@article {pmid30430196, year = {2018}, author = {Wynants, E and Frooninckx, L and Crauwels, S and Verreth, C and De Smet, J and Sandrock, C and Wohlfahrt, J and Van Schelt, J and Depraetere, S and Lievens, B and Van Miert, S and Claes, J and Van Campenhout, L}, title = {Assessing the Microbiota of Black Soldier Fly Larvae (Hermetia illucens) Reared on Organic Waste Streams on Four Different Locations at Laboratory and Large Scale.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1286-x}, pmid = {30430196}, issn = {1432-184X}, support = {RT 15/9 EDINCO//FOD Volksgezondheid, Veiligheid van de Voedselketen en Leefmilieu/ ; }, abstract = {This study aimed to gain insight into the microbial quality, safety and bacterial community composition of black soldier fly larvae (Hermetia illucens) reared at different facilities on a variety of organic waste streams. For seven rearing cycles, both on laboratory-scale and in large-scale facilities at several locations, the microbiota of the larvae was studied. Also samples of the substrate used and the residue (= leftover substrate after rearing, existing of non-consumed substrate, exuviae and faeces) were investigated. Depending on the sample, it was subjected to plate counting, Illumina Miseq sequencing and/or detection of specific food pathogens. The results revealed that the substrates applied at the various locations differed substantially in microbial numbers as well as in the bacterial community composition. Furthermore, little similarity was observed between the microbiota of the substrate and that of the larvae reared on that substrate. Despite substantial differences between the microbiota of larvae reared at several locations, 48 species-level operational taxonomic units (OTUs) were shared by all larvae, among which most belonged to the phyla Firmicutes and Proteobacteria. Although the substrate is assumed to be an important source of bacteria, our results suggest that a variety of supposedly interacting factors-both abiotic and biotic-are likely to affect the microbiota in the larvae. In some larvae and/or residue samples, potential foodborne pathogens such as Salmonella and Bacillus cereus were detected, emphasising that decontamination technologies are required when the larvae are used in feed, just as for other feed ingredients, or eventually in food.}, }
@article {pmid30429840, year = {2018}, author = {Mas-Carrió, E and Dini-Andreote, F and Brossi, MJL and Salles, JF and Olff, H}, title = {Organic Amendment Under Increasing Agricultural Intensification: Effects on Soil Bacterial Communities and Plant Productivity.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2612}, doi = {10.3389/fmicb.2018.02612}, pmid = {30429840}, issn = {1664-302X}, abstract = {The soil microbiome is a complex living network that plays essential roles in agricultural systems, regardless of the level of intensification. However, the effects of agricultural management on the soil microbiome and the association with plant productivity remain largely unclear. Here, we studied the responses of three soil systems displaying distinct levels of agriculture intensiveness (i.e., natural, organic, and conventional soil management regimes) to experimentally manipulated organic farming amendments (i.e., dung and earthworms). We aimed at (i) identifying the effect on plant productivity and (ii) elucidating the degree of shifts in bacterial communities in response to the applied organic amendments. We found plant productivity to be lower with increasing agricultural intensification. Bacterial communities shifted distinctively for each soil management regime to the organic amendments applied. In brief, greater changes were observed in the Conventional management comparatively to the Organic and Natural management, an effect largely driven by dung addition. Moreover, we found evidence that the level of agricultural intensiveness also affects the timespan for these shifts. For instance, while the Natural system reached a relatively stable community composition before the end of the experiment, treatments on the conventional soil management regime did not. Random forest analyses further revealed an increasing impact of introduced taxa from dung addition aligned with increasing agricultural intensification. These analyses suggested that earthworms regulate the introduction of species from dung into the soil bacterial community. Collectively, our results contribute to a better understanding of the outcomes of organic amendments on soils under distinct levels of agriculture intensiveness, with implications for further development in soil restorations practices.}, }
@article {pmid30429832, year = {2018}, author = {Bruno, A and Sandionigi, A and Bernasconi, M and Panio, A and Labra, M and Casiraghi, M}, title = {Changes in the Drinking Water Microbiome: Effects of Water Treatments Along the Flow of Two Drinking Water Treatment Plants in a Urbanized Area, Milan (Italy).}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2557}, doi = {10.3389/fmicb.2018.02557}, pmid = {30429832}, issn = {1664-302X}, abstract = {While safe and of high quality, drinking water can host an astounding biodiversity of microorganisms, dismantling the belief of its "biological simplicity." During the very few years, we are witnessing an exponential growth in scientific publications, exploring the ecology hidden in drinking water treatment plants (DWTPs) and drinking water distribution system (DWDS). We focused on what happens to the microbial communities from source water (groundwater) throughout the main steps of the potabilization process of a DWTP, located in an urbanized area in Northern Italy. Samples were processed by a stringent water filtration to retain even the smallest environmental bacteria and then analyzed with High-Throughput DNA Sequencing (HTS) techniques. We showed that carbon filters harbored a microbial community seeding and shaping water microbiota downstream, introducing a significant variation on incoming (groundwater) microbial community. Chlorination did not instantly affect the altered microbiota. We were also able to correctly predict (through machine learning analysis) samples belonging to groundwater (overall accuracy was 0.71), but the assignation was not reliable with carbon filter samples, which were incorrectly predicted as chlorination samples. The presence and abundance of specific microorganisms allowed us to hypothesize their role as indicators. In particular, Candidatus Adlerbacteria (Parcubacteria), together with microorganisms belonging to Alphaproteobacteria and Gammaproteobacteria, characterized treated water, but not raw water. An exception, confirming our hypothesis, is given by the samples downstream the filters renewal, which had a composition resembling groundwater. Volatility analysis illustrated how carbon filters represented an ecosystem that is stable over time, probably bearing the environmental conditions that promote the survival and growth of this peculiar microbial community.}, }
@article {pmid30429514, year = {2018}, author = {De Vrieze, J and Ijaz, UZ and Saunders, AM and Theuerl, S}, title = {Terminal restriction fragment length polymorphism is an "old school" reliable technique for swift microbial community screening in anaerobic digestion.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16818}, doi = {10.1038/s41598-018-34921-7}, pmid = {30429514}, issn = {2045-2322}, abstract = {The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades. In the last decade, high-throughput 16S rRNA gene amplicon sequencing has replaced these techniques, but the time-consuming and complex nature of high-throughput techniques is a potential bottleneck for full-scale anaerobic digestion application, when monitoring community dynamics. Here, the bacterial and archaeal TRFLP profiles were compared with 16S rRNA gene amplicon profiles (Illumina platform) of 25 full-scale anaerobic digestion plants. The α-diversity analysis revealed a higher richness based on Illumina data, compared with the TRFLP data. This coincided with a clear difference in community organisation, Pareto distribution, and co-occurrence network statistics, i.e., betweenness centrality and normalised degree. The β-diversity analysis showed a similar clustering profile for the Illumina, bacterial TRFLP and archaeal TRFLP data, based on different distance measures and independent of phylogenetic identification, with pH and temperature as the two key operational parameters determining microbial community composition. The combined knowledge of temporal dynamics and projected clustering in the β-diversity profile, based on the TRFLP data, distinctly showed that TRFLP is a reliable technique for swift microbial community dynamics screening in full-scale anaerobic digestion plants.}, }
@article {pmid30426401, year = {2018}, author = {Ver Heul, A and Planer, J and Kau, AL}, title = {The Human Microbiota and Asthma.}, journal = {Clinical reviews in allergy & immunology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12016-018-8719-7}, pmid = {30426401}, issn = {1559-0267}, support = {K08AI113184//National Institute of Allergy and Infectious Diseases (US)/ ; 5T32DK077653-27//National Institute of Diabetes and Digestive and Kidney Diseases/ ; Faculty Development Award//AAAAI Foundation/ ; }, abstract = {Over the last few decades, advances in our understanding of microbial ecology have allowed us to appreciate the important role of microbial communities in maintaining human health. While much of this research has focused on gut microbes, microbial communities in other body sites and from the environment are increasingly recognized in human disease. Here, we discuss recent advances in our understanding of host-microbiota interactions in the development and manifestation of asthma focusing on three distinct microbial compartments. First, environmental microbes originating from house dust, pets, and farm animals have been linked to asthma pathogenesis, which is often connected to their production of bioactive molecules such as lipopolysaccharide. Second, respiratory microbial communities, including newly appreciated populations of microbes in the lung have been associated with allergic airway inflammation. Current evidence suggests that the presence of particular microbes, especially Streptococcus, Haemophilus, and Morexella species within the airway may shape local immune responses and alter the severity and manifestations of airway inflammation. Third, the gut microbiota has been implicated in both experimental models and clinical studies in predisposing to asthma. There appears to be a "critical window" of colonization that occurs during early infancy in which gut microbial communities shape immune maturation and confer susceptibility to allergic airway inflammation. The mechanisms by which gut microbial communities influence lung immune responses and physiology, the "gut-lung axis," are still being defined but include the altered differentiation of immune cell populations important in asthma and the local production of metabolites that affect distal sites. Together, these findings suggest an intimate association of microbial communities with host immune development and the development of allergic airway inflammation. Improved understanding of these relationships raises the possibility of microbiota-directed therapies to improve or prevent asthma.}, }
@article {pmid30425147, year = {2018}, 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 = {Identifying and Predicting Novelty in Microbiome Studies.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, doi = {10.1128/mBio.02099-18}, pmid = {30425147}, issn = {2150-7511}, abstract = {With the expansion of microbiome sequencing globally, a key challenge is to relate new microbiome samples to the existing space of microbiome samples. Here, we present Microbiome Search Engine (MSE), which enables the rapid search of query microbiome samples against a large, well-curated reference microbiome database organized by taxonomic similarity at the whole-microbiome level. Tracking the microbiome novelty score (MNS) over 8 years of microbiome depositions based on searching in more than 100,000 global 16S rRNA gene amplicon samples, we detected that the structural novelty of human microbiomes is approaching saturation and likely bounded, whereas that in environmental habitats remains 5 times higher. Via the microbiome focus index (MFI), which is derived from the MNS and microbiome attention score (MAS), we objectively track and compare the structural-novelty and attracted-attention scores of individual microbiome samples and projects, and we predict future trends in the field. For example, marine and indoor environments and mother-baby interactions are likely to receive disproportionate additional attention based on recent trends. Therefore, MNS, MAS, and MFI are proposed "alt-metrics" for evaluating a microbiome project or prospective developments in the microbiome field, both of which are done in the context of existing microbiome big data.IMPORTANCE We introduce two concepts to quantify the novelty of a microbiome. The first, the microbiome novelty score (MNS), allows identification of microbiomes that are especially different from what is already sequenced. The second, the microbiome attention score (MAS), allows identification of microbiomes that have many close neighbors, implying that considerable scientific attention is devoted to their study. By computing a microbiome focus index based on the MNS and MAS, we objectively track and compare the novelty and attention scores of individual microbiome samples and projects over time and predict future trends in the field; i.e., we work toward yielding fundamentally new microbiomes rather than filling in the details. Therefore, MNS, MAS, and MFI can serve as "alt-metrics" for evaluating a microbiome project or prospective developments in the microbiome field, both of which are done in the context of existing microbiome big data.}, }
@article {pmid30423502, year = {2018}, author = {Ntagia, E and Fiset, E and da Silva Lima, L and Pikaar, I and Zhang, X and Jeremiasse, AW and Prévoteau, A and Rabaey, K}, title = {Anode materials for sulfide oxidation in alkaline wastewater: An activity and stability performance comparison.}, journal = {Water research}, volume = {149}, number = {}, pages = {111-119}, doi = {10.1016/j.watres.2018.11.004}, pmid = {30423502}, issn = {1879-2448}, abstract = {Electrochemical sulfide removal can be attractive as a zero-chemical-input approach for treatment of waste streams such as spent caustics coupled to caustic recovery. A key concern is possible decline in catalytic activity, due to passivation from deposited elemental sulfur (S0) on the anode surface and stability limitation, due to sulfide oxidation under highly alkaline conditions. In this study, six commercially available electrode materials (Ir Mixed Metal Oxide (MMO), Ru MMO, Pt/IrOx, Pt, PbOx and TiO2/IrTaO2 coated titanium-based electrodes) were tested to investigate the impact of the electrocatalyst on the process efficiency in terms of sulfide removal and final product of sulfide oxidation, as well as to determine the stability of the electrocatalyst under high sulfide concentrations (50 mM Na2S) and high alkalinity (pH > 12). Short-term experiments showed that the catalyst type impacts the anode potential and the sulfide oxidation reaction products. Longer-term experiments under current densities up to 200 A m-2 showed a high differentiation in stability performance among the catalysts. Ru MMO was the most active towards sulfide oxidation with a coulombic efficiency of 63.2 ± 0.5% at an average anode potential of 0.92 ± 0.17 V vs SHE. Ir MMO was the most stable, preserving 100% of its original catalyst loading during the tests. The results demonstrated that Ru MMO and Ir MMO were the most suitable electrode materials for sulfide oxidation under highly alkaline conditions, while the need for establishing a good trade-off between activity, stability and cost still persists.}, }
@article {pmid30423115, year = {2018}, author = {Romano, S and Ansorge, R}, title = {Scientific communication strategies of microbiologists in the era of social media.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fny264}, pmid = {30423115}, issn = {1574-6968}, abstract = {Over the last decades, the world of communication underwent drastic changes, and Internet and social media emerged as essential vehicles for exchanging information. Following these trends, it is important that scientists adapt to changes and adopt optimal strategies to communicate with colleagues, lay people, and institutions. We conducted an on-line survey to investigate the communication strategies of microbiologists and their colleagues from other disciplines. We collected data from 527 scholars from 57 countries, with ∼42% of them being microbiologists. We focused particularly on social media and found that > 80% of participants used them for work, and that ∼50% of interviewed actively shared and gathered scientific contents from social media. Compared to colleagues from other fields, microbiologists were less averse to use social media for work and were also less accustomed to use pre-prints as a source and vehicle of information. However, a large proportion of microbiologists declared to have planned pre-print publications in the future. Surprisingly, our data revealed that age is a poor predictor of social media usage, but it is strongly associated with the type of social media used, the activity undertaken on them, and the attitude towards pre-print publications. Considering the kaleidoscopic variety of scientific communication tools, our data might help to optimize the scientific promotion strategies among microbiologists.}, }
@article {pmid30421114, year = {2018}, author = {Chung, YA and Jumpponen, A and Rudgers, JA}, title = {Divergence in Diversity and Composition of Root-Associated Fungi Between Greenhouse and Field Studies in a Semiarid Grassland.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1277-y}, pmid = {30421114}, issn = {1432-184X}, support = {1601210//Division of Environmental Biology/ ; 1456955//Division of Environmental Biology/ ; 1748133//National Science Foundation/ ; 1440478//National Science Foundation/ ; }, abstract = {Investigations of plant-soil feedbacks (PSF) and plant-microbe interactions often rely exclusively on greenhouse experiments, yet we have little understanding of how, and when, results can be extrapolated to explain phenomena in nature. A systematic comparison of microbial communities using the same host species across study environments can inform the generalizability of such experiments. We used Illumina MiSeq sequencing to characterize the root-associated fungi of two foundation grasses from a greenhouse PSF experiment, a field PSF experiment, field monoculture stands, and naturally occurring resident plants in the field. A core community consisting < 10% of total fungal OTU richness but > 50% of total sequence abundance occurred in plants from all study types, demonstrating the ability of field and greenhouse experiments to capture the dominant component of natural communities. Fungal communities were plant species-specific across the study types, with the core community showing stronger host specificity than peripheral taxa. Roots from the greenhouse and field PSF experiments had lower among sample variability in community composition and higher diversity than those from naturally occurring, or planted monoculture plants from the field. Core and total fungal composition differed substantially across study types, and dissimilarity between fungal communities did not predict plant-soil feedbacks measured in experiments. These results suggest that rhizobiome assembly mechanisms in nature differ from the dynamics of short-term, inoculation studies. Our results validate the efficacy of common PSF experiment designs to test soil inoculum effects, and highlight the challenges of scaling the underlying microbial mechanisms of plant responses from whole-community inoculation experiments to natural ecosystems.}, }
@article {pmid30421109, year = {2018}, author = {La, A and Perré, P and Taidi, B}, title = {Process for symbiotic culture of Saccharomyces cerevisiae and Chlorella vulgaris for in situ CO2 mitigation.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-018-9506-3}, pmid = {30421109}, issn = {1432-0614}, abstract = {Industrial biotechnology relies heavily on fermentation processes that release considerable amounts of CO2. Apart from the fact that this CO2 represents a considerable part of the organic substrate, it has a negative impact on the environment. Microalgae cultures have been suggested as potential means of capturing the CO2 with further applications in high-value compounds production or directly for feed applications. We developed a sustainable process based on a mixed co-dominant culture of Saccharomyces cerevisiae and Chlorella vulgaris where the CO2 production and utilization controlled the microbial ecology of the culture. By mixing yeast and microalga in the same culture, the CO2 is produced in dissolved form and is available to the microalga avoiding degassing and dissolution phenomena. With this process, the CO2 production and utilization rates were balanced and a mutual symbiosis between the yeast and the microalga was set up in the culture. In this study, the reutilization of CO2 and growth of C. vulgaris was demonstrated. The two organism populations were balanced at approximately 20 × 106 cells ml-1 and almost all the CO2 produced by yeast was reutilized by microalga within 168 h of culture. The C. vulgaris inoculum preparation played a key role in establishing co-dominance of the two organisms. Other key factors in establishing symbiosis were the inoculum ratio of the two organisms and the growth medium design. A new method allowed the independent enumeration of each organism in a mixed culture. This study could provide a basis for the development of green processes of low environmental impact.}, }
@article {pmid30419469, year = {2018}, author = {Miao, Y and Johnson, NW and Gedalanga, PB and Adamson, D and Newell, C and Mahendra, S}, title = {Response and recovery of microbial communities subjected to oxidative and biological treatments of 1,4-dioxane and co-contaminants.}, journal = {Water research}, volume = {149}, number = {}, pages = {74-85}, doi = {10.1016/j.watres.2018.10.070}, pmid = {30419469}, issn = {1879-2448}, abstract = {Microbial community dynamics were characterized following combined oxidation and biodegradation treatment trains for mixtures of 1,4-dioxane and chlorinated volatile organic compounds (CVOCs) in laboratory microcosms. Bioremediation is generally inhibited by co-contaminate CVOCs; with only a few specific bacterial taxa reported to metabolize or cometabolize 1,4-dioxane being unaffected. Chemical oxidation by hydrogen peroxide (H2O2) as a non-selective treatment demonstrated 50-80% 1,4-dioxane removal regardless of the initial CVOC concentrations. Post-oxidation bioaugmentation with 1,4-dioxane metabolizer Pseudonocardia dioxanivorans CB1190 removed the remaining 1,4-dioxane. The intrinsic microbial population, biodiversity, richness, and biomarker gene abundances decreased immediately after the brief oxidation phase, but recovery of cultivable microbiomes and a more diverse community were observed during the subsequent 9-week biodegradation phase. Results generated from the Illumina Miseq sequencing and bioinformatics analyses established that generally oxidative stress tolerant genus Ralstonia was abundant after the oxidation step, and Cupriavidus, Pseudolabrys, Afipia, and Sphingomonas were identified as dominant genera after aerobic incubation. Multidimensional analysis elucidated the separation of microbial populations as a function of time under all conditions, suggesting that temporal succession is a determining factor that is independent of 1,4-dioxane and CVOCs mixtures. Network analysis highlighted the potential interspecies competition or commensalism, and dynamics of microbiomes during the biodegradation phase, in line with the shifts of predominant genera and various developing directions during different steps of the treatment train. Collectively, this study demonstrated that chemical oxidation followed by bioaugmentation is effective for treating 1,4-dioxane, even in the presence of high levels of CVOC mixtures and residual peroxide, a disinfectant, and enhanced our understanding of microbial ecological impacts of the treatment train. These results will be valuable for predicting treatment synergies that lead to cost savings and improved remedial outcomes in short-term active remediation as well as long-term changes to the environmental microbial communities.}, }
@article {pmid30418580, year = {2018}, author = {Lekeux, G and Crowet, JM and Nouet, C and Joris, M and Jadoul, A and Bosman, B and Carnol, M and Motte, P and Lins, L and Galleni, M and Hanikenne, M}, title = {Homology modeling and in vivo functional characterization of the zinc permeation pathway in a heavy metal P-type ATPase.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/ery353}, pmid = {30418580}, issn = {1460-2431}, abstract = {The P1B ATPase heavy metal ATPase 4 (HMA4) is responsible for zinc and cadmium translocation from roots to shoots in Arabidopsis thaliana. It couples ATP hydrolysis to cytosolic domain movements, enabling metal transport across the membrane. The detailed mechanism of metal permeation by HMA4 through the membrane remains elusive. Here, homology modeling of the HMA4 transmembrane region was conducted based on the crystal structure of a ZntA bacterial homolog. The analysis highlighted amino acids forming a metal permeation pathway, whose importance was subsequently investigated functionally through mutagenesis and complementation experiments in plants. Although the zinc pathway displayed overall conservation among the two proteins, significant differences were observed, especially in the entrance area with altered electronegativity and the presence of a ionic interaction/hydrogen bond network. The analysis also newly identified amino acids whose mutation results in total or partial loss of the protein function. In addition, comparison of zinc and cadmium accumulation in shoots of A. thaliana complemented lines revealed a number of HMA4 mutants exhibiting different abilities in zinc and cadmium translocation. These observations could be instrumental to design low cadmium-accumulating crops, hence decreasing human cadmium exposure.}, }
@article {pmid30418043, year = {2018}, author = {Muleviciene, A and D'Amico, F and Turroni, S and Candela, M and Jankauskiene, A}, title = {Iron deficiency anemia-related gut microbiota dysbiosis in infants and young children: A pilot study.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {}, number = {}, pages = {1-14}, doi = {10.1556/030.65.2018.045}, pmid = {30418043}, issn = {1217-8950}, abstract = {Nutritional iron deficiency (ID) causes not only anemia but also malfunction of the entire human organism. Recently, a role of the gut microbiota has been hypothesized, but limited data are available especially in infants. Here, we performed a pilot study to explore the gut microbiota in 10 patients with iron deficiency anemia (IDA) and 10 healthy controls aged 6-34 months. Fresh stool samples were collected from diapers, and the fecal microbiota was profiled by next-generation sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Except for diet diversity, the breastfeeding status at the enrollment, the exclusive breastfeeding duration, and the introduction of complementary foods did not differ between groups. Distinct microbial signatures were found in IDA patients, with increased relative abundance of Enterobacteriaceae (mean relative abundance, patients vs. controls, 4.4% vs. 3.0%) and Veillonellaceae (13.7% vs. 3.6%), and reduced abundance of Coriobacteriaceae (3.5% vs. 8.8%) compared to healthy controls. A decreased Bifidobacteriaceae/Enterobacteriaceae ratio was observed in IDA patients. Notwithstanding the low sample size, our data highlight microbiota dysbalance in IDA worth for further investigations, aimed at unraveling the ID impact on the microbiome trajectory in early life, and the possible long-term consequences.}, }
@article {pmid30418019, year = {2018}, author = {Shan, Y and Harms, H and Wick, LY}, title = {Electric Field Effects on Bacterial Deposition and Transport in Porous Media.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.8b03648}, pmid = {30418019}, issn = {1520-5851}, abstract = {Bacterial deposition and transport is key to microbial ecology and biotechnological applications. We therefore tested whether electrokinetic forces (electroosmotic shear force (FEOF), electrophoretic drag force (FEP)) acting on bacteria may be used to control bacterial deposition during transport in laboratory percolation columns exposed to external direct current (DC) electric fields. For different bacteria, yet similar experimental conditions we observed that DC fields either enhanced or reduced bacterial deposition efficiencies (α) relative to DC-free controls. By calculating the DLVO force of colloidal interactions, FEOF, FEP, and the hydraulic shear forces acting on single cells at a collector surface we found that DC-induced changes of α correlated to │ FEOF│ to │ FEP│ ratios: If │ FEOF│ > │ FEP│, α was clearly increased and if │ FEOF│ < │ FEP│ α was clearly decreased. Our findings allow for better prediction of the forces acting on a bacterium at collector surface and, hence, the electrokinetic control of microbial deposition in natural and manmade ecosystems.}, }
@article {pmid30417222, year = {2018}, author = {Zhang, FG and Bell, T and Zhang, QG}, title = {Experimental Testing of Dispersal Limitation in Soil Bacterial Communities with a Propagule Addition Approach.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1284-z}, pmid = {30417222}, issn = {1432-184X}, support = {31700434//National Natural Science Foundation of China/ ; 31725006 and 31670376//National Natural Science Foundation of China/ ; }, abstract = {The role of dispersal in the assembly of microbial communities remains contentious. This study tested the importance of dispersal limitation for the structuring of local soil bacterial communities using an experimental approach of propagule addition. Microbes extracted from soil pooled from samples collected at 20 localities across ~ 400 km in a temperate steppe were added to microcosms of local soils at three sites; the microcosms were then incubated in situ for 3 months. We then assessed the composition and diversity of bacterial taxa in the soils using 16S rRNA gene amplicon sequencing. The addition of the regional microbial pool did not cause significant changes in the overall composition or diversity of the total bacterial community, although a very small number of individual taxa may have been affected by the addition treatment. Our results suggest a negligible role of dispersal limitation in structuring soil bacterial communities in our study area.}, }
@article {pmid30417111, year = {2018}, author = {Minich, JJ and Humphrey, G and Benitez, RAS and Sanders, J and Swafford, A and Allen, EE and Knight, R}, title = {High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity.}, journal = {mSystems}, volume = {3}, number = {6}, pages = {}, doi = {10.1128/mSystems.00166-18}, pmid = {30417111}, issn = {2379-5077}, abstract = {Next-generation sequencing technologies have enabled many advances across biology, with microbial ecology benefiting primarily through expanded sample sizes. Although the cost of running sequencing instruments has decreased substantially over time, the price of library preparation methods has largely remained unchanged. In this study, we developed a low-cost miniaturized (5-µl volume) high-throughput (384-sample) amplicon library preparation method with the Echo 550 acoustic liquid handler. Our method reduces costs of library preparation to $1.42 per sample, a 58% reduction compared to existing automated methods and a 21-fold reduction from commercial kits, without compromising sequencing success or distorting the microbial community composition analysis. We further validated the optimized method by sampling five body sites from 46 Pacific chub mackerel fish caught across 16 sampling events over seven months from the Scripps Institution of Oceanography pier in La Jolla, CA. Fish microbiome samples were processed with the miniaturized 5-µl reaction volume with 0.2 µl of genomic DNA (gDNA) and the standard 25-µl reaction volume with 1 µl of gDNA. Between the two methods, alpha diversity was highly correlated (R2 > 0.95), while distances of technical replicates were much lower than within-body-site variation (P < 0.0001), further validating the method. The cost savings of implementing the miniaturized library preparation (going from triplicate 25-µl reactions to triplicate 5-µl reactions) are large enough to cover a MiSeq sequencing run for 768 samples while preserving accurate microbiome measurements. IMPORTANCE Reduced costs of sequencing have tremendously impacted the field of microbial ecology, allowing scientists to design more studies with larger sample sizes that often exceed 10,000 samples. Library preparation costs have not kept pace with sequencing prices, although automated liquid handling robots provide a unique opportunity to bridge this gap while also decreasing human error. Here, we take advantage of an acoustic liquid handling robot to develop a high-throughput miniaturized library preparation method of a highly cited and broadly used 16S rRNA gene amplicon reaction. We evaluate the potential negative effects of reducing the PCR volume along with varying the amount of gDNA going into the reaction. Our optimized method reduces sample-processing costs while continuing to generate a high-quality microbiome readout that is indistinguishable from the original method.}, }
@article {pmid30413836, year = {2018}, author = {Villegas-Plazas, M and Wos-Oxley, ML and Sanchez, JA and Pieper, DH and Thomas, OP and Junca, H}, title = {Variations in Microbial Diversity and Metabolite Profiles of the Tropical Marine Sponge Xestospongia muta with Season and Depth.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1285-y}, pmid = {30413836}, issn = {1432-184X}, support = {KBBE-2009-245226//MAGICPAH/ ; 652-2014//EcosNord-Colciencias/ ; JI-2012//Jóven Investigador - Colciencias/ ; MSc scholarship//Universidad de los Andes/ ; }, abstract = {Xestospongia muta is among the most emblematic sponge species inhabiting coral reefs of the Caribbean Sea. Besides being the largest sponge species growing in the Caribbean, it is also known to produce secondary metabolites. This study aimed to assess the effect of depth and season on the symbiotic bacterial dynamics and major metabolite profiles of specimens of X. muta thriving in a tropical marine biome (Portobelo Bay, Panamá), which allow us to determine whether variability patterns are similar to those reported for subtropical latitudes. The bacterial assemblages were characterized using Illumina deep-sequencing and metabolomic profiles using UHPLC-DAD-ELSD from five depths (ranging 9-28 m) across two seasons (spring and autumn). Diverse symbiotic communities, representing 24 phyla with a predominance of Proteobacteria and Chloroflexi, were found. Although several thousands of OTUs were determined, most of them belong to the rare biosphere and only 23 to a core community. There was a significant difference between the structure of the microbial communities in respect to season (autumn to spring), with a further significant difference between depths only in autumn. This was partially mirrored in the metabolome profile, where the overall metabolite composition did not differ between seasons, but a significant depth gradient was observed in autumn. At the phyla level, Cyanobacteria, Firmicutes, Actinobacteria, and Spirochaete showed a mild-moderate correlation with the metabolome profile. The metabolomic profiles were mainly characterized by known brominated polyunsaturated fatty acids. This work presents findings about the composition and dynamics of the microbial assemblages of X. muta expanding and confirming current knowledge about its remarkable diversity and geographic variability as observed in this tropical marine biome.}, }
@article {pmid30411190, year = {2018}, author = {Rossi, A and Bellone, A and Fokin, SI and Boscaro, V and Vannini, C}, title = {Detecting Associations Between Ciliated Protists and Prokaryotes with Culture-Independent Single-Cell Microbiomics: a Proof-of-Concept Study.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1279-9}, pmid = {30411190}, issn = {1432-184X}, support = {565-60%2016//University of Pisa/ ; 565-60%2017//University of Pisa/ ; 565-FFABR 2017//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; }, abstract = {Symbioses between prokaryotes and microbial eukaryotes, particularly ciliated protists, have been studied for a long time. Nevertheless, researchers have focused only on a few host genera and species, mainly due to difficulties in cultivating the hosts, and usually have considered a single symbiont at a time. Here, we present a pilot study using a single-cell microbiomic approach to circumvent these issues. Unicellular ciliate isolation followed by simultaneous amplification of eukaryotic and prokaryotic markers was used. Our preliminary test gave reliable and satisfactory results both on samples collected from different habitats (marine and freshwater) and on ciliates belonging to different taxonomic groups. Results suggest that, as already assessed for many macro-organisms like plants and metazoans, ciliated protists harbor distinct microbiomes. The applied approach detected new potential symbionts as well as new hosts for previously described ones, with relatively low time and cost effort and without culturing. When further developed, single-cell microbiomics for ciliates could be applied to a large number of studies aiming to unravel the evolutionary and ecological meaning of these symbiotic systems.}, }
@article {pmid30411189, year = {2018}, author = {Dror, H and Novak, L and Evans, JS and López-Legentil, S and Shenkar, N}, title = {Core and Dynamic Microbial Communities of Two Invasive Ascidians: Can Host-Symbiont Dynamics Plasticity Affect Invasion Capacity?.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1276-z}, pmid = {30411189}, issn = {1432-184X}, support = {2014025//United States - Israel Binational Science Foundation/ ; 2014025//United States - Israel Binational Science Foundation/ ; }, abstract = {Ascidians (Chordata, Ascidiacea) are considered to be prominent marine invaders, able to tolerate highly polluted environments and fluctuations in salinity and temperature. Here, we examined the seasonal and spatial dynamics of the microbial communities in the inner-tunic of two invasive ascidians, Styela plicata (Lesueur 1823) and Herdmania momus (Savigny 1816), in order to investigate the changes that occur in the microbiome of non-indigenous ascidians in different environments. Microbial communities were characterized using next-generation sequencing of partial (V4) 16S rRNA gene sequences. A clear differentiation between the ascidian-associated microbiome and bacterioplankton was observed, and two distinct sets of operational taxonomic units (OTUs), one core and the other dynamic, were recovered from both species. The relative abundance of the dynamic OTUs in H. momus was higher than in S. plicata, for which core OTU structure was maintained independently of location. Ten and seventeen core OTUs were identified in S. plicata and H. momus, respectively, including taxa with reported capabilities of carbon fixing, ammonia oxidization, denitrification, and heavy-metal processing. The ascidian-sourced dynamic OTUs clustered in response to site and season but significantly differed from the bacterioplankton community structure. These findings suggest that the associations between invasive ascidians and their symbionts may enhance host functionality while maintaining host adaptability to changing environmental conditions.}, }
@article {pmid30411188, year = {2018}, author = {Liu, PY and Cheng, AC and Huang, SW and Chang, HW and Oshida, T and Yu, HT}, title = {Variations in Gut Microbiota of Siberian Flying Squirrels Correspond to Seasonal Phenological Changes in Their Hokkaido Subarctic Forest Ecosystem.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1278-x}, pmid = {30411188}, issn = {1432-184X}, support = {MOST 103-2311-B-002-001//Ministry of Science and Technology, Taiwan/ ; MOST 106-2633-B-006-004//Ministry of Science and Technology, Taiwan/ ; }, abstract = {Gut microbial communities of animals are influenced by diet and seasonal weather changes. Since foraging strategies of wild animals are affected by phenological changes, gut microbial communities would differ among seasons. However, interactions of plant-animal-microbiota with seasonal changes have not been well characterized. Here, we surveyed gut microbial diversity of Siberian flying squirrels (Pteromys volans orii) from a natural forest in Hokkaido during spring and summer of 2013 and 2014. Additionally, we compared microbial diversity to temperature changes and normalized difference vegetation index (NDVI). Changes in both seasonal temperature and phenology were significantly associated with alterations in gut microbiota. There were two clusters of OTUs, below and above 20 °C that were significantly correlated with low and high temperatures, respectively. Low-temperature cluster OTUs belonged to various phyla, whereas the high-temperature cluster was only constituted by Firmicutes. In conclusion, gut microbiota of Siberian flying squirrels varied with environmental changes on an ecological scale.}, }
@article {pmid30411009, year = {2018}, author = {Van den Abbeele, P and Kamil, A and Fleige, L and Chung, Y and De Chavez, P and Marzorati, M}, title = {Different Oat Ingredients Stimulate Specific Microbial Metabolites in the Gut Microbiome of Three Human Individuals in Vitro.}, journal = {ACS omega}, volume = {3}, number = {10}, pages = {12446-12456}, doi = {10.1021/acsomega.8b01360}, pmid = {30411009}, issn = {2470-1343}, abstract = {We used a standardized in vitro simulation of the intestinal environment of three human donors to investigate the effect of six oat ingredients, which were produced by the application of different processing techniques, on the gut microbial community. Fructooligosaccharide was used as the positive control. Consistent changes in pH and gas production, on average -0.4 pH units and +32 kPa, indicated the high fermentability of the oat ingredients, and the resulting increased production of metabolites that are considered as beneficial for human health. These metabolites included acetate and lactate, but mostly propionate (+13.6 mM on average). All oat ingredients resulted in increased bifidobacteria levels with an average increase of 0.73 log. Moreover, a decreased production of proteolytic markers was observed, including branched short-chain fatty acids and ammonium. The results were donor-specific and product-specific. The results suggested an association between the total amounts of dietary fiber and the prebiotic potentials of different ingredients. Furthermore, as mechanical processing of oat products has previously been linked to increased extractability of dietary fibers, the obtained results suggest that different processing techniques might have impacted the potential functional properties of the final ingredients.}, }
@article {pmid30405584, year = {2018}, author = {Godoy-Vitorino, F and Romaguera, J and Zhao, C and Vargas-Robles, D and Ortiz-Morales, G and Vázquez-Sánchez, F and Sanchez-Vázquez, M and de la Garza-Casillas, M and Martinez-Ferrer, M and White, JR and Bittinger, K and Dominguez-Bello, MG and Blaser, MJ}, title = {Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2533}, doi = {10.3389/fmicb.2018.02533}, pmid = {30405584}, issn = {1664-302X}, abstract = {The human cervicovaginal microbiota resides at an interface between the host and the environment and may affect susceptibility to disease. Puerto Rican women have high human papillomavirus (HPV) infection and cervical cancer rates. We hypothesized that the population structure of the cervicovaginal bacterial and fungal biota changed with cervical squamous intraepithelial lesions and HPV infections. DNA was extracted from cervix, introitus, and anal sites of 62 patients attending high-risk San Juan clinics. The 16S rRNA V4 region and ITS-2 fungal regions were amplified and sequenced using Illumina technology. HPV genotyping was determined by reverse hybridization with the HPV SPF10-LiPA25 kit. HPV prevalence was 84% of which ∼44% subjects were infected with high-risk HPV, ∼35% were co-infected with as many as 9 HPV types and ∼5% were infected with exclusively low-risk HPV types. HPV diversity did not change with cervical dysplasia. Cervical bacteria were more diverse in patients with CIN3 pre-cancerous lesions. We found enrichment of Atopobium vaginae and Gardnerella vaginalis in patients with CIN3 lesions. We found no significant bacterial biomarkers associated with HPV infections. Fungal diversity was significantly higher in cervical samples with high-risk HPV and introitus samples of patients with Atypical Squamous Cells of Undetermined Significance (ASCUS). Fungal biomarker signatures for vagina and cervix include Sporidiobolaceae and Sacharomyces for ASCUS, and Malassezia for high-risk HPV infections. Our combined data suggests that specific cervicovaginal bacterial and fungal populations are related to the host epithelial microenvironment, and could play roles in cervical dysplasia.}, }
@article {pmid30405571, year = {2018}, author = {Biagi, E and Aceti, A and Quercia, S and Beghetti, I and Rampelli, S and Turroni, S and Soverini, M and Zambrini, AV and Faldella, G and Candela, M and Corvaglia, L and Brigidi, P}, title = {Microbial Community Dynamics in Mother's Milk and Infant's Mouth and Gut in Moderately Preterm Infants.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2512}, doi = {10.3389/fmicb.2018.02512}, pmid = {30405571}, issn = {1664-302X}, abstract = {Mother's own milk represents the optimal source for preterm infant nutrition, as it promotes immune defenses and gastrointestinal function, protects against necrotizing enterocolitis, improves long-term clinical outcome and is hypothesized to drive gut microbiota assembly. Preterm infants at birth usually do not receive their mother's milk directly from the breast, because active suckling and coordination between suckling, swallowing and breathing do not develop until 32-34 weeks gestational age, but actual breastfeeding is usually possible as they grow older. Here, we enrolled moderately preterm infants (gestational age 32-34 weeks) to longitudinally characterize mothers' milk and infants' gut and oral microbiomes, up to more than 200 days after birth, through 16S rRNA sequencing. This peculiar population offers the chance to disentangle the differential contribution of human milk feeding per se vs. actual breastfeeding in the development of infant microbiomes, that have both been acknowledged as crucial contributors to short and long-term infant health status. In this cohort, the milk microbiome composition seemed to change following the infant's latching to the mother's breast, shifting toward a more diverse microbial community dominated by typical oral microbes, i.e., Streptococcus and Rothia. Even if all infants in the present study were fed human milk, features typical of healthy, full term, exclusively breastfed infants, i.e., high percentages of Bifidobacterium and low abundances of Pseudomonas in fecal and oral samples, respectively, were detected in samples taken after actual breastfeeding started. These findings underline the importance of encouraging not only human milk feeding, but also an early start of actual breastfeeding in preterm infants, since the infant's latching to the mother's breast might constitute an independent factor helping the health-promoting assembly of the infant gut microbiome.}, }
@article {pmid30405545, year = {2018}, author = {Mehner-Breitfeld, D and Rathmann, C and Riedel, T and Just, I and Gerhard, R and Overmann, J and Brüser, T}, title = {Evidence for an Adaptation of a Phage-Derived Holin/Endolysin System to Toxin Transport in Clostridioides difficile.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2446}, doi = {10.3389/fmicb.2018.02446}, pmid = {30405545}, issn = {1664-302X}, abstract = {The pathogenicity locus (PaLoc) of Clostridioides difficile usually comprises five genes (tcdR, tcdB, tcdE, tcdA, tcdC). While the proteins TcdA and TcdB represent the main toxins of this pathogen, TcdR and TcdC are involved in the regulation of their production. TcdE is a holin family protein, members of which are usually involved in the transport of cell wall-degrading enzymes (endolysins) for phage-induced lysis. In the past, TcdE has been shown to contribute to the release of TcdA and TcdB, but it is unclear whether it mediates a specific transport or rather a lysis of cells. TcdE of C. difficile strains analyzed so far can be produced in three isoforms that are initiated from distinct N-terminal ATG codons. When produced in Escherichia coli, we found that the longest TcdE isoform had a moderate effect on cell growth, whereas the shortest isoform strongly induced lysis. The effect of the longest isoform was inhibitory for cell lysis, implying a regulatory function of the N-terminal 24 residues. We analyzed the PaLoc sequence of 44 C. difficile isolates and found that four of these apparently encode only the short TcdE isoforms, and the most closely related holins from C. difficile phages only possess one of these initiation codons, indicating that an N-terminal extension of TcdE evolved in C. difficile. All PaLoc sequences comprised also a conserved gene encoding a short fragment of an endolysin remnant of a phage holin/endolysin pair. We could produce this peptide, which we named TcdL, and demonstrated by bacterial two-hybrid analysis a self-interaction and an interaction with TcdB that might serve to mediate TcdE-dependent transport.}, }
@article {pmid30405201, year = {2018}, author = {Wankhade, UD and Zhong, Y and Kang, P and Alfaro, M and Chintapalli, SV and Piccolo, BD and Mercer, KE and Andres, A and Thakali, KM and Shankar, K}, title = {Maternal High-Fat Diet Programs Offspring Liver Steatosis in a Sexually Dimorphic Manner in Association with Changes in Gut Microbial Ecology in Mice.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16502}, doi = {10.1038/s41598-018-34453-0}, pmid = {30405201}, issn = {2045-2322}, support = {6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; }, abstract = {The contributions of maternal diet and obesity in shaping offspring microbiome remain unclear. Here we employed a mouse model of maternal diet-induced obesity via high-fat diet feeding (HFD, 45% fat calories) for 12 wk prior to conception on offspring gut microbial ecology. Male and female offspring were provided access to control or HFD from weaning until 17 wk of age. Maternal HFD-associated programming was sexually dimorphic, with male offspring from HFD dams showing hyper-responsive weight gain to postnatal HFD. Likewise, microbiome analysis of offspring cecal contents showed differences in α-diversity, β-diversity and higher Firmicutes in male compared to female mice. Weight gain in offspring was significantly associated with abundance of Lachnospiraceae and Clostridiaceae families and Adlercreutzia, Coprococcus and Lactococcus genera. Sex differences in metagenomic pathways relating to lipid metabolism, bile acid biosynthesis and immune response were also observed. HFD-fed male offspring from HFD dams also showed worse hepatic pathology, increased pro-inflammatory cytokines, altered expression of bile acid regulators (Cyp7a1, Cyp8b1 and Cyp39a1) and serum bile acid concentrations. These findings suggest that maternal HFD alters gut microbiota composition and weight gain of offspring in a sexually dimorphic manner, coincident with fatty liver and a pro-inflammatory state in male offspring.}, }
@article {pmid30402724, year = {2018}, author = {Veresoglou, SD and Verbruggen, E and Makarova, O and Mansour, I and Sen, R and Rillig, MC}, title = {Arbuscular Mycorrhizal Fungi Alter the Community Structure of Ammonia Oxidizers at High Fertility via Competition for Soil NH4.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1281-2}, pmid = {30402724}, issn = {1432-184X}, support = {300298//FP7 People: Marie-Curie Actions ()/ ; }, abstract = {Nitrification represents a central process in the cycling of nitrogen (N) which in high-fertility habitats can occasionally be undesirable. Here, we explore how arbuscular mycorrhiza (AM) impacts nitrification when N availability is not limiting to plant growth. We wanted to test which of the mechanisms that have been proposed in the literature best describes how AM influences nitrification. We manipulated the growth settings of Plantago lanceolata so that we could control the mycorrhizal state of our plants. AM induced no changes in the potential nitrification rates or the estimates of ammonium oxidizing (AO) bacteria. However, we could observe a moderate shift in the community of ammonia-oxidizers, which matched the shift we saw when comparing hyphosphere to rhizosphere soil samples and mirrored well changes in the availability of ammonium in soil. We interpret our results as support that it is competition for N that drives the interaction between AM and AO. Our experiment sheds light on an understudied interaction which is pertinent to typical management practices in agricultural systems.}, }
@article {pmid30397796, year = {2018}, author = {Kraus, C and Voegele, RT and Fischer, M}, title = {Temporal Development of the Culturable, Endophytic Fungal Community in Healthy Grapevine Branches and Occurrence of GTD-Associated Fungi.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1280-3}, pmid = {30397796}, issn = {1432-184X}, support = {FKZ 031A349D//Bundesministerium für Bildung und Forschung/ ; }, abstract = {Endophytic fungi play an important role in the life of grapevine, either as beneficial microorganisms or as pathogens. Many surveys concerning the fungal grapevine community have been conducted. Nevertheless, exactly how the fungal community arises within the plant and develops from young shoots to mature vines is still unknown. Therefore, it was the aim of this study to investigate the early development of endophytic fungal communities in healthy grapevine branches from 2 months to 8 years old. More than 3800 fungi belonging to 86 operational taxonomic units (OTUs) were isolated from wood samples and assigned to eight age groups. The community composition within the age groups changed and significant differences between young (≤ 1 year) and old (> 1 year) branches were found. The former were primarily dominated by ubiquitous, fast-growing fungi like Alternaria spp., Aureobasidium pullulans, Cladosporium spp., or Epicoccum nigrum, while communities of perennial branches additionally harbored many grapevine trunk disease (GTD)-associated fungi such as Diplodia seriata or Eutypa lata. This work gives an insight into the early development of fungal communities in grapevine, the nature and composition of primary settlers and core communities, as well as the emergence of GTD-associated fungi in perennial wood. This information may help grapevine growers to better estimate the risk in relation to the applied training system, producing mainly old branches or young shoots.}, }
@article {pmid30397795, year = {2018}, author = {Palacios, OA and Lopez, BR and Bashan, Y and de-Bashan, LE}, title = {Early Changes in Nutritional Conditions Affect Formation of Synthetic Mutualism Between Chlorella sorokiniana and the Bacterium Azospirillum brasilense.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1282-1}, pmid = {30397795}, issn = {1432-184X}, support = {251102//Consejo Nacional de Ciencia y Tecnología/ ; 284562//Consejo Nacional de Ciencia y Tecnología/ ; }, abstract = {The effect of three different nutritional conditions during the initial 12 h of interaction between the microalgae Chlorella sorokiniana UTEX 2714 and the plant growth-promoting bacterium Azospirillum brasilense Cd on formation of synthetic mutualism was assessed by changes in population growth, production of signal molecules tryptophan and indole-3-acetic acid, starch accumulation, and patterns of cell aggregation. When the interaction was supported by a nutrient-rich medium, production of both signal molecules was detected, but not when this interaction began with nitrogen-free (N-free) or carbon-free (C-free) media. Overall, populations of bacteria and microalgae were larger when co-immobilized. However, the highest starch production was measured in C. sorokiniana immobilized alone and growing continuously in a C-free mineral medium. In this interaction, the initial nutritional condition influenced the time at which the highest accumulation of starch occurred in Chlorella, where the N-free medium induced faster starch production and the richer medium delayed its accumulation. Formation of aggregates made of microalgae and bacteria occurred in all nutritional conditions, with maximum at 83 h in mineral medium, and coincided with declining starch content. This study demonstrates that synthetic mutualism between C. sorokiniana and A. brasilense can be modulated by the initial nutritional condition, mainly by the presence or absence of nitrogen and carbon in the medium in which they are interacting.}, }
@article {pmid30397794, year = {2018}, author = {Lau, NS and Zarkasi, KZ and Md Sah, ASR and Shu-Chien, AC}, title = {Diversity and Coding Potential of the Microbiota in the Photic and Aphotic Zones of Tropical Man-Made Lake with Intensive Aquaculture Activities: a Case Study on Temengor Lake, Malaysia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1283-0}, pmid = {30397794}, issn = {1432-184X}, abstract = {Although freshwater biomes cover less than 1% of the Earth's surface, they have disproportionate ecological significances. Attempts to study the taxonomy and function of freshwater microbiota are currently limited to samples collected from temperate lakes. In this study, we investigated samples from the photic and aphotic of an aquaculture site (disturbed) of Temengor Lake, a tropical lake in comparison with the undisturbed site of the lake using 16S rRNA amplicon and shotgun metagenomic approaches. Vertical changes in bacterial community composition and function of the Temengor Lake metagenomes were observed. The photic water layer of Temengor Lake was dominated by typical freshwater assemblages consisting of Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, and Cyanobacteria lineages. On the other hand, the aphotic water featured in addition to Proteobacteria, Bacteroidetes, Verrucomicrobia, and two more abundant bacterial phyla that are typically ubiquitous in anoxic habitats (Chloroflexi and Firmicutes). The aphotic zone of Temengor Lake exhibited genetic potential for nitrogen and sulfur metabolisms for which terminal electron acceptors other than oxygen are used in the reactions. The aphotic water of the disturbed site also showed an overrepresentation of genes associated with the metabolism of carbohydrates, likely driven by the enrichment of nutrient resulting from aquaculture activities at the site. The results presented in this study can serve as a basis for understanding the structure and functional capacity of the microbial communities in the photic and aphotic zones/water layers of tropical man-made lakes.}, }
@article {pmid30397546, year = {2018}, author = {Md Zoqratt, MZH and Eng, WWH and Thai, BT and Austin, CM and Gan, HM}, title = {Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5826}, doi = {10.7717/peerj.5826}, pmid = {30397546}, issn = {2167-8359}, abstract = {Aquaculture production of the Pacific white shrimp is the largest in the world for crustacean species. Crucial to the sustainable global production of this important seafood species is a fundamental understanding of the shrimp gut microbiota and its relationship to the microbial ecology of shrimp pond. This is especially true, given the recently recognized role of beneficial microbes in promoting shrimp nutrient intake and in conferring resistance against pathogens. Unfortunately, aquaculture-related microbiome studies are scarce in Southeast Asia countries despite the severe impact of early mortality syndrome outbreaks on shrimp production in the region. In this study, we employed the 16S rRNA amplicon (V3-V4 region) sequencing and amplicon sequence variants (ASV) method to investigate the microbial diversity of shrimp guts and pond water samples collected from aquaculture farms located in Malaysia and Vietnam. Substantial differences in the pond microbiota were observed between countries with the presence and absence of several taxa extending to the family level. Microbial diversity of the shrimp gut was found to be generally lower than that of the pond environments with a few ubiquitous genera representing a majority of the shrimp gut microbial diversity such as Vibrio and Photobacterium, indicating host-specific selection of microbial species. Given the high sequence conservation of the 16S rRNA gene, we assessed its veracity at distinguishing Vibrio species based on nucleotide alignment against type strain reference sequences and demonstrated the utility of ASV approach in uncovering a wider diversity of Vibrio species compared to the conventional OTU clustering approach.}, }
@article {pmid30350953, year = {2018}, author = {Cabernard, L and Roscher, L and Lorenz, C and Gerdts, G and Primpke, S}, title = {Comparison of Raman and Fourier Transform Infrared Spectroscopy for the Quantification of Microplastics in the Aquatic Environment.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.8b03438}, pmid = {30350953}, issn = {1520-5851}, abstract = {Microplastics (MPs, <5 mm) have been reported as emerging environmental contaminants, but reliable data are still lacking. We compared the two most promising techniques for MP analysis, namely, Raman and Fourier transform infrared (FTIR) spectroscopy, by analyzing MPs extracted from North Sea surface waters. Microplastics >500 μm were visually sorted and manually analyzed by μ-Raman and attenuated total reflection (ATR)-FTIR spectroscopy. Microplastics ≤500 μm were concentrated on gold-coated filters and analyzed by automated single-particle exploration coupled to μ-Raman (ASPEx-μ-Raman) and FTIR imaging (reflection mode). The number of identified MPs >500 μm was slightly higher for μ-Raman (+23%) than ATR-FTIR analysis. Concerning MPs ≤500 μm, ASPEx-μ-Raman quantified two-times higher MP numbers but required a four-times higher analysis time compared to FTIR imaging. Because ASPEx-μ-Raman revealed far higher MP concentrations (38-2621 particles m-3) compared to the results of previous water studies (0-559 particles m-3), the environmental concentration of MPs ≤500 μm may have been underestimated until now. This may be attributed to the exceptional increase in concentration with decreasing MP size found in this work. Our results demonstrate the need for further research to enable time-efficient routine application of ASPEx-μ-Raman for reliable MP counting down to 1 μm.}, }
@article {pmid30391860, year = {2018}, author = {van der Waals, MJ and Plugge, C and Meima-Franke, M and de Waard, P and Bodelier, PLE and Smidt, H and Gerritse, J}, title = {Ethyl tert-butyl ether (EtBE) degradation by an algal-bacterial culture obtained from contaminated groundwater.}, journal = {Water research}, volume = {148}, number = {}, pages = {314-323}, doi = {10.1016/j.watres.2018.10.050}, pmid = {30391860}, issn = {1879-2448}, abstract = {EtBE is a fuel oxygenate that is synthesized from (bio)ethanol and fossil-based isobutylene, and replaces the fossil-based MtBE. Biodegradation of EtBE to harmless metabolites or end products can reduce the environmental and human health risks after accidental release. In this study, an algal-bacterial culture enriched from contaminated groundwater was used to (i) assess the potential for EtBE degradation, (ii) resolve the EtBE degradation pathway and (iii) characterize the phylogenetic composition of the bacterial community involved in EtBE degradation in contaminated groundwater. In an unamended microcosm, algal growth was observed after eight weeks when exposed to a day-night light cycle. In the fed-batch reactor, oxygen produced by the algae Scenedesmus and Chlorella was used by bacteria to degrade 50 μM EtBE replenishments with a cumulative total of 1250 μM in a day/night cycle (650 lux), over a period of 913 days. The microbial community in the fed-batch reactor degraded EtBE, using a P450 monooxygenase and 2-hydroxyisobutyryl-CoA mutase, to tert-butyl alcohol (TBA), ethanol and CO2 as determined using 13C nuclear magnetic resonance spectroscopy (NMR) and gas chromatography. Stable isotope probing (SIP) with 13C6 labeled EtBE in a fed-batch vessel showed no significant difference in community profiles of the 13C and 12C enriched DNA fractions, with representatives of the families Halomonadaceae, Shewanellaceae, Rhodocyclaceae, Oxalobacteraceae, Comamonadaceae, Sphingomonadaceae, Hyphomicrobiaceae, Candidatus Moranbacteria, Omnitrophica, Anaerolineaceae, Nocardiaceae, and Blastocatellaceae. This is the first study describing micro-oxic degradation of EtBE by an algal-bacterial culture. This algal-bacterial culture has advantages compared with conventional aerobic treatments: (i) a lower risk of EtBE evaporation and (ii) no need for external oxygen supply in the presence of light. This study provides novel leads towards future possibilities to implement algal-bacterial consortia in field-scale groundwater or wastewater treatment.}, }
@article {pmid30390579, year = {2018}, author = {Gómez-Sagasti, MT and Epelde, L and Anza, M and Urra, J and Alkorta, I and Garbisu, C}, title = {The impact of nanoscale zero-valent iron particles on soil microbial communities is soil dependent.}, journal = {Journal of hazardous materials}, volume = {364}, number = {}, pages = {591-599}, doi = {10.1016/j.jhazmat.2018.10.034}, pmid = {30390579}, issn = {1873-3336}, abstract = {The application of nanoscale zero-valent iron particles (nZVI) for the remediation of contaminated sites is very promising. However, information concerning the ecotoxicity of nZVI on soil microbial communities and, hence, soil quality, is still scarce. We carried out a three-month experiment to evaluate the impact of the application of different concentrations of nZVI (from 1 to 20 mg g DW soil-1) on soil microbial properties in a clay-loam versus a sandy-loam soil. Data on microbial biomass (total bacteria and fungi by qPCR, microbial biomass carbon), activity (β-glucosidase, arylsulphatase and urease activities), and functional (Biolog Ecoplates™) and structural (ARISA, 16S rRNA amplicon sequencing) diversity evidenced that the sandy-loam soil was more vulnerable to the presence of nZVI than the clay-loam soil. In the sandy-loam soil, arylsulphatase activity and bacterial abundance, richness and diversity were susceptible to the presence of nZVI. The high content of clay and organic matter present in the clay-loam soil may explain the observed negligible effects of nZVI on soil microbial properties. It was concluded that the impact of nZVI on soil microbial communities and, hence, soil quality, is soil dependent.}, }
@article {pmid30388523, year = {2018}, author = {Zhang, Y and Hua, ZS and Lu, H and Oehmen, A and Guo, J}, title = {Elucidating functional microorganisms and metabolic mechanisms in a novel engineered ecosystem integrating C, N, P and S biotransformation by metagenomics.}, journal = {Water research}, volume = {148}, number = {}, pages = {219-230}, doi = {10.1016/j.watres.2018.10.061}, pmid = {30388523}, issn = {1879-2448}, abstract = {Denitrifying sulfur conversion-associated enhanced biological phosphorous removal (DS-EBPR) system is not only a novel wastewater treatment process, but also an ideal model for microbial ecology in a community context. However, it exists the knowledge gap on the roles and interactions of functional microorganisms in the DS-EBPR system for carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) bioconversions. We use genome-resolved metagenomics to build up an ecological model of microbial communities in a lab-scale DS-EBPR system with stable operation for more than 400 days. Our results yield 11 near-complete draft genomes that represent a substantial portion of the microbial community (39.4%). Sulfate-reducing bacteria (SRB) and sulfide-oxidizing bacteria (SOB) promote complex metabolic processes and interactions for C, N, P and S conversions. Bins 1-4 and 10 are considered as new potential polyphosphate-accumulating organisms (PAOs), in which Bins 1-4 can be considered as S-related PAOs (S-PAOs) with no previously cultivated or reported members. Our findings give an insight into a new ecological system with C, N, P and S simultaneous bioconversions and improve the understanding of interactions among SRB, SOB, denitrifiers and PAOs within a community context.}, }
@article {pmid30387912, year = {2018}, author = {de Nijs, EA and Hicks, LC and Leizeaga, A and Tietema, A and Rousk, J}, title = {Soil microbial moisture dependences and responses to drying-rewetting: the legacy of 18 years drought.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.14508}, pmid = {30387912}, issn = {1365-2486}, abstract = {Climate change will alter precipitation patterns with consequences for soil C cycling. An understanding of how fluctuating soil moisture affects microbial processes is therefore critical to predict responses to future global change. We investigated how long-term experimental field drought influences microbial tolerance to lower moisture levels ('resistance') and ability to recover when rewetted after drought ('resilience'), using soils from a heathland which had been subjected to experimental precipitation reduction during the summer for 18 years. We tested whether drought could induce increased resistance, resilience, and changes in the balance between respiration and bacterial growth during perturbation events, by following a two-tiered approach. We first evaluated the effects of the long-term summer drought on microbial community functioning to drought and drying-rewetting (D/RW), and second tested the ability to alter resistance and resilience through additional perturbation cycles. A history of summer drought in the field selected for increased resilience but not resistance, suggesting that rewetting after drought, rather than low moisture levels during drought, was the selective pressure shaping the microbial community functions. Laboratory D/RW cycles also selected for communities with a higher resilience rather than increased resistance. The ratio of respiration to bacterial growth during D/RW perturbation was lower for the field drought-exposed communities and decreased for both field-treatments during the D/RW cycles. This suggests that cycles of D/RW also structure microbial communities to respond quickly and efficiently to rewetting after drought. Our findings imply that microbial communities can adapt to changing climatic conditions and that this might slow the rate of SOC loss predicted to be induced by future cyclic drought. This article is protected by copyright. All rights reserved.}, }
@article {pmid30386315, year = {2018}, author = {Florez, AM and Suarez-Barrera, MO and Morales, GM and Rivera, KV and Orduz, S and Ochoa, R and Guerra, D and Muskus, C}, title = {Toxic Activity, Molecular Modeling and Docking Simulations of Bacillus thuringiensis Cry11 Toxin Variants Obtained via DNA Shuffling.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2461}, doi = {10.3389/fmicb.2018.02461}, pmid = {30386315}, issn = {1664-302X}, abstract = {The Cry11 family belongs to a large group of δ-endotoxins that share three distinct structural domains. Among the dipteran-active toxins referred to as three-domain Cry11 toxins, the Cry11Aa protein from Bacillus thuringiensis subsp. israelensis (Bti) has been the most extensively studied. Despite the potential of Bti as an effective biological control agent, the understanding of Cry11 toxins remains incomplete. In this study, five Cry11 variants obtained via DNA shuffling displayed toxic activity against Aedes aegypti and Culex quinquefasciatus. Three of these Cry11 variants (8, 23, and 79) were characterized via 3D modeling and analysis of docking with ALP1. The relevant mutations in these variants, such as deletions, insertions and point mutations, are discussed in relation to their structural domains, toxic activities and toxin-receptor interactions. Importantly, deletion of the N-terminal segment in domain I was not associated with any change in toxic activity, and domain III exhibited higher sequence variability than domains I and II. Variant 8 exhibited up to 3.78- and 6.09-fold higher toxicity to A. aegypti than Cry11Bb and Cry11Aa, respectively. Importantly, variant 79 showed an α-helix conformation at the C-terminus and formed crystals retaining toxic activity. These findings indicate that five Cry11 variants were preferentially reassembled from the cry11Aa gene during DNA shuffling. The mutations described in loop 2 and loop 3 of domain II provide valuable information regarding the activity of Cry11 toxins against A. aegypti and C. quinquefasciatus larvae and reveal new insights into the application of directed evolution strategies to study the genetic variability of specific domains in cry11 family genes.}, }
@article {pmid30384950, year = {2018}, author = {Ihekweazu, FD and Versalovic, J}, title = {Development of the Pediatric Gut Microbiome: Impact on Health and Disease.}, journal = {The American journal of the medical sciences}, volume = {356}, number = {5}, pages = {413-423}, doi = {10.1016/j.amjms.2018.08.005}, pmid = {30384950}, issn = {1538-2990}, abstract = {The intestinal microbiota are important in human growth and development. Microbial composition may yield insights into the temporal development of microbial communities and vulnerabilities to disorders of microbial ecology such as recurrent Clostridium difficile infection. Discoveries of key microbiome features of carbohydrate and amino acid metabolism are lending new insights into possible therapies or preventative strategies for inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). In this review, we summarize the current understanding of the development of the pediatric gastrointestinal microbiome, the influence of the microbiome on the developing brain through the gut-brain axis, and the impact of dysbiosis on disease development. Dysbiosis is explored in the context of pediatric allergy and asthma, recurrent C. difficile infection, IBD, IBS, and metabolic disorders. The central premise is that the human intestinal microbiome plays a vital role in health and disease, beginning in the prenatal period and extending throughout childhood.}, }
@article {pmid30379400, year = {2018}, author = {Van Hecke, T and De Vrieze, J and Boon, N and De Vos, WH and Vossen, E and De Smet, S}, title = {Combined Consumption of Beef-Based Cooked Mince and Sucrose Stimulates Oxidative Stress, Cardiac Hypertrophy, and Colonic Outgrowth of Desulfovibrionaceae in Rats.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e1800962}, doi = {10.1002/mnfr.201800962}, pmid = {30379400}, issn = {1613-4133}, abstract = {SCOPE: High consumption of red meat and sucrose increases the epidemiological risk for chronic diseases. Mechanistic hypotheses include alterations in oxidative status, gut microbial composition, fat deposition and low-grade inflammation.<br><br>METHODS AND RESULTS: For two weeks, 40 rats consumed a diet high in white or red meat (chicken-based or beef-based cooked mince respectively), and containing corn starch or sucrose in a 2 × 2 factorial design. Lard was mixed with lean chicken or beef to obtain comparable dietary fatty acid profiles. Beef (vs. chicken)-fed rats had higher lipid oxidation products (malondialdehyde, 4-hydroxy-2-nonenal and hexanal) in stomach content and blood, and lower blood glutathione. Sucrose (vs. corn starch)-fed rats showed increased blood lipid oxidation products and glutathione peroxidase activity, higher liver weight and malondialdehyde concentrations, and mesenterial and retroperitoneal fat accumulation. Beef-sucrose-fed rats had increased cardiac weight, suggesting pathophysiological effects on the cardiovascular system. The colonic microbiome of beef-sucrose-fed rats showed an outgrowth of the sulfate-reducing family of the Desulfovibrionaceae, partly in expense of the Lactobacillus genus, indicating intestinal dysbiosis. Blood C-reactive protein, a marker for inflammation, was not different among groups.<br><br>CONCLUSIONS: Consumption of a cooked beef-based meat product with sucrose increased oxidative stress parameters and promoted cardiac hypertrophy and intestinal dysbiosis. This article is protected by copyright. All rights reserved.}, }
@article {pmid30376889, year = {2018}, author = {Hale, VL and Jeraldo, P and Chen, J and Mundy, M and Yao, J and Priya, S and Keeney, G and Lyke, K and Ridlon, J and White, BA and French, AJ and Thibodeau, SN and Diener, C and Resendis-Antonio, O and Gransee, J and Dutta, T and Petterson, XM and Sung, J and Blekhman, R and Boardman, L and Larson, D and Nelson, H and Chia, N}, title = {Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers.}, journal = {Genome medicine}, volume = {10}, number = {1}, pages = {78}, doi = {10.1186/s13073-018-0586-6}, pmid = {30376889}, issn = {1756-994X}, support = {R01CA179243//National Institutes of Health/ ; R01CA170357//National Institutes of Health/ ; P30DK084567//National Institute of Diabetes and Digestive and Kidney Diseases/ ; U24DK100469//Mayo Clinic Metabolomics Resource Core/ ; }, abstract = {BACKGROUND: Links between colorectal cancer (CRC) and the gut microbiome have been established, but the specific microbial species and their role in carcinogenesis remain an active area of inquiry. Our understanding would be enhanced by better accounting for tumor subtype, microbial community interactions, metabolism, and ecology.<br><br>METHODS: We collected paired colon tumor and normal-adjacent tissue and mucosa samples from 83 individuals who underwent partial or total colectomies for CRC. Mismatch repair (MMR) status was determined in each tumor sample and classified as either deficient MMR (dMMR) or proficient MMR (pMMR) tumor subtypes. Samples underwent 16S rRNA gene sequencing and a subset of samples from 50 individuals were submitted for targeted metabolomic analysis to quantify amino acids and short-chain fatty acids. A PERMANOVA was used to identify the biological variables that explained variance within the microbial communities. dMMR and pMMR microbial communities were then analyzed separately using a generalized linear mixed effects model that accounted for MMR status, sample location, intra-subject variability, and read depth. Genome-scale metabolic models were then used to generate microbial interaction networks for dMMR and pMMR microbial communities. We assessed global network properties as well as the metabolic influence of each microbe within the dMMR and pMMR networks.<br><br>RESULTS: We demonstrate distinct roles for microbes in dMMR and pMMR CRC. Bacteroides fragilis and sulfidogenic Fusobacterium nucleatum were significantly enriched in dMMR CRC, but not pMMR CRC. These findings were further supported by metabolic modeling and metabolomics indicating suppression of B. fragilis in pMMR CRC and increased production of amino acid proxies for hydrogen sulfide in dMMR CRC.<br><br>CONCLUSIONS: Integrating tumor biology and microbial ecology highlighted distinct microbial, metabolic, and ecological properties unique to dMMR and pMMR CRC. This approach could critically improve our ability to define, predict, prevent, and treat colorectal cancers.}, }
@article {pmid30375646, year = {2018}, author = {Philip, N and Walsh, L}, title = {The potential ecological effects of Casein Phosphopeptide-Amorphous Calcium Phosphate in dental caries prevention.}, journal = {Australian dental journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/adj.12661}, pmid = {30375646}, issn = {1834-7819}, abstract = {Contemporary caries prevention protocols recommend not only effective remineralizing agents but also ecological measures to reverse the dental plaque dysbiosis responsible for the disease pathogenesis. There is a high-level of evidence supporting the remineralizing efficacy of Casein Phosphopeptide-Amorphous Calcium Phosphate (CPP-ACP) from studies around the world. There is now emerging evidence that CPP-ACP may also have a beneficial influence on the dental plaque microbial ecology and homeostasis. The ecological cariostatic effects of CPP-ACP are believed to be mediated predominantly through its anti-adhesion, buffering, and biofilm disrupting actions. This review principally discusses the ecological mechanisms of CPP-ACP and presents the current evidence for its effects on the oral microbiome ecology. This article is protected by copyright. All rights reserved.}, }
@article {pmid30374168, year = {2018}, author = {Reese, AT and Pereira, FC and Schintlmeister, A and Berry, D and Wagner, M and Hale, LP and Wu, A and Jiang, S and Durand, HK and Zhou, X and Premont, RT and Diehl, AM and O'Connell, TM and Alberts, SC and Kartzinel, TR and Pringle, RM and Dunn, RR and Wright, JP and David, LA}, title = {Microbial nitrogen limitation in the mammalian large intestine.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-018-0267-7}, pmid = {30374168}, issn = {2058-5276}, abstract = {Resource limitation is a fundamental factor governing the composition and function of ecological communities. However, the role of resource supply in structuring the intestinal microbiome has not been established and represents a challenge for mammals that rely on microbial symbionts for digestion: too little supply might starve the microbiome while too much might starve the host. We present evidence that microbiota occupy a habitat that is limited in total nitrogen supply within the large intestines of 30 mammal species. Lowering dietary protein levels in mice reduced their faecal concentrations of bacteria. A gradient of stoichiometry along the length of the gut was consistent with the hypothesis that intestinal nitrogen limitation results from host absorption of dietary nutrients. Nitrogen availability is also likely to be shaped by host-microbe interactions: levels of host-secreted nitrogen were altered in germ-free mice and when bacterial loads were reduced via experimental antibiotic treatment. Single-cell spectrometry revealed that members of the phylum Bacteroidetes consumed nitrogen in the large intestine more readily than other commensal taxa did. Our findings support a model where nitrogen limitation arises from preferential host use of dietary nutrients. We speculate that this resource limitation could enable hosts to regulate microbial communities in the large intestine. Commensal microbiota may have adapted to nitrogen-limited settings, suggesting one reason why excess dietary protein has been associated with degraded gut-microbial ecosystems.}, }
@article {pmid30372571, year = {2018}, author = {Nottingham, AT and Bååth, E and Reischke, S and Salinas, N and Meir, P}, title = {Adaptation of soil microbial growth to temperature: using a tropical elevation gradient to predict future changes.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.14502}, pmid = {30372571}, issn = {1365-2486}, abstract = {Terrestrial biogeochemical feedbacks to the climate are strongly modulated by the temperature response of soil microorganisms. Tropical forests, in particular, exert a major influence on global climate because they are the most productive terrestrial ecosystem. We used an elevation gradient across tropical forest in the Andes (a gradient of 20°C mean annual temperature, MAT), to test whether soil bacterial and fungal community growth responses are adapted to long-term temperature differences. We evaluated the temperature dependency of soil bacterial and fungal growth using the leucine- and acetate-incorporation methods, respectively, and determined indices for the temperature response of growth: Q10 and Tmin (the minimum temperature for growth). For both bacterial and fungal communities, increased MAT (decreased elevation) resulted in increases in Q10 and Tmin of growth. Across a MAT range from 6°C to 26°C, the Q10 and Tmin varied for bacterial growth (Q10-20 = 2.4 to 3.5; Tmin = -8°C to -1.5°C) and fungal growth (Q10-20 = 2.6 to 3.6; Tmin = -6°C to -1°C). Thus, bacteria and fungi did not differ in their growth temperature responses with changes in MAT. Our findings indicate that across natural temperature gradients, each increase in MAT by 1°C results in increases in Tmin of microbial growth by approximately 0.3°C and Q10-20 by 0.05, consistent with long-term temperature adaptation of soil microbial communities. A 2°C warming would increase microbial activity across a MAT gradient of 6°C to 26°C by 28% to 15%, respectively, and temperature adaptation of microbial communities would further increase activity by 1.2% to 0.3%. The impact of warming on microbial activity, and the related impact on soil carbon cycling, is thus greater in regions with lower MAT. These results can be used to predict future changes in the temperature response of microbial activity over different levels of warming and over large temperature ranges, extending to tropical regions. This article is protected by copyright. All rights reserved.}, }
@article {pmid30370317, year = {2018}, author = {Cooper, R and Tsimring, L and Hasty, J}, title = {Microfluidics-Based Analysis of Contact-dependent Bacterial Interactions.}, journal = {Bio-protocol}, volume = {8}, number = {16}, pages = {}, doi = {10.21769/BioProtoc.2970}, pmid = {30370317}, issn = {2331-8325}, abstract = {Bacteria in nature live in complex communities with multiple cell types and spatially-dependent interactions. Studying cells in well-mixed environments such as shaking culture tubes or flasks cannot capture these spatial dynamics, but cells growing in full-fledged biofilms are difficult to observe in real time. We present here a protocol for observing time-resolved, multi-species interactions at single-cell resolution. The protocol involves growing bacterial cells in a near monolayer in a microfluidic device. As a demonstration, we describe in particular observing the dynamic interactions between E. coli and Acinetobacter baylyi. In this case, the protocol is capable of observing both contact-dependent lysis of E. coli by A. baylyi via the Type VI Secretion System (T6SS) and subsequent functional horizontal gene transfer (HGT) of genes from E. coli to A. baylyi.}, }
@article {pmid30369284, year = {2018}, author = {Braga, RM and Padilla, G and Araújo, WL}, title = {The biotechnological potential of Epicoccum spp.: diversity of secondary metabolites.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-20}, doi = {10.1080/1040841X.2018.1514364}, pmid = {30369284}, issn = {1549-7828}, abstract = {Epicoccum is a genus of ubiquitous fungi typically found in air, in soil, and on decaying vegetation. They also commonly display an endophytic lifestyle and are isolated from diverse plant tissues. The fungi from the genus Epicoccum are mainly known for their use as biocontrol agents against phytopathogens and for their ability to produce many secondary metabolites with potential biotechnological applications, such as antioxidant, anticancer,r and antimicrobial compounds. Among the bioactive compounds produced by Epicoccum spp., epicocconone is a commercially available fluorophore, D8646-2-6 is a patented telomerase inhibitor, and taxol is an anticancer drug originally isolated from Taxus brevifolia. Epicoccum spp. also produces epicolactone, an antimicrobial compound with a unique and complex structure that has aroused considerable interest in the chemical-synthesis community. The main goal of the present review is to discuss the diversity of secondary metabolites produced by Epicoccum spp., their biotechnological applications, and proposed hypothetical biosynthesis. In addition, the use of Epicoccum spp. as biocontrol agents and the pigments produced by these fungi are also discussed.}, }
@article {pmid30368967, year = {2018}, author = {Feng, Y and Chen, R and Stegen, JC and Guo, Z and Zhang, J and Li, Z and Lin, X}, title = {Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.14914}, pmid = {30368967}, issn = {1365-294X}, abstract = {Belowground microbial communities strongly influence ecosystem function such that predicting function may rely on understanding ecological processes that assemble communities. Uncertainty remains, however, in what governs the relative contributions of different ecological processes. To help fill this knowledge gap we test the general hypothesis that both initial state and degree of change in environmental conditions govern the relative contributions of different ecological assembly processes. To do so we leveraged regional-scale nutrient and organic matter addition experiments and used soil organic matter (SOM) as a proxy of integrated soil environmental conditions. Consistent with our hypothesis, we found that both the initial amount of SOM and the degree of change in SOM-in response to nutrient addition-influenced the relative contributions of different ecological assembly processes. These influences were most clearly observed at the regional scale, suggesting potential scale dependence. More specifically, nutrient additions homogenized bacterial community composition due to enhanced influences of homogenizing dispersal when SOM content was initially high. In contrast, nutrient additions led to divergence in community composition due to variable selection when initial SOM was low and/or when SOM increased significantly in response to nutrient additions. Our findings indicate important connections among initial conditions, degree of change in environmental variables, and microbial community assembly processes that may influence ecosystem processes. These conceptual inferences highlight a need to strengthen connections between ecological theory and biogeochemical modeling. This article is protected by copyright. All rights reserved.}, }
@article {pmid30368524, year = {2018}, author = {Li, X and Jousset, A and de Boer, W and Carrión, VJ and Zhang, T and Wang, X and Kuramae, EE}, title = {Legacy of land use history determines reprogramming of plant physiology by soil microbiome.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-018-0300-0}, pmid = {30368524}, issn = {1751-7370}, abstract = {Microorganisms associated with roots are thought to be part of the so-called extended plant phenotypes with roles in the acquisition of nutrients, production of growth hormones, and defense against diseases. Since the crops selectively enrich most rhizosphere microbes out of the bulk soil, we hypothesized that changes in the composition of bulk soil communities caused by agricultural management affect the extended plant phenotype. In the current study, we performed shotgun metagenome sequencing of the rhizosphere microbiome of the peanut (Arachis hypogaea) and metatranscriptome analysis of the roots of peanut plants grown in the soil with different management histories, peanut monocropping and crop rotation. We found that the past planting record had a significant effect on the assembly of the microbial community in the peanut rhizosphere, indicating a soil memory effect. Monocropping resulted in a reduction of the rhizosphere microbial diversity, an enrichment of several rare species, and a reduced representation of traits related to plant performance, such as nutrients metabolism and phytohormone biosynthesis. Furthermore, peanut plants in monocropped soil exhibited a significant reduction in growth coinciding with a down-regulation of genes related to hormone production, mainly auxin and cytokinin, and up-regulation of genes related to the abscisic acid, salicylic acid, jasmonic acid, and ethylene pathways. These findings suggest that land use history affects crop rhizosphere microbiomes and plant physiology.}, }
@article {pmid30367681, year = {2018}, author = {Lian, Y and Yang, J and Lian, Y and Xiao, C and Hu, X and Xu, H}, title = {DUXAP8, a pseudogene derived lncRNA, promotes growth of pancreatic carcinoma cells by epigenetically silencing CDKN1A and KLF2.}, journal = {Cancer communications (London, England)}, volume = {38}, number = {1}, pages = {64}, doi = {10.1186/s40880-018-0333-9}, pmid = {30367681}, issn = {2523-3548}, support = {81602052//the National Natural Science Foundation of China/ ; 8160100460//the National Natural Science Foundation of China/ ; 8157040399//the National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Recent studies highlight pseudogene derived long non-coding RNAs (lncRNAs) as key regulators of cancer biology. However, few of them have been well characterized in pancreatic cancer. Here, we aimed to identify the association between pseudogene derived lncRNA DUXAP8 and growth of pancreatic cancer cells.<br><br>METHODS: We screened for pseudogene derived lncRNAs associated with human pancreatic cancer by comparative analysis of three independent datasets from GEO. Quantitative real-time reverse transcription polymerase chain reaction was used to assess the relative expression of DUXAP8 in pancreatic cancer tissues and cells. Loss-of-function approaches were used to investigate the potential functional roles of DUXAP8 in pancreatic cancer cell proliferation and apoptosis in vitro and in vivo. RNA immunoprecipitation, chromosome immunoprecipitation assay and rescue experiments were performed to analyze the association of DUXAP8 with target proteins and genes in pancreatic cancer cells.<br><br>RESULTS: Pancreatic cancer tissues had significantly higher DUXAP8 levels than paired adjacent normal tissues. High DUXAP8 expression was associated with a larger tumor size, advanced pathological stage and shorter overall survival of pancreatic cancer patients. Moreover, silencing DUXAP8 expression by siRNA or shRNA inhibited pancreatic cancer cell proliferation and promoted apoptosis in vitro and in vivo. Mechanistic analyses indicated that DUXAP8 regulates PC cell proliferation partly through downregulation of tumor suppressor CDKN1A and KLF2 expression.<br><br>CONCLUSION: Our results suggest that tumor expression of pseudogene derived lncRNA DUXAP8 plays an important role in pancreatic cancer progression. DUXAP8 may serve as a candidate biomarker and represent a novel therapeutic target of pancreatic cancer.}, }
@article {pmid30367007, year = {2018}, author = {Ren, L and Song, X and He, D and Wang, J and Tan, M and Xia, X and Li, G and Tan, Y and Wu, QL}, title = {Bacterioplankton metacommunity processes across thermal gradients: weaker species sorting but stronger niche segregation in summer than in winter subtropical bay.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02088-18}, pmid = {30367007}, issn = {1098-5336}, abstract = {Thermal effluents from nuclear power plants greatly change the environmental and ecological conditions of the receiving marine water body, but knowledge about their impact on microbial ecology is limited. Here, we used high-throughput sequencing of 16S rRNA gene to examine marine bacterioplankton metacommunity assembly across thermal gradients in two representative seasons (i.e., winter and summer) in subtropical bay locating on the northern coast of the South China Sea. We found high heterogeneity in bacterioplankton community compositions (BCCs) across thermal gradients and between seasons. The spatially structured temperature gradient created by thermal effluents was the key determinant of BCC, but its influence differed by season. Using a metacommunity approach, we found that in the thermal discharge area, i.e., where water frequently exchanges with surrounding seawater and thermal effluent water, the BCC spatial patterns were shaped by species sorting rather than mass effects from surrounding seawater or dilution of thermal effluent water by surrounding seawater. However, this effect of species sorting was weaker in summer than in winter seawater. In both seasons, bacterioplankton community structure was predominately determined by niche sharing; however, the relative importance of niche segregation was enhanced in summer seawater. Our findings suggest that for the seasonal differences in metacommunity processes, BCCs of subtropical summer seawater were more sensitive to temperature and were more difficult to predict than those of winter seawater in face of different intensity of thermal impacts.IMPORTANCE Understanding the mechanisms of bacterial community assembly across environmental gradients is one of the major goals of marine microbial ecology. Thermal effluents off two nuclear power plants in subtropical Daya Bay have been present for more than 20 years and have generated a comparatively stable and long thermal gradient (a temperature increase from 0 to 10°C). The environment patches across thermal gradients are heterogeneous and very strongly interconnected on a microbial scale, thus it is a useful model to study metacommunity processes (i.e., patch dynamics, species sorting, mass effects, and neutral processes) that underlie marine bacterioplankton assembly. The significance of our research is to understand how environmental conditions and dispersal-related processes interact to influence bacterioplankton metacommunity processes and their seasonal differences across thermal gradients. Our results may advance the understanding of marine microbial ecology under future global warming.}, }
@article {pmid30367000, year = {2018}, author = {Šulčius, S and Šimoliūnas, E and Alzbutas, G and Gasiūnas, G and Jauniškis, V and Kuznecova, J and Miettinen, S and Nilsson, E and Meškys, R and Roine, E and Paškauskas, R and Holmfeldt, K}, title = {Genomic characterization of cyanophage vB_AphaS-CL131 infecting filamentous diazotrophic cyanobacterium Aphanizomenon flos-aquae reveals novel insights into virus-bacterium interactions.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.01311-18}, pmid = {30367000}, issn = {1098-5336}, abstract = {While filamentous cyanobacteria play a crucial role in food web dynamics and biogeochemical cycling of many aquatic ecosystems around the globe, the knowledge regarding phages infecting them is limited. Here we describe the complete genome of the virulent cyanophage vB_AphaS-CL131 (CL 131), a Siphoviridae phage that infects filamentous diazotrophic bloom forming cyanobacterium Aphanizomenon flos-aquae in the brackish Baltic Sea. CL 131 features a 112793 bp dsDNA genome, encompassing 149 putative open reading frames (ORFs), of which the majority (86%) lack sequence homology to genes with known functions in other bacteriophages or bacteria. Phylogenetic analysis revealed that CL 131 possibly represents a new evolutionary lineage within the group of cyanophages infecting filamentous cyanobacteria, which form a separate cluster compared to phages infecting unicellular cyanobacteria. CL 131 encodes a putative type V-U2 CRISPR-Cas system with one spacer (out of 10) targeting a DNA primase pseudogene in a cyanobacterium and a putative type II toxin-antitoxin system, consisting of GNAT family N-acetyltransferase and a protein of unknown function containing the PRK09726 domain (characteristic of HipB antitoxins). Comparison of CL 131 proteins to reads from Baltic Sea and other available fresh- and brackish-water metagenomes and analysis of CRISPR-Cas arrays in publicly available A. flos-aquae genomes demonstrated that phages similar to CL 131 are present and dynamic in the Baltic Sea and share common history with their hosts dating back at least several decades. In addition, different CRISPR-Cas systems within individual A. flos-aquae genomes targeted several sequences in the CL 131 genome, including genes related to virion structure and morphogenesis. Altogether, these findings revealed new genomic information for exploring viral diversity and provide a model system for investigation of virus-host interactions in filamentous cyanobacteria.Importance The genomic characterization of novel cyanophage vB_AphaS-CL131 and the analysis of its genomic features in the context of other viruses, metagenomic data and host CRISPR-Cas systems contribute toward better understanding of aquatic viral diversity and distribution in general and brackish water cyanophages infecting filamentous diazotrophic cyanobacteria in the Baltic Sea in particular. The results of this study revealed previously undescribed features of cyanophage genomes (e.g. self-excising intein-containing putative dCTP deaminase, putative cyanophage-encoded CRISPR-Cas and toxin-antitoxin systems) and can therefore be used to predict potential interactions between bloom-forming cyanobacteria and their cyanophages.}, }
@article {pmid30366996, year = {2018}, author = {De Filippis, F and La Storia, A and Villani, F and Ercolini, D}, title = {Strain-level diversity analysis of Pseudomonas fragi after in situ pangenome reconstruction shows distinctive spoilage-associated metabolic traits clearly selected by different storage conditions.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02212-18}, pmid = {30366996}, issn = {1098-5336}, abstract = {Microbial spoilage of raw meat causes huge economic losses every year. Understanding the microbial ecology associated to the spoilage and its dynamics during refrigerated storage of meat can help in preventing and delaying the spoilage-related activities. Raw meat microbiota is usually complex but only few members will develop during storage and cause spoilage, upon the pressure of several external factors, such as temperature and oxygen availability. We characterized the metagenome of beef packed aerobically or under-vacuum during refrigerated storage to explore how different packaging conditions may influence microbial composition and potential spoilage-associated activities. Different population dynamics and spoilage-associated genomic repertoires occurred in beef stored in air or vacuum-packaging. Moreover, pangenomics of Pseudomonas fragi strains extracted from metagenomes was carried out. We demonstrated the presence of specific, storage-driven strain-level profiles of Pseudomonas fragi, characterized by a different gene repertoire, thus potentially able to act differently during meat spoilage. The results provide new knowledge on strain-level microbial ecology associated to meat spoilage and can be of value for future strategies of spoilage prevention and food waste reduction.IMPORTANCE This work provides insights on the mechanisms involved in raw beef spoilage during refrigerated storage and on the selective pressure exerted by the packaging conditions. We highlighted the presence of different microbial metagenomes during spoilage of beef packaged aerobically or under-vacuum. The packaging condition was able to select specific Pseudomonas fragi strains, with a distinctive genomic repertoire. This study may help in deciphering the behaviour of different biomes directly in-situ in food and in understanding the specific contribution of different strains to food spoilage.}, }
@article {pmid30366260, year = {2018}, author = {Sharma, S and Tripathi, P}, title = {Gut microbiome and type 2 diabetes: where we are and where to go?.}, journal = {The Journal of nutritional biochemistry}, volume = {63}, number = {}, pages = {101-108}, doi = {10.1016/j.jnutbio.2018.10.003}, pmid = {30366260}, issn = {1873-4847}, abstract = {Type 2 diabetes mellitus (T2D) is a highly prevalent metabolic disorder characterized by an imbalance in blood glucose level, altered lipid profile and high blood pressure. Genetic constituents, high-fat and high-energy dietary habits, and a sedentary lifestyle are three major factors that contribute to high risk of T2D. Several studies have reported gut microbiome dysbiosis as a factor in rapid progression of insulin resistance in T2D that accounts for about 90% of all diabetes cases worldwide. The gut microbiome dysbiosis may reshape intestinal barrier functions and host metabolic and signaling pathways, which are directly or indirectly related to the insulin resistance in T2D. Thousands of the metabolites derived from microbes interact with the epithelial, hepatic and cardiac cell receptors that modulate host physiology. Xenobiotics including dietary components, antibiotics and nonsteroidal anti-inflammatory drugs strongly affect the gut microbial composition and can promote dysbiosis. Any change in the gut microbiota can shift the host metabolism towards increased energy harvest during diabetes and obesity. However, the exact mechanisms behind the dynamics of gut microbes and their impact on host metabolism at the molecular level are yet to be deciphered. We reviewed the published literature for better understanding of the dynamics of gut microbiota, factors that potentially induce gut microbiome dysbiosis and their relation to the progression of T2D. Special emphasis was also given to understand the gut microbiome induced breaching of intestinal barriers and/or tight junctions and their relation to insulin resistance.}, }
@article {pmid30362214, year = {2018}, author = {Götz, F and Pjevac, P and Markert, S and McNichol, J and Becher, D and Schweder, T and Mussmann, M and Sievert, SM}, title = {Transcriptomic and Proteomic Insight into the Mechanism of Cyclooctasulfur- versus Thiosulfate-Oxidation by the Chemolithoautotroph Sulfurimonas denitrificans.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14452}, pmid = {30362214}, issn = {1462-2920}, abstract = {Chemoautotrophic bacteria belonging to the genus Sulfurimonas (class Campylobacteria) were previously identified as key players in the turnover of zero-valence sulfur, a central intermediate in the marine sulfur cycle. S. denitrificans was further shown to be able to oxidize cyclooctasulfur (S8). However, at present the mechanism of activation and metabolism of cyclooctasulfur is not known. Here, we assessed the transcriptome and proteome of S. denitrificans grown with either thiosulfate or S8 as the electron donor. While the overall expression profiles under the two growth conditions were rather similar, distinct differences were observed that could be attributed to the utilization of S8 . This included a higher abundance of expressed genes related to surface attachment in the presence of S8 , and the differential regulation of the sulfur-oxidation multienzyme complex (SOX), which in S. denitrificans is encoded in two gene clusters: soxABXY1 Z1 and soxCDY2 Z2 . While the proteins of both clusters were present with thiosulfate, only proteins of the soxCDY2 Z2 were detected at significant levels with S8 . Based on these findings a model for the oxidation of S8 is proposed. Our results have implications for interpreting metatranscriptomic and -proteomic data and for the observed high level of diversification of soxY2 Z2 among sulfur-oxidizing Campylobacteria. This article is protected by copyright. All rights reserved.}, }
@article {pmid30362076, year = {2018}, author = {Almeida, OGG and De Martinis, ECP}, title = {Bioinformatics tools to assess metagenomic data for applied microbiology.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-018-9464-9}, pmid = {30362076}, issn = {1432-0614}, support = {17/13759-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 6762/2006-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; }, abstract = {The reduction of the price of DNA sequencing has resulted in the emergence of large data sets to handle and analyze, especially in microbial ecosystems, which are characterized by high taxonomic and functional diversities. To assess the properties of these complex ecosystems, a conceptual background of the application of NGS technology and bioinformatics analysis to metagenomics is required. Accordingly, this article presents an overview of the evolution of knowledge of microbial ecology from traditional culture-dependent methods to culture-independent methods and the last frontier in knowledge, metagenomics. Topics that will be covered include sample preparation for NGS, starting with total DNA extraction and library preparation, followed by a brief discussion of the chemistry of NGS to help provide an understanding of which bioinformatics pipeline approach may be helpful for achieving a researcher's goals. The importance of selecting appropriate sequencing coverage and depth parameters to obtain a suitable measure of microbial diversity is discussed. As all DNA sequencing processes produce base-calling errors that compromise data analysis, including genome assembly and microbial functional analysis, dedicated software is presented and conceptually discussed with regard to potential applications in the general microbial ecology field.}, }
@article {pmid30359366, year = {2018}, author = {Bosmans, L and Pozo, MI and Verreth, C and Crauwels, S and Wilberts, L and Sobhy, IS and Wäckers, F and Jacquemyn, H and Lievens, B}, title = {Habitat-specific variation in gut microbial communities and pathogen prevalence in bumblebee queens (Bombus terrestris).}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0204612}, doi = {10.1371/journal.pone.0204612}, pmid = {30359366}, issn = {1932-6203}, abstract = {Gut microbial communities are critical for the health of many insect species. However, little is known about how gut microbial communities respond to anthropogenic changes and how such changes affect host-pathogen interactions. In this study, we used deep sequencing to investigate and compare the composition of gut microbial communities within the midgut and ileum (both bacteria and fungi) in Bombus terrestris queens collected from natural (forest) and urbanized habitats. Additionally, we investigated whether the variation in gut microbial communities under each habitat affected the prevalence of two important bumblebee pathogens that have recently been associated with Bombus declines (Crithidia bombi and Nosema bombi). Microbial community composition differed strongly among habitat types, both for fungi and bacteria. Fungi were almost exclusively associated with bumblebee queens from the forest habitats, and were not commonly detected in bumblebee queens from the urban sites. Further, gut bacterial communities of urban B. terrestris specimens were strongly dominated by bee-specific core bacteria like Snodgrassella (Betaproteobacteria) and Gilliamella (Gammaproteobacteria), whereas specimens from the forest sites contained a huge fraction of environmental bacteria. Pathogen infection was very low in urban populations and infection by Nosema was only observed in specimens collected from forest habitats. No significant relationship was found between pathogen prevalence and microbial gut diversity. However, there was a significant and negative relationship between prevalence of Nosema and relative abundance of the core resident Snodgrassella, supporting its role in pathogen defense. Overall, our results indicate that land-use change may lead to different microbial gut communities in bumblebees, which may have implications for bumblebee health, survival and overall fitness.}, }
@article {pmid30357428, year = {2018}, author = {Kamitani, M and Nagano, AJ and Honjo, MN and Kudoh, H}, title = {A Survey on Plant Viruses in Natural Brassicaceae Communities Using RNA-Seq.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1271-4}, pmid = {30357428}, issn = {1432-184X}, support = {JP26221106//KAKENHI/ ; 16H06171//KAKENHI/ ; JP16H01473//KAKENHI/ ; JPMJCR15O1//Core Research for Evolutional Science and Technology/ ; JPMJCR15O2//Core Research for Evolutional Science and Technology/ ; 15J00628//Grant-in-Aid for JSPS Fellows/ ; }, abstract = {Studies on plant viruses are biased towards crop diseases and little is known about viruses in natural vegetation. We conducted extensive surveys of plant viruses in wild Brassicaceae plants occurring in three local plant communities in central Japan. We applied RNA-Seq with selective depletion of rRNA, which allowed us to detect infections of all genome-reported viruses simultaneously. Infections of Turnip mosaic virus (TuMV), Cucumber mosaic virus (CMV), Brassica yellows virus, Pelargonium zonate spot virus, and Arabidopsis halleri partitivirus 1 were detected from the two perennial species, Arabidopsis halleri subsp. gemmifera and Rorippa indica. De novo assembly further detected partial sequences of a putative novel virus in Arabis fragellosa. Virus species composition and infection rate differed depending on site and plant species. Viruses were most frequently detected from the perennial clonal plant, A. halleri, in which a high clonal transmission rate of viruses across multiple years was confirmed. Phylogenetic analysis of TuMV and CMV showed that virus strains from wild Brassicaceae were included as a major clade of these viruses with other reported strains from crop plants, suggesting that viruses were shared among wild plants and crops. Our studies indicated that distribution of viruses in natural plant populations are determined by the combinations of life histories of viruses and hosts. Revealing viral distribution in the natural plant communities improves our knowledge on the ecology of plant viruses.}, }
@article {pmid30357425, year = {2018}, author = {Li, CX and Fan, YF and Luan, W and Dai, Y and Wang, MX and Wei, CM and Wang, Y and Tao, X and Mao, P and Ma, XR}, title = {Titanium Ions Inhibit the Bacteria in Vase Solutions of Freshly Cut Gerbera jamesonii and Extend the Flower Longevity.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1273-2}, pmid = {30357425}, issn = {1432-184X}, support = {2017YFD0201301//National Key Research and Development Program of China/ ; 2018NA0027//Key Research and Development Program of Sichuan/ ; }, abstract = {Titanium ions significantly promote plant growth, but the mechanism is still unclear. Cut flowers are ideal materials for the study of plant growth and senescence. In this study, freshly cut Gerbera jamesonii were used to study the effects of titanium ions (8 mg/L) on the flower longevity. Flowering observation showed that the gerbera vase life was significantly prolonged in the presence of titanium ions. Plate colony counts showed that the amounts of bacteria in the vase solution of the control group were approximately 1700 times more than that of titanium ion treatment group. High-throughput sequencing was used to determine the sequences of 16S rRNA gene V3-V4 variable regions of the vase solutions to analyze bacterial species, their average proportions, and absolute abundance. The results showed that the titanium ions reduced the entire bacterial counts as well as altered the absolute abundance of different bacterial species in the vase solution. The most prevalent bacteria were mainly Enterobacteriaceae, Pseudomonas veronii, Pseudomonas sp., Delftia sp., Agrobacterium sp., Sphingobacterium multivorum, Acinetobacter johnsonii, and Clostridiaceae. In combination with plate colony counts, we demonstrated that all the bacterial growths were significantly inhibited by titanium ions, regardless of their average proportions increased or decreased. These results showed that titanium ions could extend effectively the longevity of gerberas and possess the broad-spectrum antibacterial properties. This study provides a basis for further mechanism exploration of titanium ions action and its applications in cut flower preservation and agricultural production.}, }
@article {pmid30355963, year = {2018}, author = {Almendras, K and Leiva, D and Carú, M and Orlando, J}, title = {Carbon Consumption Patterns of Microbial Communities Associated with Peltigera Lichens from a Chilean Temperate Forest.}, journal = {Molecules (Basel, Switzerland)}, volume = {23}, number = {11}, pages = {}, doi = {10.3390/molecules23112746}, pmid = {30355963}, issn = {1420-3049}, support = {11100381 and 1181510//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; }, abstract = {Lichens are a symbiotic association between a fungus and a green alga or a cyanobacterium, or both. They can grow in practically any terrestrial environment and play crucial roles in ecosystems, such as assisting in soil formation and degrading soil organic matter. In their thalli, they can host a wide diversity of non-photoautotrophic microorganisms, including bacteria, which play important functions and are considered key components of the lichens. In this work, using the BioLog® EcoPlate system, we studied the consumption kinetics of different carbon-sources by microbial communities associated with the thallus and the substrate of Peltigera lichens growing in a Chilean temperate rain forest dominated by Nothofagus pumilio. Based on the similarity of the consumption of 31 carbon-sources, three groups were formed. Among them, one group clustered the microbial metabolic profiles of almost all the substrates from one of the sampling sites, which exhibited the highest levels of consumption of the carbon-sources, and another group gathered the microbial metabolic profiles from the lichen thalli with the most abundant mycobiont haplotypes. These results suggest that the lichen thallus has a higher impact on the metabolism of its microbiome than on the microbial community of its substrate, with the latter being more diverse in terms of the metabolized sources and whose activity level is probably related to the availability of soil nutrients. However, although significant differences were detected in the microbial consumption of several carbon-sources when comparing the lichen thallus and the underlying substrate, d-mannitol, l-asparagine, and l-serine were intensively metabolized by both communities, suggesting that they share some microbial groups. Likewise, some communities showed high consumption of 2-hydroxybenzoic acid, d-galacturonic acid, and itaconic acid; these could serve as suitable sources of microorganisms as bioresources of novel bioactive compounds with biotechnological applications.}, }
@article {pmid30355662, year = {2018}, author = {Hird, SM and Ganz, H and Eisen, JA and Boyce, WM}, title = {The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, doi = {10.1128/mSphere.00382-18}, pmid = {30355662}, issn = {2379-5042}, abstract = {Waterfowl, especially ducks of the genus Anas, are natural reservoir species for influenza A virus (IAV). Duck populations contain nearly all the known diversity of IAVs, and the birds are asymptomatic to infection. Previous work established that IAV infection status is correlated with changes in the cloacal microbiome in juvenile mallards. Here, we analyze five Anas species to determine whether these duck species have similar IAV+ and IAV- cloacal microbiomes, or if the relationships among a host, influenza virus, and the microbiome are species specific. We assessed taxonomic composition of the microbiome, alpha diversity, and beta diversity and found very few patterns related to microbiome and infection status across species, while detecting strong differences within species. A host species-specific signal was stronger in IAV- ducks than IAV+ ducks, and the effect size of host species on the microbiome was three times higher in IAV- birds than IAV+ birds. The mallards and the northern shovelers, the species with highest sample sizes but also with differing feeding ecology, showed especially contrasting patterns in microbiome composition, alpha diversity, and beta diversity. Our results indicate that the microbiome may have a unique relationship with influenza virus infection at the species level.IMPORTANCE Waterfowl are natural reservoir species for influenza A virus (IAV). Thus, they maintain high levels of pathogen diversity, are asymptomatic to the infection, and also contribute to the risk of a global influenza pandemic. An individual's microbiome is a critical part in how a vertebrate manages pathogens and illness. Here, we describe the cloacal microbiome of 300 wild ducks, from five species (four with previously undescribed microbiomes), including both IAV-negative and IAV-positive individuals. We demonstrate that there is not one consistent &quot;flu-like&quot; microbiome or response to flu across species. Individual duck species appear to have unique relationships between their microbiomes and IAV, and IAV-negative birds have a stronger tie to host species than the IAV-positive birds. In a broad context, understanding the role of the microbiome in IAV reservoir species may have future implications for avian disease management.}, }
@article {pmid30355348, year = {2018}, author = {Tackmann, J and Arora, N and Schmidt, TSB and Rodrigues, JFM and von Mering, C}, title = {Ecologically informed microbial biomarkers and accurate classification of mixed and unmixed samples in an extensive cross-study of human body sites.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {192}, doi = {10.1186/s40168-018-0565-6}, pmid = {30355348}, issn = {2049-2618}, support = {31003A-160095//Swiss National Science Foundation/ ; }, abstract = {BACKGROUND: The identification of body site-specific microbial biomarkers and their use for classification tasks have promising applications in medicine, microbial ecology, and forensics. Previous studies have characterized site-specific microbiota and shown that sample origin can be accurately predicted by microbial content. However, these studies were usually restricted to single datasets with consistent experimental methods and conditions, as well as comparatively small sample numbers. The effects of study-specific biases and statistical power on classification performance and biomarker identification thus remain poorly understood. Furthermore, reliable detection in mixtures of different body sites or with noise from environmental contamination has rarely been investigated thus far. Finally, the impact of ecological associations between microbes on biomarker discovery was usually not considered in previous work.<br><br>RESULTS: Here we present the analysis of one of the largest cross-study sequencing datasets of microbial communities from human body sites (15,082 samples from 57 publicly available studies). We show that training a Random Forest Classifier on this aggregated dataset increases prediction performance for body sites by 35% compared to a single-study classifier. Using simulated datasets, we further demonstrate that the source of different microbial contributions in mixtures of different body sites or with soil can be detected starting at 1% of the total microbial community. We apply a biomarker selection method that excludes indirect environmental associations driven by microbe-microbe associations, yielding a parsimonious set of highly predictive taxa including novel biomarkers and excluding many previously reported taxa. We find a considerable fraction of unclassified biomarkers (&quot;microbial dark matter&quot;) and observe that negatively associated taxa have a surprisingly high impact on classification performance. We further detect a significant enrichment of rod-shaped, motile, and sporulating taxa for feces biomarkers, consistent with a highly competitive environment.<br><br>CONCLUSIONS: Our machine learning model shows strong body site classification performance, both in single-source samples and mixtures, making it promising for tasks requiring high accuracy, such as forensic applications. We report a core set of ecologically informed biomarkers, inferred across a wide range of experimental protocols and conditions, providing the most concise, general, and least biased overview of body site-associated microbes to date.}, }
@article {pmid30353678, year = {2018}, author = {Tan, CK and Ikhsan, NFM and Suyub, IB and Edward, MJ and Kaman, N and Samsudin, AA}, title = {Comparative study of gut microbiota in wild and captive Malaysian Mahseer (Tor tambroides).}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e00734}, doi = {10.1002/mbo3.734}, pmid = {30353678}, issn = {2045-8827}, support = {FP0311B011//Ministry of Science, Technology and Innovation (MOSTI) of Malaysia/ ; }, abstract = {AIMS: The aim of this study was to identify and compare the gut microbial community of wild and captive Tor tambroides through 16S rDNA metagenetic sequencing followed by functions prediction.<br><br>METHODS AND RESULTS: The library of 16S rDNA V3-V4 hypervariable regions of gut microbiota was amplified and sequenced using Illumina MiSeq. The sequencing data were analyzed using Quantitative Insights into Microbial Ecology (QIIME) pipeline and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). The most abundant bacterial phyla in both wild and captive T. tambroides were Firmicutes, Proteobacteria, Fusobacteria and Bacteroidetes. Cetobacterium spp., Peptostreptococcaceae family, Bacteroides spp., Phosphate solubilizing bacteria PSB-M-3, and Vibrio spp. were five most abundant OTU in wild T. tambroides as compared to Cetobacterium spp., Citrobacter spp., Aeromonadaceae family, Peptostreptococcaceae family and Turicibacter spp. in captive T. tambroides.<br><br>CONCLUSION: In this study, the specimens of the wild T. tambroides contain more diverse gut microbiota than of the captive ones. The results suggested that Cetobacterium spp. is one of the core microbiota in guts of T. tambroides. Besides, high abundant Bacteroides spp., Citrobacter spp., Turicibacter spp., and Bacillus spp. may provide important functions in T. tambroides guts.<br><br>The results of this study provide significant information of T. tambroides gut microbiota for further understanding of their physiological functions including growth and disease resistance.}, }
