The key toxin of V. cholerae responsible for the life-threatening diarrheal disease cholera, the cholera toxin, is coded by part of the genome of a filamentous phage, CTXϕ. The replicative genome of CTXϕ is divided into two distinct modular structures and has adopted a unique strategy for its irreversible integration into the V. cholerae chromosomes. CTXϕ exploits two host-encoded tyrosine recombinases, XerC and XerD, for its integration in the highly conserved dimer resolution site (dif) of V. cholerae chromosomes. CTXϕ can replicate only in the limited number of Vibrio species. In contrast, the phage integration into the bacterial chromosome does not rely on its replication and could integrate to the dif site of large numbers of gram-negative bacteria. Recent pangenomic analysis revealed that like CTXϕ, the bacterial dif site is the integration spot for several other mobile genetic elements such as plasmids and genomic islands. In this review we discuss about current molecular insights into CTXϕ genomics and its replication and integration mechanisms into hosts. Particular emphasis has been given on the exploitation of CTXϕ genomics knowledge in developing genetic tools and designing environmentally safe recombinant live oral cholera vaccine strains.}, }
@article {pmid31272870, year = {2019}, author = {Das, B and Verma, J and Kumar, P and Ghosh, A and Ramamurthy, T}, title = {Antibiotic resistance in Vibrio cholerae: Understanding the ecology of resistance genes and mechanisms.}, journal = {Vaccine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.vaccine.2019.06.031}, pmid = {31272870}, issn = {1873-2518}, abstract = {The unique genetic makeup and remarkable competency of Vibrio cholerae are the key factors that help the cholera pathogen adapt rapidly to adverse environmental conditions and resist the detrimental effect of antimicrobial agents. In the last few decades, V. cholerae that causes acute watery diarrhoeal disease cholera has emerged as a notorious multidrug resistant (MDR) enteric pathogen. Although chromosomal mutations can contribute to antimicrobial resistance (AMR), the frequent acquisition of extrachromosomal mobile genetic elements (MGEs) from closely/distantly related bacterial species are major players in V. cholerae drug resistance. Whole genome sequence analysis of clinical and environmental V. cholerae strains revealed that the genome of most of the recent isolates harbour integrating conjugative elements (ICEs), plasmids, superintegron, transposable elements and insertion sequences, which are the key carriers of genetic traits encoding antimicrobial resistance function. Different antimicrobial resistance genes identified in V. cholerae can contribute in antibiotic resistance by facilitating one of the following three mechanisms; (i) reduced permeability or active efflux of the antibiotics, (ii) alteration of the antibiotic targets by introducing post-transcriptional/translational modifications and (iii) hydrolysis or chemical modification of antibiotics. Here, we present an overview of the present insights on the emergence and mechanisms of AMR in V. cholerae.}, }
@article {pmid31271506, year = {2019}, author = {Moeller, FU and Webster, NS and Herbold, CW and Behnam, F and Domman, D and Albertsen, M and Mooshammer, M and Markert, S and Turaev, D and Becher, D and Rattei, T and Schweder, T and Richter, A and Watzka, M and Nielsen, PH and Wagner, M}, title = {Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14732}, pmid = {31271506}, issn = {1462-2920}, support = {FP7-PEOPLE-2010-ITM Symbiomics//Marie Curie Initial Training Networks/ ; Research grants 15510; 16578//VILLUM FONDEN/ ; Advanced Grant project NITRICARE 294343//European Research Council/International ; //Marie Curie/ ; }, abstract = {Marine sponges represent one of the few eukaryotic groups that frequently harbour symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. However, in most studies, direct demonstration of ammonia-oxidation by these archaea within sponges is lacking, and little is known about sponge-specific adaptations of ammonia-oxidizing archaea (AOA). Here, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and isotope-based functional assays. 'Candidatus Nitrosospongia ianthellae' is only distantly related to cultured AOA. It is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbour nitrite-oxidizing microbes. Furthermore, this AOA is equipped with an expanded set of extracellular subtilisin-like proteases, a metalloprotease unique among archaea, as well as a putative branched-chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge-associated, but not in free-living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic-like proteins, and a DNA-phosporothioation system, represent important adaptations of AOA to life within these ancient filter-feeding animals.}, }
@article {pmid31271413, year = {2019}, author = {Dann, LM and Clanahan, M and Paterson, JS and Mitchell, JG}, title = {Distinct niche partitioning of marine and freshwater microbes during colonisation.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {8}, pages = {}, doi = {10.1093/femsec/fiz098}, pmid = {31271413}, issn = {1574-6941}, abstract = {Bacteria are ubiquitous on the Earth, and many use chemotaxis to colonise favourable microenvironments. The colonisation process is continuous, where animals, plants, protists, viruses and chemical and physical factors frequently remove bacteria from wide volume ranges. Colonisation processes are poorly understood in natural communities. Here, we investigated niche partitioning during colonisation in aquatic microbial communities using bands of bacterial chemotaxis in petri dishes from mixed-species communities. The community partitioned into loiterers, primary and secondary colonisers, each having distinct abundances and taxonomy. Within marine samples, Shewanella dominated the primary colonisers, whilst Enterobacteriaceae dominated this group within the freshwater samples. Whether the success of these specific groups translates to what occurs within natural communities is uncertain, but here we show these taxa have the capacity to colonise new, unexplored environments. A strong negative association existed between the primary colonisers and viral abundance, suggesting that successful colonisers simultaneously move toward areas of heightened resources, which correlated with lower virus-like particles. Here, we show that microbial communities constantly sort themselves into distinct taxonomic groups as they move into new environments. This sorting during colonisation may be fundamental to microbial ecology, industry, technology, and disease development by setting the initial conditions that determine the winners as a community develops.}, }
@article {pmid31267158, year = {2019}, author = {Stirling, E and Macdonald, LM and Smernik, RJ and Cavagnaro, TR}, title = {Soil Microbial Community Responses After Amendment with Thermally Altered Pinus radiata Needles.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01402-x}, pmid = {31267158}, issn = {1432-184X}, abstract = {Post-fire litter layers are composed of leaves and woody debris that predominantly fall during or soon after the fire event. These layers are distinctly different to pre-fire litters due to their common origin and deposition time. However, heterogeneity can arise from the variable thermal conditions in the canopy during fire. Therefore, in this study, we used thermally altered pine needles (heated to 40 °C, 150 °C, 260 °C and 320 °C for 1 h) in a laboratory incubation study for 43 days. These samples were measured for respiration throughout and extracted for DNA at the experiment's end; soil ribosomal RNA was analysed using Illumina sequencing (16S and internal transcribed spacer amplicons). The addition of pine needles heated to 40 °C or 150 °C caused a substantial shift in community structure, decreased alpha diversity and significantly increased soil respiration relative to the control treatment. In contrast, pine needles heated to 260 °C or 320 °C had little effect on microbial community structure or soil respiration. These results indicate that highly thermally altered needles are not microbially decomposed during the first 43 days of exposure and therefore that biomass temperature may have significant effects on post-fire litter decomposition and carbon flux. This research outlines an important knowledge gap in forest fire responses that may affect post-fire carbon emission estimates.}, }
@article {pmid31267157, year = {2019}, author = {Ou, L and Qin, X and Shi, X and Feng, Q and Zhang, S and Lu, S and Qi, Y}, title = {Alkaline phosphatase activities and regulation in three harmful Prorocentrum species from the coastal waters of the East China Sea.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01399-3}, pmid = {31267157}, issn = {1432-184X}, support = {41776121, 41176087, 41466001//National Natural Science Foundation of China/ ; }, abstract = {Harmful blooms of Prorocentrum donghaiense occur annually in the phosphorus-scarce coastal waters of the East China Sea (ECS). The enzymatic activities of alkaline phosphatase (AP) and its regulation by external phosphorus were studied during a P. donghaiense bloom in this area. The AP characteristics of P. donghaiense was further compared with Prorocentrum minimum and Prorocentrum micans in monocultures with both bulk and single-cell enzyme-labeled fluorescence AP assays. Concentrations of dissolved inorganic phosphorus (DIP) varied between 0.04 and 0.73 μmol l-1, with more than half recording stations registering concentrations below 0.10 μmol l-1. Concentrations of dissolved organic phosphorus (DOP) were comparable or even higher than those of DIP. P. donghaiense suffered phosphorus stress and expressed abundant AP, especially when DIP was lower than 0.10 μmol l-1. The AP activities showed a negative correlation with DIP but a positive correlation with DOP. The AP activities were also regulated by internal phosphorus pool. The sharp increase in AP activities was observed until cellular phosphorus was exhausted. Most AP of P. donghaiense was located on the cell surface and some were released into the water with time. Compared with P. minimum and P. micans, P. donghaiense showed a higher AP affinity for organic phosphorus substrates, a more efficient and energy-saving AP expression quantity as a response to phosphorus deficiency. The unique AP characteristic of P. donghaiense suggests that it benefits from the efficient utilization of DOP, and outcompete other species in the phosphorus-scarce ECS.}, }
@article {pmid31266970, year = {2019}, author = {Grunert, O and Robles-Aguilar, AA and Hernandez-Sanabria, E and Schrey, SD and Reheul, D and Van Labeke, MC and Vlaeminck, SE and Vandekerckhove, TGL and Mysara, M and Monsieurs, P and Temperton, VM and Boon, N and Jablonowski, ND}, title = {Tomato plants rather than fertilizers drive microbial community structure in horticultural growing media.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9561}, doi = {10.1038/s41598-019-45290-0}, pmid = {31266970}, issn = {2045-2322}, support = {603744//EC | EC Seventh Framework Programm | FP7 Environment (FP7-ENVIRONMENT - Specific Programme &amp;quot;Cooperation&amp;quot;: Environment (Including Climate Change))/ ; BioDisko 031B0406C//Bundesministerium f&amp;#x00FC;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; }, abstract = {Synthetic fertilizer production is associated with a high environmental footprint, as compounds typically dissolve rapidly leaching emissions to the atmosphere or surface waters. We tested two recovered nutrients with slower release patterns, as promising alternatives for synthetic fertilizers: struvite and a commercially available organic fertilizer. Using these fertilizers as nitrogen source, we conducted a rhizotron experiment to test their effect on plant performance and nutrient recovery in juvenile tomato plants. Plant performance was significantly improved when organic fertilizer was provided, promoting higher shoot biomass. Since the microbial community influences plant nitrogen availability, we characterized the root-associated microbial community structure and functionality. Analyses revealed distinct root microbial community structure when different fertilizers were supplied. However, plant presence significantly increased the similarity of the microbial community over time, regardless of fertilization. Additionally, the presence of the plant significantly reduced the potential ammonia oxidation rates, implying a possible role of the rhizosheath microbiome or nitrification inhibition by the plant. Our results indicate that nitrifying community members are impacted by the type of fertilizer used, while tomato plants influenced the potential ammonia-oxidizing activity of nitrogen-related rhizospheric microbial communities. These novel insights on interactions between recovered fertilizers, plant and associated microbes can contribute to develop sustainable crop production systems.}, }
@article {pmid31266879, year = {2019}, author = {Sze, MA and Topçuoğlu, BD and Lesniak, NA and Ruffin, MT and Schloss, PD}, title = {Fecal Short-Chain Fatty Acids Are Not Predictive of Colonic Tumor Status and Cannot Be Predicted Based on Bacterial Community Structure.}, journal = {mBio}, volume = {10}, number = {4}, pages = {}, doi = {10.1128/mBio.01454-19}, pmid = {31266879}, issn = {2150-7511}, support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; R01 CA215574/CA/NCI NIH HHS/United States ; UL1 TR002240/TR/NCATS NIH HHS/United States ; }, abstract = {Colonic bacterial populations are thought to have a role in the development of colorectal cancer with some protecting against inflammation and others exacerbating inflammation. Short-chain fatty acids (SCFAs) have been shown to have anti-inflammatory properties and are produced in large quantities by colonic bacteria that produce SCFAs by fermenting fiber. We assessed whether there was an association between fecal SCFA concentrations and the presence of colonic adenomas or carcinomas in a cohort of individuals using 16S rRNA gene and metagenomic shotgun sequence data. We measured the fecal concentrations of acetate, propionate, and butyrate within the cohort and found that there were no significant associations between SCFA concentration and tumor status. When we incorporated these concentrations into random forest classification models trained to differentiate between people with healthy colons and those with adenomas or carcinomas, we found that they did not significantly improve the ability of 16S rRNA gene or metagenomic gene sequence-based models to classify individuals. Finally, we generated random forest regression models trained to predict the concentration of each SCFA based on 16S rRNA gene or metagenomic gene sequence data from the same samples. These models performed poorly and were able to explain at most 14% of the observed variation in the SCFA concentrations. These results support the broader epidemiological data that questions the value of fiber consumption for reducing the risks of colorectal cancer. Although other bacterial metabolites may serve as biomarkers to detect adenomas or carcinomas, fecal SCFA concentrations have limited predictive power.IMPORTANCE Considering that colorectal cancer is the third leading cancer-related cause of death within the United States, it is important to detect colorectal tumors early and to prevent the formation of tumors. Short-chain fatty acids (SCFAs) are often used as a surrogate for measuring gut health and for being anticarcinogenic because of their anti-inflammatory properties. We evaluated the fecal SCFA concentrations of a cohort of individuals with different colonic tumor burdens who were previously analyzed to identify microbiome-based biomarkers of tumors. We were unable to find an association between SCFA concentration and tumor burden or use SCFAs to improve our microbiome-based models of classifying people based on their tumor status. Furthermore, we were unable to find an association between the fecal community structure and SCFA concentrations. Our results indicate that the association between fecal SCFAs, the gut microbiome, and tumor burden is weak.}, }
@article {pmid31265069, year = {2019}, author = {de Boer, W and Li, X and Meisner, A and Garbeva, P}, title = {Pathogen suppression by microbial volatile organic compounds in soils.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {8}, pages = {}, doi = {10.1093/femsec/fiz105}, pmid = {31265069}, issn = {1574-6941}, abstract = {There is increasing evidence that microbial volatile organic compounds (mVOCs) play an important role in interactions between microbes in soils. In this minireview, we zoom in on the possible role of mVOCs in the suppression of plant-pathogenic soil fungi. In particular, we have screened the literature to see what the actual evidence is that mVOCs in soil atmospheres can contribute to pathogen suppression. Furthermore, we discuss biotic and abiotic factors that influence the production of suppressive mVOCs in soils. Since microbes producing mVOCs in soils are part of microbial communities, community ecological aspects such as diversity and assembly play an important role in the composition of produced mVOC blends. These aspects have not received much attention so far. In addition, the fluctuating abiotic conditions in soils, such as changing moisture contents, influence mVOC production and activity. The biotic and abiotic complexity of the soil environment hampers the extrapolation of the production and suppressing activity of mVOCs by microbial isolates on artificial growth media. Yet, several pathogen suppressive mVOCs produced by pure cultures do also occur in soil atmospheres. Therefore, an integration of lab and field studies on the production of mVOCs is needed to understand and predict the composition and dynamics of mVOCs in soil atmospheres. This knowledge, together with the knowledge of the chemistry and physical behaviour of mVOCs in soils, forms the basis for the development of sustainable management strategies to enhance the natural control of soil-borne pathogens with mVOCs. Possibilities for the mVOC-based control of soil-borne pathogens are discussed.}, }
@article {pmid31263981, year = {2019}, author = {Yi, Y and Wang, H and Chen, Y and Gou, M and Xia, Z and Hu, B and Nie, Y and Tang, Y}, title = {Identification of Novel Butyrate- and Acetate-Oxidizing Bacteria in Butyrate-Fed Mesophilic Anaerobic Chemostats by DNA-Based Stable Isotope Probing.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01400-z}, pmid = {31263981}, issn = {1432-184X}, support = {2016YFE0127700//Ministry of Science and Technology of the People's Republic of China/ ; 51678378//National Natural Science Foundation of China/ ; 31200068//National Natural Science Foundation of China/ ; }, abstract = {Butyrate is one of the most important intermediates during anaerobic digestion of protein wastewater, and its oxidization is considered as a rate-limiting step during methane production. However, information on syntrophic butyrate-oxidizing bacteria (SBOB) is limited due to the difficulty in isolation of pure cultures. In this study, two anaerobic chemostats fed with butyrate as the sole carbon source were operated at different dilution rates (0.01/day and 0.05/day). Butyrate- and acetate-oxidizing bacteria in both chemostats were investigated, combining DNA-Stable Isotope Probing (DNA-SIP) and 16S rRNA gene high-throughput sequencing. The results showed that, in addition to known SBOB, Syntrophomonas, other species of unclassified Syntrophomonadaceae were putative butyrate-oxidizing bacteria. Species of Mesotoga, Aminivibrio, Acetivibrio, Desulfovibrio, Petrimonas, Sedimentibacter, unclassified Anaerolineae, unclassified Synergistaceae, unclassified Spirochaetaceae, and unclassified bacteria may contribute to acetate oxidation from butyrate metabolism. Among them, the ability of butyrate oxidation was unclear for species of Sedimentibacter, unclassified Synergistaceae, unclassified Spirochaetaceae, and unclassified bacteria. These results suggested that more unknown species participated in the degradation of butyrate. However, the corresponding function and pathway for butyrate or acetate oxidization of these labeled species need to be further investigated.}, }
@article {pmid31263456, year = {2019}, author = {Song, HS and Lee, JY and Haruta, S and Nelson, WC and Lee, DY and Lindemann, SR and Fredrickson, JK and Bernstein, HC}, title = {Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1264}, doi = {10.3389/fmicb.2019.01264}, pmid = {31263456}, issn = {1664-302X}, abstract = {An intriguing aspect in microbial communities is that pairwise interactions can be influenced by neighboring species. This creates context dependencies for microbial interactions that are based on the functional composition of the community. Context dependent interactions are ecologically important and clearly present in nature, yet firmly established theoretical methods are lacking from many modern computational investigations. Here, we propose a novel network inference method that enables predictions for interspecies interactions affected by shifts in community composition and species populations. Our approach first identifies interspecies interactions in binary communities, which is subsequently used as a basis to infer modulation in more complex multi-species communities based on the assumption that microbes minimize adjustments of pairwise interactions in response to neighbor species. We termed this rule-based inference minimal interspecies interaction adjustment (MIIA). Our critical assessment of MIIA has produced reliable predictions of shifting interspecies interactions that are dependent on the functional role of neighbor organisms. We also show how MIIA has been applied to a microbial community composed of competing soil bacteria to elucidate a new finding that - in many cases - adding fewer competitors could impose more significant impact on binary interactions. The ability to predict membership-dependent community behavior is expected to help deepen our understanding of how microbiomes are organized in nature and how they may be designed and/or controlled in the future.}, }
@article {pmid31257772, year = {2019}, author = {Hu, K and Tao, JP and He, DN and Huang, K and Wang, W}, title = {[Effects of root growth on dynamics of microbes and enzyme activities during litter decomposition.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {30}, number = {6}, pages = {1993-2001}, doi = {10.13287/j.1001-9332.201906.022}, pmid = {31257772}, issn = {1001-9332}, mesh = {Bacteria ; Biomass ; Ecosystem ; *Forests ; *Microbiota ; Plant Leaves ; Plant Roots/*growth &amp; development ; *Soil Microbiology ; }, abstract = {To understand the influence of roots of understory plant entering litter layer on litter decomposition in forest ecosystems, we examined the effects of different treatments of Lolium multiflorum root biomass on microorganisms and enzyme activities during leaf litter decomposition of Symplocos setchuensis, a dominant species in a mid-subtropical evergreen broad-leaved forest, through a litter bag simulation experiment. Results showed that diversity index of bacterial and fungal communities of leaf litter surface under three treatments, i.e. no root (N), less roots (L), more roots (M), in a 240-day decomposition process showed the following pattern: M > L > N. The effects of these different root biomass treatments on the composition and quantity of fungal community were more significant than those on bacterial community. The biomass of living roots growing in the litter bag gradually decreased at the end of the growing season of L. multiflorum. The impacts of root growth on the composition of the fungal community gradually decreased during decomposition. At the same decomposition stage, the activities of acid phosphatase, β-glucosidase, polyphenol oxidase, and peroxidase on the litter surface were higher in the treatments with roots than that without roots. These results indicated that root growth could change the composition and quantity of microbial communities and increase the extracellular enzyme activities of microbes, and thus stimulating litter decomposition.}, }
@article {pmid31253856, year = {2019}, author = {Carr, A and Diener, C and Baliga, NS and Gibbons, SM}, title = {Use and abuse of correlation analyses in microbial ecology.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0459-z}, pmid = {31253856}, issn = {1751-7370}, support = {Distinguished Investigator Award//Washington Research Foundation (WRF)/ ; Distinguished Investigator Award//Washington Research Foundation (WRF)/ ; Distinguished Investigator Award//Washington Research Foundation (WRF)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; OCE - 1558924//National Science Foundation (NSF)/ ; CBET - 1606206//National Science Foundation (NSF)/ ; MCB - 1518261//National Science Foundation (NSF)/ ; DBI-1565166//National Science Foundation (NSF)/ ; MCB-1616955//National Science Foundation (NSF)/ ; }, abstract = {Correlation analyses are often included in bioinformatic pipelines as methods for inferring taxon-taxon interactions. In this perspective, we highlight the pitfalls of inferring interactions from covariance and suggest methods, study design considerations, and additional data types for improving high-throughput interaction inferences. We conclude that correlation, even when augmented by other data types, almost never provides reliable information on direct biotic interactions in real-world ecosystems. These bioinformatically inferred associations are useful for reducing the number of potential hypotheses that we might test, but will never preclude the necessity for experimental validation.}, }
@article {pmid31252032, year = {2019}, author = {Callewaert, C and Nakatsuji, T and Knight, R and Kosciolek, T and Vrbanac, A and Kotol, P and Ardeleanu, M and Hultsch, T and Guttman-Yassky, E and Bissonnette, R and Silverberg, JI and Krueger, J and Menter, A and Graham, NMH and Pirozzi, G and Hamilton, JD and Gallo, RL}, title = {IL-4Rα Blockade by Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Atopic Dermatitis.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2019.05.024}, pmid = {31252032}, issn = {1523-1747}, abstract = {Dupilumab is a fully human antibody to interleukin-4 receptor alpha that improves the signs and symptoms of moderate-to-severe atopic dermatitis. To determine the effects of dupilumab on Staphylococcus aureus colonization and microbial diversity on the skin, bacterial DNA was analyzed from swabs collected from lesional and nonlesional skin in a double-blind, placebo-controlled study of 54 patients with moderate-to-severe atopic dermatitis randomized (1:1) and treated with either dupilumab (200 mg weekly) or placebo for 16 weeks. Microbial diversity and relative abundance of Staphylococcus were assessed by DNA sequencing of 16S rRNA, and absolute S. aureus abundance was measured by quantitative PCR. Before treatment, lesional skin had lower microbial diversity and higher overall abundance of S. aureus than nonlesional skin. During dupilumab treatment, microbial diversity increased and the abundance of S. aureus decreased. Pronounced changes were seen in nonlesional and lesional skin. Decreased S. aureus abundance during dupilumab treatment correlated with clinical improvement of atopic dermatitis and biomarkers of type 2 immunity. We conclude that clinical improvement of atopic dermatitis that is mediated by interleukin-4 receptor alpha inhibition and the subsequent suppression of type 2 inflammation is correlated with increased microbial diversity and reduced abundance of S. aureus. ClinicalTrials.gov identifier: NCT01979016.}, }
@article {pmid31250077, year = {2019}, author = {Goss-Souza, D and Mendes, LW and Rodrigues, JLM and Tsai, SM}, title = {Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01401-y}, pmid = {31250077}, issn = {1432-184X}, support = {2008/58114-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2014/50320-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 140317/2014-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; 311008/2016-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Forest-to-agriculture conversion has been identified as a major threat to soil biodiversity and soil processes resilience, although the consequences of long-term land use change to microbial community assembly and ecological processes have been often neglected. Here, we combined metagenomic approach with a large environmental dataset, to (i) identify the microbial assembly patterns and, (ii) to evaluate the ecological processes governing microbial assembly, in bulk soil and soybean rhizosphere, along a long-term forest-to-agriculture conversion chronosequence, in Eastern Amazon. We hypothesized that (i) microbial communities in bulk soil and rhizosphere have different assembly patterns and (ii) the weight of the four ecological processes governing assembly differs between bulk soil and rhizosphere and along the chronosequence in the same fraction. Community assembly in bulk soil fitted most the zero-sum multinomial (ZSM) neutral-based model, regardless of time. Low to intermediate dispersal was observed. Decreasing influence of abiotic factors was counterbalanced by increasing influence of biotic factors, as the chronosequence advanced. Undominated ecological processes of dispersal limitation and variable selection governing community assembly were observed in this soil fraction. For soybean rhizosphere, community assembly fitted most the lognormal niche-based model in all chronosequence areas. High dispersal and an increasing influence of abiotic factors coupled with a decreasing influence of biotic factors were found along the chronosequence. Thus, we found a dominant role of dispersal process governing microbial assembly with a secondary effect of homogeneous selection process, mainly driven by decreasing aluminum and increased cations saturation in soil solution, due to long-term no-till cropping. Together, our results indicate that long-term no-till lead community abundances in bulk soil to be in a transient and conditional state, while for soybean rhizosphere, community abundances reach a periodic and permanent distribution state. Dominant dispersal process in rhizosphere, coupled with homogeneous selection, brings evidences that soybean root system selects microbial taxa via trade-offs in order to keep functional resilience of soil processes.}, }
@article {pmid31250076, year = {2019}, author = {Jeong, SY and Lee, CH and Yi, T and Kim, TG}, title = {Effects of Quorum Quenching on Biofilm Metacommunity in a Membrane Bioreactor.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01397-5}, pmid = {31250076}, issn = {1432-184X}, support = {2018R1D1A1B07048872//Ministry of Education/ ; }, abstract = {Quorum quenching (QQ) has received attention for the control of biofilms, e.g., biofilms that cause biofouling in membrane bioreactors (MBRs). Despite the efficacy of QQ on biofouling, it is elusive how QQ influences biofilm formation on membranes. A pilot-scale QQ-MBR and non-QQ-MBR were identically operated for 4 days and 8 days to destructively sample the membranes. QQ prolonged the membrane filterability by 43% with no harmful influence on MBR performance. qPCR showed no effect of QQ on microbial density during either of these time periods. Community comparisons revealed that QQ influenced the bacterial and fungal community structures, and the fungal structure corresponded with the bacterial structure. Metacommunity and spatial analyses showed that QQ induced structural variation rather than compositional variation of bacteria and fungi. Moreover, QQ considerably enhanced the bacterial dispersal across membrane during the early development. As the dispersal enhancement by QQ counteracted the ecological drift, it eliminated the distance-decay relationship, reflecting a neutral theory archetype of metacommunity. Network analyses showed that QQ substantially reduced the amount and magnitude of interactions, e.g., competition and cooperation, for bacteria and fungi, and weakened their network structures, irrespective of time. Additionally, QQ suppressed the growth of specific microbial species (e.g., Acinetobacter), abundant and widespread at the early stage. These findings suggest that QQ influenced the community dynamics at the regional and local levels, correspondingly the ecological selection and dispersal processes, during the biofilm development.}, }
@article {pmid31250075, year = {2019}, author = {Lee, J and Han, G and Kim, JW and Jeon, CO and Hyun, S}, title = {Taxon-Specific Effects of Lactobacillus on Drosophila Host Development.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01404-9}, pmid = {31250075}, issn = {1432-184X}, abstract = {Commensal microbiota heavily influence metazoan host physiology. Drosophila melanogaster has been proven a valuable animal model for studying many aspects of host-microbiota interaction. Lactobacillus are the most common human probiotics and are also one of the major symbiotic bacteria in Drosophila. Although the beneficial effects of Lactobacillus on fly development and physiology have been recognized, how broadly these effects are observed across the Lactobacillus taxa remains largely unknown. In this study, four Lactobacillus species including five strains of L. plantarum were examined for their effects on fly larval development. Monoassociation of germ-free flies with L. rhamnosus (GG) most strongly accelerated fly larval development. Monoassociation with L. plantarum moderately accelerated fly development, but monoassociation with L. reuteri or L. sakei had marginal effects, despite similar bacterial loads in the host gut. An L. plantarum strain previously isolated from our lab rarely enhanced larval development, confirming the strain-specific effects of L. plantarum. The correlation between development-promoting effects and protein digestion activity in the host gut was found only among the members of L. plantarum species. Moreover, the cytoprotective response in the host gut known to be induced by L. plantarum was not correlated with development-promoting effects among any of the bacteria tested. Our results suggest that a broad range of Lactobacillus taxa are able to reside in the fly gut, but their ability to enhance host larval development is highly varied. This study may aid our understanding of the basic principles underlying the beneficial effects of probiotic commensal bacteria on metazoan development.}, }
@article {pmid31249384, year = {2019}, author = {Frau, A and Kenny, JG and Lenzi, L and Campbell, BJ and Ijaz, UZ and Duckworth, CA and Burkitt, MD and Hall, N and Anson, J and Darby, AC and Probert, CSJ}, title = {DNA extraction and amplicon production strategies deeply inf luence the outcome of gut mycobiome studies.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9328}, doi = {10.1038/s41598-019-44974-x}, pmid = {31249384}, issn = {2045-2322}, support = {M/15/4//Crohn&amp;apos;s and Colitis UK (Crohn&amp;apos;s &amp; Colitis UK)/ ; M/15/4//Crohn&amp;apos;s and Colitis UK (Crohn&amp;apos;s &amp; Colitis UK)/ ; NE/L011956/1//RCUK | Natural Environment Research Council (NERC)/ ; }, abstract = {Microbial ecology studies are often performed through extraction of metagenomic DNA followed by amplification and sequencing of a marker. It is known that each step may bias the results. These biases have been explored for the study of bacterial communities, but rarely for fungi. Our aim was therefore to evaluate methods for the study of the gut mycobiome. We first evaluated DNA extraction methods in fungal cultures relevant to the gut. Afterwards, to assess how these methods would behave with an actual sample, stool from a donor was spiked with cells from the same cultures. We found that different extraction kits favour some species and bias against others. In terms of amplicon sequencing, we evaluated five primer sets, two for ITS2 and one for ITS1, 18S and 28S rRNA. Results showed that 18S rRNA outperformed the other markers: it was able to amplify all the species in the mock community and to discriminate among them. ITS primers showed both amplification and sequencing biases, the latter related to the variable length of the product. We identified several biases in the characterisation of the gut mycobiome and showed how crucial it is to be aware of these before drawing conclusions from the results of these studies.}, }
@article {pmid31248111, year = {2019}, author = {Richardson, E and Dacks, JB}, title = {Microbial Eukaryotes in Oil Sands Environments: Heterotrophs in the Spotlight.}, journal = {Microorganisms}, volume = {7}, number = {6}, pages = {}, doi = {10.3390/microorganisms7060178}, pmid = {31248111}, issn = {2076-2607}, support = {RES0021028, RES0043758, RES0046091//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Hydrocarbon extraction and exploitation is a global, trillion-dollar industry. However, for decades it has also been known that fossil fuel usage is environmentally detrimental; the burning of hydrocarbons results in climate change, and environmental damage during extraction and transport can also occur. Substantial global efforts into mitigating this environmental disruption are underway. The global petroleum industry is moving more and more into exploiting unconventional oil reserves, such as oil sands and shale oil. The Albertan oil sands are one example of unconventional oil reserves; this mixture of sand and heavy bitumen lying under the boreal forest of Northern Alberta represent one of the world's largest hydrocarbon reserves, but extraction also requires the disturbance of a delicate northern ecosystem. Considerable effort is being made by various stakeholders to mitigate environmental impact and reclaim anthropogenically disturbed environments associated with oil sand extraction. In this review, we discuss the eukaryotic microbial communities associated with the boreal ecosystem and how this is affected by hydrocarbon extraction, with a particular emphasis on the reclamation of tailings ponds, where oil sands extraction waste is stored. Microbial eukaryotes, or protists, are an essential part of every global ecosystem, but our understanding of how they affect reclamation is limited due to our fledgling understanding of these organisms in anthropogenically hydrocarbon-associated environments and the difficulties of studying them. We advocate for an environmental DNA sequencing-based approach to determine the microbial communities of oil sands associated environments, and the importance of studying the heterotrophic components of these environments to gain a full understanding of how these environments operate and thus how they can be integrated with the natural watersheds of the region.}, }
@article {pmid31244886, year = {2019}, author = {Azarian, T and Ridgway, JP and Yin, Z and David, MZ}, title = {Long-Term Intrahost Evolution of Methicillin Resistant Staphylococcus aureus Among Cystic Fibrosis Patients With Respiratory Carriage.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {546}, doi = {10.3389/fgene.2019.00546}, pmid = {31244886}, issn = {1664-8021}, abstract = {Staphylococcus aureus is the most commonly identified airway colonizer of cystic fibrosis (CF) patients, and infections with methicillin-resistant S. aureus (MRSA) are associated with poor outcomes. Yet, little is known about the intrahost evolution of S. aureus among CF patients. We investigated convergent evolution and adaptation of MRSA among four CF patients with long-term respiratory carriage. For each patient, we performed whole-genome sequencing on an average of 21 isolates (range: 19-23) carried for a mean of 1,403 days (range: 903-1,679), including 25 pairs of isolates collected on the same day. We assessed intrahost diversity, population structure, evolutionary history, evidence of switched intergenic regions (IGRs), and signatures of adaptation in the context of patient age, antibiotic treatment, and co-colonizing microbes. Phylogenetic analysis delineated distinct multilocus sequence type ST5 (n = 3) and ST72 (n = 1) clonal populations in addition to sporadic, non-clonal isolates, and uncovered a putative transmission event. Variation in antibiotic resistance was observed within clonal populations, even among isolates collected on the same day. Rates of molecular evolution ranged from 2.21 to 8.64 nucleotide polymorphisms per year, and lineage ages were consistent with acquisition of colonization in early childhood followed by subsequent persistence of multiple sub-populations. Selection analysis of 1,622 core genes present in all four clonal populations (n = 79) found 11 genes variable in three subjects - most notably, ATP-dependent protease clpX, 2-oxoglutarate dehydrogenase odhA, fmtC, and transcription-repair coupling factor mfd. Only one gene, staphylococcal protein A (spa), was found to have evidence of gene-wide diversifying selection. We identified three instances of intrahost IGR switching events, two of which flanked genes related to quorum sensing. The complex microbial ecology of the CF airway poses challenges for management. We illustrate appreciable intrahost diversity as well as persistence of a dominant lineage. We also show that intrahost adaptation is a continual process, despite purifying selective pressure, and provide targets that should be investigated further for their function in CF adaptation.}, }
@article {pmid31243077, year = {2019}, author = {McNamara, PJ}, title = {mSphere of Influence: Engineering Microbes.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSphere.00317-19}, pmid = {31243077}, issn = {2379-5042}, abstract = {Patrick J. McNamara works in the field of environmental engineering. In this mSphere of Influence article, he reflects on how the papers &quot;Bacterial community structure in the drinking water microbiome is governed by filtration processes&quot; (A. J. Pinto, C. Xi, and L. Raskin, Environ Sci Technol 46:8851-8859, 2012, https://doi.org/10.1021/es302042t) and &quot;Differential resistance of drinking water bacterial populations to monochloramine disinfection&quot; (T. Chiao, T. M. Clancy, A. Pinto, C. Xi, and L. Raskin, Environ Sci Technol 48:4038-4047, 2014, https://doi.org/10.1021/es4055725) by Lutgarde Raskin and colleagues made an impact on him by providing a foundation for the study of microbial ecology in engineering drinking water treatment plants and drinking water distribution systems.}, }
@article {pmid31239395, year = {2019}, author = {Bayer, B and Pelikan, C and Bittner, MJ and Reinthaler, T and Könneke, M and Herndl, GJ and Offre, P}, title = {Proteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic Alphaproteobacterium.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSystems.00181-19}, pmid = {31239395}, issn = {2379-5077}, abstract = {Ammonia-oxidizing archaea (AOA) play an important role in the nitrogen cycle and account for a considerable fraction of the prokaryotic plankton in the ocean. Most AOA lack the hydrogen peroxide (H2O2)-detoxifying enzyme catalase, and some AOA have been shown to grow poorly under conditions of exposure to H2O2 However, differences in the degrees of H2O2 sensitivity of different AOA strains, the physiological status of AOA cells exposed to H2O2, and their molecular response to H2O2 remain poorly characterized. Further, AOA might rely on heterotrophic bacteria to detoxify H2O2, and yet the extent and variety of costs and benefits involved in these interactions remain unclear. Here, we used a proteomics approach to compare the protein profiles of three Nitrosopumilus strains grown in the presence and absence of catalase and in coculture with the heterotrophic alphaproteobacterium Oceanicaulis alexandrii We observed that most proteins detected at a higher relative abundance in H2O2-exposed Nitrosopumilus cells had no known function in oxidative stress defense. Instead, these proteins were putatively involved in the remodeling of the extracellular matrix, which we hypothesize to be a strategy limiting the influx of H2O2 into the cells. Using RNA-stable isotope probing, we confirmed that O. alexandrii cells growing in coculture with the Nitrosopumilus strains assimilated Nitrosopumilus-derived organic carbon, suggesting that AOA could recruit H2O2-detoxifying bacteria through the release of labile organic matter. Our results contribute new insights into the response of AOA to H2O2 and highlight the potential ecological importance of their interactions with heterotrophic free-living bacteria in marine environments.IMPORTANCE Ammonia-oxidizing archaea (AOA) are the most abundant chemolithoautotrophic microorganisms in the oxygenated water column of the global ocean. Although H2O2 appears to be a universal by-product of aerobic metabolism, genes encoding the hydrogen peroxide (H2O2)-detoxifying enzyme catalase are largely absent in genomes of marine AOA. Here, we provide evidence that closely related marine AOA have different degrees of sensitivity to H2O2, which may contribute to niche differentiation between these organisms. Furthermore, our results suggest that marine AOA rely on H2O2 detoxification during periods of high metabolic activity and release organic compounds, thereby potentially attracting heterotrophic prokaryotes that provide this missing function. In summary, this report provides insights into the metabolic interactions between AOA and heterotrophic bacteria in marine environments and suggests that AOA play an important role in the biogeochemical carbon cycle by making organic carbon available for heterotrophic microorganisms.}, }
@article {pmid31238848, year = {2019}, author = {Dimitriu, T and Marchant, L and Buckling, A and Raymond, B}, title = {Bacteria from natural populations transfer plasmids mostly towards their kin.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1905}, pages = {20191110}, doi = {10.1098/rspb.2019.1110}, pmid = {31238848}, issn = {1471-2954}, abstract = {Plasmids play a key role in microbial ecology and evolution, yet the determinants of plasmid transfer rates are poorly understood. Particularly, interactions between donor hosts and potential recipients are understudied. Here, we investigate the importance of genetic similarity between naturally co-occurring Escherichia coli isolates in plasmid transfer. We uncover extensive variability, spanning over five orders of magnitude, in the ability of isolates to donate and receive two different plasmids, R1 and RP4. Overall, transfer is strongly biased towards clone-mates, but not correlated to genetic distance when donors and recipients are not clone-mates. Transfer is limited by the presence of a functional restriction-modification system in recipients, suggesting sharing of strain-specific defence systems contributes to bias towards kin. Such restriction of transfer to kin sets the stage for longer-term coevolutionary interactions leading to mutualism between plasmids and bacterial hosts in natural communities.}, }
@article {pmid31236844, year = {2019}, author = {Kunath, BJ and Minniti, G and Skaugen, M and Hagen, LH and Vaaje-Kolstad, G and Eijsink, VGH and Pope, PB and Arntzen, MØ}, title = {Metaproteomics: Sample Preparation and Methodological Considerations.}, journal = {Advances in experimental medicine and biology}, volume = {1073}, number = {}, pages = {187-215}, doi = {10.1007/978-3-030-12298-0_8}, pmid = {31236844}, issn = {0065-2598}, mesh = {*Metagenomics ; *Microbial Consortia ; Proteins ; *Proteomics ; Specimen Handling/*methods ; }, abstract = {Meta-omic techniques have progressed rapidly in the past decade and are frequently used in microbial ecology to study microorganisms in their natural ecosystems independent from culture restrictions. Metaproteomics, in combination with metagenomics, enables quantitative assessment of expressed proteins and pathways from individual members of the consortium. Together, metaproteomics and metagenomics can provide a detailed understanding of which organisms occupy specific metabolic niches, how they interact, and how they utilize nutrients, and these insights can be obtained directly from environmental samples. Here, we outline key aspects of sample preparation, database generation, and other methodological considerations that are required for successful quantitative metaproteomic analyses and we describe case studies on the integration with metagenomics for enhanced functional output.}, }
@article {pmid31236611, year = {2019}, author = {Fiałkowska, E and Fiałkowski, W and Pajdak-Stós, A}, title = {The Relations Between Predatory Fungus and Its Rotifer Preys as a Noteworthy Example of Intraguild Predation (IGP).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01398-4}, pmid = {31236611}, issn = {1432-184X}, abstract = {Intraguild predation (IGP) is a widespread interaction combining predation and competition. We investigated a unique IGP example among predacious fungus Zoophagus sp. and two rotifers, the predacious Cephalodella gibba and the common prey Lecane inermis. We checked the influence of the fungus on its competitor C. gibba and their joint influence on shared prey L. inermis, and the impact of the competitive predator on the growth of predacious fungus. The experiment on grown mycelium showed that Zoophagus strongly, negatively influences the growth of C. gibba (intermediate consumer) whose number did not increase throughout the experiment. The intermediate consumer was also trapped by Zoophagus and become extinct when it was its only prey, whereas in the absence of the fungus and with unlimited access to prey, its number grew quickly. As only few C. gibba were trapped by fungi when common preys were present, competition for food seems to have stronger effect on intermediate consumer population than predation. The experiment with conidia of the fungus showed that intermediate consumer significantly limits the growth of Zoophagus by reducing the number of available prey. It was observed that although the fungus can trap C. gibba, the latter does not support its growth. Trapping the intermediate consumer might serve to eliminate a competitor rather than to find a source of food. The chances of survival for L. inermis under the pressure of the two competing predators are scarce. It is the first example of IGP involving representatives of two kingdoms: Fungi and Animalia.}, }
@article {pmid31234491, year = {2019}, author = {Kraemer, SA and Ramachandran, A and Perron, GG}, title = {Antibiotic Pollution in the Environment: From Microbial Ecology to Public Policy.}, journal = {Microorganisms}, volume = {7}, number = {6}, pages = {}, doi = {10.3390/microorganisms7060180}, pmid = {31234491}, issn = {2076-2607}, abstract = {The ability to fight bacterial infections with antibiotics has been a longstanding cornerstone of modern medicine. However, wide-spread overuse and misuse of antibiotics has led to unintended consequences, which in turn require large-scale changes of policy for mitigation. In this review, we address two broad classes of corollaries of antibiotics overuse and misuse. Firstly, we discuss the spread of antibiotic resistance from hotspots of resistance evolution to the environment, with special concerns given to potential vectors of resistance transmission. Secondly, we outline the effects of antibiotic pollution independent of resistance evolution on natural microbial populations, as well as invertebrates and vertebrates. We close with an overview of current regional policies tasked with curbing the effects of antibiotics pollution and outline areas in which such policies are still under development.}, }
@article {pmid31233889, year = {2019}, author = {Forger, LV and Woolf, MS and Simmons, TL and Swall, JL and Singh, B}, title = {A eukaryotic community succession based method for postmortem interval (PMI) estimation of decomposing porcine remains.}, journal = {Forensic science international}, volume = {302}, number = {}, pages = {109838}, doi = {10.1016/j.forsciint.2019.05.054}, pmid = {31233889}, issn = {1872-6283}, abstract = {Recent, short-term studies on porcine and human models (albeit with few replicates) demonstrated that the succession of the microbial community of remains may be used to estimate time since death. Using a porcine model (N=6) over an extended period of time (1703 ADD, or two months), this study characterized the eukaryote community of decomposing remains. Skin microbial samples were collected from the torso of each set of remains every day during the first week, on alternate days during the second week, and once a week for the remainder of the 60-day period; all collection intervals were recorded in accumulated degree days (ADD). The eukaryote community of each sample was determined using 18S ribosomal DNA (rDNA) MiSeq high throughput sequencing; data were analyzed in the Mothur pipeline (v1.39.5) and in IBM SPSS and R statistical packages. The relative abundance of eukaryote taxa across ADD/Days and an Analysis of Molecular Variance (AMOVA) indicated similarities between sequential ADD/Days, but significant differences in the eukaryote communities as broad stage 'milestones' of decomposition were reached. Fresh remains (0-57 ADD/0-2 Days; exhibiting a total body score (TBS) of 0-10) were characterized by the combined presence of Saccharomycetaceae, Debaryomycetaceae, Trichosporonaceae, Rhabditida, and Trichostomatia. During bloat and active decay (87-209 ADD/3-7 Days; exhibiting TBS of 11-20), Diptera was the most abundant eukaryotic taxa. During advanced decay stage (267-448 ADD/9-15 Days; exhibiting TBS of 21-25), Rhabditida was the most dominant eukaryote. Dry/skeletal remains (734-1703 ADD/26-61 Days; TBS≥26) were dominated by fungal families Dipodascaceae, Debaryomycetaceae, Trichosporonaceae, and Sporidiobolaceae. Using the family-level eukaryote taxonomic data for the entire study, random forest modelling explained 89.58% of the variation in ADD/Days, with a root mean square error (RMSE) of 177.55 ADD (≈6 days). Overall, these results highlight the importance of the microbial eukaryote community during the process of decomposition and in estimation of PMI.}, }
@article {pmid31233284, year = {2019}, author = {Zealand, AM and Mei, R and Roskilly, AP and Liu, W and Graham, DW}, title = {Molecular microbial ecology of stable versus failing rice straw anaerobic digesters.}, journal = {Microbial biotechnology}, volume = {12}, number = {5}, pages = {879-891}, doi = {10.1111/1751-7915.13438}, pmid = {31233284}, issn = {1751-7915}, support = {NE/L501748/1//Natural Environment Research Council/ ; EP/L002477/1//Energy from Rice Straw Project/ ; //DFID/ ; //DECC as part of the Energy &amp; International Development/ ; //USES programme/ ; //Sir Joseph Swan Centre for Energy Research/ ; //Xiamen-Newcastle Joint Strategic Partnership Fund/ ; }, abstract = {Waste rice straw (RS) is generated in massive quantities around the world and is often burned, creating greenhouse gas and air quality problems. Anaerobic digestion (AD) may be a better option for RS management, but RS is presumed to be comparatively refractory under anaerobic conditions without pre-treatment or co-substrates. However, this presumption assumes frequent reactor feeding regimes but less frequent feeding may be better for RS due to slow hydrolysis rates. Here, we assess how feeding frequency (FF) and organic loading rate (OLR) impacts microbial communities and biogas production in RS AD reactors. Using 16S rDNA amplicon sequencing and bioinformatics, microbial communities from five bench-scale bioreactors were characterized. At low OLR (1.0 g VS l-1 day-1), infrequently fed units (once every 21 days) had higher specific biogas yields than more frequent feeding (five in 7 days), although microbial community diversities were statistically similar (P > 0.05; ANOVA with Tukey comparison). In contrast, an increase in OLR to 2.0 g VS l-1 day-1 significantly changed Archaeal and fermenting Eubacterial sub-communities and the least frequency fed reactors failed. 'Stable' reactors were dominated by Methanobacterium, Methanosarcina and diverse Bacteroidetes, whereas 'failed' reactors saw shifts towards Clostridia and Christensenellaceae among fermenters and reduced methanogen abundances. Overall, OLR impacted RS AD microbial communities more than FF. However, combining infrequent feeding and lower OLRs may be better for RS AD because of higher specific yields.}, }
@article {pmid31232323, year = {2019}, author = {Zhong, X and Xu, G and Min, GS and Kim, S and Xu, H}, title = {Can tidal events influence monitoring surveys using periphytic ciliates based on biological trait analysis in marine ecosystems?.}, journal = {Marine pollution bulletin}, volume = {142}, number = {}, pages = {452-456}, doi = {10.1016/j.marpolbul.2019.04.005}, pmid = {31232323}, issn = {1879-3363}, mesh = {Ciliophora/*physiology ; Ecosystem ; Environmental Monitoring/instrumentation/*methods ; Multivariate Analysis ; Phenotype ; Republic of Korea ; *Seawater ; }, abstract = {To identify the influence of tidal events on community functioning of periphytic ciliates for monitoring program and community research using biological trait analysis, a 3-month baseline survey was conducted in Korean coastal waters using the polyurethane foam enveloped slide system (PFES) and conventional slide system (CS). Although the periphytic ciliate communities had similar biological trait categories, they represented considerable differences in community functioning and functional diversity measures within the PFES and CS systems. Multivariate analyses revealed different ways of the temporal shift in community functioning of the ciliates in both systems. The dispersion analysis demonstrated that the CS system was sensitive to the strong disturbance of tidal current and circulation compared to the PFES system. These findings suggest that the strong tidal event may significantly influence the output of analysis on community functioning of periphytic ciliates for bioassessment in marine ecosystems.}, }
@article {pmid31229831, year = {2019}, author = {Souza, FFC and Rissi, DV and Pedrosa, FO and Souza, EM and Baura, VA and Monteiro, RA and Balsanelli, E and Cruz, LM and Souza, RAF and Andreae, MO and Reis, RA and Godoi, RHM and Huergo, LF}, title = {Uncovering prokaryotic biodiversity within aerosols of the pristine Amazon forest.}, journal = {The Science of the total environment}, volume = {688}, number = {}, pages = {83-86}, doi = {10.1016/j.scitotenv.2019.06.218}, pmid = {31229831}, issn = {1879-1026}, abstract = {Biological aerosols (bioaerosol) are atmospheric particles that act as a dispersion unit of living organisms across the globe thereby affecting the biogeographic distribution of organisms. Despite their importance, there is virtually no knowledge about bioaerosols emitted by pristine forests. Here we provide the very first survey of the prokaryotic community of a bioaerosol collected inside pristine Amazon forest at 2 m above ground. Total atmospheric particles were collected at the Amazon Tall Tower Observatory, subjected to metagenomic DNA extraction and the prokaryotic diversity was determined by 16S rRNA gene amplicon sequencing. A total of 271,577 reads of 250 bp of the 16S rRNA gene amplicon were obtained. Only 27% of the reads could be classified using the 16S SILVA database. Most belonged to Proteobacteria, Actinobacteria and Firmicutes which is in good agreement with other bioaerosol studies. Further inspection of the reads using Blast searches and the 18S SILVA database revealed that most of the dataset was composed of Fungi sequences. The identified microbes suggest that the atmosphere may act as an important gateway to interchange bacteria between plants, soil and water ecosystems.}, }
