@article {pmid33083833, year = {2020}, author = {Arca-Suárez, J and Lasarte-Monterrubio, C and Rodiño-Janeiro, BK and Cabot, G and Vázquez-Ucha, JC and Rodríguez-Iglesias, M and Galán-Sánchez, F and Beceiro, A and González-Bello, C and Oliver, A and Bou, G}, title = {Molecular mechanisms driving the in vivo development of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDR Pseudomonas aeruginosa infections.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {}, number = {}, pages = {}, doi = {10.1093/jac/dkaa396}, pmid = {33083833}, issn = {1460-2091}, abstract = {BACKGROUND: The development of resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of Pseudomonas aeruginosa infections is concerning.<br><br>OBJECTIVES: Characterization of the mechanisms leading to the development of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDR P. aeruginosa infections.<br><br>METHODS: Four paired ceftolozane/tazobactam- and ceftazidime/avibactam-susceptible/resistant isolates were evaluated. MICs were determined by broth microdilution. STs, resistance mechanisms and genetic context of β-lactamases were determined by genotypic methods, including WGS. The OXA-10 variants were cloned in PAO1 to assess their impact on resistance. Models for the OXA-10 derivatives were constructed to evaluate the structural impact of the amino acid changes.<br><br>RESULTS: The same XDR ST253 P. aeruginosa clone was detected in all four cases evaluated. All initial isolates showed OprD deficiency, produced an OXA-10 enzyme and were susceptible to ceftazidime, ceftolozane/tazobactam, ceftazidime/avibactam and colistin. During treatment, the isolates developed resistance to all cephalosporins. Comparative genomic analysis revealed that the evolved resistant isolates had acquired mutations in the OXA-10 enzyme: OXA-14 (Gly157Asp), OXA-794 (Trp154Cys), OXA-795 (ΔPhe153-Trp154) and OXA-824 (Asn143Lys). PAO1 transformants producing the evolved OXA-10 derivatives showed enhanced ceftolozane/tazobactam and ceftazidime/avibactam resistance but decreased meropenem MICs in a PAO1 background. Imipenem/relebactam retained activity against all strains. Homology models revealed important changes in regions adjacent to the active site of the OXA-10 enzyme. The blaOXA-10 gene was plasmid borne and acquired due to transposition of Tn6746 in the pHUPM plasmid scaffold.<br><br>CONCLUSIONS: Modification of OXA-10 is a mechanism involved in the in vivo acquisition of resistance to cephalosporin/β-lactamase inhibitor combinations in P. aeruginosa.}, }
@article {pmid33082281, year = {2020}, author = {Allard, SM and Costa, MT and Bulseco, AN and Helfer, V and Wilkins, LGE and Hassenrück, C and Zengler, K and Zimmer, M and Erazo, N and Mazza Rodrigues, JL and Duke, N and Melo, VMM and Vanwonterghem, I and Junca, H and Makonde, HM and Jiménez, DJ and Tavares, TCL and Fusi, M and Daffonchio, D and Duarte, CM and Peixoto, RS and Rosado, AS and Gilbert, JA and Bowman, J}, title = {Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems.}, journal = {mSystems}, volume = {5}, number = {5}, pages = {}, pmid = {33082281}, issn = {2379-5077}, abstract = {Mangrove ecosystems provide important ecological benefits and ecosystem services, including carbon storage and coastline stabilization, but they also suffer great anthropogenic pressures. Microorganisms associated with mangrove sediments and the rhizosphere play key roles in this ecosystem and make essential contributions to its productivity and carbon budget. Understanding this nexus and moving from descriptive studies of microbial taxonomy to hypothesis-driven field and lab studies will facilitate a mechanistic understanding of mangrove ecosystem interaction webs and open opportunities for microorganism-mediated approaches to mangrove protection and rehabilitation. Such an effort calls for a multidisciplinary and collaborative approach, involving chemists, ecologists, evolutionary biologists, microbiologists, oceanographers, plant scientists, conservation biologists, and stakeholders, and it requires standardized methods to support reproducible experiments. Here, we outline the Mangrove Microbiome Initiative, which is focused around three urgent priorities and three approaches for advancing mangrove microbiome research.}, }
@article {pmid33078238, year = {2020}, author = {Jayakumar, A and Nair, IC and Radhakrishnan, EK}, title = {Environmental Adaptations of an Extremely Plant Beneficial Bacillus subtilis Dcl1 Identified Through the Genomic and Metabolomic Analysis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01605-7}, pmid = {33078238}, issn = {1432-184X}, abstract = {Bacterial endophytes ubiquitously colonize the internal tissues of plants and promote the plant growth through diverse mechanisms. The current study describes the mechanistic basis of plant-specific adaptations present in an extremely beneficial endophytic bacterium. Here, the endophytic Bacillus subtilis Dcl1 isolated from the dried rhizome of Curcuma longa was found to have the drought tolerance, IAA and ACC deaminase production and phosphate solubilization properties. The whole genome sequencing and annotation further showed the genome of B. subtilis Dcl1 to have the size of 4,321,654 bp. This also showed the presence of genes for IAA, H2S, acetoin, butanediol, flagella and siderophore production along with phosphate solubilization and biofilm formation for the B. subtilis Dcl1. In addition, the genes responsible for the synthesis of surfactin, iturin, fengycin, bacillibactin, bacillaene, bacilysin, chitinase, chitosanase, protease and glycoside hydrolase could also be annotated from the genome of B. subtilis Dcl1. Identification of genes for the glycine betaine, glutamate and trehalose further indicated the drought stress tolerance features of B. subtilis Dcl1. The presence of the genetic basis to produce the catalase, superoxide dismutase, peroxidases, gamma-glutamyltranspeptidase, glutathione and glycolate oxidase also indicated the plant oxidative stress protective effect of B. subtilis Dcl1. Identification of these properties and the demonstration of its plant probiotic effect in Vigna unguiculata confirmed the applicability of B. subtilis Dcl1 as a biofertilizer, biocontrol and bioremediator agent to enhance the agricultural productivity.}, }
@article {pmid33077749, year = {2020}, author = {Yang, FS and Nie, S and Liu, H and Shi, TL and Tian, XC and Zhou, SS and Bao, YT and Jia, KH and Guo, JF and Zhao, W and An, N and Zhang, RG and Yun, QZ and Wang, XZ and Mannapperuma, C and Porth, I and El-Kassaby, YA and Street, NR and Wang, XR and Van de Peer, Y and Mao, JF}, title = {Chromosome-level genome assembly of a parent species of widely cultivated azaleas.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5269}, doi = {10.1038/s41467-020-18771-4}, pmid = {33077749}, issn = {2041-1723}, abstract = {Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii, the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae, likely contributing to the genomic architecture of flowering time. Small-scale gene duplications contribute to the expansion of gene families involved in azalea pigment biosynthesis. We reconstruct entire metabolic pathways for anthocyanins and carotenoids and their potential regulatory networks by detailed analysis of time-ordered gene co-expression networks. MYB, bHLH, and WD40 transcription factors may collectively regulate anthocyanin accumulation in R. simsii, particularly at the initial stages of flower coloration, and with WRKY transcription factors controlling progressive flower coloring at later stages. This work provides a cornerstone for understanding the underlying genetics governing flower timing and coloration and could accelerate selective breeding in azalea.}, }
@article {pmid33075580, year = {2020}, author = {Francis, JS and Tatarko, AR and Richman, SK and Vaudo, AD and Leonard, AS}, title = {Microbes and Pollinator Behavior in the Floral Marketplace.}, journal = {Current opinion in insect science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cois.2020.10.003}, pmid = {33075580}, issn = {2214-5753}, abstract = {Pollinator foraging decisions shape microbial dispersal, and microbes change floral phenotypes in ways perceivable by pollinators. Yet, the role microbes play in the cognitive ecology of pollination is relatively unexplored. Reviewing recent literature on floral microbial ecology and pollinator behavior, we advocate for further integration between these two fields. Insights into pollinator learning, memory, and decision-making can help explain their responses to microbially-altered floral phenotypes. Specifically, considering how pollinators forage for multiple nutrients, cope with uncertainty, structure foraging bouts, and move through their environment could inform predictions about microbial dispersal within plant communities. We highlight how behavior connects microbial changes in floral phenotype to downstream effects on both microbial dispersal and plant fitness.}, }
@article {pmid33072042, year = {2020}, author = {Sabino, YNV and de Araújo, KC and de Assis, FGDV and Moreira, SM and Lopes, TDS and Mendes, TAO and Huws, SA and Mantovani, HC}, title = {In silico Screening Unveil the Great Potential of Ruminal Bacteria Synthesizing Lasso Peptides.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {576738}, doi = {10.3389/fmicb.2020.576738}, pmid = {33072042}, issn = {1664-302X}, abstract = {Studies of rumen microbial ecology suggest that the capacity to produce antimicrobial peptides could be a useful trait in species competing for ecological niches in the ruminal ecosystem. However, little is known about the synthesis of lasso peptides by ruminal microorganisms. Here we analyzed the distribution and diversity of lasso peptide gene clusters in 425 bacterial genomes from the rumen ecosystem. Genome mining was performed using antiSMASH 5, BAGEL4, and a database of well-known precursor sequences. The genomic context of the biosynthetic clusters was investigated to identify putative lasA genes and protein sequences from enzymes of the biosynthetic machinery were evaluated to identify conserved motifs. Metatranscriptome analysis evaluated the expression of the biosynthetic genes in the rumen microbiome. Several incomplete (n = 23) and complete (n = 11) putative lasso peptide clusters were detected in the genomes of ruminal bacteria. The complete gene clusters were exclusively found within the phylum Firmicutes, mainly (48%) in strains of the genus Butyrivibrio. The analysis of the genetic organization of complete putative lasso peptide clusters revealed the presence of co-occurring genes, including kinases (85%), transcriptional regulators (49%), and glycosyltransferases (36%). Moreover, a conserved pattern of cluster organization was detected between strains of the same genus/species. The maturation enzymes LasB, LasC, and LasD showed regions highly conserved, including the presence of a transglutaminase core in LasB, an asparagine synthetase domain in LasC, and an ABC-type transporter system in LasD. Phylogenetic trees of the essential biosynthetic proteins revealed that sequences split into monophyletic groups according to their shared single common ancestor. Metatranscriptome analyses indicated the expression of the lasso peptides biosynthetic genes within the active rumen microbiota. Overall, our in silico screening allowed the discovery of novel biosynthetic gene clusters in the genomes of ruminal bacteria and revealed several strains with the genetic potential to synthesize lasso peptides, suggesting that the ruminal microbiota represents a potential source of these promising peptides.}, }
@article {pmid33072023, year = {2020}, author = {Dias, T and Pimentel, V and Cogo, AJD and Costa, R and Bertolazi, AA and Miranda, C and de Souza, SB and Melo, J and Carolino, M and Varma, A and Eutrópio, F and Olivares, FL and Ramos, AC and Cruz, C}, title = {The Free-Living Stage Growth Conditions of the Endophytic Fungus Serendipita indica May Regulate Its Potential as Plant Growth Promoting Microbe.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {562238}, doi = {10.3389/fmicb.2020.562238}, pmid = {33072023}, issn = {1664-302X}, abstract = {Serendipita indica (former Piriformospora indica) is a non-obligate endophytic fungus and generally a plant growth and defence promoter with high potential to be used in agriculture. However, S. indica may switch from biotrophy to saprotrophy losing its plant growth promoting traits. Our aim was to understand if the free-living stage growth conditions (namely C availability) regulate S. indica's phenotype, and its potential as plant-growth-promoting-microbe (PGPM). We grew S. indica in its free-living stage under increasing C availabilities (2-20 g L-1 of glucose or sucrose). We first characterised the effect of C availability during free-living stage growth on fungal phenotype: colonies growth and physiology (plasma membrane proton pumps, stable isotopic signatures, and potential extracellular decomposing enzymes). The effect of the C availability during the free-living stage of the PGPM was evaluated on wheat. We observed that C availability during the free-living stage regulated S. indica's growth, ultrastructure and physiology, resulting in two distinct colony phenotypes: compact and explorer. The compact phenotype developed at low C, used peptone as the major C and N source, and displayed higher decomposing potential for C providing substrates; while the explorer phenotype developed at high C, used glucose and sucrose as major C sources and casein and yeast extract as major N sources, and displayed higher decomposing potential for N and P providing substrates. The C availability, or the C/N ratio, during the free-living stage left a legacy to the symbiosis stage, regulating S. indica's potential to promote plant growth: wheat growth promotion by the explorer phenotype was ± 40% higher than that by the compact phenotype. Our study highlights the importance of considering microbial ecology in designing PGPM/biofertilizers. Further studies are needed to test the phenotypes under more extreme conditions, and to understand if the in vitro acquired characteristics persist under field conditions.}, }
@article {pmid33072015, year = {2020}, author = {Zhu, C and Bass, D and Wang, Y and Shen, Z and Song, W and Yi, Z}, title = {Environmental Parameters and Substrate Type Drive Microeukaryotic Community Structure During Short-Term Experimental Colonization in Subtropical Eutrophic Freshwaters.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {555795}, doi = {10.3389/fmicb.2020.555795}, pmid = {33072015}, issn = {1664-302X}, abstract = {Microeukaryotes are key components of aquatic ecosystems and play crucial roles in aquatic food webs. However, influencing factors and potential assembly mechanisms for microeukaryotic community on biofilms are rarely studied. Here, those of microeukaryotic biofilms in subtropical eutrophic freshwaters were investigated for the first time based on 2,585 operational taxonomic units (OTUs) from 41 samples, across different environmental conditions and substrate types. Following conclusions were drawn: (1) Environmental parameters were more important than substrate types in structuring microeukaryotic community of biofilms in subtropical eutrophic freshwaters. (2) In the fluctuating river, there was a higher diversity of OTUs and less predictability of community composition than in the stable lake. Sessile species were more likely to be enriched on smooth surfaces of glass slides, while both free-swimming and attached organisms occurred within holes inside PFUs (polyurethane foam units). (3) Both species sorting and neutral process were mechanisms for assembly of microeukaryotic biofilms, but their importance varied depending on different habitats and substrates. (4) The effect of species sorting was slightly higher than the neutral process in river biofilms due to stronger environmental filtering. Species sorting was a stronger force structuring communities on glass slides than PFUs with more niche availability. Our study sheds light on assembly mechanisms for microeukaryotic community on different habitat and substrate types, showing that the resulting communities are determined by both sets of variables, in this case primarily habitat type. The balance of neutral process and species sorting differed between habitats, but the high alpha diversity of microeukaryotes in both led to similar sets of lifecycle traits being selected for in each case.}, }
@article {pmid33072010, year = {2020}, author = {Shang, Y and Wu, X and Wei, Q and Dou, H and Wang, X and Chen, J and Zhang, H and Ma, S and Zhang, H}, title = {Total Arsenic, pH, and Sulfate Are the Main Environmental Factors Affecting the Microbial Ecology of the Water and Sediments in Hulun Lake, China.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {548607}, doi = {10.3389/fmicb.2020.548607}, pmid = {33072010}, issn = {1664-302X}, abstract = {Bacteria have the metabolic potential to produce a diverse array of secondary metabolites, which have important roles in biogeochemical cycling processes. However, for Hulun Lake and the rivers that enter into it, the bacterial community structures and their effects have not previously been widely studied, limiting our ecological understanding of this habitat. To address this, we have analyzed the bacterial communities in the water ecosystem of the Hulun Lake Basin. 16S rRNA high-throughput sequencing identified 64 phyla, 165 classes, 218 orders, 386 families, and 740 genera of bacteria across all samples. The dominant phyla in the central area of the lake were Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria, while in all other areas, Proteobacteria, Actinobacteria, and Bacteroidetes were dominant. The microbial community structures were significantly affected by environmental factors [arsenic (As), pH, and sulfate (SO42-)] and their location in the lake. The species richness in the sediments of Hulun Lake was higher than in the water, and this ecosystem harbored the highest proportion of unclassified sequences, representing unclassified bacteria. This study provides basic data for future investigations into the Hulun lake ecosystem and for water microbial monitoring and protection measures.}, }
@article {pmid33072003, year = {2020}, author = {Brown, JM and Labonté, JM and Brown, J and Record, NR and Poulton, NJ and Sieracki, ME and Logares, R and Stepanauskas, R}, title = {Single Cell Genomics Reveals Viruses Consumed by Marine Protists.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {524828}, doi = {10.3389/fmicb.2020.524828}, pmid = {33072003}, issn = {1664-302X}, abstract = {The predominant model of the role of viruses in the marine trophic web is that of the &quot;viral shunt,&quot; where viral infection funnels a substantial fraction of the microbial primary and secondary production back to the pool of dissolved organic matter. Here, we analyzed the composition of non-eukaryotic DNA associated with individual cells of small, planktonic protists in the Gulf of Maine (GoM) and the Mediterranean Sea. We found viral DNA associated with a substantial fraction cells from the GoM (51%) and the Mediterranean Sea (35%). While Mediterranean SAGs contained a larger proportion of cells containing bacterial sequences (49%), a smaller fraction of cells contained bacterial sequences in the GoM (19%). In GoM cells, nearly identical bacteriophage and ssDNA virus sequences where found across diverse lineages of protists, suggesting many of these viruses are non-infective. The fraction of cells containing viral DNA varied among protistan lineages and reached 100% in Picozoa and Choanozoa. These two groups also contained significantly higher numbers of viral sequences than other identified taxa. We consider mechanisms that may explain the presence of viral DNA in protistan cells and conclude that protistan predation on free viral particles contributed to the observed patterns. These findings confirm prior experiments with protistan isolates and indicate that the viral shunt is complemented by a viral link in the marine microbial food web. This link may constitute a sink of viral particles in the ocean and has implications for the flow of carbon through the microbial food web.}, }