@article {pmid30352731, year = {2018}, author = {De Vrieze, J and Colica, G and Pintucci, C and Sarli, J and Pedizzi, C and Willeghems, G and Bral, A and Varga, S and Prat, D and Peng, L and Spiller, M and Buysse, J and Colsen, J and Benito, O and Carballa, M and Vlaeminck, SE}, title = {Resource recovery from pig manure via an integrated approach: A technical and economic assessment for full-scale applications.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.biortech.2018.10.024}, pmid = {30352731}, issn = {1873-2976}, abstract = {Intensive livestock farming cannot be uncoupled from the massive production of manure, requiring adequate management to avoid environmental damage. The high carbon, nitrogen and phosphorus content of pig manure enables targeted resource recovery. Here, fifteen integrated scenarios for recovery of water, nutrients and energy are compared in terms of technical feasibility and economic viability. The recovery of refined nutrients with a higher market value and quality, i.e., (NH4)2SO4 for N and struvite for P, coincided with higher net costs, compared to basic composting. The inclusion of anaerobic digestion promoted nutrient recovery efficiency, and enabled energy recovery through electricity production. Co-digestion of the manure with carbon-rich waste streams increased electricity production, but did not result in lower process costs. Overall, key drivers for the selection of the optimal manure treatment scenario will include the market demand for more refined (vs. separated or concentrated) products, and the need for renewable electricity production.}, }
@article {pmid30352325, year = {2018}, author = {Christiaens, MER and De Vrieze, J and Clinckemaillie, L and Ganigué, R and Rabaey, K}, title = {Anaerobic ureolysis of source-separated urine for NH3 recovery enables direct removal of divalent ions at the toilet.}, journal = {Water research}, volume = {148}, number = {}, pages = {97-105}, doi = {10.1016/j.watres.2018.10.021}, pmid = {30352325}, issn = {1879-2448}, abstract = {Source-separated urine is of interest for nutrient recovery. Most nitrogen recovery technologies rely on ammonia (NH3) as input, which requires ureolysis. As urease positive bacteria are widespread, source-separated urine is unstable, not only leading to NH3 release but also loss, odor nuisance, and downstream scaling. Hence, ureolysis ideally occurs in a closed controlled environment close to the toilet. We characterized microbial-induced ureolysis, subsequent divalent cation precipitation, and fermentation in anaerobic sequencing batch reactors (SBRs) at 15 °C and 28 °C. Temperatures were a proxy for urine hydrolysis in a wet well at street level or in the toilet, respectively. The need for inoculation and the metabolic stability was assessed by inoculation with autofermented urine or a mixture of anaerobic digestion and fermentation sludge. The highest specific ureolysis rates in the SBRs were achieved at 28 °C: 2107 ± 395 and 1948 ± 1121 mg N g VSS-1 d-1, for the mixed and autofermented inoculum, respectively. For Ca2+ and Mg2+ precipitation, and organics fermentation, autofermented urine at 28 °C performed best with 47.9 ± 16.4 mg Ca2+ g VSS-1 d-1, 8.2 ± 4.6 mg Mg2+ g VSS-1 d-1, and 623 ± 129 mg VFA-COD g VSS-1 d-1, respectively. This indicates the hydrolysis reactor should be close to the toilet. The selected inoculum did not impact ureolysis, whereas both Ca2+ and Mg2+ precipitation and fermentation were better in the SBRs with autofermented urine. Ureolysis was identified as the only process significantly impacting the microbial community, indicating external inoculation would not be required. A urine hydrolysis reactor in the toilet without external inoculation could thus serve as a controlled environment to release NH3 and remove divalent cations to prevent scaling in downstream transport and processing. For practical implementation in a household toilet, the reactor should be designed for user-friendly precipitate discharge and odor control.}, }
@article {pmid30349964, year = {2018}, author = {Gonzalez-Escobedo, R and Briones-Roblero, CI and López, MF and Rivera-Orduña, FN and Zúñiga, G}, title = {Changes in the Microbial Community of Pinus arizonica Saplings After Being Colonized by the Bark Beetle Dendroctonus rhizophagus (Curculionidae: Scolytinae).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1274-1}, pmid = {30349964}, issn = {1432-184X}, support = {SIP 20180686//Secretaría de Investigación y Posgrado, Instituto Politécnico Nacional/ ; }, abstract = {The death of trees is an ecological process that promotes regeneration, organic matter recycling, and the structure of communities. However, diverse biotic and abiotic factors can disturb this process. Dendroctonus bark beetles (Curculionidae: Scolytinae) are natural inhabitants of pine forests, some of which produce periodic outbreaks, killing thousands of trees in the process. These insects spend almost their entire life cycle under tree bark, where they reproduce and feed on phloem. Tunneling and feeding of the beetles result in the death of the tree and an alteration of the resident microbiota as well as the introduction of microbes that the beetles vector. To understand how microbial communities in subcortical tissues of pines change after they are colonized by the bark beetle Dendroctonus rhizophagus, we compare both the bacterial and fungal community structures in two colonization stages of Pinus arizonica (Arizona pine) employing Illumina MiSeq. Our findings showed significant differences in diversity and the dominance of bacterial community in the two colonization stages with Shannon (P = 0.004) and Simpson (P = 0.0006) indices, respectively, but not in species richness with Chao1 (P = 0.19). In contrast, fungal communities in both stages showed significant differences in species richness with Chao1 (P = 0.0003) and a diversity with Shannon index (P = 0.038), but not in the dominance with the Simpson index (P = 0.12). The β-diversity also showed significant changes in the structure of bacterial and fungal communities along the colonization stages, maintaining the dominant members in both cases. Our results suggest that microbial communities present in the Arizona pine at the tree early colonization stage by bark beetle change predictably over time.}, }
@article {pmid30348833, year = {2018}, author = {Zeng, L and Burne, RA}, title = {Essential Roles of the sppRA Fructose-Phosphate Phosphohydrolase Operon in Carbohydrate Metabolism and Virulence Expression by Streptococcus mutans.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {}, doi = {10.1128/JB.00586-18}, pmid = {30348833}, issn = {1098-5530}, abstract = {The dental caries pathogen Streptococcus mutans can ferment a variety of sugars to produce organic acids. Exposure of S. mutans to certain non-metabolizable carbohydrates such as xylitol impairs growth and can cause cell death. Recently, the presence of a sugar-phosphate stress in S. mutans was demonstrated using a mutant lacking 1-phosphofructokinase (FruK) that accumulates fructose-1-phosphate (F-1-P). Here we studied an operon in S. mutans, sppRA, which was highly expressed in the fruK mutant. Biochemical characterization of a recombinant SppA protein indicated that it possessed hexose-phosphate phosphohydrolase activity, with preferences for F-1-P and, to a lesser degree, fructose-6-phosphate (F-6-P). SppA activity was stimulated by Mg2+ and Mn2+, but inhibited by NaF. SppR, a DeoR-family regulator, repressed the expression of the sppRA operon to minimum levels in the absence of the fructose-derived metabolites, F-1-P and likely also F-6-P. Accumulation of F-1-P, as a result of growth on fructose, not only induced sppA expression, it significantly altered biofilm maturation through increased cell lysis and enhanced extracellular DNA release. Constitutive expression of sppA, via a plasmid or by deleting sppR, greatly alleviated fructose-induced stress in a fruK mutant, enhanced resistance to xylitol, and reversed effects of fructose on biofilm formation. Finally, by identifying three additional putative phosphatases that are capable of promoting sugar-phosphate tolerance, we show that S. mutans is capable of mounting a sugar-phosphate stress response by modulating the levels of certain glycolytic intermediates, functions that are interconnected with the ability of the organism to manifest key virulence behaviors.IMPORTANCEStreptococcus mutans is a major etiologic agent for dental caries, primarily due to its ability to form biofilms on tooth surface and to convert carbohydrates into organic acids. We have discovered a two-gene operon in S. mutans that regulates fructose metabolism by controlling the levels of fructose-1-phosphate, a potential signaling compound that affects bacterial behaviors. With fructose becoming increasingly common and abundant in the human diet, we reveal the ways fructose may alter bacterial development, stress tolerance, and microbial ecology in the oral cavity to promote oral diseases.}, }
@article {pmid30344635, year = {2018}, author = {Lavoie, C and Courcelle, M and Redivo, B and Derome, N}, title = {Structural and compositional mismatch between captive and wild Atlantic salmon (Salmo salar) parrs' gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods.}, journal = {Evolutionary applications}, volume = {11}, number = {9}, pages = {1671-1685}, doi = {10.1111/eva.12658}, pmid = {30344635}, issn = {1752-4571}, abstract = {Stocking methods are used in the Province of Quebec to restore Salmo salar populations. However, Atlantic salmon stocked juveniles show higher mortality rates than wild ones when introduced into nature. Hatchery environment, which greatly differs from the natural environment, is identified as the main driver of the phenotypic mismatch between captive and wild parrs. The latter is also suspected to impact the gut microbiota composition, which can be associated with essential metabolic functions for their host. We hypothesized that hatchery-raised parrs potentially recruit gut microbial communities that are different from those recruited in the wild. This study evaluated the impacts of artificial rearing on gut microbiota composition in 0+ parrs meant for stocking in two distinct Canadian rivers: Rimouski and Malbaie (Quebec, Canada). Striking differences between hatchery and wild-born parrs' gut microbiota suggest that microbiota could be another factor that could impact their survival in the targeted river, because the microbiome is narrowly related to host physiology. For instance, major commensals belonging to Enterobacteriaceae and Clostridiacea from wild parrs' gut microbiota were substituted in captive parrs by lactic acid bacteria from the Lactobacillaceae family. Overall, captive parrs host a generalist bacterial community whereas wild parrs' microbiota is much more specialized. This is the very first study demonstrating extensive impact of captive rearing on intestinal microbiota composition in Atlantic salmon intended for wild population stocking. Our results strongly suggest the need to implement microbial ecology concepts into conservation management of endangered salmon stocks supplemented with hatchery-reared parrs.}, }
@article {pmid30343437, year = {2018}, author = {Li, T and Qi, M and Gatesoupe, FJ and Tian, D and Jin, W and Li, J and Lin, Q and Wu, S and Li, H}, title = {Adaptation to Fasting in Crucian Carp (Carassius auratus): Gut Microbiota and Its Correlative Relationship with Immune Function.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1275-0}, pmid = {30343437}, issn = {1432-184X}, support = {lzujbky-2018-68//Fundamental Research Funds for the Central Universities/ ; LY18E090010//Zhejiang Provincial Natural Science Foundation of China/ ; }, abstract = {Fasting influences the overall physiology of fish, and the knowledge how the gut microbiota, growth performances, and immune function in response to intermittent and long-term fasting is still insufficient. Here, we characterized the effects of fasting on the host-gut microbiota in crucian carp, which would enhance our insight into physiological adaptation to fasting. To achieve this, we investigated the gut microbial communities of crucian carp with different fasting stress, and corresponding immune and growth parameters. The gut microbial communities were structured into four clusters according to different fasting stress, namely one control group (feed regularly), two intermittent fasting groups (fasting period and re-feeding period, respectively), and one long-term fasting group. Intermittent fasting significantly improved the activity of superoxide dismutase (SOD) and lysozyme (LZM) (ANOVA, p < 0.05) and significantly increased alpha diversity and ecosystem stability of gut microbiota (ANOVA, p < 0.05). Gut length (GL) and condition factor (CF) showed no significant difference between the control group (CG) and intermittent fasting group under re-feeding period (RIF) (ANOVA, p = 0.11), but relative gut length (RGL) in group RIF was higher than that in the CG (ANOVA, p = 0.00). The bacterial genera Bacteroides, Akkermansia, and Erysipelotrichaceae were enriched in fishes under intermittent fasting. Two Bacteroides OTUs (OTU50 and OTU1292) correlated positively with immune (SOD, complement, and LZM) and growth (GL and RGL) parameters. These results highlight the possible interplay between growth performances, immune function, and gut microbiota in response to fasting.}, }
@article {pmid30342721, year = {2018}, author = {Free, A and McDonald, MA and Pagaling, E}, title = {Diversity-Function Relationships in Natural, Applied, and Engineered Microbial Ecosystems.}, journal = {Advances in applied microbiology}, volume = {105}, number = {}, pages = {131-189}, doi = {10.1016/bs.aambs.2018.07.002}, pmid = {30342721}, issn = {0065-2164}, abstract = {The connection between ecosystem function and taxonomic diversity has been of interest and relevance to macroecologists for decades. After many years of lagging behind due to the difficulty of assigning both taxonomy and function to poorly distinguishable microscopic cells, microbial ecology now has access to a suite of powerful molecular tools which allow its practitioners to generate data relating to diversity and function of a microbial community on an unprecedented scale. Instead, the problem facing today's microbial ecologists is coupling the ease of generation of these datasets with the formulation and testing of workable hypotheses relating the diversity and function of environmental, host-associated, and engineered microbial communities. Here, we review the current state of knowledge regarding the links between taxonomic alpha- and beta-diversity and ecosystem function, comparing our knowledge in this area to that obtained by macroecologists who use more traditional techniques. We consider the methodologies that can be applied to study these properties and how successful they are at linking function to diversity, using examples from the study of model microbial ecosystems, methanogenic bioreactors (anaerobic digesters), and host-associated microbiota. Finally, we assess ways in which our newly acquired understanding might be used to manipulate diversity in ecosystems of interest in order to improve function for the benefit of us or the environment in general through the provision of ecosystem services.}, }
@article {pmid30341500, year = {2018}, author = {Deja-Sikora, E and Gołębiewski, M and Kalwasińska, A and Krawiec, A and Kosobucki, P and Walczak, M}, title = {Comamonadaceae OTU as a Remnant of an Ancient Microbial Community in Sulfidic Waters.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1270-5}, pmid = {30341500}, issn = {1432-184X}, support = {1919-B//Uniwersytet Mikolaja Kopernika w Toruniu/ ; }, abstract = {Intraterrestrial waters harbor microbial communities being extensively studied to understand microbial processes underlying subsurface ecosystem functioning. This paper provides the results of an investigation on the microbiomes of unique, subsurface sulfidic waters associated with Upper Jurassic, Cretaceous, and Miocene sediments. We used high-throughput 16S rDNA amplicon sequencing to reveal the structure of bacterial and archaeal communities in water samples differing in sulfide content (20-960 mg/dm3), salinity (1.3-3.2%), and depth of extraction (60-660 m below ground level). Composition of the bacterial communities strongly varied across the samples; however, the bacteria participating in the sulfur cycle were common in all sulfidic waters. The shallowest borehole water (60 m bgl) was dominated by sulfur-oxidizing Epsilonproteobacteria (Sulfurimonas, Sulfurovum). In the waters collected from greater depths (148-300 m bgl), the prevalence of Betaproteobacteria (Comamonadaceae) and sulfate/sulfur-reducing Deltaproteobacteria (Desulfopila, Desulfomicrobium, MSBL7) was observed. Sulfate reducers (members of Clostridia: Candidatus Desulforudis) were the most abundant bacteria in the deepest borehole water (660 m bgl). Out of 850 bacterial OTUs, only one, affiliated with the Comamonadaceae family, was found abundant (> 1% of total bacterial sequences) in all samples. Contribution of Archaea to the whole microbial communities was lower than 0.5%. Archaeal communities did not differ across the samples and they consisted of Halobacteriaceae. Out of 372 archaeal OTUs, five, belonging to the four genera Natronomonas, Halorubrum, Halobellus, and Halorhabdus, were the most numerous.}, }
@article {pmid30341452, year = {2018}, author = {Amberkar, U and Khandeparker, R and Parab, P}, title = {Nitrate Reductase Gene Expression in Idiomarina Strain cos21 Obtained from Oxygen Minimum Zone of Arabian Sea.}, journal = {Current microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00284-018-1585-y}, pmid = {30341452}, issn = {1432-0991}, abstract = {This study analyses the induction and repression of nitrate reduction activity in a batch culture of Idiomarina strain cos21. On a change from aerobic to anaerobic respiration, the culture entered a stationary phase. The onset of this phase showed 3.75 fold increase in mRNA levels for the nitrate reductase enzyme. mRNA accumulated very rapidly during a short period, after which its overall concentration declined to reach a lower value. The level of nitrite reductase protein reached a maximum value at 36 h of growth when the oxygen concentration dropped below 10 µM. The data set provided here confer new insights into the understanding of the physiological response of Idiomarina strain cos21 to change in oxygen concentration allowing the bacterium to survive and adapt to a new environment by dissimilatory reduction of nitrate to nitrite, which serves to provide energy as the bacteria adapt to anaerobiosis. Main strategy used here is to induce, measure, and track the expression of microbial genes, while they grow in culture conditions to better mimic interaction in a natural environment. This study will help us with a better understanding of the nitrate reduction process in the oxygen minimum zone.}, }
@article {pmid30340417, year = {2018}, author = {Van Houdt, R and Provoost, A and Van Assche, A and Leys, N and Lievens, B and Mijnendonckx, K and Monsieurs, P}, title = {Cupriavidus metallidurans Strains with Different Mobilomes and from Distinct Environments Have Comparable Phenomes.}, journal = {Genes}, volume = {9}, number = {10}, pages = {}, doi = {10.3390/genes9100507}, pmid = {30340417}, issn = {2073-4425}, support = {C90356//Federaal Wetenschapsbeleid/ ; }, abstract = {Cupriavidus metallidurans has been mostly studied because of its resistance to numerous heavy metals and is increasingly being recovered from other environments not typified by metal contamination. They host a large and diverse mobile gene pool, next to their native megaplasmids. Here, we used comparative genomics and global metabolic comparison to assess the impact of the mobilome on growth capabilities, nutrient utilization, and sensitivity to chemicals of type strain CH34 and three isolates (NA1, NA4 and H1130). The latter were isolated from water sources aboard the International Space Station (NA1 and NA4) and from an invasive human infection (H1130). The mobilome was expanded as prophages were predicted in NA4 and H1130, and a genomic island putatively involved in abietane diterpenoids metabolism was identified in H1130. An active CRISPR-Cas system was identified in strain NA4, providing immunity to a plasmid that integrated in CH34 and NA1. No correlation between the mobilome and isolation environment was found. In addition, our comparison indicated that the metal resistance determinants and properties are conserved among these strains and thus maintained in these environments. Furthermore, all strains were highly resistant to a wide variety of chemicals, much broader than metals. Only minor differences were observed in the phenomes (measured by phenotype microarrays), despite the large difference in mobilomes and the variable (shared by two or three strains) and strain-specific genomes.}, }
@article {pmid30327827, year = {2018}, author = {Kowalec, M and Szewczyk, T and Welc-Falęciak, R and Siński, E and Karbowiak, G and Bajer, A}, title = {Rickettsiales Occurrence and Co-occurrence in Ixodes ricinus Ticks in Natural and Urban Areas.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1269-y}, pmid = {30327827}, issn = {1432-184X}, support = {NN404795240//Ministerstwo Nauki i Szkolnictwa Wyższego/ ; The study was financially supported by the Ministry of Science and Higher Education through the Faculty of Biology, University of Warsaw intramural grant DSM #501/86 - 104911//Ministerstwo Nauki i Szkolnictwa Wyższego/ ; The study was financially supported by the Ministry of Science and Higher Education through the Faculty of Biology, University of Warsaw intramural grant DSM #501/86 - 107422//Ministerstwo Nauki i Szkolnictwa Wyższego/ ; }, abstract = {Bacteria of Rickettsiaceae and Anaplasmataceae families include disease agents spread by Ixodes ricinus ticks, the most common tick vector in Europe. The aim of the study was to compare the prevalence and co-infection prevalence of particular tick-transmitted Rickettsiales members: Rickettsia spp. (further referred as Rs), Anaplasma phagocytophilum (Ap), and &quot;Candidatus Neoehrlichia mikurensis&quot; (CNM) in I. ricinus ticks in two types of areas, different in terms of human impact: natural and urban. Using additional data, we aimed at investigating co-occurrence of these Rickettsiales with Borreliella spp. A total of 4189 tick specimens, 2363 from the urban area (Warsaw park and forests) and 1826 from the natural area (forests and park in the vicinity of National Parks), were tested for the presence of Rickettsiales DNA by PCRs. The prevalence of selected Rickettsiales was twice higher in urban than natural areas (13.2% vs. 6.9%, respectively). In total ticks, the prevalence of Rs, Ap, and CNM was 6.5%, 5.3%, and 3.6% in urban areas vs. 4.4%, 1.1%, and 2.1% in natural areas, respectively. Co-infections of Rickettsiales were also more prevalent in urban areas (2.6% vs. 0.3%, respectively). The most common Rs was R. helvetica; also R. monacensis and novel &quot;Candidatus Rickettsia mendelii&quot; were detected. Positive association between Ap and CNM infections was discovered. Rickettsiales bacteria occurrence was not associated with Borreliella occurrence, but co-infections with these two groups were more common in ticks in urban areas. In conclusion, three groups of Rickettsiales constituted the important part of the tick pathogen community in Poland, especially in the urbanized central Poland (Mazovia). In the Warsaw agglomeration, there is a greater risk of encountering the I. ricinus tick infected with Rickettsiales and co-infected with Lyme spirochaetes, in comparison to natural areas. This finding raises the question whether cities might in fact be the hot spots for TBDs.}, }
@article {pmid30326440, year = {2018}, author = {Van Winckel, T and Liu, X and Vlaeminck, SE and Takács, I and Al-Omari, A and Sturm, B and Kjellerup, BV and Murthy, SN and De Clippeleir, H}, title = {Overcoming floc formation limitations in high-rate activated sludge systems.}, journal = {Chemosphere}, volume = {215}, number = {}, pages = {342-352}, doi = {10.1016/j.chemosphere.2018.09.169}, pmid = {30326440}, issn = {1879-1298}, abstract = {High-rate activated sludge (HRAS) is an essential cornerstone of the pursuit towards energy positive sewage treatment through maximizing capture of organics. The capture efficiency heavily relies on the degree of solid separation achieved in the clarifiers. Limitations in the floc formation process commonly emerge in HRAS systems, with detrimental consequences for the capture of organics. This study pinpointed and overcame floc formation limitations present in full-scale HRAS reactors. Orthokinetic flocculation tests were performed with varying shear, sludge concentration, and coagulant or flocculant addition. These were analyzed with traditional and novel settling parameters and extracellular polymeric substances (EPS) measurements. HRAS was limited by insufficient collision efficiency and occurred because the solids retention time (SRT) was short and colloid loading was high. The limitation was predominantly caused by impaired flocculation rather than coagulation. In addition, the collision efficiency limitation was driven by EPS composition (low protein over polysaccharide ratio) instead of total EPS amount. Collision efficiency limitation was successfully overcome by bio-augmenting sludge from a biological nutrient removal reactor operating at long SRT which did not show any floc formation limitations. However, this action brought up a floc strength limitation. The latter was not correlated with EPS composition, but rather EPS amount and hindered settling parameters, which determined floc morphology. With this, an analysis toolkit was proposed that will enable design engineers and operators to tackle activated solid separation challenges found in HRAS systems and maximize the recovery potential of the process.}, }
@article {pmid30325958, year = {2018}, author = {Lee, YM and Kor, CT and Zhou, D and Lai, HC and Chang, CC and Ma, WL}, title = {Impact of age at appendectomy on development of type 2 diabetes: A population-based cohort study.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0205502}, doi = {10.1371/journal.pone.0205502}, pmid = {30325958}, issn = {1932-6203}, abstract = {AIM: Diabetes is a complex metabolic disease characterized by chronic low-grade inflammation in which genetic and environmental factors are involved. Growing evidence implicates that alterations of the gut microbiota potentially contribute to the emergence of metabolic diseases. The human appendix has more recently been recognized as a microbial reservoir for repopulating the gastrointestinal tract and an important part of the immune system. Thus, appendectomy may influence microbial ecology and immune function. This study investigated the association between appendectomy and type 2 diabetes risk.<br><br>METHODS: We analyzed a cohort of 10954 patients who underwent appendectomy between 1998 and 2013 based on the Taiwan National Health Insurance Program database. A comparison cohort of 43815 persons without appendectomy was selected randomly and matched by sex, age, comorbidities, and index year. To ensure reliability of the results, a sensitivity analysis using a propensity score-matched study was performed. We observed the subsequent development of type 2 diabetes in both cohorts.<br><br>RESULTS: Although the overall incidence of type 2 diabetes in the appendectomy patients was 7.9% higher than that in the non-appendectomy patients, it was not statistically significant (95% confidence interval [CI], 0.997-1.168) after the adjustment of confounding factors. Multivariate regression analysis revealed that the adjusted hazard ratio (HR) of type 2 diabetes was 1.347 for appendectomy patients < 30 years of age (95% CI, 1.009-1.798) compared to non-appendectomy patients. The incidence of type 2 diabetes was higher within 3 years of post-appendectomy follow-up than for non-appendectomy patients (HR, 2.017; 95% CI, 1.07-3.802). Age impacted the association between appendectomy and type 2 diabetes risk (Pinteraction = 0.002); in contrast, sex did not affect the association between appendectomy and type 2 diabetes risk (Pinteraction = 0.88).<br><br>CONCLUSIONS: Our study results suggest that appendectomy increases type 2 diabetes risk, particularly when performed prior to middle age.}, }
@article {pmid30324255, year = {2018}, author = {Szczepańska, A and Kiewra, D and Guz-Regner, K}, title = {Sensitivity of Ixodes ricinus (L., 1758) and Dermacentor reticulatus (Fabr., 1794) ticks to Bacillus thuringiensis isolates: preliminary study.}, journal = {Parasitology research}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00436-018-6096-z}, pmid = {30324255}, issn = {1432-1955}, support = {0420/2308/17//Uniwersytet Wrocławski/ ; }, abstract = {Bacillus thuringiensis is a highly specific entomopathogenic microorganism. Although defined as having properties which work against insects, its role in the control of tick populations is still insufficiently known. In our bioassay, four environmental strains of B. thuringiensis, along with one commercially available product (Vectobac), have been used against ticks. Vectobac turned out to be ineffective in the biocontrol of ticks; however, two of environmental B. thuringiensis strains proved to be efficient against both Ixodes ricinus and Dermacentor reticulatus. In those cases, the mortality rate for ticks was assessed as being up to 80%, and LC50 ranged between 9.1 × 106 and 1.3 × 1015 (cfu/ml). Dermacentor reticulatus males were the most sensitive to bacteria. The similarity between the most and least efficient B. thuringiensis strains in enzymatic profiles-including lipases, phosphatases, proteases, and chitinases-may indicate a limited role of detected enzymes in the pathogenicity profile of bacterial strains against ticks.}, }
@article {pmid30321727, year = {2018}, author = {Liu, K and Liu, Y and Han, BP and Xu, B and Zhu, L and Ju, J and Jiao, N and Xiong, J}, title = {Bacterial community changes in a glacial-fed Tibetan lake are correlated with glacial melting.}, journal = {The Science of the total environment}, volume = {651}, number = {Pt 2}, pages = {2059-2067}, doi = {10.1016/j.scitotenv.2018.10.104}, pmid = {30321727}, issn = {1879-1026}, abstract = {Climate change-induced glacial melting is a global phenomenon. The effects of climate change-induced melting on the microbial ecology in different glacial-fed aquatic systems have been well illuminated, but the resolution of seasonal dynamics was still limited. Here, we studied bacterial community composition and diversity in a glacial-fed Tibetan lake, Lake Ranwu, to elucidate how glacial-fed aquatic ecosystems respond to the seasonal glacial melting. Obvious seasonal variations of bacterial dominant groups were found in Lake Ranwu and inlet rivers. In April, the majority of OTUs belonged to the Bacteroidetes, Actinobacteria and Proteobacteria. The Proteobacteria increased to the most abundant phylum in July and November, while the Bacteroidetes and Actinobacteria decreased about 50% over seasons. Most key discriminant taxa of each season's community strongly associated with specific environmental variables, suggesting their adaptation to seasonal environments. Bacterial alpha diversity varied among seasons and exhibited strongly negative correlations with conductivity. Conductivity was the major driving force in determining the seasonal variation of bacterial community composition. Fluctuated conductivity was one of the consequences of seasonal melting of glaciers. This study offered evidence for the unique seasonal dynamics pattern of bacterial communities responding to glacial melting. Moreover, this study may provide a reference for assessing the long-term effects of glacial retreat on glacial-fed aquatic ecosystems.}, }
@article {pmid30320221, year = {2018}, author = {Stegen, JC and Goldman, AE}, title = {WHONDRS: a Community Resource for Studying Dynamic River Corridors.}, journal = {mSystems}, volume = {3}, number = {5}, pages = {}, doi = {10.1128/mSystems.00151-18}, pmid = {30320221}, issn = {2379-5077}, abstract = {The Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) aims to galvanize a global community to provide the scientific basis for improved management of dynamic river corridors. WHONDRS is a global research consortium working to understand connections among dynamic hydrology, biogeochemistry, and microbiology in river corridors from local to global scales. WHONDRS ascribes to the perspective that resources, knowledge, and data belong to the community as a whole and that science advances more rapidly and more robustly through community ownership. As such, WHONDRS provides free access to novel instrumentation, molecular analysis, and well-curated data associated with river corridor hydrology, biogeochemistry, and microbiology. There are a number of ways to be involved in WHONDRS, ranging from one-time surface water sampling to installation of WHONDRS-developed multiparameter sensors for continuous monitoring. WHONDRS hinges on broad involvement, and we encourage all interested parties to contact us and become part of the consortium.}, }
@article {pmid30320215, year = {2018}, author = {Trubl, G and Jang, HB and Roux, S and Emerson, JB and Solonenko, N and Vik, DR and Solden, L and Ellenbogen, J and Runyon, AT and Bolduc, B and Woodcroft, BJ and Saleska, SR and Tyson, GW and Wrighton, KC and Sullivan, MB and Rich, VI}, title = {Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing.}, journal = {mSystems}, volume = {3}, number = {5}, pages = {}, doi = {10.1128/mSystems.00076-18}, pmid = {30320215}, issn = {2379-5077}, abstract = {Rapidly thawing permafrost harbors ∼30 to 50% of global soil carbon, and the fate of this carbon remains unknown. Microorganisms will play a central role in its fate, and their viruses could modulate that impact via induced mortality and metabolic controls. Because of the challenges of recovering viruses from soils, little is known about soil viruses or their role(s) in microbial biogeochemical cycling. Here, we describe 53 viral populations (viral operational taxonomic units [vOTUs]) recovered from seven quantitatively derived (i.e., not multiple-displacement-amplified) viral-particle metagenomes (viromes) along a permafrost thaw gradient at the Stordalen Mire field site in northern Sweden. Only 15% of these vOTUs had genetic similarity to publicly available viruses in the RefSeq database, and ∼30% of the genes could be annotated, supporting the concept of soils as reservoirs of substantial undescribed viral genetic diversity. The vOTUs exhibited distinct ecology, with different distributions along the thaw gradient habitats, and a shift from soil-virus-like assemblages in the dry palsas to aquatic-virus-like assemblages in the inundated fen. Seventeen vOTUs were linked to microbial hosts (in silico), implicating viruses in infecting abundant microbial lineages from Acidobacteria, Verrucomicrobia, and Deltaproteobacteria, including those encoding key biogeochemical functions such as organic matter degradation. Thirty auxiliary metabolic genes (AMGs) were identified and suggested virus-mediated modulation of central carbon metabolism, soil organic matter degradation, polysaccharide binding, and regulation of sporulation. Together, these findings suggest that these soil viruses have distinct ecology, impact host-mediated biogeochemistry, and likely impact ecosystem function in the rapidly changing Arctic. IMPORTANCE This work is part of a 10-year project to examine thawing permafrost peatlands and is the first virome-particle-based approach to characterize viruses in these systems. This method yielded >2-fold-more viral populations (vOTUs) per gigabase of metagenome than vOTUs derived from bulk-soil metagenomes from the same site (J. B. Emerson, S. Roux, J. R. Brum, B. Bolduc, et al., Nat Microbiol 3:870-880, 2018, https://doi.org/10.1038/s41564-018-0190-y). We compared the ecology of the recovered vOTUs along a permafrost thaw gradient and found (i) habitat specificity, (ii) a shift in viral community identity from soil-like to aquatic-like viruses, (iii) infection of dominant microbial hosts, and (iv) carriage of host metabolic genes. These vOTUs can impact ecosystem carbon processing via top-down (inferred from lysing dominant microbial hosts) and bottom-up (inferred from carriage of auxiliary metabolic genes) controls. This work serves as a foundation which future studies can build upon to increase our understanding of the soil virosphere and how viruses affect soil ecosystem services.}, }
@article {pmid30320131, year = {2018}, author = {Ziadi, M and Bouzaiene, T and M'Hir, S and Zaafouri, K and Mokhtar, F and Hamdi, M and Boisset-Helbert, C}, title = {Evaluation of the Efficiency of Ethanol Precipitation and Ultrafiltration on the Purification and Characteristics of Exopolysaccharides Produced by Three Lactic Acid Bacteria.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {1896240}, doi = {10.1155/2018/1896240}, pmid = {30320131}, issn = {2314-6141}, abstract = {Exopolysaccharides (EPS) produced by three Lactic Acid Bacteria strains, Lactococcus lactis SLT10, Lactobacillus plantarum C7, and Leuconostoc mesenteroides B3, were isolated using two methods: ethanol precipitation (EPS-ETOH) and ultrafiltration (EPS-UF) through a 10 KDa cut-off membrane. EPS recovery by ultrafiltration was higher than ethanol precipitation for Lactococcus lactis SLT10 and Lactobacillus plantarum C7. However, it was similar with both methods for Leuconostoc mesenteroides B3. The monomer composition of the EPS fractions revealed differences in structures and molar ratios between the two studied methods. EPS isolated from Lactococcus lactis SLT10 are composed of glucose and mannose for EPS-ETOH against glucose, mannose, and rhamnose for EPS-UF. EPS extracted from Lactobacillus plantarum C7 and Leuconostoc mesenteroides B3 showed similar composition (glucose and mannose) but different molar ratios. The molecular weights of the different EPS fractions ranged from 11.6±1.83 to 62.4±2.94 kDa. Molecular weights of EPS-ETOH fractions were higher than those of EPS-UF fractions. Fourier transform infrared (FTIR) analysis revealed a similarity in the distribution of the functional groups (O-H, C-H, C=O, -COO, and C-O-C) between the EPS isolated from the three strains.}, }
@article {pmid30319569, year = {2018}, author = {D'Amico, F and Candela, M and Turroni, S and Biagi, E and Brigidi, P and Bega, A and Vancini, D and Rampelli, S}, title = {The Rootstock Regulates Microbiome Diversity in Root and Rhizosphere Compartments of Vitis vinifera Cultivar Lambrusco.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2240}, doi = {10.3389/fmicb.2018.02240}, pmid = {30319569}, issn = {1664-302X}, abstract = {Plants belonging to Vitis vinifera varieties are usually grafted on different rootstocks to enhance the plant defenses against pathogens and increase productivity under harsh environmental conditions. Particularly, in Emilia-Romagna region (Italy), Vitis vinifera cultivar Lambrusco can be grafted on a hybrid of V. berlandieri × V. riparia (5BB) or V. berlandieri × V. rupestris (1103P). However, the latter shows potassium absorption problems, with a consequent reduction in grapevine production. Since it has recently been demonstrated that the rootstock has the potential to select for different microorganisms at the root-soil interface, here we hypothesized that the potassium deficiency of 1103P could be partially accounted for by the peculiarities of the rootstock microbiome. We thus employed 16S rRNA sequencing to compare root and rhizosphere microbiomes in plants of V. vinifera cultivar Lambrusco grafted on the two aforementioned rootstocks. According to our findings, 1103P shows a reduced diversity in root and rhizosphere microbiomes, including members of potassium-solubilizing microorganisms, possibly explaining the inadequate potassium absorption of this hybrid. Besides confirming the importance of the rootstock as a determinant of the composition of plant microbiomes, our data indicate the relevance of rootstock-selected microbiomes as possible regulators of potassium absorption by V. vinifera.}, }
@article {pmid30318762, year = {2018}, author = {Van Assche, A and Crauwels, S and De Brabanter, J and Willems, KA and Lievens, B}, title = {Characterization of the bacterial community composition in water of drinking water production and distribution systems in Flanders, Belgium.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e726}, doi = {10.1002/mbo3.726}, pmid = {30318762}, issn = {2045-8827}, support = {L2010S0013X//Vlaamse Instelling voor Technologisch Onderzoek/ ; L2010S0013X//Flemish Environment Agency/ ; }, abstract = {The quality of drinking water is influenced by its chemical and microbial composition which in turn may be affected by the source water and the different processes applied in drinking water purification systems. In this study, we investigated the bacterial diversity in different water samples from the production and distribution chain of thirteen drinking water production and distribution systems from Flanders (Belgium) that use surface water or groundwater as source water. Water samples were collected over two seasons from the source water, the processed drinking water within the production facility and out of the tap in houses along its distribution network. 454-pyrosequencing of 16S ribosomal RNA gene sequences revealed a total of 1,570 species-level bacterial operational taxonomic units. Strong differences in community composition were found between processed drinking water samples originating from companies that use surface water and other that use groundwater as source water. Proteobacteria was the most abundant phylum in all samples. Yet, several phyla including Actinobacteria were significantly more abundant in surface water while Cyanobacteria were more abundant in surface water and processed water originating from surface water. Gallionella, Acinetobacter, and Pseudomonas were the three most abundant genera detected. Members of the Acinetobacter genus were even found at a relative read abundance of up to 47.5% in processed water samples, indicating a general occurrence of Acinetobacter in drinking water (systems).}, }
@article {pmid30318710, year = {2018}, author = {Liu, Y and Qin, Q and Defoirdt, T}, title = {Does quorum sensing interference affect the fitness of bacterial pathogens in the real world?.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14446}, pmid = {30318710}, issn = {1462-2920}, abstract = {Many bacterial pathogens rely on quorum sensing to control virulence gene expression. Based on numerous experiments conducted under well-defined conditions, quorum sensing interference is considered as a promising strategy to tackle infections and thus might have the potential to (partially) replace antibiotics. Despite the promising results in well-defined (artificial) laboratory experiments, there still is a lack of knowledge with respect to the impact of quorum sensing interference on the fitness of pathogens in more realistic scenarios, including interactions with a host, the external environment and complex microbial communities. In this paper, we critically evaluate the current knowledge with respect to these three facets of the real world that can affect fitness of quorum sensing bacterial pathogens. We argue that further research is needed in order to determine how these factors interplay with quorum sensing and to what extent they can influence the selective pressure that might be exerted by quorum sensing interference (and thus determine the risk of resistance development against quorum sensing interference). This kind of information is indispensable in order to optimize quorum sensing interference-based therapeutic strategies. This article is protected by copyright. All rights reserved.}, }
@article {pmid30317429, year = {2018}, author = {Mania, I and Gorra, R and Colombo, N and Freppaz, M and Martin, M and Anesio, AM}, title = {Prokaryotic Diversity and Distribution in Different Habitats of an Alpine Rock Glacier-Pond System.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1272-3}, pmid = {30317429}, issn = {1432-184X}, support = {NE/J02399X/1//Natural Environment Research Council/ ; }, abstract = {Rock glaciers (RG) are assumed to influence the biogeochemistry of downstream ecosystems because of the high ratio of rock:water in those systems, but no studies have considered the effects of a RG inflow on the microbial ecology of sediments in a downstream pond. An alpine RG-pond system, located in the NW Italian Alps has been chosen as a model, and Bacteria and Archaea 16S rRNA genes abundance, distribution and diversity have been assessed by qPCR and Illumina sequencing, coupled with geochemical analyses on sediments collected along a distance gradient from the RG inflow. RG surface material and neighbouring soil have been included in the analysis to better elucidate relationships among different habitats.Our results showed that different habitats harboured different, well-separated microbial assemblages. Across the pond, the main variations in community composition (e.g. Thaumarchaeota and Cyanobacteria relative abundance) and porewater geochemistry (pH, DOC, TDN and NH4+) were not directly linked to RG proximity, but to differences in water depth. Some microbial markers potentially linked to the presence of meltwater inputs from the RG have been recognised, although the RG seems to have a greater influence on the pond microbial communities due to its contribution in terms of sedimentary material.}, }
@article {pmid30314008, year = {2018}, author = {Sen, A and Saha, R and Sivakumar, K and Bhadury, P}, title = {Inventorizing the modern benthic foraminiferal assemblage from marginal marine environments across the North West coast of Bay of Bengal.}, journal = {Zootaxa}, volume = {4441}, number = {2}, pages = {245-260}, doi = {10.11646/zootaxa.4441.2.3}, pmid = {30314008}, issn = {1175-5334}, abstract = {Modern benthic foraminiferal assemblages are instrumental in providing information regarding changes in relative sea level as well as prevailing environmental conditions in marine environments. Marginal marine environments are coastal environments that are in most cases characterized by high influx of terrestrially originated nutrients. Inventorizing of modern benthic foraminiferal assemblages from such habitats can act as biotic indicators of water quality variations along with any changes in relative sea level. The present study documents the modern benthic foraminiferal assemblage from three major marginal marine habitats located along the North West coast of Bay of Bengal, in the Indian Ocean. Sediment samples for the purpose were thus collected from the Indian Sundarbans Delta, Chilika lagoon and the Gautami Godavari estuarine zone which encompasses the Kakinada bay. A total of 32 species of benthic foraminifera were documented during the study. The present observations were compared with previous reports of benthic foraminiferal diversity from these habitats and exhibited variability.}, }
@article {pmid30312413, year = {2018}, author = {Van Geel, M and Yu, K and Ceulemans, T and Peeters, G and van Acker, K and Geerts, W and Ramos, MM and Serafim, C and Kastendeuch, P and Najjar, G and Ameglio, T and Ngao, J and Saudreau, M and Waud, M and Lievens, B and Castro, PML and Somers, B and Honnay, O}, title = {Variation in ectomycorrhizal fungal communities associated with Silver linden (Tilia tomentosa) within and across urban areas.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiy207}, pmid = {30312413}, issn = {1574-6941}, abstract = {Trees in urban areas face harsh environmental conditions. Ectomycorrhizal fungi (EcM) form a symbiosis with many tree species and provide a range of benefits to their host through their extraradical hyphal network. Although our understanding of the environmental drivers and large scale geographical variation of EcM communities in natural ecosystems is growing, our knowledge of EcM communities within and across urban areas is still limited. Here we characterized EcM communities using Illumina miseq sequencing on 175 root samples of the urban tree Tilia tomentosa from three European cities, namely Leuven (Belgium), Strasbourg (France) and Porto (Portugal). We found strong differences in EcM richness and community composition between cities. Soil acidity, organic matter and moisture content were significantly associated with EcM community composition. In agreement, the explained variability in EcM communities was mostly attributed to general soil characteristics, whereas very little variation was explained by city and heavy metal pollution. Overall, our results suggest that EcM communities in urban areas are significantly associated with soil characteristics, while heavy metal pollution and biogeography had little or no impact. These findings deliver new insights into EcM distribution patterns in urban areas and contribute to specific inoculation strategies to improve urban tree vitality.}, }
@article {pmid30310241, year = {2017}, author = {Eisenhauer, N and Powell, JR}, title = {Plant trait effects on soil organisms and functions.}, journal = {Pedobiologia}, volume = {65}, number = {}, pages = {1-4}, doi = {10.1016/j.pedobi.2017.11.001}, pmid = {30310241}, issn = {0031-4056}, support = {677232//European Research Council/International ; }, abstract = {Global change alters the composition and functioning of ecosystems by creating novel environmental conditions and thereby selecting for specific traits of organisms. Thus, trait-based approaches are promising tools to more mechanistically understand compositional and functional shifts in ecological communities as well as the dependency of response and effect traits upon global change. Such approaches have been particularly successful for the study of plant communities in terrestrial ecosystems. However, given the intimate linkages between aboveground and belowground compartments as well as the significance of plants as integrating organisms across those compartments, the role of plant traits in affecting soils communities has been understudied. This special issue contains empirical studies and reviews of plant trait effects on soil organisms and functions. Based on those contributions, we discuss here plasticity in trait expression, the context-dependency of plant trait effects, time lags in soil biotic responses to trait expression, and limitations of measured plant traits. We conclude that plant trait-based approaches are an important tool to advance soil ecological research, but also identify critical limitations and next steps.}, }
@article {pmid30310127, year = {2018}, author = {Cuer, CA and Rodrigues, RAR and Balieiro, FC and Jesus, J and Silva, EP and Alves, BJR and Rachid, CTCC}, title = {Short-term effect of Eucalyptus plantations on soil microbial communities and soil-atmosphere methane and nitrous oxide exchange.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {15133}, doi = {10.1038/s41598-018-33594-6}, pmid = {30310127}, issn = {2045-2322}, abstract = {Soil greenhouse gas (GHG) emissions are a significant environmental problem resulting from microbially-mediated nitrogen (N) and carbon (C) cycling. This study aimed to investigate the impact of Eucalyptus plantations on the structure and function of a soil microbial community, and how resulting alterations may be linked to GHG fluxes. We sampled and monitored two adjacent Eucalyptus plantations-a recently logged site that harbored new seedlings and an adult plantation-and compared them to a site hosting native vegetation. We used 16S rRNA gene sequencing and qPCR amplifications of key nitrogen and methane cycle genes to characterize microbial structure and functional gene abundance and compared our data with soil parameters and GHG fluxes. Both microbial community attributes were significantly affected by land use and logging of Eucalyptus plantations. The genes nosZ and archaeal amoA were significantly more abundant in native forest than in either young or old Eucalyptus plantations. Statistical analyses suggest that land use type has a greater impact on microbial community structure and functional gene abundance than Eucalyptus rotation. There was no correlation between GHG fluxes and shifts in microbial community, suggesting that microbial community structure and functional gene abundance are not the main drivers of GHG fluxes in this system.}, }
@article {pmid30308860, year = {2019}, author = {Karmakar, R and Bindiya, S and Hariprasad, P}, title = {Convergent evolution in bacteria from multiple origins under antibiotic and heavy metal stress, and endophytic conditions of host plant.}, journal = {The Science of the total environment}, volume = {650}, number = {Pt 1}, pages = {858-867}, doi = {10.1016/j.scitotenv.2018.09.078}, pmid = {30308860}, issn = {1879-1026}, abstract = {The focus of this work is to study the convergent evolution in bacteria from multiple origins under antibiotic and heavy metal stress, and endophytic conditions of host plant cultivated on the Yamuna river bank. Forty-one endophytic bacteria (EB) were isolated from green leafy vegetables (GLV's) and were found to be resistant to a wide range of antibiotics (AB) and heavy metals (HM) tested. Further, they showed susceptibility to Quinolones group of antibiotics, and the HM, Cadmium, Chromium, and Mercury. Twenty-seven percent of these bacteria endowed with Class I integron. The probability of co-existence of HM resistance with β‑lactams was higher, whereas quinolones group of AB recorded lesser values. These EB owned a wide array of beneficial traits, through which they improved the plant health under HM and salt stress conditions. Bacterial identity revealed the association of both plant beneficial and human pathogenic bacteria as an endophyte with GLV's. Principal component analysis showed a pattern of convergent evolution irrespective of their origin. In conclusion, under the selection pressure of AB and HM, the susceptible EB population may reduce with time and the resistant native/introduced bacteria might survive. The vertical and horizontal gene transfer between introduced and native bacteria is the crucial factor in enhancing their fitness along with the host plant to survive under abiotic stress conditions.}, }
@article {pmid30308834, year = {2019}, author = {Lourenço, KS and Rossetto, R and Vitti, AC and Montezano, ZF and Soares, JR and Sousa, RM and do Carmo, JB and Kuramae, EE and Cantarella, H}, title = {Strategies to mitigate the nitrous oxide emissions from nitrogen fertilizer applied with organic fertilizers in sugarcane.}, journal = {The Science of the total environment}, volume = {650}, number = {Pt 1}, pages = {1476-1486}, doi = {10.1016/j.scitotenv.2018.09.037}, pmid = {30308834}, issn = {1879-1026}, abstract = {Vinasse is a major byproduct of the sugarcane biofuel industry, recycled in the fields. However, there is evidence that the application of vinasse with mineral nitrogen (N) fertilizers in sugarcane enhances the emission of greenhouse gases (GHGs). Therefore, strategies are needed to decrease the environmental impacts caused by both inputs. We carried out three sugarcane field experiments by applying N fertilizer (ammonium nitrate) with types of vinasses (concentrated-CV and standard-V) in different combinations (vinasses with N fertilizer and vinasses one month before or after mineral N fertilization). The gases nitrous oxide (N2O), carbon dioxide (CO2), and methane (CH4) were measured in one experiment fertilized in the beginning (fall/winter = dry season) and two experiments fertilized in the end (spring = rainy season) of the harvest season. Sugarcane fields were sinks rather than sources of CH4, while total carbon emitted as CO2 was similar between seasons and treatments. The effect of mineral fertilization and vinasses (CV and V) on N2O emissions was highly dependent on soil moisture (rain events). The N2O-N fertilizer emission factor (EF) varied from 0.07% to 0.51%, whereas the average EF of V and CV were 0.66% and 0.34%, respectively. On average across the three experiments, the combination of vinasse (CV or V) with N fertilizer increased the N2O emissions 2.9-fold compared to that of N fertilizer alone. For CV + N, the EF was 0.94% of the applied N and 0.23% of the ammonium nitrate-N, and for V + N (EF = 0.47%), increased emissions were observed in two out of three experiments. The strategy of anticipating or postponing vinasse application by one month with respect to mineral N reduced the N2O emissions by 51% for CV, but not for V. Therefore, to avoid boosting N2O emissions, we suggest applying vinasses (CV and V) before or after mineral N fertilization.}, }
@article {pmid30308248, year = {2018}, author = {Hessler, T and Harrison, STL and Huddy, RJ}, title = {Stratification of microbial communities throughout a biological sulphate reducing up-flow anaerobic packed bed reactor, revealed through 16S metagenomics.}, journal = {Research in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.resmic.2018.09.003}, pmid = {30308248}, issn = {1769-7123}, abstract = {Biological sulphate reduction (BSR) is a promising low-cost treatment of acid rock drainage effluents. In this paper, the system performance and microbial ecology of a lactate supplemented BSR up-flow anaerobic packed bed reactor (UAPBR) are evaluated across reactor height and compared to a continuous stirred tank reactor (CSTR). The biomass concentrations of planktonic and biofilm communities were quantified and subsequently characterised by 16S rRNA gene amplicon sequencing. The defined microbial communities were shown to correlate with differing availability of lactate, volatile fatty acids produced from lactate degradation and sulphate concentration. The UAPBR was able to achieve near complete sulphate conversion at a 4-day hydraulic residence time (HRT) at a sulphate feed concentration of 10.41 mM (1 g/L). The high volumetric sulphate reduction rate of 0.184 mM/L.h achieved in the first third of the reactor was attributed to OTUs present in the planktonic and biofilm communities. While the scavenging of sulphate within the final third of the UAPBR was attributed to an acetate oxidising genus of SRB which was not detected in the lactate-fed CSTR. The detailed analyses of the microbial communities throughout the UAPBR and CSTR contribute to the growing understanding of the impact of the microbial communities of BSR reactors on system performance.}, }
@article {pmid30305843, year = {2018}, author = {Cassman, NA and Lourenço, KS and do Carmo, JB and Cantarella, H and Kuramae, EE}, title = {Correction to: Genome-resolved metagenomics of sugarcane vinasse bacteria.}, journal = {Biotechnology for biofuels}, volume = {11}, number = {}, pages = {270}, doi = {10.1186/s13068-018-1254-1}, pmid = {30305843}, issn = {1754-6834}, abstract = {[This corrects the article DOI: 10.1186/s13068-018-1036-9.].}, }
@article {pmid30303297, year = {2018}, author = {Ghosh, A and Bhadury, P}, title = {Exploring biogeographic patterns of bacterioplankton communities across global estuaries.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e741}, doi = {10.1002/mbo3.741}, pmid = {30303297}, issn = {2045-8827}, support = {//IISER Kolkata/ ; }, abstract = {Estuaries provide an ideal niche to study structure and function of bacterioplankton communities owing to the presence of a multitude of environmental stressors. Bacterioplankton community structures from nine global estuaries were compared to understand their broad-scale biogeographic patterns. Bacterioplankton community structure from four estuaries of Sundarbans, namely Mooriganga, Thakuran, Matla, and Harinbhanga, was elucidated using Illumina sequencing. Bacterioplankton communities from these estuaries were compared against available bacterioplankton sequence data from Columbia, Delaware, Jiulong, Pearl, and Hangzhou estuaries. All nine estuaries were dominated by Proteobacteria. Other abundant phyla included Bacteroidetes, Firmicutes, Acidobacteria, Actinobacteria, Cyanobacteria, Planctomycetes, and Verrucomicrobia. The abundant bacterial phyla showed a ubiquitous presence across the estuaries. At class level, the overwhelming abundance of Gammaproteobacteria in the estuaries of Sundarbans and Columbia estuary clearly stood out amidst high abundance of Alphaproteobacteria observed in the other estuaries. Abundant bacterial families including Rhodobacteriaceae, Shingomonadaceae, Acidobacteriaceae, Vibrionaceae, and Xanthomondaceae also showed ubiquitous presence in the studied estuaries. However, rare taxa including Chloroflexi, Tenericutes, Nitrospirae, and Deinococcus-Thermus showed clear site-specific distribution patterns. Such distribution patterns were also reinstated by nMDS ordination plots. Such clustering patterns could hint toward the potential role of environmental parameters and substrate specificity which could result in distinct bacterioplankton communities at specific sites. The ubiquitous presence of abundant bacterioplankton groups along with their strong correlation with surface water temperature and dissolved nutrient concentrations indicates the role of such environmental parameters in shaping bacterioplankton community structure in estuaries. Overall, studies on biogeographic patters of bacterioplankton communities can provide interesting insights into ecosystem functioning and health of global estuaries.}, }
@article {pmid30301807, year = {2018}, author = {Weber, Y and Sinninghe Damsté, JS and Zopfi, J and De Jonge, C and Gilli, A and Schubert, CJ and Lepori, F and Lehmann, MF and Niemann, H}, title = {Redox-dependent niche differentiation provides evidence for multiple bacterial sources of glycerol tetraether lipids in lakes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {43}, pages = {10926-10931}, doi = {10.1073/pnas.1805186115}, pmid = {30301807}, issn = {1091-6490}, abstract = {Terrestrial paleoclimate archives such as lake sediments are essential for our understanding of the continental climate system and for the modeling of future climate scenarios. However, quantitative proxies for the determination of paleotemperatures are sparse. The relative abundances of certain bacterial lipids, i.e., branched glycerol dialkyl glycerol tetraethers (brGDGTs), respond to changes in environmental temperature, and thus have great potential for climate reconstruction. Their application to lake deposits, however, is hampered by the lack of fundamental knowledge on the ecology of brGDGT-producing microbes in lakes. Here, we show that brGDGTs are synthesized by multiple groups of bacteria thriving under contrasting redox regimes in a deep meromictic Swiss lake (Lake Lugano). This niche partitioning is evidenced by highly distinct brGDGT inventories in oxic vs. anoxic water masses, and corresponding vertical patterns in bacterial 16S rRNA gene abundances, implying that sedimentary brGDGT records are affected by temperature-independent changes in the community composition of their microbial producers. Furthermore, the stable carbon isotope composition (δ13C) of brGDGTs in Lake Lugano and 34 other (peri-)Alpine lakes attests to the widespread heterotrophic incorporation of 13C-depleted, methane-derived biomass at the redox transition zone of mesotrophic to eutrophic lake systems. The brGDGTs produced under such hypoxic/methanotrophic conditions reflect near-bottom water temperatures, and are characterized by comparatively low δ13C values. Depending on climate zone and water depth, lake sediment archives predominated by deeper water/low-13C brGDGTs may provide more reliable records of climate variability than those where brGDGTs derive from terrestrial and/or aquatic sources with distinct temperature imprints.}, }
@article {pmid30298251, year = {2018}, author = {Hall, M and Beiko, RG}, title = {16S rRNA Gene Analysis with QIIME2.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {113-129}, doi = {10.1007/978-1-4939-8728-3_8}, pmid = {30298251}, issn = {1940-6029}, abstract = {Microbial marker-gene sequence data can be used to generate comprehensive taxonomic profiles of the microorganisms present in a given community and for other community diversity analyses. The process of going from raw gene sequences to taxonomic profiles or diversity measures involves a series of data transformations performed by numerous computational tools. This includes tools for sequence quality checking, denoising, taxonomic classification, alignment, and phylogenetic tree building. In this chapter, we demonstrate how the Quantitative Insights Into Microbial Ecology version 2 (QIIME2) software suite can simplify 16S rRNA marker-gene analysis. We walk through an example data set extracted from the guts of bumblebees in order to show how QIIME2 can transform raw sequences into taxonomic bar plots, phylogenetic trees, principal co-ordinates analyses, and other visualizations of microbial diversity.}, }
@article {pmid30297403, year = {2018}, author = {García, FC and Bestion, E and Warfield, R and Yvon-Durocher, G}, title = {Changes in temperature alter the relationship between biodiversity and ecosystem functioning.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {43}, pages = {10989-10994}, doi = {10.1073/pnas.1805518115}, pmid = {30297403}, issn = {1091-6490}, abstract = {Global warming and the loss of biodiversity through human activities (e.g., land-use change, pollution, invasive species) are two of the most profound threats to the functional integrity of the Earth's ecosystems. These factors are, however, most frequently investigated separately, ignoring the potential for synergistic effects of biodiversity loss and environmental warming on ecosystem functioning. Here we use high-throughput experiments with microbial communities to investigate how changes in temperature affect the relationship between biodiversity and ecosystem functioning. We found that changes in temperature systematically altered the relationship between biodiversity and ecosystem functioning. As temperatures departed from ambient conditions the exponent of the diversity-functioning relationship increased, meaning that more species were required to maintain ecosystem functioning under thermal stress. This key result was driven by two processes linked to variability in the thermal tolerance curves of taxa. First, more diverse communities had a greater chance of including species with thermal traits that enabled them to maintain productivity as temperatures shifted from ambient conditions. Second, we found a pronounced increase in the contribution of complementarity to the net biodiversity effect at high and low temperatures, indicating that changes in species interactions played a critical role in mediating the impacts of temperature change on the relationship between biodiversity and ecosystem functioning. Our results highlight that if biodiversity loss occurs independently of species' thermal tolerance traits, then the additional impacts of environmental warming will result in sharp declines in ecosystem function.}, }
@article {pmid30297041, year = {2019}, author = {Ssepuuya, G and Wynants, E and Verreth, C and Crauwels, S and Lievens, B and Claes, J and Nakimbugwe, D and Van Campenhout, L}, title = {Microbial characterisation of the edible grasshopper Ruspolia differens in raw condition after wild-harvesting in Uganda.}, journal = {Food microbiology}, volume = {77}, number = {}, pages = {106-117}, doi = {10.1016/j.fm.2018.09.005}, pmid = {30297041}, issn = {1095-9998}, abstract = {This research aimed at establishing the chemical intrinsic properties and the microbial quality of an edible grasshopper Ruspolia differens and the effect of its source (geographical area) in Uganda, trading point, swarming season and plucking on these parameters. The intrinsic properties of the grasshopper can support the growth of a wide variety of microorganisms. High counts of total aerobic microbes, Enterobacteriaceae, lactic acid bacteria, total aerobic spores, and yeasts and moulds were obtained. Metagenetic analyses yielded 1793 Operational Taxonomic Units (OTUs) belonging to 24 phyla. Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria and Proteobacteria were the most abundant phyla, while members of the genera Acinetobacter, Buttiauxella, Lactococcus, Staphylococcus and Undibacterium were the most abundant OTUs. A number of genera harbouring potential pathogens (Acinetobacter, Bacillus, Buttiauxella, Campylobacter, Clostridium, Staphylococcus, Pseudomonas and Neisseria) were identified. The geographical area, trading point, swarming season and plucking significantly influenced microbial counts and bacterial diversity. The high microbial counts predispose R. differens to fast microbial spoilage, while the presence of Clostridium and Campylobacter makes this grasshopper a potential source of food borne diseases. Further research should identify the specific spoilage microorganisms of R. differens and assess the characteristics of this grasshopper that support growth of food pathogens.}, }
@article {pmid30294625, year = {2018}, author = {Urra, J and Alkorta, I and Mijangos, I and Garbisu, C}, title = {Data on links between structural and functional prokaryotic diversity in long-term sewage sludge amended soil.}, journal = {Data in brief}, volume = {20}, number = {}, pages = {1787-1796}, doi = {10.1016/j.dib.2018.09.025}, pmid = {30294625}, issn = {2352-3409}, abstract = {The application of sewage sludge to agricultural soil induces co-exposure of prokaryotic populations to antibiotics and heavy metals, thus exerting a selection pressure that may lead to the development of antibiotic resistance. Here, soil samples from a long-term factorial field experiment in which sewage sludge was applied to agricultural soil, at different rates (40 and 80 t ha-1) and frequencies (every 1, 2 and 4 years) of application, were studied to assess: (i) the effect of sewage sludge application on prokaryotic community composition, (ii) the links between prokaryotic community composition and antibiotic resistance profiles, and (iii) the links between antibiotic resistance and metal(oid) concentrations in amended soil. We found no significant impact of sewage sludge on prokaryotic community composition. Some antibiotic resistance genes (ARGs) correlated positively with particular prokaryotic taxa, being Gemmatimonadetes the taxon with the greatest number of positive correlations at phylum level. No positive correlation was found between prokaryotic taxa and genes encoding resistance to sulfonamides and FCA. All metal(oid)s showed positive correlations with, at least, one ARG. Metal(oid) concentrations in soil also showed positive correlations with mobile genetic element genes, particularly with the gene tnpA-07. These data provide useful information on the links between soil prokaryotic composition and resistome profiles, and between antibiotic resistance and metal(oid) concentrations, in agricultural soils amended with sewage sludge.}, }
@article {pmid30294306, year = {2018}, author = {Purahong, W and Wubet, T and Lentendu, G and Hoppe, B and Jariyavidyanont, K and Arnstadt, T and Baber, K and Otto, P and Kellner, H and Hofrichter, M and Bauhus, J and Weisser, WW and Krüger, D and Schulze, ED and Kahl, T and Buscot, F}, title = {Determinants of Deadwood-Inhabiting Fungal Communities in Temperate Forests: Molecular Evidence From a Large Scale Deadwood Decomposition Experiment.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2120}, doi = {10.3389/fmicb.2018.02120}, pmid = {30294306}, issn = {1664-302X}, abstract = {Despite the important role of wood-inhabiting fungi (WIF) in deadwood decomposition, our knowledge of the factors shaping the dynamics of their species richness and community composition is scarce. This is due to limitations regarding the resolution of classical methods used for characterizing WIF communities and to a lack of well-replicated long-term experiments with sufficient numbers of tree species. Here, we used a large scale experiment with logs of 11 tree species at an early stage of decomposition, distributed across three regions of Germany, to identify the factors shaping WIF community composition and Operational Taxonomic Unit (OTU) richness using next generation sequencing. We found that tree species identity was the most significant factor, corresponding to (P < 0.001) and explaining 10% (representing 48% of the explainable variance) of the overall WIF community composition. The next important group of variables were wood-physicochemical properties, of which wood pH was the only factor that consistently corresponded to WIF community composition. For overall WIF richness patterns, we found that approximately 20% of the total variance was explained by wood N content, location, tree species identity and wood density. It is noteworthy that the importance of determinants of WIF community composition and richness appeared to depend greatly on tree species group (broadleaved vs. coniferous) and it differed between the fungal phyla Ascomycota and Basidiomycota.}, }
@article {pmid30290356, year = {2019}, author = {Cipullo, S and Negrin, I and Claveau, L and Snapir, B and Tardif, S and Pulleyblank, C and Prpich, G and Campo, P and Coulon, F}, title = {Linking bioavailability and toxicity changes of complex chemicals mixture to support decision making for remediation endpoint of contaminated soils.}, journal = {The Science of the total environment}, volume = {650}, number = {Pt 2}, pages = {2150-2163}, doi = {10.1016/j.scitotenv.2018.09.339}, pmid = {30290356}, issn = {1879-1026}, abstract = {A six-month laboratory scale study was carried out to investigate the effect of biochar and compost amendments on complex chemical mixtures of tar, heavy metals and metalloids in two genuine contaminated soils. An integrated approach, where organic and inorganic contaminants bioavailability and distribution changes, along with a range of microbiological indicators and ecotoxicological bioassays, was used to provide multiple lines of evidence to support the risk characterisation and assess the remediation end-point. Both compost and biochar amendment (p = 0.005) as well as incubation time (p = 0.001) significantly affected the total and bioavailable concentrations of the total petroleum hydrocarbons (TPH) in the two soils. Specifically, TPH concentration decreased by 46% and 30% in Soil 1 and Soil 2 amended with compost. These decreases were accompanied by a reduction of 78% (Soil 1) and 6% (Soil 2) of the bioavailable hydrocarbons and the most significant decrease was observed for the medium to long chain aliphatic compounds (EC16-35) and medium molecular weight aromatic compounds (EC16-21). Compost amendment enhanced the degradation of both the aliphatic and aromatic fractions in the two soils, while biochar contributed to lock the hydrocarbons in the contaminated soils. Neither compost nor biochar affected the distribution and behaviour of the heavy metals (HM) and metalloids in the different soil phases, suggesting that the co-presence of heavy metals and metalloids posed a low risk. Strong negative correlations were observed between the bioavailable hydrocarbon fractions and the ecotoxicological assays suggesting that when bioavailable concentrations decreased, the toxicity also decreased. This study showed that adopting a combined diagnostic approach can significantly help to identify optimal remediation strategies and contribute to change the over-conservative nature of the current risk assessments thus reducing the costs associated with remediation endpoint.}, }
@article {pmid30288545, year = {2018}, author = {Benucci, GMN and Bonito, V and Bonito, G}, title = {Fungal, Bacterial, and Archaeal Diversity in Soils Beneath Native and Introduced Plants in Fiji, South Pacific.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1266-1}, pmid = {30288545}, issn = {1432-184X}, support = {project MICL02416//Michigan State University AgBioResearch NIFA/ ; DEB1737898//National Science Foundation/ ; }, abstract = {The Fiji Islands is an archipelago of more than 330 islands located in the tropics of the South Pacific Ocean. Microbial diversity and biogeography in this region is still not understood. Here, we present the first molecular characterization of fungal, bacterial, and archaeal communities in soils from different habitats within the largest Fijian island, Viti Levu. Soil samples were collected from under native vegetation in maritime-, forest-, stream-, grassland-, and casuarina-dominated habitats, as well as from under the introduced agricultural crops sugarcane, cassava, pine, and mahogany. Soil microbial diversity was analyzed through MiSeq amplicon sequencing of 16S (for prokaryotes), ITS, LSU ribosomal DNA (for fungi). Prokaryotic communities were dominated by Proteobacteria (~ 25%), Acidobacteria (~ 19%), and Actinobacteria (~ 17%), and there were no indicator species associated with particular habitats. ITS and LSU were congruent in β-diversity patterns of fungi, and fungal communities were dominated by Ascomycota (~ 57-64%), followed by Basidiomycota (~ 20-23%) and Mucoromycota (~ 10%) according to ITS, or Chytridiomycota (~ 9%) according to LSU. Indicator species analysis of fungi found statistical associations of Cenococcum, Wilcoxina, and Rhizopogon to Pinus caribaea. We hypothesize these obligate biotrophic fungi were co-introduced with their host plant. Entoloma was statistically associated with grassland soils, and Fusarium and Lecythophora with soils under cassava. Observed richness varied from 65 (casuarina) to 404 OTUs (cassava) for fungi according to ITS region, and from 1268 (pine) to 2931 OTUs (cassava) for bacteria and archaea. A major finding of this research is that nearly 25% of the fungal OTUs are poorly classified, indicative of novel biodiversity in this region. This preliminary survey provides important baseline data on fungal, bacterial, and archaeal diversity and biogeography in the Fiji Islands.}, }
@article {pmid30288544, year = {2018}, author = {Peters, MJ and Suwannapong, G and Pelin, A and Corradi, N}, title = {Genetic and Genome Analyses Reveal Genetically Distinct Populations of the Bee Pathogen Nosema ceranae from Thailand.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1268-z}, pmid = {30288544}, issn = {1432-184X}, support = {ER13-09-190//Ministry of Research, Innovation and Science/ ; }, abstract = {The recent global decline in Western honeybee (Apis mellifera) populations is of great concern for pollination and honey production worldwide. Declining honeybee populations are frequently infected by the microsporidian pathogen Nosema ceranae. This species was originally described in the Asiatic honeybee (Apis cerana), and its identification in global A. mellifera hives could result from a recent host transfer. Recent genome studies have found that global populations of this parasite are polyploid and that humans may have fueled their global expansion. To better understand N. ceranae biology, we investigated its genetic diversity within part of their native range (Thailand) and among different hosts (A. mellifera, A. cerana) using both PCR and genome-based methods. We find that Thai N. ceranae populations share many SNPs with other global populations and appear to be clonal. However, in stark contrast with previous studies, we found that these populations also carry many SNPs not found elsewhere, indicating that these populations have evolved in their current geographic location for some time. Our genome analyses also indicate the potential presence of diploidy within Thai populations of N. ceranae.}, }
@article {pmid30288176, year = {2018}, author = {Walker, TWN and Kaiser, C and Strasser, F and Herbold, CW and Leblans, NIW and Woebken, D and Janssens, IA and Sigurdsson, BD and Richter, A}, title = {Microbial temperature sensitivity and biomass change explain soil carbon loss with warming.}, journal = {Nature climate change}, volume = {8}, number = {10}, pages = {885-889}, doi = {10.1038/s41558-018-0259-x}, pmid = {30288176}, issn = {1758-678X}, support = {294343//European Research Council/International ; 610028//European Research Council/International ; 636928//European Research Council/International ; }, abstract = {Soil microorganisms control carbon losses from soils to the atmosphere1-3, yet their responses to climate warming are often short-lived and unpredictable4-7. Two mechanisms, microbial acclimation and substrate depletion, have been proposed to explain temporary warming effects on soil microbial activity8-10. However, empirical support for either mechanism is unconvincing. Here we used geothermal temperature gradients (> 50 years of field warming)11 and a short-term experiment to show that microbial activity (gross rates of growth, turnover, respiration and carbon uptake) is intrinsically temperature sensitive and does not acclimate to warming (+ 6 ºC) over weeks or decades. Permanently accelerated microbial activity caused carbon loss from soil. However, soil carbon loss was temporary because substrate depletion reduced microbial biomass and constrained the influence of microbes over the ecosystem. A microbial biogeochemical model12-14 showed that these observations are reproducible through a modest, but permanent, acceleration in microbial physiology. These findings reveal a mechanism by which intrinsic microbial temperature sensitivity and substrate depletion together dictate warming effects on soil carbon loss via their control over microbial biomass. We thus provide a framework for interpreting the links between temperature, microbial activity and soil carbon loss on timescales relevant to Earth's climate system.}, }
@article {pmid30287354, year = {2018}, author = {Staley, C and Sadowsky, MJ}, title = {Practical considerations for sampling and data analysis in contemporary metagenomics-based environmental studies.}, journal = {Journal of microbiological methods}, volume = {154}, number = {}, pages = {14-18}, doi = {10.1016/j.mimet.2018.09.020}, pmid = {30287354}, issn = {1872-8359}, abstract = {Recent advancements in metagenomic-based studies, especially analyses of amplicon-based DNA sequencing targeting taxonomic marker genes, has led to an unprecedented characterization of microbial communities from diverse ecosystems around the world. While originally constrained by a lack of appropriate analytical tools and sequencing depth, new technologies and computational and statistical algorithms have been developed to handle highly dimensional, next-generation sequencing datasets. Both these tools allow for the robust analysis of structural and distributional patterns of microbiota essential for the understanding of microbial ecology and biogeography. Furthermore, consortia of individual laboratories working on large interdisciplinary research programs, like the Human and Earth Microbiome Projects, have developed standardized protocols for DNA extraction, sequencing pipelines, and bioinformatics. These approaches provide large repositories of publicly available data to serve as references for on-going and future, hypothesis-driven studies to better characterize the roles of microbial communities in diverse ecosystems. In this review, we outline the currently available statistical approaches and tools to aid in statistically powered study designs and analyses. Given what is now known about the enormous diversity and variability of the microbial communities in aquatic and terrestrial habitats, we also discuss practical considerations for sample collection. Due to the extensive advances made in the field of metagenomics over the last decade, rigorous, well replicated, hypothesis-driven studies are: 1) needed, 2) now possible, and 3) essential to make best use of sequencing-based technologies to characterize the roles of microbial communities in the structure and function of diverse ecosystems.}, }
@article {pmid30285851, year = {2018}, author = {Mehrshad, M and Salcher, MM and Okazaki, Y and Nakano, SI and Šimek, K and Andrei, AS and Ghai, R}, title = {Hidden in plain sight-highly abundant and diverse planktonic freshwater Chloroflexi.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {176}, doi = {10.1186/s40168-018-0563-8}, pmid = {30285851}, issn = {2049-2618}, abstract = {BACKGROUND: Representatives of the phylum Chloroflexi, though reportedly highly abundant in the extensive deep water habitats of both marine (SAR202 up to 30% of total prokaryotes) and freshwater (CL500-11 up to 26% of total prokaryotes), remain uncultivated and uncharacterized. There are few metagenomic studies on marine Chloroflexi representatives, while the pelagic freshwater Chloroflexi community is largely unknown except for a single metagenome-assembled genome of CL500-11.<br><br>RESULTS: Here, we provide the first extensive examination of the community composition of this cosmopolitan phylum in a range of pelagic habitats (176 datasets) and highlight the impact of salinity and depth on their phylogenomic composition. Reconstructed genomes (53 in total) provide a perspective on the phylogeny, metabolism, and distribution of three novel classes and two family-level taxa within the phylum Chloroflexi. We unraveled a remarkable genomic diversity of pelagic freshwater Chloroflexi representatives that thrive not only in the hypolimnion as previously suspected, but also in the epilimnion. Our results suggest that the lake hypolimnion provides a globally stable habitat reflected in lower species diversity among hypolimnion-specific CL500-11 and TK10 clusters in distantly related lakes compared to a higher species diversity of the epilimnion-specific SL56 cluster. Cell volume analyses show that the CL500-11 are among the largest prokaryotic cells in the water column of deep lakes and with a biomass to abundance ratio of two they significantly contribute to the deep lake carbon flow. Metabolic insights indicate participation of JG30-KF-CM66 representatives in the global cobalamin production via cobinamide to cobalamin salvage pathway.<br><br>CONCLUSIONS: Extending phylogenomic comparisons to brackish and marine habitats suggests salinity as the major influencer of the community composition of the deep-dwelling Chloroflexi in marine (SAR202) and freshwater (CL500-11) habitats as both counterparts thrive in intermediate brackish salinity; however, freshwater habitats harbor the most phylogenetically diverse community of pelagic Chloroflexi representatives that reside both in epi- and hypolimnion.}, }
@article {pmid30285747, year = {2018}, author = {Lebre, PH and Aliyu, H and De Maayer, P and Cowan, DA}, title = {In silico characterization of the global Geobacillus and Parageobacillus secretome.}, journal = {Microbial cell factories}, volume = {17}, number = {1}, pages = {156}, doi = {10.1186/s12934-018-1005-9}, pmid = {30285747}, issn = {1475-2859}, abstract = {BACKGROUND: Geobacillus and Parageobacillus are two ecologically diverse thermophilic genera within the phylum Firmicutes. These taxa have long been of biotechnological interest due to their ability to secrete thermostable enzymes and other biomolecules that have direct applications in various industrial and clinical fields. Despite the commercial and industrial interest in these microorganisms, the full scope of the secreted protein, i.e. the secretome, of Geobacillus and Parageobacillus species remains largely unexplored, with most studies focusing on single enzymes. A genome-wide exploration of the global secretome can provide a platform for understanding the extracellular functional &quot;protein cloud&quot; and the roles that secreted proteins play in the survival and adaptation of these biotechnologically relevant organisms.<br><br>RESULTS: In the present study, the global secretion profile of 64 Geobacillus and Parageobacillus strains, comprising 772 distinct proteins, was predicted using comparative genomic approaches. Thirty-one of these proteins are shared across all strains used in this study and function in cell-wall/membrane biogenesis as well as transport and metabolism of carbohydrates, amino acids and inorganic ions. An analysis of the clustering patterns of the secretomes of the 64 strains according to shared functional orthology revealed a correlation between the secreted profiles of different strains and their phylogeny, with Geobacillus and Parageobacillus species forming two distinct functional clades.<br><br>CONCLUSIONS: The in silico characterization of the global secretome revealed a metabolically diverse set of secreted proteins, which include proteases, glycoside hydrolases, nutrient binding proteins and toxins.}, }
@article {pmid30284602, year = {2018}, author = {Lin, X and Hetharua, B and Lin, L and Xu, H and Zheng, T and He, Z and Tian, Y}, title = {Mangrove Sediment Microbiome: Adaptive Microbial Assemblages and Their Routed Biogeochemical Processes in Yunxiao Mangrove National Nature Reserve, China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1261-6}, pmid = {30284602}, issn = {1432-184X}, support = {2017YFC05061001//National Key Research and Development Program of China/ ; }, abstract = {Microorganisms play important roles in mangrove ecosystems. However, we know little about the ecological implications of mangrove microbiomes for high productivity and the efficient circulation of elements in mangrove ecosystems. Here, we focused on mangrove sediments located at the Yunxiao National Mangrove Reserve in southeast China, uncovering the mangrove microbiome using the 16S rRNA gene and shotgun metagenome sequencing approaches. Physicochemical assays characterized the Yunxiao mangrove sediments as carbon (C)-rich, sulfur (S)-rich, and nitrogen (N)-limited environment. Then phylogenetic analysis profiling a distinctive microbiome with an unexpected high frequency of Chloroflexi and Nitrospirae appeared to be an adaptive characteristic of microbial structure in S-rich habitat. Metagenome sequencing analysis revealed that the metabolic pathways of N and S cycling at the community-level were routed through ammonification and dissimilatory nitrate reduction to ammonium for N conservation in this N-limited habitat, and dissimilatory sulfate reduction along with polysulfide formation for generating bioavailable S resource avoiding the biotoxicity of sulfide in mangrove sediments. In addition, methane metabolism acted as a bridge to connect C cycling to N and S cycling. Further identification of possible biogeochemical linkers suggested Syntrophobacter, Sulfurovum, Nitrospira, and Anaerolinea potentially drive the coupling of C, N, and S cycling. These results highlighting the adaptive routed metabolism flow, a previously undescribed property of mangrove sediment microbiome, appears to be a defining characteristic of this habitat and may significantly contribute to the high productivity of mangrove ecosystems, which could be used as indicators for the health and biodiversity of mangrove ecosystems.}, }
@article {pmid30283424, year = {2018}, author = {El-Chakhtoura, J and Saikaly, PE and van Loosdrecht, MCM and Vrouwenvelder, JS}, title = {Impact of Distribution and Network Flushing on the Drinking Water Microbiome.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2205}, doi = {10.3389/fmicb.2018.02205}, pmid = {30283424}, issn = {1664-302X}, abstract = {We sampled the tap water of seven unique, full-scale drinking water distribution systems at different locations as well as the corresponding treatment plant effluents to evaluate the impact of distribution and the potential presence of a core drinking water microbiome. The water was also sampled during network flushing to examine its effect on the microbial ecology. While a core microbiome dominated by Gammaproteobacteria was found using 16S rRNA gene pyrosequencing, an increase in biomass was detected in the networks, especially during flushing. Water age did not significantly impact the microbiology. Irrespective of differences in treatment plants, tap water bacterial communities in the distinct networks converged and highly resembled the flushed water communities. Piping biofilm and sediment communities therefore largely determine the final tap water microbial quality, attenuating the impact of water source and treatment strategy and highlighting the fundamental role of local physicochemical conditions and microbial processes within infrastructure micro-niches.}, }
@article {pmid30283421, year = {2018}, author = {Durán, P and Tortella, G and Viscardi, S and Barra, PJ and Carrión, VJ and Mora, ML and Pozo, MJ}, title = {Microbial Community Composition in Take-All Suppressive Soils.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2198}, doi = {10.3389/fmicb.2018.02198}, pmid = {30283421}, issn = {1664-302X}, abstract = {Gaeumannomyces graminis var. tritici (Ggt) is the main soilborne factor that affects wheat production around the world. Recently we reported the occurrence of six suppressive soils in monoculture areas from indigenous &quot;Mapuche&quot; communities, and evidenced that the suppression relied on the biotic component of those soils. Here, we compare the rhizosphere and endosphere microbial community structure (total bacteria, actinomycetes, total fungi, and ascomycetes) of wheat plants grown in suppressive and conducive soils. Our results suggested that Ggt suppression could be mediated mostly by bacterial endophytes, rather than rhizosphere microorganisms, since the community structure was similar in all suppressive soils as compared with conducive. Interestingly, we found that despite the lower incidence of take-all disease in suppressive soils, the Ggt concentration in roots was not significantly reduced in all suppressive soils compared to those growing in conducive soil. Therefore, the disease suppression is not always related to a reduction of the pathogen biomass. Furthermore, we isolated endophytic bacteria from wheat roots growing in suppressive soils. Among them we identified Serratia spp. and Enterobacter spp. able to inhibit Ggt growth in vitro. Since the disease, but not always pathogen amount, was reduced in the suppressive soils, we propose that take all disease suppressiveness is not only related to direct antagonism to the pathogen.}, }
@article {pmid30283052, year = {2018}, author = {Boers, SA and Prest, EI and Taučer-Kapteijn, M and Knezev, A and Schaap, PG and Hays, JP and Jansen, R}, title = {Monitoring of microbial dynamics in a drinking water distribution system using the culture-free, user-friendly, MYcrobiota platform.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14727}, doi = {10.1038/s41598-018-32987-x}, pmid = {30283052}, issn = {2045-2322}, abstract = {Drinking water utilities currently rely on a range of microbiological detection techniques to evaluate the quality of their drinking water (DW). However, microbiota profiling using culture-free 16S rRNA gene next-generation sequencing (NGS) provides an opportunity for improved monitoring of the microbial ecology and quality of DW. Here, we evaluated the utility of a previously validated microbiota profiling platform (MYcrobiota) to investigate the microbial dynamics of a full-scale, non-chlorinated DW distribution system (DWDS). In contrast to conventional methods, we observed spatial and temporal bacterial genus changes (expressed as operational taxonomic units - OTUs) within the DWDS. Further, a small subset of bacterial OTUs dominated with abundances that shifted across the length of the DWDS, and were particularly affected by a post-disinfection step. We also found seasonal variation in OTUs within the DWDS and that many OTUs could not be identified, even though MYcrobiota is specifically designed to reduce potential PCR sequencing artefacts. This suggests that our current knowledge about the microbial ecology of DW communities is limited. Our findings demonstrate that the user-friendly MYcrobiota platform facilitates culture-free, standardized microbial dynamics monitoring and has the capacity to facilitate the introduction of microbiota profiling into the management of drinking water quality.}, }
@article {pmid30281902, year = {2018}, author = {Sollai, M and Villanueva, L and Hopmans, EC and Reichart, GJ and Sinninghe Damsté, JS}, title = {A combined lipidomic and 16S rRNA gene amplicon sequencing approach reveals archaeal sources of intact polar lipids in the stratified Black Sea water column.}, journal = {Geobiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gbi.12316}, pmid = {30281902}, issn = {1472-4669}, support = {024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek - Soehngen Institute for Anaerobic Microbiology (SIAM)/ ; 024.002.001//Nederlandse Organisatie voor Wetenschappelijk Onderzoek - Netherlands Earth System Science Center (NESSC)/ ; 3012//Darwin Center for Biogeosciences/ ; 822.01013//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, abstract = {Archaea are important players in marine biogeochemical cycles, and their membrane lipids are useful biomarkers in environmental and geobiological studies. However, many archaeal groups remain uncultured and their lipid composition unknown. Here, we aim to expand the knowledge on archaeal lipid biomarkers and determine the potential sources of those lipids in the water column of the euxinic Black Sea. The archaeal community was evaluated by 16S rRNA gene amplicon sequencing and by quantitative PCR. The archaeal intact polar lipids (IPLs) were investigated by ultra-high-pressure liquid chromatography coupled to high-resolution mass spectrometry. Our study revealed both a complex archaeal community and large changes with water depth in the IPL assemblages. In the oxic/upper suboxic waters (<105 m), the archaeal community was dominated by marine group (MG) I Thaumarchaeota, coinciding with a higher relative abundance of hexose phosphohexose crenarchaeol, a known marker for Thaumarchaeota. In the suboxic waters (80-110 m), MGI Nitrosopumilus sp. dominated and produced predominantly monohexose glycerol dibiphytanyl glycerol tetraethers (GDGTs) and hydroxy-GDGTs. Two clades of MGII Euryarchaeota were present in the oxic and upper suboxic zones in much lower abundances, preventing the detection of their specific IPLs. In the deep sulfidic waters (>110 m), archaea belonging to the DPANN Woesearchaeota, Bathyarchaeota, and ANME-1b clades dominated. Correlation analyses suggest that the IPLs GDGT-0, GDGT-1, and GDGT-2 with two phosphatidylglycerol (PG) head groups and archaeol with a PG, phosphatidylethanolamine, and phosphatidylserine head groups were produced by ANME-1b archaea. Bathyarchaeota represented 55% of the archaea in the deeper part of the euxinic zone and likely produces archaeol with phospho-dihexose and hexose-glucuronic acid head groups.}, }
@article {pmid30280234, year = {2018}, author = {Boixel, AL and Delestre, G and Legeay, J and Chelle, M and Suffert, F}, title = {Phenotyping Thermal Responses of Yeasts and Yeast-like Microorganisms at the Individual and Population Levels: Proof-of-Concept, Development and Application of an Experimental Framework to a Plant Pathogen.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1253-6}, pmid = {30280234}, issn = {1432-184X}, support = {ANR-11-LABX-0034//Agence Nationale de la Recherche/ ; }, abstract = {Deciphering the responses of microbial populations to spatiotemporal changes in their thermal environment is instrumental in improving our understanding of their eco-evolutionary dynamics. Recent studies have shown that current phenotyping protocols do not adequately address all dimensions of phenotype expression. Therefore, these methods can give biased assessments of sensitivity to temperature, leading to misunderstandings concerning the ecological processes underlying thermal plasticity. We describe here a new robust and versatile experimental framework for the accurate investigation of thermal performance and phenotypic diversity in yeasts and yeast-like microorganisms, at the individual and population levels. In addition to proof-of-concept, the application of this framework to the fungal wheat pathogen Zymoseptoria tritici resulted in detailed characterisations for this yeast-like microorganism of (i) the patterns of temperature-dependent changes in performance for four fitness traits; (ii) the consistency in thermal sensitivity rankings of strains between in planta and in vitro growth assessments; (iii) significant interindividual variation in thermal responses, with four principal thermotypes detected in a sample of 66 strains; and (iv) the ecological consequences of this diversity for population-level processes through pairwise competition experiments highlighting temperature-dependent outcomes. These findings extend our knowledge and ability to quantify and categorise the phenotypic heterogeneity of thermal responses. As such, they lay the foundations for further studies elucidating local adaptation patterns and the effects of temperature variations on eco-evolutionary and epidemiological processes.}, }
@article {pmid30280026, year = {2018}, author = {Li, J and Lin, J and Pei, C and Lai, K and Jeffries, TC and Tang, G}, title = {Variation of soil bacterial communities along a chronosequence of Eucalyptus plantation.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5648}, doi = {10.7717/peerj.5648}, pmid = {30280026}, issn = {2167-8359}, abstract = {Eucalyptus is harvested for wood and fiber production in many tropical and sub-tropical habitats globally. Plantation has been controversial because of its influence on the surrounding environment, however, the influence of massive Eucalyptus planting on soil microbial communities is unclear. Here we applied high-throughput sequencing of the 16S rRNA gene to assess the microbial community composition and diversity of planting chronosequences, involving two, five and ten years of Eucalyptus plantation, comparing to that of secondary-forest in South China. We found that significant changes in the composition of soil bacteria occurred when the forests were converted from secondary-forest to Eucalyptus. The bacterial community structure was clearly distinct from control and five year samples after Eucalyptus was grown for 2 and 10 years, highlighting the influence of this plantation on local soil microbial communities. These groupings indicated a cycle of impact (2 and 10 year plantations) and low impact (5-year plantations) in this chronosequence of Eucalyptus plantation. Community patterns were underpinned by shifts in soil properties such as pH and phosphorus concentration. Concurrently, key soil taxonomic groups such as Actinobacteria showed abundance shifts, increasing in impacted plantations and decreasing in low impacted samples. Shifts in taxonomy were reflected in a shift in metabolic potential, including pathways for nutrient cycles such as carbon fixation, which changed in abundance over time following Eucalyptus plantation. Combined these results confirm that Eucalyptus plantation can change the community structure and diversity of soil microorganisms with strong implications for land-management and maintaining the health of these ecosystems.}, }
@article {pmid30279438, year = {2018}, author = {Quintanilla, E and Ramírez-Portilla, C and Adu-Oppong, B and Walljasper, G and Glaeser, SP and Wilke, T and Muñoz, AR and Sánchez, JA}, title = {Local confinement of disease-related microbiome facilitates recovery of gorgonian sea fans from necrotic-patch disease.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14636}, doi = {10.1038/s41598-018-33007-8}, pmid = {30279438}, issn = {2045-2322}, abstract = {Microbiome disruptions triggering disease outbreaks are increasingly threatening corals worldwide. In the Tropical Eastern Pacific, a necrotic-patch disease affecting gorgonian corals (sea fans, Pacifigorgia spp.) has been observed in recent years. However, the composition of the microbiome and its disease-related disruptions remain unknown in these gorgonian corals. Therefore, we analysed 16S rRNA gene amplicons from tissues of healthy colonies (n = 19) and from symptomatic-asymptomatic tissues of diseased colonies (n = 19) of Pacifigorgia cairnsi (Gorgoniidae: Octocorallia) in order to test for disease-related changes in the bacterial microbiome. We found that potential endosymbionts (mostly Endozoicomonas spp.) dominate the core microbiome in healthy colonies. Moreover, healthy tissues differed in community composition and functional profile from those of the symptomatic tissues but did not show differences to asymptomatic tissues of the diseased colonies. A more diverse set of bacteria was observed in symptomatic tissues, together with the decline in abundance of the potential endosymbionts from the healthy core microbiome. Furthermore, according to a comparative taxonomy-based functional profiling, these symptomatic tissues were characterized by the increase in heterotrophic, ammonia oxidizer and dehalogenating bacteria and by the depletion of nitrite and sulphate reducers. Overall, our results suggest that the bacterial microbiome associated with the disease behaves opportunistically and is likely in a state of microbial dysbiosis. We also conclude that the confinement of the disease-related consortium to symptomatic tissues may facilitate colony recovery.}, }
@article {pmid30276419, year = {2018}, author = {Renoz, F and Pons, I and Vanderpoorten, A and Bataille, G and Noël, C and Foray, V and Pierson, V and Hance, T}, title = {Evidence for Gut-Associated Serratia symbiotica in Wild Aphids and Ants Provides New Perspectives on the Evolution of Bacterial Mutualism in Insects.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1265-2}, pmid = {30276419}, issn = {1432-184X}, support = {1.E074.14//Fonds pour la Formation à la Recherche dans l'Industrie et dans l'Agriculture/ ; }, abstract = {Many insects engage in symbiotic associations with diverse assemblages of bacterial symbionts that can deeply impact on their ecology and evolution. The intraspecific variation of symbionts remains poorly assessed while phenotypic effects and transmission behaviors, which are key processes for the persistence and evolution of symbioses, may differ widely depending on the symbiont strains. Serratia symbiotica is one of the most frequent symbiont species in aphids and a valuable model to assess this intraspecific variation since it includes both facultative and obligate symbiotic strains. Despite evidence that some facultative S. symbiotica strains exhibit a free-living capacity, the presence of these strains in wild aphid populations, as well as in insects with which they maintain regular contact, has never been demonstrated. Here, we examined the prevalence, diversity, and tissue tropism of S. symbiotica in wild aphids and associated ants. We found a high occurrence of S. symbiotica infection in ant populations, especially when having tended infected aphid colonies. We also found that the S. symbiotica diversity includes strains found located within the gut of aphids and ants. In the latter, this tissue tropism was found restricted to the proventriculus. Altogether, these findings highlight the extraordinary diversity and versatility of an insect symbiont and suggest the existence of novel routes for symbiont acquisition in insects.}, }
@article {pmid30274898, year = {2018}, author = {Blachier, F and Beaumont, M and Portune, KJ and Steuer, N and Lan, A and Audebert, M and Khodorova, N and Andriamihaja, M and Airinei, G and Benamouzig, R and Davila, AM and Armand, L and Rampelli, S and Brigidi, P and Tomé, D and Claus, SP and Sanz, Y}, title = {High-protein diets for weight management: Interactions with the intestinal microbiota and consequences for gut health. A position paper by the my new gut study group.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.clnu.2018.09.016}, pmid = {30274898}, issn = {1532-1983}, abstract = {BACKGROUND &amp; AIMS: This review examines to what extent high-protein diets (HPD), which may favor body weight loss and improve metabolic outcomes in overweight and obese individuals, may also impact the gut environment, shaping the microbiota and the host-microbe (co)metabolic pathways and products, possibly affecting large intestine mucosa homeostasis.<br><br>METHODS: PubMed-referenced publications were analyzed with an emphasis on dietary intervention studies involving human volunteers in order to clarify the beneficial vs. deleterious effects of HPD in terms of both metabolic and gut-related health parameters; taking into account the interactions with the gut microbiota.<br><br>RESULTS: HPD generally decrease body weight and improve blood metabolic parameters, but also modify the fecal and urinary contents in various bacterial metabolites and co-metabolites. The effects of HPD on the intestinal microbiota composition appear rather heterogeneous depending on the type of dietary intervention. Recently, HPD consumption was shown to modify the expression of genes playing key roles in homeostatic processes in the rectal mucosa, without evidence of intestinal inflammation. Importantly, the effects of HPD on the gut were dependent on the protein source (i.e. from plant or animal sources), a result which should be considered for further investigations.<br><br>CONCLUSION: Although HPD appear to be efficient for weight loss, the effects of HPD on microbiota-derived metabolites and gene expression in the gut raise new questions on the impact of HPD on the large intestine mucosa homeostasis leading the authors to recommend some caution regarding the utilization of HPD, notably in a recurrent and/or long-term ways.}, }
@article {pmid30273809, year = {2018}, author = {De Vrieze, J and Arends, JBA and Verbeeck, K and Gildemyn, S and Rabaey, K}, title = {Interfacing anaerobic digestion with (bio)electrochemical systems: Potentials and challenges.}, journal = {Water research}, volume = {146}, number = {}, pages = {244-255}, doi = {10.1016/j.watres.2018.08.045}, pmid = {30273809}, issn = {1879-2448}, abstract = {For over a century, anaerobic digestion has been a key technology in stabilizing organic waste streams, while at the same time enabling the recovery of energy. The anticipated transition to a bio-based economy will only increase the quantity and diversity of organic waste streams to be treated, and, at the same time, increase the demand for additional and effective resource recovery schemes for nutrients and organic matter. The performance of anaerobic digestion can be supported and enhanced by (bio)electrochemical systems in a wide variety of hybrid technologies. Here, the possible benefits of combining anaerobic digestion with (bio)electrochemical systems were reviewed in terms of (1) process monitoring, control, and stabilization, (2) nutrient recovery, (3) effluent polishing, and (4) biogas upgrading. The interaction between microorganisms and electrodes with respect to niche creation is discussed, and the potential impact of this interaction on process performance is evaluated. The strength of combining anaerobic digestion with (bio)electrochemical technologies resides in the complementary character of both technologies, and this perspective was used to distinguish transient trends from schemes with potential for full-scale application. This is supported by an operational costs assessment, showing that the economic potential of combining anaerobic digestion with a (bio)electrochemical system is highly case-specific, and strongly depends on engineering challenges with respect to full-scale applications.}, }
@article {pmid30273364, year = {2018}, author = {Tam, J and Hoffmann, T and Fischer, S and Bornstein, S and Gräßler, J and Noack, B}, title = {Obesity alters composition and diversity of the oral microbiota in patients with type 2 diabetes mellitus independently of glycemic control.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0204724}, doi = {10.1371/journal.pone.0204724}, pmid = {30273364}, issn = {1932-6203}, abstract = {BACKGROUND AND OBJECTIVE: The involvement of the oral microbiota as a possible link between periodontitis, type 2 diabetes mellitus and obesity is still not well understood. The objective of the study was to investigate if glycemic control and obesity play a role in modulating the composition and diversity of the oral microbial ecology.<br><br>MATERIAL AND METHODS: A cohort of patients with type 2 diabetes mellitus (n = 18) was recruited. Participants demonstrating improved glycemic control after 3 months (n = 6) were included in a second examination. A full mouth examination was performed to estimate periodontitis severity followed by sample collection (subgingival plaque and saliva). Generation of large sequence libraries was performed using the high-throughput Illumina MiSeq sequencing platform.<br><br>RESULTS: The majority of participants (94.4%, n = 17) presented with moderate or severe forms of periodontitis. Differences in microbial composition and diversity between obese (BMI ≥ 30 kg/m2) and non-obese (BMI < 30 kg/m2) groups were statistically significant. Cross-sectional and longitudinal approaches failed to reveal statistically significant associations between HbA1c level and species composition or diversity.<br><br>CONCLUSIONS: Obesity was significantly associated with the oral microbial composition. The impact of glycemic control on oral microbiota, however, could not be assured statistically.}, }
@article {pmid30272014, year = {2018}, author = {de Araujo, ASF and Mendes, LW and Lemos, LN and Antunes, JEL and Beserra, JEA and de Lyra, MDCCP and Figueiredo, MDVB and Lopes, ÂCA and Gomes, RLF and Bezerra, WM and Melo, VMM and de Araujo, FF and Geisen, S}, title = {Protist species richness and soil microbiome complexity increase towards climax vegetation in the Brazilian Cerrado.}, journal = {Communications biology}, volume = {1}, number = {}, pages = {135}, doi = {10.1038/s42003-018-0129-0}, pmid = {30272014}, issn = {2399-3642}, abstract = {Biodiversity underlies ecosystem functioning. While aboveground biodiversity is often well studied, the belowground microbiome, in particular protists, remains largely unknown. Indeed, holistic insights into soil microbiome structures in natural soils, especially in hyperdiverse biomes such as the Brazilian Cerrado, remain unexplored. Here, we study the soil microbiome across four major vegetation zones of the Cerrado, ranging from grass-dominated to tree-dominated vegetation with a focus on protists. We show that protist taxon richness increases towards the tree-dominated climax vegetation. Early successional habitats consisting of primary grass vegetation host most potential plant pathogens and least animal parasites. Using network analyses combining protist with prokaryotic and fungal sequences, we show that microbiome complexity increases towards climax vegetation. Together, this suggests that protists are key microbiome components and that vegetation succession towards climax vegetation is stimulated by higher loads of animal and plant pathogens. At the same time, an increase in microbiome complexity towards climax vegetation might enhance system stability.}, }
@article {pmid30269410, year = {2018}, author = {Bovio, P and Cabezas, A and Etchebehere, C}, title = {Preliminary analysis of Chloroflexi populations in full scale UASB methanogenic reactors.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.14115}, pmid = {30269410}, issn = {1365-2672}, abstract = {AIMS: The phylum Chloroflexi is frequently found in high abundance in methanogenic reactors, but, their role is still unclear as most of them remain uncultured and understudied. Hence, a detailed analysis was performed in samples from five Up-flow anaerobic sludge blanket (UASB) full-scale reactors fed with different industrial wastewaters.<br><br>METHODS AND RESULTS: Quantitative PCR show that the phylum Chloroflexi was abundant in all UASB methanogenic reactors, with higher abundance in the reactors operated for a long period of time, which presented granular biomass. Both T-RFLP and 16S rRNA gene amplicon sequencing revealed diverse Chloroflexi populations apparently determined by the different inocula. According to the phylogenetic analysis the sequences from the dominant Chloroflexi were positioned in branches where no sequences of the cultured representative strains is placed. FISH analysis performed in two of the reactors showed filamentous morphology of the hybridizing cells.<br><br>CONCLUSIONS: While members of the Anaerolineae class within phylum Chloroflexi were predominant, their diversity is still poorly described in anaerobic reactors. Due to their filamentous morphology, Chloroflexi may have a key role in the granulation in methanogenic UASB reactors.<br><br>Our results bring new insights about the diversity, stability, dynamics and abundance of this phylum in full scale UASB reactors which aid in understanding their function within the reactor biomass. However, new methodological approaches and analysis of bulking biomass is needed to completely unravel their role in these reactors. Combining all this knowledge with reactor operational parameters will allow to understand their participation in granulation and bulking episodes and design strategies to prevent Chloroflexi overgrowth. This article is protected by copyright. All rights reserved.}, }
@article {pmid30267172, year = {2018}, author = {Staley, C and Kaiser, T and Khoruts, A}, title = {Clinician Guide to Microbiome Testing.}, journal = {Digestive diseases and sciences}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10620-018-5299-6}, pmid = {30267172}, issn = {1573-2568}, abstract = {Recent recognition that the intestinal microbiome plays potential roles in the pathogenesis of multiple common diseases has led to a growing interest in personalized microbiome analysis among clinical investigators and patients. Permissibility of direct access testing has allowed the emergence of commercial companies offering microbiome analysis to patients seeking to gain a better understanding of their symptoms and disease conditions. In turn, physicians are often asked to help with interpretation of such tests or even requested by their patients to order them. Therefore, physicians need to have a basic understanding of the current state of microbiome science. This review examines how the perspective of microbial ecology, which is fundamental to understanding the microbiome, updates the classical version of the germ theory of disease. We provide the essential vocabulary of microbiome science and describe its current limitations. We look forward to the future when microbiome diagnostics may live up to its potential of becoming integral to clinical care that will become increasingly individualized, and microbiome analysis may become incorporated into that future paradigm. However, we caution patients and providers that the current microbiome tests, given the state of knowledge and technology, do not provide much value in clinical decisions. Considerable research remains to be carried out to make this objective a reality.}, }
@article {pmid30267129, year = {2018}, author = {Miller, SR and Carvey, D}, title = {Ecological Divergence with Gene Flow in a Thermophilic Cyanobacterium.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1267-0}, pmid = {30267129}, issn = {1432-184X}, support = {EF-0801999//National Science Foundation/ ; }, abstract = {How ecological diversity is maintained and distributed within populations is a longstanding question in microbial ecology. In the thermophilic cyanobacterium Synechococcus B', high observed levels of recombination are predicted to maintain ecological variation despite the simultaneous action of diverse selective pressures on different regions of the genome. To investigate ecological diversity in these bacteria, we directly isolated laboratory strains of Synechococcus B' from samples collected along the thermal gradients of two geothermal environments in Yellowstone National Park. Extensive recombination was evident for a multi-locus sequence data set, and, consequently, our sample did not exhibit the sequence clustering expected for distinct ecotypes evolving by periodic clonal selection. Evidence for local selective sweeps at specific loci suggests that sweeps may be common but that recombination is effective for maintaining diversity of unlinked genomic regions. Thermal performance for strain growth was positively associated with the temperature of the environment, indicating that Synechococcus B' populations consist of locally adapted ecological specialists that occupy specific thermal niches. Because this ecological differentiation is observed despite the absence of dispersal barriers among sites, we conclude that these bacteria may freely exchange much of the genome but that barriers to gene flow exist for loci under direct temperature selection.}, }
@article {pmid30266729, year = {2018}, author = {Vital, M and Howe, A and Bergeron, N and Krauss, RM and Jansson, JK and Tiedje, JM}, title = {Metagenomic insights into resistant starch degradation by human gut microbiota.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.01562-18}, pmid = {30266729}, issn = {1098-5336}, abstract = {Several studies monitoring alterations of the community structure upon resistant starch (RS) interventions are available, although comprehensive function-based analyses are lacking. Recently, a multiomics approach based on 16S rRNA gene-sequencing, metaproteomics and metabolomics on fecal samples from individuals subjected to high and low doses of type-2 RS (RS2; 48 g and 3 g/2500 kcal, respectively, daily for 2 weeks) in a cross-over intervention experiment was performed. In the present study, we did pathway-based metagenomic analyses on samples from a subset of individuals (n=12) from that study to get additional, detailed insights into the functional structure at high resolution during RS2 intervention. A mechanistic framework based on obtained results is proposed where primary degradation was governed by Firmicutes, with Ruminococcus bromii as a major taxon involved, providing fermentation substrates and increased acetate concentrations for growth of various major butyrate-producers exhibiting the enzyme butyryl-CoA:acetate CoA-transferase. H2-scavenging sulfite reducers and acetogens concurrently increased. Individual responses of gut microbiota were noted where seven of the 12 participants displayed all features of the outlined pattern, whereas four individuals showed mixed behavior and one subject was unresponsive. Intervention order did not affect the outcome emphasizing a constant substrate supply for maintaining specific functional communities.Significance Manipulating gut microbiota is increasingly recognized as a promising approach to reduce various non-communicable diseases such as obesity and type-2-diabetes. Specific dietary supplements including resistant starches (RS) are often in focus, yet comprehensive insights into functional responses of microbiota are largely lacking. Furthermore, unresponsiveness in certain individuals is only poorly understood. Our data indicate that distinct parts of microbiota work jointly to degrade RS and successively form health-promoting fermentation end products. It highlights the need to consider both primary degraders and specific, more downstream acting bacterial groups in order to achieve desired intervention outcomes. The gained insights will assist the design of personalized treatment strategies based on individual's microbiota.}, }
@article {pmid30266244, year = {2018}, author = {Miller, ET and Svanbäck, R and Bohannan, BJM}, title = {Microbiomes as Metacommunities: Understanding Host-Associated Microbes through Metacommunity Ecology.}, journal = {Trends in ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2018.09.002}, pmid = {30266244}, issn = {1872-8383}, abstract = {Interest in host-associated microbiomes has skyrocketed recently, yet our ability to explain microbiome variation has remained stubbornly low. Considering scales of interaction beyond the level of the individual host could lead to new insights. Metacommunity theory has many of the tools necessary for modeling multiscale processes and has been successfully applied to host microbiomes. However, the biotic nature of the host requires an expansion of theory to incorporate feedback between the habitat patch (host) and their local (microbial) community. This feedback can have unexpected effects, is predicted to be common, and can arise through a variety of mechanisms, including developmental, ecological, and evolutionary processes. We propose a new way forward for both metacommunity theory and host microbiome research that incorporates this feedback.}, }
@article {pmid30265892, year = {2018}, author = {Fiorentino, A and Cucciniello, R and Di Cesare, A and Fontaneto, D and Prete, P and Rizzo, L and Corno, G and Proto, A}, title = {Disinfection of urban wastewater by a new photo-Fenton like process using Cu-iminodisuccinic acid complex as catalyst at neutral pH.}, journal = {Water research}, volume = {146}, number = {}, pages = {206-215}, doi = {10.1016/j.watres.2018.08.024}, pmid = {30265892}, issn = {1879-2448}, abstract = {Photo-Fenton process is among the most effective advanced oxidation processes (AOPs) in urban wastewater treatment and disinfection, but its application as tertiary treatment at full scale has not been a feasible/attractive option so far because optimum conditions are typically achieved under acidic pH. In this work a new photo Fenton like process (UV-C/H2O2/IDS-Cu) using iminodisuccinic acid (IDS)-Cu complex as catalyst, was compared to other processes (UV-C/H2O2/Cu, UV-C/H2O2/Fe, H2O2 and UV-C) in urban wastewater disinfection. Since this is the first time that IDS-Cu complex was isolated and used as catalyst, preliminary tests to evaluate the mineralization of a model compound (phenol, 25 mg L-1 initial concentration) in water by UV-C/H2O2/IDS-Cu were carried out. Almost complete mineralization of phenol (95%) was observed after 60 min treatment, being the process more effective than all other investigated AOPs (Fenton and photo-Fenton processes). This process was also proven to be more effective in the inactivation of E. coli (complete inactivation (3.5 log units) in 10 min) at natural pH (7.8 ± 0.5) in real wastewater, than the other processes investigated. Unlike of what observed for E. coli inactivation, the investigated processes only partially inactivated total bacterial population (from 18% for UV-C to 43% for UV-C/H2O2/Cu), according to flow cytometry measurements. In particular, Cu based photo-Fenton processes resulted in the higher percentage of inactivated total cells, thus being consistent with the results of E. coli inactivation. It is worthy to note that, as H2O2 was decreased, UV-C/H2O2/Cu-IDS was more effective than UV-C/H2O2/Cu process. Moreover, the formation of small and large clusters decreased in the presence of Cu and Cu-IDS complex, and process efficiency improved accordingly; these results show that Cu based AOPs can more effectively disaggregate clusters, thus making disinfection process more effective than Fe based AOPs.}, }