@article {pmid31229570, year = {2019}, author = {Boyle, MA and Kearney, A and Carling, PC and Humphreys, H}, title = {'Off the rails': hospital bed rail design, contamination, and the evaluation of their microbial ecology.}, journal = {The Journal of hospital infection}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhin.2019.06.008}, pmid = {31229570}, issn = {1532-2939}, abstract = {Microbial contamination of the near-patient environment is an acknowledged reservoir for nosocomial pathogens. The hospital bed and specifically bed rails have been shown to be frequently and heavily contaminated in observational and interventional studies. Whereas the complexity of bed rail design has evolved over the years, the microbial contamination of these surfaces has been incompletely evaluated. In many published studies, key design variables are not described, compromising the extrapolation of results to other settings. This report reviews the evolving structure of hospital beds and bed rails, the possible impact of different design elements on microbial contamination and their role in pathogen transmission. Our findings support the need for clearly defined standardized assessment protocols to accurately assess bed rail and similar patient zone surface levels of contamination, as part of environmental hygiene investigations.}, }
@article {pmid31227816, year = {2019}, author = {Jung, MY and Gwak, JH and Rohe, L and Giesemann, A and Kim, JG and Well, R and Madsen, EL and Herbold, CW and Wagner, M and Rhee, SK}, title = {Indications for enzymatic denitrification to N2O at low pH in an ammonia-oxidizing archaeon.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0460-6}, pmid = {31227816}, issn = {1751-7370}, support = {NRF-2015R1A4A1041869//National Research Foundation of Korea (NRF)/ ; NRF-2015M3D3A1A01064881//National Research Foundation of Korea (NRF)/ ; NRF-2018R1A2B6008861//National Research Foundation of Korea (NRF)/ ; NIBR201701107//MOE | National Institute of Biological Resources (NIBR)/ ; }, abstract = {Nitrous oxide (N2O) is a key climate change gas and nitrifying microbes living in terrestrial ecosystems contribute significantly to its formation. Many soils are acidic and global change will cause acidification of aquatic and terrestrial ecosystems, but the effect of decreasing pH on N2O formation by nitrifiers is poorly understood. Here, we used isotope-ratio mass spectrometry to investigate the effect of acidification on production of N2O by pure cultures of two ammonia-oxidizing archaea (AOA; Nitrosocosmicus oleophilus and Nitrosotenuis chungbukensis) and an ammonia-oxidizing bacterium (AOB; Nitrosomonas europaea). For all three strains acidification led to increased emission of N2O. However, changes of 15N site preference (SP) values within the N2O molecule (as indicators of pathways for N2O formation), caused by decreasing pH, were highly different between the tested AOA and AOB. While acidification decreased the SP value in the AOB strain, SP values increased to a maximum value of 29‰ in N. oleophilus. In addition, 15N-nitrite tracer experiments showed that acidification boosted nitrite transformation into N2O in all strains, but the incorporation rate was different for each ammonia oxidizer. Unexpectedly, for N. oleophilus more than 50% of the N2O produced at pH 5.5 had both nitrogen atoms from nitrite and we demonstrated that under these conditions expression of a putative cytochrome P450 NO reductase is strongly upregulated. Collectively, our results indicate that N. oleophilus might be able to enzymatically denitrify nitrite to N2O at low pH.}, }
@article {pmid31227556, year = {2019}, author = {Webster, TM and Fierer, N}, title = {Microbial Dynamics of Biosand Filters and Contributions of the Microbial Food Web to Effective Treatment of Wastewater-Impacted Water Sources.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {17}, pages = {}, doi = {10.1128/AEM.01142-19}, pmid = {31227556}, issn = {1098-5336}, abstract = {Biosand filtration systems are widely used for drinking water treatment, from household-level, intermittently operated filters to large-scale continuous municipal systems. While it is well-established that microbial activity within the filter is essential for the removal of potential pathogens and other contaminants, the microbial ecology of these systems and how microbial succession relates to their performance remain poorly resolved. We determined how different source waters influence the composition, temporal dynamics, and performance of microbial communities in intermittently operated biosand filters. We operated lab-scale biosand filters, adding daily inputs from two contrasting water sources with differing nutrient concentrations and found that total coliform removal increased and became less variable after 4 weeks, regardless of water source. Total effluent biomass was also lower than total influent biomass for both water sources. Bacterial community composition, assessed via cultivation-independent DNA sequencing, varied by water source, sample type (influent, effluent, or sand), and time. Despite these differences, we identified specific taxa that were consistently removed, including common aquatic and wastewater bacteria. In contrast, taxa consistently more abundant in the sand and effluent included predatory, intracellular, and symbiotic bacteria.IMPORTANCE Although microbial activities are known to contribute to the effectiveness of biosand filtration for drinking water treatment, we have a limited understanding of what microbial groups are most effectively removed, colonize the sand, or make it through the filter. This study tracked the microbial communities in the influent, sand, and effluent of lab-scale, intermittently operated biosand filters over 8 weeks. These results represent the most detailed and time-resolved investigation of the microbial communities in biosand filters typical of those implemented at the household level in many developing countries. We show the importance of the microbial food web in biosand filtration, and we identified taxa that are preferentially removed from wastewater-impacted water sources. We found consistent patterns in filter effectiveness from source waters with differing nutrient loads and, likewise, identified specific bacterial taxa that were consistently more abundant in effluent waters, taxa that are important targets for further study and posttreatment.}, }
@article {pmid31226149, year = {2019}, author = {Wang, S and Zheng, X and Xia, H and Shi, D and Fan, J and Wang, P and Yan, Z}, title = {Archaeal community variation in the Qinhuangdao coastal aquaculture zone revealed by high-throughput sequencing.}, journal = {PloS one}, volume = {14}, number = {6}, pages = {e0218611}, doi = {10.1371/journal.pone.0218611}, pmid = {31226149}, issn = {1932-6203}, abstract = {The differences in archaeal diversity and community composition in the sediments and waters of the Qinhuangdao coastal aquaculture zone were investigated. Furthermore, the associations between dominant archaeal taxa with geographic and environmental variables were evaluated. High-throughput sequencing of archaeal 16S rRNA genes yielded a total of 176,211 quality-filtered reads and 1,178 operational taxonomic units (OTUs) overall. The most abundant phylum and class among all communities were Thaumarchaeota and Nitrososphaeria, respectively. Beta diversity analysis indicated that community composition was divided into two groups according to the habitat type (i.e., sediments or waters). Only 9.8% OTUs were shared by communities from the two habitats, while 73.9% and 16.3% of the OTUs were unique to sediment or water communities, respectively. Furthermore, the relative abundances of the dominant OTUs differed with habitat type. Investigations of relationships between dominant OTUs and environmental variables indicated that some dominant OTUs were more sensitive to variation in environmental factors, which could be due to individual taxonomic differences in lifestyles and biological processes. Overall, the investigation of archaeal community variation within the Qinhuangdao coastal aquaculture zone provides an important baseline understanding of the microbial ecology in this important ecosystem.}, }
@article {pmid31225613, year = {2019}, author = {Brehony, C and McGrath, E and Brennan, W and Tuohy, A and Whyte, T and Brisse, S and Maiden, M and Jolley, K and Morris, D and Cormican, M}, title = {An MLST approach to support tracking of plasmids carrying OXA-48-like carbapenemase.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {7}, pages = {1856-1862}, doi = {10.1093/jac/dkz136}, pmid = {31225613}, issn = {1460-2091}, abstract = {OBJECTIVES: The prevalence of infections caused by OXA-48-like carbapenemase-producing organisms in Ireland has increased dramatically since 2011 and is an urgent public health issue. Genome-based high-resolution genotyping was used to analyse clinical isolates submitted to the Irish Carbapenemase-Producing Enterobacteriaceae Reference Laboratory Service for a 13 month period (2016-17).<br><br>METHODS: A total of 109 OXA-48-producing non-duplicate clinical isolates from 16 submitting centres were sequenced. Using a gene-by-gene approach, isolate genomes were characterized by MLST and core genome MLST, and the presence of antimicrobial resistance determinants was determined. Reference mapping and a novel plasmid MLST-type approach was applied to determine plasmid background.<br><br>RESULTS: The OXA-48-like-producing isolates were Escherichia coli (n = 56), Klebsiella spp. (n = 46) and Enterobacter cloacae (n = 7). Amongst the E. coli isolates there were 37 different STs and amongst the Klebsiella spp. isolates there were 27 different STs. blaOXA-48 was present in 105/109 (96.3%) of isolates. Based on mapping analysis and detection of the pOXA-48 IncL-type plasmid replicon and backbone genes, a pOXA-48-like plasmid was identified in 93/109 isolates (85.3%). The remaining isolates (n = 16; 14.7%) harboured blaOXA-48-like genes in unknown environments. Using a gene-by-gene approach two pOXA-48-like plasmid groups with 2/71 pOXA-48-like locus differences between them were identified.<br><br>CONCLUSIONS: In Ireland we found a diversity of genotypes associated with OXA-48-like-producing clinical isolates with the IncL pOXA-48 plasmid type predominating as the blaOXA-48 genetic environment. A plasmid MLST approach can rapidly identify plasmids associated with outbreaks and monitor spread of types temporally and geographically.}, }
@article {pmid31222757, year = {2019}, author = {Hammerbacher, A and Coutinho, TA and Gershenzon, J}, title = {Roles of plant volatiles in defence against microbial pathogens and microbial exploitation of volatiles.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.13602}, pmid = {31222757}, issn = {1365-3040}, support = {//Max Planck Society/ ; //University of Pretoria/ ; //National Research Foundation of South Africa/ ; }, abstract = {Plants emit a large variety of volatile organic compounds during infection by pathogenic microbes, including terpenes, aromatics, nitrogen-containing compounds, and fatty acid derivatives, as well as the volatile plant hormones, methyl jasmonate, and methyl salicylate. Given the general antimicrobial activity of plant volatiles and the timing of emission following infection, these compounds have often been assumed to function in defence against pathogens without much solid evidence. In this review, we critically evaluate current knowledge on the toxicity of volatiles to fungi, bacteria, and viruses and their role in plant resistance as well as how they act to induce systemic resistance in uninfected parts of the plant and in neighbouring plants. We also discuss how microbes can detoxify plant volatiles and exploit them as nutrients, attractants for insect vectors, and inducers of volatile emissions, which stimulate immune responses that make plants more susceptible to infection. Although much more is known about plant volatile-herbivore interactions, knowledge of volatile-microbe interactions is growing and it may eventually be possible to harness plant volatiles to reduce disease in agriculture and forestry. Future research in this field can be facilitated by making use of the analytical and molecular tools generated by the prolific research on plant-herbivore interactions.}, }
@article {pmid31220587, year = {2019}, author = {Trifi, H and Najjari, A and Achouak, W and Barakat, M and Ghedira, K and Mrad, F and Saidi, M and Sghaier, H}, title = {Metataxonomics of Tunisian phosphogypsum based on five bioinformatics pipelines: Insights for bioremediation.}, journal = {Genomics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ygeno.2019.06.014}, pmid = {31220587}, issn = {1089-8646}, abstract = {Phosphogypsum (PG) is an acidic by-product from the phosphate fertilizer industry and it is characterized by a low nutrient availability and the presence of radionuclides and heavy metals which pose a serious problem in its management. Here, we have applied Illumina MiSeq sequencing technology and five bioinformatics pipelines to explore the phylogenetic communities in Tunisian PG. Taking One Codex as a reference method, we present the results of 16S-rDNA-gene-based metataxonomics abundances with four other alternative bioinformatics pipelines (MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST), mothur, MICrobial Community Analysis (MICCA) and Quantitative Insights into Microbial Ecology (QIIME)), when analyzing the Tunisian PG. Importantly, based on 16S rDNA datasets, the functional capabilities of microbial communities of PG were deciphered. They suggested the presence of PG autochthonous bacteria valorizable into (1) removal of radioactive elements and toxic heavy metals, (2) promotion of plant growth, (3) oxidation and (4) reduction of sulfate. These bacteria can be explored further for applications in the bioremediation of by-products, like PG, by different processes.}, }
@article {pmid31219789, year = {2019}, author = {Myer, PR}, title = {Bovine Genome-Microbiome Interactions: Metagenomic Frontier for the Selection of Efficient Productivity in Cattle Systems.}, journal = {mSystems}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSystems.00103-19}, pmid = {31219789}, issn = {2379-5077}, abstract = {The mutualistic, commensal, and parasitic microorganisms that reside in the rumen and lower gastrointestinal tract of cattle and other ruminants exert enormous influence over animal physiology and performance. Because these microbial communities are critical for host nutrient utilization and contribute to the metabolic capacity of the rumen, past research has aimed to define host-microbe symbioses in cattle by examining the rumen and lower gut microbiomes with respect to production phenotypes, such as feed efficiency. However, as the field of bovine gut microbial ecology progresses, multidisciplinary approaches must be employed, combining host genomics and other omics-based techniques to understand the complex host-microbe network. In this perspective, I discuss the direction of the field of bovine gut microbial ecology with regard to feed efficiency and explore how the grand challenge of such research will be to maintain host-efficient gut microbiomes in cattle production through manipulations of genome-microbiome interactions.}, }
@article {pmid31219680, year = {2019}, author = {Tedersoo, L and Anslan, S}, title = {Towards PacBio-based pan-eukaryote metabarcoding using full-length ITS sequences.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.12776}, pmid = {31219680}, issn = {1758-2229}, abstract = {Development of high-throughput sequencing techniques has greatly benefited our understanding about microbial ecology, yet the methods producing short reads suffer from species-level resolution and uncertainty of identification. Here, we optimize Pacific Biosciences-based metabarcoding protocols covering the internal transcribed spacer (ITS region) and partial small subunit of the rRNA gene for species-level identification of all eukaryotes, with a specific focus on Fungi (including Glomeromycota) and Stramenopila (particularly Oomycota). Based on tests on composite soil samples and mock communities, we propose best suitable degenerate primers, ITS9munngs + ITS4ngsUni for eukaryotes and selected groups therein and discuss the pros and cons of long read-based identification of eukaryotes.}, }
@article {pmid31218384, year = {2019}, author = {Della Mónica, IF and Godeas, AM and Scervino, JM}, title = {In Vivo Modulation of Arbuscular Mycorrhizal Symbiosis and Soil Quality by Fungal P Solubilizers.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01396-6}, pmid = {31218384}, issn = {1432-184X}, support = {PICT 2012 0285//Agencia Nacional de Promoción Científica y Tecnológica/ ; }, abstract = {Phosphorus (P) is an essential nutrient with low bioavailability in soils for plant growth. The use of P solubilization fungi (PSF) has arisen as an eco-friendly strategy to increase this nutrient's bioavailability. The effect of PSF inoculation and its combination with P-transporting organisms (arbuscular mycorrhizal fungi, AMF) on plant growth has been previously studied. However, these studies did not evaluate the combined effect of PSF and AMF inoculation on plant growth, symbiosis, and soil quality. Therefore, the aim of this study is to assess the impact of PSF on the AMF-wheat symbiosis establishment and efficiency, considering the effect on plant growth and soil quality. We performed a greenhouse experiment with wheat under different treatments (+/-AMF: Rhizophagus irregularis; +/-PSF strains: Talaromyces flavus, T. helicus L7B, T. helicus N24, and T. diversus) and measured plant growth, AMF root colonization, symbiotic efficiency, and soil quality indicators. No interaction between PSF and R. irregularis was found in wheat growth, showcasing that their combination is not better than single inoculation. T. helicus strains did not interfere with the AMF-wheat symbiosis establishment, while T. diversus and T. flavus decreased it. The symbiotic efficiency was increased by T. flavus and T. helicus N24, and unchanged with T. helicus L7B and T. diversus inoculation. The soil quality indicators were higher with microbial co-inoculation, particularly the alkaline phosphatases parameter, showing the beneficial role of fungi in soil. This work highlights the importance of microbial interactions in the rhizosphere for crop sustainability and soil quality improvement, assessing the effects of PSF on AMF-wheat symbiosis.}, }
@article {pmid31217455, year = {2019}, author = {Fan, Z and Lu, S and Liu, S and Guo, H and Wang, T and Zhou, J and Peng, X}, title = {Changes in Plant Rhizosphere Microbial Communities under Different Vegetation Restoration Patterns in Karst and Non-karst Ecosystems.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {8761}, doi = {10.1038/s41598-019-44985-8}, pmid = {31217455}, issn = {2045-2322}, abstract = {Understanding how patterns of recovery and geological conditions affect microbial communities is important for determining the stability of karst ecosystems. Here, we investigated the diversity and composition of microorganisms in karst and non-karst environments under natural restoration and artificial rehabilitation conditions. The results showed no significant differences in soil microbial diversity, but the microbial communities associated with geological conditions and tree species differed significantly. Variation partitioning analysis (VPA) showed that a total of 77.3% of the variation in bacteria and a total of 69.3% of the variation in fungi could be explained by vegetation type and geological background. There were significant differences in six bacterial classes (Actinobacteria, Alphaproteobacteria, Ktedonobacteria, TK10, Gammaproteobacteria, and Anaerolineae) and nine fungal classes (Eurotiomycetes, Agaricomycetes, unclassified _p_Ascomycota, Sordariomycetes, Tremellomycetes, norank_k_Fungi, Pezizomycetes, Leotiomycetes and Archaeorhizomycetes) among the soils collected from six plots. A Spearman correlation heatmap showed that the microbial community was affected by the major soil properties. Principal coordinates analysis indicated that the microbial community of Pinus yunnanensis in the artificial forest, which was established for the protection of the environment was most similar to that in the natural secondary forest in the karst ecosystem. These findings further our understanding of microbial responses to vegetation restoration and geological conditions.}, }
@article {pmid31214149, year = {2019}, author = {Hounmanou, YMG and Mdegela, RH and Dougnon, TV and Madsen, H and Withey, JH and Olsen, JE and Dalsgaard, A}, title = {Tilapia (Oreochromis niloticus) as a Putative Reservoir Host for Survival and Transmission of Vibrio cholerae O1 Biotype El Tor in the Aquatic Environment.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1215}, doi = {10.3389/fmicb.2019.01215}, pmid = {31214149}, issn = {1664-302X}, support = {R01 AI127390/AI/NIAID NIH HHS/United States ; }, abstract = {Studies have reported the occurrence of Vibrio cholerae in fish but little is known about the interaction between fish and toxigenic V. cholerae as opposed to phytoplankton, which are well-established aquatic reservoirs for V. cholerae. The present study determined the role of tilapia (Oreochromis niloticus) as a reservoir host for survival and transmission of V. cholerae in aquatic environments. Three experiments were performed with one repetition each, where O. niloticus (∼2 g) kept in beakers were inoculated with four V. cholerae strains (5 × 107 cfu/mL). Firstly, infected tilapia were kept in stagnant water and fed live brine shrimp (Artemia salina) larvae daily. Secondly, infected tilapia were kept without feeding and water was changed every 24 h. Thirdly, infected tilapia were fed and water was renewed daily. Infected tilapia and non-infected controls were sacrificed on days 1, 2, 3, 7, and 14 post-inoculation and V. cholerae were enumerated in intestinal content and water. Another experiment assessed the transmission of V. cholerae from infected to non-infected tilapia. The study revealed that El Tor biotype V. cholerae O1 and V. cholerae non-O1 colonized tilapia intestines and persisted at stable concentrations during the second week of the experiment whereas the Classical biotype was undetectable after 1 week. In stagnant water with feeding, V. cholerae counts dropped to 105 cfu/ml in water and from 107 to 104 cfu/intestine in fish after 14 days. When water was renewed, counts in water decreased from 107 to 103 cfu/ml and intestinal counts went from 106 to 102 cfu/intestine regardless of feeding. All strains were transmitted from infected to naïve fish after 24 h of cohabitation. Tilapia like other fish may play an essential role in the survival and dissemination of V. cholerae O1 in aquatic environments, e.g., the seventh pandemic strains mostly. In this study, tilapia were exposed to high concentrations of V. cholerae to ensure initial uptake and follow-up studies with lower doses resembling natural concentrations of V. cholerae in the aquatic environment are needed to confirm our findings.}, }
@article {pmid31214145, year = {2019}, author = {El Hage, R and Hernandez-Sanabria, E and Calatayud Arroyo, M and Props, R and Van de Wiele, T}, title = {Propionate-Producing Consortium Restores Antibiotic-Induced Dysbiosis in a Dynamic in vitro Model of the Human Intestinal Microbial Ecosystem.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1206}, doi = {10.3389/fmicb.2019.01206}, pmid = {31214145}, issn = {1664-302X}, abstract = {Metabolic syndrome is a growing public health concern. Efforts at searching for links with the gut microbiome have revealed that propionate is a major fermentation product in the gut with several health benefits toward energy homeostasis. For instance, propionate stimulates satiety-inducing hormones, leading to lower energy intake and reducing weight gain and associated risk factors. In (disease) scenarios where microbial dysbiosis is apparent, gut microbial production of propionate may be decreased. Here, we investigated the effect of a propionogenic bacterial consortium composed of Lactobacillusplantarum, Bacteroidesthetaiotaomicron, Ruminococcusobeum, Coprococcuscatus, Bacteroidesvulgatus, Akkermansiamuciniphila, and Veillonellaparvula for its potential to restore in vitro propionate concentrations upon antibiotic-induced microbial dysbiosis. Using the mucosal simulator of the human intestinal microbial ecosystem (M-SHIME), we challenged the simulated colon microbiome with clindamycin. Addition of the propionogenic consortium resulted in successful colonization and subsequent restoration of propionate levels, while a positive effect on the mitochondrial membrane potential (ΔΨm) was observed in comparison with the controls. Our results support the development and application of next generation probiotics, which are composed of multiple bacterial strains with diverse functionality and phylogenetic background.}, }
@article {pmid31214144, year = {2019}, author = {Dai, D and Wang, T and Wu, S and Gao, NL and Chen, WH}, title = {Metabolic Dependencies Underlie Interaction Patterns of Gut Microbiota During Enteropathogenesis.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1205}, doi = {10.3389/fmicb.2019.01205}, pmid = {31214144}, issn = {1664-302X}, abstract = {In recent decades, increasing evidence has strongly suggested that gut microbiota play an important role in many intestinal diseases including inflammatory bowel disease (IBD) and colorectal cancer (CRC). The composition of gut microbiota is thought to be largely shaped by interspecies competition for available resources and also by cooperative interactions. However, to what extent the changes could be attributed to external factors such as diet of choice and internal factors including mutual relationships among gut microbiota, respectively, are yet to be elucidated. Due to the advances of high-throughput sequencing technologies, flood of (meta)-genome sequence information and high-throughput biological data are available for gut microbiota and their association with intestinal diseases, making it easier to gain understanding of microbial physiology at the systems level. In addition, the newly developed genome-scale metabolic models that cover significant proportion of known gut microbes enable researchers to analyze and simulate the system-level metabolic response in response to different stimuli in the gut, providing deeper biological insights. Using metabolic interaction network based on pair-wise metabolic dependencies, we found the same interaction pattern in two IBD datasets and one CRC datasets. We report here for the first time that the growth of significantly enriched bacteria in IBD and CRC patients could be boosted by other bacteria including other significantly increased ones. Conversely, the growth of probiotics could be strongly inhibited from other species, including other probiotics. Therefore, it is very important to take the mutual interaction of probiotics into consideration when developing probiotics or &quot;microbial based therapies.&quot; Together, our metabolic interaction network analysis can predict majority of the changes in terms of the changed directions in the gut microbiota during enteropathogenesis. Our results thus revealed unappreciated interaction patterns between species could underlie alterations in gut microbiota during enteropathogenesis, and between probiotics and other microbes. Our methods provided a new framework for studying interactions in gut microbiome and their roles in health and disease.}, }
@article {pmid31214131, year = {2019}, author = {You, YA and Yoo, JY and Kwon, EJ and Kim, YJ}, title = {Blood Microbial Communities During Pregnancy Are Associated With Preterm Birth.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1122}, doi = {10.3389/fmicb.2019.01122}, pmid = {31214131}, issn = {1664-302X}, abstract = {Microbial infection of the placenta, amniotic fluid, vaginal canal, and oral cavity is known to significantly contribute to preterm birth (PTB). Although microbes can be translocated into the blood, little is known regarding the blood microbiota during pregnancy. To assess changes in the microbiome during pregnancy, blood samples were obtained 2 or 3 times during pregnancy from a cohort of 45 pregnant women enrolled between 2008 and 2010. To analyze the association with PTB, we conducted a case-control study involving 41 pregnant women upon admission for preterm labor and rupture of membrane (20 with term delivery; 21 with PTB). Bacterial diversity was assessed in number and composition between the first, second, and third trimesters in term delivered women according to 16S rRNA gene amplicon sequencing, and data were analyzed using Quantitative Insight Into Microbial Ecology (QIIME). Taxonomy was assigned using the GreenGenes 8.15.13 database. Dominant microorganisms at the phylum level in all pregnant women were identified as Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. However, the number and composition of bacteria in women with PTB differed from that in women with term delivery. Firmicutes and Bacteroidetes were more abundant in women with PTB than in women with term delivery, while Proteobacteria was less prevalent in women with PTB. At the genus level, Bacteroides, Lactobacillus, Sphingomonas, Fastidiosipila, Weissella, and Butyricicoccus were enriched in PTB samples. These observational results suggest that several taxa in the maternal blood microbiome are associated with PTB. Further studies are needed to confirm the composition of the blood microbiota in women with PTB. Additionally, the mechanism by which pathogenic microbes in maternal blood cause infection and PTB requires further analysis.}, }
@article {pmid31207046, year = {2019}, author = {Czechowska, K and Lannigan, J and Wang, L and Arcidiacono, J and Ashhurst, TM and Barnard, RM and Bauer, S and Bispo, C and Bonilla, DL and Brinkman, RR and Cabanski, M and Chang, HD and Chakrabarti, L and Chojnowski, G and Cotleur, B and Degheidy, H and Dela Cruz, GV and Eck, S and Elliott, J and Errington, R and Filby, A and Gagnon, D and Gardner, R and Green, C and Gregory, M and Groves, CJ and Hall, C and Hammes, F and Hedrick, M and Hoffman, R and Icha, J and Ivaska, J and Jenner, DC and Jones, D and Kerckhof, FM and Kukat, C and Lanham, D and Leavesley, S and Lee, M and Lin-Gibson, S and Litwin, V and Liu, Y and Molloy, J and Moore, JS and Müller, S and Nedbal, J and Niesner, R and Nitta, N and Ohlsson-Wilhelm, B and Paul, NE and Perfetto, S and Portat, Z and Props, R and Radtke, S and Rayanki, R and Rieger, A and Rogers, S and Rubbens, P and Salomon, R and Schiemann, M and Sharpe, J and Sonder, SU and Stewart, JJ and Sun, Y and Ulrich, H and Van Isterdael, G and Vitaliti, A and van Vreden, C and Weber, M and Zimmermann, J and Vacca, G and Wallace, P and Tárnok, A}, title = {Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2018 Conference Workshops.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {95}, number = {6}, pages = {598-644}, doi = {10.1002/cyto.a.23777}, pmid = {31207046}, issn = {1552-4930}, }
@article {pmid31205409, year = {2019}, author = {Yao, R and Xu, L and Lu, G and Zhu, L}, title = {Evaluation of the Function of Wild Animal Gut Microbiomes Using Next-Generation Sequencing and Bioinformatics and its Relevance to Animal Conservation.}, journal = {Evolutionary bioinformatics online}, volume = {15}, number = {}, pages = {1176934319848438}, doi = {10.1177/1176934319848438}, pmid = {31205409}, issn = {1176-9343}, abstract = {The relationship between animal conservation and the animal gut microbiome is a hot topic in current microbial ecology research. Our group has recently revealed that the occurrence of diverse combinations of gut microbial compositions and functions (metagenomics) in Père David's deer (Elaphurus davidianus) populations is likely to lead to increased evolutionary potential and resilience in response to environmental changes. Thus, considering the effects of diet on the gut microbiome and the importance of a stable gut microbial community to host health, we suggest that a transitional buffer period (with feeding on a regular diet and a diet from the translocation habitat) is needed before animal translocation. When the gut microbiome enters into relatively stable stages and adapts to the new diet from the translocation site, the time is suitable for translocation. Long-term monitoring of the gut microbiomes of translocated animals (by collecting fresh feces and carrying out next-generation sequencing) is still necessary after their translocation.}, }
@article {pmid31204896, year = {2019}, author = {Tian, H and Hui, M and Pan, P and Huang, J and Chen, L and Zhao, J}, title = {Performance and microbial ecology of biofilms adhering on aerated membrane with distinctive conditions for the treatment of domestic sewage.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-9}, doi = {10.1080/09593330.2019.1631890}, pmid = {31204896}, issn = {1479-487X}, abstract = {When used to treat domestic wastewater, biofilms adhering to oxygen-permeable membranes are generally altered by environmental conditions. In this study, the effect of common conditions, including salinity, temperature, air-supplying pressure, flow velocity, influent COD, and NH4-N on the biofilm structure were determined. Principal component analysis revealed that archaeal community was more easily affected by the changing conditions than bacteria. The subsequent redundancy analysis showed that salinity had the most influence on bacteria, followed by temperature, influent COD, flow velocity, pressure, and influent NH4-N. In archaea, temperature had the highest effect, followed by flow velocity, salinity, influent NH4-N, pressure, and influent COD. The key bacterial class Anaerolineae was not easily influenced by the above conditions, but the population probably contributed to the nitrogen removal. Gammaproteobacteria was promoted significantly by influent NH4-N concentration, salinity, and pressure. Betaproteobacteria and Deltaproteobacteria were apparently inhibited by the high salinity and contributed to the organic compound degradation. Flow velocity primarily promoted the growth of Alphaproteobacteria. Candidatus Nitrososphaera had a higher tolerance for salinity but lower tolerance for influent NH4-N than Nitrosomonas. The former probably played a more crucial role in ammoxidation. Methanomethylovorans might disrupt nitrogen removal because it could consume the carbon source for denitrification.}, }
@article {pmid31202406, year = {2019}, author = {Wedel, C and Wenning, M and Dettling, A and Scherer, S and Hinrichs, J}, title = {Resistance of thermophilic spore formers isolated from milk and whey products towards cleaning-in-place conditions: Influence of pH, temperature and milk residues.}, journal = {Food microbiology}, volume = {83}, number = {}, pages = {150-158}, doi = {10.1016/j.fm.2019.05.002}, pmid = {31202406}, issn = {1095-9998}, abstract = {The occurrence of thermophilic spore formers in dairy powders is a major concern for producers worldwide. This study aims to investigate the resistance of thermophilic endospores towards cleaning solutions typically used for cleaning-in-place in dairy manufacturing plants. From eleven tested strains, all were able to survive an alkaline treatment (NaOH) at 65 °C for 10 min (0.5%), whereas at concentrations of 2% eight strains withstood the treatment. Acid solutions were more sporicidal. At 0.5% of HNO3, only three strains survived the treatment. Milk impurities reduced the inactivation effect of the NaOH solutions towards thermophilic spore formers. For two selected strains, a detailed kinetic inactivation in NaOH and HNO3 solutions at different temperatures was performed and non-log-linear inactivation curves were observed. This study highlights the risk of reusing cleaning solutions in dairies.}, }
@article {pmid31202277, year = {2019}, author = {Soverini, M and Turroni, S and Biagi, E and Brigidi, P and Candela, M and Rampelli, S}, title = {HumanMycobiomeScan: a new bioinformatics tool for the characterization of the fungal fraction in metagenomic samples.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {496}, doi = {10.1186/s12864-019-5883-y}, pmid = {31202277}, issn = {1471-2164}, abstract = {BACKGROUND: Modern metagenomic analysis of complex microbial communities produces large amounts of sequence data containing information on the microbiome in terms of bacterial, archaeal, viral and eukaryotic composition. The bioinformatics tools available are mainly devoted to profiling the bacterial and viral fractions and only a few software packages consider fungi. As the human fungal microbiome (human mycobiome) can play an important role in the onset and progression of diseases, a comprehensive description of host-microbiota interactions cannot ignore this component.<br><br>RESULTS: HumanMycobiomeScan is a bioinformatics tool for the taxonomic profiling of the mycobiome directly from raw data of next-generation sequencing. The tool uses hierarchical databases of fungi in order to unambiguously assign reads to fungal species more accurately and > 10,000 times faster than other comparable approaches. HumanMycobiomeScan was validated using in silico generated synthetic communities and then applied to metagenomic data, to characterize the intestinal fungal components in subjects adhering to different subsistence strategies.<br><br>CONCLUSIONS: Although blind to unknown species, HumanMycobiomeScan allows the characterization of the fungal fraction of complex microbial ecosystems with good performance in terms of sample denoising from reads belonging to other microorganisms. HumanMycobiomeScan is most appropriate for well-studied microbiomes, for which most of the fungal species have been fully sequenced. This released version is functionally implemented to work with human-associated microbiota samples. In combination with other microbial profiling tools, HumanMycobiomeScan is a frugal and efficient tool for comprehensive characterization of microbial ecosystems through shotgun metagenomics sequencing.}, }
@article {pmid31201518, year = {2019}, author = {Moisan, K and Cordovez, V and van de Zande, EM and Raaijmakers, JM and Dicke, M and Lucas-Barbosa, D}, title = {Volatiles of pathogenic and non-pathogenic soil-borne fungi affect plant development and resistance to insects.}, journal = {Oecologia}, volume = {190}, number = {3}, pages = {589-604}, doi = {10.1007/s00442-019-04433-w}, pmid = {31201518}, issn = {1432-1939}, abstract = {Plants are ubiquitously exposed to a wide diversity of (micro)organisms, including mutualists and antagonists. Prior to direct contact, plants can perceive microbial organic and inorganic volatile compounds (hereafter: volatiles) from a distance that, in turn, may affect plant development and resistance. To date, however, the specificity of plant responses to volatiles emitted by pathogenic and non-pathogenic fungi and the ecological consequences of such responses remain largely elusive. We investigated whether Arabidopsis thaliana plants can differentiate between volatiles of pathogenic and non-pathogenic soil-borne fungi. We profiled volatile organic compounds (VOCs) and measured CO2 emission of 11 fungi. We assessed the main effects of fungal volatiles on plant development and insect resistance. Despite distinct differences in VOC profiles between the pathogenic and non-pathogenic fungi, plants did not discriminate, based on plant phenotypic responses, between pathogenic and non-pathogenic fungi. Overall, plant growth was promoted and flowering was accelerated upon exposure to fungal volatiles, irrespectively of fungal CO2 emission levels. In addition, plants became significantly more susceptible to a generalist insect leaf-chewing herbivore upon exposure to the volatiles of some of the fungi, demonstrating that a prior fungal volatile exposure can negatively affect plant resistance. These data indicate that plant development and resistance can be modulated in response to exposure to fungal volatiles.}, }
@article {pmid31201356, year = {2019}, author = {Szafrański, SP and Kilian, M and Yang, I and Bei der Wieden, G and Winkel, A and Hegermann, J and Stiesch, M}, title = {Diversity patterns of bacteriophages infecting Aggregatibacter and Haemophilus species across clades and niches.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-019-0450-8}, pmid = {31201356}, issn = {1751-7370}, abstract = {Aggregatibacter and Haemophilus species are relevant human commensals and opportunistic pathogens. Consequently, their bacteriophages may have significant impact on human microbial ecology and pathologies. Our aim was to reveal the prevalence and diversity of bacteriophages infecting Aggregatibacter and Haemophilus species that colonize the human body. Genome mining with comparative genomics, screening of clinical isolates, and profiling of metagenomes allowed characterization of 346 phages grouped in 52 clusters and 18 superclusters. Less than 10% of the identified phage clusters were represented by previously characterized phages. Prophage diversity patterns varied significantly for different phage types, host clades, and environmental niches. A more diverse phage community lysogenizes Haemophilus influenzae and Haemophilus parainfluenzae strains than Aggregatibacter actinomycetemcomitans and &quot;Haemophilus ducreyi&quot;. Co-infections occurred more often in &quot;H. ducreyi&quot;. Phages from Aggregatibacter actinomycetemcomitans preferably lysogenized strains of specific serotype. Prophage patterns shared by subspecies clades of different bacterial species suggest similar ecoevolutionary drivers. Changes in frequencies of DNA uptake signal sequences and guanine-cytosine content reflect phage-host long-term coevolution. Aggregatibacter and Haemophilus phages were prevalent at multiple oral sites. Together, these findings should help exploring the ecoevolutionary forces shaping virus-host interactions in the human microbiome. Putative lytic phages, especially phiKZ-like, may provide new therapeutic options.}, }
@article {pmid31195956, year = {2019}, author = {Hirano, H and Takemoto, K}, title = {Difficulty in inferring microbial community structure based on co-occurrence network approaches.}, journal = {BMC bioinformatics}, volume = {20}, number = {1}, pages = {329}, doi = {10.1186/s12859-019-2915-1}, pmid = {31195956}, issn = {1471-2105}, support = {JP17H04703//Japan Society for the Promotion of Science/ ; }, mesh = {*Ecosystem ; *Microbiota ; Models, Biological ; }, abstract = {BACKGROUND: Co-occurrence networks-ecological associations between sampled populations of microbial communities inferred from taxonomic composition data obtained from high-throughput sequencing techniques-are widely used in microbial ecology. Several co-occurrence network methods have been proposed. Co-occurrence network methods only infer ecological associations and are often used to discuss species interactions. However, validity of this application of co-occurrence network methods is currently debated. In particular, they simply evaluate using parametric statistical models, even though microbial compositions are determined through population dynamics.<br><br>RESULTS: We comprehensively evaluated the validity of common methods for inferring microbial ecological networks through realistic simulations. We evaluated how correctly nine widely used methods describe interaction patterns in ecological communities. Contrary to previous studies, the performance of the co-occurrence network methods on compositional data was almost equal to or less than that of classical methods (e.g., Pearson's correlation). The methods described the interaction patterns in dense and/or heterogeneous networks rather inadequately. Co-occurrence network performance also depended upon interaction types; specifically, the interaction patterns in competitive communities were relatively accurately predicted while those in predator-prey (parasitic) communities were relatively inadequately predicted.<br><br>CONCLUSIONS: Our findings indicated that co-occurrence network approaches may be insufficient in interpreting species interactions in microbiome studies. However, the results do not diminish the importance of these approaches. Rather, they highlight the need for further careful evaluation of the validity of these much-used methods and the development of more suitable methods for inferring microbial ecological networks.}, }
@article {pmid31194939, year = {2019}, author = {Johnson, AJ and Vangay, P and Al-Ghalith, GA and Hillmann, BM and Ward, TL and Shields-Cutler, RR and Kim, AD and Shmagel, AK and Syed, AN and ,  and Walter, J and Menon, R and Koecher, K and Knights, D}, title = {Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans.}, journal = {Cell host &amp; microbe}, volume = {25}, number = {6}, pages = {789-802.e5}, doi = {10.1016/j.chom.2019.05.005}, pmid = {31194939}, issn = {1934-6069}, abstract = {Diet is a key determinant of human gut microbiome variation. However, the fine-scale relationships between daily food choices and human gut microbiome composition remain unexplored. Here, we used multivariate methods to integrate 24-h food records and fecal shotgun metagenomes from 34 healthy human subjects collected daily over 17 days. Microbiome composition depended on multiple days of dietary history and was more strongly associated with food choices than with conventional nutrient profiles, and daily microbial responses to diet were highly personalized. Data from two subjects consuming only meal replacement beverages suggest that a monotonous diet does not induce microbiome stability in humans, and instead, overall dietary diversity associates with microbiome stability. Our work provides key methodological insights for future diet-microbiome studies and suggests that food-based interventions seeking to modulate the gut microbiota may need to be tailored to the individual microbiome. Trial Registration: ClinicalTrials.gov: NCT03610477.}, }
@article {pmid31194515, year = {2019}, author = {Ali, M and Wang, Z and Salam, KW and Hari, AR and Pronk, M and van Loosdrecht, MCM and Saikaly, PE}, title = {Importance of Species Sorting and Immigration on the Bacterial Assembly of Different-Sized Aggregates in a Full-Scale Aerobic Granular Sludge Plant.}, journal = {Environmental science &amp; technology}, volume = {53}, number = {14}, pages = {8291-8301}, doi = {10.1021/acs.est.8b07303}, pmid = {31194515}, issn = {1520-5851}, abstract = {In aerobic granular sludge (AGS) systems, different-sized microbial aggregates having different solids retention time (SRT) coexist in the same reactor compartment and are subjected to the same influent wastewater. Thus, the AGS system provides a unique ecosystem to study the importance of local (species sorting) and regional (immigration) processes in bacterial community assembly. The microbial communities of different-sized aggregates (flocs <0.2 mm, small granules (0.2-1.0 mm) and large granules >1.0 mm), influent wastewater, excess sludge and effluent of a full-scale AGS plant were characterized over a steady-state operation period of 6 months. Amplicon sequencing was integrated with mass balance to determine the SRT and net growth rate of operational taxonomic units (OTUs). We found strong evidence of species sorting as opposed to immigration, which was significantly higher at short SRT (i.e., flocs and small granules) than that at long SRT (large granules). Rare OTUs in wastewater belonging to putative functional groups responsible for nitrogen and phosphorus removal were progressively enriched with an increase in microbial aggregates size. In contrast, fecal- and sewage infrastructure-derived microbes progressively decreased in relative abundance with increase in microbial aggregate size. These findings highlight the importance of AGS as a unique model ecosystem to study fundamental microbial ecology concepts.}, }
@article {pmid31191599, year = {2019}, author = {Zhang, B and Xu, S and Xu, W and Chen, Q and Chen, Z and Yan, C and Fan, Y and Zhang, H and Liu, Q and Yang, J and Yang, J and Xiao, C and Xu, H and Ren, J}, title = {Leveraging Fecal Bacterial Survey Data to Predict Colorectal Tumors.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {447}, doi = {10.3389/fgene.2019.00447}, pmid = {31191599}, issn = {1664-8021}, abstract = {Colorectal cancer (CRC) ranks second in cancer-associated mortality and third in the incidence worldwide. Most of CRC follow adenoma-carcinoma sequence, and have more than 90% chance of survival if diagnosed at early stage. But the recommended screening by colonoscopy is invasive, expensive, and poorly adhered to. Recently, several studies reported that the fecal bacteria might provide non-invasive biomarkers for CRC and precancerous tumors. Therefore, we collected and uniformly re-analyzed these published fecal 16S rDNA sequencing datasets to verify the association and identify biomarkers to classify and predict colorectal tumors by random forest method. A total of 1674 samples (330 CRC, 357 advanced adenoma, 141 adenoma, and 846 control) from 7 studies were analyzed in this study. By random effects model and fixed effects model, we observed significant differences in alpha-diversity and beta-diversity between individuals with CRC and the normal colon, but not between adenoma and the normal. We identified various bacterial genera with significant odds ratios for colorectal tumors at different stages. Through building random forest model with 10-fold cross-validation as well as new test datasets, we classified individuals with CRC, advanced adenoma, adenoma and normal colon. All approaches obtained comparable performance at entire OTU level, entire genus level, and the common genus level as measured using AUC. When combined all samples, the AUC of random forest model based on 12 common genera reached 0.846 for CRC, although the predication performed poorly for advance adenoma and adenoma.}, }
@article {pmid31191490, year = {2019}, author = {Chronopoulou, PM and Salonen, I and Bird, C and Reichart, GJ and Koho, KA}, title = {Metabarcoding Insights Into the Trophic Behavior and Identity of Intertidal Benthic Foraminifera.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1169}, doi = {10.3389/fmicb.2019.01169}, pmid = {31191490}, issn = {1664-302X}, abstract = {Foraminifera are ubiquitous marine protists with an important role in the benthic carbon cycle. However, morphological observations often fail to resolve their exact taxonomic placement and there is a lack of field studies on their particular trophic preferences. Here, we propose the application of metabarcoding as a tool for the elucidation of the in situ feeding behavior of benthic foraminifera, while also allowing the correct taxonomic assignment of the feeder, using the V9 region of the 18S (small subunit; SSU) rRNA gene. Living foraminiferal specimens were collected from two intertidal mudflats of the Wadden Sea and DNA was extracted from foraminiferal individuals and from the surrounding sediments. Molecular analysis allowed us to confirm that our foraminiferal specimens belong to three genetic types: Ammonia sp. T6, Elphidium sp. S5 and Haynesina sp. S16. Foraminiferal intracellular eukaryote communities reflected to an extent those of the surrounding sediments but at different relative abundances. Unlike sediment eukaryote communities, which were largely determined by the sampling site, foraminiferal intracellular eukaryote communities were driven by foraminiferal species, followed by sediment depth. Our data suggests that Ammonia sp. T6 can predate on metazoan classes, whereas Elphidium sp. S5 and Haynesina sp. S16 are more likely to ingest diatoms. These observations, alongside the use of metabarcoding in similar ecological studies, significantly contribute to our overall understanding of the ecological roles of these protists in intertidal benthic environments and their position and function in the benthic food webs.}, }
@article {pmid31189482, year = {2019}, author = {Bouslimani, A and da Silva, R and Kosciolek, T and Janssen, S and Callewaert, C and Amir, A and Dorrestein, K and Melnik, AV and Zaramela, LS and Kim, JN and Humphrey, G and Schwartz, T and Sanders, K and Brennan, C and Luzzatto-Knaan, T and Ackermann, G and McDonald, D and Zengler, K and Knight, R and Dorrestein, PC}, title = {The impact of skin care products on skin chemistry and microbiome dynamics.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {47}, doi = {10.1186/s12915-019-0660-6}, pmid = {31189482}, issn = {1741-7007}, abstract = {BACKGROUND: Use of skin personal care products on a regular basis is nearly ubiquitous, but their effects on molecular and microbial diversity of the skin are unknown. We evaluated the impact of four beauty products (a facial lotion, a moisturizer, a foot powder, and a deodorant) on 11 volunteers over 9 weeks.<br><br>RESULTS: Mass spectrometry and 16S rRNA inventories of the skin revealed decreases in chemical as well as in bacterial and archaeal diversity on halting deodorant use. Specific compounds from beauty products used before the study remain detectable with half-lives of 0.5-1.9 weeks. The deodorant and foot powder increased molecular, bacterial, and archaeal diversity, while arm and face lotions had little effect on bacterial and archaeal but increased chemical diversity. Personal care product effects last for weeks and produce highly individualized responses, including alterations in steroid and pheromone levels and in bacterial and archaeal ecosystem structure and dynamics.<br><br>CONCLUSIONS: These findings may lead to next-generation precision beauty products and therapies for skin disorders.}, }
@article {pmid31187884, year = {2019}, author = {Vissenaekens, H and Grootaert, C and Rajkovic, A and Van De Wiele, T and Calatayud, M}, title = {The response of five intestinal cell lines to anoxic conditions in vitro.}, journal = {Biology of the cell}, volume = {111}, number = {9}, pages = {232-244}, doi = {10.1111/boc.201800076}, pmid = {31187884}, issn = {1768-322X}, support = {BOF (01B04212)//Universiteit Gent/ ; 1S18417N//Fonds Wetenschappelijk Onderzoek/ ; FWO/12R2717N//Fonds Wetenschappelijk Onderzoek/ ; }, abstract = {BACKGROUND INFORMATION: In vivo oxygen levels in tissues range from 1% to 15%, while mechanistic cell culture studies employ an atmospheric oxygen level of 21% to grow cells. These oxygen concentrations are therefore not representative for conditions where the cell response is dependent on oxygen partial pressure. In pathological situation, such as (colon) cancer or chronic inflammation, tissue oxygenation is severely affected, and even under physiological conditions a steep oxygen gradient is present in the large intestine, where epithelial cells co-exist with microbial species, resulting in almost anoxia at the midpoint of the lumen. In these situations, a better characterisation of the essential cellular behaviour under hypoxia or anoxia is required.<br><br>RESULTS: We have characterised the cellular response of commonly used cell cultures for the study of intestinal epithelial processes and colon cancer development (Caco-2, HT-29, SW480, HCT 116 and LoVo) under conventional normoxic conditions (21% O2) and in an anoxic (<0.1% O2) environment generated in an anaerobic chamber. In general, anoxic conditions led to lower levels of oxidative stress, a reduction in reduced glutathione/oxidised glutathione (GSH/GSSG) ratio, the shift of the redox status to oxidised glutathione levels, reduced cell proliferation, decreased barrier function and higher glycolysis rates at the expense of oxidative respiration.<br><br>CONCLUSIONS: Continuous exposure to anoxic conditions, such as occurring at the host-microbe interface in the intestine, may create an adaptive metabolic cellular response of the cells.<br><br>SIGNIFICANCE: Considering adequate oxygen levels is essential for creating more physiologically relevant models for the study of host-microbe interactions and colon cancer development.}, }
@article {pmid31187177, year = {2019}, author = {Johnke, J and Fraune, S and Bosch, TCG and Hentschel, U and Schulenburg, H}, title = {Bdellovibrio and Like Organisms Are Predictors of Microbiome Diversity in Distinct Host Groups.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01395-7}, pmid = {31187177}, issn = {1432-184X}, support = {CRC 1182, project A4//Deutsche Forschungsgemeinschaft (DE)/ ; CRC 1182, project B2//Deutsche Forschungsgemeinschaft (DE)/ ; CRC 1182, project B2//Deutsche Forschungsgemeinschaft (DE)/ ; CRC 1182, project A4//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Biodiversity is generally believed to be a main determinant of ecosystem functioning. This principle also applies to the microbiome and could consequently contribute to host health. According to ecological theory, communities are shaped by top predators whose direct and indirect interactions with community members cause stability and diversity. Bdellovibrio and like organisms (BALOs) are a neglected group of predatory bacteria that feed on Gram-negative bacteria and can thereby influence microbiome composition. We asked whether BALOs can predict biodiversity levels in microbiomes from distinct host groups and environments. We demonstrate that genetic signatures of BALOs are commonly found within the 16S rRNA reads from diverse host taxa. In many cases, their presence, abundance, and especially richness are positively correlated with overall microbiome diversity. Our findings suggest that BALOs can act as drivers of microbial alpha-diversity and should therefore be considered candidates for the restoration of microbiomes and the prevention of dysbiosis.}, }