@article {pmid33070212, year = {2020}, author = {Xu, S and Jiang, L and Qiao, G and Chen, J}, title = {Diversity of bacterial symbionts associated with Myzus persicae (Sulzer) (Hemiptera: Aphididae: Aphidinae) revealed by 16S rRNA Illumina sequencing.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01622-6}, pmid = {33070212}, issn = {1432-184X}, support = {2016YFE0203100//National Key R &amp; D Program of China/ ; 31620103916//National Natural Science Foundation of China (CN)/ ; 31772492//National Natural Science Foundation of China/ ; XDA19050303//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2020087//Youth Innovation Promotion Association of Chinese Academy of Sciences/ ; }, abstract = {Aphids are known to be associated with a variety of symbiotic bacteria. To improve our knowledge of the bacterial diversity of polyphagous aphids, in the present study, we investigated the microbiota of the cosmopolitan agricultural pest Myzus persicae (Sulzer). Ninety-two aphid samples collected from different host plants in various regions of China were examined using high-throughput amplicon sequencing. We comprehensively characterized the symbiont diversity of M. persicae and assessed the variations in aphid-associated symbiont communities. We detected a higher diversity of symbionts than has been previously observed. M. persicae hosted the primary endosymbiont Buchnera aphidicola and seven secondary symbionts, among which Wolbachia was the most prevalent and Rickettsia, Arsenophonus, and Spiroplasma were reported for the first time. Ordination analyses and statistical tests revealed that the symbiont flora associated with M. persicae did not change with respect to host plant or geography, which may be due to frequent migrations between different aphid populations. These findings will advance our knowledge of the microbiota of polyphagous insects and will enrich our understanding of assembly of host-microbiome systems.}, }
@article {pmid33069997, year = {2020}, author = {Dai, H and Gao, J and Li, D and Wang, Z and Duan, W}, title = {Metagenomics combined with DNA-based stable isotope probing provide comprehensive insights of active triclosan-degrading bacteria in wastewater treatment.}, journal = {Journal of hazardous materials}, volume = {404}, number = {Pt B}, pages = {124192}, doi = {10.1016/j.jhazmat.2020.124192}, pmid = {33069997}, issn = {1873-3336}, abstract = {The biotransformation of triclosan (TCS) during wastewater treatment occurred frequently, while little researches are known the identity of microorganisms involved in the biodegradation process. In this work, DNA-based stable isotope probing (DNA-SIP) was occupied to investigate the TCS assimilation microbes originated from a full-scale cyclic activated sludge system in Beijing. Results of TCS removal pathway showed that the TCS removal in nitrification process was mainly contributed by the metabolism of heterotrophic bacteria, accounting for about 18.54%. DNA-SIP assay indicated that Sphingobium dominated the degradation of TCS. Oligotyping analysis further indicated that oligotype GCTAAT and ATGTTA of Sphingobium played important roles in degrading TCS. Furthermore, the Kyoto Encyclopedia of Genes and Genomes functional abundance statistics based on PICRUSt2 showed that glutathione transferase was the most prevalent enzyme involved in TCS metabolism, and TCS might be removed through microbial carbon metabolism. Metagenomics made clear that Sphingobium might play irrelevant role on the propagation of antibiotics resistance genes (ARGs), even though, it could degrade TCS. Thauera and Dechloromonas were identified as the key hosts of most ARGs. This study revealed the potential metabolic pathway and microbial ecology of TCS biodegradation in nitrification process of wastewater treatment system.}, }
@article {pmid33068395, year = {2020}, author = {Lebre, PH and Bottos, E and Makhalanyane, TP and Hogg, I and Cowan, DA}, title = {Islands in the sand: Are all hypolithic microbial communities the same?.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaa216}, pmid = {33068395}, issn = {1574-6941}, abstract = {Hypolithic microbial communities (hypolithons) are complex assemblages of phototrophic and heterotrophic organisms associated with the ventral surfaces of translucent minerals embedded in soil surfaces. Past studies on the assembly, structure and function of hypolithic communities have tended to use composite samples (i.e. bulked hypolithic biomass) with the underlying assumption that samples collected from within a 'homogeneous' locality are phylogenetically homogeneous. In this study, we question this assumption by analysing the prokaryote phylogenetic diversity of multiple individual hypolithons: i.e. asking the seemingly simple question of 'Are all hypolithons the same'? Using 16S rRNA gene-based phylogenetic analysis of hypolithons recovered for a localised moraine region in the Taylor Valley, McMurdo Dry Valleys, Antarctica, we demonstrate that these communities are heterogeneous at very small spatial scales (<5 m). Using null models of phylogenetic turnover, we showed that this heterogeneity between hypolithons is probably due to stochastic effects such as dispersal limitations, which is entirely consistent with the physically isolated nature of the hypolithic communities ('islands in the sand') and the almost complete absence of a liquid continuum as a mode of microbial transport between communities.}, }
@article {pmid33067657, year = {2020}, author = {Han, D and Richter-Heitmann, T and Kim, IN and Choy, E and Park, KT and Unno, T and Kim, J and Nam, SI}, title = {Survey of Bacterial Phylogenetic Diversity During the Glacier Melting Season in an Arctic Fjord.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01616-4}, pmid = {33067657}, issn = {1432-184X}, support = {NRF-2015M1A5A1037243//National Research Foundation of Korea/ ; NRF-2018R1D1A3B07041743//National Research Foundation of Korea/ ; NRF-2019R1I1A1A01058140//National Research Foundation of Korea/ ; }, abstract = {To understand bacterial biogeography in response to the hydrographic impact of climate change derived from the Arctic glacier melting, we surveyed bacterial diversity and community composition using bacterial 16S rRNA gene metabarcoding in the seawaters of Kongsfjorden, Svalbard, during summer 2016. In the present study, bacterial biogeography in the Kongsfjorden seawaters showed distinct habitat patterns according to water mass classification and habitat transition between Atlantic and fjord surface waters. Moreover, we estimated phylogenetic diversity of bacterial communities using the net relatedness, nearest taxon, and beta nearest taxon indices. We found the influence of freshwater input from glacier melting in shaping bacterial assemblage composition through the stochastic model. We further evaluated bacterial contributions to phytoplankton-derived dimethylsulfoniopropionate (DMSP) using a quantitative PCR (qPCR) measurement with demethylation (dmdA) and cleavage (dddP) genes of two fundamentally different processes. Our qPCR results imply that bacterial DMSP degradation follows the Atlantic inflow during summer in Kongsfjorden. These findings suggest that the Atlantic inflow and glacial melting influence bacterial community composition and assembly processes and thus affect the degradation of phytoplankton-derived organic matter in an Arctic fjord.}, }
@article {pmid33067588, year = {2020}, author = {Mueller, AJ and Jung, MY and Strachan, CR and Herbold, CW and Kirkegaard, RH and Wagner, M and Daims, H}, title = {Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-020-00809-6}, pmid = {33067588}, issn = {1751-7370}, support = {W1257//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; W1257//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 294343//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, abstract = {Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the most abundant, known NOB in the oceans. To date, only two closely affiliated Nitrospinae species have been isolated, which are only distantly related to the environmentally abundant uncultured Nitrospinae clades. Here, we applied live cell sorting, activity screening, and subcultivation on marine nitrite-oxidizing enrichments to obtain novel marine Nitrospinae. Two binary cultures were obtained, each containing one Nitrospinae strain and one alphaproteobacterial heterotroph. The Nitrospinae strains represent two new genera, and one strain is more closely related to environmentally abundant Nitrospinae than previously cultured NOB. With an apparent half-saturation constant of 8.7 ± 2.5 µM, this strain has the highest affinity for nitrite among characterized marine NOB, while the other strain (16.2 ± 1.6 µM) and Nitrospina gracilis (20.1 ± 2.1 µM) displayed slightly lower nitrite affinities. The new strains and N. gracilis share core metabolic pathways for nitrite oxidation and CO2 fixation but differ remarkably in their genomic repertoires of terminal oxidases, use of organic N sources, alternative energy metabolisms, osmotic stress and phage defense. The new strains, tentatively named &quot;Candidatus Nitrohelix vancouverensis&quot; and &quot;Candidatus Nitronauta litoralis&quot;, shed light on the niche differentiation and potential ecological roles of Nitrospinae.}, }
@article {pmid33067398, year = {2020}, author = {Shibl, AA and Isaac, A and Ochsenkühn, MA and Cárdenas, A and Fei, C and Behringer, G and Arnoux, M and Drou, N and Santos, MP and Gunsalus, KC and Voolstra, CR and Amin, SA}, title = {Diatom modulation of select bacteria through use of two unique secondary metabolites.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, pmid = {33067398}, issn = {1091-6490}, abstract = {Unicellular eukaryotic phytoplankton, such as diatoms, rely on microbial communities for survival despite lacking specialized compartments to house microbiomes (e.g., animal gut). Microbial communities have been widely shown to benefit from diatom excretions that accumulate within the microenvironment surrounding phytoplankton cells, known as the phycosphere. However, mechanisms that enable diatoms and other unicellular eukaryotes to nurture specific microbiomes by fostering beneficial bacteria and repelling harmful ones are mostly unknown. We hypothesized that diatom exudates may tune microbial communities and employed an integrated multiomics approach using the ubiquitous diatom Asterionellopsis glacialis to reveal how it modulates its naturally associated bacteria. We show that A. glacialis reprograms its transcriptional and metabolic profiles in response to bacteria to secrete a suite of central metabolites and two unusual secondary metabolites, rosmarinic acid and azelaic acid. While central metabolites are utilized by potential bacterial symbionts and opportunists alike, rosmarinic acid promotes attachment of beneficial bacteria to the diatom and simultaneously suppresses the attachment of opportunists. Similarly, azelaic acid enhances growth of beneficial bacteria while simultaneously inhibiting growth of opportunistic ones. We further show that the bacterial response to azelaic acid is numerically rare but globally distributed in the world's oceans and taxonomically restricted to a handful of bacterial genera. Our results demonstrate the innate ability of an important unicellular eukaryotic group to modulate select bacteria in their microbial consortia, similar to higher eukaryotes, using unique secondary metabolites that regulate bacterial growth and behavior inversely across different bacterial populations.}, }
@article {pmid33066774, year = {2020}, author = {Yan, H and Yu, B and Degroote, J and Spranghers, T and Van Noten, N and Majdeddin, M and Van Poucke, M and Peelman, L and De Vrieze, J and Boon, N and Gielen, I and Smet, S and Chen, D and Michiels, J}, title = {Antibiotic affects the gut microbiota composition and expression of genes related to lipid metabolism and myofiber types in skeletal muscle of piglets.}, journal = {BMC veterinary research}, volume = {16}, number = {1}, pages = {392}, doi = {10.1186/s12917-020-02592-0}, pmid = {33066774}, issn = {1746-6148}, support = {CARS-36//earmarked fund for the China Agriculture Research System/ ; 31672436//National Natural Science Foundation of China/ ; 31730091//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Early-life antibiotic administration is known to affect gut microbiota and host adiposity, but the effects of antibiotic exposure on skeletal muscle properties remain unknown. The present study evaluated the changes in skeletal muscle properties including myofiber characteristics and composition, as well as intramuscular fat (IMF) content in skeletal muscle of piglets when exposed to a tylosin-containing diet.<br><br>RESULTS: A total of 18 piglets (28 days of age) were randomly allocated into two groups: control basal diet (Control) and Control + 100 mg tylosin phosphate/kg of feed (Antibiotic). The trial lasted for 39 days. High-throughput amplicon sequencing revealed that no significant difference in initial gut microbiota composition was existed between Control and Antibiotic groups. Antibiotic administration increased body weight and growth rate and decreased feed to gain ratio of pigs (P < 0.05). The carcass lean and fat volumes of pigs were increased by the tylosin administration (P < 0.05). Antibiotic treatment increased myofiber density and the expression of genes related to type I and type IIb myofibers in longissimus muscle (P < 0.05). The IMF content in longissimus muscle was increased by antibiotic exposure (P < 0.05). Antibiotic administration increased expression of genes related to fatty acid uptake and de novo synthesis, and decreased expression of genes related to triglyceride hydrolysis (P < 0.05). Tylosin administration affected taxonomic distribution and beta diversity of the caecal and colonic microbiota of piglets.<br><br>CONCLUSION: These results confirm that the growth performance, myofiber composition and muscle lipid metabolism are affected by antibiotic administration, which may be associated with an altered gut microbiota, suggesting that the gut microbiota could be served as a potential target for modulating skeletal muscle properties of host.}, }
@article {pmid33066697, year = {2020}, author = {Amat, S and Lantz, H and Munyaka, PM and Willing, BP}, title = {Prevotella in Pigs: The Positive and Negative Associations with Production and Health.}, journal = {Microorganisms}, volume = {8}, number = {10}, pages = {}, doi = {10.3390/microorganisms8101584}, pmid = {33066697}, issn = {2076-2607}, abstract = {A diverse and dynamic microbial community (known as microbiota) resides within the pig gastrointestinal tract (GIT). The microbiota contributes to host health and performance by mediating nutrient metabolism, stimulating the immune system, and providing colonization resistance against pathogens. Manipulation of gut microbiota to enhance growth performance and disease resilience in pigs has recently become an active area of research in an era defined by increasing scrutiny of antimicrobial use in swine production. In order to develop microbiota-targeted strategies, or to identify potential next-generation probiotic strains originating from the endogenous members of GIT microbiota in pigs, it is necessary to understand the role of key commensal members in host health. Many, though not all, correlative studies have associated members of the genus Prevotella with positive outcomes in pig production, including growth performance and immune response; therefore, a comprehensive review of the genus in the context of pig production is needed. In the present review, we summarize the current state of knowledge about the genus Prevotella in the intestinal microbial community of pigs, including relevant information from other animal species that provide mechanistic insights, and identify gaps in knowledge that must be addressed before development of Prevotella species as next-generation probiotics can be supported.}, }
@article {pmid33065340, year = {2020}, author = {Jacquemyn, H and Pozo, MI and Álvarez-Pérez, S and Lievens, B and Fukami, T}, title = {Yeast-nectar interactions: metacommunities and effects on pollinators.}, journal = {Current opinion in insect science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cois.2020.09.014}, pmid = {33065340}, issn = {2214-5753}, abstract = {About 90% of all flowering plant species are pollinated by animals. Animals are attracted to flowers because they often provide food in the form of nectar and pollen. While floral nectar is assumed to be initially sterile, it commonly becomes colonized by yeasts after animals have visited the flowers. Although yeast communities in floral nectar appear simple, community assembly depends on a complex interaction between multiple factors. Yeast colonization has a significant effect on the scent of floral nectar, foraging behavior of insects and nectar consumption. Consumption of nectar colonized by yeasts has been shown to improve bee fitness, but effects largely depended on yeast species. Altogether, these results indicate that dispersal, colonization history and nectar chemistry strongly interact and have pronounced effects on yeast metacommunities and as result bee foraging behavior and fitness. Future research directions to better understand the dynamics of plant-microbe-pollinator interactions are discussed.}, }
@article {pmid33062716, year = {2020}, author = {Almugadam, BS and Liu, Y and Chen, SM and Wang, CH and Shao, CY and Ren, BW and Tang, L}, title = {Alterations of Gut Microbiota in Type 2 Diabetes Individuals and the Confounding Effect of Antidiabetic Agents.}, journal = {Journal of diabetes research}, volume = {2020}, number = {}, pages = {7253978}, doi = {10.1155/2020/7253978}, pmid = {33062716}, issn = {2314-6753}, abstract = {Type 2 diabetes is a leading cause of morbidity and a common risk of several disorders. Identifying the microbial ecology changes is essential for disease prediction, therapy, and prevention. Thus, our study is aimed at investigating the intestinal microbiota among healthy and type 2 diabetes individuals and exploring the effect of antidiabetic agents on gut bacterial flora. 24 type 2 diabetes (metformin, glimepiride, and nontherapeutic subgroups; N = 8) and 24 healthy control subjects were enrolled in this study, and intestinal bacterial microbiota was investigated by analyzing V3-V4 regions of 16S rRNA gene sequence. Numerous alterations were observed in the gut microbial community of diabetic individuals. These changes were characterized by a significant lowered abundance of Faecalibacterium, Fusobacterium, Dialister, and Elusimicrobium in the nontherapeutic subgroup compared to the healthy control group. Likewise, correlation analysis showed a substantial decline in gut microbiota richness and diversity with the duration of illness. Furthermore, antidiabetic agents restored to some extent the richness and diversity of gut microbiota and improved the abundance of many beneficial bacteria with a significant increase of Methanobrevibacter in the metformin subcategory compared to the nontherapeutic subgroup. In return, they decreased the abundance of some opportunistic pathogens. The findings of this study have added a novel understanding about the pathogenesis of the disease and the mechanisms underlying antidiabetic therapy, which are of potential interest for therapeutic lines and further studies.}, }
@article {pmid33059158, year = {2020}, author = {Chique, C and Hynds, P and Burke, LP and Morris, D and Ryan, MP and O'Dwyer, J}, title = {Contamination of domestic groundwater systems by verotoxigenic escherichia coli (VTEC), 2003-2019: A global scoping review.}, journal = {Water research}, volume = {188}, number = {}, pages = {116496}, doi = {10.1016/j.watres.2020.116496}, pmid = {33059158}, issn = {1879-2448}, abstract = {Verocytotoxin-producing E. coli (VTEC) are important agents of diarrhoeal disease in humans globally. As a noted waterborne disease, emphasis has been given to the study VTEC in surface waters, readily susceptible to microbial contamination. Conversely, the status of VTEC in potable groundwater sources, generally regarded as a &quot;safe&quot; drinking-water supply remains largely understudied. As such, this investigation presents the first scoping review seeking to determine the global prevalence of VTEC in groundwater supply sources intended for human consumption. Twenty-three peer-reviewed studies were identified and included for data extraction. Groundwater sample and supply detection rates (estimated 0.6 and 1.3%, respectively) indicate VTEC is infrequently present in domestic groundwater sources. However, where generic (fecal indicator) E. coli are present, the VTEC to E. coli ratio was found to be 9.9%, representing a latent health concern for groundwater consumers. Geographically, extracted data indicates higher VTEC detection rates in urban (5.4%) and peri‑urban (4.9%) environments than in rural areas (0.9%); however, this finding is confounded by the predominance of research studies in lower income regions. Climate trends indicate local environments classified as 'temperate' (14/554; 2.5%) and 'cold' (8/392; 2%) accounted for a majority of supply sources with VTEC present, with similar detection rates encountered among supplies sampled during periods typically characterized by 'high' precipitation (15/649; 2.3%). Proposed prevalence figures may find application in preventive risk-based catchment and groundwater quality management including development of Quantitative Microbial Risk Assessments (QMRA). Notwithstanding, to an extent, a large geographical disparity in available investigations, lack of standardized reporting, and bias in source selection, restrict the transferability of research findings. Overall, the mechanisms responsible for VTEC transport and ingress into groundwater supplies remain ambiguous, representing a critical knowledge gap, and denoting a distinctive lack of integration between hydrogeological and public health research. Key recommendations and guidelines are provided for prospective studies directed at increasingly integrative and multi-disciplinary research.}, }