@article {pmid30262203, year = {2018}, author = {Tomuschat, C and Virbel, CR and O'Donnell, AM and Puri, P}, title = {Reduced expression of the NLRP6 inflammasome in the colon of patients with Hirschsprung's disease.}, journal = {Journal of pediatric surgery}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jpedsurg.2018.08.059}, pmid = {30262203}, issn = {1531-5037}, abstract = {PURPOSE: Hirschsprung's associated enterocolitis (HAEC) is the most common cause of morbidity and mortality in Hirschsprung's Disease (HSCR). The pathogenesis of HAEC remains unsatisfactorily understood. Mounting evidence of an altered microbiome in patients with HSCR adds a new angle to the pathogenesis of HAEC. NLRP6 is a member of the nucleotide-binding domain, leucine-rich-repeat-containing (NLR) innate immune receptor family, a multiprotein complex that functions as a sensor of damage-associated molecular patterns. Known as inflammasomes they have been implicated in the regulation of colonic microbial ecology and by alteration, regulators of inflammation. We designed this study to test the hypothesis that NLRP6 expression is altered in the colon of patients with HSCR.<br><br>METHODS: We investigated NLPR6 protein expression in both the aganglionic and ganglionic regions of HSCR patients (n = 10) versus healthy control colon (n = 10). Protein distribution was assessed by using immunofluorescence and confocal microscopy. Gene and protein expressions were quantified using quantitative real-time polymerase chain reaction (qPCR), Western blot analysis, and densitometry.<br><br>MAIN RESULTS: qPCR and Western blot analysis revealed that NLRP6 is expressed in the colon of patients with HSCR. NLRP6 expression was significantly decreased (p < 0.003) in the ganglionic and aganglionic bowel in HSCR compared to controls. Confocal microscopy revealed that NLRP6 expression in colonic epithelium was markedly decreased in HSCR specimens compared to controls.<br><br>CONCLUSION: We demonstrate for the first time the expression and distribution of NLRP6 in patients with HSCR. The observed decreased expression of NLRP6 may contribute to an altered colonic microbiome in patients with HSCR and increases the susceptibility to develop HAEC.}, }
@article {pmid30261358, year = {2018}, author = {Friedman, L and Mamane, H and Avisar, D and Chandran, K}, title = {The role of influent organic carbon-to-nitrogen (COD/N) ratio in removal rates and shaping microbial ecology in soil aquifer treatment (SAT).}, journal = {Water research}, volume = {146}, number = {}, pages = {197-205}, doi = {10.1016/j.watres.2018.09.014}, pmid = {30261358}, issn = {1879-2448}, abstract = {Soil columns simulating soil aquifer treatment (SAT), fed with synthetic secondary effluent by intermittent infiltration of flooding/drying cycles, were characterized for nitrogen and organic carbon removal, and microbial ecology and biokinetics. The columns differed in the concentration ratio of chemical oxygen demand (COD) to the summed NH4+, NO2- and organic nitrogen-2 (C/N2) or 5 (C/N5). Chemical profiles along the column demonstrated a preference for COD oxidation over nitrification and coupled denitrification, with higher nitrogen loss (57% vs. 16%) in the C/N5 column. Unexpectedly, significant dominance of the genus Nitrospira over the genus Nitrobacter and ammonia-oxidizing bacteria (AOB) was strongly correlated at column depths where NH4+ removal occurred. Moreover, the Nitrospira profile had the strongest correlation to the profile of NH4+ (positive) and NO3- (negative), strongly indicating complete ammonia oxidation. 16S sequencing analysis of the topsoil in C/N2 vs. C/N5 columns revealed double the abundance of microbial aerobic potential (64% vs. 32%) vs. one-third the denitrification potential (13% vs. 31%). The concentrations and degradability levels of organic carbon were the most influential parameters shaping community structure. Niche differentiation within the biofilm attached to the soil is suggested to have an important role in the process's anoxic activity and nitrogen removal.}, }
@article {pmid30259511, year = {2018}, author = {Pimentel, SP and Fontes, M and Ribeiro, FV and Corrêa, MG and Nishii, D and Cirano, FR and Casati, MZ and Casarin, RCV}, title = {Smoking habit modulates peri-implant microbiome: A case-control study.}, journal = {Journal of periodontal research}, volume = {53}, number = {6}, pages = {983-991}, doi = {10.1111/jre.12597}, pmid = {30259511}, issn = {1600-0765}, abstract = {BACKGROUND AND OBJECTIVE: Smoking is a recognized risk factor for peri-implant disease and leads to microbiological changes in mucositis and peri-implantitis. However, there is no knowledge about the impact of smoking in healthy peri-implant tissue. The aim of the study was to evaluate the microbiome in a peri-implant environment in smokers with healthy peri-implant conditions.<br><br>METHODS: Peri-implant biofilm was collected around single clinically healthy, screwed-retained, teeth-surrounded implants in 12 non-smoker (NSMK) and 12 smoker (SMK) non-periodontitis subjects (no bleeding and probing depth <4 mm). Bacterial DNA was isolated and 16S ribosomal RNA gene libraries were sequenced using pyrosequencing, targeting the V3-V4 region. Datasets were processed using the Quantitative Insights into Microbial Ecology, Greengenes and the Human Oral Microbiome Database databases.<br><br>RESULTS: An evident difference in the SMK peri-implant microbiome was observed compared to the NSMK microbiome, with a large abundance of species, even with a healthy peri-implant. The SMK core-microbiome showed an abundance of Fusobacterium, Tannerella and Mogibacterium, while the NSMK core revealed an abundance of Actinomyces, Capnocytophaga and Streptococcus, genera that are usually related to periodontal health. The microbiome inter-relationship was shown to be more inter-generic in SMK then in NSMK, indicating different microbiome cohesion.<br><br>CONCLUSION: Smoking negatively affected the peri-implant microbiome, leading to a disease-associated state, even in clinically healthy individuals.}, }
@article {pmid30259168, year = {2018}, author = {Cardinale, M and Suarez, C and Steffens, D and Ratering, S and Schnell, S}, title = {Effect of Different Soil Phosphate Sources on the Active Bacterial Microbiota Is Greater in the Rhizosphere than in the Endorhiza of Barley (Hordeum vulgare L.).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1264-3}, pmid = {30259168}, issn = {1432-184X}, abstract = {Phosphate is a macronutrient and often the limiting growing factor of many ecosystems. The aim of this work was to assess the effect of various phosphate sources on the active bacterial microbiota of barley rhizosphere and endorhiza. Barley was grown on poor soil supplemented with either Ca(H2PO4)2 (CaP), Gafsa rock phosphate (Gafsa), sodium hexaphytate (NaHex), or not amended (P0). RNA was extracted and cDNA synthesized via reverse transcription from both rhizosphere and endorhiza of barley roots; the obtained 16S rRNA cDNA was sequenced by Ion Torrent and analyzed with QIIME and co-occurrence network analysis. Phosphatase activity was measured in the rhizosphere. The phosphate source significantly affected alpha- and beta-diversities of the active microbiota, especially in the rhizosphere. CaP enriched the relative abundance of a broad range of taxa, while NaHex and Gafsa specifically enriched one dominant Massilia-related OTU. Co-occurrence network analysis showed that the most abundant OTUs were affected by phosphate source and, at the same time, were low connected to other OTUs (thus they were relatively &quot;independent&quot; from other bacteria); this indicates a successful adaptation to the specific abiotic conditions. In the rhizosphere, the phosphatase activities were correlated to several OTUs. Moreover, the phosphodiesterase/alk. phosphomonoesterase ratio was highly correlated to the dominance index of the microbiota and to the relative abundance of the dominant Massilia OTU. This study shows the differential response of the rhizosphere- and endorhiza bacterial microbiota of barley to various phosphate sources in soil, thus providing insights onto this largely unknown aspect of the soil microbiome ecology and plant-microbe interactions.}, }
@article {pmid30258074, year = {2018}, author = {Cheung, MK and Wong, CK and Chu, KH and Kwan, HS}, title = {Community Structure, Dynamics and Interactions of Bacteria, Archaea and Fungi in Subtropical Coastal Wetland Sediments.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14397}, doi = {10.1038/s41598-018-32529-5}, pmid = {30258074}, issn = {2045-2322}, abstract = {Bacteria, archaea and fungi play crucial roles in wetland biogeochemical processes. However, little is known about their community structure, dynamics and interactions in subtropical coastal wetlands. Here, we examined communities of the three kingdoms in mangrove and mudflat sediments of a subtropical coastal wetland using Ion Torrent amplicon sequencing and co-occurrence network analysis. Bacterial, archaeal and fungal communities comprised mainly of members from the phyla Proteobacteria and Bacteroidetes, Bathyarchaeota and Euryarchaeota, and Ascomycota, respectively. Species richness and Shannon diversity were highest in bacteria, followed by archaea and were lowest in fungi. Distinct spatiotemporal patterns were observed, with bacterial and fungal communities varying, to different extent, between wet and dry seasons and between mangrove and mudflat, and archaeal community remaining relatively stable between seasons and regions. Redundancy analysis revealed temperature as the major driver of the seasonal patterns of bacterial and fungal communities but also highlighted the importance of interkingdom biotic factors in shaping the community structure of all three kingdoms. Potential ecological interactions and putative keystone taxa were identified based on co-occurrence network analysis. These findings facilitate current understanding of the microbial ecology of subtropical coastal wetlands and provide a basis for better modelling of ecological processes in this important ecosystem.}, }
@article {pmid30255115, year = {2018}, author = {Anza, M and Salazar, O and Epelde, L and Garbisu, C}, title = {Data on the selection of biostimulating agents for the bioremediation of soil simultaneously contaminated with lindane and zinc.}, journal = {Data in brief}, volume = {20}, number = {}, pages = {1371-1377}, doi = {10.1016/j.dib.2018.08.203}, pmid = {30255115}, issn = {2352-3409}, abstract = {The bioremediation of contaminated soil often involves the addition of organic/inorganic amendments and mobilizing agents (e.g. surfactants, detergents), in order to stimulate the growth and degrading activity of soil microbial populations and increase contaminant bioavailability. For this data article we carried out an experiment to select biostimulating agents for the bioremediation of soil simultaneously contaminated with lindane (HCH, 10 mg kg-1 DW soil) and Zinc (Zn, 1500 mg kg-1 DW soil). To this purpose, a factorial design was used to test the effect of three organic amendments (i.e. hen manure, composted horse manure, cow slurry) and three mobilizing agents (i.e. sodium dodecylbenzenesulfonate (SDS), rhamnolipids and Tween-80) on the reduction of total HCH and bioavailable Zn concentration in soil. Similarly, the effect of the addition of cyclohexane, as chemical inducer of HCH degradation, was also studied. The addition of SDS, rhamnolipids and Tween-80 significantly reduced HCH concentration in soil, regardless of the presence of other biostimulating agents. When added individually, the three organic amendments (hen manure, composted horse manure, cow slurry) significantly reduced bioavailable Zn concentration in soil. These data provide useful information for the bioremediation, through biostimulation, of soils simultaneously contaminated with HCH and Zn.}, }
@article {pmid30254509, year = {2018}, author = {Krzmarzick, MJ and Taylor, DK and Fu, X and McCutchan, AL}, title = {Diversity and Niche of Archaea in Bioremediation.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2018}, number = {}, pages = {3194108}, doi = {10.1155/2018/3194108}, pmid = {30254509}, issn = {1472-3654}, abstract = {Bioremediation is the use of microorganisms for the degradation or removal of contaminants. Most bioremediation research has focused on processes performed by the domain Bacteria; however, Archaea are known to play important roles in many situations. In extreme conditions, such as halophilic or acidophilic environments, Archaea are well suited for bioremediation. In other conditions, Archaea collaboratively work alongside Bacteria during biodegradation. In this review, the various roles that Archaea have in bioremediation is covered, including halophilic hydrocarbon degradation, acidophilic hydrocarbon degradation, hydrocarbon degradation in nonextreme environments such as soils and oceans, metal remediation, acid mine drainage, and dehalogenation. Research needs are addressed in these areas. Beyond bioremediation, these processes are important for wastewater treatment (particularly industrial wastewater treatment) and help in the understanding of the natural microbial ecology of several Archaea genera.}, }
@article {pmid30252869, year = {2018}, author = {Chen, X and Liu, X and Du, Y and Wang, B and Zhao, N and Geng, Z}, title = {Green forage and fattening duration differentially modulate cecal microbiome of Wanxi white geese.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0204210}, doi = {10.1371/journal.pone.0204210}, pmid = {30252869}, issn = {1932-6203}, abstract = {Gut microbial ecology is responsible for fatty acid metabolism in ruminants. The cecal microbiota composition of geese and their adaptation to fiber inclusion and feeding timeswere investigated in this study. A total of 116 Wanxi white geese were randomly selected at 70 days old. Eight geese were subjected to cecal sampling at 70 d of age, and the remaining 108 geese were divided into four groups with three replicates each (9 geese in each replicate). The geese in the four groups were fed 0, 15, 30, and 45% green forage (relative to dry matter), respectively. Three birds from each replicate were selected for cecal sampling at 80, 90, and 100 days old. All samples were subjected to 16S rRNA gene sequencing using the Illumina Ion Personal Genome Machine platform. Bacterial abundance was analyzed using two-way ANOVA analysis, and the relationship between the relative abundance of bacteria (phylum level) and fatty acids was analyzed using acanonical correspondence analysis. Cecal microbiota in geese were mainly composed of Bacteroidetes (68.46%), Firmicutes (20.04%), and Proteobacteria (7.89%). Dietary treatments had no significant effect on the α-diversity indices of the cecal bacterial community (P > 0.05), but a numerical increase occurred with increased fattening duration and green forage inclusion. The Selenomonadales order (P = 0.024), Negativicutes class (P = 0.026), and Megamonas (P = 0.012) and Oscillospira (P = 0.042) genera were affected by green forageinclusion level, and microflora abundance was mainly influenced by the fattening duration. Bacteria phyla were mostly set along the line of linolenic acid and oleic acid. Finally, Bacteroidales might be an intestinal promoter that improves unsaturated fatty acid synthesis in geese.}, }
@article {pmid30251120, year = {2018}, author = {Oh, S and Choi, D}, title = {Microbial Community Enhances Biodegradation of Bisphenol A Through Selection of Sphingomonadaceae.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1263-4}, pmid = {30251120}, issn = {1432-184X}, support = {NRF-2017R1C1B5076367//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIP; Ministry of Science, ICT &amp; Future Planning)/ ; }, abstract = {Bisphenol A (BPA) is a common ingredient in plastic wares and epoxy resins that are essential for our daily life. Despite the obvious benefits, BPA may act as an environmental endocrine disruptor, causing metabolic, reproductive, and/or developmental consequences and diseases in humans and other organisms. Although previous studies have yielded progress toward the microbial breakdown of BPA, the work has primarily been focused on pure cultures rather than complex microbial communities. In this study, we examined microbial communities in bioreactors that control the fate of BPA at various levels (up to 5000 μg L-1). Microbial communities rapidly increased removal rates of 500-5000 μg L-1 BPA from 23-29 to 89-99% during the first 2 weeks of the acclimation period, after which > 90% stable removal rates were maintained over 3 months. Biochemical assays demonstrated that BPA was removed by biodegradation, rather than other abiotic removal routes (e.g., adsorption and volatilization). The 16S rRNA gene-based community analysis revealed that 50-5000 μg L-1 of BPA exposure systematically selected for three Sphingomonadaceae species (Sphingobium, Novosphingobium, and Sphingopyxis). The Sphingomonadaceae-enriched communities acclimated to BPA showed a 7.0-L gVSS-1 day-1 BPA degradation rate constant, which is comparable to that (4.1-6.3) of Sphingomonadaceae isolates and is higher than other potential BPA degraders. Taken together, our results advanced the understanding of how microbial communities acclimate to environmentally relevant levels of BPA, gradually enhancing BPA degradation via selective enrichment of a few Sphingomonadaceae populations with higher BPA metabolic activity.}, }
@article {pmid30251018, year = {2018}, author = {Sanchis-Chordà, J and Del Pulgar, EMG and Carrasco-Luna, J and Benítez-Páez, A and Sanz, Y and Codoñer-Franch, P}, title = {Bifidobacterium pseudocatenulatum CECT 7765 supplementation improves inflammatory status in insulin-resistant obese children.}, journal = {European journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00394-018-1828-5}, pmid = {30251018}, issn = {1436-6215}, support = {AGL2014-52101-P//Spanish Ministry of Economy and Competitiveness/ ; FPU13/03753//Spanish Training University Lecturers Programme/ ; No. 613979//EU Project MyNewGut/ ; }, abstract = {PURPOSE: The relationships between gut microbiota and obesity-related co-morbidities have been increasingly recognized. Low-grade inflammation may be the main factor in the pathogenesis of such disorders. We investigated the effect of the potential probiotic Bifidobacterium pseudocatenulatum CECT 7765 on cardiometabolic risk factors, inflammatory cytokines and gut microbiota composition in obese children with insulin resistance.<br><br>METHODS: The study included 48 obese children (10-15 years old) with insulin resistance. They received dietary advice and were assigned to take the capsules with or without probiotic (109-10 CFU) daily for 13 weeks. Clinical, biochemical and gut microbiome measurements were made at baseline and at the end of the intervention.<br><br>RESULTS: There was a significant improvement in body mass index in all children after the intervention, suggesting that weight changes are related to the dietary advice. A significant decrease in circulating high-sensitive C-reactive protein (P = 0.026) and monocyte chemoattractant protein-1 (P = 0.032) and an increase in high-density lipoprotein cholesterol (P = 0.035) and omentin-1 (P = 0.023) in children receiving probiotic supplementation were observed compared to the control group. Regarding gut microbiota, probiotic administration significantly increased the proportion of the Rikenellaceae family members, particularly of the Alistipes genus.<br><br>CONCLUSIONS: The beneficial effects of the intervention on inflammatory markers and lipid profile suggest that B. pseudocatenulatum CECT 7765 intake together with dietary recommendations can improve inflammatory status in children with obesity and insulin resistance. These effects are parallel to increases in bacterial groups associated with a lean phenotype. The modulation of gut microbiota with probiotic supplementation can be considered an effective tool to ameliorate some obesity-related disorders in children.}, }
@article {pmid30250249, year = {2018}, author = {Takano, Y and Chikaraishi, Y and Imachi, H and Miyairi, Y and Ogawa, NO and Kaneko, M and Yokoyama, Y and Krüger, M and Ohkouchi, N}, title = {Insight into anaerobic methanotrophy from 13C/12C- amino acids and 14C/12C-ANME cells in seafloor microbial ecology.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14070}, doi = {10.1038/s41598-018-31004-5}, pmid = {30250249}, issn = {2045-2322}, abstract = {Oceanic methane from global deep-sea sediment is largely consumed through microbially mediated sulfate-coupled oxidation, resulting in 13C-depleted cell biomass of anaerobic methanotrophic archaea (ANME). The general ecological importance of subseafloor ANME has been well recognized in the last two decades. However, the crucial biochemical pathways for the overall anaerobic oxidation of methane (AOM) still remain enigmatic. Here, methanotrophic pathways were analyzed to trace 13C-depleted amino acid biosynthesis in two clades of ANME (ANME-1 and ANME-2) from the Black Sea. Compound-specific analysis of ANME-dominated microbial mats showed a significant 13C-depletion trend in association with increasing carbon numbers in protein-derived amino acid families (e.g., the pyruvate family in the order of alanine, valine, isoleucine and leucine was down to -114‰). This result indicates a stepwise elongation of 13C-depleted carbon during amino acid biosynthesis. The overall results suggest that intracellular protein amino acids and the most 13C-depleted signature of leucine, which has a specific branched-chain structure, are potentially propagated as isoprenoid precursor molecules into archaeal biosynthesis, resulting in the extremely 13C- and 14C-depleted nature of ANME cells in the deep microbial oasis.}, }
@article {pmid30250138, year = {2018}, author = {Ventorino, V and Pascale, A and Adamo, P and Rocco, C and Fiorentino, N and Mori, M and Faraco, V and Pepe, O and Fagnano, M}, title = {Comparative assessment of autochthonous bacterial and fungal communities and microbial biomarkers of polluted agricultural soils of the Terra dei Fuochi.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14281}, doi = {10.1038/s41598-018-32688-5}, pmid = {30250138}, issn = {2045-2322}, support = {LIFE11/ENV/IT/275//European Commission (EC)/ ; LIFE11/ENV/IT/275//European Commission (EC)/ ; LIFE11/ENV/IT/275//European Commission (EC)/ ; LIFE11/ENV/IT/275//European Commission (EC)/ ; LIFE11/ENV/IT/275//European Commission (EC)/ ; LIFE11/ENV/IT/275//European Commission (EC)/ ; LIFE11/ENV/IT/275//European Commission (EC)/ ; LIFE11/ENV/IT/275//European Commission (EC)/ ; LIFE11/ENV/IT/275//European Commission (EC)/ ; }, abstract = {Organic and inorganic xenobiotic compounds can affect the potential ecological function of the soil, altering its biodiversity. Therefore, the response of microbial communities to environmental pollution is a critical issue in soil ecology. Here, a high-throughput sequencing approach was used to investigate the indigenous bacterial and fungal community structure as well as the impact of pollutants on their diversity and richness in contaminated and noncontaminated soils of a National Interest Priority Site of Campania Region (Italy) called &quot;Terra dei Fuochi&quot;. The microbial populations shifted in the polluted soils via their mechanism of adaptation to contamination, establishing a new balance among prokaryotic and eukaryotic populations. Statistical analyses showed that the indigenous microbial communities were most strongly affected by contamination rather than by site of origin. Overabundant taxa and Actinobacteria were identified as sensitive biomarkers for assessing soil pollution and could provide general information on the health of the environment. This study has important implications for microbial ecology in contaminated environments, increasing our knowledge of the capacity of natural ecosystems to develop microbiota adapted to polluted soil in sites with high agricultural potential and providing a possible approach for modeling pollution indicators for bioremediation purposes.}, }
@article {pmid30249184, year = {2018}, author = {Byloos, B and Monsieurs, P and Mysara, M and Leys, N and Boon, N and Van Houdt, R}, title = {Characterization of the bacterial communities on recent Icelandic volcanic deposits of different ages.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {122}, doi = {10.1186/s12866-018-1262-0}, pmid = {30249184}, issn = {1471-2180}, support = {E-GEM/BIOROCK//Federaal Wetenschapsbeleid/ ; TD1308//European Cooperation in Science and Technology/ ; IUAP 305 P7/25//Federaal Wetenschapsbeleid (BE)/ ; }, abstract = {BACKGROUND: Basalt is the most common igneous rock on the Earth's surface covering. Basalt-associated microorganisms drive the cycling and sequestration of different elements such as nitrogen, carbon and other nutrients, which facilitate subsequent pioneer and plant development, impacting long-term regulation of the Earth's temperature and biosphere. The initial processes of colonization and subsequent rock weathering by microbial communities are still poorly understood and relatively few data are available on the diversity and richness of the communities inhabiting successive and chronological lava flows. In this study, the bacterial communities present on lava deposits from different eruptions of the 1975-84 Krafla Fires (32-, 35- and 39-year old, respectively) at the Krafla, Iceland, were determined.<br><br>RESULTS: Three sites were sampled for each deposit (32-, 35- and 39-year old), two proximal sites (at 10 m distance) and one more distant site (at 100 m from the two other sites). The determined chemical composition and metal concentrations were similar for the three basalt deposits. No significant differences were observed in the total number of cells in each flow. 16S rRNA gene amplicon sequencing showed that the most abundant classified phylum across the 3 flows was Proteobacteria, although predominance of Acidobacteria, Actinobacteria and Firmicutes was observed for some sampling sites. In addition, a considerable fraction of the operational taxonomic units remained unclassified. Alpha diversity (Shannon, inverse Simpson and Chao), HOMOVA and AMOVA only showed a significant difference for Shannon between the 32- and 39-year old flow (p < 0.05). Nonmetric multidimensional scaling (NMDS) analysis showed that age significantly (p = 0.026) influenced the leftward movement along NMDS axis 1.<br><br>CONCLUSIONS: Although NMDS indicated that the (relatively small) age difference of the deposits appeared to impact the bacterial community, this analysis was not consistent with AMOVA and HOMOVA, indicating no significant difference in community structure. The combined results drive us to conclude that the (relatively small) age differences of the deposits do not appear to be the main factor shaping the microbial communities. Probably other factors such as spatial heterogeneity, associated carbon content, exogenous rain precipitations and wind also affect the diversity and dynamics.}, }
@article {pmid30249049, year = {2018}, author = {Sivakumar, G and Uccella, NA and Gentile, L}, title = {Probing Downstream Olive Biophenol Secoiridoids.}, journal = {International journal of molecular sciences}, volume = {19}, number = {10}, pages = {}, doi = {10.3390/ijms19102892}, pmid = {30249049}, issn = {1422-0067}, abstract = {Numerous bioactive biophenol secoiridoids (BPsecos) are found in the fruit, leaves, and oil of olives. These BPsecos play important roles in both the taste of food and human health. The main BPseco bioactive from green olive fruits, leaves, and table olives is oleuropein, while olive oil is rich in oleuropein downstream pathway molecules. The aim of this study was to probe olive BPseco downstream molecular pathways that are alike in biological and olive processing systems at different pHs and reaction times. The downstream molecular pathway were analyzed by high performance liquid chromatography coupled with electrospray ionization mass spectrometry (HPLC-ESI/MS) and typed neglected of different overlap (TNDO) computational methods. Our study showed oleuropein highest occupied molecular orbital (HOMO) and HOMO-1 triggered the free radical processes, while HOMO-2 and lowest unoccupied molecular orbital (LUMO) were polar reactions of glucoside and ester groups. Olive BPsecos were found to be stable under acid and base catalylic experiments. Oleuropein aglycone opened to diales and rearranged to hydroxytyrosil-elenolate under strong reaction conditions. The results suggest that competition among olive BPseco HOMOs could induce glucoside hydrolysis during olive milling due to native olive β-glucosidases. The underlined olive BPsecos downstream molecular mechanism herein could provide new insights into the olive milling process to improve BPseco bioactives in olive oil and table olives, which would enhance both the functional food and the nutraceuticals that are produced from olives.}, }
@article {pmid30248830, year = {2018}, author = {Qi, Y and Yang, X and Pelaez, AM and Huerta Lwanga, E and Beriot, N and Gertsen, H and Garbeva, P and Geissen, V}, title = {Macro- and micro- plastics in soil-plant system: Effects of plastic mulch film residues on wheat (Triticum aestivum) growth.}, journal = {The Science of the total environment}, volume = {645}, number = {}, pages = {1048-1056}, doi = {10.1016/j.scitotenv.2018.07.229}, pmid = {30248830}, issn = {1879-1026}, abstract = {Plastic residues have become a serious environmental problem in the regions with intensive use of plastic mulching. Even though plastic mulch is widely used, the effects of macro- and micro- plastic residues on the soil-plant system and the agroecosystem are largely unknown. In this study, low density polyethylene and one type of starch-based biodegradable plastic mulch film were selected and used as examples of macro- and micro- sized plastic residues. A pot experiment was performed in a climate chamber to determine what effect mixing 1% concentration of residues of these plastics with sandy soil would have on wheat growth in the presence and absence of earthworms. The results showed that macro- and micro- plastic residues affected both above-ground and below-ground parts of the wheat plant during both vegetative and reproductive growth. The type of plastic mulch films used had a strong effect on wheat growth with the biodegradable plastic mulch showing stronger negative effects as compared to polyethylene. The presence of earthworms had an overall positive effect on the wheat growth and chiefly alleviated the impairments made by plastic residues.}, }
@article {pmid30247566, year = {2018}, author = {Otte, JM and Blackwell, N and Soos, V and Rughöft, S and Maisch, M and Kappler, A and Kleindienst, S and Schmidt, C}, title = {Sterilization impacts on marine sediment---Are we able to inactivate microorganisms in environmental samples?.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {12}, pages = {}, doi = {10.1093/femsec/fiy189}, pmid = {30247566}, issn = {1574-6941}, abstract = {To distinguish between biotic and abiotic processes in laboratory experiments with environmental samples, an effective sterilization method is required that prevents biological activity but does not change physico-geochemical properties of samples. We compared standard sterilization methods with respect to their impact on microbial abundance and activity. We exposed marine sediment to (i) autoclaving, (ii) gamma-radiation or (iii) sodium azide (NaN3) and determined how nucleic acids, microbial productivity, colony forming units (CFUs) and community composition of microorganisms, fungi, unicellular protists and protozoa were affected. In autoclaved and gamma-sterilized sediments, only few colonies formed within 16 days. After addition of NaN3 to the sediment, numerous CFUs (>50) but lower 3H-leucine incorporation rates, i.e. lower protein biosynthesis rates, were found compared to the other two sterilization techniques. Extractable RNA was detected immediately after all sterilization treatments (0.2-17.9 ng/g dry sediment) but decreased substantially by 84%-98% after 16 days of incubation. The total organic carbon content increased from 18 mg L-1 to 220 mg L-1 (autoclaving) and 150 mg L-1 (gamma-radiation) after sterilization. We compare advantages and disadvantages for each tested sterilization method and provide a helpful decision-making resource for choosing the appropriate sterilization technique for environmental studies, particularly for marine sediments.}, }
@article {pmid30247563, year = {2018}, author = {Cieplak, T and Wiese, M and Nielsen, S and Van de Wiele, T and van den Berg, F and Nielsen, DS}, title = {The Smallest Intestine (TSI)-a low volume in vitro model of the small intestine with increased throughput.}, journal = {FEMS microbiology letters}, volume = {365}, number = {21}, pages = {}, doi = {10.1093/femsle/fny231}, pmid = {30247563}, issn = {1574-6968}, abstract = {There is a growing interest in understanding the fate and behaviour of probiotic microorganisms and bioactive compounds during passage of the human gastrointestinal tract (GIT). Here, we report the development of a small volume in vitro model called The smallest Intestine (TSI) with increased throughput focusing on simulating passage through the stomach and small intestine (SI). The basic TSI module consists of five reactors, with a working volume of 12 ml each. During the simulated passage through the SI, bile is absorbed and pH is adjusted to physiologically relevant values for duodenum, jejunum and ileum. A consortium of seven representative bacterial members of the ileum microbiota is included in the ileal stage of the model. The behaviour of three putative probiotic Lactobacillus strains during in vitro simulated upper GIT passage was tested in the model and results were compared to previous studies describing probiotic survival. It was found, that probiotic persistence is strongly related to whether food was ingested, but also to presence of the ileal microbiota, which significantly impacted probiotic survival. In conclusion, TSI allows testing a substantial number of samples, at low cost and short time, and is thus suitable as an in vitro screening platform.}, }
@article {pmid30245683, year = {2018}, author = {Hernandez-Agreda, A and Leggat, W and Ainsworth, TD}, title = {A Comparative Analysis of Microbial DNA Preparation Methods for Use With Massive and Branching Coral Growth Forms.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2146}, doi = {10.3389/fmicb.2018.02146}, pmid = {30245683}, issn = {1664-302X}, abstract = {In the last two decades, over 100 studies have investigated the structure of the coral microbiome. However, as yet there are no standardized methods applied to sample preservation and preparation, with different studies using distinct methods. There have also been several comparisons made of microbiome data generated across different studies, which have not addressed the influence of the methodology employed over each of the microbiome datasets. Here, we assess three different preservation methods; salt saturated dimethyl sulfoxide (DMSO) - EDTA, snap freezing with liquid nitrogen and 4% paraformaldehyde solution, and two different preparation methodologies; bead beating and crushing, that have been applied to study the coral microbiome. We compare the resultant bacterial assemblage data for two coral growth forms, the massive coral Goniastrea edwardsi and the branching coral Isopora palifera. We show that microbiome datasets generated from differing preservation and processing protocols are comparable in composition (presence/absence). Significant discrepancies between preservation and homogenization methods are observed in structure (relative abundance), and in the occurrence and dominance of taxa, with rare (low abundance and low occurrence) phylotypes being the most variable fraction of the microbial community. Finally, we provide evidence to support chemical preservation with DMSO as effective as snap freezing samples for generating reliable and robust microbiome datasets. In conclusion, we recommend where possible a standardized preservation and extraction method be taken up by the field to provide the best possible practices for detailed assessments of symbiotic and conserved bacterial associations.}, }
@article {pmid30245425, year = {2019}, author = {Li, B and Cao, Y and Guan, X and Li, Y and Hao, Z and Hu, W and Chen, L}, title = {Microbial assessments of soil with a 40-year history of reclaimed wastewater irrigation.}, journal = {The Science of the total environment}, volume = {651}, number = {Pt 1}, pages = {696-705}, doi = {10.1016/j.scitotenv.2018.09.193}, pmid = {30245425}, issn = {1879-1026}, abstract = {The long-term effects on soil microorganisms from 40 years of irrigating soil with reclaimed wastewater was investigated by determining the quantity, composition, and inter-species connection of microorganisms. No significant difference in microbial quantity and composition were identified in the reclaimed wastewater- and groundwater-irrigated soils. The dominant bacterial phylum in both irrigation water sources and soils was Proteobacteria, which commonly exists in soil. From the analysis of four (4) alpha diversity metrics, including the observed number of operational taxonomic units (OTUs), Chao1, and the Shannon and Simpson diversity, there was no significant difference between the reclaimed wastewater- and groundwater-irrigated soils. Three zones (shallow, medium and deep) were identified in the reclaimed wastewater- and groundwater-irrigated soils based on the taxonomic networks and clusters generated by graphical lasso and random walk algorithm. The cluster profiles (shallow, medium and deep zones) appear to be different in the reclaimed wastewater- and groundwater-irrigated soils. Soil irrigated with reclaimed wastewater showed less depth of clustered profile in medium zone than that in soil irrigated with groundwater (20-60 cm of reclaimed wastewater-irrigated soil compared to 20-100 cm of groundwater-irrigated soil), although the significance of such a variance (the depth of medium zone of reclaimed wastewater-irrigated soil decreased 40 cm than that of groundwater-irrigated soil) is not clear at this time. Positive influence has been identified in the growth and yield of eggplant, tomato and cucumber between the reclaimed wastewater- and groundwater-irrigated soils, suggesting that reclaimed wastewater irrigation can potentially substitute groundwater irrigation, despite the variance in inter-species clustering profiles in soil microbes in certain soil zones. Nevertheless, the possible negative influence of pathogens, organic compounds and pharmaceuticals should be seriously considered during the reclaimed wastewater irrigation.}, }
@article {pmid30244277, year = {2018}, author = {Shteindel, N and Yankelev, D and Gerchman, Y}, title = {High-Throughput Quantitative Measurement of Bacterial Attachment Kinetics on Seconds Time Scale.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1254-5}, pmid = {30244277}, issn = {1432-184X}, abstract = {Surface attachment is an important factor in the life of many microbial species. Late stages of attachment (i.e., mature biofilms) are rigorously studied, but data on the very early stages is scarce. The lack of robust research methods may go a long way in explaining this situation. We have developed a method that allows the rapid kinetic measurement of bacterial attachment, with seconds to minute's temporal resolution, in a high-throughput setting. The method requires the use of a commercially available microtiter plate reader capable of fluorescence measurement from the bottom, standard microtiter plates, fluorescently tagged bacteria, and a common dye. The high temporal resolution reveals nuanced, fast, and dynamic behaviors in the very early phases of attachment. To demonstrate potential applications, we tested the effect of various conditions on attachment kinetics-specie, substratum, salt concentration, and culture density. Results are in good agreement with crystal violet staining (correlation R2 > 0.95 in all cases) and reproducing published data but show much greater detail and fidelity.}, }
@article {pmid30244124, year = {2018}, author = {Podduturi, R and Jørgensen, NOG}, title = {Conidia-based fluorescence quantification of Streptomyces.}, journal = {Journal of microbiological methods}, volume = {153}, number = {}, pages = {104-107}, doi = {10.1016/j.mimet.2018.09.010}, pmid = {30244124}, issn = {1872-8359}, abstract = {Determination of cell numbers in filamentous bacteria, such as Streptomyces, is challenging due to the tangled and twisted structure of the filaments and formation of cell clumps in liquid cultures. Here, we developed a conidia-based approach, in which fluorescence of conidia, after staining with the DNA-binding stain SYBR Green 1, was related to SYBR Green 1 fluorescence of DNA in Streptomyces. When cell number in Streptomyces filaments, determined by the conidia assay, was compared to number obtained by a qPCR assay, 34 to 62% of cells in the Streptomyces filaments were recovered. The difference in numbers probably reflects an insufficient extraction of DNA from the Gram-positive bacteria, rather than underestimation of the actual cell number by the conidia-based determination. The conidia-based approach appears to be a fast and reliable procedure for counting cell numbers in Streptomyces filaments but it can also be used for other filamentous bacteria, if proper standard curves can be made.}, }
@article {pmid30243206, year = {2018}, author = {Wen, D and Chang, NB and Wanielista, MP}, title = {Comparative copper toxicity impact and enzymatic cascade effect on Biosorption Activated Media and woodchips for nutrient removal in stormwater treatment.}, journal = {Chemosphere}, volume = {213}, number = {}, pages = {403-413}, doi = {10.1016/j.chemosphere.2018.09.062}, pmid = {30243206}, issn = {1879-1298}, abstract = {Copper, a commonly occurring heavy metal in stormwater runoff, was tested for its inhibitory effects on key nitrogen cycle bacteria in Biosorption Activated Media (BAM) and woodchip. The information in this paper is used to show that copper can enhance the denitrification process through enzyme cascade reactions since nitrous reductase is the enzyme responsible for the last step of denitrification and is largely dependent on copper as its cofactor. However, media characteristics are critical for assessing multi-enzymatic cascade reactions from the microbial ecology point of view. Moreover, both media showed significant copper removal through various mechanisms at 30 cm depth. The bioactivity evaluation indicates that other bacteria (fermentative bacteria, etc.) can be largely depressed with the presence of copper, hence the biofilm structure would be more vulnerable under shearing effects, which may result in holistic depression on the microbial community.}, }
@article {pmid30241680, year = {2018}, author = {Mergoni, G and Percudani, D and Lodi, G and Bertani, P and Manfredi, M}, title = {Prevalence of Candida Species in Endodontic Infections: Systematic Review and Meta-analysis.}, journal = {Journal of endodontics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.joen.2018.07.016}, pmid = {30241680}, issn = {1878-3554}, abstract = {INTRODUCTION: Candida in endodontic infections has been investigated in a large number of studies, but its role as an endodontic pathogen is still debatable. The aim of this study was to systematically review the literature on the prevalence of Candida species in root canal infections.<br><br>METHODS: Extensive literature research was performed in the most important electronic biomedical databases, and additional studies have been identified from references from relevant articles. Studies were critically appraised using a modified version of the Joanna Briggs Institute Critical Appraisal Checklist.<br><br>RESULTS: From 2225 unique records, 2118 were excluded on the basis of title and abstract. Of the remaining 107 studies, 50 were excluded after full-text review, and 57 were included for qualitative and quantitative analysis. The overall prevalence of Candida spp. in root canal infections was 8.20% (95% confidence interval, 5.56%-11.21%). Candida albicans was the most frequently isolated species. Significant heterogeneity among studies was observed (P < .001, I2 = 86.07%). Subgroup analyses revealed a higher prevalence of Candida spp. from African samples. All studies considered, a high or unclear risk of bias was prevalent regarding 6 out of the 8 items considered in the critical appraisal.<br><br>CONCLUSIONS: Candida spp. occurred in a small proportion of root canal infections. Further and better designed research is needed to investigate the real contribution of Candida spp. to the microbial ecology in infected root canals.}, }
@article {pmid30239657, year = {2018}, author = {Van Herreweghen, F and De Paepe, K and Roume, H and Kerckhof, FM and Van de Wiele, T}, title = {Mucin degradation niche as a driver of microbiome composition and Akkermansia muciniphila abundance in a dynamic gut model is donor independent.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {12}, pages = {}, doi = {10.1093/femsec/fiy186}, pmid = {30239657}, issn = {1574-6941}, abstract = {Akkermansia muciniphila, an abundant mucin degrading intestinal bacterium, has been correlated with human health in various studies. The in vitro SHIME model was used to reach a mechanistic understanding of A. muciniphila's colonization preferences and its response to environmental parameters such as colon pH and mucins. These insight can help to identify the optimal conditions for successful in vivo application. After a period of mucin deprivation, we found that mucin supplementation resulted in significantly different microbial communities, with more Akkermansia, Bacteroides and Ruminococcus. Mucin treatment accounted for 26% of the observed variation in the microbial community at OTU level (P = 0.001), whereas the donor effect was limited (8%) (P = 0.035), indicating mucins to constitute an important ecological niche shaping the microbiota composition. The effect of colonic pH had a less profound impact on the microbiome with both pH and donor origin explaining around 10% of the variability in the dataset. Yet, higher simulated colonic pH had a positive impact on Akkermansia abundance while short chain fatty acid analysis displayed a preference for propionate production with higher colonic pH. Our results show that mucins as nutritional resource are a more important modulator of the gut microbiome than colon pH as environmental factor.}, }
@article {pmid30238141, year = {2018}, author = {Roussel, C and Galia, W and Leriche, F and Chalancon, S and Denis, S and Van de Wiele, T and Blanquet-Diot, S}, title = {Comparison of conventional plating, PMA-qPCR, and flow cytometry for the determination of viable enterotoxigenic Escherichia coli along a gastrointestinal in vitro model.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {22}, pages = {9793-9802}, doi = {10.1007/s00253-018-9380-z}, pmid = {30238141}, issn = {1432-0614}, abstract = {Recent technological advances for bacterial viability assessment using molecular methods or flow cytometry can provide meaningful interest for the demarcation between live and dead microorganisms. Nonetheless, these methods have been scarcely applied to foodborne pathogens and never for directly assessing their viability within the human digestive environment. The purpose of this study was to compare two methods based on membrane integrity (propidium monoazide (PMA) q-PCR and Live/Dead flow cytometry) and the classical plate-count method to determine the viability of a common foodborne pathogen, enterotoxigenic Escherichia coli (ETEC), during its transit trough simulated human gastrointestinal environment. Viable ETEC counts in the gastric and small intestinal compartments of the gastrointestinal TIM model indicated a consensus between the three tested methods (PMA-qPCR, flow cytometry, and plate counts). In a further step, flow cytometry analysis appeared as the preferred method to elucidate ETEC physiological states in the in vitro digestive environment by discriminating four subpopulations, while PMA-qPCR can only distinguish two. The defined viable/altered ETEC population was found during all in vitro digestions, but mainly in the gastric compartment. Being able to discriminate the particular physiological states of pathogenic microorganisms in the digestive environment is of high interest, because if some cells are not observable on culture media, they might keep their ability to express virulence functions.}, }
@article {pmid30237506, year = {2018}, author = {Erşan, YÇ and Van Tittelboom, K and Boon, N and De Belie, N}, title = {Nitrite producing bacteria inhibit reinforcement bar corrosion in cementitious materials.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14092}, doi = {10.1038/s41598-018-32463-6}, pmid = {30237506}, issn = {2045-2322}, abstract = {Chemicals and synthetic coatings are widely used to protect steel against corrosion. Bio-based corrosion inhibition strategies can be an alternative in the arising bioeconomy era. To maintain the good state of steel reinforcement in cracked concrete, microbe-based self-healing cementitious composites (MSCC) have been developed. Yet, proposed strategies involve reasonably slow crack filling by biomineralization and thus risk the possible rebar corrosion during crack healing. Here we upgrade the rebar protection to a higher level by combining MSCC with microbial induced corrosion inhibition. Presented NO3- reducing bacterial granules inhibit rebar corrosion by producing the anodic corrosion inhibitor NO2- and meanwhile heal a 300-µm-wide crack in 28 days. During 120 days exposure to 0.5 M Cl- solution, the rebars in cracked MSCC keep showing open circuit potentials above the critical value of -250 mV and they lose less than 2% of the total rebar material which corresponds to half the material loss in cracked plain mortar. Overall, the obtained rebar protection performance is comparable with that of uncracked mortar and mortar containing chemical inhibitor, hence the microbe-based system becomes an alternative to the traditional methods.}, }
@article {pmid30235606, year = {2019}, author = {Fiorentino, A and Di Cesare, A and Eckert, EM and Rizzo, L and Fontaneto, D and Yang, Y and Corno, G}, title = {Impact of industrial wastewater on the dynamics of antibiotic resistance genes in a full-scale urban wastewater treatment plant.}, journal = {The Science of the total environment}, volume = {646}, number = {}, pages = {1204-1210}, doi = {10.1016/j.scitotenv.2018.07.370}, pmid = {30235606}, issn = {1879-1026}, abstract = {Urban Wastewater Treatment Plants (UWTPs) treating mixed urban sewage and industrial wastewater are among the major hotspots for the spread of Antibiotic Resistance Genes (ARGs) into the environment. This study addresses the impact of the wastewater origin on ARG dynamics in a full-scale UWTP (15,000 Population Equivalent, PE) by operating the plant with and without industrial wastewater. Composite samples (4 L) from different treatment points were characterized for their chemical composition, bacterial abundance and for the abundance of four resistance genes against tetracycline, sulfonamides, erythromycin, and quinolones (tetA, sul2, ermB, and qnrS), and of the class 1 integrons (intI1). Although the chemical composition of the outflow significantly differed when the plant operated with or without industrial wastewater, the system efficiency in the removal of bacterial cells, ARGs, and intI1 was constant. The final disinfection by peracetic acid (PAA) did not affect the removal of ARGs, independently of the wastewater origin and the chemical characteristics of the inflows. Our results demonstrated that a well-functioning small size UWTP could treat a significant amount of industrial wastewater mixed in the urban sewage without affecting the overall ARGs and class 1 integrons released into the environment.}, }
@article {pmid30234420, year = {2018}, author = {De Mulder, T and Rasschaert, G and Van Coillie, E and Van den Meersche, T and Haegeman, A and Ruttink, T and de Wiele, TV and Heyndrickx, M}, title = {Impact of Cross-Contamination Concentrations of Doxycycline Hyclate on the Microbial Ecosystem in an Ex Vivo Model of the Pig's Cecum.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {}, number = {}, pages = {}, doi = {10.1089/mdr.2018.0034}, pmid = {30234420}, issn = {1931-8448}, abstract = {AIMS: Cross-contamination of feed with antibiotics causes pigs to become unintentionally exposed to low concentrations of antibiotics. This study investigates the effect of residues of doxycycline hyclate (DOX) in an ex vivo model of the intestinal tract of pigs, focusing on the microbial community, microbial activity, and the enrichment of resistant bacteria and resistance genes.<br><br>RESULTS: The effect of three concentrations DOX were tested; 1 and 4 mg/L correspond to the intestinal concentrations when pigs are fed a compound feed containing 3% of a therapeutic dose, and a reference concentration of 16 mg/L. These were continuously administered to a chemostat, simulating the microbial ecosystem of the pig cecum and inoculated with cecal content of organically grown pigs. The administration of even the lowest DOX concentration caused a significant decrease in bacterial activity, while the microbial community profile appeared to remain unaffected by any of the concentrations. A concentration of 1 mg/L DOX caused minor selection pressure for tetracycline-resistant Escherichia coli but no other groups enumerated with plate cultivation, while 4 mg/L induced major enrichment of tetracycline-resistant E. coli, Enterobacteriaceae and total anaerobes. High abundances of tet(Q), tet(M), tet(W), tet(O), and tet(B) were detected in the inoculum and also before antibiotic administration in the chemostat and did not significantly increase during administration of 1 and 4 mg/L DOX. Only 16 mg/L DOX caused minor enrichments.<br><br>CONCLUSIONS: Cross-contamination concentrations of doxycycline, as a result of cross-contamination, cause a selection pressure for resistant bacteria and negatively affect microbial activity.}, }
@article {pmid30233537, year = {2018}, author = {Teurlincx, S and Heijboer, A and Veraart, AJ and Kowalchuk, GA and Declerck, SAJ}, title = {Local Functioning, Landscape Structuring: Drivers of Soil Microbial Community Structure and Function in Peatlands.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2060}, doi = {10.3389/fmicb.2018.02060}, pmid = {30233537}, issn = {1664-302X}, abstract = {Agricultural peatlands are essential for a myriad of ecosystem functions and play an important role in the global carbon (C) cycle through C sequestration. Management of these agricultural peatlands takes place at different spatial scales, ranging from local to landscape management, and drivers of soil microbial community structure and function may be scale-dependent. Effective management for an optimal biogeochemical functioning thus requires knowledge of the drivers on soil microbial community structure and functioning, as well as the spatial scales upon which they are influenced. During two field campaigns, we examined the importance of different drivers (i.e., soil characteristics, nutrient management, vegetation composition) at two spatial scales (local vs. landscape) for, respectively, the soil microbial community structure (determined by PLFA) and soil microbial community functional capacity (as assessed by CLPP) in agricultural peatlands. First, we show by an analysis of PLFA profiles that the total microbial biomass changes with soil moisture and relative C:P nutrient availability. Secondly, we showed that soil communities are controlled by a distinct set of drivers at the local, as opposed to landscape, scale. Community structure was found to be markedly different between areas, in contrast to community function which showed high variability within areas. We further found that microbial structure appears to be controlled more at a landscape scale by nutrient-related variables, whereas microbial functional capacity is driven locally through plant community feedbacks. Optimal management strategies within such peatlands should therefore consider the scale-dependent action of soil microbial community drivers, for example by first optimizing microbial structure at the landscape scale by targeted areal management, and then optimizing soil microbial function by local vegetation management.}, }
@article {pmid30232167, year = {2018}, author = {Ingala, MR and Simmons, NB and Perkins, SL}, title = {Bats Are an Untapped System for Understanding Microbiome Evolution in Mammals.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, doi = {10.1128/mSphere.00397-18}, pmid = {30232167}, issn = {2379-5042}, abstract = {Mammals evolved in a microbial world, and consequently, microbial symbionts have played a role in their evolution. An exciting new subdiscipline of metagenomics considers the ways in which microbes, particularly those found in the gut, have facilitated the ecological and phylogenetic radiation of mammals. However, the vast majority of such studies focus on domestic animals, laboratory models, or charismatic megafauna (e.g., pandas and chimpanzees). The result is a plethora of studies covering few taxa across the mammal tree of life, leaving broad patterns of microbiome function and evolution unclear. Wildlife microbiome research urgently needs a model system in which to test hypotheses about metagenomic involvement in host ecology and evolution. We propose that bats (Order: Chiroptera) represent a model system ideal for comparative microbiome research, affording opportunities to examine host phylogeny, diet, and other natural history characteristics in relation to the evolution of the gut microbiome.}, }
@article {pmid30231985, year = {2018}, author = {Malik, A and Sharma, D and Malireddi, RKS and Guy, CS and Chang, TC and Olsen, SR and Neale, G and Vogel, P and Kanneganti, TD}, title = {SYK-CARD9 Signaling Axis Promotes Gut Fungi-Mediated Inflammasome Activation to Restrict Colitis and Colon Cancer.}, journal = {Immunity}, volume = {49}, number = {3}, pages = {515-530.e5}, doi = {10.1016/j.immuni.2018.08.024}, pmid = {30231985}, issn = {1097-4180}, abstract = {Fungi represent a significant proportion of the gut microbiota. Aberrant immune responses to fungi are frequently observed in inflammatory bowel diseases (IBD) and colorectal cancer (CRC), and mutations in the fungal-sensing pathways are associated with the pathogenesis of IBD. Fungal recognition receptors trigger downstream signaling via the common adaptor protein CARD9 and the kinase SYK. Here we found that commensal gut fungi promoted inflammasome activation during AOM-DSS-induced colitis. Myeloid cell-specific deletion of Card9 or Syk reduced inflammasome activation and interleukin (IL)-18 maturation and increased susceptibility to colitis and CRC. IL-18 promoted epithelial barrier restitution and interferon-γ production by intestinal CD8+ T cells. Supplementation of IL-18 or transfer of wild-type myeloid cells reduced tumor burden in AOM-DSS-treated Card9-/- and Sykfl/flLysMCre/+ mice, whereas treatment with anti-fungal agents exacerbated colitis and CRC. CARD9 deletion changes the gut microbial landscape, suggesting that SYK-CARD9 signaling maintains a microbial ecology that promotes inflammasome activation and thereby restrains colitis and colon tumorigenesis.}, }
@article {pmid30231921, year = {2018}, author = {Vavourakis, CD and Andrei, AS and Mehrshad, M and Ghai, R and Sorokin, DY and Muyzer, G}, title = {A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {168}, doi = {10.1186/s40168-018-0548-7}, pmid = {30231921}, issn = {2049-2618}, support = {322551//European Research Council/International ; 322551//European Research Council/International ; L200961651//Czech Academy of Science/ ; 16-14-00121//Russian Science Support Foundation/ ; 24002002//Dutch Ministry of Education and Science/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; 17-04828S//Grant Agency of the Czech Republic/ ; 17-04828S//Grant Agency of the Czech Republic/ ; }, abstract = {BACKGROUND: Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages.<br><br>RESULTS: We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L-1. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria.<br><br>CONCLUSIONS: Our first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments.}, }
@article {pmid30231187, year = {2018}, author = {Wu, T and Grootaert, C and Pitart, J and Vidovic, NK and Kamiloglu, S and Possemiers, S and Glibetic, M and Smagghe, G and Raes, K and Van de Wiele, T and Van Camp, J}, title = {Aronia (Aronia melanocarpa) Polyphenols Modulate the Microbial Community in a Simulator of the Human Intestinal Microbial Ecosystem (SHIME) and Decrease Secretion of Proinflammatory Markers in a Caco-2/endothelial Cell Coculture Model.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e1800607}, doi = {10.1002/mnfr.201800607}, pmid = {30231187}, issn = {1613-4133}, support = {//China Scholarship Council (CSC)/ ; //Ghent University/ ; 01B04212//BOF/ ; FP7/2007-2013//Project BACCHUS/ ; 312090//Project BACCHUS/ ; }, abstract = {SCOPE: To explore the mechanisms behind the health effects of Aronia (Aronia melanocarpa), the microbial community modulating and anti-inflammatory effects of Aronia polyphenols are investigated by combining the similutor of the human intestinal microbial ecosystem (SHIME) with a coculture of intestinal and endothelial cells.<br><br>RESULTS: Administration of Aronia juice (6.5g L-1) to the SHIME for 2 weeks increases the abundance of firmicutes to 92% in the ascending colon (AC), 85% in the transverse colon (TC), and 82% in the descending colon (DC; p < 0.001), proteobacteria (6.7% in AC, p < 0.001), and Akkermansia (14% in TC and 18% in DC, p < 0.001) and decreases the abundance of Bifidobacterium species, associated with a decrease of acetate and increase of propionate and butyrate, whereas no significant difference is observed upon placebo juice treatment. After addition of the digests to TNF-α challenged Caco-2/endothelial cocultures, intercellular adhesion molecule (ICAM)-1, IL-8, and monocyte chemoattractant protein-1 levels are significantly downregulated. Interestingly, Aronia juice treats digests from each colon compartment resulting in a stronger decrease of the ICAM-1 secretion (up to 73%, p < 0.001) compared to their corresponding placebo treated digests, thereby pointing to a polyphenol-dependent effect.<br><br>CONCLUSIONS: Aronia polyphenols modulate intestinal microbial composition, induce beneficial short chain fatty acid production, and prevent inflammatory stress in endothelial cells. This opens perspectives for the use of Aronia polyphenols as prebiotics in the context of intestinal and cardiovascular health.}, }
@article {pmid30229264, year = {2018}, author = {Ziller, A and Fraissinet-Tachet, L}, title = {Metallothionein diversity and distribution in the tree of life: a multifunctional protein.}, journal = {Metallomics : integrated biometal science}, volume = {}, number = {}, pages = {}, doi = {10.1039/c8mt00165k}, pmid = {30229264}, issn = {1756-591X}, abstract = {MTs are small cysteine-rich proteins that chelate metal ions such as Cu+ and Zn2+, and are widely distributed in several life domains, in particular the eukaryotic one. They are present in the following phyla: Opisthokonta (mainly Fungi and Metazoa), Chloroplastida, Alveolata (ciliates) and Excavata (Trichomonas) for Eukaryota and Cyanobacteria, Actinobacteria, Proteobacteria and Firmicutes for Bacteria. However, their absence in some phyla underlines that MTs are far from being fully known. The MT amino acid sequences show a great diversity of sizes and structures both in terms of cysteine motifs and organization of these motifs. This review also highlights the different oxidized, apoprotein and metalated forms of MTs, the diversity of interactions they can establish with different molecules and their central and multifunctional cellular role. We present MTs as a protein system that could be a hub in molecular interaction networks. Studying MTs as a hub in cellular interaction networks should provide new insights for a better understanding of MT functioning and cellular processes.}, }
@article {pmid30228802, year = {2018}, author = {Gacesa, R and Baranasic, D and Starcevic, A and Diminic, J and Korlević, M and Najdek, M and Blažina, M and Oršolić, D and Kolesarić, D and Long, PF and Cullum, J and Hranueli, D and Orlic, S and Zucko, J}, title = {Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from 
Northern Adriatic Sea Sediments.}, journal = {Food technology and biotechnology}, volume = {56}, number = {2}, pages = {270-277}, doi = {10.17113/ftb.56.02.18.5393}, pmid = {30228802}, issn = {1330-9862}, abstract = {Three metagenomic libraries were constructed using surface sediment samples from the northern Adriatic Sea. Two of the samples were taken from a highly polluted and an unpolluted site respectively. The third sample from a polluted site had been enriched using crude oil. The results of the metagenome analyses were incorporated in the REDPET relational database (http://redpet.bioinfo.pbf.hr/REDPET), which was generated using the previously developed MEGGASENSE platform. The database includes taxonomic data to allow the assessment of the biodiversity of metagenomic libraries and a general functional analysis of genes using hidden Markov model (HMM) profiles based on the KEGG database. A set of 22 specialised HMM profiles was developed to detect putative genes for hydrocarbon-degrading enzymes. Use of these profiles showed that the metagenomic library generated after selection on crude oil had enriched genes for aerobic n-alkane degradation. The use of this system for bioprospecting was exemplified using potential alkB and almA genes from this library.}, }
@article {pmid30228389, year = {2018}, author = {Mechmeche, M and Kachouri, F and Ksontini, H and Setti, K and Hamdi, M}, title = {Bioprocess development and preservation of functional food from tomato seed isolate fermented by kefir culture mixture.}, journal = {Journal of food science and technology}, volume = {55}, number = {10}, pages = {3911-3921}, doi = {10.1007/s13197-018-3315-7}, pmid = {30228389}, issn = {0022-1155}, abstract = {The aim of this work was to explore the use of protein isolate from tomato seed enriched with the sucrose and the ascorbic acid as a medium for the growth of kefir mixture culture to develop a new non-dairy functional food. Unstructured mathematical and logistic models were proposed to describe cell growth, kefiran production, nutriment consumption and antioxidant activity. It was found that the maximal cell mass in the culture reached 8.38 g L-1 after 24 h of fermentation. A significant amount of kefiran was also produced (0.65 g L-1). The kefir culture growth significantly decreased protein content and enhanced the antioxidant activity during varied fermentation through the production of bio active peptides. After 24 h of fermentation, IC50 value for protein isolate was estimated to be about 10.48 µg mL-1. The proposed models adequately described the changes during fermentation and as observed as a promising approach for the formulation of tomato seed-based functional foods. The preservation of the isolate was also investigated through a spray-drying process. The effect of spray-drying on the viability of lactic acid bacteria and stability of protein content and the antioxidant activity of the powder was also carried out. Results showed that the spray-drying method has great potential for the synthesis of powder from the fermented isolate that are rich in desirable properties. However, it was appropriate to preserve the powder for 10 days at 37 °C for the preservation of protein functionality.}, }
@article {pmid30223892, year = {2018}, author = {Sitaraman, R}, title = {Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {163}, doi = {10.1186/s40168-018-0551-z}, pmid = {30223892}, issn = {2049-2618}, abstract = {The ubiquity of horizontal gene transfer in the living world, especially among prokaryotes, raises interesting and important scientific questions regarding its effects on the human holobiont i.e., the human and its resident bacterial communities considered together as a unit of selection. Specifically, it would be interesting to determine how particular gene transfer events have influenced holobiont phenotypes in particular ecological niches and, conversely, how specific holobiont phenotypes have influenced gene transfer events. In this synthetic review, we list some notable and recent discoveries of horizontal gene transfer among the prokaryotic component of the human microbiota, and analyze their potential impact on the holobiont from an ecological-evolutionary viewpoint. Finally, the human-Helicobacter pylori association is presented as an illustration of these considerations, followed by a delineation of unresolved questions and avenues for future research.}, }
@article {pmid30218926, year = {2018}, author = {Zhang, X and Prévoteau, A and Louro, RO and Paquete, CM and Rabaey, K}, title = {Periodic polarization of electroactive biofilms increases current density and charge carriers concentration while modifying biofilm structure.}, journal = {Biosensors &amp; bioelectronics}, volume = {121}, number = {}, pages = {183-191}, doi = {10.1016/j.bios.2018.08.045}, pmid = {30218926}, issn = {1873-4235}, abstract = {Anodic electroactive biofilms (EABs) need to overcome low current densities for applications such as microbial fuel cells or biosensors. EABs can store charge in self-produced redox proteins when temporarily left in open circuit, and discharge them once the electrode is appropriately repolarized, thus behaving as pseudocapacitors. Here we investigated the effect of such periodic polarization on the intrinsic nature of the EABs during their entire growth (i.e. starting from inoculation and for 10 days) on glassy carbon electrodes. An optimal periodic polarization (half-period of 10 s) greatly increased the maximum steady-state current density delivered by the Geobacter-dominated EABs (up to 1.10 ± 0.02 mA cm-2, n = 3 electrodes) when compared to continuously polarized EABs (0.41 ± 0.04 mA cm-2); and increased the amount of electric charges produced per hour by 69 ± 17% even taking into account the half-periods of open circuit. This enhancement was highly correlated with a substantial increase in charge carriers concentration (10.6 ± 0.5 mMe- vs. 2.9 ± 0.6 mMe-), allowing higher charge storage capacity and higher electron mobility across the EABs. Our results suggest that appropriate periodic polarizations may upregulate the expression of heme-containing redox proteins associated with the matrix, such as c-type cytochromes. The EABs grown under periodic polarization presented mushroom-like structures on their top layers, while EABs grown under continuous polarization were flat.}, }
@article {pmid30218130, year = {2018}, author = {Bernasconi, R and Stat, M and Koenders, A and Huggett, MJ}, title = {Global Networks of Symbiodinium-Bacteria Within the Coral Holobiont.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1255-4}, pmid = {30218130}, issn = {1432-184X}, abstract = {Scleractinian corals form the framework of coral reefs and host abundant and diverse microbial communities that are fundamental to their success. A very limited number of studies have examined the co-occurrence of multiple partners within the coral 'holobiont' and their pattern of specificity over different geographical scales. In this study, we explored two molecular sequence datasets representing associations between corals and dinoflagellates in the genus Symbiodinium and between corals and bacteria, across the globe. Through a network theory approach, we characterised patterns of co-occurrences between bacteria and Symbiodinium with 13 coral genera across six water basins. The majority of the bacteria-Symbiodinium co-occurrences were specific to either a coral genus or water basin, emphasising both coral host and environment as important factors driving the diversity of coral assemblages. Yet, results also identified bacteria and Symbiodinium that were shared by multiple coral genera across several water basins. The analyses indicate that shared co-occurrences are independent of the phylogenetic and biogeographic relationship of coral hosts.}, }
@article {pmid30218129, year = {2018}, author = {Biswas, S and Mukherjee, P and Manna, T and Dutta, K and Guchhait, KC and Karmakar, A and Karmakar, M and Dua, P and Panda, AK and Ghosh, C}, title = {Quorum Sensing Autoinducer(s) and Flagellum Independently Mediate EPS Signaling in Vibrio cholerae Through LuxO-Independent Mechanism.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1262-5}, pmid = {30218129}, issn = {1432-184X}, support = {SR/SO/HS-43/2006//Department of Science and Technology/ ; BT/PR3802/BRB/10/981/2011//Department of Biotechnology , Ministry of Science and Technology/ ; }, abstract = {Vibrio cholerae, the Gram-negative bacterium causing lethal diarrheal disease cholera, forms biofilm on solid surfaces to gain adaptive advantage for successful survival in aquatic reservoirs. Expression of exopolysaccharide (EPS), an extracellular matrix material, has been found critical for biofilm-based environmental persistence. In a subset of epidemic-causing V. cholerae, absence of flagellum but not motility was identified to induce elevated exopolysaccharide expression. Identification of the role played by quorum sensing autoinducer molecules, i.e., cholera autoinducer 1 (CAI-1) and autoinducer 2 (AI-2) as well as central regulator LuxO on EPS expression in the subset was explored. Deletion mutations were introduced in vital genes responsible for synthesizing CAI-1 (cqsA), AI-2 (luxS), flagellum (flaA), LuxO (luxO), flagellar motor (motX), and VpsR (vpsR) in the model strain MO10. Subsequent phenotypic alterations in terms of colony morphology, EPS expression, biofilm formation, and transcription level of relevant genes were analyzed. Autoinducer cross-feeding experiment confirmed the role of autoinducers in EPS signaling. Results reveal that autoinducers and flagellum are the two major EPS signaling units in this subset where one unit becomes predominant for EPS production in absence of the other. Moreover, either unit exerts negative influence on EPS induction by the other. Both the EPS signaling cascades are independent of LuxO contribution and essentially involve sodium-driven flagellar motor and VpsR. A cell density and flagellum-mediated, but LuxO-independent, EPS signaling mechanism is considered to be functional in these organisms that confers their survival fitness.}, }
@article {pmid30217848, year = {2018}, author = {Mbareche, H and Veillette, M and Bilodeau, GJ and Duchaine, C}, title = {Bioaerosol Sampler Choice Should Consider Efficiency and Ability of Samplers to Cover Microbial Diversity.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.01589-18}, pmid = {30217848}, issn = {1098-5336}, abstract = {Bioaerosol studies tend to describe the microbial content and understand the aerosolization processes linked to diseases. Air samplers are used to collect, identify and quantify bioaerosols. Studies comparing the performance of air samplers have typically used a culture approach or have targeted a specific microorganism in laboratory settings. The objective of this study was to use environmental field samples to compare the efficiency of 3 high airflow rate samplers for describing bioaerosol diversity using a next-generation sequencing approach. Two liquid cyclonic impactors and one electrostatic filter dry sampler were used in four wastewater treatment plants to target bacterial diversity and in five dairy farms to target fungal diversity. The dry electrostatic sampler was consistently more powerful in collecting more fungal and bacterial OTUs. Substantial differences in OTU abundance between liquid and dry sampling were revealed. The majority of the diversity revealed by dry electrostatic sampling was not identified using the cyclonic liquid impactors. The findings on this work suggest that the choice of a bioaerosol sampler should include information about the efficiency and ability of samplers to cover microbial diversity. Although these results suggest that electrostatic filters result in better coverage of the microbial diversity amongst the tested air samplers, further studies are needed to confirm this hypothesis. While it is difficult to determine a single universally optimal air sampler, this work provides an in-depth look at some of the considerations that are essential when choosing an air sampler for studying the microbial ecology of bioaerosols.Importance Associating bioaerosol exposure and health problems is challenging and adequate exposure monitoring is a priority for scientist in the field. Conclusions that can be drawn from bioaerosol exposure studies are highly dependent on the design of the study and the methodologies used. The air sampling strategy is the first methodological step leading to an accurate interpretation of what is present in the air. Applying new molecular approaches to evaluate the efficiency of the different types of samplers used in the field is a necessary work around the traditional approaches and the biases they introduce to such studies. The results and conclusions provided in this manuscript should be taken in considerations when conducting a bioaerosol study.}, }
@article {pmid30214003, year = {2018}, author = {Lindeboom, REF and Ilgrande, C and Carvajal-Arroyo, JM and Coninx, I and Van Hoey, O and Roume, H and Morozova, J and Udert, KM and Sas, B and Paille, C and Lasseur, C and Ilyin, V and Clauwaert, P and Leys, N and Vlaeminck, SE}, title = {Nitrogen cycle microorganisms can be reactivated after Space exposure.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {13783}, doi = {10.1038/s41598-018-32055-4}, pmid = {30214003}, issn = {2045-2322}, abstract = {Long-term human Space missions depend on regenerative life support systems (RLSS) to produce food, water and oxygen from waste and metabolic products. Microbial biotechnology is efficient for nitrogen conversion, with nitrate or nitrogen gas as desirable products. A prerequisite to bioreactor operation in Space is the feasibility to reactivate cells exposed to microgravity and radiation. In this study, microorganisms capable of essential nitrogen cycle conversions were sent on a 44-days FOTON-M4 flight to Low Earth Orbit (LEO) and exposed to 10-3-10-4 g (gravitational constant) and 687 ± 170 µGy (Gray) d-1 (20 ± 4 °C), about the double of the radiation prevailing in the International Space Station (ISS). After return to Earth, axenic cultures, defined and reactor communities of ureolytic bacteria, ammonia oxidizing archaea and bacteria, nitrite oxidizing bacteria, denitrifiers and anammox bacteria could all be reactivated. Space exposure generally yielded similar or even higher nitrogen conversion rates as terrestrial preservation at a similar temperature, while terrestrial storage at 4 °C mostly resulted in the highest rates. Refrigerated Space exposure is proposed as a strategy to maximize the reactivation potential. For the first time, the combined potential of ureolysis, nitritation, nitratation, denitrification (nitrate reducing activity) and anammox is demonstrated as key enabler for resource recovery in human Space exploration.}, }
@article {pmid30213542, year = {2018}, author = {Lee, K and Yu, H and Zhang, X and Choo, KH}, title = {Quorum sensing and quenching in membrane bioreactors: Opportunities and challenges for biofouling control.}, journal = {Bioresource technology}, volume = {270}, number = {}, pages = {656-668}, doi = {10.1016/j.biortech.2018.09.019}, pmid = {30213542}, issn = {1873-2976}, abstract = {Membrane biofouling, due to biofilm growth after planktonic bacteria attachment to a membrane, is a major bottleneck limiting the energy-efficient operation and maintenance of membrane bioreactors (MBRs). Microbial communications, known as quorum sensing (QS), are responsible for this biofouling behavior. Novel strategies for stopping this communication, known as quorum quenching (QQ), appear to be successful for biofouling control in MBRs used for wastewater treatment. This review describes recent information regarding the signal molecules and mechanisms responsible for QS behaviors, promising approaches for QQ (enzymatic, bacterial, fungal, photocatalytic, mimicking, and biostimulating methods), and efficient fabrication and use of QQ media for MBR applications. We discuss the opportunities and challenges of QQ techniques for their further improvement and practical use in MBRs.}, }
@article {pmid30210468, year = {2018}, author = {Nguyen, NL and Yu, WJ and Gwak, JH and Kim, SJ and Park, SJ and Herbold, CW and Kim, JG and Jung, MY and Rhee, SK}, title = {Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1982}, doi = {10.3389/fmicb.2018.01982}, pmid = {30210468}, issn = {1664-302X}, abstract = {Soil acidification is accelerated by anthropogenic and agricultural activities, which could significantly affect global methane cycles. However, detailed knowledge of the genomic properties of methanotrophs adapted to acidic soils remains scarce. Using metagenomic approaches, we analyzed methane-utilizing communities enriched from acidic forest soils with pH 3 and 4, and recovered near-complete genomes of proteobacterial methanotrophs. Novel methanotroph genomes designated KS32 and KS41, belonging to two representative clades of methanotrophs (Methylocystis of Alphaproteobacteria and Methylobacter of Gammaproteobacteria), were dominant. Comparative genomic analysis revealed diverse systems of membrane transporters for ensuring pH homeostasis and defense against toxic chemicals. Various potassium transporter systems, sodium/proton antiporters, and two copies of proton-translocating F1F0-type ATP synthase genes were identified, which might participate in the key pH homeostasis mechanisms in KS32. In addition, the V-type ATP synthase and urea assimilation genes might be used for pH homeostasis in KS41. Genes involved in the modification of membranes by incorporation of cyclopropane fatty acids and hopanoid lipids might be used for reducing proton influx into cells. The two methanotroph genomes possess genes for elaborate heavy metal efflux pumping systems, possibly owing to increased heavy metal toxicity in acidic conditions. Phylogenies of key genes involved in acid adaptation, methane oxidation, and antiviral defense in KS41 were incongruent with that of 16S rRNA. Thus, the detailed analysis of the genome sequences provides new insights into the ecology of methanotrophs responding to soil acidification.}, }
@article {pmid30209587, year = {2018}, author = {Hernández-Gómez, O and Briggler, JT and Williams, RN}, title = {Captivity-Induced Changes in the Skin Microbial Communities of Hellbenders (Cryptobranchus alleganiensis).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1258-1}, pmid = {30209587}, issn = {1432-184X}, abstract = {Variation in environmental conditions can result in disparate associations between hosts and microbial symbionts. As such, it is imperative to evaluate how environmental variables (e.g., habitat quality) can influence host-associated microbiome composition. Within wildlife conservation programs, captive conditions can negatively influence the establishment and maintenance of &quot;wild-type&quot; microbiotas within a host. Alternative microbial communities can result in the proliferation of disease among captive stock or upon reintroduction. Hellbenders (Cryptobranchus alleganiensis) are a threatened salamander for which extensive captive management is currently employed. Using metabarcoding, we characterized the skin microbiota of wild and captive hellbenders from two subspecies in the state of Missouri, the eastern (C. a. alleganiensis) and the Ozark hellbender (C. a. bishopi). Both subspecies in our study included wild adults and captive juveniles that were collected from the wild as eggs. Our objectives were to investigate differences in the skin microbial communities' richness/diversity, composition, and functional profiles of microbes between wild and captive individuals. Captive eastern hellbenders possessed richer communities than wild cohorts, whereas the opposite pattern was observed within the Ozark subspecies. We found significant microbial community structure between wild and captive populations of both subspecies. Microbiota structure translated into differences in the predicted metagenome of wild and captive individuals as well. As such, we can expect captive hellbenders to experience alternative microbial structure and function upon reintroduction into the wild. Our study provides a baseline for the effect of captivity on the skin microbial communities of hellbenders, and highlights the need to incorporate microbiota management in current captive-rearing programs.}, }
@article {pmid30209586, year = {2018}, author = {Manjunatha, BS and Paul, S and Aggarwal, C and Bandeppa, S and Govindasamy, V and Dukare, AS and Rathi, MS and Satyavathi, CT and Annapurna, K}, title = {Diversity and Tissue Preference of Osmotolerant Bacterial Endophytes Associated with Pearl Millet Genotypes Having Differential Drought Susceptibilities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1257-2}, pmid = {30209586}, issn = {1432-184X}, abstract = {Genetic and functional diversity of osmotolerant bacterial endophytes colonizing the root, stem, and leaf tissues of pearl millet genotypes differing in their drought susceptibility was assessed. Two genotypes of pearl millet, viz., the drought tolerant genotype TT-1 and the drought susceptible genotype PPMI-69, were used in the present study. Diazotrophs were found to be the predominant colonizers, followed by the Gram positive bacteria in most of the tissues of both the genotypes. Higher proportion of bacterial endophytes obtained from the drought tolerant genotype was found to be osmotolerant. Results of 16S rRNA gene-ARDRA analysis grouped 50 of the highly osmotolerant isolates into 16 clusters, out of which nine clusters had only one isolate each, indicating their uniqueness. One cluster had 21 isolates and remaining clusters were represented by isolates ranging from two to four. The representative isolates from each cluster were identified, and Bacillus was found to be the most prevalent osmotolerant genera with many different species. Other endophytic bacteria belonged to Pseudomonas sp., Stenotrophomonas sp., and Macrococcus caseolyticus. High phylogenetic diversity was observed in the roots of the drought tolerant genotype while different tissues of the drought susceptible genotype showed less diversity. Isolates of Bacillus axarquiensis were present in all the tissues of both the genotypes of pearl millet. However, most of the other endophytic bacteria showed tissue/genotype specificity. With the exception of B. axarquiensis and B. thuringiensis, rest all the species of Bacillus were found colonizing only the drought-tolerant genotype; while M. caseolyticus colonized all the tissues of only the drought susceptible genotype. There was high incidence of IAA producers and low incidence of ACC deaminase producers among the isolates from the root tissues of the drought-tolerant genotype while reverse was the case for the drought-susceptible genotype. Thus, host played an important role in the selection of endophytes based on both phylogenetic and functional traits.}, }
@article {pmid30209585, year = {2018}, author = {Houfani, AA and Větrovský, T and Navarrete, OU and Štursová, M and Tláskal, V and Beiko, RG and Boucherba, N and Baldrian, P and Benallaoua, S and Jorquera, MA}, title = {Cellulase-Hemicellulase Activities and Bacterial Community Composition of Different Soils from Algerian Ecosystems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1251-8}, pmid = {30209585}, issn = {1432-184X}, support = {LM2015055//Ministry of Education, Youth and Sports of the Czech Republic/ ; 1160302//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; }, abstract = {Soil microorganisms are important mediators of carbon cycling in nature. Although cellulose- and hemicellulose-degrading bacteria have been isolated from Algerian ecosystems, the information on the composition of soil bacterial communities and thus the potential of their members to decompose plant residues is still limited. The objective of the present study was to describe and compare the bacterial community composition in Algerian soils (crop, forest, garden, and desert) and the activity of cellulose- and hemicellulose-degrading enzymes. Bacterial communities were characterized by high-throughput 16S amplicon sequencing followed by the in silico prediction of their functional potential. The highest lignocellulolytic activity was recorded in forest and garden soils whereas activities in the agricultural and desert soils were typically low. The bacterial phyla Proteobacteria (in particular classes α-proteobacteria, δ-proteobacteria, and γ-proteobacteria), Firmicutes, and Actinobacteria dominated in all soils. Forest and garden soils exhibited higher diversity than agricultural and desert soils. Endocellulase activity was elevated in forest and garden soils. In silico analysis predicted higher share of genes assigned to general metabolism in forest and garden soils compared with agricultural and arid soils, particularly in carbohydrate metabolism. The highest potential of lignocellulose decomposition was predicted for forest soils, which is in agreement with the highest activity of corresponding enzymes.}, }
@article {pmid30209011, year = {2018}, author = {Shade, A and Dunn, RR and Blowes, SA and Keil, P and Bohannan, BJM and Herrmann, M and Küsel, K and Lennon, JT and Sanders, NJ and Storch, D and Chase, J}, title = {Macroecology to Unite All Life, Large and Small.}, journal = {Trends in ecology &amp; evolution}, volume = {33}, number = {10}, pages = {731-744}, doi = {10.1016/j.tree.2018.08.005}, pmid = {30209011}, issn = {1872-8383}, abstract = {Macroecology is the study of the mechanisms underlying general patterns of ecology across scales. Research in microbial ecology and macroecology have long been detached. Here, we argue that it is time to bridge the gap, as they share a common currency of species and individuals, and a common goal of understanding the causes and consequences of changes in biodiversity. Microbial ecology and macroecology will mutually benefit from a unified research agenda and shared datasets that span the entirety of the biodiversity of life and the geographic expanse of the Earth.}, }
@article {pmid30206025, year = {2018}, author = {Kispal, ZF and Vajda, P and Kardos, D and Klymiuk, I and Moissl-Eichinger, C and Castellani, C and Singer, G and Till, H}, title = {The local microbiome after pediatric bladder augmentation: intestinal segments and the native urinary bladder host similar mucosal microbiota.}, journal = {Journal of pediatric urology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jpurol.2018.07.028}, pmid = {30206025}, issn = {1873-4898}, abstract = {INTRODUCTION: Next-generation sequencing (NGS) techniques have provided novel insights into the microbiome of the urinary bladder (UB). In children after bladder augmentation using either ileum (ileocystoplasty, ICP) or colon (colocystoplasty, CCP), the fate of the mucosal microbiome introduced into the urinary tract remains unknown.<br><br>OBJECTIVE: The aim was to compare the mucosal microbiome of the native UB vs the augmented intestinal segment (IS) using NGS.<br><br>STUDY DESIGN: Twelve children after bladder augmentation (ICP n = 6, CCP n = 6) were included. Biopsies were taken during routine postoperative cystoscopy from the native UB and the IS. Specimens underwent whole-genome DNA extraction, 16S rRNA gene amplification, NGS, and Quantitative Insights Into Microbial Ecology (QIIME) data analysis. Downstream statistical data analyses were performed in Calypso.<br><br>RESULTS: Patients' median age at the time of surgery was 11 years (6-17 years), and the median interval between augmentation and sampling was 7 years (4-13 years). α-Diversity (Shannon diversity index) was not significantly different between IS vs UB, ICP vs CCP, and male vs female. No general differences in the overall bacterial pattern (β-diversity) were found between IS, UB, ICP, and CCP groups. The groups overlapped in principal coordinate analysis (PCoA) and non-metric multidimensional scaling (NMDS) analysis (Figure). Age at sampling had a statistically significant influence on β-diversity at the genus level. Corynebacterium, Pseudoxanthomonas, Lactobacillus, Flavobacterium, and Micrococcus were the most dominating taxa detected over all samples. There was an obvious dominance of the genus Corynebacterium in the samples taken from the UB and IS in both ICP and CCP patients. Limitations of this study include the relatively small number of patients.<br><br>CONCLUSION: After bladder augmentation, the native UB and augmented ISs (ICP and CCP) host similar microbiota despite their distinct differences of originating mucosal anatomy.}, }
@article {pmid30204767, year = {2018}, author = {Lee, JZ and Everroad, RC and Karaoz, U and Detweiler, AM and Pett-Ridge, J and Weber, PK and Prufert-Bebout, L and Bebout, BM}, title = {Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0202792}, doi = {10.1371/journal.pone.0202792}, pmid = {30204767}, issn = {1932-6203}, abstract = {Hypersaline photosynthetic microbial mats are stratified microbial communities known for their taxonomic and metabolic diversity and strong light-driven day-night environmental gradients. In this study of the upper photosynthetic zone of hypersaline microbial mats of Elkhorn Slough, California (USA), we show how metagenome sequencing can be used to meaningfully assess microbial ecology and genetic partitioning in these complex microbial systems. Mapping of metagenome reads to the dominant Cyanobacteria observed in the system, Coleofasciculus (Microcoleus) chthonoplastes, was used to examine strain variants within these metagenomes. Highly conserved gene subsystems indicated a core genome for the species, and a number of variant genes and subsystems suggested strain level differentiation, especially for nutrient utilization and stress response. Metagenome sequence coverage binning was used to assess ecosystem partitioning of remaining microbes to both reconstruct the model organisms in silico and identify their ecosystem functions as well as to identify novel clades and propose their role in the biogeochemical cycling of mats. Functional gene annotation of these bins (primarily of Proteobacteria, Bacteroidetes, and Cyanobacteria) recapitulated the known biogeochemical functions in microbial mats using a genetic basis, and revealed significant diversity in the Bacteroidetes, presumably in heterotrophic cycling. This analysis also revealed evidence of putative phototrophs within the Gemmatimonadetes and Gammaproteobacteria residing in microbial mats. This study shows that metagenomic analysis can produce insights into the systems biology of microbial ecosystems from a genetic perspective and to suggest further studies of novel microbes.}, }
@article {pmid30199845, year = {2018}, author = {Dolan, JR}, title = {The Villefranche Strombidium sulcatum: A review.}, journal = {European journal of protistology}, volume = {66}, number = {}, pages = {68-76}, doi = {10.1016/j.ejop.2018.08.002}, pmid = {30199845}, issn = {1618-0429}, abstract = {The marine oligotrich ciliate Strombidium sulcatum, the best known marine oligotrich of the marine microozoplankton, was first cultured in Villefranche-sur-Mer 35 years ago. Cultures were maintained from 1983 to 2003 and used in 22 studies investigating a very wide variety of questions. Here we review the major findings of these studies and underline their contributions to our knowledge of planktonic ciliate ecology and microbial ecology in general. We conclude with the observation that while ecophysiology has apparently fallen out of fashion, culture work will likely return as an invaluable resource in our present 'omics' era.}, }
@article {pmid30199026, year = {2018}, author = {Couper, L and Swei, A}, title = {Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {138}, pages = {}, doi = {10.3791/58239}, pmid = {30199026}, issn = {1940-087X}, abstract = {In recent decades, vector-borne diseases have re-emerged and expanded at alarming rates, causing considerable morbidity and mortality worldwide. Effective and widely available vaccines are lacking for a majority of these diseases, necessitating the development of novel disease mitigation strategies. To this end, a promising avenue of disease control involves targeting the vector microbiome, the community of microbes inhabiting the vector. The vector microbiome plays a pivotal role in pathogen dynamics, and manipulations of the microbiome have led to reduced vector abundance or pathogen transmission for a handful of vector-borne diseases. However, translating these findings into disease control applications requires a thorough understanding of vector microbial ecology, historically limited by insufficient technology in this field. The advent of next-generation sequencing approaches has enabled rapid, highly parallel sequencing of diverse microbial communities. Targeting the highly-conserved 16S rRNA gene has facilitated characterizations of microbes present within vectors under varying ecological and experimental conditions. This technique involves amplification of the 16S rRNA gene, sample barcoding via PCR, loading samples onto a flow cell for sequencing, and bioinformatics approaches to match sequence data with phylogenetic information. Species or genus-level identification for a high number of replicates can typically be achieved through this approach, thus circumventing challenges of low detection, resolution, and output from traditional culturing, microscopy, or histological staining techniques. Therefore, this method is well-suited for characterizing vector microbes under diverse conditions but cannot currently provide information on microbial function, location within the vector, or response to antibiotic treatment. Overall, 16S next-generation sequencing is a powerful technique for better understanding the identity and role of vector microbes in disease dynamics.}, }
@article {pmid30197411, year = {2018}, author = {Mise, K and Fujita, K and Kunito, T and Senoo, K and Otsuka, S}, title = {Phosphorus-mineralizing Communities Reflect Nutrient-Rich Characteristics in Japanese Arable Andisols.}, journal = {Microbes and environments}, volume = {33}, number = {3}, pages = {282-289}, doi = {10.1264/jsme2.ME18043}, pmid = {30197411}, issn = {1347-4405}, abstract = {Elucidating the soil phosphorus cycle driven by soil microbes is a vital question in soil microbial ecology. The Japanese arable Andisols, occupying half of the Japanese cropland, are known for their high phosphorus sorption capacity. However, limited information is currently available on microbially driven phosphorus mineralization in arable Andisols. We herein report that the phosphorus-mineralizing community in the Japanese arable Andisols showed characteristic distribution and composition patterns, from those in other types of soils. We performed a chemical analysis and microbial community analysis of 43 arable Andisols along the Japanese archipelago. Soil phosphomonoesterase activities measured at pH 11 were approximately 70% of those at pH 6.5, which indicates that alkaline phosphatase contributes to phosphorus cycling, although most soil samples were acidic. Functional gene predictions based on 16S rRNA gene sequencing indicated that the alkaline phosphatase gene phoD was more abundant than other alkaline phosphatase genes and, thus, plays major roles. Hence, amplicon sequencing targeting phoD was performed and the results obtained showed that alphaproteobacterial phoD was dominant. This is in contrast to previously reported phoD compositions in other soils and may be attributed to the nutrient conditions in arable Andisols, which favor copiotrophic Alphaproteobacteria. Furthermore, the composition of phoD correlated with soil pH and bioavailable phosphorus concentrations rather than carbon or nitrogen concentrations. These results were partly different from previous findings, varying in the soil types and geographic ranges of sampling sites. Collectively, the present results indicate that the phosphorus-mineralizing community in the Japanese arable Andisols is regulated differently from those in other soil types.}, }
@article {pmid30196926, year = {2018}, author = {Šulčius, S and Mazur-Marzec, H and Vitonytė, I and Kvederavičiūtė, K and Kuznecova, J and Šimoliūnas, E and Holmfeldt, K}, title = {Insights into cyanophage-mediated dynamics of nodularin and other non-ribosomal peptides in Nodularia spumigena.}, journal = {Harmful algae}, volume = {78}, number = {}, pages = {69-74}, doi = {10.1016/j.hal.2018.07.004}, pmid = {30196926}, issn = {1878-1470}, abstract = {The effect of cyanophage infection and lysis on the dynamics of the hepatotoxin nodularin (NOD) and other non-ribosomal peptides (NRPs) produced by cyanobacteria is poorly understood. In this study, changes in concentration of NOD and other NRPs during cyanophage infection of the filamentous cyanobacteria Nodularia spumigena were assessed using incubation experiments. Viral infection and lysis were associated with a significant reduction (93% at the 96 h post infection) of N. spumigena cell density. While no correlation between N. spumigena abundance and total concentration of NOD (ng mL-1) within the infected cells was observed, cellular NOD quota (ng cell-1) gradually increased in the remaining cyanophage resistant N. spumigena subpopulation. Lysis of N. spumigena cells resulted in a substantial increase (>57 times) of dissolved NOD concentration in the culture medium. The relative concentration of other cyclic (anabaenopeptins) and linear (aeruginosins, spumigins) NRPs produced by N. spumigena also increased in response to cyanophage addition. This study highlights the importance of cyanophage infection on the population toxicity of filamentous cyanobacteria and demonstrates a significant contribution of virus-mediated cell lysis on the conversion of NOD from the particulate to dissolved phase.}, }
@article {pmid30196314, year = {2018}, author = {Ullah, A and Akbar, A and Luo, Q and Khan, AH and Manghwar, H and Shaban, M and Yang, X}, title = {Microbiome Diversity in Cotton Rhizosphere Under Normal and Drought Conditions.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1260-7}, pmid = {30196314}, issn = {1432-184X}, support = {2016YFD0101006//National Key Project of Research and Development Plan/ ; 2016ZX08005-004-002//Transgenic Crops of Transgenic Crops of Ministry of Science and Technology of China/ ; }, abstract = {Climate change contributes to drought stress and subsequently affects crop growth, development, and yield. The microbial community, such as fungi and bacteria in the rhizosphere, is of special importance to plant productivity. In this study, soil collected from a cotton research field was used to grow cotton plants (Gossypium hirsutum cv. Jin668) under controlled environment conditions. Drought stress was applied at flowering stage, while control plants were regularly watered. At the same time, the soil without plants was also subjected to drought, while control pots were regularly watered. The soil was collected in sterilized tubes and microbial DNA was isolated and high-throughput sequencing of 16S rRNA genes was carried out. The alpha diversity of bacteria community significantly increased in the soil with cotton plants compared to the soil without cotton plants. Taxonomic analysis revealed that the bacterial community structure of the cotton rhizosphere predominantly consisted of the phyla Proteobacteria (31.7%), Actinobacteria (29.6%), Gemmatimonadetes (9.8%), Chloroflexi (9%), Cyanobacteria (5.6%), and Acidobacteria. In the drought-treated rhizosphere, Chloroflexi and Gemmatimonadetes were the dominant phyla. This study reveals that the cotton rhizosphere has a rich pool of bacterial communities even under drought stress, and which may improve drought tolerance in plants. These data will underpin future improvement of drought tolerance of cotton via the soil microbial community.}, }
@article {pmid30195549, year = {2018}, author = {Jamar, G and Santamarina, AB and Dias, GC and Masquio, DCL and de Rosso, VV and Pisani, LP}, title = {Relationship between fatty acids intake and Clostridium coccoides in obese individuals with metabolic syndrome.}, journal = {Food research international (Ottawa, Ont.)}, volume = {113}, number = {}, pages = {86-92}, doi = {10.1016/j.foodres.2018.07.002}, pmid = {30195549}, issn = {1873-7145}, abstract = {Dietary habits exert a strong influence on gut microbial composition and may result in an imbalance of gut microbes, representing a predisposition to obesity and metabolic disorders. We aimed to investigate a potential relationship between gut bacterial species and metabolic parameters and dietary intake. Bacterial DNA was extracted from feces of 34 obese subjects with and without metabolic syndrome (MS and n-MS group, respectively). We then used real-time polymerase chain reaction (qPCR) for quantifying specific sequences to Akkermansia muciniphila, Bifidobacterium spp., Clostridium coccoides, and Lactobacillus spp. and analyzed them with respect to clinical characteristics. Our data showed that the MS group had a 6.7-fold higher level of C. coccoides in their stool samples than the n-MS group. The abundance of C. coccoides was positively correlated with a high intake of monounsaturated fatty acids (MUFA) and polyunsaturated fatty acids. Furthermore, an excessive dietary level of MUFA was identified as a predictor of C. coccoides abundance. Alterations in the gut microbial ecology were positively correlated with levels of triacylglycerol in obese individuals. Therefore, the type and quantity of dietary fat may alter the gut microbial ecology in obese individuals with MS and may predispose them to dyslipidemia.}, }
@article {pmid30195522, year = {2018}, author = {Nash, V and Ranadheera, CS and Georgousopoulou, EN and Mellor, DD and Panagiotakos, DB and McKune, AJ and Kellett, J and Naumovski, N}, title = {The effects of grape and red wine polyphenols on gut microbiota - A systematic review.}, journal = {Food research international (Ottawa, Ont.)}, volume = {113}, number = {}, pages = {277-287}, doi = {10.1016/j.foodres.2018.07.019}, pmid = {30195522}, issn = {1873-7145}, abstract = {There is a growing body of evidence implicating the gut 'microbiome' role in overall human health. Bacterial species belonging to the genera Lactobacillus and Bifidobacterium are generally considered to be beneficial and are commonly used in probiotic applications, whereas increases in some genera including Clostridum, Eubacterium and Bacteroides are implicated in negative health outcomes. Dietary polyphenols are bioactive compounds that have been found to increase the numbers of beneficial bacteria and antimicrobial actions against pathogenic bacteria, however most studies have been conducted in animal models or in-vitro colonic models. The aim of this systematic review was to provide an overview of recent trials on the effect of dietary grape and red wine polyphenols on the gut microbiota in humans. Following PRISMA guidelines, a systematic review was conducted of electronic databases (PubMed, CINAHL, Cochrane Library, Wed of Science and Scopus) to identify human intervention trials examining the effect of grape or wine polyphenols on gut microbiota. Seven trials met the inclusion criteria. One study looked at changes in gut microbiota following the ingestion of de-alcoholised red wine or red wine, and six studies referred to gut microbiota as intermediates in formation of phenolic metabolites. All studies confirmed that ingested polyphenols from grape and red wine, were modulated by gut microbiota, increasing numbers of polyphenolic metabolites which were found in blood, urine, ileal fluid and faeces. Intake of polyphenols derived from grape and red wine can modulate gut microbiota and contribute to beneficial microbial ecology that can enhance human health benefits. Additionally, grape and red wine polyphenols were modulated by the gut microbiota and there is a potential for a two-way relationship between the gut microbiota and polyphenolic compounds. Nevertheless, additional research is required to fully understand the complex relationship between gut microbiota and dietary polyphenols before any health claims can be made in relation to human health.}, }
@article {pmid30195437, year = {2018}, author = {Medlock, GL and Carey, MA and McDuffie, DG and Mundy, MB and Giallourou, N and Swann, JR and Kolling, GL and Papin, JA}, title = {Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota.}, journal = {Cell systems}, volume = {7}, number = {3}, pages = {245-257.e7}, doi = {10.1016/j.cels.2018.08.003}, pmid = {30195437}, issn = {2405-4712}, support = {R01 GM108501/GM/NIGMS NIH HHS/United States ; T32 GM008136/GM/NIGMS NIH HHS/United States ; T32 LM012416/LM/NLM NIH HHS/United States ; }, abstract = {The diversity and number of species present within microbial communities create the potential for a multitude of interspecies metabolic interactions. Here, we develop, apply, and experimentally test a framework for inferring metabolic mechanisms associated with interspecies interactions. We perform pairwise growth and metabolome profiling of co-cultures of strains from a model mouse microbiota. We then apply our framework to dissect emergent metabolic behaviors that occur in co-culture. Based on one of the inferences from this framework, we identify and interrogate an amino acid cross-feeding interaction and validate that the proposed interaction leads to a growth benefit in vitro. Our results reveal the type and extent of emergent metabolic behavior in microbial communities composed of gut microbes. We focus on growth-modulating interactions, but the framework can be applied to interspecies interactions that modulate any phenotype of interest within microbial communities.}, }
@article {pmid30194506, year = {2018}, author = {da Silveira, APD and Iório, RPF and Marcos, FCC and Fernandes, AO and de Souza, SACD and Kuramae, EE and Cipriano, MAP}, title = {Exploitation of new endophytic bacteria and their ability to promote sugarcane growth and nitrogen nutrition.}, journal = {Antonie van Leeuwenhoek}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10482-018-1157-y}, pmid = {30194506}, issn = {1572-9699}, support = {2008/56147-1//FAPESP/ ; 456420/2013-4//CNPq/NWO/ ; 729.004.013//NWO/ ; }, abstract = {Few studies have evaluated endophytic bacteria in relation to plant growth promotion, nitrogen uptake and biological control. The aim of this study was to molecularly and physiologically characterize thirteen endophytic bacteria strains, evaluate their biological control properties and their ability to promote plant growth and plant N nutrition. All the strains produced indole acetic acid and promoted increase of plant biomass, N accumulative amount and N-use efficiency index. None of the strains carries the nifH gene. Four strains stimulated plant nitrate reductase activity, four solubilized phosphate, nine produced siderophores and none produced HCN. Seven strains inhibited Bipolaris sacchari growth and one was antagonistic to Ceratocystis paradoxa. The pathogens were inhibited by the production of diffusible and volatile metabolites by the bacterial strains. Moreover, this is the first study to demonstrate the effect of Delftia acidovorans on sugarcane plant growth, nitrogen metabolism improvement and antagonism to B. sacchari. The most efficient strains in promoting plant growth and exhibiting antagonistic activities towards fungal pathogens were Herbaspirillum frinsingense (IAC-BECa-152) and three Pantoea dispersa strains (IAC-BECa-128, IAC-BECa-129, and IAC-BECa-132). These bacteria show potential to be used as inoculants for sustainable agricultural management, mainly at the seedling production phase.}, }
@article {pmid30194484, year = {2018}, author = {Szubert-Kruszyńska, A and Stańczak, J and Cieniuch, S and Podsiadły, E and Postawa, T and Michalik, J}, title = {Correction to: Bartonella and Rickettsia Infections in Haematophagous Spinturnix myoti Mites (Acari: Mesostigmata) and their Bat Host, Myotis myotis (Yangochiroptera: Vespertilionidae), from Poland.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1259-0}, pmid = {30194484}, issn = {1432-184X}, abstract = {The original version of this article published online (27 August 2018) unfortunately contained a mistake regarding an affiliation of Dr. Edyta Podsiadły, one of the authors.}, }
@article {pmid30194483, year = {2018}, author = {Eichmeier, A and Kiss, T and Necas, T and Penazova, E and Tekielska, D and Bohunicka, M and Valentova, L and Cmejla, R and Morais, D and Baldrian, P}, title = {High-Throughput Sequencing Analysis of the Bacterial Community in Stone Fruit Phloem Tissues Infected by &quot;Candidatus Phytoplasma prunorum&quot;.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1250-9}, pmid = {30194483}, issn = {1432-184X}, support = {QJ1510352//Ministry of Agriculture of the Czech Republic/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; LM2015042//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; }, abstract = {&quot;Candidatus Phytoplasma prunorum&quot; (CPp) is a highly destructive phytopathogenic agent in many stone fruit-growing regions in Europe and the surrounding countries. In this work, we focused on documenting entire bacterial community in the phloem tissues of 60 stone fruit trees. Nested PCR and two real-time PCR assays were used to select CPp-positive (group A) and CPp-negative samples (group B). Afterwards, high-throughput amplicon sequencing was performed to assess bacterial community compositions in phloem tissues. The bacterial composition in phloem tissue consisted of 118 distinct genera, represented mainly by Pseudomonas, Acinetobacter, Methylobacterium, Sphingomonas, and Rhizobium. Statistics showed that CPp influenced the bacterial composition of infected plants (group A) and that the bacterial community depended on the geographical origin of the sample. This is the first work focusing on an analysis of the influence of CPp on the bacteria coexisting in the phloem tissues of stone fruit trees.}, }
@article {pmid30194105, year = {2018}, author = {Cordovez, V and Schop, S and Hordijk, K and de Boulois, HD and Coppens, F and Hanssen, I and Raaijmakers, JM and Carrion, VJ}, title = {Priming of plant growth promotion by volatiles of root-associated Microbacterium.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.01865-18}, pmid = {30194105}, issn = {1098-5336}, abstract = {Volatile compounds produced by plant-associated microorganisms represent a diverse resource to promote plant growth and health. Here we investigated the effect of volatiles from root-associated Microbacterium species on plant growth and development. Volatiles of eight strains induced significant increases in shoot and root biomass of Arabidopsis, but differed in their effects on root architecture. Microbacterium strain EC8 also enhanced root and shoot biomass of lettuce and tomato. Biomass increases were also observed for plants exposed only shortly to volatiles from EC8 prior to transplantation of the seedlings to soil. These results indicate that volatiles from EC8 can prime plants for growth promotion without direct and prolonged contact. We further showed that the induction of plant growth promotion is tissue specific: exposure of roots to volatiles from EC8 led to an increase in plant biomass whereas shoot exposure resulted in no or less growth promotion. GC-QTOF analysis revealed that EC8 produces a wide array of sulfur containing compounds as well as ketones. Bioassays with synthetic sulfur volatile compounds revealed that the plant growth response to dimethyl trisulfide was concentration-dependent with a significant increase in shoot weight at 1 μM and negative effects on plant biomass at concentrations higher than 1 mM. Genome-wide transcriptome analysis of volatile-exposed Arabidopsis seedlings showed up-regulation of genes involved in assimilation and transport of sulfate and nitrate. Collectively, these results show that root-associated Microbacterium primes plants, via the roots, for growth promotion most likely via modulation of sulfur and nitrogen metabolism.Importance In the past decade, various studies have described the effects of microbial volatiles on other (micro)organisms in vitro, but their broad-spectrum activity in vivo and the mechanisms underlying volatile-mediated plant growth promotion have not been addressed in detail. Here, we revealed that volatiles from root-associated bacteria of the genus Microbacterium can enhance growth of different plant species and can prime plants for growth promotion without direct and prolonged contact between the bacterium and the plant. Collectively, these results provide new opportunities for sustainable agriculture and horticulture by exposing roots of plants only briefly to a specific blend of microbial volatile compounds prior to transplantation of the seedlings to the greenhouse or field. This strategy has no need for large-scale introduction, root colonization and survival of the microbial inoculant.}, }
@article {pmid30192223, year = {2018}, author = {Borel, N and Bavoil, P and Greub, G and Horn, M}, title = {International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Chlamydiae. Minutes of the closed meeting, 9 April 2017, Charlotte, USA.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {68}, number = {1}, pages = {3369-3370}, doi = {10.1099/ijsem.0.003010}, pmid = {30192223}, issn = {1466-5034}, }
@article {pmid30191255, year = {2018}, author = {Tarnecki, AM and Brennan, NP and Schloesser, RW and Rhody, NR}, title = {Shifts in the Skin-Associated Microbiota of Hatchery-Reared Common Snook Centropomus undecimalis During Acclimation to the Wild.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1252-7}, pmid = {30191255}, issn = {1432-184X}, support = {R/LR-A-54//Florida Sea Grant, University of Florida/ ; }, abstract = {The skin-associated microbiota of fish competes against pathogens for space and nutrients, preventing colonization by harmful bacteria encountered during environmental transitions such as those faced during stock enhancement. Thus, alterations in bacterial community structure during release of cultured fish have important implications for health of these individuals. This study investigated microbiota structure during acclimation of juvenile hatchery-reared common snook Centropomus undecimalis to the wild by comparing skin-associated microflora among snook in captivity, after 48 h of acclimation at release sites, and from the wild. After two days of acclimation, the microbiota of hatchery-reared snook mirrored that observed on wild snook. Relative abundances of potential pathogens were higher in captive fish, whereas acclimated and wild fish harbored bacterial taxa influenced by geographical factors and water quality at release sites. Predicted microbiota function of acclimated and wild fish showed higher production of protective amino acids and antimicrobials, identifying a mechanism for microbial supplementation of the immune defense of these fish. The two-day transition to wild-type microbiota suggests a temporal scale of hours associated with bacterial succession indicating that the microbiota, whose structure is vital to fish health, aids in acclimation of fish to new environments during stock enhancement efforts.}, }
@article {pmid30190715, year = {2018}, author = {Safonov, AV and Babich, TL and Sokolova, DS and Grouzdev, DS and Tourova, TP and Poltaraus, AB and Zakharova, EV and Merkel, AY and Novikov, AP and Nazina, TN}, title = {Microbial Community and in situ Bioremediation of Groundwater by Nitrate Removal in the Zone of a Radioactive Waste Surface Repository.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1985}, doi = {10.3389/fmicb.2018.01985}, pmid = {30190715}, issn = {1664-302X}, abstract = {The goal of the present work was to investigate the physicochemical and radiochemical conditions and the composition of the microbial community in the groundwater of a suspended surface repository for radioactive waste (Russia) and to determine the possibility of in situ groundwater bioremediation by removal of nitrate ions. Groundwater in the repository area (10-m depth) had elevated concentrations of strontium, tritium, nitrate, sulfate, and bicarbonate ions. High-throughput sequencing of the V3-V4/V4 region of the 16S rRNA gene revealed the presence of members of the phyla Proteobacteria (genera Acidovorax, Simplicispira, Thermomonas, Thiobacillus, Pseudomonas, Brevundimonas, and uncultured Oxalobacteraceae), Firmicutes (genera Bacillus and Paenibacillus), and Actinobacteria (Candidatus Planktophila, Gaiella). Canonical correspondence analysis suggested that major contaminant - nitrate, uranium, and sulfate shaped the composition of groundwater microbial community. Groundwater samples contained culturable aerobic organotrophic, as well as anaerobic fermenting, iron-reducing, and denitrifying bacteria. Pure cultures of 33 bacterial strains belonging to 15 genera were isolated. Members of the genera Pseudomonas, Rhizobium, Cupriavidus, Shewanella, Ensifer, and Thermomonas reduced nitrate to nitrite and/or dinitrogen. Application of specific primers revealed the nirS and nirK genes encoding nitrite reductases in bacteria of the genera Pseudomonas, Rhizobium, and Ensifer. Nitrate reduction by pure bacterial cultures resulted in decreased ambient Eh. Among the organic substrates tested, sodium acetate and milk whey were the best for stimulation of denitrification by the microcosms with groundwater microorganisms. Injection of these substrates into the subterranean horizon (single-well push-pull test) resulted in temporary removal of nitrate ions in the area of the suspended radioactive waste repository and confirmed the possibility for in situ application of this method for bioremediation.}, }
@article {pmid30190707, year = {2018}, author = {Hicks, N and Liu, X and Gregory, R and Kenny, J and Lucaci, A and Lenzi, L and Paterson, DM and Duncan, KR}, title = {Temperature Driven Changes in Benthic Bacterial Diversity Influences Biogeochemical Cycling in Coastal Sediments.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1730}, doi = {10.3389/fmicb.2018.01730}, pmid = {30190707}, issn = {1664-302X}, abstract = {Marine sediments are important sites for global biogeochemical cycling, mediated by macrofauna and microalgae. However, it is the microorganisms that drive these key processes. There is strong evidence that coastal benthic habitats will be affected by changing environmental variables (rising temperature, elevated CO2), and research has generally focused on the impact on macrofaunal biodiversity and ecosystem services. Despite their importance, there is less understanding of how microbial community assemblages will respond to environmental changes. In this study, a manipulative mesocosm experiment was employed, using next-generation sequencing to assess changes in microbial communities under future environmental change scenarios. Illumina sequencing generated over 11 million 16S rRNA gene sequences (using a primer set biased toward bacteria) and revealed Bacteroidetes and Proteobacteria dominated the total bacterial community of sediment samples. In this study, the sequencing coverage and depth revealed clear changes in species abundance within some phyla. Bacterial community composition was correlated with simulated environmental conditions, and species level community composition was significantly influenced by the mean temperature of the environmental regime (p = 0.002), but not by variation in CO2 or diurnal temperature variation. Species level changes with increasing mean temperature corresponded with changes in NH4 concentration, suggesting there is no functional redundancy in microbial communities for nitrogen cycling. Marine coastal biogeochemical cycling under future environmental conditions is likely to be driven by changes in nutrient availability as a direct result of microbial activity.}, }
@article {pmid30188995, year = {2018}, author = {Shibl, AA and Ngugi, DK and Talarmin, A and Thompson, LR and Blom, J and Stingl, U}, title = {The genome of a novel isolate of Prochlorococcus from the Red Sea contains transcribed genes for compatible solute biosynthesis.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {12}, pages = {}, doi = {10.1093/femsec/fiy182}, pmid = {30188995}, issn = {1574-6941}, abstract = {Marine microbes possess genomic and physiological adaptations to cope with varying environmental conditions. So far, the effects of high salinity on the most abundant marine photoautotrophic organism, Prochlorococcus, in marine oligotrophic environments, are mostly unknown. Here, we report the isolation of a new Prochlorococcus strain (RSP50) belonging to high-light (HL) clade II from the Red Sea, one of the warmest and most saline bodies of water in the global oceans. A comparative genomic analysis identified a set of 59 genes that were exclusive to RSP50 relative to currently available Prochlorococcus genomes, the majority of which (70%) encode for hypothetical proteins of unknown function. However, three of the unique genes encode for a complete pathway for the biosynthesis of the compatible solute glucosylglycerol, and are homologous to enzymes found in the sister lineage Synechococcus. Metatranscriptomic analyses of this metabolic pathway in the water column of the Red Sea revealed that the corresponding genes were constitutively transcribed, independent of depth and light, suggesting that osmoregulation using glucosylglycerol is a general feature of HL II Prochlorococcus in the Red Sea.}, }