@article {pmid31187139, year = {2019}, author = {Pacheco, AR and Segrè, D}, title = {A multidimensional perspective on microbial interactions.}, journal = {FEMS microbiology letters}, volume = {366}, number = {11}, pages = {}, doi = {10.1093/femsle/fnz125}, pmid = {31187139}, issn = {1574-6968}, abstract = {Beyond being simply positive or negative, beneficial or inhibitory, microbial interactions can involve a diverse set of mechanisms, dependencies and dynamical properties. These more nuanced features have been described in great detail for some specific types of interactions, (e.g. pairwise metabolic cross-feeding, quorum sensing or antibiotic killing), often with the use of quantitative measurements and insight derived from modeling. With a growing understanding of the composition and dynamics of complex microbial communities for human health and other applications, we face the challenge of integrating information about these different interactions into comprehensive quantitative frameworks. Here, we review the literature on a wide set of microbial interactions, and explore the potential value of a formal categorization based on multidimensional vectors of attributes. We propose that such an encoding can facilitate systematic, direct comparisons of interaction mechanisms and dependencies, and we discuss the relevance of an atlas of interactions for future modeling and rational design efforts.}, }
@article {pmid31186361, year = {2019}, author = {Kehe, J and Kulesa, A and Ortiz, A and Ackerman, CM and Thakku, SG and Sellers, D and Kuehn, S and Gore, J and Friedman, J and Blainey, PC}, title = {Massively parallel screening of synthetic microbial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {26}, pages = {12804-12809}, doi = {10.1073/pnas.1900102116}, pmid = {31186361}, issn = {1091-6490}, support = {F32 CA236425/CA/NCI NIH HHS/United States ; }, abstract = {Microbial communities have numerous potential applications in biotechnology, agriculture, and medicine. Nevertheless, the limited accuracy with which we can predict interspecies interactions and environmental dependencies hinders efforts to rationally engineer beneficial consortia. Empirical screening is a complementary approach wherein synthetic communities are combinatorially constructed and assayed in high throughput. However, assembling many combinations of microbes is logistically complex and difficult to achieve on a timescale commensurate with microbial growth. Here, we introduce the kChip, a droplets-based platform that performs rapid, massively parallel, bottom-up construction and screening of synthetic microbial communities. We first show that the kChip enables phenotypic characterization of microbes across environmental conditions. Next, in a screen of ∼100,000 multispecies communities comprising up to 19 soil isolates, we identified sets that promote the growth of the model plant symbiont Herbaspirillum frisingense in a manner robust to carbon source variation and the presence of additional species. Broadly, kChip screening can identify multispecies consortia possessing any optically assayable function, including facilitation of biocontrol agents, suppression of pathogens, degradation of recalcitrant substrates, and robustness of these functions to perturbation, with many applications across basic and applied microbial ecology.}, }
@article {pmid31186282, year = {2019}, author = {Biancalani, T and Gore, J}, title = {Disentangling bacterial invasiveness from lethality in an experimental host-pathogen system.}, journal = {Molecular systems biology}, volume = {15}, number = {6}, pages = {e8707}, doi = {10.15252/msb.20188707}, pmid = {31186282}, issn = {1744-4292}, abstract = {Quantifying virulence remains a central problem in human health, pest control, disease ecology, and evolutionary biology. Bacterial virulence is typically quantified by the LT50 (i.e., the time taken to kill 50% of infected hosts); however, such an indicator cannot account for the full complexity of the infection process, such as distinguishing between the pathogen's ability to colonize versus kill the hosts. Indeed, the pathogen needs to breach the primary defenses in order to colonize, find a suitable environment to replicate, and finally express the virulence factors that cause disease. Here, we show that two virulence attributes, namely pathogen lethality and invasiveness, can be disentangled from the survival curves of a laboratory population of Caenorhabditis elegans nematodes exposed to three bacterial pathogens: Pseudomonas aeruginosa, Serratia marcescens, and Salmonella enterica We first show that the host population eventually experiences a constant mortality rate, which quantifies the lethality of the pathogen. We then show that the time necessary to reach this constant mortality rate regime depends on the pathogen growth rate and colonization rate, and thus determines the pathogen invasiveness. Our framework reveals that Serratia marcescens is particularly good at the initial colonization of the host, whereas Salmonella enterica is a poor colonizer yet just as lethal once established. Pseudomonas aeruginosa, on the other hand, is both a good colonizer and highly lethal after becoming established. The ability to quantitatively characterize the ability of different pathogens to perform each of these steps has implications for treatment and prevention of disease and for the evolution and ecology of pathogens.}, }
@article {pmid31180804, year = {2019}, author = {Welch, JLM and Dewhirst, FE and Borisy, GG}, title = {Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis.}, journal = {Annual review of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-micro-090817-062503}, pmid = {31180804}, issn = {1545-3251}, abstract = {Microbial communities are complex and dynamic, composed of hundreds of taxa interacting across multiple spatial scales. Advances in sequencing and imaging technology have led to great strides in understanding both the composition and the spatial organization of these complex communities. In the human mouth, sequencing results indicate that distinct sites host microbial communities that not only are distinguishable but to a meaningful degree are composed of entirely different microbes. Imaging suggests that the spatial organization of these communities is also distinct. Together, the literature supports the idea that most oral microbes are site specialists. A clear understanding of microbiota structure at different sites in the mouth enables mechanistic studies, informs the generation of hypotheses, and strengthens the position of oral microbiology as a model system for microbial ecology in general. Expected final online publication date for the Annual Review of Microbiology Volume 73 is September 9, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid31178845, year = {2019}, author = {Berlanas, C and Berbegal, M and Elena, G and Laidani, M and Cibriain, JF and Sagües, A and Gramaje, D}, title = {The Fungal and Bacterial Rhizosphere Microbiome Associated With Grapevine Rootstock Genotypes in Mature and Young Vineyards.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1142}, doi = {10.3389/fmicb.2019.01142}, pmid = {31178845}, issn = {1664-302X}, abstract = {The microbiota colonizing the rhizosphere and the endorhizosphere contribute to plant growth, productivity, carbon sequestration, and phytoremediation. Several studies suggested that different plants types and even genotypes of the same plant species harbor partially different microbiomes. Here, we characterize the rhizosphere bacterial and fungal microbiota across five grapevine rootstock genotypes cultivated in the same soil at two vineyards and sampling dates over 2 years by 16S rRNA gene and ITS high-throughput amplicon sequencing. In addition, we use quantitative PCR (qPCR) approach to measure the relative abundance and dynamic changes of fungal pathogens associated with black-foot disease. The objectives were to (1) unravel the effects of rootstock genotype on microbial communities in the rhizosphere of grapevine and (2) to compare the relative abundances of sequence reads and DNA amount of black-foot disease pathogens. Host genetic control of the microbiome was evident in the rhizosphere of the mature vineyard. Microbiome composition also shifted as year of sampling, and fungal diversity varied with sampling moments. Linear discriminant analysis identified specific bacterial (i.e., Bacillus) and fungal (i.e., Glomus) taxa associated with grapevine rootstocks. Host genotype did not predict any summary metrics of rhizosphere α- and β-diversity in the young vineyard. Regarding black-foot associated pathogens, a significant correlation between sequencing reads and qPCR was observed. In conclusion, grapevine rootstock genotypes in the mature vineyard were associated with different rhizosphere microbiomes. The latter could also have been affected by age of the vineyard, soil properties or field management practices. A more comprehensive study is needed to decipher the cause of the rootstock microbiome selection and the mechanisms by which grapevines are able to shape their associated microbial community. Understanding the vast diversity of bacteria and fungi in the rhizosphere and the interactions between microbiota and grapevine will facilitate the development of future strategies for grapevine protection.}, }
@article {pmid31177395, year = {2019}, author = {Liu, H and Wu, M and Liu, J and Qu, Y and Gao, Y and Ren, A}, title = {Tripartite Interactions Between Endophytic Fungi, Arbuscular Mycorrhizal Fungi, and Leymus chinensis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01394-8}, pmid = {31177395}, issn = {1432-184X}, support = {31570433//National Natural Science Foundation of China/ ; 2016YFC0500702//National Key Research and Development Program/ ; }, abstract = {Grasses often establish multiple simultaneous symbiotic associations with endophytic fungi and arbuscular mycorrhizal fungi (AMF). Many studies have examined pair-wise interactions between plants and endophytic fungi or between plants and AMF, overlooking the interplays among multiple endosymbionts and their combined impacts on hosts. Here, we examined both the way in which each symbiont affects the other symbionts and the tripartite interactions between leaf endophytic fungi, AMF, and Leymus chinensis. As for AMF, different species (Glomus etunicatum, GE; Glomus mosseae, GM; Glomus claroideum, GC; and Glomus intraradices, GI) and AMF richness (no AMF, single AMF taxa, double AMF mixtures, triple AMF mixtures, and all four together) were considered. Our results showed that significant interactions were observed between endophytes and AMF, with endophytes interacting antagonistically with GM but synergistically with GI. No definitive interactions were observed between the endophytes and GE or GC. Additionally, the concentration of endophytes in the leaf sheath was positively correlated with the concentration of AMF in the roots under low AMF richness. The shoot biomass of L. chinensis was positively related to both endophyte concentration and AMF concentration, with only endophytes contributing to shoot biomass more than AMF. Endophytes and AMF increased shoot growth by contributing to phosphorus uptake. The interactive effects of endophytes and AMF on host growth were affected by the identity of AMF species. The beneficial effect of the endophytes decreased in response to GM but increased in response to GI. However, no influences were observed with other GC and GE. In addition, endophyte presence can alter the response of host plants to AMF richness. When leaf endophytes were absent, shoot biomass increased with higher AMF richness, only the influence of AMF species identity outweighed that of AMF richness. However, when leaf endophytes were present, no significant association was observed between AMF richness and shoot biomass. AMF species identity rather than AMF richness promoted shoot growth. The results of this study demonstrate that the outcomes of interspecific symbiotic interactions are very complex and vary with partner identity such that the effects of simultaneous symbioses cannot be generalized and highlight the need for studies to evaluate fitness response of all three species, as the interactive effects may not be the same for each partner.}, }
@article {pmid31176264, year = {2019}, author = {Patel, R and Kunjadia, P and Koringa, P and Joshi, C and Kunjadiya, A}, title = {Microbiological profiles in clinical and subclinical cases of mastitis in milking Jafarabadi buffalo.}, journal = {Research in veterinary science}, volume = {125}, number = {}, pages = {94-99}, doi = {10.1016/j.rvsc.2019.05.012}, pmid = {31176264}, issn = {1532-2661}, abstract = {Mastitis is one of the important diseases affecting the dairy industry across the globe. Identification of bacterial pathogens associated with mastitis becomes essential in order to understand the etiology of disease which in turn will help to new strategies to control it. Microbial diversity analysis using pyrosequencing is widely studied for mastitis pathogens in dairy cows. However it is unexplored in case of buffalo. In the present study 16SrDNA gene pyrosequencing was used to characterize microbiota associated with clinical and subclinical mastitis in 28 Jafarabadi buffalo. The obtained sequencing data were analyzed by Quantitative Insights into Microbial Ecology (QIIME) and statistical analysis was done using Paleontological Statistics (PAST). Pyrosequencing produced 47.3 million base pairs reads. Phylogenetic profiles using ribosomal database revealed differences in abundance of Staphylococcus (25.95%, 10.09% and 0.03%), Enterococcus (10.80%, 8.72% and 0.36%), Escherichia (8.88%, 0.38% and 0.00%), Streptococcus (3.97%, 0.42% and 0.00%), Lactococcus (3.73%, 23.96% and 0.01%), and Ralstonia (0.54%, 12.72% and 0.00%), genera in clinical, subclinical and healthy samples, respectively. Different microbial profiles in clinical and subclinical mastitis in buffalo suggest the composition of bacteria in the milk is more diverse and complex hence single therapeutic regimes cannot be applied.}, }
@article {pmid31175190, year = {2019}, author = {Schmidt, JE and Vannette, RL and Igwe, A and Blundell, R and Casteel, CL and Gaudin, ACM}, title = {Effects of Agricultural Management on Rhizosphere Microbial Structure and Function in Processing Tomato Plants.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {16}, pages = {}, doi = {10.1128/AEM.01064-19}, pmid = {31175190}, issn = {1098-5336}, abstract = {Agricultural management practices affect bulk soil microbial communities and the functions they carry out, but it remains unclear how these effects extend to the rhizosphere in different agroecosystem contexts. Given close linkages between rhizosphere processes and plant nutrition and productivity, understanding how management practices impact this critical zone is of great importance to optimize plant-soil interactions for agricultural sustainability. A comparison of six paired conventional-organic processing tomato farms was conducted to investigate relationships between management, soil physicochemical parameters, and rhizosphere microbial community composition and functions. Organically managed fields were higher in soil total N and NO3-N, total and labile C, plant Ca, S, and Cu, and other essential nutrients, while soil pH was higher in conventionally managed fields. Differential abundance, indicator species, and random forest analyses of rhizosphere communities revealed compositional differences between organic and conventional systems and identified management-specific microbial taxa. Phylogeny-based trait prediction showed that these differences translated into more abundant pathogenesis-related gene functions in conventional systems. Structural equation modeling revealed a greater effect of soil biological communities than physicochemical parameters on plant outcomes. These results highlight the importance of rhizosphere-specific studies, as plant selection likely interacts with management in regulating microbial communities and functions that impact agricultural productivity.IMPORTANCE Agriculture relies, in part, on close linkages between plants and the microorganisms that live in association with plant roots. These rhizosphere bacteria and fungi are distinct from microbial communities found in the rest of the soil and are even more important to plant nutrient uptake and health. Evidence from field studies shows that agricultural management practices such as fertilization and tillage shape microbial communities in bulk soil, but little is known about how these practices affect the rhizosphere. We investigated how agricultural management affects plant-soil-microbe interactions by comparing soil physical and chemical properties, plant nutrients, and rhizosphere microbial communities from paired fields under organic and conventional management. Our results show that human management effects extend even to microorganisms living in close association with plant roots and highlight the importance of these bacteria and fungi to crop nutrition and productivity.}, }
@article {pmid31173081, year = {2019}, author = {Roodt, D and Li, Z and Van de Peer, Y and Mizrachi, E}, title = {Loss of Wood Formation Genes in Monocot Genomes.}, journal = {Genome biology and evolution}, volume = {11}, number = {7}, pages = {1986-1996}, doi = {10.1093/gbe/evz115}, pmid = {31173081}, issn = {1759-6653}, abstract = {Woodiness (secondary xylem derived from vascular cambium) has been gained and lost multiple times in the angiosperms, but has been lost ancestrally in all monocots. Here, we investigate the conservation of genes involved in xylogenesis in fully sequenced angiosperm genomes, hypothesizing that monocots have lost some essential orthologs involved in this process. We analyzed the conservation of genes preferentially expressed in the developing secondary xylem of two eudicot trees in the sequenced genomes of 26 eudicot and seven monocot species, and the early diverging angiosperm Amborella trichopoda. We also reconstructed a regulatory model of early vascular cambial cell identity and differentiation and investigated the conservation of orthologs across the angiosperms. Additionally, we analyzed the genome of the aquatic seagrass Zostera marina for additional losses of genes otherwise essential to, especially, secondary cell wall formation. Despite almost complete conservation of orthology within the early cambial differentiation gene network, we show a clear pattern of loss of genes preferentially expressed in secondary xylem in the monocots that are highly conserved across eudicot species. Our study provides candidate genes that may have led to the loss of vascular cambium in the monocots, and, by comparing terrestrial angiosperms to an aquatic monocot, highlights genes essential to vasculature on land.}, }
@article {pmid31171824, year = {2019}, author = {Verspecht, T and Rodriguez Herrero, E and Khodaparast, L and Khodaparast, L and Boon, N and Bernaerts, K and Quirynen, M and Teughels, W}, title = {Development of antiseptic adaptation and cross-adapatation in selected oral pathogens in vitro.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {8326}, doi = {10.1038/s41598-019-44822-y}, pmid = {31171824}, issn = {2045-2322}, support = {C24/17/086//KU Leuven (Katholieke Universiteit Leuven)/ ; C24/17/086//KU Leuven (Katholieke Universiteit Leuven)/ ; C24/17/086//KU Leuven (Katholieke Universiteit Leuven)/ ; C24/17/086//KU Leuven (Katholieke Universiteit Leuven)/ ; C24/17/086//KU Leuven (Katholieke Universiteit Leuven)/ ; C24/17/086//KU Leuven (Katholieke Universiteit Leuven)/ ; C24/17/086//KU Leuven (Katholieke Universiteit Leuven)/ ; }, abstract = {There is evidence that pathogenic bacteria can adapt to antiseptics upon repeated exposure. More alarming is the concomitant increase in antibiotic resistance that has been described for some pathogens. Unfortunately, effects of adaptation and cross-adaptation are hardly known for oral pathogens, which are very frequently exposed to antiseptics. Therefore, this study aimed to determine the in vitro increase in minimum inhibitory concentrations (MICs) in oral pathogens after repeated exposure to chlorhexidine or cetylpyridinium chloride, to examine if (cross-)adaptation to antiseptics/antibiotics occurs, if (cross-)adaptation is reversible and what the potential underlying mechanisms are. When the pathogens were exposed to antiseptics, their MICs significantly increased. This increase was in general at least partially conserved after regrowth without antiseptics. Some of the adapted species also showed cross-adaptation, as shown by increased MICs of antibiotics and the other antiseptic. In most antiseptic-adapted bacteria, cell-surface hydrophobicity was increased and mass-spectrometry analysis revealed changes in expression of proteins involved in a wide range of functional domains. These in vitro data shows the adaptation and cross-adaptation of oral pathogens to antiseptics and antibiotics. This was related to changes in cell surface hydrophobicity and in expression of proteins involved in membrane transport, virulence, oxidative stress protection and metabolism.}, }
@article {pmid31171429, year = {2019}, author = {Raskin, L and Nielsen, PH}, title = {Editorial overview: Integrating biotechnology and microbial ecology in urban water infrastructure through a microbiome continuum viewpoint.}, journal = {Current opinion in biotechnology}, volume = {57}, number = {}, pages = {iii-vi}, doi = {10.1016/j.copbio.2019.05.001}, pmid = {31171429}, issn = {1879-0429}, }
@article {pmid31167950, year = {2019}, author = {Ghashghavi, M and Belova, SE and Bodelier, PLE and Dedysh, SN and Kox, MAR and Speth, DR and Frenzel, P and Jetten, MSM and Lücker, S and Lüke, C}, title = {Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSphere.00631-18}, pmid = {31167950}, issn = {2379-5042}, abstract = {Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial methanotrophs belong to the Proteobacteria, Verrucomicrobia, and NC10 phyla. Within the Proteobacteria phylum, they can be divided into type Ia, type Ib, and type II methanotrophs. Type Ia and type II are well represented by isolates. Contrastingly, the vast majority of type Ib methanotrophs have not been able to be cultivated so far. Here, we compared the distributions of type Ib lineages in different environments. Whereas the cultivated type Ib methanotrophs (Methylococcus and Methylocaldum) are found in landfill and upland soils, lineages that are not represented by isolates are mostly dominant in freshwater environments, such as paddy fields and lake sediments. Thus, we observed a clear niche differentiation within type Ib methanotrophs. Our subsequent isolation attempts resulted in obtaining a pure culture of a novel type Ib methanotroph, tentatively named &quot;Methylotetracoccus oryzae&quot; C50C1. Strain C50C1 was further characterized to be an obligate methanotroph, containing C16:1ω9c as the major membrane phospholipid fatty acid, which has not been found in other methanotrophs. Genome analysis of strain C50C1 showed the presence of two pmoCAB operon copies and XoxF5-type methanol dehydrogenase in addition to MxaFI. The genome also contained genes involved in nitrogen and sulfur cycling, but it remains to be demonstrated if and how these help this type Ib methanotroph to adapt to fluctuating environmental conditions in freshwater ecosystems.IMPORTANCE Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study focused on the diversity and adaptation of aerobic methane-oxidizing bacteria in different environments by comparing their phenotypic and genotypic properties. We used lab-scale microcosms to create a countergradient of oxygen and methane for preenrichment, followed by classical isolation techniques to obtain methane-oxidizing bacteria from a freshwater environment. This resulted in the discovery and isolation of a novel methanotroph with interesting physiological and genomic properties that could possibly make this bacterium able to cope with fluctuating environmental conditions.}, }
@article {pmid31166992, year = {2019}, author = {Weinroth, MD and Britton, BC and McCullough, KR and Martin, JN and Geornaras, I and Knight, R and Belk, KE and Metcalf, JL}, title = {Ground beef microbiome changes with antimicrobial decontamination interventions and product storage.}, journal = {PloS one}, volume = {14}, number = {6}, pages = {e0217947}, doi = {10.1371/journal.pone.0217947}, pmid = {31166992}, issn = {1932-6203}, abstract = {Ground beef makes up more than half of the beef consumed in the U.S. market. Although numerous studies have been conducted on microbial safety and shelf life of ground beef limited work has been done using a culture-independent approach. While past studies have allowed for the evaluation of a few organisms of interest, there is limited work on the microbial community associated with fresh ground beef. In order to have a more complete picture of the microbial ecology of the product, a culture-independent approach utilizing 16S rRNA gene amplicon sequencing was used. The objectives of this study were to characterize the fresh ground beef microbiome and the effect that antimicrobial interventions and antioxidants, applied to beef trim before grinding, and product storage have on community composition using 16S rRNA gene amplicon sequencing. Beef trimmings were treated with antimicrobials and an antioxidant. Samples were ground, loafed, and overwrapped before being packaged in modified-atmosphere packaging. Samples were in dark storage for 21 days followed by five days in retail display. Periodically during storage, samples were collected for microbiological analysis and DNA isolation. Due to low microbial biomass, only 52 of 210 samples were included in the final analysis. These samples represented two antimicrobial treatments (peroxyacetic acid, and a sulfuric acid and sodium sulfate blend) and a control, from day-15 of dark storage and day-5 of retail display. As sample age increased, so did the number of raw reads (P < 0.001) and aerobic plate counts (P < 0.001), which were correlated (r = 0.94, P = 0.017). Across all samples, lactic acid bacteria were most abundant followed by Enterobacteriaceae; several rare taxa were also identified (namely Geobacillus, Thermus, and Sporosarcina). Antimicrobial treatment altered the bacterial alpha (P < 0.001) and beta (P = 0.001) diversity, while storage day altered alpha (P = 0.001) diversity. Enterobacteriaceae relative abundance differed (P < 0.05) among treatments and was highest in control samples. In addition to confirming previously described dominant microbial differences in culture-dependent results, these data identified genera not typically associated with ground beef and allowed for study of shifts in the entire microbiome and not just a subset of indicator organisms.}, }
@article {pmid31166650, year = {2019}, author = {Maaroufi, NI and Nordin, A and Palmqvist, K and Hasselquist, NJ and Forsmark, B and Rosenstock, NP and Wallander, H and Gundale, MJ}, title = {Anthropogenic nitrogen enrichment enhances soil carbon accumulation by impacting saprotrophs rather than ectomycorrhizal fungal activity.}, journal = {Global change biology}, volume = {25}, number = {9}, pages = {2900-2914}, doi = {10.1111/gcb.14722}, pmid = {31166650}, issn = {1365-2486}, support = {CMF1122373//Center for Environmental Research in Umeå/ ; H14-0018-GBN//Royal Swedish Academy of Agrilculture and Forestry/ ; 2014-00497//Svenska Forskningsrådet Formas/ ; }, abstract = {There is evidence that anthropogenic nitrogen (N) deposition enhances carbon (C) sequestration in boreal forest soils. However, it is unclear how free-living saprotrophs (bacteria and fungi, SAP) and ectomycorrhizal (EM) fungi responses to N addition impact soil C dynamics. Our aim was to investigate how SAP and EM communities are impacted by N enrichment and to estimate whether these changes influence decay of litter and humus. We conducted a long-term experiment in northern Sweden, maintained since 2004, consisting of ambient, low N additions (0, 3, 6, and 12 kg N ha-1 year-1) simulating current N deposition rates in the boreal region, as well as a high N addition (50 kg N ha-1 year-1). Our data showed that long-term N enrichment impeded mass loss of litter, but not of humus, and only in response to the highest N addition treatment. Furthermore, our data showed that EM fungi reduced the mass of N and P in both substrates during the incubation period compared to when only SAP organisms were present. Low N additions had no effect on microbial community structure, while the high N addition decreased fungal and bacterial biomasses and altered EM fungi and SAP community composition. Actinomycetes were the only bacterial SAP to show increased biomass in response to the highest N addition. These results provide a mechanistic understanding of how anthropogenic N enrichment can influence soil C accumulation rates and suggest that current N deposition rates in the boreal region (≤12 kg N ha-1 year-1) are likely to have a minor impact on the soil microbial community and the decomposition of humus and litter.}, }
@article {pmid31165188, year = {2019}, author = {Li, Y and Guo, Q and He, F and Li, Y and Xue, Q and Lai, H}, title = {Biocontrol of Root Diseases and Growth Promotion of the Tuberous Plant Aconitum carmichaelii Induced by Actinomycetes Are Related to Shifts in the Rhizosphere Microbiota.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01388-6}, pmid = {31165188}, issn = {1432-184X}, support = {31600407//Youth Fund of the National Natural Science Foundation of China/ ; Z109021616//Fundamental Research Funds for the Central Universities of China/ ; 2012BAD14B11//National Key Technology R&amp;D Program of China/ ; }, abstract = {Soil Actinomycetes have been used as biocontrol agents against soil-borne plant diseases, yet little is known about their effects on the structure of the rhizosphere microbiota and the long-term effects on crop yield and disease intensity after the application of Actinomycetes is stopped. Here, we conducted 3-year plot experiments to investigate the roles of two Actinomycetes strains (Streptomyces pactum Act12 and Streptomyces rochei D74) in the biocontrol of soil-borne root diseases and growth promotion of monkhood (Aconitum carmichaelii). We also examined their long-term effects after soil application of a mixed Actinomycetes preparation (spore powder) was completed. High-throughput sequencing was used to analyze shifts in the rhizosphere microbiota. The antifungal activity and root colonization ability of the two Actinomycetes were also tested. Disease severity of southern blight and root rot decreased following application of the Actinomycetes preparation, whereas biomass yield of tubers increased compared with the control group. Significant effects of disease control and plant growth promotion were also observed after application was stopped. The Actinomycetes preparation induced marked increases in the abundance of beneficial microbes and decreases in the abundance of harmful microbes in rhizosphere soil. Adding cell-free culture filtrates of both strains Act12 and D74 inhibited the growth of fungal pathogens capable of causing southern blight (Sclerotium rolfsii) and root rot (Fusarium oxysporum) in A. carmichaelii. A GFP-labeled strain was used to show that D74 can colonize roots of A. carmichaelii. In conclusion, a preparation of two Actinomycetes plays a role in the biocontrol of root diseases and growth promotion of A. carmichaelii by inhibiting pathogen growth and shaping the rhizosphere microbiota.}, }
@article {pmid31165187, year = {2019}, author = {Kruger, A}, title = {Functional Redundancy of Batrachochytrium dendrobatidis Inhibition in Bacterial Communities Isolated from Lithobates clamitans Skin.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01387-7}, pmid = {31165187}, issn = {1432-184X}, abstract = {The cutaneous microbial community can influence the health of amphibians exposed to Batrachochytrium dendrobatidis (Bd), a fungal pathogen that has contributed to recent amphibian declines. Resistance to Bd in amphibian populations is correlated with the presence of anti-Bd cutaneous microbes, which confer disease resistance by inhibiting Bd growth. I aimed to determine if green frogs (Lithobates clamitans), an abundant and widely distributed species in New Jersey, harbored bacteria that inhibit Bd and whether the presence and identity of these microbes varied among sites. I used in vitro challenge assays to determine if bacteria isolated from green frog skin could inhibit or enhance the growth of Bd. I found that green frogs at all sites harbored anti-Bd bacteria. However, there were differences in Bd inhibition capabilities among bacterial isolates identified as the same operational taxonomic unit (OTU), lending support to the idea that phylogenetic relatedness does not always predict Bd inhibition status. Additionally, anti-Bd bacterial richness did not vary by site, but the composition of anti-Bd bacterial taxa was distinct at each site. This suggests that there is functional redundancy of Bd inhibition across unique communities of anti-Bd symbionts found on frogs at different sites. These findings highlight the need to better elucidate the structure-function relationship of microbiomes and their role in disease resistance.}, }
@article {pmid31164870, year = {2019}, author = {Guarcello, R and Gaglio, R and Todaro, A and Alfonzo, A and Schicchi, R and Cirlincione, F and Moschetti, G and Francesca, N}, title = {Insights Into the Cultivable Microbial Ecology of &quot;Manna&quot; Ash Products Extracted From Fraxinus angustifolia (Oleaceae) Trees in Sicily, Italy.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {984}, doi = {10.3389/fmicb.2019.00984}, pmid = {31164870}, issn = {1664-302X}, abstract = {Microbial communities characterizing a specific food matrix, generally, strongly contribute to both its composition, and properties for food applications. To our knowledge, this is the first study to investigate the cultivable microbial ecology of Sicilian &quot;Manna&quot; ash products in order to acquire new information on the hygienic quality, shelf-life and potential application of this traditional food. To this purpose, several manna samples belonging to different commercial categories were collected and subjected to the analysis of bacteria, yeasts, and filamentous fungi. Furthermore, an investigation of the sugar content and physicochemical parameters was performed. The results of our study followed the trend generally reported for other sugary foods. Conversely, as regards microbiological analyses, in the present study, the presence of microorganisms at high levels confirmed their survival in stressing conditions characterizing this food matrix in a viable and cultivable form. Most species were osmophilic, endophytic bacteria, antagonistic of fungi pathogen of plants. Yeasts were the most abundant microbial populations and a total of six species were identified: Candida aaseri, Candida lactis-condensi, Citeromyces matritensis, Lachancea thermotolerans, Saccharomyces cerevisiae, and Zygosaccharomyces bailii. Filamentous fungi included five genera, which were considered common contaminants of honey and of other foods due to their xerophilic characteristics. Interestingly, our results suggest that the strains of L. thermotolerans isolated in this study might be evaluated for their potential to act as starters either singly or in multi-combination for food applications.}, }
@article {pmid31164404, year = {2019}, author = {Bik, HM}, title = {Microbial Metazoa Are Microbes Too.}, journal = {mSystems}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSystems.00109-19}, pmid = {31164404}, issn = {2379-5077}, abstract = {Microbial metazoa inhabit a certain &quot;Goldilocks zone,&quot; where conditions are just right for the continued ignorance of these taxa. These microscopic animal species have body sizes of <1 mm and include diverse groups such as nematodes, tardigrades, kinorhynchs, loriciferans, and platyhelminths. The majority of species are too large to be considered in single-cell genomics approaches, yet too small to be wrapped into international genome sequencing initiatives. Other microbial eukaryote groups (namely the fungal and protist communities) have gained significant momentum in recent years, driven by a strong community of researchers united behind a common goal of culturing and sequencing new representatives. However, due to historical factors and difficult taxonomy, persistent research silos still exist for most microbial metazoan groups, and public molecular databases remain sparsely populated. Here, I argue that small metazoa should be embraced as a key component of microbial ecology studies, promoting a holistic and cutting-edge view of natural ecosystems.}, }
@article {pmid31163430, year = {2019}, author = {Philip, N and Leishman, SJ and Bandara, HMHN and Walsh, LJ}, title = {Casein Phosphopeptide-Amorphous Calcium Phosphate Attenuates Virulence and Modulates Microbial Ecology of Saliva-Derived Polymicrobial Biofilms.}, journal = {Caries research}, volume = {}, number = {}, pages = {1-7}, doi = {10.1159/000499869}, pmid = {31163430}, issn = {1421-976X}, abstract = {BACKGROUND: Casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) acts as a salivary biomimetic that provides bioavailable calcium and phosphate ions to augment fluoride-mediated remineralisation of early caries lesions. However, there are indications that it may also have beneficial ecological effects on the oral microbiome.<br><br>OBJECTIVE: This in vitro study investigated whether CPP-ACP could influence microbial counts, acidogenicity, and the relative abundance of specific caries- and health-associated bacterial -species in polymicrobial biofilms.<br><br>METHODS: Saliva-derived polymicrobial biofilms were grown for 96 h in a cariogenic environment and treated every 12 h with 2% CPP-ACP or vehicle control. Colony forming units (CFUs) and acidogenicity were estimated from the treated biofilms. Microbial ecological effects of CPP-ACP were assessed based on the relative abundance of 14 specific caries- and health-associated -bacterial species using a real-time quantitative PCR assay. -Results: CPP-ACP-treated biofilms showed relatively modest, but significant, reductions in microbial CFUs (21% reduction, p = 0.008) and acidogenicity (33% reduction, p < 0.001), compared to the control-treated biofilms. The CPP-ACP treated biofilms also exhibited significantly lower bacterial loads of cariogenic Scardovia wiggsiae (fold change 0.017, p < 0.001) and Prevotella denticola(fold change 0.005, p < 0.001), and higher bacterial loads of commensal Streptococcus sanguinis(fold change 30.22, p < 0.001), S. mitis/oralis(fold change 9.66, p = 0.012), and S. salivarius/thermophilus(fold change 89.35, p < 0.001) than the control-treated biofilms.<br><br>CONCLUSIONS: The results indicate that CPP-ACP has virulence-attenuating attributes that can influence a beneficial microbial ecological change in the biofilm.}, }
@article {pmid31163257, year = {2019}, author = {Momper, L and Hu, E and Moore, KR and Skoog, EJ and Tyler, M and Evans, AJ and Bosak, T}, title = {Metabolic versatility in a modern lineage of cyanobacteria from terrestrial hot springs.}, journal = {Free radical biology &amp; medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.freeradbiomed.2019.05.036}, pmid = {31163257}, issn = {1873-4596}, abstract = {The extent of oxygenated environments on the early Earth was much lower than today, and cyanobacteria were critical players in Earth's shift from widespread anoxia to oxygenated surface environments. Extant cyanobacteria that aggregate into cones, tufts and ridges are used to understand the long record of photosynthesis and microbe-mineral interactions during times when oxygen was much lower, i.e., the Archean and the Proterozoic. To better understand the metabolic versatility and physiological properties of these organisms, we examined publicly available genomes of cyanobacteria from modern terrestrial hydrothermal systems and a newly sequenced genome of a cyanobacterium isolated from conical and ridged microbialites that grow in occasionally sulfidic hydrothermal springs in Yellowstone National Park, USA. Phylogenomic analyses reveal that cyanobacteria from globally distributed terrestrial and shallow marine hydrothermal systems form a monophyletic clade within the Cyanobacteria phylum. Comparative genomics of this clade reveals the genetic capacity for oxygenic photosynthesis that uses photosystems I and II, and anoxygenic photosynthesis that uses a putative sulfide quinone reductase to oxidize sulfide and bypass photosystem II. Surprisingly large proportions of the newly sequenced genome from Yellowstone National Park are also dedicated to secondary metabolite production (15.1-15.6%), of which ∼6% can be attributed to antibiotic production and resistance genes. All this may be advantageous to benthic, mat-forming photosynthesizers that have to compete for light and nutrients in sporadically or permanently sulfidic environments, and may have also improved the tolerance of ancient counterparts of these cyanobacteria to sulfidic conditions in benthic communities that colonized the coastal margins in the Archean and the Proterozoic.}, }
@article {pmid31162610, year = {2019}, author = {Etienne-Mesmin, L and Chassaing, B and Desvaux, M and De Paepe, K and Gresse, R and Sauvaitre, T and Forano, E and Van de Wiele, T and Schüller, S and Juge, N and Blanquet-Diot, S}, title = {Experimental models to study intestinal microbes-mucus interactions in health and disease.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuz013}, pmid = {31162610}, issn = {1574-6976}, abstract = {A close symbiotic relationship exists between the intestinal microbiota and its host. A critical component of gut homeostasis is the presence of a mucus layer covering the gastrointestinal tract. Mucus is a viscoelastic gel at the interface between the luminal content and the host tissue that provides a habitat to the gut microbiota and protects the intestinal epithelium. The review starts by setting up the biological context underpinning the need for experimental models to study gut bacteria-mucus interactions in the digestive environment. We provide an overview of the structure and function of intestinal mucus and mucins, their interactions with intestinal bacteria (including commensal, probiotics and pathogenic microorganisms) and their role in modulating health and disease states. We then describe the characteristics and potentials of experimental models currently available to study the mechanisms underpinning the interaction of mucus with gut microbes, including in vitro, ex vivo and in vivo models. We then discuss the limitations and challenges facing this field of research.}, }
@article {pmid31161957, year = {2019}, author = {Ilgrande, C and Mastroleo, F and Christiaens, MER and Lindeboom, REF and Prat, D and Van Hoey, O and Ambrozova, I and Coninx, I and Heylen, W and Pommerening-Roser, A and Spieck, E and Boon, N and Vlaeminck, SE and Leys, N and Clauwaert, P}, title = {Reactivation of Microbial Strains and Synthetic Communities After a Spaceflight to the International Space Station: Corroborating the Feasibility of Essential Conversions in the MELiSSA Loop.}, journal = {Astrobiology}, volume = {19}, number = {9}, pages = {1167-1176}, doi = {10.1089/ast.2018.1973}, pmid = {31161957}, issn = {1557-8070}, abstract = {To sustain human deep space exploration or extra-terrestrial settlements where no resupply from the Earth or other planets is possible, technologies for in situ food production, water, air, and waste recovery need to be developed. The Micro-Ecological Life Support System Alternative (MELiSSA) is such a Regenerative Life Support System (RLSS) and it builds on several bacterial bioprocesses. However, alterations in gravity, temperature, and radiation associated with the space environment can affect survival and functionality of the microorganisms. In this study, representative strains of different carbon and nitrogen metabolisms with application in the MELiSSA were selected for launch and Low Earth Orbit (LEO) exposure. An edible photoautotrophic strain (Arthrospira sp. PCC 8005), a photoheterotrophic strain (Rhodospirillum rubrum S1H), a ureolytic heterotrophic strain (Cupriavidus pinatubonensis 1245), and combinations of C. pinatubonensis 1245 and autotrophic ammonia and nitrite oxidizing strains (Nitrosomonas europaea ATCC19718, Nitrosomonas ureae Nm10, and Nitrobacter winogradskyi Nb255) were sent to the International Space Station (ISS) for 7 days. There, the samples were exposed to 2.8 mGy, a dose 140 times higher than on the Earth, and a temperature of 22°C ± 1°C. On return to the Earth, the cultures were reactivated and their growth and activity were compared with terrestrial controls stored under refrigerated (5°C ± 2°C) or room temperature (22°C ± 1°C and 21°C ± 0°C) conditions. Overall, no difference was observed between terrestrial and ISS samples. Most cultures presented lower cell viability after the test, regardless of the type of exposure, indicating a harsher effect of the storage and sample preparation than the spaceflight itself. Postmission analysis revealed the successful survival and proliferation of all cultures except for Arthrospira, which suffered from the premission depressurization test. These observations validate the possibility of launching, storing, and reactivating bacteria with essential functionalities for microbial bioprocesses in RLSS.}, }
@article {pmid31161232, year = {2019}, author = {Mojica, KDA and Carlson, CA and Behrenfeld, MJ}, title = {Regulation of Low and High Nucleic Acid Fluorescent Heterotrophic Prokaryote Subpopulations and Links to Viral-Induced Mortality Within Natural Prokaryote-Virus Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01393-9}, pmid = {31161232}, issn = {1432-184X}, support = {NNX15AF30G//National Aeronautics and Space Administration/ ; 1537943//National Science Foundation/ ; }, abstract = {Flow cytometric analysis of marine prokaryotes routinely reveals two distinct clusters of heterotrophic cells referred to as high nucleic acid fluorescent (HNA) and low nucleic acid fluorescent (LNA) populations. Evidence suggests that these may represent physiologically and ecologically distinct prokaryote populations. According to the &quot;kill the winner&quot; hypothesis, viral lysis reduces the efficiency of the microbial loop by decreasing the biomass and activity of the most abundant and active members of a population (i.e., competition specialist). Thus, viral-induced mortality may vary according to the physiology of HNA and LNA cells, with implications for the marine carbon cycle. Here, the abundance and production of heterotrophic prokaryotic populations were assessed in the North Atlantic during two phases of the annual plankton cycle and related to bottom-up (i.e., organic carbon variability) and top-down processes (i.e., viral abundance and lytic production). Our results demonstrate that the relative abundance of HNA and LNA heterotrophic cells and heterotrophic prokaryote production vary according to organic carbon variability in the water column, which can be strongly influenced by the physical eddy field (i.e., type of eddy: cyclonic, anticyclonic, or no eddy). In addition, the abundance and lytic production of virus subpopulations were correlated with the cellular production and abundance of heterotrophic HNA and LNA prokaryote communities. Our data suggest group- and activity-specific linkages between hosts and viruses (i.e., HNA-V1 and LNA-V2). Specifically, V1 had a greater contribution to total viral production (i.e., 2.6-fold higher than V2 viruses), similar to their putative host. Finally, we explore potential implications of group- and activity-specific linkages between host and virus groups on the flux of carbon through the microbial food web.}, }
@article {pmid31159875, year = {2019}, author = {Wright, RJ and Gibson, MI and Christie-Oleza, JA}, title = {Understanding microbial community dynamics to improve optimal microbiome selection.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {85}, doi = {10.1186/s40168-019-0702-x}, pmid = {31159875}, issn = {2049-2618}, support = {NE/K009044/1//Natural Environment Research Council/ ; BB/M01116X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; 638631//European Research Council/International ; }, abstract = {BACKGROUND: Artificial selection of microbial communities that perform better at a desired process has seduced scientists for over a decade, but the method has not been systematically optimised nor the mechanisms behind its success, or failure, determined. Microbial communities are highly dynamic and, hence, go through distinct and rapid stages of community succession, but the consequent effect this may have on artificially selected communities is unknown.<br><br>RESULTS: Using chitin as a case study, we successfully selected for microbial communities with enhanced chitinase activities but found that continuous optimisation of incubation times between selective transfers was of utmost importance. The analysis of the community composition over the entire selection process revealed fundamental aspects in microbial ecology: when incubation times between transfers were optimal, the system was dominated by Gammaproteobacteria (i.e. main bearers of chitinase enzymes and drivers of chitin degradation), before being succeeded by cheating, cross-feeding and grazing organisms.<br><br>CONCLUSIONS: The selection of microbiomes to enhance a desired process is widely used, though the success of artificially selecting microbial communities appears to require optimal incubation times in order to avoid the loss of the desired trait as a consequence of an inevitable community succession. A comprehensive understanding of microbial community dynamics will improve the success of future community selection studies.}, }
@article {pmid31158321, year = {2019}, author = {Jaba, A and Dagher, F and Hamidi Oskouei, AM and Guertin, C and Constant, P}, title = {Physiological traits and relative abundance of species as explanatory variables of co-occurrence pattern of cultivable bacteria associated with chia seeds.}, journal = {Canadian journal of microbiology}, volume = {65}, number = {9}, pages = {668-680}, doi = {10.1139/cjm-2019-0052}, pmid = {31158321}, issn = {1480-3275}, abstract = {Deciphering the rules defining microbial community assemblage is envisioned as a promising strategy to improve predictions of pathogens colonization and proliferation in food. Despite the increasing number of studies reporting microbial co-occurrence patterns, only a few attempts have been made to challenge them in experimental or theoretical frameworks. Here, we tested the hypothesis that observed variations in co-occurrence patterns can be explained by taxonomy, relative abundance, and physiological traits of microbial species. We used PCR amplicon sequencing of taxonomic markers to assess distribution and co-occurrence patterns of bacterial and fungal species found in 25 chia (Salvia hispanica L.) samples originating from eight different sources. The use of nutrient-rich and oligotrophic media enabled isolation of 71 strains encompassing 16 bacterial species, of which five corresponded to phylotypes represented in the molecular survey. Tolerance to different growth inhibitors and antibiotics was tested to assess the physiological traits of these isolates. Divergence of physiological traits and relative abundance of each pair of species explained 69% of the co-occurrence profile displayed by cultivable bacterial phylotypes in chia. Validation of this ecological network conceptualization approach to more food products is required to integrate microbial species co-occurrence patterns in predictive microbiology.}, }
@article {pmid31156569, year = {2019}, author = {Joyner, JL and Kerwin, J and Deeb, M and Lozefski, G and Prithiviraj, B and Paltseva, A and McLaughlin, J and Groffman, P and Cheng, Z and Muth, TR}, title = {Green Infrastructure Design Influences Communities of Urban Soil Bacteria.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {982}, doi = {10.3389/fmicb.2019.00982}, pmid = {31156569}, issn = {1664-302X}, abstract = {The importance of natural ecosystem processes is often overlooked in urban areas. Green Infrastructure (GI) features have been constructed in urban areas as elements to capture and treat excess urban runoff while providing a range of ancillary benefits, e.g., ecosystem processes mediated by microorganisms that improve air and water quality, in addition to the associations with plant and tree rhizospheres. The objective of this study was to characterize the bacterial community and diversity in engineered soils (Technosols) of five types of GI in New York City; vegetated swales, right of way bioswales (ROWB; including street-side infiltration systems and enhanced tree pits), and an urban forest. The design of ROWB GI features directly connects with the road to manage street runoff, which can increase the Technosol saturation and exposure to urban contaminants washed from the street and carried into the GI feature. This GI design specifically accommodates dramatic pulses of water that influence the bacterial community composition and diversity through the selective pressure of contaminants or by disturbance. The ROWB had the highest biodiversity, but no significant correlation with levels of soil organic matter and microbially-mediated biogeochemical functions. Another important biogeochemical parameter for soil bacterial communities is pH, which influenced the bacterial community composition, consistent with studies in non-urban soils. Bacterial community composition in GI features showed signs of anthropogenic disturbance, including exposure to animal feces and chemical contaminants, such as petroleum products. Results suggest the overall design and management of GI features with a channeled connection with street runoff, such as ROWB, have a comprehensive effect on soil parameters (particularly organic matter) and the bacterial community. One key consideration for future assessments of GI microbial community would be to determine the source of organic matter and elucidate the relationship between vegetation, Technosol, and bacteria in the designed GI features.}, }
@article {pmid31154270, year = {2019}, author = {Yue, SJ and Liu, J and Wang, WX and Wang, AT and Yang, XY and Guan, HS and Wang, CY and Yan, D}, title = {Berberine treatment-emergent mild diarrhea associated with gut microbiota dysbiosis.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {116}, number = {}, pages = {109002}, doi = {10.1016/j.biopha.2019.109002}, pmid = {31154270}, issn = {1950-6007}, abstract = {Berberine (BBR) is a non-prescription drug to treat various bacteria-associated diarrheas. However, BBR has also been reported to cause diarrhea in clinic, with underlying mechanisms poorly understood. Because altered gut microbial ecology is a potential basis for diarrhea, this study was conducted to investigate the impact of BBR on gut microbiota of treatment-emergent diarrhea. BBR treatment (200 mg/kg, i.g.) in normal rats exhibited no significant changes in serum biochemical parameters but mild diarrhea occurred, accompanied with the decreased gastrointestinal transit time and increased fecal moisture, suggestive of the local effects of BBR in the intestine. Colon histology revealed the decreased abundance of mucus-filled goblet cells in BBR group. Although BBR-treated rats had the enlarged cecum with watery caecal digesta, short-chain fatty acids concentration was significantly lower than control group. Additionally, BBR caused gut microbiota dysbiosis by evaluating the decreased observed species number and Shannon index. BBR increased the relative abundances of families Porphyromonadaceae and Prevotellaceae as well as genera Parabacteroides, Prevotellaceae_UCG-001 and Prevotellaceae_NK3B31_group. Spearman's correlation analysis revealed family Prevotellaceae and genus Prevotellaceae_UCG-001 as the most prominent drivers of the BBR treatment-emergent diarrhea, correlating positively with fecal moisture but negatively with gastrointestinal transit time. This study therefore demonstrated that the treatment-emergent mild diarrhea of BBR was most likely due to the dysbiosis of the gut microbiota.}, }
@article {pmid31152013, year = {2019}, author = {Herlemann, DPR and Markert, S and Meeske, C and Andersson, AF and de Bruijn, I and Hentschker, C and Unfried, F and Becher, D and Jürgens, K and Schweder, T}, title = {Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {15}, pages = {}, doi = {10.1128/AEM.00825-19}, pmid = {31152013}, issn = {1098-5336}, abstract = {Enclosure experiments are frequently used to investigate the impact of changing environmental conditions on microbial assemblages. Yet, how the incubation itself challenges complex bacterial communities is thus far unknown. In this study, metaproteomic profiling, 16S rRNA gene analyses, and cell counts were combined to evaluate bacterial communities derived from marine, mesohaline, and oligohaline conditions after long-term batch incubations. Early in the experiment, the three bacterial communities were highly diverse and differed significantly in their compositions. Manipulation of the enclosures with terrigenous dissolved organic carbon resulted in notable differences compared to the control enclosures at this early phase of the experiment. However, after 55 days, bacterial communities in the manipulated and the control enclosures under marine and mesohaline conditions were all dominated by gammaproteobacterium Spongiibacter In the oligohaline enclosures, actinobacterial cluster I of the hgc group (hgc-I) remained abundant in the late phase of the incubation. Metaproteome analyses suggested that the ability to use outer membrane-based internal energy stores, in addition to the previously described grazing resistance, may enable the gammaproteobacterium Spongiibacter to prevail in long-time incubations. Under oligohaline conditions, the utilization of external recalcitrant carbon appeared to be more important (hgc-I). Enclosure experiments with complex natural microbial communities are important tools to investigate the effects of manipulations. However, species-specific properties, such as individual carbon storage strategies, can cause manipulation-independent effects and need to be considered when interpreting results from enclosures.IMPORTANCE In microbial ecology, enclosure studies are often used to investigate the effect of single environmental factors on complex bacterial communities. However, in addition to the manipulation, unintended effects (&quot;bottle effect&quot;) may occur due to the enclosure itself. In this study, we analyzed the bacterial communities that originated from three different salinities of the Baltic Sea, comparing their compositions and physiological activities both at the early stage and after 55 days of incubation. Our results suggested that internal carbon storage strategies impact the success of certain bacterial species, independent of the experimental manipulation. Thus, while enclosure experiments remain valid tools in environmental research, microbial community composition shifts must be critically followed. This investigation of the metaproteome during long-term batch enclosures expanded our current understanding of the so-called &quot;bottle effect,&quot; which is well known to occur during enclosure experiments.}, }