@article {pmid33059136, year = {2020}, author = {Ávila, C and García-Galán, MJ and Borrego, CM and Rodríguez-Mozaz, S and García, J and Barceló, D}, title = {New insights on the combined removal of antibiotics and ARGs in urban wastewater through the use of two configurations of vertical subsurface flow constructed wetlands.}, journal = {The Science of the total environment}, volume = {755}, number = {Pt 2}, pages = {142554}, doi = {10.1016/j.scitotenv.2020.142554}, pmid = {33059136}, issn = {1879-1026}, abstract = {The occurrence and removal of 49 antibiotics and 11 selected antibiotic resistance genes (ARGs) were investigated in 2 vertical subsurface flow (VF) constructed wetlands (1.5 m2 each): an unsaturated (UVF) unit and a partially saturated (SVF) unit (0.35 m saturated out of 0.8 m) operating in parallel and treating urban wastewater. Thirteen antibiotics were detected in influent wastewater, 6 of which were present in all samples. The SVF showed statistical significance on the removal of 4 compounds (namely ciprofloxacin, ofloxacin, pipemidic acid and azithromycin), suggesting that the wider range of pH and/or redox conditions of this configuration might promote the microbial degradation of some antibiotics. In contrast, the concentration of the latter (except pipemidic acid) and also clindamycin was higher in the effluent than in the influent of the UVF. Five ARGs were detected in influent wastewater, sul1 and sul2, blaTEM, ermB and qnrS. All of them were detected also in the biofilm of both wetlands, except qnrS. Average removal rates of ARGs showed no statistical differences between both wetland units, and ranged between 46 and 97% for sul1, 33 and 97% for sul2, 9 and 99% for ermB, 18 and 97% for qnrS and 11 and 98% for blaTEM.}, }
@article {pmid33054775, year = {2020}, author = {Roussel, C and De Paepe, K and Galia, W and De Bodt, J and Chalancon, S and Leriche, F and Ballet, N and Denis, S and Alric, M and Van de Wiele, T and Blanquet-Diot, S}, title = {Spatial and temporal modulation of enterotoxigenic E. coli H10407 pathogenesis and interplay with microbiota in human gut models.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {141}, doi = {10.1186/s12915-020-00860-x}, pmid = {33054775}, issn = {1741-7007}, abstract = {BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) substantially contributes to the burden of diarrheal illnesses in developing countries. With the use of complementary in vitro models of the human digestive environment, TNO gastrointestinal model (TIM-1), and Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME), we provided the first detailed report on the spatial-temporal modulation of ETEC H10407 survival, virulence, and its interplay with gut microbiota. These systems integrate the main physicochemical parameters of the human upper digestion (TIM-1) and simulate the ileum vs ascending colon microbial communities and luminal vs mucosal microenvironments, captured from six fecal donors (M-SHIME).<br><br>RESULTS: A loss of ETEC viability was noticed upon gastric digestion, while a growth renewal was found at the end of jejunal and ileal digestion. The remarkable ETEC mucosal attachment helped to maintain luminal concentrations above 6 log10 mL-1 in the ileum and ascending colon up to 5 days post-infection. Seven ETEC virulence genes were monitored. Most of them were switched on in the stomach and switched off in the TIM-1 ileal effluents and in a late post-infectious stage in the M-SHIME ascending colon. No heat-labile enterotoxin production was measured in the stomach in contrast to the ileum and ascending colon. Using 16S rRNA gene-based amplicon sequencing, ETEC infection modulated the microbial community structure of the ileum mucus and ascending colon lumen.<br><br>CONCLUSIONS: This study provides a better understanding of the interplay between ETEC and gastrointestinal cues and may serve to complete knowledge on ETEC pathogenesis and inspire novel prophylactic strategies for diarrheal diseases.}, }
@article {pmid33054212, year = {2020}, author = {Li, Y and Wang, T and Camps-Arbestain, M and Suárez-Abelenda, M and Whitby, CP}, title = {Lime and/or Phosphate Application Affects the Stability of Soil Organic Carbon: Evidence from Changes in Quantity and Chemistry of the Soil Water-Extractable Organic Matter.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.0c01341}, pmid = {33054212}, issn = {1520-5851}, abstract = {The mechanisms by which lime and/or phosphate addition impacts the preservation of soil organic matter (OM) are poorly understood. We explored the changes in quantity and chemistry of water-extractable organic matter (WEOM) in the bulk soil and its heavy density fraction (>1.6 g/cm3) of an unmanaged C-rich volcanic soil caused by lime and/or phosphate application. The addition of lime or phosphate caused (i) a significant increase in the WEOM, along with a decrease in its C/N ratio and an increase in its aromaticity, and (ii) changes in the WEOM chemical composition, measured with pyrolysis-gas chromatography/mass spectrometry, this being most impacted by lime application. The combined effect of lime and phosphate addition on the quantity and chemistry of WEOM was larger than the effects of separate lime and phosphate additions. By comparing the response of the bulk soil and the heavy fraction, we infer that phosphate has a greater contribution to the destabilization of vulnerable particulate OM, while lime causes a comparable disruption in the particulate OM and that in the heavy fraction. These findings provide a mechanistic insight into the decreased OM stability after liming and/or P fertilizing Andosols. They have implications for designing climate-smart management practices for these soils.}, }
@article {pmid33051738, year = {2020}, author = {Zhang, W and Wang, X and Li, Y and Liu, Z and Li, D and Wen, X and Feng, Y and Zhang, X}, title = {Pinewood Nematode Alters the Endophytic and Rhizospheric Microbial Communities of Pinus massoniana.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01619-1}, pmid = {33051738}, issn = {1432-184X}, support = {2018YFC1200400//National Key R &amp; D Program of China/ ; 31901315//Young Scientists Fund/ ; }, abstract = {Pinewood nematode, Bursaphelenchus xylophilus, is one of the greatest threats to pine trees and is spreading all over the world. During the nematode's pathogenesis, plant microorganisms play important roles. However, many microbial communities, such as that in Pinus massoniana, a major host of B. xylophilus that is widely distributed in China, are not well studied, especially the fungal communities. Here, the endophytic and rhizospheric bacterial and fungal communities associated with healthy and B. xylophilus-infected P. massoniana were analyzed. The results showed that 7639 bacterial and 3108 fungal OTUs were annotated from samples of P. massoniana, the rhizosphere, and B. xylophilus. There were significant diversity differences of endophytic microbes between healthy and infected P. massoniana. The abundances of endophytic bacteria Paenibacillus, unidentified_Burkholderiaceae, Serratia, Erwinia, and Pseudoxanthomonas and fungi Penicillifer, Zygoascus, Kirschsteiniothelia, Cyberlindnera, and Sporothrix in infected pines were greater than those in healthy pines, suggesting an association of particular microbial abundances with the pathogenesis of B. xylophilus in pines. Meanwhile, the abundances of microbes of unidentified_Burkholderiaceae, Saitozyma, and Pestalotiopsis were greater and Acidothermus and Trichoderma were lower in the rhizosphere under infected pines than those under healthy pines and the differences might be caused by B. xylophilus-induced weakening of the health of pines. Our study explored the endophytic and rhizospheric microbial community changes potentially caused by B. xylophilus infection of pines.}, }
@article {pmid33049639, year = {2020}, author = {Ni, N and Li, X and Yao, S and Shi, R and Kong, D and Bian, Y and Jiang, X and Song, Y}, title = {Biochar applications combined with paddy-upland rotation cropping systems benefit the safe use of PAH-contaminated soils: From risk assessment to microbial ecology.}, journal = {Journal of hazardous materials}, volume = {404}, number = {Pt A}, pages = {124123}, doi = {10.1016/j.jhazmat.2020.124123}, pmid = {33049639}, issn = {1873-3336}, abstract = {This study aimed to establish a method allowing the safe use of polycyclic aromatic hydrocarbon (PAH)-contaminated soils through the combination of biochar applications and different cropping systems. The impact of biochar applications under different cropping systems on the human health risks of PAHs and soil microbiology was elucidated. The residual PAHs were the lowest in rhizosphere soils amended with 2% corn straw-derived biochar pyrolyzed at 300 °C (CB300) under the paddy-upland rotation cropping (PURC) system. Human health risks resulting from the ingestion of PAH-contaminated carrot roots / rice grains under the PURC system were significantly lower than those under continuous upland cropping systems. The greatest diversity, richness and network complexity of soil microbial communities occurred under the PURC system combined with the 2% CB300 treatment. Soil microbial functions associated with soil health and PAH biodegradation were enhanced under this strategy, while the pathogen group was inhibited. Primarily owing to its high sorption capacity, bamboo-derived biochar pyrolyzed at 700 °C realized in the reduction of PAHs, but weakly influenced shifts in soil microbial communities. Overall, the combination of PURC systems and low-temperature-pyrolyzed nutrient-rich biochar could efficiently reduce the human health risks of PAHs and improve soil microbial ecology in agricultural fields.}, }
@article {pmid33047413, year = {2020}, author = {Dini-Andreote, F and Kowalchuk, GA and Prosser, JI and Raaijmakers, JM}, title = {Towards meaningful scales in ecosystem microbiome research.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15276}, pmid = {33047413}, issn = {1462-2920}, abstract = {Studies of microbial communities in natural ecosystems have been generally focused on mapping patterns of species and gene distributions. Although highly instrumental in expanding our understanding of microbial diversity and distribution patterns, such census studies often lack a meaningful and explicit definition of scale. Here, we discuss the importance of scale in environmental microbiology assessments and consider how patterning ecology can be redirected towards advancing concept and theory formation in ecosystem microbiome research. This article is protected by copyright. All rights reserved.}, }
@article {pmid33043868, year = {2020}, author = {Seto, M and Iwasa, Y}, title = {Microbial material cycling, energetic constraints and ecosystem expansion in subsurface ecosystems.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1931}, pages = {20200610}, doi = {10.1098/rspb.2020.0610}, pmid = {33043868}, issn = {1471-2954}, abstract = {To harvest energy from chemical reactions, microbes engage in diverse catabolic interactions that drive material cycles in the environment. Here, we consider a simple mathematical model for cycling reactions between alternative forms of an element (A and Ae), where reaction 1 converts A to Ae and reaction 2 converts Ae to A. There are two types of microbes: type 1 microbes harness reaction 1, and type 2 microbes harness reaction 2. Each type receives its own catabolic resources from the other type and provides the other type with the by-products as the catabolic resources. Analyses of the model show that each type increases its steady-state abundance in the presence of the other type. The flux of material flow becomes faster in the presence of microbes. By coupling two catabolic reactions, types 1 and 2 can also expand their realized niches through the abundant resource premium, the effect of relative quantities of products and reactants on the available chemical energy, which is especially important for microbes under strong energetic limitations. The plausibility of mutually beneficial interactions is controlled by the available chemical energy (Gibbs energy) of the system. We conclude that mutualistic catabolic interactions can be an important factor that enables microbes in subsurface ecosystems to increase ecosystem productivity and expand the ecosystem.}, }
@article {pmid33042180, year = {2020}, author = {Otlewska, A and Migliore, M and Dybka-Stępień, K and Manfredini, A and Struszczyk-Świta, K and Napoli, R and Białkowska, A and Canfora, L and Pinzari, F}, title = {When Salt Meddles Between Plant, Soil, and Microorganisms.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {553087}, pmid = {33042180}, issn = {1664-462X}, abstract = {In extreme environments, the relationships between species are often exclusive and based on complex mechanisms. This review aims to give an overview of the microbial ecology of saline soils, but in particular of what is known about the interaction between plants and their soil microbiome, and the mechanisms linked to higher resistance of some plants to harsh saline soil conditions. Agricultural soils affected by salinity is a matter of concern in many countries. Soil salinization is caused by readily soluble salts containing anions like chloride, sulphate and nitrate, as well as sodium and potassium cations. Salinity harms plants because it affects their photosynthesis, respiration, distribution of assimilates and causes wilting, drying, and death of entire organs. Despite these life-unfavorable conditions, saline soils are unique ecological niches inhabited by extremophilic microorganisms that have specific adaptation strategies. Important traits related to the resistance to salinity are also associated with the rhizosphere-microbiota and the endophytic compartments of plants. For some years now, there have been studies dedicated to the isolation and characterization of species of plants' endophytes living in extreme environments. The metabolic and biotechnological potential of some of these microorganisms is promising. However, the selection of microorganisms capable of living in association with host plants and promoting their survival under stressful conditions is only just beginning. Understanding the mechanisms of these processes and the specificity of such interactions will allow us to focus our efforts on species that can potentially be used as beneficial bioinoculants for crops.}, }
@article {pmid33040164, year = {2020}, author = {Wisnoski, NI and Lennon, JT}, title = {Microbial community assembly in a multi-layer dendritic metacommunity.}, journal = {Oecologia}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00442-020-04767-w}, pmid = {33040164}, issn = {1432-1939}, support = {DEB-1442246//National Science Foundation (US)/ ; W911NF-14-1-0411//Army Research Office/ ; }, abstract = {A major goal of metacommunity ecology is to infer the local- and regional-scale processes that underlie community assembly. In dendritic ecological networks, branching patterns and directional flow can alter the balance between local and regional factors during assembly. Vertical habitat structure may further affect community assembly in dendritic metacommunities. In this study, we analyzed the bacterial metacommunity of a fifth-order mountain stream network to assess differences in community assembly (1) between planktonic and benthic habitats, (2) across spatial scales, and (3) between headwater and downstream regions of the network. Using taxonomic and phylogenetic null modeling, we found habitat-specific spatial patterns of community assembly across the dendritic network. Compositional differences between planktonic and benthic communities were maintained by variable selection, but we also found evidence of local dispersal limitation between the two habitats. Planktonic community assembly was scale dependent, transitioning from homogeneous selection at local scales to variable selection at regional scales, while benthic community assembly was less scale dependent. Variable selection structured headwaters in both habitat types, but downstream communities were primarily structured by homogeneous selection, especially in sediments. Taken together, our results show that vertical habitat structure contributes to the scale-dependent processes of community assembly across the dendritic metacommunity.}, }
@article {pmid33039899, year = {2020}, author = {Douterelo, I and Dutilh, BE and Calero, C and Rosales, E and Martin, K and Husband, S}, title = {Impact of phosphate dosing on the microbial ecology of drinking water distribution systems: Fieldwork studies in chlorinated networks.}, journal = {Water research}, volume = {187}, number = {}, pages = {116416}, doi = {10.1016/j.watres.2020.116416}, pmid = {33039899}, issn = {1879-2448}, abstract = {Phosphate is routinely dosed to ensure regulatory compliance for lead in drinking water distribution systems. Little is known about the impact of the phosphate dose on the microbial ecology in these systems and in particular the endemic biofilms. Disturbance of the biofilms and embedded material in distribution can cause regulatory failures for turbidity and metals. To investigate the impact of phosphate on developing biofilms, pipe wall material from four independent pipe sections was mobilised and collected using two twin-flushing operations a year apart in a chlorinated UK network pre- and post-phosphate dosing. Intensive monitoring was undertaken, including turbidity and water physico-chemistry, traditional microbial culture-based indicators, and microbial community structure via sequencing the 16S rRNA gene for bacteria and the ITS2 gene for fungi. Whole metagenome sequencing was used to study shifts in functional characteristics following the addition of phosphate. As an operational consequence, turbidity responses from the phosphate-enriched water were increased, particularly from cast iron pipes. Differences in the taxonomic composition of both bacteria and fungi were also observed, emphasising a community shift towards microorganisms able to use or metabolise phosphate. Phosphate increased the relative abundance of bacteria such as Pseudomonas, Paenibacillus, Massilia, Acinetobacter and the fungi Cadophora, Rhizophagus and Eupenicillium. Whole metagenome sequencing showed with phosphate a favouring of sequences related to Gram-negative bacterium type cell wall function, virions and thylakoids, but a reduction in the number of sequences associated to vitamin binding, methanogenesis and toxin biosynthesis. With current faecal indicator tests only providing risk detection in bulk water samples, this work improves understanding of how network changes effect microbial ecology and highlights the potential for new approaches to inform future monitoring or control strategies to protect drinking water quality.}, }
@article {pmid33039841, year = {2020}, author = {Alloul, A and Muys, M and Hertoghs, N and Kerckhof, FM and Vlaeminck, SE}, title = {Cocultivating aerobic heterotrophs and purple bacteria for microbial protein in sequential photo- and chemotrophic reactors.}, journal = {Bioresource technology}, volume = {319}, number = {}, pages = {124192}, doi = {10.1016/j.biortech.2020.124192}, pmid = {33039841}, issn = {1873-2976}, abstract = {Aerobic heterotrophic bacteria (AHB) and purple non-sulfur bacteria (PNSB) are typically explored as two separate types of microbial protein, yet their properties as respectively a bulk and added-value feed ingredient make them appealing for combined use. The feasibility of cocultivation in a sequential photo- and chemotrophic approach was investigated. First, mapping the chemotrophic growth kinetics for four Rhodobacter, Rhodopseudomonas and Rhodospirillum species on different carbon sources showed a preference for fructose (µmax 2.4-3.9 d-1 28 °C; protein 36-59%DW). Secondly, a continuous photobioreactor inoculated with Rhodobacter capsulatus (VFA as C-source) delivered the starter culture for an aerobic batch reactor (fructose as C-source). This two-stage system showed an improved nutritional quality compared to AHB production: higher protein content (45-71%DW), more attractive amino/fatty acid profile and contained up to 10% PNSB. The findings strengthen protein production with cocultures and might enable the implementation of the technology for resource recovery on streams such as wastewater.}, }