@article {pmid30188282, year = {2018}, author = {Coats, ER and Eyre, K and Bryant, C and Woodland, T and Brinkman, CK}, title = {Assessing the Effects of RAS Fermentation on EBPR Performance and Associated Microbial Ecology.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {90}, number = {7}, pages = {659-671}, doi = {10.2175/106143017X15131012153130}, pmid = {30188282}, issn = {1061-4303}, abstract = {Enhanced biological phosphorus removal (EBPR) is an engineered water resource recovery facility (WRRF) process configuration that can produce effluent P < 0.5 mg/L. To consistently achieve low effluent P concentrations, EBPR requires volatile fatty acids (VFAs) to induce requisite biochemical reactions. Moreover, returned activated sludge (RAS) nitrate concentrations must be minimized. Returned activated sludge fermentation can potentially address process needs. However, research detailed herein highlights concerns with RAS fermentation integrated with EBPR. Under 2 and 4 hours of RAS fermentation periods, no consequential VFA production was observed; similar results were observed in batch tests with RAS from a full-scale EBPR WRRF. More critically, EBPR performance was poor, with average effluent concentrations of 1.0 to 2.4 mg/L. Furthermore, the glycogen accumulating organism (GAO) fraction under RAS fermentation was 4.3 to 8.7 times higher than in a conventional EBPR mixed microbial consortium (MMC). Integrated RAS fermentation-EBPR only performed well under &quot;high&quot; RAS nitrate; thus, should RAS fermentation be implemented, careful control to prevent anaerobic conditions in the fermentation zone is required.}, }
@article {pmid30187987, year = {2018}, author = {Hooper, R and Brealey, JC and van der Valk, T and Alberdi, A and Durban, JW and Fearnbach, H and Robertson, KM and Baird, RW and Bradley Hanson, M and Wade, P and Gilbert, MTP and Morin, PA and Wolf, JBW and Foote, AD and Guschanski, K}, title = {Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.14860}, pmid = {30187987}, issn = {1365-294X}, support = {//Lindblad Expeditions/National Geographic Conservation Fund/ ; ERCStG-336536//European Research Council/International ; DNRF94//Danish National Research Foundation/ ; //Antarctic Science Bursary/ ; //Welsh Government and Higher Education Funding Council for Wales through the Sêr Cymru National Research Network for Low Carbon, Energy and Environment/ ; 663830//European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie/ ; SR17/1227//British Ecological Society/ ; 2016-00835//FORMAS/ ; 5051-00033//Danish Council for Independent Research-DFF/ ; R250-2017-1351//Lundbeckfonden/ ; }, abstract = {Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.}, }
@article {pmid30187089, year = {2018}, author = {Chan, YF and Chiang, KP and Ku, Y and Gong, GC}, title = {Abiotic and Biotic Factors Affecting the Ingestion Rates of Mixotrophic Nanoflagellates (Haptophyta).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1249-2}, pmid = {30187089}, issn = {1432-184X}, abstract = {Mixotrophic haptophytes comprise one of several important groups of mixotrophic nanoflagellates in the pelagic environment. This study aimed to investigate if phagotrophy in mixotrophic haptophytes is regulated by light or other factors in the surface (SE) and bottom (BE) of the euphotic zone in the subtropical northwestern Pacific Ocean. We estimated the rates of bacterial ingestion by haptophytes using fluorescently labeled bacteria (FLBs) and fluorescence in situ hybridization. Haptophyte diversity and abundance were also investigated in the same sampling area. The annual mean abundance of haptophytes was 419 ± 85.6 cells mL-1 in both SE and BE. Cells 3-5 μm in size were the dominant group in all haptophytes and accounted for majority of bacteria standing stock removed by haptophytes (53%). Most haptophyte ingestion rates (IRs) were not significantly different between the two layers (average SE ingestion rate: 12.5 ± 2.29 bac Hap-1 h-1; BE: 14.7 ± 3.03 bac Hap-1 h-1). Furthermore, the haptophyte IRs were negatively correlated with nitrate concentrations in the SE and positively correlated with bacterial abundances in the BE, which accounts for the significantly high IRs in August 2012 and 2013. These findings imply that mixotrophic haptophytes in this region had different factors affecting phagotrophy to adapt to the ambient light intensity alterations between SE and BE.}, }
@article {pmid30187088, year = {2018}, author = {Vallesi, A and Sjödin, A and Petrelli, D and Luporini, P and Taddei, AR and Thelaus, J and Öhrman, C and Nilsson, E and Di Giuseppe, G and Gutiérrez, G and Villalobo, E}, title = {A New Species of the γ-Proteobacterium Francisella, F. adeliensis Sp. Nov., Endocytobiont in an Antarctic Marine Ciliate and Potential Evolutionary Forerunner of Pathogenic Species.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1256-3}, pmid = {30187088}, issn = {1432-184X}, abstract = {The study of the draft genome of an Antarctic marine ciliate, Euplotes petzi, revealed foreign sequences of bacterial origin belonging to the γ-proteobacterium Francisella that includes pathogenic and environmental species. TEM and FISH analyses confirmed the presence of a Francisella endocytobiont in E. petzi. This endocytobiont was isolated and found to be a new species, named F. adeliensis sp. nov.. F. adeliensis grows well at wide ranges of temperature, salinity, and carbon dioxide concentrations implying that it may colonize new organisms living in deeply diversified habitats. The F. adeliensis genome includes the igl and pdp gene sets (pdpC and pdpE excepted) of the Francisella pathogenicity island needed for intracellular growth. Consistently with an F. adeliensis ancient symbiotic lifestyle, it also contains a single insertion-sequence element. Instead, it lacks genes for the biosynthesis of essential amino acids such as cysteine, lysine, methionine, and tyrosine. In a genome-based phylogenetic tree, F. adeliensis forms a new early branching clade, basal to the evolution of pathogenic species. The correlations of this clade with the other clades raise doubts about a genuine free-living nature of the environmental Francisella species isolated from natural and man-made environments, and suggest to look at F. adeliensis as a pioneer in the Francisella colonization of eukaryotic organisms.}, }
@article {pmid30186247, year = {2018}, author = {Olivares, M and Schüppel, V and Hassan, AM and Beaumont, M and Neyrinck, AM and Bindels, LB and Benítez-Páez, A and Sanz, Y and Haller, D and Holzer, P and Delzenne, NM}, title = {The Potential Role of the Dipeptidyl Peptidase-4-Like Activity From the Gut Microbiota on the Host Health.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1900}, doi = {10.3389/fmicb.2018.01900}, pmid = {30186247}, issn = {1664-302X}, abstract = {The Dipeptidyl peptidase-4 (DPP-4) activity influences metabolic, behavioral and intestinal disorders through the cleavage of key hormones and peptides. Some studies describe the existence of human DPP-4 homologs in commensal bacteria, for instance in Prevotella or Lactobacillus. However, the role of the gut microbiota as a source of DPP-4-like activity has never been investigated. Through the comparison of the DPP-4 activity in the cecal content of germ-free mice (GFM) and gnotobiotic mice colonized with the gut microbiota of a healthy subject, we bring the proof of concept that a significant DPP-4-like activity occurs in the microbiota. By analyzing the existing literature, we propose that DPP-4-like activity encoded by the intestinal microbiome could constitute a novel mechanism to modulate protein digestion as well as host metabolism and behavior.}, }
@article {pmid30185512, year = {2018}, author = {Rohwer, RR and Hamilton, JJ and Newton, RJ and McMahon, KD}, title = {TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, doi = {10.1128/mSphere.00327-18}, pmid = {30185512}, issn = {2379-5042}, abstract = {Taxonomy assignment of freshwater microbial communities is limited by the minimally curated phylogenies used for large taxonomy databases. Here we introduce TaxAss, a taxonomy assignment workflow that classifies 16S rRNA gene amplicon data using two taxonomy reference databases: a large comprehensive database and a small ecosystem-specific database rigorously curated by scientists within a field. We applied TaxAss to five different freshwater data sets using the comprehensive SILVA database and the freshwater-specific FreshTrain database. TaxAss increased the percentage of the data set classified compared to using only SILVA, especially at fine-resolution family to species taxon levels, while across the freshwater test data sets classifications increased by as much as 11 to 40% of total reads. A similar increase in classifications was not observed in a control mouse gut data set, which was not expected to contain freshwater bacteria. TaxAss also maintained taxonomic richness compared to using only the FreshTrain across all taxon levels from phylum to species. Without TaxAss, most organisms not represented in the FreshTrain were unclassified, but at fine taxon levels, incorrect classifications became significant. We validated TaxAss using simulated amplicon data derived from full-length clone libraries and found that 96 to 99% of test sequences were correctly classified at fine resolution. TaxAss splits a data set's sequences into two groups based on their percent identity to reference sequences in the ecosystem-specific database. Sequences with high similarity to sequences in the ecosystem-specific database are classified using that database, and the others are classified using the comprehensive database. TaxAss is free and open source and is available at https://www.github.com/McMahonLab/TaxAssIMPORTANCE Microbial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon data sets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at the phylum, class, and order levels lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or unique sequences. These fine-resolution groupings are more ecologically relevant, but OTU definitions are data set dependent and cannot be compared between data sets. Microbial ecologists studying freshwater have curated a small, ecosystem-specific taxonomy database to provide consistent and up-to-date terminology. We created TaxAss, a workflow that leverages this database to assign taxonomy. We found that TaxAss improves fine-resolution taxonomic classifications (family, genus, and species). Fine taxonomic groupings are more ecologically relevant, so they provide an alternative to OTU-based analyses that is consistent and comparable between data sets.}, }
@article {pmid30184128, year = {2018}, author = {Mangin, I and Dossou-Yovo, F and Lévêque, C and Dessoy, MV and Sawoo, O and Suau, A and Pochart, P}, title = {Oral administration of viable Bifidobacterium pseudolongum strain Patronus modified colonic microbiota and increased mucus layer thickness in rat.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {11}, pages = {}, doi = {10.1093/femsec/fiy177}, pmid = {30184128}, issn = {1574-6941}, abstract = {This study aimed at evaluating the alteration of the colonic microbiota and the changes in the mucus layer thickness induced by oral administration of living bifidobacteria in rats. The study was performed on rats fed with Bifidobacterium pseudolongum strain Patronus (1010 bacteria per day for 7 days). This bacterial administration led to a large increase of mucus thickness (57%, P < 0.05). Both quantitative PCR and high-throughput sequencing of bacterial 16S rRNA gene revealed a significant increase of the amount of the Bifidobacterium genus in the microbiota of rats fed with the strain Patronus, associated with a decrease of Akkermansia muciniphila. The increase in mucus thickness could be due to an increase of the bifidobacteria per se or via the decrease of A. muciniphila, a major mucin-degrading species. As the mucus layer plays an essential role in gut protection, our data enlighten the importance of studying mucus-degrading bacteria for understanding the underlying etiology of diseases such as intestinal bowel diseases and to implement new therapeutic strategies.}, }
@article {pmid30181663, year = {2018}, author = {Castelle, CJ and Brown, CT and Anantharaman, K and Probst, AJ and Huang, RH and Banfield, JF}, title = {Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {10}, pages = {629-645}, doi = {10.1038/s41579-018-0076-2}, pmid = {30181663}, issn = {1740-1534}, abstract = {Candidate phyla radiation (CPR) bacteria and DPANN (an acronym of the names of the first included phyla) archaea are massive radiations of organisms that are widely distributed across Earth's environments, yet we know little about them. Initial indications are that they are consistently distinct from essentially all other bacteria and archaea owing to their small cell and genome sizes, limited metabolic capacities and often episymbiotic associations with other bacteria and archaea. In this Analysis, we investigate their biology and variations in metabolic capacities by analysis of approximately 1,000 genomes reconstructed from several metagenomics-based studies. We find that they are not monolithic in terms of metabolism but rather harbour a diversity of capacities consistent with a range of lifestyles and degrees of dependence on other organisms. Notably, however, certain CPR and DPANN groups seem to have exceedingly minimal biosynthetic capacities, whereas others could potentially be free living. Understanding of these microorganisms is important from the perspective of evolutionary studies and because their interactions with other organisms are likely to shape natural microbiome function.}, }
@article {pmid30180359, year = {2019}, author = {Evans, SE and Dueker, ME and Logan, JR and Weathers, KC}, title = {The biology of fog: results from coastal Maine and Namib Desert reveal common drivers of fog microbial composition.}, journal = {The Science of the total environment}, volume = {647}, number = {}, pages = {1547-1556}, doi = {10.1016/j.scitotenv.2018.08.045}, pmid = {30180359}, issn = {1879-1026}, abstract = {Fog supplies water and nutrients to systems ranging from coastal forests to inland deserts. Fog droplets can also contain bacterial and fungal aerosols, but our understanding of fog biology is limited. Using metagenomic tools and culturing, we provide a unique look at fungal and bacterial communities in fog at two fog-dominated sites: coastal Maine (USA) and the Namib Desert (Namibia). Microbial communities in the fog at both sites were diverse, distinct from clear aerosols, and influenced by both soil and marine sources. Fog from both sites contained Actinobacteria and Firmicutes, commonly soil- and air-associated phyla, but also contained bacterial taxa associated with marine environments including Cyanobacteria, Oceanospirillales, Novosphingobium, Pseudoalteromonas, and Bradyrhizobiaceae. Marine influence on fog communities was greatest near the coast, but still evident in Namib fogs 50 km inland. In both systems, differences between pre- and post-fog aerosol communities suggest that fog events can significantly alter microbial aerosol diversity and composition. Fog is likely to enhance viability of transported microbes and facilitate their deposition, making fog biology ecologically important in fog-dominated environments. Fog may introduce novel species to terrestrial ecosystems, including human and plant pathogens, warranting further work on the drivers of this important and underrecognized aerobiological transfer between marine and terrestrial systems.}, }
@article {pmid30180347, year = {2019}, author = {Urra, J and Alkorta, I and Mijangos, I and Epelde, L and Garbisu, C}, title = {Application of sewage sludge to agricultural soil increases the abundance of antibiotic resistance genes without altering the composition of prokaryotic communities.}, journal = {The Science of the total environment}, volume = {647}, number = {}, pages = {1410-1420}, doi = {10.1016/j.scitotenv.2018.08.092}, pmid = {30180347}, issn = {1879-1026}, abstract = {The application of sewage sludge as soil amendment is a common agricultural practice. However, wastewater treatment plants, sewage sludge and sewage sludge-amended soils have been reported as hotspots for the appearance and dissemination of antibiotic resistance, driven, among other factors, by selection pressure exerted by co-exposure to antibiotics and heavy metals. To address this threat to environmental and human health, soil samples from a long-term (24 years) field experiment, carried out to study the impact of thermally dried and anaerobically digested sewage sludge (at different doses and frequencies of application) on agricultural soil quality, were investigated for the presence of genes encoding antibiotic resistance (ARGs) and mobile genetic elements (MGEs). Sewage sludge-induced changes in specific soil physicochemical and microbial properties, as indicators of soil quality, were also investigated. The application of sewage sludge increased the total concentration of copper and zinc in amended soils, but without affecting the bioavailability of these metals, possibly due to the high values of soil pH and organic matter content. Soil microbal quality, as reflected by the value of the Soil Quality Index, was higher in sewage sludge-amended soils. Similarly, the application of sewage sludge increased soil microbial activity and biomass, as well as the abundance of ARGs and MGE genes, posing a risk of dissemination of antibiotic resistance. In contrast, the composition of soil prokaryotic communities was not significantly altered by the application of sewage sludge. We found correlation between soil Cu and Zn concentrations and the abundance of ARGs and MGE genes. It was concluded that sewage sludge-derived amendments must be properly treated and managed if they are to be applied to agricultural soil.}, }
@article {pmid30179784, year = {2018}, author = {Perez, S and Czerner, M and Patat, ML and Zaritzky, NE and Murialdo, SE and Yeannes, MI}, title = {Monitoring the characteristics of cultivable halophilic microbial community during salted-ripened anchovy (Engraulis anchoita) production.}, journal = {International journal of food microbiology}, volume = {286}, number = {}, pages = {179-189}, doi = {10.1016/j.ijfoodmicro.2018.08.013}, pmid = {30179784}, issn = {1879-3460}, abstract = {The halophilic microbial community of the salted-ripened anchovy process was studied. Samples from raw materials (salt and fresh anchovies) and from the stages of brining and ripening were collected and analyzed for their bacterial counts at 15 and 20% NaCl. No halophilic colonies were found in fresh anchovy and counts of about 103 CFU/g were determined in salt samples. A fluctuation of bacterial counts during the process was found. At the end of brining, ~104 CFU/g were determined in anchovy samples and this value was reduced to not detectable counts at the beginning of the ripening stage. After one month, counts increased to ~104 CFU/g and remained stable until the end of the process. From each sample, colonies having different morphotypes were isolated and submitted to a macro and microscopic characterization, a study of salt requirement for growth, and biochemical and phenotypic tests. The results were submitted to Univariate, Bivariate and Multiple Correspondence Factorial Analysis (MCFA). A total of 79 colonies were isolated during the salting-ripening anchovy process. Among the isolates, about 40-50% was positive for indole production and lipolytic activity and a 25% showed ability to produce H2S and proteolytic capacity. Proteolytic and lipolytic activities were well balanced along the process and resulted independent from the isolation stage, which is a desirable condition due to the contribution of microbial proteolysis and lipolysis to the development of texture and final aroma, respectively. H2S and indole producers practically were not detected during ripening. This fact is important because indole and H2S are associated with the development of off-flavors and spoilage in salted fish products. MFCA and Cluster Analyses complemented the Bivariate Analyses. The factor map showed proximity between the isolates from salt samples and from ripening. Isolates were statistically clustered in two groups. Cluster 1 grouped non-desirable activities (H2S and indole production) with cultures proceeding from brining whereas Cluster 2 related isolates mainly from salt samples and during ripening with some desirable microbial capacities (Cytochrome oxidase activity and non-H2S and non-indole production). These results would indicate that during the ripening process of salted anchovies, a natural selection of beneficial microorganisms for the development of the typical product sensory attributes occurred.}, }
@article {pmid30179231, year = {2018}, author = {Berube, PM and Biller, SJ and Hackl, T and Hogle, SL and Satinsky, BM and Becker, JW and Braakman, R and Collins, SB and Kelly, L and Berta-Thompson, J and Coe, A and Bergauer, K and Bouman, HA and Browning, TJ and De Corte, D and Hassler, C and Hulata, Y and Jacquot, JE and Maas, EW and Reinthaler, T and Sintes, E and Yokokawa, T and Lindell, D and Stepanauskas, R and Chisholm, SW}, title = {Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180154}, doi = {10.1038/sdata.2018.154}, pmid = {30179231}, issn = {2052-4463}, abstract = {Prochlorococcus and Synechococcus are the dominant primary producers in marine ecosystems and perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with a diverse microbial community that coexists with them. Comparative genomics of cultivated isolates has helped address questions regarding patterns of evolution and diversity among microbes, but the fraction that can be cultivated is miniscule compared to the diversity in the wild. To further probe the diversity of these groups and extend the utility of reference sequence databases, we report a data set of single cell genomes for 489 Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190 additional microorganisms from a diverse range of bacterial, archaeal, and viral groups. Many of these uncultivated single cell genomes are derived from samples obtained on GEOTRACES cruises and at well-studied oceanographic stations, each with extensive suites of physical, chemical, and biological measurements. The genomic data reported here greatly increases the number of available Prochlorococcus genomes and will facilitate studies on evolutionary biology, microbial ecology, and biological oceanography.}, }
@article {pmid30178561, year = {2018}, author = {Kilian, M}, title = {The oral microbiome - friend or foe?.}, journal = {European journal of oral sciences}, volume = {126 Suppl 1}, number = {}, pages = {5-12}, doi = {10.1111/eos.12527}, pmid = {30178561}, issn = {1600-0722}, abstract = {The microbiome and the human body constitute an integrated superorganism, which is the result of millions of years of coevolution with mutual adaptation and functional integration, and confers significant benefits for both parties. This evolutionary process has resulted in a highly diverse oral microbiome, which covers the full spectrum of acidogenic, aciduric, inflammatory, and anti-inflammatory properties. The relative proportions of members of the microbiome are affected by factors associated with modern life, such as general diet patterns, sugar consumption, tobacco smoking, oral hygiene, use of antibiotics and other antimicrobials, and vaccines. A perturbed balance in the oral microbiome may result in caries, periodontal disease, or candidiasis, and oral bacteria passively transferred to normally sterile parts of the body may cause extra-oral infections. Nevertheless, it should never be our goal to eliminate the oral microbiome, but rather we have to develop ways to re-establish a harmonious coexistence that is lost because of the modern lifestyle. With regard to oral diseases, this goal can normally be achieved by optimal oral hygiene, exposure to fluoride, reduction of sucrose consumption, stimulation of our innate immune defense, smoking cessation, and control of diabetes.}, }
@article {pmid30178387, year = {2018}, author = {Xu, WF and Ren, HS and Ou, T and Lei, T and Wei, JH and Huang, CS and Li, T and Strobel, G and Zhou, ZY and Xie, J}, title = {Genomic and Functional Characterization of the Endophytic Bacillus subtilis 7PJ-16 Strain, a Potential Biocontrol Agent of Mulberry Fruit Sclerotiniose.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1247-4}, pmid = {30178387}, issn = {1432-184X}, support = {31601678//National Natural Science Foundation of China/ ; XDJK2018D020//Fundamental Research Funds for the Central Universities/ ; cstc2015jcyjys80001//Natural Science Foundation of Chongqing/ ; }, abstract = {Bacillus sp. 7PJ-16, an endophytic bacterium isolated from a healthy mulberry stem and previously identified as Bacillus tequilensis 7PJ-16, exhibits strong antifungal activity and has the capacity to promote plant growth. This strain was studied for its effectiveness as a biocontrol agent to reduce mulberry fruit sclerotiniose in the field and as a growth-promoting agent for mulberry in the greenhouse. In field studies, the cell suspension and supernatant of strain 7PJ-16 exhibited biocontrol efficacy and the lowest disease incidence was reduced down to only 0.80%. In greenhouse experiments, the cell suspension (1.0 × 106 and 1.0 × 105 CFU/mL) and the cell-free supernatant (100-fold and 1000-fold dilution) stimulated mulberry seed germination and promoted mulberry seedling growth. In addition, to accurately identify the 7PJ-16 strain and further explore the mechanisms of its antifungal and growth-promoting properties, the complete genome of this strain was sequenced and annotated. The 7PJ-16 genome is comprised of two circular plasmids and a 4,209,045-bp circular chromosome, containing 4492 protein-coding genes and 116 RNA genes. This strain was ultimately designed as Bacillus subtilis based on core genome sequence analyses using a phylogenomic approach. In this genome, we identified a series of gene clusters that function in the synthesis of non-ribosomal peptides (surfactin, fengycin, bacillibactin, and bacilysin) as well as the ribosome-dependent synthesis of tasA and bacteriocins (subtilin, subtilosin A), which are responsible for the biosynthesis of numerous antimicrobial metabolites. Additionally, several genes with function that promote plant growth, such as indole-3-acetic acid biosynthesis, the production of volatile substances, and siderophores synthesis, were also identified. The information described in this study has established a good foundation for understanding the beneficial interactions between endophytes and host plants, and facilitates the further application of B. subtilis 7PJ-16 as an agricultural biofertilizer and biocontrol agent.}, }
@article {pmid30175237, year = {2018}, author = {Coenen, AR and Weitz, JS}, title = {Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities.}, journal = {mSystems}, volume = {3}, number = {4}, pages = {}, doi = {10.1128/mSystems.00084-18}, pmid = {30175237}, issn = {2379-5077}, abstract = {Microbes are present in high abundances in the environment and in human-associated microbiomes, often exceeding 1 million per ml. Viruses of microbes are present in even higher abundances and are important in shaping microbial populations, communities, and ecosystems. Given the relative specificity of viral infection, it is essential to identify the functional linkages between viruses and their microbial hosts, particularly given dynamic changes in virus and host abundances. Multiple approaches have been proposed to infer infection networks from time series of in situ communities, among which correlation-based approaches have emerged as the de facto standard. In this work, we evaluate the accuracy of correlation-based inference methods using an in silico approach. In doing so, we compare predicted networks to actual networks to assess the self-consistency of correlation-based inference. At odds with assumptions underlying its widespread use, we find that correlation is a poor predictor of interactions in the context of viral infection and lysis of microbial hosts. The failure to predict interactions holds for methods that leverage product-moment, time-lagged, and relative-abundance-based correlations. In closing, we discuss alternative inference methods, particularly model-based methods, as a means to infer interactions in complex microbial communities with viruses. IMPORTANCE Inferring interactions from population time series is an active and ongoing area of research. It is relevant across many biological systems-particularly in virus-microbe communities, but also in gene regulatory networks, neural networks, and ecological communities broadly. Correlation-based inference-using correlations to predict interactions-is widespread. However, it is well-known that &quot;correlation does not imply causation.&quot; Despite this, many studies apply correlation-based inference methods to experimental time series without first assessing the potential scope for accurate inference. Here, we find that several correlation-based inference methods fail to recover interactions within in silico virus-microbe communities, raising questions on their relevance when applied in situ.}, }
@article {pmid30175122, year = {2018}, author = {Asses, N and Ayed, L and Hkiri, N and Hamdi, M}, title = {Congo Red Decolorization and Detoxification by Aspergillus niger: Removal Mechanisms and Dye Degradation Pathway.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {3049686}, doi = {10.1155/2018/3049686}, pmid = {30175122}, issn = {2314-6141}, abstract = {Congo red is one of the best known and used azo dyes which has two azo bonds (-N=N-) chromophore in its molecular structure. Its structural stability makes it highly toxic and resistant to biodegradation. The objective of this study was to assess the congo red biodegradation and detoxification by Aspergillus niger. The effects of pH, initial dye concentration, temperature, and shaking speed on the decolorization rate and enzymes production were studied. The maximum decolorization was correlated with lignin peroxidase and manganese peroxidase production. Above 97% were obtained when 2 g mycelia were incubated at pH 5, in presence of 200 mg/L of dye during 6 days at 28°C and under 120 to 150 rpm shaking speed. The degraded metabolites were characterized by using LC-MS/MS analyses and the biodegradation mechanism was also studied. Congo red bioconversion formed degradation metabolites mainly by peroxidases activities, i.e., the sodium naphthalene sulfonate (m/z = 227) and the cycloheptadienylium (m/z = 91). Phytotoxicity and microtoxicity tests confirmed that degradation metabolites were less toxic than original dye.}, }
@article {pmid30175029, year = {2018}, author = {Li, Y and Jiang, W and Gao, R and Cai, Y and Guan, Z and Liao, X}, title = {Fe(III)-based immobilized metal-affinity chromatography (IMAC) method for the separation of the catechol siderophore from Bacillus tequilensis CD36.}, journal = {3 Biotech}, volume = {8}, number = {9}, pages = {392}, doi = {10.1007/s13205-018-1396-7}, pmid = {30175029}, issn = {2190-572X}, abstract = {Catechol siderophore plays an important role in microbial ecology, agriculture, and medicine, but its research is often limited by the difficulty in acquisition of it in large quantities. Based on evidence from the coordination chemistry and chemical biology, catechol siderophore could chelate Fe3+ with high affinity. Therefore, Fe(III)-based immobilized metal-affinity chromatography (IMAC) was applied to capture siderophore from the culture filtrate of Bacillus tequilensis CD36. The ethanol-precipitated sample and the separated sample from Fe(III)-based IMAC were analyzed by liquid chromatography-mass spectrometry. According to the result, the pure siderophore DHB-Gly-Thr could be extracted from the ethanol-precipitated sample. Compared with other purifications, Fe(III)-based IMAC was convenient and had fewer steps. In addition, it also reduced the use of toxic chemical solvents in some traditional extraction process, such as extraction and ion exchange chromatography. Fe(III)-based IMAC was successfully used in separation of the catechol siderophore from B. tequilensis CD36. The results revealed that Fe(III)-based IMAC was an efficient and environmentally friendly method for the separation and purification of catechol siderophore.}, }
@article {pmid30172443, year = {2018}, author = {Gänzle, MG and Zheng, J}, title = {Lifestyles of sourdough lactobacilli - Do they matter for microbial ecology and bread quality?.}, journal = {International journal of food microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijfoodmicro.2018.08.019}, pmid = {30172443}, issn = {1879-3460}, abstract = {Sourdough is used in production of (steamed) bread as leavening agent (type I sourdoughs) or as baking improver to enhance flavour, texture, and shelf life of bread (type II sourdoughs). The long-term propagation of sourdoughs eliminates dispersal limitation and consistently leads to sourdough microbiota that are composed of host adapted lactobacilli. In contrast, community assembly in spontaneous cereal fermentations is limited by dispersal and nomadic or environmental lactic acid bacteria are the first colonizers of these sourdoughs. Propagation of sourdoughs for use as sole leavening agent (type I sourdoughs) dictates fermentation conditions that select for rapid growth. Type I wheat- and rye sourdoughs are consistently populated by insect-adapted lactobacilli, particularly Lactobacillus sanfranciscensis, which is characterized by a small genome size and a restricted metabolic potential. The diverse fermentation conditions employed in industrial or artisanal Type II sourdough fermentation processes also result in a more diverse microbiota. Nevertheless, type II sourdoughs are typically populated by vertebrate host adapted lactobacilli of the L. delbrueckii and L. reuteri groups. Metabolic traits of host-adapted lactobacilli that enhance competitiveness in intestinal ecosystems also provide technological functionality in bread making. Examples include formation of exopolysaccharides, arginine-, glutamine- and glutamate based mechanisms of acid resistance, and glycosyl hydrolases that reduce FODMAP levels in sourdough and sourdough bread. In conclusion, consideration of the lifestyle of sourdough lactobacilli facilitates the selection of competitive and functional sourdough starter cultures.}, }
@article {pmid30172137, year = {2019}, author = {Macintosh, KA and Doody, DG and Withers, PJA and McDowell, RW and Smith, DR and Johnson, LT and Bruulsema, TW and O'Flaherty, V and McGrath, JW}, title = {Transforming soil phosphorus fertility management strategies to support the delivery of multiple ecosystem services from agricultural systems.}, journal = {The Science of the total environment}, volume = {649}, number = {}, pages = {90-98}, doi = {10.1016/j.scitotenv.2018.08.272}, pmid = {30172137}, issn = {1879-1026}, abstract = {Despite greater emphasis on holistic phosphorus (P) management, current nutrient advice delivered at farm-scale still focuses almost exclusively on agricultural production. This limits our ability to address national and international strategies for the delivery of multiple ecosystem services (ES). Currently there is no operational framework in place to manage P fertility for multiple ES delivery and to identify the costs of potentially sacrificing crop yield and/or quality. As soil P fertility plays a central role in ES delivery, we argue that soil test phosphorus (STP) concentration provides a suitable common unit of measure by which delivering multiple ES can be economically valued relative to maximum potential yield, in $ ha-1 yr-1 units. This value can then be traded, or payments made against one another, at spatio-temporal scales relevant for farmer and national policy objectives. Implementation of this framework into current P fertility management strategies would allow for the integration and interaction of different stakeholder interests in ES delivery on-farm and in the wider landscape. Further progress in biophysical modeling of soil P dynamics is needed to inform its adoption across diverse landscapes.}, }
@article {pmid30171270, year = {2018}, author = {Szafranek-Nakonieczna, A and Wolińska, A and Zielenkiewicz, U and Kowalczyk, A and Stępniewska, Z and Błaszczyk, M}, title = {Activity and Identification of Methanotrophic Bacteria in Arable and No-Tillage Soils from Lublin Region (Poland).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1248-3}, pmid = {30171270}, issn = {1432-184X}, support = {DEC-2013/09/D/NZ9/02482//Narodowe Centrum Nauki/ ; }, abstract = {Methanotrophic bacteria are able to use methane (CH4) as a sole carbon and energy source. Photochemical oxidation of methane takes place in the stratosphere, whereas in the troposphere, this process is carried out by methanotrophic bacteria. On the one hand, it is known that the efficiency of biological CH4 oxidation is dependent on the mode of land use but, on the other hand, the knowledge of this impact on methanotrophic activity (MTA) is still limited. Thus, the aim of the study was to determine the CH4 oxidation ability of methanotrophic bacteria inhabiting selected arable and no-tillage soils from the Lublin region (Albic Luvisol, Brunic Arenosol, Haplic Chernozem, Calcaric Cambisol) and to identify bacteria involved in this process. MTA was determined based on incubation of soils in air with addition of methane at the concentrations of 0.002, 0.5, 1, 5, and 10%. The experiment was conducted in a temperature range of 10-30 °C. Methanotrophs in soils were identified by next-generation sequencing (NGS). MTA was confirmed in all investigated soils (in the entire range of the tested methane concentrations and temperatures, except for the arable Albic Luvisol). Importantly, the MTA values in the no-tillage soil were nearly two-fold higher than in the cultivated soils. Statistical analysis indicated a significant influence of land use, type of soil, temperature, and especially methane concentration (p < 0.05) on MTA. Metagenomic analysis confirmed the presence of methanotrophs from the genus Methylocystis (Alphaproteobacteria) in the studied soils (except for the arable Albic Luvisol). Our results also proved the ability of methanotrophic bacteria to oxidize methane although they constituted only up to 0.1% of the total bacterial community.}, }
@article {pmid30168107, year = {2018}, author = {Xu, G and Abdullah Al, M and Sikder, MNA and Warren, A and Xu, H}, title = {Identifying indicator redundancy of biofilm-dwelling protozoa for bioassessment in marine ecosystems.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {30}, pages = {30441-30450}, doi = {10.1007/s11356-018-3063-2}, pmid = {30168107}, issn = {1614-7499}, abstract = {A multivariate peeling method of data analysis was applied to determine indicator redundancy and for identifying indicator units (IUs) among biofilm-dwelling ciliate communities used for bioassessment of marine water quality. Samples were taken monthly over a 1-year period at four stations in coastal waters of the Yellow Sea: one heavily polluted, one moderately polluted, one intermittently polluted, and one unpolluted. Four IUs (IU1-4) were identified consisting of 22, 13, 14, and 17 species, respectively, out of a total of 144 species. The IUs showed significant correlation with temporal and spatial variations in environmental variables. The redundancy levels of IUs were interchangeable in time and space. However, IU1 and IU2 generally dominated the communities in moderately and intermittently polluted areas during cool (e.g., early spring, late autumn, and winter) and warm (late spring and early autumn) seasons; IU3 dominated in warm seasons (e.g., late spring to autumn) in the heavily polluted area; and IU4 mainly dominated the samples in the unpolluted and moderately polluted areas during the late summer and early autumn. Furthermore, different trophic-functional groupings were represented within the four IUs and these were generally associated with water quality status. These findings suggest that there is high indicator redundancy in marine biofilm-dwelling ciliate communities subjected to different levels of water quality.}, }
@article {pmid30166150, year = {2018}, author = {Houngbédji, M and Johansen, P and Padonou, SW and Akissoé, N and Arneborg, N and Nielsen, DS and Hounhouigan, DJ and Jespersen, L}, title = {Occurrence of lactic acid bacteria and yeasts at species and strain level during spontaneous fermentation of mawè, a cereal dough produced in West Africa.}, journal = {Food microbiology}, volume = {76}, number = {}, pages = {267-278}, doi = {10.1016/j.fm.2018.06.005}, pmid = {30166150}, issn = {1095-9998}, abstract = {Mawè is a West African spontaneous fermented cereal-based dough. Different types of mawè exist varying in type of cereal and/or production condition, with fermentations lasting 24-48 h. With the aim of obtaining a comprehensive understanding of the microbial ecology of mawè processing, a microbiological characterisation was performed for four mawè types, produced at eight sites in Benin. At the onset of the fermentations lactic acid bacteria (LAB) and yeast counts were on average 7.5 ± 1.03 and 4.8 ± 0.79 Log10 cfu/g, which increased to 9.2 ± 0.38 and 7.4 ± 0.42 Log10 cfu/g, respectively, at the end of the fermentations. LAB (n = 321) and yeasts (n = 298), isolated during the fermentations, were identified. The predominant LAB and yeast species were Lactobacillus fermentum and Pichia kudriavzevii, respectively, followed by Kluyveromyces marxianus, all present throughout the mawè fermentations. Further, microbial successions took place with Weissella confusa occurring mostly at the onset, while Pediococcus acidilactici and Saccharomyces cerevisiae were mainly associated with the end of the fermentations. Species diversity was influenced both by type of cereal and production condition. The dominating strain clusters of L. fermentum and P. kudriavzevii were ubiquitous and strain diversities were influenced by type of cereal and production site.}, }
@article {pmid30158906, year = {2018}, author = {Mackelprang, R and Grube, AM and Lamendella, R and Jesus, EDC and Copeland, A and Liang, C and Jackson, RD and Rice, CW and Kapucija, S and Parsa, B and Tringe, SG and Tiedje, JM and Jansson, JK}, title = {Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1775}, doi = {10.3389/fmicb.2018.01775}, pmid = {30158906}, issn = {1664-302X}, abstract = {The North American prairie covered about 3.6 million-km2 of the continent prior to European contact. Only 1-2% of the original prairie remains, but the soils that developed under these prairies are some of the most productive and fertile in the world, containing over 35% of the soil carbon in the continental United States. Cultivation may alter microbial diversity and composition, influencing the metabolism of carbon, nitrogen, and other elements. Here, we explored the structure and functional potential of the soil microbiome in paired cultivated-corn (at the time of sampling) and never-cultivated native prairie soils across a three-states transect (Wisconsin, Iowa, and Kansas) using metagenomic and 16S rRNA gene sequencing and lipid analysis. At the Wisconsin site, we also sampled adjacent restored prairie and switchgrass plots. We found that agricultural practices drove differences in community composition and diversity across the transect. Microbial biomass in prairie samples was twice that of cultivated soils, but alpha diversity was higher with cultivation. Metagenome analyses revealed denitrification and starch degradation genes were abundant across all soils, as were core genes involved in response to osmotic stress, resource transport, and environmental sensing. Together, these data indicate that cultivation shifted the microbiome in consistent ways across different regions of the prairie, but also suggest that many functions are resilient to changes caused by land management practices - perhaps reflecting adaptations to conditions common to tallgrass prairie soils in the region (e.g., soil type, parent material, development under grasses, temperature and rainfall patterns, and annual freeze-thaw cycles). These findings are important for understanding the long-term consequences of land management practices to prairie soil microbial communities and their genetic potential to carry out key functions.}, }
@article {pmid30155556, year = {2018}, author = {Ma, ZS}, title = {Sketching the Human Microbiome Biogeography with DAR (Diversity-Area Relationship) Profiles.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1245-6}, pmid = {30155556}, issn = {1432-184X}, abstract = {SAR (species area relationship) is a classic ecological theory that has been extensively investigated and applied in the studies of global biogeography and biodiversity conservation in macro-ecology. It has also found important applications in microbial ecology in recent years thanks to the breakthroughs in metagenomic sequencing technology. Nevertheless, SAR has a serious limitation for practical applications-ignoring the species abundance and treating all species as equally abundant. This study aims to explore the biogeography discoveries of human microbiome over 18 sites of 5 major microbiome habitats, establish the baseline DAR (diversity-area scaling relationship) parameters, and perform comparisons with the classic SAR. The extension from SAR to DAR by adopting the Hill numbers as diversity measures not only overcomes the previously mentioned flaw of SAR but also allows for obtaining a series of important findings on the human microbiome biodiversity and biogeography. Specifically, two types of DAR models were built, the traditional power law (PL) and power law with exponential cutoff (PLEC), using comprehensive datasets from the HMP (human microbiome project). Furthermore, the biogeography &quot;maps&quot; for 18 human microbiome sites using their DAR profiles for assessing and predicting the diversity scaling across individuals, PDO profiles (pair-wise diversity overlap) for measuring diversity overlap (similarity), and MAD profile (for predicting the maximal accrual diversity in a population) were sketched out. The baseline biogeography maps for the healthy human microbiome diversity can offer guidelines for conserving human microbiome diversity and investigating the health implications of the human microbiome diversity and heterogeneity.}, }
@article {pmid30154827, year = {2018}, author = {Cairns, J and Jokela, R and Hultman, J and Tamminen, M and Virta, M and Hiltunen, T}, title = {Construction and Characterization of Synthetic Bacterial Community for Experimental Ecology and Evolution.}, journal = {Frontiers in genetics}, volume = {9}, number = {}, pages = {312}, doi = {10.3389/fgene.2018.00312}, pmid = {30154827}, issn = {1664-8021}, abstract = {Experimental microbial ecology and evolution have yielded foundational insights into ecological and evolutionary processes using simple microcosm setups and phenotypic assays with one- or two-species model systems. The fields are now increasingly incorporating more complex systems and exploration of the molecular basis of observations. For this purpose, simplified, manageable and well-defined multispecies model systems are required that can be easily investigated using culturing and high-throughput sequencing approaches, bridging the gap between simpler and more complex synthetic or natural systems. Here we address this need by constructing a completely synthetic 33 bacterial strain community that can be cultured in simple laboratory conditions. We provide whole-genome data for all the strains as well as metadata about genomic features and phenotypic traits that allow resolving individual strains by amplicon sequencing and facilitate a variety of envisioned mechanistic studies. We further show that a large proportion of the strains exhibit coexistence in co-culture over serial transfer for 48 days in the absence of any experimental manipulation to maintain diversity. The constructed bacterial community can be a valuable resource in future experimental work.}, }
@article {pmid30154761, year = {2018}, author = {Plominsky, AM and Henríquez-Castillo, C and Delherbe, N and Podell, S and Ramirez-Flandes, S and Ugalde, JA and Santibañez, JF and van den Engh, G and Hanselmann, K and Ulloa, O and De la Iglesia, R and Allen, EE and Trefault, N}, title = {Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1800}, doi = {10.3389/fmicb.2018.01800}, pmid = {30154761}, issn = {1664-302X}, abstract = {Hypersaline environments represent some of the most challenging settings for life on Earth. Extremely halophilic microorganisms have been selected to colonize and thrive in these extreme environments by virtue of a broad spectrum of adaptations to counter high salinity and osmotic stress. Although there is substantial data on microbial taxonomic diversity in these challenging ecosystems and their primary osmoadaptation mechanisms, less is known about how hypersaline environments shape the genomes of microbial inhabitants at the functional level. In this study, we analyzed the microbial communities in five ponds along the discontinuous salinity gradient from brackish to salt-saturated environments and sequenced the metagenome of the salt (halite) precipitation pond in the artisanal Cáhuil Solar Saltern system. We combined field measurements with spectrophotometric pigment analysis and flow cytometry to characterize the microbial ecology of the pond ecosystems, including primary producers and applied metagenomic sequencing for analysis of archaeal and bacterial taxonomic diversity of the salt crystallizer harvest pond. Comparative metagenomic analysis of the Cáhuil salt crystallizer pond against microbial communities from other salt-saturated aquatic environments revealed a dominance of the archaeal genus Halorubrum and showed an unexpectedly low abundance of Haloquadratum in the Cáhuil system. Functional comparison of 26 hypersaline microbial metagenomes revealed a high proportion of sequences associated with nucleotide excision repair, helicases, replication and restriction-methylation systems in all of them. Moreover, we found distinctive functional signatures between the microbial communities from salt-saturated (>30% [w/v] total salinity) compared to sub-saturated hypersaline environments mainly due to a higher representation of sequences related to replication, recombination and DNA repair in the former. The current study expands our understanding of the diversity and distribution of halophilic microbial populations inhabiting salt-saturated habitats and the functional attributes that sustain them.}, }
@article {pmid30153641, year = {2018}, author = {Xie, H and Wang, H and Ji, F and Liang, Y and Song, M and Zhang, J}, title = {Tetrabromobisphenol A alters soil microbial community via selective antibacterial activity.}, journal = {Ecotoxicology and environmental safety}, volume = {164}, number = {}, pages = {597-603}, doi = {10.1016/j.ecoenv.2018.08.053}, pmid = {30153641}, issn = {1090-2414}, abstract = {Tetrabromobisphenol A (TBBPA) is the most widely used brominated flame retardant. Most studies regarding TBBPA have concentrated on its occurrence, distribution, toxicity and degradation in the environment. However, little is known about its ecological effects on soil microbial communities. In this study, we investigated the effect of TBBPA on soil microbial community. Overall, the data suggested that the growth and composition of soil microorganisms were correlated to the TBBPA concentration and exposure time. Phospholipid-derived fatty acid analysis (PLFAs) showed that significant microbial growth inhibitions were 46.1% and 46.9% in 40 mg/kg TBBPA-treated soils after 45-day incubation under aerobic and anaerobic conditions, respectively. Results of PLFAs and llumina sequencing indicated that TBBPA mainly inhibited Gram-positive bacteria, but not Gram-negative bacteria. The selective antibacterial activity of TBBPA toward Gram-positive bacteria was further confirmed in pure bacteria cultures. These data suggested that, in addition to their effect on microbial growth and composition, TBBPA may affect the microbial ecology. Additional research should be carried out to identify the ecological risk of TBBPA in soil.}, }
@article {pmid30153548, year = {2018}, author = {Vandekerckhove, TGL and De Mulder, C and Boon, N and Vlaeminck, SE}, title = {Temperature impact on sludge yield, settleability and kinetics of three heterotrophic conversions corroborates the prospect of thermophilic biological nitrogen removal.}, journal = {Bioresource technology}, volume = {269}, number = {}, pages = {104-112}, doi = {10.1016/j.biortech.2018.08.012}, pmid = {30153548}, issn = {1873-2976}, mesh = {*Bioreactors ; *Denitrification ; Kinetics ; Nitrogen ; *Sewage ; Temperature ; Waste Disposal, Fluid ; }, abstract = {In specific municipal and industrial cases, thermophilic wastewater treatment (>45 °C) might bring cost advantages over commonly applied mesophilic processes (10-35 °C). To develop such a novel process, one needs sound parameters on kinetics, sludge yield and sludge settleability of three heterotrophic conversions: aerobic carbon removal, denitritation and denitrification. These features were evaluated in acetate-fed sequencing batch reactors (30, 40, 50 and 60 °C). Higher temperatures were accompanied by lower sludge production and maximum specific removal rates, resulting mainly from lower maximum growth rates. Thermophilic denitritation was demonstrated for the first time, with lower sludge production (18-26%), higher nitrogen removal rates (24-92%) and lower carbon requirement (40%) compared to denitrification. Acceptable settling of thermophilic aerobic (60 °C) and anoxic biomass (50 and 60 °C) was obtained. Overall, this parameter set may catalyze the establishment of thermophilic nitrogen removal, once nitritation and nitratation are characterized. Furthermore, waters with low COD/N ratio might benefit from thermophilic nitritation/denitritation.}, }
@article {pmid30152425, year = {2018}, author = {Samanta, A and Patra, A and Mandal, S and Roy, S and Das, K and Kar, S and Nandi, DK}, title = {Hypoxia: A cause of acute renal failure and alteration of gastrointestinal microbial ecology.}, journal = {Saudi journal of kidney diseases and transplantation : an official publication of the Saudi Center for Organ Transplantation, Saudi Arabia}, volume = {29}, number = {4}, pages = {879-888}, doi = {10.4103/1319-2442.239653}, pmid = {30152425}, issn = {1319-2442}, abstract = {Oxygen is very important to the existence of life. Oxygen deficiency, defined as hypoxia, elicits adaptive responses in cells and tissues. Lower oxygen concentration can cause the alteration of renal function, affects the maintenance of a balance of the body fluids, electrolytes, pH, and blood pressure homeostasis. Impaired fluid regulation could, in addition, contribute to the precipitation of pulmonary edema and exacerbate hypoxemia which may accelerate the progression of chronic kidney disease. In this context, the present study attempted to evaluate the association of renal injury and oxidative stress at different atmospheric pressures (1829, 3657, and 5486 m). Limited fecal analysis of experimental animals was also done to evaluate the impact of hypobaric hypoxia on the composition of dominant gastrointestinal microbiota. The study was performed on 24 male Wister strain rats and divided into four groups (C, HA-I, HA-II, and HA-III), and exposure was carried out for seven days period. In hypoxic exposure rats, plasma urea, creatinine, electrolytes and malonaldehyde level elevated and catalase and superoxide dismutase level diminished significantly compared to the controls. Increase in blood uremia profile, toxicity markers, and lipid peroxidation marker enzymes indicated that hypoxia causes renal failure. Histological structures of the kidney of group HA-II and HA-III animals showed severe disorganization of glomerulus and dilation of renal tubules. These results indicate nephrotoxicity or acute renal failure can occur at hypobaric hypoxia and it also affected the gut microbial population. This alteration was observed significantly above 3000 m.}, }
@article {pmid30152327, year = {2018}, author = {Bittleston, LS and Wolock, CJ and Yahya, BE and Chan, XY and Chan, KG and Pierce, NE and Pringle, A}, title = {Convergence between the microcosms of Southeast Asian and North American pitcher plants.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, doi = {10.7554/eLife.36741}, pmid = {30152327}, issn = {2050-084X}, support = {NSF Graduate Fellowship and Doctoral Dissertation Improvement Grant DEB-1400982//National Science Foundation/International ; Foundational Questions In Evolutionary Biology//John Templeton Foundation/International ; Putnam Expedition Grant//Harvard University Museum of Comparative Zoology/International ; High Impact Research Grant, UM-MOHE HIR Grant UM.C/625/1/HIR/MOHE/CHAN/14/1//Universiti Malaya/International ; SES-0750480//National Science Foundation/International ; High Impact Research Grant, H-50001-A000027//Universiti Malaya/International ; High Impact Research Grant, A-000001-50001//Universiti Malaya/International ; Foundational Questions In Evolutionary Biology//Templeton Foundation/International ; Putnam Grant//Harvard University Museum of Comparative Zoology Putnam Expedition Grant/International ; UM-MOHE HIR Grant UM.C/625/1/HIR/MOHE/CHAN/14/1//University of Malaya High Impact Research Grant/International ; H-50001-A000027//University of Malaya High Impact Research Grant/International ; A-000001-50001//University of Malaya High Impact Research Grant/International ; }, abstract = {The 'pitchers' of carnivorous pitcher plants are exquisite examples of convergent evolution. An open question is whether the living communities housed in pitchers also converge in structure or function. Using samples from more than 330 field-collected pitchers of eight species of Southeast Asian Nepenthes and six species of North American Sarracenia, we demonstrate that the pitcher microcosms, or miniature ecosystems with complex communities, are strikingly similar. Compared to communities from surrounding habitats, pitcher communities house fewer species. While communities associated with the two genera contain different microbial organisms and arthropods, the species are predominantly from the same phylogenetic clades. Microbiomes from both genera are enriched in degradation pathways and have high abundances of key degradation enzymes. Moreover, in a manipulative field experiment, Nepenthes pitchers placed in a North American bog assembled Sarracenia-like communities. An understanding of the convergent interactions in pitcher microcosms facilitates identification of selective pressures shaping the communities.}, }
@article {pmid30152021, year = {2018}, author = {Peyyala, R and Emecen-Huja, P and Ebersole, JL}, title = {Environmental lead effects on gene expression in oral epithelial cells.}, journal = {Journal of periodontal research}, volume = {53}, number = {6}, pages = {961-971}, doi = {10.1111/jre.12594}, pmid = {30152021}, issn = {1600-0765}, support = {GM103538//National Institute of General Medical Sciences/ ; //Center for Oral Health Research in the University of Kentucky College of Dentistry/ ; }, abstract = {BACKGROUND AND OBJECTIVE: Host responses in periodontitis span a range of local and emigrating cell types and biomolecules. Accumulating evidence regarding the expression of this disease across the population suggests some component of genetic variation that controls onset and severity of disease, in concert with the qualitative and quantitative parameters of the oral microbiome at sites of disease. However, there remains little information regarding the capacity of accruing environmental stressors or modifiers over a lifespan at both the host genetic and microbial ecology levels to understand fully the population variation in disease. This study evaluated the impact of environmental lead exposure on the responses of oral epithelial cells to challenge with a model pathogenic oral biofilm.<br><br>METHODS AND RESULTS: Using NanoString technology to quantify gene expression profiles of an array of 511 host response-associated genes in the epithelial cells, we identified an interesting primary panel of basal responses of the cells with numerous genes not previously considered as major response markers for epithelial cells, eg, interleukin (IL)-32, CTNNB1, CD59, MIF, CD44 and CD99. Even high levels of environment lead had little effect on these constitutive responses. Challenge of the cells with the biofilms (Streptococcus gordonii/Fusobacterium nucleatum/Porphyromonas gingivalis) resulted in significant increases in an array of host immune-related genes (134 of 511). The greatest magnitude in differential expression was observed with many genes not previously described as major response genes in epithelial cells, including IL-32, CD44, NFKBIA, CTSC, TNFAIP3, IL-1A, IL-1B, IL-8 and CCL20. The effects of environmental lead on responses to the biofilms were mixed, although levels of IL-8, CCL20 and CD70 were significantly decreased at lead concentrations of 1 and/or 5 μmol/L.<br><br>CONCLUSION: The results provided new information on a portfolio of genes expressed by oral epithelial cells, targeted substantial increases in an array of immune-related genes post-biofilm challenge, and a focused impact of environmental lead on these induced responses.}, }
@article {pmid30151669, year = {2018}, author = {Szubert-Kruszyńska, A and Stańczak, J and Cieniuch, S and Podsiadły, E and Postawa, T and Michalik, J}, title = {Bartonella and Rickettsia Infections in Haematophagous Spinturnix myoti Mites (Acari: Mesostigmata) and their Bat Host, Myotis myotis (Yangochiroptera: Vespertilionidae), from Poland.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1246-5}, pmid = {30151669}, issn = {1432-184X}, support = {N N303819640//Ministerstwo Nauki i Szkolnictwa Wyższego/ ; }, abstract = {Hematophagous Spinturnix myoti mites and their host, the greater mouse-eared bat (Myotis myotis), were tested for the presence of Bartonella spp., Rickettsia spp., and Anaplasma phagocytophilum. In total, Bartonella spp. DNA was amplified in 28% of 134 mite pools and in 25% of 59 bats tested by PCR targeting a fragment of citrate synthase gltA gen. Adult mites were at least threefold more frequently infected compared to immature stages. The overall infection prevalence among mite pools from cave-dwelling bats was higher than for those collected from attic shelters. Three distinct genotypes were detected. The most prevalent genotype in mites and bats matched closely with Candidatus Bartonella hemsundetiensis identified in bats from Finland and was relatively distant from bat-borne Bartonella strains described in the UK and France. Importantly, most sequences were close to those reported in forest workers from Poland. The presence of identical genotype among S. myoti samples and M. myotis bats suggests that bartonellae can be shared between mites and their bat hosts. In this case, wing mites could serve as vectors, whereas their hosts as reservoirs. One blood sample was positive by PCR for the msp2 gene of A. phagocytophilum. Two mite pools yielded Rickettsia spp. DNA. Both sequences were distinct from any known species but can be classified as spotted fever group Rickettsia spp. Our findings expanded our knowledge on the role of spinturnicid mites in the ecology and epidemiology of bacterial infections associated with vespertilionid bats, especially regarding the genus Bartonella.}, }
@article {pmid30150233, year = {2018}, author = {Perault, AI and Cotter, PA}, title = {Three distinct contact-dependent growth inhibition systems mediate interbacterial competition by the cystic fibrosis pathogen Burkholderia dolosa.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {}, doi = {10.1128/JB.00428-18}, pmid = {30150233}, issn = {1098-5530}, abstract = {The respiratory tracts of individuals afflicted with cystic fibrosis (CF) harbor complex polymicrobial communities. By an unknown mechanism, species of the Gram-negative Burkholderia cepacia complex, such as Burkholderia dolosa, can displace other bacteria in the CF lung, causing cepacia syndrome, which has a poor prognosis. The genome of B. dolosa strain AU0158 (BdAU0158) contains three loci that are predicted to encode Contact-Dependent growth Inhibition (CDI) systems. CDI systems function by translocating the toxic C-terminus of a large exoprotein directly into target cells, resulting in growth inhibition or death unless the target cells produce a cognate immunity protein. We demonstrate here that each of the three bcpAIOB loci in BdAU0158 encodes a distinct CDI system that mediates interbacterial competition in an allele-specific manner. While only two of the three bcpAIOB loci are expressed under the in vitro conditions tested, the third conferred immunity under these conditions due to the presence of an internal promoter driving expression of the bcpI gene. One BdAU0158 bcpAIOB allele is highly similar to bcpAIOB in Burkholderia thailandensis strain E264 (BtE264), and we showed that their BcpI proteins are functionally interchangeable, but Contact-Dependent Signaling (CDS) phenotypes were not observed in BdAU0158. Our findings suggest that the CDI systems of BdAU0158 may provide this pathogen an ecological advantage during polymicrobial infections of the CF respiratory tract.IMPORTANCE Human-associated polymicrobial communities can promote health and disease, and interbacterial interactions influence the microbial ecology of such communities. Polymicrobial infections of the cystic fibrosis respiratory tract impair lung function and lead to death of individuals suffering from this disorder; therefore, a greater understanding of these microbial communities is necessary for improving treatment strategies. Bacteria utilize contact-dependent growth inhibition systems to kill neighboring competitors and maintain their niche within multicellular communities. Several cystic fibrosis pathogens have the potential to gain an ecological advantage during infection via contact-dependent growth inhibition systems, including Burkholderia dolosa Our research is significant as it has identified three functional contact-dependent growth inhibition systems in B. dolosa that may provide this pathogen a competitive advantage during polymicrobial infections.}, }
@article {pmid30149801, year = {2018}, author = {Bascuñán, P and Niño-Garcia, JP and Galeano-Castañeda, Y and Serre, D and Correa, MM}, title = {Factors shaping the gut bacterial community assembly in two main Colombian malaria vectors.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {148}, doi = {10.1186/s40168-018-0528-y}, pmid = {30149801}, issn = {2049-2618}, support = {project code No. 2015-8423//Departamento Administrativo de Ciencia, Tecnología e Innovación - Colciencias and Universidad de Antioquia/ ; Code No. ES84160123//Estrategia para la Sostenibilidad de Grupos de Investigación, Universidad de Antioquia 2016-2017/ ; grant No. 656-2014 &quot;Es tiempo de volver&quot;//PB is a postdoctoral fellow of Colciencias/ ; }, abstract = {BACKGROUND: The understanding of the roles of gut bacteria in the fitness and vectorial capacity of mosquitoes that transmit malaria, is improving; however, the factors shaping the composition and structure of such bacterial communities remain elusive. In this study, a high-throughput 16S rRNA gene sequencing was conducted to understand the effect of developmental stage, feeding status, species, and geography on the composition of the gut bacterial microbiota of two main Colombian malaria vectors, Anopheles nuneztovari and Anopheles darlingi.<br><br>RESULTS: The results revealed that mosquito developmental stage, followed by geographical location, are more important determinants of the gut bacterial composition than mosquito species or adult feeding status. Further, they showed that mosquito gut is a major filter for environmental bacteria colonization.<br><br>CONCLUSIONS: The sampling design and analytical approach of this study allowed to untangle the influence of factors that are simultaneously shaping the microbiota composition of two Latin-American malaria vectors, essential aspect for the design of vector biocontrol strategies.}, }
@article {pmid30146914, year = {2018}, author = {Papathanasiou, P and Erdmann, S and Leon-Sobrino, C and Sharma, K and Urlaub, H and Garrett, RA and Peng, X}, title = {Stable maintenance of the rudivirus SIRV3 in a carrier state in Sulfolobus islandicus despite activation of the CRISPR-Cas immune response by a second virus SMV1.}, journal = {RNA biology}, volume = {}, number = {}, pages = {1-9}, doi = {10.1080/15476286.2018.1511674}, pmid = {30146914}, issn = {1555-8584}, abstract = {Carrier state viral infection constitutes an equilibrium state in which a limited fraction of a cellular population is infected while the remaining cells are transiently resistant to infection. This type of infection has been characterized for several bacteriophages but not, to date, for archaeal viruses. Here we demonstrate that the rudivirus SIRV3 can produce a host-dependent carrier state infection in the model crenarchaeon Sulfolobus. SIRV3 only infected a fraction of a Sulfolobus islandicus REY15A culture over several days during which host growth was unimpaired and no chromosomal DNA degradation was observed. CRISPR spacer acquisition from SIRV3 DNA was induced by coinfecting with the monocaudavirus SMV1 and it was coincident with increased transcript levels from subtype I-A adaptation and interference cas genes. However, this response did not significantly affect the carrier state infection of SIRV3 and both viruses were maintained in the culture over 12 days during which SIRV3 anti-CRISPR genes were shown to be expressed. Transcriptome and proteome analyses demonstrated that most SIRV3 genes were expressed at varying levels over time whereas SMV1 gene expression was generally low. The study yields insights into the basis for the stable infection of SIRV3 and the resistance to the different host CRISPR-Cas interference mechanisms. It also provides a rationale for the commonly observed coinfection of archaeal cells by different viruses in natural environments.}, }
@article {pmid30145477, year = {2018}, author = {Daghio, M and Vaiopoulou, E and Aulenta, F and Sherry, A and Head, I and Franzetti, A and Rabaey, K}, title = {Anode potential selection for sulfide removal in contaminated marine sediments.}, journal = {Journal of hazardous materials}, volume = {360}, number = {}, pages = {498-503}, doi = {10.1016/j.jhazmat.2018.08.016}, pmid = {30145477}, issn = {1873-3336}, abstract = {Sulfate reducing microorganisms are typically involved in hydrocarbon biodegradation in the sea sediment, with their metabolism resulting in the by-production of toxic sulfide. In this context, it is of utmost importance identifying the optimal value for anodic potential which ensures efficient toxic sulfide removal. Along this line, in this study the (bio)electrochemical removal of sulfide was tested at anodic potentials of -205 mV, +195 mV and +300 mV (vs Ag/AgCl), also in the presence of a pure culture of the sulfur-oxidizing bacterium Desulfobulbus propionicus. Current production, sulfide concentration and sulfate concentration were monitored over time. At the end of the experiment sulfur deposition on the electrodes and the microbial communities were characterized by SEM-EDS and by next generation sequencing of the 16S rRNA gene respectively. Results confirmed that current production was linked to sulfide removal and D. propionicus promoted back oxidation of deposited sulfur to sulfate. The highest electron recovery was observed at +195 mV vs Ag/AgCl, and the lowest sulfur deposition was obtained at -205 mV vs Ag/AgCl anode polarization.}, }
@article {pmid30145102, year = {2018}, author = {Chen, L and Xu, W and Lee, A and He, J and Huang, B and Zheng, W and Su, T and Lai, S and Long, Y and Chu, H and Chen, Y and Wang, L and Wang, K and Si, J and Chen, S}, title = {The impact of Helicobacter pylori infection, eradication therapy and probiotic supplementation on gut microenvironment homeostasis: An open-label, randomized clinical trial.}, journal = {EBioMedicine}, volume = {35}, number = {}, pages = {87-96}, doi = {10.1016/j.ebiom.2018.08.028}, pmid = {30145102}, issn = {2352-3964}, support = {KL2 TR002241/TR/NCATS NIH HHS/United States ; }, abstract = {BACKGROUND: Helicobacter pylori (H. pylori) infection is associated with remodeling of gastric microbiota. However, comprehensive analyses of the impact of H. pylori infection, eradication therapy and probiotic supplementation on gut microbiota are still lacking. We aimed to provide evidence for clinical decision making.<br><br>METHODS: Seventy H. pylori-positive and 35 H. pylori-negative patients (group C) were enrolled. H. pylori-positive patients were randomly assigned to group A (14-day bismuth-containing quadruple therapy) and group B (quadruple therapy supplemented with Clostridium butyricum). Stool samples of group A and B were collected on day 0, 14 and 56 while stool samples of group C were collected on day 0. Gut microbiota was investigated by 16S rRNA sequencing.<br><br>FINDINGS: The Sobs index (richness estimator) was significantly higher in H. pylori-positive samples than H. pylori-negative samples (p < .05). Several metabolic pathways were more abundant in H. pylori-positive communities while some disease-associated pathways had higher potential in H. pylori-negative community through KEGG pathway analysis. Abundances of most butyrate-producing bacteria significantly decreased, while several detrimental bacteria increased after eradication therapy. Probiotic supplementation was associated with improved gastrointestinal symptoms as well as increased Bacteroidetes:Firmicutes ratio.<br><br>INTERPRETATION: While H. pylori infection may not be necessarily detrimental in all patients, eradication of H. pylori was associated with widespread changes in gut microbial ecology and structure. Probiotic supplementation could relieve more gastrointestinal symptoms by inducing alterations in gut microbiota and host immune responses. As such, the decision to eradicate H. pylori should be based on comprehensive analysis of individual patients.}, }
@article {pmid30143799, year = {2018}, author = {Hall, EK and Bernhardt, ES and Bier, RL and Bradford, MA and Boot, CM and Cotner, JB and Del Giorgio, PA and Evans, SE and Graham, EB and Jones, SE and Lennon, JT and Locey, KJ and Nemergut, D and Osborne, BB and Rocca, JD and Schimel, JP and Waldrop, MP and Wallenstein, MD}, title = {Understanding how microbiomes influence the systems they inhabit.}, journal = {Nature microbiology}, volume = {3}, number = {9}, pages = {977-982}, doi = {10.1038/s41564-018-0201-z}, pmid = {30143799}, issn = {2058-5276}, abstract = {Translating the ever-increasing wealth of information on microbiomes (environment, host or built environment) to advance our understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes that they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here, we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system-level processes that they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted using constituent taxa (community-aggregated traits) from those properties that cannot currently be predicted using constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these three categories of microbial characteristics and connect them with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.}, }
@article {pmid30143666, year = {2018}, author = {Benicio, LM and Simionato, AS and Novello, CR and Guimarães, JR and Felicidade, I and de Oliveira, AG and de Mello, JCP and Mantovani, MS and Chryssafidis, AL and Andrade, G and de Syllos Colus, IM and de Oliveira, MT}, title = {RNAm expression profile of cancer marker genes in HepG2 cells treated with different concentrations of a new indolin-3-one from Pseudomonas aeruginosa.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12781}, doi = {10.1038/s41598-018-30893-w}, pmid = {30143666}, issn = {2045-2322}, abstract = {The present study tested the effects of a newly identified indolin-3-one compound (compound 1), produced by Pseudomonas aeruginosa, on HepG2 cells. The MTT assays demonstrated decreased metabolic activities in HepG2 cells treated with compound 1, with dose- and time-dependent intensifying effect, starting at a concentration of 40 µM. The IC50 after 24, 48, 72, and 96 h treatments were 41.35, 52.7, 92.79 and 66.65 μM of compound 1, respectively. Below 80 µM, no significative damage on erythrocytes membranes was observed by the hemolytic assays. The RT-qPCR revealed that the compound modulated key genes involved in carcinogenesis process, indicating possible indolin-3-one mechanisms of action. The data showed that gene expression alterations promoted by compound 1, in concentrations up to 60 μM after 48 h, led to a decrease in cellular progression and there was no direct cellular damage. In addition, non-cytotoxic concentrations of compound 1 halved the concentration of the chemotherapeutic doxorubicin, maintaining similar therapeutic effect against HepG2 cells. The novelty of the molecule and the biological activities observed in the present study emphasize the potential of the compound 1 in cancer therapy research.}, }
@article {pmid30142153, year = {2018}, author = {Pace, NR}, title = {The small things can matter.}, journal = {PLoS biology}, volume = {16}, number = {8}, pages = {e3000009}, doi = {10.1371/journal.pbio.3000009}, pmid = {30142153}, issn = {1545-7885}, abstract = {In the context of biology as a whole and of our own personal lives, seemingly small things can prove surprisingly influential. Here, I consider the powerful impact of small organisms-the inhabitants of the microbial world-and the small events that shaped my own development as a scientist. I reflect on the early days of the fields of molecular biology and microbial ecology and my own role in the origin story of what we now call &quot;metagenomics&quot;.}, }
@article {pmid30141128, year = {2018}, author = {Li, H and Mishra, M and Ding, S and Miyamoto, MM}, title = {Diversity and Dynamics of &quot;Candidatus Endobugula&quot; and Other Symbiotic Bacteria in Chinese Populations of the Bryozoan, Bugula neritina.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1233-x}, pmid = {30141128}, issn = {1432-184X}, support = {201205024-2//Public Welfare Project of the State Oceanic Administration/ ; 2013FY110700//National Basic Research Foundation of China/ ; }, abstract = {Bugula neritina is a common invasive cosmopolitan bryozoan that harbors (like many sessile marine invertebrates) a symbiotic bacterial (SB) community. Among the SB of B. neritina, &quot;Candidatus Endobugula sertula&quot; continues to receive the greatest attention, because it is the source of bryostatins. The bryostatins are potent bioactive polyketides, which have been investigated for their therapeutic potential to treat various cancers, Alzheimer's disease, and AIDS. In this study, we compare the metagenomics sequences for the 16S ribosomal RNA gene of the SB communities from different geographic and life cycle samples of Chinese B. neritina. Using a variety of approaches for estimating alpha/beta diversity and taxonomic abundance, we find that the SB communities vary geographically with invertebrate and fish mariculture and with latitude and environmental temperature. During the B. neritina life cycle, we find that the diversity and taxonomic abundances of the SB communities change with the onset of host metamorphosis, filter feeding, colony formation, reproduction, and increased bryostatin production. &quot;Ca. Endobugula sertula&quot; is confirmed as the symbiont of the Chinese &quot;Ca. Endobugula&quot;/B. neritina symbiosis. Our study extends our knowledge about B. neritina symbiosis from the New to the Old World and offers new insights into the environmental and life cycle factors that can influence its SB communities, &quot;Ca. Endobugula,&quot; and bryostatins more globally.}, }
@article {pmid30141127, year = {2018}, author = {Choi, Y and Banerjee, A and McNish, S and Couch, KS and Torralba, MG and Lucas, S and Tovchigrechko, A and Madupu, R and Yooseph, S and Nelson, KE and Shanmugam, VK and Chan, AP}, title = {Co-occurrence of Anaerobes in Human Chronic Wounds.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1231-z}, pmid = {30141127}, issn = {1432-184X}, support = {R01NR013888//National Institute of Nursing Research/ ; UL1 TR000075//National Center for Advancing Translational Sciences/ ; }, abstract = {Chronic wounds are wounds that have failed to heal after 3 months of appropriate wound care. Previous reports have identified a diverse collection of bacteria in chronic wounds, and it has been postulated that bacterial profile may contribute to delayed healing. The purpose of this study was to perform a microbiome assessment of the Wound Healing and Etiology (WE-HEAL) Study cohort, including underlying comorbidities less commonly studied in the context of chronic wounds, such as autoimmune diseases, and investigate possible relationships of the wound microbiota with clinical healing trends. We examined chronic wound specimens from 60 patients collected through the WE-HEAL Study using 16S ribosomal RNA gene sequencing. A group of co-occurring obligate anaerobes was identified from taxonomic analysis guided by Dirichlet multinomial mixtures (DMM) modeling. The group includes members of the Gram-positive anaerobic cocci (GPAC) of the Clostridia class (i.e., Anaerococcus, Finegoldia, and Peptoniphilus) and additional strict anaerobes (i.e., Porphyromonas and Prevotella). We showed that the co-occurring group of obligate anaerobes not only co-exists with commonly identified wound species (such as Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas, Corynebacterium, and Streptococcus), but importantly, they could also predominate the wound microbiota. Furthermore, examination of clinical comorbidities of the WE-HEAL specimens showed that specific obligate and facultative anaerobes were significantly reduced in wounds presented with autoimmune disease. With respect to future healing trends, no association with the wound microbiome community or the abundance of individual wound species could be established. In conclusion, we identified a co-occurring obligate anaerobic community type that predominated some human chronic wounds and underrepresentation of anaerobes in wounds associated with autoimmune diseases. Possible elucidation of host environments or key factors that influence anaerobe colonization warrants further investigation in a larger cohort.}, }
@article {pmid30138752, year = {2018}, author = {Zeineldin, M and Barakat, R and Elolimy, A and Salem, AZM and Elghandour, MMY and Monroy, JC}, title = {Synergetic action between the rumen microbiota and bovine health.}, journal = {Microbial pathogenesis}, volume = {124}, number = {}, pages = {106-115}, doi = {10.1016/j.micpath.2018.08.038}, pmid = {30138752}, issn = {1096-1208}, abstract = {Host-rumen-microbe interactions are essential components of many physiological processes, and therefore can affect ruminant health. Classical knowledge of rumen microbiology is based on culture-dependent methodologies, which only account for 10-20% of the rumen bacterial communities. While, the advancement in DNA sequencing and bioinformatics platforms provide novel approaches to investigate the composition and dynamics of the rumen microbiota. Recent studies demonstrated that the ruminal ecosystem is highly diverse and harbors numerous microbial communities. The composition of these microbial communities are affected by various environmental factors such as nutrition and different management strategies. Disturbance in the microbial ecology of the rumen is associated with the development of various diseases. Despite the flow of recent rumen-based studies, rumen microbiota is still not fully characterized. This review provides an overview of recent efforts to characterize rumen microbiota and its potential role in rumen health and disease. Moreover, the recent effects of dietary interventions and probiotics on rumen microbiota are discussed.}, }
@article {pmid30137564, year = {2018}, author = {Lekeux, G and Laurent, C and Joris, M and Jadoul, A and Jiang, D and Bosman, B and Carnol, M and Motte, P and Xiao, Z and Galleni, M and Hanikenne, M}, title = {di-Cysteine motifs in the C-terminus of plant HMA4 proteins confer nanomolar affinity for zinc and are essential for HMA4 function in vivo.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/ery311}, pmid = {30137564}, issn = {1460-2431}, abstract = {The PIB ATPase Heavy Metal ATPase 4 (HMA4) has a central role in the zinc homeostasis network of Arabidopsis thaliana. This membrane protein loads metal from the pericycle cells into the xylem in roots, thereby allowing root to shoot metal translocation. Moreover, HMA4 is key for zinc hyperaccumulation as well as zinc and cadmium hypertolerance in the pseudometallophyte Arabidopsis halleri. The plant-specific cytosolic C-terminal extension of HMA4 is rich in putative metal-binding residues and substantially diverged between A. thaliana and A. halleri. To clarify the function of the domain in both species, protein variants with truncated C-terminal extension, as well as with mutated di-Cys motifs and/or a His-stretch, were functionally characterized. We show that di-Cys motifs, but not the His-stretch, contribute to high affinity zinc binding and function in planta. We suggest that the HMA4 C-terminal extension is at least partly responsible for protein targeting to the plasma membrane. Finally, we reveal that the C-terminal extensions of both A. thaliana and A. halleri HMA4 proteins share similar function, despite marginally different zinc-binding capacity.}, }
@article {pmid30137345, year = {2018}, author = {Luk, AW and Beckmann, S and Manefield, M}, title = {Dependency of DNA extraction efficiency on cell concentration confounds molecular quantification of microorganisms in groundwater.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {10}, pages = {}, doi = {10.1093/femsec/fiy146}, pmid = {30137345}, issn = {1574-6941}, abstract = {Quantification of microbes in water systems is essential to industrial practices ranging from drinking water and wastewater treatment to groundwater remediation. While quantification using DNA-based molecular methods is precise, the accuracy is dependent on DNA extraction efficiencies. We show that the DNA yield is strongly impacted by the cell concentration in groundwater samples (r = -0.92, P < 0.0001). This has major implications for industrial applications using quantitative polymerase chain reaction (qPCR) to determine cell concentrations in water, including bioremediation. We propose a simple normalization method using a DNA recovery ratio, calculated with the total cell count and DNA yield. Application of this method to enumeration of bacteria and archaea in groundwater samples targeting phylogenetic markers (16S rRNA) demonstrated an increased goodness of fit after normalization (7.04 vs 0.94 difference in Akaike's information criteria). Furthermore, normalization was applied to qPCR quantification of functional genes and combined with DNA sequencing of archaeal and bacterial 16S rRNA genes to monitor changes in abundance of methanogenic archaea and sulphate-reducing bacteria in groundwater. The integration of qPCR and DNA sequencing with appropriate normalization enables high-throughput quantification of microbial groups using increasingly affordable and accessible techniques. This research has implications for microbial ecology and engineering research as well as industrial practice.}, }
@article {pmid30137328, year = {2018}, author = {Geesink, P and Tyc, O and Küsel, K and Taubert, M and van de Velde, C and Kumar, S and Garbeva, P}, title = {Growth promotion and inhibition induced by interactions of groundwater bacteria.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {11}, pages = {}, doi = {10.1093/femsec/fiy164}, pmid = {30137328}, issn = {1574-6941}, abstract = {Microorganisms can produce a plethora of secondary metabolites, some acting as signaling compounds and others as suppressing agents. As yet, the potential of groundwater microbes to produce antimicrobial compounds to increase their competitiveness against other bacteria has not been examined. In this study, we developed an AlamarBlue® based high-throughput screening method that allowed for a fast and highly standardized evaluation of both growth-inhibiting and -promoting metabolites. With this technique, 149 screened bacterial isolates were grown in monocultures and in 1402 co-cultures. Co-cultivation did not increase the frequency of growth inhibition against the two tested model organisms (Staphylococcus aureus 533R4 and Escherichia coli WA321) compared to monocultures. Mainly co-cultivation of Proteobacteria induced growth inhibition of both model organisms. Only slightly increased growth promotion of S. aureus 533R4 was observed. Growth-promoting effects on E. coli WA321 were observed by supernatants from co-cultures between Bacteroidetes and Firmicutes. With the standardized screening for both growth-inhibiting and -promoting effects, this method will enable further studies to elaborate and better understand complex inter-specific interactions and networks in aquatic communities as well as in other environments.}, }
@article {pmid30135980, year = {2018}, author = {Vikström, K and Wikner, J}, title = {Importance of Bacterial Maintenance Respiration in a Subarctic Estuary: a Proof of Concept from the Field.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1244-7}, pmid = {30135980}, issn = {1432-184X}, abstract = {Bacterial respiration contributes to atmospheric carbon dioxide accumulation and development of hypoxia and is a critical, often overlooked, component of ecosystem function. This study investigates the concept that maintenance respiration is a significant proportion of bacterial respiration at natural nutrient levels in the field, advancing our understanding of bacterial living conditions and energy strategies. Two river-sea transects of respiration and specific growth rates were analyzed representing low- and high-productivity conditions (by in situ bacterial biomass production) in a subarctic estuary, using an established ecophysiological linear model (the Pirt model) estimating maintenance respiration. The Pirt model was applicable to field conditions during high, but not low, bacterial biomass production. However, a quadratic model provided a better fit to observed data, accounting for the maintained respiration at low μ. A first estimate of maintenance respiration was 0.58 fmol O2 day-1 cell-1 by the quadratic model. Twenty percent to nearly all of the bacterial respiration was due to maintenance respiration over the observed range of μ (0.21-0.002 day-1). In the less productive condition, bacterial specific respiration was high and without dependence on μ, suggesting enhanced bacterial energy expenditure during starvation. Annual maintenance respiration accounted for 58% of the total bacterioplankton respiration based on μ from monitoring data. Phosphorus availability occasionally, but inconsistently, explained some of the remaining variation in bacterial specific respiration. Bacterial maintenance respiration can constitute a large share of pelagic respiration and merit further study to understand bacterial energetics and oxygen dynamics in the aquatic environment.}, }
@article {pmid30131799, year = {2018}, author = {Seugendo, M and Janssen, I and Lang, V and Hasibuan, I and Bohne, W and Cooper, P and Daniel, R and Gunka, K and Kusumawati, RL and Mshana, SE and von Müller, L and Okamo, B and Ortlepp, JR and Overmann, J and Riedel, T and Rupnik, M and Zimmermann, O and Groß, U}, title = {Prevalence and Strain Characterization of Clostridioides (Clostridium) difficile in Representative Regions of Germany, Ghana, Tanzania and Indonesia - A Comparative Multi-Center Cross-Sectional Study.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1843}, doi = {10.3389/fmicb.2018.01843}, pmid = {30131799}, issn = {1664-302X}, abstract = {Clostridioides (Clostridium) difficile infections (CDI) are considered worldwide as emerging health threat. Uptake of C. difficile spores may result in asymptomatic carrier status or lead to CDI that could range from mild diarrhea, eventually developing into pseudomembranous colitis up to a toxic megacolon that often results in high mortality. Most epidemiological studies to date have been performed in middle- and high income countries. Beside others, the use of antibiotics and the composition of the microbiome have been identified as major risk factors for the development of CDI. We therefore postulate that prevalence rates of CDI and the distribution of C. difficile strains differ between geographical regions depending on the regional use of antibiotics and food habits. A total of 593 healthy control individuals and 608 patients suffering from diarrhea in communities in Germany, Ghana, Tanzania and Indonesia were selected for a comparative multi-center cross-sectional study. The study populations were screened for the presence of C. difficile in stool samples. Cultured C. difficile strains (n = 84) were further subtyped and characterized using PCR-ribotyping, determination of toxin production, and antibiotic susceptibility testing. Prevalence rates of C. difficile varied widely between the countries. Whereas high prevalence rates were observed in symptomatic patients living in Germany and Indonesia (24.0 and 14.7%), patients from Ghana and Tanzania showed low detection rates (4.5 and 6.4%). Differences were also obvious for ribotype distribution and toxin repertoires. Toxin A+/B+ ribotypes 001/072 and 078 predominated in Germany, whereas most strains isolated from Indonesian patients belonged to toxin A+/B+ ribotype SLO160 and toxin A-/B+ ribotype 017. With 42.9-73.3%, non-toxigenic strains were most abundant in Africa, but were also found in Indonesia at a rate of 18.2%. All isolates were susceptible to vancomycin and metronidazole. Mirroring the antibiotic use, however, moxifloxacin resistance was absent in African C. difficile isolates but present in Indonesian (24.2%) and German ones (65.5%). This study showed that CDI is a global health threat with geographically different prevalence rates which might reflect distinct use of antibiotics. Significant differences for distributions of ribotypes, toxin production, and antibiotic susceptibilities were observed.}, }
@article {pmid30130114, year = {2018}, author = {Eshrati, M and Amadei, F and Van de Wiele, T and Veschgini, M and Kaufmann, S and Tanaka, M}, title = {Biopolymer-Based Minimal Formulations Boost Viability and Metabolic Functionality of Probiotics Lactobacillus rhamnosus GG through Gastrointestinal Passage.}, journal = {Langmuir : the ACS journal of surfaces and colloids}, volume = {34}, number = {37}, pages = {11167-11175}, doi = {10.1021/acs.langmuir.8b01915}, pmid = {30130114}, issn = {1520-5827}, abstract = {The delivery of probiotic microorganisms as food additives via oral administration is a straightforward strategy to improve the intestinal microbiota. To protect probiotics from the harsh environments in the stomach and small intestine, it is necessary to formulate them in biocompatible carriers, which finally release them in the ileum and colon without losing their viability and functions. Despite major progresses in various polymer-based formulations, many of them are highly heterogeneous and too large in size and hence often &quot;felt&quot; by the tongue. In this study, we established a new formulation for probiotics Lactobacillus rhamnosus GG (LGG) and systematically correlated the physicochemical properties of formulations with the functions of probiotics after the delivery to different gastrointestinal compartments. By reducing the stirring speed by 1 order of magnitude during the emulsification of polyalginate in the presence of xanthan gum, we fabricated microparticles with a size well below the limit of human oral sensory systems. To improve the chemical stability, we deposited chitosan and polyalginate layers on particle surfaces and found that the deposition of a 20 nm-thick layer is already sufficient to perfectly sustain the viability of all LGG. Compared to free LGG, the colony-forming units of LGG in these formulations were by factors of 107 larger in stomach fluid and 104 larger in small intestine fluid. The metabolic functionality of LGG in polymer formulations was assessed by measuring the amount of lactate produced by LGG in a human gastrointestinal simulator, showing 5 orders of magnitude larger values compared to free LGG. The obtained results have demonstrated that the minimal formulation of LGG established here boosts not only the viability but also the metabolic functionality of probiotics throughout oral uptake, passage through the gastrointestinal tract, and delivery to the ileum and colon.}, }
@article {pmid30128178, year = {2018}, author = {Wallace, J and Laforest-Lapointe, I and Kembel, SW}, title = {Variation in the leaf and root microbiome of sugar maple (Acer saccharum) at an elevational range limit.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5293}, doi = {10.7717/peerj.5293}, pmid = {30128178}, issn = {2167-8359}, abstract = {Background: Bacteria, archaea, viruses and fungi live in various plant compartments including leaves and roots. These plant-associated microbial communities have many effects on host fitness and function. Global climate change is impacting plant species distributions, a phenomenon that will affect plant-microbe interactions both directly and indirectly. In order to predict plant responses to global climate change, it will be crucial to improve our understanding of plant-microbe interactions within and at the edge of plant species natural ranges. While microbes affect their hosts, in turn the plant's attributes and the surrounding environment drive the structure and assembly of the microbial communities themselves. However, the patterns and dynamics of these interactions and their causes are poorly understood.<br><br>Methods: In this study, we quantified the microbial communities of the leaves and roots of seedlings of the deciduous tree species sugar maple (Acer saccharum Marshall) within its natural range and at the species' elevational range limit at Mont-Mégantic, Quebec. Using high-throughput DNA sequencing, we quantified the bacterial and fungal community structure in four plant compartments: the epiphytes and endophytes of leaves and roots. We also quantified endophytic fungal communities in roots.<br><br>Results: The bacterial and fungal communities of A. saccharum seedlings differ across elevational range limits for all four plant compartments. Distinct microbial communities colonize each compartment, although the microbial communities inside a plant's structure (endophytes) were found to be a subset of the communities found outside the plant's structure (epiphytes). Plant-associated bacterial communities were dominated by the phyla Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes while the main fungal taxa present were Ascomycota.<br><br>Discussion: We demonstrate that microbial communities associated with sugar maple seedlings at the edge of the species' elevational range differ from those within the natural range. Variation in microbial communities differed among plant components, suggesting the importance of each compartment's exposure to changes in biotic and abiotic conditions in determining variability in community structure. These findings provide a greater understanding of the ecological processes driving the structure and diversity of plant-associated microbial communities within and at the edge of a plant species range, and suggest the potential for biotic interactions between plants and their associated microbiota to influence the dynamics of plant range edge boundaries and responses to global change.}, }
@article {pmid30127345, year = {2018}, author = {Gilbert, JA and Stephens, B}, title = {Microbiology of the built environment.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {11}, pages = {661-670}, doi = {10.1038/s41579-018-0065-5}, pmid = {30127345}, issn = {1740-1534}, abstract = {The built environment comprises all structures built by humans, including our homes, workplaces, schools and vehicles. As in any ecosystem on Earth, microorganisms have been found in every part of the built environment that has been studied. They exist in the air, on surfaces and on building materials, usually dispersed by humans, animals and outdoor sources. Those microbial communities and their metabolites have been implied to cause (or exacerbate) and prevent (or mitigate) human disease. In this Review, we outline the history of the field of microbiology of the built environment and discuss recent insights that have been gained into microbial ecology, adaptation and evolution of this ecosystem. Finally, we consider the implications of this research, specifically, how it is changing the types of materials we use in buildings and how our built environments affect human health.}, }
@article {pmid30126070, year = {2018}, author = {De Paepe, K and Verspreet, J and Verbeke, K and Raes, J and Courtin, CM and Van de Wiele, T}, title = {Introducing insoluble wheat bran as a gut microbiota niche in an in vitro dynamic gut model stimulates propionate and butyrate production and induces colon region specific shifts in the luminal and mucosal microbial community.}, journal = {Environmental microbiology}, volume = {20}, number = {9}, pages = {3406-3426}, doi = {10.1111/1462-2920.14381}, pmid = {30126070}, issn = {1462-2920}, support = {IWT130028//Fonds Wetenschappelijk Onderzoek/ ; }, abstract = {The spatial organization of gut microorganisms is important with respect to their functional role in the gut ecosystem. Regional differences in the longitudinal and lateral direction are, however, not frequently studied, given the difficulty to sample these human gut regions in vivo. Particularly the insoluble food particle-associated microbiota is poorly studied. Therefore, the long-term effects of insoluble wheat bran supplementation on the composition and functionality of the gut microbial community derived from six individuals were explored in the Dietary Particle-Mucosal-Simulator of the Human Intestinal Microbial Ecosystem in vitro model. Wheat bran stimulated propionate and butyrate production and induced shifts in the luminal and mucosal microbial community composition. The insoluble wheat bran residue and the mucus layer were identified as crucial platforms in sustaining diversity by selectively enriching species, which are not thriving in the luminal environment, including Lactobacillus, Bifidobacterium and Dialister species, Roseburia faecis, Prevotella copri and Bacteroides ovatus. Despite the evident habitat preference, some parallels could be drawn between the enrichment of taxa on bran platforms and their stimulation in the luminal and mucosal communities. Removing wheat bran during the wash-out period reversed the functional effects and gave rise to a blooming of some taxa that are considered opportunistic pathogens.}, }
@article {pmid30124400, year = {2018}, author = {Jung, MY and Islam, MA and Gwak, JH and Kim, JG and Rhee, SK}, title = {Nitrosarchaeum koreense gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon member of the phylum Thaumarchaeota isolated from agricultural soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {68}, number = {10}, pages = {3084-3095}, doi = {10.1099/ijsem.0.002926}, pmid = {30124400}, issn = {1466-5034}, mesh = {Agriculture ; Ammonia/*metabolism ; Archaea/*classification/genetics/isolation &amp; purification ; Base Composition ; Genes, Archaeal ; Glyceryl Ethers/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {A mesophilic, chemolithoautotrophic, neutrophilic and aerobic ammonia-oxidizing archaeon, designated strain MY1T, was isolated from agricultural soil. Microscopic observation revealed short, rod-shaped cells with a diameter of 0.3-0.5 µm and length of 0.6-1.0 µm. The isolate had no flagella and pili, and possessed no genes associated with archaeal flagella synthesis. The major membrane lipids consisted mainly of the glycerol dibiphytanyl glycerol tetraether (GDGT) lipids GDGT-0 to GDGT-4 and crenarchaeol. The major intact polar lipids (IPLs) were determined as hexose plus phosphohexose IPL and dihexose IPL. Strain MY1T obtains energy by aerobically oxidizing ammonia and carbon by fixing CO2. An optimal growth was observed at 25 °C, at pH 7 and with 0.2-0.4 % (w/v) salinity that corresponds with its terrestrial habitat. The addition of α-keto acids was necessary to stimulate growth. The strain tolerated ammonium and nitrite concentrations up to 10 and 5 mM, respectively. The MY1T genome has a DNA G+C content of 32.7 mol%. Phylogenetic analysis based on the 16S rRNA gene showed that strain MY1T belongs to the family Nitrosopumilaceaeof the phylum Thaumarchaeota, sharing the highest 16S rRNA gene sequence similarity (96.6-97.1 %) with marine isolates of the genus Nitrosopumilus. The average nucleotide identity was 78 % between strain MY1T and Nitrosopumilus maritimus SCM1T, indicating distant relatedness. Based on the phenotypic, phylogenetic and genomic analyses, it was concluded that strain MY1T belongs to the novel genus Nitrosarchaeum, under which the name Nitrosarchaeum koreense sp. nov. is proposed as the type species. The type strain is MY1T (=JCM 31640T=KCTC 4249T).}, }
@article {pmid30123820, year = {2018}, author = {Williamson, IA and Arnold, JW and Samsa, LA and Gaynor, L and DiSalvo, M and Cocchiaro, JL and Carroll, I and Azcarate-Peril, MA and Rawls, JF and Allbritton, NL and Magness, ST}, title = {A High-Throughput Organoid Microinjection Platform to Study Gastrointestinal Microbiota and Luminal Physiology.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {6}, number = {3}, pages = {301-319}, doi = {10.1016/j.jcmgh.2018.05.004}, pmid = {30123820}, issn = {2352-345X}, support = {UL1 TR001111/TR/NCATS NIH HHS/United States ; R01 DK091427/DK/NIDDK NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; R01 DK081426/DK/NIDDK NIH HHS/United States ; R01 DK109559/DK/NIDDK NIH HHS/United States ; UL1 TR001117/TR/NCATS NIH HHS/United States ; }, abstract = {Background &amp; Aims: The human gut microbiota is becoming increasingly recognized as a key factor in homeostasis and disease. The lack of physiologically relevant in vitro models to investigate host-microbe interactions is considered a substantial bottleneck for microbiota research. Organoids represent an attractive model system because they are derived from primary tissues and embody key properties of the native gut lumen; however, access to the organoid lumen for experimental perturbation is challenging. Here, we report the development and validation of a high-throughput organoid microinjection system for cargo delivery to the organoid lumen and high-content sampling.<br><br>Methods: A microinjection platform was engineered using off-the-shelf and 3-dimensional printed components. Microinjection needles were modified for vertical trajectories and reproducible injection volumes. Computer vision (CVis) and microfabricated CellRaft Arrays (Cell Microsystems, Research Triangle Park, NC) were used to increase throughput and enable high-content sampling of mock bacterial communities. Modeling preformed using the COMSOL Multiphysics platform predicted a hypoxic luminal environment that was functionally validated by transplantation of fecal-derived microbial communities and monocultures of a nonsporulating anaerobe.<br><br>Results: CVis identified and logged locations of organoids suitable for injection. Reproducible loads of 0.2 nL could be microinjected into the organoid lumen at approximately 90 organoids/h. CVis analyzed and confirmed retention of injected cargos in approximately 500 organoids over 18 hours and showed the requirement to normalize for organoid growth for accurate assessment of barrier function. CVis analyzed growth dynamics of a mock community of green fluorescent protein- or Discosoma sp. red fluorescent protein-expressing bacteria, which grew within the organoid lumen even in the presence of antibiotics to control media contamination. Complex microbiota communities from fecal samples survived and grew in the colonoid lumen without appreciable changes in complexity.<br><br>Conclusions: High-throughput microinjection into organoids represents a next-generation in vitro approach to investigate gastrointestinal luminal physiology and the gastrointestinal microbiota.}, }
@article {pmid30121434, year = {2018}, author = {Props, R and Rubbens, P and Besmer, M and Buysschaert, B and Sigrist, J and Weilenmann, H and Waegeman, W and Boon, N and Hammes, F}, title = {Detection of microbial disturbances in a drinking water microbial community through continuous acquisition and advanced analysis of flow cytometry data.}, journal = {Water research}, volume = {145}, number = {}, pages = {73-82}, doi = {10.1016/j.watres.2018.08.013}, pmid = {30121434}, issn = {1879-2448}, abstract = {Detecting disturbances in microbial communities is an important aspect of managing natural and engineered microbial communities. Here, we implemented a custom-built continuous staining device in combination with real-time flow cytometry (RT-FCM) data acquisition, which, combined with advanced FCM fingerprinting methods, presents a powerful new approach to track and quantify disturbances in aquatic microbial communities. Through this new approach we were able to resolve various natural community and single-species microbial contaminations in a flow-through drinking water reactor. Next to conventional FCM metrics, we applied metrics from a recently developed fingerprinting technique in order to gain additional insight into the microbial dynamics during these contamination events. Importantly, we found that multiple community FCM metrics based on different statistical approaches were required to fully characterize all contaminations. Furthermore we found that for accurate cell concentration measurements and accurate inference from the FCM metrics (coefficient of variation ≤ 5%), at least 1000 cells should be measured, which makes the achievable temporal resolution a function of the prevalent bacterial concentration in the system-of-interest. The integrated RT-FCM acquisition and analysis approach presented herein provides a considerable improvement in the temporal resolution by which microbial disturbances can be observed and simultaneously provides a multi-faceted toolset to characterize such disturbances.}, }
@article {pmid30121040, year = {2019}, author = {Petersen, NB and Madsen, T and Glaring, MA and Dobbs, FC and Jørgensen, NOG}, title = {Ballast water treatment and bacteria: Analysis of bacterial activity and diversity after treatment of simulated ballast water by electrochlorination and UV exposure.}, journal = {The Science of the total environment}, volume = {648}, number = {}, pages = {408-421}, doi = {10.1016/j.scitotenv.2018.08.080}, pmid = {30121040}, issn = {1879-1026}, abstract = {Effects of ballast water (BW) treatment by ultra-violet (UV) light and electrochlorination (EC) on survival, activity and diversity of marine bacterioplankton and release of organic matter from cell damage were examined at discharge in a large-scale BW test facility (250 m3 tanks) at Hundested harbour, Denmark. The tests were performed in accordance with the requirements for type approval testing by International Maritime Organization (IMO) and US Coast Guard. After treatment, the water was held in the tanks for one day (EC) before discharge, or 6 days (UV, including also a final UV re-treatment) before discharge. In the discharged and treated water, numbers of viable bacteria and bacterial growth rate had decreased significantly relative to the untreated water, but the total number of bacteria only was reduced in the EC-treated water. After additional storage for up to 10 days in small-scale laboratory incubations, significant regrowth of bacteria was observed after either treatment. Sequencing of 16S rRNA gene amplicons demonstrated that α-Proteobacteria initially were dominant, but γ-Proteobacteria dominated after regrowth. Bacteria used to document BW treatment efficiency (E. coli, Vibrio spp., enterococci) survived both treatments; neither treatment reduced the risk of pathogen dispersal. Concentrations of amino acids in the water were used as indicators of treatment-induced cell damage and demonstrated higher concentrations at discharge, but only after the EC treatments. Our results indicate that activity of bacteria, rather than their abundances, should be used when examining effects by ballast water treatment on microorganisms and that none of the examined treatment technologies could eliminate pathogenic bacteria.}, }
@article {pmid30117593, year = {2018}, author = {Ngo, TTN and Senior, AM and Culina, A and Santos, ESA and Vlak, JM and Zwart, MP}, title = {Quantitative analysis of the dose-response of white spot syndrome virus in shrimp.}, journal = {Journal of fish diseases}, volume = {41}, number = {11}, pages = {1733-1744}, doi = {10.1111/jfd.12877}, pmid = {30117593}, issn = {1365-2761}, abstract = {White spot syndrome virus (WSSV) is an important cause of mortality and economic losses in shrimp farming. Although WSSV-induced mortality is virus dose dependent and WSSV infection does not necessarily lead to mortality, the relationships between virus-particle dose, infection and mortality have not been analysed quantitatively. Here, we explored WSSV dose-response by a combination of experiments, modelling and meta-analysis. We performed dose-response experiments in Penaeus vannamei postlarvae, recorded host mortality and detected WSSV infection. When we fitted infection models to these data, two models-differing in whether they incorporated heterogeneous host susceptibility to the virus or not-were supported for two independent experiments. To determine the generality of these results, we reanalysed published data sets and then performed a meta-analysis. We found that WSSV dose-response kinetics is indeed variable over experiments. We could not clearly identify which specific infection model has the most support by meta-analysis, but we argue that these results also are most concordant with a model incorporating varying levels of heterogeneous host susceptibility to WSSV. We have identified suitable models for analysing WSSV dose-response, which can elucidate the most basic virus-host interactions and help to avoid underestimating WSSV infection at low virus doses.}, }
@article {pmid30115327, year = {2018}, author = {Zimudzi, J and van der Waals, JE and Coutinho, TA and Cowan, DA and Valverde, A}, title = {Temporal shifts of fungal communities in the rhizosphere and on tubers in potato fields.}, journal = {Fungal biology}, volume = {122}, number = {9}, pages = {928-934}, doi = {10.1016/j.funbio.2018.05.008}, pmid = {30115327}, issn = {1878-6146}, abstract = {Soil fungal communities perform important ecological roles determining, at least in part, agricultural productivity. This study aimed at examining the fungal community dynamics in the potato rhizosphere across different development stages in two consecutive growing seasons (winter and summer). Microbial fingerprinting of rhizosphere soil samples collected at pre-planting, tuber initiation, flowering and at senescence was performed using ARISA in conjunction with Next Generation Sequencing (Illumina MiSeq). The epiphytic fungal communities on tubers at harvest were also investigated. Alpha-diversity was stable over time within and across the two seasons. In contrast, rhizospheric fungal community structure and composition were different between the two seasons and in the different plant growth stages within a given season, indicating the significance of the rhizosphere in shaping microbial communities. The phylum Ascomycota was dominant in the potato fungal rhizosphere, with Operational Taxonomic Units (OTUs) belonging to the genus Peyronellaea being the most abundant in all samples. Important fungal pathogens of potato, together with potential biological control agents and saprophytic species, were identified as indicator OTUs at different plant growth stages. These findings indicate that potato rhizosphere fungal communities are functionally diverse, which may contribute to soil health.}, }
@article {pmid30115122, year = {2018}, author = {Pérez-Jaramillo, JE and Carrión, VJ and de Hollander, M and Raaijmakers, JM}, title = {The wild side of plant microbiomes.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {143}, doi = {10.1186/s40168-018-0519-z}, pmid = {30115122}, issn = {2049-2618}, support = {568-2012-15517825//Departamento Administrativo de Ciencia, Tecnología e Innovación/ ; Back to the Roots//Stichting voor de Technische Wetenschappen/ ; Back to the Roots//Stichting voor de Technische Wetenschappen/ ; }, }
@article {pmid30110640, year = {2018}, author = {Kearney, SM and Gibbons, SM and Erdman, SE and Alm, EJ}, title = {Orthogonal Dietary Niche Enables Reversible Engraftment of a Gut Bacterial Commensal.}, journal = {Cell reports}, volume = {24}, number = {7}, pages = {1842-1851}, doi = {10.1016/j.celrep.2018.07.032}, pmid = {30110640}, issn = {2211-1247}, abstract = {Interest in manipulating the gut microbiota to treat disease has led to a need for understanding how organisms can establish themselves when introduced into a host with an intact microbial community. Here, we employ the concept of orthogonal niche engineering: a resource typically absent from the diet, seaweed, creates a customized niche for an introduced organism. In the short term, co-introduction of this resource at 1% in the diet along with an organism with exclusive access to this resource, Bacteroides plebeius DSM 17135, enables it to colonize at a median abundance of 1% and frequently up to 10 or more percent, both on pulsed and constant seaweed diets. In a two-month follow-up after the initial treatment period, B. plebeius stops responding to seaweed in mice initially on the constant seaweed diet, suggesting treatment regime will affect controllability. These results offer potential for diet-based intervention to introduce and control target organisms.}, }
@article {pmid30108568, year = {2018}, author = {van Kruistum, H and Bodelier, PLE and Ho, A and Meima-Franke, M and Veraart, AJ}, title = {Resistance and Recovery of Methane-Oxidizing Communities Depends on Stress Regime and History; A Microcosm Study.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1714}, doi = {10.3389/fmicb.2018.01714}, pmid = {30108568}, issn = {1664-302X}, abstract = {Although soil microbes are responsible for important ecosystem functions, and soils are under increasing environmental pressure, little is known about their resistance and resilience to multiple stressors. Here, we test resistance and recovery of soil methane-oxidizing communities to two different, repeated, perturbations: soil drying, ammonium addition and their combination. In replicated soil microcosms we measured methane oxidation before and after perturbations, while monitoring microbial abundance and community composition using quantitative PCR assays for the bacterial 16S rRNA and pmoA gene, and sequencing of the bacterial 16S rRNA gene. Although microbial community composition changed after soil drying, methane oxidation rates recovered, even after four desiccation events. Moreover, microcosms subjected to soil drying recovered significantly better from ammonium addition compared to microcosms not subjected to soil drying. Our results show the flexibility of microbial communities, even if abundances of dominant populations drop, ecosystem functions can recover. In addition, a history of stress may induce changes in community composition and functioning, which may in turn affect its future tolerance to different stressors.}, }
@article {pmid30106224, year = {2018}, author = {Otwell, AE and López García de Lomana, A and Gibbons, SM and Orellana, MV and Baliga, NS}, title = {Systems biology approaches towards predictive microbial ecology.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14378}, pmid = {30106224}, issn = {1462-2920}, support = {//Washington Research Foundation/ ; //Office of Science/ ; //U.S. Department of Energy/ ; //Lawrence Berkeley National Laboratory/ ; //National Science Foundation/ ; }, abstract = {Through complex interspecies interactions, microbial processes drive nutrient cycling and biogeochemistry. However, we still struggle to predict specifically which organisms, communities and biotic and abiotic processes are determining ecosystem function and how environmental changes will alter their roles and stability. While the tools to create such a predictive microbial ecology capability exist, cross-disciplinary integration of high-resolution field measurements, detailed laboratory studies and computation is essential. In this perspective, we emphasize the importance of pursuing a multiscale, systems approach to iteratively link ecological processes measured in the field to testable hypotheses that drive high-throughput laboratory experimentation. Mechanistic understanding of microbial processes gained in controlled lab systems will lead to the development of theory that can be tested back in the field. Using N2 O production as an example, we review the current status of field and laboratory research and layout a plausible path to the kind of integration that is needed to enable prediction of how N-cycling microbial communities will respond to environmental changes. We advocate for the development of realistic and predictive gene regulatory network models for environmental responses that extend from single-cell resolution to ecosystems, which is essential to understand how microbial communities involved in N2 O production and consumption will respond to future environmental conditions.}, }
@article {pmid30105506, year = {2018}, author = {Hotaling, S and Quackenbush, CR and Bennett-Ponsford, J and New, DD and Arias-Rodriguez, L and Tobler, M and Kelley, JL}, title = {Bacterial Diversity in Replicated Hydrogen Sulfide-Rich Streams.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1237-6}, pmid = {30105506}, issn = {1432-184X}, support = {IOS-1557860//National Science Foundation/ ; IOS-1557795//National Science Foundation/ ; W911NF-15-1-0175//United States Army Research Office/ ; }, abstract = {Extreme environments typically require costly adaptations for survival, an attribute that often translates to an elevated influence of habitat conditions on biotic communities. Microbes, primarily bacteria, are successful colonizers of extreme environments worldwide, yet in many instances, the interplay between harsh conditions, dispersal, and microbial biogeography remains unclear. This lack of clarity is particularly true for habitats where extreme temperature is not the overarching stressor, highlighting a need for studies that focus on the role other primary stressors (e.g., toxicants) play in shaping biogeographic patterns. In this study, we leveraged a naturally paired stream system in southern Mexico to explore how elevated hydrogen sulfide (H2S) influences microbial diversity. We sequenced a portion of the 16S rRNA gene using bacterial primers for water sampled from three geographically proximate pairings of streams with high (> 20 μM) or low (~ 0 μM) H2S concentrations. After exploring bacterial diversity within and among sites, we compared our results to a previous study of macroinvertebrates and fish for the same sites. By spanning multiple organismal groups, we were able to illuminate how H2S may differentially affect biodiversity. The presence of elevated H2S had no effect on overall bacterial diversity (p = 0.21), a large effect on community composition (25.8% of variation explained, p < 0.0001), and variable influence depending upon the group-whether fish, macroinvertebrates, or bacteria-being considered. For bacterial diversity, we recovered nine abundant operational taxonomic units (OTUs) that comprised a core H2S-rich stream microbiome in the region. Many H2S-associated OTUs were members of the Epsilonproteobacteria and Gammaproteobacteria, which both have been implicated in endosymbiotic relationships between sulfur-oxidizing bacteria and eukaryotes, suggesting the potential for symbioses that remain to be discovered in these habitats.}, }
@article {pmid30105505, year = {2018}, author = {Castelli, M and Serra, V and Senra, MVX and Basuri, CK and Soares, CAG and Fokin, SI and Modeo, L and Petroni, G}, title = {The Hidden World of Rickettsiales Symbionts: &quot;Candidatus Spectririckettsia obscura,&quot; a Novel Bacterium Found in Brazilian and Indian Paramecium caudatum.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1243-8}, pmid = {30105505}, issn = {1432-184X}, support = {247658//FP7 People: Marie-Curie Actions/ ; PRA_2016_58//Università di Pisa/ ; }, abstract = {Symbioses between bacteria and eukaryotes are widespread and may have significant impact on the evolutionary history of symbiotic partners. The order Rickettsiales is a lineage of intracellular Alphaproteobacteria characterized by an obligate association with a wide range of eukaryotic hosts, including several unicellular organisms, such as ciliates and amoebas. In this work, we characterized the Rickettsiales symbionts associated with two different genotypes of the freshwater ciliate Paramecium caudatum originated from freshwater environments in distant geographical areas. Phylogenetic analyses based on 16S rRNA gene showed that the two symbionts are closely related to each other (99.4% identity), belong to the family Rickettsiaceae, but are far-related with respect to previously characterized Rickettsiales. Consequently, they were assigned to a new species of a novel genus, namely &quot;Candidatus Spectririckettsia obscura.&quot; Screening on a database of short reads from 16S rRNA gene amplicon-based profiling studies confirmed that bacterial sequences related to the new symbiont are preferentially retrieved from freshwater environments, apparently with extremely scarce occurrence (< 0.1% positive samples). The present work provides new information on the still under-explored biodiversity of Rickettsiales, in particular those associated to ciliate host cells.}, }