@article {pmid31150591, year = {2019}, author = {Gleason, ML and Zhang, R and Batzer, JC and Sun, G}, title = {Stealth Pathogens: The Sooty Blotch and Flyspeck Fungal Complex.}, journal = {Annual review of phytopathology}, volume = {57}, number = {}, pages = {135-164}, doi = {10.1146/annurev-phyto-082718-100237}, pmid = {31150591}, issn = {1545-2107}, abstract = {Sooty blotch and flyspeck (SBFS) fungi produce superficial, dark-colored colonies on fruits, stems, and leaves of many plant genera. These blemishes are economically damaging on fruit, primarily apple and pear, because they reduce the sale price of fresh fruit. Fungicide spray programs can control SBFS but are costly and impair human and environmental health; thus, less chemically intensive management strategies are needed. Although the scientific study of SBFS fungi began nearly 200 years ago, recent DNA-driven studies revealed an unexpectedly diverse complex: more than 100 species in 30 genera of Ascomycota and Basidiomycota. Analysis of evolutionary phylogenetics and phylogenomics indicates that the evolution of SBFS fungi from plant-penetrating ancestors to noninvasive ectophytic parasites was accompanied by a massive contraction of pathogenicity-related genes, including plant cell wall-degrading enzymes and effectors, and an expansion of cuticle-degradation genes. This article reviews progress in understanding SBFS taxonomy and ecology and improving disease management. We also highlight recent breakthroughs in reconstructing the evolutionary origins of these unusual plant pathogens and delineating adaptations to their ectophytic niche.}, }
@article {pmid31147731, year = {2019}, author = {Arias, A and Saiz, E and Calbet, A}, title = {Towards an Understanding of Diel Feeding Rhythms in Marine Protists: Consequences of Light Manipulation.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01390-y}, pmid = {31147731}, issn = {1432-184X}, support = {FERMI (CGL2014-59227-R)//MINECO/FEDER, UE/ ; FPI (BES-2015-074092)//MINECO/ ; }, abstract = {Temporal programs synchronised with the daily cycle are of adaptive importance for organisms exposed to periodic fluctuations. This study deepens into several aspects of the exogenous and endogenous nature of microbial grazers. We investigated the diel rhythms of cell division and feeding activity of four marine protists under different light regimes. In particular, we tested if the feeding cycle of protistan grazers could be mediated by a light-aided enhancement of prey digestion, and also explored the consequences of cell division on diel feeding rhythms. Cell division occurred at night for the heterotrophic dinoflagellates Gyrodinium dominans and Oxyrrhis marina. In contrast, the mixotrophic dinoflagellate Karlodinium armiger and the ciliate Strombidium sp. mostly divided during the day. Additionally, a significant diurnal feeding rhythm was observed in all species. When exposed to continuous darkness, nearly all species maintained the cell division rhythm, but lost the feeding cycle within several hours/days (with the exception of O. marina that kept the rhythm for 9.5 days). Additional feeding experiments under continuous light also showed the same pattern. We conclude that the feeding rhythms of protistan grazers are generally regulated not by cell division nor by the enhancement of digestion by light. Our study, moreover, indicates that the cell division cycle is under endogenous control, whereas an external trigger is required to maintain the feeding rhythm, at least for most of the species studied here.}, }
@article {pmid31145076, year = {2019}, author = {Farfour, E and Henry, A and Razillard, A and Cardot, E and Limousin, L and Cahen, P and Jolly, E and Vasse, M and Mathonnet, D}, title = {Rapid identification of Escherichia coli colonies from clinical sample inoculated on CHROMagar Orientation media (Becton Dickinson).}, journal = {Annales de biologie clinique}, volume = {77}, number = {3}, pages = {350-352}, doi = {10.1684/abc.2019.1446}, pmid = {31145076}, issn = {1950-6112}, abstract = {CHROMmagar Orientation media (Becton Dickinson) was developed and validated for the culture of urinary samples. It allows a direct identification of E. coli colonies without additional tests. As CHROMmagar Orientation media is superior to non-chromogenic media for the distinction of enterobacterial colonies, it is used for the inoculation of a large variety of samples in clinical laboratories. Direct identification of E. coli colonies cultured from these samples is not validated by the manufacturer. The difference in microbial ecology and the nature of the sample may impact CHROMagar Orientation performances for this use. We evaluated these media for the direct identification of E. coli colonies from 410 samples (excluding urine). Its sensitivity of 99% allows a direct identification of E. coli colonies cultured from a wide variety of samples. On-site testing using a large number of representative samples, allows laboratories to assess agar media performance and adapt their uses. Suppliers who are aware of frequent and non-recommended use of their culture media should perform tests and if conclusive, adapt their technical instructions.}, }
@article {pmid31144710, year = {2019}, author = {Villa-Rodriguez, JA and Ifie, I and Gonzalez-Aguilar, GA and Roopchand, DE}, title = {The Gastrointestinal Tract as Prime Site for Cardiometabolic Protection by Dietary Polyphenols.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/advances/nmz038}, pmid = {31144710}, issn = {2156-5376}, support = {K01 AT008829/AT/NCCIH NIH HHS/United States ; R01 AT010242/AT/NCCIH NIH HHS/United States ; }, abstract = {Substantial evidence from nutritional epidemiology links polyphenol-rich diets with reduced incidence of chronic disorders; however, biological mechanisms underlying polyphenol-disease relations remain enigmatic. Emerging evidence is beginning to unmask the contribution of the gastrointestinal tract on whole-body energy homeostasis, suggesting that the intestine may be a prime target for intervention and a fundamental site for the metabolic actions of polyphenols. During their transit through the gastrointestinal tract, polyphenols may activate enteric nutrient sensors ensuing appropriate responses from other peripheral organs to regulate metabolic homeostasis. Furthermore, polyphenols can modulate the absorption of glucose, attenuating exaggerated hormonal responses and metabolic imbalances. Polyphenols that escape absorption are metabolized by the gut microbiota and the resulting catabolites may act locally, activating nuclear receptors that control enteric functions such as intestinal permeability. Finally, polyphenols modulate gut microbial ecology, which can have profound effects on cardiometabolic health.}, }
@article {pmid31144004, year = {2019}, author = {Clairmont, LK and Slawson, RM}, title = {Contrasting Water Quality Treatments Result in Structural and Functional Changes to Wetland Plant-Associated Microbial Communities in Lab-Scale Mesocosms.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01389-5}, pmid = {31144004}, issn = {1432-184X}, support = {GR-RGPGP 2014-00060-R//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada/ ; 471103-2015, PGSD//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {The impact of contrasting water quality treatments on wetland plant-associated microbial communities was investigated in this study using 12 lab-scale wetland mesocosms (subsurface flow design) planted with reed canary grass (Phalaris arundinacea) or water speedwell (Veronica anagallis-aquatica) over a 13-week period. Mesocosms received water collected from two sites along the Grand River (Ontario, Canada) designated as having either high or poor water quality according to Grand River Conservation Authority classifications. All mesocosms were established using sediment collected from the high water quality site and received water from this source pre-treatment. Resulting changes to microbial community structure were assessed using PCR-denaturing gel gradient electrophoresis (DGGE) on microbial 16S rDNA sequences extracted from rhizoplane, rhizosphere, and water samples before and after exposure to water quality treatments. Functional community changes were determined using Biolog™ EcoPlates which assess community-level carbon source utilization profiles. Wetland mesocosm removal of inorganic nutrients (N, P) and fecal coliforms was also determined, and compared among treatments. Treatment-specific effects were assessed using a repeated measures restricted maximum likelihood (REML) analysis. Structural and functional characteristics of rhizoplane microbial communities were significantly influenced by the interaction between plant species and water treatment (P = 0.04, P = 0.01). Plant species-specific effects were observed for rhizosphere structural diversity (P = 0.01) and wetland water community metabolic diversity (P = 0.03). The effect of water treatment alone was significant for structural diversity measurements in wetland water communities (P = 0.03). The effect of plant species, water quality treatment, and the interaction between the two is dependent on the microhabitat type (rhizoplane, rhizosphere, or water). Rhizoplane communities appear to be more sensitive to water quality-specific environmental changes and may be a good candidate for microbial community-based monitoring of wetland ecosystems.}, }
@article {pmid31144003, year = {2019}, author = {Han, D and Kang, HY and Kang, CK and Unno, T and Hur, HG}, title = {Seasonal Mixing-Driven System in Estuarine-Coastal Zone Triggers an Ecological Shift in Bacterial Assemblages Involved in Phytoplankton-Derived DMSP Degradation.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01392-w}, pmid = {31144003}, issn = {1432-184X}, support = {Long-term Marine Ecosystem Research//Ministry of Oceans and Fisheries/ ; NRF-2016R1A6A3A11931896//National Research Foundation of Korea/ ; }, abstract = {The coastal zone has distinguishable but tightly connected ecosystems from rivers to the ocean and globally contributes to nutrient cycling including phytoplankton-derived organic matter. Particularly, bacterial contributions to phytoplankton-derived dimethylsulfoniopropionate (DMSP) degradation have been recently evaluated by using advanced sequencing technologies to understand their role in the marine microbial food web. Here, we surveyed the bacterial diversity and community composition under seasonal water mixing in the bay of Gwangyang (GW), a semi-enclosed estuary at the southern tip of the Korea Peninsula. We detected phylogenetic dissimilarities among season-specific habitats in GW and their specific bacterial taxa. Additionally, bacterial contribution to degradation of phytoplankton-derived DMSP from estuarine to coastal waters at euphotic depths in GW was investigated as the presence or absence of DMSP demethylation gene, encoded by dmdA. Among the operational taxonomic units (OTUs) in GW bacterial communities, the most dominant and ubiquitous OTU1 was affiliated with the SAR11 clade (SAR11-OTU). The population dynamics of SAR11-OTU in dmdA-detected GW waters suggest that water mass mixing plays a major role in shaping bacterial communities involved in phytoplankton-derived DMSP demethylation.}, }
@article {pmid31144002, year = {2019}, author = {Bittar, C and Machado, RRG and Comelis, MT and Bueno, LM and Beguelini, MR and Morielle-Versute, E and Nogueira, ML and Rahal, P}, title = {Alphacoronavirus Detection in Lungs, Liver, and Intestines of Bats from Brazil.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01391-x}, pmid = {31144002}, issn = {1432-184X}, support = {2015/09704-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 165802/2015-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Bats are flying mammals distributed worldwide known to host several types of Coronavirus (CoV). Since they were reported as the probable source of spillover of highly pathogenic CoV into the human population, investigating the circulation of this virus in bats around the world became of great importance. We analyzed samples from 103 bats from two distinct regions in Brazil. Coronavirus from the Alphacoronavirus genus was detected in 12 animals, 11 from São José do Rio Preto-SP region and 1 from Barreiras-BA region, resulting in a prevalence of 17.18% and 2.56% respectively. The virus was detected not only in intestines but also in lungs and liver. Phylogenetic analysis based on nsP12 genomic region suggests that the sequences group according to host family and sampling location. Studies on the circulation of these viruses in bats remain important to understand the ecology and evolutionary relationship of these pathogens.}, }
@article {pmid31143408, year = {2019}, author = {Conrads, G and Wendt, LK and Hetrodt, F and Deng, ZL and Pieper, D and Abdelbary, MMH and Barg, A and Wagner-Döbler, I and Apel, C}, title = {Deep sequencing of biofilm microbiomes on dental composite materials.}, journal = {Journal of oral microbiology}, volume = {11}, number = {1}, pages = {1617013}, doi = {10.1080/20002297.2019.1617013}, pmid = {31143408}, issn = {2000-2297}, abstract = {Background: The microbiome on dental composites has not been studied in detail before. It has not been conclusively clarified whether restorative materials influence the oral microbiome. Methods: We used Illumina Miseq next-generation sequencing of the 16S V1-V2 region to compare the colonisation patterns of bovine enamel (BE) and the composite materials Grandio Flow (GF) and Grandio Blocs (GB) after 48 h in vivo in 14 volunteers. Applying a new method to maintain the oral microbiome ex vivo for 48 h also, we compared the microbiome on GF alone and with the new antimicrobial substance carolacton (GF+C). Results: All in vitro biofilm communities showed a higher diversity and richness than those grown in vivo but the very different atmospheric conditions must be considered. Contrary to expectations, there were only a few significant differences between BE and the composite materials GB and GF either in vivo or in vitro: Oribacterium, Peptostreptococcaceae [XI][G-1] and Streptococcus mutans were more prevalent and Megasphaera, Prevotella oulorum, Veillonella atypica, V. parvula, Gemella morbillorum, and Fusobacterium periodonticum were less prevalent on BE than on composites. In vivo, such preferences were only significant for Granulicatella adiacens (more prevalent on BE) and Fusobacterium nucleatum subsp. animalis (more prevalent on composites). On DNA sequence level, there were no significant differences between the biofilm communities on GF and GF+C. Conclusion: We found that the oral microbiome showed an increased richness when grown on various composites compared to BE in vitro, but otherwise changed only slightly independent of the in vivo or in vitro condition. Our new ex vivo biofilm model might be useful for pre-clinical testing of preventive strategies.}, }
@article {pmid31143165, year = {2019}, author = {Miller, JI and Techtmann, S and Fortney, J and Mahmoudi, N and Joyner, D and Liu, J and Olesen, S and Alm, E and Fernandez, A and Gardinali, P and GaraJayeva, N and Askerov, FS and Hazen, TC}, title = {Oil Hydrocarbon Degradation by Caspian Sea Microbial Communities.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {995}, doi = {10.3389/fmicb.2019.00995}, pmid = {31143165}, issn = {1664-302X}, abstract = {The Caspian Sea, which is the largest landlocked body of water on the planet, receives substantial annual hydrocarbon input from anthropogenic sources (e.g., industry, agriculture, oil exploration, and extraction) and natural sources (e.g., mud volcanoes and oil seeps). The Caspian Sea also receives substantial amounts of runoff from agricultural and municipal sources, containing nutrients that have caused eutrophication and subsequent hypoxia in the deep, cold waters. The effect of decreasing oxygen saturation and cold temperatures on oil hydrocarbon biodegradation by a microbial community is not well characterized. The purpose of this study was to investigate the effect of oxic and anoxic conditions on oil hydrocarbon biodegradation at cold temperatures by microbial communities derived from the Caspian Sea. Water samples were collected from the Caspian Sea for study in experimental microcosms. Major taxonomic orders observed in the ambient water samples included Flavobacteriales, Actinomycetales, and Oceanospirillales. Microcosms were inoculated with microbial communities from the deepest waters and amended with oil hydrocarbons for 17 days. Hydrocarbon degradation and shifts in microbial community structure were measured. Surprisingly, oil hydrocarbon biodegradation under anoxic conditions exceeded that under oxic conditions; this was particularly evident in the degradation of aromatic hydrocarbons. Important microbial taxa associated with the anoxic microcosms included known oil degraders such as Oceanospirillaceae. This study provides knowledge about the ambient community structure of the Caspian Sea, which serves as an important reference point for future studies. Furthermore, this may be the first report in which anaerobic biodegradation of oil hydrocarbons exceeds aerobic biodegradation.}, }
@article {pmid31143163, year = {2019}, author = {Kuramae, EE and Leite, MFA and Suleiman, AKA and Gough, CM and Castillo, BT and Faller, L and Franklin, RB and Syring, J}, title = {Wood Decay Characteristics and Interspecific Interactions Control Bacterial Community Succession in Populus grandidentata (Bigtooth Aspen).}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {979}, doi = {10.3389/fmicb.2019.00979}, pmid = {31143163}, issn = {1664-302X}, abstract = {Few studies have investigated bacterial community succession and the role of bacterial decomposition over a continuum of wood decay. Here, we identified how (i) the diversity and abundance of bacteria changed along a chronosequence of decay in Populus grandidentata (bigtooth aspen); (ii) bacterial community succession was dependent on the physical and chemical characteristics of the wood; (iii) interspecific bacterial interactions may mediate community structure. Four hundred and fifty-nine taxa were identified through Illumina sequencing of 16S rRNA amplicons from samples taken along a continuum of decay, representing standing dead trees, downed wood, and soil. Community diversity increased as decomposition progressed, peaking in the most decomposed trees. While a small proportion of taxa displayed a significant pattern in regards to decay status of the host log, many bacterial taxa followed a stochastic distribution. Changes in the water availability and chemical composition of standing dead and downed trees and soil were strongly coupled with shifts in bacterial communities. Nitrogen was a major driver of succession and nitrogen-fixing taxa of the order Rhizobiales were abundant early in decomposition. Recently downed logs shared 65% of their bacterial abundance with the microbiomes of standing dead trees while only sharing 16% with soil. As decay proceeds, bacterial communities appear to respond less to shifting resource availability and more to interspecific bacterial interactions - we report an increase in both the proportion (+9.3%) and the intensity (+62.3%) of interspecific interactions in later stages of decomposition, suggesting the emergence of a more complex community structure as wood decay progresses.}, }
@article {pmid31139578, year = {2019}, author = {Castillo, DJ and Rifkin, RF and Cowan, DA and Potgieter, M}, title = {The Healthy Human Blood Microbiome: Fact or Fiction?.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {148}, doi = {10.3389/fcimb.2019.00148}, pmid = {31139578}, issn = {2235-2988}, abstract = {The blood that flows perpetually through our veins and arteries performs numerous functions essential to our survival. Besides distributing oxygen, this vast circulatory system facilitates nutrient transport, deters infection and dispenses heat throughout our bodies. Since human blood has traditionally been considered to be an entirely sterile environment, comprising only blood-cells, platelets and plasma, the detection of microbes in blood was consistently interpreted as an indication of infection. However, although a contentious concept, evidence for the existence of a healthy human blood-microbiome is steadily accumulating. While the origins, identities and functions of these unanticipated micro-organisms remain to be elucidated, information on blood-borne microbial phylogeny is gradually increasing. Given recent advances in microbial-hematology, we review current literature concerning the composition and origin of the human blood-microbiome, focusing on bacteria and their role in the configuration of both the diseased and healthy human blood-microbiomes. Specifically, we explore the ways in which dysbiosis in the supposedly innocuous blood-borne bacterial microbiome may stimulate pathogenesis. In addition to exploring the relationship between blood-borne bacteria and the development of complex disorders, we also address the matter of contamination, citing the influence of contaminants on the interpretation of blood-derived microbial datasets and urging the routine analysis of laboratory controls to ascertain the taxonomic and metabolic characteristics of environmentally-derived contaminant-taxa.}, }
@article {pmid31139170, year = {2019}, author = {León-Sobrino, C and Ramond, JB and Maggs-Kölling, G and Cowan, DA}, title = {Nutrient Acquisition, Rather Than Stress Response Over Diel Cycles, Drives Microbial Transcription in a Hyper-Arid Namib Desert Soil.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1054}, doi = {10.3389/fmicb.2019.01054}, pmid = {31139170}, issn = {1664-302X}, abstract = {Hot desert surface soils are characterized by extremely low water activities for large parts of any annual cycle. It is widely assumed that microbial processes in such soils are very limited. Here we present the first metatranscriptomic survey of microbial community function in a low water activity hyperarid desert soil. Sequencing of total mRNA revealed a diverse and active community, dominated by Actinobacteria. Metatranscriptomic analysis of samples taken at different times over 3 days indicated that functional diel variations were limited at the whole community level, and mostly affected the eukaryotic subpopulation which was induced during the cooler night hours. High levels of transcription of chemoautotrophic carbon fixation genes contrasted with limited expression of photosynthetic genes, indicating that chemoautotrophy is an important alternative to photosynthesis for carbon cycling in desiccated desert soils. Analysis of the transcriptional levels of key N-cycling genes provided strong evidence that soil nitrate was the dominant nitrogen input source. Transcriptional network analyses and taxon-resolved functional profiling suggested that nutrient acquisition processes, and not diurnal environmental variation, were the main drivers of community activity in hyperarid Namib Desert soil. While we also observed significant levels of expression of common stress response genes, these genes were not dominant hubs in the co-occurrence network.}, }
@article {pmid31138723, year = {2019}, author = {Emerson, JB}, title = {Soil Viruses: A New Hope.}, journal = {mSystems}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSystems.00120-19}, pmid = {31138723}, issn = {2379-5077}, abstract = {As abundant members of microbial communities, viruses impact microbial mortality, carbon and nutrient cycling, and food web dynamics. Although most of our information about viral communities comes from marine systems, evidence is mounting to suggest that viruses are similarly important in soil. Here I outline soil viral metagenomic approaches and the current state of soil viral ecology as a field, and then I highlight existing knowledge gaps that we can begin to fill. We are poised to elucidate soil viral contributions to terrestrial ecosystem processes, considering: the full suite of potential hosts across trophic scales, the ecological impacts of different viral replication strategies, links to economically relevant outcomes like crop productivity, and measurable in situ virus-host population dynamics across spatiotemporal scales and environmental conditions. Soon, we will learn how soil viruses contribute to food webs linked to organic matter decomposition, carbon and nutrient cycling, greenhouse gas emissions, and agricultural productivity.}, }
@article {pmid31138673, year = {2019}, author = {Benítez-Páez, A and Kjølbæk, L and Gómez Del Pulgar, EM and Brahe, LK and Astrup, A and Matysik, S and Schött, HF and Krautbauer, S and Liebisch, G and Boberska, J and Claus, S and Rampelli, S and Brigidi, P and Larsen, LH and Sanz, Y}, title = {A Multi-omics Approach to Unraveling the Microbiome-Mediated Effects of Arabinoxylan Oligosaccharides in Overweight Humans.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSystems.00209-19}, pmid = {31138673}, issn = {2379-5077}, abstract = {Long-term consumption of dietary fiber is generally considered beneficial for weight management and metabolic health, but the results of interventions vary greatly depending on the type of dietary fibers involved. This study provides a comprehensive evaluation of the effects of a specific dietary fiber consisting of a wheat-bran extract enriched in arabinoxylan-oligosaccharides (AXOS) in a human intervention trial. An integrated multi-omics analysis has been carried out to evaluate the effects of an intervention trial with an AXOS-enriched diet in overweight individuals with indices of metabolic syndrome. Microbiome analyses were performed by shotgun DNA sequencing in feces; in-depth metabolomics using nuclear magnetic resonance in fecal, urine, and plasma samples; and massive lipid profiling using mass spectrometry in fecal and serum/plasma samples. In addition to their bifidogenic effect, we observed that AXOS boost the proportion of Prevotella species. Metagenome analysis showed increases in the presence of bacterial genes involved in vitamin/cofactor production, glycan metabolism, and neurotransmitter biosynthesis as a result of AXOS intake. Furthermore, lipidomics analysis revealed reductions in plasma ceramide levels. Finally, we observed associations between Prevotella abundance and short-chain fatty acids (SCFAs) and succinate concentration in feces and identified a potential protective role of Eubacterium rectale against metabolic disease given that its abundance was positively associated with plasma phosphatidylcholine levels, thus hypothetically reducing bioavailability of choline for methylamine biosynthesis. The metagenomics, lipidomics, and metabolomics data integration indicates that sustained consumption of AXOS orchestrates a wide variety of changes in the gut microbiome and the host metabolism that collectively would impact on glucose homeostasis. (This study has been registered at ClinicalTrials.gov under identifier NCT02215343)IMPORTANCE The use of dietary fiber food supplementation as a strategy to reduce the burden of diet-related diseases is a matter of study given its cost-effectiveness and the positive results demonstrated in clinical trials. This multi-omics assessment, on different biological samples of overweight subjects with signs of metabolic syndrome, sheds light on the early and less evident effects of short-term AXOS intake on intestinal microbiota and host metabolism. We observed a deep influence of AXOS on gut microbiota beyond their recognized bifidogenic effect by boosting concomitantly a wide diversity of butyrate producers and Prevotella copri, a microbial species abundant in non-Westernized populations with traditional lifestyle and diets enriched in fresh unprocessed foods. A comprehensive evaluation of hundreds of metabolites unveiled new benefits of the AXOS intake, such as reducing the plasma ceramide levels. Globally, we observed that multiple effects of AXOS consumption seem to converge in reversing the glucose homeostasis impairment.}, }
@article {pmid31132623, year = {2019}, author = {Liu, L and Wu, L and Knauth, S and Eickhorst, T}, title = {Degradation of transgenic Bt-rice straw incorporated with two different paddy soils.}, journal = {Journal of environmental management}, volume = {244}, number = {}, pages = {415-421}, doi = {10.1016/j.jenvman.2019.05.075}, pmid = {31132623}, issn = {1095-8630}, abstract = {Transgenic Bt-rice is rice that has been genetically modified to produce insecticidal proteins (Cry1Ab/Ac) within the plant. Rice straw is incorporated into paddy soils after harvest for fertilization or to improve the soil structure. The incorporation of straw from transgenic Bt-rice may pose risks to the paddy soil system. The decomposition of Bt-rice straw and degradation of Cry1Ab/Ac proteins from the straw were investigated under laboratory conditions. In addition, effects of the incorporation with chopped rice straw on microbial communities in differently textured paddy soils were studied. The results indicated that the incorporation of straw from transgenic Bt-rice might have a slight influence on soil respiration and CH4 emissions in two paddy soils, i.e. the Silt Loam soil and the Silty Clay soil. Differences were also observed in the cumulative emissions of CO2 between the two amended paddy soils in addition to the well-known increase in emissions of both CO2 and CH4 due to straw incorporation. The Cry1Ab/Ac proteins from straw of transgenic Bt-rice were degraded in paddy soils. The rate of decline in the concentration of Cry1Ab/Ac proteins was different in the two soils. After 29 d of incubation, 61% and 42% of initial Cry1Ab/Ac proteins were detected in the silt loam and silty clay, respectively. As a result of the presence of the rice straw, the abundance of bacteria, archaea, and total cells were increased in two soils. The numbers of bacteria and total cells were 6.4% and 11.5% higher in the silt loam amended with straw of Bt-rice than non-Bt-rice, respectively. The silty clay displayed a similar trend as the silt loam.}, }
@article {pmid31130935, year = {2019}, author = {Cramm, MA and Chakraborty, A and Li, C and Ruff, SE and Jørgensen, BB and Hubert, CRJ}, title = {Freezing Tolerance of Thermophilic Bacterial Endospores in Marine Sediments.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {945}, doi = {10.3389/fmicb.2019.00945}, pmid = {31130935}, issn = {1664-302X}, abstract = {Dormant endospores of anaerobic, thermophilic bacteria found in cold marine sediments offer a useful model for studying microbial biogeography, dispersal, and survival. The dormant endospore phenotype confers resistance to unfavorable environmental conditions, allowing dispersal to be isolated and studied independently of other factors such as environmental selection. To study the resilience of thermospores to conditions relevant for survival in extreme cold conditions, their viability following different freezing treatments was tested. Marine sediment was frozen at either -80°C or -20°C for 10 days prior to pasteurization and incubation at +50°C for 21 days to assess thermospore viability. Sulfate reduction commenced at +50°C following both freezing pretreatments indicating persistence of thermophilic endospores of sulfate-reducing bacteria. The onset of sulfate reduction at +50°C was delayed in -80°C pretreated microcosms, which exhibited more variability between triplicates, compared to -20°C pretreated microcosms and parallel controls that were not frozen in advance. Microbial communities were evaluated by 16S rRNA gene amplicon sequencing, revealing an increase in the relative sequence abundance of thermophilic endospore-forming Firmicutes in all microcosms. Different freezing pretreatments (-80°C and -20°C) did not appreciably influence the shift in overall bacterial community composition that occurred during the +50°C incubations. Communities that had been frozen prior to +50°C incubation showed an increase in the relative sequence abundance of operational taxonomic units (OTUs) affiliated with the class Bacilli, relative to unfrozen controls. These results show that freezing impacts but does not obliterate thermospore populations and their ability to germinate and grow under appropriate conditions. Indeed the majority of the thermospore OTUs detected in this study (21 of 22) could be observed following one or both freezing treatments. These results are important for assessing thermospore viability in frozen samples and following cold exposure such as the very low temperatures that would be encountered during panspermia.}, }
@article {pmid31129882, year = {2019}, author = {Huh, YJ and Seo, JY and Nam, J and Yang, J and McDowell, A and Kim, YK and Lee, JH}, title = {Bariatric/Metabolic Surgery Induces Noticeable Changes of Microbiota and Their Secreting Extracellular Vesicle Composition in the Gut.}, journal = {Obesity surgery}, volume = {29}, number = {8}, pages = {2470-2484}, doi = {10.1007/s11695-019-03852-1}, pmid = {31129882}, issn = {1708-0428}, support = {NRF-2016R1D1A1B03932360//National Research Foundation of Korea/ ; }, abstract = {INTRODUCTION: Microbial ecology is reported to be an important regulator of energy homeostasis and glucose metabolism. Microbes secrete extracellular vesicles (EVs) during their proliferation and death to communicate with other cells. To investigate the roles of gut microbiota in glucose metabolism, we analyzed serial changes of gut microbe and microbial EV composition before and after bariatric/metabolic surgery (BMS).<br><br>METHODS: Twenty-eight Wistar rats were fed on high-fat diet (HFD) to induce obesity and diabetes. Five of them compared with 5 rats fed on regular chow diet (RCD). Among the remaining 23 rats, Roux-en-Y gastric bypass (RYGB) (n = 10), sleeve gastrectomy (SG) (n = 10), or sham operation (n = 3) was randomly performed. Gut microbiota and EVs from fecal samples were analyzed by 16S rDNA amplicon sequencing.<br><br>RESULTS: The present study showed that microbial diversity was decreased in HFD-fed rats versus RCD-fed rats. In addition, BMS reversed glucose intolerance and microbial richness which were induced by HFD. In terms of microbiota and microbial EV composition, both RYGB and SG enhance the composition of phyla Proteobacteria, Verrucomicrobia, and their secreting EVs, but decrease phylum Firmicutes and its EVs. We tried to demonstrate specific genera showed a significant compositional difference in obesity/diabetes-induced rats compared with normal rats and then restored similarly toward normal rats' level after BMS. At the genus level, Lactococcus, Ruminococcus, Dorea in Firmicutes(p), Psychrobacter in Proteobacteria(p), and Akkermansia in Verrucomicrobia(p) fit these conditions after BMS.<br><br>CONCLUSION: We suggest that these genera are the candidates contributing to obesity and diabetes improvement mechanism after BMS.}, }
@article {pmid31129376, year = {2019}, author = {Meng, Y and Zhou, Z and Meng, F}, title = {Impacts of diel temperature variations on nitrogen removal and metacommunity of anammox biofilm reactors.}, journal = {Water research}, volume = {160}, number = {}, pages = {1-9}, doi = {10.1016/j.watres.2019.05.021}, pmid = {31129376}, issn = {1879-2448}, abstract = {The influence of diel temperature variations (DTVs) on nitrogen removal and bacterial communities was investigated in two parallel anammox reactors (i.e., control and DTV reactors). The control reactor was operated at a constant temperature of 30 °C, whereas the DTV reactor was operated in a temperature fluctuation mode with a cycle of 12/12 h of high/low temperatures. Nine water temperature variations for the day/night periods were set from 30/30 °C (i.e., Δ0 °C) to 38/22 °C (i.e., Δ16 °C). An increase in DTVs from Δ8 °C (34/26 °C) to Δ16 °C (38/22 °C) caused a significant decline in reactor performance and a shift in bacterial diversity. Compared to the control reactor, for instance, nitrogen removal efficiency decreased (P < 0.05) when temperature fluctuations exceeded Δ8 °C in the DTV reactor with a decreasing ΔNO3-/ΔNH4+ ratio (from 0.21 ± 0.15 to 0.16 ± 0.04). The results of 16S rRNA gene sequencing showed that the initial disturbance of temperature variations led to increased levels of bacterial diversity (i.e., alpha diversity) and decreased community levels of anammox consortia whereas they slightly recovered at the end of each DTV phase. Notably, Candidatus Jettenia was more sensitive to strong water temperature fluctuations, with the lower relative abundance at Δ14 °C (17.11 ± 5.01%) and Δ16 °C (17.83 ± 7.22%) than at Δ4 °C (39.82 ± 0.01%). In contrast, Ca. Brocadia and Ca. Kuenenia had higher relative abundance at Δ14 °C (i.e., 0.24 ± 0.07% and 0.09 ± 0.02%, respectively) and Δ16 °C (i.e., 0.28 ± 0.05% and 0.12 ± 0.03%, respectively) compared to that at Δ4 °C (i.e., 0.15 ± 0.04% and 0.04 ± 0.01%, respectively). Nitrifiers (i.e., unidentified_Nitrospiraceae and Nitrosomonas) and denitrifiers (i.e., Denitratisoma) were also capable of tolerating high temperature perturbations. Overall this study furthers our knowledge of responses of the microbial ecology of anammox bacteria to DTVs in anammox processes, which could aid us in optimizing anammox-related wastewater treatment systems and in understanding the nitrogen cycles of natural ecosystems.}, }
@article {pmid31128471, year = {2019}, author = {Tsao, HF and Scheikl, U and Herbold, C and Indra, A and Walochnik, J and Horn, M}, title = {The cooling tower water microbiota: Seasonal dynamics and co-occurrence of bacterial and protist phylotypes.}, journal = {Water research}, volume = {159}, number = {}, pages = {464-479}, doi = {10.1016/j.watres.2019.04.028}, pmid = {31128471}, issn = {1879-2448}, abstract = {Cooling towers for heating, ventilation and air conditioning are ubiquitous in the built environment. Often located on rooftops, their semi-open water basins provide a suitable environment for microbial growth. They are recognized as a potential source of bacterial pathogens and have been associated with disease outbreaks such as Legionnaires' disease. While measures to minimize public health risks are in place, the general microbial and protist community structure and dynamics in these systems remain largely elusive. In this study, we analysed the microbiome of the bulk water from the basins of three cooling towers by 16S and 18S rRNA gene amplicon sequencing over the course of one year. Bacterial diversity in all three towers was broadly comparable to other freshwater systems, yet less diverse than natural environments; the most abundant taxa are also frequently found in freshwater or drinking water. While each cooling tower had a pronounced site-specific microbial community, taxa shared among all locations mainly included groups generally associated with biofilm formation. We also detected several groups related to known opportunistic pathogens, such as Legionella, Mycobacterium, and Pseudomonas species, albeit at generally low abundance. Although cooling towers represent a rather stable environment, microbial community composition was highly dynamic and subject to seasonal change. Protists are important members of the cooling tower water microbiome and known reservoirs for bacterial pathogens. Co-occurrence analysis of bacteria and protist taxa successfully captured known interactions between amoeba-associated bacteria and their hosts, and predicted a large number of additional relationships involving ciliates and other protists. Together, this study provides an unbiased and comprehensive overview of microbial diversity of cooling tower water basins, establishing a framework for investigating and assessing public health risks associated with these man-made freshwater environments.}, }
@article {pmid31125804, year = {2019}, author = {Zhou, LJ and Han, P and Yu, Y and Wang, B and Men, Y and Wagner, M and Wu, QL}, title = {Cometabolic biotransformation and microbial-mediated abiotic transformation of sulfonamides by three ammonia oxidizers.}, journal = {Water research}, volume = {159}, number = {}, pages = {444-453}, doi = {10.1016/j.watres.2019.05.031}, pmid = {31125804}, issn = {1879-2448}, abstract = {The abilities of three phylogenetically distant ammonia oxidizers, Nitrososphaera gargensis, an ammonia-oxidizing archaeon (AOA); Nitrosomomas nitrosa Nm90, an ammonia-oxidizing bacterium (AOB); and Nitrospira inopinata, the only complete ammonia oxidizer (comammox) available as a pure culture, to biotransform seven sulfonamides (SAs) were investigated. The removals and protein-normalized biotransformation rate constants indicated that the AOA strain N. gargensis exhibited the highest SA biotransformation rates, followed by N. inopinata and N. nitrosa Nm90. The transformation products (TPs) of sulfadiazine (SDZ), sulfamethazine (SMZ) and sulfamethoxazole (SMX) and the biotransformation mechanisms were evaluated. Based on the analysis of the TP formulas and approximate structures, it was found that during biotransformation, i) the AOA strain carried out SA deamination, hydroxylation, and nitration; ii) the AOB strain mainly performed SA deamination; and iii) the comammox isolate participated only in deamination reactions. It is proposed that deamination was catalyzed by deaminases while hydroxylation and nitration were mediated by nonspecific activities of the ammonia monooxygenase (AMO). Additionally, it was demonstrated that among the three ammonia oxidizers, only AOB contributed to the formation of pterin-SA conjugates. The biotransformation of SDZ, SMZ and SMX occurred only when ammonia oxidation was active, suggesting a cometabolic transformation mechanism. Interestingly, SAs could also be transformed by hydroxylamine, an intermediate of ammonia oxidation, suggesting that in addition to enzymatic conversions, a microbially induced abiotic mechanism contributes to SA transformation during ammonia oxidation. Overall, using experiments with pure cultures, this study provides important insights into the roles played by ammonia oxidizers in SA biotransformation.}, }
@article {pmid31120557, year = {2019}, author = {Dove, NC and Stark, JM and Newman, GS and Hart, SC}, title = {Carbon control on terrestrial ecosystem function across contrasting site productivities: the carbon connection revisited.}, journal = {Ecology}, volume = {100}, number = {7}, pages = {e02695}, doi = {10.1002/ecy.2695}, pmid = {31120557}, issn = {1939-9170}, support = {92-37101-7976//U.S. Department of Agriculture Co-operative State Research Service/ ; }, abstract = {Understanding how altered soil organic carbon (SOC) availability affects microbial communities and their function is imperative in predicting impacts of global change on soil carbon (C) storage and ecosystem function. However, the response of soil microbial communities and their function to depleted C availability in situ is unclear. We evaluated the role of soil C inputs in controlling microbial biomass, community composition, physiology, and function by (1) experimentally excluding plant C inputs in situ for 9 yr in four temperate forest ecosystems along a productivity gradient in Oregon, USA; and (2) integrating these findings with published data from similar C-exclusion studies into a global meta-analysis. Excluding plant C inputs for 9 yr resulted in a 13% decrease in SOC across the four Oregon sites and an overall shift in the microbial community composition, with a 45% decrease in the fungal : bacterial ratio and a 13% increase in Gram-positive : Gram-negative bacterial ratio. Although gross N mineralization decreased under C exclusion, decreases in gross N immobilization were greater, resulting in increased net N mineralization rates in all but the lowest-productivity site. Microbial biomass showed a variable response to C exclusion that was method dependent; however, we detected a 29% decrease in C-use efficiency across the sites, with greater declines occurring in less-productive sites. Although extracellular enzyme activity increased with C exclusion, C exclusion resulted in a 31% decrease in microbial respiration across all sites. Our meta-analyses of published data with similar C-exclusion treatments were largely consistent with our experimental results, showing decreased SOC, fungal : bacterial ratios, and microbial respiration, and increased Gram-positive : Gram-negative bacterial ratio following exclusion of C inputs to soil. Effect sizes of SOC and respiration correlated negatively with the duration of C exclusion; however, there were immediate effects of C exclusion on microbial community composition and biomass that were unaltered by duration of treatment. Our field-based experimental results and analyses demonstrate unequivocally the dominant control of C availability on soil microbial biomass, community composition, and function, and provide additional insight into the mechanisms for these effects in forest ecosystems.}, }
@article {pmid31119088, year = {2019}, author = {Roux, S and Trubl, G and Goudeau, D and Nath, N and Couradeau, E and Ahlgren, NA and Zhan, Y and Marsan, D and Chen, F and Fuhrman, JA and Northen, TR and Sullivan, MB and Rich, VI and Malmstrom, RR and Eloe-Fadrosh, EA}, title = {Optimizing de novo genome assembly from PCR-amplified metagenomes.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6902}, doi = {10.7717/peerj.6902}, pmid = {31119088}, issn = {2167-8359}, abstract = {Background: Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes.<br><br>Methods: Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10 kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes.<br><br>Results: Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥10 kb by 10 to 100-fold for low input metagenomes.<br><br>Conclusions: PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.}, }
@article {pmid31118299, year = {2019}, author = {Sze, MA and Schloss, PD}, title = {The Impact of DNA Polymerase and Number of Rounds of Amplification in PCR on 16S rRNA Gene Sequence Data.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSphere.00163-19}, pmid = {31118299}, issn = {2379-5042}, support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; R01 CA215574/CA/NCI NIH HHS/United States ; UL1 TR002240/TR/NCATS NIH HHS/United States ; }, abstract = {PCR amplification of 16S rRNA genes is a critical yet underappreciated step in the generation of sequence data to describe the taxonomic composition of microbial communities. Numerous factors in the design of PCR can impact the sequencing error rate, the abundance of chimeric sequences, and the degree to which the fragments in the product represent their abundance in the original sample (i.e., bias). We compared the performance of high fidelity polymerases and various numbers of rounds of amplification when amplifying a mock community and human stool samples. Although it was impossible to derive specific recommendations, we did observe general trends. Namely, using a polymerase with the highest possible fidelity and minimizing the number of rounds of PCR reduced the sequencing error rate, fraction of chimeric sequences, and bias. Evidence of bias at the sequence level was subtle and could not be ascribed to the fragments' fraction of bases that were guanines or cytosines. When analyzing mock community data, the amount that the community deviated from the expected composition increased with the number of rounds of PCR. This bias was inconsistent for human stool samples. Overall, the results underscore the difficulty of comparing sequence data that are generated by different PCR protocols. However, the results indicate that the variation in human stool samples is generally larger than that introduced by the choice of polymerase or number of rounds of PCR.IMPORTANCE A steep decline in sequencing costs drove an explosion in studies characterizing microbial communities from diverse environments. Although a significant amount of effort has gone into understanding the error profiles of DNA sequencers, little has been done to understand the downstream effects of the PCR amplification protocol. We quantified the effects of the choice of polymerase and number of PCR cycles on the quality of downstream data. We found that these choices can have a profound impact on the way that a microbial community is represented in the sequence data. The effects are relatively small compared to the variation in human stool samples; however, care should be taken to use polymerases with the highest possible fidelity and to minimize the number of rounds of PCR. These results also underscore that it is not possible to directly compare sequence data generated under different PCR conditions.}, }
@article {pmid31117021, year = {2019}, author = {Beinart, RA}, title = {The Significance of Microbial Symbionts in Ecosystem Processes.}, journal = {mSystems}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSystems.00127-19}, pmid = {31117021}, issn = {2379-5077}, abstract = {It is increasingly accepted that the microbial symbionts of eukaryotes can have profound effects on host ecology and evolution. However, the relative contribution that they make directly to ecosystem processes, like energy and nutrient flows, is less explicitly acknowledged and, in many cases, only poorly constrained. Here, I explore the idea that, in some habitats, host-associated microbes may have an outsized role in ecosystem processes relative to functionally equivalent free-living microbes due to key aspects of the physiology, ecology, and evolution of symbiotic interactions. My research quantifying symbiont metabolism has shown that microbial symbionts have the potential to make a substantial impact on carbon and sulfur cycling. It is my perspective that direct measurement of symbiont activity and comparison to free-living counterparts will expand our understanding of the significance of microbial symbioses and, more broadly, the role of microbial processes in ecosystems.}, }
@article {pmid31114556, year = {2019}, author = {Hounmanou, YMG and Leekitcharoenphon, P and Hendriksen, RS and Dougnon, TV and Mdegela, RH and Olsen, JE and Dalsgaard, A}, title = {Surveillance and Genomics of Toxigenic Vibrio cholerae O1 From Fish, Phytoplankton and Water in Lake Victoria, Tanzania.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {901}, doi = {10.3389/fmicb.2019.00901}, pmid = {31114556}, issn = {1664-302X}, abstract = {The occurrence of toxigenic Vibrio cholerae O1 during a non- outbreak period in Lake Victoria was studied and genetic characteristics for environmental persistence and relatedness to pandemic strains were assessed. We analyzed 360 samples of carps, phytoplankton and water collected in 2017 during dry and rainy seasons in the Tanzanian basin of Lake Victoria. Samples were tested using PCR (ompW and ctxA) with DNA extracted from bacterial isolates and samples enriched in alkaline peptone water. Isolates were screened with polyvalent antiserum O1 followed by antimicrobial susceptibility testing. Whole genome sequencing and bioinformatics tools were employed to investigate the genomic characteristics of the isolates. More V. cholerae positive samples were recovered by PCR when DNA was obtained from enriched samples than from isolates (69.0% vs. 21.3%, p < 0.05), irrespectively of season. We identified ten V. cholerae O1 among 22 ctxA-positive isolates. Further studies are needed to serotype the remaining ctxA-positive non-O1 strains. Sequenced strains belonged to El Tor atypical biotype of V. cholerae O1 of MLST ST69 harboring the seventh pandemic gene. Major virulence genes, ctxA, ctxB, zot, ace, tcpA, hlyA, rtxA, ompU, toxR, T6SS, alsD, makA and pathogenicity islands VPI-1, VPI-2, VSP-1, and VSP-2 were found in all strains. The strains contained Vibrio polysaccharide biosynthesis enzymes, the mshA gene and two-component response regulator proteins involved in stress response and autoinducers for quorum sensing and biofilm formation. They carried the SXT integrative conjugative element with phenotypic and genotypic resistance to aminoglycoside, sulfamethoxazole, trimethoprim, phenicol, and quinolones. Strains contained a multidrug efflux pump component and were resistant to toxic compounds with copper homeostasis and cobalt-zinc-cadmium resistance proteins. The environmental strains belonged to the third wave of the seventh pandemic and most are genetically closely related to recent outbreak strains from Tanzania, Kenya, and Uganda with as low as three SNPs difference. Some strains have persisted longer in the environment and were more related to older outbreak strains in the region. V. cholerae O1 of outbreak potential seem to persist in Lake Victoria through interactions with fish and phytoplankton supported by the optimum water parameters and intrinsic genetic features enhancing survival in the aquatic environment.}, }
@article {pmid31114015, year = {2019}, author = {Worrich, A and Musat, N and Harms, H}, title = {Associational effects in the microbial neighborhood.}, journal = {The ISME journal}, volume = {13}, number = {9}, pages = {2143-2149}, doi = {10.1038/s41396-019-0444-6}, pmid = {31114015}, issn = {1751-7370}, abstract = {Even though &quot;perfect&quot; metagenomes or metatranscriptomes are close at hand, the implicit assumption of spatial homogeneity in the &quot;omic&quot; approaches makes it difficult if not impossible to relate those data to ecological processes occurring in natural and man-made ecosystems. In fact, the distribution of microbes in their habitats is far from being uniform and random. Microbial communities show a high degree of spatial organization that stems from environmental gradients and local interactions. These interactions can be very complex and may involve multiple species. Several studies highlighted the importance of indirect interactions for community stability, but the absence of a theoretical framework for microbial ecology restricts the possibilities to strike a balance between the investigation of simple communities with purely pairwise interactions and the attempts to understand interaction patterns in whole communities based on meta-omics studies. Here we suggest adapting the concept of Associational Effects (AE) from plant ecology, to better understand the link between ecological interactions, spatial arrangement, and stability in microbial communities. By bringing together a conceptual framework developed for plants and observations made for microbes, this perspective article fosters synthesis of related disciplines to yield novel insights into the advancing field of spatial microbial ecology. To promote the integration into microbial ecology, we (i) outline the theoretical background of AE, (ii) collect underlying mechanisms by literature synthesis, (iii) propose a three-point roadmap for the investigation of AE in microbial communities, and (iv) discuss its implications for microbial ecology research.}, }
@article {pmid31112792, year = {2019}, author = {Michels, N and Van de Wiele, T and Fouhy, F and O'Mahony, S and Clarke, G and Keane, J}, title = {Gut microbiome patterns depending on children's psychosocial stress: Reports versus biomarkers.}, journal = {Brain, behavior, and immunity}, volume = {80}, number = {}, pages = {751-762}, doi = {10.1016/j.bbi.2019.05.024}, pmid = {31112792}, issn = {1090-2139}, abstract = {AIM: Chronic stress increases disease vulnerability factors including inflammation, a pathological characteristic potentially regulated by the gut microbiota. We checked the association between the gut microbiome and psychosocial stress in children/adolescents and investigated which stress parameter (negative versus positive emotion, self-report versus parental report, events versus emotions, biomarker cortisol versus parasympathetic activity) is the most relevant indicator herein.<br><br>METHODS: Gut microbiome sequencing was completed in fecal samples from 93 Belgian 8-16y olds. Stress measures included negative events, negative emotions, emotional problems reported by parents, happiness, hair cortisol and heart rate variability (pnn50 parameter reflecting parasympathetic activity). Alpha diversity, beta diversity and linear discriminant analysis were the unadjusted analyses. Age, sex, socio-economic status, diet, physical activity, sleep and weight status were adjusted for via a redundancy analysis and differential abundance via zero-inflated negative binomial regression.<br><br>RESULTS: High stress as reflected by low pnn50 and more negative events were associated with a lower alpha diversity as indicated by the Simpson index. Happiness and pnn50 showed significant differences between high and low stress groups based on weighted UniFrac distance, and this remained significant after confounder adjustment. Adjusted and unadjusted taxonomic differences were also most pronounced for happiness and pnn50 being associated respectively with 24 OTU (=11.8% of bacterial counts) and 31 OTU (=13.0%). As a general pattern, high stress was associated with lower Firmicutes at the phylum level and higher Bacteroides, Parabacteroides, Rhodococcus, Methanobrevibacter and Roseburia but lower Phascolarctobacterium at genus level. Several genera gave conflicting results between different stress measures e.g. Ruminococcaceae UCG014, Tenericutes, Eubacterium coprostanoligenes, Prevotella 9 and Christensenellaceae R7. Differential results in preadolescents versus adolescents were also evident.<br><br>CONCLUSION: Even in this young healthy population, stress parameters were cross-sectionally associated with gut microbial composition but this relationship was instrument specific. Positive emotions and parasympathetic activity appeared the strongest parameters and should be integrated in future microbiota projects amongst other stress measures.}, }
@article {pmid31111178, year = {2019}, author = {Mesquita, MCB and Prestes, ACC and Gomes, AMA and Marinho, MM}, title = {Direct Effects of Temperature on Growth of Different Tropical Phytoplankton Species.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01384-w}, pmid = {31111178}, issn = {1432-184X}, support = {478440/2011-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Temperature increase may influence competition among phytoplankton species, potentially intensifying cyanobacteria blooms that can be favored by direct and indirect effects of temperature. In this study, we aimed to clarify how cyanobacteria can be favored by the direct effects of increased temperature compared to diatoms and chlorophytes. Strains of the most representative species of a eutrophic coastal lagoon (Microcystis aeruginosa, Planktothrix agardhii, Desmodesmus communis, and Cyclotella meneghiniana) were used to test the hypothesis that cyanobacteria would be favored by the direct effect of temperature increase. First, we evaluated the effect of temperature increase on growth in monocultures (batch and chemostats) at 25 and 30 °C and after in mixed cultures (chemostats). In batch monocultures, the cyanobacteria showed higher growth rates in 30 °C than in 25 °C. However, in continuous culture experiments (chemostats), growth rates of M. aeruginosa and P. agardhii were not affected by temperature, but the strains showed higher biovolume in steady-state with the temperature increase. In continuous mixed cultures, M. aeruginosa was always dominant and C. meneghiniana was excluded, regardless of temperature tested. D. communis was able to coexist with lower biomass. This study shows that rising temperatures can be detrimental to diatoms, even for a tropical strain. Although some studies indicate that the dominance of cyanobacteria in warmer climates may be due to the indirect effect of warming that will promote physical conditions in the environment more favorable to cyanobacteria, the outcomes of mixed cultures demonstrate that the direct effect of temperature can also favor the dominance of cyanobacteria.}, }