@article {pmid33037304, year = {2020}, author = {De Rudder, C and Garcia-Tímermans, C and De Boeck, I and Lebeer, S and Van de Wiele, T and Calatayud Arroyo, M}, title = {Lacticaseibacillus casei AMBR2 modulates the epithelial barrier function and immune response in a donor-derived nasal microbiota manner.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {16939}, doi = {10.1038/s41598-020-73857-9}, pmid = {33037304}, issn = {2045-2322}, support = {SBO 150052//Fonds Wetenschappelijk Onderzoek/ ; G020119N//Fonds Wetenschappelijk Onderzoek/ ; SBO 150052//Fonds Wetenschappelijk Onderzoek/ ; SBO 150052//Fonds Wetenschappelijk Onderzoek/ ; 118499/12R2717N LV//Fonds Wetenschappelijk Onderzoek/ ; }, abstract = {Live biotherapeutic products (LBP) are emerging as alternative treatment strategies for chronic rhinosinusitis. The selection of interesting candidate LBPs often involves model systems that do not include the polymicrobial background (i.e. the host microbiota) in which they will be introduced. Here, we performed a screening in a simplified model system of upper respiratory epithelium to assess the effect of nasal microbiota composition on the ability to attach and grow of a potential LBP, Lacticaseibacillus casei AMBR2, in this polymicrobial background. After selecting the most permissive and least permissive donor, L. casei AMBR2 colonisation in their respective polymicrobial backgrounds was assessed in more physiologically relevant model systems. We examined cytotoxicity, epithelial barrier function, and cytokine secretion, as well as bacterial cell density and phenotypic diversity in differentiated airway epithelium based models, with or without macrophage-like cells. L. casei AMBR2 could colonize in the presence of both selected donor microbiota and increased epithelial barrier resistance in presence of donor-derived nasal bacteria, as well as anti-inflammatory cytokine secretion in the presence of macrophage-like cells. This study highlights the potential of L. casei AMBR2 as LBP and the necessity to employ physiologically relevant model systems to investigate host-microbe interaction in LBP research.}, }
@article {pmid33033618, year = {2020}, author = {Medina, WRM and Eramo, A and Tu, M and Fahrenfeld, NL}, title = {Sewer biofilm microbiome and antibiotic resistance genes as function of pipe material, source of microbes, and disinfection: field and laboratory studies.}, journal = {Environmental science : water research &amp; technology}, volume = {6}, number = {8}, pages = {2122-2137}, pmid = {33033618}, issn = {2053-1400}, support = {R25 GM058389/GM/NIGMS NIH HHS/United States ; }, abstract = {Wastewater systems are recognized pathways for the spread of antibiotic resistant bacteria, but relatively little is known about the microbial ecology of the sewer environment. Sewer biofilm colonization by antibiotic resistance gene (ARG) carrying bacteria may impact interpretations of sewage epidemiology data, water quality during sewer overflows, and hazard to utility workers. The objectives of this research were to evaluate the (1) microbiome of real and simulated sewer biofilms and their potential to accumulate ARGs and (2) susceptibility of simulated sewer biofilms to bleach disinfection. First, biofilm samples were collected from sewer municipal systems. Next, an annular biofilm reactor was used to simulate the sewer environment while controlling the pipe material (concrete vs. PVC). The reactor was operated either as fed semi-batch with sewer sediment and synthetic wastewater (Sed-SB) or fed with a continuous flow of raw sewage (WW-CF). The abundance of ARGs, human fecal marker HF183, and 16S rRNA gene copies in these biofilm samples was measured with qPCR. Amplicon sequencing was performed to compare the prokaryotic diversity between samples. Finally, the susceptibility of reactor biofilm to a 4.6% bleach disnfection protocol was evaluated using viability qPCR and amplicon sequencing. Field and WW-CF biofilms contained the most ARG copies and the microbial community compositions varied between the different biofilm samples (field, Sed-SB, and WW-CF). Pipe material did not affect the abundance of ARGs in the reactor samples. However, log removal following bleach treatment suggested that the biofilm grown on PVC surface was primarily dislodged from the surface by the bleach treatment whereas more bacteria were lysed within the biofilm that remained on the concrete surface. Viable bacteria carrying ARGs were observed following 10 minutes of treatment. This study showed that sewer biofilms can accumulate bacteria carrying ARGs and that while bleach can reduce sewer biofilm density, the protocol tested here will not completely remove the biofilms.}, }
@article {pmid33033140, year = {2020}, author = {Peruzzo, A and Salerno, B and Tiengo, A and Petrin, S and Barco, L and Losasso, C and Orsini, M}, title = {Genome Sequence of a Persistent Campylobacter jejuni Strain, 2016-IZSVE-19-111250.}, journal = {Microbiology resource announcements}, volume = {9}, number = {41}, pages = {}, pmid = {33033140}, issn = {2576-098X}, abstract = {In this report, we present the whole-genome sequence of a Campylobacter jejuni strain isolated recursively for the last 3 years from an Italian poultry farm.}, }
@article {pmid33032584, year = {2020}, author = {Zhu, L and Xu, F and Wan, W and Yu, B and Tang, L and Yang, Y and Du, Y and Chen, Z and Xu, H}, title = {Correction to: Gut microbial characteristics of adult patients with allergy rhinitis.}, journal = {Microbial cell factories}, volume = {19}, number = {1}, pages = {192}, pmid = {33032584}, issn = {1475-2859}, abstract = {An amendment to this paper has been published and can be accessed via the original article.}, }
@article {pmid33032128, year = {2020}, author = {Zhang, S and Xia, X and Ke, Y and Song, S and Shen, Z and Cheung, S and Liu, H}, title = {Population dynamics and interactions of Noctiluca scintillans and Mesodinium rubrum during their successive blooms in a subtropical coastal water.}, journal = {The Science of the total environment}, volume = {755}, number = {Pt 1}, pages = {142349}, doi = {10.1016/j.scitotenv.2020.142349}, pmid = {33032128}, issn = {1879-1026}, abstract = {A time series field survey were conducted in Port Shelter, a subtropical coastal water in NW Pacific, beginning before the onset of a chain of Noctiluca scintillans and/or Mesodinium rubrum blooms, and ending after the blooms had declined. At the first mixed bloom stage, seed of N. scintillans and the consequent outbreak of both N. scintillans and M. rubrum were largely due to the physical forcing. Plenty food supply and their different feeding habits supported N. scintillans and M. rubrum to bloom massively and concomitantly. Following that, there was a small N. scintillans bloom followed by a small crest of M. rubrum. Their initiation and scale were mainly affected by limited food supply and/or the inferior food source. Sudden change of wind from mild northeast wind to strong southeast wind might contribute to the termination of N. scintillans bloom. Finally, physical accumulation was the most important driving factors of the formation and dispersal of the third and largest bloom of N. scintillans. Formation of these bloom events may involve vertical migration and/or the concentrating mechanism of M. rubrum and N. scintillans. Meanwhile, biotic interactions such as mutual supportive relationship between N. scintillans and M. rubrum, and O. hongkongense fed on the progametes of N. scintillans, as well as other abiotic factors like seawater temperature and rainfall, also play important roles in this series of bloom events. Our findings have important implications for coastal zones worldwide, which are affected recurrently by these two ubiquitous red tide-forming species.}, }
@article {pmid33031481, year = {2020}, author = {Klaps, J and de Vega, C and Herrera, CM and Junker, RR and Lievens, B and Álvarez-Pérez, S}, title = {Candida metrosideri pro tempore sp. nov. and Candida ohialehuae pro tempore sp. nov., two antifungal-resistant yeasts associated with Metrosideros polymorpha flowers in Hawaii.}, journal = {PloS one}, volume = {15}, number = {10}, pages = {e0240093}, doi = {10.1371/journal.pone.0240093}, pmid = {33031481}, issn = {1932-6203}, abstract = {Flowers produce an array of nutrient-rich exudates in which microbes can thrive, making them hotspots for microbial abundance and diversity. During a diversity study of yeasts inhabiting the flowers of Metrosideros polymorpha (Myrtaceae) in the Hawai'i Volcanoes National Park (HI, USA), five isolates were found to represent two novel species. Morphological and physiological characterization, and sequence analysis of the small subunit ribosomal RNA (rRNA) genes, the D1/D2 domains of the large subunit rRNA genes, the internal transcribed spacer (ITS) regions, and the genes encoding the largest and second largest subunits of the RNA polymerase II (RPB1 and RPB2, respectively), classified both species in the family Metschnikowiaceae, and we propose the names Candida metrosideri pro tempore sp. nov. (JK22T = CBS 16091 = MUCL 57821) and Candida ohialehuae pro tempore sp. nov. (JK58.2T = CBS 16092 = MUCL 57822) for such new taxa. Both novel Candida species form a well-supported subclade in the Metschnikowiaceae containing species associated with insects, flowers, and a few species of clinical importance. The ascosporic state of the novel species was not observed. The two novel yeast species showed elevated minimum inhibitory concentrations to the antifungal drug amphotericin B (>4 μg/mL). The ecology and phylogenetic relationships of C. metrosideri and C. ohialehuae are also discussed.}, }
@article {pmid33027736, year = {2020}, author = {Dettling, A and Wedel, C and Huptas, C and Hinrichs, J and Scherer, S and Wenning, M}, title = {High counts of thermophilic spore formers in dairy powders originate from persisting strains in processing lines.}, journal = {International journal of food microbiology}, volume = {335}, number = {}, pages = {108888}, doi = {10.1016/j.ijfoodmicro.2020.108888}, pmid = {33027736}, issn = {1879-3460}, abstract = {During the last decades, thermophilic spore counts became a very important quality parameter for manufacturers with regard to powdered dairy products. Low-spore count powders are highly demanded but challenging to produce when high production volume and long process times are intended. In this study a detailed monitoring of microbial levels in three skim milk powder plants was conducted. Anoxybacillus flavithermus was found to be primarily responsible for increased spore levels with increasing spore numbers being detected after 6-8 h already during initial processing steps. Simultaneously, the species composition shifted from a diverse bulk tank milk microbiota where different Bacillus species represented around 90% of the thermophilic bacteria to a dominance of A. flavithermus in the end product. The analysis of A. flavithermus isolates from different powder batches with RAPD PCR revealed recurring patterns in each of the eight German manufacturers sampled over several months. The high relatedness of isolates exhibiting identical RAPD patterns was exemplified by cgMLST based on whole genome sequences. We assume that A. flavithermus strains persisted in production plants and were not eliminated by cleaning. It is concluded that such persisting strains recurrently recontaminated subsequent powder productions. The data highlight that a targeted optimization of cleaning and disinfection procedures is the most promising measure to effectively reduce thermophilic spore counts in German dairy powders.}, }
@article {pmid33026073, year = {2020}, author = {Thomas, S and Lucie, EM and Adeline, S and Pascale, M and Christophe, C and Tom, VW and Stéphanie, BD}, title = {Tripartite relationship between gut microbiota, intestinal mucus and dietary fibers: towards preventive strategies against enteric infections.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuaa052}, pmid = {33026073}, issn = {1574-6976}, abstract = {The human gut is inhabited by a large variety of microorganims involved in many physiological processes and collectively refered as to gut microbiota. Disrupted microbiome has been associated with negative health outcomes and especially could promote the onset of enteric infections. To sustain their growth and persistence within the human digestive tract, gut microbes and enteric pathogens rely on two main polysaccharide compartments, namely dietary fibers and mucus carbohydrates. Several evidences suggest that the three-way relationship between gut microbiota, dietary fibers and mucus layer could unravel the capacity of enteric pathogens to colonize the human digestive tract and ultimately lead to infection. The review starts by shedding light on similarities and differences between dietary fibers and mucus carbohydrates structures and functions. Next, we provide an overview of the interactions of these two components with the third partner, namely the gut microbiota, under health and diseased situations. The review will then provide insights into the relevance of using dietary fibers interventions to prevent enteric infections with a focus on gut microbial imbalance and impaired-mucus integrity. Facing the numerous challenges in studying microbiota-pathogen-dietary fiber-mucus interactions, we lastly describe the characteristics and potentialities of currently available in vitro models of the human gut.}, }
@article {pmid33025063, year = {2020}, author = {Gomard, Y and Flores, O and Vittecoq, M and Blanchon, T and Toty, C and Duron, O and Mavingui, P and Tortosa, P and McCoy, KD}, title = {Changes in Bacterial Diversity, Composition and Interactions During the Development of the Seabird Tick Ornithodoros maritimus (Argasidae).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01611-9}, pmid = {33025063}, issn = {1432-184X}, support = {ESPEVEC (ANR blanc ANR-13-BSV7-0018-01)//Agence Nationale de la Recherche/ ; DISTIC//Labex CeMEB (Centre Méditerranéen de l'Environnement et de la Biodiversité)/ ; }, abstract = {Characterising within-host microbial interactions is essential to understand the drivers that shape these interactions and their consequences for host ecology and evolution. Here, we examined the bacterial microbiota hosted by the seabird soft tick Ornithodoros maritimus (Argasidae) in order to uncover bacterial interactions within ticks and how these interactions change over tick development. Bacterial communities were characterised through next-generation sequencing of the V3-V4 hypervariable region of the bacterial 16S ribosomal RNA gene. Bacterial co-occurrence and co-exclusion were determined by analysing networks generated from the metagenomic data obtained at each life stage. Overall, the microbiota of O. maritimus was dominated by four bacterial genera, namely Coxiella, Rickettsia, Brevibacterium and Arsenophonus, representing almost 60% of the reads. Bacterial diversity increased over tick development, and adult male ticks showed higher diversity than did adult female ticks. Bacterial networks showed that co-occurrence was more frequent than co-exclusion and highlighted substantial shifts across tick life stages; interaction networks changed from one stage to the next with a steady increase in the number of interactions through development. Although many bacterial interactions appeared unstable across life stages, some were maintained throughout development and were found in both sexes, such as Coxiella and Arsenophonus. Our data support the existence of a few stable interactions in O. maritimus ticks, on top of which bacterial taxa accumulate from hosts and/or the environment during development. We propose that stable associations delineate core microbial interactions, which are likely to be responsible for key biological functions.}, }
@article {pmid33025062, year = {2020}, author = {Baeza, N and Mercade, E}, title = {Relationship Between Membrane Vesicles, Extracellular ATP and Biofilm Formation in Antarctic Gram-Negative Bacteria.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01614-6}, pmid = {33025062}, issn = {1432-184X}, support = {CTQ2014-59632-R//Ministerio de Ciencia, Innovación y Universidades/ ; BES-2015-074582//Ministerio de Ciencia, Innovación y Universidades/ ; 2014SGR1017//Departament d'Innovació, Universitats i Empresa, Generalitat de Catalunya/ ; }, abstract = {Biofilms offer a safe environment that favors bacterial survival; for this reason, most pathogenic and environmental bacteria live integrated in biofilm communities. The development of biofilms is complex and involves many factors, which need to be studied in order to understand bacterial behavior and control biofilm formation when necessary. We used a collection of cold-adapted Antarctic Gram-negative bacteria to study whether their ability to form biofilms is associated with a capacity to produce membrane vesicles and secrete extracellular ATP. In most of the studied strains, no correlation was found between biofilm formation and these two factors. Only Shewanella vesiculosa M7T secreted high levels of extracellular ATP, and its membrane vesicles caused a significant increase in the speed and amount of biofilm formation. In this strain, an important portion of the exogenous ATP was contained in membrane vesicles, where it was protected from apyrase treatment. These results confirm that ATP influences biofilm formation. Although the role of extracellular ATP in prokaryotes is still not well understood, the metabolic cost of its production suggests it has an important function, such as a role in biofilm formation. Thus, the liberation of extracellular ATP through membrane vesicles and its function deserve further study.}, }
@article {pmid33025061, year = {2020}, author = {Boraks, A and Plunkett, GM and Doro, TM and Alo, F and Sam, C and Tuiwawa, M and Ticktin, T and Amend, AS}, title = {Scale-Dependent Influences of Distance and Vegetation on the Composition of Aboveground and Belowground Tropical Fungal Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01608-4}, pmid = {33025061}, issn = {1432-184X}, support = {1555793//National Science Foundation (US)/ ; 1555657//National Science Foundation/ ; }, abstract = {Fungi provide essential ecosystem services and engage in a variety of symbiotic relationships with trees. In this study, we investigate the spatial relationship of trees and fungi at a community level. We characterized the spatial dynamics for above- and belowground fungi using a series of forest monitoring plots, at nested spatial scales, located in the tropical South Pacific, in Vanuatu. Fungal communities from different habitats were sampled using metagenomic analysis of the nuclear ribosomal ITS1 region. Fungal communities exhibited strong distance-decay of similarity across our entire sampling range (3-110,000 m) and also at small spatial scales (< 50 m). Unexpectedly, this pattern was inverted at an intermediate scale (3.7-26 km). At large scales (80-110 km), belowground and aboveground fungal communities responded inversely to increasing geographic distance. Aboveground fungal community turnover (beta diversity) was best explained, at all scales, by geographic distance. In contrast, belowground fungal community turnover was best explained by geographic distance at small scales and tree community composition at large scales. Fungal communities from various habitats respond differently to the influences of habitat and geographic distance. At large geographic distances (80-110 km), community turnover for aboveground fungi is better explained by spatial distance, whereas community turnover for belowground fungi is better explained by plant community turnover. Future syntheses of spatial dynamics among fungal communities must explicitly consider geographic scale to appropriately contextualize community turnover.}, }