@article {pmid30105504, year = {2018}, author = {Albright, MBN and Timalsina, B and Martiny, JBH and Dunbar, J}, title = {Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1239-4}, pmid = {30105504}, issn = {1432-184X}, support = {F260LANL2018//U.S. Department of Energy, Office of Science, Biological and Environmental Research Division/ ; Graduate Student Research (SCGSR) Fellowship//U.S. Department of Energy, Office of Science/ ; }, abstract = {Despite the explosion of metagenomic sequencing data, using -omics data to predict environmental biogeochemistry remains a challenge. One or a few genes (referred to as marker genes) in a metabolic pathway of interest in meta-omic data are typically used to represent the prevalence of a biogeochemical reaction. This approach often fails to demonstrate a consistent relationship between gene abundance and an ecosystem process rate. One reason this may occur is if a marker gene is not a good representative of a complete pathway. Here, we map the presence of 11 nitrogen (N)-cycling pathways in over 6000 complete bacterial and archaeal genomes using the Integrated Microbial Genomes database. Incomplete N-cycling pathways occurred in 39% of surveyed archaeal and bacterial species revealing a weakness in current marker-gene analyses. Furthermore, we found that most organisms have limited ability to utilize inorganic N in multiple oxidation states. This suggests that inter-organism exchange of inorganic N compounds is common, highlighting the importance of both community composition and spatial structure in determining the extent of recycling versus loss in an ecosystem.}, }
@article {pmid30105011, year = {2018}, author = {Doster, E and Rovira, P and Noyes, NR and Burgess, BA and Yang, X and Weinroth, MD and Lakin, SM and Dean, CJ and Linke, L and Magnuson, R and Jones, KI and Boucher, C and Ruiz, J and Belk, KE and Morley, PS}, title = {Investigating Effects of Tulathromycin Metaphylaxis on the Fecal Resistome and Microbiome of Commercial Feedlot Cattle Early in the Feeding Period.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1715}, doi = {10.3389/fmicb.2018.01715}, pmid = {30105011}, issn = {1664-302X}, abstract = {The objective was to examine effects of treating commercial beef feedlot cattle with therapeutic doses of tulathromycin, a macrolide antimicrobial drug, on changes in the fecal resistome and microbiome using shotgun metagenomic sequencing. Two pens of cattle were used, with all cattle in one pen receiving metaphylaxis treatment (800 mg subcutaneous tulathromycin) at arrival to the feedlot, and all cattle in the other pen remaining unexposed to parenteral antibiotics throughout the study period. Fecal samples were collected from 15 selected cattle in each group just prior to treatment (Day 1), and again 11 days later (Day 11). Shotgun sequencing was performed on isolated metagenomic DNA, and reads were aligned to a resistance and a taxonomic database to identify alignments to antimicrobial resistance (AMR) gene accessions and microbiome content. Overall, we identified AMR genes accessions encompassing 9 classes of AMR drugs and encoding 24 unique AMR mechanisms. Statistical analysis was used to identify differences in the resistome and microbiome between the untreated and treated groups at both timepoints, as well as over time. Based on composition and ordination analyses, the resistome and microbiome were not significantly different between the two groups on Day 1 or on Day 11. However, both the resistome and microbiome changed significantly between these two sampling dates. These results indicate that the transition into the feedlot-and associated changes in diet, geography, conspecific exposure, and environment-may exert a greater influence over the fecal resistome and microbiome of feedlot cattle than common metaphylactic antimicrobial drug treatment.}, }
@article {pmid30103819, year = {2018}, author = {Lourenço, KS and Suleiman, AKA and Pijl, A and van Veen, JA and Cantarella, H and Kuramae, EE}, title = {Resilience of the resident soil microbiome to organic and inorganic amendment disturbances and to temporary bacterial invasion.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {142}, doi = {10.1186/s40168-018-0525-1}, pmid = {30103819}, issn = {2049-2618}, support = {729.004.003//NWO/ ; 2013/50365-5//FAPESP/ ; 2014/24141-5, 2013/12716-0//FAPESP/ ; }, abstract = {BACKGROUND: Vinasse, a by-product of sugarcane ethanol production, is recycled by sugarcane plantations as a fertilizer due to its rich nutrient content. However, the impacts of the chemical and microbial composition of vinasse on soil microbiome dynamics are unknown. Here, we evaluate the recovery of the native soil microbiome after multiple disturbances caused by the application of organic vinasse residue, inorganic nitrogen, or a combination of both during the sugarcane crop-growing season (389 days). Additionally, we evaluated the resistance of the resident soil microbial community to the vinasse microbiome.<br><br>RESULTS: Vinasse applied alone or 30 days prior to N resulted in similar changes in the soil microbial community. Furthermore, the impact of the application of vinasse together with N fertilizer on the soil microbial community differed from that of N fertilizer alone. Organic vinasse is a source of microbes, nutrients, and organic matter, and the combination of these factors drove the changes in the resident soil microbial community. However, these changes were restricted to a short period of time due to the capacity of the soil community to recover. The invasive bacteria present in the vinasse microbiome were unable to survive in the soil conditions and disappeared after 31 days, with the exception of the Acetobacteraceae (native in the soil) and Lactobacillaceae families.<br><br>CONCLUSION: Our analysis showed that the resident soil microbial community was not resistant to vinasse and inorganic N application but was highly resilient.}, }
@article {pmid30101801, year = {2018}, author = {Muys, M and Coppens, J and Boon, N and Vlaeminck, SE}, title = {Photosynthetic oxygenation for urine nitrification.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {78}, number = {1-2}, pages = {183-194}, doi = {10.2166/wst.2018.200}, pmid = {30101801}, issn = {0273-1223}, abstract = {Human urine accounts for only a fraction of the sewage volume, but it contains the majority of valuable nutrient load in wastewater. In this study, synthetic urine was nitrified in a closed photo-bioreactor through photosynthetic oxygenation by means of a consortium of microalgae and nitrifying bacteria. In situ production of oxygen by photosynthetic organisms has the potential to reduce the energy costs linked to conventional aeration. This energy-efficient strategy results in stable urine for further nutrient recovery, while part of the nutrients are biologically recovered in the form of valuable biomass. In this study, urine was nitrified for the first time without conventional aeration at a maximum photosynthetic oxygenation rate of 160 mg O2 gVSS-1 d-1 (VSS: volatile suspended solids). A maximum volumetric nitrification rate of 67 mg N L-1 d-1 was achieved on 12% diluted synthetic urine. Chemical oxygen demand (COD) removal efficiencies were situated between 44% and 83% at a removal rate of 24 mg COD gVSS-1 d-1. After 180 days, microscopic observations revealed that Scenedesmus sp. was the dominant microalga. Overall, photosynthetic oxygenation for urine nitrification is promising as a highly electricity efficient approach for further nutrient recovery.}, }
@article {pmid30098679, year = {2018}, author = {Kroon, SJ and Ravel, J and Huston, WM}, title = {Cervicovaginal microbiota, women's health, and reproductive outcomes.}, journal = {Fertility and sterility}, volume = {110}, number = {3}, pages = {327-336}, doi = {10.1016/j.fertnstert.2018.06.036}, pmid = {30098679}, issn = {1556-5653}, abstract = {The human microbiome project has shown a remarkable diversity of microbial ecology within the human body. The vaginal microbiota is unique in that in many women it is most often dominated by Lactobacillus species. However, in some women it lacks Lactobacillus spp. and is comprised of a wide array of strict and facultative anaerobes, a state that broadly correlates with increased risk for infection, disease, and poor reproductive and obstetric outcomes. Interestingly, the level of protection against infection can also vary by species and strains of Lactobacillus, and some species although dominant are not always optimal. This factors into the risk of contracting sexually transmitted infections and possibly influences the occurrence of resultant adverse reproductive outcomes such as tubal factor infertility. The composition and function of the vaginal microbiota appear to play an important role in pregnancy and fertility treatment outcomes and future research in this field will shed further translational mechanistic understanding onto the interplay of the vaginal microbiota with women's health and reproduction.}, }
@article {pmid30097682, year = {2018}, author = {Green, TJ and Siboni, N and King, WL and Labbate, M and Seymour, JR and Raftos, D}, title = {Simulated Marine Heat Wave Alters Abundance and Structure of Vibrio Populations Associated with the Pacific Oyster Resulting in a Mass Mortality Event.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1242-9}, pmid = {30097682}, issn = {1432-184X}, support = {9201300681//Macquarie University/ ; FT130100218//Australian Research Council/ ; LP160101785//Australian Research Council/ ; }, abstract = {Marine heat waves are predicted to become more frequent and intense due to anthropogenically induced climate change, which will impact global production of seafood. Links between rising seawater temperature and disease have been documented for many aquaculture species, including the Pacific oyster Crassostrea gigas. The oyster harbours a diverse microbial community that may act as a source of opportunistic pathogens during temperature stress. We rapidly raised the seawater temperature from 20 °C to 25 °C resulting in an oyster mortality rate of 77.4%. Under the same temperature conditions and with the addition of antibiotics, the mortality rate was only 4.3%, strongly indicating a role for bacteria in temperature-induced mortality. 16S rRNA amplicon sequencing revealed a change in the oyster microbiome when the temperature was increased to 25 °C, with a notable increase in the proportion of Vibrio sequences. This pattern was confirmed by qPCR, which revealed heat stress increased the abundance of Vibrio harveyi and Vibrio fortis by 324-fold and 10-fold, respectively. Our findings indicate that heat stress-induced mortality of C. gigas coincides with an increase in the abundance of putative bacterial pathogens in the oyster microbiome and highlights the negative consequences of marine heat waves on food production from aquaculture.}, }
@article {pmid30097447, year = {2018}, author = {Burns, AS and Padilla, CC and Pratte, ZA and Gilde, K and Regensburger, M and Hall, E and Dove, ADM and Stewart, FJ}, title = {Broad Phylogenetic Diversity Associated with Nitrogen Loss through Sulfur Oxidation in a Large Public Marine Aquarium.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {20}, pages = {}, doi = {10.1128/AEM.01250-18}, pmid = {30097447}, issn = {1098-5336}, abstract = {Denitrification by sulfur-oxidizing bacteria is an effective nitrate removal strategy in engineered aquatic systems. However, the community taxonomic and metabolic diversity of sulfur-driven denitrification (SDN) systems, as well as the relationship between nitrate removal and SDN community structure, remains underexplored. This is particularly true for SDN reactors applied to marine aquaria, despite the increasing use of this technology to supplement filtration. We applied 16S rRNA gene, metagenomic, and metatranscriptomic analyses to explore the microbial basis of SDN reactors operating on Georgia Aquarium's Ocean Voyager, the largest indoor closed-system seawater exhibit in the United States. The exhibit's two SDN systems vary in water retention time and nitrate removal efficiency. The systems also support significantly different microbial communities. These communities contain canonical SDN bacteria, including a strain related to Thiobacillus thioparus that dominates the system with the higher water retention time and nitrate removal but is effectively absent from the other system. Both systems contain a wide diversity of other microbes whose metagenome-assembled genomes contain genes of SDN metabolism. These include hundreds of strains of the epsilonproteobacterium Sulfurimonas, as well as gammaproteobacterial sulfur oxidizers of the Thiotrichales and Chromatiales, and a relative of Sedimenticolathiotaurini with complete denitrification potential. The SDN genes are transcribed and the taxonomic richness of the transcript pool varies markedly among the enzymatic steps, with some steps dominated by transcripts from noncanonical SDN taxa. These results indicate complex and variable SDN communities that may involve chemical dependencies among taxa as well as the potential for altering community structure to optimize nitrate removal.IMPORTANCE Engineered aquatic systems such as aquaria and aquaculture facilities have large societal value. Ensuring the health of animals in these systems requires understanding how microorganisms contribute to chemical cycling and waste removal. Focusing on the largest seawater aquarium in the United States, we explore the microbial communities in specialized reactors designed to remove excess nitrogen through the metabolic activity of sulfur-consuming microbes. We show that the diversity of microbes in these reactors is both high and highly variable, with distinct community types associated with significant differences in nitrogen removal rate. We also show that the genes encoding the metabolic steps of nitrogen removal are distributed broadly throughout community members, suggesting that the chemical transformations in this system are likely a result of microbes relying on other microbes. These results provide a framework for future studies exploring the contributions of different community members, both in waste removal and in structuring microbial biodiversity.}, }
@article {pmid30094615, year = {2018}, author = {Ren, F and Kovalchuk, A and Mukrimin, M and Liu, M and Zeng, Z and Ghimire, RP and Kivimäenpää, M and Holopainen, JK and Sun, H and Asiegbu, FO}, title = {Tissue Microbiome of Norway Spruce Affected by Heterobasidion-Induced Wood Decay.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1240-y}, pmid = {30094615}, issn = {1432-184X}, support = {276862//Academy of Finland/ ; 278424//Academy of Finland/ ; 165010015//Jiangsu Specially-Appointed Professor, China/ ; }, abstract = {Plants live in close association with microbial symbionts, which may affect the host fitness, productivity, and tolerance against biotic and abiotic stressors. The composition of plant microbial communities is influenced by many biotic and abiotic factors, but little is known about the effect of plant pathogens on the structure of these communities. In this study, we investigated the structure of bacterial communities associated with different tissues of asymptomatic and symptomatic (Heterobasidion-rotten) Norway spruce (Picea abies (L.) Karst.) trees. Our results demonstrated that each of the investigated anatomic tissues (root, bark, down stem, upper stem, and needles) harbored a unique bacterial assemblage. However, the health status of the host trees had little effect on the structure of bacterial communities, as the only significant differences among asymptomatic and symptomatic trees were found in the composition of the bacterial communities of needles. Proteobacteria was predominant in all anatomic regions with the highest abundance in needles (86.7%), whereas Actinobacteria showed an opposite trend, being more abundant in the woody tissues than in needles. Additionally, we performed profiling of terpenoid compounds present in spruce xylem and phloem. Total concentrations of monoterpenes and sesquiterpenes were considerably higher in asymptomatic trees. However, we found no significant correlations between terpenoid profiles of spruce trees and the composition of their bacterial communities. Our results provide an insight into the diversity of bacteria associated with Norway spruce tree tissues. At the same time, the health status and terpenoid content of host trees had a limited effect on the composition of bacterial communities in our survey.}, }
@article {pmid30093611, year = {2018}, author = {Liang, J and Zhou, Z and Huo, C and Shi, Z and Cole, JR and Huang, L and Konstantinidis, KT and Li, X and Liu, B and Luo, Z and Penton, CR and Schuur, EAG and Tiedje, JM and Wang, YP and Wu, L and Xia, J and Zhou, J and Luo, Y}, title = {More replenishment than priming loss of soil organic carbon with additional carbon input.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {3175}, doi = {10.1038/s41467-018-05667-7}, pmid = {30093611}, issn = {2041-1723}, support = {DE SC00114085//U.S. Department of Energy (DOE)/ ; DE SC0004601//U.S. Department of Energy (DOE)/ ; DE SC0010715//U.S. Department of Energy (DOE)/ ; OIA-1301789//National Science Foundation (NSF)/ ; }, abstract = {Increases in carbon (C) inputs to soil can replenish soil organic C (SOC) through various mechanisms. However, recent studies have suggested that the increased C input can also stimulate the decomposition of old SOC via priming. Whether the loss of old SOC by priming can override C replenishment has not been rigorously examined. Here we show, through data-model synthesis, that the magnitude of replenishment is greater than that of priming, resulting in a net increase in SOC by a mean of 32% of the added new C. The magnitude of the net increase in SOC is positively correlated with the nitrogen-to-C ratio of the added substrates. Additionally, model evaluation indicates that a two-pool interactive model is a parsimonious model to represent the SOC decomposition with priming and replenishment. Our findings suggest that increasing C input to soils likely promote SOC accumulation despite the enhanced decomposition of old C via priming.}, }
@article {pmid30092404, year = {2018}, author = {Lian, Y and Yan, C and Xu, H and Yang, J and Yu, Y and Zhou, J and Shi, Y and Ren, J and Ji, G and Wang, K}, title = {A Novel lncRNA, LINC00460, Affects Cell Proliferation and Apoptosis by Regulating KLF2 and CUL4A Expression in Colorectal Cancer.}, journal = {Molecular therapy. Nucleic acids}, volume = {12}, number = {}, pages = {684-697}, doi = {10.1016/j.omtn.2018.06.012}, pmid = {30092404}, issn = {2162-2531}, abstract = {Emerging evidence has proven that long noncoding RNAs (lncRNAs) play important roles in human colorectal cancer (CRC) biology, although few lncRNAs have been characterized in CRC. Therefore, the functional significance of lncRNAs in the malignant progression of CRC still needs to be further explored. In this study, through analyzing TCGA RNA sequencing data and other publicly available microarray data, we found a novel lncRNA, LINC00460, whose expression was significantly upregulated in CRC tissues compared to adjacent normal tissues. Consistently, real-time qPCR results also verified that LINC00460 was overexpressed in CRC tissues and cells. Furthermore, high LINC00460 expression levels in CRC specimens were correlated with larger tumor size, advanced tumor stage, lymph node metastasis and shorter overall survival. In vitro and in vivo assays of LINC00460 alterations revealed a complex integrated phenotype affecting cell growth and apoptosis. Mechanistically, LINC00460 repressed Krüppel-like factor 2 (KLF2) transcription by binding to enhancer of zeste homolog 2 (EZH2). LINC00460 also functioned as a molecular sponge for miR-149-5p, antagonizing its ability to repress cullin 4A (CUL4A) protein translation. Taken together, our findings support a model in which the LINC00460/EZH2/KLF2 and LINC00460/miR-149-5p/CUL4A crosstalk serve as critical effectors in CRC tumorigenesis and progression, suggesting new therapeutic directions in CRC.}, }
@article {pmid30088464, year = {2018}, author = {Gil-Pulido, B and Tarpey, E and Finnegan, W and Zhan, X and Dobson, AD and O'Leary, N}, title = {Dominance of the genus Polaromonas in the microbial ecology of an Intermittently Aerated Sequencing Batch Reactor (IASBR) treating dairy processing wastewater under varying aeration rates.}, journal = {The Journal of dairy research}, volume = {85}, number = {3}, pages = {388-390}, doi = {10.1017/S0022029918000572}, pmid = {30088464}, issn = {1469-7629}, abstract = {In this Research Communication we investigate potential correlations between key bacterial groups and nutrient removal efficiency in an Intermittently Aerated Sequencing Batch Reactor (IASBR) treating synthetic dairy processing wastewater. Reactor aeration rates of 0·6 and 0·4 litre per minute (LPM) were applied to an 8 l laboratory scale system and the relative impacts on IASBR microbial community structure and orthophosphate (PO4-P) and ammonium (NH4-N) removal efficiencies compared. Aeration at 0·6 LPM over several sludge retention times (SRTs) resulted in approximately 92% removal efficiencies for both PO4-P and NH4-N. Biomass samples subjected to next-generation sequencing (NGS), 16S rRNA profiling revealed a concomitant enrichment of Polaromonas under 0·6 LPM conditions, up to ~50% relative abundance within the reactor biomass. The subsequent shift in reactor aeration to 0·4 LPM, over a period of 3 SRTs, resulted in markedly reduced nutrient removal efficiencies for PO4-P (50%) and NH4-N (45%). An 85·7% reduction in the genus level relative abundance of Polaromonas was observed under 0·4 LPM aeration conditions over the same period.}, }
@article {pmid30088023, year = {2018}, author = {Polano, C and Martini, M and Savian, F and Moruzzi, S and Ermacora, P and Firrao, G}, title = {Genome Sequence and Antifungal Activity of Two Niche-Sharing Pseudomonas protegens Related Strains Isolated from Hydroponics.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1238-5}, pmid = {30088023}, issn = {1432-184X}, support = {2370 - STAYFRESH//Ager - Agroalimentare e Ricerca/ ; }, abstract = {This work reports the comparison of the genome sequence and the ability to inhibit fungal growth of two Pseudomonas protegens related strains that were isolated from the same hydroponic culture of lamb's lettuce. The two strains were very similar in their core genome but one strain, Pf4, contained three gene clusters for the production of secondary metabolites, i.e., pyoluteorin (plt), pyrrolnitrin (prn), and rhizoxin (rzx), that were missing in the other strain, Pf11. The difference between the two strains was not due to simple insertion events, but to a relatively complex differentiation focused on the accessory genomes. In dual culture assays, both strains inhibited nearly all tested fungal strains, yet Pf4 exerted a significantly stronger fungal growth inhibition than Pf11. In addition to the differences in the secondary metabolite production associated genes abundance, the genome of Pf4 was more stable, smaller in size and with a lower number of transposons. The preservation of a dynamic equilibrium within natural populations of different strains comprised in the same species but differing in their secondary metabolite repertoire and in their genome stability may be functional to the adaptation to environmental changes.}, }
@article {pmid30087659, year = {2018}, author = {Trivedi, CB and Lau, GE and Grasby, SE and Templeton, AS and Spear, JR}, title = {Low-Temperature Sulfidic-Ice Microbial Communities, Borup Fiord Pass, Canadian High Arctic.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1622}, doi = {10.3389/fmicb.2018.01622}, pmid = {30087659}, issn = {1664-302X}, abstract = {A sulfur-dominated supraglacial spring system found at Borup Fiord Pass (BFP), Ellesmere Island, Nunavut, Canada, is a unique sulfur-on-ice system expressed along the toe of a glacier. BFP has an intermittent flowing, subsurface-derived, glacial spring that creates a large white-yellow icing (aufeis) that extends down-valley. Over field campaigns in 2014, 2016, and 2017, numerous samples were collected and analyzed for both microbial community composition and aqueous geochemistry. Samples were collected from multiple site types: spring discharge fluid, aufeis (spring-derived ice), melt pools with sedimented cryoconite material, and mineral precipitate scrapings, to probe how microbial communities differed between site types in a dynamic freeze/thaw sulfur-rich system. Dissolved sulfate varied between 0.07 and 11.6 mM and was correlated with chloride concentrations, where the fluids were saltiest among spring fluids. The highest sulfate samples exhibited high dissolved sulfide values between 0.22 and 2.25 mM. 16S rRNA gene sequencing from melt pool and aufeis samples from the 2014 campaign were highly abundant in operational taxonomic units (OTUs) closely related to sulfur-oxidizing microorganisms (SOM; Sulfurimonas, Sulfurovum, and Sulfuricurvum). Subsequent sampling 2 weeks later had fewer SOMs and showed an increased abundance of the genus Flavobacterium. Desulfocapsa, an organism that specializes in the disproportionation of inorganic sulfur compounds was also found. Samples from 2016 and 2017 revealed that microorganisms present were highly similar in community composition to 2014 samples, primarily echoed by the continued presence of Flavobacterium sp. Results suggest that while there may be acute events where sulfur cycling organisms dominate, a basal community structure appears to dominate over time and site type. These results further enhance our knowledge of low-temperature sulfur systems on Earth, and help to guide the search for potential life on extraterrestrial worlds, such as Europa, where similar low-temperature sulfur-rich conditions may exist.}, }
@article {pmid30087358, year = {2018}, author = {Chaib De Mares, M and Jiménez, DJ and Palladino, G and Gutleben, J and Lebrun, LA and Muller, EEL and Wilmes, P and Sipkema, D and van Elsas, JD}, title = {Expressed protein profile of a Tectomicrobium and other microbial symbionts in the marine sponge Aplysina aerophoba as evidenced by metaproteomics.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {11795}, doi = {10.1038/s41598-018-30134-0}, pmid = {30087358}, issn = {2045-2322}, support = {607786//EC | Seventh Framework Programme (European Union Seventh Framework Programme)/ ; 607786//EC | Seventh Framework Programme (European Union Seventh Framework Programme)/ ; 607786//EC | Seventh Framework Programme (European Union Seventh Framework Programme)/ ; 607786//EC | Seventh Framework Programme (European Union Seventh Framework Programme)/ ; }, abstract = {Aplysina aerophoba is an emerging model marine sponge, with a well-characterized microbial community in terms of diversity and structure. However, little is known about the expressed functional capabilities of its associated microbes. Here, we present the first metaproteomics-based study of the microbiome of A. aerophoba. We found that transport and degradation of halogenated and chloroaromatic compounds are common active processes in the sponge microbiomes. Our data further reveal that the highest number of proteins were affiliated to a sponge-associated Tectomicrobium, presumably from the family Entotheonellaceae, as well as to the well-known symbiont &quot;Candidatus Synechococcus spongiarium&quot;, suggesting a high metabolic activity of these two microorganisms in situ. Evidence for nitric oxide (NO) conversion to nitrous oxide was consistently observed for Tectomicrobia across replicates, by production of the NorQ protein. Moreover, we found a potential energy-yielding pathway through CO oxidation by putative Chloroflexi bacteria. Finally, we observed expression of enzymes that may be involved in the transformation of chitin, glycoproteins, glycolipids and glucans into smaller molecules, consistent with glycosyl hydrolases predicted from analyses of the genomes of Poribacteria sponge symbionts. Thus, this study provides crucial links between expressed proteins and specific members of the A. aerophoba microbiome.}, }
@article {pmid30086814, year = {2018}, author = {Yurchenko, V and Lukeš, J}, title = {Parasites and their (endo)symbiotic microbes.}, journal = {Parasitology}, volume = {145}, number = {10}, pages = {1261-1264}, doi = {10.1017/S0031182018001257}, pmid = {30086814}, issn = {1469-8161}, abstract = {Thanks to modern molecular biology methods, our understanding of the impact of (endo)symbiotic bacteria on parasitic protists and helminths is growing fast. In this issue, 9 papers have been brought together that describe various facets of the relationships between these microorganisms, reveal their range and high frequency, as well as their capacity to create novel biological complexity. Comparative analyses of these host-endosymbiont interactions indicate that there may be no discrete types of relationships but rather a continuum ranging from a dispensable endosymbiont minimally integrated within the host cell to organelles, such as mitochondria and plastids that evolved into an indispensable, deeply integrated components of the cell. We hope that this series of studies on parasites and (endo)symbiotic bacteria will increase awareness about these relationships and their representation in microbial ecology models.}, }
@article {pmid30084932, year = {2018}, author = {Cantos-Parra, E and Ramió-Pujol, S and Colprim, J and Puig, S and Bañeras, L}, title = {Specific detection of &quot;Clostridium autoethanogenum&quot;, Clostridium ljungdahlii and Clostridium carboxidivorans in complex bioreactor samples.}, journal = {FEMS microbiology letters}, volume = {365}, number = {18}, pages = {}, doi = {10.1093/femsle/fny191}, pmid = {30084932}, issn = {1574-6968}, abstract = {The high genetic similarity between some carboxydotrophic bacteria does not allow for the use of common sequencing techniques targeting the 16S rRNA gene for species identification. 16S rRNA sequencing fails to discriminate among Clostridium ljungdahlii and 'Clostridium autoethanogenum', despite this two species exhibit significant differences in CO2 assimilation and alcohol production. In this work we designed PCR primers targeting for the DNA gyrase subunit A (gyrA) and a putative formate/nitrite transporter (fnt) to specifically detect the presence of 'C. autoethanogenum', C. ljungdahlii or Clostridium carboxidivorans. We could confirm the simultaneous presence of C. ljungdahlii and 'C. autoethanogenum' in different bioreactors, and a preference of the latter for high CO2 content.}, }
@article {pmid30083828, year = {2018}, author = {Bai, M and Sen, B and Wang, Q and Xie, Y and He, Y and Wang, G}, title = {Molecular Detection and Spatiotemporal Characterization of Labyrinthulomycete Protist Diversity in the Coastal Waters Along the Pearl River Delta.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1235-8}, pmid = {30083828}, issn = {1432-184X}, support = {31670044//National Natural Science Foundation of China/ ; 91751115//National Natural Science Foundation of China/ ; 2017YFC1404500//National Key R&amp;D program of China/ ; }, abstract = {The heterotrophic labyrinthulomycete protists have long been known to play an important role in the nutrient cycling of coastal seawater. Yet, their spatiotemporal abundance and diversity in polluted coastal waters remain poorly discussed, due in part to the paucity of a rapid detection method. To this end, we developed a qPCR detection method based on a newly designed primer pair targeting their 18S rRNA gene. Using this method, we studied the population dynamics of labyrinthulomycete protists in nutrient-rich (Shenzhen Bay) and low-nutrient (Daya) coastal habitats along the Pearl River Delta. We found a significantly (P < 0.05) higher abundance of Labyrinthulomycetes in the Shenzhen bay (average 3455 gene copies mL-1) than that in Daya Bay (average 378 gene copies mL-1). Their abundance gradient positively correlated (P < 0.05) with the levels of inorganic nitrogen and phosphates. Further characterization of the molecular diversity of these protists in Shenzhen Bay using different primer sets revealed the presence of several genera besides a large number of unclassified OTUs. Regardless of the primer biases, our results show significant (P < 0.05) spatiotemporal changes in the molecular abundance and diversity of these heterotrophic protists. Overall, this study provides a rapid molecular detection tool for Labyrinthulomycetes and expands our current understanding of their dynamics controlled by physicochemical gradients in coastal waters.}, }
@article {pmid30083827, year = {2018}, author = {Weinisch, L and Kirchner, I and Grimm, M and Kühner, S and Pierik, AJ and Rosselló-Móra, R and Filker, S}, title = {Correction to: Glycine Betaine and Ectoine Are the Major Compatible Solutes Used by Four Different Halophilic Heterotrophic Ciliates.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1241-x}, pmid = {30083827}, issn = {1432-184X}, abstract = {The original version of this article unfortunately contained mistakes in the author affiliation, the references given in two tables and in a figure legend.}, }
@article {pmid30083145, year = {2018}, author = {Costa, OYA and Raaijmakers, JM and Kuramae, EE}, title = {Microbial Extracellular Polymeric Substances: Ecological Function and Impact on Soil Aggregation.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1636}, doi = {10.3389/fmicb.2018.01636}, pmid = {30083145}, issn = {1664-302X}, abstract = {A wide range of microorganisms produce extracellular polymeric substances (EPS), highly hydrated polymers that are mainly composed of polysaccharides, proteins, and DNA. EPS are fundamental for microbial life and provide an ideal environment for chemical reactions, nutrient entrapment, and protection against environmental stresses such as salinity and drought. Microbial EPS can enhance the aggregation of soil particles and benefit plants by maintaining the moisture of the environment and trapping nutrients. In addition, EPS have unique characteristics, such as biocompatibility, gelling, and thickening capabilities, with industrial applications. However, despite decades of research on the industrial potential of EPS, only a few polymers are widely used in different areas, especially in agriculture. This review provides an overview of current knowledge on the ecological functions of microbial EPSs and their application in agricultural soils to improve soil particle aggregation, an important factor for soil structure, health, and fertility.}, }
@article {pmid30083144, year = {2018}, author = {Kroeger, ME and Delmont, TO and Eren, AM and Meyer, KM and Guo, J and Khan, K and Rodrigues, JLM and Bohannan, BJM and Tringe, SG and Borges, CD and Tiedje, JM and Tsai, SM and Nüsslein, K}, title = {New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1635}, doi = {10.3389/fmicb.2018.01635}, pmid = {30083144}, issn = {1664-302X}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; }, abstract = {Deforestation in the Brazilian Amazon occurs at an alarming rate, which has broad effects on global greenhouse gas emissions, carbon storage, and biogeochemical cycles. In this study, soil metagenomes and metagenome-assembled genomes (MAGs) were analyzed for alterations to microbial community composition, functional groups, and putative physiology as it related to land-use change and tropical soil. A total of 28 MAGs were assembled encompassing 10 phyla, including both dominant and rare biosphere lineages. Amazon Acidobacteria subdivision 3, Melainabacteria, Microgenomates, and Parcubacteria were found exclusively in pasture soil samples, while Candidatus Rokubacteria was predominant in the adjacent rainforest soil. These shifts in relative abundance between land-use types were supported by the different putative physiologies and life strategies employed by the taxa. This research provides unique biological insights into candidate phyla in tropical soil and how deforestation may impact the carbon cycle and affect climate change.}, }
@article {pmid30081136, year = {2018}, author = {Losasso, C and Di Cesare, A and Mastrorilli, E and Patuzzi, I and Cibin, V and Eckert, EM and Fontaneto, D and Vanzo, A and Ricci, A and Corno, G}, title = {Assessing antimicrobial resistance gene load in vegan, vegetarian and omnivore human gut microbiota.}, journal = {International journal of antimicrobial agents}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijantimicag.2018.07.023}, pmid = {30081136}, issn = {1872-7913}, abstract = {Massive antimicrobial use in animal farming is considered as the greatest contributor to the presence of antimicrobial-resistant bacteria (ARB) in food of animal origin. Nevertheless, sewage from treated animals may impact on vegetables grown on fertilised fields, but it is largely unknown whether and to what extent ARB are transferred to vegetables and the human gut. It could be hypothesised that food of animal and vegetal origin have a different role in ARB transfer to the human gut and that different diets could be characterised by different antimicrobial resistance gene (ARG) loads. This study included three groups comprising vegans (n = 26), vegetarians (n = 32) and omnivores (n = 43). Metadata regarding food consumption and anthropometric parameters were collected. Gut microbial communities were investigated by 16S rDNA analysis. Four ARGs (sul2, tetA, blaTEM and strB) were quantified by qPCR. The results showed a lower total load of investigated ARGs in vegan diet (pairwise comparison adjusted results: omnivorous-vegan, P = 0.0119; omnivorous-vegetarian, P = 0.7416; and vegan-vegetarian, P = 0.0119). No significant differences in abundance of each gene separately were found between the three groups. Neither the amount of animal protein nor the occurrence of ARGs was significant in explaining differences in the gut microbial community of individuals, and a large proportion of the differences between community composition (PERMANOVA, 46.87%) was not explained by the analysed variables. The results support the role of omnivorous and vegetarian diets in accumulating ARGs, suggesting a possible role for animal-derived food consumption.}, }
@article {pmid30078567, year = {2018}, author = {Cordero, RJB and Robert, V and Cardinali, G and Arinze, ES and Thon, SM and Casadevall, A}, title = {Impact of Yeast Pigmentation on Heat Capture and Latitudinal Distribution.}, journal = {Current biology : CB}, volume = {28}, number = {16}, pages = {2657-2664.e3}, doi = {10.1016/j.cub.2018.06.034}, pmid = {30078567}, issn = {1879-0445}, abstract = {Pigmentation is a fundamental characteristic of living organisms that is used to absorb radiation energy and to regulate temperature. Since darker pigments absorb more radiation than lighter ones, they stream more heat, which can provide an adaptive advantage at higher latitudes and a disadvantage near the Tropics, because of the risk of overheating. This intuitive process of color-mediated thermoregulation, also known as the theory of thermal melanism (TTM), has been only tested in ectothermic animal models [1-8]. Here, we report an association between yeast pigmentation and their latitude of isolation, with dark-pigmented isolates being more frequent away from the Tropics. To measure the impact of microbial pigmentation in energy capture from radiation, we generated 20 pigmented variants of Cryptococcus neoformans and Candida spp. Infrared thermography revealed that dark-pigmented yeasts heated up faster and reached higher temperatures (up to 2-fold) than lighter ones following irradiation. Melanin-pigmented C. neoformans exhibited a growth advantage relative to non-melanized yeasts when incubated under the light at 4°C but increased thermal susceptibility at 25°C ambient temperatures. Our results extend the TTM to microbiology and suggest pigmentation as an ancient adaptation mechanism for gaining thermal energy from radiation. The contribution of microbial pigmentation in heat absorption is relevant to microbial ecology and for estimating global temperatures. The color variations available in yeasts provide new opportunities in chromatology to quantify radiative heat transfer and validate biophysical models of heat flow [9] that are not possible with plants or animals.}, }
@article {pmid30077912, year = {2018}, author = {Seuntjens, D and Carvajal-Arroyo, JM and Ruopp, M and Bunse, P and De Mulder, CP and Lochmatter, S and Agrawal, S and Boon, N and Lackner, S and Vlaeminck, SE}, title = {High-resolution mapping and modeling of anammox recovery from recurrent oxygen exposure.}, journal = {Water research}, volume = {144}, number = {}, pages = {522-531}, doi = {10.1016/j.watres.2018.07.024}, pmid = {30077912}, issn = {1879-2448}, abstract = {Oxygen inhibits anammox, a bioconversion executed by anoxic ammonium oxidizing bacteria (AnAOB). Nonetheless, oxygen is mostly found in the proximity of AnAOB in nitrogen removal applications, being a substrate for nitritation. The experiments performed to date were mostly limited to batch activity tests where AnAOB activity is estimated during oxygen exposure. However, little attention has been paid to the recovery and reversibility of activity following aerobic conditions, of direct relevance for bioreactor operation. In this work, anoxic and autotrophic reactor cultivation at 20 °C yielded an enriched microbial community in AnAOB, consisting for 75% of a member of the genus Brocadia. High-resolution kinetic data were obtained with online ammonium measurements and further processed with a newly developed Python data pipeline. The experimentally obtained AnAOB response showed complete inhibition until micro-aerobic conditions were reached again (<0.02 mg O2 L-1). After oxygen inhibition, AnAOB recovered gradually, with recovery times of 5-37 h to reach a steady-state activity, dependent on the perceived inhibition. The recovery immediately after inhibition was lowest when exposed to higher oxygen concentrations (range: 0.5-8 mg O2 L-1) with long contact times (range: 9-24 h). The experimental data did not fit well with a conventional 'instant recovery' Monod-type inhibition model. Yet, the fit greatly improved by incorporating a dynamic growth rate formula accurately describing gradual activity recovery. With the upgraded model, long-term kinetic simulations for partial nitritation/anammox (PN/A) with intermittent aeration showed a decrease in growth rate compared to the instant recovery mode. These results indicate that recovery of AnAOB after oxygen exposure was previously overlooked. It is recommended to account for this effect in the intensification of partial nitritation/anammox.}, }
@article {pmid30077104, year = {2018}, author = {Zhou, L and Xu, X and Xia, S}, title = {Effects of sulfate on simultaneous nitrate and selenate removal in a hydrogen-based membrane biofilm reactor for groundwater treatment: Performance and biofilm microbial ecology.}, journal = {Chemosphere}, volume = {211}, number = {}, pages = {254-260}, doi = {10.1016/j.chemosphere.2018.07.092}, pmid = {30077104}, issn = {1879-1298}, mesh = {Biofilms/*drug effects ; Bioreactors/*microbiology ; Groundwater/*chemistry ; Hydrogen/*chemistry ; Nitrates/*chemistry ; Selenic Acid/*chemistry ; Sulfates/*chemistry ; }, abstract = {Effects of sulfate on simultaneous nitrate and selenate removal in a hydrogen-based membrane biofilm reactor (MBfR) for groundwater treatment was identified with performance and biofilm microbial ecology. In whole operation, MBfR had almost 100% removal of nitration even with 50 mg mL-1 sulfate. Moreover, selenate degradation increased from 95% to approximate 100% with sulfate addition, indicating that sulfate had no obvious effects on nitrate degradation, and even partly promoted selenate removal. Short-term sulfate effect experiment further showed that Gibbs free energy of reduction (majority) and abiotic sulfide oxidation (especially between sulfate and selenate) contributed to degradable performance with sulfate. Microbial ecology showed that high percentage of Hydrogenophaga (≥75%) was one of the contributors for the stable and efficient nitrate degradation. Chemoheterotrophy (ratio>0.3) and dark hydrogen oxidation (ratio>0.3) were the majority of functional profile for biofilm in MBfR, and sulfate led to profiles of sulfate respiration and respiration of sulfur compounds in biofilm. Additionally, no special bacteria for selenate degradation was identified in biofilm microbial ecology, and selenate degradation was relied on Hydrogenophaga (75% of ecology percentage with sulfate addition) and Desulfovibrionaceae (4% of ecology percentage with sulfate addition). But with overloading sulfate, Desulfovibrionaceae was prior to sulfate degradation for energy supply and thus inhibited selenate removal.}, }
@article {pmid30076592, year = {2018}, author = {Nottingham, AT and Fierer, N and Turner, BL and Whitaker, J and Ostle, NJ and McNamara, NP and Bardgett, RD and Leff, JW and Salinas, N and Silman, MR and Kruuk, LEB and Meir, P}, title = {Microbes follow Humboldt: temperature drives plant and soil microbial diversity patterns from the Amazon to the Andes.}, journal = {Ecology}, volume = {}, number = {}, pages = {}, doi = {10.1002/ecy.2482}, pmid = {30076592}, issn = {0012-9658}, support = {NE/G018278/1//UK Natural Environment Research Council (NERC)/ ; NE/N006852/1//UK Natural Environment Research Council (NERC)/ ; DP170104091//Australian Research Council (ARC)/ ; FT1110100453//Australian Research Council (ARC)/ ; FP7-2012-329360//European Union Marie-Curie Fellowship/ ; }, abstract = {More than 200 years ago, Alexander von Humboldt reported that tropical plant species richness decreased with increasing elevation and decreasing temperature. Surprisingly, coordinated patterns in plant, bacterial, and fungal diversity on tropical mountains have not yet been observed, despite the central role of soil microorganisms in terrestrial biogeochemistry and ecology. We studied an Andean transect traversing 3.5 km in elevation to test whether the species diversity and composition of tropical forest plants, soil bacteria, and fungi follow similar biogeographical patterns with shared environmental drivers. We found coordinated changes with elevation in all three groups: species richness declined as elevation increased, and the compositional dissimilarity among communities increased with increased separation in elevation, although changes in plant diversity were larger than in bacteria and fungi. Temperature was the dominant driver of these diversity gradients, with weak influences of edaphic properties, including soil pH. The gradients in microbial diversity were strongly correlated with the activities of enzymes involved in organic matter cycling, and were accompanied by a transition in microbial traits towards slower-growing, oligotrophic taxa at higher elevations. We provide the first evidence of coordinated temperature-driven patterns in the diversity and distribution of three major biotic groups in tropical ecosystems: soil bacteria, fungi, and plants. These findings suggest that interrelated and fundamental patterns of plant and microbial communities with shared environmental drivers occur across landscape scales. These patterns are revealed where soil pH is relatively constant, and have implications for tropical forest communities under future climate change.}, }
@article {pmid30070653, year = {2018}, author = {Winkelmann, T and Smalla, K and Amelung, W and Baab, G and Grunewaldt-Stöcker, G and Kanfra, X and Meyhöfer, R and Reim, S and Schmitz, M and Vetterlein, D and Wrede, A and Zühlke, S and Grunewaldt, J and Weiß, S and Schloter, M}, title = {Apple Replant Disease: Causes and Mitigation Strategies.}, journal = {Current issues in molecular biology}, volume = {30}, number = {}, pages = {89-106}, doi = {10.21775/cimb.030.089}, pmid = {30070653}, issn = {1467-3045}, abstract = {After replanting apple (Malus domestica Borkh.) on the same site severe growth suppressions, and a decline in yield and fruit quality are observed in all apple producing areas worldwide. The causes of this complex phenomenon, called apple replant disease (ARD), are only poorly understood up to now which is in part due to inconsistencies in terms and methodologies. Therefore we suggest the following definition for ARD: ARD describes a harmfully disturbed physiological and morphological reaction of apple plants to soils that faced alterations in their (micro-) biome due to the previous apple cultures. The underlying interactions likely have multiple causes that extend beyond common analytical tools in microbial ecology. They are influenced by soil properties, faunal vectors, and trophic cascades, with genotype-specific effects on plant secondary metabolism, particularly phytoalexin biosynthesis. Yet, emerging tools allow to unravel the soil and rhizosphere (micro-) biome, to characterize alterations of habitat quality, and to decipher the plant reactions. Thereby, deep insights into the reactions taking place at the root rhizosphere interface will be gained. Counteractions are suggested, taking into account that culture management should emphasize on improving soil microbial and faunal diversity as well as habitat quality rather than focus on soil disinfection.}, }
@article {pmid30069710, year = {2018}, author = {McFrederick, QS and Rehan, SM}, title = {Wild Bee Pollen Usage and Microbial Communities Co-vary Across Landscapes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1232-y}, pmid = {30069710}, issn = {1432-184X}, support = {CA-R-ENT-5109-H//National Institute of Food and Agriculture/ ; NC1173//National Institute of Food and Agriculture/ ; 1638728//Directorate for Biological Sciences/ ; 1456296//Directorate for Biological Sciences/ ; 9659-15//National Geographic Society/ ; }, abstract = {Bees forage for pollen and nectar at flowers but simultaneously acquire pathogenic, commensal, and likely beneficial microbes from these same flowers. Characterizing pollen usage of wild bees is therefore crucial to their conservation yet remains a challenging task. To understand pollen usage across landscapes and how this affects microbial communities found in the pollen provisions collected from flowers, we studied the generalist small carpenter bee Ceratina australensis. We collected C. australensis nests from three different climatic zones across eastern and southern Australia. To characterize the plant, fungal, and bacterial composition of these pollen provisions, we used a metabarcoding and next-generation sequencing approach. We found that the species richness of plant types, fungi, and bacteria was highest in a subtropical zone compared to a temperate or a grassland zone. The composition of these communities also differentiated by zone, particularly in pollen composition and fungal communities. Moreover, pollen composition strongly correlated with fungal community composition, suggesting that variation in pollen usage across landscapes results in variation in microbial communities. While how these pollen usage and microbial community patterns affect bee health merits additional work, these data further our understanding of how flowering plant community composition affects not only the pollen usage of a generalist bee but also its associated microbial communities.}, }
@article {pmid30065892, year = {2018}, author = {Schlemper, TR and Dimitrov, MR and Silva Gutierrez, FAO and van Veen, JA and Silveira, APD and Kuramae, EE}, title = {Effect of Burkholderia tropica and Herbaspirillum frisingense strains on sorghum growth is plant genotype dependent.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5346}, doi = {10.7717/peerj.5346}, pmid = {30065892}, issn = {2167-8359}, abstract = {Sorghum is a multipurpose crop that is cultivated worldwide. Plant growth-promoting bacteria (PGPB) have important roles in enhancing sorghum biomass and nutrient uptake and suppressing plant pathogens. The aim of this research was to test the effects of the endophytic bacterial species Kosakonia radicincitans strain IAC/BECa 99, Enterobacter asburiae strain IAC/BECa 128, Pseudomonas fluorescens strain IAC/BECa 141, Burkholderia tropica strain IAC/BECa 135 and Herbaspirillum frisingense strain IAC/BECa 152 on the growth and root architecture of four sorghum cultivars (SRN-39, Shanqui-Red, BRS330, BRS509), with different uses and strigolactone profiles. We hypothesized that the different bacterial species would trigger different growth plant responses in different sorghum cultivars. Burkholderia tropica and H. frisingense significantly increased the plant biomass of cultivars SRN-39 and BRS330. Moreover, cultivar BRS330 inoculated with either strain displayed isolates significant decrease in average root diameter. This study shows that Burkholderia tropica strain IAC/BECa 135 and H. frisingense strain IAC/BECa 152 are promising PGPB strains for use as inocula for sustainable sorghum cultivation.}, }
@article {pmid30065353, year = {2018}, author = {Rahlff, J and Ribas-Ribas, M and Brown, SM and Mustaffa, NIH and Renz, J and Peck, MA and Bird, K and Cunliffe, M and Melkonian, K and Zappa, CJ}, title = {Blue pigmentation of neustonic copepods benefits exploitation of a prey-rich niche at the air-sea boundary.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {11510}, doi = {10.1038/s41598-018-29869-7}, pmid = {30065353}, issn = {2045-2322}, support = {GA336408//EC | European Research Council (ERC)/ ; GA336408//EC | European Research Council (ERC)/ ; GA336408//EC | European Research Council (ERC)/ ; }, abstract = {The sea-surface microlayer (SML) at the air-sea interface is a distinct, under-studied habitat compared to the subsurface and copepods, important components of ocean food webs, have developed key adaptations to exploit this niche. By using automated SML sampling, high-throughput sequencing and unmanned aerial vehicles, we report on the distribution and abundance of pontellid copepods in relation to the unique biophysicochemical signature of the SML. We found copepods in the SML even during high exposure to sun-derived ultraviolet radiation and their abundance was significantly correlated to increased algal biomass. We additionally investigated the significance of the pontellids' blue pigmentation and found that the reflectance peak of the blue pigment matched the water-leaving spectral radiance of the ocean surface. This feature could reduce high visibility at the air-sea boundary and potentially provide camouflage of copepods from their predators.}, }
@article {pmid30063956, year = {2018}, author = {Thompson, HF and Lesaulnier, C and Pelikan, C and Gutierrez, T}, title = {Visualisation of the obligate hydrocarbonoclastic bacteria Polycyclovorans algicola and Algiphilus aromaticivorans in co-cultures with micro-algae by CARD-FISH.}, journal = {Journal of microbiological methods}, volume = {152}, number = {}, pages = {73-79}, doi = {10.1016/j.mimet.2018.07.016}, pmid = {30063956}, issn = {1872-8359}, abstract = {Some studies have described the isolation and 16S rRNA gene sequence-based identification of hydrocarbon-degrading bacteria living associated with marine eukaryotic phytoplankton, and thus far the direct visual observation of these bacteria on micro-algal cell surfaces ('phycosphere') has not yet been reported. Here, we developed two new 16S rRNA-targeted oligonucleotide probes, PCY223 and ALGAR209, to respectively detect and enumerate the obligate hydrocarbonoclastic bacteria Polycyclovorans algicola and Algiphilus aromaticivorans by Catalyzed Reporter Deposition Fluorescence in situ Hybridization (CARD-FISH). To enhance the hybridization specificity with the ALGAR209 probe, a competitor probe was developed. These probes were tested and optimized using pure cultures, and then used in enrichment experiments with laboratory cultures of micro-algae exposed to phenanthrene, and with coastal water enriched with crude oil. Microscopic analysis revealed these bacteria are found in culture with the micro-algal cells, some of which were found attached to algal cells, and whose abundance increased after phenanthrene or crude oil enrichment. These new probes are a valuable tool for identifying and studying the ecology of P. algicola and A. aromaticivorans in laboratory and field samples of micro-algae, as well as opening new fields of research that could harness their ability to enhance the bioremediation of contaminated sites.}, }
@article {pmid30061909, year = {2018}, author = {Sobhy, IS and Baets, D and Goelen, T and Herrera-Malaver, B and Bosmans, L and Van den Ende, W and Verstrepen, KJ and Wäckers, F and Jacquemyn, H and Lievens, B}, title = {Sweet Scents: Nectar Specialist Yeasts Enhance Nectar Attraction of a Generalist Aphid Parasitoid Without Affecting Survival.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1009}, doi = {10.3389/fpls.2018.01009}, pmid = {30061909}, issn = {1664-462X}, abstract = {Floral nectar is commonly inhabited by microorganisms, mostly yeasts and bacteria, which can have a strong impact on nectar chemistry and scent. Yet, little is known about the effects of nectar microbes on the behavior and survival of insects belonging to the third trophic level such as parasitoids. Here, we used five nectar-inhabiting yeast species to test the hypothesis that yeast species that almost solely occur in nectar, and therefore substantially rely on floral visitors for dispersal, produce volatile compounds that enhance insect attraction without compromising insect life history parameters, such as survival. Experiments were performed using two nectar specialist yeasts (Metschnikowia gruessii and M. reukaufii) and three generalist species (Aureobasidium pullulans, Hanseniaspora uvarum, and Sporobolomyces roseus). Saccharomyces cerevisiae was included as a reference yeast. We compared olfactory responses of the generalist aphid parasitoid Aphidius ervi (Haliday) (Hymenoptera: Braconidae) when exposed to these microorganisms inoculated in synthetic nectar. Nectar-inhabiting yeasts had a significant impact on nectar chemistry and produced distinct volatile blends, some of which were attractive, while others were neutral or repellent. Among the different yeast species tested, the nectar specialists M. gruessii and M. reukaufii were the only species that produced a highly attractive nectar to parasitoid females, which simultaneously had no adverse effects on longevity and survival of adults. By contrast, parasitoids that fed on nectars fermented with the reference strain, A. pullulans, H. uvarum or S. roseus showed shortest longevity and lowest survival. Additionally, nectars fermented by A. pullulans or S. roseus were consumed significantly less, suggesting a lack of important nutrients or undesirable changes in the nectar chemical profiles. Altogether our results indicate that nectar-inhabiting yeasts play an important, but so far largely overlooked, role in plant-insect interactions by modulating the chemical composition of nectar, and may have important ecological consequences for plant pollination and biological control of herbivorous insects.}, }
@article {pmid30061657, year = {2018}, author = {Butler, S and O'Dwyer, JP}, title = {Stability criteria for complex microbial communities.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2970}, doi = {10.1038/s41467-018-05308-z}, pmid = {30061657}, issn = {2041-1723}, abstract = {Competition and mutualism are inevitable processes in microbial ecology, and a central question is which and how many taxa will persist in the face of these interactions. Ecological theory has demonstrated that when direct, pairwise interactions among a group of species are too numerous, or too strong, then the coexistence of these species will be unstable to any slight perturbation. Here, we refine and to some extent overturn that understanding, by considering explicitly the resources that microbes consume and produce. In contrast to more complex organisms, microbial cells consume primarily abiotic resources, and mutualistic interactions are often mediated through the mechanism of crossfeeding. We show that if microbes consume, but do not produce resources, then any positive equilibrium will always be stable to small perturbations. We go on to show that in the presence of crossfeeding, stability is no longer guaranteed. However, positive equilibria remain stable whenever mutualistic interactions are either sufficiently weak, or when all pairs of taxa reciprocate each other's assistance.}, }
@article {pmid30061355, year = {2018}, author = {van der Aart, LT and Spijksma, GK and Harms, A and Vollmer, W and Hankemeier, T and van Wezel, GP}, title = {High-Resolution Analysis of the Peptidoglycan Composition in Streptomyces coelicolor.}, journal = {Journal of bacteriology}, volume = {200}, number = {20}, pages = {}, doi = {10.1128/JB.00290-18}, pmid = {30061355}, issn = {1098-5530}, abstract = {The bacterial cell wall maintains cell shape and protects against bursting by turgor. A major constituent of the cell wall is peptidoglycan (PG), which is continuously modified to enable cell growth and differentiation through the concerted activity of biosynthetic and hydrolytic enzymes. Streptomycetes are Gram-positive bacteria with a complex multicellular life style alternating between mycelial growth and the formation of reproductive spores. This involves cell wall remodeling at apical sites of the hyphae during cell elongation and autolytic degradation of the vegetative mycelium during the onset of development and antibiotic production. Here, we show that there are distinct differences in the cross-linking and maturation of the PGs between exponentially growing vegetative hyphae and the aerial hyphae that undergo sporulation. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis identified over 80 different muropeptides, revealing that major PG hydrolysis takes place over the course of mycelial growth. Half of the dimers lacked one of the disaccharide units in transition-phase cells, most likely due to autolytic activity. The deacetylation of MurNAc to MurN was particularly pronounced in spores and strongly reduced in sporulation mutants with a deletion of bldD or whiG, suggesting that MurN is developmentally regulated. Altogether, our work highlights the dynamic and growth phase-dependent changes in the composition of the PG in StreptomycesIMPORTANCE Streptomycetes are bacteria with a complex lifestyle and are model organisms for bacterial multicellularity. From a single spore, a large multigenomic multicellular mycelium is formed, which differentiates to form spores. Programmed cell death is an important event during the onset of morphological differentiation. In this work, we provide new insights into the changes in the peptidoglycan composition and over time, highlighting changes over the course of development and between growing mycelia and spores. This revealed dynamic changes in the peptidoglycan when the mycelia aged, with extensive peptidoglycan hydrolysis and, in particular, an increase in the proportion of 3-3 cross-links. Additionally, we identified a muropeptide that accumulates predominantly in the spores and may provide clues toward spore development.}, }
@article {pmid30060765, year = {2018}, author = {Seal, BS and Drider, D and Oakley, BB and Brüssow, H and Bikard, D and Rich, JO and Miller, S and Devillard, E and Kwan, J and Bertin, G and Reeves, S and Swift, SM and Raicek, M and Gay, CG}, title = {Microbial-derived products as potential new antimicrobials.}, journal = {Veterinary research}, volume = {49}, number = {1}, pages = {66}, doi = {10.1186/s13567-018-0563-5}, pmid = {30060765}, issn = {1297-9716}, mesh = {Animal Diseases/prevention &amp; control ; *Animal Husbandry ; Animals ; Anti-Infective Agents/*analysis ; Bacteriocins ; Bacteriophages ; CRISPR-Cas Systems ; *Drug Discovery ; France ; Livestock ; }, abstract = {Due to the continuing global concerns involving antibiotic resistance, there is a need for scientific forums to assess advancements in the development of antimicrobials and their alternatives that might reduce development and spread of antibiotic resistance among bacterial pathogens. The objectives of the 2nd International Symposium on Alternatives to Antibiotics were to highlight promising research results and novel technologies that can provide alternatives to antibiotics for use in animal health and production, assess challenges associated with their authorization and commercialization for use, and provide actionable strategies to support their development. The session on microbial-derived products was directed at presenting novel technologies that included exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials, probiotics development via fecal microbiome transplants among monogastric production animals such as chickens and mining microbial sources such as bacteria or yeast to identify new antimicrobial compounds. Other research has included continuing development of antimicrobial peptides such as newly discovered bacteriocins as alternatives to antibiotics, use of bacteriophages accompanied by development of unique lytic proteins with specific cell-wall binding domains and novel approaches such as microbial-ecology guided discovery of anti-biofilm compounds discovered in marine environments. The symposium was held at the Headquarters of the World Organisation for Animal Health (OIE) in Paris, France during 12-15 December 2016.}, }
@article {pmid30058041, year = {2018}, author = {Farhat, A and Miladi, B and Hamdi, M and Bouallagui, H}, title = {Fermentative hydrogen and methane co-production from anaerobic co-digestion of organic wastes at high loading rate coupling continuously and sequencing batch digesters.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {28}, pages = {27945-27958}, doi = {10.1007/s11356-018-2796-2}, pmid = {30058041}, issn = {1614-7499}, abstract = {The anaerobic co-digestion of the most abundant organic wastes was investigated for enhancing biogas production rate and quality. The used feedstock was composed of fruit and vegetable waste (FVW), waste-activated sludge (WAS), olive mill wastewater (OMW) and cattle manure (CM). A considerable methane yield of 340 L/kg volatile solid (VS) inlet was obtained using single-stage anaerobic sequencing batch reactors (ASBRs). However, VS biodegradation becomes difficult at high organic loading rate (OLR). Therefore, a continuously stirred tank reactor (CSTR) was integrated to the ASBR for waste pre-digestion. The dark fermentation leads to the improvement of organic matter solubilisation and bio-hydrogen productivity, reaching 0.73 L/L/day (H2 content of 49.8%) when pH decreased to 5.8. Therefore, methane productivity increased from 0.6 to 1.86 L/L/day in the methanogenic reactor with a better VS biodegradation (91.1%) at high OLR. Furthermore, the bio-hythane production was performed through a controlled biogas recirculation from the dark fermentation stage into the methaniser to reach 842.4 L/kg VS inlet. The produced biogas was composed of 8% H2, 28.5% CO2 and 63.5% CH4. Therefore, two-stage anaerobic co-digestion with coupled CH4 and H2 recuperation may be an important contribution for pollution control and high-rate bioenergy recovery (21.1 kJ/g VS inlet) from organic wastes.}, }
@article {pmid30056833, year = {2018}, author = {Mercer, F and Johnson, PJ}, title = {Trichomonas vaginalis: Pathogenesis, Symbiont Interactions, and Host Cell Immune Responses.}, journal = {Trends in parasitology}, volume = {34}, number = {8}, pages = {683-693}, doi = {10.1016/j.pt.2018.05.006}, pmid = {30056833}, issn = {1471-5007}, abstract = {The parasite Trichomonas vaginalis (Tv) causes a highly prevalent sexually transmitted infection. As an extracellular pathogen, the parasite mediates adherence to epithelial cells to colonize the human host. In addition, the parasite interfaces with the host immune system and the vaginal microbiota. Modes of Tv pathogenesis include damage to host tissue mediated by parasite killing of host cells, disruption of steady-state vaginal microbial ecology, and eliciting inflammation by activating the host immune response. Recent Tv research has uncovered new players that contribute to multifactorial mechanisms of host-parasite adherence and killing, and has examined the relationship between Tv and vaginal bacteria. Mechanisms that may lead to parasite recognition and killing, or the evasion of host immune cells, have also been revealed.}, }
@article {pmid30056235, year = {2019}, author = {Lupatini, M and Korthals, GW and Roesch, LFW and Kuramae, EE}, title = {Long-term farming systems modulate multi-trophic responses.}, journal = {The Science of the total environment}, volume = {646}, number = {}, pages = {480-490}, doi = {10.1016/j.scitotenv.2018.07.323}, pmid = {30056235}, issn = {1879-1026}, abstract = {Soil microbiome and multi-trophic relationships are essential for the stability and functioning of agroecosystems. However, little is known about how farming systems and alternative methods for controlling plant pathogens modulate microbial communities, soil mesofauna and plant productivity. In this study, we assessed the composition of eukaryotic microbial groups using a high-throughput sequencing approach (18S rRNA gene marker), the populations of parasitic and free-living nematodes, plant productivity and their inter-relationships in long-term conventional and organic farming systems. The diversity of the fungal community increased in the organic farming system compared to the conventional farming system, whereas the diversity of the protist community was similar between the two farming systems. Compared to conventional farming, organic farming increased the population of free-living nematodes and suppressed plant parasitic nematodes belonging to Meloidogynidae and Pratylenchidae. Fungal diversity and community structure appeared to be related to nematode suppression in the system receiving organic fertilizer, which was characterized by component microbial groups known to be involved in the suppression of soil pathogens. Unraveling the microbiome and multi-trophic interactions in different farming systems may permit the management of the soil environment toward more sustainable control of plant pathogens.}, }
@article {pmid30056005, year = {2018}, author = {Bankevich, A and Pevzner, PA}, title = {Joint Analysis of Long and Short Reads Enables Accurate Estimates of Microbiome Complexity.}, journal = {Cell systems}, volume = {7}, number = {2}, pages = {192-200.e3}, doi = {10.1016/j.cels.2018.06.009}, pmid = {30056005}, issn = {2405-4712}, abstract = {Reduced microbiome diversity has been linked to several diseases. However, estimating the diversity of bacterial communities-the number and the total length of distinct genomes within a metagenome-remains an open problem in microbial ecology. Here, we describe an algorithm for estimating the microbial diversity in a metagenomic sample based on a joint analysis of short and long reads. Unlike previous approaches, the algorithm does not make any assumptions on the distribution of the frequencies of genomes within a metagenome (as in parametric methods) and does not require a large database that covers the total diversity (as in non-parametric methods). We estimate that genomes comprising a human gut metagenome have total length varying from 1.3 to 3.5 billion nucleotides, with genomes responsible for 50% of total abundance having total length varying from only 25 to 61 million nucleotides. In contrast, genomes comprising an aquifer sediment metagenome have more than two orders of magnitude larger total length (≈840 billion nucleotides).}, }
@article {pmid30055451, year = {2018}, author = {Mayta-Apaza, AC and Pottgen, E and De Bodt, J and Papp, N and Marasini, D and Howard, L and Abranko, L and Van de Wiele, T and Lee, SO and Carbonero, F}, title = {Impact of tart cherries polyphenols on the human gut microbiota and phenolic metabolites in vitro and in vivo.}, journal = {The Journal of nutritional biochemistry}, volume = {59}, number = {}, pages = {160-172}, doi = {10.1016/j.jnutbio.2018.04.001}, pmid = {30055451}, issn = {1873-4847}, abstract = {Tart cherries have been reported to exert potential health benefits attributed to their specific and abundant polyphenol content. However, there is a need to study the impact and fate of tart cherries polyphenols in the gut microbiota. Here, tart cherries, pure polyphenols (and apricots) were submitted to in vitro bacterial fermentation assays and assessed through 16S rRNA gene sequence sequencing and metabolomics. A short-term (5 days, 8 oz. daily) human dietary intervention study was also conducted for microbiota analyses. Tart cherry concentrate juices were found to contain expected abundances of anthocyanins (cyanidin-glycosylrutinoside) and flavonoids (quercetin-rutinoside) and high amounts of chlorogenic and neochlorogenic acids. Targeted metabolomics confirmed that gut microbes were able to degrade those polyphenols mainly to 4-hydroxyphenylpropionic acids and to lower amounts of epicatechin and 4-hydroxybenzoic acids. Tart cherries were found to induce a large increase of Bacteroides in vitro, likely due to the input of polysaccharides, but prebiotic effect was also suggested by Bifidobacterium increase from chlorogenic acid. In the human study, two distinct and inverse responses to tart cherry consumption were associated with initial levels of Bacteroides. High-Bacteroides individuals responded with a decrease in Bacteroides and Bifidobacterium, and an increase of Lachnospiraceae, Ruminococcus and Collinsella. Low-Bacteroides individuals responded with an increase in Bacteroides or Prevotella and Bifidobacterium, and a decrease of Lachnospiraceae, Ruminococcus and Collinsella. These data confirm that gut microbiota metabolism, in particular the potential existence of different metabotypes, needs to be considered in studies attempting to link tart cherries consumption and health.}, }
@article {pmid30055017, year = {2018}, author = {Lemay, MA and Martone, PT and Hind, KR and Lindstrom, SC and Wegener Parfrey, L}, title = {Alternate life history phases of a common seaweed have distinct microbial surface communities.}, journal = {Molecular ecology}, volume = {27}, number = {17}, pages = {3555-3568}, doi = {10.1111/mec.14815}, pmid = {30055017}, issn = {1365-294X}, abstract = {Macroalgal life histories are complex, often involving the alternation of distinct free-living life history phases that differ in morphology, longevity and ploidy. The surfaces of marine macroalgae support diverse microbial biofilms, yet the degree of microbial variation between alternate phases is unknown. We quantified bacterial (16S rRNA gene) and microeukaryote (18S rRNA gene) communities on the surface of the common intertidal seaweed, Mastocarpus spp., which alternates between gametophyte (foliose, haploid) and sporophyte (encrusting, diploid) life history phases. A large portion (97%) of bacterial taxa on the surface Mastocarpus was also present in samples from the environment, indicating that macroalgal surface communities are largely assembled from the surrounding seawater. Still, changes in the relative abundance of bacterial taxa result in significantly different communities on alternate Mastocarpus life history phases, rocky substrate and seawater at all intertidal elevations. For microeukaryote assemblages, only high intertidal samples had significant differences between life history phases although sporophytes were not different from the rocky substrate at this elevation; gametophytes and sporophytes did not differ in microeukaryote communities in the mid and low zones. By sequencing three host genes, we identified three cryptic species of Mastocarpus in our data set, which co-occur in the mid-to-low intertidal zone. In these samples, M. alaskensis sporophytes harboured distinct bacterial communities compared to M. agardhii and M. intermedius sporophytes, which were not distinguishable. Conversely, microeukaryote communities did not differ among species.}, }
@article {pmid30054367, year = {2018}, author = {Endo, A and Maeno, S and Tanizawa, Y and Kneifel, W and Arita, M and Dicks, L and Salminen, S}, title = {Fructophilic Lactic Acid Bacteria, a Unique Group of Fructose-Fermenting Microbes.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {19}, pages = {}, doi = {10.1128/AEM.01290-18}, pmid = {30054367}, issn = {1098-5336}, abstract = {Fructophilic lactic acid bacteria (FLAB) are a recently discovered group, consisting of a few Fructobacillus and Lactobacillus species. Because of their unique characteristics, including poor growth on glucose and preference of oxygen, they are regarded as &quot;unconventional&quot; lactic acid bacteria (LAB). Their unusual growth characteristics are due to an incomplete gene encoding a bifunctional alcohol/acetaldehyde dehydrogenase (adhE). This results in the imbalance of NAD/NADH and the requirement of additional electron acceptors to metabolize glucose. Oxygen, fructose, and pyruvate are used as electron acceptors. FLAB have significantly fewer genes for carbohydrate metabolism than other LAB, especially due to the lack of complete phosphotransferase system (PTS) transporters. They have been isolated from fructose-rich environments, including flowers, fruits, fermented fruits, and the guts of insects that feed on plants rich in fructose, and are separated into two groups on the basis of their habitats. One group is associated with flowers, grapes, wines, and insects, and the second group is associated with ripe fruits and fruit fermentations. Species associated with insects may play a role in the health of their host and are regarded as suitable vectors for paratransgenesis in honey bees. Besides their impact on insect health, FLAB may be promising candidates for the promotion of human health. Further studies are required to explore their beneficial properties in animals and humans and their applications in the food industry.}, }
@article {pmid30054363, year = {2018}, author = {Philips, J and Van den Driessche, N and De Paepe, K and Prévoteau, A and Gralnick, JA and Arends, JBA and Rabaey, K}, title = {A Novel Shewanella Isolate Enhances Corrosion by Using Metallic Iron as the Electron Donor with Fumarate as the Electron Acceptor.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {20}, pages = {}, doi = {10.1128/AEM.01154-18}, pmid = {30054363}, issn = {1098-5336}, abstract = {The involvement of Shewanella spp. in biocorrosion is often attributed to their Fe(III)-reducing properties, but they could also affect corrosion by using metallic iron as an electron donor. Previously, we isolated Shewanella strain 4t3-1-2LB from an acetogenic community enriched with Fe(0) as the sole electron donor. Here, we investigated its use of Fe(0) as an electron donor with fumarate as an electron acceptor and explored its corrosion-enhancing mechanism. Without Fe(0), strain 4t3-1-2LB fermented fumarate to succinate and CO2, as was shown by the reaction stoichiometry and pH. With Fe(0), strain 4t3-1-2LB completely reduced fumarate to succinate and increased the Fe(0) corrosion rate (7.0 ± 0.6)-fold in comparison to that of abiotic controls (based on the succinate-versus-abiotic hydrogen formation rate). Fumarate reduction by strain 4t3-1-2LB was, at least in part, supported by chemical hydrogen formation on Fe(0). Filter-sterilized spent medium increased the hydrogen generation rate only 1.5-fold, and thus extracellular hydrogenase enzymes appear to be insufficient to explain the enhanced corrosion rate. Electrochemical measurements suggested that strain 4t3-1-2LB did not excrete dissolved redox mediators. Exchanging the medium and scanning electron microscopy (SEM) imaging indicated that cells were attached to Fe(0). It is possible that strain 4t3-1-2LB used a direct mechanism to withdraw electrons from Fe(0) or favored chemical hydrogen formation on Fe(0) through maintaining low hydrogen concentrations. In coculture with an Acetobacterium strain, strain 4t3-1-2LB did not enhance acetogenesis from Fe(0). This work describes a strong corrosion enhancement by a Shewanella strain through its use of Fe(0) as an electron donor and provides insights into its corrosion-enhancing mechanism.IMPORTANCEShewanella spp. are frequently found on corroded metal structures. Their role in microbial influenced corrosion has been attributed mainly to their Fe(III)-reducing properties and, therefore, has been studied with the addition of an electron donor (lactate). Shewanella spp., however, can also use solid electron donors, such as cathodes and potentially Fe(0). In this work, we show that the electron acceptor fumarate supported the use of Fe(0) as the electron donor by Shewanella strain 4t3-1-2LB, which caused a (7.0 ± 0.6)-fold increase of the corrosion rate. The corrosion-enhancing mechanism likely involved cell surface-associated components in direct contact with the Fe(0) surface or maintenance of low hydrogen levels by attached cells, thereby favoring chemical hydrogen formation by Fe(0). This work sheds new light on the role of Shewanella spp. in biocorrosion, while the insights into the corrosion-enhancing mechanism contribute to the understanding of extracellular electron uptake processes.}, }
@article {pmid30054356, year = {2018}, author = {Peng, M and Salaheen, S and Buchanan, RL and Biswas, D}, title = {Alterations of Salmonella enterica Serovar Typhimurium Antibiotic Resistance under Environmental Pressure.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {19}, pages = {}, doi = {10.1128/AEM.01173-18}, pmid = {30054356}, issn = {1098-5336}, abstract = {Microbial horizontal gene transfer is a continuous process that shapes bacterial genomic adaptation to the environment and the composition of concurrent microbial ecology. This includes the potential impact of synthetic antibiotic utilization in farm animal production on overall antibiotic resistance issues; however, the mechanisms behind the evolution of microbial communities are not fully understood. We explored potential mechanisms by experimentally examining the relatedness of phylogenetic inference between multidrug-resistant Salmonella enterica serovar Typhimurium isolates and pathogenic Salmonella Typhimurium strains based on genome-wide single-nucleotide polymorphism (SNP) comparisons. Antibiotic-resistant S Typhimurium isolates in a simulated farm environment barely lost their resistance, whereas sensitive S Typhimurium isolates in soils gradually acquired higher tetracycline resistance under antibiotic pressure and manipulated differential expression of antibiotic-resistant genes. The expeditious development of antibiotic resistance and the ensuing genetic alterations in antimicrobial resistance genes in S Typhimurium warrant effective actions to control the dissemination of Salmonella antibiotic resistance.IMPORTANCE Antibiotic resistance is attributed to the misuse or overuse of antibiotics in agriculture, and antibiotic resistance genes can also be transferred to bacteria under environmental stress. In this study, we report a unidirectional alteration in antibiotic resistance from susceptibility to increased resistance. Highly sensitive Salmonella enterica serovar Typhimurium isolates from organic farm systems quickly acquired tetracycline resistance under antibiotic pressure in simulated farm soil environments within 2 weeks, with expression of antibiotic resistance-related genes that was significantly upregulated. Conversely, originally resistant S Typhimurium isolates from conventional farm systems lost little of their resistance when transferred to environments without antibiotic pressure. Additionally, multidrug-resistant S Typhimurium isolates genetically shared relevancy with pathogenic S Typhimurium isolates, whereas susceptible isolates clustered with nonpathogenic strains. These results provide detailed discussion and explanation about the genetic alterations and simultaneous acquisition of antibiotic resistance in S Typhimurium in agricultural environments.}, }
@article {pmid30052926, year = {2018}, author = {Stedtfeld, RD and Guo, X and Stedtfeld, TM and Sheng, H and Williams, MR and Hauschild, K and Gunturu, S and Tift, L and Wang, F and Howe, A and Chai, B and Yin, D and Cole, JR and Tiedje, JM and Hashsham, SA}, title = {Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {9}, pages = {}, doi = {10.1093/femsec/fiy130}, pmid = {30052926}, issn = {1574-6941}, abstract = {The high-throughput antibiotic resistance gene (ARG) qPCR array, initially published in 2012, is increasingly used to quantify resistance and mobile determinants in environmental matrices. Continued utility of the array; however, necessitates improvements such as removing or redesigning questionable primer sets, updating targeted genes and coverage of available sequences. Towards this goal, a new primer design tool (EcoFunPrimer) was used to aid in identification of conserved regions of diverse genes. The total number of assays used for diverse genes was reduced from 91 old primer sets to 52 new primer sets, with only a 10% loss in sequence coverage. While the old and new array both contain 384 primer sets, a reduction in old primer sets permitted 147 additional ARGs and mobile genetic elements to be targeted. Results of validating the updated array with a mock community of strains resulted in over 98% of tested instances incurring true positive/negative calls. Common queries related to sensitivity, quantification and conventional data analysis (e.g. Ct cutoff value, and estimated genomic copies without standard curves) were also explored. A combined list of new and previously used primer sets is provided with a recommended set based on redesign of primer sets and results of validation.}, }
@article {pmid30051940, year = {2018}, author = {Averill, C and Dietze, MC and Bhatnagar, JM}, title = {Continental-scale nitrogen pollution is shifting forest mycorrhizal associations and soil carbon stocks.}, journal = {Global change biology}, volume = {24}, number = {10}, pages = {4544-4553}, doi = {10.1111/gcb.14368}, pmid = {30051940}, issn = {1365-2486}, support = {//National Oceanic and Atmospheric Administration/ ; 1638577//National Science Foundation/ ; //Peter Paul Professorship/ ; }, abstract = {Most tree roots on Earth form a symbiosis with either ecto- or arbuscular mycorrhizal fungi. Nitrogen fertilization is hypothesized to favor arbuscular mycorrhizal tree species at the expense of ectomycorrhizal species due to differences in fungal nitrogen acquisition strategies, and this may alter soil carbon balance, as differences in forest mycorrhizal associations are linked to differences in soil carbon pools. Combining nitrogen deposition data with continental-scale US forest data, we show that nitrogen pollution is spatially associated with a decline in ectomycorrhizal vs. arbuscular mycorrhizal trees. Furthermore, nitrogen deposition has contrasting effects on arbuscular vs. ectomycorrhizal demographic processes, favoring arbuscular mycorrhizal trees at the expense of ectomycorrhizal trees, and is spatially correlated with reduced soil carbon stocks. This implies future changes in nitrogen deposition may alter the capacity of forests to sequester carbon and offset climate change via interactions with the forest microbiome.}, }
@article {pmid30051650, year = {2018}, author = {Müller, AL and Pelikan, C and de Rezende, JR and Wasmund, K and Putz, M and Glombitza, C and Kjeldsen, KU and Jørgensen, BB and Loy, A}, title = {Bacterial interactions during sequential degradation of cyanobacterial necromass in a sulfidic arctic marine sediment.}, journal = {Environmental microbiology}, volume = {20}, number = {8}, pages = {2927-2940}, doi = {10.1111/1462-2920.14297}, pmid = {30051650}, issn = {1462-2920}, support = {FWF, P29426-B29 to KW//Austrian Science Fund/ ; P25111-B22 to AL//Austrian Science Fund/ ; DSS1431//CARD-FISH probe/ ; }, abstract = {Seafloor microorganisms impact global carbon cycling by mineralizing vast quantities of organic matter (OM) from pelagic primary production, which is predicted to increase in the Arctic because of diminishing sea ice cover. We studied microbial interspecies-carbon-flow during anaerobic OM degradation in arctic marine sediment using stable isotope probing. We supplemented sediment incubations with 13 C-labeled cyanobacterial necromass (spirulina), mimicking fresh OM input, or acetate, an important OM degradation intermediate and monitored sulfate reduction rates and concentrations of volatile fatty acids (VFAs) during substrate degradation. Sequential 16S rRNA gene and transcript amplicon sequencing and fluorescence in situ hybridization combined with Raman microspectroscopy revealed that only few bacterial species were the main degraders of 13 C-spirulina necromass. Psychrilyobacter, Psychromonas, Marinifilum, Colwellia, Marinilabiaceae and Clostridiales species were likely involved in the primary hydrolysis and fermentation of spirulina. VFAs, mainly acetate, produced from spirulina degradation were mineralized by sulfate-reducing bacteria and an Arcobacter species. Cellular activity of Desulfobacteraceae and Desulfobulbaceae species during acetoclastic sulfate reduction was largely decoupled from relative 16S rRNA gene abundance shifts. Our findings provide new insights into the identities and physiological constraints that determine the population dynamics of key microorganisms during complex OM degradation in arctic marine sediments.© 2018 Society for Applied Microbiology and John Wiley &amp; Sons Ltd.}, }
@article {pmid30051173, year = {2018}, author = {Weinisch, L and Kirchner, I and Grimm, M and Kühner, S and Pierik, AJ and Rosselló-Móra, R and Filker, S}, title = {Glycine Betaine and Ectoine Are the Major Compatible Solutes Used by Four Different Halophilic Heterotrophic Ciliates.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1230-0}, pmid = {30051173}, issn = {1432-184X}, abstract = {One decisive factor controlling the distribution of organisms in their natural habitats is the cellular response to environmental factors. Compared to prokaryotes, our knowledge about salt adaptation strategies of microbial eukaryotes is very limited. We, here, used a recently introduced approach (implementing proton nuclear magnetic resonance spectroscopy) to investigate the presence of compatible solutes in halophilic, heterotrophic ciliates. Therefore, we isolated four ciliates from solar salterns, which were identified as Cyclidium glaucoma, Euplotes sp., Fabrea salina, and Pseudocohnilembus persalinus based on their 18S rRNA gene signatures and electron microscopy. The results of 1H-NMR spectroscopy revealed that all four ciliates employ the &quot;low-salt-in&quot; strategy by accumulating glycine betaine and ectoine as main osmoprotectants. We recorded a linear increase of these compatible solutes with increasing salinity of the external medium. Ectoine in particular stands out as its use as compatible solute was thought to be exclusive to prokaryotes. However, our findings and those recently made on two other heterotroph species call for a re-evaluation of this notion. The observation of varying relative proportions of compatible solutes within the four ciliates points to slight differences in haloadaptive strategies by regulatory action of the ciliates. Based on this finding, we provide an explanatory hypothesis for the distribution of protistan diversity along salinity gradients.}, }
@article {pmid30050987, year = {2018}, author = {Zumstein, MT and Schintlmeister, A and Nelson, TF and Baumgartner, R and Woebken, D and Wagner, M and Kohler, HE and McNeill, K and Sander, M}, title = {Biodegradation of synthetic polymers in soils: Tracking carbon into CO2 and microbial biomass.}, journal = {Science advances}, volume = {4}, number = {7}, pages = {eaas9024}, doi = {10.1126/sciadv.aas9024}, pmid = {30050987}, issn = {2375-2548}, abstract = {Plastic materials are widely used in agricultural applications to achieve food security for the growing world population. The use of biodegradable instead of nonbiodegradable polymers in single-use agricultural applications, including plastic mulching, promises to reduce plastic accumulation in the environment. We present a novel approach that allows tracking of carbon from biodegradable polymers into CO2 and microbial biomass. The approach is based on 13C-labeled polymers and on isotope-specific analytical methods, including nanoscale secondary ion mass spectrometry (NanoSIMS). Our results unequivocally demonstrate the biodegradability of poly(butylene adipate-co-terephthalate) (PBAT), an important polyester used in agriculture, in soil. Carbon from each monomer unit of PBAT was used by soil microorganisms, including filamentous fungi, to gain energy and to form biomass. This work advances both our conceptual understanding of polymer biodegradation and the methodological capabilities to assess this process in natural and engineered environments.}, }
@article {pmid30048866, year = {2018}, author = {Beganskas, S and Gorski, G and Weathers, T and Fisher, AT and Schmidt, C and Saltikov, C and Redford, K and Stoneburner, B and Harmon, R and Weir, W}, title = {A horizontal permeable reactive barrier stimulates nitrate removal and shifts microbial ecology during rapid infiltration for managed recharge.}, journal = {Water research}, volume = {144}, number = {}, pages = {274-284}, doi = {10.1016/j.watres.2018.07.039}, pmid = {30048866}, issn = {1879-2448}, abstract = {We present results from field experiments linking hydrology, geochemistry, and microbiology during infiltration at a field site that is used for managed aquifer recharge (MAR). These experiments measured how a horizontal permeable reactive barrier (PRB) made of woodchips impacted subsurface nitrate removal and microbial ecology. Concentrations of dissolved organic carbon consistently increased in infiltrating water below the PRB, but not in un-amended native soil. The average nitrate removal rate in soils below the PRB was 1.5 g/m2/day NO3-N, despite rapid infiltration (up to 1.9 m/d) and a short fluid residence time within the woodchips (≤6 h). In contrast, 0.09 g/m2/day NO3-N was removed on average in native soil. Residual nitrate in infiltrating water below the PRB was enriched in δ15N and δ18O, with low and variable isotopic enrichment factors that are consistent with denitrification during rapid infiltration. Many putative denitrifying bacteria were significantly enhanced in the soil below a PRB; Methylotenera mobilis and genera Microbacterium, Polaromonas, and Novosphingobium had log2 fold-changes of +4.9, +5.6, +7.2, and +11.8, respectively. These bacteria were present before infiltration and were not enhanced in native soil. It appears that the woodchip PRB contributed to favorable conditions in the underlying soil for enhanced nitrate removal, quantitatively shifting soil microbial ecology. These results suggest that using a horizontal PRB could improve water quality during rapid infiltration for MAR.}, }
@article {pmid30047254, year = {2018}, author = {Biagi, E and D'Amico, F and Soverini, M and Angelini, V and Barone, M and Turroni, S and Rampelli, S and Pari, S and Brigidi, P and Candela, M}, title = {Faecal bacterial communities from Mediterranean loggerhead sea turtles (Caretta caretta).}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.12683}, pmid = {30047254}, issn = {1758-2229}, support = {LIFE12 NAT/IT/000937//LIFE-EU project TartaLife/ ; }, abstract = {The loggerhead sea turtle (Caretta caretta) is the most widespread sea turtle species in the Mediterranean Sea and a relevant pollution 'flagship species'. Here, we profiled the faecal microbiota from 29 C. caretta from a rescue centre, and explored the impact of several variables linked to both the animal itself and the environment (i.e., tank water ecosystem). We show that loggerhead turtles share more gut microbiota features with carnivorous marine mammals, than with phylogenetically close, but herbivorous, turtles, as a confirmation of the gut microbiota adaptive function to diet and environment. We also highlight a relation between the microbiota composition and the size (and consequently the age) of the turtles. Finally, we point out that the gut microbiota of sea turtles shows unexpectedly low exchange of microbes with the aquatic environment and is resilient to the stress induced by short-time captivity.}, }
@article {pmid30047191, year = {2018}, author = {Ma, X and Coleman, ML and Waldbauer, JR}, title = {Distinct molecular signatures in dissolved organic matter produced by viral lysis of marine cyanobacteria.}, journal = {Environmental microbiology}, volume = {20}, number = {8}, pages = {3001-3011}, doi = {10.1111/1462-2920.14338}, pmid = {30047191}, issn = {1462-2920}, support = {3305//Gordon and Betty Moore Foundation/ ; }, abstract = {Dissolved organic matter (DOM) plays a central role in the microbial ecology and biogeochemistry of aquatic environments, yet little is known about how the mechanism of DOM release from its ultimate source, primary producer biomass, affects the molecular composition of the inputs to the dissolved pool. Here we used a model marine phytoplankton, the picocyanobacterium Synechococcus WH7803, to compare the composition of DOM released by three mechanisms: exudation, mechanical cell lysis and infection by the lytic phage S-SM1. A broad, untargeted analytical approach reveals the complexity of this freshly sourced DOM, and comparative analysis between DOM produced by the different mechanisms suggests that exudation and viral lysis are sources of unsaturated, oxygen-rich and possibly novel biomolecules. Furthermore, viral lysis of WH7803 by S-SM1 releases abundant peptides derived from specific proteolysis of the major light-harvesting protein phycoerythrin, raising the possibility that phage infection of these abundant cyanobacteria could be a significant source of high molecular weight dissolved organic nitrogen compounds.}, }
@article {pmid30046860, year = {2018}, author = {Zhang, H and Feng, J and Chen, S and Zhao, Z and Li, B and Wang, Y and Jia, J and Li, S and Wang, Y and Yan, M and Lu, K and Hao, H}, title = {Geographical Patterns of nirS Gene Abundance and nirS-Type Denitrifying Bacterial Community Associated with Activated Sludge from Different Wastewater Treatment Plants.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1236-7}, pmid = {30046860}, issn = {1432-184X}, support = {2016YFC0400706//the National Key Research and Development Program of China/ ; CSC No. 201708610028//Foundation of China Scholarship Council/ ; 2018KW-011//International Science and Technology Cooperation Program/ ; }, abstract = {Denitrifying bacteria is a driver of nitrogen removal process in wastewater treatment ecosystem. However, the geographical characteristics of denitrifying bacterial communities associated with activated sludge from diverse wastewater treatment plants (WWTPs) are still unclear. Here, quantitative PCR and next-generation sequencing of the nirS gene were applied to characterize the abundance and denitrifying bacterial communities from 18 geographically distributed WWTPs. The results showed that the nirS abundance ranged from 4.6 × 102 to 2.4 × 103 copies per ng DNA, while nirS-type denitrifying bacterial populations were diverse and distinct from activated sludge communities. Among WWTPs, total nitrogen removal efficiencies varied from 25.8 to 84%, which was positively correlated with diversity indices, whereas abundance-based coverage estimator index decreased with an increase in latitude. The dominant phyla across all samples were proteobacteria, accounting for 46.23% (ranging from 17.98 to 87.07%) of the sequences. Eight of the 22 genera detected were dominant: Thauera sp., Alicycliphilus sp., and Pseudomonas sp., etc. Based on network analysis, the coexistence and interaction between dominant genera may be vital for regulating the nitrogen and carbon removal behaviors. Multivariate statistical analysis revealed that both geographic location and wastewater factors concurrently govern the distribution patterns of nirS-type denitrifying bacterial community harbored in WWTPs. Taking together, these results from the present study provide novel insights into the nirS gene abundance and nirS-type denitrifying bacterial community composition in geographically distributed WWTPs. Moreover, the knowledge gained will improve the operation and management of WWTPs for nitrogen removal.}, }
@article {pmid30045954, year = {2018}, author = {Van den Bergh, B and Swings, T and Fauvart, M and Michiels, J}, title = {Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {82}, number = {3}, pages = {}, doi = {10.1128/MMBR.00008-18}, pmid = {30045954}, issn = {1098-5557}, abstract = {In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.}, }
@article {pmid30043185, year = {2018}, author = {Mörkl, S and Lackner, S and Meinitzer, A and Mangge, H and Lehofer, M and Halwachs, B and Gorkiewicz, G and Kashofer, K and Painold, A and Holl, AK and Bengesser, SA and Müller, W and Holzer, P and Holasek, SJ}, title = {Gut microbiota, dietary intakes and intestinal permeability reflected by serum zonulin in women.}, journal = {European journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00394-018-1784-0}, pmid = {30043185}, issn = {1436-6215}, support = {A16 - 028180/2009/0143//Stadt Graz/ ; }, abstract = {PURPOSE: Increased gut permeability causes the trespass of antigens into the blood stream which leads to inflammation. Gut permeability reflected by serum zonulin and diversity of the gut microbiome were investigated in this cross-sectional study involving female study participants with different activity and BMI levels.<br><br>METHODS: 102 women were included (BMI range 13.24-46.89 kg m-2): Anorexia nervosa patients (n = 17), athletes (n = 20), normal weight (n = 25), overweight (n = 21) and obese women (n = 19). DNA was extracted from stool samples and subjected to 16S rRNA gene analysis (V1-V2). Quantitative Insights Into Microbial Ecology (QIIME) was used to analyze data. Zonulin was measured with ELISA. Nutrient intake was assessed by repeated 24-h dietary recalls. We used the median of serum zonulin concentration to divide our participants into a &quot;high-zonulin&quot; (> 53.64 ng/ml) and &quot;low-zonulin&quot; (< 53.64 ng/ml) group.<br><br>RESULTS: The alpha-diversity (Shannon Index, Simpson Index, equitability) and beta-diversity (unweighted and weighted UniFrac distances) of the gut microbiome were not significantly different between the groups. Zonulin concentrations correlated significantly with total calorie-, protein-, carbohydrate-, sodium- and vitamin B12 intake. Linear discriminant analysis effect size (LEfSe) identified Ruminococcaceae (LDA = 4.163, p = 0.003) and Faecalibacterium (LDA = 4.151, p = 0.0002) as significantly more abundant in the low zonulin group.<br><br>CONCLUSION: Butyrate-producing gut bacteria such as Faecalibacteria could decrease gut permeability and lower inflammation. The diversity of the gut microbiota in women does not seem to be correlated with the serum zonulin concentration. Further interventional studies are needed to investigate gut mucosal permeability and the gut microbiome in the context of dietary factors.}, }
@article {pmid30042197, year = {2018}, author = {Murray, AK and Zhang, L and Yin, X and Zhang, T and Buckling, A and Snape, J and Gaze, WH}, title = {Novel Insights into Selection for Antibiotic Resistance in Complex Microbial Communities.}, journal = {mBio}, volume = {9}, number = {4}, pages = {}, doi = {10.1128/mBio.00969-18}, pmid = {30042197}, issn = {2150-7511}, abstract = {Recent research has demonstrated that selection for antibiotic resistance occurs at very low antibiotic concentrations in single-species experiments, but the relevance of these findings when species are embedded in complex microbial communities is unclear. We show that the strength of selection for naturally occurring resistance alleles in a complex community remains constant from low subinhibitory to above clinically relevant concentrations. Selection increases with antibiotic concentration before reaching a plateau where selection remains constant over a 2-order-magnitude concentration range. This is likely to be due to cross protection of the susceptible bacteria in the community following rapid extracellular antibiotic degradation by the resistant population, shown experimentally through a combination of chemical quantification and bacterial growth experiments. Metagenome and 16S rRNA analyses of sewage-derived bacterial communities evolved under cefotaxime exposure show preferential enrichment for blaCTX-M genes over all other beta-lactamase genes, as well as positive selection and co-selection for antibiotic resistant, opportunistic pathogens. These findings have far-reaching implications for our understanding of the evolution of antibiotic resistance, by challenging the long-standing assumption that selection occurs in a dose-dependent manner.IMPORTANCE Antibiotic resistance is one of the greatest global issues facing society. Still, comparatively little is known about selection for resistance at very low antibiotic concentrations. We show that the strength of selection for clinically important resistance genes within a complex bacterial community can remain constant across a large antibiotic concentration range (wide selective space). Therefore, largely understudied ecological compartments could be just as important as clinical environments for selection of antibiotic resistance.}, }
@article {pmid30041461, year = {2018}, author = {Romano, S and Jackson, SA and Patry, S and Dobson, ADW}, title = {Extending the &quot;One Strain Many Compounds&quot; (OSMAC) Principle to Marine Microorganisms.}, journal = {Marine drugs}, volume = {16}, number = {7}, pages = {}, doi = {10.3390/md16070244}, pmid = {30041461}, issn = {1660-3397}, abstract = {Genomic data often highlights an inconsistency between the number of gene clusters identified using bioinformatic approaches as potentially producing secondary metabolites and the actual number of chemically characterized secondary metabolites produced by any given microorganism. Such gene clusters are generally considered as &quot;silent&quot;, meaning that they are not expressed under laboratory conditions. Triggering expression of these &quot;silent&quot; clusters could result in unlocking the chemical diversity they control, allowing the discovery of novel molecules of both medical and biotechnological interest. Therefore, both genetic and cultivation-based techniques have been developed aimed at stimulating expression of these &quot;silent&quot; genes. The principles behind the cultivation based approaches have been conceptualized in the &quot;one strain many compounds&quot; (OSMAC) framework, which underlines how a single strain can produce different molecules when grown under different environmental conditions. Parameters such as, nutrient content, temperature, and rate of aeration can be easily changed, altering the global physiology of a microbial strain and in turn significantly affecting its secondary metabolism. As a direct extension of such approaches, co-cultivation strategies and the addition of chemical elicitors have also been used as cues to activate &quot;silent&quot; clusters. In this review, we aim to provide a focused and comprehensive overview of these strategies as they pertain to marine microbes. Moreover, we underline how changes in some parameters which have provided important results in terrestrial microbes, but which have rarely been considered in marine microorganisms, may represent additional strategies to awaken &quot;silent&quot; gene clusters in marine microbes. Unfortunately, the empirical nature of the OSMAC approach forces scientists to perform extensive laboratory experiments. Nevertheless, we believe that some computation and experimental based techniques which are used in other disciplines, and which we discuss; could be effectively employed to help streamline the OSMAC based approaches. We believe that natural products discovery in marine microorganisms would be greatly aided through the integration of basic microbiological approaches, computational methods, and technological innovations, thereby helping unearth much of the as yet untapped potential of these microorganisms.}, }
@article {pmid30040385, year = {2018}, author = {Garner, E and McLain, J and Bowers, J and Engelthaler, DM and Edwards, MA and Pruden, A}, title = {Microbial Ecology and Water Chemistry Impact Regrowth of Opportunistic Pathogens in Full-Scale Reclaimed Water Distribution Systems.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {16}, pages = {9056-9068}, doi = {10.1021/acs.est.8b02818}, pmid = {30040385}, issn = {1520-5851}, abstract = {Need for global water security has spurred growing interest in wastewater reuse to offset demand for municipal water. While reclaimed (i.e., nonpotable) microbial water quality regulations target fecal indicator bacteria, opportunistic pathogens (OPs), which are subject to regrowth in distribution systems and spread via aerosol inhalation and other noningestion routes, may be more relevant. This study compares the occurrences of five OP gene markers (Acanthamoeba spp., Legionella spp., Mycobacterium spp., Naegleria fowleri, Pseudomonas aeruginosa) in reclaimed versus potable water distribution systems and characterizes factors potentially contributing to their regrowth. Samples were collected over four sampling events at the point of compliance for water exiting treatment plants and at five points of use at four U.S. utilities bearing both reclaimed and potable water distribution systems. Reclaimed water systems harbored unique water chemistry (e.g., elevated nutrients), microbial community composition, and OP occurrence patterns compared to potable systems examined here and reported in the literature. Legionella spp. genes, Mycobacterium spp. genes, and total bacteria, represented by 16S rRNA genes, were more abundant in reclaimed than potable water distribution system samples (p ≤ 0.0001). This work suggests that further consideration should be given to managing reclaimed water distribution systems with respect to nonpotable exposures to OPs.}, }
@article {pmid30039872, year = {2018}, author = {De Bodt, J and Defoirdt, T}, title = {Impact of the organic load on the efficacy of chlorine disinfection against acute hepatopancreatic necrosis disease-causing Vibrio parahaemolyticus.}, journal = {Journal of fish diseases}, volume = {41}, number = {10}, pages = {1609-1612}, doi = {10.1111/jfd.12866}, pmid = {30039872}, issn = {1365-2761}, }
@article {pmid30038663, year = {2018}, author = {Calusinska, M and Goux, X and Fossépré, M and Muller, EEL and Wilmes, P and Delfosse, P}, title = {A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems.}, journal = {Biotechnology for biofuels}, volume = {11}, number = {}, pages = {196}, doi = {10.1186/s13068-018-1195-8}, pmid = {30038663}, issn = {1754-6834}, abstract = {Background: Anaerobic digestion (AD) is a microbe-driven process of biomass decomposition to CH4 and CO2. In addition to renewable and cost-effective energy production, AD has emerged in the European Union as an environmentally friendly model of bio-waste valorisation and nutrient recycling. Nevertheless, due to the high diversity of uncharacterised microbes, a typical AD microbiome is still considered as &quot;dark matter&quot;.<br><br>Results: Using the high-throughput sequencing of small rRNA gene, and a monthly monitoring of the physicochemical parameters for 20 different mesophilic full-scale bioreactors over 1 year, we generated a detailed view of AD microbial ecology towards a better understanding of factors that influence and shape these communities. By studying the broadly distributed OTUs present in over 80% of analysed samples, we identified putatively important core bacteria and archaea to the AD process that accounted for over 70% of the whole microbial community relative abundances. AD reactors localised at the wastewater treatment plants were shown to operate with distinct core microbiomes than the agricultural and bio-waste treating biogas units. We also showed that both the core microbiomes were composed of low (with average community abundance ≤ 1%) and highly abundant microbial populations; the vast majority of which remains yet uncharacterised, e.g. abundant candidate Cloacimonetes. Using non-metric multidimensional scaling, we observed microorganisms grouping into clusters that well reflected the origin of the samples, e.g. wastewater versus agricultural and bio-waste treating biogas units. The calculated diversity patterns differed markedly between the different community clusters, mainly due to the presence of highly diverse and dynamic transient species. Core microbial communities appeared relatively stable over the monitoring period.<br><br>Conclusions: In this study, we characterised microbial communities in different AD systems that were monitored over a 1-year period. Evidences were shown to support the concept of a core community driving the AD process, whereas the vast majority of dominant microorganisms remain yet to be characterised.}, }
@article {pmid30035767, year = {2018}, author = {Calatayud Arroyo, M and Van de Wiele, T and Hernandez-Sanabria, E}, title = {Assessing the Viability of a Synthetic Bacterial Consortium on the In Vitro Gut Host-microbe Interface.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {137}, pages = {}, doi = {10.3791/57699}, pmid = {30035767}, issn = {1940-087X}, mesh = {Gastrointestinal Microbiome/*physiology ; Humans ; Intestines/*microbiology ; }, abstract = {The interplay between host and microbiota has been long recognized and extensively described. The mouth is similar to other sections of the gastrointestinal tract, as resident microbiota occurs and prevents colonisation by exogenous bacteria. Indeed, more than 600 species of bacteria are found in the oral cavity, and a single individual may carry around 100 different at any time. Oral bacteria possess the ability to adhere to the various niches in the oral ecosystem, thus becoming integrated within the resident microbial communities, and favouring growth and survival. However, the flow of bacteria into the gut during swallowing has been proposed to disturb the balance of the gut microbiota. In fact, oral administration of P. gingivalis shifted bacterial composition in the ileal microflora. We used a synthetic community as a simplified representation of the natural oral ecosystem, to elucidate the survival and viability of oral bacteria subjected to simulated gastrointestinal transit conditions. Fourteen species were selected, subjected to in vitro salivary, gastric, and intestinal digestion processes, and presented to a multicompartment cell model containing Caco-2 and HT29-MTX cells to simulate the gut mucosal epithelium. This model served to unravel the impact of swallowed bacteria on cells involved in the enterohepatic circulation. Using synthetic communities allows for controllability and reproducibility. Thus, this methodology can be adapted to assess pathogen viability and subsequent inflammation-associated changes, colonization capacity of probiotic mixtures, and ultimately, potential bacterial impact on the presystemic circulation.}, }
@article {pmid30033973, year = {2018}, author = {Choi, HJ and Jeong, TY and Yoon, H and Oh, BY and Han, YS and Hur, MJ and Kang, S and Kim, JG}, title = {Comparative microbial communities in tidal flats sediment on Incheon, South Korea.}, journal = {The Journal of general and applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.2323/jgam.2017.12.007}, pmid = {30033973}, issn = {1349-8037}, abstract = {Coastal ecosystems, play critical ecological roles of which tidal flats are a significant component of coastal wetlands, such as habitat and nutrient cycling in aquatic biology. Microbial communities in tidal flats are known to play vital roles of self-purification. And the microbial ecology of the sediment is easily affected by human activities and pollution. In this paper, we applied pyrosequencing technology to investigate microbial communities in three different tidal flats (Ganghwa Island, Ongnyeon land region and Yeongjong Island) on the Incheon, Korea peninsula. A total of 16,906 sequences were obtained. We used these sequences to identify the dominant phyla in the three tidal flats: Proteobacteria, Chloroflexi, Actinobacteria, and Bacteroidetes. The composition of the bacterial community of Ganghwa Island and the Ongnyeon region were more similar to each other than they were to the bacterial community of Yeongjong Island. Simpson's dominance index of Yeongjong Island was higher than that of the other regions, and the Shannon diversity index of this region was the lowest. Previous research of samples in these regions indicated that the three tidal flats had similar geochemical characteristics. However, their bacterial communities were rather distinct. This might be because the analysis of microbial communities and physiochemical analysis have different perspectives. Therefore, the pyrosequencing of a bacterial community with physiochemical analysis is recommended as an effective monitoring tool for the comprehensive management of tidal flats.}, }
@article {pmid30033500, year = {2018}, author = {Clemmons, BA and Voy, BH and Myer, PR}, title = {Altering the Gut Microbiome of Cattle: Considerations of Host-Microbiome Interactions for Persistent Microbiome Manipulation.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1234-9}, pmid = {30033500}, issn = {1432-184X}, abstract = {The beef cattle industry represents a significant portion of the USA's agricultural sect, with beef cattle accounting for the most red meat consumed in the USA. Feed represents the largest input cost in the beef industry, accounting for approximately 70% of total input cost. Given that, novel methods need to be employed to optimize feed efficiency in cattle to reduce monetary cost as well as environmental cost associated with livestock industries, such as methane production and nitrogen release into the environment. The rumen microbiome contributes to feed efficiency by breaking down low-quality feedstuffs into energy substrates that can subsequently be utilized by the host animal. Attempts to manipulate the rumen microbiome have been met with mixed success, though persistent changes have not yet been achieved beyond changing diet. Recent technological advances have made analyzing host-wide effects of the rumen microbiome possible, as well as provided finer resolution of those effects. This manuscript reviews contributing factors to the rumen microbiome establishment or re-establishment following rumen microbiome perturbation, as well as host-microbiome interactions that may be responsible for possible host specificity of the rumen microbiome. Understanding and accounting for the variety of factors contributing to rumen microbiome establishment or re-establishment in cattle will ultimately lead to identification of biomarkers of feed efficiency that will result in improved selection criteria, as well as aid to determine methods for persistent microbiome manipulation to optimize production phenotypes.}, }
@article {pmid30033172, year = {2018}, author = {Sanz, Y and Romaní-Perez, M and Benítez-Páez, A and Portune, KJ and Brigidi, P and Rampelli, S and Dinan, T and Stanton, C and Delzenne, N and Blachier, F and Neyrinck, AM and Beaumont, M and Olivares, M and Holzer, P and Günther, K and Wolters, M and Ahrens, W and Claus, SP and Campoy, C and Murphy, R and Sadler, C and Fernández, L and Kamp, JV}, title = {Towards microbiome-informed dietary recommendations for promoting metabolic and mental health: Opinion papers of the MyNewGut project.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.clnu.2018.07.007}, pmid = {30033172}, issn = {1532-1983}, abstract = {The gut microbiota coexists in partnership with the human host through adaptations to environmental and physiological changes that help maintain dynamic homeostatic healthy states. Break-down of this delicate balance under sustained exposure to stressors (e.g. unhealthy diets) can, however, contribute to the onset of disease. Diet is a key modifiable environmental factor that modulates the gut microbiota and its metabolic capacities that, in turn, could impact human physiology. On this basis, the diet and the gut microbiota could act as synergistic forces that provide resilience against disease or that speed the progress from health to disease states. Associations between unhealthy dietary patterns, non-communicable diseases and intestinal dysbiosis can be explained by this hypothesis. Translational studies showing that dietary-induced alterations in microbial communities recapitulate some of the pathological features of the original host further support this notion. In this introductory paper by the European project MyNewGut, we briefly summarize the investigations conducted to better understand the role of dietary patterns and food components in metabolic and mental health and the specificities of the microbiome-mediating mechanisms. We also discuss how advances in the understanding of the microbiome's role in dietary health effects can help to provide acceptable scientific grounds on which to base dietary advice for promoting healthy living.}, }
@article {pmid30032189, year = {2018}, author = {Donhauser, J and Frey, B}, title = {Alpine soil microbial ecology in a changing world.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {9}, pages = {}, doi = {10.1093/femsec/fiy099}, pmid = {30032189}, issn = {1574-6941}, abstract = {Climate change has a disproportionally large impact on alpine soil ecosystems, leading to pronounced changes in soil microbial diversity and function associated with effects on biogeochemical processes at the local and supraregional scales. However, due to restricted accessibility, high-altitude soils remain largely understudied and a considerable heterogeneity hampers the comparability of different alpine studies. Here, we highlight differences and similarities between alpine and arctic ecosystems, and we discuss the impact of climatic variables and associated vegetation and soil properties on microbial ecology. We consider how microbial alpha-diversity, community structures and function change along altitudinal gradients and with other topographic features such as slope aspect. In addition, we focus on alpine permafrost soils, harboring a surprisingly large unknown microbial diversity and on microbial succession along glacier forefield chronosequences constituting the most thoroughly studied alpine habitat. Finally, highlighting experimental approaches, we present climate change studies showing shifts in microbial community structures and function in response to warming and altered moisture, interestingly with some contradiction. Collectively, despite harsh environmental conditions, many specially adapted microorganisms are able to thrive in alpine environments. Their community structures strongly correlate with climatic, vegetation and soil properties and thus closely mirror the complexity and small-scale heterogeneity of alpine soils.}, }
@article {pmid30031405, year = {2018}, author = {Zhang, AN and Li, LG and Ma, L and Gillings, MR and Tiedje, JM and Zhang, T}, title = {Conserved phylogenetic distribution and limited antibiotic resistance of class 1 integrons revealed by assessing the bacterial genome and plasmid collection.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {130}, doi = {10.1186/s40168-018-0516-2}, pmid = {30031405}, issn = {2049-2618}, abstract = {BACKGROUND: Integrons, especially the class 1 integrons, are major contributors to the acquisition and dissemination of antibiotic resistance genes (ARGs). However, comprehensive knowledge of the types, content, and distribution of integrons in bacterial taxa is lacking to evaluate their contribution.<br><br>RESULTS: We have constructed a new integrase database and developed a pipeline that provides comprehensive recovery of class 1 integrons. Previous PCR-based techniques might only detect one fourth of the integron-integrases and integrons recovered in this study. By exploring the class 1 integrons in over 73,000 currently available complete and draft bacterial genomes, the contribution of class 1 integrons in spreading and acquiring ARGs was evaluated. Firstly, the host species of class 1 integrons are highly conserved within (96%) in class Gammaproteobacteria, dominated by four pathogenic species of &quot;ESKAPE.&quot; Secondly, more than half of class 1 integrons are embedded in chromosomes with less potential for horizontal gene transfer. Finally, ARGs that have been acquired by these integrons only cover 11% of all the ARG genotypes detected in bacterial genomes.<br><br>CONCLUSIONS: The above observations indicated that there are both biological and ecological limitations to class 1 integrons in acquiring and spreading ARGs across different classes of the domain Bacteria.}, }
@article {pmid30031243, year = {2018}, author = {Paul, W and Marta, C and Tom, VW}, title = {Resolving host-microbe interactions in the gut: the promise of in vitro models to complement in vivo research.}, journal = {Current opinion in microbiology}, volume = {44}, number = {}, pages = {28-33}, doi = {10.1016/j.mib.2018.07.001}, pmid = {30031243}, issn = {1879-0364}, abstract = {While animal models remain essential for inferring causality, they exhibit important limitations, which restrict the direct translation of findings into new approaches aimed at steering host-microbe interactions for the improvement of human health. Different in vitro models have therefore been developed which incorporate human cell types and microbiota. By virtue of their intricate designs, these models result in human and microbial read-outs reflective of in vivo gut physiology, and present important alternatives to animal models. However, to allow systematic investigations of the interactions between gut microbiota and different human cell types and body systems, ever more complex cell assemblies are necessary which will culminate in the establishment of personalized in vitro models. Such models will allow the unravelling of human-microbe interdependencies and will open exciting new avenues for microbiome-tailored nutrition and drug development.}, }