@article {pmid31110670, year = {2019}, author = {Silva, DP and Duarte, G and Villela, HDM and Santos, HF and Rosado, PM and Rosado, JG and Rosado, AS and Ferreira, EM and Soriano, AU and Peixoto, RS}, title = {Adaptable mesocosm facility to study oil spill impacts on corals.}, journal = {Ecology and evolution}, volume = {9}, number = {9}, pages = {5172-5185}, doi = {10.1002/ece3.5095}, pmid = {31110670}, issn = {2045-7758}, abstract = {Although numerous studies have been carried out on the impacts of oil spills on coral physiology, most have relied on laboratory assays. This scarcity is partly explained by the difficulty of reproducing realistic conditions in a laboratory setting or of performing experiments with toxic compounds in the field. Mesocosm systems provide the opportunity to carry out such studies with safe handling of contaminants while reproducing natural conditions required by living organisms. The mesocosm design is crucial and can lead to the development of innovative technologies to mitigate environmental impacts. Therefore, this study aimed to develop a mesocosm system for studies simulating oil spills with several key advantages, including true replication and the use of gravity to control flow-through that reduces reliance on pumps that can clog thereby decreasing errors and costs. This adaptable system can be configured to (a) have continuous flow-through; (b) operate as an open or closed system; (c) be fed by gravity; (d) have separate mesocosm sections that can be used for individual and simultaneous experiments; and (e) simulate the migration of oil from ocean oil spills to the nearby reefs. The mesocosm performance was assessed with two experiments using the hydrocoral Millepora alcicornis and different configurations to simulate two magnitudes of oil spills. With few exceptions, physical and chemical parameters remained stable within replicates and within treatments throughout the experiments. Physical and chemical parameters that expressed change during the experiment were still within the range of natural conditions observed in Brazilian marine environments. The photosynthetic potential (Fv/Fm) of the algae associated with M. alcicornis decreased in response to an 1% crude-oil contamination, suggesting a successful delivery of the toxic contaminant to the targeted replicates. This mesocosm is customizable and adjustable for several types of experiments and proved to be effective for studies of oil spills.}, }
@article {pmid31109532, year = {2019}, author = {Qi, H and Wei, Z and Zhang, J and Zhao, Y and Wu, J and Gao, X and Liu, Z and Li, Y}, title = {Effect of MnO2 on biotic and abiotic pathways of humic-like substance formation during composting of different raw materials.}, journal = {Waste management (New York, N.Y.)}, volume = {87}, number = {}, pages = {326-334}, doi = {10.1016/j.wasman.2019.02.022}, pmid = {31109532}, issn = {1879-2456}, abstract = {The humic-like substances (HLS) are proposed to be formed by biotic and abiotic pathways. The abiotic pathways were neglected in existed composting studies. The present study aims to accelerate the abiotic pathways, and to investigate how MnO2 drives the HLS transformation via changing the contribution of abiotic and biotic pathways during composting with different materials. Parallel factor analysis model (PARAFAC), hetero two-dimensional correlation spectra (hetero-2DCOS) and variance partitioning were used to identify the effects of MnO2 on the formation of humic acid (HA) and fluvic acid (FA) during composting of chicken manure (CM) and corn straw (CS). The addition of MnO2 could change the structures of HLS during CS and CM composting, mainly promoting the formation of complex components in HA and FA during CS composting, as well as the complex components of FA during CM composting. Meanwhile, the addition of MnO2 could reshape the microbial ecology, which enhanced the correlation between microbes and complex components formation during composting, especially in CM composting. Variance partitioning showed that both abiotic and biotic pathways were stimulated in conversion of HLS components after adding MnO2 during CS composting, especially for the abiotic pathways. During CM composting, the MnO2 promoted biotic effects on the conversion of HLS components. Above all, the addition of MnO2 could stimulate pathways of biotic, abiotic or both of them to improve the humification degree of HLS by changing microbial ecology, which could be a promising way for promoting the application value of composting products.}, }
@article {pmid31105660, year = {2019}, author = {Jørgensen, BB and Findlay, AJ and Pellerin, A}, title = {The Biogeochemical Sulfur Cycle of Marine Sediments.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {849}, doi = {10.3389/fmicb.2019.00849}, pmid = {31105660}, issn = {1664-302X}, abstract = {Microbial dissimilatory sulfate reduction to sulfide is a predominant terminal pathway of organic matter mineralization in the anoxic seabed. Chemical or microbial oxidation of the produced sulfide establishes a complex network of pathways in the sulfur cycle, leading to intermediate sulfur species and partly back to sulfate. The intermediates include elemental sulfur, polysulfides, thiosulfate, and sulfite, which are all substrates for further microbial oxidation, reduction or disproportionation. New microbiological discoveries, such as long-distance electron transfer through sulfide oxidizing cable bacteria, add to the complexity. Isotope exchange reactions play an important role for the stable isotope geochemistry and for the experimental study of sulfur transformations using radiotracers. Microbially catalyzed processes are partly reversible whereby the back-reaction affects our interpretation of radiotracer experiments and provides a mechanism for isotope fractionation. We here review the progress and current status in our understanding of the sulfur cycle in the seabed with respect to its microbial ecology, biogeochemistry, and isotope geochemistry.}, }
@article {pmid31100891, year = {2019}, author = {Jeong, Y and Kim, JW and You, HJ and Park, SJ and Lee, J and Ju, JH and Park, MS and Jin, H and Cho, ML and Kwon, B and Park, SH and Ji, GE}, title = {Gut Microbial Composition and Function Are Altered in Patients with Early Rheumatoid Arthritis.}, journal = {Journal of clinical medicine}, volume = {8}, number = {5}, pages = {}, doi = {10.3390/jcm8050693}, pmid = {31100891}, issn = {2077-0383}, support = {NRF-2017M3A9F3041045//National Research Foundation/ ; NRF-2017M3A9F3041747//National Research Foundation/ ; }, abstract = {Rheumatoid arthritis (RA) is an autoimmune disease characterized by synovial inflammation of the joints and extra-articular manifestations. Recent studies have shown that microorganisms affect RA pathogenesis. However, few studies have examined the microbial distribution of early RA patients, particularly female patients. In the present study, we investigated the gut microbiome profile and microbial functions in early RA female patients, including preclinical and clinically apparent RA cases. Changes in microbiological diversity, composition, and function in each group were analyzed using quantitative insights into microbial ecology (QIIME) and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt). The results revealed the dysbiosis due to decreased diversity in the early RA patients compared with healthy subjects. There were significant differences in the microbial distribution of various taxa from phylum to genus levels between healthy subjects and early RA patients. Phylum Bacteroidetes was enriched in early RA patients, while Actinobacteria, including the genus Collinsella, was enriched in healthy subjects. Functional analysis based on clusters of orthologous groups revealed that the genes related to the biosynthesis of menaquinone, known to be derived from gram-positive bacteria, were enriched in healthy subjects, while iron transport-related genes were enriched in early RA patients. Genes related to the biosynthesis of lipopolysaccharide, the gram-negative bacterial endotoxin, were enriched in clinically apparent RA patients. The obvious differences in microbial diversity, taxa, and associated functions of the gut microbiota between healthy subjects and early RA patients highlight the involvement of the gut microbiome in the early stages of RA.}, }
@article {pmid31100615, year = {2019}, author = {Bautista-de Los Santos, QM and Chavarria, KA and Nelson, KL}, title = {Understanding the impacts of intermittent supply on the drinking water microbiome.}, journal = {Current opinion in biotechnology}, volume = {57}, number = {}, pages = {167-174}, doi = {10.1016/j.copbio.2019.04.003}, pmid = {31100615}, issn = {1879-0429}, abstract = {Increasing access to piped water in low-income and middle-income countries combined with the many factors that threaten our drinking water supply infrastructure mean that intermittent water supply (IWS) will remain a common practice around the world. Common features of IWS include water stagnation, pipe drainage, intrusion, backflow, first flush events, and household storage. IWS has been shown to cause degradation as measured by traditional microbial water quality indicators. In this review, we build on new insights into the microbial ecology of continuous water supply systems revealed by sequencing methods to speculate about how intermittent supply conditions may further influence the drinking water microbiome, and identify priorities for future research.}, }
@article {pmid31099963, year = {2019}, author = {Nguyen, B and Rubbens, P and Kerckhof, FM and Boon, N and De Baets, B and Waegeman, W}, title = {Learning Single-Cell Distances from Cytometry Data.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {95}, number = {7}, pages = {782-791}, doi = {10.1002/cyto.a.23792}, pmid = {31099963}, issn = {1552-4930}, support = {BOF15/DOS/039//Universiteit Gent/ ; BOFSTA2015000501//Universiteit Gent/ ; }, abstract = {Recent years have seen an increased interest in employing data analysis techniques for the automated identification of cell populations in the field of cytometry. These techniques highly depend on the use of a distance metric, a function that quantifies the distances between single-cell measurements. In most cases, researchers simply use the Euclidean distance metric. In this article, we exploit the availability of single-cell labels to find an optimal Mahalanobis distance metric derived from the data. We show that such a Mahalanobis distance metric results in an improved identification of cell populations compared with the Euclidean distance metric. Once determined, it can be used for the analysis of multiple samples that were measured under the same experimental setup. We illustrate this approach for cytometry data from two different origins, that is, flow cytometry applied to microbial cells and mass cytometry for the analysis of human blood cells. We also illustrate that such a distance metric results in an improved identification of cell populations when clustering methods are employed. Generally, these results imply that the performance of data analysis techniques can be improved by using a more advanced distance metric. © 2019 International Society for Advancement of Cytometry.}, }
@article {pmid31098412, year = {2019}, author = {Sato, Y and Hori, T and Koike, H and Navarro, RR and Ogata, A and Habe, H}, title = {Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {179}, doi = {10.1038/s42003-019-0418-2}, pmid = {31098412}, issn = {2399-3642}, abstract = {Although metagenomics researches have illuminated microbial diversity in numerous biospheres, understanding individual microbial functions is yet difficult due to the complexity of ecosystems. To address this issue, we applied a metagenome-independent, de novo assembly-based metatranscriptomics to a complex microbiome, activated sludge, which has been used for wastewater treatment for over a century. Even though two bioreactors were operated under the same conditions, their performances differed from each other with unknown causes. Metatranscriptome profiles in high- and low-performance reactors demonstrated that denitrifiers contributed to the anaerobic degradation of heavy oil; however, no marked difference in the gene expression was found. Instead, gene expression-based nitrification activities that fueled the denitrifiers by providing the respiratory substrate were notably high in the high-performance reactor only. Nitrifiers-small minorities with relative abundances of <0.25%-governed the heavy-oil degradation performances of the reactors, unveiling an unexpected linkage of carbon- and nitrogen-metabolisms of the complex microbiome.}, }
@article {pmid31097577, year = {2019}, author = {Brumley, DR and Carrara, F and Hein, AM and Yawata, Y and Levin, SA and Stocker, R}, title = {Bacteria push the limits of chemotactic precision to navigate dynamic chemical gradients.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {22}, pages = {10792-10797}, doi = {10.1073/pnas.1816621116}, pmid = {31097577}, issn = {1091-6490}, abstract = {Ephemeral aggregations of bacteria are ubiquitous in the environment, where they serve as hotbeds of metabolic activity, nutrient cycling, and horizontal gene transfer. In many cases, these regions of high bacterial concentration are thought to form when motile cells use chemotaxis to navigate to chemical hotspots. However, what governs the dynamics of bacterial aggregations is unclear. Here, we use an experimental platform to create realistic submillimeter-scale nutrient pulses with controlled nutrient concentrations. By combining experiments, mathematical theory, and agent-based simulations, we show that individual Vibrio ordalii bacteria begin chemotaxis toward hotspots of dissolved organic matter (DOM) when the magnitude of the chemical gradient rises sufficiently far above the sensory noise that is generated by stochastic encounters with chemoattractant molecules. Each DOM hotspot is surrounded by a dynamic ring of chemotaxing cells, which congregate in regions of high DOM concentration before dispersing as DOM diffuses and gradients become too noisy for cells to respond to. We demonstrate that V. ordalii operates close to the theoretical limits on chemotactic precision. Numerical simulations of chemotactic bacteria, in which molecule counting noise is explicitly taken into account, point at a tradeoff between nutrient acquisition and the cost of chemotactic precision. More generally, our results illustrate how limits on sensory precision can be used to understand the location, spatial extent, and lifespan of bacterial behavioral responses in ecologically relevant environments.}, }
@article {pmid31095604, year = {2019}, author = {Di Lonardo, DP and de Boer, W and Zweers, H and van der Wal, A}, title = {Effect of the amount of organic trigger compounds, nitrogen and soil microbial biomass on the magnitude of priming of soil organic matter.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0216730}, doi = {10.1371/journal.pone.0216730}, pmid = {31095604}, issn = {1932-6203}, abstract = {Priming effects (PEs) are defined as short-term changes in the turnover of soil organic matter (SOM) caused by the addition of easily degradable organic compounds to the soil. PEs are ubiquitous but the direction (acceleration or retardation of SOM decomposition) and magnitude are not easy to predict. It has been suggested that the ratio between the amount of added PE-triggering substrate to the size of initial soil microbial biomass is an important factor influencing PEs. However, this is mainly based on comparison of different studies and not on direct experimentation. The aim of the current study is to examine the impact of glucose-to-microbial biomass ratios on PEs for three different ecosystems. We did this by adding three different amounts of 13C-glucose with or without addition of mineral N (NH4NO3) to soils collected from arable lands, grasslands and forests. The addition of 13C-glucose was equivalent to 15%, 50% and 200% of microbial biomass C. After one month of incubation, glucose had induced positive PEs for almost all the treatments, with differences in magnitude related to the soil origin and the amount of glucose added. For arable and forest soils, the primed C increased with increasing amount of glucose added, whereas for grassland soils this relationship was negative. We found positive correlations between glucose-derived C and primed C and the strength of these correlations was different among the three ecosystems considered. Generally, additions of mineral N next to glucose (C:N = 15:1) had little effect on the flux of substrate-derived C and primed C. Overall, our study does not support the hypothesis that the trigger-substrate to microbial biomass ratio can be an important predictor of PEs. Rather our results indicate that the amount of energy obtained from decomposing trigger substrates is an important factor for the magnitude of PEs.}, }
@article {pmid31093727, year = {2019}, author = {Woodhams, DC and Rollins-Smith, LA and Reinert, LK and Lam, BA and Harris, RN and Briggs, CJ and Vredenburg, VT and Patel, BT and Caprioli, RM and Chaurand, P and Hunziker, P and Bigler, L}, title = {Probiotics Modulate a Novel Amphibian Skin Defense Peptide That Is Antifungal and Facilitates Growth of Antifungal Bacteria.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01385-9}, pmid = {31093727}, issn = {1432-184X}, support = {0640373//National Science Foundation/ ; 1121758//National Science Foundation/ ; 31-125099//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, abstract = {Probiotics can ameliorate diseases of humans and wildlife, but the mechanisms remain unclear. Host responses to interventions that change their microbiota are largely uncharacterized. We applied a consortium of four natural antifungal bacteria to the skin of endangered Sierra Nevada yellow-legged frogs, Rana sierrae, before experimental exposure to the pathogenic fungus Batrachochytrium dendrobatidis (Bd). The probiotic microbes did not persist, nor did they protect hosts, and skin peptide sampling indicated immune modulation. We characterized a novel skin defense peptide brevinin-1Ma (FLPILAGLAANLVPKLICSITKKC) that was downregulated by the probiotic treatment. Brevinin-1Ma was tested against a range of amphibian skin cultures and found to inhibit growth of fungal pathogens Bd and B. salamandrivorans, but enhanced the growth of probiotic bacteria including Janthinobacterium lividum, Chryseobacterium ureilyticum, Serratia grimesii, and Pseudomonas sp. While commonly thought of as antimicrobial peptides, here brevinin-1Ma showed promicrobial function, facilitating microbial growth. Thus, skin exposure to probiotic bacterial cultures induced a shift in skin defense peptide profiles that appeared to act as an immune response functioning to regulate the microbiome. In addition to direct microbial antagonism, probiotic-host interactions may be a critical mechanism affecting disease resistance.}, }
@article {pmid31093726, year = {2019}, author = {Hernández-Gómez, O and Wuerthner, V and Hua, J}, title = {Amphibian Host and Skin Microbiota Response to a Common Agricultural Antimicrobial and Internal Parasite.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01351-5}, pmid = {31093726}, issn = {1432-184X}, support = {1655190//Division of Environmental Biology/ ; 1708926//Directorate for Biological Sciences/ ; }, abstract = {Holistic approaches that simultaneously characterize responses of both microbial symbionts and their hosts to environmental shifts are imperative to understanding the role of microbiotas on host health. Using the northern leopard frog (Lithobates pipiens) as our model, we investigated the effects of a common trematode (family Echinostomatidae), a common agricultural antimicrobial (Sulfadimethoxine; SDM), and their interaction on amphibian skin microbiota and amphibian health (growth metrics and susceptibility to parasites). In the trematode-exposed individuals, we noted an increase in alpha diversity and a shift in microbial communities. In the SDM-treated individuals, we found a change in the composition of the skin microbiota similar to those induced by the trematode treatment. Groups treated with SDM, echinostomes, or a combination of SDM and echinostomes, had higher relative abundances of OTUs assigned to Flavobacterium and Acinetobacter. Both of these genera have been associated with infectious disease in amphibians and the production of anti-pathogen metabolites. Similar changes in microbial community composition between SDM and trematode exposed individuals may have resulted from stress-related disruption of host immunity. Despite changes in the microbiota, we found no effect of echinostomes and SDM on host health. Given the current disease- and pollution-related threats facing amphibians, our study highlights the need to continue to evaluate the influence of natural and anthropogenic stressors on host-associated microbial communities.}, }
@article {pmid31091418, year = {2019}, author = {Cordovez, V and Dini-Andreote, F and Carrión, VJ and Raaijmakers, JM}, title = {Ecology and Evolution of Plant Microbiomes.}, journal = {Annual review of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-micro-090817-062524}, pmid = {31091418}, issn = {1545-3251}, abstract = {Microorganisms colonizing plant surfaces and internal tissues provide a number of life-support functions for their host. Despite increasing recognition of the vast functional capabilities of the plant microbiome, our understanding of the ecology and evolution of the taxonomically hyperdiverse microbial communities is limited. Here, we review current knowledge of plant genotypic and phenotypic traits as well as allogenic and autogenic factors that shape microbiome composition and functions. We give specific emphasis to the impact of plant domestication on microbiome assembly and how insights into microbiomes of wild plant relatives and native habitats can contribute to reinstate or enrich for microorganisms with beneficial effects on plant growth, development, and health. Finally, we introduce new concepts and perspectives in plant microbiome research, in particular how community ecology theory can provide a mechanistic framework to unravel the interplay of distinct ecological processes-i.e., selection, dispersal, drift, diversification-that structure the plant microbiome. Expected final online publication date for the Annual Review of Microbiology Volume 73 is September 9, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid31088922, year = {2019}, author = {König, L and Wentrup, C and Schulz, F and Wascher, F and Escola, S and Swanson, MS and Buchrieser, C and Horn, M}, title = {Symbiont-Mediated Defense against Legionella pneumophila in Amoebae.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, doi = {10.1128/mBio.00333-19}, pmid = {31088922}, issn = {2150-7511}, mesh = {Acanthamoeba castellanii/*microbiology/physiology ; Chlamydiales/*physiology ; Gene Expression ; Humans ; Legionella pneumophila/*pathogenicity ; *Symbiosis ; Virulence ; }, abstract = {Legionella pneumophila is an important opportunistic pathogen for which environmental reservoirs are crucial for the infection of humans. In the environment, free-living amoebae represent key hosts providing nutrients and shelter for highly efficient intracellular proliferation of L. pneumophila, which eventually leads to lysis of the protist. However, the significance of other bacterial players for L. pneumophila ecology is poorly understood. In this study, we used a ubiquitous amoeba and bacterial endosymbiont to investigate the impact of this common association on L. pneumophila infection. We demonstrate that L. pneumophila proliferation was severely suppressed in Acanthamoeba castellanii harboring the chlamydial symbiont Protochlamydia amoebophila The amoebae survived the infection and were able to resume growth. Different environmental amoeba isolates containing the symbiont were equally well protected as different L. pneumophila isolates were diminished, suggesting ecological relevance of this symbiont-mediated defense. Furthermore, protection was not mediated by impaired L. pneumophila uptake. Instead, we observed reduced virulence of L. pneumophila released from symbiont-containing amoebae. Pronounced gene expression changes in the presence of the symbiont indicate that interference with the transition to the transmissive phase impedes the L. pneumophila infection. Finally, our data show that the defensive response of amoebae harboring P. amoebophila leaves the amoebae with superior fitness reminiscent of immunological memory. Given that mutualistic associations between bacteria and amoebae are widely distributed, P. amoebophila and potentially other amoeba endosymbionts could be key in shaping environmental survival, abundance, and virulence of this important pathogen, thereby affecting the frequency of human infection.IMPORTANCE Bacterial pathogens are generally investigated in the context of disease. To prevent outbreaks, it is essential to understand their lifestyle and interactions with other microbes in their natural environment. Legionella pneumophila is an important human respiratory pathogen that survives and multiplies in biofilms or intracellularly within protists, such as amoebae. Importantly, transmission to humans occurs from these environmental sources. Legionella infection generally leads to rapid host cell lysis. It was therefore surprising to observe that amoebae, including fresh environmental isolates, were well protected during Legionella infection when the bacterial symbiont Protochlamydia amoebophila was also present. Legionella was not prevented from invading amoebae but was impeded in its ability to develop fully virulent progeny and were ultimately cleared in the presence of the symbiont. This study highlights how ecology and virulence of an important human pathogen is affected by a defensive amoeba symbiont, with possibly major consequences for public health.}, }
@article {pmid31087742, year = {2019}, author = {Geiger, RA and Junghare, M and Mergelsberg, M and Ebenau-Jehle, C and Jesenofsky, VJ and Jehmlich, N and von Bergen, M and Schink, B and Boll, M}, title = {Enzymes involved in phthalate degradation in sulphate-reducing bacteria.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14681}, pmid = {31087742}, issn = {1462-2920}, support = {BO 1565/16-1//German research council/ ; }, abstract = {The complete degradation of the xenobiotic and environmentally harmful phthalate esters is initiated by hydrolysis to alcohols and o-phthalate (phthalate) by esterases. While further catabolism of phthalate has been studied in aerobic and denitrifying microorganisms, the degradation in obligately anaerobic bacteria has remained obscure. Here, we demonstrate a previously overseen growth of the δ-proteobacterium Desulfosarcina cetonica with phthalate/sulphate as only carbon and energy sources. Differential proteome and CoA ester pool analyses together with in vitro enzyme assays identified the genes, enzymes and metabolites involved in phthalate uptake and degradation in D. cetonica. Phthalate is initially activated to the short-lived phthaloyl-CoA by an ATP-dependent phthalate CoA ligase (PCL) followed by decarboxylation to the central intermediate benzoyl-CoA by an UbiD-like phthaloyl-CoA decarboxylase (PCD) containing a prenylated flavin cofactor. Genome/metagenome analyses predicted phthalate degradation capacity also in the sulphate-reducing Desulfobacula toluolica, strain NaphS2, and other δ-proteobacteria. Our results suggest that phthalate degradation proceeds in all anaerobic bacteria via the labile phthaloyl-CoA that is captured and decarboxylated by highly abundant PCDs. In contrast, two alternative strategies have been established for the formation of phthaloyl-CoA, the possibly most unstable CoA ester in biology.}, }
@article {pmid31086312, year = {2019}, author = {Wu, L and Ning, D and Zhang, B and Li, Y and Zhang, P and Shan, X and Zhang, Q and Brown, M and Li, Z and Van Nostrand, JD and Ling, F and Xiao, N and Zhang, Y and Vierheilig, J and Wells, GF and Yang, Y and Deng, Y and Tu, Q and Wang, A and ,  and Zhang, T and He, Z and Keller, J and Nielsen, PH and Alvarez, PJJ and Criddle, CS and Wagner, M and Tiedje, JM and He, Q and Curtis, TP and Stahl, DA and Alvarez-Cohen, L and Rittmann, BE and Wen, X and Zhou, J}, title = {Global diversity and biogeography of bacterial communities in wastewater treatment plants.}, journal = {Nature microbiology}, volume = {4}, number = {7}, pages = {1183-1195}, doi = {10.1038/s41564-019-0426-5}, pmid = {31086312}, issn = {2058-5276}, abstract = {Microorganisms in wastewater treatment plants (WWTPs) are essential for water purification to protect public and environmental health. However, the diversity of microorganisms and the factors that control it are poorly understood. Using a systematic global-sampling effort, we analysed the 16S ribosomal RNA gene sequences from ~1,200 activated sludge samples taken from 269 WWTPs in 23 countries on 6 continents. Our analyses revealed that the global activated sludge bacterial communities contain ~1 billion bacterial phylotypes with a Poisson lognormal diversity distribution. Despite this high diversity, activated sludge has a small, global core bacterial community (n = 28 operational taxonomic units) that is strongly linked to activated sludge performance. Meta-analyses with global datasets associate the activated sludge microbiomes most closely to freshwater populations. In contrast to macroorganism diversity, activated sludge bacterial communities show no latitudinal gradient. Furthermore, their spatial turnover is scale-dependent and appears to be largely driven by stochastic processes (dispersal and drift), although deterministic factors (temperature and organic input) are also important. Our findings enhance our mechanistic understanding of the global diversity and biogeography of activated sludge bacterial communities within a theoretical ecology framework and have important implications for microbial ecology and wastewater treatment processes.}, }
@article {pmid31079748, year = {2019}, author = {López, JC and Porca, E and Collins, G and Clifford, E and Quijano, G and Muñoz, R}, title = {Ammonium influences kinetics and structure of methanotrophic consortia.}, journal = {Waste management (New York, N.Y.)}, volume = {89}, number = {}, pages = {345-353}, doi = {10.1016/j.wasman.2019.04.028}, pmid = {31079748}, issn = {1879-2456}, abstract = {The literature is conflicted on the influence of ammonium on the kinetics and microbial ecology of methanotrophy. In this study, methanotrophic cultures were enriched, under ammonium concentrations ranging from 0 to 200 mM, from an inoculum comprising leachate and top-cover soil from a landfill. Specific CH4 biodegradation rates were highest (7.8 × 10-4 ± 6.0 × 10-5 gCH4 gX-1 h-1) in cultures enriched at 4 mM NH4+, which were mainly dominated by type II methanotrophs belonging to Methylocystis spp. Lower specific CH4 oxidation rates (average values of 1.8-3.6 × 10-4 gCH4 gX-1 h-1) were achieved by cultures enriched at higher NH4+ concentrations (20 and 80 mM), and had higher affinity for CH4 compared to 4 mM enrichments. These lower affinities were attributed to lower diversity dominated by type I methanotrophs, of the Methylosarcina, Methylobacter and Methylomicrobium genera, encountered with increasing concentrations of NH4+. The study indicates that CH4 oxidation biotechnologies applied at low NH4+ concentrations can support efficient abatement of CH4 and high diversity of methanotrophic consortia, whilst enriching type II methanotrophs.}, }
@article {pmid31079198, year = {2019}, author = {Wanner, M and Birkhofer, K and Fischer, T and Shimizu, M and Shimano, S and Puppe, D}, title = {Soil Testate Amoebae and Diatoms as Bioindicators of an Old Heavy Metal Contaminated Floodplain in Japan.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01383-x}, pmid = {31079198}, issn = {1432-184X}, support = {PU 626/2-1//Deutsche Forschungsgemeinschaft/ ; S16738//Japan Society for the Promotion of Science/ ; Kakenhi 15H02858//Japan Society for the Promotion of Science/ ; }, abstract = {Soil protists are rarely included in ecotoxicological investigations, despite their fundamental role in ecological processes. Moreover, testate amoebae and diatoms contribute considerably to silicon fluxes in soils. We investigated the effects of heavy metals on testate amoebae (species and individual densities) and diatoms (individual densities) in aged soils of a floodplain (Watarase retarding basin, Japan) taking soil samples from two unpolluted reference sites and two polluted sites. The total concentrations of Cu, Pb, and Zn in soil were higher at the polluted sites as compared with the reference sites. The available concentrations of Co, Cu, and Zn in CaCl2 extracts were higher at the polluted sites but available Pb was not detectable. Testate amoeba taxonomic richness was higher in the reference sites (45/38 taxa) than in the polluted sites (36/27 taxa). The reference sites had higher diatom and amoeba densities than the polluted sites. There was a significant negative correlation between total testate amoeba density and heavy metal concentration (available Co), while significant negative correlations were found between diatom density and Co, Cu, and Zn (available and total concentration). Densities of Cyclopyxis kahli cyclostoma, Centropyxis spp., and Trinema complanatum were negatively correlated to concentrations of available heavy metals. The observed decrease in individual numbers due to heavy metal pollution resulted in a considerable decline in protozoic (testate amoebae) and protophytic (pennate diatoms) silicon pools. Our data suggest that heavy metal pollution affects biogeochemical cycling in this system.}, }
@article {pmid31079197, year = {2019}, author = {Pillot, G and Davidson, S and Auria, R and Combet-Blanc, Y and Godfroy, A and Liebgott, PP}, title = {Production of Current by Syntrophy Between Exoelectrogenic and Fermentative Hyperthermophilic Microorganisms in Heterotrophic Biofilm from a Deep-Sea Hydrothermal Chimney.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01381-z}, pmid = {31079197}, issn = {1432-184X}, support = {PEPS-ExoMod 2016//Institut National des Sciences de l'Univers, Centre National de la Recherche Scientifique/ ; 1166-39417//European Regional Development Fund/ ; }, abstract = {To study the role of exoelectrogens within the trophic network of deep-sea hydrothermal vents, we performed successive subcultures of a hyperthermophilic community from a hydrothermal chimney sample on a mix of electron donors in a microbial fuel cell system. Electrode (the electron acceptor) was swapped every week to enable fresh development from spent media as inoculum. The MFC at 80 °C yielded maximum current production increasing from 159 to 247 mA m-2 over the subcultures. The experiments demonstrated direct production of electric current from acetate, pyruvate, and H2 and indirect production from yeast extract and peptone through the production of H2 and acetate from fermentation. The microorganisms found in on-electrode communities were mainly affiliated to exoelectrogenic Archaeoglobales and Thermococcales species, whereas in liquid media, the communities were mainly affiliated to fermentative Bacillales and Thermococcales species. The work shows interactions between fermentative microorganisms degrading complex organic matter into fermentation products that are then used by exoelectrogenic microorganisms oxidizing these reduced compounds while respiring on a conductive support. The results confirmed that with carbon cycling, the syntrophic relations between fermentative microorganisms and exoelectrogens could enable some microbes to survive as biofilm in extremely unstable conditions. Graphical Abstract Schematic representation of cross-feeding between fermentative and exoelectrogenic microbes on the surface of the conductive support. B, Bacillus/Geobacillus spp.; Tc, Thermococcales; Gg, Geoglobus spp.; Py, pyruvate; Ac, acetate.}, }
@article {pmid31074596, year = {2019}, author = {Feng, M and Tripathi, BM and Shi, Y and Adams, JM and Zhu, YG and Chu, H}, title = {Interpreting distance-decay pattern of soil bacteria via quantifying the assembly processes at multiple spatial scales.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e851}, doi = {10.1002/mbo3.851}, pmid = {31074596}, issn = {2045-8827}, support = {XDB15010101//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2017YFC0504002//National Key Research and Development Program of China/ ; 2017YFD0200604//National Key Research and Development Program of China/ ; //China Biodiversity Observation Networks (Sino BON)/ ; }, abstract = {It has been widely accepted that there is a distance-decay pattern in the soil microbiome. However, few studies have attempted to interpret the microbial distance-decay pattern from the perspective of quantifying underlying processes. In this study, we examined the processes governing bacterial community assembly at multiple spatial scales in maize fields of Northeast China using Illumina MiSeq sequencing. Results showed that the processes governing spatial turnover in bacterial community composition shifted regularly with spatial scale, with homogenizing dispersal dominating at small spatial scales and variable selection dominating at larger scales, which in turn explained the distance-decay pattern that closer located sites tended to have higher community similarity. Together, homogenizing dispersal and dispersal limitation resulting from geographic factors governed about 33% of spatial turnover in bacterial community composition. Deterministic selection processes had the strongest influence, at 57%, with biotic factors and abiotic environmental filtering (mainly imposed by soil pH) respectively contributing about 37% and 63% of variation. Our results provided a novel and comprehensive way to explain the distance-decay pattern of soil microbiome via quantifying the assembly processes at multiple spatial scales, as well as the method to quantify the influence of abiotic, biotic, and geographic factors in shaping microbial community structure, thus enabling understanding of widely acknowledged microbial biogeographic patterns and microbial ecology.}, }
@article {pmid31065700, year = {2019}, author = {Mohammed, AA and Jiang, S and Jacobs, JA and Cheng, HW}, title = {Effect of a synbiotic supplement on cecal microbial ecology, antioxidant status, and immune response of broiler chickens reared under heat stress.}, journal = {Poultry science}, volume = {}, number = {}, pages = {}, doi = {10.3382/ps/pez246}, pmid = {31065700}, issn = {1525-3171}, abstract = {The aim of this study was to examine the effect of a dietary synbiotic supplement on the cecal microflora, antioxidant status, and immune response of broiler chickens under heat stress (HS). A total of 360 one-day-old male Ross 708 broiler chicks were randomly distributed among 3 dietary treatments containing a synbiotic (PoultryStar consists of Bifidobacterium animalis, Enterococcus faecium, Lactobacillus reuteri, Pediococcus acidilactici, and fructooligosaccharides) at 0 (control), 0.5 (0.5X), and 1.0 (1.0X) g/kg. Each treatment contained 8 replicates of 15 birds each housed in floor pens. Heat stimulation was at 32°C for 9 h daily from day 15 to 42. Heat stress-induced changes of cecal bacteria were detected using bacteria-specific agars, and spleen protein concentration and mRNA expression of interleukins and antioxidants were examined using ELISA and real-time PCR, respectively. Under the HS condition, synbiotic fed broilers regardless of dose had lower cecal enumerations of Escherichia coli and coliforms, and a lower heterophil/lymphocyte (H/L) ratio (P < 0.05) compared to controls. 1.0X group also had higher cecal enumerations of Bifidobacterium spp. and Lactobacillus spp., spleen glutathione peroxidase (GPx), and plasma nuclear factor erythroid 2-related factor 2 (Nrf-2), and a lower H/L ratio compared to both control and 0.5X groups (P < 0.05). However, there were no treatment effects on the levels of Enterococcus spp., the circulating monocytes, eosinophils, and basophils, Toll like receptor-4 (TLR-4), interleukin-6 (IL-6), interlukin-10 (IL-10), and their mRNA expression, as well as plasma Kelch-like ECH-associated protein 1 (Keap-1) (P > 0.05). These results suggest that the synbiotic could inhibit the negative effects of HS on broiler health through the reduction of cecal pathogens, regulation of stress reactions, and improvement of antioxidant status.}, }
@article {pmid31064055, year = {2019}, author = {Pineda-Quiroga, C and Borda-Molina, D and Chaves-Moreno, D and Ruiz, R and Atxaerandio, R and Camarinha-Silva, A and García-Rodríguez, A}, title = {Microbial and Functional Profile of the Ceca from Laying Hens Affected by Feeding Prebiotics, Probiotics, and Synbiotics.}, journal = {Microorganisms}, volume = {7}, number = {5}, pages = {}, doi = {10.3390/microorganisms7050123}, pmid = {31064055}, issn = {2076-2607}, support = {LIFE11/ENV/ES/000639//LIFE program of the European Union/ ; PRE/2013/1/1077//Department of Education, Language Policy and Culture, Scholarship, , Basque Government, Vitoria-Gasteiz, Spain/ ; }, abstract = {Diet has an essential influence in the establishment of the cecum microbial communities in poultry, so its supplementation with safe additives, such as probiotics, prebiotics, and synbiotics might improve animal health and performance. This study showed the ceca microbiome modulations of laying hens, after feeding with dry whey powder as prebiotics, Pediococcus acidilactici as probiotics, and the combination of both as synbiotics. A clear grouping of the samples induced per diet was observed (p < 0.05). Operational taxonomic units (OTUs) identified as Olsenella spp., and Lactobacilluscrispatus increased their abundance in prebiotic and synbiotic treatments. A core of the main functions was shared between all metagenomes (45.5%), although the genes encoding for the metabolism of butanoate, propanoate, inositol phosphate, and galactose were more abundant in the prebiotic diet. The results indicated that dietary induced-changes in microbial composition did not imply a disturbance in the principal biological roles, while the specific functions were affected.}, }
@article {pmid31063726, year = {2019}, author = {Lindemann, SR}, title = {Microbial Ecology: Functional 'Modules' Drive Assembly of Polysaccharide-Degrading Marine Microbial Communities.}, journal = {Current biology : CB}, volume = {29}, number = {9}, pages = {R330-R332}, doi = {10.1016/j.cub.2019.03.056}, pmid = {31063726}, issn = {1879-0445}, abstract = {Although ecological principles governing the competition of microbes for simple substrates are well-understood, less is known about how complex, structured substrates influence ecological outcomes in microbial communities. A new study sheds light on how marine microbial communities assemble on polysaccharide particles modeling marine snow.}, }
@article {pmid31060399, year = {2019}, author = {Panebianco, C and Pazienza, V}, title = {Body site-dependent variations of microbiota in pancreatic cancer pathophysiology.}, journal = {Critical reviews in clinical laboratory sciences}, volume = {56}, number = {4}, pages = {260-273}, doi = {10.1080/10408363.2019.1615407}, pmid = {31060399}, issn = {1549-781X}, abstract = {Lack of specific symptoms and reliable biomarkers, along with aggressive nature and resistance to therapies makes pancreatic cancer (PC) one of the leading causes of death from cancer worldwide. The search for new diagnostic, prognostic, predictive, and therapeutic tools that could improve clinical outcomes of patients has led, in recent years, to the investigation of potential roles for the microbiota in the pathogenesis of this disease. The human microbiota encompasses trillions of microorganisms residing within several body tissues and organs, where they provide beneficial functions for host homeostasis and health. Derangements of the microbial ecology in different anatomic districts have been described in PC, as in many other diseases, both in patients and in animal models. In detail, infection from the gastric pathogen Helicobacter pylori and changes in composition and diversity of oral, intestinal, and pancreatic microbiota have been found to associate with PC. Future research should assess how to potentially exploit such differences in microbiota composition as diagnostic, prognostic, or predictive biomarkers, and as targets for therapeutic interventions, in the hope of improving the dismal prognosis of this insidious cancer.}, }
@article {pmid31058277, year = {2018}, author = {Photos-Jones, E}, title = {From mine to apothecary: an archaeo-biomedical approach to the study of the Greco-Roman lithotherapeutics industry.}, journal = {World archaeology}, volume = {50}, number = {3}, pages = {418-433}, doi = {10.1080/00438243.2018.1515034}, pmid = {31058277}, issn = {0043-8243}, abstract = {Western biomedicine has only partially developed its own tradition of mineral medicinals (lithotherapeutics), at least compared to botanicals. This is perhaps because these minerals were site-specific, and fundamental information associated with the empirical processes of mineral extraction, beneficiation, storage, trade and preparation was not widely available. In other words, there are many and serious breaks in the multi-link chain from mine to apothecary. This long-term investigation aims to rebuild this chain, on a mineral-by-mineral basis, by pulling together the extant documentary record, material culture, mineralogy, geochemistry and microbial ecology, as well as by testing against known pathogens as an indicator of their antimicrobial activity. Critical to understanding the nature and efficacy of lithotherapeutics is the recognition that these materials need to be investigated simultaneously at two levels: the empirical (ancient sources and practices); and the biomedical (application of physical and biological sciences). Both approaches require the same starting point, namely the field (mine or quarry) and in particular the 'point of contact' (relationship) between minerals and their microbiome.}, }
@article {pmid31055618, year = {2019}, author = {Ben Yahia, H and Chairat, S and Gharsa, H and Alonso, CA and Ben Sallem, R and Porres-Osante, N and Hamdi, N and Torres, C and Ben Slama, K}, title = {First Report of KPC-2 and KPC-3-Producing Enterobacteriaceae in Wild Birds in Africa.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01375-x}, pmid = {31055618}, issn = {1432-184X}, abstract = {The increased incidence of antibiotic-resistant Enterobacteriaceae is a public health problem worldwide. The aim of this study was to analyze the potential role of wild birds, given their capacity of migrating over long distances, in the spreading of carbapenemase, extended-spectrum β-lactamase (ESBL), and acquired-AmpC beta-lactamase-producing Enterobacteriaceae in the environment. Fecal and pellet samples were recovered from 150 wild birds in seven Tunisian regions and were inoculated in MacConkey-agar plates for Enterobacteriaceae recovery (one isolate/animal). Ninety-nine isolates were obtained and acquired resistance mechanisms were characterized in the five detected imipenem-resistant and/or cefotaxime-resistant isolates, by PCR and sequencing. The following ESBL, carbapenemase, and acquired-AmpC beta-lactamase genes were detected: blaCTX-M-15 (two Escherichia fergusonii and one Klebsiella oxytoca isolates), blaKPC-2 (one K. oxytoca), blaKPC-3 (one E. fergusonii), blaACT-36, and blaACC-2 (two K. oxytoca, four E. fergusonii, and two E. coli). The IncFIIs, IncF, IncFIB, IncK, IncP, and IncX replicons were detected among these beta-lactamase Enterobacteriaceae producers. The blaKPC-2, tetA, sul3, qnrB, and cmlA determinants were co-transferred by conjugation from K. oxytoca strain to E. coli J153, in association with IncK and IncF replicons. Our results support the implication of wild birds as a biological vector for carbapenemase, ESBL, and acquired-AmpC-producing Enterobacteriaceae.}, }
@article {pmid31054240, year = {2019}, author = {Ma, S and De Frenne, P and Boon, N and Brunet, J and Cousins, SAO and Decocq, G and Kolb, A and Lemke, I and Liira, J and Naaf, T and Orczewska, A and Plue, J and Wulf, M and Verheyen, K}, title = {Plant species identity and soil characteristics determine rhizosphere soil bacteria community composition in European temperate forests.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {6}, pages = {}, doi = {10.1093/femsec/fiz063}, pmid = {31054240}, issn = {1574-6941}, abstract = {Soil bacteria and understorey plants interact and drive forest ecosystem functioning. Yet, knowledge about biotic and abiotic factors that affect the composition of the bacterial community in the rhizosphere of understorey plants is largely lacking. Here, we assessed the effects of plant species identity (Milium effusum vs. Stachys sylvatica), rhizospheric soil characteristics, large-scale environmental conditions (temperature, precipitation and nitrogen (N) deposition), and land-use history (ancient vs. recent forests) on bacterial community composition in rhizosphere soil in temperate forests along a 1700 km latitudinal gradient in Europe. The dominant bacterial phyla in the rhizosphere soil of both plant species were Acidobacteria, Actinobacteria and Proteobacteria. Bacterial community composition differed significantly between the two plant species. Within plant species, soil chemistry was the most important factor determining soil bacterial community composition. More precisely, soil acidity correlated with the presence of multiple phyla, e.g. Acidobacteria (negatively), Chlamydiae (negatively) and Nitrospirae (positively), in both plant species. Large-scale environmental conditions were only important in S. sylvatica and land-use history was not important in either of the plant species. The observed role of understorey plant species identity and rhizosphere soil characteristics in determining soil bacterial community composition extends our understanding of plant-soil bacteria interactions in forest ecosystem functioning.}, }
@article {pmid31053974, year = {2019}, author = {Krstin, L and Katanić, Z and Repar, J and Ježić, M and Kobaš, A and Ćurković-Perica, M}, title = {Genetic Diversity of Cryphonectria hypovirus 1, a Biocontrol Agent of Chestnut Blight, in Croatia and Slovenia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01377-9}, pmid = {31053974}, issn = {1432-184X}, support = {IZ73Z0_152525/1//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; IZIP-2016-54//Sveučilište Josipa Jurja Strossmayera u Osijeku/ ; }, abstract = {Transmissible hypovirulence associated with Cryphonectria hypovirus 1 (CHV1) has been used for biological control of chestnut blight, devastating disease of chestnut caused by the fungus Cryphonectria parasitica. The main aims of this study were to provide molecular characterization of CHV1 from Croatia and Slovenia and to reveal its genetic variability, phylogeny, and diversification of populations. Fifty-one CHV1 haplotypes were detected among 54 partially sequenced CHV1 isolates, all belonging to Italian subtype (I). Diversity was mainly generated by point mutations while evidence of recombination was not found. The level of conservation over analyzed parts of ORF-A proteins p29 and p40 varied, but functional sites were highly conserved. Phylogenetic analysis revealed close relatedness and intermixing of Croatian and Slovenian CHV1 populations. Our CHV1 isolates were also related to Swiss and Bosnian hypoviruses supporting previously suggested course of CHV1 invasion in Europe. Overall, this study indicates that phylogeny of CHV1 subtype I in Europe is complex and characterized with frequent point mutations resulting in many closely related variants of the virus. Possible association between variations within CHV1 ORF-A and growth of the hypovirulent fungal isolates is tested and presented.}, }
@article {pmid31050730, year = {2019}, author = {Moraïs, S and Mizrahi, I}, title = {Islands in the stream: from individual to communal fiber degradation in the rumen ecosystem.}, journal = {FEMS microbiology reviews}, volume = {43}, number = {4}, pages = {362-379}, doi = {10.1093/femsre/fuz007}, pmid = {31050730}, issn = {1574-6976}, mesh = {Anaerobiosis ; Animal Nutritional Physiological Phenomena ; Animals ; Dietary Fiber/*metabolism ; *Ecosystem ; Rumen/*microbiology ; Ruminants/metabolism/microbiology ; }, abstract = {The herbivore rumen ecosystem constitutes an extremely efficient degradation machinery for the intricate chemical structure of fiber biomass, thus, enabling the hosting animal to digest its feed. The challenging task of deconstructing and metabolizing fiber is performed by microorganisms inhabiting the rumen. Since most of the ingested feed is comprised of plant fiber, these fiber-degrading microorganisms are of cardinal importance to the ecology of the rumen microbial community and to the hosting animal, and have a great impact on our environment and food sustainability. We summarize herein the enzymological fundamentals of fiber degradation, how the genes encoding these enzymes are spread across fiber-degrading microbes, and these microbes' interactions with other members of the rumen microbial community and potential effect on community structure. An understanding of these concepts has applied value for agriculture and our environment, and will also contribute to a better understanding of microbial ecology and evolution in anaerobic ecosystems.}, }
@article {pmid31050668, year = {2019}, author = {Melo-Bolívar, JF and Ruiz Pardo, RY and Hume, ME and Nisbet, DJ and Rodríguez-Villamizar, F and Alzate, JF and Junca, H and Villamil Díaz, LM}, title = {Establishment and characterization of a competitive exclusion bacterial culture derived from Nile tilapia (Oreochromis niloticus) gut microbiomes showing antibacterial activity against pathogenic Streptococcus agalactiae.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0215375}, doi = {10.1371/journal.pone.0215375}, pmid = {31050668}, issn = {1932-6203}, abstract = {This study reports the characterization of the microbial community composition, and the establishment and dynamics of a continuous-flow competitive exclusion culture (CFCEC) derived from gut microbiomes of Nile tilapia (Oreochromis niloticus) specimens reared on aquaculture farms in Colombia. 16S rRNA gene amplicon Illumina sequencing was used to identify taxonomical changes in the CFCEC microbial community over time. The CFCEC was developed from adult tilapia from two farms in Colombia, and CFCEC samples were collected over two months. The pH varied from 6.25 to 6.35 throughout culturing, while anaerobic and aerobic cell counts stabilized at day 9, at 109 CFU mL-1 and were maintained to day 68. A variation in the CFCEC bacterial composition was observed over time. Cetobacterium was the most abundant in the first two days and coincided with a higher CFCEC supernatant antimicrobial effect against the fish pathogen Streptococcus agalactiae. Antimicrobial activity against S. agalactiae disappeared by day 3. Changes in bacterial composition continued to day 33 with Lactococcus spp. becoming the most abundant member of the community. In conclusion, the study of the CFCEC from intestinal tract of Nile tilapia (Oreochromis niloticus) by 16S rRNA gene sequencing allowed identification of predominant bacterial genera in the continuous-flow competitive exclusion culture exhibiting antibacterial activity against the fish pathogen Streptococcus agalactiae.}, }
@article {pmid31049616, year = {2019}, author = {Ma, GC and Worthing, KA and Ward, MP and Norris, JM}, title = {Commensal Staphylococci Including Methicillin-Resistant Staphylococcus aureus from Dogs and Cats in Remote New South Wales, Australia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01382-y}, pmid = {31049616}, issn = {1432-184X}, abstract = {Staphylococci are important opportunistic pathogens in human and veterinary medicine in addition to being part of the normal flora of the skin and mucous membranes of mammals and birds. The rise of antimicrobial resistance amongst staphylococci warrants closer investigation of the diversity of skin commensal organisms-including coagulase-negative staphylococci (CoNS)-due to their potential as a source of resistance genes. This study is aimed at characterising the commensal staphylococci-including methicillin-resistant Staphylococcus species (spp.)-from mucocutaneous sites of dogs and cats from remote New South Wales (NSW), Australia. Pet dogs and cats were recruited from participants in a community companion animal health programme in six communities in western NSW. Three swabs were collected from each animal (anterior nares, oropharynx, and perineum) and from skin lesions or wounds if present and cultured on selective media for Staphylococcus spp. In total, 383 pets (303 dogs, 80 cats) were enrolled. Staphylococcus spp. were isolated from 67.3% of dogs and 73.8% of cats (494 isolates). The diversity of CoNS was high (20 species) whilst only three coagulase-positive spp. were isolated (S. pseudintermedius, S. aureus, S. intermedius). The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) carriage in dogs was high (2.6%) relative to other studies but was only a small proportion of overall commensal staphylococci. No cats carried MRSA and no MRSP was isolated from either species. Dogs were significantly more likely to carry coagulase-positive staphylococci than cats (P < 0.001). Amongst dogs, males and those with skin lesions were more likely to carry S. pseudintermedius. This study highlights important differences in the diversity and patterns of carriage of commensal staphylococci between dogs and cats in remote NSW, Australia.}, }