@article {pmid33025060, year = {2020}, author = {Fernandes, NM and Campello-Nunes, PH and Paiva, TS and Soraes, CAG and Silva-Neto, ID}, title = {Ciliate Diversity From Aquatic Environments in the Brazilian Atlantic Forest as Revealed by High-Throughput DNA Sequencing.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01612-8}, pmid = {33025060}, issn = {1432-184X}, support = {E-26/202.325/2018//Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; E-26/202.326/2018//Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; 426648/2016-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Rainforest aquatic ecosystems include complex habitats with scarce information on their unicellular eukaryote diversity and community structure. We have investigated the diversity of ciliates in freshwater and brackish environments along the Brazilian Atlantic Forest, based on the hypervariable V4 region of the 18S-rDNA obtained by high-throughput DNA sequencing. Our analyses detected 409 ciliate taxonomic units (OTUs), mostly attributed to the classes Oligohymenophorea and Spirotrichea. A total of 11 classes, 12 subclasses, 112 genera, and 144 species were reported. We found the following: (a) the ciliate communities are more diverse in freshwater- than in Atlantic Forest-associated brackish environments; (b) the ciliate communities are composed by a small amount of highly abundant OTUs, but a high number of low-abundant or rare OTUs; (c) nearly one-third of the ciliate OTUs share less than 97% sequence identity to reference sequences and (d) phylogenetic inference supports the hypothesis that the V4 region of the Ciliophora 18S-rDNA is a suitable marker for accurate evolutionary inferences at class level. Our results showed that a considerable fraction of the HTS-detected diversity of ciliates from Brazilian Atlantic Forest is not represented in the currently available molecular databases.}, }
@article {pmid33024291, year = {2020}, author = {Giguere, AT and Eichorst, SA and Meier, DV and Herbold, CW and Richter, A and Greening, C and Woebken, D}, title = {Acidobacteria are active and abundant members of diverse atmospheric H2-oxidizing communities detected in temperate soils.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-020-00750-8}, pmid = {33024291}, issn = {1751-7370}, support = {P26392-B20//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 636928//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, abstract = {Significant rates of atmospheric hydrogen (H2) consumption have been observed in temperate soils due to the activity of high-affinity enzymes, such as the group 1h [NiFe]-hydrogenase. We designed broadly inclusive primers targeting the large subunit gene (hhyL) of group 1h [NiFe]-hydrogenases for long-read sequencing to explore its taxonomic distribution across soils. This approach revealed a diverse collection of microorganisms harboring hhyL, including previously unknown groups and taxonomically not assignable sequences. Acidobacterial group 1h [NiFe]-hydrogenase genes were abundant and expressed in temperate soils. To support the participation of acidobacteria in H2 consumption, we studied two representative mesophilic soil acidobacteria, which expressed group 1h [NiFe]-hydrogenases and consumed atmospheric H2 during carbon starvation. This is the first time mesophilic acidobacteria, which are abundant in ubiquitous temperate soils, have been shown to oxidize H2 down to below atmospheric concentrations. As this physiology allows bacteria to survive periods of carbon starvation, it could explain the success of soil acidobacteria. With our long-read sequencing approach of group 1h [NiFe]-hydrogenase genes, we show that the ability to oxidize atmospheric levels of H2 is more widely distributed among soil bacteria than previously recognized and could represent a common mechanism enabling bacteria to persist during periods of carbon deprivation.}, }
@article {pmid33022257, year = {2020}, author = {Koskella, B}, title = {The phyllosphere.}, journal = {Current biology : CB}, volume = {30}, number = {19}, pages = {R1143-R1146}, doi = {10.1016/j.cub.2020.07.037}, pmid = {33022257}, issn = {1879-0445}, abstract = {There is longstanding interest in studying microbial communities below ground, while little attention has historically been paid to the above ground portions of plants (the phyllosphere). The phyllosphere has been estimated to make up around 60% of the biomass across all taxa on Earth, making it a key habitat for microbial organisms. The more we study these complex and dynamic communities, the more we come to realize their importance to the health of plant hosts. Overall, the phyllosphere is proving to be both an important microbial habitat and a tractable model system for asking questions in microbial ecology and evolution.}, }
@article {pmid33021904, year = {2020}, author = {Taparia, T and Hendrix, E and Hendriks, M and Krijger, M and de Boer, W and Van der Wolf, J}, title = {Comparative studies on the disease prevalence and population dynamics of ginger blotch and brown blotch pathogens of button mushrooms.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-06-20-1260-RE}, pmid = {33021904}, issn = {0191-2917}, abstract = {INTRODUCTION: Bacterial blotch is one of the most economically important diseases of button mushrooms. Knowledge on mechanisms of disease expression, inoculum thresholds and disease management is limited to the most-well known pathogen, Pseudomonas tolaasii. Recent outbreaks in Western Europe have been attributed to 'P. gingeri' and P. salomonii for ginger and brown blotch, respectively, although information on their identity, infection dynamics and pathogenicity is largely lacking.<br><br>METHODS: The disease pressure in an experimental mushroom cultivation facility was evaluated for 'P. gingeri' and P. salomonii over varying inoculation densities, casing soil types, environmental humidity and cultivation cycles. The pathogen population structures in the casing soils were simultaneously tracked across the cropping cycle using highly specific and sensitive TaqmanTM-qPCR assays.<br><br>RESULTS: 'P. gingeri' caused disease outbreaks at lower inoculum thresholds (104 cfu/g) in the soil than P. salomonii (105 cfu/g). Ginger blotch generically declined in later harvest cycles, although brown blotch did not. Casing soils were differentially suppressive to blotch diseases, based on their composition and supplementation. Endemic pathogen populations increased across the cultivation cycle although the inoculated pathogen populations were consistent between the 1st and 2nd flush.<br><br>CONCLUSION: 'P. gingeri' and P. salomonii have unique infection and population dynamics, that vary over soil types. Their endemic populations are also differently abundant in peat-based casing soils. This knowledge is essential to interpret diagnostic results from screening mushroom farms and design localized disease control strategies.}, }
@article {pmid33021677, year = {2020}, author = {Kolátková, V and Čepička, I and Hoffman, R and Vohník, M}, title = {Marinomyxa Gen. Nov. Accommodates Gall-Forming Parasites of the Tropical to Subtropical Seagrass Genus Halophila and Constitutes a Novel Deep-Branching Lineage Within Phytomyxea (Rhizaria: Endomyxa).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01615-5}, pmid = {33021677}, issn = {1432-184X}, support = {1308218//Grantová Agentura, Univerzita Karlova/ ; }, abstract = {Marine representatives of Phytomyxea (SAR: Rhizaria: Endomyxa), a peculiar class of obligate endobiotic parasites, are a greatly understudied ecological group of protists infecting many algal, diatom, and seagrass species. Very little is known about the actual diversity, ecology, and pathogenic potential of these organisms and their taxonomic treatment in many cases follows outdated morphotaxonomic concepts. Here we focused on resolving the phylogenetic relations of the phytomyxean parasites of the widespread seagrass genus Halophila. We report the first finding of Plasmodiophora halophilae, the parasite of ovate-leaf Halophila species, after more than 100 years since its original description in 1913. We provide additional information on its anatomy, morphology, distribution, and host range, together with a phylogenetic evidence that it is congeneric with the recently rediscovered species infecting the invasive seagrass Halophila stipulacea in the Mediterranean Sea. Despite the previously hypothesized affiliation of the latter to Tetramyxa, our phylogenetic analyses of the 18S rRNA gene place Tetramyxa parasitica (a parasite of brackish water phanerogams and the type species of the genus) in the freshwater/terrestrial phytomyxean order Plasmodiophorida and reveal that phytomyxids associated with Halophila spp. form a separate deep-branching clade within the class proposed here as Marinomyxa gen. nov. We further argue that M. marina infecting H. stipulacea is most likely a species-specific parasite and implies their comigration through the Suez Canal.}, }
@article {pmid33013993, year = {2020}, author = {Jueterbock, A and Boström, C and Coyer, JA and Olsen, JL and Kopp, M and Dhanasiri, AKS and Smolina, I and Arnaud-Haond, S and Van de Peer, Y and Hoarau, G}, title = {The Seagrass Methylome Is Associated With Variation in Photosynthetic Performance Among Clonal Shoots.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {571646}, pmid = {33013993}, issn = {1664-462X}, abstract = {Evolutionary theory predicts that clonal organisms are more susceptible to extinction than sexually reproducing organisms, due to low genetic variation and slow rates of evolution. In agreement, conservation management considers genetic variation as the ultimate measure of a population's ability to survive over time. However, clonal plants are among the oldest living organisms on our planet. Here, we test the hypothesis that clonal seagrass meadows display epigenetic variation that complements genetic variation as a source of phenotypic variation. In a clonal meadow of the seagrass Zostera marina, we characterized DNA methylation among 42 shoots. We also sequenced the whole genome of 10 shoots to correlate methylation patterns with photosynthetic performance under exposure to and recovery from 27°C, while controlling for somatic mutations. Here, we show for the first time that clonal seagrass shoots display DNA methylation variation that is independent from underlying genetic variation, and associated with variation in photosynthetic performance under experimental conditions. It remains unknown to what degree this association could be influenced by epigenetic responses to transplantation-related stress, given that the methylomes showed a strong shift under acclimation to laboratory conditions. The lack of untreated control samples in the heat stress experiment did not allow us to distinguish methylome shifts induced by acclimation from such induced by heat stress. Notwithstanding, the co-variation in DNA methylation and photosynthetic performance may be linked via gene expression because methylation patterns varied in functionally relevant genes involved in photosynthesis, and in the repair and prevention of heat-induced protein damage. While genotypic diversity has been shown to enhance stress resilience in seagrass meadows, we suggest that epigenetic variation plays a similar role in meadows dominated by a single genotype. Consequently, conservation management of clonal plants should consider epigenetic variation as indicator of resilience and stability.}, }
@article {pmid33013873, year = {2020}, author = {Ou, J and Liang, S and Guo, XK and Hu, X}, title = {α-Defensins Promote Bacteroides Colonization on Mucosal Reservoir to Prevent Antibiotic-Induced Dysbiosis.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {2065}, pmid = {33013873}, issn = {1664-3224}, abstract = {In addition to their established functions in host defense, accumulating evidence has suggested an emerging role for antimicrobial proteins (AMPs) in shaping commensal microbiota. However, the role of α-defensins, the most abundant AMPs of intestine, in regulating microbial ecology remains inconclusive. Here, we report that α-defensins promote commensal Bacteroides colonization by enhancing bacterial adhesion to the mucosal reservoir. Experiments utilizing mice deficient in matrix metalloproteinase 7 (MMP7), the α-defensin-activating enzyme, with rigorous littermate controls showed that α-defensin deficiency did not significantly influence steady-state intestinal microbiota. In contrast, α-defensins are essential for replenishment of commensal Bacteroides from the mucosal reservoir following antibiotics-induced dysbiosis, shown by markedly compromised recovery of Bacteroides in Mmp7-/- animals. Mechanistically, α-defensins promote Bacteroides colonization on epithelial surfaces in vivo and adhesion to epithelial cells in vitro. Moreover, α-defensins unexpectedly does not show any microbicidal activities against Bacteroides. Together, we propose that α-defensins promote commensal bacterial colonization and recovery to maintain microbial diversity upon environmental challenges.}, }
@article {pmid33013780, year = {2020}, author = {Yang, Y and Zhang, Y and Cápiro, NL and Yan, J}, title = {Genomic Characteristics Distinguish Geographically Distributed Dehalococcoidia.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {546063}, pmid = {33013780}, issn = {1664-302X}, abstract = {Dehalococcoidia (Dia) class microorganisms are frequently found in various pristine and contaminated environments. Metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) studies have substantially improved the understanding of Dia microbial ecology and evolution; however, an updated thorough investigation on the genomic and evolutionary characteristics of Dia microorganisms distributed in geographically distinct environments has not been implemented. In this study, we analyzed available genomic data to unravel Dia evolutionary and metabolic traits. Based on the phylogeny of 16S rRNA genes retrieved from sixty-seven genomes, Dia microorganisms can be categorized into three groups, the terrestrial cluster that contains all Dehalococcoides and Dehalogenimonas strains, the marine cluster I, and the marine cluster II. These results reveal that a higher ratio of horizontally transferred genetic materials was found in the Dia marine clusters compared to that of the Dia terrestrial cluster. Pangenome analysis further suggests that Dia microorganisms have evolved cluster-specific enzymes (e.g., dehalogenase in terrestrial Dia, sulfite reductase in marine Dia) and biosynthesis capabilities (e.g., siroheme biosynthesis in marine Dia). Marine Dia microorganisms are likely adapted to versatile metabolisms for energy conservation besides organohalide respiration. The genomic differences between marine and terrestrial Dia may suggest distinct functions and roles in element cycling (e.g., carbon, sulfur, chlorine), which require interdisciplinary approaches to unravel the physiology and evolution of Dia in various environments.}, }
@article {pmid33013755, year = {2020}, author = {Whitworth, DE and Jurkevitch, E and Pérez, J and Fuhrmann, G and Koval, SF}, title = {Editorial: Mechanisms of Prokaryotic Predation.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {2071}, doi = {10.3389/fmicb.2020.02071}, pmid = {33013755}, issn = {1664-302X}, }
@article {pmid33013480, year = {2020}, author = {Turroni, S and Magnani, M and Kc, P and Lesnik, P and Vidal, H and Heer, M}, title = {Gut Microbiome and Space Travelers' Health: State of the Art and Possible Pro/Prebiotic Strategies for Long-Term Space Missions.}, journal = {Frontiers in physiology}, volume = {11}, number = {}, pages = {553929}, pmid = {33013480}, issn = {1664-042X}, abstract = {The upcoming exploration missions will imply a much longer duration than any of the missions flown so far. In these missions, physiological adaptation to the new environment leads to changes in different body systems, such as the cardiovascular and musculoskeletal systems, metabolic and neurobehavioral health and immune function. To keep space travelers healthy on their trip to Moon, Mars and beyond and their return to Earth, a variety of countermeasures need to be provided to maintain body functionality. From research on the International Space Station (ISS) we know today, that for instance prescribing an adequate training regime for each individual with the devices available in the respective spacecraft is still a challenge. Nutrient supply is not yet optimal and must be optimized in exploration missions. Food intake is intrinsically linked to changes in the gut microbiome composition. Most of the microbes that inhabit our body supply ecosystem benefit to the host-microbe system, including production of important resources, bioconversion of nutrients, and protection against pathogenic microbes. The gut microbiome has also the ability to signal the host, regulating the processes of energy storage and appetite perception, and influencing immune and neurobehavioral function. The composition and functionality of the microbiome most likely changes during spaceflight. Supporting a healthy microbiome by respective measures in space travelers might maintain their health during the mission but also support rehabilitation when being back on Earth. In this review we are summarizing the changes in the gut microbiome observed in spaceflight and analog models, focusing particularly on the effects on metabolism, the musculoskeletal and immune systems and neurobehavioral disorders. Since space travelers are healthy volunteers, we focus on the potential of countermeasures based on pre- and probiotics supplements.}, }
@article {pmid33008820, year = {2020}, author = {Stracke, C and Meyer, BH and Hagemann, A and Jo, E and Lee, A and Albers, SV and Cha, J and Bräsen, C and Siebers, B}, title = {Sulfolobus acidocaldarius uses a complex trehalose metabolism for salt stress response involving a novel TPS/TPP pathway.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.01565-20}, pmid = {33008820}, issn = {1098-5336}, abstract = {The Crenarchaeon Sulfolobus acidocaldarius has been described to synthesize trehalose via the maltooligosyltrehalose synthase (TreY) and maltooligosyltrehalose trehalohydrolase (TreZ) pathway and the trehalose glycosyltransferring synthase (TreT) pathway has been predicted. Deletion mutant analysis of single and double deletion strains of ΔtreY and ΔtreT in S. acidocaldarius revealed that next to these two pathways a third, novel trehalose biosynthesis pathway is operative in vivo: the trehalose-6-phosphate (T6P) synthase/T6P phosphatase (TPS/TPP) pathway. In contrast to known TPS proteins, which belong to the GT20 family, the S. acidocaldarius TPS belongs to the GT4 family establishing a new function within this group of enzymes. This novel GT4-like TPS turned out to be mainly present in the Sulfolobales. The ΔtreY/ΔtreT/Δtps triple mutant of S. acidocaldarius lacking the ability to synthesize trehalose showed no altered phenotype under standard conditions or heat stress, but was unable to grow under salt stress. Accordingly, in the wild type strain a significant increase of intracellular trehalose formation was observed under salt stress. Quantitative real-time PCR showed a salt stress mediated induction of all three trehalose synthesizing pathways. This demonstrates in Archaea that trehalose plays an essential role for growth under high salt conditions.ImportanceThe metabolism and function of trehalose as compatible solute was not well understood in Archaea. This combined genetic and enzymatic approach at the interface of microbiology, physiology and microbial ecology gives important insights into survival under stress, adaptation to extreme environments, and the role of compatible solutes in Archaea. Here we unravelled the complexity of trehalose metabolism and present a comprehensive study on trehalose function in stress response in S. acidocaldarius This sheds light on the general microbiology and the fascinating metabolic repertoire of Archaea involving many novel biocatalysts such as glycosyltransferases with great potential in biotechnology.}, }
@article {pmid33007535, year = {2020}, author = {Wang, H and Chen, J and Ren, P and Zhang, Y and Omondi Onyango, S}, title = {Ultrasound irradiation alters the spatial structure and improves the antioxidant activity of the yellow tea polysaccharide.}, journal = {Ultrasonics sonochemistry}, volume = {70}, number = {}, pages = {105355}, doi = {10.1016/j.ultsonch.2020.105355}, pmid = {33007535}, issn = {1873-2828}, abstract = {In this study, the impact of ultrasound irradiation on the structural characteristics and antioxidant properties of yellow tea polysaccharides with different molecular weights (Mw) were investigated. Native yellow tea polysaccharide containing YTPS-3N, YTPS-5N and YTPS-7N were prepared through precipitation with ethanol at various concentrations of 30%, 50%, and 70%, respectively, and irradiated with high intensity ultrasound (20 kHz) for 55 min to yield yellow tea polysaccharide including YTPS-3U, YTPS-5U and YTPS-7U. The molecular weight (Mw) of YTPS-3N (from 37.7 to 15.1 kDa) and YTPS-5N (from 14.6 to 5.2 kDa) sharply decreased upon ultrasound irradiation, coincidentally particle size (Zavg) was also significantly reduced for YTPS-3N (40%), YTPS-5N (48%) and YTPS-7N (54%). The high-performance liquid chromatography and Fourier transform-infrared spectroscopy analysis revealed a partial degradation of native yellow tea polysaccharide treated with ultrasound, though the monosaccharide composition was not altered. Furthermore, changes in morphology and the breakdown of native yellow tea polysaccharide upon irradiation was confirmed with the circular dichroism spectrum, atomic force and scanning electron microscopy. As a consequence, irradiation of yellow tea polysaccharide increased free radical scavenging activity with YTPS-7U exhibiting the highest levels of 2, 2-diphenyl-1-picrylhydrazyl free radical, superoxide and hydroxyl radicals scavenging activity. These results suggest that the alteration of the spatial structure of yellow tea polysaccharide can enhance its antioxidant activity which is an important property for functional foods or medicines.}, }