@article {pmid30029141, year = {2018}, author = {Cipullo, S and Snapir, B and Tardif, S and Campo, P and Prpich, G and Coulon, F}, title = {Insights into mixed contaminants interactions and its implication for heavy metals and metalloids mobility, bioavailability and risk assessment.}, journal = {The Science of the total environment}, volume = {645}, number = {}, pages = {662-673}, doi = {10.1016/j.scitotenv.2018.07.179}, pmid = {30029141}, issn = {1879-1026}, abstract = {Mobility of heavy metals at contaminated sites is mainly influenced by the soil physicochemical properties and environmental conditions, therefore assessing heavy metals (HMs) and metalloids fractionation can provide insights into their potential risk and the mechanisms that regulate bioavailability. A 12-months mesocosms experiment was setup to investigate the effect of physicochemical factors (pH, moisture, and temperature) and weathering (time) on HMs and metalloids fractionation in three different multi-contaminated soil matrices (low, medium, and high contamination) collected from a soil treatment facility located in the United Kingdom, and two rural contaminated soil samples. The study demonstrates that even though Pb and Zn were found associated with the exchangeable fraction in the soil with the highest contamination (total average Pb 3400 mg/kg, and total average Zn 2100 mg/kg in Soil C), neither the condition applied nor the weathering caused an increase in their mobility. Although it was expected that lower pH (4.5) would favours the dissociation of HMs and metalloids, no significant differences were observed, potentially due to the initial alkaline pH of the genuine-contaminated soil samples. The results show that even though total concentration of Pb, Cu, and Zn exceed the soil standards and guideline values, HMs were predominantly associated with the non-exchangeable fraction, while only 5% were dissolved in the pore water fraction (potentially bioavailable). In addition, the mobility and bioavailability of HMs remained constant over the 12 months monitoring, suggesting that these soils pose negligible risk to the environment.}, }
@article {pmid30029114, year = {2018}, author = {McGillicuddy, E and Morrison, L and Cormican, M and Dockery, P and Morris, D}, title = {Activated charcoal as a capture material for silver nanoparticles in environmental water samples.}, journal = {The Science of the total environment}, volume = {645}, number = {}, pages = {356-362}, doi = {10.1016/j.scitotenv.2018.07.145}, pmid = {30029114}, issn = {1879-1026}, abstract = {Silver nanoparticles (AgNPs), due to their antibacterial activity, have been incorporated into numerous consumer products. Their environmental impact however, is currently unclear. Uncertainties surround the concentration, fate, and effects of AgNPs in aquatic environments. This study examined the suitability of activated charcoal as a capture material for AgNPs from water. Samples of 100 ppb AgNPs were initially generated and exposed to activated charcoal for 24 h to examine the ability of charcoal to capture AgNPs. The decrease in Ag concentration was measured using ICP-MS. Following initial investigations, the surface area of the charcoal was increased firstly with a pestle and mortar and secondly by milling the charcoal using a ball mill. The increased surface area of the milled charcoal increased the capture of the AgNPs from 11.9% to 63.6% for the 100 ppb samples. Further investigations were carried out examining the effect on the capture of AgNP concentration (with concentration ranging from 10 to 100 ppb), particle coating and the effect of exposure time to the activated charcoal. The capture of AgNP increased with decreasing concentration. A hydrochloric acid (HCl) leaching procedure was also developed which successfully removed the captured silver allowing the fraction captured by the charcoal to be quantified with an average of 94.8% recovery. The results show that milled activated charcoal, can successfully capture AgNPs from water samples, and that therefore, activated charcoal may prove to be a cost effective material for the remediation of waters impacted by AgNP or other nano-wastes.}, }
@article {pmid30028282, year = {2018}, author = {Sultanpuram, VR and Mothe, T}, title = {Thalassorhabdus alkalitolerans gen. nov., sp. nov., a novel Bacillaceae member isolated from marine sediment.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {68}, number = {9}, pages = {2969-2976}, doi = {10.1099/ijsem.0.002931}, pmid = {30028282}, issn = {1466-5034}, mesh = {Bacillaceae/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; Cell Wall/chemistry ; DNA, Bacterial/genetics ; Diaminopimelic Acid/chemistry ; Fatty Acids/chemistry ; Geologic Sediments/*microbiology ; India ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry ; Phosphatidylglycerols/analysis ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {A novel Gram-stain-variable, rod-shaped, non-motile and non-endospore-forming bacterium (strain G27T) was isolated from near Dhuvaran, Gujarat, India. Based on 16S rRNA gene sequence analysis, strain G27T was identified as a member of the class Firmibacteria and was most closely related to Bacillus populi FJAT-45347T (94.9 % sequence similarity), Salipaludibacillus aurantiacus S9T (94.9 %), Salipaludibacillus neizhouensis KCTC 13187T (94.7 %), Alteribacillus iranensis DSM 23995T (94.6 %) and other Firmibacteria (<94.6 %). The DNA G+C content of strain G27T was 43.4±0.6 mol%. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and five unidentified lipids. The predominant isoprenoid quinone was menaquinone MK-7. Major fatty acids (>5 %) included anteiso-C15:0, iso-C15 : 0, anteiso-C17:0, C16 : 0 and iso-C16 : 0. The results of phylogenetic, chemotaxonomic and biochemical tests allowed the clear differentiation of strain G27T from all other members of the family Bacillaceae.It is therefore considered to represent a novel species of a new genus, for which the name Thalassorhabdus alkalitolerans gen. nov., sp. nov., is proposed. The type strain of Thalassorhabdus alkalitolerans is G27T (=MCC 3411T=CGMCC 1.15772T=KCTC 33941T).}, }
@article {pmid30025176, year = {2018}, author = {Liang, Z and Shen, Z and Zhang, Y and Ji, D and Li, J and Warren, A and Lin, X}, title = {Morphology and Phylogeny of Four New Vorticella Species (Ciliophora: Peritrichia) from Coastal Waters of Southern China.}, journal = {The Journal of eukaryotic microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jeu.12668}, pmid = {30025176}, issn = {1550-7408}, abstract = {Four new species of Vorticella, V. parachiangi sp. n., V. scapiformis sp. n., V. sphaeroidalis sp. n., and V. paralima sp. n., were isolated from coastal brackish waters of southern China. Their morphology, infraciliature, and silverline system were investigated based on observations of specimens both in vivo and following silver staining. Vorticella parachiangi sp. n. is distinguished by: a J-shaped macronucleus; a single dorsally located contractile vacuole; a two-rowed infundibular polykinetid 3, in which row 1 is shorter than row 2; 21-31 silverlines between peristome and aboral trochal band, 6-11 between aboral trochal band and scopula. Vorticella scapiformis sp. n. is characterized by its conspicuously thin and irregularly edged peristomial lip; a J-shaped macronucleus; a single, ventrally located contractile vacuole; row 1 of the infundibular polykinetid 3 proximally shortened; 18-25 silverlines between peristome and aboral trochal band, 8-12 between aboral trochal band and scopula. Vorticella sphaeroidalis sp. n. can be identified by its small, sub-spherical zooid; a C-shaped macronucleus; a ventrally located contractile vacuole; an aboral trochal band adjacent to the scopula; 16-18 silverlines between persitome and aboral trochal band, two between aboral trochal band and scopula. Vorticella paralima sp. n. can be identified by its ovoidal zooid; a J-shaped macronucleus; a dorsally positioned contractile vacuole; rows 1 and 2 of the infundibular polykinetid 3 proximally shortened; 26-35 silverlines from peristome to aboral trochal band, and 7-13 from aboral trochal band to scopula. The SSU rDNA genes of these four species were sequenced and their phylogeny was analyzed.}, }
@article {pmid30023789, year = {2018}, author = {Mukherjee, I and Ghosh, A and Bhadury, P and De, P}, title = {Leucine-Based Polymer Architecture-Induced Antimicrobial Properties and Bacterial Cell Morphology Switching.}, journal = {ACS omega}, volume = {3}, number = {1}, pages = {769-780}, doi = {10.1021/acsomega.7b01674}, pmid = {30023789}, issn = {2470-1343}, abstract = {To evaluate the comparative antibacterial activity of leucine-based cationic polymers having linear, hyperbranched, and star architectures containing both hydrophilic and hydrophobic segments against Gram-negative bacterium, Escherichia coli (E. coli), herein we performed zone of inhibition study, minimum inhibitory concentration (MIC) calculation, and bacterial growth experiment. The highest antibacterial activity in terms of the MIC value was found in hyperbranched and star architectures because of the greater extent of cationic and hydrophobic functionality, enhancing cell wall penetration ability compared to that of the linear polymer. The absence of the bacterial regrowth stage in the growth curve exhibited the highest bactericidal capacity of star polymers, when untreated cells (control) already reached to the stationary phase, whereas the bacterial regrowth stage with a delayed lag phase was critically observed for linear and hyperbranched architectures displaying lower bactericidal efficacy. Coagulation of E. coli cells, switching of cell morphology from rod to sphere, and lengthening due to stacking in an antimicrobial polymer-treated environment at the bacterial regrowth stage in liquid media were visualized critically by field emission scanning electron microscopy and confocal fluorescence microscopy instruments in the presence of 4',6-diamidino-2-phenylindole stain.}, }
@article {pmid30022610, year = {2018}, author = {Di Cesare, A and Petrin, S and Fontaneto, D and Losasso, C and Eckert, EM and Tassistro, G and Borello, A and Ricci, A and Wilson, WH and Pruzzo, C and Vezzulli, L}, title = {ddPCR applied on archived Continuous Plankton Recorder samples reveals long-term occurrence of class 1 integrons and a sulphonamide resistance gene in marine plankton communities.}, journal = {Environmental microbiology reports}, volume = {10}, number = {4}, pages = {458-464}, doi = {10.1111/1758-2229.12665}, pmid = {30022610}, issn = {1758-2229}, abstract = {Antibiotic resistance is a rising threat for human health. Although in clinical settings and terrestrial environments the rise of antibiotic resistant bacteria is well documented, their dissemination and spread in the marine environment, covering almost two-thirds of the Earth's surface, is still poorly understood. In this study, the presence and abundance of sulphonamide resistance gene (sul2) and class 1 integron-integrase gene (intI1), used as markers for the occurrence and spread of antibiotic resistance genes since the beginning of the antibiotic era, were investigated. Twenty-nine archived formalin-fixed samples, collected by the Continuous Plankton Recorder (CPR) survey in the Atlantic Ocean and North Sea from 1970 to 2011, were analysed using Droplet Digital PCR (ddPCR) applied for the first time on CPR samples. The two marker genes were present in a large fraction of the samples (48% for sul2 and 76% for intI1). In contrast, results from Real-Time PCR performed on the same samples greatly underestimate their occurrence (21% for sul2 and 52% for intI1). Overall, besides providing successful use of ddPCR for the molecular analysis of CPR samples, this study reveals long-term occurrence and spread of sul2 gene and class 1 integrons in the plankton-associated bacterial communities in the ocean.}, }
@article {pmid30022245, year = {2018}, author = {Kopejtka, K and Tomasch, J and Bunk, B and Spröer, C and Wagner-Döbler, I and Koblížek, M}, title = {The complete genome sequence of Rhodobaca barguzinensis alga05 (DSM 19920) documents its adaptation for life in soda lakes.}, journal = {Extremophiles : life under extreme conditions}, volume = {22}, number = {6}, pages = {839-849}, doi = {10.1007/s00792-018-1041-8}, pmid = {30022245}, issn = {1433-4909}, support = {Algatech Plus (LO1416)//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; Transregio 51 &quot;Roseobacter&quot;//Deutsche Forschungsgemeinschaft/ ; 57155424//Deutscher Akademischer Austauschdienst/ ; P501/12/G055//Grantová Agentura České Republiky/ ; }, abstract = {Soda lakes, with their high salinity and high pH, pose a very challenging environment for life. Microorganisms living in these harsh conditions have had to adapt their physiology and gene inventory. Therefore, we analyzed the complete genome of the haloalkaliphilic photoheterotrophic bacterium Rhodobaca barguzinensis strain alga05. It consists of a 3,899,419 bp circular chromosome with 3624 predicted coding sequences. In contrast to most of Rhodobacterales, this strain lacks any extrachromosomal elements. To identify the genes responsible for adaptation to high pH, we compared the gene inventory in the alga05 genome with genomes of 17 reference strains belonging to order Rhodobacterales. We found that all haloalkaliphilic strains contain the mrpB gene coding for the B subunit of the MRP Na+/H+ antiporter, while this gene is absent in all non-alkaliphilic strains, which indicates its importance for adaptation to high pH. Further analysis showed that alga05 requires organic carbon sources for growth, but it also contains genes encoding the ethylmalonyl-CoA pathway for CO2 fixation. Remarkable is the genetic potential to utilize organophosphorus compounds as a source of phosphorus. In summary, its genetic inventory indicates a large flexibility of the alga05 metabolism, which is advantageous in rapidly changing environmental conditions in soda lakes.}, }
@article {pmid30021874, year = {2018}, author = {Glassman, SI and Martiny, JBH}, title = {Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units.}, journal = {mSphere}, volume = {3}, number = {4}, pages = {}, doi = {10.1128/mSphere.00148-18}, pmid = {30021874}, issn = {2379-5042}, abstract = {Recent discussion focuses on the best method for delineating microbial taxa, based on either exact sequence variants (ESVs) or traditional operational taxonomic units (OTUs) of marker gene sequences. We sought to test if the binning approach (ESVs versus 97% OTUs) affected the ecological conclusions of a large field study. The data set included sequences targeting all bacteria (16S rRNA) and fungi (internal transcribed spacer [ITS]), across multiple environments diverging markedly in abiotic conditions, over three collection times. Despite quantitative differences in microbial richness, we found that all α and β diversity metrics were highly positively correlated (r > 0.90) between samples analyzed with both approaches. Moreover, the community composition of the dominant taxa did not vary between approaches. Consequently, statistical inferences were nearly indistinguishable. Furthermore, ESVs only moderately increased the genetic resolution of fungal and bacterial diversity (1.3 and 2.1 times OTU richness, respectively). We conclude that for broadscale (e.g., all bacteria or all fungi) α and β diversity analyses, ESV or OTU methods will often reveal similar ecological results. Thus, while there are good reasons to employ ESVs, we need not question the validity of results based on OTUs.IMPORTANCE Microbial ecologists have made exceptional improvements in our understanding of microbiomes in the last decade due to breakthroughs in sequencing technologies. These advances have wide-ranging implications for fields ranging from agriculture to human health. Due to limitations in databases, the majority of microbial ecology studies use a binning approach to approximate taxonomy based on DNA sequence similarity. There remains extensive debate on the best way to bin and approximate this taxonomy. Here we examine two popular approaches using a large field-based data set examining both bacteria and fungi and conclude that there are not major differences in the ecological outcomes. Thus, it appears that standard microbial community analyses are not overly sensitive to the particulars of binning approaches.}, }
@article {pmid30019110, year = {2018}, author = {Broman, E and Li, L and Fridlund, J and Svensson, F and Legrand, C and Dopson, M}, title = {Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1229-6}, pmid = {30019110}, issn = {1432-184X}, abstract = {Two annual Baltic Sea phytoplankton blooms occur in spring and summer. The bloom intensity is determined by nutrient concentrations in the water, while the period depends on weather conditions. During the course of the bloom, dead cells sink to the sediment where their degradation consumes oxygen to create hypoxic zones (< 2 mg/L dissolved oxygen). These zones prevent the establishment of benthic communities and may result in fish mortality. The aim of the study was to determine how the spring and autumn sediment chemistry and microbial community composition changed due to degradation of diatom or cyanobacterial biomass, respectively. Results from incubation of sediment cores showed some typical anaerobic microbial processes after biomass addition such as a decrease in NO2- + NO3- in the sediment surface (0-1 cm) and iron in the underlying layer (1-2 cm). In addition, an increase in NO2- + NO3- was observed in the overlying benthic water in all amended and control incubations. The combination of NO2- + NO3- diffusion plus nitrification could not account for this increase. Based on 16S rRNA gene sequences, the addition of cyanobacterial biomass during autumn caused a large increase in ferrous iron-oxidizing archaea while diatom biomass amendment during spring caused minor changes in the microbial community. Considering that OTUs sharing lineages with acidophilic microorganisms had a high relative abundance during autumn, it was suggested that specific niches developed in sediment microenvironments. These findings highlight the importance of nitrogen cycling and early microbial community changes in the sediment due to sinking phytoplankton before potential hypoxia occurs.}, }
@article {pmid30018864, year = {2018}, author = {Lydon, KA and Lipp, EK}, title = {Taxonomic annotation errors incorrectly assign the family Pseudoalteromonadaceae to the order Vibrionales in Greengenes: implications for microbial community assessments.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5248}, doi = {10.7717/peerj.5248}, pmid = {30018864}, issn = {2167-8359}, abstract = {Next-generation sequencing has provided powerful tools to conduct microbial ecology studies. Analysis of community composition relies on annotated databases of curated sequences to provide taxonomic assignments; however, these databases occasionally have errors with implications for downstream analyses. Systemic taxonomic errors were discovered in Greengenes database (v13_5 and 13_8) related to orders Vibrionales and Alteromonadales. These orders have family level annotations that were erroneous at least one taxonomic level, e.g., 100% of sequences assigned to the Pseudoalteromonadaceae family were placed improperly in Vibrionales (rather than Alteromonadales) and >20% of these sequences were indeed Vibrio spp. but were improperly assigned to the Pseudoalteromonadaceae family (rather than to Vibrionaceae). Use of this database is common; we identified 68 peer-reviewed papers since 2013 that likely included erroneous annotations specifically associated with Vibrionales and Pseudoalteromonadaceae, with 20 explicitly stating the incorrect taxonomy. Erroneous assignments using these specific versions of Greengenes can lead to incorrect conclusions, especially in marine systems where these taxa are commonly encountered as conditionally rare organisms and potential pathogens.}, }
@article {pmid30018368, year = {2018}, author = {Mendes, LW and Mendes, R and Raaijmakers, JM and Tsai, SM}, title = {Breeding for soil-borne pathogen resistance impacts active rhizosphere microbiome of common bean.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-018-0234-6}, pmid = {30018368}, issn = {1751-7370}, support = {88887.185941/2018-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brazilian Federal Agency for the Support and Evaluation of Graduate Education)/ ; 2015/00251-9 and 2014/03217-3//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; }, abstract = {Over the past century, plant breeding programs have substantially improved plant growth and health, but have not yet considered the potential effects on the plant microbiome. Here, we conducted metatranscriptome analysis to determine if and how breeding for resistance of common bean against the root pathogen Fusarium oxysporum (Fox) affected gene expression in the rhizobacterial community. Our data revealed that the microbiome of the Fox-resistant cultivar presented a significantly higher expression of genes associated with nutrient metabolism, motility, chemotaxis, and the biosynthesis of the antifungal compounds phenazine and colicin V. Network analysis further revealed a more complex community for Fox-resistant cultivar and indicated Paenibacillus as a keystone genus in the rhizosphere microbiome. We suggest that resistance breeding in common bean has unintentionally co-selected for plant traits that strengthen the rhizosphere microbiome network structure and enrich for specific beneficial bacterial genera that express antifungal traits involved in plant protection against infections by root pathogens.}, }
@article {pmid30014981, year = {2018}, author = {De Paepe, J and Lindeboom, REF and Vanoppen, M and De Paepe, K and Demey, D and Coessens, W and Lamaze, B and Verliefde, ARD and Clauwaert, P and Vlaeminck, SE}, title = {Refinery and concentration of nutrients from urine with electrodialysis enabled by upstream precipitation and nitrification.}, journal = {Water research}, volume = {144}, number = {}, pages = {76-86}, doi = {10.1016/j.watres.2018.07.016}, pmid = {30014981}, issn = {1879-2448}, abstract = {Human urine is a valuable resource for nutrient recovery, given its high levels of nitrogen, phosphorus and potassium, but the compositional complexity of urine presents a challenge for an energy-efficient concentration and refinery of nutrients. In this study, a pilot installation combining precipitation, nitrification and electrodialysis (ED), designed for one person equivalent (1.2 Lurine d-1), was continuously operated for ∼7 months. First, NaOH addition yielded calcium and magnesium precipitation, preventing scaling in ED. Second, a moving bed biofilm reactor oxidized organics, preventing downstream biofouling, and yielded complete nitrification on diluted urine (20-40%, i.e. dilution factors 5 and 2.5) at an average loading rate of 215 mg N L-1 d-1. Batch tests demonstrated the halotolerance of the nitrifying community, with nitrification rates not affected up to an electrical conductivity of 40 mS cm-1 and gradually decreasing, yet ongoing, activity up to 96 mS cm-1 at 18% of the maximum rate. Next-generation 16S rRNA gene amplicon sequencing revealed that switching from a synthetic influent to real urine induced a profound shift in microbial community and that the AOB community was dominated by halophilic species closely related to Nitrosomonas aestuarii and Nitrosomonas marina. Third, nitrate, phosphate and potassium in the filtered (0.1 μm) bioreactor effluent were concentrated by factors 4.3, 2.6 and 4.6, respectively, with ED. Doubling the urine concentration from 20% to 40% further increased the ED recovery efficiency by ∼10%. Batch experiments at pH 6, 7 and 8 indicated a more efficient phosphate transport to the concentrate at pH 7. The newly proposed three-stage strategy opens up opportunities for energy- and chemical-efficient nutrient recovery from urine. Precipitation and nitrification enabled the long-term continuous operation of ED on fresh urine requiring minimal maintenance, which has, to the best of our knowledge, never been achieved before.}, }
@article {pmid30014593, year = {2018}, author = {Våge, S and Bratbak, G and Egge, J and Heldal, M and Larsen, A and Norland, S and Lund Paulsen, M and Pree, B and Sandaa, RA and Skjoldal, EF and Tsagaraki, TM and Øvreås, L and Thingstad, TF}, title = {Simple models combining competition, defence and resource availability have broad implications in pelagic microbial food webs.}, journal = {Ecology letters}, volume = {21}, number = {9}, pages = {1440-1452}, doi = {10.1111/ele.13122}, pmid = {30014593}, issn = {1461-0248}, abstract = {In food webs, interactions between competition and defence control the partitioning of limiting resources. As a result, simple models of these interactions contain links between biogeochemistry, diversity, food web structure and ecosystem function. Working at hierarchical levels, these mechanisms also produce self-similarity and therefore suggest how complexity can be generated from repeated application of simple underlying principles. Reviewing theoretical and experimental literature relevant to the marine photic zone, we argue that there is a wide spectrum of phenomena, including single cell activity of prokaryotes, microbial biodiversity at different levels of resolution, ecosystem functioning, regional biogeochemical features and evolution at different timescales; that all can be understood as variations over a common principle, summarised in what has been termed the 'Killing-the-Winner' (KtW) motif. Considering food webs as assemblages of such motifs may thus allow for a more integrated approach to aquatic microbial ecology.}, }
@article {pmid30013541, year = {2018}, author = {Aguinaga, OE and McMahon, A and White, KN and Dean, AP and Pittman, JK}, title = {Microbial Community Shifts in Response to Acid Mine Drainage Pollution Within a Natural Wetland Ecosystem.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1445}, doi = {10.3389/fmicb.2018.01445}, pmid = {30013541}, issn = {1664-302X}, abstract = {Natural wetlands are known to play an important role in pollutant remediation, such as remediating acid mine drainage (AMD) from abandoned mine sites. However, many aspects of the microbiological mechanisms underlying AMD remediation within wetlands are poorly understood, including the role and composition of associated microbial communities. We have utilized an AMD-polluted river-wetland system to perform rRNA sequence analysis of microbial communities that play a role in biogeochemical activities that are linked to water quality improvement. Next-generation sequencing of bacterial 16S rRNA gene amplicons from river and wetland sediment samples identified variation in bacterial community structure and diversity on the basis of dissolved and particulate metal concentrations, sediment metal concentrations and other water chemistry parameters (pH and conductivity), and wetland plant presence. Metabolic reconstruction analysis allowed prediction of relative abundance of microbial metabolic pathways and revealed differences between samples that cluster on the basis of the severity of AMD pollution. Global metabolic activity was predicted to be significantly higher in unpolluted and wetland sediments in contrast to polluted river sediments, indicating a metabolic stress response to AMD pollution. This is one of the first studies to explore microbial community structure dynamics within a natural wetland exposed to AMD and our findings indicate that wetland ecosystems play critical roles in maintaining diversity and metabolic structure of sediment microbial communities subject to high levels of acidity and metal pollution. Moreover, these microbial communities are predicted to be important for the remediation action of the wetland.}, }
@article {pmid30013236, year = {2018}, author = {Emerson, JB and Roux, S and Brum, JR and Bolduc, B and Woodcroft, BJ and Jang, HB and Singleton, CM and Solden, LM and Naas, AE and Boyd, JA and Hodgkins, SB and Wilson, RM and Trubl, G and Li, C and Frolking, S and Pope, PB and Wrighton, KC and Crill, PM and Chanton, JP and Saleska, SR and Tyson, GW and Rich, VI and Sullivan, MB}, title = {Host-linked soil viral ecology along a permafrost thaw gradient.}, journal = {Nature microbiology}, volume = {3}, number = {8}, pages = {870-880}, doi = {10.1038/s41564-018-0190-y}, pmid = {30013236}, issn = {2058-5276}, abstract = {Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood1-7. The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans8-10, remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling.}, }
@article {pmid30009332, year = {2018}, author = {Bag, S and Ghosh, TS and Banerjee, S and Mehta, O and Verma, J and Dayal, M and Desigamani, A and Kumar, P and Saha, B and Kedia, S and Ahuja, V and Ramamurthy, T and Das, B}, title = {Molecular Insights into Antimicrobial Resistance Traits of Commensal Human Gut Microbiota.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1228-7}, pmid = {30009332}, issn = {1432-184X}, support = {BT/MB/THSTI/HMC-SFC/2011//Department of Biotechnology , Ministry of Science and Technology/ ; }, abstract = {Antimicrobial resistance (AMR) among bacterial species that resides in complex ecosystems is a natural phenomenon. Indiscriminate use of antimicrobials in healthcare, livestock, and agriculture provides an evolutionary advantage to the resistant variants to dominate the ecosystem. Ascendency of resistant variants threatens the efficacy of most, if not all, of the antimicrobial drugs commonly used to prevent and/or cure microbial infections. Resistant phenotype is very common in enteric bacteria. The most common mechanisms of AMR are enzymatic modifications to the antimicrobials or their target molecules. In enteric bacteria, most of the resistance traits are acquired by horizontal gene transfer from closely or distantly related bacterial population. AMR traits are generally linked with mobile genetic elements (MGEs) and could rapidly disseminate to the bacterial species through horizontal gene transfer (HGT) from a pool of resistance genes. Although prevalence of AMR genes among pathogenic bacteria is widely studied in the interest of infectious disease management, the resistance profile and the genetic traits that encode resistance to the commensal microbiota residing in the gut of healthy humans are not well-studied. In the present study, we have characterized AMR phenotypes and genotypes of five dominant commensal enteric bacteria isolated from the gut of healthy Indians. Our study revealed that like pathogenic bacteria, enteric commensals are also multidrug-resistant. The genes encoding antibiotic resistance are physically linked with MGEs and could disseminate vertically to the progeny and laterally to the distantly related microbial species. Consequently, the AMR genes present in the chromosome of commensal gut bacteria could be a potential source of resistance functions for other enteric pathogens.}, }
@article {pmid30007724, year = {2018}, author = {Lukša, J and Vepštaitė-Monstavičė, I and Yurchenko, V and Serva, S and Servienė, E}, title = {High content analysis of sea buckthorn, black chokeberry, red and white currants microbiota - A pilot study.}, journal = {Food research international (Ottawa, Ont.)}, volume = {111}, number = {}, pages = {597-606}, doi = {10.1016/j.foodres.2018.05.060}, pmid = {30007724}, issn = {1873-7145}, abstract = {The high potential of sea buckthorn, black chokeberry, red and white currants in healthy food industry boosted interest in the plant cultivation. The present study is the first work providing comprehensive information on microbial populations of these berries. Next Generation Sequencing allowed identification of eukaryotic and prokaryotic microorganisms prevalent on specific berries, including uncultivable microorganisms. Our study revealed the broad diversity of berries-associated bacterial and fungal microorganisms. Analysis of representative microbial OTUs showed a clear separation among inhabitants of sea buckthorn, black chokeberry and both currants, indicating plant-defined differences in the composition of the bacterial and fungal microbiota. Among the microorganisms distributed on tested berries, we documented potentially beneficial fungi and bacteria along with potential phytopathogens or those harmful for humans. Thus, plant microbiota appears to be highly relevant for the evaluation of the microbiota impact on food quality and human health.}, }
@article {pmid30007669, year = {2018}, author = {Zheng, X and Liu, F and Li, K and Shi, X and Ni, Y and Li, B and Zhuge, B}, title = {Evaluating the microbial ecology and metabolite profile in Kazak artisanal cheeses from Xinjiang, China.}, journal = {Food research international (Ottawa, Ont.)}, volume = {111}, number = {}, pages = {130-136}, doi = {10.1016/j.foodres.2018.05.019}, pmid = {30007669}, issn = {1873-7145}, abstract = {Kazak artisanal cheese is one of the famous fermented food in Uighur Autonomy Region of Xinjiang, China. However, the microbial ecology in Kazak artisanal cheeses across different regions is unclear. In this study, we determined the microbial community composition through amplicon sequencing and measured the flavor profile of 10 cheese samples from different regions of Xinjiang. The associations between microbial communities, flavors and environmental factors were examined by redundancy analysis and Monte Carlo permutation test. Cheeses from different regions had different microbial communities, which was mainly reflected in the relative abundance of Lactobacillus, Streptococcus, Issatchenkia, Debaryomyces and Kluyveromyces. In addition, Pichia and Torulaspora were also the key microbial groups, according to the high relative abundance and large co-occurrence incidence in the correlation network. Using the microbe-metabolites correlation analysis, the major flavor-producing taxa were identified as Kluyveromyces, Anoxybacillus, Torulaspora, Lactobacillus, Streptococcus and Dipodascus. Environmental factors accounted for the majority of the microbial community variations, 88.54% for bacteria and 75.71% for fungi. Compared to physico-chemical factors (temperature, moisture, and pH), geographical factors (longitude, latitude and elevation) had a stronger effect on microbial communities in cheese samples from different regions of Xinjiang.}, }
@article {pmid30006398, year = {2018}, author = {Kougias, PG and Campanaro, S and Treu, L and Tsapekos, P and Armani, A and Angelidaki, I}, title = {Spatial Distribution and Diverse Metabolic Functions of Lignocellulose-Degrading Uncultured Bacteria as Revealed by Genome-Centric Metagenomics.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {18}, pages = {}, doi = {10.1128/AEM.01244-18}, pmid = {30006398}, issn = {1098-5336}, abstract = {The mechanisms by which specific anaerobic microorganisms remain firmly attached to lignocellulosic material, allowing them to efficiently decompose organic matter, have yet to be elucidated. To circumvent this issue, microbiomes collected from anaerobic digesters treating pig manure and meadow grass were fractionated to separate the planktonic microbes from those adhered to lignocellulosic substrate. Assembly of shotgun reads, followed by a binning process, recovered 151 population genomes, 80 out of which were completely new and were not previously deposited in any database. Genome coverage allowed the identification of microbial spatial distribution in the engineered ecosystem. Moreover, a composite bioinformatic analysis using multiple databases for functional annotation revealed that uncultured members of the Bacteroidetes and Firmicutes follow diverse metabolic strategies for polysaccharide degradation. The structure of cellulosome in Firmicutes species can differ depending on the number and functional roles of carbohydrate-binding modules. In contrast, members of the Bacteroidetes are able to adhere to and degrade lignocellulose due to the presence of multiple carbohydrate-binding family 6 modules in beta-xylosidase and endoglucanase proteins or S-layer homology modules in unknown proteins. This study combines the concept of variability in spatial distribution with genome-centric metagenomics, allowing a functional and taxonomical exploration of the biogas microbiome.IMPORTANCE This work contributes new knowledge about lignocellulose degradation in engineered ecosystems. Specifically, the combination of the spatial distribution of uncultured microbes with genome-centric metagenomics provides novel insights into the metabolic properties of planktonic and firmly attached to plant biomass bacteria. Moreover, the knowledge obtained in this study enabled us to understand the diverse metabolic strategies for polysaccharide degradation in different species of Bacteroidetes and Clostridiales Even though structural elements of cellulosome were restricted to Clostridiales species, our study identified a putative mechanism in Bacteroidetes species for biomass decomposition, which is based on a gene cluster responsible for cellulose degradation, disaccharide cleavage to glucose, and transport to cytoplasm.}, }
@article {pmid30006234, year = {2018}, author = {Aliyu, H and Lebre, P and Blom, J and Cowan, D and De Maayer, P}, title = {Corrigendum to &quot;Phylogenomic re-assessment of the thermophilic genus Geobacillus&quot; [Syst. Appl. Microbiol. 39 (2016) 527-533].}, journal = {Systematic and applied microbiology}, volume = {41}, number = {5}, pages = {529-530}, doi = {10.1016/j.syapm.2018.07.001}, pmid = {30006234}, issn = {1618-0984}, }
@article {pmid30005805, year = {2018}, author = {Driscoll, CB and Meyer, KA and Šulčius, S and Brown, NM and Dick, GJ and Cao, H and Gasiūnas, G and Timinskas, A and Yin, Y and Landry, ZC and Otten, TG and Davis, TW and Watson, SB and Dreher, TW}, title = {A closely-related clade of globally distributed bloom-forming cyanobacteria within the Nostocales.}, journal = {Harmful algae}, volume = {77}, number = {}, pages = {93-107}, doi = {10.1016/j.hal.2018.05.009}, pmid = {30005805}, issn = {1878-1470}, abstract = {In order to better understand the relationships among current Nostocales cyanobacterial blooms, eight genomes were sequenced from cultured isolates or from environmental metagenomes of recent planktonic Nostocales blooms. Phylogenomic analysis of publicly available sequences placed the new genomes among a group of 15 genomes from four continents in a distinct ADA clade (Anabaena/Dolichospermum/Aphanizomenon) within the Nostocales. This clade contains four species-level groups, two of which include members with both Anabaena-like and Aphanizomenon flos-aquae-like morphology. The genomes contain many repetitive genetic elements and a sizable pangenome, in which ABC-type transporters are highly represented. Alongside common core genes for photosynthesis, the differentiation of N2-fixing heterocysts, and the uptake and incorporation of the major nutrients P, N and S, we identified several gene pathways in the pangenome that may contribute to niche partitioning. Genes for problematic secondary metabolites-cyanotoxins and taste-and-odor compounds-were sporadically present, as were other polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters. By contrast, genes predicted to encode the ribosomally generated bacteriocin peptides were found in all genomes.}, }
@article {pmid30004677, year = {2018}, author = {Yu, Y and Han, P and Zhou, LJ and Li, Z and Wagner, M and Men, Y}, title = {Ammonia Monooxygenase-Mediated Cometabolic Biotransformation and Hydroxylamine-Mediated Abiotic Transformation of Micropollutants in an AOB/NOB Coculture.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {16}, pages = {9196-9205}, doi = {10.1021/acs.est.8b02801}, pmid = {30004677}, issn = {1520-5851}, abstract = {Biotransformation of various micropollutants (MPs) has been found to be positively correlated with nitrification in activated sludge communities. To further elucidate the roles played by ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), we investigated the biotransformation capabilities of an NOB pure culture (Nitrobacter sp.) and an AOB (Nitrosomonas europaea)/NOB (Nitrobacter sp.) coculture for 15 MPs, whose biotransformation was reported previously to be associated with nitrification. The NOB pure culture did not biotransform any investigated MP, whereas the AOB/NOB coculture was capable of biotransforming six MPs (i.e., asulam, bezafibrate, fenhexamid, furosemide, indomethacin, and rufinamide). Transformation products (TPs) were identified, and tentative structures were proposed. Inhibition studies with octyne, an ammonia monooxygenase (AMO) inhibitor, suggested that AMO was the responsible enzyme for MP transformation that occurred cometabolically. For the first time, hydroxylamine, a key intermediate of all aerobic ammonia oxidizers, was found to react with several MPs at concentrations typically occurring in AOB batch cultures. All of these MPs were also biotransformed by the AOB/NOB coculture. Moreover, the same asulam TPs were detected in both biotransformation and hydroxylamine-treated abiotic transformation experiments, whereas rufinamide TPs formed from biological transformation were not detected during hydroxylamine-mediated abiotic transformation, which was consistent with the inability of rufinamide abiotic transformation by hydroxylamine. Thus, in addition to cometabolism likely carried out by AMO, an abiotic transformation route indirectly mediated by AMO might also contribute to MP biotransformation by AOB.}, }
@article {pmid30003276, year = {2018}, author = {Miranda, V and Rothen, C and Yela, N and Aranda-Rickert, A and Barros, J and Calcagno, J and Fracchia, S}, title = {Subterranean Desert Rodents (Genus Ctenomys) Create Soil Patches Enriched in Root Endophytic Fungal Propagules.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1227-8}, pmid = {30003276}, issn = {1432-184X}, support = {PICT 0546//Consejo Nacional de Innovación, Ciencia y Tecnología/ ; }, abstract = {Subterranean rodents are considered major soil engineers, as they can locally modify soil properties by their burrowing activities. In this study, the effect of a subterranean rodent of the genus Ctenomys on soil properties and root endophytic fungal propagules in a shrub desert of northwest Argentina was examined. Our main goal was to include among root endophytic fungi not only arbuscular mycorrhiza but also the dark septate endophytes. We compared the abundance of fungal propagules as well as several microbiological and physicochemical parameters between soils from burrows and those from the surrounding landscape. Our results show that food haulage, the deposition of excretions, and soil mixing by rodents' burrowing promote soil patchiness by (1) the enrichment in both types of root endophytic fungal propagules; (2) the increase in organic matter and nutrients; and (3) changes in soil edaphic properties including moisture, field capacity, and texture. These patches may play a critical role as a source of soil heterogeneity in desert ecosystems, where burrows constructed in interpatches of bare soil can act, once abandoned, as &quot;islands of fertility,&quot; promoting the establishment of plants in an otherwise hostile environment.}, }
@article {pmid30003158, year = {2018}, author = {Samanta, B and Bhadury, P}, title = {Study of diatom assemblages in Sundarbans mangrove water based on light microscopy and rbcL gene sequencing.}, journal = {Heliyon}, volume = {4}, number = {6}, pages = {e00663}, doi = {10.1016/j.heliyon.2018.e00663}, pmid = {30003158}, issn = {2405-8440}, abstract = {Sundarbans, the world's largest mangrove deltaic region, is one of the most productive ecosystems in tropical and subtropical latitudes and also serve as a nursery ground for rich coastal fisheries. In this study, we highlighted diatom assemblages from the Indian part of Sundarbans Biosphere Reserve (SBR) area for the first time based on light microscopy and rbcL gene sequencing and phylogeny. In total, 15 diatom species (11 centric forms and 4 pennate forms) were documented using light microscopy, and 3 major clades of diatoms were detected in rbcL phylogeny. Out of 15 diatom species, 7 were the first record from Sundarbans mangrove water. One of the species, Thalassiosira ferelineata Hasle and Fryxell, was reported for the first time in an Asian mangrove ecosystem based on light microscopy. Our study suggests the importance of establishing cultures and their polyphasic taxonomy are the future necessity to create an authenticated diatom database from mangrove water, which is still overlooked globally.}, }
@article {pmid30002454, year = {2018}, author = {Phoma, S and Vikram, S and Jansson, JK and Ansorge, IJ and Cowan, DA and Van de Peer, Y and Makhalanyane, TP}, title = {Agulhas Current properties shape microbial community diversity and potential functionality.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10542}, doi = {10.1038/s41598-018-28939-0}, pmid = {30002454}, issn = {2045-2322}, abstract = {Understanding the impact of oceanographic features on marine microbial ecosystems remains a major ecological endeavour. Here we assess microbial diversity, community structure and functional capacity along the Agulhas Current system and the Subtropical Front in the South Indian Ocean (SIO). Samples collected from the epipelagic, oxygen minimum and bathypelagic zones were analysed by 16S rRNA gene amplicon and metagenomic sequencing. In contrast to previous studies, we found high taxonomic richness in surface and deep water samples, but generally low richness for OMZ communities. Beta-diversity analysis revealed significant dissimilarity between the three water depths. Most microbial communities were dominated by marine Gammaproteobacteria, with strikingly low levels of picocyanobacteria. Community composition was strongly influenced by specific environmental factors including depth, salinity, and the availability of both oxygen and light. Carbon, nitrogen and sulfur cycling capacity in the SIO was linked to several autotrophic and copiotrophic Alphaproteobacteria and Gammaproteobacteria. Taken together, our data suggest that the environmental conditions in the Agulhas Current system, particularly depth-related parameters, substantially influence microbial community structure. In addition, the capacity for biogeochemical cycling of nitrogen and sulfur is linked primarily to the dominant Gammaproteobacteria taxa, whereas ecologically rare taxa drive carbon cycling.}, }
@article {pmid30002323, year = {2018}, author = {Barrett, HL and Gomez-Arango, LF and Wilkinson, SA and McIntyre, HD and Callaway, LK and Morrison, M and Dekker Nitert, M}, title = {A Vegetarian Diet Is a Major Determinant of Gut Microbiota Composition in Early Pregnancy.}, journal = {Nutrients}, volume = {10}, number = {7}, pages = {}, doi = {10.3390/nu10070890}, pmid = {30002323}, issn = {2072-6643}, abstract = {The composition of the gut microbiota can be influenced by dietary composition. In pregnancy, the maternal gut microbiome has associations with maternal and infant metabolic status. There is little known regarding the impact of a vegetarian diet in pregnancy on maternal gut microbiota. This study explored the gut microbiota profile in women who were vegetarian or omnivorous in early gestation. Women were selected from participants in the Study of PRobiotics IN Gestational diabetes (SPRING) randomised controlled trial. Nine women identified as vegetarians were matched to omnivorous women in a 1:2 ratio. Microbiota analyses were performed using 16S rRNA gene amplicon sequencing and analysed using the Quantitative Insights Into Microbial Ecology (QIIME) and Calypso software tools. There was no difference in alpha diversity, but beta diversity was slightly reduced in vegetarians. There were differences seen in the relative abundance of several genera in those on a vegetarian diet, specifically a reduction in Collinsella, Holdemania, and increases in the relative abundances of Roseburia and Lachnospiraceae. In this sub-analysis of gut microbiota from women in early pregnancy, a vegetarian as compared to omnivorous diet, was associated with a different gut microbiome, with features suggesting alterations in fermentation end products from a mixed acid fermentation towards more acetate/butyrate.}, }
@article {pmid30001854, year = {2018}, author = {Berry, D and Loy, A}, title = {Stable-Isotope Probing of Human and Animal Microbiome Function.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2018.06.004}, pmid = {30001854}, issn = {1878-4380}, abstract = {Humans and animals host diverse communities of microorganisms important to their physiology and health. Despite extensive sequencing-based characterization of host-associated microbiomes, there remains a dramatic lack of understanding of microbial functions. Stable-isotope probing (SIP) is a powerful strategy to elucidate the ecophysiology of microorganisms in complex host-associated microbiotas. Here, we suggest that SIP methodologies should be more frequently exploited as part of a holistic functional microbiomics approach. We provide examples of how SIP has been used to study host-associated microbes in vivo and ex vivo. We highlight recent developments in SIP technologies and discuss future directions that will facilitate deeper insights into the function of human and animal microbiomes.}, }
@article {pmid29997457, year = {2018}, author = {Majeed, M and Nagabhushanam, K and Arumugam, S and Majeed, S and Ali, F}, title = {Bacillus coagulans MTCC 5856 for the management of major depression with irritable bowel syndrome: a randomised, double-blind, placebo controlled, multi-centre, pilot clinical study.}, journal = {Food &amp; nutrition research}, volume = {62}, number = {}, pages = {}, doi = {10.29219/fnr.v62.1218}, pmid = {29997457}, issn = {1654-661X}, abstract = {Background: The modification of microbial ecology in human gut by supplementing probiotics may be an alternative strategy to ameliorate or prevent depression.<br><br>Objective: The current study was conducted to assess the safety and efficacy of the probiotic strain Bacillus coagulans MTCC 5856 for major depressive disorder (MDD) in IBS patients.<br><br>Method: Patients (n = 40) diagnosed for MDD with IBS were randomized (1:1) to receive placebo or B. coagulans MTCC 5856 at a daily dose of 2 × 109 cfu (2 billion spores) and were maintained to the end of double-blind treatment (90 days). Changes from baseline in clinical symptoms of MDD and IBS were evaluated through questionnaires.<br><br>Results: Significant change (p = 0.01) in favour of the B. coagulans MTCC 5856 was observed for the primary efficacy measure Hamilton Rating Scale for Depression (HAM-D), Montgomery-Asberg Depression Rating Scale (MADRS), Center for Epidemiological Studies Depression Scale (CES-D) and Irritable bowel syndrome quality of life questionnaire (IBS-QOL). Secondary efficacy measures i.e. Clinical Global Impression-Improvement rating Scale (CGI-I), Clinical Global Impression Severity rating Scale (CGI-S), Gastrointestinal Discomfort Questionnaire (GI-DQ) and Modified Epworth Sleepiness Scale (mESS) also showed significant results (p = 0.01) in B. coagulans MTCC 5856 group compared to placebo group except dementia total reaction scoring. Serum myeloperoxidase, an inflammatory biomarker was also significantly reduced (p < 0.01) when compared with the baseline and end of the study. All the safety parameters remained well within the normal clinical range and had no clinically significant difference between the screening and at the end of the study.<br><br>Conclusion: B. coagulans MTCC 5856 showed robust efficacy for the treatment of patients experiencing IBS symptoms with major depressive disorder. The improvement in depression and IBS symptoms was statistically significant and clinically meaningful. These findings support B. coagulans MTCC 5856 as an important new treatment option for major depressive disorder in IBS patients.}, }
@article {pmid29995395, year = {2018}, author = {Du, Q and Mu, Q and Cheng, T and Li, N and Wang, X}, title = {Real-Time Imaging Revealed That Exoelectrogens from Wastewater Are Selected at the Center of a Gradient Electric Field.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {15}, pages = {8939-8946}, doi = {10.1021/acs.est.8b01468}, pmid = {29995395}, issn = {1520-5851}, abstract = {Exoelectrogens acclimated from the environment are the key to energy recovery from waste in bioelectrochemical systems. However, it is still unknown how these bacteria are selectively enriched on the electrode. Here we confirmed for the first time that the electric field (EF) intensity selects exoelectrogens from wastewater using an integrated electrovisual system with a gradient EF. Under the operating conditions (I = 3 × 10-3A), the EF intensity on the working electrode ranged from 6.00 V/cm at the center to 1.08 V/cm at the edge. A thick biofilm (88.9 μm) with spherical pink aggregates was observed at the center, while the color became gray at the edge (33.8 μm). The coverage of the biofilm also increased linearly with EF intensity from 0.42 at the edge (12 mm to the center) to 0.78 at the center. The biofilm at the center contained 76% Geobacter, which was 25% higher than that at the edge (60%). Geobacter anodireducens was the main species induced by the EF (50% at the center vs 24% at the edge). These results improve our fundamental knowledge of exoelectrogen acclimation and mixed electroactive biofilm formation, which has broader implications for energy recovery from waste and general understanding of microbial ecology.}, }
@article {pmid29992097, year = {2018}, author = {Gil-Pulido, B and Tarpey, E and Almeida, EL and Finnegan, W and Zhan, X and Dobson, ADW and O'Leary, N}, title = {Evaluation of dairy processing wastewater biotreatment in an IASBR system: Aeration rate impacts on performance and microbial ecology.}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {19}, number = {}, pages = {e00263}, doi = {10.1016/j.btre.2018.e00263}, pmid = {29992097}, issn = {2215-017X}, abstract = {Dairy processing generates large volumes of wastewater that require extensive nutrient remediation prior to discharge. Significant commercial opportunities exist therefore for cost-effective biotechnologies capable of achieving this requirement. In this study the authors evaluated the use of intermittently aerated sequencing batch reactors, (IASBRs), as a single-tank biotreatment system for co-removal of COD, nitrogen and phosphorus from synthetic dairy processing wastewater. Variation of the IASBR aeration rates, (0.8, 0.6 and 0.4 L/min), had significant impacts on the respective nutrient removal efficiencies and underlying microbial diversity profiles. Aeration at 0.6 L/min was most effective and resulted in >90% co-removal of orthophosphate and ammonium. 16S rRNA based pyrosequencing of biomass DNA samples revealed the family Comamonadaceae was notably enriched (>80% relative abundance) under these conditions. In silico predictive metabolic modelling also identified Comamonadaceae as the major contributor of several known genes for nitrogen and phosphorus assimilation (nirK, nosZ, norB, ppK, ppX and phbC).}, }
@article {pmid29991589, year = {2018}, author = {Kitzinger, K and Koch, H and Lücker, S and Sedlacek, CJ and Herbold, C and Schwarz, J and Daebeler, A and Mueller, AJ and Lukumbuzya, M and Romano, S and Leisch, N and Karst, SM and Kirkegaard, R and Albertsen, M and Nielsen, PH and Wagner, M and Daims, H}, title = {Characterization of the First &quot;Candidatus Nitrotoga&quot; Isolate Reveals Metabolic Versatility and Separate Evolution of Widespread Nitrite-Oxidizing Bacteria.}, journal = {mBio}, volume = {9}, number = {4}, pages = {}, doi = {10.1128/mBio.01186-18}, pmid = {29991589}, issn = {2150-7511}, abstract = {Nitrification is a key process of the biogeochemical nitrogen cycle and of biological wastewater treatment. The second step, nitrite oxidation to nitrate, is catalyzed by phylogenetically diverse, chemolithoautotrophic nitrite-oxidizing bacteria (NOB). Uncultured NOB from the genus &quot;Candidatus Nitrotoga&quot; are widespread in natural and engineered ecosystems. Knowledge about their biology is sparse, because no genomic information and no pure &quot;Ca Nitrotoga&quot; culture was available. Here we obtained the first &quot;Ca Nitrotoga&quot; isolate from activated sludge. This organism, &quot;Candidatus Nitrotoga fabula,&quot; prefers higher temperatures (>20°C; optimum, 24 to 28°C) than previous &quot;Ca Nitrotoga&quot; enrichments, which were described as cold-adapted NOB. &quot;Ca Nitrotoga fabula&quot; also showed an unusually high tolerance to nitrite (activity at 30 mM NO2-) and nitrate (up to 25 mM NO3-). Nitrite oxidation followed Michaelis-Menten kinetics, with an apparent Km (Km(app)) of ~89 µM nitrite and a Vmax of ~28 µmol of nitrite per mg of protein per h. Key metabolic pathways of &quot;Ca Nitrotoga fabula&quot; were reconstructed from the closed genome. &quot;Ca Nitrotoga fabula&quot; possesses a new type of periplasmic nitrite oxidoreductase belonging to a lineage of mostly uncharacterized proteins. This novel enzyme indicates (i) separate evolution of nitrite oxidation in &quot;Ca Nitrotoga&quot; and other NOB, (ii) the possible existence of phylogenetically diverse, unrecognized NOB, and (iii) together with new metagenomic data, the potential existence of nitrite-oxidizing archaea. For carbon fixation, &quot;Ca Nitrotoga fabula&quot; uses the Calvin-Benson-Bassham cycle. It also carries genes encoding complete pathways for hydrogen and sulfite oxidation, suggesting that alternative energy metabolisms enable &quot;Ca Nitrotoga fabula&quot; to survive nitrite depletion and colonize new niches.IMPORTANCE Nitrite-oxidizing bacteria (NOB) are major players in the biogeochemical nitrogen cycle and critical for wastewater treatment. However, most NOB remain uncultured, and their biology is poorly understood. Here, we obtained the first isolate from the environmentally widespread NOB genus &quot;Candidatus Nitrotoga&quot; and performed a detailed physiological and genomic characterization of this organism (&quot;Candidatus Nitrotoga fabula&quot;). Differences between key phenotypic properties of &quot;Ca Nitrotoga fabula&quot; and those of previously enriched &quot;Ca Nitrotoga&quot; members reveal an unexpectedly broad range of physiological adaptations in this genus. Moreover, genes encoding components of energy metabolisms outside nitrification suggest that &quot;Ca Nitrotoga&quot; are ecologically more flexible than previously anticipated. The identification of a novel nitrite-oxidizing enzyme in &quot;Ca Nitrotoga fabula&quot; expands our picture of the evolutionary history of nitrification and might lead to discoveries of novel nitrite oxidizers. Altogether, this study provides urgently needed insights into the biology of understudied but environmentally and biotechnologically important microorganisms.}, }
@article {pmid29990812, year = {2018}, author = {Ajmi, K and Vismara, E and Manai, I and Haddad, M and Hamdi, M and Bouallagui, H}, title = {Polyvinyl acetate processing wastewater treatment using combined Fenton's reagent and fungal consortium: Application of central composite design for conditions optimization.}, journal = {Journal of hazardous materials}, volume = {358}, number = {}, pages = {243-255}, doi = {10.1016/j.jhazmat.2018.06.050}, pmid = {29990812}, issn = {1873-3336}, abstract = {The Fenton reaction as an oxidative degradation process was used for industrial chemical wastewater (ICW) pretreatment. The biodegradation of pretreated ICW was performed, in aqueous environment under aerobic condition, by a defined fungal consortium. The central composite design (CCD) was used to study the effect of nitrogen and phosphorus addition and the concentration of the pollution on the removal of polyvinyl alcohol (PVA) and organic compounds. The interaction between parameters was modeled using the response surface methodology (RSM). Results of optimization showed COD, PVA and color removal yields of 97.8%, 98.5% and 99.75%, respectively with a supplementof 1.4 gL-1 of (NH4)2SO4, 1.2 gL-1 of KH2PO4 and 75% of concentrated ICW. Enzymatic analysis proved that laccase and lignin peroxidase were involved in the biodegradation with 45 UIL-1 and 450 UIL-1, respectively. Furthermore, the analysis of metabolic products using Fourier transforms infrared spectroscopy (FTIR) and nuclear magnetic resonance (1HNMR) showed clearly the mineralization of organic compounds and the formation of formic acid and ethanol. Therefore, the effective treatment of ICW was achieved by developing an integrated chemical and biological process which met the requirement for a safety effluent respectful for environment without risks for public health.}, }
@article {pmid29989429, year = {2018}, author = {Ronholm, J and Goordial, J and Sapers, HM and Izawa, MRM and Applin, DM and Pontefract, A and Omelon, CR and Lamarche-Gagnon, G and Cloutis, EA and Whyte, LG}, title = {Characterization of Microbial Communities Hosted in Quartzofeldspathic and Serpentinite Lithologies in Jeffrey Mine, Canada.}, journal = {Astrobiology}, volume = {18}, number = {8}, pages = {1008-1022}, doi = {10.1089/ast.2017.1685}, pmid = {29989429}, issn = {1557-8070}, abstract = {The microbial ecology and activity of serpentine deposits and associated hydrated minerals are largely unknown. Previous research has largely focused on microbial communities in active serpentinizing systems, whereas relatively little research has demonstrated the ability of serpentine deposits to host microbial communities after the cessation of serpentinization. Given the potential role of serpentinization reactions fueling primitive microbial metabolisms on early Earth and the identification of serpentine deposits on Mars, knowledge of these geobiological relationships and potential for serpentine to host extant microbial communities and preserve biosignatures is increasingly important for planetary exploration seeking signs of life. The selection of habitable sites most likely to yield putative biosignatures is crucial to mission success. In this study, we aimed to characterize, on the basis of both metabolic activity and taxonomic composition, the microbial communities hosted in two naturally co-occurring and mineralogically distinct substrates within the serpentine-rich Jeffrey Mine pit-igneous quartzofeldspathic intrusives and serpentinite. Detection of heterotrophic activity in both lithologies at 24°C, and in serpentinite at -5°C, demonstrated that each substrate had the ability to host a viable microbial community, at Mars-relevant temperatures. Targeted amplicon sequencing subsequently showed the presence of bacterial, fungal, and photosynthetic microbial communities in both substrates. Here, we have demonstrated the presence of a viable lithic microbial community within two rock types in the Jeffrey Mine and provided evidence that lithologies associated with serpentine deposits and proximal hydrated minerals have the ability to support diverse prokaryotic and eukaryotic microbial colonization.}, }
@article {pmid29987529, year = {2018}, author = {King, WL and Jenkins, C and Go, J and Siboni, N and Seymour, JR and Labbate, M}, title = {Characterisation of the Pacific Oyster Microbiome During a Summer Mortality Event.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1226-9}, pmid = {29987529}, issn = {1432-184X}, abstract = {The Pacific oyster, Crassostrea gigas, is a key commercial species that is cultivated globally. In recent years, disease outbreaks have heavily impacted C. gigas stocks worldwide, with many losses incurred during summer. A number of infectious agents have been associated with these summer mortality events, including viruses (particularly Ostreid herpesvirus 1, OsHV-1) and bacteria; however, cases where no known aetiological agent can be identified are common. In this study, we examined the microbiome of disease-affected and disease-unaffected C. gigas during a 2013-2014 summer mortality event in Port Stephens (Australia) where known oyster pathogens including OsHV-1 were not detected. The adductor muscle microbiomes of 70 C. gigas samples across 12 study sites in the Port Stephens estuary were characterised using 16S rRNA (V1-V3 region) amplicon sequencing, with the aim of comparing the influence of spatial location and disease state on the oyster microbiome. Spatial location was found to be a significant determinant of the disease-affected oyster microbiome. Furthermore, microbiome comparisons between disease states identified a significant increase in rare operational taxonomic units (OTUs) belonging to Vibrio harveyi and an unidentified member of the Vibrio genus in the disease-affected microbiome. This is indicative of a potential role of Vibrio species in oyster disease and supportive of previous culture-based examination of this mortality event.}, }
@article {pmid29986719, year = {2018}, author = {Mohr, T and Aliyu, H and Küchlin, R and Polliack, S and Zwick, M and Neumann, A and Cowan, D and de Maayer, P}, title = {CO-dependent hydrogen production by the facultative anaerobe Parageobacillus thermoglucosidasius.}, journal = {Microbial cell factories}, volume = {17}, number = {1}, pages = {108}, doi = {10.1186/s12934-018-0954-3}, pmid = {29986719}, issn = {1475-2859}, support = {031B0180//Bundesministerium für Bildung und Forschung/ ; 109137//National Research Foundation of South Africa/ ; }, abstract = {BACKGROUND: The overreliance on dwindling fossil fuel reserves and the negative climatic effects of using such fuels are driving the development of new clean energy sources. One such alternative source is hydrogen (H2), which can be generated from renewable sources. Parageobacillus thermoglucosidasius is a facultative anaerobic thermophilic bacterium which is frequently isolated from high temperature environments including hot springs and compost.<br><br>RESULTS: Comparative genomics performed in the present study showed that P. thermoglucosidasius encodes two evolutionary distinct H2-uptake [Ni-Fe]-hydrogenases and one H2-evolving hydrogenases. In addition, genes encoding an anaerobic CO dehydrogenase (CODH) are co-localized with genes encoding a putative H2-evolving hydrogenase. The co-localized of CODH and uptake hydrogenase form an enzyme complex that might potentially be involved in catalyzing the water-gas shift reaction (CO + H2O → CO2 + H2) in P. thermoglucosidasius. Cultivation of P. thermoglucosidasius DSM 2542T with an initial gas atmosphere of 50% CO and 50% air showed it to be capable of growth at elevated CO concentrations (50%). Furthermore, GC analyses showed that it was capable of producing hydrogen at an equimolar conversion with a final yield of 1.08 H2/CO.<br><br>CONCLUSIONS: This study highlights the potential of the facultative anaerobic P. thermoglucosidasius DSM 2542T for developing new strategies for the biohydrogen production.}, }
@article {pmid29986237, year = {2018}, author = {Zhang, Q and Vlaeminck, SE and DeBarbadillo, C and Su, C and Al-Omari, A and Wett, B and Pümpel, T and Shaw, A and Chandran, K and Murthy, S and De Clippeleir, H}, title = {Supernatant organics from anaerobic digestion after thermal hydrolysis cause direct and/or diffusional activity loss for nitritation and anammox.}, journal = {Water research}, volume = {143}, number = {}, pages = {270-281}, doi = {10.1016/j.watres.2018.06.037}, pmid = {29986237}, issn = {1879-2448}, abstract = {Treatment of sewage sludge with a thermal hydrolysis process (THP) followed by anaerobic digestion (AD) enables to boost biogas production and minimize residual sludge volumes. However, the reject water can cause inhibition to aerobic and anoxic ammonium-oxidizing bacteria (AerAOB &amp; AnAOB), the two key microbial groups involved in the deammonification process. Firstly, a detailed investigation elucidated the impact of different organic fractions present in THP-AD return liquor on AerAOB and AnAOB activity. For AnAOB, soluble compounds linked to THP conditions and AD performance caused the main inhibition. Direct inhibition by dissolved organics was also observed for AerAOB, but could be overcome by treating the filtrate with extended aerobic or anaerobic incubation or with activated carbon. AerAOB additionally suffered from particulate and colloidal organics limiting the diffusion of substrates. This was resolved by improving the dewatering process through an optimized flocculant polymer dose and/or addition of coagulant polymer to better capture the large colloidal fraction, especially in case of unstable AD performance. Secondly, a new inhibition model for AerAOB included diffusion-limiting compounds based on the porter-equation, and achieved the best fit with the experimental data, highlighting that AerAOB were highly sensitive to large colloids. Overall, this paper for the first time provides separate identification of organic fractions within THP-AD filtrate causing differential types of inhibition. Moreover, it highlights the combined effect of the performance of THP, AD and dewatering on the downstream autotrophic nitrogen removal kinetics.}, }
@article {pmid29985435, year = {2018}, author = {Mori, G and Rampelli, S and Orena, BS and Rengucci, C and De Maio, G and Barbieri, G and Passardi, A and Casadei Gardini, A and Frassineti, GL and Gaiarsa, S and Albertini, AM and Ranzani, GN and Calistri, D and Pasca, MR}, title = {Shifts of Faecal Microbiota During Sporadic Colorectal Carcinogenesis.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10329}, doi = {10.1038/s41598-018-28671-9}, pmid = {29985435}, issn = {2045-2322}, abstract = {Gut microbiota has been implicated in the etiopathogenesis of colorectal cancer. The development of colorectal cancer is a multistep process by which healthy epithelium slowly develops into preneoplastic lesions, which in turn progress into malignant carcinomas over time. In particular, sporadic colorectal cancers can arise from adenomas (about 85% of cases) or serrated polyps through the &quot;adenoma-carcinoma&quot; or the &quot;serrated polyp-carcinoma&quot; sequences, respectively. In this study, we performed 16 S rRNA gene sequencing of bacterial DNA extracted from faecal samples to compare the microbiota of healthy subjects and patients with different preneoplastic and neoplastic lesions. We identified putative microbial biomarkers associated with stage-specific progression of colorectal cancer. In particular, bacteria belonging to the Firmicutes and Actinobacteria phyla, as well as members of the Lachnospiraceae family, proved to be specific of the faecal microbiota of patients with preneoplastic lesions, including adenomas and hyperplastic polyps. On the other hand, two families of the Proteobacteria phylum, Alcaligeneaceae and Enterobacteriaceae, with Sutterella and Escherichia/Shigella being the most representative genera, appeared to be associated with malignancy. These findings, once confirmed on larger cohorts of patients, can represent an important step towards the development of more effective diagnostic strategies.}, }
@article {pmid29984314, year = {2018}, author = {Danczak, RE and Johnston, MD and Kenah, C and Slattery, M and Wilkins, MJ}, title = {Microbial Community Cohesion Mediates Community Turnover in Unperturbed Aquifers.}, journal = {mSystems}, volume = {3}, number = {4}, pages = {}, doi = {10.1128/mSystems.00066-18}, pmid = {29984314}, issn = {2379-5077}, abstract = {Microbial ecological processes are frequently studied in the presence of perturbations rather than in undisturbed environments, despite the relatively stable conditions dominating many microbial habitats. To examine processes influencing microbial community structuring in the absence of strong external perturbations, three unperturbed aquifers in Ohio (Greene, Licking, and Athens) were sampled over 2 years and analyzed using geochemical measurements, 16S rRNA gene sequencing, and ecological modeling. Redox conditions ranging from highly reducing to more oxidizing distinguished aquifer geochemistry across the three locations. Distinct microbial communities were present in each aquifer, and overall community structure was related to geochemistry, although community composition was more similar between the Athens and Licking locations. The ecological processes acting upon microbial assemblages within aquifers were varied; geochemical changes affected the Athens location, while time or some unknown factor affected Greene County. Stochastic processes, however, dominated the Licking aquifer, suggesting a decoupling between environmental fluctuations and community development. Although physicochemical differences might be expected to drive variable selection, dispersal limitation (inability to mix) explained differences between Athens and Licking. Finally, community complexity as measured by &quot;cohesion&quot; indicated that less-interconnected communities experienced higher turnover and were more likely to be affected by stochastic processes. Conversely, more-interconnected communities experienced lower turnover and susceptibility to homogenizing selection. Based upon these data, we support the hypothesis that unperturbed environments house dynamic microbial communities due to external and internal forces. IMPORTANCE Many microbial ecology studies have examined community structuring processes in dynamic or perturbed situations, while stable environments have been investigated to a lesser extent. Researchers have predicted that environmental communities never truly reach a steady state but rather exist in states of constant flux due to internal, rather than external, dynamics. The research presented here utilized a combined null model approach to examine the deterministic and stochastic processes responsible for observed community differences in unperturbed, groundwater ecosystems. Additionally, internal dynamics were investigated by relating a recently published measure of community complexity (cohesion) to ecological structuring processes. The data presented here suggest that communities that are more cohesive, and therefore more complex, are more likely affected by homogenizing selection, while less-complex communities are more susceptible to dispersal. By understanding the relationship between internal dynamics and community structuring processes, insight about microbial population development in natural systems can be obtained.}, }
@article {pmid29978357, year = {2018}, author = {Kearns, PJ and Bulseco-McKim, AN and Hoyt, H and Angell, JH and Bowen, JL}, title = {Nutrient Enrichment Alters Salt Marsh Fungal Communities and Promotes Putative Fungal Denitrifiers.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1223-z}, pmid = {29978357}, issn = {1432-184X}, support = {1350491//National Science Foundation (US)/ ; 1353140//National Science Foundation (US)/ ; DBI-1359241//National Science Foundation (US)/ ; OCE0924287//National Science Foundation (US)/ ; OCE0923689//National Science Foundation (US)/ ; DEB0213767//National Science Foundation (US)/ ; DEB1354494//National Science Foundation (US)/ ; OCE1353140//National Science Foundation (US)/ ; OCE 1673630//National Science Foundation (US)/ ; OCE0423565//National Science Foundation (US)/ ; OCE1058747//National Science Foundation (US)/ ; }, abstract = {Enrichment of ecosystems with excess nutrients is occurring at an alarming rate and has fundamentally altered ecosystems worldwide. Salt marshes, which lie at the land-sea interface, are highly effective at removing anthropogenic nutrients through the action of macrophytes and through microbial processes in coastal sediments. The response of salt marsh bacteria to excess nitrogen has been documented; however, the role of fungi and their response to excess nitrogen in salt marsh sediments is not fully understood. Here, we document the response of salt marsh fungal communities to long-term excess nitrate in four distinct marsh habitats within a northern temperate marsh complex. We show that salt marsh fungal communities varied as a function of salt marsh habitat, with both fungal abundance and diversity increasing with carbon quantity. Nutrient enrichment altered fungal communities in all habitats through an increase in fungal abundance and the proliferation of putative fungal denitrifiers. Nutrient enrichment also altered marsh carbon quality in low marsh surface sediments where fungal response to nutrient enrichment was most dramatic, suggesting nutrient enrichment can alter organic matter quality in coastal sediments. Our results indicate that fungi, in addition to bacteria, likely play an important role in anaerobic decomposition of salt marsh sediment organic matter.}, }
@article {pmid29978356, year = {2018}, author = {Ferrándiz, MJ and Cercenado, MI and Domenech, M and Tirado-Vélez, JM and Escolano-Martínez, MS and Yuste, J and García, E and de la Campa, AG and Martín-Galiano, AJ}, title = {An Uncharacterized Member of the Gls24 Protein Superfamily Is a Putative Sensor of Essential Amino Acid Availability in Streptococcus pneumoniae.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1218-9}, pmid = {29978356}, issn = {1432-184X}, support = {BIO2014-55462-R//Ministerio de Economía y Competitividad/ ; SAF2012-39444-C02//Ministerio de Economía y Competitividad/ ; }, abstract = {Proteins belonging to the Gls24 superfamily are involved in survival of pathogenic Gram-positive cocci under oligotrophic conditions and other types of stress, by a still unknown molecular mechanism. In Firmicutes, this superfamily includes three different valine-rich orthologal families (Gls24A, B, C) with different potential interactive partners. Whereas the Streptococcus pneumoniae Δgls24A deletion mutant experienced a general long growth delay, the Δgls24B mutant grew as the parental strain in the semisynthetic AGCH medium but failed to grow in the complex Todd-Hewitt medium. Bovine seroalbumin (BSA) was the component responsible for this phenotype. The effect of BSA on growth was concentration-dependent and was maintained when the protein was proteolyzed but not when heat-denatured, suggesting that BSA dependence was related to oligopeptide supplementation. Global transcriptional analyses of the knockout mutant revealed catabolic derepression and induction of chaperone and oligopeptide transport genes. This mutant also showed increased sensibility to cadmium and high temperature. The Δgls24B mutant behaved as a poor colonizer in the nasopharynx of mice and showed 20-fold competence impairment. Experimental data suggest that Gls24B plays a central role as a sensor of amino acid availability and its connection to sugar catabolism. This metabolic rewiring can be compensated in vitro, at the expenses of external oligopeptide supplementation, but reduce important bacteria skills prior to efficiently address systemic virulence traits. This is an example of how metabolic factors conserved in enterococci, streptococci, and staphylococci can be essential for survival in poor oligopeptide environments prior to infection progression.}, }
@article {pmid29974320, year = {2018}, author = {Makita, H}, title = {Iron-oxidizing bacteria in marine environments: recent progresses and future directions.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {34}, number = {8}, pages = {110}, doi = {10.1007/s11274-018-2491-y}, pmid = {29974320}, issn = {1573-0972}, support = {JP 26820389//JSPS KAKENHI/ ; JP 18K04595//JSPS KAKENHI/ ; }, mesh = {Bacteria/*classification/*metabolism ; Biodiversity ; Corrosion ; Hydrogen-Ion Concentration ; Iron/*metabolism ; Marine Biology ; Oxidation-Reduction ; Oxygen/metabolism ; *Phylogeny ; Phylogeography ; Proteobacteria/classification/cytology/metabolism ; Seawater/*microbiology ; }, abstract = {Iron-oxidizing bacteria (FeOB) refers to a group of bacteria with the ability to exchange and accumulate divalent iron dissolved in water as trivalent iron inside and outside the bacterial cell. Most FeOB belong the largest bacterial phylum, Proteobacteria. Within this phylum, FeOB with varying physiology with regards to their response to oxygen (obligate aerobes, facultative and obligate anaerobes) and pH optimum for proliferation (neutrophiles, moderate and extreme acidophiles) can be found. Although FeOB have been reported from a wide variety of environments, most of them have not been isolated and their biochemical characteristics remain largely unknown. This is especially true for those living in the marine realm, where the properties of FeOB was not known until the isolation of the Zetaproteobacteria Mariprofundus ferrooxydans, first reported in 2007. Since the proposal of Zetaproteobacteria by Emerson et al., the detection and isolation of those microorganisms from the marine environment has greatly escalated. Furthermore, FeOB have also recently been reported from works on ocean drilling and metal corrosion. This review aims to summarize the current state of phylogenetic and physiological diversity in marine FeOB, the significance of their roles in their environments (on both global and local scales), as well as their growing importance and applications in the industry.}, }
@article {pmid29974184, year = {2018}, author = {Pierangelini, M and Glaser, K and Mikhailyuk, T and Karsten, U and Holzinger, A}, title = {Light and Dehydration but Not Temperature Drive Photosynthetic Adaptations of Basal Streptophytes (Hormidiella, Streptosarcina and Streptofilum) Living in Terrestrial Habitats.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1225-x}, pmid = {29974184}, issn = {1432-184X}, support = {I 1951-B16//Austrian Science Fund/ ; Ref. No. 06-1000014-6216//Alexander von Humboldt-Stiftung/ ; KA899/16//Deutsche Forschungsgemeinschaft/ ; GL 909/1-1//Deutsche Forschungsgemeinschaft (DE) Priority Program 1991 &quot;Taxon-omics&quot;/ ; }, abstract = {Streptophyte algae are the ancestors of land plants, and several classes contain taxa that are adapted to an aero-terrestrial lifestyle. In this study, four basal terrestrial streptophytes from the class Klebsormidiophyceae, including Hormidiella parvula; two species of the newly described genus Streptosarcina (S. costaricana and S. arenaria); and the newly described Streptofilum capillatum were investigated for their responses to radiation, desiccation and temperature stress conditions. All the strains showed low-light adaptation (Ik < 70 μmol photons m-2 s-1) but differed in photoprotective capacities (such as non-photochemical quenching). Acclimation to enhanced photon fluence rates (160 μmol photons m-2 s-1) increased photosynthetic performance in H. parvula and S. costaricana but not in S. arenaria, showing that low-light adaptation is a constitutive trait for S. arenaria. This lower-light adaptation of S. arenaria was coupled with a higher desiccation tolerance, providing further evidence that dehydration is a selective force shaping species occurrence in low light. For protection against ultraviolet radiation, all species synthesised and accumulated different amounts of mycosporine-like amino acids (MAAs). Biochemically, MAAs synthesised by Hormidiella and Streptosarcina were similar to MAAs from closely related Klebsormidium spp. but differed in retention time and spectral characteristics in S. capillatum. Unlike the different radiation and dehydration tolerances, Hormidiella, Streptosarcina and Streptofilum displayed preferences for similar thermal conditions. These species showed a temperature dependence of photosynthesis similar to respiration, contrasting with Klebsormidium spp. and highlighting an interspecific diversity in thermal requirements, which could regulate species distributions under temperature changes.}, }
@article {pmid29973712, year = {2018}, author = {Das, B and Ghosh, TS and Kedia, S and Rampal, R and Saxena, S and Bag, S and Mitra, R and Dayal, M and Mehta, O and Surendranath, A and Travis, SPL and Tripathi, P and Nair, GB and Ahuja, V}, title = {Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10104}, doi = {10.1038/s41598-018-28550-3}, pmid = {29973712}, issn = {2045-2322}, support = {BT/MB/THSTI/HMC-SFC/2011//Department of Biotechnology, Ministry of Science and Technology (DBT)/ ; INT/UK/P-116/14//Department of Science and Technology, Ministry of Science and Technology (DST)/ ; }, abstract = {The diversity and basic functional attributes of the gut microbiome of healthy Indians is not well understood. This study investigated the gut microbiome of three Indian communities: individuals residing in rural and urban (n = 49) sea level Ballabhgarh areas and in rural high altitude areas of Leh, Ladakh in North India (n = 35). Our study revealed that the gut microbiome of Indian communities is dominated by Firmicutes followed by Bacteroidetes, Actinobateria and Proteobacteria. Although, 54 core bacterial genera were detected across the three distinct communities, the gut bacterial composition displayed specific signatures and was observed to be influenced by the topographical location and dietary intake of the individuals. The gut microbiome of individuals living in Leh was observed to be significantly similar with a high representation of Bacteroidetes and low abundance of Proteobacteria. In contrast, the gut microbiome of individuals living in Ballabhgarh areas harbored higher number of Firmicutes and Proteobacteria and is enriched with microbial xenobiotic degradation pathways. The rural community residing in sea level Ballabhgarh areas has unique microbiome characterized not only by a higher diversity, but also a higher degree of interindividual homogeneity.}, }
@article {pmid29967922, year = {2018}, author = {Nesvorna, M and Bittner, V and Hubert, J}, title = {The Mite Tyrophagus putrescentiae Hosts Population-Specific Microbiomes That Respond Weakly to Starvation.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1224-y}, pmid = {29967922}, issn = {1432-184X}, support = {GA15-09038S//Grantová Agentura České Republiky/ ; }, abstract = {The effect of short-term nutrient deprivation was studied in five populations of the mite Tyrophagus putrescentiae with different microbiomes. The fresh weight, nutrient status, respiration, and population growth of the mites were observed for the five mite population-scale samples. The starvation caused the larvae and nymphs to be eliminated, resulting in a significant increase in the fresh weight of starved adult specimens. Three populations were negatively influenced by starvation, and the starved specimens were characterized by a decrease in nutrient status, respiration, and population growth. One population was not influenced or was slightly influenced by starvation, which had no effect on population growth or nutrient contents but caused a significant decrease in respiration. One population was positively influenced by starvation; the population growth increased in starved specimens, and starvation had no effect on respiration. Although starvation altered the bacterial profiles of the microbiomes, these differences were much smaller than those between the populations. The bacterial profiles of Staphylococcus, Bacillus, Kocuria, Brevibacterium, and unidentified Micrococcaceae and Enterobacteriaceae increased in starved specimens, whereas those of Bartonella and Solitalea-like genera were reduced in the starved mite populations. The profiles of the intracellular symbiont Cardinium decreased in the starved specimens, and the Wolbachia profile changes were dependent on the mite population. In mite populations, when the symbionts were rare, their profiles varied stochastically. Correlations between changes in the profiles of the bacterial taxa and mite fitness parameters, including nutrient status (lipids, proteins, saccharides, and glycogen contents), mite population growth, and respiration, were observed. Although the microbiomes were resistant to the perturbations caused by nutrition deficiency, the responses of the mites differed in terms of their population growth, respiration, and nutrient status.}, }
@article {pmid29966083, year = {2018}, author = {Palermo, A and Forsberg, EM and Warth, B and Aisporna, AE and Billings, E and Kuang, E and Benton, HP and Berry, D and Siuzdak, G}, title = {Fluorinated Gold Nanoparticles for Nanostructure Imaging Mass Spectrometry.}, journal = {ACS nano}, volume = {12}, number = {7}, pages = {6938-6948}, doi = {10.1021/acsnano.8b02376}, pmid = {29966083}, issn = {1936-086X}, abstract = {Nanostructure imaging mass spectrometry (NIMS) with fluorinated gold nanoparticles (f-AuNPs) is a nanoparticle assisted laser desorption/ionization approach that requires low laser energy and has demonstrated high sensitivity. Here we describe NIMS with f-AuNPs for the comprehensive analysis of metabolites in biological tissues. F-AuNPs assist in desorption/ionization by laser-induced release of the fluorocarbon chains with minimal background noise. Since the energy barrier required to release the fluorocarbons from the AuNPs is minimal, the energy of the laser is maintained in the low μJ/pulse range, thus limiting metabolite in-source fragmentation. Electron microscopy analysis of tissue samples after f-AuNP NIMS shows a distinct &quot;raising&quot; of the surface as compared to matrix assisted laser desorption ionization ablation, indicative of a gentle desorption mechanism aiding in the generation of intact molecular ions. Moreover, the use of perfluorohexane to distribute the f-AuNPs on the tissue creates a hydrophobic environment minimizing metabolite solubilization and spatial dislocation. The transfer of the energy from the incident laser to the analytes through the release of the fluorocarbon chains similarly enhances the desorption/ionization of metabolites of different chemical nature, resulting in heterogeneous metabolome coverage. We performed the approach in a comparative study of the colon of mice exposed to three different diets. F-AuNP NIMS allows the direct detection of carbohydrates, lipids, bile acids, sulfur metabolites, amino acids, nucleotide precursors as well as other small molecules of varied biological origins. Ultimately, the diversified molecular coverage obtained provides a broad picture of a tissue's metabolic organization.}, }
@article {pmid29965364, year = {2017}, author = {Zhou, HY and Han, ML and Qiu, TL and Gao, M and Sun, XB and Wang, XM}, title = {[Ammonia Removal Rate and Microbial Community Structures in Different Biofilters for Treating Aquaculture Wastewater].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {38}, number = {6}, pages = {2444-2452}, doi = {10.13227/j.hjkx.201610142}, pmid = {29965364}, issn = {0250-3301}, abstract = {Three MBBRs and three curtain type trickling filters (CTFs) with different carriers were operated in lab-scale simulated RASs. The characteristics of biofilms, ammonia removal rates and microbial communities in six reactors were compared with each other. Compared with the biofilms of MBBRs, the biofilms of CTFs were heavier and grew faster. The weight of biofilms on CTFs with carbon fiber carriers was the maximum (45.97 g·m-2), and the ammonia nitrogen removal efficiency (86.76%) of this CTFs was higher than the other filters or reactors (61.96%~78.76%). In addition, the concentration of the accumulated nitrite in the carbon fiber CTFs was the lowest in all the six reactors. The microbial communities of biofilms in the six biofilters were evaluated by the high-throughput Illumina-MiSeq sequencing technology. The results showed that the microbial (bacteria and eukaryote) community in biofilms of CTFs was different from that in biofilms of MBBRs. At both bacteria and micro-eukaryote level, the species richness and biological diversity of biofilms in the trickling filters were higher than those in the MBBRs. On the contrary, the Simpson index of bacterial community in biofilms of MBBRs was higher than that in the trickling filters. In all the six biofilters, Nitrospira and Nakamurella were the dominated bacterial genera. Saprospiraceae was more abundant in CTFs than in MBBRs, but Comamonadaceae was enriched in the MBBRs. At the micro-eukaryote genus level, Rhabditida norank genus was more abundant in CTFs, while Chlorophyceae norank genus was more abundant in the MBBRs. The results provide useful information about microbial ecology that can be used for the application of CTFs in RAS.}, }
@article {pmid29963907, year = {2018}, author = {Kiewra, D and Szymanowski, M and Zalewska, G and Dobracka, B and Dobracki, W and Klakočar, J and Czułowska, A and Plewa-Tutaj, K}, title = {Seroprevalence of Borrelia burgdorferi in forest workers from inspectorates with different forest types in Lower Silesia, SW Poland: preliminary study.}, journal = {International journal of environmental health research}, volume = {28}, number = {5}, pages = {502-510}, doi = {10.1080/09603123.2018.1489954}, pmid = {29963907}, issn = {1369-1619}, abstract = {To estimate the Lyme borreliosis (LB) risk for forest workers, totally 646 blood samples were tested for IgG and IgM anti-Borrelia burgdorferi s.l. (anti-B.b.) antibody occurrence using ELISA tests confirmed with western blot. To clarify the varied LB risk, additionally, the data from the Forest Data Bank determining the detailed forest habitat type in particular forest inspectorates were used. The occurrence of the anti-B.b. antibody was confirmed in 22% (8.7% IgM, 17.8% IgG) of forest workers. Analysis of the influence of the habitat type (forest types) indicated the significant positive impact of the occurrence of the deciduous and mixed-deciduous forests on the seroprevalence of anti-B.b. IgG level among forestry workers. However, the share of forest type cannot be the only factor taken into account when assessing risk.}, }
@article {pmid29963641, year = {2018}, author = {Tsukayama, P and Boolchandani, M and Patel, S and Pehrsson, EC and Gibson, MK and Chiou, KL and Jolly, CJ and Rogers, J and Phillips-Conroy, JE and Dantas, G}, title = {Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes.}, journal = {mSystems}, volume = {3}, number = {3}, pages = {}, doi = {10.1128/mSystems.00016-18}, pmid = {29963641}, issn = {2379-5077}, support = {DP2 DK098089/DK/NIDDK NIH HHS/United States ; R01 GM099538/GM/NIGMS NIH HHS/United States ; }, abstract = {Environmental microbes have harbored the capacity for antibiotic production for millions of years, spanning the evolution of humans and other vertebrates. However, the industrial-scale use of antibiotics in clinical and agricultural practice over the past century has led to a substantial increase in exposure of these agents to human and environmental microbiota. This perturbation is predicted to alter the ecology of microbial communities and to promote the evolution and transfer of antibiotic resistance (AR) genes. We studied wild and captive baboon populations to understand the effects of exposure to humans and human activities (e.g., antibiotic therapy) on the composition of the primate fecal microbiota and the antibiotic-resistant genes that it collectively harbors (the &quot;resistome&quot;). Using a culture-independent metagenomic approach, we identified functional antibiotic resistance genes in the gut microbiota of wild and captive baboon groups and saw marked variation in microbiota architecture and resistomes across habitats and lifeways. Our results support the view that antibiotic resistance is an ancient feature of gut microbial communities and that sharing habitats with humans may have important effects on the structure and function of the primate microbiota. IMPORTANCE Antibiotic exposure results in acute and persistent shifts in the composition and function of microbial communities associated with vertebrate hosts. However, little is known about the state of these communities in the era before the widespread introduction of antibiotics into clinical and agricultural practice. We characterized the fecal microbiota and antibiotic resistomes of wild and captive baboon populations to understand the effect of human exposure and to understand how the primate microbiota may have been altered during the antibiotic era. We used culture-independent and bioinformatics methods to identify functional resistance genes in the guts of wild and captive baboons and show that exposure to humans is associated with changes in microbiota composition and resistome expansion compared to wild baboon groups. Our results suggest that captivity and lifestyle changes associated with human contact can lead to marked changes in the ecology of primate gut communities.}, }
@article {pmid29963639, year = {2018}, author = {Nieves-Ramírez, ME and Partida-Rodríguez, O and Laforest-Lapointe, I and Reynolds, LA and Brown, EM and Valdez-Salazar, A and Morán-Silva, P and Rojas-Velázquez, L and Morien, E and Parfrey, LW and Jin, M and Walter, J and Torres, J and Arrieta, MC and Ximénez-García, C and Finlay, BB}, title = {Asymptomatic Intestinal Colonization with Protist Blastocystis Is Strongly Associated with Distinct Microbiome Ecological Patterns.}, journal = {mSystems}, volume = {3}, number = {3}, pages = {}, doi = {10.1128/mSystems.00007-18}, pmid = {29963639}, issn = {2379-5077}, abstract = {Blastocystis is the most prevalent protist of the human intestine, colonizing approximately 20% of the North American population and up to 100% in some nonindustrialized settings. Blastocystis is associated with gastrointestinal and systemic disease but can also be an asymptomatic colonizer in large populations. While recent findings in humans have shown bacterial microbiota changes associated with this protist, it is unknown whether these occur due to the presence of Blastocystis or as a result of inflammation. To explore this, we evaluated the fecal bacterial and eukaryotic microbiota in 156 asymptomatic adult subjects from a rural population in Xoxocotla, Mexico. Colonization with Blastocystis was strongly associated with an increase in bacterial alpha diversity and broad changes in beta diversity and with more discrete changes to the microbial eukaryome. More than 230 operational taxonomic units (OTUs), including those of dominant species Prevotella copri and Ruminococcus bromii, were differentially abundant in Blastocystis-colonized individuals. Large functional changes accompanied these observations, with differential abundances of 202 (out of 266) predicted metabolic pathways (PICRUSt), as well as lower fecal concentrations of acetate, butyrate, and propionate in colonized individuals. Fecal calprotectin was markedly decreased in association with Blastocystis colonization, suggesting that this ecological shift induces subclinical immune consequences to the asymptomatic host. This work is the first to show a direct association between the presence of Blastocystis and shifts in the gut bacterial and eukaryotic microbiome in the absence of gastrointestinal disease or inflammation. These results prompt further investigation of the role Blastocystis and other eukaryotes play within the human microbiome. IMPORTANCE Given the results of our study and other reports of the effects of the most common human gut protist on the diversity and composition of the bacterial microbiome, Blastocystis and, possibly, other gut protists should be studied as ecosystem engineers that drive community diversity and composition.}, }
@article {pmid29960932, year = {2018}, author = {Proia, L and Anzil, A and Borrego, C and Farrè, M and Llorca, M and Sanchis, J and Bogaerts, P and Balcázar, JL and Servais, P}, title = {Occurrence and persistence of carbapenemases genes in hospital and wastewater treatment plants and propagation in the receiving river.}, journal = {Journal of hazardous materials}, volume = {358}, number = {}, pages = {33-43}, doi = {10.1016/j.jhazmat.2018.06.058}, pmid = {29960932}, issn = {1873-3336}, abstract = {This study aims to investigate the prevalence of clinically relevant carbapenemases genes (blaKPC, blaNDM and blaOXA-48) in water samples collected over one-year period from hospital (H), raw and treated wastewater of two wastewater treatment plants (WWTPs) as well as along the Zenne River (Belgium). The genes were quantified in both particle-attached (PAB) and free-living (FLB) bacteria. Our results showed that absolute abundances were the highest in H waters. Although absolute abundances were significantly reduced in WWTP effluents, the relative abundance (normalized per 16S rRNA) was never lowered through wastewater treatment. Particularly, for the PAB the relative abundances were significantly higher in the effluents respect to the influents of both WWTPs for all the genes. The absolute abundances along the Zenne River increased from upstream to downstream, peaking after the release of WWTPs effluents, in both fractions. Our results demonstrated that blaKPC, blaNDM and blaOXA-48 are widely distributed in the Zenne as a consequence of chronic discharge from WWTPs. To conclude, the levels of carbapenemases genes are significantly lower than other genes conferring resistance to more widely used antibiotics (analyzed in previous studies carried out at the same sites), but could raise up to the levels of high prevalent resistance genes.}, }
@article {pmid29959406, year = {2018}, author = {Kearns, PJ and Shade, A}, title = {Trait-based patterns of microbial dynamics in dormancy potential and heterotrophic strategy: case studies of resource-based and post-press succession.}, journal = {The ISME journal}, volume = {12}, number = {11}, pages = {2575-2581}, doi = {10.1038/s41396-018-0194-x}, pmid = {29959406}, issn = {1751-7370}, abstract = {Understanding the relationship between microbial community structure and function is a major challenge in microbial ecology. Recent work has shown that community weighted mean 16S rRNA gene copies, as a proxy for heterotrophic growth strategy, is a microbial community trait that decreases predictably over successional trajectories that are underpinned by changes in resource availability. However, it has been challenging to identify other microbial traits that are predictive of community functions and have consistent patterns with succession. Trait-based patterns of secondary succession (e.g., after a disturbance) are less often considered, and these responses may be underpinned by abiotic drivers other than changes in resources. In this perspectives piece, we present hypotheses about microbial traits important for microbial succession in resource-based and post-press disturbance scenarios, as synthesized from previous works and extended within this work. Using four case studies, we compare two traits, heterotrophic strategy and dormancy potential, and two different types of succession, resource-based (endogenous heterotrophic) and post-press. There were decreases in weighted ribosomal operon counts and in dormancy genes over resource-based succession. Both traits also were lower in post-press succession as compared to reference conditions, but increased with time from disturbance. Thus, dormancy potential may be an additional trait that changes predictably with succession. Finally, considering changes in microbial community traits over post-press succession is as important as over resource-based succession. These patterns need to be interpreted carefully and reference and recovering samples can be collected to improve interpretation of changes in community traits over post-press succession.}, }
@article {pmid29958172, year = {2018}, author = {Li, H and Zhou, L and Lin, H and Xu, X and Jia, R and Xia, S}, title = {Dynamic response of biofilm microbial ecology to para-chloronitrobenzene biodegradation in a hydrogen-based, denitrifying and sulfate-reducing membrane biofilm reactor.}, journal = {The Science of the total environment}, volume = {643}, number = {}, pages = {842-849}, doi = {10.1016/j.scitotenv.2018.06.245}, pmid = {29958172}, issn = {1879-1026}, abstract = {The dynamic response of biofilm microbial ecology to para-chloronitrobenzene (p-CNB) biodegradation was systematically evaluated according to the composition and loading of electron acceptors and H2 availability (controlled by H2 pressure) in a hydrogen-based, denitrifying and sulfate-reducing membrane biofilm reactor (MBfR). To accomplish this, a laboratory-scale MBfR was set up and operated with different influent p-CNB concentrations (0, 2, and 5 mg p-CNB/L) and H2 pressures (0.04 and 0.05 MPa). Polymerase chain reaction-denaturing gel electrophoresis (PCR-DGGE) and cloning were then applied to investigate the bacterial diversity response of biofilm during p-CNB biodegradation. The results showed that denitrification and sulfate reduction largely controlled the total demand for H2. Additionally, the DGGE fingerprint demonstrated that the addition of p-CNB, which acted as an electron acceptor, was a critical factor in the dynamics of the MBfR biofilm microbial ecology. The presence of p-CNB also had a more advantageous effect on the biofilm microbial community. Additionally, clone library analysis showed that Proteobacteria (especially beta- and gamma-) comprised the majority of the microbial biofilm response to p-CNB biodegradation, and that Pseudomonas sp. (Gammaproteobacteria) played a significant role in the biotransformation of p-CNB to aniline.}, }
@article {pmid29957118, year = {2018}, author = {Moravej, H and Moravej, Z and Yazdanparast, M and Heiat, M and Mirhosseini, A and Moosazadeh Moghaddam, M and Mirnejad, R}, title = {Antimicrobial Peptides: Features, Action, and Their Resistance Mechanisms in Bacteria.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {24}, number = {6}, pages = {747-767}, doi = {10.1089/mdr.2017.0392}, pmid = {29957118}, issn = {1931-8448}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Antimicrobial Cationic Peptides/*pharmacology/*therapeutic use ; Bacteria/*drug effects ; Biofilms/drug effects ; Drug Resistance, Bacterial/*drug effects ; Humans ; Immunity, Innate/drug effects ; }, abstract = {In recent years, because of increased resistance to conventional antimicrobials, many researchers have started to study the synthesis of new antibiotics to control the disease-causing effects of infectious pathogens. Antimicrobial peptides (AMPs) are among the newest antibiotics; these peptides are integral compounds in all kinds of organisms and play a significant role in microbial ecology, and critically contribute to the innate immunity of organisms by destroying invading microorganisms. Moreover, AMPs may encourage cells to produce chemokines, stimulate angiogenesis, accelerate wound healing, and influence programmed cell death in multicellular organisms. Bacteria differ in their inherent susceptibility and resistance mechanisms to these peptides when responding to the antimicrobial effects of AMPs. Generally, the development of AMP resistance mechanisms is driven by direct competition between bacterial species, and host and pathogen interactions. Several studies have shown diverse mechanisms of bacterial resistance to AMPs, for example, some bacteria produce proteases and trapping proteins; some modify cell surface charge, change membrane fluidity, and activate efflux pumps; and some species make use of biofilms and exopolymers, and develop sensing systems by selective gene expression. A closer understanding of bacterial resistance mechanisms may help in developing novel therapeutic approaches for the treatment of infections caused by pathogenic organisms that are successful in developing extensive resistance to AMPs. Based on these observations, this review discusses the properties of AMPs, their targeting mechanisms, and bacterial resistance mechanisms against AMPs.}, }
@article {pmid29954432, year = {2018}, author = {Faust, K and Bauchinger, F and Laroche, B and de Buyl, S and Lahti, L and Washburne, AD and Gonze, D and Widder, S}, title = {Signatures of ecological processes in microbial community time series.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {120}, doi = {10.1186/s40168-018-0496-2}, pmid = {29954432}, issn = {2049-2618}, support = {295741; 307127//Academy of Finland/ ; Elise Richter V585-B31//Austrian Science Fund/ ; }, abstract = {BACKGROUND: Growth rates, interactions between community members, stochasticity, and immigration are important drivers of microbial community dynamics. In sequencing data analysis, such as network construction and community model parameterization, we make implicit assumptions about the nature of these drivers and thereby restrict model outcome. Despite apparent risk of methodological bias, the validity of the assumptions is rarely tested, as comprehensive procedures are lacking. Here, we propose a classification scheme to determine the processes that gave rise to the observed time series and to enable better model selection.<br><br>RESULTS: We implemented a three-step classification scheme in R that first determines whether dependence between successive time steps (temporal structure) is present in the time series and then assesses with a recently developed neutrality test whether interactions between species are required for the dynamics. If the first and second tests confirm the presence of temporal structure and interactions, then parameters for interaction models are estimated. To quantify the importance of temporal structure, we compute the noise-type profile of the community, which ranges from black in case of strong dependency to white in the absence of any dependency. We applied this scheme to simulated time series generated with the Dirichlet-multinomial (DM) distribution, Hubbell's neutral model, the generalized Lotka-Volterra model and its discrete variant (the Ricker model), and a self-organized instability model, as well as to human stool microbiota time series. The noise-type profiles for all but DM data clearly indicated distinctive structures. The neutrality test correctly classified all but DM and neutral time series as non-neutral. The procedure reliably identified time series for which interaction inference was suitable. Both tests were required, as we demonstrated that all structured time series, including those generated with the neutral model, achieved a moderate to high goodness of fit to the Ricker model.<br><br>CONCLUSIONS: We present a fast and robust scheme to classify community structure and to assess the prevalence of interactions directly from microbial time series data. The procedure not only serves to determine ecological drivers of microbial dynamics, but also to guide selection of appropriate community models for prediction and follow-up analysis.}, }
@article {pmid29951743, year = {2018}, author = {Xiao, F and Bi, Y and Li, X and Huang, J and Yu, Y and Xie, Z and Fang, T and Cao, X and He, Z and Juneau, P and Yan, Q}, title = {The Impact of Anthropogenic Disturbance on Bacterioplankton Communities During the Construction of Donghu Tunnel (Wuhan, China).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1222-0}, pmid = {29951743}, issn = {1432-184X}, support = {31672262//National Natural Science Foundation of China/ ; }, abstract = {Bacterioplankton are both primary producers and primary consumers in aquatic ecosystems, which were commonly investigated to reflect environmental changes, evaluate primary productivity, and assess biogeochemical cycles. However, there is relatively less understanding of their responses to anthropogenic disturbances such as constructions of dams/tunnels/roads that may significantly affect the aquatic ecosystem. To fill such gap, this study focused on the bacterioplankton communities' diversity and turnover during a tunnel construction across an urban lake (Lake Donghu, Wuhan, China), and five batches of samples were collected within 2 months according to the tunnel construction progress. Results indicated that both resources and predator factors contributed significant to the variations of bacterioplankton communities, but the closed area and open areas showed different diversity patterns due to the impacts of tunnel construction. Briefly, the phytoplankton, TN, and TP in water were still significantly correlated with the bacterioplankton composition and diversity like that in normal conditions. Additionally, the organic matter, TN, and NH4-N in sediments also showed clear effects on the bacterioplankton. However, the predator effects on the bacterioplankton in the closed-off construction area mainly derived from large zooplankton (i.e., cladocerans), while small zooplankton such as protozoa and rotifers are only responsible for weak predator effects on the bacterioplankton in the open areas. Further analysis about the ecological driving forces indicated that the bacterioplankton communities' turnover during the tunnel construction was mainly governed by the homogeneous selection due to similar environments within the closed area or the open areas at two different stages. This finding suggests that bacterioplankton communities can quickly adapt to the environmental modifications resulting from tunnel construction activities. This study can also give references to enhance our understanding on bacterioplankton communities' response to ecological and environmental changes due to intensification of construction and urbanization in and around lake ecosystems.}, }
@article {pmid29951048, year = {2018}, author = {Zinke, LA and Reese, BK and McManus, J and Wheat, CG and Orcutt, BN and Amend, JP}, title = {Sediment Microbial Communities Influenced by Cool Hydrothermal Fluid Migration.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1249}, doi = {10.3389/fmicb.2018.01249}, pmid = {29951048}, issn = {1664-302X}, abstract = {Cool hydrothermal systems (CHSs) are prevalent across the seafloor and discharge fluid volumes that rival oceanic input from rivers, yet the microbial ecology of these systems are poorly constrained. The Dorado Outcrop on the ridge flank of the Cocos Plate in the northeastern tropical Pacific Ocean is the first confirmed CHS, discharging minimally altered <15°C fluid from the shallow lithosphere through diffuse venting and seepage. In this paper, we characterize the resident sediment microbial communities influenced by cool hydrothermal advection, which is evident from nitrate and oxygen concentrations. 16S rRNA gene sequencing revealed that Thaumarchaea, Proteobacteria, and Planctomycetes were the most abundant phyla in all sediments across the system regardless of influence from seepage. Members of the Thaumarchaeota (Marine Group I), Alphaproteobacteria (Rhodospirillales), Nitrospirae, Nitrospina, Acidobacteria, and Gemmatimonadetes were enriched in the sediments influenced by CHS advection. Of the various geochemical parameters investigated, nitrate concentrations correlated best with microbial community structure, indicating structuring based on seepage of nitrate-rich fluids. A comparison of microbial communities from hydrothermal sediments, seafloor basalts, and local seawater at Dorado Outcrop showed differences that highlight the distinct niche space in CHS. Sediment microbial communities from Dorado Outcrop differ from those at previously characterized, warmer CHS sediment, but are similar to deep-sea sediment habitats with surficial ferromanganese nodules, such as the Clarion Clipperton Zone. We conclude that cool hydrothermal venting at seafloor outcrops can alter the local sedimentary oxidation-reduction pathways, which in turn influences the microbial communities within the fluid discharge affected sediment.}, }
@article {pmid29950696, year = {2018}, author = {Petersen, JM and Kemper, A and Gruber-Vodicka, H and Cardini, U and van der Geest, M and Kleiner, M and Bulgheresi, S and Mußmann, M and Herbold, C and Seah, BKB and Antony, CP and Liu, D and Belitz, A and Weber, M}, title = {Author Correction: Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation.}, journal = {Nature microbiology}, volume = {3}, number = {8}, pages = {961}, doi = {10.1038/s41564-018-0196-5}, pmid = {29950696}, issn = {2058-5276}, abstract = {In this Article, the completeness and number of contigs for draft genomes from two individuals of Laxus oneistus are incorrect in the main text, although the correct information is included in Table 1. The original and corrected versions of the relevant sentence are shown in the correction notice.}, }
@article {pmid29950677, year = {2018}, author = {Candry, P and Van Daele, T and Denis, K and Amerlinck, Y and Andersen, SJ and Ganigué, R and Arends, JBA and Nopens, I and Rabaey, K}, title = {A novel high-throughput method for kinetic characterisation of anaerobic bioproduction strains, applied to Clostridium kluyveri.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {9724}, doi = {10.1038/s41598-018-27594-9}, pmid = {29950677}, issn = {2045-2322}, abstract = {Hexanoic acid (HA), also called caproic acid, can be used as an antimicrobial agent and as a precursor to various chemicals, such as fuels, solvents and fragrances. HA can be produced from ethanol and acetate by the mesophilic anaerobic bacterium Clostridium kluyveri, via two successive elongation steps over butyrate. A high-throughput anaerobic growth curve technique was coupled to a data analysis framework to assess growth kinetics for a range of substrate and product concentrations. Using this method, growth rates and several kinetic parameters were determined for C. kluyveri. A maximum growth rate (µmax) of 0.24 ± 0.01 h-1 was found, with a half-saturation index for acetic acid (KS,AA) of 3.8 ± 0.9 mM. Inhibition by butyric acid occurred at of 124.7 ± 5.7 mM (KI,BA), while the final product, HA, linearly inhibited growth with complete inhibition above 91.3 ± 10.8 mM (KHA of 10.9*10-3 ± 1.3*10-3 mM-1) at pH = 7, indicating that the hexanoate anion also exerts toxicity. These parameters were used to create a dynamic mass-balance model for bioproduction of HA. By coupling data collection and analysis to this modelling framework, we have produced a powerful tool to assess the kinetics of anaerobic micro-organisms, demonstrated here with C. kluyveri, in order further explore the potential of micro-organisms for chemicals production.}, }
@article {pmid29950381, year = {2018}, author = {Jenior, ML and Leslie, JL and Young, VB and Schloss, PD}, title = {Clostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization.}, journal = {mSphere}, volume = {3}, number = {3}, pages = {}, doi = {10.1128/mSphere.00261-18}, pmid = {29950381}, issn = {2379-5042}, mesh = {Animals ; Anti-Bacterial Agents/*administration &amp; dosage/adverse effects ; Cecum/*chemistry/*microbiology ; Clostridium Infections/*microbiology ; Clostridium difficile/*growth &amp; development ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Metabolomics ; Metagenomics ; Mice ; }, abstract = {Susceptibility to Clostridium difficile infection (CDI) is primarily associated with previous exposure to antibiotics, which compromise the structure and function of the gut bacterial community. Specific antibiotic classes correlate more strongly with recurrent or persistent C. difficile infection. As such, we utilized a mouse model of infection to explore the effect of distinct antibiotic classes on the impact that infection has on community-level transcription and metabolic signatures shortly following pathogen colonization and how those changes may associate with persistence of C. difficile Untargeted metabolomic analysis revealed that C. difficile infection had significantly larger impacts on the metabolic environment across cefoperazone- and streptomycin-pretreated mice, which became persistently colonized compared to clindamycin-pretreated mice, where infection quickly became undetectable. Through metagenome-enabled metatranscriptomics, we observed that transcripts for genes associated with carbon and energy acquisition were greatly reduced in infected animals, suggesting that those niches were instead occupied by C. difficile Furthermore, the largest changes in transcription were seen in the least abundant species, indicating that C. difficile may &quot;attack the loser&quot; in gut environments where sustained infection occurs more readily. Overall, our results suggest that C. difficile is able to restructure the nutrient-niche landscape in the gut to promote persistent infection.IMPORTANCEClostridium difficile has become the most common single cause of hospital-acquired infection over the last decade in the United States. Colonization resistance to the nosocomial pathogen is primarily provided by the gut microbiota, which is also involved in clearing the infection as the community recovers from perturbation. As distinct antibiotics are associated with different risk levels for CDI, we utilized a mouse model of infection with 3 separate antibiotic pretreatment regimens to generate alternative gut microbiomes that each allowed for C. difficile colonization but varied in clearance rate. To assess community-level dynamics, we implemented an integrative multi-omics approach that revealed that infection significantly changed many aspects of the gut community. The degree to which the community changed was inversely correlated with clearance during the first 6 days of infection, suggesting that C. difficile differentially modifies the gut environment to promote persistence. This is the first time that metagenome-enabled metatranscriptomics have been employed to study the behavior of a host-associated microbiota in response to an infection. Our results allow for a previously unseen understanding of the ecology associated with C. difficile infection and provide the groundwork for identification of context-specific probiotic therapies.}, }
@article {pmid29948019, year = {2018}, author = {Lin, L and Liu, W and Zhang, M and Lin, X and Zhang, Y and Tian, Y}, title = {Different Height Forms of Spartina alterniflora Might Select Their Own Rhizospheric Bacterial Communities in Southern Coast of China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1208-y}, pmid = {29948019}, issn = {1432-184X}, support = {20720150097//the Fundamental Research Funds for the Central Universities/ ; }, abstract = {In the southernmost part of coast of China, two height forms of Spartina alterniflora, tall and short, have invaded Leizhou Peninsula within the last decade. However, the effect of different height forms of Spartina alterniflora on plant-microbe interaction has not been clarified. Here, the community structures of rhizosphere bacteria and the abundance of N- and S-cycling functional genes associated with selected S. alterniflora were investigated in the field and a common garden. The community structure of tall-form S. alterniflora was distinct from short-form S. alterniflora at OTU level in the field, even after transplantation into a common garden. The abundance of bacterial amoA, nirS, and nosZ in tall S. alterniflora was significantly greater than those in short S. alterniflora in the field; however, this difference disappeared in a 1-year common garden experiment. These results suggested that compared with the tall-form S. alterniflora, the rhizosphere of short-form S. alterniflora harbored fewer nitrification-denitrification related microorganisms, which might benefit from conserving N in an N limited habitat. Together, our results suggested that tall- and short-form S. alterniflora can host their specific rhizosphere microbial communities and had different strategies of N usage via selecting the composition of rhizosphere bacterial assemblages, which in turn might determine the growth and invasiveness of S. alterniflora in its introduced range.}, }
@article {pmid29948018, year = {2018}, author = {Kamutando, CN and Vikram, S and Kamgan-Nkuekam, G and Makhalanyane, TP and Greve, M and Le Roux, JJ and Richardson, DM and Cowan, DA and Valverde, A}, title = {The Functional Potential of the Rhizospheric Microbiome of an Invasive Tree Species, Acacia dealbata.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1214-0}, pmid = {29948018}, issn = {1432-184X}, support = {CPRR14071676470//National Research Foundation of South Africa (NRF)/ ; }, abstract = {Plant-microbe interactions mediate both the invasiveness of introduced plant species and the impacts that they have in invaded ecosystems. Although the phylogenetic composition of the rhizospheric microbiome of Acacia dealbata (an invasive Australian tree species) has been investigated, little is known about the functional potential of the constituents of these altered microbial communities. We used shotgun DNA sequencing to better understand the link between bacterial community composition and functional capacity in the rhizospheric microbiomes associated with invasive A. dealbata populations in South Africa. Our analysis showed that several genes associated with plant growth-promoting (PGP) traits were significantly overrepresented in the rhizospheric metagenomes compared to neighbouring bulk soils collected away from A. dealbata stands. The majority of these genes are involved in the metabolism of nitrogen, carbohydrates and vitamins, and in various membrane transport systems. Overrepresented genes were linked to a limited number of bacterial taxa, mostly Bradyrhizobium species, the preferred N-fixing rhizobial symbiont of Australian acacias. Overall, these findings suggest that A. dealbata enriches rhizosphere soils with potentially beneficial microbial taxa, and that members of the genus Bradyrhizobium may play an integral role in mediating PGP processes that may influence the success of this invader when colonizing novel environments.}, }
@article {pmid29948017, year = {2018}, author = {Mason, CJ and Campbell, AM and Scully, ED and Hoover, K}, title = {Bacterial and Fungal Midgut Community Dynamics and Transfer Between Mother and Brood in the Asian Longhorned Beetle (Anoplophora glabripennis), an Invasive Xylophage.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1205-1}, pmid = {29948017}, issn = {1432-184X}, support = {2015-67013-23287//National Institute of Food and Agriculture/ ; }, abstract = {Microbial symbionts play pivotal roles in the ecology and physiology of insects feeding in woody plants. Both eukaryotic and bacterial members occur in these systems where they facilitate digestive and nutrient provisioning. The larval gut of the Asian longhorned beetle (Anoplophora glabripennis) is associated with a microbial consortium that fulfills these metabolic roles. While members of the community vary in presence and abundance among individuals from different hosts, A. glabripennis is consistently associated with a fungus in the Fusarium solani species complex (FSSC). We used amplicon sequencing, taxon-specific PCR, culturing, and imaging to determine how bacterial and fungal communities differ between life stages and possible modes of symbiont transfer. The bacterial and fungal communities of adult guts were more diverse than those from larvae and eggs. The communities of larvae and eggs were more similar to those from oviposition sites than from adult female guts. FSSC isolates were not detected in the reproductive tissues of adult females, but were consistently detected on egg surfaces after oviposition and in frass. These results demonstrate that frass can serve as a vehicle of transmission of a subset for the beetle gut microbiota. Vertically transmitted symbionts are often beneficial to their host, warranting subsequent functional studies.}, }