@article {pmid31049565, year = {2019}, author = {Samba-Louaka, A and Delafont, V and Rodier, MH and Cateau, E and Héchard, Y}, title = {Free-living amoebae and squatters in the wild: ecological and molecular features.}, journal = {FEMS microbiology reviews}, volume = {43}, number = {4}, pages = {415-434}, doi = {10.1093/femsre/fuz011}, pmid = {31049565}, issn = {1574-6976}, mesh = {Amoeba/genetics/*physiology/virology ; Bacteria/*classification/virology ; Bacterial Physiological Phenomena ; Biological Evolution ; *Ecosystem ; Genetic Variation ; }, abstract = {Free-living amoebae are protists frequently found in water and soils. They feed on other microorganisms, mainly bacteria, and digest them through phagocytosis. It is accepted that these amoebae play an important role in the microbial ecology of these environments. There is a renewed interest for the free-living amoebae since the discovery of pathogenic bacteria that can resist phagocytosis and of giant viruses, underlying that amoebae might play a role in the evolution of other microorganisms, including several human pathogens. Recent advances, using molecular methods, allow to bring together new information about free-living amoebae. This review aims to provide a comprehensive overview of the newly gathered insights into (1) the free-living amoeba diversity, assessed with molecular tools, (2) the gene functions described to decipher the biology of the amoebae and (3) their interactions with other microorganisms in the environment.}, }
@article {pmid31048756, year = {2019}, author = {Schwank, K and Bornemann, TLV and Dombrowski, N and Spang, A and Banfield, JF and Probst, AJ}, title = {An archaeal symbiont-host association from the deep terrestrial subsurface.}, journal = {The ISME journal}, volume = {13}, number = {8}, pages = {2135-2139}, doi = {10.1038/s41396-019-0421-0}, pmid = {31048756}, issn = {1751-7370}, abstract = {DPANN archaea have reduced metabolic capacities and are diverse and abundant in deep aquifer ecosystems, yet little is known about their interactions with other microorganisms that reside there. Here, we provide evidence for an archaeal host-symbiont association from a deep aquifer system at the Colorado Plateau (Utah, USA). The symbiont, Candidatus Huberiarchaeum crystalense, and its host, Ca. Altiarchaeum hamiconexum, show a highly significant co-occurrence pattern over 65 metagenome samples collected over six years. The physical association of the two organisms was confirmed with genome-informed fluorescence in situ hybridization depicting small cocci of Ca. H. crystalense attached to Ca. A. hamiconexum cells. Based on genomic information, Ca. H. crystalense potentially scavenges vitamins, sugars, nucleotides, and reduced redox-equivalents from its host and thus has a similar metabolism as Nanoarchaeum equitans. These results provide insight into host-symbiont interactions among members of two uncultivated archaeal phyla that thrive in a deep subsurface aquifer.}, }
@article {pmid31048390, year = {2019}, author = {Bryce, C and Blackwell, N and Straub, D and Kleindienst, S and Kappler, A}, title = {Draft Genome Sequence of Chlorobium sp. Strain N1, a Marine Fe(II)-Oxidizing Green Sulfur Bacterium.}, journal = {Microbiology resource announcements}, volume = {8}, number = {18}, pages = {}, doi = {10.1128/MRA.00080-19}, pmid = {31048390}, issn = {2576-098X}, abstract = {Here, we present the draft genome sequence of the halotolerant photoferrotroph Chlorobium sp. strain N1. This draft genome provides insights into the genomic potential of the only marine Fe(II)-oxidizing green sulfur bacterium (GSB) available in culture and expands our views on the metabolic capabilities of Fe(II)-oxidizing GSB more generally.}, }
@article {pmid31046835, year = {2019}, author = {Sharma, A and Richardson, M and Cralle, L and Stamper, CE and Maestre, JP and Stearns-Yoder, KA and Postolache, TT and Bates, KL and Kinney, KA and Brenner, LA and Lowry, CA and Gilbert, JA and Hoisington, AJ}, title = {Longitudinal homogenization of the microbiome between both occupants and the built environment in a cohort of United States Air Force Cadets.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {70}, doi = {10.1186/s40168-019-0686-6}, pmid = {31046835}, issn = {2049-2618}, support = {G-2016-7077//Alfred P. Sloan Foundation/ ; }, abstract = {BACKGROUND: The microbiome of the built environment has important implications for human health and wellbeing; however, bidirectional exchange of microbes between occupants and surfaces can be confounded by lifestyle, architecture, and external environmental exposures. Here, we present a longitudinal study of United States Air Force Academy cadets (n = 34), which have substantial homogeneity in lifestyle, diet, and age, all factors that influence the human microbiome. We characterized bacterial communities associated with (1) skin and gut samples from roommate pairs, (2) four built environment sample locations inside the pairs' dormitory rooms, (3) four built environment sample locations within shared spaces in the dormitory, and (4) room-matched outdoor samples from the window ledge of their rooms.<br><br>RESULTS: We analyzed 2,170 samples, which generated 21,866 unique amplicon sequence variants. Linear convergence of microbial composition and structure was observed between an occupants' skin and the dormitory surfaces that were only used by that occupant (i.e., desk). Conversely, bacterial community beta diversity (weighted Unifrac) convergence between the skin of both roommates and the shared dormitory floor between the two cadet's beds was not seen across the entire study population. The sampling period included two semester breaks in which the occupants vacated their rooms; upon their return, the beta diversity similarity between their skin and the surfaces had significantly decreased compared to before the break (p < 0.05). There was no apparent convergence between the gut and building microbiota, with the exception of communal bathroom door-handles, which suggests that neither co-occupancy, diet, or lifestyle homogenization had a significant impact on gut microbiome similarity between these cadets over the observed time frame. As a result, predictive classifier models were able to identify an individual more accurately based on the gut microbiota (74%) compared to skin (51%).<br><br>CONCLUSIONS: To the best of our knowledge, this is the first study to show an increase in skin microbial similarity of two individuals who start living together for the first time and who are not genetically related or romantically involved. Cohabitation was significantly associated with increased skin microbiota similarity but did not significantly influence the gut microbiota. Following a departure from the occupied space of several weeks, the skin microbiota, but not the gut microbiota, showed a significant reduction in similarity relative to the building. Overall, longitudinal observation of these dynamics enables us to dissect the influence of occupation, diet, and lifestyle factors on occupant and built environment microbial ecology.}, }
@article {pmid31040329, year = {2019}, author = {Engel, F and Attermeyer, K and Ayala, AI and Fischer, H and Kirchesch, V and Pierson, DC and Weyhenmeyer, GA}, title = {Phytoplankton gross primary production increases along cascading impoundments in a temperate, low-discharge river: Insights from high frequency water quality monitoring.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6701}, doi = {10.1038/s41598-019-43008-w}, pmid = {31040329}, issn = {2045-2322}, support = {2016-04153//Vetenskapsr&amp;#x00E5;det (Swedish Research Council)/ ; 643052//EC | Horizon 2020 (Horizon 2020 - Research and Innovation Framework Programme)/ ; KAW project//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; }, abstract = {Damming alters carbon processing along river continua. Estimating carbon transport along rivers intersected by multiple dams requires an understanding of the effects of cascading impoundments on the riverine metabolism. We analyzed patterns of riverine metabolism and phytoplankton biomass (chlorophyll a; Chla) along a 74.4-km river reach intersected by six low-head navigation dams. Calculating gross primary production (GPP) from continuous measurements of dissolved oxygen concentration, we found a maximum increase in the mean GPP by a factor of 3.5 (absolute difference of 0.45 g C m-3 d-1) along the first 26.5 km of the study reach, while Chla increased over the entire reach by a factor of 2.9 (8.7 µg l-1). In the intermittently stratified section of the deepest impoundment the mean GPP between the 1 and 4 m water layer differed by a factor of 1.4 (0.31 g C m-3 d-1). Due to the strong increase in GPP, the river featured a wide range of conditions characteristic of low- to medium-production rivers. We suggest that cascading impoundments have the potential to stimulate riverine GPP, and conclude that phytoplankton CO2 uptake is an important carbon flux in the river Saar, where a considerable amount of organic matter is of autochthonous origin.}, }
@article {pmid31038352, year = {2019}, author = {Dong, Y and Sanford, RA and Inskeep, WP and Srivastava, V and Bulone, V and Fields, CJ and Yau, PM and Sivaguru, M and Ahrén, D and Fouke, KW and Weber, J and Werth, CR and Cann, IK and Keating, KM and Khetani, RS and Hernandez, AG and Wright, C and Band, M and Imai, BS and Fried, GA and Fouke, BW}, title = {Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats.}, journal = {Astrobiology}, volume = {}, number = {}, pages = {}, doi = {10.1089/ast.2018.1965}, pmid = {31038352}, issn = {1557-8070}, abstract = {The evolutionarily ancient Aquificales bacterium Sulfurihydrogenibium spp. dominates filamentous microbial mat communities in shallow, fast-flowing, and dysoxic hot-spring drainage systems around the world. In the present study, field observations of these fettuccini-like microbial mats at Mammoth Hot Springs in Yellowstone National Park are integrated with geology, geochemistry, hydrology, microscopy, and multi-omic molecular biology analyses. Strategic sampling of living filamentous mats along with the hot-spring CaCO3 (travertine) in which they are actively being entombed and fossilized has permitted the first direct linkage of Sulfurihydrogenibium spp. physiology and metabolism with the formation of distinct travertine streamer microbial biomarkers. Results indicate that, during chemoautotrophy and CO2 carbon fixation, the 87-98% Sulfurihydrogenibium-dominated mats utilize chaperons to facilitate enzyme stability and function. High-abundance transcripts and proteins for type IV pili and extracellular polymeric substances (EPSs) are consistent with their strong mucus-rich filaments tens of centimeters long that withstand hydrodynamic shear as they become encrusted by more than 5 mm of travertine per day. Their primary energy source is the oxidation of reduced sulfur (e.g., sulfide, sulfur, or thiosulfate) and the simultaneous uptake of extremely low concentrations of dissolved O2 facilitated by bd-type cytochromes. The formation of elevated travertine ridges permits the Sulfurihydrogenibium-dominated mats to create a shallow platform from which to access low levels of dissolved oxygen at the virtual exclusion of other microorganisms. These ridged travertine streamer microbial biomarkers are well preserved and create a robust fossil record of microbial physiological and metabolic activities in modern and ancient hot-spring ecosystems.}, }
@article {pmid31037377, year = {2019}, author = {Wu, C and Kan, J and Liu, H and Pujari, L and Guo, C and Wang, X and Sun, J}, title = {Heterotrophic Bacteria Dominate the Diazotrophic Community in the Eastern Indian Ocean (EIO) during Pre-Southwest Monsoon.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01355-1}, pmid = {31037377}, issn = {1432-184X}, support = {41276124//the National Natural Science Foundation of China/ ; 41676112//the National Natural Science Foundation of China/ ; NORC2017-10//NSFC open research cruises/ ; TD12-5003//the Science Fund for University Creative Research Groups in Tianjin/ ; 41876134//Foundation for the Author of National Excellent Doctoral Dissertation of the People's Republic of China (CN)/ ; }, abstract = {The diazotrophic communities play an important role in sustaining primary productivity through adding new nitrogen to oligotrophic marine ecosystems. Yet, their composition in the oligotrophic Indian Ocean is poorly understood. Here, we report the first observation of phylogenetic diversity and distribution of diazotrophs in the Eastern Indian Ocean (EIO) surface water (to 200 m) during the pre-southwest monsoon period. Through high throughput sequencing of nifH genes, we identified diverse groups of diazotrophs in the EIO including both non-cyanobacterial and cyanobacterial phylotypes. Proteobacteria (mainly Alpha-, Beta-, and Gamma-proteobacteria) were the most diverse and abundant groups within all the diazotrophs, which accounted for more than 86.9% of the total sequences. Cyanobacteria were also retrieved, and they were dominated by the filamentous non-heterocystous cyanobacteria Trichodesmium spp. Other cyanobacteria such as unicellular diazotrophic cyanobacteria were detected sporadically. Interestingly, our qPCR analysis demonstrated that the depth-integrated gene abundances of the diazotrophic communities exhibited spatial heterogeneity with Trichodesmium spp. appeared to be more abundant in the Bay of Bengal (p < 0.05), while Sagittula castanea (Alphaproteobacteria) was found to be more dominating in the equatorial region and offshores (p < 0.05). Non-metric multidimensional scaling analysis (NMDS) further confirmed distinct vertical and horizontal spatial variations in the EIO. Canonical correspondence analysis (CCA) indicated that temperature, salinity, and phosphate were the major environmental factors driving the distribution of the diazotroph communities. Overall, our study provides the first insight into the diversity and distribution of the diazotrophic communities in EIO. The findings from this study highlight distinct contributions of both non-cyanobacteria and cyanobacteria to N2 fixation. Moreover, our study reveals information that is critical for understanding spatial heterogeneity and distribution of diazotrophs, and their vital roles in nitrogen and carbon cycling.}, }
@article {pmid31037376, year = {2019}, author = {Robledo-Mahón, T and Silva-Castro, GA and Kuhar, U and Jamnikar-Ciglenečki, U and Barlič-Maganja, D and Aranda, E and Calvo, C}, title = {Effect of Composting Under Semipermeable Film on the Sewage Sludge Virome.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01365-z}, pmid = {31037376}, issn = {1432-184X}, abstract = {The addition of compost from sewage sludge to soils represents a sustainable option from an environmental and economic point of view, which involves the valorisation of these wastes. However, before their use as a soil amendment, compost has to reach the quality levels according to the normative, including microbial parameters. Viruses are not included in this regulation and they can produce agricultural problems and human diseases if the compost is not well sanitised. In this study, we carried out the analysis of the viral populations during a composting process with sewage sludge at an industrial scale, using semipermeable cover technology. Viral community was characterised by the presence of plant viruses and bacteriophages of enteric bacteria. The phytopathogen viruses were the group with the highest relative abundance in the sewage sludge sample and at 70 days of the composting process. The diversity of bacterial viruses and their specificity, with respect to the more abundant bacterial taxa throughout the process, highlights the importance of the interrelations between viral and bacterial communities in the control of pathogenic communities. These results suggest the possibility of using them as a tool to predict the effectiveness of the process.}, }
@article {pmid31031958, year = {2019}, author = {Collins, GE and Hogg, ID and Baxter, JR and Maggs-Kölling, G and Cowan, DA}, title = {Ancient landscapes of the Namib Desert harbor high levels of genetic variability and deeply divergent lineages for Collembola.}, journal = {Ecology and evolution}, volume = {9}, number = {8}, pages = {4969-4979}, doi = {10.1002/ece3.5103}, pmid = {31031958}, issn = {2045-7758}, abstract = {Aim: To assess spatial patterns of genetic and species-level diversity for Namib Desert Collembola using mitochondrial DNA cytochrome c oxidase subunit I (COI) gene sequences.<br><br>Location: Namib Desert gravel plains.<br><br>Taxon: Collembola (springtails).<br><br>Methods: A total of 77 soil samples were collected along NE-SW (60 km) and E-W (160 km) transects from within a 4,000 km2 area of the Namib Desert gravel plains. We extracted 434 springtails from the 37 samples which contained Collembola and sequenced them at the COI gene locus. In the absence of specific taxonomic keys and previous genetic data for these taxa, we used Generalized Mixed Yule Coalescent (GMYC) analyses to provide putative species-level designations.<br><br>Results: We obtained 341 successful COI sequences, 175 of which were unique haplotypes. GMYC analyses identified 30 putative species, with up to 28% sequence divergence (uncorrected p-distance). The distribution of genetic variants was disjunct, with 97% of haplotypes and 70% of &quot;GMYC species&quot; found only at single sites.<br><br>Main conclusions: Dispersal events, although rare, may be facilitated by environmental events such as prevailing onshore winds or occasional flow of rainwater to the coast. We conclude that the high genetic diversity we observed is the result of ancient springtail lineages, patchy distribution of suitable habitats, and limited dispersal (gene flow) among habitable locations.}, }
@article {pmid31031435, year = {2019}, author = {Gomes, J and Khandeparker, R and Meena, RM and Ramaiah, N}, title = {Bacterial Community Composition Markedly Altered by Coastal Hypoxia.}, journal = {Indian journal of microbiology}, volume = {59}, number = {2}, pages = {200-208}, doi = {10.1007/s12088-019-00790-5}, pmid = {31031435}, issn = {0046-8991}, abstract = {Monsoonal upwelling along south and central west coast of India leads to intense biological productivity. As a consequence of excess organic matter production following upwelling during June-October and low dissolved oxygen in the upwelled waters, denitrification occurs in the near shore waters. Implicitly, these processes ought to bring alterations in microbial communities. Therefore, diversity and community structure of bacteria from subsurface layers of a tropical region experiencing intense seasonal lows of oxygen were analyzed through sequencing of 16S rRNA gene clones. The overall diversity was more during hypoxic period of Fall intermonsoon (FIM, October) compared either to Spring intermonsoon (SIM, March) or summer monsoon (SuM, June) months. As many as 14 lineages of bacterial domains: Gammaproteobacteria (37%), Alphaproteobacteria (21%), Cyanobacteria (20%), Deltaproteobacteria (3%), Firmicutes (3%), Betaproteobacteria (2%), Acidobacteria (2%), Actinobacteria (7%), Marinimicrobia (2%), Bacteroidetes (1%), Verrucomicrobia (1%), Planctomycetes (0.4%), Chloroflexi (0.2%) and Omnitrophica bacterium (0.2%), were recognized from our coastal location. Notably, sequences of Planctomycetes, Chloroflexi and Omnitrophica bacterium were found exclusively during FIM. A generally higher representation of sequences of Betaproteobacteria during SuM and of Actinobacteria and Firmicutes during SIM was discernible. This study is thus useful to recognize that microbial community might undergo strong temporal shifts in the monsoon affected tropical coastal ecosystems.}, }
@article {pmid31031118, year = {2019}, author = {Enke, TN and Datta, MS and Schwartzman, J and Cermak, N and Schmitz, D and Barrere, J and Pascual-García, A and Cordero, OX}, title = {Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities.}, journal = {Current biology : CB}, volume = {29}, number = {9}, pages = {1528-1535.e6}, doi = {10.1016/j.cub.2019.03.047}, pmid = {31031118}, issn = {1879-0445}, abstract = {Understanding the principles that govern the assembly of microbial communities across earth's biomes is a major challenge in modern microbial ecology. This pursuit is complicated by the difficulties of mapping functional roles and interactions onto communities with immense taxonomic diversity and of identifying the scale at which microbes interact [1]. To address this challenge, here, we focused on the bacterial communities that colonize and degrade particulate organic matter in the ocean [2-4]. We show that the assembly of these communities can be simplified as a linear combination of functional modules. Using synthetic polysaccharide particles immersed in natural bacterioplankton assemblages [1, 5], we showed that successional particle colonization dynamics are driven by the interaction of two types of modules: a first type made of narrowly specialized primary degraders, whose dynamics are controlled by particle polysaccharide composition, and a second type containing substrate-independent taxa whose dynamics are controlled by interspecific interactions-in particular, cross-feeding via organic acids, amino acids, and other metabolic byproducts. We show that, as a consequence of this trophic structure, communities can assemble modularly-i.e., by a simple sum of substrate-specific primary degrader modules, one for each complex polysaccharide in the particle, connected to a single broad-niche range consumer module. Consistent with this model, a linear combination of the communities on single-polysaccharide particles accurately predicts community composition on mixed-polysaccharide particles. Our results suggest that the assembly of heterotrophic communities that degrade complex organic materials follows simple design principles that could be exploited to engineer heterotrophic microbiomes.}, }
@article {pmid31031092, year = {2019}, author = {Hull, NM and Ling, F and Pinto, AJ and Albertsen, M and Jang, HG and Hong, PY and Konstantinidis, KT and LeChevallier, M and Colwell, RR and Liu, WT}, title = {Drinking Water Microbiome Project: Is it Time?.}, journal = {Trends in microbiology}, volume = {27}, number = {8}, pages = {670-677}, doi = {10.1016/j.tim.2019.03.011}, pmid = {31031092}, issn = {1878-4380}, abstract = {Now is an opportune time to foster collaborations across sectors and geographical boundaries to enable development of best practices for drinking water (DW) microbiome research, focusing on accuracy and reproducibility of meta-omic techniques (while learning from past microbiome projects). A large-scale coordinated effort that builds on this foundation will enable the urgently needed comprehensive spatiotemporal understanding and control of DW microbiomes by engineering interventions to protect public health. This opinion paper highlights the need to initiate and conduct a large-scale coordinated DW microbiome project by addressing key knowledge gaps and recommends a roadmap for this effort.}, }
@article {pmid31030239, year = {2019}, author = {Omae, K and Fukuyama, Y and Yasuda, H and Mise, K and Yoshida, T and Sako, Y}, title = {Diversity and distribution of thermophilic hydrogenogenic carboxydotrophs revealed by microbial community analysis in sediments from multiple hydrothermal environments in Japan.}, journal = {Archives of microbiology}, volume = {201}, number = {7}, pages = {969-982}, doi = {10.1007/s00203-019-01661-9}, pmid = {31030239}, issn = {1432-072X}, support = {16J11269//Grant-in-Aid from the Japan Society for the Promotion of Science (JSPS) Fellows/ ; 25252038//Japan Society for the Promotion of Science/ ; 16H06381//Japan Society for the Promotion of Science/ ; }, abstract = {In hydrothermal environments, carbon monoxide (CO) utilisation by thermophilic hydrogenogenic carboxydotrophs may play an important role in microbial ecology by reducing toxic levels of CO and providing H2 for fuelling microbial communities. We evaluated thermophilic hydrogenogenic carboxydotrophs by microbial community analysis. First, we analysed the correlation between carbon monoxide dehydrogenase (CODH)-energy-converting hydrogenase (ECH) gene cluster and taxonomic affiliation by surveying an increasing genomic database. We identified 71 genome-encoded CODH-ECH gene clusters, including 46 whose owners were not reported as hydrogenogenic carboxydotrophs. We identified 13 phylotypes showing > 98.7% identity with these taxa as potential hydrogenogenic carboxydotrophs in hot springs. Of these, Firmicutes phylotypes such as Parageobacillus, Carboxydocella, Caldanaerobacter, and Carboxydothermus were found in different environmental conditions and distinct microbial communities. The relative abundance of the potential thermophilic hydrogenogenic carboxydotrophs was low. Most of them did not show any symbiotic networks with other microbes, implying that their metabolic activities might be low.}, }
@article {pmid31026580, year = {2019}, author = {Han, M and Dsouza, M and Zhou, C and Li, H and Zhang, J and Chen, C and Yao, Q and Zhong, C and Zhou, H and Gilbert, JA and Wang, Z and Ning, K}, title = {Agricultural Risk Factors Influence Microbial Ecology in Honghu Lake.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {17}, number = {1}, pages = {76-90}, doi = {10.1016/j.gpb.2018.04.008}, pmid = {31026580}, issn = {2210-3244}, mesh = {*Agriculture ; Animals ; Anti-Bacterial Agents/*analysis ; China ; Eutrophication ; Geologic Sediments/chemistry/microbiology ; Lakes/chemistry/*microbiology ; *Microbiota ; Risk Factors ; Water Pollutants, Chemical/*analysis ; }, abstract = {Agricultural activities, including stock-farming, planting industry, and fish aquaculture, can affect the physicochemical and biological characters of freshwater lakes. However, the effects of pollution producing by agricultural activities on microbial ecosystem of lakes remain unclear. Hence, in this work, we selected Honghu Lake as a typical lake that is influenced by agriculture activities. We collected water and sediment samples from 18 sites, which span a wide range of areas from impacted and less-impacted areas. We performed a geospatial analysis on the composition of microbial communities associated with physicochemical properties and antibiotic pollution of samples. The co-occurrence networks of water and sediment were also built and analyzed. Our results showed that the microbial communities of impacted and less-impacted samples of water were largely driven by the concentrations of TN, TP, NO3--N, and NO2--N, while those of sediment were affected by the concentrations of Sed-OM and Sed-TN. Antibiotics have also played important roles in shaping these microbial communities: the concentrations of oxytetracycline and tetracycline clearly reflected the variance in taxonomic diversity and predicted functional diversity between impacted and less-impacted sites in water and sediment samples, respectively. Furthermore, for samples from both water and sediment, large differences of network topology structures between impacted and less-impacted were also observed. Our results provide compelling evidence that the microbial community can be used as a sentinel of eutrophication and antibiotics pollution risk associated with agricultural activity; and that proper monitoring of this environment is vital to maintain a sustainable environment in Honghu Lake.}, }
@article {pmid31025063, year = {2019}, author = {Negi, A and Sarethy, IP}, title = {Microbial Biodeterioration of Cultural Heritage: Events, Colonization, and Analyses.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01366-y}, pmid = {31025063}, issn = {1432-184X}, abstract = {Geochemical cycles result in the chemical, physical, and mineralogical modification of rocks, eventually leading to formation of soil. However, when the stones and rocks are a part of historic buildings and monuments, the effects are deleterious. In addition, microorganisms also colonize these monuments over a period of time, resulting in formation of biofilms; their metabolites lead to physical weakening and discoloration of stone eventually. This process, known as biodeterioration, leads to a significant loss of cultural heritage. For formulating effective conservation strategies to prevent biodeterioration and restore monuments, it is important to know which microorganisms are colonizing the substrate and the different energy sources they consume to sustain themselves. With this view in scope, this review focuses on studies that have attempted to understand the process of biodeterioration, the mechanisms by which they colonize and affect the monuments, the techniques used for assessment of biodeterioration, and conservation strategies that aim to preserve the original integrity of the monuments. This review also includes the &quot;omics&quot; technologies that have started playing a large role in elucidating the nature of microorganisms, and how they can play a role in hastening the formulation of effective conservation strategies.}, }
@article {pmid31025062, year = {2019}, author = {Zhao, Z and Zhang, X and Cheng, M and Song, X and Zhang, Y and Zhong, X}, title = {Influences of Iron Compounds on Microbial Diversity and Improvements in Organic C, N, and P Removal Performances in Constructed Wetlands.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01379-7}, pmid = {31025062}, issn = {1432-184X}, support = {D-8005-18-0068-1/2//China Postdoctoral Science Foundation/ ; 51679041//National Natural Science Foundation of China/ ; A2-0203-00-100356//Shanghai Ocean University Ph. D Start-Up Fund/ ; 2017B020236002//program of. science and technology in Guangdong Province/ ; }, abstract = {The effects of various combinations of iron compounds on the contaminant removal performance in constructed wetlands (CWs) were explored under various initial iron concentrations, contaminant concentrations, different hydraulic retention time (HRT), and different temperatures. The Combo 6 (nanoscale zero-valent iron combined with Fe3+) in CW treatments showed the highest pollutant removal performance under the conditions of C2 initial iron dosage concentration (total iron 0.2 mM) and I2 initial contaminant concentration (COD:TN:TP = 60 mg/L:60 mg/L:1 mg/L) in influent after 72-h HRT. These results were directly verified by two different microbial tests (Biolog test and high-throughput pyrosequencing) and microbial community analysis (principal component analysis of community-level physiological profile, biodiversity index, cluster tree, relative abundance at order of taxonomy level). Specific bacteria related to significant improvements in contaminant removal were domesticated by various combinations of iron compounds. Iron dosage was advised as a green, new, and effective option for wastewater treatment. Graphical Abstract .}, }
@article {pmid31024771, year = {2019}, author = {Cipriano, MAP and Suleiman, AKA and da Silveira, APD and do Carmo, JB and Kuramae, EE}, title = {Bacterial community composition and diversity of two different forms of an organic residue of bioenergy crop.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6768}, doi = {10.7717/peerj.6768}, pmid = {31024771}, issn = {2167-8359}, abstract = {The use of residue of sugarcane ethanol industry named vinasse in fertirrigation is an established and widespread practice in Brazil. Both non-concentrated vinasse (NCV) and concentrated vinasse (CV) are used in fertirrigation, particularly to replace the potassium fertilizer. Although studies on the chemical and organic composition of vinasse and their impact on nitrous oxide emissions when applied in soil have been carried out, no studies have evaluated the microbial community composition and diversity in different forms of vinasse. We assessed the bacterial community composition of NCV and CV by non-culturable and culturable approaches. The non-culturable bacterial community was assessed by next generation sequencing of the 16S rRNA gene and culturable community by isolation of bacterial strains and molecular and biochemical characterization. Additionally, we assessed in the bacterial strains the presence of genes of nitrogen cycle nitrification and denitrification pathways. The microbial community based on 16S rRNA sequences of NCV was overrepresented by Bacilli and Negativicutes while CV was mainly represented by Bacilli class. The isolated strains from the two types of vinasse belong to class Bacilli, similar to Lysinibacillus, encode for nirK gene related to denitrification pathway. This study highlights the bacterial microbial composition particularly in CV what residue is currently recycled and recommended as a sustainable practice in sugarcane cultivation in the tropics.}, }
@article {pmid31024471, year = {2019}, author = {Lacerda-Júnior, GV and Noronha, MF and Cabral, L and Delforno, TP and de Sousa, STP and Fernandes-Júnior, PI and Melo, IS and Oliveira, VM}, title = {Land Use and Seasonal Effects on the Soil Microbiome of a Brazilian Dry Forest.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {648}, doi = {10.3389/fmicb.2019.00648}, pmid = {31024471}, issn = {1664-302X}, abstract = {Drylands occupy approximately 41% of the Earth's terrestrial surface. Climate change and land use practices are expected to affect biogeochemical cycling by the soil microbiome in these ecosystems. Understanding how soil microbial community might respond to these drivers is extremely important to mitigate the processes of land degradation and desertification. The Caatinga, an exclusively Brazilian biome composed of an extensive seasonal tropical dry forest, is exposed to variable spatiotemporal rainfall patterns as well as strong human-driven pressures. Herein, an integrated analysis of shotgun metagenomics approach coupled to meteorological data was employed to unravel the impact of seasonality and land use change on soil microbiome from preserved and agriculture-affected experimental fields in Caatinga drylands. Multivariate analysis suggested that microbial communities of preserved soils under seasonal changes were shaped primarily by water deficit, with a strong increase of Actinobacteria and Proteobacteria members in the dry and rainy seasons, respectively. In contrast, nutrient availability notably played a critical role in driving the microbial community in agriculture-affected soils. The strong enrichment of bacterial genera belonging to the poorly-known phylum Acidobacteria ('Candidatus Solibacter' and 'Candidatus Koribacter') in soils from dry season affected by ferti-irrigation practices presupposes a contrasting copiotrophic lifestyle and ecological role in mitigating the impact of chemical fertilization. Functional analyses identify overrepresented genes related to osmotic stress response (synthesis of osmoprotectant compounds, accumulation of potassium ions) and preferential carbon and nitrogen utilization when comparing the microbiome of preserved soils under seasonal changes, reflecting differences in the genetic potential for nutrient cycling and C acquisition in the environment. However, the prevalence of nitrosative stress and denitrification functions in irrigation/fertilization-affected soils of the dry season clearly suggest that nutrient input and disruption of natural water regime may impact biogeochemical cycles linked to the microbial processes, with potential impacts on the ecosystem functionality. These findings help to better understand how natural seasonality and agricultural management differentially affect soil microbial ecology from dry forests, providing support for the development of more sustainable land management in dryland ecosystems.}, }
@article {pmid31021624, year = {2019}, author = {Mani, T and Primpke, S and Lorenz, C and Gerdts, G and Burkhardt-Holm, P}, title = {Microplastic Pollution in Benthic Midstream Sediments of the Rhine River.}, journal = {Environmental science &amp; technology}, volume = {53}, number = {10}, pages = {6053-6062}, doi = {10.1021/acs.est.9b01363}, pmid = {31021624}, issn = {1520-5851}, abstract = {Rivers are major transport vectors for microplastics (MP) toward the sea. However, there is evidence that MP can temporarily or permanently be inhibited from migrating downstream by retention in sediments or ingestion by organisms. MP concentrations, compositions, and fate within the different compartments of the fluvial environment are poorly understood. Here, benthic, midstream sediments of two undammed, open-flowing stretches were investigated in the Rhine River, one of the world's busiest inland waterways. Twenty-five samples were collected at ten sites via riverbed access through a diving bell or dredging. We performed the first comprehensive analysis of riverbed sediment aliquots that avoids visual selection bias using state-of-the art automated micro-Fourier-transform infrared spectroscopy (μFTIR) imaging. MP numbers ranged between 0.26 ± 0.01 and 11.07 ± 0.6 × 103 MP kg-1 while MP particles <75 μm accounted for a mean numerical proportion ± SD of 96 ± 6%. MP concentrations decreased with sediment depth. Eighteen polymers were identified in the size range of 11-500 μm; the acrylates/polyurethane/varnish (APV) cluster was found at all sites (mean numerical proportion, 70 ± 19%), possibly indicating particulate pollution from ship antifouling paint. Overall, polymers denser than freshwater (>1 g cm-3) dominated (85 ± 18%), which contrasts the large proportions of low-density polymers previously reported in near-surface compartments of the Rhine.}, }
@article {pmid31019271, year = {2019}, author = {Averill, C and Cates, LL and Dietze, MC and Bhatnagar, JM}, title = {Spatial vs. temporal controls over soil fungal community similarity at continental and global scales.}, journal = {The ISME journal}, volume = {13}, number = {8}, pages = {2082-2093}, doi = {10.1038/s41396-019-0420-1}, pmid = {31019271}, issn = {1751-7370}, support = {1638577//National Science Foundation (NSF)/ ; Boston University BRITE Research Experiences for Undergraduates Program//National Science Foundation (NSF)/ ; 1638577//National Science Foundation (NSF)/ ; 1638577//National Science Foundation (NSF)/ ; Climate and Global Change Postdoctoral Fellowship//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; }, abstract = {Large-scale environmental sequencing efforts have transformed our understanding of the spatial controls over soil microbial community composition and turnover. Yet, our knowledge of temporal controls is comparatively limited. This is a major uncertainty in microbial ecology, as there is increasing evidence that microbial community composition is important for predicting microbial community function in the future. Here, we use continental- and global-scale soil fungal community surveys, focused within northern temperate latitudes, to estimate the relative contribution of time and space to soil fungal community turnover. We detected large intra-annual temporal differences in soil fungal community similarity, where fungal communities differed most among seasons, equivalent to the community turnover observed over thousands of kilometers in space. inter-annual community turnover was comparatively smaller than intra-annual turnover. Certain environmental covariates, particularly climate covariates, explained some spatial-temporal effects, though it is unlikely the same mechanisms drive spatial vs. temporal turnover. However, these commonly measured environmental covariates could not fully explain relationships between space, time and community composition. These baseline estimates of fungal community turnover in time provide a starting point to estimate the potential duration of legacies in microbial community composition and function.}, }
@article {pmid31016338, year = {2019}, author = {Nappi, J and Soldi, E and Egan, S}, title = {Diversity and Distribution of Bacteria Producing Known Secondary Metabolites.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01380-0}, pmid = {31016338}, issn = {1432-184X}, support = {FT130100828//Australian Research Council/ ; }, abstract = {There is an increasing interest in the utilisation of marine bioactive compounds as novel biopharmaceuticals and agrichemicals; however, little is known about the environmental distribution for many of these molecules. Here, we aimed to elucidate the environmental distribution and to detect the biosynthetic gene clusters in environmental samples of four bioactive compounds, namely violacein, tropodithietic acid (TDA), tambjamine and the antibacterial protein AlpP. Our database analyses revealed high bacterial diversity for AlpP and violacein producers, while TDA-producing bacteria were mostly associated with marine surfaces and all belonged to the roseobacter group. In contrast, the tambjamine cluster was only found in the genomes of two Pseudoalteromonas species and in one terrestrial species belonging to the Cupriavidus genus. Using a PCR-based screen of different marine samples, we detected TDA and violacein genes associated with the microbiome of Ulva and Protohyale niger and tambjamine genes associated with Nodilittorina unifasciata; however, alpP was not detected. These results highlight the variable distribution of the genes encoding these four bioactive compounds, including their detection from the surface of multiple marine eukaryotic hosts. Determining the natural distribution of these gene clusters will help to understand the ecological importance of these metabolites and the bacteria that produce them.}, }
@article {pmid31015413, year = {2019}, author = {Kits, KD and Jung, MY and Vierheilig, J and Pjevac, P and Sedlacek, CJ and Liu, S and Herbold, C and Stein, LY and Richter, A and Wissel, H and Brüggemann, N and Wagner, M and Daims, H}, title = {Low yield and abiotic origin of N2O formed by the complete nitrifier Nitrospira inopinata.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1836}, doi = {10.1038/s41467-019-09790-x}, pmid = {31015413}, issn = {2041-1723}, mesh = {Ammonia/*metabolism ; Archaea/metabolism ; Bacteria/drug effects/*metabolism ; Climate Change ; Cyclic N-Oxides/pharmacology ; Imidazoles/pharmacology ; Metabolic Networks and Pathways/drug effects/physiology ; Nitric Oxide/*metabolism ; Nitrification/drug effects/physiology ; Nitrous Oxide/*metabolism ; Oxidation-Reduction ; Soil Microbiology ; }, abstract = {Nitrous oxide (N2O) and nitric oxide (NO) are atmospheric trace gases that contribute to climate change and affect stratospheric and ground-level ozone concentrations. Ammonia oxidizing bacteria (AOB) and archaea (AOA) are key players in the nitrogen cycle and major producers of N2O and NO globally. However, nothing is known about N2O and NO production by the recently discovered and widely distributed complete ammonia oxidizers (comammox). Here, we show that the comammox bacterium Nitrospira inopinata is sensitive to inhibition by an NO scavenger, cannot denitrify to N2O, and emits N2O at levels that are comparable to AOA but much lower than AOB. Furthermore, we demonstrate that N2O formed by N. inopinata formed under varying oxygen regimes originates from abiotic conversion of hydroxylamine. Our findings indicate that comammox microbes may produce less N2O during nitrification than AOB.}, }
@article {pmid31015324, year = {2019}, author = {Easton, AV and Quiñones, M and Vujkovic-Cvijin, I and Oliveira, RG and Kepha, S and Odiere, MR and Anderson, RM and Belkaid, Y and Nutman, TB}, title = {The Impact of Anthelmintic Treatment on Human Gut Microbiota Based on Cross-Sectional and Pre- and Postdeworming Comparisons in Western Kenya.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, doi = {10.1128/mBio.00519-19}, pmid = {31015324}, issn = {2150-7511}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anthelmintics/*administration &amp; dosage ; Ascariasis/*drug therapy ; Bacteria/*classification/genetics ; Child ; Child, Preschool ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Kenya ; Metagenomics ; Microbiota/*drug effects ; Middle Aged ; Necatoriasis/*drug therapy ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Rural Population ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Murine studies suggest that the presence of some species of intestinal helminths is associated with changes in host microbiota composition and diversity. However, studies in humans have produced varied conclusions, and the impact appears to vary widely depending on the helminth species present. To demonstrate how molecular approaches to the human gut microbiome can provide insights into the complex interplay among disparate organisms, DNA was extracted from cryopreserved stools collected from residents of 5 rural Kenyan villages prior to and 3 weeks and 3 months following albendazole (ALB) therapy. Samples were analyzed by quantitative PCR (qPCR) for the presence of 8 species of intestinal parasites and by MiSeq 16S rRNA gene sequencing. Based on pretreatment results, the presence of neither Ascaris lumbricoides nor Necator americanus infection significantly altered the overall diversity of the microbiota in comparison with age-matched controls. Following ALB therapy and clearance of soil-transmitted helminths (STH), there were significant increases in the proportion of the microbiota made up by Clostridiales (P = 0.0002; average fold change, 0.57) and reductions in the proportion made up by Enterobacteriales (P = 0.0004; average fold change, -0.58). There was a significant posttreatment decrease in Chao1 richness, even among individuals who were uninfected pretreatment, suggesting that antimicrobial effects must be considered in any posttreatment setting. Nevertheless, the helminth-associated changes in Clostridiales and Enterobacteriales suggest that clearance of STH, and of N. americanus in particular, alters the gut microbiota.IMPORTANCE The gut microbiome is an important factor in human health. It is affected by what we eat, what medicines we take, and what infections we acquire. In turn, it affects the way we absorb nutrients and whether we have excessive intestinal inflammation. Intestinal worms may have an important impact on the composition of the gut microbiome. Without a complete understanding of the impact of mass deworming programs on the microbiome, it is impossible to accurately calculate the cost-effectiveness of such public health interventions and to guard against any possible deleterious side effects. Our research examines this question in a &quot;real-world&quot; setting, using a longitudinal cohort, in which individuals with and without worm infections are treated with deworming medication and followed up at both three weeks and three months posttreatment. We quantify the impact of roundworms and hookworms on gut microbial composition, suggesting that the impact is small, but that treatment of hookworm infection results in significant changes. This work points to the need for follow-up studies to further examine the impact of hookworm on the gut microbiota and determine the health consequences of the observed changes.}, }
@article {pmid31015144, year = {2019}, author = {Corno, G and Yang, Y and Eckert, EM and Fontaneto, D and Fiorentino, A and Galafassi, S and Zhang, T and Di Cesare, A}, title = {Effluents of wastewater treatment plants promote the rapid stabilization of the antibiotic resistome in receiving freshwater bodies.}, journal = {Water research}, volume = {158}, number = {}, pages = {72-81}, doi = {10.1016/j.watres.2019.04.031}, pmid = {31015144}, issn = {1879-2448}, abstract = {Treated wastewater discharged into the environment acts as a disturbance of the natural microbial communities in terms of taxonomic composition and of functional gene pool, including antibiotic resistance genes. We tested whether stochastic and heterogeneous site-specific trajectories or generalities, potentially driven by deterministic processes, control the fate of allochthonous bacteria from anthropogenic sources and the persistence of their functional traits in freshwater. Finding generalities would allow the identification of wastewater treatments that could be effective in abating determinants of antibiotic resistance. We analysed the short-term response of native bacterial communities in waters exposed to the disturbance of wastewater at different dilutions, using a metagenomic approach that revealed both microbial community composition and the scope and abundance of the resistome that can pose indirect risks to human health. We found that the taxonomic composition of the communities after the disturbance was driven by case-specific stochastic processes, whereas the resistome had a deterministic trajectory, rapidly stabilising its functional traits with higher proportions of wastewater effluents, regardless of differences in taxonomic composition, richness of antibiotic resistance genes and of bacterial taxa, phenotypic features of the bacterial communities, and type of wastewater treatment. The observed deterministic proliferation of resistomes in freshwater bodies receiving wastewater effluents, suggests that this process may contribute to the global propagation of antibiotic resistance, and thus calls for new legislations promoting alternative tertiary treatments for the wastewater reuse, and targeting bacterial functional traits and not only bacterial abundances.}, }
@article {pmid31009873, year = {2019}, author = {Lin, S and Wang, TY and Xu, HR and Zhang, XN and Wang, Q and Liu, R and Li, Q and Bi, KS}, title = {A systemic combined nontargeted and targeted LC-MS based metabolomic strategy of plasma and liver on pathology exploration of alpha-naphthylisothiocyanate induced cholestatic liver injury in mice.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {171}, number = {}, pages = {180-192}, doi = {10.1016/j.jpba.2019.04.009}, pmid = {31009873}, issn = {1873-264X}, abstract = {The pathology of cholestatic liver injury (CLI) was complicated, which has limited the development of anti-cholestatic drugs for a long period. Metabolomic researches focused on global and dynamic changes of the organism could shed some light on mechanism investigation. In order to characterize and validate metabolite alterations of alpha-naphthylisothiocyanate (ANIT) induced CLI in C57BL/6 mice, a systemic metabolomic approach combining nontargeted HPLC-ESI-QTOF-MS and targeted UFLC-ESI-MS/MS technologies were developed innovatively. Multivariate data analysis was applied to determine the changes of metabolites in processed plasma and liver samples between control and model groups. Afterwards, 38 potential plasma biomarkers and 17 potential liver biomarkers involved in bile acid (BA) biosynthesis, phospholipid biosynthesis, sphingolipid metabolism, alpha linolenic acid and linoleic acid metabolism, as well as arachidonic acid metabolism were found and attributed as potential biomarkers and influential pathways of cholestasis. Based on correlation analysis, BA biosynthesis played the most important role in ANIT induced CLI, thereinto, major BAs were carried out with quantitative analysis. Targeted metabolomic results showed that the increase of BAs might have an impact on intestinal microbial ecology which could aggravate liver injury probably, among which cholic acid (CA) and taurocholic acid (TCA) were the most sensitive indicators of ANIT induced CLI in both plasma and liver. In conclusion, CLI might correlate significantly with hepatocyte necrosis, metabolic disorders and imbalance of intestinal microbiome ecology triggered by BA accumulation.}, }
@article {pmid31005840, year = {2019}, author = {Qian, X and Gu, J and Sun, W and Wang, X and Li, H}, title = {Effects of passivators on antibiotic resistance genes and related mechanisms during composting of copper-enriched pig manure.}, journal = {The Science of the total environment}, volume = {674}, number = {}, pages = {383-391}, doi = {10.1016/j.scitotenv.2019.04.197}, pmid = {31005840}, issn = {1879-1026}, mesh = {Animals ; Charcoal/chemistry ; Composting/*methods ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; Manure/microbiology ; Zeolites/chemistry ; }, abstract = {Due to the intensive use of feed additives in livestock farming, animal manure has become a hotspot for antibiotics, heavy metals, and antibiotic resistance genes (ARGs). Unlike antibiotics, heavy metals cannot be degraded during composting and thus could pose a persistent co-selective pressure in the proliferation of antibiotic resistance. Passivators are commonly applied to immobilize metals and improve the safety of compost. However, little is known about the effects of various passivators on ARGs and mobile genetic elements (MGEs) during composting and the underlying mechanisms involved. Thus, three typical passivators (biochar, fly ash, and zeolite) were applied during the composting of copper-enriched pig manure, and their effects on ARGs, copper resistance genes, MGEs, and the bacterial communities were examined. Compared to the control, all passivator treatments reduced the abundances of at least six ARGs (tetC, tetG, tetQ, tetX, sul1, and ermB) by 0.23-1.09 logs and of two MGEs (intI1 and ISCR1) by 26-85% after composting. Biochar and fly ash also significantly reduced the abundances of intI2 and Tn914/1545. In contrast, abundances of copper resistance genes were not reduced by passivators, implying that the decreased co-selective pressure may not be a major contributor to ARG reductions in this study. Procrustes analysis and redundancy analysis demonstrated that shifts in the bacterial community determined the changes in the abundances of ARGs, and the variation in MGEs and DTPA-Cu can also partially explain the ARG variance. Overall, all of three passivators can be used to reduce the health risks associated with ARGs in livestock manure, and biochar performed the best at reducing ARGs and MGEs.}, }
@article {pmid31001657, year = {2019}, author = {Mastan, A and Bharadwaj, R and Kushwaha, RK and Vivek Babu, CS}, title = {Functional Fungal Endophytes in Coleus forskohlii Regulate Labdane Diterpene Biosynthesis for Elevated Forskolin Accumulation in Roots.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01376-w}, pmid = {31001657}, issn = {1432-184X}, abstract = {Coleus forskohlii is a perennial medicinal shrub cultivated mainly for its forskolin content. The plant has been used since ancient times in ayurvedic traditional medicines for the treatment of hypertension, glaucoma, asthma, congestive heart failures, obesity, and cancer. Use of endophytic microorganisms presents a special interest for the development of value-added bioactive compounds through agriculture. Limited investigations have been undertaken on in planta enhancement of forskolin content using endophytic fungus in sustainable agriculture. Here we report specific roles of three fungal endophytes, Fusarium redolens (RF1), Phialemoniopsis cornearis (SF1), and Macrophomina pseudophaseolina (SF2), functionally acting as plant probiotic fungus, regulating secondary metabolite (forskolin) biosynthesis in C. forskohlii. The root endophyte, RF1, and shoot endophytes, SF1 and SF2, were found to enhance forskolin content by 52 to 88% in pot and 60 to 84% in field experiments as compared to uninoculated control plants. The three endophytes also enhanced total biomass owing to plant growth promoting properties. The expression of diterpene synthases (CfTPSs) like CfTPS1, CfTPS2, CfTPS3, and CfTPS4 were significantly upregulated in endophyte-treated C. forskohlii plants. Elevated expression of key diterpene synthases (CfTPS2) in the forskolin biosynthesis pathway, exclusively present in the root cork of C. forskohlii, was observed following SF2 endophyte treatment. Furthermore, endophyte treatments conferred a variety of antagonistic activity against nematode galls (80%) and plant pathogens like Fusarium oxysporum, Colletotricum gloeosporioides, and Sclerotium rolfsii. RF1 and SF1 fungal endophytes showed positive for IAA production; however, SF1 also indicated phosphate solubilization activity. Overall, the qualitative and quantitative improvement of in planta forskolin enhancement represents an area of high commercial interest, and hence, our work focused on novel insights for the application of three fungal endophytes for in planta enhancement of forskolin content for C. forskohlii cultivation by a sustainable approach.}, }
@article {pmid31000488, year = {2019}, author = {Ladau, J and Eloe-Fadrosh, EA}, title = {Spatial, Temporal, and Phylogenetic Scales of Microbial Ecology.}, journal = {Trends in microbiology}, volume = {27}, number = {8}, pages = {662-669}, doi = {10.1016/j.tim.2019.03.003}, pmid = {31000488}, issn = {1878-4380}, abstract = {Microbial communities play a major role in disease, biogeochemical cycling, agriculture, and bioremediation. However, identifying the ecological processes that govern microbial community assembly and disentangling the relative impacts of those processes has proven challenging. Here, we propose that this discord is due to microbial systems being studied at different spatial, temporal, and phylogenetic scales. We argue that different processes dominate at different scales, and that through a more explicit consideration of spatial, temporal, and phylogenetic grains and extents (the two components of scale) a more accurate, clear, and useful understanding of microbial community assembly can be developed. We demonstrate the value of applying ecological concepts of scale to microbiology, specifically examining their application to nestedness, legacy effects, and taxa-area relationships of microbial systems. These proposed considerations of scale will help resolve long-standing debates in microbial ecology regarding the processes determining the assembly of microbial communities, and provide organizing principles around which hypotheses and theories can be developed.}, }
@article {pmid30993370, year = {2019}, author = {Li, W and Wang, M and Burgaud, G and Yu, H and Cai, L}, title = {Fungal Community Composition and Potential Depth-Related Driving Factors Impacting Distribution Pattern and Trophic Modes from Epi- to Abyssopelagic Zones of the Western Pacific Ocean.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01374-y}, pmid = {30993370}, issn = {1432-184X}, abstract = {Fungi play an important role in cycling organic matter and nutrients in marine ecosystems. However, the distribution of fungal communities in the ocean, especially the vertical distribution along depth in the water column, remained poorly understood. Here, we assess the depth-related distribution pattern of fungal communities along the water column from epi- to abyssopelagic zones of the Western Pacific Ocean using internal transcribed spacer 2 (ITS2) metabarcoding. Majority of the assigned OTUs were affiliated to Ascomycota, followed by three other minor phyla (Basidiomycota, Chytridiomycota, and Mucoromycota). The epipelagic zone harbored a higher OTU richness with distinct fungal communities as compared with meso-, bathy-, and abyssopelagic zones. Across the whole water column, depth appears as a key parameter for both fungal α- and β-diversity. However, when the dataset was split into the upper (5-500 m) and deeper (below 500 m) layers, no significant correlation was observed between depth and community compositions. In the upper layer, temperature and dissolved oxygen were recognized as the primary environmental factors shaping fungal α- and β- diversity. By parsing fungal OTUs into ecological categories, multi-trophic mode of nutrition was found to be more prevalent with increasing depth, suggesting a potential adaptation to the extreme conditions of the deep sea. This study provides new and meaningful information on the depth-stratified fungal diversity, community structure, and putative ecological roles in the open sea.}, }