@article {pmid33006023, year = {2020}, author = {Gao, X and Xu, H and Yuan, X}, title = {The Overlooked Genetic Diversity in the Dryland Soil Surface-Dwelling Cyanobacterium Nostoc flagelliforme as Revealed by the Marker Gene wspA.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01610-w}, pmid = {33006023}, issn = {1432-184X}, support = {31670104//the National Natural Science Foundation of China/ ; 2020JZ-51//Natural Science Foundation of Shaanxi Province (CN)/ ; }, abstract = {Biodiversity is recognized to be relatively low in the dryland ecosystem. However, we might overlook the accumulating genetic variation in those dryland micro-populations, which should eventually increase the dryland biodiversity. In the xeric steppes of western and northwestern China, there are two soil surface-dwelling and genetically close cyanobacterial species, Nostoc commune and Nostoc flagelliforme. They respectively exhibit lamellate and filamentous colony shapes. Their individual colony is consisted of hundreds of trichomes and the common exopolysaccharide matrix. N. flagelliforme is exclusively distributed in the dryland and supposed to be evolved from N. commune. We previously reported that the morphological diversity of N. flagelliforme colonies was very limited, being either cylindrical or strip-like. In this communication, we performed single-nucleotide polymorphism (SNP) analysis of the marker gene wspA as well as phylogenetic analysis of the WspA protein in N. flagelliforme colonies to gain insights into its genetic diversity. SNP analysis suggested that there existed plentiful nucleotide variations in the individual colonies and meanwhile these variations shared certain evolutionary regularity. Phylogenetic analysis of the deduced proteins from the cloned wspA sequences suggested that the relatively regular variations were possibly dispersed in the N. flagelliforme populations of different regions. Thus, these results presented a scenario of the underestimated genetic diversity hidden behind the limited morphotype of dryland cyanobacteria. Maybe, we can consider the individual cyanobacterial colony as a potential biodiversity pool in the drylands.}, }
@article {pmid33004967, year = {2020}, author = {Walker, SP and Barrett, M and Hogan, G and Flores Bueso, Y and Claesson, MJ and Tangney, M}, title = {Non-specific amplification of human DNA is a major challenge for 16S rRNA gene sequence analysis.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {16356}, pmid = {33004967}, issn = {2045-2322}, support = {12/RC/2273/SFI_/Science Foundation Ireland/Ireland ; 15/CDA/3630/SFI_/Science Foundation Ireland/Ireland ; MRCG2016-25/HRBI_/Health Research Board/Ireland ; }, abstract = {The targeted sequencing of the 16S rRNA gene is one of the most frequently employed techniques in the field of microbial ecology, with the bacterial communities of a wide variety of niches in the human body have been characterised in this way. This is performed by targeting one or more hypervariable (V) regions within the 16S rRNA gene in order to produce an amplicon suitable in size for next generation sequencing. To date, all technical research has focused on the ability of different V regions to accurately resolve the composition of bacterial communities. We present here an underreported artefact associated with 16S rRNA gene sequencing, namely the off-target amplification of human DNA. By analysing 16S rRNA gene sequencing data from a selection of human sites we highlighted samples susceptible to this off-target amplification when using the popular primer pair targeting the V3-V4 region of the gene. The most severely affected sample type identified (breast tumour samples) were then re-analysed using the V1-V2 primer set, showing considerable reduction in off target amplification. Our data indicate that human biopsy samples should preferably be amplified using primers targeting the V1-V2 region. It is shown here that these primers result in on average 80% less human genome aligning reads, allowing for more statistically significant analysis of the bacterial communities residing in these samples.}, }
@article {pmid33002118, year = {2020}, author = {Song, J and Klümper, U and Riber, L and Dechesne, A and Smets, BF and Sørensen, SJ and Brandt, KK}, title = {A converging subset of soil bacterial taxa is permissive to the IncP-1 plasmid pKJK5 across a range of soil copper contamination.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaa200}, pmid = {33002118}, issn = {1574-6941}, abstract = {Stressors like metals or antibiotics can affect bacterial community permissiveness for plasmid uptake, but there is little knowledge about long-term effects of such stressors on the evolution of community permissiveness. We assessed the effect of more than 90 years of soil Cu contamination on bacterial community permissiveness (i.e. uptake ability) towards a gfp-tagged IncP-1 plasmid (pKJK5) introduced via an Escherichia coli donor. Plasmid transfer events from the donor to the recipient soil bacterial community were quantified and transconjugants were subsequently isolated by fluorescence activated cell sorting and identified by 16S rRNA gene amplicon sequencing. Transfer frequency of plasmid pKJK5 was reduced in bacterial communities extracted from highly Cu contaminated (4526 mg kg-1) soil compared to corresponding communities extracted from moderately (458 mg kg-1) Cu contaminated soil and a low Cu reference soil (15 mg kg-1). The taxonomic composition of the transconjugal pools showed remarkable similarities irrespective of the degree of soil Cu contamination and despite contrasting compositions of the extracted recipient communities and the original soil communities. Permissiveness assessed at the level of individual operational taxonomic units (OTUs; 16S rRNA gene 97% sequence similarity threshold) was only slightly affected by soil Cu level and high replicate variability of OTU-level permissiveness indicated a role of stochastic events in IncP-1 plasmid transfer or strain-to-strain permissiveness variability.}, }
@article {pmid33001506, year = {2020}, author = {Beier, S and Andersson, AF and Galand, PE and Hochart, C and Logue, JB and McMahon, K and Bertilsson, S}, title = {The environment drives microbial trait variability in aquatic habitats.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15656}, pmid = {33001506}, issn = {1365-294X}, abstract = {A prerequisite to improve the predictability of microbial community dynamics is to understand microbial assembly mechanisms. To study factors that contribute to microbial community assembly, we examined temporal dynamics of genes in five aquatic metagenome time-series, originating from marine off-shore or coastal sites and one lake. With this trait-based approach we expected to find gene-specific patterns of temporal allele variability that depended on the seasonal metacommunity size of carrier-taxa and the variability of the milieu and the substrates that the resulting proteins were exposed to. In more detail, we hypothesized that a larger seasonal metacommunity size would result in increased temporal variability of functional units (i.e. gene alleles), as shown previously for taxonomic units. We further hypothesized that multi-copy genes would feature higher temporal variability than single-copy genes, as gene multiplication can result from high variability in substrate quality and quantity. Finally, we hypothesized that direct exposure of proteins to the extracellular environment would result in increased temporal variability of the respective gene compared to intracellular proteins that are less exposed to environmental fluctuations. The first two hypotheses were confirmed in all datasets, while significant effects of the subcellular location of gene-products was only seen in three out of the five time-series. The gene with the highest allele variability throughout all datasets was an iron transporter, also representing a target for phage infection. Earlier work emphasizes the role of phage-prokaryote interactions as a major driver of microbial diversity. Our finding therefore points to a potentially important role of iron transporter mediated phage infections for the assembly and maintenance of diversity in aquatic prokaryotes.}, }
@article {pmid33001224, year = {2020}, author = {Yavitt, JB and Roco, CA and Debenport, SJ and Barnett, SE and Shapleigh, JP}, title = {Community Organization and Metagenomics of Bacterial Assemblages Across Local Scale pH Gradients in Northern Forest Soils.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01613-7}, pmid = {33001224}, issn = {1432-184X}, support = {1007286//Agricultural Research Service/ ; }, abstract = {Soil pH has shown to predict bacterial diversity, but mechanisms are still poorly understood. To investigate how bacteria distribute themselves as a function of soil pH, we assessed community composition, diversity, assembly, and gene abundance across local (ca. 1 km) scale gradients in soil pH from ~ 3.8 to 6.5 created by differences in soil parent material in three northern forests. Plant species were the same on all sites, with no evidence of agriculture in the past. Concentrations of extractable calcium, iron, and phosphorus also varied significantly across the pH gradients. Among taxa, Alphaproteobacteria and Acidobacteria were more common in soils with acidic pH values. Overall richness and diversity of OTUs peaked at intermediate pH values. Variations in OTU richness and diversity also had a quadratic fit with concentrations of extractable calcium and phosphorus. Community assembly was via homogeneous deterministic processes in soils with acidic pH values, whereas stochastic processes dominated in soils with near-neutral pH values. Although we expected selection via genes for acid tolerance response in acidic soils, genes for genetic information processing were more selective. Taxa in higher pH soils had differential abundance of transporter genes, suggesting adaptation to acquire metabolic substrates from soils. Soil bacterial communities in northern forest soils are incredibly diverse, and we still have much to learn about how soil pH and co-varying soil parameters directly drive gene selection in this critical component of ecosystem structure.}, }
@article {pmid33001029, year = {2020}, author = {Nelson, CW and Ardern, Z and Goldberg, TL and Meng, C and Kuo, CH and Ludwig, C and Kolokotronis, SO and Wei, X}, title = {Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, doi = {10.7554/eLife.59633}, pmid = {33001029}, issn = {2050-084X}, support = {Postdoctoral Research Fellowship//Academia Sinica/ ; Grant//National Philanthropic Trust/ ; John D. MacArthur Professorship Chair//University of Wisconsin-Madison/ ; IOS grants #1755370 and #1758800//National Science Foundation/ ; }, abstract = {Understanding the emergence of novel viruses requires an accurate and comprehensive annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have been associated with pandemics, but are still widely overlooked. We identify and characterize ORF3d, a novel OLG in SARS-CoV-2 that is also present in Guangxi pangolin-CoVs but not other closely related pangolin-CoVs or bat-CoVs. We then document evidence of ORF3d translation, characterize its protein sequence, and conduct an evolutionary analysis at three levels: between taxa (21 members of Severe acute respiratory syndrome-related coronavirus), between human hosts (3978 SARS-CoV-2 consensus sequences), and within human hosts (401 deeply sequenced SARS-CoV-2 samples). ORF3d has been independently identified and shown to elicit a strong antibody response in COVID-19 patients. However, it has been misclassified as the unrelated gene ORF3b, leading to confusion. Our results liken ORF3d to other accessory genes in emerging viruses and highlight the importance of OLGs.}, }
@article {pmid33000311, year = {2020}, author = {Silva-Lima, AW and Froes, AM and Garcia, GD and Tonon, LAC and Swings, J and Cosenza, CAN and Medina, M and Penn, K and Thompson, JR and Thompson, CC and Thompson, FL}, title = {Mussismilia braziliensis White Plague Disease Is Characterized by an Affected Coral Immune System and Dysbiosis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01588-5}, pmid = {33000311}, issn = {1432-184X}, support = {Biocomp, IODP//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; PQ//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/ ; CNE//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; }, abstract = {Infectious diseases are one of the major drivers of coral reef decline worldwide. White plague-like disease (WPL) is a widespread disease with a complex etiology that infects several coral species, including the Brazilian endemic species Mussismilia braziliensis. Gene expression profiles of healthy and WPL-affected M. braziliensis were analyzed in winter and summer seasons. The de novo assembly of the M. braziliensis transcriptome from healthy and white plague samples produced a reference transcriptome containing 119,088 transcripts. WPL-diseased samples were characterized by repression of immune system and cellular defense processes. Autophagy and cellular adhesion transcripts were also repressed in WPL samples, suggesting exhaustion of the coral host defenses. Seasonal variation leads to plasticity in transcription with upregulation of intracellular signal transduction, apoptosis regulation, and oocyte development in the summer. Analysis of the active bacterial rRNA indicated that Pantoea bacteria were more abundant in WPL corals, while Tistlia, Fulvivirga, and Gammaproteobacteria Ga0077536 were more abundant in healthy samples. Cyanobacteria proliferation was also observed in WPL, mostly in the winter. These results indicate a scenario of dysbiosis in WPL-affected M. braziliensis, with the loss of potentially symbiotic bacteria and proliferation of opportunistic microbes after the start of the infection process.}, }
@article {pmid32998695, year = {2020}, author = {Soverini, M and Rampelli, S and Turroni, S and Brigidi, P and Biagi, E and Candela, M}, title = {Do the human gut metagenomic species possess the minimal set of core functionalities necessary for life?.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {678}, pmid = {32998695}, issn = {1471-2164}, abstract = {BACKGROUND: Advances in bioinformatics recently allowed for the recovery of 'metagenomes assembled genomes' from human microbiome studies carried on with shotgun sequencing techniques. Such approach is used as a mean to discover new unclassified metagenomic species, putative biological entities having distinct metabolic traits.<br><br>RESULTS: In the present analysis we compare 400 genomes from isolates available on NCBI database and 10,000 human gut metagenomic species, screening all of them for the presence of a minimal set of core functionalities necessary, but not sufficient, for life. As a result, the metagenome-assembled genomes resulted systematically depleted in genes encoding for essential functions apparently needed to support autonomous bacterial life.<br><br>CONCLUSIONS: The relevant degree of lacking core functionalities that we observed in metagenome-assembled genomes raises some concerns about the effective completeness of metagenome-assembled genomes, suggesting caution in extrapolating biological information about their metabolic propensity and ecology in a complex environment like the human gastrointestinal tract.}, }
@article {pmid32996612, year = {2020}, author = {Moisan, K and Raaijmakers, JM and Dicke, M and Lucas-Barbosa, D and Cordovez, V}, title = {Volatiles from soil-borne fungi affect directional growth of roots.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.13890}, pmid = {32996612}, issn = {1365-3040}, abstract = {Volatiles play major roles in mediating ecological interactions between soil (micro)organisms and plants. It is well-established that microbial volatiles can increase root biomass and lateral root formation. To date, however, it is unknown whether microbial volatiles can affect directional root growth. Here, we present a novel method to study belowground volatile-mediated interactions. As proof-of-concept, we designed a root Y-tube olfactometer, and tested the effects of volatiles from four different soil-borne fungi on directional growth of Brassica rapa roots in soil. Subsequently, we compared the fungal volatile organic compounds (VOCs) previously profiled with Gas Chromatography-Mass Spectrometry (GC-MS). Using our newly designed setup, we show that directional root growth in soil is differentially affected by fungal volatiles. Roots grew more frequently toward volatiles from the root pathogen Rhizoctonia solani, whereas volatiles from the other three saprophytic fungi did not impact directional root growth. GC-MS profiling showed that six VOCs were exclusively emitted by R. solani. These findings verify that this novel method is suitable to unravel the intriguing chemical cross-talk between roots and soil-borne fungi and its impact on root growth.}, }
@article {pmid32996237, year = {2020}, author = {Barbera, P and Czech, L and Lutteropp, S and Stamatakis, A}, title = {SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13255}, pmid = {32996237}, issn = {1755-0998}, support = {//Klaus Tschira Stiftung/ ; }, abstract = {Microbial ecology research is currently driven by the continuously decreasing cost of DNA sequencing and the improving accuracy of data analysis methods. One such analysis method is phylogenetic placement, which establishes the phylogenetic identity of the anonymous environmental sequences in a sample by means of a given phylogenetic reference tree. However, assessing the diversity of a sample remains challenging, as traditional methods do not scale well with the increasing data volumes and/or do not leverage the phylogenetic placement information. Here, we present scrapp, a highly parallel and scalable tool that uses a molecular species delimitation algorithm to quantify the diversity distribution over the reference phylogeny for a given phylogenetic placement of the sample. scrapp employs a novel approach to cluster phylogenetic placements, called placement space clustering, to efficiently perform dimensionality reduction, so as to scale on large data volumes. Furthermore, it uses the phylogeny-aware molecular species delimitation method mPTP to quantify diversity. We evaluated scrapp using both, simulated and empirical data sets. We use simulated data to verify our approach. Tests on an empirical data set show that scrapp-derived metrics can classify samples by their diversity-correlated features equally well or better than existing, commonly used approaches. scrapp is available at https://github.com/pbdas/scrapp.}, }
@article {pmid32995929, year = {2020}, author = {Wang, H and Zhang, Y and Bartlett, DH and Xiao, X}, title = {Transcriptomic Analysis Reveals Common Adaptation Mechanisms Under Different Stresses for Moderately Piezophilic Bacteria.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01609-3}, pmid = {32995929}, issn = {1432-184X}, support = {2018YFC0309800//National Key Research and Development Program of China/ ; 41776173//National Natural Science Foundation of China/ ; 41530967//National Natural Science Foundation of China/ ; 91951117//National Natural Science Foundation of China/ ; 41921006//National Natural Science Foundation of China/ ; }, abstract = {Piezophiles, by the commonly accepted definition, grow faster under high hydrostatic pressure (HHP) than under ambient pressure and are believed to exist only in pressurized environments where life has adapted to HHP during evolution. However, recent findings suggest that piezophiles have developed a common adaptation strategy to cope with multiple types of stresses including HHP. These results raise a question on the ecological niches of piezophiles: are piezophiles restricted to habitats with HHP? In this study, we observed that the bacterial strains Sporosarcina psychrophila DSM 6497 and Lysinibacillus sphaericus LMG 22257, which were isolated from surface environments and then transferred under ambient pressure for half a century, possess moderately piezophilic characteristics with optimal growth pressures of 7 and 20 MPa, respectively. Their tolerance to HHP was further enhanced by MgCl2 supplementation under the highest tested pressure of 50 MPa. Transcriptomic analysis was performed to compare gene expression with and without MgCl2 supplementation under 50 MPa for S. psychrophila DSM 6497. Among 4390 genes or transcripts obtained, 915 differentially expressed genes (DEGs) were identified. These DEGs are primarily associated with the antioxidant defense system, intracellular compatible solute accumulation, and membrane lipid biosynthesis, which have been reported to be essential for cells to cope with HHP. These findings indicate no in situ pressure barrier for piezophile isolation, and cells may adopt a common adaptation strategy to cope with different stresses.}, }