@article {pmid29948016, year = {2018}, author = {Maki, J}, title = {Introduction.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {1}, doi = {10.1007/s00248-018-1216-y}, pmid = {29948016}, issn = {1432-184X}, }
@article {pmid29948015, year = {2018}, author = {Väisänen, M and Gavazov, K and Krab, EJ and Dorrepaal, E}, title = {The Legacy Effects of Winter Climate on Microbial Functioning After Snowmelt in a Subarctic Tundra.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1213-1}, pmid = {29948015}, issn = {1432-184X}, abstract = {Warming-induced increases in microbial CO2 release in northern tundra may positively feedback to climate change. However, shifts in microbial extracellular enzyme activities (EEAs) may alter the impacts of warming over the longer term. We investigated the in situ effects of 3 years of winter warming in combination with the in vitro effects of a rapid warming (6 days) on microbial CO2 release and EEAs in a subarctic tundra heath after snowmelt in spring. Winter warming did not change microbial CO2 release at ambient (10 °C) or at rapidly increased temperatures, i.e., a warm spell (18 °C) but induced changes (P < 0.1) in the Q10 of microbial respiration and an oxidative EEA. Thus, although warmer winters may induce legacy effects in microbial temperature acclimation, we found no evidence for changes in potential carbon mineralization after spring thaw.}, }
@article {pmid29947838, year = {2018}, author = {Melo-Nascimento, AODS and Treumann, C and Neves, C and Andrade, E and Andrade, AC and Edwards, R and Dinsdale, E and Bruce, T}, title = {Functional characterization of ligninolytic Klebsiella spp. strains associated with soil and freshwater.}, journal = {Archives of microbiology}, volume = {200}, number = {8}, pages = {1267-1278}, doi = {10.1007/s00203-018-1532-0}, pmid = {29947838}, issn = {1432-072X}, support = {JCB0064/2013//Fundação de Amparo à Pesquisa do Estado da Bahia/ ; 23038.009420/201271//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; JCB0064/2013//Fundação de Amparo à Pesquisa do Estado da Bahia (BR)/ ; 13330800//National Science Foundation/ ; }, abstract = {Overcoming recalcitrance of lignin has motivated bioprospecting of high-yielding enzymes from environmental ligninolytic microorganisms associated with lignocellulose degrading-systems. Here, we performed isolation of 21 ligninolytic strains belonging to the genus Klebsiella spp., driven by the presence of lignin in the media. The fastest-growing strains (FP10-5.23, FP10-5.22 and P3TM1) reached the stationary phase in approximately 24 h, in the media containing lignin as the main carbon source. The strains showed biochemical evidence of ligninolytic potential in liquid- and solid media-converting dyes, which the molecular structures are similar to lignin fragments. In liquid medium, higher levels of dye decolorization was observed for P3TM.1 in the presence of methylene blue, reaching 98% decolorization in 48 h. The highest index values (1.25) were found for isolates P3TM.1 and FP10-5.23, in the presence of toluidine blue. The genomic analysis revealed the presence of more than 20 genes associated with known prokaryotic lignin-degrading systems. Identification of peroxidases (lignin peroxidase-LiP, dye-decolorizing peroxidase-DyP, manganese peroxidase-MnP) and auxiliary activities (AA2, AA3, AA6 and AA10 families) among the genetic repertoire suggest the ability to produce extracellular enzymes able to attack phenolic and non-phenolic lignin structures. Our results suggest that the Klebsiella spp. associated with fresh water and soil may play important role in the cycling of recalcitrant molecules in the Caatinga (desert-like Brazilian biome), and represent a potential source of lignin-degrading enzymes with biotechnological applications.}, }
@article {pmid29946784, year = {2018}, author = {Sakoda, S and Aisu, K and Imagami, H and Matsuda, Y}, title = {Comparison of Actinomycete Community Composition on the Surface and Inside of Japanese Black Pine (Pinus thunbergii) Tree Roots Colonized by the Ectomycorrhizal Fungus Cenococcum geophilum.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1221-1}, pmid = {29946784}, issn = {1432-184X}, abstract = {Various bacteria are associated with ectomycorrhizal roots, which are symbiotic complexes formed between plant roots and fungi. Among these associated bacteria, actinomycetes have received attention for their ubiquity and diverse roles in forest ecosystems. Here, to examine the association of actinomycetes with ectomycorrhizal root tips, we compared the bacterial and actinomycete communities on the surface and inside of root tips of coastal Japanese black pine (Pinus thunbergii) colonized by the fungus Cenococcum geophilum. Next-generation sequences of 16S rDNA of bacteria communities using the Ion Torrent Personal Genome Machine showed that the number of bacterial classes in the surface of C. geophilum ECM roots was significantly higher than that in non-ECM roots. The bacterial community structure of surface, inside, and non-ECM roots was significantly discriminated each other. For an isolation method, a total of 762 and 335 actinomycete isolates were obtained from the surface and inside of the roots, respectively. In addition, the isolation ratio of actinomycetes in these root tips varied depending on the age of the tree and the season. Identification of the isolates based on partial 16S rDNA sequencing revealed that the isolates belonged to nine genera of the order Actinomycetales. On the surface of the roots, most of the isolates belonged to genus Streptomyces (90.4%); inside of the roots, most of the isolates belonged to genus Actinoallomurus (40.0%), which is a relatively new taxon. Our results suggest that actinomycetes as well as bacteria are ubiquitously associated with C. geophilum ectomycorrhizal roots of P. thunbergii, although their communities can vary either surface or inside of individual root tips.}, }
@article {pmid29946053, year = {2018}, author = {MeGraw, VE and Brown, AR and Boothman, C and Goodacre, R and Morris, K and Sigee, D and Anderson, L and Lloyd, JR}, title = {A Novel Adaptation Mechanism Underpinning Algal Colonization of a Nuclear Fuel Storage Pond.}, journal = {mBio}, volume = {9}, number = {3}, pages = {}, doi = {10.1128/mBio.02395-17}, pmid = {29946053}, issn = {2150-7511}, abstract = {Geochemical analyses alongside molecular techniques were used to characterize the microbial ecology and biogeochemistry of an outdoor spent nuclear fuel storage pond at Sellafield, United Kingdom, that is susceptible to seasonal algal blooms that cause plant downtime. 18S rRNA gene profiling of the filtered biomass samples showed the increasing dominance of a species closely related to the alga Haematococcus pluvialis, alongside 16S rRNA genes affiliated with a diversity of freshwater bacteria, including Proteobacteria and Cyanobacteria High retention of 137Cs and 90Sr on pond water filters coincided with high levels of microbial biomass in the pond, suggesting that microbial colonization may have an important control on radionuclide fate in the pond. To interpret the unexpected dominance of Haematococcus species during bloom events in this extreme environment, the physiological response of H. pluvialis to environmentally relevant ionizing radiation doses was assessed. Irradiated laboratory cultures produced significant quantities of the antioxidant astaxanthin, consistent with pigmentation observed in pond samples. Fourier transform infrared (FT-IR) spectroscopy suggested that radiation did not have a widespread impact on the metabolic fingerprint of H. pluvialis in laboratory experiments, despite the 80-Gy dose. This study suggests that the production of astaxanthin-rich encysted cells may be related to the preservation of the Haematococcus phenotype, potentially allowing it to survive oxidative stress arising from radiation doses associated with the spent nuclear fuel. The oligotrophic and radiologically extreme conditions in this environment do not prevent extensive colonization by microbial communities, which play a defining role in controlling the biogeochemical fate of major radioactive species present.IMPORTANCE Spent nuclear fuel is stored underwater in large ponds prior to processing and disposal. Such environments are intensively radioactive but can be colonized by microorganisms. Colonization of such inhospitable radioactive ponds is surprising, and the survival mechanisms that microbes use is of fundamental interest. It is also important to study these unusual ecosystems, as microbes growing in the pond waters may accumulate radionuclides present in the waters (for bioremediation applications), while high cell loads can hamper management of the ponds due to poor visibility. In this study, an outdoor pond at the U.K. Sellafield facility was colonized by a seasonal bloom of microorganisms, able to accumulate high levels of 137Cs and 90Sr and dominated by the alga Haematococcus This organism is not normally associated with deep water bodies, but it can adapt to radioactive environments via the production of the pigment astaxanthin, which protects the cells from radiation damage.}, }
@article {pmid29945195, year = {2018}, author = {Liu, X and Wu, Y and Wilson, FP and Yu, K and Lintner, C and Cupples, AM and Mattes, TE}, title = {Integrated methodological approach reveals microbial diversity and functions in aerobic groundwater microcosms adapted to vinyl chloride.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {9}, pages = {}, doi = {10.1093/femsec/fiy124}, pmid = {29945195}, issn = {1574-6941}, abstract = {Vinyl chloride (VC), a known human carcinogen, is often formed in groundwater (GW) by incomplete reductive dechlorination of chlorinated ethenes. An integrated microbial ecology approach involving bacterial enrichments and isolations, carbon stable-isotope probing (SIP) and metagenome and genome sequencing was applied to ethene-fed GW microcosms that rapidly transitioned to aerobic growth on VC. Actinobacteria, Proteobacteria and Bacteroidetes dominated the microbial communities in ethene- and VC-grown cultures. SIP with 13C2-VC demonstrated that Nocardioides spp. significantly participated in carbon uptake from VC (52.1%-75.7% enriched in heavy fractions). Sediminibacterium, Pedobacter and Pseudomonas spp. also incorporated 13C from VC into genomic DNA. Ethene- and VC-assimilating Nocardioides sp. strain XL1 was isolated. Sequencing revealed a large (∼300 kbp) plasmid harboring genes encoding alkene monooxygenase and epoxyalkane: coenzyme M transferase, enzymes known to participate in aerobic VC and ethene biodegradation. The plasmid was 100% identical to pNOCA01 found in VC-assimilating Nocardioides sp. strain JS614. Metagenomic analysis of enrichment cultures indicated other bacteria implicated in carbon uptake from VC possessed the genetic potential to detoxify epoxides via epoxide hydrolase or glutathione S-transferase (Pseudomonas) and/or metabolize VC epoxide breakdown products and downstream VC metabolites. This study provides new functional insights into aerobic VC metabolism within a GW microbial community.}, }
@article {pmid29944836, year = {2018}, author = {Guo, X and Stedtfeld, RD and Hedman, H and Eisenberg, JNS and Trueba, G and Yin, D and Tiedje, JM and Zhang, L}, title = {Antibiotic Resistome Associated with Small-Scale Poultry Production in Rural Ecuador.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {15}, pages = {8165-8172}, doi = {10.1021/acs.est.8b01667}, pmid = {29944836}, issn = {1520-5851}, abstract = {Small-scale poultry farming is common in rural communities across the developing world. To examine the extent to which small-scale poultry farming serves as a reservoir for resistance determinants, the resistome of fecal samples was compared between production chickens that received antibiotics and free-ranging household chickens that received no antibiotics from a rural village in northern Ecuador. A qPCR array was used to quantify antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) using 248 primer pairs; and the microbiome structure was analyzed via 16S rRNA gene sequencing. A large number of ARGs (148) and MGEs (29) were detected. The ARG richness in production chickens was significantly higher than that of household chickens with an average of 15 more genes detected (p < 0.01). Moreover, ARGs and MGEs were much more abundant in production chickens than in household chickens (up to a 157-fold difference). Production chicken samples had significantly lower taxonomic diversity and were more abundant in Gammaproteobacteria, Betaproteobacteria, and Flavobacteria. The high abundance and diversity of ARGs and MGEs found in small-scale poultry farming was comparable to the levels previously found in large scale animal production, suggesting that these chickens could act as a local reservoir for spreading ARGs into rural communities.}, }
@article {pmid29941858, year = {2018}, author = {Pimenoff, VN and Houldcroft, CJ and Rifkin, RF and Underdown, S}, title = {The Role of aDNA in Understanding the Coevolutionary Patterns of Human Sexually Transmitted Infections.}, journal = {Genes}, volume = {9}, number = {7}, pages = {}, doi = {10.3390/genes9070317}, pmid = {29941858}, issn = {2073-4425}, abstract = {Analysis of pathogen genome data sequenced from clinical and historical samples has made it possible to perform phylogenetic analyses of sexually transmitted infections on a global scale, and to estimate the diversity, distribution, and coevolutionary host relationships of these pathogens, providing insights into pathogen emergence and disease prevention. Deep-sequenced pathogen genomes from clinical studies and ancient samples yield estimates of within-host and between-host evolutionary rates and provide data on changes in pathogen genomic stability and evolutionary responses. Here we examine three groups of pathogens transmitted mainly through sexual contact between modern humans to provide insight into ancient human behavior and history with their pathogens. Exploring ancient pathogen genomic divergence and the ancient viral-host parallel evolutionary histories will help us to reconstruct the origin of present-day geographical distribution and diversity of clinical pathogen infections, and will hopefully allow us to foresee possible environmentally induced pathogen evolutionary responses. Lastly, we emphasize that ancient pathogen DNA research should be combined with modern clinical pathogen data, and be equitable and provide advantages for all researchers worldwide, e.g., through shared data.}, }
@article {pmid29937879, year = {2017}, author = {Nabee, Z and Jeewon, R and Pugo-Gunsam, P}, title = {Oral dysbacteriosis in type 2 diabetes and its role in the progression to cardiovascular disease.}, journal = {African health sciences}, volume = {17}, number = {4}, pages = {1082-1091}, doi = {10.4314/ahs.v17i4.16}, pmid = {29937879}, issn = {1729-0503}, mesh = {Adult ; Aged ; Buffers ; Cardiovascular Diseases/*microbiology ; Case-Control Studies ; DMF Index ; Dental Caries/*microbiology ; Diabetes Mellitus, Type 2/diagnosis/*microbiology ; Disease Progression ; Dysbiosis ; Female ; Humans ; Hydrogen-Ion Concentration ; Lactobacillus/*isolation &amp; purification ; Male ; Middle Aged ; Oral Health ; Saliva/*microbiology ; Streptococcus mutans/*isolation &amp; purification ; }, abstract = {Background: Salivary changes and proliferation of specific bacterial communities are known to result in oral disease which may adversely impact on systemic conditions like diabetes and cardiovascular diseases.<br><br>Objectives: This study reports on the changes in oral ecology of healthy and diseased adults and the possible role in disease causation.<br><br>Methods: The study comprised 150 participants divided into control (healthy), diabetic and cardiac groups. After dental examination for (Decayed Missing Filled Teeth (DMFT) and Oral Rating Index (ORI), stimulated saliva was sampled to determine flow rate and buffering capacity. Salivary microbial load of Streptococcus mutans and Lactobacilli were subsequently quantified.<br><br>Results: DMFT, ORI, buffering capacity and flow rate were inferior for both diabetic and cardiac patients, who had higher bacterial counts (p<0.05). Long standing diabetics harboured a higher load of Streptococcus mutans. The microbial load of Streptococcus mutans in cardiac patients was double that of diabetics.<br><br>Conclusion: Disruption in the salivary environment and changes in microbial ecology with increased load of cariogenic bacteria were found in diabetic and cardiac patients. This study brings forward new evidence of a markedly higher load of Streptococcus mutans in cardiac patients which may underlie the progression of diabetes to cardiovascular disease in this population.}, }
@article {pmid29934850, year = {2018}, author = {Kostina, EV and Sinyakov, AN and Ryabinin, VA}, title = {A many probes-one spot hybridization oligonucleotide microarray.}, journal = {Analytical and bioanalytical chemistry}, volume = {410}, number = {23}, pages = {5817-5823}, doi = {10.1007/s00216-018-1190-8}, pmid = {29934850}, issn = {1618-2650}, mesh = {Base Sequence ; DNA, Viral/*analysis/genetics ; Equipment Design ; Immobilized Nucleic Acids/chemistry/genetics ; *Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis/*instrumentation ; Oligonucleotide Probes/chemistry/genetics ; Orthopoxvirus/chemistry/*genetics ; Poxviridae Infections/virology ; }, abstract = {A variant of the hybridization oligonucleotide microarray, utilizing the principle of many probes-one spot (MPOS-microarrays), is proposed. A case study based on Orthopoxviruses (Variola, Monkeypox, and Ectromelia viruses) demonstrates a considerable increase in the fluorescence signal (up to 100-fold) when several oligonucleotide probes are printed to one spot. Moreover, the specificity of detection also increases (almost 1000-fold), allowing the use of probes that individually lack such high specificity. The optimal probes have a Tm of 32-37 °C and length of 13-15 bases. We suggest that the high specificity and sensitivity of the MPOS-microarray is a result of cooperativity of DNA binding with all probes immobilized in the spot. This variant of DNA detection can be useful for designing biosensors, tools for point-of-care (POC) diagnostics, microbial ecology, analysis of clustered regularly interspaced short palindromic repeats (CRISPR), and others. Graphical abstract ᅟ.}, }
@article {pmid29931762, year = {2018}, author = {Quercia, S and Freccero, F and Castagnetti, C and Soverini, M and Turroni, S and Biagi, E and Rampelli, S and Lanci, A and Mariella, J and Chinellato, E and Brigidi, P and Candela, M}, title = {Early colonisation and temporal dynamics of the gut microbial ecosystem in Standardbred foals.}, journal = {Equine veterinary journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/evj.12983}, pmid = {29931762}, issn = {2042-3306}, abstract = {BACKGROUND: Even if horses strictly depend on the gut microbiota for energy homeostasis, only a few molecular studies have focused on its characterisation and none on the perinatal gut microbial colonisation process.<br><br>OBJECTIVES: To explore the perinatal colonisation process of the foal gut microbial ecosystem and the temporal dynamics of the ecosystem assembly during the first days of life.<br><br>STUDY DESIGN: Longitudinal study.<br><br>METHODS: Thirteen Standardbred mare-foal pairs were included in the study. For each pair, at delivery we collected the mare amniotic fluid, faeces and colostrum, and the foal meconium. Milk samples and faeces of both mare and foal were also taken longitudinally, until day 10 post-partum. Samples were analysed by means of next-generation sequencing of the 16S rRNA gene on Illumina MiSeq.<br><br>RESULTS: Our findings suggest that microbial components derived from the mare symbiont communities establishes in the foal gut since fetal life. After birth, an external transmission route of mare microorganisms takes place. This involves a rapid and dynamic process of assembling the mature foal gut microbiome, in which the founder microbial species are derived from both the milk and the gut microbial ecosystems of the mare.<br><br>MAIN LIMITATIONS: The inability to discriminate between live and dead cells, the possible presence of contaminating bacteria in low biomass samples (e.g. meconium and amniotic fluid), the limits of the phylogenetic assignment down to species level, and the presence of unassigned operational taxonomic units.<br><br>CONCLUSIONS: Our data highlight the importance of mare microbiomes as a key factor for the establishment of the gut microbial ecosystem of the foal.}, }
@article {pmid29931623, year = {2018}, author = {Arai, H and Hirano, T and Akizuki, N and Abe, A and Nakai, M and Kunimi, Y and Inoue, MN}, title = {Multiple Infection and Reproductive Manipulations of Wolbachia in Homona magnanima (Lepidoptera: Tortricidae).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1210-4}, pmid = {29931623}, issn = {1432-184X}, abstract = {Endosymbiotic bacterium Wolbachia interacts with host in either a mutualistic or parasitic manner. Wolbachia is frequently identified in various arthropod species, and to date, Wolbachia infections have been detected in different insects. Here, we found a triple Wolbachia infection in Homona magnanima, a serious tea pest, and investigated the effects of three infecting Wolbachia strains (wHm-a, -b, and -c) on the host. Starting with the triple-infected host line (Wabc), which was collected in western Tokyo in 1999 and maintained in laboratory, we established an uninfected line (W-) and three singly infected lines (Wa, Wb, and Wc) using antibiotics. Mating experiments with the host lines revealed that only wHm-b induced cytoplasmic incompatibility (CI) in H. magnanima, with the intensities of CI different between the Wb and Wabc lines. Regarding mutualistic effects, wHm-c shortened larval development time and increased pupal weight in both the Wc and Wabc lines to the same extent, whereas no distinct phenotype was observed in lines singly infected with wHm-a. Based on quantitative PCR analysis, Wolbachia density in the Wa line was higher than in the other host lines (p < 0.01, n = 10). Wolbachia density in the Wb line was also higher than in the Wc and Wabc lines, while no difference was observed between the Wc and Wabc lines. These results indicate that the difference in the CI intensity between a single or multiple infection may be attributed to the difference in wHm-b density. However, no correlation was observed between mutualistic effects and Wolbachia density.}, }
@article {pmid29930350, year = {2018}, author = {Dini-Andreote, F and van Elsas, JD and Olff, H and Salles, JF}, title = {Dispersal-competition tradeoff in microbiomes in the quest for land colonization.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {9451}, doi = {10.1038/s41598-018-27783-6}, pmid = {29930350}, issn = {2045-2322}, abstract = {Ancestor microbes started colonizing inland habitats approximately 2.7 to 3.5 billion years ago. With some exceptions, the key physiological adaptations of microbiomes associated with marine-to-land transitions have remained elusive. This is essentially caused by the lack of suitable systems that depict changes in microbiomes across sufficiently large time scales. Here, we investigate the adaptive routes taken by microbiomes along a contemporary gradient of land formation. Using functional trait-based metagenomics, we show that a switch from a microbial 'dispersal' to a 'competition' response modus best characterizes the microbial trait changes during this eco-evolutionary trajectory. The 'dispersal' modus prevails in microbiomes at the boundary sites between land and sea. It encompasses traits conferring cell chemosensory and motile behaviors, thus allowing the local microbes to exploit short-lived nutritional patches in high-diffusion microhabitats. A systematic transition towards the 'competition' modus occurs progressively as the soil matures, which is likely due to forces of viscosity or strain that favor traits for competition and chemical defense. Concomitantly, progressive increases in the abundances of genes encoding antibiotic resistance and complex organic substrate degradation were found. Our findings constitute a novel perspective on the ecology and evolution of microbiome traits, tracking back one of the most seminal transitions in the evolutionary history of life.}, }
@article {pmid29928771, year = {2018}, author = {Cristea, A and Baricz, A and Leopold, N and Floare, CG and Borodi, G and Kacso, I and Tripon, S and Bulzu, PA and Andrei, AȘ and Cadar, O and Levei, EA and Banciu, HL}, title = {Polyhydroxybutyrate production by an extremely halotolerant Halomonas elongata strain isolated from the hypersaline meromictic Fără Fund Lake (Transylvanian Basin, Romania).}, journal = {Journal of applied microbiology}, volume = {125}, number = {5}, pages = {1343-1357}, doi = {10.1111/jam.14029}, pmid = {29928771}, issn = {1365-2672}, support = {PN-II-ID-PCE-2011-3-0546//Romanian National Authority for Scientific Research, CNCS-UEFISCDI/ ; PN-II-ID-PCE-2011-3-0765//Romanian National Authority for Scientific Research, CNCS-UEFISCDI/ ; PN-III-P4-ID-PCE-2016-0303//Romanian National Authority for Scientific Research, CNCS-UEFISCDI/ ; Core Program, PN18-03 02 01//Ministry of Research and Innovation, MCI/ ; 31773.3//Babes-Bolyai University/ ; }, abstract = {AIM: This study aimed at unprecedented physical and chemical evaluation of the 'green plastics' polyhydroxyalkanoates (PHAs), in an extremely halotolerant Halomonas elongata strain 2FF under high-salt concentration.<br><br>METHODS AND RESULTS: The investigated bacterial strain was isolated from the surface water of the hypersaline Fără Fund Lake. The 16S rRNA gene sequence phylogeny and phenotypic analysis indicated that the isolate belonged to H. elongata. PHA inclusions were observed by Sudan Black B, Nile Red staining, and transmission electron microscopy during growth at high salinity (10%, w/v, NaCl) on 1% (w/v) d-glucose. The produced polymer was quantitatively and qualitatively assessed using crotonic acid assay, elemental analysis, Fourier transform infrared and Raman spectroscopies. Additionally, X-ray powder diffraction, 1 H-NMR spectroscopy, and differential scanning calorimetry were applied. The investigations showed that the intracellular polymer was polyhydroxybutyrate (PHB) of which the strain produced up to 40 wt% of total cell dry weight after 48 h. The analysis of phaC gene from the isolated H. elongata strain indicated that the encoded PHA synthase belongs to Class I PHA synthase family.<br><br>CONCLUSIONS: Overall, our investigations pointed out that the halotolerant H. elongata strain 2FF was capable to produce significant amounts of PHB from d-glucose, and PHAs from various carbon substrates at high-salt concentrations.<br><br>The tested strain showed the ability for significant production of natural, biodegradable polymers under nutrient limitation and hypersaline conditions suggesting its potentiality for further metabolic and molecular investigations towards enhanced biopolymer production. Additionally, this study reports on the unprecedented use of Raman and XPRD techniques to investigate PHAs of an extremely halotolerant bacterium, thus expanding the repertoire of physical methods to study green plastics derived from extremophilic microorganisms.}, }
@article {pmid29927545, year = {2018}, author = {Bäumel, S and Tytgat, HLP and Nemec, B and Schmidt, R and Chia, LW and Smidt, H}, title = {Fifty Percent Human - how art brings us in touch with our microbial cohabitants.}, journal = {Microbial biotechnology}, volume = {11}, number = {4}, pages = {571-574}, doi = {10.1111/1751-7915.13285}, pmid = {29927545}, issn = {1751-7915}, abstract = {The Human Microbiome, as well as the exploration of the microorganisms inhabiting the human body, are not only integral to the field of microbiology but represent an intrinsic part of all human beings. Consequently, along with scientists, artists have been inspired by the microbiome: transforming it in to tangible artefacts in order to critically question, reflect on and break down the barrier between humans and their microcohabitants. By artistic means, artists help us to understand how microbial research topics are inevitably affected by societal influences, including (health) politics, economics and the arts. Fifty Percent Human is a multidisciplinary artistic research project that aims to reshape our understanding of the human body and its environment as well as to explore possibilities for conscious coexistence in order to bridge the gap between science and society.}, }
@article {pmid29926340, year = {2018}, author = {Řezanka, T and Palyzová, A and Sigler, K}, title = {Isolation and identification of siderophores produced by cyanobacteria.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12223-018-0626-z}, pmid = {29926340}, issn = {1874-9356}, support = {LO1509//Ministry of Education, Youth and Sports of the Czech Republic/ ; }, abstract = {Cyanobacteria are one of the most successful and oldest forms of life that are present on Earth. They are prokaryotic photoautotrophic microorganisms that colonize so diverse environments as soil, seawater, and freshwater, but also stones, plants, or extreme habitats such as snow and ice as well as hot springs. This diversity in the type of environment they live in requires a successful adaptation to completely different conditions. For this reason, cyanobacteria form a wide range of different secondary metabolites. In particular, the cyanobacteria living in both freshwater and sea produce many metabolites that have biological activity. In this review, we focus on metabolites called siderophores, which are low molecular weight chemical compounds specifically binding iron ions. They have a relatively low molecular weight and are produced by bacteria and also by fungi. The main role of siderophores is to obtain iron from the environment and to create a soluble complex available to microbial cells. Siderophores play an important role in microbial ecology; for example, in agriculture they support the growth of many plants and increase their production by increasing the availability of Fe in plants. The aim of this review is to demonstrate the modern use of physico-chemical methods for the detection of siderophores in cyanobacteria and the use of these methods for the detection and characterization of the siderophore-producing microorganisms. Using high-performance liquid chromatography-mass spectrometry (LC-MS), it is possible not only to discover new chemical structures but also to identify potential interactions between microorganisms. Based on tandem mass spectrometry (MS/MS) analyses, previous siderophore knowledge can be used to interpret MS/MS data to examine both known and new siderophores.}, }
@article {pmid29926147, year = {2018}, author = {Schaub, I and Baum, C and Schumann, R and Karsten, U}, title = {Effects of an Early Successional Biological Soil Crust from a Temperate Coastal Sand Dune (NE Germany) on Soil Elemental Stoichiometry and Phosphatase Activity.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1220-2}, pmid = {29926147}, issn = {1432-184X}, support = {SAS-2015-IOW-LWC//Leibniz-Gemeinschaft/ ; }, abstract = {Early successional biological soil crusts (BSCs), a consortium of bacteria, cyanobacteria, and other microalgae, are one of the first settlement stages on temperate coastal sand dunes. In this study, we investigated the algal biomass (Chlorophyll a (Chl a)), algal (Calgal) and microbial carbon (Cmic), elemental stoichiometry (C:N:P), and acid and alkaline phosphatase activity (AcidPA and AlkPA) of two algae-dominated BSCs from a coastal white dune (northeast Germany, on the southwestern Baltic Sea) which differed in the exposure to wind forces. The dune sediment (DS) was generally low in total carbon (TC), nitrogen (TN), and phosphorus (TP). These elements, together with the soil organic matter (SOM) accumulated in the BSC layer and in the sediment underneath (crust sediment CS), leading to initial soil development. The more disturbed BSC (BSC1) exhibited lower algal and microbial biomass and lower Calgal/Cmic ratios than the undisturbed BSC (BSC2). The BSC1 accumulated more organic carbon (OC) than BSC2. However, the OC in the BSC2 was more effectively incorporated into Cmic than in the BSC1, as indicated by lower OC:Cmic ratios. The AcidPA (1.1-1.3 μmol g-1 DM h-1 or 147-178 μg g-1 DM h-1) and AlkPA (2.7-5.5 μmol g-1 DM h-1 or 372-764 μg g-1 DM h-1) were low in both BSCs. The PA, together with the elemental stoichiometry, indicated no P limitation of both BSCs but rather water limitation followed by N limitation for the algae community and a carbon limitation for the microbial community. Our results explain the observed distribution of early successional and more developed BSCs on the sand dune.}, }
@article {pmid29925614, year = {2018}, author = {Brothers, CJ and Van Der Pol, WJ and Morrow, CD and Hakim, JA and Koo, H and McClintock, JB}, title = {Ocean warming alters predicted microbiome functionality in a common sea urchin.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1881}, pages = {}, doi = {10.1098/rspb.2018.0340}, pmid = {29925614}, issn = {1471-2954}, abstract = {The microbiome of sea urchins plays a role in maintaining digestive health and innate immunity. Here, we investigated the effects of long-term (90 day) exposure to elevated seawater temperatures on the microbiome of the common, subtropical sea urchin Lytechinus variegatus The community composition and diversity of microbes varied according to the type of sample collected from the sea urchin (seawater, feed, intestines, coelomic fluid, digested pellet and faeces), with the lowest microbial diversity (predominately the order Campylobacterales) located in the intestinal tissue. Sea urchins exposed to near-future seawater temperatures maintained the community structure and diversity of microbes associated with their tissues. However, marginal, non-significant shifts in microbial community structure with elevated temperature resulted in significant changes in predicted metagenomic functions such as membrane transport and amino acid and carbohydrate metabolism. The predicted changes in key metabolic categories suggest that near-future climate-induced increases in seawater temperature could shift microbial community function and impact sea urchin digestive and immune physiology.}, }
@article {pmid29923792, year = {2018}, author = {Obase, K and Douhan, GW and Matsuda, Y and Smith, ME}, title = {Isolation source matters: sclerotia and ectomycorrhizal roots provide different views of genetic diversity in Cenococcum geophilum.}, journal = {Mycologia}, volume = {110}, number = {3}, pages = {473-481}, doi = {10.1080/00275514.2018.1463130}, pmid = {29923792}, issn = {1557-2536}, abstract = {Cenococcum geophilum forms sclerotia and ectomycorrhizas with host plants in forest soils. We demonstrated the differences in genetic diversity of C. geophilum between cultured isolates from sclerotia and those from ectomycorrhizal roots in the same 73 soil samples based on glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene sequences and newly developed microsatellite markers. Based on GAPDH sequences, 759 cultured isolates (553 from sclerotia and 206 from ectomycorrhizas) were classified into 107 &quot;genotypes&quot; with sequence variation of up to 8.6%. The total number of GAPDH genotypes per soil sample ranged from 1 to 9, but genotypes that were shared between sclerotia and ectomycorrhizas were uncommon (0-3 per soil sample). More than 50% of GAPDH genotypes were unique to one source in most soil samples. Unique GAPDH genotypes were detected from either scleotia or ectomycorrhizal roots in most of the soil samples. Multilocus analysis using nine microsatellite markers provided additional resolution to differentiate fungal individuals and supported the results of GAPDH genotyping. The results indicated that sampling both sclerotia and ectomycorrhizal roots maximizes the detection of diversity at the soil core scale. On the other hand, when all isolates were viewed together, 82 GAPDH genotypes were unique to sclerotia whereas only 6 GAPDH genotypes were unique to ectomycorrhizas. Rarefaction analysis indicated that GAPDH genotypic diversity is significantly higher in sclerotia than ectomycorrhizal roots and the diversity within sclerotia is nearly the same as that of both sclerotia and ectomycorrhizas together. These findings suggest that sampling sclerotia alone is likely to detect the majority of GAPDH genotypes in Cenococcum at the regional scale. When deciding whether to sample sclerotia, ectomycorrhizas, or both types of tissues from Cenococcum, it is critical to consider the spatial scale and also the main questions and hypotheses of the study.}, }
@article {pmid29923399, year = {2018}, author = {Pikaar, I and Matassa, S and Bodirsky, BL and Weindl, I and Humpenöder, F and Rabaey, K and Boon, N and Bruschi, M and Yuan, Z and van Zanten, H and Herrero, M and Verstraete, W and Popp, A}, title = {Decoupling Livestock from Land Use through Industrial Feed Production Pathways.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {13}, pages = {7351-7359}, doi = {10.1021/acs.est.8b00216}, pmid = {29923399}, issn = {1520-5851}, abstract = {One of the main challenges for the 21st century is to balance the increasing demand for high-quality proteins while mitigating environmental impacts. In particular, cropland-based production of protein-rich animal feed for livestock rearing results in large-scale agricultural land-expansion, nitrogen pollution, and greenhouse gas emissions. Here we propose and analyze the long-term potential of alternative animal feed supply routes based on industrial production of microbial proteins (MP). Our analysis reveals that by 2050, MP can replace, depending on socio-economic development and MP production pathways, between 10-19% of conventional crop-based animal feed protein demand. As a result, global cropland area, global nitrogen losses from croplands and agricultural greenhouse gas emissions can be decreased by 6% (0-13%), 8% (-3-8%), and 7% (-6-9%), respectively. Interestingly, the technology to industrially produce MP at competitive costs is directly accessible for implementation and has the potential to cause a major structural change in the agro-food system.}, }
@article {pmid29922904, year = {2018}, author = {Ghiloufi, W and Seo, J and Kim, J and Chaieb, M and Kang, H}, title = {Effects of Biological Soil Crusts on Enzyme Activities and Microbial Community in Soils of an Arid Ecosystem.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1219-8}, pmid = {29922904}, issn = {1432-184X}, support = {2016R1D1A1A02937049//National Research Foundation of Korea/ ; 20110030040//National Research Foundation of Korea/ ; 2016R1D1A1A02937049//National Research Foundation of Korea/ ; 2017096A001719BB01//Korea Forest Service/ ; }, abstract = {Arid ecosystems constitute 41% of land's surface and play an important role in global carbon cycle. In particular, biological soil crusts (BSC) are known to be a hotspot of carbon fixation as well as mineralization in arid ecosystems. However, little information is available on carbon decomposition and microbes in BSC and key controlling variables for microbial activities in arid ecosystems. The current study, carried out in South Mediterranean arid ecosystem, aimed to evaluate the effects of intact and removed cyanobacteria/lichen crusts on soil properties, soil enzyme activities, and microbial abundances (bacteria and fungi). We compared five different treatments (bare soil, soil with intact cyanobacteria, soil with cyanobacteria removed, soil with intact lichens, and soil with lichens removed) in four different soil layers (0-5, 5-10, 10-15, and 15-20 cm). Regardless of soil treatments, activities of hydrolases and water content increased with increasing soil depth. The presence of lichens increased significantly hydrolase activities, which appeared to be associated with greater organic matter, nitrogen, and water contents. However, phenol oxidase was mainly controlled by pH and oxygen availability. Neither fungal nor bacterial abundance exhibited a significant correlation with enzyme activities suggesting that soil enzyme activities are mainly controlled by edaphic and environmental conditions rather than source microbes. Interestingly, the presence of lichens reduced the abundance of bacteria of which mechanism is still to be investigated.}, }
@article {pmid29920927, year = {2018}, author = {Lee, JR and Magruder, M and Zhang, L and Westblade, LF and Satlin, MJ and Robertson, A and Edusei, E and Crawford, C and Ling, L and Taur, Y and Schluter, J and Lubetzky, M and Dadhania, D and Pamer, E and Suthanthiran, M}, title = {Gut microbiota dysbiosis and diarrhea in kidney transplant recipients.}, journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons}, volume = {}, number = {}, pages = {}, doi = {10.1111/ajt.14974}, pmid = {29920927}, issn = {1600-6143}, support = {K23 AI124464/AI/NIAID NIH HHS/United States ; R37 AI051652/AI/NIAID NIH HHS/United States ; }, abstract = {Posttransplant diarrhea is associated with kidney allograft failure and death, but its etiology remains unknown in the majority of cases. Because altered gut microbial ecology is a potential basis for diarrhea, we investigated whether posttransplant diarrhea is associated with gut dysbiosis. We enrolled 71 kidney allograft recipients for serial fecal specimen collections in the first 3 months of transplantation and profiled the gut microbiota using 16S ribosomal RNA (rRNA) gene V4-V5 deep sequencing. The Shannon diversity index was significantly lower in 28 diarrheal fecal specimens from 25 recipients with posttransplant diarrhea than in 112 fecal specimens from 46 recipients without posttransplant diarrhea. We found a lower relative abundance of 13 commensal genera (Benjamini-Hochberg adjusted P ≤ .15) in the diarrheal fecal specimens including the same 4 genera identified in our prior study. The 28 diarrheal fecal specimens were also evaluated by a multiplexed polymerase chain reaction (PCR) assay for 22 bacterial, viral, and protozoan gastrointestinal pathogens, and 26 specimens were negative for infectious etiologies. Using PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) to predict metagenomic functions, we found that diarrheal fecal specimens had a lower abundance of metabolic genes. Our findings suggest that posttransplant diarrhea is not associated with common infectious diarrheal pathogens but with a gut dysbiosis.}, }
@article {pmid29920462, year = {2018}, author = {Ferguson, RMW and Coulon, F and Villa, R}, title = {Understanding microbial ecology can help improve biogas production in AD.}, journal = {The Science of the total environment}, volume = {642}, number = {}, pages = {754-763}, doi = {10.1016/j.scitotenv.2018.06.007}, pmid = {29920462}, issn = {1879-1026}, abstract = {454-Pyrosequencing and lipid fingerprinting were used to link anaerobic digestion (AD) process parameters (pH, alkalinity, volatile fatty acids (VFAs), biogas production and methane content) with the reactor microbial community structure and composition. AD microbial communities underwent stress conditions after changes in organic loading rate and digestion substrates. 454-Pyrosequencing analysis showed that, irrespectively of the substrate digested, methane content and pH were always significantly, and positively, correlated with community evenness. In AD, microbial communities with more even distributions of diversity are able to use parallel metabolic pathways and have greater functional stability; hence, they are capable of adapting and responding to disturbances. In all reactors, a decrease in methane content to <30% was always correlated with a 50% increase of Firmicutes sequences (particularly in operational taxonomic units (OTUs) related to Ruminococcaceae and Veillonellaceae). Whereas digesters producing higher methane content (above 60%), contained a high number of sequences related to Synergistetes and unidentified bacterial OTUs. Finally, lipid fingerprinting demonstrated that, under stress, the decrease in archaeal biomass was higher than the bacterial one, and that archaeal Phospholipid etherlipids (PLEL) levels were correlated to reactor performances. These results demonstrate that, across a number of parameters such as lipids, alpha and beta diversity, and OTUs, knowledge of the microbial community structure can be used to predict, monitor, or optimise AD performance.}, }
@article {pmid29916010, year = {2018}, author = {Wentzel, LCP and Inforsato, FJ and Montoya, QV and Rossin, BG and Nascimento, NR and Rodrigues, A and Sette, LD}, title = {Fungi from Admiralty Bay (King George Island, Antarctica) Soils and Marine Sediments.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1217-x}, pmid = {29916010}, issn = {1432-184X}, support = {2013/19486-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2016/07957-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 304103/2013-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 305341/2015-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Extreme environments such as the Antarctic can lead to the discovery of new microbial taxa, as well as to new microbial-derived natural products. Considering that little is known yet about the diversity and the genetic resources present in these habitats, the main objective of this study was to evaluate the fungal communities from extreme environments collected at Aldmiralty Bay (Antarctica). A total of 891 and 226 isolates was obtained from soil and marine sediment samples, respectively. The most abundant isolates from soil samples were representatives of the genera Leucosporidium, Pseudogymnoascus, and a non-identified Ascomycota NIA6. Metschnikowia sp. was the most abundant taxon from marine samples, followed by isolates from the genera Penicillium and Pseudogymnoascus. Many of the genera were exclusive in marine sediment or terrestrial samples. However, representatives of eight genera were found in both types of samples. Data from non-metric multidimensional scaling showed that each sampling site is unique in their physical-chemical composition and fungal community. Biotechnological potential in relation to enzymatic production at low/moderate temperatures was also investigated. Ligninolytic enzymes were produced by few isolates from root-associated soil. Among the fungi isolated from marine sediments, 16 yeasts and nine fungi showed lipase activity and three yeasts and six filamentous fungi protease activity. The present study permitted increasing our knowledge on the diversity of fungi that inhabit the Antarctic, finding genera that have never been reported in this environment before and discovering putative new species of fungi.}, }
@article {pmid29915106, year = {2018}, author = {Bryce, C and Franz-Wachtel, M and Nalpas, NC and Miot, J and Benzerara, K and Byrne, JM and Kleindienst, S and Macek, B and Kappler, A}, title = {Proteome Response of a Metabolically Flexible Anoxygenic Phototroph to Fe(II) Oxidation.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {16}, pages = {}, doi = {10.1128/AEM.01166-18}, pmid = {29915106}, issn = {1098-5336}, abstract = {The oxidation of Fe(II) by anoxygenic photosynthetic bacteria was likely a key contributor to Earth's biosphere prior to the evolution of oxygenic photosynthesis and is still found in a diverse range of modern environments. All known phototrophic Fe(II) oxidizers can utilize a wide range of substrates, thus making them very metabolically flexible. However, the underlying adaptations required to oxidize Fe(II), a potential stressor, are not completely understood. We used a combination of quantitative proteomics and cryogenic transmission electron microscopy (cryo-TEM) to compare cells of Rhodopseudomonas palustris TIE-1 grown photoautotrophically with Fe(II) or H2 and photoheterotrophically with acetate. We observed unique proteome profiles for each condition, with differences primarily driven by carbon source. However, these differences were not related to carbon fixation but to growth and light harvesting processes, such as pigment synthesis. Cryo-TEM showed stunted development of photosynthetic membranes in photoautotrophic cultures. Growth on Fe(II) was characterized by a response typical of iron homeostasis, which included an increased abundance of proteins required for metal efflux (particularly copper) and decreased abundance of iron import proteins, including siderophore receptors, with no evidence of further stressors, such as oxidative damage. This study suggests that the main challenge facing anoxygenic phototrophic Fe(II) oxidizers comes from growth limitations imposed by autotrophy, and, once this challenge is overcome, iron stress can be mitigated using iron management mechanisms common to diverse bacteria (e.g., by control of iron influx and efflux).IMPORTANCE The cycling of iron between redox states leads to the precipitation and dissolution of minerals, which can in turn impact other major biogeochemical cycles, such as those of carbon, nitrogen, phosphorus and sulfur. Anoxygenic phototrophs are one of the few drivers of Fe(II) oxidation in anoxic environments and are thought to contribute significantly to iron cycling in both modern and ancient environments. These organisms thrive at high Fe(II) concentrations, yet the adaptations required to tolerate the stresses associated with this are unclear. Despite the general consensus that high Fe(II) concentrations pose numerous stresses on these organisms, our study of the large-scale proteome response of a model anoxygenic phototroph to Fe(II) oxidation demonstrates that common iron homeostasis strategies are adequate to manage this. The bulk of the proteome response is not driven by adaptations to Fe(II) stress but to adaptations required to utilize an inorganic carbon source. Such a global overview of the adaptation of these organisms to Fe(II) oxidation provides valuable insights into the physiology of these biogeochemically important organisms and suggests that Fe(II) oxidation may not pose as many challenges to anoxygenic phototrophs as previously thought.}, }
@article {pmid29915105, year = {2018}, author = {Rosenfeld, CE and James, BR and Santelli, CM}, title = {Persistent Bacterial and Fungal Community Shifts Exhibited in Selenium-Contaminated Reclaimed Mine Soils.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {16}, pages = {}, doi = {10.1128/AEM.01394-18}, pmid = {29915105}, issn = {1098-5336}, abstract = {Mining and other industrial activities worldwide have resulted in Se-enriched surface soils, which pose risks to human and environmental health. Although not well studied, microbial activity can alter Se bioavailability and distribution, even in oxic environments. We used high-throughput sequencing to profile bacterial and fungal communities inhabiting mine soils in southeastern Idaho, comparing mined and unmined locations within two reclaimed phosphate mine areas containing various Se concentrations. The goal was to determine whether microbial communities differed in (i) different mines, (ii) mined areas compared to unmined areas, and (iii) various soil Se concentrations. Though reclamation occurred 20 to 30 years ago, microbial community structures in mined soils were significantly altered compared to unmined soils, suggesting persistent mining-related impacts on soil processes. Additionally, operational taxonomic unit with a 97% sequence similarity cutoff (OTU0.03) richness and diversity were significantly diminished with increasing Se, though not with other geochemical parameters, suggesting that Se contamination shapes communities in favor of Se-tolerant microorganisms. Two bacterial phyla, Actinobacteria and Gemmatimonadetes, were enriched in high-Se soils, while for fungi, Ascomycota dominated all soils regardless of Se concentration. Combining diversity analyses and taxonomic patterns enables us to move toward connecting physiological function of microbial groups to Se biogeochemical cycling in oxic soil environments.IMPORTANCE Selenium contamination in natural environments is of great concern globally, and microbial processes are known to mediate Se transformations. Such transformations alter Se mobility, bioavailability, and toxicity, which can amplify or mitigate Se pollution. To date, nearly all studies investigating Se-microbe interactions have used culture-based approaches with anaerobic bacteria despite growing knowledge that (i) aerobic Se transformations can occur, (ii) such transformations can be mediated by microorganisms other than bacteria, and (iii) microbial community dynamics, rather than individual organismal activities, are important for metal(loid) cycling in natural environments. We examined bacterial and fungal communities in Se-contaminated reclaimed mine soils and found significant declines in diversity at high Se concentrations. Additionally, we identified specific taxonomic groups that tolerate excess Se and may be useful for bioremediation purposes. These patterns were similar across mines of different ages, suggesting that microbial community impacts may persist long after physicochemical parameters indicate complete site recovery.}, }
@article {pmid29913582, year = {2018}, author = {Zhang, S and Sheng, B and Lin, W and Meng, F}, title = {Day/night temperature differences (DNTD) trigger changes in nutrient removal and functional bacteria in membrane bioreactors.}, journal = {The Science of the total environment}, volume = {636}, number = {}, pages = {1202-1210}, doi = {10.1016/j.scitotenv.2018.04.373}, pmid = {29913582}, issn = {1879-1026}, mesh = {Bioreactors/*microbiology ; *Membranes, Artificial ; Microbiota ; Temperature ; Waste Disposal, Fluid/*methods ; Waste Water ; }, abstract = {Temperature is a well-known environmental stress that influences both microbial metabolism and community structure in the biological wastewater treatment systems. In this study, responses of biological performance and sludge microbiota to the long-term day/night temperature differences (DNTD) were investigated in membrane bioreactors (MBRs). The results showed that the functional bacteria could sustained their ecological functions at low DNTD (20/30 °C), resulting in relatively stable performance with respect to nutrient removal. However, when the activated sludge was subjected to a high DNTD (17/33 °C), the effluent concentrations of COD, TN and TP were significantly higher in MBR-B than that in MBR-A. In addition, more severe membrane fouling occurred under the perturbation of high DNTD as revealed by the transmembrane pressure (TMP) profile, which was mainly attributed to the accumulation of extracellular polymeric substances (EPS). The results of 16S rRNA gene sequencing showed that DNTD showed negligible effect on the bacterial community structures. Nonetheless, the functional bacteria responded differently to DNTD, which were in accordance with the bioreactor performances. Specifically, Nitrospina (NOB) and Tetrasphaera (PAOs) appeared to be sensitive to both low and high DNTD. In contrast, a low DNTD showed marginal effects on the denitrifiers, while a high DNTD significantly decreased their abundances. More strikingly, filamentous bulking bacteria were found to be well-adapted to DNTD, indicating their tolerance to the daily temperature fluctuation. This study will advance our knowledge regarding the response of microbial ecology of activated sludge to daily temperature variations in full-scale MBRs.}, }
@article {pmid29912320, year = {2018}, author = {Kumar, V and Thakur, V and Ambika,  and Kumar, S and Singh, D}, title = {Bioplastic reservoir of diverse bacterial communities revealed along altitude gradient of Pangi-Chamba trans-Himalayan region.}, journal = {FEMS microbiology letters}, volume = {365}, number = {14}, pages = {}, doi = {10.1093/femsle/fny144}, pmid = {29912320}, issn = {1574-6968}, abstract = {Himalaya hosts a unique environment for microbial ecology. The present study aimed to explore the bioplastic producing bacterial communities along altitude gradient of Pangi-Chamba trans-Himalayan region. A total of 411 bacteria were isolated and 70 characterized at the molecular level for potential polyhydroxyalkanoates (PHA) producers. The most abundant phylum for PHA synthesis was Proteobacteria (73%), followed by Actinobacteria (11%), Firmicutes (10%) and Bacteroidetes (6%). However, at the genus level, Pseudomonas and Janthinobacterium were dominantly reported. Also, the ability to synthesize PHA was reported for the first time for few genera such as Collimonas, Pseudarthrobacter and Paenarthrobacter. Phylogenetic analysis of partial 16S rDNA and phaC genes revealed conservation in phaC and possibility of horizontal gene transfer among distant taxa. Furthermore, GC-MS also confirmed the ability of potential bacterial isolates to synthesize PHA. In fact, we found that PHA-positive bacteria are dominant in the high altitude of Himalaya, suggesting the vital role of PHA in bacterial adaptation and survival. Together, these findings had revealed the rich bacterial diversity and genetic machinery for PHA synthesis which does have potential for further utilization in the commercial applications.}, }
@article {pmid29910792, year = {2018}, author = {Daniel, R and Simon, M and Wemheuer, B}, title = {Editorial: Molecular Ecology and Genetic Diversity of the Roseobacter Clade.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1185}, doi = {10.3389/fmicb.2018.01185}, pmid = {29910792}, issn = {1664-302X}, }
@article {pmid29909752, year = {2018}, author = {Subramaniam, A and Van Der Pol, WJ and Ptacek, T and Lobashevsky, E and Neely, C and Biggio, JR and Lefkowitz, EJ and Morrow, CD and Edwards, RK}, title = {Midtrimester microbial DNA variations in maternal serum of women who experience spontaneous preterm birth.}, journal = {The journal of maternal-fetal &amp; neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians}, volume = {}, number = {}, pages = {1-9}, doi = {10.1080/14767058.2018.1490721}, pmid = {29909752}, issn = {1476-4954}, abstract = {OBJECTIVES: To evaluate if midtrimester maternal serum contains microbial DNA and whether it differs between women with spontaneous preterm birth (SPTB) and those delivering at term.<br><br>STUDY DESIGN: In this retrospective case-control study, we identified 20 healthy nulliparas with SPTB at 24-33 weeks of a nonanomalous singleton in 2014. Each case was matched by race/ethnicity to a control delivering at 39-40 weeks. Serum samples, collected at 15-20 weeks and stored at -80 C, were thawed and DNA extracted. PCR with primers targeting the 16S rDNA V4 region were used to prepare an amplicon library, sequenced using Illumina MiSeq, and analyzed using quantitative insight into microbial ecology (QIIME). Taxonomy was assigned using Ribosomal Database program (RDP) Classifier (threshold 0.8) against a modified Greengenes database. Differences in number of observed species, microbial alpha-diversity and beta-diversity, and taxa level analyses were undertaken.<br><br>RESULTS: All 40 samples were included. Women with SPTB had more unique observed species (p = .046) and higher mean alpha-diversity by Shannon index (but not Chao1 or Simpson) (p = .024). Microbial composition was different between groups by Bray-Curtis clustering (p = .03) but not by weighted (p = .13) or unweighted Unifrac (p = .11). Numerous taxa in the Firmicutes, Proteobacteria, and Actinobacteria phyla differed between groups (p < .05).<br><br>CONCLUSIONS: SPTB is associated with distinct microbial DNA changes detected in midtrimester maternal serum.}, }
@article {pmid29905870, year = {2018}, author = {Rodriguez-R, LM and Gunturu, S and Harvey, WT and Rosselló-Mora, R and Tiedje, JM and Cole, JR and Konstantinidis, KT}, title = {The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.}, journal = {Nucleic acids research}, volume = {46}, number = {W1}, pages = {W282-W288}, doi = {10.1093/nar/gky467}, pmid = {29905870}, issn = {1362-4962}, abstract = {The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species and communities but it offers limited resolution at the species and finer levels, and cannot represent the whole-genome diversity and fluidity. To overcome these limitations, we introduced the Microbial Genomes Atlas (MiGA), a webserver that allows the classification of an unknown query genomic sequence, complete or partial, against all taxonomically classified taxa with available genome sequences, as well as comparisons to other related genomes including uncultivated ones, based on the genome-aggregate Average Nucleotide and Amino Acid Identity (ANI/AAI) concepts. MiGA integrates best practices in sequence quality trimming and assembly and allows input to be raw reads or assemblies from isolate genomes, single-cell sequences, and metagenome-assembled genomes (MAGs). Further, MiGA can take as input hundreds of closely related genomes of the same or closely related species (a so-called 'Clade Project') to assess their gene content diversity and evolutionary relationships, and calculate important clade properties such as the pangenome and core gene sets. Therefore, MiGA is expected to facilitate a range of genome-based taxonomic and diversity studies, and quality assessment across environmental and clinical settings. MiGA is available at http://microbial-genomes.org/.}, }
@article {pmid29905791, year = {2018}, author = {Merlino, G and Barozzi, A and Michoud, G and Ngugi, DK and Daffonchio, D}, title = {Microbial ecology of deep-sea hypersaline anoxic basins.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {7}, pages = {}, doi = {10.1093/femsec/fiy085}, pmid = {29905791}, issn = {1574-6941}, abstract = {Deep hypersaline anoxic basins (DHABs) are unique water bodies occurring within fractures at the bottom of the sea, where the dissolution of anciently buried evaporites created dense anoxic brines that are separated by a chemocline/pycnocline from the overlying oxygenated deep-seawater column. DHABs have been described in the Gulf of Mexico, the Mediterranean Sea, the Black Sea and the Red Sea. They are characterized by prolonged historical separation of the brines from the upper water column due to lack of mixing and by extreme conditions of salinity, anoxia, and relatively high hydrostatic pressure and temperatures. Due to these combined selection factors, unique microbial assemblages thrive in these polyextreme ecosystems. The topological localization of the different taxa in the brine-seawater transition zone coupled with the metabolic interactions and niche adaptations determine the metabolic functioning and biogeochemistry of DHABs. In particular, inherent metabolic strategies accompanied by genetic adaptations have provided insights on how prokaryotic communities can adapt to salt-saturated conditions. Here, we review the current knowledge of the diversity, genomics, metabolisms and ecology of prokaryotes in DHABs.}, }
@article {pmid29904373, year = {2018}, author = {Le Moine Bauer, S and Stensland, A and Daae, FL and Sandaa, RA and Thorseth, IH and Steen, IH and Dahle, H}, title = {Water Masses and Depth Structure Prokaryotic and T4-Like Viral Communities Around Hydrothermal Systems of the Nordic Seas.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1002}, doi = {10.3389/fmicb.2018.01002}, pmid = {29904373}, issn = {1664-302X}, abstract = {The oceanographic features of the Nordic Seas, situated between Iceland and Svalbard, have been extensively studied over the last decades. As well, the Nordic Seas hydrothermal systems situated on the Arctic Mid-Ocean Ridge System have received an increasing interest. However, there is very little knowledge on the microbial communities inhabiting the water column of the Nordic Seas, and nothing is known about the influence of the different water masses and hydrothermal plumes on the microbial community structures. In this study, we aimed at characterizing the impact of hydrothermal plumes on prokaryotic and T4-like viral communities around the island of Jan Mayen. To this end, we used 16S rRNA-gene and g23-gene profiling as well as flow cytometry counts to examine prokaryotic and viral communities in 27 samples obtained from different water masses in this area. While Thaumarchaeota and Marine group II Archaea dominated the waters deeper than 500 m, members of Flavobacteria generally dominated the shallower waters. Furthermore, extensive chemical and physical characteristics of all samples were obtained, including temperature measurements and concentrations of major ions and gases. The effect of these physiochemical variables on the communities was measured by using constrained and unconstrained multivariate analyzes, Mantel tests, network analyzes, phylogenetic analyzes, taxonomic analyzes and temperature-salinity (Θ-S) plots. Our results suggest that hydrothermal activity has little effect on pelagic microbial communities in hydrothermal plumes of the Nordic Seas. However, we provide evidences that observed differences in prokaryotic community structure can largely be attributed to which water mass each sample was taken from. In contrast, depth was the major factor structuring the T4-like viral communities. Our results also show that it is crucial to include water masses when studying the influence of hydrothermal plumes on microbial communities, as it could prevent to falsely associate a change in community structure with the presence of a plume.}, }
@article {pmid29904372, year = {2018}, author = {Guo, X and Zhou, X and Hale, L and Yuan, M and Feng, J and Ning, D and Shi, Z and Qin, Y and Liu, F and Wu, L and He, Z and Van Nostrand, JD and Liu, X and Luo, Y and Tiedje, JM and Zhou, J}, title = {Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {954}, doi = {10.3389/fmicb.2018.00954}, pmid = {29904372}, issn = {1664-302X}, abstract = {Clipping, removal of aboveground plant biomass, is an important issue in grassland ecology. However, few studies have focused on the effect of clipping on belowground microbial communities. Using integrated metagenomic technologies, we examined the taxonomic and functional responses of soil microbial communities to annual clipping (2010-2014) in a grassland ecosystem of the Great Plains of North America. Our results indicated that clipping significantly (P < 0.05) increased root and microbial respiration rates. Annual temporal variation within the microbial communities was much greater than the significant changes introduced by clipping, but cumulative effects of clipping were still observed in the long-term scale. The abundances of some bacterial and fungal lineages including Actinobacteria and Bacteroidetes were significantly (P < 0.05) changed by clipping. Clipping significantly (P < 0.05) increased the abundances of labile carbon (C) degrading genes. More importantly, the abundances of recalcitrant C degrading genes were consistently and significantly (P < 0.05) increased by clipping in the last 2 years, which could accelerate recalcitrant C degradation and weaken long-term soil carbon stability. Furthermore, genes involved in nutrient-cycling processes including nitrogen cycling and phosphorus utilization were also significantly increased by clipping. The shifts of microbial communities were significantly correlated with soil respiration and plant productivity. Intriguingly, clipping effects on microbial function may be highly regulated by precipitation at the interannual scale. Altogether, our results illustrated the potential of soil microbial communities for increased soil organic matter decomposition under clipping land-use practices.}, }
@article {pmid29902436, year = {2018}, author = {Makki, K and Deehan, EC and Walter, J and Bäckhed, F}, title = {The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease.}, journal = {Cell host &amp; microbe}, volume = {23}, number = {6}, pages = {705-715}, doi = {10.1016/j.chom.2018.05.012}, pmid = {29902436}, issn = {1934-6069}, abstract = {Food is a primordial need for our survival and well-being. However, diet is not only essential to maintain human growth, reproduction, and health, but it also modulates and supports the symbiotic microbial communities that colonize the digestive tract-the gut microbiota. Type, quality, and origin of our food shape our gut microbes and affect their composition and function, impacting host-microbe interactions. In this review, we will focus on dietary fibers, which interact directly with gut microbes and lead to the production of key metabolites such as short-chain fatty acids, and discuss how dietary fiber impacts gut microbial ecology, host physiology, and health. Hippocrates' notion &quot;Let food be thy medicine and medicine be thy food&quot; remains highly relevant millennia later, but requires consideration of how diet can be used for modulation of gut microbial ecology to promote health.}, }
@article {pmid29902263, year = {2018}, author = {Bednarz, VN and Naumann, MS and Cardini, U and van Hoytema, N and Rix, L and Al-Rshaidat, MMD and Wild, C}, title = {Contrasting seasonal responses in dinitrogen fixation between shallow and deep-water colonies of the model coral Stylophora pistillata in the northern Red Sea.}, journal = {PloS one}, volume = {13}, number = {6}, pages = {e0199022}, doi = {10.1371/journal.pone.0199022}, pmid = {29902263}, issn = {1932-6203}, abstract = {Tropical corals are often associated with dinitrogen (N2)-fixing bacteria (diazotrophs), and seasonal changes in key environmental parameters, such as dissolved inorganic nitrogen (DIN) availability and seawater temperature, are known to affect N2 fixation in coral-microbial holobionts. Despite, then, such potential for seasonal and depth-related changes in N2 fixation in reef corals, such variation has not yet been investigated. Therefore, this study quantified seasonal (winter vs. summer) N2 fixation rates associated with the reef-building coral Stylophora pistillata collected from depths of 5, 10 and 20 m in the northern Gulf of Aqaba (Red Sea). Findings revealed that corals from all depths exhibited the highest N2 fixation rates during the oligotrophic summer season, when up to 11% of their photo-metabolic nitrogen demand (CPND) could be met by N2 fixation. While N2 fixation remained seasonally stable for deep corals (20 m), it significantly decreased for the shallow corals (5 and 10 m) during the DIN-enriched winter season, accounting for less than 2% of the corals' CPND. This contrasting seasonal response in N2 fixation across corals of different depths could be driven by 1) release rates of coral-derived organic matter, 2) the community composition of the associated diazotrophs, and/or 3) nutrient acquisition by the Symbiodinium community.}, }
@article {pmid29899600, year = {2018}, author = {Saha, M and Goecke, F and Bhadury, P}, title = {Minireview: algal natural compounds and extracts as antifoulants.}, journal = {Journal of applied phycology}, volume = {30}, number = {3}, pages = {1859-1874}, doi = {10.1007/s10811-017-1322-0}, pmid = {29899600}, issn = {0921-8971}, abstract = {Marine biofouling is a paramount phenomenon in the marine environment and causes serious problems to maritime industries worldwide. Marine algae are known to produce a wide variety of chemical compounds with antibacterial, antifungal, antialgal, and anti-macrofouling properties, inhibiting the settlement and growth of other marine fouling organisms. Significant investigations and progress have been made in this field in the last two decades and several antifouling extracts and compounds have been isolated from micro- and macroalgae. In this minireview, we have summarized and evaluated antifouling compounds isolated and identified from macroalgae and microalgae between January 2010 and June 2016. Future directions for their commercialization through metabolic engineering and industrial scale up have been discussed. Upon comparing biogeographical regions, investigations from Southeast Asian waters were found to be rather scarce. Thus, we have also discussed the need to conduct more chemical ecology based research in relatively less explored areas with high algal biodiversity like Southeast Asia.}, }
@article {pmid29899517, year = {2018}, author = {Carrión, VJ and Cordovez, V and Tyc, O and Etalo, DW and de Bruijn, I and de Jager, VCL and Medema, MH and Eberl, L and Raaijmakers, JM}, title = {Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils.}, journal = {The ISME journal}, volume = {12}, number = {9}, pages = {2307-2321}, doi = {10.1038/s41396-018-0186-x}, pmid = {29899517}, issn = {1751-7370}, abstract = {Disease-suppressive soils are ecosystems in which plants suffer less from root infections due to the activities of specific microbial consortia. The characteristics of soils suppressive to specific fungal root pathogens are comparable to those of adaptive immunity in animals, as reported by Raaijmakers and Mazzola (Science 352:1392-3, 2016), but the mechanisms and microbial species involved in the soil suppressiveness are largely unknown. Previous taxonomic and metatranscriptome analyses of a soil suppressive to the fungal root pathogen Rhizoctonia solani revealed that members of the Burkholderiaceae family were more abundant and more active in suppressive than in non-suppressive soils. Here, isolation, phylogeny, and soil bioassays revealed a significant disease-suppressive activity for representative isolates of Burkholderia pyrrocinia, Paraburkholderia caledonica, P. graminis, P. hospita, and P. terricola. In vitro antifungal activity was only observed for P. graminis. Comparative genomics and metabolite profiling further showed that the antifungal activity of P. graminis PHS1 was associated with the production of sulfurous volatile compounds encoded by genes not found in the other four genera. Site-directed mutagenesis of two of these genes, encoding a dimethyl sulfoxide reductase and a cysteine desulfurase, resulted in a loss of antifungal activity both in vitro and in situ. These results indicate that specific members of the Burkholderiaceae family contribute to soil suppressiveness via the production of sulfurous volatile compounds.}, }
@article {pmid29897884, year = {2018}, author = {Platzer, A and Polzin, J and Rembart, K and Han, PP and Rauer, D and Nussbaumer, T}, title = {BioSankey: Visualization of Microbial Communities Over Time.}, journal = {Journal of integrative bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1515/jib-2017-0063}, pmid = {29897884}, issn = {1613-4516}, abstract = {Metagenomics provides quantitative measurements for microbial species over time. To obtain a global overview of an experiment and to explore the full potential of a given dataset, intuitive and interactive visualization tools are needed. Therefore, we established BioSankey to visualize microbial species in microbiome studies over time as a Sankey diagram. These diagrams are embedded into a project-specific webpage which depends only on JavaScript and Google API to allow searches of interesting species without requiring a web server or connection to a database. BioSankey is a valuable tool to visualize different data elements from single or dual RNA-seq datasets and additionally enables a straightforward exchange of results among collaboration partners.}, }
@article {pmid29896162, year = {2018}, author = {Haq, IU and Zwahlen, RD and Yang, P and van Elsas, JD}, title = {The Response of Paraburkholderia terrae Strains to Two Soil Fungi and the Potential Role of Oxalate.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {989}, doi = {10.3389/fmicb.2018.00989}, pmid = {29896162}, issn = {1664-302X}, abstract = {Fungal-associated Paraburkholderia terrae strains in soil have been extensively studied, but their sensing strategies to locate fungi in soil have remained largely elusive. In this study, we investigated the behavior of five mycosphere-isolated P. terrae strains [including the type-3 secretion system negative mutant BS001-ΔsctD and the type strain DSM 17804T] with respect to their fungal-sensing strategies. The putative role of oxalic acid as a signaling molecule in the chemotaxis toward soil fungi, as well as a potential carbon source, was assessed. First, all P. terrae strains, including the type strain, were found to sense, and show a chemotactic response toward, the different levels of oxalic acid (0.1, 0.5, and 0.8%) applied at a distance. The chemotactic responses were faster and stronger at lower concentrations (0.1%) than at higher ones. We then tested the chemotactic responses of all strains toward exudates of the soil fungi Lyophyllum sp. strain Karsten and Trichoderma asperellum 302 used in different dilutions (undiluted, 1:10, 1:100 diluted) versus the control. All P. terrae strains showed significant directed chemotactic behavior toward the exudate source, with full-strength exudates inciting the strongest responses. In a separate experiment, strain BS001 was shown to be able to grow on oxalate-amended (0.1 and 0.5%) mineral medium M9. Chemical analyses of the fungal secretomes using proton nuclear magnetic resonance (1H NMR), next to high-performance liquid chromatography (HPLC), indeed revealed the presence of oxalic acid (next to glycerol, acetic acid, formic acid, and fumaric acid) in the supernatants of both fungi. In addition, citric acid was found in the Lyophyllum sp. strain Karsten exudates. Given the fact that, next to oxalic acid, the other compounds can also serve as C and energy sources for P. terrae, the two fungi clearly offer ecological benefits to this bacterium. The oxalic acid released by the two fungi may have primarily acted as a signaling molecule, and, as a &quot;second option,&quot; a carbon source for P. terrae strains like BS001.}, }
@article {pmid29893876, year = {2018}, author = {Algya, KM and Cross, TL and Leuck, KN and Kastner, ME and Baba, T and Lye, L and de Godoy, MRC and Swanson, KS}, title = {Apparent Total Tract Macronutrient Digestibility, Serum Chemistry, Urinalysis, and Fecal Characteristics, Metabolites and Microbiota of Adult Dogs Fed Extruded, Mildly Cooked, and Raw Diets.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/sky235}, pmid = {29893876}, issn = {1525-3163}, abstract = {Despite their popularity, little research has been performed on lightly cooked and raw diet formats for pets. Therefore, the objective of this study was to determine the apparent total tract macronutrient digestibility (ATTD); fecal characteristics, metabolites, and microbiota; serum chemistry metabolites; urinalysis; and voluntary physical activity levels of adult dogs fed commercial diets differing in processing type. The diets included: 1) Extruded Dry Kibble (EXT) diet; 2) High-Moisture Roasted Refrigerated (RR) diet; 3) High-Moisture Grain-Free Roasted Refrigerated (GFRR) diet; and 4) Raw (RAW) diet. Eight dogs (mean age = 3.6; mean BW = 13.0 kg) were used in a replicated 4x4 Latin square design. Each period consisted of 28 d, with a 14-d adaptation phase followed by a 7-d phase for measuring voluntary physical activity, 1-d adaptation phase to metabolic cages, 5-d phase for fecal and urine collection, and 1 d for blood collection. Except for microbiota, all data were analyzed statistically by mixed models using SAS. Microbiota data were analyzed using Quantitative Insights Into Microbial Ecology (QIIME) and Statistical Analyses of Metagenomic Profiles (STAMP) software. Many differences in digestibility were observed, including greater (P<0.05) ATTD of crude protein and fat in dogs fed GFRR and RR than dogs fed EXT. Dogs fed RAW had the lowest fecal pH and dry matter %, but fecal scores were not affected. Dogs fed RR had higher (P<0.05) fecal indole and total phenol and indole concentrations than dogs fed the other diets. Dogs fed RAW had a higher (P<0.05) fecal ammonia concentration than dogs fed the other diets. Fecal microbial diversity was altered by diet, with dogs fed GFRR and RAW having reduced species richness than dogs fed EXT. Dogs fed RR, GFRR, or RAW had lower (P<0.05) Actinobacteria and higher (P<0.05) Fusobacteria than dogs fed EXT. Dogs fed RAW or GFRR had higher (P<0.05) Proteobacteria than dogs fed EXT or RR. Dogs fed RAW had higher (P<0.05) Bacteroidetes and lower (P<0.05) Firmicutes than dogs fed EXT. Serum triglycerides were within reference ranges, but greater (P<0.05) in dogs fed EXT than dogs fed GFRR and RAW. All diets were well tolerated and dogs remained healthy throughout the study. In conclusion, the lightly cooked and raw diets tested were highly palatable, highly digestible, reduced blood triglycerides, maintained fecal quality and serum chemistry, and modified the fecal microbial community of healthy adult dogs.}, }
@article {pmid29892374, year = {2018}, author = {Harrison, JP and Boardman, C and O'Callaghan, K and Delort, AM and Song, J}, title = {Biodegradability standards for carrier bags and plastic films in aquatic environments: a critical review.}, journal = {Royal Society open science}, volume = {5}, number = {5}, pages = {171792}, doi = {10.1098/rsos.171792}, pmid = {29892374}, issn = {2054-5703}, abstract = {Plastic litter is encountered in aquatic ecosystems across the globe, including polar environments and the deep sea. To mitigate the adverse societal and ecological impacts of this waste, there has been debate on whether 'biodegradable' materials should be granted exemptions from plastic bag bans and levies. However, great care must be exercised when attempting to define this term, due to the broad and complex range of physical and chemical conditions encountered within natural ecosystems. Here, we review existing international industry standards and regional test methods for evaluating the biodegradability of plastics within aquatic environments (wastewater, unmanaged freshwater and marine habitats). We argue that current standards and test methods are insufficient in their ability to realistically predict the biodegradability of carrier bags in these environments, due to several shortcomings in experimental procedures and a paucity of information in the scientific literature. Moreover, existing biodegradability standards and test methods for aquatic environments do not involve toxicity testing or account for the potentially adverse ecological impacts of carrier bags, plastic additives, polymer degradation products or small (microscopic) plastic particles that can arise via fragmentation. Successfully addressing these knowledge gaps is a key requirement for developing new biodegradability standard(s) for lightweight carrier bags.}, }
@article {pmid29892072, year = {2018}, author = {Krause, SMB and Meima-Franke, M and Veraart, AJ and Ren, G and Ho, A and Bodelier, PLE}, title = {Environmental legacy contributes to the resilience of methane consumption in a laboratory microcosm system.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8862}, doi = {10.1038/s41598-018-27168-9}, pmid = {29892072}, issn = {2045-2322}, abstract = {The increase of extreme drought and precipitation events due to climate change will alter microbial processes. Perturbation experiments demonstrated that microbes are sensitive to environmental alterations. However, only little is known on the legacy effects in microbial systems. Here, we designed a laboratory microcosm experiment using aerobic methane-consuming communities as a model system to test basic principles of microbial resilience and the role of changes in biomass and the presence of non-methanotrophic microbes in this process. We focused on enrichments from soil, sediment, and water reflecting communities with different legacy with respect to exposure to drought. Recovery rates, a recently proposed early warning indicator of a critical transition, were utilized as a measure to detect resilience loss of methane consumption during a series of dry/wet cycle perturbations. We observed a slowed recovery of enrichments originating from water samples, which suggests that the community's legacy with a perturbation is a contributing factor for the resilience of microbial functioning.}, }
@article {pmid29891000, year = {2018}, author = {Lammel, DR and Barth, G and Ovaskainen, O and Cruz, LM and Zanatta, JA and Ryo, M and de Souza, EM and Pedrosa, FO}, title = {Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {106}, doi = {10.1186/s40168-018-0482-8}, pmid = {29891000}, issn = {2049-2618}, support = {1273253/284601/273253//Academy of Finland/ ; 223257//Norges Forskningsråd/ ; }, abstract = {BACKGROUND: pH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to &quot;spillover effects&quot; on other chemical parameters (e.g., availability of Al, Fe, Mn, Zn, and Cu) and plant growth, but these indirect effects on the microbial communities are rarely investigated. Usually, pH also co-varies with some confounding factors, such as land use, soil management (e.g., tillage and chemical inputs), plant cover, and/or edapho-climatic conditions. So, a more comprehensive analysis of the direct and indirect effects of pH brings a better understanding of the mechanisms driving prokaryotic (archaeal and bacterial) community structures.<br><br>RESULTS: We evaluated an agricultural soil pH gradient (from 4 to 6, the typical range for tropical farms), in a liming gradient with confounding factors minimized, investigating relationships between prokaryotic communities (16S rRNA) and physical-chemical parameters (indirect effects). Correlations, hierarchical modeling of species communities (HMSC), and random forest (RF) modeling indicated that both direct and indirect effects of the pH gradient affected the prokaryotic communities. Some OTUs were more affected by the pH changes (e.g., some Actinobacteria), while others were more affected by the indirect pH effects (e.g., some Proteobacteria). HMSC detected a phylogenetic signal related to the effects. Both HMSC and RF indicated that the main indirect effect was the pH changes on the availability of some elements (e.g., Al, Fe, and Cu), and secondarily, effects on plant growth and nutrient cycling also affected the OTUs. Additionally, we found that some of the OTUs that responded to pH also correlated with CO2, CH4, and N2O greenhouse gas fluxes.<br><br>CONCLUSIONS: Our results indicate that there are two distinct pH-related mechanisms driving prokaryotic community structures, the direct effect and &quot;spillover effects&quot; of pH (indirect effects). Moreover, the indirect effects are highly relevant for some OTUs and consequently for the community structure; therefore, it is a mechanism that should be further investigated in microbial ecology.}, }
@article {pmid29888841, year = {2018}, author = {Alster, CJ and Weller, ZD and von Fischer, JC}, title = {A meta-analysis of temperature sensitivity as a microbial trait.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.14342}, pmid = {29888841}, issn = {1365-2486}, abstract = {Traits-based approaches in microbial ecology provide a valuable way to abstract organismal interaction with the environment and to generate hypotheses about community function. Using macromolecular rate theory (MMRT), we recently identified that temperature sensitivity can be characterized as a distinct microbial trait. As temperature is fundamental in controlling biological reactions, variation in temperature sensitivity across communities, organisms, and processes has the potential to vastly improve understanding of microbial response to climate change. These microbial temperature sensitivity traits include the heat capacity (ΔCP‡), temperature optimum (Topt), and point of maximum temperature sensitivity (TSmax), each of which provide unique insights about organismal response to changes in temperature. In this meta-analysis, we analyzed the distribution of these temperature sensitivity traits from bacteria, fungi, and mixed communities across a variety of biological systems (e.g., soils, oceans, foods, wastewater treatment plants) in order to identify commonalities in temperature responses across these diverse organisms and reaction rates. Our analysis of temperature sensitivity traits from over 350 temperature response curves reveals a wide distribution of temperature sensitivity traits, with Topt and TSmax well within biological relevant temperatures. We find that traits vary significantly depending on organism type, microbial diversity, source environment, and biological process, with higher temperature sensitivity found in fungi than bacteria and in less diverse systems. Carbon dioxide production was found to be less temperature sensitive than denitrification, suggesting that changes in temperature will have a potentially larger impact on nitrogen-related processes. As climate changes, these results have important implications for basic understanding of the temperature sensitivity of biological reactions and for ecological understanding of species' trait distributions, as well as for improved treatment of temperature sensitivity in models.}, }
@article {pmid29887367, year = {2018}, author = {Acosta, N and De Vrieze, J and Sandoval, V and Sinche, D and Wierinck, I and Rabaey, K}, title = {Cocoa residues as viable biomass for renewable energy production through anaerobic digestion.}, journal = {Bioresource technology}, volume = {265}, number = {}, pages = {568-572}, doi = {10.1016/j.biortech.2018.05.100}, pmid = {29887367}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Biofuels ; Biological Oxygen Demand Analysis ; Biomass ; Bioreactors ; Methane/*biosynthesis ; *Renewable Energy ; }, abstract = {The aim of this work was to evaluate the bioenergy potential of cocoa residue via anaerobic digestion. Batch and fed-batch lab-scale reactors were operated under low and high solids conditions. In the batch tests, 59 ± 4% of Chemical Oxygen Demand (COD) was recovered as methane. This corresponded with an average methane yield of 174 (wet) and 193 (dry) L kg-1 volatile solids fed, whereas a series of fed-batch reactors produced 70 ± 24 (wet) and 107 ± 39 (dry) L CH4 kg-1 volatile solids fed during stable conditions. A case study was developed for canton Balao (Ecuador) based on our experimental data, operational estimates and available cocoa waste in the area. Annually, 8341 MWh could be produced, meeting 88% of the current electricity demand in Balao. This case study proves the potential for cocoa waste as a source of renewable energy in rural areas.}, }
@article {pmid29886983, year = {2018}, author = {Xu, G and Zhong, X and Al, MA and Warren, A and Xu, H}, title = {Identifying bioindicators across trait-taxon space for assessing water quality in marine environments.}, journal = {Marine pollution bulletin}, volume = {131}, number = {Pt A}, pages = {565-571}, doi = {10.1016/j.marpolbul.2018.04.044}, pmid = {29886983}, issn = {1879-3363}, abstract = {The response units of protozoan communities, based on a community-weighted mean (CWM) dataset across trait-taxon space, were investigated in order to determine their utility as bioindicators of marine water quality. From a total of 17 functional categories of seven biological traits, three functional response units (FRUs) were identified at correlation levels of >0.75. FRUs 1 and 3 generally dominated the communities in more polluted areas during warm seasons, while FRU2 appeared to prefer less polluted waters and dominated the communities in spring and winter. Correlation analysis demonstrated that the CWM values of FRUs 1 and 3 were significantly positively correlated to the concentrations of chemical oxygen demand (COD), whereas those of FRU2 were negatively correlated to COD. Across taxon-function space, 16 species were identified as potential bioindicators of water quality. These results suggest that redundancy analysis across trait-taxon space is a useful tool for identifying indicators of environmental quality.}, }
@article {pmid29884244, year = {2018}, author = {Liu, X and Li, M and Castelle, CJ and Probst, AJ and Zhou, Z and Pan, J and Liu, Y and Banfield, JF and Gu, JD}, title = {Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {102}, doi = {10.1186/s40168-018-0488-2}, pmid = {29884244}, issn = {2049-2618}, support = {41506163//National Natural Science Foundation of China/ ; 31622002//National Natural Science Foundation of China/ ; 3160010182//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: As a recently discovered member of the DPANN superphylum, Woesearchaeota account for a wide diversity of 16S rRNA gene sequences, but their ecology, evolution, and metabolism remain largely unknown.<br><br>RESULTS: Here, we assembled 133 global clone libraries/studies and 19 publicly available genomes to profile these patterns for Woesearchaeota. Phylogenetic analysis shows a high diversity with 26 proposed subgroups for this recently discovered archaeal phylum, which are widely distributed in different biotopes but primarily in inland anoxic environments. Ecological patterns analysis and ancestor state reconstruction for specific subgroups reveal that oxic status of the environments is the key factor driving the distribution and evolutionary diversity of Woesearchaeota. A selective distribution to different biotopes and an adaptive colonization from anoxic to oxic environments can be proposed and supported by evidence of the presence of ferredoxin-dependent pathways in the genomes only from anoxic biotopes but not from oxic biotopes. Metabolic reconstructions support an anaerobic heterotrophic lifestyle with conspicuous metabolic deficiencies, suggesting the requirement for metabolic complementarity with other microbes. Both lineage abundance distribution and co-occurrence network analyses across diverse biotopes confirmed metabolic complementation and revealed a potential syntrophic relationship between Woesearchaeota and methanogens, which is supported by metabolic modeling. If correct, Woesearchaeota may impact methanogenesis in inland ecosystems.<br><br>CONCLUSIONS: The findings provide an ecological and evolutionary framework for Woesearchaeota at a global scale and indicate their potential ecological roles, especially in methanogenesis.}, }
@article {pmid29882155, year = {2018}, author = {Mikhailov, IS and Zakharova, YR and Bukin, YS and Galachyants, YP and Petrova, DP and Sakirko, MV and Likhoshway, YV}, title = {Co-occurrence Networks Among Bacteria and Microbial Eukaryotes of Lake Baikal During a Spring Phytoplankton Bloom.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1212-2}, pmid = {29882155}, issn = {1432-184X}, support = {0345-2016-0005//Federal Agency of Scientific Organizations of Russia/ ; 0345-2016-0001//Federal Agency of Scientific Organizations of Russia/ ; }, abstract = {The pelagic zone of Lake Baikal is an ecological niche where phytoplankton bloom causes increasing microbial abundance in spring which plays a key role in carbon turnover in the freshwater lake. Co-occurrence patterns revealed among different microbes can be applied to predict interactions between the microbes and environmental conditions in the ecosystem. We used 454 pyrosequencing of 16S rRNA and 18S rRNA genes to study bacterial and microbial eukaryotic communities and their co-occurrence patterns at the pelagic zone of Lake Baikal during a spring phytoplankton bloom. We found that microbes within one domain mostly correlated positively with each other and are highly interconnected. The highly connected taxa in co-occurrence networks were operational taxonomic units (OTUs) of Actinobacteria, Bacteroidetes, Alphaproteobacteria, and autotrophic and unclassified Eukaryota which might be analogous to microbial keystone taxa. Constrained correspondence analysis revealed the relationships of bacterial and microbial eukaryotic communities with geographical location.}, }
@article {pmid29882154, year = {2018}, author = {Kerfahi, D and Tripathi, BM and Dong, K and Kim, M and Kim, H and Ferry Slik, JW and Go, R and Adams, JM}, title = {From the High Arctic to the Equator: Do Soil Metagenomes Differ According to Our Expectations?.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1215-z}, pmid = {29882154}, issn = {1432-184X}, support = {0409-20140091//Korea Polar Research Institute/ ; NRF-0409-20150076//National Research Foundation of Korea/ ; }, abstract = {Comparing the functional gene composition of soils at opposite extremes of environmental gradients may allow testing of hypotheses about community and ecosystem function. Here, we were interested in comparing how tropical microbial ecosystems differ from those of polar climates. We sampled several sites in the equatorial rainforest of Malaysia and Brunei, and the high Arctic of Svalbard, Canada, and Greenland, comparing the composition and the functional attributes of soil biota between the two extremes of latitude, using shotgun metagenomic Illumina HiSeq2000 sequencing. Based upon &quot;classical&quot; views of how tropical and higher latitude ecosystems differ, we made a series of predictions as to how various gene function categories would differ in relative abundance between tropical and polar environments. Results showed that in some respects our predictions were correct: the polar samples had higher relative abundance of dormancy related genes, and lower relative abundance of genes associated with respiration, and with metabolism of aromatic compounds. The network complexity of the Arctic was also lower than the tropics. However, in various other respects, the pattern was not as predicted; there were no differences in relative abundance of stress response genes or in genes associated with secondary metabolism. Conversely, CRISPR genes, phage-related genes, and virulence disease and defense genes, were unexpectedly more abundant in the Arctic, suggesting more intense biotic interaction. Also, eukaryote diversity and bacterial diversity were higher in the Arctic of Svalbard compared to tropical Brunei, which is consistent with what may expected from amplicon studies in terms of the higher pH of the Svalbard soil. Our results in some respects confirm expectations of how tropical versus polar nature may differ, and in other respects challenge them.}, }
@article {pmid29880912, year = {2018}, author = {Mo, Y and Zhang, W and Yang, J and Lin, Y and Yu, Z and Lin, S}, title = {Biogeographic patterns of abundant and rare bacterioplankton in three subtropical bays resulting from selective and neutral processes.}, journal = {The ISME journal}, volume = {12}, number = {9}, pages = {2198-2210}, doi = {10.1038/s41396-018-0153-6}, pmid = {29880912}, issn = {1751-7370}, abstract = {Unraveling the relative importance of ecological processes regulating microbial community structure is a central goal in microbial ecology. Here, we used high-throughput sequencing to examine the relative contribution of selective and neutral processes in the assembly of abundant and rare subcommunities from three subtropical bays of China. We found that abundant and rare bacterial taxa were distinctly different in diversity, despite the similar biogeographic patterns and strong distance-decay relationships, but the dispersal of rare bacterial taxa was more limited than that of abundant taxa. Furthermore, the environmental (selective processes) and spatial (neutral processes) factors seemed to govern the assembly and biogeography of abundant and rare bacterial subcommunities, although both factors explained only a small fraction of variation within the rare subcommunity. More importantly, variation partitioning (based on adjusted R2 in redundancy analysis) showed that spatial factors exhibited a slightly greater influence on both abundant and rare subcommunities compared to environmental selection; however, the abundant subcommunity had a much stronger response to spatial factors (17.3% of pure variance was explained) than that shown by the rare bacteria (3.5%). These results demonstrate that environmental selection and neutral processes explained the similar biogeographic patterns of abundant and rare subcommunities, but a large proportion of unexplained variation in the rare taxa (91.1%) implies that more complex assembly mechanisms may exist to shape the rare bacterial assemblages in the three subtropical bays.}, }
@article {pmid29878056, year = {2018}, author = {Martinez-Vernon, A and Farrell, F and Soyer, OS}, title = {MetQy - an R package to query metabolic functions of genes and genomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/bty447}, pmid = {29878056}, issn = {1367-4811}, support = {BB/M017982/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Summary: With the rapid accumulation of sequencing data from genomic and metagenomic studies, there is an acute need for better tools that facilitate their analyses against biological functions. To this end, we developed MetQy, an open-source R package designed for query-based analysis of functional units in [meta]genomes and/or sets of genes using the The Kyoto Encyclopedia of Genes and Genomes (KEGG). Furthermore, MetQy contains visualisation and analysis tools and facilitates KEGG's flat file manipulation. Thus, MetQy enables better understanding of metabolic capabilities of known genomes or user-specified [meta]genomes by using the available information and can help guide studies in microbial ecology, metabolic engineering and synthetic biology.<br><br>The MetQy R package is freely available and can be downloaded from our group's website (http://osslab.lifesci.warwick.ac.uk) or GitHub (https://github.com/OSS-Lab/MetQy).<br><br>Contact: O.Soyer@warwick.ac.uk.}, }
@article {pmid29876609, year = {2018}, author = {Weiss, H and Hertzberg, VS and Dupont, C and Espinoza, JL and Levy, S and Nelson, K and Norris, S and , }, title = {The Airplane Cabin Microbiome.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1191-3}, pmid = {29876609}, issn = {1432-184X}, support = {2001-041-1//The Boeing Company/ ; }, abstract = {Serving over three billion passengers annually, air travel serves as a conduit for infectious disease spread, including emerging infections and pandemics. Over two dozen cases of in-flight transmissions have been documented. To understand these risks, a characterization of the airplane cabin microbiome is necessary. Our study team collected 229 environmental samples on ten transcontinental US flights with subsequent 16S rRNA sequencing. We found that bacterial communities were largely derived from human skin and oral commensals, as well as environmental generalist bacteria. We identified clear signatures for air versus touch surface microbiome, but not for individual types of touch surfaces. We also found large flight-to-flight beta diversity variations with no distinguishing signatures of individual flights, rather a high between-flight diversity for all touch surfaces and particularly for air samples. There was no systematic pattern of microbial community change from pre- to post-flight. Our findings are similar to those of other recent studies of the microbiome of built environments. In summary, the airplane cabin microbiome has immense airplane to airplane variability. The vast majority of airplane-associated microbes are human commensals or non-pathogenic, and the results provide a baseline for non-crisis-level airplane microbiome conditions.}, }
@article {pmid29876608, year = {2018}, author = {Suffert, F and Delestre, G and Gélisse, S}, title = {Sexual Reproduction in the Fungal Foliar Pathogen Zymoseptoria tritici Is Driven by Antagonistic Density Dependence Mechanisms.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1211-3}, pmid = {29876608}, issn = {1432-184X}, support = {634179//Horizon 2020 Framework Programme (EMPHASIS)/ ; }, abstract = {This study provides empirical evidence for antagonistic density dependence mechanisms driving sexual reproduction in the wheat fungal pathogen Zymoseptoria tritici. Biparental crosses with 12 increasing inoculum concentrations, in controlled conditions, showed that sexual reproduction in Z. tritici was impacted by an Allee effect due to mate limitation and a competition with asexual multiplication for resource allocation. The highest number of ascospores discharged was reached at intermediate inoculum concentrations (from 5 × 104 conidia mL-1 to 106 conidia mL-1). Consistent with these results for controlled co-inoculation, we found that the intensity of sexual reproduction varied with both cropping period and the vertical position of the host tissues in the field, with a maximum between 25 and 35 cm above the ground. An optimal lesion density (disease severity of 30 to 45%) maximizing offspring (ascospores) number was established, and its eco-evolutionary consequences are considered here. Two ecological mechanisms may be involved: competition for resources between the two modes of reproduction (decrease in the host resources available for sexual reproduction due to their prior use in asexual multiplication), and competitive disequilibrium between the two parental isolates, due to differential interaction dynamics with the host, for example, leading to an imbalance between mating types. A conceptual model based on these results suggests that sexual reproduction plays a key role in the evolution of pathogenicity traits, including virulence and aggressiveness. Ecological knowledge about the determinants of sexual reproduction in Z. tritici may, therefore, open up new perspectives for the management of other fungal foliar pathogens with dual modes of reproduction.}, }
@article {pmid29875749, year = {2018}, author = {Rapp, JZ and Fernández-Méndez, M and Bienhold, C and Boetius, A}, title = {Effects of Ice-Algal Aggregate Export on the Connectivity of Bacterial Communities in the Central Arctic Ocean.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1035}, doi = {10.3389/fmicb.2018.01035}, pmid = {29875749}, issn = {1664-302X}, support = {294757//European Research Council/International ; }, abstract = {In summer 2012, Arctic sea ice declined to a record minimum and, as a consequence of the melting, large amounts of aggregated ice-algae sank to the seafloor at more than 4,000 m depth. In this study, we assessed the composition, turnover and connectivity of bacterial and microbial eukaryotic communities across Arctic habitats from sea ice, algal aggregates and surface waters to the seafloor. Eukaryotic communities were dominated by diatoms, dinoflagellates and other alveolates in all samples, and showed highest richness and diversity in sea-ice habitats (∼400-500 OTUs). Flavobacteriia and Gammaproteobacteria were the predominant bacterial classes across all investigated Arctic habitats. Bacterial community richness and diversity peaked in deep-sea samples (∼1,700 OTUs). Algal aggregate-associated bacterial communities were mainly recruited from the sea-ice community, and were transported to the seafloor with the sinking ice algae. The algal deposits at the seafloor had a unique community structure, with some shared sequences with both the original sea-ice community (22% OTU overlap), as well as with the deep-sea sediment community (17% OTU overlap). We conclude that ice-algal aggregate export does not only affect carbon export from the surface to the seafloor, but may change microbial community composition in central Arctic habitats with potential effects for benthic ecosystem functioning in the future.}, }
@article {pmid29875400, year = {2018}, author = {Harrison, CA and Laubitz, D and Ohland, CL and Midura-Kiela, MT and Patil, K and Besselsen, DG and Jamwal, DR and Jobin, C and Ghishan, FK and Kiela, PR}, title = {Microbial dysbiosis associated with impaired intestinal Na+/H+ exchange accelerates and exacerbates colitis in ex-germ free mice.}, journal = {Mucosal immunology}, volume = {11}, number = {5}, pages = {1329-1341}, doi = {10.1038/s41385-018-0035-2}, pmid = {29875400}, issn = {1935-3456}, support = {R01 DK041274/DK/NIDDK NIH HHS/United States ; R01 DK073338/DK/NIDDK NIH HHS/United States ; }, abstract = {Intestinal epithelial Na+/H+ exchange facilitated by the apical NHE3 (Slc9a3) is a highly regulated process inhibited by intestinal pathogens and in inflammatory bowel diseases. NHE3-/- mice develop spontaneous, bacterially mediated colitis, and IBD-like dysbiosis. Disruption of epithelial Na+/H+ exchange in IBD may thus represent a host response contributing to the altered gut microbial ecology, and may play a pivotal role in modulating the severity of inflammation in a microbiome-dependent manner. To test whether microbiome fostered in an NHE3-deficient environment is able to drive mucosal immune responses affecting the onset or severity of colitis, we performed a series of cohousing experiments and fecal microbiome transplants into germ-free Rag-deficient or IL-10-/- mice. We determined that in the settings where the microbiome of NHE3-deficient mice was stably engrafted in the recipient host, it was able accelerate the onset and amplify severity of experimental colitis. NHE3-deficiency was characterized by the reduction in pH-sensitive butyrate-producing Firmicutes families Lachnospiraceae and Ruminococcaceae (Clostridia clusters IV and XIVa), with an expansion of inflammation-associated Bacteroidaceae. We conclude that the microbiome fostered by impaired epithelial Na+/H+ exchange enhances the onset and severity of colitis through disruption of the gut microbial ecology.}, }
@article {pmid29867972, year = {2018}, author = {Malik, S and Awasthi, A}, title = {Transcriptional Control of Th9 Cells: Role of Foxo1 in Interleukin-9 Induction.}, journal = {Frontiers in immunology}, volume = {9}, number = {}, pages = {995}, doi = {10.3389/fimmu.2018.00995}, pmid = {29867972}, issn = {1664-3224}, abstract = {Interleukin (IL) 9-producing helper T (Th) 9 cells play a major role in contributing immunity against extracellular pathogens. In addition, the role of Th9 cells was demonstrated in the pathogenesis of allergic, skin, and intestinal inflammation. The functions of Th9 cells were further extended in antitumor immune response, as Th9 cells were suggested to be potent antitumor Th cells. Given the pleotropic functions of IL-9 in various pathophysiological conditions, it is essential to understand the differentiation and stability of Th9 cells and other IL-9-producing T cells. In addition to Th9 cells, Th2 and Th17 cells as well as induced Foxp3+ regulatory T cells (iTregs) cells also produce IL-9, but how IL-9 production is regulated in these cell types is not yet clearly defined. Although Th2, Th9 and Th17 cells as well as iTregs develop in the presence of distinct differentiating factors, yet they all express IL-9 together with their own lineage specific cytokines. Here, in this review, we summarize the current understanding of signaling pathways that lead to the promotion of differentiation of Th9 cells and IL-9 induction in Th2 and Th17 cells, as well as in iTregs. We further discuss the transcriptional regulation of Th9 cells in context of Foxo1, as an essential transcription factor required for the development and functions of Th9 and other IL-9-producing T cells.}, }
@article {pmid29867840, year = {2018}, author = {Hücker, SM and Vanderhaeghen, S and Abellan-Schneyder, I and Scherer, S and Neuhaus, K}, title = {The Novel Anaerobiosis-Responsive Overlapping Gene ano Is Overlapping Antisense to the Annotated Gene ECs2385 of Escherichia coli O157:H7 Sakai.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {931}, doi = {10.3389/fmicb.2018.00931}, pmid = {29867840}, issn = {1664-302X}, abstract = {Current notion presumes that only one protein is encoded at a given bacterial genetic locus. However, transcription and translation of an overlapping open reading frame (ORF) of 186 bp length were discovered by RNAseq and RIBOseq experiments. This ORF is almost completely embedded in the annotated L,D-transpeptidase gene ECs2385 of Escherichia coli O157:H7 Sakai in the antisense reading frame -3. The ORF is transcribed as part of a bicistronic mRNA, which includes the annotated upstream gene ECs2384, encoding a murein lipoprotein. The transcriptional start site of the operon resides 38 bp upstream of the ECs2384 start codon and is driven by a predicted σ70 promoter, which is constitutively active under different growth conditions. The bicistronic operon contains a ρ-independent terminator just upstream of the novel gene, significantly decreasing its transcription. The novel gene can be stably expressed as an EGFP-fusion protein and a translationally arrested mutant of ano, unable to produce the protein, shows a growth advantage in competitive growth experiments compared to the wild type under anaerobiosis. Therefore, the novel antisense overlapping gene is named ano (anaerobiosis responsive overlapping gene). A phylostratigraphic analysis indicates that ano originated very recently de novo by overprinting after the Escherichia/Shigella clade separated from other enterobacteria. Therefore, ano is one of the very rare cases of overlapping genes known in the genus Escherichia.}, }
@article {pmid29867833, year = {2018}, author = {Woo, HL and Hazen, TC}, title = {Enrichment of Bacteria From Eastern Mediterranean Sea Involved in Lignin Degradation via the Phenylacetyl-CoA Pathway.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {922}, doi = {10.3389/fmicb.2018.00922}, pmid = {29867833}, issn = {1664-302X}, abstract = {The degradation of allochthonous terrestrial organic matter, such as recalcitrant lignin and hemicellulose from plants, occurs in the ocean. We hypothesize that bacteria instead of white-rot fungi, the model organisms of aerobic lignin degradation within terrestrial environments, are responsible for lignin degradation in the ocean due to the ocean's oligotrophy and hypersalinity. Warm oxic seawater from the Eastern Mediterranean Sea was enriched on lignin in laboratory microcosms. Lignin mineralization rates by the lignin-adapted consortia improved after two sequential incubations. Shotgun metagenomic sequencing detected a higher abundance of aromatic compound degradation genes in response to lignin, particularly phenylacetyl-CoA, which may be an effective strategy for marine microbes in fluctuating oxygen concentrations. 16S rRNA gene amplicon sequencing detected a higher abundance of Gammaproteobacteria and Alphaproteobacteria bacteria such as taxonomic families Idiomarinaceae, Alcanivoraceae, and Alteromonadaceae in response to lignin. Meanwhile, fungal Ascomycetes and Basidiomycetes remained at very low abundance. Our findings demonstrate the significant potential of bacteria and microbes utilizing the phenylacetyl-CoA pathway to contribute to lignin degradation in the Eastern Mediterranean where environmental conditions are unfavorable for fungi. Exploring the diversity of bacterial lignin degraders may provide important enzymes for lignin conversion in industry. Enzymes may be key in breaking down high molecular weight lignin and enabling industry to use it as a low-cost and sustainable feedstock for biofuels or other higher-value products.}, }
@article {pmid29867788, year = {2018}, author = {Pratama, AA and Chaib De Mares, M and van Elsas, JD}, title = {Evolutionary History of Bacteriophages in the Genus Paraburkholderia.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {835}, doi = {10.3389/fmicb.2018.00835}, pmid = {29867788}, issn = {1664-302X}, abstract = {The genus Paraburkholderia encompasses mostly environmental isolates with diverse predicted lifestyles. Genome analyses have shown that bacteriophages form a considerable portion of some Paraburkholderia genomes. Here, we analyzed the evolutionary history of prophages across all Paraburkholderia spp. Specifically, we investigated to what extent the presence of prophages and their distribution affect the diversity/diversification of Paraburkholderia spp., as well as to what extent phages coevolved with their respective hosts. Particular attention was given to the presence of CRISPR-Cas arrays as a reflection of past interactions with phages. We thus analyzed 36 genomes of Paraburkholderia spp., including those of 11 new strains, next to those of three Burkholderia species. Most genomes were found to contain at least one full prophage sequence. The highest number was found in Paraburkholderia sp. strain MF2-27; the nine prophages found amount to up to 4% of its genome. Among all prophages, potential moron genes (e.g., DNA adenine methylase) were found that might be advantageous for host cell fitness. Co-phylogenetic analyses indicated the existence of complex evolutionary scenarios between the different Paraburkholderia hosts and their prophages, including short-term co-speciation, duplication, host-switching and phage loss events. Analysis of the CRISPR-Cas systems showed a record of diverse, potentially recent, phage infections. We conclude that, overall, different phages have interacted in diverse ways with their Paraburkholderia hosts over evolutionary time.}, }
@article {pmid29860637, year = {2018}, author = {Torres, PJ and Thompson, J and McLean, JS and Kelley, ST and Edlund, A}, title = {Discovery of a Novel Periodontal Disease-Associated Bacterium.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1200-6}, pmid = {29860637}, issn = {1432-184X}, support = {R00 DE024543/DE/NIDCR NIH HHS/United States ; R01 DE023810/DE/NIDCR NIH HHS/United States ; U26IHS300292//National Institutes of Health/ ; }, abstract = {One of the world's most common infectious disease, periodontitis (PD), derives from largely uncharacterized communities of oral bacteria growing as biofilms (a.k.a. plaque) on teeth and gum surfaces in periodontal pockets. Bacteria associated with periodontal disease trigger inflammatory responses in immune cells, which in later stages of the disease cause loss of both soft and hard tissue structures supporting teeth. Thus far, only a handful of bacteria have been characterized as infectious agents of PD. Although deep sequencing technologies, such as whole community shotgun sequencing have the potential to capture a detailed picture of highly complex bacterial communities in any given environment, we still lack major reference genomes for the oral microbiome associated with PD and other diseases. In recent work, by using a combination of supervised machine learning and genome assembly, we identified a genome from a novel member of the Bacteroidetes phylum in periodontal samples. Here, by applying a comparative metagenomics read-classification approach, including 272 metagenomes from various human body sites, and our previously assembled draft genome of the uncultivated Candidatus Bacteroides periocalifornicus (CBP) bacterium, we show CBP's ubiquitous distribution in dental plaque, as well as its strong association with the well-known pathogenic &quot;red complex&quot; that resides in deep periodontal pockets.}, }
@article {pmid29860594, year = {2018}, author = {Vieira, A and Ribera-Guardia, A and Marques, R and Barreto Crespo, MT and Oehmen, A and Carvalho, G}, title = {The link between the microbial ecology, gene expression, and biokinetics of denitrifying polyphosphate-accumulating systems under different electron acceptor combinations.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {15}, pages = {6725-6737}, doi = {10.1007/s00253-018-9077-3}, pmid = {29860594}, issn = {1432-0614}, support = {PTDC/AAC-AMB/120581/2010//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/97640/2013//Fundação para a Ciência e a Tecnologia/ ; Water JPI project 196//H2020 Environment/ ; COST Action ES1202//Horizon 2020/ ; UID/Multi/04378/2013//Portuguese Government/ ; POCI-01- 0145-FEDER-007728//European Regional Development Fund/ ; LISBOA-01-0145-FEDER-007344//European Regional Development Fund/ ; BES-2012-052753//Secretaría de Estado de Investigación, Desarrollo e Innovación/ ; }, mesh = {Bacteria/classification/*drug effects ; Bioreactors ; Denitrification ; Electrons ; Gene Expression/*drug effects ; Microbiota/drug effects ; Nitrates/chemistry/*pharmacology ; Nitrites/chemistry/*pharmacology ; Nitrous Oxide/chemistry/metabolism/*pharmacology ; Phylogeny ; Polyphosphates/metabolism ; }, abstract = {The emission of the greenhouse gas nitrous oxide (N2O) can occur during biological nutrient removal. Denitrifying enhanced biological phosphorus removal (d-EBPR) systems are an efficient means of removing phosphate and nitrogen, performed by denitrifying polyphosphate-accumulating organisms (d-PAOs). The aim of this work was to study the effect of various combinations of electron acceptors, nitrate (NO3-), nitrite (NO2-), and N2O, on the denitrification pathway of a d-EBPR system. Batch tests were performed with different electron acceptor combinations, to explore the denitrification pathway. Reverse transcriptase-qPCR (RT-qPCR) and high-throughput sequencing, combined with chemical analysis, were used to study gene expression, microbial diversity, and denitrification kinetics. The potential for N2O production was greater than the potential for its reduction in most tests. A strong correlation was observed between the N2O reduction rate and the relative gene expression of nitrous oxide reductase per nitrite reductase (nosZ/(nirS + nirK)), suggesting that the expression of denitrifying marker genes is a strong predictor of the N2O reduction rate. The d-EBPR community maintained a core population with low variations throughout the study. Furthermore, phylogenetic analyses of the studied marker genes revealed that the organisms actively involved in denitrification were closely related to Thauera sp., Candidatus Accumulibacter phosphatis, and Candidatus Competibacter denitrificans. Moreover, Competibacter-related OTUs seem to be important contributors to the N2O reduction capacity of the system, likely scavenging the N2O produced by other organisms. Overall, this study contributes to a better understanding of the microbial biochemistry and the genetics involving biological denitrification removal, important to minimize N2O emissions in wastewater treatment plants.}, }
@article {pmid29858666, year = {2018}, author = {Magill, DJ and McGrath, JW and O'Flaherty, V and Quinn, JP and Kulakov, LA}, title = {Insights into the structural dynamics of the bacteriophage T7 DNA polymerase and its complexes.}, journal = {Journal of molecular modeling}, volume = {24}, number = {7}, pages = {144}, doi = {10.1007/s00894-018-3671-2}, pmid = {29858666}, issn = {0948-5023}, support = {14/IA/2371//Science Foundation Ireland/Ireland ; }, mesh = {Bacteriophage T7/*enzymology ; Binding Sites ; Cluster Analysis ; DNA/chemistry/metabolism ; DNA-Directed DNA Polymerase/*chemistry/metabolism ; Hydrogen/chemistry ; Hydrogen-Ion Concentration ; *Molecular Dynamics Simulation ; Protein Binding ; Protein Conformation ; Structure-Activity Relationship ; Viral Proteins/chemistry ; }, abstract = {The T7 DNA polymerase is dependent on the host protein thioredoxin (trx) for its processivity and fidelity. Using all-atom molecular dynamics, we demonstrate the specific interactions between trx and the T7 polymerase, and show that trx docking to its binding domain on the polymerase results in a significant level of stability and exposes a series of basic residues within the domain that interact with the phosphodiester backbone of the DNA template. We also characterize the nature of interactions between the T7 DNA polymerase and its DNA template. We show that the trx-binding domain acts as an intrinsic clamp, constraining the DNA via a two-step hinge motion, and characterize the interactions necessary for this to occur. Together, these insights provide a significantly improved understanding of the interactions responsible for highly processive DNA replication by T7 polymerase.}, }
@article {pmid29858646, year = {2018}, author = {McGee, KM and Eaton, WD and Shokralla, S and Hajibabaei, M}, title = {Determinants of Soil Bacterial and Fungal Community Composition Toward Carbon-Use Efficiency Across Primary and Secondary Forests in a Costa Rican Conservation Area.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1206-0}, pmid = {29858646}, issn = {1432-184X}, support = {1262907//Directorate for Biological Sciences/ ; }, abstract = {Tropical secondary forests currently represent over half of the world's remaining tropical forests and are critical candidates for maintaining global biodiversity and enhancing potential carbon-use efficiency (CUE) and, thus, carbon sequestration. However, these ecosystems can exhibit multiple successional pathways, which have hindered our understanding of the soil microbial drivers that facilitate improved CUE. To begin to address this, we examined soil % C; % N; C:N ratio; soil microbial biomass C (Cmic); NO3-; NH4+; pH; % moisture; % sand, silt, and clay; and elevation, along with soil bacterial and fungal community composition, and determined which soil abiotic properties structure the soil Cmic and the soil bacterial and fungal communities across a primary forest, 33-year-old secondary forest, and 22-year-old young secondary in the Northern Zone of Costa Rica. We provide evidence that soil microbial communities were mostly distinct across the habitat types and that these habitats appear to have affected the soil ectomycorrhizal fungi and the soil microbial groups associated with the degradation of complex carbon compounds. We found that soil Cmic levels increased along the management gradient from young, to old secondary, to primary forest. In addition, the changes in soil Cmic and soil fungal community structure were significantly related to levels of soil NO3-. Our analyses showed that even after 33 years of natural forest regrowth, the clearing of tropical forests can have persistent effects on soil microbial communities and that it may take a longer time than we realized for secondary forests to develop carbon-utilization efficiencies similar to that of a primary forest. Our results also indicated that forms of inorganic N may be an important factor in structuring soil Cmic and the soil microbial communities, leading to improved CUE in regenerating secondary forests. This study is the first in the region to highlight some of the factors which appear to be structuring the soil Cmic and soil microbial communities such that they are more conducive for enhanced CUE in secondary forests.}, }