@article {pmid30992445, year = {2019}, author = {Lax, S and Cardona, C and Zhao, D and Winton, VJ and Goodney, G and Gao, P and Gottel, N and Hartmann, EM and Henry, C and Thomas, PM and Kelley, ST and Stephens, B and Gilbert, JA}, title = {Microbial and metabolic succession on common building materials under high humidity conditions.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1767}, doi = {10.1038/s41467-019-09764-z}, pmid = {30992445}, issn = {2041-1723}, support = {T32 EB009412/EB/NIBIB NIH HHS/United States ; }, mesh = {Bacteria/genetics/isolation &amp; purification/*metabolism ; Construction Materials/*microbiology ; Environmental Monitoring/*methods ; Fungi/genetics/isolation &amp; purification/*metabolism ; Humidity ; Phylogeny ; RNA, Ribosomal, 16S/isolation &amp; purification ; Viruses/genetics/isolation &amp; purification/*metabolism ; }, abstract = {Despite considerable efforts to characterize the microbial ecology of the built environment, the metabolic mechanisms underpinning microbial colonization and successional dynamics remain unclear, particularly at high moisture conditions. Here, we applied bacterial/viral particle counting, qPCR, amplicon sequencing of the genes encoding 16S and ITS rRNA, and metabolomics to longitudinally characterize the ecological dynamics of four common building materials maintained at high humidity. We varied the natural inoculum provided to each material and wet half of the samples to simulate a potable water leak. Wetted materials had higher growth rates and lower alpha diversity compared to non-wetted materials, and wetting described the majority of the variance in bacterial, fungal, and metabolite structure. Inoculation location was weakly associated with bacterial and fungal beta diversity. Material type influenced bacterial and viral particle abundance and bacterial and metabolic (but not fungal) diversity. Metabolites indicative of microbial activity were identified, and they too differed by material.}, }
@article {pmid30989355, year = {2019}, author = {Nilsson, LKJ and de Oliveira, MR and Marinotti, O and Rocha, EM and Håkansson, S and Tadei, WP and de Souza, AQL and Terenius, O}, title = {Characterization of Bacterial Communities in Breeding Waters of Anopheles darlingi in Manaus in the Amazon Basin Malaria-Endemic Area.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01369-9}, pmid = {30989355}, issn = {1432-184X}, support = {348-2012-622//Vetenskapsrådet/ ; }, abstract = {The microbiota in mosquito breeding waters can affect ovipositing mosquitoes, have effects on larval development, and can modify adult mosquito-gut bacterial composition. This, in turn, can affect transmission of human pathogens such as malaria parasites. Here, we explore the microbiota of four breeding sites for Anopheles darlingi, the most important malaria vector in Latin America. The sites are located in Manaus in the Amazon basin in Brazil, an area of active malaria transmission. Using 16S rRNA gene sequencing by MiSeq, we found that all sites were dominated by Proteobacteria and Firmicutes and that 94% of the total number of reads belonged to 36 operational taxonomic units (OTUs) identified in all sites. Of these, the most common OTUs belonged to Escherichia/Shigella, Staphylococcus, and Pseudomonas. Of the remaining 6% of the reads, the OTUs found to differentiate between the four sites belonged to the orders Burkholderiales, Actinomycetales, and Clostridiales. We conclude that An. darlingi can develop in breeding waters with different surface-water bacteria, but that the common microbiota found in all breeding sites might indicate or contribute to a suitable habitat for this important malaria vector.}, }
@article {pmid30989354, year = {2019}, author = {Newsham, KK and Tripathi, BM and Dong, K and Yamamoto, N and Adams, JM and Hopkins, DW}, title = {Bacterial Community Composition and Diversity Respond to Nutrient Amendment but Not Warming in a Maritime Antarctic Soil.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01373-z}, pmid = {30989354}, issn = {1432-184X}, support = {NE/D00893X/1//Natural Environment Research Council/ ; 2018R1C1B6007755//National Research Foundation of Korea/ ; }, abstract = {A resumption of climate warming in maritime Antarctica, arising from continued greenhouse gas emissions to the atmosphere, is predicted to lead to further expansions of plant populations across the region, with consequent increases in nutrient inputs to soils. Here, we test the main and interactive effects of warming, applied with open top chambers (OTCs), and nutrient amendment with tryptic soy broth (TSB), an artificial growth substrate, on bacterial community composition and diversity using Illumina sequencing of 16S rRNA genes in soil from a field experiment in the southern maritime Antarctic. Substantial effects of TSB application on bacterial communities were identified after 49 months, including reduced diversity, altered phylogenetic community assembly processes, increased Proteobacteria-to-Acidobacteria ratios and significant divergence in community composition, notably increases in the relative abundances of the gram-positive genera Arthrobacter, Paeniglutamicibacter and Planococcus. Contrary to previous observations from other maritime Antarctic field warming experiments, we recorded no effects of warming with OTCs, or interactive effects of OTCs and TSB application, on bacterial community composition or diversity. Based on these findings, we conclude that further warming of the maritime Antarctic is unlikely to influence soil bacterial community composition or diversity directly, but that increased nutrient inputs arising from enhanced plant growth across the region may affect the composition of soil bacterial communities, with possible effects on ecosystem productivity.}, }
@article {pmid30988401, year = {2019}, author = {Tanaka, SE and Dayi, M and Maeda, Y and Tsai, IJ and Tanaka, R and Bligh, M and Takeuchi-Kaneko, Y and Fukuda, K and Kanzaki, N and Kikuchi, T}, title = {Stage-specific transcriptome of Bursaphelenchus xylophilus reveals temporal regulation of effector genes and roles of the dauer-like stages in the lifecycle.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6080}, doi = {10.1038/s41598-019-42570-7}, pmid = {30988401}, issn = {2045-2322}, support = {15H04514&amp;#x2019;//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 26292178//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 16H04722//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 15H04521//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, abstract = {The pine wood nematode Bursaphelenchus xylophilus is the causal agent of pine wilt disease, one of the most devastating forest diseases in East Asian and West European countries. The lifecycle of B. xylophilus includes four propagative larval stages and gonochoristic adults which are involved in the pathogenicity, and two stages of dispersal larvae involved in the spread of the disease. To elucidate the ecological roles of each developmental stage in the pathogenic life cycle, we performed a comprehensive transcriptome analysis using RNA-seq generated from all developmental stages of B. xylophilus and compared transcriptomes between stages. We found more than 9000 genes are differentially expressed in at least one stage of the life cycle including genes involved in general nematode biology such as reproduction and moulting but also effector genes likely to be involved in parasitism. The dispersal-stage transcriptome revealed its analogy to C. elegans dauer and the distinct roles of the two larval stages from each other regarding survival and transmission. This study provides important insights and resources to understand B. xylophilus parasitic biology.}, }
@article {pmid30980672, year = {2019}, author = {Pratama, AA and van Elsas, JD}, title = {Gene mobility in microbiomes of the mycosphere and mycorrhizosphere -role of plasmids and bacteriophages.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {5}, pages = {}, doi = {10.1093/femsec/fiz053}, pmid = {30980672}, issn = {1574-6941}, abstract = {Microbial activity in soil, including horizontal gene transfer (HGT), occurs in soil hot spots and at &quot;hot moments&quot;. Given their capacities to explore soil for nutrients, soil fungi (associated or not with plant roots) can act as (1) selectors of myco(rrhizo)sphere-adapted organisms and (2) accelerators of HGT processes across the cell populations that are locally present. This minireview critically examines our current understanding of the drivers of gene mobility in the myco(rrhizo)sphere. We place a special focus on the role of two major groups of gene mobility agents, i.e. plasmids and bacteriophages. With respect to plasmids, there is mounting evidence that broad-host-range (IncP-1β and PromA group) plasmids are prominent drivers of gene mobility across mycosphere inhabitants. A role of IncP-1β plasmids in Fe uptake processes has been revealed. Moreover, a screening of typical mycosphere-inhabiting Paraburkholderia spp. revealed carriage of integrated plasmids, next to prophages, that presumably confer fitness enhancements. In particular, functions involved in biofilm formation and nutrient uptake were thus identified. The potential of the respective gene mobility agents to promote the movement of such genes is critically examined.}, }
@article {pmid30980101, year = {2019}, author = {Ogwu, MC and Srinivasan, S and Dong, K and Ramasamy, D and Waldman, B and Adams, JM}, title = {Community Ecology of Deinococcus in Irradiated Soil.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01343-5}, pmid = {30980101}, issn = {1432-184X}, support = {2016E1D1A1B03930385//National Research Foundation Korea/ ; 2017R1D1A1B03035583//National Foundation foundation Korea/ ; }, abstract = {Deinococcus is a genus of soil bacteria known for radiation resistance. However, the effects of radiation exposure on its community structure are unknown. We exposed soil to three levels of gamma radiation, 0.1 kGy/h (low), 1 kGy/h (medium), and 3 kGy/h (high), once a week for 6 weeks and then extracted soil DNA for 16S rRNA amplicon sequencing. We found the following: (1) Increasing radiation dose produced a major increase in relative abundance of Deinococcus, reaching ~ 80% of reads at the highest doses. Differing abundances of the various Deinococcus species in relation to exposure levels indicate distinct &quot;radiation niches.&quot; At 3 kGy/h, a single OTU identified as D. ficus overwhelmingly dominated the mesocosms. (2) Corresponding published genome data show that the dominant species at 3 kGy/h, D. ficus, has a larger and more complex genome than other Deinococcus species with a greater proportion of genes related to DNA and nucleotide metabolism, cell wall, membrane, and envelope biogenesis as well as more cell cycle control, cell division, and chromosome partitioning-related genes. Deinococcus ficus also has a higher guanine-cytosine ratio than most other Deinococcus. These features may be linked to genome stability and may explain its greater abundance in this apparently competitive system, under high-radiation exposures. (3) Genomic analysis suggests that Deinococcus, including D. ficus, are capable of utilizing diverse carbon sources derived from both microbial cells killed by the radiation (including C5-C12-containing compounds, like arabinose, lactose, N-acetyl-D-glucosamine) and plant-derived organic matter in the soil (e.g., cellulose and hemicellulose). (4) Overall, based on its metagenome, even the most highly irradiated (3 kGy/h) soil possesses a wide range of the activities necessary for a functional soil system. Future studies may consider the resilience and sustainability of such soils in a high-radiation environment.}, }
@article {pmid30980037, year = {2019}, author = {Lee, KS and Palatinszky, M and Pereira, FC and Nguyen, J and Fernandez, VI and Mueller, AJ and Menolascina, F and Daims, H and Berry, D and Wagner, M and Stocker, R}, title = {Publisher Correction: An automated Raman-based platform for the sorting of live cells by functional properties.}, journal = {Nature microbiology}, volume = {4}, number = {5}, pages = {902-903}, doi = {10.1038/s41564-019-0446-1}, pmid = {30980037}, issn = {2058-5276}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid30977724, year = {2019}, author = {Gralka, M and Hallatschek, O}, title = {Environmental heterogeneity can tip the population genetics of range expansions.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, doi = {10.7554/eLife.44359}, pmid = {30977724}, issn = {2050-084X}, support = {R01 GM115851/GM/NIGMS NIH HHS/United States ; }, abstract = {The population genetics of most range expansions is thought to be shaped by the competition between Darwinian selection and random genetic drift at the range margins. Here, we show that the evolutionary dynamics during range expansions is highly sensitive to additional fluctuations induced by environmental heterogeneities. Tracking mutant clones with a tunable fitness effect in bacterial colonies grown on randomly patterned surfaces we found that environmental heterogeneity can dramatically reduce the efficacy of selection. Time-lapse microscopy and computer simulations suggest that this effect arises generically from a local 'pinning' of the expansion front, whereby stretches of the front are slowed down on a length scale that depends on the structure of the environmental heterogeneity. This pinning focuses the range expansion into a small number of 'lucky' individuals with access to expansion paths, altering the neutral evolutionary dynamics and increasing the importance of chance relative to selection.}, }
@article {pmid30976843, year = {2019}, author = {Salerno, C and Berardi, G and Laera, G and Pollice, A}, title = {Functional Response of MBR Microbial Consortia to Substrate Stress as Revealed by Metaproteomics.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01360-4}, pmid = {30976843}, issn = {1432-184X}, abstract = {Bacterial consortia have a primary role in the biological degradations occurring in activated sludge for wastewater treatment, for their capacities to metabolize the polluting matter. Therefore, the knowledge of the main metabolic pathways for the degradation of pollutants becomes critical for a correct design and operation of wastewater treatment plants. The metabolic activity of the different bacterial groups in activated sludge is commonly investigated through respirometry. Furthermore, in the last years, the development of &quot;omic&quot; approaches has offered more opportunities to integrate or substitute the conventional microbiological assays and to deeply understand the taxonomy and dynamics of complex microbial consortia. In the present work, an experimental membrane bioreactor (MBR) was set up and operated for the treatment of municipal wastewater, and the effects of a sudden decrease of the organic supply on the activated sludge were investigated. Both respirometric and metaproteomic approaches revealed a resistance of autotrophic bacteria to the substrate stress, and particularly of nitrifying bacteria. Furthermore, metaproteomics allowed the identification of the taxonomy of the microbial consortium based on its protein expression, unveiling the prevalence of Sorangium and Nitrosomonas genera both before and after the organic load decrease. Moreover, it confirmed the results obtained through respirometry and revealed a general expression of proteins involved in metabolism and transport of nitrogen, or belonging to nitrifying species like Nitrosomonas europeae, Nitrosomonas sp. AL212, or Nitrospira defluvii.}, }
@article {pmid30976842, year = {2019}, author = {Vieira, LC and da Silva, DKA and de Melo, MAC and Escobar, IEC and Oehl, F and da Silva, GA}, title = {Edaphic Factors Influence the Distribution of Arbuscular Mycorrhizal Fungi Along an Altitudinal Gradient of a Tropical Mountain.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01354-2}, pmid = {30976842}, issn = {1432-184X}, abstract = {Changes in relief in montane areas, with increasing altitude, provide different biotic and abiotic conditions, acting on the species of arbuscular mycorrhizal fungi (AMF). The objective of this work was to determine the influence of altitude, edaphic factors, and vegetation on the AMF species in a mountainous area. The list of AMF species was obtained from morphological identification of the spores, with 72 species recovered from field samples and trap cultures. Lower levels of Shannon's diversity occurred only at lower altitude; however, there was no difference in AMF richness. The structure of the AMF assembly between the two highest altitudes was similar and differed in relation to the lower altitude. There was variation in the distribution of AMF species, which was related to soil texture and chemical factors along the altitude gradient. Some species, genera, and families were indicative of a certain altitude, showing the preference of fungi for certain environmental conditions, which may aid in decisions to conserve montane ecosystems.}, }
@article {pmid30976841, year = {2019}, author = {Sedlacek, CJ and McGowan, B and Suwa, Y and Sayavedra-Soto, L and Laanbroek, HJ and Stein, LY and Norton, JM and Klotz, MG and Bollmann, A}, title = {A Physiological and Genomic Comparison of Nitrosomonas Cluster 6a and 7 Ammonia-Oxidizing Bacteria.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01378-8}, pmid = {30976841}, issn = {1432-184X}, support = {1120443//National Science Foundation/ ; 0541797//National Science Foundation/ ; 0541797//National Science Foundation/ ; }, abstract = {Ammonia-oxidizing bacteria (AOB) within the genus Nitrosomonas perform the first step in nitrification, ammonia oxidation, and are found in diverse aquatic and terrestrial environments. Nitrosomonas AOB were grouped into six defined clusters, which correlate with physiological characteristics that contribute to adaptations to a variety of abiotic environmental factors. A fundamental physiological trait differentiating Nitrosomonas AOB is the adaptation to either low (cluster 6a) or high (cluster 7) ammonium concentrations. Here, we present physiological growth studies and genome analysis of Nitrosomonas cluster 6a and 7 AOB. Cluster 6a AOB displayed maximum growth rates at ≤ 1 mM ammonium, while cluster 7 AOB had maximum growth rates at ≥ 5 mM ammonium. In addition, cluster 7 AOB were more tolerant of high initial ammonium and nitrite concentrations than cluster 6a AOB. Cluster 6a AOB were completely inhibited by an initial nitrite concentration of 5 mM. Genomic comparisons were used to link genomic traits to observed physiological adaptations. Cluster 7 AOB encode a suite of genes related to nitrogen oxide detoxification and multiple terminal oxidases, which are absent in cluster 6a AOB. Cluster 6a AOB possess two distinct forms of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and select species encode genes for hydrogen or urea utilization. Several, but not all, cluster 6a AOB can utilize urea as a source of ammonium. Hence, although Nitrosomonas cluster 6a and 7 AOB have the capacity to fulfill the same functional role in microbial communities, i.e., ammonia oxidation, differentiating species-specific and cluster-conserved adaptations is crucial in understanding how AOB community succession can affect overall ecosystem function.}, }
@article {pmid30975748, year = {2019}, author = {Baker, JL and Hendrickson, EL and Tang, X and Lux, R and He, X and Edlund, A and McLean, JS and Shi, W}, title = {Klebsiella and Providencia emerge as lone survivors following long-term starvation of oral microbiota.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {17}, pages = {8499-8504}, doi = {10.1073/pnas.1820594116}, pmid = {30975748}, issn = {1091-6490}, support = {F32 DE026947/DE/NIDCR NIH HHS/United States ; R00 DE024543/DE/NIDCR NIH HHS/United States ; R01 DE020102/DE/NIDCR NIH HHS/United States ; R01 DE026186/DE/NIDCR NIH HHS/United States ; }, abstract = {It is well-understood that many bacteria have evolved to survive catastrophic events using a variety of mechanisms, which include expression of stress-response genes, quiescence, necrotrophy, and metabolic advantages obtained through mutation. However, the dynamics of individuals leveraging these abilities to gain a competitive advantage in an ecologically complex setting remain unstudied. In this study, we observed the saliva microbiome throughout the ecological perturbation of long-term starvation, allowing only the species best equipped to access and use the limited resources to survive. During the first several days, the community underwent a death phase that resulted in a ∼50-100-fold reduction in the number of viable cells. Interestingly, after this death phase, only three species, Klebsiella pneumoniae, Klebsiella oxytoca, and Providencia alcalifaciens, all members of the family Enterobacteriaceae, appeared to be transcriptionally active and recoverable. Klebsiella are significant human pathogens, frequently resistant to multiple antibiotics, and recently, ectopic colonization of the gut by oral Klebsiella was documented to induce dysbiosis and inflammation. MetaOmics analyses provided several leads for further investigation regarding the ecological success of the Enterobacteriaceae. The isolates accumulated single nucleotide polymorphisms in known growth advantage in stationary phase alleles and produced natural products closely resembling antimicrobial cyclic depsipeptides. The results presented in this study suggest that pathogenic Enterobacteriaceae persist much longer than their more benign neighbors in the salivary microbiome when faced with starvation. This is particularly significant, given that hospital surfaces contaminated with oral fluids, especially sinks and drains, are well-established sources of outbreaks of drug-resistant Enterobacteriaceae.}, }
@article {pmid30974353, year = {2019}, author = {Cahill, N and O'Connor, L and Mahon, B and Varley, Á and McGrath, E and Ryan, P and Cormican, M and Brehony, C and Jolley, KA and Maiden, MC and Brisse, S and Morris, D}, title = {Hospital effluent: A reservoir for carbapenemase-producing Enterobacterales?.}, journal = {The Science of the total environment}, volume = {672}, number = {}, pages = {618-624}, doi = {10.1016/j.scitotenv.2019.03.428}, pmid = {30974353}, issn = {1879-1026}, mesh = {Bacterial Proteins/*analysis/metabolism ; Enterobacteriaceae/*growth &amp; development ; Hospitals ; Waste Water/*microbiology ; *Water Microbiology ; Water Pollutants/analysis/*metabolism ; beta-Lactamases/*analysis/metabolism ; }, abstract = {Antimicrobial resistance is a major public health concern. Carbapenemase-producing Enterobacterales (CPE) represent a significant health threat as some strains are resistant to almost all available antibiotics. The aim of this research was to examine hospital effluent and municipal wastewater in an urban area in Ireland for CPE. Samples of hospital effluent (n = 5), municipal wastewater before (n = 5) and after (n = 4) the hospital effluent stream joined the municipal wastewater stream were collected over a nine-week period (May-June 2017). All samples were examined for CPE by direct plating onto Brilliance CRE agar. Isolates were selected for susceptibility testing to 15 antimicrobial agents in accordance with EUCAST criteria. Where relevant, isolates were tested for carbapenemase-encoding genes by real-time PCR. CPE were detected in five samples of hospital effluent, one sample of pre-hospital wastewater and three samples of post-hospital wastewater. Our findings suggest hospital effluent is a major contributor to CPE in municipal wastewater. Monitoring of hospital effluent for CPE could have important applications in detection and risk management of unrecognised dissemination of CPE in both the healthcare setting and the environment.}, }
@article {pmid30973888, year = {2019}, author = {Nakato, GV and Fuentes Rojas, JL and Verniere, C and Blondin, L and Coutinho, T and Mahuku, G and Wicker, E}, title = {A new Multi Locus Variable Number of Tandem Repeat Analysis Scheme for epidemiological surveillance of Xanthomonas vasicola pv. musacearum, the plant pathogen causing bacterial wilt on banana and enset.}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0215090}, doi = {10.1371/journal.pone.0215090}, pmid = {30973888}, issn = {1932-6203}, abstract = {Xanthomonas vasicola pv. musacearum (Xvm) which causes Xanthomonas wilt (XW) on banana (Musa accuminata x balbisiana) and enset (Ensete ventricosum), is closely related to the species Xanthomonas vasicola that contains the pathovars vasculorum (Xvv) and holcicola (Xvh), respectively pathogenic to sugarcane and sorghum. Xvm is considered a monomorphic bacterium whose intra-pathovar diversity remains poorly understood. With the sudden emergence of Xvm within east and central Africa coupled with the unknown origin of one of the two sublineages suggested for Xvm, attention has shifted to adapting technologies that focus on identifying the origin and distribution of the genetic diversity within this pathogen. Although microbiological and conventional molecular diagnostics have been useful in pathogen identification. Recent advances have ushered in an era of genomic epidemiology that aids in characterizing monomorphic pathogens. To unravel the origin and pathways of the recent emergence of XW in Eastern and Central Africa, there was a need for a genotyping tool adapted for molecular epidemiology. Multi-Locus Variable Number of Tandem Repeat Analysis (MLVA) is able to resolve the evolutionary patterns and invasion routes of a pathogen. In this study, we identified microsatellite loci from nine published Xvm genome sequences. Of the 36 detected microsatellite loci, 21 were selected for primer design and 19 determined to be highly typeable, specific, reproducible and polymorphic with two- to four- alleles per locus on a sub-collection. The 19 markers were multiplexed and applied to genotype 335 Xvm strains isolated from seven countries over several years. The microsatellite markers grouped the Xvm collection into three clusters; with two similar to the SNP-based sublineages 1 and 2 and a new cluster 3, revealing an unknown diversity in Ethiopia. Five of the 19 markers had alleles present in both Xvm and Xanthomonas vasicola pathovars holcicola and vasculorum, supporting the phylogenetic closeliness of these three pathovars. Thank to the public availability of the haplotypes on the MLVABank database, this highly reliable and polymorphic genotyping tool can be further used in a transnational surveillance network to monitor the spread and evolution of XW throughout Africa.. It will inform and guide management of Xvm both in banana-based and enset-based cropping systems. Due to the suitability of MLVA-19 markers for population genetic analyses, this genotyping tool will also be used in future microevolution studies.}, }
@article {pmid30973887, year = {2019}, author = {Perona-Vico, E and Blasco-Gómez, R and Colprim, J and Puig, S and Bañeras, L}, title = {[NiFe]-hydrogenases are constitutively expressed in an enriched Methanobacterium sp. population during electromethanogenesis.}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0215029}, doi = {10.1371/journal.pone.0215029}, pmid = {30973887}, issn = {1932-6203}, abstract = {Electromethanogenesis is the bioreduction of carbon dioxide (CO2) to methane (CH4) utilizing an electrode as electron donor. Some studies have reported the active participation of Methanobacterium sp. in electron capturing, although no conclusive results are available. In this study, we aimed at determining short-time changes in the expression levels of [NiFe]-hydrogenases (Eha, Ehb and Mvh), heterodisulfide reductase (Hdr), coenzyme F420-reducing [NiFe]-hydrogenase (Frh), and hydrogenase maturation protein (HypD), according to the electron flow in independently connected carbon cloth cathodes poised at- 800 mV vs. standard hydrogen electrode (SHE). Amplicon massive sequencing of cathode biofilm confirmed the presence of an enriched Methanobacterium sp. population (>70% of sequence reads), which remained in an active state (78% of cDNA reads), tagging this archaeon as the main methane producer in the system. Quantitative RT-PCR determinations of ehaB, ehbL, mvhA, hdrA, frhA, and hypD genes resulted in only slight (up to 1.5 fold) changes for four out of six genes analyzed when cells were exposed to open (disconnected) or closed (connected) electric circuit events. The presented results suggested that suspected mechanisms for electron capturing were not regulated at the transcriptional level in Methanobacterium sp. for short time exposures of the cells to connected-disconnected circuits. Additional tests are needed in order to confirm proteins that participate in electron capturing in Methanobacterium sp.}, }
@article {pmid30972435, year = {2019}, author = {Wei, W and Wang, N and Cai, L and Zhang, C and Jiao, N and Zhang, R}, title = {Impacts of Freshwater and Seawater Mixing on the Production and Decay of Virioplankton in a Subtropical Estuary.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01362-2}, pmid = {30972435}, issn = {1432-184X}, support = {41522603//National Natural Science Foundation of China/ ; 31570172//National Natural Science Foundation of China/ ; 91428308//National Natural Science Foundation of China/ ; 41673073//National Natural Science Foundation of China/ ; 41861144018//National Natural Science Foundation of China/ ; QNLM2016ORP0303//Qingdao National Laboratory for Marine Science and Technology/ ; }, abstract = {Virioplankton is an important component of the aquatic ecosystem and plays multiple ecological and biogeochemical roles. Although the spatial and temporal distributions and dynamics of virioplankton have been well investigated in riverine and marine environments, little is known about the dynamics and environmental controlling mechanisms of virioplankton in estuaries. In this study, viral abundance, production and decay were examined in the Pearl River Estuary (PRE), one of the largest estuaries in China. The influences of freshwater and seawater mixing on viral ecological dynamics were evaluated with several cross-transplant experiments. In PRE, viral abundance, production and decay rates varied from 2.72 ± 0.09 to 27.5 ± 1.07 × 106 viruses ml-1, 7.98 ± 2.33 to 16.27 ± 2.85% h-1 and 0.80 ± 0.23 to 3.74 ± 0.98% h-1, respectively. When the riverine and marine microbial community were transferred into simulated brackish water, viral production rates were markedly inhibited by 83.8% and 47.3%, respectively. The decay of riverine and marine virioplankton was inhibited by 21.1% and 34.2%, respectively, in simulated brackish water. These results indicate change of estuarine environmental factors significantly alters the dynamics of riverine and marine virioplankton. In addition, the effects of mixing on viral production and decay differed between high- and low-fluorescence viruses. High-fluorescence viruses seemed more resistant to decay than low-fluorescence viruses, whereas the production of marine low-fluorescence viruses seemed more resistant to inhibition than that of marine high-fluorescence viruses. Together, these results provide new insights into the ecological dynamics of virioplankton in estuarine environments.}, }
@article {pmid30967122, year = {2019}, author = {Ai, D and Li, X and Pan, H and Chen, J and Cram, JA and Xia, LC}, title = {Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 2}, pages = {185}, doi = {10.1186/s12864-019-5469-8}, pmid = {30967122}, issn = {1471-2164}, mesh = {*Algorithms ; Bacteria/*classification/genetics ; Biodiversity ; Computational Biology/*methods ; *Metagenome ; *Microbial Interactions ; *Microbiota ; *Software ; }, abstract = {BACKGROUND: Discovering the key microbial species and environmental factors of microbial community and characterizing their relationships with other members are critical to ecosystem studies. The microbial co-occurrence patterns across a variety of environmental settings have been extensively characterized. However, previous studies were limited by their restriction toward pairwise relationships, while there was ample evidence of third-party mediated co-occurrence in microbial communities.<br><br>METHODS: We implemented and applied the triplet-based liquid association analysis in combination with the local similarity analysis procedure to microbial ecology data. We developed an intuitive scheme to visualize those complex triplet associations along with pairwise correlations. Using a time series from the marine microbial ecosystem as example, we identified pairs of operational taxonomic units (OTUs) where the strength of their associations appeared to relate to the values of a third &quot;mediator&quot; variable. These &quot;mediator&quot; variables appear to modulate the associations between pairs of bacteria.<br><br>RESULTS: Using this analysis, we were able to assess the OTUs' ability to regulate its functional partners in the community, typically not manifested in the pairwise correlation patterns. For example, we identified Flavobacteria as a multifaceted player in the marine microbial ecosystem, and its clades were involved in mediating other OTU pairs. By contrast, SAR11 clades were not active mediators of the community, despite being abundant and highly correlated with other OTUs. Our results suggested that Flavobacteria are more likely to respond to situations where particles and unusual sources of dissolved organic material are prevalent, such as after a plankton bloom. On the other hand, SAR11s are oligotrophic chemoheterotrophs with inflexible metabolisms, and their relationships with other organisms may be less governed by environmental or biological factors.<br><br>CONCLUSIONS: By integrating liquid association with local similarity analysis to explore the mediated co-varying dynamics, we presented a novel perspective and a useful toolkit to analyze and interpret time series data from microbial community. Our augmented association network analysis is thus more representative of the true underlying dynamic structure of the microbial community. The analytic software in this study was implemented as new functionalities of the ELSA (Extended local similarity analysis) tool, which is available for free download (http://bitbucket.org/charade/elsa).}, }
@article {pmid30963868, year = {2019}, author = {Barbaro, L and Allan, E and Ampoorter, E and Castagneyrol, B and Charbonnier, Y and De Wandeler, H and Kerbiriou, C and Milligan, HT and Vialatte, A and Carnol, M and Deconchat, M and De Smedt, P and Jactel, H and Koricheva, J and Le Viol, I and Muys, B and Scherer-Lorenzen, M and Verheyen, K and van der Plas, F}, title = {Biotic predictors complement models of bat and bird responses to climate and tree diversity in European forests.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1894}, pages = {20182193}, doi = {10.1098/rspb.2018.2193}, pmid = {30963868}, issn = {1471-2954}, abstract = {Bats and birds are key providers of ecosystem services in forests. How climate and habitat jointly shape their communities is well studied, but whether biotic predictors from other trophic levels may improve bird and bat diversity models is less known, especially across large bioclimatic gradients. Here, we achieved multi-taxa surveys in 209 mature forests replicated in six European countries from Spain to Finland, to investigate the importance of biotic predictors (i.e. the abundance or activity of defoliating insects, spiders, earthworms and wild ungulates) for bat and bird taxonomic and functional diversity. We found that nine out of 12 bird and bat diversity metrics were best explained when biotic factors were added to models including climate and habitat variables, with a mean gain in explained variance of 38% for birds and 15% for bats. Tree functional diversity was the most important habitat predictor for birds, while bats responded more to understorey structure. The best biotic predictors for birds were spider abundance and defoliating insect activity, while only bat functional evenness responded positively to insect herbivory. Accounting for potential biotic interactions between bats, birds and other taxa of lower trophic levels will help to understand how environmental changes along large biogeographical gradients affect higher-level predator diversity in forest ecosystems.}, }
@article {pmid30962365, year = {2019}, author = {Tveit, AT and Hestnes, AG and Robinson, SL and Schintlmeister, A and Dedysh, SN and Jehmlich, N and von Bergen, M and Herbold, C and Wagner, M and Richter, A and Svenning, MM}, title = {Widespread soil bacterium that oxidizes atmospheric methane.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {17}, pages = {8515-8524}, doi = {10.1073/pnas.1817812116}, pmid = {30962365}, issn = {1091-6490}, abstract = {The global atmospheric level of methane (CH4), the second most important greenhouse gas, is currently increasing by ∼10 million tons per year. Microbial oxidation in unsaturated soils is the only known biological process that removes CH4 from the atmosphere, but so far, bacteria that can grow on atmospheric CH4 have eluded all cultivation efforts. In this study, we have isolated a pure culture of a bacterium, strain MG08 that grows on air at atmospheric concentrations of CH4 [1.86 parts per million volume (p.p.m.v.)]. This organism, named Methylocapsa gorgona, is globally distributed in soils and closely related to uncultured members of the upland soil cluster α. CH4 oxidation experiments and 13C-single cell isotope analyses demonstrated that it oxidizes atmospheric CH4 aerobically and assimilates carbon from both CH4 and CO2 Its estimated specific affinity for CH4 (a0s) is the highest for any cultivated methanotroph. However, growth on ambient air was also confirmed for Methylocapsa acidiphila and Methylocapsa aurea, close relatives with a lower specific affinity for CH4, suggesting that the ability to utilize atmospheric CH4 for growth is more widespread than previously believed. The closed genome of M. gorgona MG08 encodes a single particulate methane monooxygenase, the serine cycle for assimilation of carbon from CH4 and CO2, and CO2 fixation via the recently postulated reductive glycine pathway. It also fixes dinitrogen and expresses the genes for a high-affinity hydrogenase and carbon monoxide dehydrogenase, suggesting that atmospheric CH4 oxidizers harvest additional energy from oxidation of the atmospheric trace gases carbon monoxide (0.2 p.p.m.v.) and hydrogen (0.5 p.p.m.v.).}, }
@article {pmid30961521, year = {2019}, author = {Dos Santos, HRM and Argolo, CS and Argôlo-Filho, RC and Loguercio, LL}, title = {A 16S rDNA PCR-based theoretical to actual delta approach on culturable mock communities revealed severe losses of diversity information.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {74}, doi = {10.1186/s12866-019-1446-2}, pmid = {30961521}, issn = {1471-2180}, abstract = {BACKGROUND: Subunits of ribosomal RNA genes (rDNAs) characterized by PCR-based protocols have been the proxy for studies in microbial taxonomy, phylogenetics, evolution and ecology. However, relevant factors have shown to interfere in the experimental outputs in a variety of systems. In this work, a 'theoretical' to 'actual' delta approach was applied to data on culturable mock bacterial communities (MBCs) to study the levels of losses in operational taxonomic units (OTUs) detectability. Computational and lab-bench strategies based on 16S rDNA amplification by 799F and U1492R primers were employed, using a fingerprinting method with highly improved detectability of fragments as a case-study tool. MBCs were of two major types: in silico MBCs, assembled with database-retrieved sequences, and in vitro MBCs, with AluI digestions of PCR data generated from culturable endophytes isolated from cacao trees.<br><br>RESULTS: Interfering factors for the 16 s rDNA amplifications, such as the type of template, direct and nested PCR, proportion of chloroplast DNA from a tropical plant source (Virola officinalis), and biased-amplification by the primers resulted in altered bacterial 16S rDNA amplification, both on MBCs and V. officinalis leaf-extracted DNA. For the theoretical data, the maximum number of fragments for in silico and in vitro cuts were not significantly different from each other. Primers' preferences for certain sequences were detected, depending on the MBCs' composition prior to PCR. The results indicated overall losses from 2.3 up to 8.2 times in the number of OTUs detected from actual AluI digestions of MBCs when compared to in silico and in vitro theoretical data.<br><br>CONCLUSIONS: Due to all those effects, the final amplification profile of the bacterial community assembled was remarkably simplified when compared to the expected number of detectable fragments known to be present in the MBC. From these findings, the scope of hypotheses generation and conclusions from experiments based on PCR amplifications of bacterial communities was discussed.}, }
@article {pmid30958642, year = {2019}, author = {Kim, J and Gómez-Pastora, J and Weigand, M and Potgieter, M and A Walters, N and Reátegui, E and F Palmer, A and Yazer, M and Zborowski, M and Chalmers, JJ}, title = {A Subpopulation of Monocytes in Normal Human Blood Has Significant Magnetic Susceptibility: Quantification and Potential Implications.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {95}, number = {5}, pages = {478-487}, doi = {10.1002/cyto.a.23755}, pmid = {30958642}, issn = {1552-4930}, support = {BAA07-21//Defense Advanced Research Projects Agency/ ; 1R01HL131720-01A1//National Heart, Lung, and Blood Institute/ ; }, abstract = {The presence of iron in circulating monocytes is well known as they play essential roles in iron recycling. Also, the storage of this metal as well as its incorrect uptake and/or release are important data to diagnose different pathologies. It has been demonstrated that iron storage in human blood cells can be measured through their magnetic behavior with high accuracy; however, the magnetic characteristics of monocytes have not been reported so far to the best of our knowledge. Therefore, in this work, we report, for the first time, the physical and magnetic properties of human monocytes, along with plasma platelets, oxyhemoglobin red blood cells (oxyHb-RBCs), and methemoglobin red blood cells (metHb-RBCs). The different cell populations were separated by Ficoll-density gradient centrifugation, followed by a flow sorting step to isolate monocytes from peripheral blood mononuclear cells. The different fractions were analyzed by Coulter Counter (for determining the size distribution and concentration) and the sorted monocytes were qualitatively analyzed on ImageStream, a state-of-the-art imaging cytometer. The analysis of the Coulter Counter and ImageStream data suggests that although there exists contamination in the monocyte fraction, the integrity of the sorted monocytes appears to be intact and the concentration was high enough to precisely measure their magnetic velocity by Cell Tracking Velocimetry. Surprisingly, monocytes reported the highest magnetic mobility from the four fractions under analysis, with an average magnetic velocity 7.8 times higher than MetHb-RBCs, which is the only type of cells with positive magnetic velocities. This value is equivalent to a susceptibility 2.5 times higher than the value reported by fresh MetHb-RBCs. It should be noted that this is the first study that reports that a subpopulation of human monocytes is much more magnetic than MetHb-RBCs, opening the door to the possible isolation of human monocytes by label-free magnetic techniques. Further, it is suggested that these magnetic monocytes could &quot;contaminate&quot; positively selected, immunomagnetically labeled blood cells (i.e., during a process using magnetically conjugated antibodies targeting cells, such as CD34 positive cells). Conversely, these magnetic monocytes could be inadvertently removed from a desired blood population when one is using a negative magnetic isolation technique to target cells for removal. © 2019 International Society for Advancement of Cytometry.}, }
@article {pmid30957419, year = {2019}, author = {Fanin, N and Kardol, P and Farrell, M and Kempel, A and Ciobanu, M and Nilsson, MC and Gundale, MJ and Wardle, DA}, title = {Effects of plant functional group removal on structure and function of soil communities across contrasting ecosystems.}, journal = {Ecology letters}, volume = {22}, number = {7}, pages = {1095-1103}, doi = {10.1111/ele.13266}, pmid = {30957419}, issn = {1461-0248}, support = {//Vetenskapsrådet/ ; }, mesh = {*Biodiversity ; *Ecosystem ; Islands ; Plants ; Soil ; *Soil Microbiology ; Sweden ; }, abstract = {Loss of plant diversity has an impact on ecosystems worldwide, but we lack a mechanistic understanding of how this loss may influence below-ground biota and ecosystem functions across contrasting ecosystems in the long term. We used the longest running biodiversity manipulation experiment across contrasting ecosystems in existence to explore the below-ground consequences of 19 years of plant functional group removals for each of 30 contrasting forested lake islands in northern Sweden. We found that, against expectations, the effects of plant removals on the communities of key groups of soil organisms (bacteria, fungi and nematodes), and organic matter quality and soil ecosystem functioning (decomposition and microbial activity) were relatively similar among islands that varied greatly in productivity and soil fertility. This highlights that, in contrast to what has been shown for plant productivity, plant biodiversity loss effects on below-ground functions can be relatively insensitive to environmental context or variation among widely contrasting ecosystems.}, }
@article {pmid30956127, year = {2019}, author = {Abad, ED and Ferreira, DC and Cavalcante, FS and Saintive, S and Goudouris, E and Prado, EA and Hofer, C and Ribeiro, M and da Silva, AMP and Rosado, AS and van Elsas, JD and Dos Santos, KRN}, title = {High incidence of acquiring methicillin-resistant Staphylococcus aureus in Brazilian children with Atopic Dermatitis and associated risk factors.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jmii.2018.12.014}, pmid = {30956127}, issn = {1995-9133}, abstract = {BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) colonization in Atopic Dermatitis (AD) patients can contribute to worsening their clinical condition.<br><br>OBJECTIVE: A cohort study was carried out to determine the incidence of MRSA acquisition and its risk factors in AD children.<br><br>METHODS: Patients with AD (2 months-14 years old) were followed up for about 1 year at a reference center for AD treatment in Rio de Janeiro, Brazil, from September 2011 to February 2014. Nasal swabs from patients and contacts were collected every 2 months. The SCORAD system assessed the severity of the AD. S. aureus isolates were evaluated to determine the methicillin resistance and the clonal lineages.<br><br>RESULTS: Among 117 AD patients, 97 (82.9%) were already colonized with S. aureus and 26 (22.2%) had MRSA at the first evaluation. The incidence of MRSA acquisition in the cohort study was 27.47% (n = 25). The SCORAD assessments were: mild (46.15%), moderate (37.36%) or severe (16.48%). Risk factors were: colonized MRSA contacts (HR = 2.27; 95% CI: 1.16-7.54), use of cyclosporine (HR = 5.84; 95% CI: 1.70-19.98), moderate or severe AD (HR = 3.26; 95% CI: 1.13-9.37). Protective factors were: availability of running water (HR = 0.21; 95% CI: 0.049-0.96) and use of antihistamines (HR = 0.21; 95% IC: 0.64-0.75). MRSA isolates carried the SCCmec type IV and most of them were typed as USA800/ST5.<br><br>CONCLUSIONS: The high incidence of MRSA acquisition found among AD patients and the risk factors associated show that an effective surveillance of MRSA colonization in these patients is needed.}, }
@article {pmid30955771, year = {2019}, author = {Cotta, SR and Cadete, LL and van Elsas, JD and Andreote, FD and Dias, ACF}, title = {Exploring bacterial functionality in mangrove sediments and its capability to overcome anthropogenic activity.}, journal = {Marine pollution bulletin}, volume = {141}, number = {}, pages = {586-594}, doi = {10.1016/j.marpolbul.2019.03.001}, pmid = {30955771}, issn = {1879-3363}, mesh = {Bacteria/genetics/metabolism ; Biodiversity ; Brazil ; Carbon/metabolism ; Ecosystem ; Gene Transfer, Horizontal ; Geologic Sediments/*microbiology ; Metagenomics ; *Microbiota/genetics ; Sulfur/metabolism ; *Wetlands ; }, abstract = {Mangrove forests are highly productive yet vulnerable ecosystems that act as important carbon sinks (&quot;blue carbon&quot;). The objective of this work was to analyze the impact of anthropogenic activities on microbiome structure and functioning. The metagenomic analysis revealed that the taxonomic compositions were grossly similar across all mangrove microbiomes. Remarkably, these microbiomes, along the gradient of anthropogenic impact, showed fluctuations in the relative abundances of bacterial taxa predicted to be involved in sulfur cycling processes. Functions involved in sulfur metabolism, such as APS pathways (associated with sulfate reduction and sulfur oxidation processes) were prevalent across the microbiomes, being sox and dsrAB genes highly expressed on anthropogenically-impacted areas. Apparently, the oil-impacted microbiomes were more affected in taxonomic than in functional terms, as high functional redundancies were noted across them. The microbial gene diversity found was typical for a functional system, even following the previous disturbance.}, }
@article {pmid30953090, year = {2019}, author = {Stamou, GP and Monokrousos, N and Gwynn-Jones, D and Whitworth, DE and Papatheodorou, EM}, title = {A Polyphasic Approach for Assessing Eco-System Connectivity Demonstrates that Perturbation Remodels Network Architecture in Soil Microcosms.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01367-x}, pmid = {30953090}, issn = {1432-184X}, support = {No. Project 89434//Research Committee, Aristotle University of Thessaloniki/ ; }, abstract = {Network analysis was used to show changes in network attributes by analyzing the relations among the main soil microbial groups in a potted tomato soil inoculated with arbuscular mycorrhizal fungus, treated with low doses of Mentha spicata essential oil, or both, and then exposed to tenfold higher oil addition (stress pulse). Pretreatments were chosen since they can induce changes in the composition of the microbial community. Cellular phospholipid fatty acids (PLFAs) and the activity of six soil enzymes, mainly involved in the N-cycle were measured. Networks were constructed based on correlated changes in PLFA abundances. The values of all parameters were significantly different from those of random networks indicating modular architecture. Networks ranked from the lowest to highest modularity: control, non-pretreated and stressed, inoculated and stressed, oil treated and stressed, inoculated and treated with oil and stressed. The high values of network density and 1st/2nd eigenvalue ratio are related to arylamidase activity while N-acetyl-glucosaminidase, acid phosphomoesterase, and asparaginase activities related to high values of the clustering coefficient index. We concluded that modularity may be an efficient indicator of changes in the network of interactions among the members of the soil microbial community and the modular structure of the network may be related to the activity of specific enzymes. Communities that were stressed without a pretreatment were relatively resistant but prone to sudden transition towards instability, while oil or inoculation pretreatments gave networks which could be considered adaptable and susceptible to gradual change.}, }
@article {pmid30953089, year = {2019}, author = {Han, J and Wang, S and Fan, D and Guo, Y and Liu, C and Zhu, Y}, title = {Time-Dependent Hormetic Response of Soil Alkaline Phosphatase Induced by Cd and the Association with Bacterial Community Composition.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01371-1}, pmid = {30953089}, issn = {1432-184X}, support = {No. 41375149//National Natural Science Foundation of China/ ; No. 41471191//National Natural Science Foundation of China/ ; }, abstract = {Hormetic dose-response that involved Cd in soils is increasingly paid attentions for risk assessment of Cd toxicity, but insufficient studies were conducted to define the temporary modification of soil enzyme and the potential microbial responses. The present study chooses soil alkaline phosphatase (ALP) as endpoint to uncover the time-dependent hormetic responses to low doses of Cd and its association with bacterial community composition. The results showed that addition of 0.01-3.0 mg kg-1 Cd significantly increased ALP's activities with maximum stimulatory magnitude of 11.4-27.2%, indicating a typical hormesis. The response started at 12 h after Cd addition and maintained about 24 h. This demonstrated that the hormetic response is time-dependent and transient. Changes of soil bacterial community composition showed that, at 6 h, relative abundances (RAs) of Proteobacteria and Firmicutes at phylum and Pontibacter, Bacillaceae-Bacillus, Bacillaceae1-Bacillus, and Paenisporosarcina at genus significantly correlated with ALP's activities at 12-36 h (P < 0.05). This suggests that soil bacteria likely showed an earlier response to Cd and potentially contributes to the subsequent soil enzyme's hormesis. In addition, it was found that Gram-negative bacteria other than Gram-positive bacteria are prone to exhibiting a hormetic response under Cd stress. Our findings provide much insight into ecotoxicological risk assessment for soil Cd pollution.}, }
@article {pmid30952994, year = {2019}, author = {Martiny, AC}, title = {High proportions of bacteria are culturable across major biomes.}, journal = {The ISME journal}, volume = {13}, number = {8}, pages = {2125-2128}, doi = {10.1038/s41396-019-0410-3}, pmid = {30952994}, issn = {1751-7370}, support = {1848576//NSF | Directorate for Geosciences (GEO)/ ; 1559002//NSF | Directorate for Geosciences (GEO)/ ; 1457160//NSF | BIO | Division of Environmental Biology (DEB)/ ; SC0016410//DOE | SC | Biological and Environmental Research (BER)/ ; }, abstract = {The paradigm that only 1% of microbes are culturable has had a profound impact on our understanding of microbial ecology and is still a major motivation for mostly using molecular tools to characterize microbial communities. However, this point is often expressed vaguely, suggesting that some scientists have different interpretations of the paradigm. In addition, there have been substantial advances in cultivation techniques suggesting that this paradigm may no longer be correct. To quantify bacterial culturability across six major biomes, I found that the median 16S rRNA similarity of bacteria to known cultured relatives was 97.3 ± 2.3% (s.d.). Furthermore, 52.0 ± 24% of sequences and 34.9 ± 23% of taxa (defined as >97% similar) had a closely related cultured relative. Thus, many cells and taxa across environments are culturable with known techniques, suggesting that the 1% paradigm is no longer correct.}, }
@article {pmid30952863, year = {2019}, author = {Wilschut, RA and van der Putten, WH and Garbeva, P and Harkes, P and Konings, W and Kulkarni, P and Martens, H and Geisen, S}, title = {Root traits and belowground herbivores relate to plant-soil feedback variation among congeners.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1564}, doi = {10.1038/s41467-019-09615-x}, pmid = {30952863}, issn = {2041-1723}, mesh = {Animals ; Geranium/genetics/microbiology/*physiology ; Herbivory/*physiology ; Microbiota ; Nematoda/physiology ; Phylogeny ; Plant Roots/genetics/microbiology/physiology ; Rhizosphere ; *Soil ; }, abstract = {Plant-soil feedbacks contribute to vegetation dynamics by species-specific interactions between plants and soil biota. Variation in plant-soil feedbacks can be predicted by root traits, successional position, and plant nativeness. However, it is unknown whether closely related plant species develop more similar plant-soil feedbacks than more distantly related species. Where previous comparisons included plant species from distant phylogenetic positions, we studied plant-soil feedbacks of congeneric species. Using eight intra-continentally range-expanding and native Geranium species, we tested relations between phylogenetic distances, chemical and structural root traits, root microbiomes, and plant-soil feedbacks. We show that root chemistry and specific root length better predict bacterial and fungal community composition than phylogenetic distance. Negative plant-soil feedback strength correlates with root-feeding nematode numbers, whereas microbiome dissimilarity, nativeness, or phylogeny does not predict plant-soil feedbacks. We conclude that root microbiome variation among congeners is best explained by root traits, and that root-feeding nematode abundances predict plant-soil feedbacks.}, }
@article {pmid30951891, year = {2019}, author = {Philip, N and Bandara, HMHN and Leishman, SJ and Walsh, LJ}, title = {Effect of polyphenol-rich cranberry extracts on cariogenic biofilm properties and microbial composition of polymicrobial biofilms.}, journal = {Archives of oral biology}, volume = {102}, number = {}, pages = {1-6}, doi = {10.1016/j.archoralbio.2019.03.026}, pmid = {30951891}, issn = {1879-1506}, abstract = {OBJECTIVE: To investigate the effect of cranberry extracts on saliva-derived polymicrobial biofilms with regards to biofilm biomass, acidogenicity, exopolysaccharide (EPS)/microbial biovolumes, colony forming unit (CFU) counts, and the relative abundance of specific caries- and health-associated bacteria.<br><br>METHODS: Saliva-derived polymicrobial biofilms were grown for 96 h in a cariogenic environment and treated for 2 min every 12 h over the entire biofilm growth period with 500 μg/mL cranberry extract or vehicle control. The effect of the cranberry extract on biofilm behaviour was evaluated using different assays and its influence on key cariogenic and health-associated bacterial populations was assessed with a microarray real-time quantitative PCR method.<br><br>RESULTS: Cranberry-treated biofilms showed significant drops in biomass (38% reduction, P < 0.001), acidogenicity (44% reduction, P < 0.001), EPS/microbial biovolume ratios (P = 0.033), and CFU counts (51% reduction, P = 0.001). Furthermore, the cranberry extracts effected a significantly lower relative abundance of caries-associated Streptococcus sobrinus (fold change 0.004, P = 0.002) and Provotella denticola (0.002, P < 0.001), and a significantly higher relative abundance of the health-associated Streptococcus sanguinis (fold change 90.715, P = 0.001).<br><br>CONCLUSIONS: The cranberry extract lowered biofilm biomass, acidogenicity, EPS/microbial biovolumes, CFU counts, and modulated a beneficial microbial ecological change in saliva-derived polymicrobial biofilms.}, }