@article {pmid32994415, year = {2020}, author = {Guo, X and Gao, Q and Yuan, M and Wang, G and Zhou, X and Feng, J and Shi, Z and Hale, L and Wu, L and Zhou, A and Tian, R and Liu, F and Wu, B and Chen, L and Jung, CG and Niu, S and Li, D and Xu, X and Jiang, L and Escalas, A and Wu, L and He, Z and Van Nostrand, JD and Ning, D and Liu, X and Yang, Y and Schuur, EAG and Konstantinidis, KT and Cole, JR and Penton, CR and Luo, Y and Tiedje, JM and Zhou, J}, title = {Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4897}, doi = {10.1038/s41467-020-18706-z}, pmid = {32994415}, issn = {2041-1723}, abstract = {Soil microbial respiration is an important source of uncertainty in projecting future climate and carbon (C) cycle feedbacks. However, its feedbacks to climate warming and underlying microbial mechanisms are still poorly understood. Here we show that the temperature sensitivity of soil microbial respiration (Q10) in a temperate grassland ecosystem persistently decreases by 12.0 ± 3.7% across 7 years of warming. Also, the shifts of microbial communities play critical roles in regulating thermal adaptation of soil respiration. Incorporating microbial functional gene abundance data into a microbially-enabled ecosystem model significantly improves the modeling performance of soil microbial respiration by 5-19%, and reduces model parametric uncertainty by 55-71%. In addition, modeling analyses show that the microbial thermal adaptation can lead to considerably less heterotrophic respiration (11.6 ± 7.5%), and hence less soil C loss. If such microbially mediated dampening effects occur generally across different spatial and temporal scales, the potential positive feedback of soil microbial respiration in response to climate warming may be less than previously predicted.}, }
@article {pmid32994285, year = {2020}, author = {Trego, AC and O'Sullivan, S and Quince, C and Mills, S and Ijaz, UZ and Collins, G}, title = {Size Shapes the Active Microbiome of Methanogenic Granules, Corroborating a Biofilm Life Cycle.}, journal = {mSystems}, volume = {5}, number = {5}, pages = {}, pmid = {32994285}, issn = {2379-5077}, abstract = {Methanogenic archaea are key players in cycling organic matter in nature but also in engineered waste treatment systems, where they generate methane, which can be used as a renewable energy source. In such systems in the built environment, complex methanogenic consortia are known to aggregate into highly organized, spherical granular biofilms comprising the interdependent microbial trophic groups mediating the successive stages of the anaerobic digestion (AD) process. This study separated methanogenic granules into a range of discrete size fractions, hypothesizing different biofilm growth stages, and separately supplied each with specific substrates to stimulate the activity of key AD trophic groups, including syntrophic acid oxidizers and methanogens. Rates of specific methanogenic activity were measured, and amplicon sequencing of 16S rRNA gene transcripts was used to resolve phylotranscriptomes across the series of size fractions. Increased rates of methane production were observed in each of the size fractions when hydrogen was supplied as the substrate compared with those of volatile fatty acids (acetate, propionate, and butyrate). This was connected to a shift toward hydrogenotrophic methanogenesis dominated by Methanobacterium and Methanolinea Interestingly, the specific active microbiomes measured in this way indicated that size was significantly more important than substrate in driving the structure of the active community in granules. Multivariate integration studywise discriminant analysis identified 56 genera shaping changes in the active community across both substrate and size. Half of those were found to be upregulated in the medium-sized granules, which were also the most active and potentially of the most important size, or life stage, for precision management of AD systems.IMPORTANCE Biological wastewater conversion processes collectively constitute one of the single biggest worldwide applications of microbial communities. There is an obvious requirement, therefore, to study the microbial systems central to the success of such technologies. Methanogenic granules, in particular, are architecturally fascinating biofilms that facilitate highly organized cooperation within the metabolic network of the anaerobic digestion (AD) process and, thus, are especially intriguing model systems for microbial ecology. This study, in a way not previously reported, provoked syntrophic and methanogenic activity and the structure of the microbial community, using specific substrates targeting the key trophic groups in AD. Unexpectedly, granule size more strongly than substrate shaped the active portion of the microbial community. Importantly, the findings suggest the size, or age, of granules inherently shapes the active microbiome linked to a life cycle. This provides exciting insights into the function of, and the potential for additional modeling of biofilm development in, methanogenic granules.}, }
@article {pmid32993824, year = {2020}, author = {Hanley-Cook, GT and Argaw, AA and de Kok, BP and Vanslambrouck, KW and Toe, LC and Kolsteren, PW and Jones, AD and Lachat, CK}, title = {EAT-Lancet Diet Score Requires Minimum Intake Values to Predict Higher Micronutrient Adequacy of Diets in Rural Women of Reproductive Age from Five Low- and Middle-Income Countries.}, journal = {The British journal of nutrition}, volume = {}, number = {}, pages = {1-26}, doi = {10.1017/S0007114520003864}, pmid = {32993824}, issn = {1475-2662}, abstract = {The EAT-Lancet Commission on Food, Planet, Health promulgated a universal reference diet. Subsequently, researchers constructed an EAT-Lancet diet score (0-14 points), with lower bound intake values for various dietary components set at 0 g/d, and reported inverse associations with risks of major health outcomes in a high-income population. We assessed associations between EAT-Lancet diet scores, without or with (>0 g/d) minimum intake values, and the Mean Probability of Micronutrient Adequacy (MPA) in food and nutrition insecure women of reproductive age (WRA) from low- and middle-income countries (LMICs). We analysed single 24-h diet recall data (n=1,950) from studies in rural Democratic Republic of the Congo, Ecuador, Kenya, Sri Lanka, and Vietnam. Associations between EAT-Lancet diet scores and MPA were assessed by fitting linear mixed-effects models with random intercept and slope. EAT-Lancet diet scores (mean ± SD) were 8.8 ± 1.3 and 1.9 ± 1.1 without or with minimum intake values, respectively. Furthermore, pooled MPA was 0.58 ± 0.22 and total energy intake was 2521 ± 1100 kcal/d. One-point increase in the EAT-Lancet diet score, without minimum intake values, was associated with a 2.6 ± 0.7 percentage points decrease in MPA (P<0.001). In contrast, the EAT-Lancet diet score, with minimum intake values, was associated with a 2.4 ± 1.3 percentage points increase in MPA (P=0.07). Further analysis indicated positive associations between EAT-Lancet diet scores and MPA adjusted for total energy intake (P<0.05). Our findings indicate that the EAT-Lancet diet score requires minimum intake values for nutrient-dense dietary components to avoid positively scoring non-consumption of food groups and subsequently predicting lower MPA of diets, when applied to rural WRA in LMICs.}, }
@article {pmid32993503, year = {2020}, author = {De Maayer, P and Pillay, T and Coutinho, TA}, title = {Flagella by numbers: comparative genomic analysis of the supernumerary flagellar systems among the Enterobacterales.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {670}, pmid = {32993503}, issn = {1471-2164}, support = {SFH180109299856//National Research Foundation/ ; }, abstract = {BACKGROUND: Flagellar motility is an efficient means of movement that allows bacteria to successfully colonize and compete with other microorganisms within their respective environments. The production and functioning of flagella is highly energy intensive and therefore flagellar motility is a tightly regulated process. Despite this, some bacteria have been observed to possess multiple flagellar systems which allow distinct forms of motility.<br><br>RESULTS: Comparative genomic analyses showed that, in addition to the previously identified primary peritrichous (flag-1) and secondary, lateral (flag-2) flagellar loci, three novel types of flagellar loci, varying in both gene content and gene order, are encoded on the genomes of members of the order Enterobacterales. The flag-3 and flag-4 loci encode predicted peritrichous flagellar systems while the flag-5 locus encodes a polar flagellum. In total, 798/4028 (~ 20%) of the studied taxa incorporate dual flagellar systems, while nineteen taxa incorporate three distinct flagellar loci. Phylogenetic analyses indicate the complex evolutionary histories of the flagellar systems among the Enterobacterales.<br><br>CONCLUSIONS: Supernumerary flagellar loci are relatively common features across a broad taxonomic spectrum in the order Enterobacterales. Here, we report the occurrence of five (flag-1 to flag-5) flagellar loci on the genomes of enterobacterial taxa, as well as the occurrence of three flagellar systems in select members of the Enterobacterales. Considering the energetic burden of maintaining and operating multiple flagellar systems, they are likely to play a role in the ecological success of members of this family and we postulate on their potential biological functions.}, }
@article {pmid32992776, year = {2020}, author = {García-Vega, ÁS and Corrales-Agudelo, V and Reyes, A and Escobar, JS}, title = {Diet Quality, Food Groups and Nutrients Associated with the Gut Microbiota in a Nonwestern Population.}, journal = {Nutrients}, volume = {12}, number = {10}, pages = {}, doi = {10.3390/nu12102938}, pmid = {32992776}, issn = {2072-6643}, abstract = {Diet plays an important role in shaping gut microbiota. However, much remains to be learned regarding this association. We analyzed dietary intake and gut microbiota in a community-dwelling cohort of 441 Colombians. Diet quality, intake of food groups and nutrient consumption were paired with microbial diversity and composition using linear regressions, Procrustes analyses and a random-forest machine-learning algorithm. Analyses were adjusted for potential confounders, including the five cities from where the participants originated, sex (male, female), age group (18-40 and 41-62 years), BMI (lean, overweight, obese) and socioeconomic status. Microbial diversity was higher in individuals with increased intake of nutrients obtained from plant-food sources, whereas the intake of food groups and nutrients correlated with microbiota structure. Random-forest regressions identified microbial communities associated with different diet components. Two remarkable results confirmed previous expectations regarding the link between diet and microbiota: communities composed of short-chain fatty acid (SCFA) producers were more prevalent in the microbiota of individuals consuming diets rich in fiber and plant-food sources, such as fruits, vegetables and beans. In contrast, an inflammatory microbiota composed of bile-tolerant and putrefactive microorganisms along with opportunistic pathogens thrived in individuals consuming diets enriched in animal-food sources and of low quality, i.e., enriched in ultraprocessed foods and depleted in dietary fiber. This study expands our understanding of the relationship between dietary intake and gut microbiota. We provide evidence that diet is strongly associated with the gut microbial community and highlight generalizable connections between them.}, }
@article {pmid32990279, year = {2020}, author = {Zhu, Y and Xiong, Y and Gu, Y and Li, Q and Liu, Y}, title = {Chiropractic Therapy Modulated Gut Microbiota and Attenuated Allergic Airway Inflammation in an Immature Rat Model.}, journal = {Medical science monitor : international medical journal of experimental and clinical research}, volume = {26}, number = {}, pages = {e926039}, doi = {10.12659/MSM.926039}, pmid = {32990279}, issn = {1643-3750}, abstract = {BACKGROUND As a type of traditional Chinese massage, chiropractic therapy is applied to prevent and treat children with asthma in China. However, its mechanism of action is unclear. Allergic airway inflammation plays a key role in the occurrence and development of asthma, in which changes in gut microbiota are involved. The present study investigated the influence of chiropractic therapy on allergic airway inflammation (AAI) and gut microbiota in an immature rat model. MATERIAL AND METHODS Three-week-old male Sprague-Dawley rats were divided randomly into control (CN), AAI, and chiropractic (CP) groups. AAI and CP groups were sensitized and challenged with ovalbumin (OVA) to induce AAI. The CP group received chiropractic therapy during AAI modelling. AAI was assessed by cell counts in bronchoalveolar lavage fluid and HE staining of lung tissues. Plasma OVA-sIgE, IFN-γ, IL-4, and IL-10 levels were detected by ELISA. DNA extraction from feces samples was used for 16S rRNA gene sequencing and analyzed for gut microbiota by Quantitative Insights Into Microbial Ecology (QIIME). RESULTS AAI group had significantly lower richness and diversity of gut microbiota along with Th2 response and allergic airway inflammation. Moreover, the AAI group had lower abundance of butyrate-producing bacterial taxa with more Lactobacillus. Chiropractic therapy significantly increased the richness and diversity of gut microbiota and increased butyrate-producing bacterial taxa and decreased Lactobacillus, along with attenuating Th2 response and allergic airway inflammation during AAI modelling. CONCLUSIONS Chiropractic therapy attenuated allergic airway inflammation and optimized gut microbiota in an immature rat model, which might promote the development of adult-like butyrogenic milieu, immunotolerance, and inflammation attenuation.}, }
@article {pmid32989484, year = {2020}, author = {González-Hourcade, M and Del Campo, EM and Casano, LM}, title = {The Under-explored Extracellular Proteome of Aero-Terrestrial Microalgae Provides Clues on Different Mechanisms of Desiccation Tolerance in Non-Model Organisms.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01604-8}, pmid = {32989484}, issn = {1432-184X}, support = {CGL2016-80259-P//Ministerio de Ciencia, Innovación y Universidades/ ; }, abstract = {Trebouxia sp. (TR9) and Coccomyxa simplex (Csol) are desiccation-tolerant lichen microalgae with different adaptive strategies in accordance with the prevailing conditions of their habitats. The remodelling of cell wall and extracellular polysaccharides depending on water availability are key elements in the tolerance to desiccation of both microalgae. Currently, there is no information about the extracellular proteins of these algae and other aero-terrestrial microalgae in response to limited water availability. To our knowledge, this is the first report on the proteins associated with the extracellular polymeric substances (EPS) of aero-terrestrial microalgae subjected to cyclic desiccation/rehydration. LC-MS/MS and bioinformatic analyses of the EPS-associated proteins in the two lichen microalgae submitted to four desiccation/rehydration cycles allowed the compilation of 111 and 121 identified proteins for TR9 and Csol, respectively. Both sets of EPS-associated proteins shared a variety of predicted biological functions but showed a constitutive expression in Csol and partially inducible in TR9. In both algae, the EPS-associated proteins included a number of proteins of unknown functions, some of which could be considered as small intrinsically disordered proteins related with desiccation-tolerant organisms. Differences in the composition and the expression pattern between the studied EPS-associated proteins would be oriented to preserve the biochemical and biophysical properties of the extracellular structures under the different conditions of water availability in which each alga thrives.}, }
@article {pmid32984478, year = {2020}, author = {Hassen, AI and Pierneef, R and Swanevelder, ZH and Bopape, FL}, title = {Microbial and functional diversity of Cyclopia intermedia rhizosphere microbiome revealed by analysis of shotgun metagenomics sequence data.}, journal = {Data in brief}, volume = {32}, number = {}, pages = {106288}, pmid = {32984478}, issn = {2352-3409}, abstract = {Cyclopia spp., commonly referred to as honeybush due to the honey scented flowers, are indigenous legumes mainly growing in the Cape Floristic Region of the Western Cape, South Africa. Dozens of species, including Cyclopia intermedia, C. subternata, C. plicata, C. genistoides are used to make the well-known, popular and widely enjoyed beverage called 'honeybush tea'. In the past, most rhizosphere microbial studies associated with Cyclopia spp. focused mainly on the taxonomy and diversity of the root nodule associated symbiotic nitrogen fixing rhizobia. The work presented here is the first report on the microbial and functional diversity of rhizosphere microbiome associated with Cyclopia intermedia. Metagenomic shotgun sequencing was performed on the rhizosphere soil sample collected from this Cyclopia sp. using illumina Hiseq 2500 platform which resulted in an α- diversity of 312 species. Analysis of the metagenome sequence using the Metagenomic analysis server (MG-RAST) indicated that bacteria constitute the dominant domain followed by Eukaryota, Archaea and other sequences derived from fungi and viruses. Functional diversity of the metagenome based on analysis using the Cluster Orthologous Group (COG) method showed metabolism as the most important function in the community. The raw sequence data is uploaded in FASTQ format on MG-RAST server with ID mgm4855911.3 which can be accessed at http://www.mg-rast.org/linkin.cgi?project=mgp90368. The data on the microbial and functional diversity of the rhizosphere community of Cyclopia intermedia generates a baseline information about the microbial ecology of this indigenous legume. The microbial profile data can also be used as indicators of soil health characteristic of the rhizosphere of this important legume.}, }
@article {pmid32983401, year = {2020}, author = {Lequime, S and Bastide, P and Dellicour, S and Lemey, P and Baele, G}, title = {nosoi: A stochastic agent-based transmission chain simulation framework in r.}, journal = {Methods in ecology and evolution}, volume = {11}, number = {8}, pages = {1002-1007}, pmid = {32983401}, issn = {2041-210X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {The transmission process of an infectious agent creates a connected chain of hosts linked by transmission events, known as a transmission chain. Reconstructing transmission chains remains a challenging endeavour, except in rare cases characterized by intense surveillance and epidemiological inquiry. Inference frameworks attempt to estimate or approximate these transmission chains but the accuracy and validity of such methods generally lack formal assessment on datasets for which the actual transmission chain was observed.We here introduce nosoi, an open-source r package that offers a complete, tunable and expandable agent-based framework to simulate transmission chains under a wide range of epidemiological scenarios for single-host and dual-host epidemics. nosoi is accessible through GitHub and CRAN, and is accompanied by extensive documentation, providing help and practical examples to assist users in setting up their own simulations.Once infected, each host or agent can undergo a series of events during each time step, such as moving (between locations) or transmitting the infection, all of these being driven by user-specified rules or data, such as travel patterns between locations. nosoi is able to generate a multitude of epidemic scenarios, that can-for example-be used to validate a wide range of reconstruction methods, including epidemic modelling and phylodynamic analyses. nosoi also offers a comprehensive framework to leverage empirically acquired data, allowing the user to explore how variations in parameters can affect epidemic potential. Aside from research questions, nosoi can provide lecturers with a complete teaching tool to offer students a hands-on exploration of the dynamics of epidemiological processes and the factors that impact it. Because the package does not rely on mathematical formalism but uses a more intuitive algorithmic approach, even extensive changes of the entire model can be easily and quickly implemented.}, }