@article {pmid29858645, year = {2018}, author = {Gao, CH and Zhang, M and Wu, Y and Huang, Q and Cai, P}, title = {Divergent Influence to a Pathogen Invader by Resident Bacteria with Different Social Interactions.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1207-z}, pmid = {29858645}, issn = {1432-184X}, support = {2016YFD0800206//National Key R&amp;D Program of China/ ; 41522106//National Natural Science Foundation of China/ ; }, abstract = {Bacterial social interaction is a potential influencing factor in determining the fate of invading pathogens in diverse environments. In this study, interactions between two representative resident species (Bacillus subtilis and Pseudomonas putida) and a leading food-borne disease causative pathogen (Vibrio parahaemolyticus) were examined. An antagonistic effect toward V. parahaemolyticus was observed for B. subtilis but not for P. putida. However, the relative richness of the pathogen remained rather high in B. subtilis co-cultures and was, unexpectedly, not sensitive to the initial inoculation ratios. Furthermore, two approaches were found to be efficient at modulating the relative richness of the pathogen. (1) The addition of trace glycerol and manganese to Luria-Bertani medium (LBGM) reduced the richness of V. parahaemolyticus in the co-culture with B. subtilis and in contrast, increased its richness in the co-culture with P. putida, although it did not affect the growth of V. parahaemolyticus by its own. (2) The relative richness of V. parahaemolyticus on semisolid medium decreased significantly as a function of an agar gradient, ranging from 0 to 2%. Furthermore, we explored the molecular basis of bacterial interaction through transcriptomic analysis. In summary, we investigated the interactions between a pathogen invader and two resident bacteria species, showing that the different influences on a pathogen by different types of interactions can be modulated by chemicals and medium fluidity.}, }
@article {pmid29858203, year = {2018}, author = {Almeida, C and Silva Pereira, C and Gonzalez-Menendez, V and Bills, G and Pascual, J and Sánchez-Hidalgo, M and Kehraus, S and Genilloud, O}, title = {Unveiling concealed functions of endosymbiotic bacteria harboured in the Ascomycota Stachylidium bicolor.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.00660-18}, pmid = {29858203}, issn = {1098-5336}, abstract = {Amongst the plethora of unusual secondary metabolites isolated from Stachylidium bicolor are the tetrapeptidic endolides A and B. Both tetrapeptides contain 3-(3-furyl)-alanine residues, previously proposed to originate from bacterial metabolism. Inspired by this observation, we aimed to identify the presence of endosymbiotic bacteria in S. bicolor and to discover the true producer of the endolides. The endobacterium Burkholderia contaminans was initially detected by 16S rRNA gene amplicon sequencing from the fungal metagenome and was subsequently isolated. It was confirmed that the tetrapeptides were produced by the axenic B. contaminans only when in latency. Fungal colonies unable to produce conidia and the tetrapeptides were isolated and confirmed to be free of B. contaminans A second endosymbiont identified as related to Sphingomonas leidyi was also isolated. In situ imaging of the mycelium supported an endosymbiotic relationship between S. bicolor and the two endobacteria. Besides the technical novelty, our in situ analyses revealed that the two endobacteria are compartmentalised in defined fungal cells, prevailing mostly in latency when in symbiosis. Within the emerging field of intracellular bacterial symbioses, fungi are the least studied eukaryotic hosts. Our study further supports the Fungi as a valuable model for understanding endobacterial symbioses in eukaryotes.Importance Discovery of two bacterial endosymbionts harboured in Stachylidium bicolor mycelium: Burkholderia contaminans and Sphingomonas leidyi. Production of tetrapeptides inside the mycelium is ensured by B. contaminans, and fungal sporulation is influenced by the endosymbionts. Herein we illustrate the bacterial endosymbiotic origin of secondary metabolites in an Ascomycota host.}, }
@article {pmid29857194, year = {2018}, author = {Egert, M and Weis, S and Schnell, S}, title = {RNA-based stable isotope probing (RNA-SIP) to unravel intestinal host-microbe interactions.}, journal = {Methods (San Diego, Calif.)}, volume = {149}, number = {}, pages = {25-30}, doi = {10.1016/j.ymeth.2018.05.022}, pmid = {29857194}, issn = {1095-9130}, abstract = {The RNA-SIP technology, introduced into molecular microbial ecology in 2002, is an elegant technique to link the structure and function of complex microbial communities, i.e. to identify microbial key-players involved in distinct degradation and assimilation processes under in-situ conditions. Due to its dependence of microbial RNA, this technique is particularly suited for environments with high numbers of very active, i.e. significantly RNA-expressing, bacteria. So far, it was mainly used in environmental studies using microbiotas from soil or water habitats. Here we outline and summarize our application of RNA-SIP for the identification of bacteria involved in the degradation and assimilation of prebiotic carbohydrates in intestinal samples of human and animal origin. Following an isotope label from a prebiotic substrate into the RNA of distinct bacterial taxa will help to better understand the functionality of these medically and economically important nutrients in an intestinal environment.}, }
@article {pmid29856843, year = {2018}, author = {Roley, SS and Duncan, DS and Liang, D and Garoutte, A and Jackson, RD and Tiedje, JM and Robertson, GP}, title = {Associative nitrogen fixation (ANF) in switchgrass (Panicum virgatum) across a nitrogen input gradient.}, journal = {PloS one}, volume = {13}, number = {6}, pages = {e0197320}, doi = {10.1371/journal.pone.0197320}, pmid = {29856843}, issn = {1932-6203}, abstract = {Associative N fixation (ANF), the process by which dinitrogen gas is converted to ammonia by bacteria in casual association with plants, has not been well-studied in temperate ecosystems. We examined the ANF potential of switchgrass (Panicum virgatum L.), a North American prairie grass whose productivity is often unresponsive to N fertilizer addition, via separate short-term 15N2 incubations of rhizosphere soils and excised roots four times during the growing season. Measurements occurred along N fertilization gradients at two sites with contrasting soil fertility (Wisconsin, USA Mollisols and Michigan, USA Alfisols). In general, we found that ANF potentials declined with long-term N addition, corresponding with increased soil N availability. Although we hypothesized that ANF potential would track plant N demand through the growing season, the highest root fixation rates occurred after plants senesced, suggesting that root diazotrophs exploit carbon (C) released during senescence, as C is translocated from aboveground tissues to roots for wintertime storage. Measured ANF potentials, coupled with mass balance calculations, suggest that ANF appears to be an important source of N to unfertilized switchgrass, and, by extension, to temperate grasslands in general.}, }
@article {pmid29854953, year = {2018}, author = {Cardona, C and Lax, S and Larsen, P and Stephens, B and Hampton-Marcell, J and Edwardson, CF and Henry, C and Van Bonn, B and Gilbert, JA}, title = {Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics.}, journal = {mSystems}, volume = {3}, number = {3}, pages = {}, doi = {10.1128/mSystems.00052-18}, pmid = {29854953}, issn = {2379-5077}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; }, abstract = {Host-associated microbial dynamics are influenced by dietary and immune factors, but how exogenous microbial exposure shapes host-microbe dynamics remains poorly characterized. To investigate this phenomenon, we characterized the skin, rectum, and respiratory tract-associated microbiota in four aquarium-housed dolphins daily over a period of 6 weeks, including administration of a probiotic during weeks 4 to 6. The environmental bacterial sources were also characterized, including the animals' human handlers, the aquarium air and water, and the dolphins' food supply. Continuous microbial exposure occurred between all sites, yet each environment maintained a characteristic microbiota, suggesting that the majority of exposure events do not result in colonization. Small changes in water physicochemistry had a significant but weak correlation with change in dolphin-associated bacterial richness but had no influence on phylogenetic diversity. Food and air microbiota were the richest and had the largest conditional influence on other microbiota in the absence of probiotics, but during probiotic administration, food alone had the largest influence on the stability of the dolphin microbiota. Our results suggest that respiratory tract and gastrointestinal epithelium interactions with air- and food-associated microbes had the biggest influence on host-microbiota dynamics, while other interactions, such as skin transmission, played only a minor role. Finally, direct oral stimulation with a foreign exogenous microbial source can have a profound effect on microbial stability. IMPORTANCE These results provide valuable insights into the ecological influence of exogenous microbial exposure, as well as laying the foundation for improving aquarium management practices. By comparing data for dolphins from aquaria that use natural versus artificial seawater, we demonstrate the potential influence of aquarium water disinfection procedures on dolphin microbial dynamics.}, }
@article {pmid29854043, year = {2017}, author = {Hakkaart, XDV and Pronk, JT and van Maris, AJA}, title = {A Simulator-Assisted Workshop for Teaching Chemostat Cultivation in Academic Classes on Microbial Physiology.}, journal = {Journal of microbiology &amp; biology education}, volume = {18}, number = {3}, pages = {}, doi = {10.1128/jmbe.v18i3.1292}, pmid = {29854043}, issn = {1935-7877}, abstract = {Understanding microbial growth and metabolism is a key learning objective of microbiology and biotechnology courses, essential for understanding microbial ecology, microbial biotechnology and medical microbiology. Chemostat cultivation, a key research tool in microbial physiology that enables quantitative analysis of growth and metabolism under tightly defined conditions, provides a powerful platform to teach key features of microbial growth and metabolism. Substrate-limited chemostat cultivation can be mathematically described by four equations. These encompass mass balances for biomass and substrate, an empirical relation that describes distribution of consumed substrate over growth and maintenance energy requirements (Pirt equation), and a Monod-type equation that describes the relation between substrate concentration and substrate-consumption rate. The authors felt that the abstract nature of these mathematical equations and a lack of visualization contributed to a suboptimal operative understanding of quantitative microbial physiology among students who followed their Microbial Physiology B.Sc. courses. The studio-classroom workshop presented here was developed to improve student understanding of quantitative physiology by a set of question-guided simulations. Simulations are run on Chemostatus, a specially developed MATLAB-based program, which visualizes key parameters of simulated chemostat cultures as they proceed from dynamic growth conditions to steady state. In practice, the workshop stimulated active discussion between students and with their teachers. Moreover, its introduction coincided with increased average exam scores for questions on quantitative microbial physiology. The workshop can be easily implemented in formal microbial physiology courses or used by individuals seeking to test and improve their understanding of quantitative microbial physiology and/or chemostat cultivation.}, }
@article {pmid29850933, year = {2018}, author = {Gołębiewski, M and Tarasek, A and Sikora, M and Deja-Sikora, E and Tretyn, A and Niklińska, M}, title = {Rapid Microbial Community Changes During Initial Stages of Pine Litter Decomposition.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1209-x}, pmid = {29850933}, issn = {1432-184X}, support = {UMO-2012/05/NZ8/001362//Narodowe Centrum Nauki/ ; DS758//Uniwersytet Jagielloński w Krakowie/ ; DS759//Uniwersytet Jagielloński w Krakowie/ ; DSC//Uniwersytet Jagielloński w Krakowie/ ; }, abstract = {Plant litter decomposition is a process enabling biogeochemical cycles closing in ecosystems, and decomposition in forests constitutes the largest part of this process taking place in terrestrial biomes. Microbial communities during litter decomposition were studied mainly with low-throughput techniques not allowing detailed insight, particularly into coniferous litter, as it is more difficult to obtain high quality DNA required for analyses. Motivated by these problems, we analyzed archaeal, bacterial, and eukaryotic communities at three decomposition stages: fresh, 3- and 8-month-old litter by 16/18S rDNA pyrosequencing, aiming at detailed insight into early stages of pine litter decomposition. Archaea were absent from our libraries. Bacterial and eukaryotic diversity was greatest in 8-month-old litter and the same applied to bacterial and fungal rDNA content. Community structure was different at various stages of decomposition, and phyllospheric organisms (bacteria: Acetobacteraceae and Pseudomonadaceae members, fungi: Lophodermium, Phoma) were replaced by communities with metabolic capabilities adapted to the particular stage of decomposition. Sphingomonadaceae and Xanthomonadaceae and fungal genera Sistotrema, Ceuthospora, and Athelia were characteristic for 3-month-old samples, while 8-month-old ones were characterized by Bradyrhizobiaceae and nematodes (Plectus). We suggest that bacterial and eukaryotic decomposer communities change at different stages of pine litter decomposition in a way similar to that in broadleaf litter. Interactions between bacteria and eukaryotes appear to be one of the key drivers of microbial community structure.}, }
@article {pmid29850857, year = {2018}, author = {Alfano, M and Ferrarese, R and Locatelli, I and Ventimiglia, E and Ippolito, S and Gallina, P and Cesana, D and Canducci, F and Pagliardini, L and Viganò, P and Clementi, M and Nebuloni, M and Montorsi, F and Salonia, A}, title = {Testicular microbiome in azoospermic men-first evidence of the impact of an altered microenvironment.}, journal = {Human reproduction (Oxford, England)}, volume = {33}, number = {7}, pages = {1212-1217}, doi = {10.1093/humrep/dey116}, pmid = {29850857}, issn = {1460-2350}, abstract = {STUDY QUESTION: Given the relevant role of the extracellular microenvironment in regulating tissue homeostasis, is testicular bacterial microbiome (BM) associated with germ cell aplasia in idiopathic non-obstructive azoospermia (iNOA)?<br><br>SUMMARY ANSWER: A steady increase of dysbiosis was observed among testis with normal spermatogenesis vs. iNOA with positive sperm retrieval and iNOA with complete germ cell aplasia.<br><br>WHAT IS KNOWN ALREADY: Tissue-associated BM has been reported to be a biologically important extracellular microenvironment component for numerous body habitats, but not yet for the human testis.<br><br>STUDY DESIGN, SIZE, DURATION: Cross-sectional study, investigating tissue-associated BM in the testis of (i) five men with iNOA and negative sperm retrieval at microdissection testicular sperm extraction (microTESE); (ii) five men with iNOA and positive sperm retrieval at microTESE; and (iii) five normozoospermic men upon orchiectomy. Every testicular specimen was histologically classified and analyzed in terms of bacterial community.<br><br>Massive ultra-deep pyrosequencing was applied to investigate testis microbiome. Metagenome was analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Tissue-associated bacterial load was quantified by digital droplet PCR.<br><br>Normozoospermic men showed small amounts of bacteria in the testis, with Actinobacteria, Bacteroidetes, Firmicutes Proteobacteria as the dominating phyla; iNOA individuals had increased amounts of bacterial DNA (P = 0.02), associated with decreased taxa richness due to the lack of Bacteroidetes and Proteobacteria (P = 2 × 10-5). Specimens with negative sperm retrieval at microTESE depicted complete germ cell aplasia and a further decrease in terms of Firmicutes and Clostridia (P < 0.05), a complete lack of Peptoniphilus asaccharolyticus, but increased amount of Actinobacteria.<br><br>The limited number of specimens analyzed in this preliminary study deserves external validation. The paraneoplastic microenvironment could have an impact on the residential bacterial flora.<br><br>Human testicular microenvironment is not microbiologically sterile, containing low amounts of Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. A dysbiotic bacterial community was associated with iNOA and complete germ cell aplasia. Novel findings on testicular BM could support future translational therapies of male-factor infertility.<br><br>This work was supported by URI-Urological Research Institute free funds. Authors declared no conflict of interest.<br><br>TRIAL REGISTRATION NUMBER: N/A.}, }
@article {pmid29849169, year = {2018}, author = {Dong, X and Greening, C and Brüls, T and Conrad, R and Guo, K and Blaskowski, S and Kaschani, F and Kaiser, M and Laban, NA and Meckenstock, RU}, title = {Fermentative Spirochaetes mediate necromass recycling in anoxic hydrocarbon-contaminated habitats.}, journal = {The ISME journal}, volume = {12}, number = {8}, pages = {2039-2050}, doi = {10.1038/s41396-018-0148-3}, pmid = {29849169}, issn = {1751-7370}, abstract = {Spirochaetes are frequently detected in anoxic hydrocarbon- and organohalide-polluted groundwater, but their role in such ecosystems has remained unclear. To address this, we studied a sulfate-reducing, naphthalene-degrading enrichment culture, mainly comprising the sulfate reducer Desulfobacterium N47 and the rod-shaped Spirochete Rectinema cohabitans HM. Genome sequencing and proteome analysis suggested that the Spirochete is an obligate fermenter that catabolizes proteins and carbohydrates, resulting in acetate, ethanol, and molecular hydrogen (H2) production. Physiological experiments inferred that hydrogen is an important link between the two bacteria in the enrichment culture, with H2 derived from fermentation by R. cohabitans used as reductant for sulfate reduction by Desulfobacterium N47. Differential proteomics and physiological experiments showed that R. cohabitans utilizes biomass (proteins and carbohydrates) released from dead cells of Desulfobacterium N47. Further comparative and community genome analyses indicated that other Rectinema phylotypes are widespread in contaminated environments and may perform a hydrogenogenic fermentative lifestyle similar to R. cohabitans. Together, these findings indicate that environmental Spirochaetes scavenge detrital biomass and in turn drive necromass recycling at anoxic hydrocarbon-contaminated sites and potentially other habitats.}, }
@article {pmid29848762, year = {2018}, author = {Garcia, SL and Buck, M and Hamilton, JJ and Wurzbacher, C and Grossart, HP and McMahon, KD and Eiler, A}, title = {Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.}, journal = {mSphere}, volume = {3}, number = {3}, pages = {}, doi = {10.1128/mSphere.00202-18}, pmid = {29848762}, issn = {2379-5042}, mesh = {Bacteria/*metabolism ; Fresh Water/*microbiology ; *Metabolism ; *Microbial Consortia ; Microbial Interactions ; }, abstract = {Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.}, }
@article {pmid29844191, year = {2018}, author = {Kleiner, M and Dong, X and Hinzke, T and Wippler, J and Thorson, E and Mayer, B and Strous, M}, title = {Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {24}, pages = {E5576-E5584}, doi = {10.1073/pnas.1722325115}, pmid = {29844191}, issn = {1091-6490}, mesh = {Animals ; Carbon/*metabolism ; Carbon Isotopes/metabolism ; Environmental Microbiology ; Isotope Labeling/methods ; Metabolic Networks and Pathways/*physiology ; Microbiota/*physiology ; Proteome/*metabolism ; Proteomics/*methods ; Software ; Symbiosis/physiology ; }, abstract = {Measurements of stable carbon isotope ratios (δ13C) are widely used in biology to address questions regarding food sources and metabolic pathways used by organisms. The analysis of these so-called stable isotope fingerprints (SIFs) for microbes involved in biogeochemical cycling and microbiota of plants and animals has led to major discoveries in environmental microbiology. Currently, obtaining SIFs for microbial communities is challenging as the available methods either only provide low taxonomic resolution, such as the use of lipid biomarkers, or are limited in throughput, such as nanoscale secondary ion MS imaging of single cells. Here we present &quot;direct protein-SIF&quot; and the Calis-p software package (https://sourceforge.net/projects/calis-p/), which enable high-throughput measurements of accurate δ13C values for individual species within a microbial community. We benchmark the method using 20 pure culture microorganisms and show that the method reproducibly provides SIF values consistent with gold-standard bulk measurements performed with an isotope ratio mass spectrometer. Using mock community samples, we demonstrate that SIF values can also be obtained for individual species within a microbial community. Finally, a case study of an obligate bacteria-animal symbiosis shows that direct protein-SIF confirms previous physiological hypotheses and can provide unexpected insights into the symbionts' metabolism. This confirms the usefulness of this approach to accurately determine δ13C values for different species in microbial community samples.}, }
@article {pmid29809120, year = {2018}, author = {Kim, SH and Kim, JG and Jung, MY and Kim, SJ and Gwak, JH and Yu, WJ and Roh, SW and Kim, YH and Rhee, SK}, title = {Ketobacter alkanivorans gen. nov., sp. nov., an n-alkane-degrading bacterium isolated from seawater.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {68}, number = {7}, pages = {2258-2264}, doi = {10.1099/ijsem.0.002823}, pmid = {29809120}, issn = {1466-5034}, mesh = {Alcanivoraceae/*classification/genetics/isolation &amp; purification ; Alkanes/*metabolism ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Seawater/*microbiology ; Sequence Analysis, DNA ; Ubiquinone/chemistry ; }, abstract = {Strain GI5T was isolated from a surface seawater sample collected from Garorim Bay (West Sea, Republic of Korea). The isolated strain was aerobic, Gram-stain-negative, rod-shaped, motile by means of a polar flagellum, negative for catalase and weakly positive for oxidase. The optimum growth pH, salinity and temperature were determined to be pH 7.5-8.0, 3 % NaCl (w/v) and 25 °C, respectively; the growth ranges were pH 6.0-9.0, 1-7 % NaCl (w/v) and 18-40 °C. The results of phylogenetic analysis of 16S rRNA gene sequences indicated that GI5T clustered within the family Alcanivoracaceae, and most closely with Alcanivorax dieseloleiB-5T and Alcanivorax marinusR8-12T (91.9 % and 91.6 % similarity, respectively). The major cellular fatty acids in GI5T were C18 : 1ω7c/C18 : 1ω6c (44.45 %), C16 : 1ω6c/C16 : 1ω7c (14.17 %) and C16 : 0 (10.19 %); this profile was distinct from those of the closely related species. The major respiratory quinone of GI5T was Q-8. The main polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Two putative alkane hydroxylase (alkB) genes were identified in GI5T. The G+C content of the genomic DNA of GI5T was determined to be 51.2 mol%. On the basis of the results of phenotypic, chemotaxonomic and phylogenetic studies, strain GI5T represents a novel species of a novel genus of the family Alcanivoracaceae, for which we propose the name Ketobacter alkanivorans gen. nov., sp. nov.; the type strain is GI5T (=KCTC 52659T=JCM 31835T).}, }
@article {pmid29808411, year = {2018}, author = {Kumar, A and Ng, DHP and Wu, Y and Cao, B}, title = {Microbial Community Composition and Putative Biogeochemical Functions in the Sediment and Water of Tropical Granite Quarry Lakes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1204-2}, pmid = {29808411}, issn = {1432-184X}, support = {L2NICCFP1-2013-3//Singapore Ministry of National Development and National Research Foundation/ ; }, abstract = {Re-naturalized quarry lakes are important ecosystems, which support complex communities of flora and fauna. Microorganisms associated with sediment and water form the lowest trophic level in these ecosystems and drive biogeochemical cycles. A direct comparison of microbial taxa in water and sediment microbial communities is lacking, which limits our understanding of the dominant functions that are carried out by the water and sediment microbial communities in quarry lakes. In this study, using the 16S rDNA amplicon sequencing approach, we compared microbial communities in the water and sediment in two re-naturalized quarry lakes in Singapore and elucidated putative functions of the sediment and water microbial communities in driving major biogeochemical processes. The richness and diversity of microbial communities in sediments of the quarry lakes were higher than those in the water. The composition of the microbial communities in the sediments from the two quarries was highly similar to one another, while those in the water differed greatly. Although the microbial communities of the sediment and water samples shared some common members, a large number of microbial taxa (at the phylum and genus levels) were prevalent either in sediment or water alone. Our results provide valuable insights into the prevalent biogeochemical processes carried out by water and sediment microbial communities in tropical granite quarry lakes, highlighting distinct microbial processes in water and sediment that contribute to the natural purification of the resident water.}, }
@article {pmid29806601, year = {2018}, author = {Lekshmi, N and Joseph, I and Ramamurthy, T and Thomas, S}, title = {Changing facades of Vibrio cholerae: An enigma in the epidemiology of cholera.}, journal = {The Indian journal of medical research}, volume = {147}, number = {2}, pages = {133-141}, doi = {10.4103/ijmr.IJMR_280_17}, pmid = {29806601}, issn = {0971-5916}, mesh = {Anti-Bacterial Agents/therapeutic use ; Biofilms/drug effects ; Cholera/*epidemiology/genetics/microbiology/*therapy ; Disease Outbreaks ; Humans ; Vibrio cholerae O1/*pathogenicity ; }, abstract = {Cholera, caused by the Gram-negative bacterium Vibrio cholerae, has ravaged humanity from time immemorial. Although the disease can be treated using antibiotics along with administration of oral rehydration salts and controlled by good sanitation, cholera is known to have produced mayhems in ancient times when little was known about the pathogen. By the 21st century, ample information about the pathogen, its epidemiology, genetics, treatment and control strategies was revealed. However, there is still fear of cholera outbreaks in developing countries, especially in the wake of natural calamities. Studies have proved that the bacterium is mutating and evolving, out-competing all our efforts to treat the disease with previously used antibiotics and control with existing vaccines. In this review, the major scientific insights of cholera research are discussed. Considering the important role of biofilm formation in the V. cholerae life cycle, the vast availability of next-generation sequencing data of the pathogen and multi-omic approach, the review thrusts on the identification of suitable biofilm-inhibiting targets and the discovery of anti-biofilm drugs from nature to control the disease.}, }
@article {pmid29804046, year = {2018}, author = {Bae, HS and Huang, L and White, JR and Wang, J and DeLaune, RD and Ogram, A}, title = {Response of microbial populations regulating nutrient biogeochemical cycles to oiling of coastal saltmarshes from the Deepwater Horizon oil spill.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {241}, number = {}, pages = {136-147}, doi = {10.1016/j.envpol.2018.05.033}, pmid = {29804046}, issn = {1873-6424}, abstract = {Microbial communities play vital roles in the biogeochemistry of nutrients in coastal saltmarshes, ultimately controlling water quality, nutrient cycling, and detoxification. We determined the structure of microbial populations inhabiting coastal saltmarsh sediments from northern Barataria Bay, Louisiana, USA to gain insight into impacts on the biogeochemical cycles affected by Macondo oil from the 2010 Deepwater Horizon well blowout two years after the accident. Quantitative PCR directed toward specific functional genes revealed that oiled marshes were greatly diminished in the population sizes of diazotrophs, denitrifiers, nitrate-reducers to ammonia, methanogens, sulfate-reducers and anaerobic aromatic degraders, and harbored elevated numbers of alkane-degraders. Illumina 16S rRNA gene sequencing indicated that oiling greatly changed the structure of the microbial communities, including significant decreases in diversity. Oil-driven changes were also demonstrated in the structure of two functional populations, denitrifying and sulfate reducing prokaryotes, using nirS and dsrB as biomarkers, respectively. Collectively, the results from 16S rRNA and functional genes indicated that oiling not only markedly altered the microbial community structures, but also the sizes and structures of populations involved in (or regulating) a number of important nutrient biogeochemical cycles in the saltmarshes. Alterations such as these are associated with potential deterioration of ecological services, and further studies are necessary to assess the trajectory of recovery of microbial-mediated ecosystem functions over time in oiled saltmarsh sediment.}, }
@article {pmid29802797, year = {2018}, author = {Liang, J and Xia, J and Shi, Z and Jiang, L and Ma, S and Lu, X and Mauritz, M and Natali, SM and Pegoraro, E and Penton, CR and Plaza, C and Salmon, VG and Celis, G and Cole, JR and Konstantinidis, KT and Tiedje, JM and Zhou, J and Schuur, EAG and Luo, Y}, title = {Biotic responses buffer warming-induced soil organic carbon loss in Arctic tundra.}, journal = {Global change biology}, volume = {24}, number = {10}, pages = {4946-4959}, doi = {10.1111/gcb.14325}, pmid = {29802797}, issn = {1365-2486}, support = {DE SC00114085//US Department of Energy, Terrestrial Ecosystem Sciences/ ; DE-SC0004601//Biological Systems Research on the Role of Microbial Communities in Carbon Cycling Program/ ; DE-SC0010715//Biological Systems Research on the Role of Microbial Communities in Carbon Cycling Program/ ; EF 1137293//US National Science Foundation (NSF)/ ; OIA-1301789//US National Science Foundation (NSF)/ ; 654132//European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie/ ; }, abstract = {Climate warming can result in both abiotic (e.g., permafrost thaw) and biotic (e.g., microbial functional genes) changes in Arctic tundra. Recent research has incorporated dynamic permafrost thaw in Earth system models (ESMs) and indicates that Arctic tundra could be a significant future carbon (C) source due to the enhanced decomposition of thawed deep soil C. However, warming-induced biotic changes may influence biologically related parameters and the consequent projections in ESMs. How model parameters associated with biotic responses will change under warming and to what extent these changes affect projected C budgets have not been carefully examined. In this study, we synthesized six data sets over 5 years from a soil warming experiment at the Eight Mile Lake, Alaska, into the Terrestrial ECOsystem (TECO) model with a probabilistic inversion approach. The TECO model used multiple soil layers to track dynamics of thawed soil under different treatments. Our results show that warming increased light use efficiency of vegetation photosynthesis but decreased baseline (i.e., environment-corrected) turnover rates of SOC in both the fast and slow pools in comparison with those under control. Moreover, the parameter changes generally amplified over time, suggesting processes of gradual physiological acclimation and functional gene shifts of both plants and microbes. The TECO model predicted that field warming from 2009 to 2013 resulted in cumulative C losses of 224 or 87 g/m2 , respectively, without or with changes in those parameters. Thus, warming-induced parameter changes reduced predicted soil C loss by 61%. Our study suggests that it is critical to incorporate biotic changes in ESMs to improve the model performance in predicting C dynamics in permafrost regions.}, }
@article {pmid29802607, year = {2018}, author = {Masood, N and Halimoon, N and Aris, AZ and Zakaria, MP and Vaezzadeh, V and Magam, SM and Mustafa, S and Ali, MM and Keshavarzifard, M and Alkhadher, SAA and Bong, CW and Alsalahi, MA}, title = {Seasonal variability of anthropogenic indices of PAHs in sediment from the Kuala Selangor River, west coast Peninsular Malaysia.}, journal = {Environmental geochemistry and health}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10653-018-0122-z}, pmid = {29802607}, issn = {1573-2983}, support = {6379005//Ministry of Higher Education, Malaysia (MY), HICoE-MOHE Grant IOES-2014/ ; }, abstract = {Rapid increase in industrialization and urbanization in the west coast of Peninsular Malaysia has led to the intense release of petroleum and products of petroleum into the environment. Surface sediment samples were collected from the Selangor River in the west coast of Peninsular Malaysia during four climatic seasons and analyzed for PAHs and biomarkers (hopanes). Sediments were soxhlet extracted and further purified and fractionated through first and second step column chromatography. A gas chromatography-mass spectrometry (GC-MS) was used for analysis of PAHs and hopanes fractions. The average concentrations of total PAHs ranged from 219.7 to 672.3 ng g-1 dw. The highest concentrations of PAHs were detected at 964.7 ng g-1 dw in station S5 in the mouth of the Selangor River during the wet inter-monsoonal season. Both pyrogenic and petrogenic PAHs were detected in the sediments with a predominance of the former. The composition of hopanes was homogeneous showing that petroleum hydrocarbons share an identical source in the study area. Diagnostic ratios of hopanes indicated that some of the sediment samples carry the crankcase oil signature.}, }
@article {pmid29802478, year = {2018}, author = {Roussel, C and Sivignon, A and de Vallée, A and Garrait, G and Denis, S and Tsilia, V and Ballet, N and Vandekerckove, P and Van de Wiele, T and Barnich, N and Blanquet-Diot, S}, title = {Anti-infectious properties of the probiotic Saccharomyces cerevisiae CNCM I-3856 on enterotoxigenic E. coli (ETEC) strain H10407.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {14}, pages = {6175-6189}, doi = {10.1007/s00253-018-9053-y}, pmid = {29802478}, issn = {1432-0614}, mesh = {Animals ; Antibiosis/*physiology ; Caco-2 Cells ; Enterotoxigenic Escherichia coli/*physiology ; Escherichia coli Infections/*microbiology ; Humans ; Mice ; *Probiotics ; Saccharomyces cerevisiae/*physiology ; }, abstract = {Enterotoxigenic Escherichia coli (ETEC) are major food-borne pathogens responsible for traveler's diarrhea. The production of adhesins and the secretion of enterotoxins constitute the major virulence traits of the bacteria. Treatments are mainly symptomatic and can involve antibiotherapy. However, given the rise of antibiotic resistance worldwide, there is an urgent need for the development of new preventive strategies for the control of ETEC infections. Among them, a promising approach is the use of probiotics. The aim of this study was to investigate, using complementary in vitro and in vivo approaches, the inhibitory potential of the yeast Saccharomyces cerevisiae CNCM I-3856 against the human ETEC reference strain H10407. In conventional culture media, S. cerevisiae significantly reduced ETEC growth and toxin production. The yeast also inhibited bacterial adhesion to mucin-agar and intestinal Caco-2/TC7 cells in a dose-dependent manner. Lastly, pre-treatment with S. cerevisiae inhibited interleukin-8 production by ETEC-infected intestinal cells. In streptomycin-treated mice, the probiotic yeast decreased bacterial colonization, mainly in the ileum, the main site of ETEC pathogenesis. For the first time, this study shows that the probiotic yeast S. cerevisiae CNCM I-3856 can exert an anti-infectious activity against a human ETEC strain through a multi-targeted approach, including inhibition of bacterial growth and toxin production, reduction of bacterial adhesion to mucins and intestinal epithelial cells, and suppression of ETEC-induced inflammation. Interestingly, the highest activity was obtained with a prophylactic treatment. Further studies will aim to assess the effect of the yeast on ETEC survival and virulence under human simulated digestive conditions.}, }
@article {pmid29802242, year = {2018}, author = {Wilhelmson, AS and Lantero Rodriguez, M and Stubelius, A and Fogelstrand, P and Johansson, I and Buechler, MB and Lianoglou, S and Kapoor, VN and Johansson, ME and Fagman, JB and Duhlin, A and Tripathi, P and Camponeschi, A and Porse, BT and Rolink, AG and Nissbrandt, H and Turley, SJ and Carlsten, H and Mårtensson, IL and Karlsson, MCI and Tivesten, Å}, title = {Testosterone is an endogenous regulator of BAFF and splenic B cell number.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2067}, doi = {10.1038/s41467-018-04408-0}, pmid = {29802242}, issn = {2041-1723}, abstract = {Testosterone deficiency in men is associated with increased risk for autoimmunity and increased B cell numbers through unknown mechanisms. Here we show that testosterone regulates the cytokine BAFF, an essential survival factor for B cells. Male mice lacking the androgen receptor have increased splenic B cell numbers, serum BAFF levels and splenic Baff mRNA. Testosterone deficiency by castration causes expansion of BAFF-producing fibroblastic reticular cells (FRCs) in spleen, which may be coupled to lower splenic noradrenaline levels in castrated males, as an α-adrenergic agonist decreases splenic FRC number in vitro. Antibody-mediated blockade of the BAFF receptor or treatment with the neurotoxin 6-hydroxydopamine revert the increased splenic B cell numbers induced by castration. Among healthy men, serum BAFF levels are higher in men with low testosterone. Our study uncovers a previously unrecognized regulation of BAFF by testosterone and raises important questions about BAFF in testosterone-mediated protection against autoimmunity.}, }
@article {pmid29802195, year = {2018}, author = {Mertens, J and Aliyu, H and Cowan, DA}, title = {LEA Proteins and the Evolution of the WHy Domain.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {15}, pages = {}, doi = {10.1128/AEM.00539-18}, pmid = {29802195}, issn = {1098-5336}, abstract = {The late embryogenesis abundant (LEA) family is composed of a diverse collection of multidomain and multifunctional proteins found in all three domains of the tree of life, but they are particularly common in plants. Most members of the family are known to play an important role in abiotic stress response and stress tolerance in plants but are also part of the plant hypersensitive response to pathogen infection. The mechanistic basis for LEA protein functionality is still poorly understood. The group of LEA 2 proteins harbor one or more copies of a unique domain, the water stress and hypersensitive response (WHy) domain. This domain sequence has recently been identified as a unique open reading frame (ORF) in some bacterial genomes (mostly in the phylum Firmicutes), and the recombinant bacterial WHy protein has been shown to exhibit a stress tolerance phenotype in Escherichia coli and an in vitro protein denaturation protective function. Multidomain phylogenetic analyses suggest that the WHy protein gene sequence may have ancestral origins in the domain Archaea, with subsequent acquisition in Bacteria and eukaryotes via endosymbiont or horizontal gene transfer mechanisms. Here, we review the structure, function, and nomenclature of LEA proteins, with a focus on the WHy domain as an integral component of the LEA constructs and as an independent protein.}, }
@article {pmid29796758, year = {2018}, author = {Pessi, IS and Pushkareva, E and Lara, Y and Borderie, F and Wilmotte, A and Elster, J}, title = {Marked Succession of Cyanobacterial Communities Following Glacier Retreat in the High Arctic.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1203-3}, pmid = {29796758}, issn = {1432-184X}, support = {LM2010009//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; RVO67985939//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CRCH1011-1513911//Fonds De La Recherche Scientifique - FNRS/ ; FRFC2457009//Fonds De La Recherche Scientifique - FNRS/ ; }, abstract = {Cyanobacteria are important colonizers of recently deglaciated proglacial soil but an in-depth investigation of cyanobacterial succession following glacier retreat has not yet been carried out. Here, we report on the successional trajectories of cyanobacterial communities in biological soil crusts (BSCs) along a 100-year deglaciation gradient in three glacier forefields in central Svalbard, High Arctic. Distance from the glacier terminus was used as a proxy for soil age (years since deglaciation), and cyanobacterial abundance and community composition were evaluated by epifluorescence microscopy and pyrosequencing of partial 16S rRNA gene sequences, respectively. Succession was characterized by a decrease in phylotype richness and a marked shift in community structure, resulting in a clear separation between early (10-20 years since deglaciation), mid (30-50 years), and late (80-100 years) communities. Changes in cyanobacterial community structure were mainly connected with soil age and associated shifts in soil chemical composition (mainly moisture, SOC, SMN, K, and Na concentrations). Phylotypes associated with early communities were related either to potentially novel lineages (< 97.5% similar to sequences currently available in GenBank) or lineages predominantly restricted to polar and alpine biotopes, suggesting that the initial colonization of proglacial soil is accomplished by cyanobacteria transported from nearby glacial environments. Late communities, on the other hand, included more widely distributed genotypes, which appear to establish only after the microenvironment has been modified by the pioneering taxa.}, }
@article {pmid29795328, year = {2018}, author = {Knight, R and Vrbanac, A and Taylor, BC and Aksenov, A and Callewaert, C and Debelius, J and Gonzalez, A and Kosciolek, T and McCall, LI and McDonald, D and Melnik, AV and Morton, JT and Navas, J and Quinn, RA and Sanders, JG and Swafford, AD and Thompson, LR and Tripathi, A and Xu, ZZ and Zaneveld, JR and Zhu, Q and Caporaso, JG and Dorrestein, PC}, title = {Best practices for analysing microbiomes.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {7}, pages = {410-422}, doi = {10.1038/s41579-018-0029-9}, pmid = {29795328}, issn = {1740-1534}, abstract = {Complex microbial communities shape the dynamics of various environments, ranging from the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies and data analysis have provided drastic improvements in microbiome analyses, for example, in taxonomic resolution, false discovery rate control and other properties, over earlier methods. In this Review, we discuss the best practices for performing a microbiome study, including experimental design, choice of molecular analysis technology, methods for data analysis and the integration of multiple omics data sets. We focus on recent findings that suggest that operational taxonomic unit-based analyses should be replaced with new methods that are based on exact sequence variants, methods for integrating metagenomic and metabolomic data, and issues surrounding compositional data analysis, where advances have been particularly rapid. We note that although some of these approaches are new, it is important to keep sight of the classic issues that arise during experimental design and relate to research reproducibility. We describe how keeping these issues in mind allows researchers to obtain more insight from their microbiome data sets.}, }
@article {pmid29789680, year = {2018}, author = {Banerjee, S and Schlaeppi, K and van der Heijden, MGA}, title = {Keystone taxa as drivers of microbiome structure and functioning.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {9}, pages = {567-576}, doi = {10.1038/s41579-018-0024-1}, pmid = {29789680}, issn = {1740-1534}, abstract = {Microorganisms have a pivotal role in the functioning of ecosystems. Recent studies have shown that microbial communities harbour keystone taxa, which drive community composition and function irrespective of their abundance. In this Opinion article, we propose a definition of keystone taxa in microbial ecology and summarize over 200 microbial keystone taxa that have been identified in soil, plant and marine ecosystems, as well as in the human microbiome. We explore the importance of keystone taxa and keystone guilds for microbiome structure and functioning and discuss the factors that determine their distribution and activities.}, }
@article {pmid29788358, year = {2018}, author = {Waldschmitt, N and Metwaly, A and Fischer, S and Haller, D}, title = {Microbial Signatures as a Predictive Tool in IBD-Pearls and Pitfalls.}, journal = {Inflammatory bowel diseases}, volume = {24}, number = {6}, pages = {1123-1132}, doi = {10.1093/ibd/izy059}, pmid = {29788358}, issn = {1536-4844}, abstract = {Studies of microbial signatures have improved our understanding of the role of dysbiosis in gut microbiota for the pathogenesis of inflammatory bowel disease (IBD). New technological advances such as next-generation sequencing facilitate investigations on large patient cohorts, but require methodological considerations regarding study design, sample processing, data analysis, and integration. Here, we summarize recent study approaches in microbial ecology with respect to IBD research and discuss crucial process steps for the production and integration of adequate data sets.}, }
@article {pmid29787679, year = {2018}, author = {Bader, M and Dunkel, A and Wenning, M and Kohler, B and Medard, G and Del Castillo, E and Gholami, A and Kuster, B and Scherer, S and Hofmann, T}, title = {Dynamic Proteome Alteration and Functional Modulation of Human Saliva Induced by Dietary Chemosensory Stimuli.}, journal = {Journal of agricultural and food chemistry}, volume = {66}, number = {22}, pages = {5621-5634}, doi = {10.1021/acs.jafc.8b02092}, pmid = {29787679}, issn = {1520-5118}, mesh = {Adult ; Aspartame/metabolism ; Catechols/metabolism ; Citric Acid/metabolism ; Electrophoresis, Polyacrylamide Gel ; Fatty Alcohols/metabolism ; Female ; Humans ; Male ; Muramidase/analysis/metabolism ; Peroxidase/metabolism ; Proteome/*chemistry/metabolism ; Saliva/chemistry/*metabolism ; Sodium Glutamate/metabolism ; Tandem Mass Spectrometry ; Taste ; Young Adult ; }, abstract = {Saliva flow measurements and SDS-PAGE separation of human whole saliva freshly collected after oral stimulation with citric acid (sour), aspartame (sweet), iso-α-acids (bitter), mono sodium l-glutamate (umami), NaCl (salty), 6-gingerol (pungent), hydroxy-α-sanshool (tingling), and hydroxy-β-sanshool (numbing), followed by tryptic digestion, nano-HPLC-MS/MS, and label-free protein quantitation demonstrated a stimulus- and time-dependent influence of the dietary chemosensates on salivation and the salivary proteome composition. Gene ontology enrichment analysis showed evidence for stimulus-induced alterations of the saliva proteome to boot an efficient molecular defense network of the oral cavity, e.g., 6-gingerol increased salivary lactoperoxidase activity, catalyzing the oxidation of thiocyanate to produce the antimicrobial and antifungal hypothiocyanate, from 0.37 ± 0.02 to 0.91 ± 0.05 mU/mL 45 s after stimulation. In comparison, oral citric acid stimulation induced an increase of myeloperoxidase activity, catalyzing the chloride oxidation to generate antimicrobial hypochloride in saliva, from 0.24 ± 0.04 to 0.70 ± 0.1 mU/mL as well as an increase of salivary levels of lysozyme, exhibiting antimicrobial activity on Gram-positive bacteria, from 6.0-10 to 100-150 μg/mL. Finally, microbial growth experiments clearly demonstrated for the first time that the increase of the salivary lysozyme abundance upon oral citric acid stimulation translates into an enhanced biological function, that is an almost complete growth inhibition of the two lysozyme-sensitive Gram-positive bacteria tested.}, }
@article {pmid29787677, year = {2018}, author = {Seuntjens, D and Van Tendeloo, M and Chatzigiannidou, I and Carvajal-Arroyo, JM and Vandendriessche, S and Vlaeminck, SE and Boon, N}, title = {Synergistic Exposure of Return-Sludge to Anaerobic Starvation, Sulfide, and Free Ammonia to Suppress Nitrite Oxidizing Bacteria.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {15}, pages = {8725-8732}, doi = {10.1021/acs.est.7b06591}, pmid = {29787677}, issn = {1520-5851}, abstract = {A key step toward energy-positive sewage treatment is the development of mainstream partial nitritation/anammox, a nitrogen removal technology where aerobic ammonium-oxidizing bacteria (AerAOB) are desired, while nitrite-oxidizing bacteria (NOB) are not. To suppress NOB, a novel return-sludge treatment was investigated. Single and combined effects of sulfide (0-600 mg S L-1), anaerobic starvation (0-8 days), and a free ammonia (FA) shock (30 mg FA-N L-1 for 1 h) were tested for immediate effects and long-term recovery. AerAOB and NOB were inhibited immediately and proportionally by sulfide, with AerAOB better coping with the inhibition, while the short FA shock and anaerobic starvation had minor effects. Combinatory effects inhibited AerAOB and NOB more strongly. A combined treatment of sulfide (150 mg S L-1), 2 days of anaerobic starvation, and FA shock (30 mg FA-N L-1) inhibited AerAOB 14% more strongly compared to sulfide addition alone, while the AerAOB/NOB activity ratio remained constant. Despite no positive change being observed in the immediate-stress response, AerAOB recovered much faster than NOB, with a nitrite accumulation ratio (effluent nitrite on nitrite + nitrate) peak of 50% after 12 days. Studying long-term recovery is therefore crucial for design of an optimal NOB-suppression treatment, while applying combined stressors regularly may lead toward practical implementation.}, }
@article {pmid29785352, year = {2018}, author = {Gajigan, AP and Yñiguez, AT and Villanoy, CL and San Diego-McGlone, ML and Jacinto, GS and Conaco, C}, title = {Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4781}, doi = {10.7717/peerj.4781}, pmid = {29785352}, issn = {2167-8359}, abstract = {Microbes are central to the structuring and functioning of marine ecosystems. Given the remarkable diversity of the ocean microbiome, uncovering marine microbial taxa remains a fundamental challenge in microbial ecology. However, there has been little effort, thus far, to describe the diversity of marine microorganisms in the region of high marine biodiversity around the Philippines. Here, we present data on the taxonomic diversity of bacteria and archaea in Benham Rise, Philippines, Western Pacific Ocean, using 16S V4 rRNA gene sequencing. The major bacterial and archaeal phyla identified in the Benham Rise are Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Marinimicrobia, Thaumarchaeota and, Euryarchaeota. The upper mesopelagic layer exhibited greater microbial diversity and richness compared to surface waters. Vertical zonation of the microbial community is evident and may be attributed to physical stratification of the water column acting as a dispersal barrier. Canonical Correspondence Analysis (CCA) recapitulated previously known associations of taxa and physicochemical parameters in the environment, such as the association of oligotrophic clades with low nutrient surface water and deep water clades that have the capacity to oxidize ammonia or nitrite at the upper mesopelagic layer. These findings provide foundational information on the diversity of marine microbes in Philippine waters. Further studies are warranted to gain a more comprehensive picture of microbial diversity within the region.}, }
@article {pmid29784985, year = {2018}, author = {Chalermwatanachai, T and Vilchez-Vargas, R and Holtappels, G and Lacoere, T and Jáuregui, R and Kerckhof, FM and Pieper, DH and Van de Wiele, T and Vaneechoutte, M and Van Zele, T and Bachert, C}, title = {Chronic rhinosinusitis with nasal polyps is characterized by dysbacteriosis of the nasal microbiota.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {7926}, doi = {10.1038/s41598-018-26327-2}, pmid = {29784985}, issn = {2045-2322}, abstract = {Chronic rhinosinusitis with nasal polyp (CRSwNP) patients are often characterized by asthma comorbidity and a type-2 inflammation of the sinonasal mucosa. The mucosal microbiota has been suggested to be implicated in the persistence of inflammation, but associations have not been well defined. To compare the bacterial communities of healthy subjects with CRSwNP patients, we collected nasal swabs from 17 healthy subjects, 21 CRSwNP patients without asthma (CRSwNP-A), and 20 CRSwNP patients with co-morbid asthma (CRSwNP+A). We analysed the microbiota using high-throughput sequencing of the bacterial 16S rRNA. Bacterial communities were different between the three groups. Haemophilus influenzae was significantly enriched in CRSwNP patients, Propionibacterium acnes in the healthy group; Staphylococcus aureus was abundant in the CRSwNP-A group, even though present in 57% of patients. Escherichia coli was found in high amounts in CRSwNP+A patients. Nasal tissues of CRSwNP+A patients expressed significantly higher concentrations of IgE, SE-IgE, and IL-5 compared to those of CRSwNP-A patients. Co-cultivation demonstrated that P. acnes growth was inhibited by H. influenzae, E. coli and S. aureus. The nasal microbiota of healthy subjects are different from those of CRSwNP-A and CRSwNP+A patients. However, the most abundant species in healthy status could not inhibit those in CRSwNP disease.}, }
@article {pmid29783165, year = {2018}, author = {Miller, HC and Morgan, MJ and Walsh, T and Wylie, JT and Kaksonen, AH and Puzon, GJ}, title = {Preferential feeding in Naegleria fowleri; intracellular bacteria isolated from amoebae in operational drinking water distribution systems.}, journal = {Water research}, volume = {141}, number = {}, pages = {126-134}, doi = {10.1016/j.watres.2018.05.004}, pmid = {29783165}, issn = {1879-2448}, mesh = {Biofilms ; Deinococcus/genetics/*isolation &amp; purification/physiology ; Drinking Water/*microbiology ; Environmental Monitoring ; Naegleria fowleri/isolation &amp; purification/*microbiology ; RNA, Ribosomal, 16S ; Water Pollutants/isolation &amp; purification ; }, abstract = {The amoeba Naegleria fowleri is the causative agent of the highly fatal disease, primary amoebic meningoencephalitis, and estimated to cause 16 deaths per year in the United States alone. Colonisation of drinking water distribution systems (DWDSs) by the N. fowleri is a significant public health issue. Understanding the factors which enable this pathogen to colonise and thrive in DWDSs is critical for proper management. The microbial ecology within DWDSs may influence the ability of N. fowleri to colonise DWDSs by facilitating the availability of an appropriate food source. Using biofilm samples obtained from operational DWDSs, 16S rRNA amplicon metabarcoding was combined with genus-specific PCR and Sanger sequencing of intracellular associated bacteria from isolated amoeba and their parental biofilms to identify Meiothermus chliarophilus as a potential food source for N. fowleri. Meiothermus was confirmed as a food source for N. fowleri following successful serial culturing of axenic N. fowleri with M. chliarophilus or M. ruber as the sole food source. The ability to identify environmental and ecological conditions favourable to N. fowleri colonisation, including the detection of appropriate food sources such as Meiothermus, could provide water utilities with a predictive tool for managing N. fowleri colonisation within the DWDS.}, }
@article {pmid29782923, year = {2018}, author = {Wong, SH and Kwong, TNY and Wu, CY and Yu, J}, title = {Clinical applications of gut microbiota in cancer biology.}, journal = {Seminars in cancer biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.semcancer.2018.05.003}, pmid = {29782923}, issn = {1096-3650}, abstract = {The involvement of microorganisms in cancer has been increasing recognized. Collectively, microorganisms have been estimated to account for ∼20% of all cancers worldwide. Recent advances in metagenomics and bioinformatics have provided new insights on the microbial ecology in different tumors, pinpointing the roles of microorganisms in cancer formation, development and response to treatments. Furthermore, studies have emphasized the importance of host-microbial and inter-microbial interactions in the cancer microbiota. These studies have not only revolutionized our understanding of cancer biology, but also opened up new opportunities for cancer prevention, diagnosis, prognostication and treatment. This review article aims to summarize the microbiota in various cancers and their treatments, and explore clinical applications for such relevance.}, }
@article {pmid29780377, year = {2018}, author = {Egerton, S and Culloty, S and Whooley, J and Stanton, C and Ross, RP}, title = {The Gut Microbiota of Marine Fish.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {873}, doi = {10.3389/fmicb.2018.00873}, pmid = {29780377}, issn = {1664-302X}, abstract = {The body of work relating to the gut microbiota of fish is dwarfed by that on humans and mammals. However, it is a field that has had historical interest and has grown significantly along with the expansion of the aquaculture industry and developments in microbiome research. Research is now moving quickly in this field. Much recent focus has been on nutritional manipulation and modification of the gut microbiota to meet the needs of fish farming, while trying to maintain host health and welfare. However, the diversity amongst fish means that baseline data from wild fish and a clear understanding of the role that specific gut microbiota play is still lacking. We review here the factors shaping marine fish gut microbiota and highlight gaps in the research.}, }
@article {pmid29779128, year = {2018}, author = {Kurina, IV and Li, H}, title = {Why Do Testate Amoeba Optima Related to Water Table Depth Vary?.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1202-4}, pmid = {29779128}, issn = {1432-184X}, support = {16-34-60057//Russian Foundation for Basic Research/ ; }, abstract = {This study focusses on the ecology of testate amoeba species in peatlands of the southern taiga of Western Siberia. To estimate the influence of the trophic state of mires on species optima related to water table depth, a separate study of three calibration datasets including ombrotrophic, minerotrophic and the combined habitats was conducted. In the datasets obtained separately from ombrotrophic and minerotrophic mires, the water table depth was the main factor affecting testate amoeba assemblages. However, the trophic state (specifically pH and ash content) was more important factor in the combined dataset, including all of the studied mires. For 36 testate amoeba species, which were found in the ombrotrophic and minerotrophic mire habitats, their species optima, obtained separately in ombrotrophic and minerotrophic datasets, differed significantly from each other. Some of these species preferred minerotrophic conditions, while others preferred ombrotrophic ones. For all species, the trophic state of the mires affected the values of the species optima related to water table depth, as revealed in the form of a threshold effect. In extreme conditions, the species were more sensitive to the trophic status than to the water table depth, and their optimum related to water table depth was distorted. Variation of the optimum was observed in those species that inhabited both ombrotrophic and minerotrophic mires due to the fact that mires with a different trophic status were included in the training sets. The optima did not vary for species inhabiting only ombrotrophic or only minerotrophic mires.}, }
@article {pmid29776729, year = {2018}, author = {Farhat, A and Manai, I and Gtari, M and Bouallagui, H}, title = {Effect of enhancing nutrient balance in anaerobic digester feedstock by co-substrate addition on the microbial diversity and energy production from municipal sewage sludge.}, journal = {Journal of bioscience and bioengineering}, volume = {126}, number = {4}, pages = {497-506}, doi = {10.1016/j.jbiosc.2018.04.014}, pmid = {29776729}, issn = {1347-4421}, abstract = {Enhancement of methane production during anaerobic digestion of waste activated sludge (WAS) could improve the energy self sufficiency of the municipal wastewater treatment plants (WWTPs). Therefore, mixing WAS with organic wastes improved process performance and stability. In this work, the anaerobic co-digestion of WAS combined with the olive processing wastewater (OPW) was investigated and associated with the energetic benefits and microbial populations shifts. The bio-methane potential (BMP) of various WAS and OPW mixtures corresponding to increased phenols concentrations were tested. The anaerobic digestion of better proportions (90%/10% and 80%/20%) was performed in anaerobic sequencing batch reactors (ASBRs). The biodegradation of phenols at concentrations up to 0.76 g/L was confirmed by Sephadex gel filtration showing that ASBR, which is suspended growth reactor, can handle much higher concentration of toxic compounds. Microbial analysis showed that phenols induced significantly the archaea community dynamic, which showed highly richness and diversity in the well performed reactor. The dominant bacteria and archaea phylotypes were affiliated to Proteobacteria and Methanosarcinales, respectively. Therefore, OPW addition increased total energy production from 24.6 kWh/ton to 64.7 kWh/ton, which would provide 0.43 M€/year net benefits only from the electric power. In addition it brings a payback time on investment of 2 years for WWTPs modification, which was considered interesting.}, }
@article {pmid29774016, year = {2018}, author = {Cheaib, B and Le Boulch, M and Mercier, PL and Derome, N}, title = {Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {869}, doi = {10.3389/fmicb.2018.00869}, pmid = {29774016}, issn = {1664-302X}, abstract = {Adaptation of microbial communities to anthropogenic stressors can lead to reductions in microbial diversity and disequilibrium of ecosystem services. Such adaptation can change the molecular signatures of communities with differences in taxonomic and functional composition. Understanding the relationship between taxonomic and functional variation remains a critical issue in microbial ecology. Here, we assessed the taxonomic and functional diversity of a lake metacommunity system along a polymetallic pollution gradient caused by 60 years of chronic exposure to acid mine drainage (AMD). Our results highlight three adaptive signatures. First, a signature of taxon-function decoupling was detected in the microbial communities of moderately and highly polluted lakes. Second, parallel shifts in taxonomic composition occurred between polluted and unpolluted lakes. Third, variation in the abundance of functional modules suggested a gradual deterioration of ecosystem services (i.e., photosynthesis) and secondary metabolism in highly polluted lakes. Overall, changes in the abundance of taxa, function, and more importantly the polymetallic resistance genes such as copA, copB, czcA, cadR, cCusA, were correlated with trace metal content (mainly Cadmium) and acidity. Our findings highlight the impact of polymetallic pollution gradient at the lowest trophic levels.}, }
@article {pmid29774012, year = {2018}, author = {Schultz-Johansen, M and Bech, PK and Hennessy, RC and Glaring, MA and Barbeyron, T and Czjzek, M and Stougaard, P}, title = {A Novel Enzyme Portfolio for Red Algal Polysaccharide Degradation in the Marine Bacterium Paraglaciecola hydrolytica S66T Encoded in a Sizeable Polysaccharide Utilization Locus.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {839}, doi = {10.3389/fmicb.2018.00839}, pmid = {29774012}, issn = {1664-302X}, abstract = {Marine microbes are a rich source of enzymes for the degradation of diverse polysaccharides. Paraglaciecola hydrolytica S66T is a marine bacterium capable of hydrolyzing polysaccharides found in the cell wall of red macroalgae. In this study, we applied an approach combining genomic mining with functional analysis to uncover the potential of this bacterium to produce enzymes for the hydrolysis of complex marine polysaccharides. A special feature of P. hydrolytica S66T is the presence of a large genomic region harboring an array of carbohydrate-active enzymes (CAZymes) notably agarases and carrageenases. Based on a first functional characterization combined with a comparative sequence analysis, we confirmed the enzymatic activities of several enzymes required for red algal polysaccharide degradation by the bacterium. In particular, we report for the first time, the discovery of novel enzyme activities targeting furcellaran, a hybrid carrageenan containing both β-carrageenan and κ/β-carrageenan motifs. Some of these enzymes represent a new subfamily within the CAZy classification. From the combined analyses, we propose models for the complete degradation of agar and κ/β-type carrageenan by P. hydrolytica S66T. The novel enzymes described here may find value in new bio-based industries and advance our understanding of the mechanisms responsible for recycling of red algal polysaccharides in marine ecosystems.}, }
@article {pmid29772177, year = {2018}, author = {Alloul, A and Ganigué, R and Spiller, M and Meerburg, F and Cagnetta, C and Rabaey, K and Vlaeminck, SE}, title = {Capture-Ferment-Upgrade: A Three-Step Approach for the Valorization of Sewage Organics as Commodities.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {12}, pages = {6729-6742}, doi = {10.1021/acs.est.7b05712}, pmid = {29772177}, issn = {1520-5851}, abstract = {This critical review outlines a roadmap for the conversion of chemical oxygen demand (COD) contained in sewage to commodities based on three-steps: capture COD as sludge, ferment it to volatile fatty acids (VFA), and upgrade VFA to products. The article analyzes the state-of-the-art of this three-step approach and discusses the bottlenecks and challenges. The potential of this approach is illustrated for the European Union's 28 member states (EU-28) through Monte Carlo simulations. High-rate contact stabilization captures the highest amount of COD (66-86 g COD person equivalent-1 day-1 in 60% of the iterations). Combined with thermal hydrolysis, this would lead to a VFA-yield of 23-44 g COD person equivalent-1 day-1. Upgrading VFA generated by the EU-28 would allow, in 60% of the simulations, for a yearly production of 0.2-2.0 megatonnes of esters, 0.7-1.4 megatonnes of polyhydroxyalkanoates or 0.6-2.2 megatonnes of microbial protein substituting, respectively, 20-273%, 70-140% or 21-72% of their global counterparts (i.e., petrochemical-based esters, bioplastics or fishmeal). From these flows, we conclude that sewage has a strong potential as biorefinery feedstock, although research is needed to enhance capture, fermentation and upgrading efficiencies. These developments need to be supported by economic/environmental analyses and policies that incentivize a more sustainable management of our resources.}, }
@article {pmid29771325, year = {2018}, author = {Armada, E and Leite, MFA and Medina, A and Azcón, R and Kuramae, EE}, title = {Native bacteria promote plant growth under drought stress condition without impacting the rhizomicrobiome.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {7}, pages = {}, doi = {10.1093/femsec/fiy092}, pmid = {29771325}, issn = {1574-6941}, abstract = {Inoculation of plants with beneficial plant growth-promoting bacteria (PGPB) emerges a valuable strategy for ecosystem recovery. However, drought conditions might compromise plant-microbe interactions especially in semiarid regions. This study highlights the effect of native PGPB after 1 year inoculation on autochthonous shrubs growth and rhizosphere microbial community composition and activity under drought stress conditions. We inoculated three plant species of semiarid Mediterranean zones, Thymus vulgaris, Santolina chamaecyparissus and Lavandula dentata with a Bacillus thuringiensis strain IAM 12077 and evaluated the impact on plant biomass, plant nutrient contents, arbuscular mycorrhiza fungi (AMF) colonization, soil rhizosphere microbial activity and both the bacterial and fungal communities. Inoculation with strain IAM 12077 improved the ability of all three plants species to uptake nutrients from the soil, promoted L. dentata shoot growth (>65.8%), and doubled the AMF root colonization of S. chamaecyparissus. Inoculation did not change the rhizosphere microbial community. Moreover, changes in rhizosphere microbial activity were mainly plant species-specific and strongly associated with plant nutrients. In conclusion, the strain IAM 12077 induced positive effects on plant growth and nutrient acquisition with no impact on the rhizosphere microbiome, indicating a rhizosphere microbial community resilient to native bacteria inoculation.}, }
@article {pmid29769378, year = {2018}, author = {Warren, FJ and Fukuma, NM and Mikkelsen, D and Flanagan, BM and Williams, BA and Lisle, AT and Ó Cuív, P and Morrison, M and Gidley, MJ}, title = {Food Starch Structure Impacts Gut Microbiome Composition.}, journal = {mSphere}, volume = {3}, number = {3}, pages = {}, doi = {10.1128/mSphere.00086-18}, pmid = {29769378}, issn = {2379-5042}, mesh = {Animals ; Fermentation ; *Food Analysis ; Gastrointestinal Microbiome/*drug effects ; Models, Biological ; Starch/*administration &amp; dosage/*metabolism ; Swine ; }, abstract = {Starch is a major source of energy in the human diet and is consumed in diverse forms. Resistant starch (RS) escapes small intestinal digestion and is fermented in the colon by the resident microbiota, with beneficial impacts on colonic function and host health, but the impacts of the micro- and nanoscale structure of different physical forms of food starch on the broader microbial community have not been described previously. Here, we use a porcine in vitro fermentation model to establish that starch structure dramatically impacts microbiome composition, including the key amylolytic species, and markedly alters both digestion kinetics and fermentation outcomes. We show that three characteristic food forms of starch that survive digestion in the small intestine each give rise to substantial and distinct changes in the microbiome and in fermentation products. Our results highlight the complexity of starch fermentation processes and indicate that not all forms of RS in foods are degraded or fermented in the same way. This work points the way for the design of RS with tailored degradation by defined microbial communities, informed by an understanding of how substrate structure influences the gut microbiome, to improve nutritive value and/or health benefits.IMPORTANCE Dietary starch is a major component in the human diet. A proportion of the starch in our diet escapes digestion in the small intestine and is fermented in the colon. In this study, we use a model of the colon, seeded with porcine feces, in which we investigate the fermentation of a variety of starches with structures typical of those found in foods. We show that the microbial community changes over time in our model colon are highly dependent on the structure of the substrate and how accessible the starch is to colonic microbes. These findings have important implications for how we classify starches reaching the colon and for the design of foods with improved nutritional properties.}, }
@article {pmid29769279, year = {2018}, author = {Granchelli, AM and Adler, FR and Keogh, RH and Kartsonaki, C and Cox, DR and Liou, TG}, title = {Microbial Interactions in the Cystic Fibrosis Airway.}, journal = {Journal of clinical microbiology}, volume = {56}, number = {8}, pages = {}, doi = {10.1128/JCM.00354-18}, pmid = {29769279}, issn = {1098-660X}, support = {R01 HL125520/HL/NHLBI NIH HHS/United States ; T32 HL105321/HL/NHLBI NIH HHS/United States ; U54 CA209978/CA/NCI NIH HHS/United States ; }, abstract = {Interactions in the airway ecology of cystic fibrosis may alter organism persistence and clinical outcomes. Better understanding of such interactions could guide clinical decisions. We used generalized estimating equations to fit logistic regression models to longitudinal 2-year patient cohorts in the Cystic Fibrosis Foundation Patient Registry, 2003 to 2011, in order to study associations between the airway organisms present in each calendar year and their presence in the subsequent year. Models were adjusted for clinical characteristics and multiple observations per patient. Adjusted models were tested for sensitivity to cystic fibrosis-specific treatments. The study included 28,042 patients aged 6 years and older from 257 accredited U.S. care centers and affiliates. These patients had produced sputum specimens for at least two consecutive years that were cultured for methicillin-sensitive Staphylococcus aureus, methicillin-resistant S. aureus, Pseudomonas aeruginosa, Burkholderia cepacia complex, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, and Candida and Aspergillus species. We analyzed 99.8% of 538,458 sputum cultures from the patients during the study period. Methicillin-sensitive S. aureus was negatively associated with subsequent Paeruginosa. Paeruginosa was negatively associated with subsequent B. cepacia complex, Axylosoxidans, and Smaltophilia. Bcepacia complex was negatively associated with the future presence of all bacteria studied, as well as with that of Aspergillus species. Paeruginosa, B. cepacia complex, and S. maltophilia were each reciprocally and positively associated with Aspergillus species. Independently of patient characteristics, the organisms studied interact and alter the outcomes of treatment decisions, sometimes in unexpected ways. By inhibiting P. aeruginosa, methicillin-sensitive S. aureus may delay lung disease progression. Paeruginosa and B. cepacia complex may inhibit other organisms by decreasing airway biodiversity, potentially worsening lung disease.}, }
@article {pmid29767159, year = {2017}, author = {Luo, D and Gao, Y and Lu, Y and Qu, M and Xiong, X and Xu, L and Zhao, X and Pan, K and Ouyang, K}, title = {Niacin alters the ruminal microbial composition of cattle under high-concentrate condition.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {3}, number = {2}, pages = {180-185}, doi = {10.1016/j.aninu.2017.04.005}, pmid = {29767159}, issn = {2405-6383}, abstract = {To understand the effects of niacin on the ruminal microbial ecology of cattle under high-concentrate diet condition, Illumina MiSeq sequencing technology was used. Three cattle with rumen cannula were used in a 3 × 3 Latin-square design trial. Three diets were fed to these cattle during 3 periods for 3 days, respectively: high-forage diet (HF; forage-to-concentrate ratio = 80:20), high-concentrate diet (HC; forage-to-concentrate ratio = 20:80), and HC supplemented with 800 mg/kg niacin (HCN). Ruminal pH was measured before feeding and every 2 h after initiating feeding. Ruminal fluid was sampled at the end of each period for microbial DNA extraction. Overall, our findings revealed that subacute ruminal acidosis (SARA) was induced and the α-diversity of ruminal bacterial community decreased in the cattle of HC group. Adding niacin in HC could relieve the symptoms of SARA in the cattle but the ruminal pH value and the Shannon index of ruminal bacterial community of HCN group were still lower than those of HF group. Whatever the diet was, the ruminal bacterial community of cattle was dominated by Bacteroidetes, Firmicutes and Proteobacteria. High-concentrate diet significantly increased the abundance of Prevotella, and decreased the abundance of Paraprevotella, Sporobacter, Ruminococcus and Treponema than HF. Compared with HC, HCN had a trend to decrease the percentage of Prevotella, and to increase the abundance of Succiniclasticum, Acetivibrio and Treponema. Increasing concentrate ratio could decrease ruminal pH value, and change the ruminal microbial composition. Adding niacin in HC could increase the ruminal pH value, alter the ruminal microbial composition.}, }
@article {pmid29766224, year = {2018}, author = {García-Bonilla, E and Brandão, PFB and Pérez, T and Junca, H}, title = {Stable and Enriched Cenarchaeum symbiosum and Uncultured Betaproteobacteria HF1 in the Microbiome of the Mediterranean Sponge Haliclona fulva (Demospongiae: Haplosclerida).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1201-5}, pmid = {29766224}, issn = {1432-184X}, support = {Doctoral Grant (Convocatoria 528-2011)//Colciencias-Colfuturo/ ; Projects (2012-2014 and 2015-2017//EcosNord-Colciencias/ ; }, abstract = {Sponges harbor characteristic microbiomes derived from symbiotic relationships shaping their lifestyle and survival. Haliclona fulva is encrusting marine sponge species dwelling in coralligenous accretions or semidark caves of the Mediterranean Sea and the near Atlantic Ocean. In this work, we characterized the abundance and core microbial community composition found in specimens of H. fulva by means of electron microscopy and 16S amplicon Illumina sequencing. We provide evidence of its low microbial abundance (LMA) nature. We found that the H. fulva core microbiome is dominated by sequences belonging to the orders Nitrosomonadales and Cenarchaeales. Seventy percent of the reads assigned to these phylotypes grouped in a very small number of high-frequency operational taxonomic units, representing niche-specific species Cenarchaeum symbiosum and uncultured Betaproteobacteria HF1, a new eubacterial ribotype variant found in H. fulva. The microbial composition of H. fulva is quite distinct from those reported in sponge species of the same Haliclona genus. We also detected evidence of an excretion/capturing loop between these abundant microorganisms and planktonic microbes by analyzing shifts in seawater planktonic microbial content exposed to healthy sponge specimens maintained in aquaria. Our results suggest that horizontal transmission is very likely the main mechanism for symbionts' acquisition by H. fulva. So far, this is the first shallow water sponge species harboring such a specific and predominant assemblage composed of these eubacterial and archaeal ribotypes. Our data suggests that this symbiotic relationship is very stable over time, indicating that the identified core microbial symbionts may play key roles in the holobiont functioning.}, }
@article {pmid29763867, year = {2018}, author = {Brehony, C and Cullinan, J and Cormican, M and Morris, D}, title = {Shiga toxigenic Escherichia coli incidence is related to small area variation in cattle density in a region in Ireland.}, journal = {The Science of the total environment}, volume = {637-638}, number = {}, pages = {865-870}, doi = {10.1016/j.scitotenv.2018.05.038}, pmid = {29763867}, issn = {1879-1026}, abstract = {Shiga toxigenic Escherichia coli (STEC) are pathogenic E. coli that cause infectious diarrhoea. In some cases infection may be complicated by renal failure and death. The incidence of human infection with STEC in Ireland is the highest in Europe. The objective of the study was to examine the spatial incidence of human STEC infection in a region of Ireland with significantly higher rates of STEC incidence than the national average and to identify possible risk factors of STEC incidence at area level. Anonymised laboratory records (n = 379) from 2009 to 2015 were obtained from laboratories serving three counties in the West of Ireland. Data included location and sample date. Population and electoral division (ED) data were obtained from the Irish 2011 Census of Population. STEC incidence was calculated for each ED (n = 498) and used to map hotspots/coldspots using the Getis-Ord Gi* spatial statistic and significant spatial clustering using the Anselin's Local Moran's I statistic. Multivariable regression analysis was used to consider the importance of a number of potential predictors of STEC incidence. Incidence rates for the seven-year period ranged from 0 to 10.9 cases per 1000. A number of areas with significant local clustering of STEC incidence as well as variation in the spatial distribution of the two main serogroups associated with disease in the region i.e. O26 and O157 were identified. Cattle density was found to be a statistically significant predictor of STEC in the region. GIS analysis of routine data indicates that cattle density is associated STEC infection in this high incidence region. This finding points to the importance of agricultural practices for human health and the importance of a &quot;one-health&quot; approach to public policy in relation to agriculture, health and environment.}, }
@article {pmid29762668, year = {2018}, author = {Almeida, A and Mitchell, AL and Tarkowska, A and Finn, RD}, title = {Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments.}, journal = {GigaScience}, volume = {7}, number = {5}, pages = {}, doi = {10.1093/gigascience/giy054}, pmid = {29762668}, issn = {2047-217X}, abstract = {Background: Taxonomic profiling of ribosomal RNA (rRNA) sequences has been the accepted norm for inferring the composition of complex microbial ecosystems. Quantitative Insights Into Microbial Ecology (QIIME) and mothur have been the most widely used taxonomic analysis tools for this purpose, with MAPseq and QIIME 2 being two recently released alternatives. However, no independent and direct comparison between these four main tools has been performed. Here, we compared the default classifiers of MAPseq, mothur, QIIME, and QIIME 2 using synthetic simulated datasets comprised of some of the most abundant genera found in the human gut, ocean, and soil environments. We evaluate their accuracy when paired with both different reference databases and variable sub-regions of the 16S rRNA gene.<br><br>Findings: We show that QIIME 2 provided the best recall and F-scores at genus and family levels, together with the lowest distance estimates between the observed and simulated samples. However, MAPseq showed the highest precision, with miscall rates consistently <2%. Notably, QIIME 2 was the most computationally expensive tool, with CPU time and memory usage almost 2 and 30 times higher than MAPseq, respectively. Using the SILVA database generally yielded a higher recall than using Greengenes, while assignment results of different 16S rRNA variable sub-regions varied up to 40% between samples analysed with the same pipeline.<br><br>Conclusions: Our results support the use of either QIIME 2 or MAPseq for optimal 16S rRNA gene profiling, and we suggest that the choice between the two should be based on the level of recall, precision, and/or computational performance required.}, }
@article {pmid29760683, year = {2018}, author = {Angel, R and Nepel, M and Panhölzl, C and Schmidt, H and Herbold, CW and Eichorst, SA and Woebken, D}, title = {Evaluation of Primers Targeting the Diazotroph Functional Gene and Development of NifMAP - A Bioinformatics Pipeline for Analyzing nifH Amplicon Data.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {703}, doi = {10.3389/fmicb.2018.00703}, pmid = {29760683}, issn = {1664-302X}, abstract = {Diazotrophic microorganisms introduce biologically available nitrogen (N) to the global N cycle through the activity of the nitrogenase enzyme. The genetically conserved dinitrogenase reductase (nifH) gene is phylogenetically distributed across four clusters (I-IV) and is widely used as a marker gene for N2 fixation, permitting investigators to study the genetic diversity of diazotrophs in nature and target potential participants in N2 fixation. To date there have been limited, standardized pipelines for analyzing the nifH functional gene, which is in stark contrast to the 16S rRNA gene. Here we present a bioinformatics pipeline for processing nifH amplicon datasets - NifMAP (&quot;NifH MiSeq Illumina Amplicon Analysis Pipeline&quot;), which as a novel aspect uses Hidden-Markov Models to filter out homologous genes to nifH. By using this pipeline, we evaluated the broadly inclusive primer pairs (Ueda19F-R6, IGK3-DVV, and F2-R6) that target the nifH gene. To evaluate any systematic biases, the nifH gene was amplified with the aforementioned primer pairs in a diverse collection of environmental samples (soils, rhizosphere and roots samples, biological soil crusts and estuarine samples), in addition to a nifH mock community consisting of six phylogenetically diverse members. We noted that all primer pairs co-amplified nifH homologs to varying degrees; up to 90% of the amplicons were nifH homologs with IGK3-DVV in some samples (rhizosphere and roots from tall oat-grass). In regards to specificity, we observed some degree of bias across the primer pairs. For example, primer pair F2-R6 discriminated against cyanobacteria (amongst others), yet captured many sequences from subclusters IIIE and IIIL-N. These aforementioned subclusters were largely missing by the primer pair IGK3-DVV, which also tended to discriminate against Alphaproteobacteria, but amplified sequences within clusters IIIC (affiliated with Clostridia) and clusters IVB and IVC. Primer pair Ueda19F-R6 exhibited the least bias and successfully captured diazotrophs in cluster I and subclusters IIIE, IIIL, IIIM, and IIIN, but tended to discriminate against Firmicutes and subcluster IIIC. Taken together, our newly established bioinformatics pipeline, NifMAP, along with our systematic evaluations of nifH primer pairs permit more robust, high-throughput investigations of diazotrophs in diverse environments.}, }
@article {pmid29759899, year = {2018}, author = {Belgini, DRB and Siqueira, VM and Oliveira, DM and Fonseca, SG and Piccin-Santos, V and Dias, RS and Quartaroli, L and Souza, RS and Torres, APR and Sousa, MP and Silva, CM and Silva, CC and De Paula, SO and Oliveira, VM}, title = {Integrated diversity analysis of the microbial community in a reverse osmosis system from a Brazilian oil refinery.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {5}, pages = {473-486}, doi = {10.1016/j.syapm.2018.03.007}, pmid = {29759899}, issn = {1618-0984}, abstract = {Oil refineries are known for the large volume of water used in their processes, as well as the amount of wastewater generated at the end of the production chain. Due to strict environmental regulations, the recycling of water has now become a viable alternative for refineries. Among the many methods available to treat wastewater for reuse, the use of membranes in reverse osmosis systems stands out due to several economic and environmental benefits. However, these systems are vulnerable to contamination and deposition of microorganisms, mainly because of the feedwater quality. In this study, the microbial diversity of feedwater and reverse osmosis membranes was investigated using a combination of culture-dependent and culture-independent methods in order to characterize the microorganisms colonizing and deteriorating the membranes. In total, 37 bacterial isolates, 17 filamentous fungi and approximately 400 clones were obtained and analyzed. Among the bacterial genera identified, the most represented were Sphingobium, Acidovorax, Microbacterium, Rhizobium and Shinella. The results revealed genera that acted as candidate key players in initial biofilm formation in membrane systems, and provided important information concerning the microbial ecology of oligotrophic aquatic systems.}, }
@article {pmid29758429, year = {2018}, author = {Najar, IN and Sherpa, MT and Das, S and Das, S and Thakur, N}, title = {Microbial ecology of two hot springs of Sikkim: Predominate population and geochemistry.}, journal = {The Science of the total environment}, volume = {637-638}, number = {}, pages = {730-745}, doi = {10.1016/j.scitotenv.2018.05.037}, pmid = {29758429}, issn = {1879-1026}, abstract = {Northeastern regions of India are known for their floral and faunal biodiversity. Especially the state of Sikkim lies in the eastern Himalayan ecological hotspot region. The state harbors many sulfur rich hot springs which have therapeutic and spiritual values. However, these hot springs are yet to be explored for their microbial ecology. The development of neo generation techniques such as metagenomics has provided an opportunity for inclusive study of microbial community of different environment. The present study describes the microbial diversity in two hot springs of Sikkim that is Polok and Borong with the assist of culture dependent and culture independent approaches. The culture independent techniques used in this study were next generation sequencing (NGS) and Phospholipid Fatty Acid Analysis (PLFA). Having relatively distinct geochemistry both the hot springs are thermophilic environments with the temperature range of 50-77 °C and pH range of 5-8. Metagenomic data revealed the dominance of bacteria over archaea. The most abundant phyla were Proteobacteria and Bacteroidetes although other phyla were also present such as Acidobacteria, Nitrospirae, Firmicutes, Proteobacteria, Parcubacteria and Spirochaetes. The PLFA studies have shown the abundance of Gram Positive bacteria followed by Gram negative bacteria. The culture dependent technique was correlative with PLFA studies. Most abundant bacteria as isolated and identified were Gram-positive genus Geobacillus and Anoxybacillus. The genus Geobacillus has been reported for the first time in North-Eastern states of India. The Geobacillus species obtained from the concerned hot springs were Geobacillus toebii, Geobacillus lituanicus, Geobacillus Kaustophillus and the Anoxybacillus species includes Anoxybacillus gonensis and Anoxybacillus Caldiproteolyticus. The distribution of major genera and their statistical correlation analyses with the geochemistry of the springs predicted that the temperature, pH, alkalinity, Ca2+, Mg2+, Cl2+, and sulfur were main environmental variables influencing the microbial community composition and diversity. Also the piper diagram suggested that the water of both the hot springs are Ca-HCO3- type and can be predicted as shallow fresh ground waters. This study has provided an insight into the ecological interaction of the diverse microbial communities and associated physicochemical parameters, which will help in determining the future studies on different biogeochemical pathways in these hot springs.}, }
@article {pmid29757994, year = {2018}, author = {Ibrahim, B and Arkhipova, K and Andeweg, AC and Posada-Céspedes, S and Enault, F and Gruber, A and Koonin, EV and Kupczok, A and Lemey, P and McHardy, AC and McMahon, DP and Pickett, BE and Robertson, DL and Scheuermann, RH and Zhernakova, A and Zwart, MP and Schönhuth, A and Dutilh, BE and Marz, M}, title = {Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.}, journal = {Viruses}, volume = {10}, number = {5}, pages = {}, doi = {10.3390/v10050256}, pmid = {29757994}, issn = {1999-4915}, abstract = {The Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions. Approximately 120 researchers from around the world attended the Second Annual Meeting of the EVBC this year, including 15 renowned international speakers. This report presents an overview of new developments and novel research findings that emerged during the meeting.}, }
@article {pmid29755700, year = {2018}, author = {Sharma, P and Maherchandani, S and Shringi, BN and Kashyap, SK and Sundar, KSG}, title = {Temporal variations in patterns of Escherichia coli strain diversity and antimicrobial resistance in the migrant Egyptian vulture.}, journal = {Infection ecology &amp; epidemiology}, volume = {8}, number = {1}, pages = {1450590}, doi = {10.1080/20008686.2018.1450590}, pmid = {29755700}, issn = {2000-8686}, abstract = {Aims: Multiple antimicrobial resistance in Escherichia coli of wild vertebrates is a global concern with scarce assessments on the subject from developing countries that have high human-wild species interactions. We studied the ecology of E. coli in a wintering population of Egyptian Vultures in India to understand temporal changes in both E. coli strains and patterns of antimicrobial resistance. Methods and Results: We ribotyped E. coli strains and assessed antimicrobial resistance from wintering vultures at a highly synanthropic carcass dump in north-west India. Both E. coli occurence (90.32%) and resistance to multiple antimicrobials (71.43%) were very high. Clear temporal patterns were apparent. Diversity of strains changed and homogenized at the end of the Vultures' wintering period, while the resistance pattern showed significantly difference inter-annually, as well as between arrival and departing individuals within a wintering cycle. Significance of study: The carcass dump environment altered both E. coli strains and multiple antimicrobial resistance in migratory Egyptian Vultures within a season. Long-distance migratory species could therefore disseminate resistant E. coli strains across broad geographical scales rendering regional mitigation strategies to control multiple antimicrobial resistance in bacteria ineffective.}, }
@article {pmid29755434, year = {2018}, author = {Pérez-Cataluña, A and Collado, L and Salgado, O and Lefiñanco, V and Figueras, MJ}, title = {A Polyphasic and Taxogenomic Evaluation Uncovers Arcobacter cryaerophilus as a Species Complex That Embraces Four Genomovars.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {805}, doi = {10.3389/fmicb.2018.00805}, pmid = {29755434}, issn = {1664-302X}, abstract = {The species Arcobacter cryaerophilus is found in many food products of animal origin and is the dominating species in wastewater. In addition, it is associated with cases of farm animal and human infectious diseases,. The species embraces two subgroups i.e., 1A (LMG 24291T = LMG 9904T) and 1B (LMG 10829) that can be differentiated by their 16S rRNA-RFLP pattern. However, some authors, on the basis of the shared intermediate levels of DNA-DNA hybridization, have suggested abandoning the subgroup classification. This contradiction indicates that the taxonomy of this species is not yet resolved. The objective of the present study was to perform a taxonomic evaluation of the diversity of A. cryaerophilus. Genomic information was used along with a Multilocus Phylogenetic Analysis (MLPA) and phenotypic characterization on a group of 52 temporally and geographically dispersed strains, coming from different types of samples and hosts from nine countries. The MLPA analysis showed that those strains formed four clusters (I-IV). Values of Average Nucleotide Identity (ANI) and in silico DNA-DNA Hybridization (isDDH) obtained between 13 genomes representing strains of the four clusters were below the proposed cut-offs of 96 and 70%, respectively, confirming that each of the clusters represented a different genomic species. However, none of the evaluated phenotypic tests enabled their unequivocal differentiation into species. Therefore, the genomic delimited clusters should be considered genomovars of the species A. cryaerophilus. These genomovars could have different clinical importance, since only the cluster I included strains isolated from human specimens. The discovery of at least one stable distinctive phenotypic character would be needed to define each cluster or genomovar as a different species. Until then, we propose naming them &quot;A. cryaerophilus gv. pseudocryaerophilus&quot; (Cluster I = LMG 10229T), &quot;A. cryaerophilus gv. crypticus&quot; (Cluster II = LMG 9065T), &quot;A. cryaerophilus gv. cryaerophilus&quot; (Cluster III = LMG 24291T) and &quot;A. cryaerophilus gv. occultus&quot; (Cluster IV = LMG 29976T).}, }
@article {pmid29752058, year = {2018}, author = {Deng, D and Weidhaas, JL and Lin, LS}, title = {Corrigendum to &quot; Kinetics and microbial ecology of batch sulfidogenic bioreactors for co-treatment of municipal wastewater and acid mine drainage&quot; [J. Hazard. Mater. (2016) 10.1016/j.jhazmat.2015.11.041].}, journal = {Journal of hazardous materials}, volume = {353}, number = {}, pages = {552}, doi = {10.1016/j.jhazmat.2018.04.046}, pmid = {29752058}, issn = {1873-3336}, }
@article {pmid29747113, year = {2018}, author = {Rousk, J and Rousk, K}, title = {Responses of microbial tolerance to heavy metals along a century-old metal ore pollution gradient in a subarctic birch forest.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {240}, number = {}, pages = {297-305}, doi = {10.1016/j.envpol.2018.04.087}, pmid = {29747113}, issn = {1873-6424}, mesh = {Bacteria ; Betula ; Betulaceae ; Biomass ; Drug Tolerance ; Ecosystem ; *Environmental Monitoring ; Environmental Pollution ; *Forests ; Metals, Heavy/analysis/*toxicity ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/analysis/*toxicity ; }, abstract = {Heavy metals are some of the most persistent and potent anthropogenic environmental contaminants. Although heavy metals may compromise microbial communities and soil fertility, it is challenging to causally link microbial responses to heavy metals due to various confounding factors, including correlated soil physicochemistry or nutrient availability. A solution is to investigate whether tolerance to the pollutant has been induced, called Pollution Induced Community Tolerance (PICT). In this study, we investigated soil microbial responses to a century-old gradient of metal ore pollution in an otherwise pristine subarctic birch forest generated by a railway source of iron ore transportation. To do this, we determined microbial biomass, growth, and respiration rates, and bacterial tolerance to Zn and Cu in replicated distance transects (1 m-4 km) perpendicular to the railway. Microbial biomass, growth and respiration rates were stable across the pollution gradient. The microbial community structure could be distinguished between sampled distances, but most of the variation was explained by soil pH differences, and it did not align with distance from the railroad pollution source. Bacterial tolerance to Zn and Cu started from background levels at 4 km distance from the pollution source, and remained at background levels for Cu throughout the gradient. Yet, bacterial tolerance to Zn increased 10-fold 100 m from the railway source. Our results show that the microbial community structure, size and performance remained unaffected by the metal ore exposure, suggesting no impact on ecosystem functioning.}, }
@article {pmid29745026, year = {2018}, author = {De Vrieze, J and Boon, N and Verstraete, W}, title = {Taking the technical microbiome into the next decade.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14269}, pmid = {29745026}, issn = {1462-2920}, abstract = {The 'microbiome' has become a buzzword. Multiple new technologies allow to gather information about microbial communities as they evolve under stable and variable environmental conditions. The challenge of the next decade will be to develop strategies to compose and manage microbiomes. Here, key aspects are considered that will be of crucial importance for future microbial technological developments. First, the need to deal not only with genotypes but also particularly with phenotypes is addressed. Microbial technologies are often highly dependent on specific core organisms to obtain the desired process outcome. Hence, it is essential to combine omics data with phenotypic information to invoke and control specific phenotypes in the microbiome. Second, the development and application of synthetic microbiomes is evaluated. The central importance of the core species is a no-brainer, but the implementation of proper satellite species is an important route to explore. Overall, for the next decade, microbiome research should no longer almost exclusively focus on its capacity to degrade and dissipate but rather on its remarkable capability to capture disordered components and upgrade them into high-value microbial products. These products can become valuable commodities in the cyclic economy, as reflected in the case of 'reversed sanitation', which is introduced here.}, }
@article {pmid29744532, year = {2018}, author = {Peng, C and Wang, H and Jiang, Y and Yang, J and Lai, H and Wei, X}, title = {Exploring the Abundance and Diversity of Bacterial Communities and Quantifying Antibiotic-Related Genes Along an Elevational Gradient in Taibai Mountain, China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1197-x}, pmid = {29744532}, issn = {1432-184X}, support = {2012BAD14B11//National Sci-Tech Support Plan of China/ ; 2016KTZDNY03-03-02//Shaanxi Science &amp; Technology Co-ordination &amp; Innovation Project/ ; 2452017313//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Thus far, no studies have investigated the soil microbial diversity over an elevational gradient in Taibai Mountain, the central massif of the Qinling Mountain Range. Here, we used Illumina sequencing and quantitative PCR of the 16S rRNA gene to assess the diversity and abundance of bacterial communities along an elevational gradient in representative vegetation soils in Taibai Mountain. We identified the soil, climate, and vegetation factors driving the variations in soil bacterial community structure by Pearson correlation and redundancy analysis. We also evaluated the potential for antibiotic discovery by quantitative PCR of the PKS-I, PKS-II, and NRPS genes from Actinobacteria. The results showed that soil bacterial alpha diversity increased first and then decreased with an elevational rise in both the northern and southern slopes of Taibai Mountain. The bacterial abundance was significantly correlated with soil organic matter and nitrate nitrogen. The average relative abundance of Actinobacteria in Taibai Mountain was markedly higher than those in other mountain forest soils. The absolute abundance of PKS and NPRS gene was significantly higher in the tested soils compared with the gene copy numbers reported in tropical urban soils. Taibai Mountain is rich in actinomycete resources and has great potential for antibiotic excavation.}, }
@article {pmid29744531, year = {2018}, author = {Gioacchini, G and Ciani, E and Pessina, A and Cecchini, C and Silvi, S and Rodiles, A and Merrifield, DL and Olivotto, I and Carnevali, O}, title = {Correction to: Effects of Lactogen 13, a New Probiotic Preparation, on Gut Microbiota and Endocrine Signals Controlling Growth and Appetite of Oreochromis niloticus Juveniles.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1194-0}, pmid = {29744531}, issn = {1432-184X}, abstract = {The original version of this article unfortunately contained mistakes in Authors First name/Family name order. Please refer to this paper as Gioacchini et al. and not as Giorgia et al.}, }
@article {pmid29743637, year = {2018}, author = {Ghasemian, E and Inic-Kanada, A and Collingro, A and Tagini, F and Stein, E and Alchalabi, H and Schuerer, N and Keše, D and Babiker, BE and Borel, N and Greub, G and Barisani-Asenbauer, T}, title = {Detection of Chlamydiaceae and Chlamydia-like organisms on the ocular surface of children and adults from a trachoma-endemic region.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {7432}, doi = {10.1038/s41598-018-23887-1}, pmid = {29743637}, issn = {2045-2322}, abstract = {Trachoma, the leading infectious cause of blindness, is caused by Chlamydia trachomatis (Ct), a bacterium of the phylum Chlamydiae. Recent investigations revealed the existence of additional families within the phylum Chlamydiae, also termed Chlamydia-like organisms (CLOs). In this study, the frequency of Ct and CLOs was examined in the eyes of healthy Sudanese (control) participants and those with trachoma (case). We tested 96 children (54 cases and 42 controls) and 93 adults (51 cases and 42 controls) using broad-range Chlamydiae and Ct-specific (omcB) real-time PCR. Samples positive by broad-range Chlamydiae testing were subjected to DNA sequencing. Overall Chlamydiae prevalence was 36%. Sequences corresponded to unclassified and classified Chlamydiae. Ct infection rate was significantly higher in children (31.5%) compared to adults (0%) with trachoma (p < 0.0001). In general, 21.5% of adults and 4.2% of children tested positive for CLOs (p = 0.0003). Our findings are consistent with previous investigations describing the central role of Ct in trachoma among children. This is the first study examining human eyes for the presence of CLOs. We found an age-dependent distribution of CLO DNA in human eyes with significantly higher positivity in adults. Further studies are needed to understand the impact of CLOs in trachoma pathogenicity and/or protection.}, }
@article {pmid29743566, year = {2018}, author = {Willemsen, A and Carrasco, JL and Elena, SF and Zwart, MP}, title = {Going, going, gone: predicting the fate of genomic insertions in plant RNA viruses.}, journal = {Heredity}, volume = {121}, number = {5}, pages = {499-509}, doi = {10.1038/s41437-018-0086-x}, pmid = {29743566}, issn = {1365-2540}, abstract = {Horizontal gene transfer is common among viruses, while they also have highly compact genomes and tend to lose artificial genomic insertions rapidly. Understanding the stability of genomic insertions in viral genomes is therefore relevant for explaining and predicting their evolutionary patterns. Here, we revisit a large body of experimental research on a plant RNA virus, tobacco etch potyvirus (TEV), to identify the patterns underlying the stability of a range of homologous and heterologous insertions in the viral genome. We obtained a wide range of estimates for the recombination rate-the rate at which deletions removing the insertion occur-and these appeared to be independent of the type of insertion and its location. Of the factors we considered, recombination rate was the best predictor of insertion stability, although we could not identify the specific sequence characteristics that would help predict insertion instability. We also considered experimentally the possibility that functional insertions lead to higher mutational robustness through increased redundancy. However, our observations suggest that both functional and non-functional increases in genome size decreased the mutational robustness. Our results therefore demonstrate the importance of recombination rates for predicting the long-term stability and evolution of viral RNA genomes and suggest that there are unexpected drawbacks to increases in genome size for mutational robustness.}, }
@article {pmid29740008, year = {2018}, author = {Defoirdt, T and Mai Anh, NT and De Schryver, P}, title = {Virulence-inhibitory activity of the degradation product 3-hydroxybutyrate explains the protective effect of poly-β-hydroxybutyrate against the major aquaculture pathogen Vibrio campbellii.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {7245}, doi = {10.1038/s41598-018-25385-w}, pmid = {29740008}, issn = {2045-2322}, abstract = {The bacterial storage compound poly-β-hydroxybutyrate, a polymer of the short-chain fatty acid 3-hydroxybutyrate, has been reported to protect various aquatic animals from bacterial disease. In order to obtain a better mechanistic insight, we aimed to (1) investigate whether 3-hydroxybutyrate is released from poly-β-hydroxybutyrate within sterile brine shrimp larvae, (2) determine the impact of 3-hydroxybutyrate on the virulence of Vibrio campbellii to brine shrimp larvae and on its cell density in the shrimp, and (3) determine the impact of this compound on virulence factor production in the pathogen. We detected 3-hydroxybutyrate in poly-β-hydroxybutyrate-fed brine shrimp, resulting in 24 mM 3-hydroxybutyrate in the intestinal tract of shrimp reared in the presence of 1000 mg l-1 poly-β-hydroxybutyrate. We further demonstrate that this concentration of 3-hydroxybutyrate does not affect the growth of V. campbellii, whereas it decreases the production of different virulence factors, including hemolysin, phospholipase and protease activities, and swimming motility. We hypothesize that by affecting all these virulence factors at once, 3-hydroxybutyrate (and thus also poly-β-hydroxybutyrate) can exert a significant impact on the virulence of V. campbellii. This hypothesis was confirmed in a challenge test showing that 3-hydroxybutyrate protected gnotobiotic brine shrimp from pathogenic V. campbellii, without affecting the number of host-associated vibrios.}, }
@article {pmid29738975, year = {2018}, author = {Theuerl, S and Klang, J and Heiermann, M and De Vrieze, J}, title = {Marker microbiome clusters are determined by operational parameters and specific key taxa combinations in anaerobic digestion.}, journal = {Bioresource technology}, volume = {263}, number = {}, pages = {128-135}, doi = {10.1016/j.biortech.2018.04.111}, pmid = {29738975}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Biofuels ; *Bioreactors ; *Microbiota ; Sewage ; }, abstract = {In this study, microbiomes of 36 full-scale anaerobic digesters originated from 22 different biogas plants were compared by terminal restriction fragment length polymorphism (TRFLP) analysis. Regarding the differences in microbial community composition, a weighting of the environmental parameters could be derived from higher to lower importance as follows: (i) temperature, (ii) TAN and NH3 concentrations and conductivity, and (iii) the chemical composition of the supplied feedstocks. Biotic interactions between specific bacterial and archaeal community arrangements were revealed, whereby members of the phyla Bacteroidetes and Cloacimonetes combined with the archaeal genus Methanothrix dominated the conversion of homogeneous feedstocks, such as waste water sludge or industrial waste. As most of the detected TRFs were only found in a certain number of anaerobic digestion plants, each plant develops its unique microbiome. The putative rare species, the specialists, are potentially hidden drivers of microbiome functioning as they provide necessary traits under, e.g., process-inconvenient conditions.}, }
@article {pmid29738306, year = {2018}, author = {Svenningsen, NB and Martínez-García, E and Nicolaisen, MH and de Lorenzo, V and Nybroe, O}, title = {The biofilm matrix polysaccharides cellulose and alginate both protect Pseudomonas putida mt-2 against reactive oxygen species generated under matric stress and copper exposure.}, journal = {Microbiology (Reading, England)}, volume = {164}, number = {6}, pages = {883-888}, doi = {10.1099/mic.0.000667}, pmid = {29738306}, issn = {1465-2080}, abstract = {In natural environments most bacteria live in biofilms embedded in complex matrices of extracellular polymeric substances (EPS). This lifestyle is known to increase protection against environmental stress. Pseudomonas putida mt-2 harbours genes for the production of at least four different EPS polysaccharides, including alginate and cellulose. Little is known about the functional properties of cellulose, while alginate attenuates the accumulation of reactive oxygen species (ROS) caused by matric stress. By using mutants that are deficient in either alginate or cellulose production we show that even cellulose attenuates the accumulation of matric stress-induced ROS for cells in biofilms. Further, both cellulose and alginate attenuate ROS generated through exposure to copper. Interestingly, the two EPS polysaccharides protect cells in both liquid culture and in biofilms against ROS caused by matric stress, indicating that cellulose and alginate do not need to be produced as an integral part of the biofilm lifestyle to provide tolerance towards environmental stressors.}, }
@article {pmid29738088, year = {2018}, author = {Faure, D and Simon, JC and Heulin, T}, title = {Holobiont: a conceptual framework to explore the eco-evolutionary and functional implications of host-microbiota interactions in all ecosystems.}, journal = {The New phytologist}, volume = {218}, number = {4}, pages = {1321-1324}, doi = {10.1111/nph.15199}, pmid = {29738088}, issn = {1469-8137}, }
@article {pmid29737382, year = {2018}, author = {Delafont, V and Rodier, MH and Maisonneuve, E and Cateau, E}, title = {Vermamoeba vermiformis: a Free-Living Amoeba of Interest.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {991-1001}, doi = {10.1007/s00248-018-1199-8}, pmid = {29737382}, issn = {1432-184X}, abstract = {Free-living amoebae are protists that are widely distributed in the environment including water, soil, and air. Although the amoebae of the genus Acanthamoeba are still the most studied, other species, such as Vermamoeba vermiformis (formerly Hartmannella vermiformis), are the subject of increased interest. Found in natural or man-made aquatic environments, V. vermiformis can support the multiplication of other microorganisms and is able to harbor and potentially protect pathogenic bacteria or viruses. This feature is to be noted because of the presence of this thermotolerant amoeba in hospital water networks. As a consequence, this protist could be implicated in health concerns and be indirectly responsible for healthcare-related infections. This review highlights, among others, the consequences of V. vermiformis relationships with other microorganisms and shows that this free-living amoeba species is therefore of interest for public health.}, }
@article {pmid29736898, year = {2018}, author = {Arias-Jayo, N and Abecia, L and Alonso-Sáez, L and Ramirez-Garcia, A and Rodriguez, A and Pardo, MA}, title = {High-Fat Diet Consumption Induces Microbiota Dysbiosis and Intestinal Inflammation in Zebrafish.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-018-1198-9}, pmid = {29736898}, issn = {1432-184X}, abstract = {Energy-dense foods and overnutrition represent major starting points altering lipid metabolism, systemic inflammation and gut microbiota. The aim of this work was to investigate the effects of a high-fat diet (HFD) over a period of 25 days on intestinal microbiota and inflammation in zebrafish. Microbial composition of HFD-fed animals was analysed and compared to controls by 16S rRNA sequencing and quantitative PCR. The expression level on several genes related to inflammation was tested. Furthermore, microscopic assessment of the intestine was performed in both conditions. The consumption of the HFD resulted in microbial dysbiosis, characterised by an increase in the relative abundance of the phylum Bacteroidetes. Moreover, an emerging intestinal inflammation via NF-κβ activation was confirmed by the overexpression of several genes related to signalling receptors, antimicrobial metabolism and the inflammatory cascade. The intestinal barrier was also damaged, with an increase of goblet cell mucin production. This is the first study performed in zebrafish which suggests that the consumption of a diet enriched with 10% fat changes the intestinal microbial community composition, which was correlated with low-grade inflammation.}, }
@article {pmid29736335, year = {2018}, author = {Stewart, CJ and Auchtung, TA and Ajami, NJ and Velasquez, K and Smith, DP and De La Garza, R and Salas, R and Petrosino, JF}, title = {Effects of tobacco smoke and electronic cigarette vapor exposure on the oral and gut microbiota in humans: a pilot study.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4693}, doi = {10.7717/peerj.4693}, pmid = {29736335}, issn = {2167-8359}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; }, abstract = {Background: The use of electronic cigarettes (ECs) has increased drastically over the past five years, primarily as an alternative to smoking tobacco cigarettes. However, the adverse effects of acute and long-term use of ECs on the microbiota have not been explored. In this pilot study, we sought to determine if ECs or tobacco smoking alter the oral and gut microbiota in comparison to non-smoking controls.<br><br>Methods: We examined a human cohort consisting of 30 individuals: 10 EC users, 10 tobacco smokers, and 10 controls. We collected cross-sectional fecal, buccal swabs, and saliva samples from each participant. All samples underwent V4 16S rRNA gene sequencing.<br><br>Results: Tobacco smoking had a significant effect on the bacterial profiles in all sample types when compared to controls, and in feces and buccal swabs when compared to EC users. The most significant associations were found in the gut, with an increased relative abundance of Prevotella (P = 0.006) and decreased Bacteroides (P = 0.036) in tobacco smokers. The Shannon diversity was also significantly reduced (P = 0.009) in fecal samples collected from tobacco smokers compared to controls. No significant difference was found in the alpha diversity, beta-diversity or taxonomic relative abundances between EC users and controls.<br><br>Discussion: From a microbial ecology perspective, the current pilot data demonstrate that the use of ECs may represent a safer alternative compared to tobacco smoking. However, validation in larger cohorts and greater understanding of the short and long-term impact of EC use on microbiota composition and function is warranted.}, }
@article {pmid29735671, year = {2018}, author = {Bjerg, JT and Boschker, HTS and Larsen, S and Berry, D and Schmid, M and Millo, D and Tataru, P and Meysman, FJR and Wagner, M and Nielsen, LP and Schramm, A}, title = {Long-distance electron transport in individual, living cable bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {22}, pages = {5786-5791}, doi = {10.1073/pnas.1800367115}, pmid = {29735671}, issn = {1091-6490}, mesh = {Bacteria/*chemistry/*metabolism ; Cytochromes/metabolism ; Electron Transport/*physiology ; Geologic Sediments/microbiology ; Oxidation-Reduction ; Oxygen/metabolism ; Spectrum Analysis, Raman ; Sulfides/metabolism ; }, abstract = {Electron transport within living cells is essential for energy conservation in all respiring and photosynthetic organisms. While a few bacteria transport electrons over micrometer distances to their surroundings, filaments of cable bacteria are hypothesized to conduct electric currents over centimeter distances. We used resonance Raman microscopy to analyze cytochrome redox states in living cable bacteria. Cable-bacteria filaments were placed in microscope chambers with sulfide as electron source and oxygen as electron sink at opposite ends. Along individual filaments a gradient in cytochrome redox potential was detected, which immediately broke down upon removal of oxygen or laser cutting of the filaments. Without access to oxygen, a rapid shift toward more reduced cytochromes was observed, as electrons were no longer drained from the filament but accumulated in the cellular cytochromes. These results provide direct evidence for long-distance electron transport in living multicellular bacteria.}, }
@article {pmid29735061, year = {2018}, author = {Martins, MCF and Freitas, R and Deuvaux, JC and Eller, MR and Nero, LA and Carvalho, AF}, title = {Bacterial diversity of artisanal cheese from the Amazonian region of Brazil during the dry and rainy seasons.}, journal = {Food research international (Ottawa, Ont.)}, volume = {108}, number = {}, pages = {295-300}, doi = {10.1016/j.foodres.2018.03.060}, pmid = {29735061}, issn = {1873-7145}, abstract = {The microbiota from artisanal cheeses produced in the Amazonian region is evaluated. Samples of artisanal cheeses were obtained from markets in Conceição do Araguaia and Redenção (Pará, Brazil) over rainy and dry seasons, and their biodiversity was assessed by culture-dependent and culture-independent methods. Mean counts of lactic acid bacteria (LAB) in cheeses ranged from 7.32 to 8.84 log CFU/g, for both seasons. Members of genera Lactobacillus, Lactococcus, Weissella, Enterococcus, Pediococcus, and Leuconostoc were predominant. The amplification of the 16S rRNA V6-V9 region, followed by a temporal temperature-gradient gel electrophoresis (TTGE) and sequencing of the TTGE bands revealed important differences in the microbial composition variability between samples from the two seasons and among cheese samples analyzed. TTGE showed the presence of microorganisms that are frequently found in cheese, such as L. lactis subsp. lactis, as well as other non-usual species, such as Macrococcus caseolyticus and Corynebacterium variabile. Moreover, TTGE analysis revealed the presence of microorganisms that have been isolated from other types of foods (Paralactobacillus selangorenses) along with some not usually found in foods, such as Exiguobacterium acetylicum, plus the presence of pathogenic microorganisms (Granulicatella elegans and Aerococcus sanguinicola). The present molecular approaches combined with culture-dependent methods provided a more detailed description of the microbial ecology of traditional cheeses from the Amazonian region in northern Brazil.}, }
@article {pmid29734762, year = {2018}, author = {Semedo-Aguiar, AP and Pereira-Leal, JB and Leite, RB}, title = {Microbial Diversity and Toxin Risk in Tropical Freshwater Reservoirs of Cape Verde.}, journal = {Toxins}, volume = {10}, number = {5}, pages = {}, doi = {10.3390/toxins10050186}, pmid = {29734762}, issn = {2072-6651}, abstract = {The Cape Verde islands are part of the African Sahelian arid belt that possesses an erratic rain pattern prompting the need for water reservoirs, which are now critical for the country&amp;rsquo;s sustainability. Worldwide, freshwater cyanobacterial blooms are increasing in frequency due to global climate change and the eutrophication of water bodies, particularly in reservoirs. To date, there have been no risk assessments of cyanobacterial toxin production in these man-made structures. We evaluated this potential risk using 16S rRNA gene amplicon sequencing and full metagenome sequencing in freshwater reservoirs of Cape Verde. Our analysis revealed the presence of several potentially toxic cyanobacterial genera in all sampled reservoirs. Faveta potentially toxic and bloom-forming Microcystis sp., dominated our samples, while a Cryptomonas green algae and Gammaproteobacteria dominated Saquinho and Poil&amp;atilde;o reservoirs. We reconstructed and assembled the Microcystis genome, extracted from the metagenome of bulk DNA from Faveta water. Phylogenetic analysis of Microcystis cf. aeruginosa CV01&amp;rsquo;s genome revealed its close relationship with other Microcystis genomes, as well as clustering with other continental African strains, suggesting geographical coherency. In addition, it revealed several clusters of known toxin-producing genes. This survey reinforces the need to better understand the country&amp;rsquo;s microbial ecology as a whole of water reservoirs on the rise.}, }
@article {pmid29728707, year = {2018}, author = {Li, B and Li, Z and Sun, X and Wang, Q and Xiao, E and Sun, W}, title = {DNA-SIP Reveals the Diversity of Chemolithoautotrophic Bacteria Inhabiting Three Different Soil Types in Typical Karst Rocky Desertification Ecosystems in Southwest China.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {976-990}, doi = {10.1007/s00248-018-1196-y}, pmid = {29728707}, issn = {1432-184X}, support = {41771301, 41420104007//the National Natural Science Foundation of China/ ; 2016GDASRC-0103//the High-Level Leading Talent Introduction Program of GDAS/ ; 2018GDASCX-0601 and 2017GDASCX-0106//1000 Youth Talents Program, the GDAS' Special Project of Science and Technology Development/ ; 2016B070701015//the Science and Technology Planning Project of Guangdong Province/ ; }, abstract = {Autotrophs that inhabit soils receive less attention than their counterparts in other ecosystems, such as deep-sea and subsurface sediments, due to the low abundance of autotrophs in soils with high organic contents. However, the karst rocky desertification region is a unique ecosystem that may have a low level of organic compounds. Therefore, we propose that karst rocky desertification ecosystems may harbor diverse autotrophic microbial communities. In this study, DNA-SIP was employed to identify the chemolithoautotrophic bacteria inhabiting three soil types (i.e., grass, forest, and agriculture) of the karst rocky desertification ecosystems. The results indicated that potential chemolithoautotrophic population was observed in each soil type, even at different time points after amending 13C-NaHCO3, confirming our hypothesis that diverse autotrophs contribute to the carbon cycle in karst soils. Bacteria, such as Ralstonia, Ochrobactrum, Brevibacterium, Acinetobacter, and Corynebacterium, demonstrated their potential to assimilate inorganic carbon and reduce nitrate or thiosulfate as electron acceptors. Putative mixotrophs were identified by DNA-SIP as well, suggesting the metabolic versatility of soil microbiota. A co-occurrence network further indicated that autotrophs and heterotrophs may form associated communities to sustain the ecosystem function. Our current study revealed the metabolic diversity of autotrophic bacteria in soil habitats and demonstrated the potentially important role of chemoautotrophs in karst rocky desertification ecosystems.}, }
@article {pmid29727966, year = {2018}, author = {Pershina, EV and Ivanova, EA and Korvigo, IO and Chirak, EL and Sergaliev, NH and Abakumov, EV and Provorov, NA and Andronov, EE}, title = {Investigation of the core microbiome in main soil types from the East European plain.}, journal = {The Science of the total environment}, volume = {631-632}, number = {}, pages = {1421-1430}, doi = {10.1016/j.scitotenv.2018.03.136}, pmid = {29727966}, issn = {1879-1026}, mesh = {Bacteria/genetics ; *Environmental Monitoring ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Russia ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The main goal of modern microbial ecology is to determine the key factors influencing the global diversity of microorganisms. Because of their complexity, soil communities are largely underexplored in this context. We studied soil genesis (combination of various soil-forming processes, specific to a particular soil type) that is driven by microbial activity. To investigate the interrelation between soil type and microbial diversity, we analyzed six soil types that are common