@article {pmid30949751, year = {2019}, author = {Hughey, MC and Sokol, ER and Walke, JB and Becker, MH and Belden, LK}, title = {Ecological Correlates of Large-Scale Turnover in the Dominant Members of Pseudacris crucifer Skin Bacterial Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01372-0}, pmid = {30949751}, issn = {1432-184X}, support = {DEB-1136640//National Science Foundation/ ; D10ZO-028//Morris Animal Foundation/ ; }, abstract = {Animals host a wide diversity of symbiotic microorganisms that contribute important functions to host health, and our knowledge of what drives variation in the composition of these complex communities continues to grow. Microbiome studies at larger spatial scales present opportunities to evaluate the contribution of large-scale factors to variation in the microbiome. We conducted a large-scale field study to assess variation in the bacterial symbiont communities on adult frog skin (Pseudacris crucifer), characterized using 16S rRNA gene amplicon sequencing. We found that skin bacterial communities on frogs were less diverse than, and structurally distinct from, the surrounding habitat. Frog skin was typically dominated by one of two bacterial OTUs: at western sites, a Proteobacteria dominated the community, whereas eastern sites were dominated by an Actinobacteria. Using a metacommunity framework, we then sought to identify factors explaining small- and large-scale variation in community structure-that is, among hosts within a pond, and among ponds spanning the study transect. We focused on the presence of a fungal skin pathogen, Batrachochytrium dendrobatidis (Bd) as one potential driver of variation. We found no direct link between skin bacterial community structure and Bd infection status of individual frog hosts. Differences in pond-level community structure, however, were explained by Bd infection prevalence. Importantly, Bd infection prevalence itself was correlated with numerous other environmental factors; thus, skin bacterial diversity may be influenced by a complex suite of extrinsic factors. Our findings indicate that large-scale factors and processes merit consideration when seeking to understand microbiome diversity.}, }
@article {pmid30949750, year = {2019}, author = {Lan, S and Thomas, AD and Tooth, S and Wu, L and Hu, C}, title = {Small-Scale Spatial Heterogeneity of Photosynthetic Fluorescence Associated with Biological Soil Crust Succession in the Tengger Desert, China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01356-0}, pmid = {30949750}, issn = {1432-184X}, support = {31670456 and 31300322//National Natural Science Foundation of China/ ; 2017385//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 663830//European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant/ ; }, abstract = {In dryland regions, biological soil crusts (BSCs) have numerous important ecosystem functions. Crust species and functions are, however, highly spatially heterogeneous and remain poorly understood at a range of scales. In this study, chlorophyll fluorescence imaging was used to quantify millimeter-scale patterns in the distribution and activity of photosynthetic organisms in BSCs of different successional stages (including cyanobacterial, lichen, moss three main successional stages and three intermixed transitional stages) from the Tengger Desert, China. Chlorophyll fluorescence images derived from the Imaging PAM (Pulse Amplitude Modulation) showed that with the succession from cyanobacterial to lichen and to moss crusts, crust photosynthetic efficiency (including the maximum and effective photosynthetic efficiency, respectively) and fluorescence coverage increased significantly (P < 0.05), and that increasing photosynthetically active radiation (PAR) reduced the effective photosynthetic efficiency (Yield). The distribution of photosynthetic organisms in crusts determined Fv/Fm (ratio of variable fluorescence to maximum fluorescence) frequency pattern, although the photosynthetic heterogeneity (SHI index) was not significantly different (P > 0.05) between cyanobacterial and moss crusts, and showed a unimodal pattern of Fv/Fm values. In contrast, photosynthetic heterogeneity was significantly higher in lichen, cyanobacteria-moss and lichen-moss crusts (P < 0.05), with a bimodal pattern of Fv/Fm values. Point pattern analysis showed that the distribution pattern of chlorophyll fluorescence varied at different spatial scales and also among the different crust types. These new results provide a detailed (millimeter-scale) insight into crust photosynthetic mechanisms and spatial distribution patterns associated with their community types. Collectively, this information provides an improved theoretical basis for crust maintenance and management in dryland regions.}, }
@article {pmid30948795, year = {2019}, author = {D'Amico, F and Soverini, M and Zama, D and Consolandi, C and Severgnini, M and Prete, A and Pession, A and Barone, M and Turroni, S and Biagi, E and Brigidi, P and Masetti, R and Rampelli, S and Candela, M}, title = {Gut resistome plasticity in pediatric patients undergoing hematopoietic stem cell transplantation.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5649}, doi = {10.1038/s41598-019-42222-w}, pmid = {30948795}, issn = {2045-2322}, abstract = {The gut microbiome of pediatric patients undergoing allo-hematopoietic stem cell transplantation (HSCT) has recently been considered as a potential reservoir of antimicrobial resistance, with important implications in terms of patient mortality rate. By means of shotgun metagenomics, here we explored the dynamics of the gut resistome - i.e. the pattern of antibiotic resistance genes provided by the gut microbiome - in eight pediatric patients undergoing HSCT, half of whom developed acute Graft-versus-Host Disease (aGvHD). According to our findings, the patients developing aGvHD are characterized by post-HSCT expansion of their gut resistome, involving the acquisition of new resistances, as well as the consolidation of those already present before HSCT. Interestingly, the aGvHD-associated bloom in resistome diversity is not limited to genes coding for resistance to the antibiotics administered along the therapeutic course, but rather involves a broad pattern of different resistance classes, including multidrug resistance, as well as resistance to macrolides, aminoglycosides, tetracyclines and beta-lactams. Our data stress the relevance of mapping the gut resistome in HSCT pediatric patients to define the most appropriate anti-infective treatment post HSCT.}, }
@article {pmid30945554, year = {2019}, author = {Miclotte, L and Van de Wiele, T}, title = {Food processing, gut microbiota and the globesity problem.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-14}, doi = {10.1080/10408398.2019.1596878}, pmid = {30945554}, issn = {1549-7852}, abstract = {In the context of diseases of affluence, western diets have in the past years mainly been studied on their fat and sugar content and lack of dietary fiber. Yet, the more general aspect of food processing has recently sparked scientific interest as well. In addition, the gut microbiota have been put forward as an important link between diet, obesity and non-communicable diseases (NCD). Western dietary patterns, containing large amounts of processed foods might create an imbalance in the gut system by affecting gut bacteria and their metabolism. Here we discuss what has been already published regarding the relationship between several recently researched features of processed foods and the etiology of obesity and NCD. The addressed features concern micronutrient and energy density, several types of food additives and the generation of advanced glycation end products by thermal treatment during food processing. Overall, literature indicates that all discussed aspects can be linked to western ailments and that they can have a potential negative impact on human microbiota. Therefore, we propose that the thesis that a distressed gut microbiota is a mechanism that might explain how food processing features could harm human health is gaining empirical evidence. Future research will need to address the question whether the alteration of the gut microbiota is a direct or an indirect (via the host) effect. These conclusions are important assets in the fight against the continuing worldwide upsurge of obesity and NCD.}, }
@article {pmid30944882, year = {2019}, author = {Jiao, S and Xu, Y and Zhang, J and Hao, X and Lu, Y}, title = {Core Microbiota in Agricultural Soils and Their Potential Associations with Nutrient Cycling.}, journal = {mSystems}, volume = {4}, number = {2}, pages = {}, doi = {10.1128/mSystems.00313-18}, pmid = {30944882}, issn = {2379-5077}, abstract = {Revealing the ecological roles of the core microbiota in community maintaining and soil nutrient cycling is crucial for understanding ecosystem function, yet there is a dearth of continental-scale studies on this fundamental topic in microbial ecology. Here, we collected 251 soil samples from adjacent pairs of maize and rice fields at a continental scale in eastern China. We revealed the major ecological roles of the core microbiota in maintaining complex connections between bacterial taxa and their associations with belowground multinutrient cycling. By identifying the habitat preferences of the core microbiota, we built a continental atlas for mapping the spatial distributions of bacteria in agro-soils, which helps forecast the responses of agricultural ecosystems to anthropogenic disturbance. The multinutrient cycling index for maize and rice soils was related to bacterial α-diversity and β-diversity, respectively. Rice soils exhibited higher bacterial diversity and closer bacterial cooccurrence relationships than maize soils. In contrast to the macro- or microecological latitudinal richness patterns in natural terrestrial ecosystems, the bacteria in maize soils showed higher richness at high latitudes; however, this trend was not observed in rice soils. This study provides a new perspective on the distinct bacterial biogeographic patterns to predict the ecological roles of the core microbiota in agro-soils and thus helps manage soil bacterial communities for better provisioning of key ecosystem services. IMPORTANCE Disentangling the roles of the core microbiota in community maintaining and soil nutrient cycling is an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the spatial atlas and ecological roles of the core microbiota. A systematic, continental-scale survey was conducted using agro-soils in adjacent pairs of maize (dryland) and rice (wetland) fields across eastern China. The results indicate that the core microbiota play major ecological roles in maintaining complex connections between bacterial taxa and are associated with belowground multinutrient cycling. A continental atlas was built for mapping the bacterial spatial distributions in agro-soils through identifying their habitat preferences. This study represents a significant advance in forecasting the responses of agricultural ecosystems to anthropogenic disturbance and thus helps manage soil bacterial communities for better provisioning of key ecosystem services-the ultimate goal of microbial ecology.}, }
@article {pmid30944878, year = {2019}, author = {Tong, X and Leung, MHY and Wilkins, D and Cheung, HHL and Lee, PKH}, title = {Neutral Processes Drive Seasonal Assembly of the Skin Mycobiome.}, journal = {mSystems}, volume = {4}, number = {2}, pages = {}, doi = {10.1128/mSystems.00004-19}, pmid = {30944878}, issn = {2379-5077}, abstract = {The importance of microorganisms to human skin health has led to a growing interest in the temporal stability of skin microbiota. Here we investigated the dynamics and assembly of skin fungal communities (mycobiomes) with amplicon sequencing of samples collected from multiple sites on 24 healthy Chinese individuals across four seasons (in the order of winter, spring, summer, and autumn in a calendar year). We found a significant difference in community compositions between individuals, and intrapersonal community variation increased over time at all body sites. Within each season, the frequency of occurrence of most operational taxonomic units (OTUs) was well fitted by a neutral model, highlighting the importance of stochastic forces such as passive dispersal and ecological drift in skin community assembly. Despite the significant richness contributed by neutrally distributed OTUs, skin coassociation networks were dominated by taxa well-adapted to multiple body sites (forehead, forearm, and palm), although hub species were disproportionately rare. Taken together, these results suggest that while skin mycobiome assembly is a predominantly neutral process, taxa that could be under the influence of selective forces (e.g., host selection) are potentially key to the structure of a community network. IMPORTANCE Fungi are well recognized members of the human skin microbiota and are crucial to cutaneous health. Common cutaneous diseases such as seborrheic dermatitis and dermatophytes are linked to fungal species. Most studies related to skin microbial community dynamics have focused on Western subjects, while non-Western individuals are understudied. In this study, we explore the seasonal changes of the skin mycobiome in a healthy Chinese cohort and identify ecological processes that could possibly give rise to such variations. Our work reveals the dynamic nature of host skin fungal community, highlighting the dominant roles neutral forces play in the seasonal assembly of skin mycobiome. This study provides insight into the microbial ecology of the human skin microbiome and fills a knowledge gap in the literature regarding the dynamics of skin fungal community.}, }
@article {pmid30944853, year = {2019}, author = {Pärnänen, KMM and Narciso-da-Rocha, C and Kneis, D and Berendonk, TU and Cacace, D and Do, TT and Elpers, C and Fatta-Kassinos, D and Henriques, I and Jaeger, T and Karkman, A and Martinez, JL and Michael, SG and Michael-Kordatou, I and O'Sullivan, K and Rodriguez-Mozaz, S and Schwartz, T and Sheng, H and Sørum, H and Stedtfeld, RD and Tiedje, JM and Giustina, SVD and Walsh, F and Vaz-Moreira, I and Virta, M and Manaia, CM}, title = {Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence.}, journal = {Science advances}, volume = {5}, number = {3}, pages = {eaau9124}, doi = {10.1126/sciadv.aau9124}, pmid = {30944853}, issn = {2375-2548}, abstract = {Integrated antibiotic resistance (AR) surveillance is one of the objectives of the World Health Organization global action plan on antimicrobial resistance. Urban wastewater treatment plants (UWTPs) are among the most important receptors and sources of environmental AR. On the basis of the consistent observation of an increasing north-to-south clinical AR prevalence in Europe, this study compared the influent and final effluent of 12 UWTPs located in seven countries (Portugal, Spain, Ireland, Cyprus, Germany, Finland, and Norway). Using highly parallel quantitative polymerase chain reaction, we analyzed 229 resistance genes and 25 mobile genetic elements. This first trans-Europe surveillance showed that UWTP AR profiles mirror the AR gradient observed in clinics. Antibiotic use, environmental temperature, and UWTP size were important factors related with resistance persistence and spread in the environment. These results highlight the need to implement regular surveillance and control measures, which may need to be appropriate for the geographic regions.}, }
@article {pmid30941803, year = {2019}, author = {Björk, JR and Dasari, M and Grieneisen, L and Archie, EA}, title = {Primate microbiomes over time: Longitudinal answers to standing questions in microbiome research.}, journal = {American journal of primatology}, volume = {}, number = {}, pages = {e22970}, doi = {10.1002/ajp.22970}, pmid = {30941803}, issn = {1098-2345}, abstract = {To date, most insights into the processes shaping vertebrate gut microbiomes have emerged from studies with cross-sectional designs. While this approach has been valuable, emerging time series analyses on vertebrate gut microbiomes show that gut microbial composition can change rapidly from 1 day to the next, with consequences for host physical functioning, health, and fitness. Hence, the next frontier of microbiome research will require longitudinal perspectives. Here we argue that primatologists, with their traditional focus on tracking the lives of individual animals and familiarity with longitudinal fecal sampling, are well positioned to conduct research at the forefront of gut microbiome dynamics. We begin by reviewing some of the most important ecological processes governing microbiome change over time, and briefly summarizing statistical challenges and approaches to microbiome time series analysis. We then introduce five questions of general interest to microbiome science where we think field-based primate studies are especially well positioned to fill major gaps: (a) Do early life events shape gut microbiome composition in adulthood? (b) Do shifting social landscapes cause gut microbial change? (c) Are gut microbiome phenotypes heritable across variable environments? (d) Does the gut microbiome show signs of host aging? And (e) do gut microbiome composition and dynamics predict host health and fitness? For all of these questions, we highlight areas where primatologists are uniquely positioned to make substantial contributions. We review preliminary evidence, discuss possible study designs, and suggest future directions.}, }
@article {pmid30941446, year = {2019}, author = {Johansen, R and Albright, M and Gallegos-Graves, V and Lopez, D and Runde, A and Yoshida, T and Dunbar, J}, title = {Tracking Replicate Divergence in Microbial Community Composition and Function in Experimental Microcosms.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01368-w}, pmid = {30941446}, issn = {1432-184X}, support = {SFA 2015F260//U.S. Department of Energy/ ; }, abstract = {The study of microbial community functions necessitates replicating microbial communities. Variation in community development over time renders this an imperfect process. Thus, anticipating the likely degree of variation among replicate communities may aid in experimental design. We examined divergence in replicate community composition and function among 128 naturally assembled starting communities obtained from soils, each replicated three times, following a 30-day microcosm incubation period. Bacterial and fungal communities diverged in both composition and function among replicates, but remained much more similar to each other than to communities from different starting inocula. Variation in bacterial community composition among replicates was, however, correlated with variation in dissolved organic carbon production. A smaller-scale experiment testing nine starting communities showed that divergence was similar whether replicates were incubated on sterile or non-sterile pine litter, suggesting the impact of a pre-existing community on replicate divergence is minor. However, replicates in this experiment which were incubated for 114 days diverged more than those incubated for 30 days, suggesting experiments that run over long time periods will likely see greater variation among replicate community composition. These results suggest that while replicates diverge at a community level, such divergence is unlikely to severely impede the study of community function.}, }
@article {pmid30937143, year = {2019}, author = {Chiu, CY and Chan, YL and Tsai, MH and Wang, CJ and Chiang, MH and Chiu, CC}, title = {Gut microbial dysbiosis is associated with allergen-specific IgE responses in young children with airway allergies.}, journal = {The World Allergy Organization journal}, volume = {12}, number = {3}, pages = {100021}, doi = {10.1016/j.waojou.2019.100021}, pmid = {30937143}, issn = {1939-4551}, abstract = {Background: There is increasing evidence linking alterations of the gut microbial composition during early infancy to the development of atopic diseases and asthma. However, few studies have addressed the association of dysbiotic gut microbiota with allergic reactions through evaluation of feces in young children with allergic airway diseases.<br><br>Methods: We sought to evaluate relationships among gut microbiota, total fecal immunoglobulin E (IgE) levels, serum allergic sensitization, and their relevance to childhood allergic rhinitis and asthma. Microbial composition and diversity were analyzed with Illumina-based 16S rRNA gene sequencing of 89 stool samples collected from children with asthma (n = 35) and allergic rhinitis (n = 28), and from healthy controls (n = 26). Data analysis was performed using Quantitative Insights into Microbial Ecology (QIIME) software.<br><br>Results: A significantly lower abundance of organisms of the phylum Firmicutes were found in children with asthma and allergic rhinitis than in the healthy controls. Relatively lower Chao1 and Shannon indices were also found in children with allergic airway diseases but without any significant difference. Total fecal IgE levels in early childhood were strongly correlated with serum D. pteronyssinus- and D. farinae-specific IgE but not with food-specific IgE levels. In comparison with healthy controls, the genus Dorea was less abundant and negatively correlated with total fecal IgE levels in children with rhinitis, whereas the genus Clostridium was abundant and positively correlated with fecal IgE levels in children with asthma.<br><br>Conclusions: An interaction between particular subsets of gut microbial dysbiosis and IgE-mediated responses to allergens may contribute to the susceptibility to allergic rhinitis and asthma in early childhood.}, }
@article {pmid30936485, year = {2019}, author = {Bulzu, PA and Andrei, AŞ and Salcher, MM and Mehrshad, M and Inoue, K and Kandori, H and Beja, O and Ghai, R and Banciu, HL}, title = {Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche.}, journal = {Nature microbiology}, volume = {4}, number = {7}, pages = {1129-1137}, doi = {10.1038/s41564-019-0404-y}, pmid = {30936485}, issn = {2058-5276}, abstract = {Recent advances in phylogenomic analyses and increased genomic sampling of uncultured prokaryotic lineages have brought compelling evidence in support of the emergence of eukaryotes from within the archaeal domain of life (eocyte hypothesis)1,2. The discovery of Asgardarchaeota and its supposed position at the base of the eukaryotic tree of life3,4 provided cues about the long-awaited identity of the eocytic lineage from which the nucleated cells (Eukaryota) emerged. While it is apparent that Asgardarchaeota encode a plethora of eukaryotic-specific proteins (the highest number identified yet in prokaryotes)5, the lack of genomic information and metabolic characterization has precluded inferences about their lifestyles and the metabolic landscape that favoured the emergence of the protoeukaryote ancestor. Here, we use advanced phylogenetic analyses for inferring the deep ancestry of eukaryotes, and genome-scale metabolic reconstructions for shedding light on the metabolic milieu of Asgardarchaeota. In doing so, we: (1) show that Heimdallarchaeia (the closest eocytic lineage to eukaryotes to date) are likely to have a microoxic niche, based on their genomic potential, with aerobic metabolic pathways that are unique among Archaea (that is, the kynurenine pathway); (2) provide evidence of mixotrophy within Asgardarchaeota; and (3) describe a previously unknown family of rhodopsins encoded within the recovered genomes.}, }
@article {pmid30929045, year = {2019}, author = {Hogue, SR and Gomez, MF and da Silva, WV and Pierce, CM}, title = {A Customized At-Home Stool Collection Protocol for Use in Microbiome Studies Conducted in Cancer Patient Populations.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01346-2}, pmid = {30929045}, issn = {1432-184X}, support = {02-25999-18-46//Florida Academic Cancer Center Alliance/ ; P30-CA076292//H. Lee Moffitt Cancer Center and Research Institute/ ; }, abstract = {Fecal specimen collection in the clinical setting is often unfeasible for large population studies, especially because cancer patients on immunotherapy often experience constipation. A method for constructing and using an at-home stool collection kit designed for epidemiological studies in cancer patients is presented. Participation and compliance rates of the collection kit among late-stage cancer patients from an ongoing, longitudinal study are also discussed. The kit includes three different media on which samples are introduced. Using one stool sample, patients collect specimens by smearing stool onto a fecal occult blood test (FOBT) card, containing three slides for collection. Additional specimens from the same stool sample are added to one tube containing 8 mL of RNAlater preservative and one tube containing 8 mL of 95% ethanol. Stool specimens are stored at room temperature and returned to researchers within 3 days of collection. The purpose of this kit is to yield stool specimens on a variety of media that can be preserved for extended periods of time at room temperature and are compatible with multi-omics approaches for specimen analysis. According to leading microbiome researchers and published literature, each collection method is considered optimal for use in large epidemiological studies. Moreover, the kit is comprised of various components that make stool collection easy, so as not to burden the patient and hence maximize overall compliance. Use of this kit in a study of late-stage lung cancer patients had a participation rate of 83% and baseline compliance rate of 58%.}, }
@article {pmid30929044, year = {2019}, author = {Semenec, L and Vergara, IA and Laloo, AE and Mathews, ER and Bond, PL and Franks, AE}, title = {Correction to: Enhanced Growth of Pilin-Deficient Geobacter sulfurreducens Mutants in Carbon Poor and Electron Donor Limiting Conditions.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01370-2}, pmid = {30929044}, issn = {1432-184X}, abstract = {The published version of this article contained an old version of Fig. 2.}, }
@article {pmid30926316, year = {2019}, author = {Brown, MR and Hands, CL and Coello-Garcia, T and Sani, BS and Ott, AIG and Smith, SJ and Davenport, RJ}, title = {A flow cytometry method for bacterial quantification and biomass estimates in activated sludge.}, journal = {Journal of microbiological methods}, volume = {160}, number = {}, pages = {73-83}, doi = {10.1016/j.mimet.2019.03.022}, pmid = {30926316}, issn = {1872-8359}, abstract = {Absolute bacterial quantification receives little serious attention in the literature compared to sequencing, conceivably because it is considered unimportant and facile, or because existing methods are tedious, laborious and/or biased in nature. This is particularly true in engineered systems, including activated sludge, where such information underpins their design and operation. To overcome these limitations we built upon existing work and optimised and comprehensively validated, through comparison with epifluorescence microscopy (EFM), a rapid and precise flow cytometric protocol to enumerate total bacterial numbers in activated sludge. Insights into potential biases were evaluated using appropriate statistical analyses on this comparison, which spanned four orders of magnitude, as well as comparing volatile suspended solid (VSS) concentrations. The results suggest flow cytometry (FCM) is a rapid, reproducible and economical technique for quantifying total bacterial numbers and biomass concentrations in activated sludge, despite within order of magnitude discrepancies with EFM counts, which had inherent and evidently greater errors and biases than FCM. The use of FCM for routine monitoring over both EFM and VSS should help further understanding of the microbial ecology in, and the operation of, engineered systems.}, }
@article {pmid30923872, year = {2019}, author = {Wu, RN and Meng, H and Wang, YF and Gu, JD}, title = {Functional dominance and community compositions of ammonia-oxidizing archaea in extremely acidic soils of natural forests.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {10}, pages = {4229-4240}, doi = {10.1007/s00253-019-09721-2}, pmid = {30923872}, issn = {1432-0614}, support = {31470562//National Natural Science Foundation of China/ ; }, mesh = {Ammonia/*metabolism ; Archaea/*classification/enzymology/genetics/*metabolism ; *Forests ; Hydrogen-Ion Concentration ; *Microbiota ; Oxidation-Reduction ; Oxidoreductases/analysis/genetics ; RNA, Messenger/analysis/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Extremely acidic soils of natural forests in Nanling National Nature Reserve have been previously investigated and revisited in two successive years to reveal the active ammonia oxidizers. Ammonia-oxidizing archaea (AOA) rather than ammonia-oxidizing bacteria (AOB) were found more functionally important in the extremely acidic soils of the natural forests in Nanling National Nature Reserve. The relative abundances of Nitrosotalea, Nitrososphaera sister group, and Nitrososphaera lineages recovered by ammonia monooxygenase subunit A (amoA) transcripts were reassessed and compared to AOA communities formerly detected by genomic DNA. Nitrosotalea, previously found the most abundant AOA, were the second-most-active lineage after Nitrososphaera sister group. Our field study results, therefore, propose the acidophilic AOA, Nitrosotalea, can better reside in extremely acidic soils while they may not contribute to nitrification proportionately according to their abundances or they are less functionally active. In contrast, the functional importance of Nitrososphaera sister group may be previously underestimated and the functional dominance further extends their ecological distribution as little has been reported. Nitrososphaera gargensis-like AOA, the third abundant lineage, were more active in summer. The analyses of AOA community composition and its correlation with environmental parameters support the previous observations of the potential impact of organic matter on AOA composition. Al3+, however, did not show a strong adverse correlation with the abundances of functional AOA unlike in the DNA-based study. The new data further emphasize the functional dominance of AOA in extremely acidic soils, and unveil the relative contributions of AOA lineages to nitrification and their community transitions under the environmental influences.}, }
@article {pmid30923814, year = {2019}, author = {Tiedje, JM}, title = {Editorial: Environmental aspects of antibiotic resistance.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {4}, pages = {}, doi = {10.1093/femsec/fiz019}, pmid = {30923814}, issn = {1574-6941}, }
@article {pmid30919752, year = {2019}, author = {Cabezas, A and Bovio, P and Etchebehere, C}, title = {Commercial formulation amendment transiently affects the microbial composition but not the biogas production of a full scale methanogenic UASB reactor.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/09593330.2019.1600042}, pmid = {30919752}, issn = {1479-487X}, abstract = {The treatment of dairy wastewater in methanogenic reactors cause several problems due to their high lipid content. One strategy to overcome these problems is the use of commercial formulations. Here we studied the effect of adding a commercial formulation, designed to improve fat degradation, on both the microbial community composition and reactor performance. Samples from two full-scale Up-flow Anaerobic Sludge Blanket (UASB) reactors in parallel arrangement were analysed. The commercial product was added to one of the reactors while the other was used as control. The amendment increased significantly the fat removal but an accumulation of volatile fatty acids was detected. Nevertheless, no significant differences were observed in the total Chemical Oxygen Demand (COD) removal and biogas production between reactors. A significant change in the bacterial community was not detected by 16S rRNA gene Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis probably due to the limitation of the technique. A strong change in the composition of the phylum Firmicutes was detected with 16S rRNA gene amplicon sequencing; however, it didn't persist during the whole operation period. The relative abundance of minor Operational Taxonomic Units (OTUs) with sequences related to syntrophic bacteria increased with the amendment. Although a better hydrolytic capacity was obtained when adding the commercial product, the overall process did not improve and no increase in biogas production was detected. Alternative strategies could be applied to avoid the accumulation of intermediary products and improve biogas production as intermittent addition of the commercial product or batch operation of reactors.}, }
@article {pmid30918994, year = {2019}, author = {Klima, CL and Holman, DB and Ralston, BJ and Stanford, K and Zaheer, R and Alexander, TW and McAllister, TA}, title = {Lower Respiratory Tract Microbiome and Resistome of Bovine Respiratory Disease Mortalities.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {446-456}, doi = {10.1007/s00248-019-01361-3}, pmid = {30918994}, issn = {1432-184X}, support = {2015R025R//Alberta Livestock and Meat Agency/ ; 001//Growing Forward II/ ; 001//Genomics Research Initiative/ ; }, mesh = {Alberta ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/*isolation &amp; purification ; Bacterial Infections/microbiology/mortality/*veterinary ; Cattle ; Cattle Diseases/*microbiology/mortality ; *Drug Resistance, Bacterial ; *Microbiota ; Respiratory System/*microbiology ; Respiratory Tract Diseases/microbiology/mortality/*veterinary ; }, abstract = {Bovine respiratory disease (BRD) continues to be a serious health problem in beef cattle production. A multifactorial condition, BRD encompasses several types of pneumonia that are associated with multiple viral and bacterial agents. Comprehensive identification of microbes associated with BRD fatalities could enhance our understanding of the range of pathogens that contribute to the disease and identify new therapeutic targets. This study used metagenomic analysis to describe the lower respiratory tract microbiome and resistome of 15 feedlot cattle BRD and 3 non-BRD mortalities along with any affiliated integrative and conjugative elements (ICEs). Known bacterial pathogens associated with BRD, including Histophilus somni, Mannheimia haemolytica, and Mycoplasma bovis, were relatively abundant (> 5%) in most, but not all samples. Other relatively abundant genera (> 1%) included Acinetobacter, Bacillus, Bacteroides, Clostridium, Enterococcus, and Pseudomonas. Antimicrobial resistance genes (ARGs) comprised up to 0.5% of sequences and many of these genes were associated with ICEs previously described within the Pasteurellaceae family. A total of 20 putative ICEs were detected among 16 samples. These results document the wide diversity of microorganisms in the lower respiratory tract of cattle that have succumbed to BRD. The data also strongly suggest that antimicrobial-resistant Pasteurellaceae strains are prevalent in BRD cases in Alberta and that the resistance observed is associated with ICEs. The presence of ICEs harboring a wide array of ARGs holds significant consequence for the effectiveness of drug therapies for the control of BRD in beef cattle.}, }
@article {pmid30915518, year = {2019}, author = {Kolasa, M and Ścibior, R and Mazur, MA and Kubisz, D and Dudek, K and Kajtoch, Ł}, title = {How Hosts Taxonomy, Trophy, and Endosymbionts Shape Microbiome Diversity in Beetles.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01358-y}, pmid = {30915518}, issn = {1432-184X}, support = {DEC-2013/11/D/NZ8/00583//National Science Centre, Poland/ ; small grants for young researchers//Polish Ministry of Science and Higher Education/ ; }, abstract = {Bacterial communities play a crucial role in the biology, ecology, and evolution of multicellular organisms. In this research, the microbiome of 24 selected beetle species representing five families (Carabidae, Staphylinidae, Curculionidae, Chrysomelidae, Scarabaeidae) and three trophic guilds (carnivorous, herbivorous, detrivorous) was examined using 16S rDNA sequencing on the Illumina platform. The aim of the study was to compare diversity within and among species on various levels of organization, including evaluation of the impact of endosymbiotic bacteria. Collected data showed that beetles possess various bacterial communities and that microbiota of individuals of particular species hosts are intermixed. The most diverse microbiota were found in Carabidae and Scarabaeidae; the least diverse, in Staphylinidae. On higher organization levels, the diversity of bacteria was more dissimilar between families, while the most distinct with respect to their microbiomes were trophic guilds. Moreover, eight taxa of endosymbiotic bacteria were detected including common genera such as Wolbachia, Rickettsia, and Spiroplasma, as well as the rarely detected Cardinium, Arsenophonus, Buchnera, Sulcia, Regiella, and Serratia. There were no correlations among the abundance of the most common Wolbachia and Rickettsia; a finding that does not support the hypothesis that these bacteria occur interchangeably. The abundance of endosymbionts only weakly and negatively correlates with diversity of the whole microbiome in beetles. Overall, microbiome diversity was found to be more dependent on host phylogeny than on the abundance of endosymbionts. This is the first study in which bacteria diversity is compared between numerous species of beetles in a standardized manner.}, }
@article {pmid30915517, year = {2019}, author = {Neupane, S and Modry, D and Pafčo, B and Zurek, L}, title = {Correction to: Bacterial Community of the Digestive Tract of the European Medicinal Leech (Hirudo verbana) from the Danube River.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {1091}, doi = {10.1007/s00248-019-01363-1}, pmid = {30915517}, issn = {1432-184X}, abstract = {The original published version of this article had mistakes in figure legends. Correct figure legends are presented below.}, }
@article {pmid30915050, year = {2019}, author = {Wang, W and Luo, X and Chen, Y and Ye, X and Wang, H and Cao, Z and Ran, W and Cui, Z}, title = {Succession of Composition and Function of Soil Bacterial Communities During Key Rice Growth Stages.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {421}, doi = {10.3389/fmicb.2019.00421}, pmid = {30915050}, issn = {1664-302X}, abstract = {Elucidating the succession of soil microbial communities and microbial functions at key plant growth stages is a major goal of microbial ecology research. In this study, we investigated the succession of soil bacteria during four fertilizer treatments (control, NPK, NPK + pig manure, and NPK + straw) and at three crucial rice growth stages (tillering, heading, and ripening) in paddy soil from a rice-wheat cropping system over a 10-year period. The results showed that the bacterial community and function composition of the control treatment was significantly different from that of the other treatments with NPK fertilizers, and S1 from others stages (ANOSIM, p < 0.05). The application of pig manure could reduce the effects of applying NPK fertilizers on bacterial communities in heading and ripening stages, but the effects of straw returning is not obvious. Variance partitioning analyses (VPA) suggested that pH, OM, and AK appeared to be key factors responsible for the microbial community changes observed in all the treatments or stages. The correlation results showed the bacterial families different between S1 and other stages such as Micromonosporaceae, Nocardioidaceae, Gaiellaceae, and Anaerolineaceae etc., were correlated with bacterial KEGG metabolic pathways. In addition, the topological of the soil bacterial community network with more nodes, links and higher Maximal degree at the heading stage and maintained relatively similar topological structures at the heading and ripening stages. However, the topological of the functional networks at the ripening stage were a small yet complicated co-occurring network with 209 nodes, 789 links, higher Average connectivity (avgK), and Maximal degree. These results suggest an obvious succession of soil bacteria and bacterial function at the key rice growth stages, but the topological of functional network structure of bacteria changes a little in the early and middle stages of rice, while its changes significantly in the ripening stage of rice growth.}, }
@article {pmid30914267, year = {2019}, author = {Zhang, X and Fan, L and Wu, J and Xu, H and Leung, WY and Fu, K and Wu, J and Liu, K and Man, K and Yang, X and Han, J and Ren, J and Yu, J}, title = {Macrophage p38α promotes nutritional steatohepatitis through M1 polarization.}, journal = {Journal of hepatology}, volume = {71}, number = {1}, pages = {163-174}, doi = {10.1016/j.jhep.2019.03.014}, pmid = {30914267}, issn = {1600-0641}, abstract = {BACKGROUND &amp; AIMS: p38 mitogen-activated protein kinases are important inflammatory factors. p38α alteration has been implicated in both human and mouse inflammatory disease models. Therefore, we aimed to characterize the cell type-specific role of p38α in non-alcoholic steatohepatitis (NASH).<br><br>METHODS: Human liver tissues were obtained from 27 patients with non-alcoholic fatty liver disease (NAFLD) and 20 control individuals. NASH was established and compared between hepatocyte-specific p38α knockout (p38αΔHep), macrophage-specific p38α knockout (p38αΔMΦ) and wild-type (p38αfl/fl) mice fed with high-fat diet (HFD), high-fat/high-cholesterol diet (HFHC), or methionine-and choline-deficient diet (MCD). p38 inhibitors were administered to HFHC-fed wild-type mice for disease treatment.<br><br>RESULTS: p38α was significantly upregulated in the liver tissues of patients with NAFLD. Compared to p38αfl/fl littermates, p38αΔHep mice developed significant nutritional steatohepatitis induced by HFD, HFHC or MCD. Meanwhile, p38αΔMΦ mice exhibited less severe steatohepatitis and insulin resistance than p38αfl/fl mice in response to a HFHC or MCD. The effect of macrophage p38α in promoting steatohepatitis was mediated by the induction of pro-inflammatory factors (CXCL2, IL-1β, CXCL10 and IL-6) secreted by M1 macrophages and associated signaling pathways. p38αΔMΦ mice exhibited M2 anti-inflammatory polarization as demonstrated by increased CD45+F4/80+CD11b+CD206+ M2 macrophages and enhanced arginase activity in liver tissues. Primary hepatocytes from p38αΔMΦ mice showed decreased steatosis and inflammatory damage. In a co-culture system, p38α deleted macrophages attenuated steatohepatitic changes in hepatocytes through decreased secretion of pro-inflammatory cytokines (TNF-α, CXCL10 and IL-6), which mediate M1 macrophage polarization in p38αΔMΦ mice. Restoration of TNF-α, CXCL10 or IL-6 induced lipid accumulation and inflammatory responses in p38αfl/fl hepatocytes co-cultured with p38αΔMΦ macrophages. Moreover, pharmacological p38 inhibitors suppressed HFHC-induced steatohepatitis.<br><br>CONCLUSIONS: Macrophage p38α promotes the progression of steatohepatitis by inducing pro-inflammatory cytokine secretion and M1 polarization. p38 inhibition protects against steatohepatitis. LAY SUMMARY: p38 mitogen-activated protein kinases are important inflammatory factors. In the present study, we demonstrated that p38α is upregulated in liver tissues of patients with non-alcoholic fatty liver diseases. Genetic deletion of p38α in macrophages led to ameliorated nutritional steatohepatitis in mice through decreased pro-inflammatory cytokine secretion and increased M2 macrophage polarization.}, }
@article {pmid30912268, year = {2019}, author = {Timmis, K and Cavicchioli, R and Garcia, JL and Nogales, B and Chavarría, M and Stein, L and McGenity, TJ and Webster, N and Singh, BK and Handelsman, J and de Lorenzo, V and Pruzzo, C and Timmis, J and Martín, JLR and Verstraete, W and Jetten, M and Danchin, A and Huang, W and Gilbert, J and Lal, R and Santos, H and Lee, SY and Sessitsch, A and Bonfante, P and Gram, L and Lin, RTP and Ron, E and Karahan, ZC and van der Meer, JR and Artunkal, S and Jahn, D and Harper, L}, title = {The urgent need for microbiology literacy in society.}, journal = {Environmental microbiology}, volume = {21}, number = {5}, pages = {1513-1528}, doi = {10.1111/1462-2920.14611}, pmid = {30912268}, issn = {1462-2920}, }
@article {pmid30911770, year = {2019}, author = {Pan, Y and Wu, Y and Li, X and Zeng, J and Lin, X}, title = {Continuing Impacts of Selective Inhibition on Bacterial and Fungal Communities in an Agricultural Soil.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01364-0}, pmid = {30911770}, issn = {1432-184X}, support = {41671266//National Natural Science Foundation of China/ ; }, abstract = {Selective inhibition (SI) has been routinely used to differentiate the contributions of bacteria and fungi to soil ecological processes. SI experiments typically measured rapid responses within hours since the addition of inhibitor, but the long-term effects of selective biocides on microbial community composition and function were largely unknown. In this study, a microcosm experiment was performed with an agricultural soil to explore the effectiveness of two bactericides (bronopol, streptomycin) and two fungicides (cycloheximide, captan), which were applied at two different concentrations (2 and 10 mg g-1). The microcosms were incubated for 6 weeks. A radiolabeled substrate, [1,2,3,4,4a,9a-14C] anthracene, was spiked to all microcosms, and the derived CO2 was monitored during the incubation. The abundance and composition of bacteria and fungi were assessed by qPCR and Miseq sequencing of ribosomal rRNA genes. It was demonstrated that only 2 mg g-1 bronopol and cycloheximide significantly changed the bacteria to fungi ratio without apparent non-target inhibition on the abundances; however, community shifts were observed in all treatments after 6 weeks incubation. The enrichment of specific taxa implicated a selection of resistant or adapted microbes by these biocides. Mineralization of anthracene was continuingly suppressed in all SI microcosms, which may result in biased estimate of bacterial and fungal contributions to pollutant degradation. These findings highlight the risks of long-term application of selective inhibition, and a preliminary assessment of biocide selection and concentration is highly recommended.}, }
@article {pmid30911147, year = {2019}, author = {Guo, X and Zhou, X and Hale, L and Yuan, M and Ning, D and Feng, J and Shi, Z and Li, Z and Feng, B and Gao, Q and Wu, L and Shi, W and Zhou, A and Fu, Y and Wu, L and He, Z and Van Nostrand, JD and Qiu, G and Liu, X and Luo, Y and Tiedje, JM and Yang, Y and Zhou, J}, title = {Climate warming accelerates temporal scaling of grassland soil microbial biodiversity.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {4}, pages = {612-619}, doi = {10.1038/s41559-019-0848-8}, pmid = {30911147}, issn = {2397-334X}, mesh = {Bacteria/genetics/isolation &amp; purification ; *Biodiversity ; *Climate Change ; DNA, Bacterial/analysis ; DNA, Fungal/analysis ; Fungi/genetics/isolation &amp; purification ; *Grassland ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Determining the temporal scaling of biodiversity, typically described as species-time relationships (STRs), in the face of global climate change is a central issue in ecology because it is fundamental to biodiversity preservation and ecosystem management. However, whether and how climate change affects microbial STRs remains unclear, mainly due to the scarcity of long-term experimental data. Here, we examine the STRs and phylogenetic-time relationships (PTRs) of soil bacteria and fungi in a long-term multifactorial global change experiment with warming (+3 °C), half precipitation (-50%), double precipitation (+100%) and clipping (annual plant biomass removal). Soil bacteria and fungi all exhibited strong STRs and PTRs across the 12 experimental conditions. Strikingly, warming accelerated the bacterial and fungal STR and PTR exponents (that is, the w values), yielding significantly (P < 0.001) higher temporal scaling rates. While the STRs and PTRs were significantly shifted by altered precipitation, clipping and their combinations, warming played the predominant role. In addition, comparison with the previous literature revealed that soil bacteria and fungi had considerably higher overall temporal scaling rates (w = 0.39-0.64) than those of plants and animals (w = 0.21-0.38). Our results on warming-enhanced temporal scaling of microbial biodiversity suggest that the strategies of soil biodiversity preservation and ecosystem management may need to be adjusted in a warmer world.}, }
@article {pmid30910952, year = {2019}, author = {Penn, JL and Weber, T and Chang, BX and Deutsch, C}, title = {Microbial ecosystem dynamics drive fluctuating nitrogen loss in marine anoxic zones.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {15}, pages = {7220-7225}, doi = {10.1073/pnas.1818014116}, pmid = {30910952}, issn = {1091-6490}, mesh = {Ammonia/metabolism ; Aquatic Organisms/*physiology ; Bacteria, Anaerobic/*physiology ; *Climate ; Denitrification/physiology ; *Ecosystem ; Microbial Consortia/*physiology ; Nitrogen/*metabolism ; Oxygen/metabolism ; }, abstract = {The dynamics of nitrogen (N) loss in the ocean's oxygen-deficient zones (ODZs) are thought to be driven by climate impacts on ocean circulation and biological productivity. Here we analyze a data-constrained model of the microbial ecosystem in an ODZ and find that species interactions drive fluctuations in local- and regional-scale rates of N loss, even in the absence of climate variability. By consuming O2 to nanomolar levels, aerobic nitrifying microbes cede their competitive advantage for scarce forms of N to anaerobic denitrifying bacteria. Because anaerobes cannot sustain their own low-O2 niche, the physical O2 supply restores competitive advantage to aerobic populations, resetting the cycle. The resulting ecosystem oscillations induce a unique geochemical signature within the ODZ-short-lived spikes of ammonium that are found in measured profiles. The microbial ecosystem dynamics also give rise to variable ratios of anammox to heterotrophic denitrification, providing a mechanism for the unexplained variability of these pathways observed in the ocean.}, }
@article {pmid30904989, year = {2019}, author = {Yoo, K and Han, I and Ko, KS and Lee, TK and Yoo, H and Khan, MI and Tiedje, JM and Park, J}, title = {Bacillus-Dominant Airborne Bacterial Communities Identified During Asian Dust Events.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01348-0}, pmid = {30904989}, issn = {1432-184X}, support = {2018R1A6A1A08025348//National Research Foundation of Korea/ ; }, abstract = {Asian dust (AD) events have received significant attention due to their adverse effects on ecosystems and human health. However, detailed information about airborne pathogens associated with AD events is limited. This study monitored airborne bacterial communities and identified AD-specific bacteria and the potential hazards associated with these bacteria during AD events. Over a 33-month period, 40 air samples were collected under normal atmospheric conditions (non-AD events; n = 34) and during AD events (n = 6). The airborne bacterial communities in the air samples collected during non-AD events (non-AD sample) and AD events (AD sample) were evaluated using both culture-dependent and culture-independent methods. The bacterial diversity increased significantly, along with the 16S rRNA gene copy number, in AD samples (p < 0.05) and was positively correlated with PM10 concentration. High throughput sequencing of the 16S rRNA gene revealed that the relative abundance of the phylum Firmicutes increased substantially in AD samples (44.3 ± 5.0%) compared with non-AD samples (27.8 ± 4.3%). Within the phylum Firmicutes, AD samples included a greater abundance of Bacillus species (almost 23.8%) than non-AD samples (almost 13.3%). Both culture-dependent and culture-independent methods detected common predominant species closely related to Bacillus cereus during AD events. Subsequent multilocus sequence typing (MLST) and enterotoxin gene assays confirmed the presence of virulence factors in B. cereus isolates from AD samples. Furthermore, the abundance of bceT, encoding enterotoxin in B. cereus, was significantly higher in AD samples (p < 0.05). The systematic characterization of airborne bacterial communities in AD samples in this study suggests that B. cereus pose risks to public health.}, }
@article {pmid30904709, year = {2019}, author = {Vandekerckhove, TGL and Kerckhof, FM and De Mulder, C and Vlaeminck, SE and Boon, N}, title = {Determining stoichiometry and kinetics of two thermophilic nitrifying communities as a crucial step in the development of thermophilic nitrogen removal.}, journal = {Water research}, volume = {156}, number = {}, pages = {34-45}, doi = {10.1016/j.watres.2019.03.008}, pmid = {30904709}, issn = {1879-2448}, abstract = {Nitrification and denitrification, the key biological processes for thermophilic nitrogen removal, have separately been established in bioreactors at 50 °C. A well-characterized set of kinetic parameters is essential to integrate these processes while safeguarding the autotrophs performing nitrification. Knowledge on thermophilic nitrifying kinetics is restricted to isolated or highly enriched batch cultures, which do not represent bioreactor conditions. This study characterized the stoichiometry and kinetics of two thermophilic (50 °C) nitrifying communities. The most abundant ammonia oxidizing archaea (AOA) were related to the Nitrososphaera genus, clustering relatively far from known species Nitrososphaera gargensis (95.5% 16S rRNA gene sequence identity). The most abundant nitrite oxidizing bacteria (NOB) were related to Nitrospira calida (97% 16S rRNA gene sequence identity). The nitrification biomass yield was 0.20-0.24 g VSS g-1 N, resulting mainly from a high AOA yield (0.16-0.20 g VSS g-1 N), which was reflected in a high AOA abundance in the community (57-76%) compared to NOB (5-11%). Batch-wise determination of decay rates (AOA: 0.23-0.29 d-1; NOB: 0.32-0.43 d-1) rendered an overestimation compared to in situ estimations of overall decay rate (0.026-0.078 d-1). Possibly, the inactivation rate rather than the actual decay rate was determined in batch experiments. Maximum growth rates of AOA and NOB were 0.12-0.15 d-1 and 0.13-0.33 d-1 respectively. NOB were susceptible to nitrite, opening up opportunities for shortcut nitrogen removal. However, NOB had a similar growth rate and oxygen affinity (0.15-0.55 mg O2 L-1) as AOA and were resilient towards free ammonia (IC50 > 16 mg NH3-N L-1). This might complicate NOB outselection using common practices to establish shortcut nitrogen removal (SRT control; aeration control; free ammonia shocks). Overall, the obtained insights can assist in integrating thermophilic conversions and facilitate single-sludge nitrification/denitrification.}, }
@article {pmid30904186, year = {2019}, author = {Delzenne, NM and Olivares, M and Neyrinck, AM and Beaumont, M and Kjølbæk, L and Larsen, TM and Benítez-Páez, A and Romaní-Pérez, M and Garcia-Campayo, V and Bosscher, D and Sanz, Y and van der Kamp, JW}, title = {Nutritional interest of dietary fiber and prebiotics in obesity: Lessons from the MyNewGut consortium.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.clnu.2019.03.002}, pmid = {30904186}, issn = {1532-1983}, abstract = {The aim of EU project MyNewGut is to contribute to future public health-related recommendations supported by new insight in gut microbiome and nutrition-host relationship. In this Opinion Paper, we first revisit the concept of dietary fiber, taking into account their interaction with the gut microbiota. This paper also summarizes the main effects of dietary fibers with prebiotic properties in intervention studies in humans, with a particular emphasis on the effects of arabinoxylans and arabinoxylo-oligosaccharides on metabolic alterations associated with obesity. Based on the existing state of the art and future development, we elaborate the steps required to propose dietary guidelines related to dietary fibers, taking into account their interaction with the gut microbiota.}, }
@article {pmid30903203, year = {2019}, author = {Hu, J and Liu, S and Yang, W and He, Z and Wang, J and Liu, H and Zheng, P and Xi, C and Ma, F and Hu, B}, title = {Ecological Success of the Nitrosopumilus and Nitrosospira Clusters in the Intertidal Zone.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01359-x}, pmid = {30903203}, issn = {1432-184X}, support = {No.41773074//National Natural Science Foundation of China/ ; No. 31828001//National Natural Science Foundation of China/ ; No.41641031//National Natural Science Foundation of China/ ; No. QAK201714//Open Project of State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology/ ; }, abstract = {The intertidal zone is an important buffer and a nitrogen sink between land and sea. Ammonia oxidation is the rate-limiting step of nitrification, conducted by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, it remains a debatable issue regarding dominant ammonia oxidizers in this region, and environmental factors driving their spatiotemporal niche differentiation have yet to be identified. In this study, intertidal and subtidal zones of Zhoushan Islands were selected for seasonal sampling. Ammonia-oxidizing activity, quantitative PCR, and 454 high-throughput sequencing were performed to study the nitrification potential, abundance, and community structure of ammonia-oxidizing archaea and bacteria. AOA and AOB amoA abundance (107-108amoA gene copies/g dry weight sediment) varied spatiotemporally independently of environmental factors. AOA surpassed AOB in most samples, driven by sediment temperature, moisture, and total nitrogen. The diversity of both AOA and AOB differed spatiotemporally. The Nitrosopumilus and Nitrosospira clusters accounted for an absolutely dominant percentage of AOA (> 99%) and AOB (> 99%) respectively, indicating a negligible contribution of other clusters to ammonia oxidation. However, there was no significant correlation between nitrification potential and the abundance of AOA or AOB. Overall, the present study showed that AOA dominated over AOB spatiotemporally in the intertidal zone of Zhoushan Islands due to fluctuations in environmental factors, and the Nitrosopumilus and Nitrosospira clusters ecologically succeeded in the intertidal zone of Zhoushan Islands.}, }
@article {pmid30903202, year = {2019}, author = {Borg Dahl, M and Brejnrod, AD and Russel, J and Sørensen, SJ and Schnittler, M}, title = {Different Degrees of Niche Differentiation for Bacteria, Fungi, and Myxomycetes Within an Elevational Transect in the German Alps.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01347-1}, pmid = {30903202}, issn = {1432-18