@article {pmid32983187, year = {2020}, author = {de Souza, RSC and Armanhi, JSL and Arruda, P}, title = {From Microbiome to Traits: Designing Synthetic Microbial Communities for Improved Crop Resiliency.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {1179}, pmid = {32983187}, issn = {1664-462X}, abstract = {Plants teem with microorganisms, whose tremendous diversity and role in plant-microbe interactions are being increasingly explored. Microbial communities create a functional bond with their hosts and express beneficial traits capable of enhancing plant performance. Therefore, a significant task of microbiome research has been identifying novel beneficial microbial traits that can contribute to crop productivity, particularly under adverse environmental conditions. However, although knowledge has exponentially accumulated in recent years, few novel methods regarding the process of designing inoculants for agriculture have been presented. A recently introduced approach is the use of synthetic microbial communities (SynComs), which involves applying concepts from both microbial ecology and genetics to design inoculants. Here, we discuss how to translate this rationale for delivering stable and effective inoculants for agriculture by tailoring SynComs with microorganisms possessing traits for robust colonization, prevalence throughout plant development and specific beneficial functions for plants. Computational methods, including machine learning and artificial intelligence, will leverage the approaches of screening and identifying beneficial microbes while improving the process of determining the best combination of microbes for a desired plant phenotype. We focus on recent advances that deepen our knowledge of plant-microbe interactions and critically discuss the prospect of using microbes to create SynComs capable of enhancing crop resiliency against stressful conditions.}, }
@article {pmid32983012, year = {2020}, author = {Hounmanou, YMG and Dalsgaard, A and Sopacua, TF and Uddin, GMN and Leekitcharoenphon, P and Hendriksen, RS and Olsen, JE and Larsen, MH}, title = {Molecular Characteristics and Zoonotic Potential of Salmonella Weltevreden From Cultured Shrimp and Tilapia in Vietnam and China.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1985}, pmid = {32983012}, issn = {1664-302X}, abstract = {Salmonella Weltevreden is increasingly reported from aquatic environments, seafood, and patients in several Southeast Asian countries. Using genome-wide analysis, we characterized S. Weltevreden isolated from cultured shrimp and tilapia from Vietnam and China to study their genetic characteristics and relatedness to clinical isolates of S. Weltevreden ST-365. The phylogenetic analysis revealed up to 312 single-nucleotide polymorphism (SNP) difference between tilapia isolates, whereas isolates from shrimp were genetically more closely related. Epidemiologically unrelated isolates from Vietnam were closely related to isolates from China, e.g., 20 SNPs differences between strains 28V and 75C. In comparison with strains from other parts of the world, our environmental isolates predominantly clustered within the continental South Asia lineage, constituted mostly of strains from human stool with as low as seven SNPs difference, e.g., 30V versus Cont_ERR495254. All sequenced isolates were MLST type ST-365 and contained the major virulence-related genes encoded by the Salmonella Pathogenicity Islands 1-5. Ten of the isolates harbored the IncFII(S) plasmid similar to the virulence genes-mediated plasmid pSPCV of S. Paratyphi C, and one isolate had the IncQ1 plasmid on the same contig with strA/B, sul2, and tetA resistance genes similar to the IncQ1 type, pNUC of S. Typhimurium. A pangenomic analysis yielded 7891 genes including a core genome of 4892 genes, with a closely related accessory genome content between clinical and environmental isolates (Benjamini p > 0.05). In a search for differences that could explain the higher prevalence of S. Weltevreden in aquatic samples, genomes were compared with those of other Salmonella enterica serovars. S. Weltevreden revealed specific regions harboring glpX (Fructose-1;6-bisphosphatase; class II), rfbC (dTDP-4-dehydrorhamnose 3;5-epimerase), and cmtB (PTS Mannitol-specific cryptic phosphotransferase enzyme IIA component) involved in carbohydrate biosynthesis pathways. Our study builds grounds for future experiments to determine genes or pathways that are essential when S. Weltevreden are in aquatic environments and microbial interactions providing survival advantages to S. Weltevreden in such environments.}, }
@article {pmid32982988, year = {2020}, author = {van der Goot, E and van Spronsen, FJ and Falcão Salles, J and van der Zee, EA}, title = {A Microbial Community Ecology Perspective on the Gut-Microbiome-Brain Axis.}, journal = {Frontiers in endocrinology}, volume = {11}, number = {}, pages = {611}, pmid = {32982988}, issn = {1664-2392}, }
@article {pmid32979812, year = {2020}, author = {Meyer, KM and Morris, AH and Webster, K and Klein, AM and Kroeger, ME and Meredith, LK and Brændholt, A and Nakamura, F and Venturini, A and Fonseca de Souza, L and Shek, KL and Danielson, R and van Haren, J and Barbosa de Camargo, P and Tsai, SM and Dini-Andreote, F and de Mauro, JMS and Barlow, J and Berenguer, E and Nüsslein, K and Saleska, S and Rodrigues, JLM and Bohannan, BJM}, title = {Belowground changes to community structure alter methane-cycling dynamics in Amazonia.}, journal = {Environment international}, volume = {145}, number = {}, pages = {106131}, doi = {10.1016/j.envint.2020.106131}, pmid = {32979812}, issn = {1873-6750}, abstract = {Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with increases in soil methane (CH4) emission. To better understand the drivers of this change, we measured soil CH4 flux, environmental conditions, and belowground microbial community structure across primary forests, cattle pastures, and secondary forests in two Amazonian regions. We show that pasture soils emit high levels of CH4 (mean: 3454.6 ± 9482.3 μg CH4 m-2 d-1), consistent with previous reports, while forest soils on average emit CH4 at modest rates (mean: 9.8 ± 120.5 μg CH4 m-2 d-1), but often act as CH4 sinks. We report that secondary forest soils tend to consume CH4 (mean: -10.2 ± 35.7 μg CH4 m-2 d-1), demonstrating that pasture CH4 emissions can be reversed. We apply a novel computational approach to identify microbial community attributes associated with flux independent of soil chemistry. While this revealed taxa known to produce or consume CH4 directly (i.e. methanogens and methanotrophs, respectively), the vast majority of identified taxa are not known to cycle CH4. Each land use type had a unique subset of taxa associated with CH4 flux, suggesting that land use change alters CH4 cycling through shifts in microbial community composition. Taken together, we show that microbial composition is crucial for understanding the observed CH4 dynamics and that microorganisms provide explanatory power that cannot be captured by environmental variables.}, }
@article {pmid32978127, year = {2020}, author = {Xia, W and Zhao, J and Zheng, Y and Zhang, H and Zhang, J and Chen, R and Lin, X and Jia, Z}, title = {Active soil nitrifying communities revealed by in situ transcriptomics and microcosm-based stable isotope probing.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.01807-20}, pmid = {32978127}, issn = {1098-5336}, abstract = {Long-term nitrogen (N) field fertilization often results in significant changes in nitrifying communities that catalyze a key step in the global N cycle. However, whether microcosm studies are able to inform the dynamic changes of ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities under field conditions remains poorly understood. This study aimed to evaluate the transcriptional activities of nitrifying communities under in situ conditions, and we found that they were largely similar to 13C-labeled nitrifying communities in the urea-amended microcosms of soils that had received different N fertilization regimes for 22 years. High-throughput sequencing of 16S rRNA genes and transcripts suggested that Nitrosospira cluster 3 -like AOB and Nitrososphaera viennensis-like AOA were significantly stimulated in N fertilized fresh soils. Real-time quantitative PCR demonstrated that the significant increase of AOA and AOB in fresh soils upon nitrogen fertilization could be preserved in the air-dried soils. DNA-based stable isotope probing (SIP) further revealed the greatest labeling of Nitrosospira cluster 3-like AOB and N. viennensis-like AOA, despite the strong advantage of AOB over AOA in the N fertilized soils. Nitrobacter-like nitrite-oxidizing bacteria (NOB) played more important roles than Nitrospira-like NOB in urea-amended SIP microcosms, while the situation was opposite under field conditions. Our results suggest that long-term fertilization selected for physiologically versatile AOB and AOA that could have been adapted to a wide range of substrate ammonium concentrations. It also provides compelling evidences that the dominant communities of transcriptionally active nitrifiers under field conditions were largely similar to those revealed in 13C-labeled microcosms.IMPORTANCEThe role of manipulated microcosm in microbial ecology has been much debated because it cannot entirely represent the in situ situation. We collected soil samples from 20 field plots including 5 different treatments with and without nitrogen fertilizers for 22 years, in order to assess active nitrifying communities by in situ transcriptomics and microcosm-based stable isotope probing. The results showed that chronic N enrichment led to competitive advantages of Nitrosospira cluster 3-like AOB over N. viennensis-like AOA in soils under field conditions. Microcosm labeling revealed similar results of active AOA and AOB, although apparent discrepancy was observed for nitrite-oxidizing bacteria. This study suggests that soil microbiome represents a relatively stable community resulting from complex evolutionary processes over a large time scale, and microcosm can serve as a powerful tool to test the theory of environmental filtering on the key functional microbial guilds.}, }
@article {pmid32975888, year = {2020}, author = {Goelen, T and Vuts, J and Sobhy, IS and Wäckers, F and Caulfield, JC and Birkett, MA and Rediers, H and Jacquemyn, H and Lievens, B}, title = {Identification and application of bacterial volatiles to attract a generalist aphid parasitoid: from laboratory to greenhouse assays.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.6102}, pmid = {32975888}, issn = {1526-4998}, abstract = {BACKGROUND: Recent studies have shown that microorganisms emit volatile compounds that affect insect behaviour. However, it remains largely unclear whether microbes can be exploited as a source of attractants to improve biological control of insect pests. In this study, we used a combination of coupled gas chromatography-electroantennography (GC-EAG) and Y-tube olfactometer bioassays to identify attractive compounds in the volatile extracts of three bacterial strains that are associated with the habitat of the generalist aphid parasitoid Aphidius colemani, and to create mixtures of synthetic compounds to find attractive blends for A. colemani. Subsequently, the most attractive blend was evaluated in two-choice cage experiments under greenhouse conditions.<br><br>RESULTS: GC-EAG analysis revealed 20 compounds that were linked to behaviourally attractive bacterial strains. A mixture of two EAG-active compounds, styrene and benzaldehyde applied at a respective dose of 1 μg and 10 ng, was more attractive than the single compounds or the culture medium of the bacteria in Y-tube olfactometer bioassays. Application of this synthetic mixture under greenhouse conditions resulted in significant attraction of the parasitoids, and outperformed application of the bacterial culture medium.<br><br>CONCLUSION: Compounds isolated from bacterial blends were capable of attracting parasitoids both in laboratory and greenhouse assays, indicating that microbial cultures are an effective source of insect attractants. This opens new opportunities to attract and retain natural enemies of pest species and to enhance biological pest control. This article is protected by copyright. All rights reserved.}, }
@article {pmid32975751, year = {2020}, author = {Garbisu, C and Alkorta, I and Kidd, P and Epelde, L and Mench, M}, title = {Keep and promote biodiversity at polluted sites under phytomanagement.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-020-10854-5}, pmid = {32975751}, issn = {1614-7499}, support = {SOE1/P5/E0189//Interreg/ ; }, abstract = {The phytomanagement concept combines a sustainable reduction of pollutant linkages at risk-assessed contaminated sites with the generation of both valuable biomass for the (bio)economy and ecosystem services. One of the potential benefits of phytomanagement is the possibility to increase biodiversity in polluted sites. However, the unique biodiversity present in some polluted sites can be severely impacted by the implementation of phytomanagement practices, even resulting in the local extinction of endemic ecotypes or species of great conservation value. Here, we highlight the importance of promoting measures to minimise the potential adverse impact of phytomanagement on biodiversity at polluted sites, as well as recommend practices to increase biodiversity at phytomanaged sites without compromising its effectiveness in terms of reduction of pollutant linkages and the generation of valuable biomass and ecosystem services.}, }
@article {pmid32975677, year = {2020}, author = {Ouarabi, L and Drider, D and Taminiau, B and Daube, G and Bendali, F and Lucau-Danila, A}, title = {Vaginal Microbiota: Age Dynamic and Ethnic Particularities of Algerian Women.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01606-6}, pmid = {32975677}, issn = {1432-184X}, abstract = {The composition of the vaginal microbiota is a key element for maintaining gynecological and reproductive health. With the aim of obtaining an accurate overview of the vaginal microbiota of Algerian women, in terms of their age and ethnic group, we conducted a 16S rRNA gene targeted metagenomic analysis of 100 vaginal samples taken from healthy childbearing and menopausal women. These data were used to establish the pattern of the vaginal microbiota during reproductive and postreproductive phases. Hormone levels were correlated to changes in microbial composition for menopausal women. The ethnic comparison revealed a particular microbiota profile for Algerian women, with a dominance of CST III and CST I. A rapid qPCR method developed by the authors was successfully used to identify the vaginal bacterial pattern for a customized gynecological management.}, }
@article {pmid32975666, year = {2020}, author = {Lee, CW and Lim, JH and Heng, PL and Marican, NF and Narayanan, K and Sim, EUH and Bong, CW}, title = {Influence of elevated river flow on hypoxia occurrence, nutrient concentration and microbial dynamics in a tropical estuary.}, journal = {Environmental monitoring and assessment}, volume = {192}, number = {10}, pages = {660}, doi = {10.1007/s10661-020-08625-3}, pmid = {32975666}, issn = {1573-2959}, support = {HiCOE (IOES-2014D)//Ministry of Higher Education/ ; FRGS (FP061-2018A)//Ministry of Higher Education/ ; }, mesh = {Chlorophyll A ; Environmental Monitoring ; *Estuaries ; Humans ; Hypoxia ; Nutrients ; *Rivers ; Seasons ; }, abstract = {We sampled the Klang estuary during the inter-monsoon and northeast monsoon period (July-Nov 2011, Oct-Nov 2012), which coincided with higher rainfall and elevated Klang River flow. The increased freshwater inflow into the estuary resulted in water column stratification that was observed during both sampling periods. Dissolved oxygen (DO) dropped below 63 μM, and hypoxia was observed. Elevated river flow also transported dissolved inorganic nutrients, chlorophyll a and bacteria to the estuary. However, bacterial production did not correlate with DO concentration in this study. As hypoxia was probably not due to in situ heterotrophic processes, deoxygenated waters were probably from upstream. We surmised this as DO correlated with salinity (R2 = 0.664, df = 86, p < 0.001). DO also decreased with increasing flushing time (R2 = 0.556, df = 11, p < 0.01), suggesting that when flushing time (> 6.7 h), hypoxia could occur at the Klang estuary. Here, we presented a model that related riverine flow rate to the post-heavy rainfall hypoxia that explicated the episodic hypoxia at Klang estuary. As Klang estuary supports aquaculture and cockle culture, our results could help protect the aquaculture and cockle culture industry here.}, }
@article {pmid32975419, year = {2020}, author = {Trueba-Santiso, A and Wasmund, K and Soder-Walz, JM and Marco-Urrea, E and Adrian, L}, title = {Genome Sequence, Proteome Profile, and Identification of a Multiprotein Reductive Dehalogenase Complex in Dehalogenimonas alkenigignens Strain BRE15M.}, journal = {Journal of proteome research}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jproteome.0c00569}, pmid = {32975419}, issn = {1535-3907}, abstract = {Bacteria of the genus Dehalogenimonas respire with vicinally halogenated alkanes via dihaloelimination. We aimed to describe involved proteins and their supermolecular organization. Metagenomic sequencing of a Dehalogenimonas-containing culture resulted in a 1.65 Mbp draft genome of Dehalogenimonas alkenigignens strain BRE15M. It contained 31 full-length reductive dehalogenase homologous genes (rdhA), but only eight had cognate rdhB gene coding for membrane-anchoring proteins. Shotgun proteomics of cells grown with 1,2-dichloropropane as an electron acceptor identified 1152 proteins representing more than 60% of the total proteome. Ten RdhA proteins were detected, including a DcpA ortholog, which was the strongest expressed RdhA. Blue native gel electrophoresis (BNE) demonstrating maximum activity was localized in a protein complex of 146-242 kDa. Protein mass spectrometry revealed the presence of DcpA, its membrane-anchoring protein DcpB, two hydrogen uptake hydrogenase subunits (HupL and HupS), an iron-sulfur protein (HupX), and subunits of a redox protein with a molybdopterin-binding motif (OmeA and OmeB) in the complex. BNE after protein solubilization with different detergent concentrations revealed no evidence for an interaction between the putative respiratory electron input module (HupLS) and the OmeA/OmeB/HupX module. All detected RdhAs comigrated with the organohalide respiration complex. Based on genomic and proteomic analysis, we propose quinone-independent respiration in Dehalogenimonas.}, }
@article {pmid32974747, year = {2020}, author = {Souza, UA and Webster, A and Dall'Agnol, B and Morel, AP and Peters, FB and Favarini, MO and Mazim, FD and Soares, JBG and Tirelli, FP and Tortato, MA and de Lemos, ERS and Trigo, TC and Soares, JF and Reck, J}, title = {Molecular and Serological Survey of the Cat-Scratch Disease Agent (Bartonella henselae) in Free-Ranging Leopardus geoffroyi and Leopardus wiedii (Carnivora: Felidae) From Pampa Biome, Brazil.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01601-x}, pmid = {32974747}, issn = {1432-184X}, abstract = {The genus Bartonella comprises emerging bacteria that affect humans and other mammals worldwide. Felids represent an important reservoir for several Bartonella species. Domestic cats are the main reservoir of Bartonella henselae, the agent of cat scratch disease (CSD). It can be transmitted directly by scratches and bites from infected cats and via cat fleas. This study aims to investigate the circulation of Bartonella spp. in free-ranging Neotropical wild felids from Southern Brazil using serological and molecular methods. In this study, 53 live-trapped free-ranging wild felids were sampled, 39 Leopardus geoffroyi and 14 Leopardus wiedii, from five municipalities in the Rio Grande, do Sul state, southern Brazil. All captured animals were clinically healthy. Two blood samples of L. geoffroyi were positive, by PCR, for the presence of B. henselae DNA. Conversely, none of L. wiedii blood samples were positive when tested using PCR. Indirect immunofluorescence assay (IFA) showed that 28% of serum samples of wild felids were reactive (seropositive) for B. henselae by immunofluorescence, with titers ranging from 64 to 256. The results presented here provide the first evidence of a Bartonella-enzootic cycle involving L. geoffroyi and L. wiedii, which may account for the spillover of the emerging zoonotic pathogen B. henselae for the indigenous fauna in Southern Brazil.}, }
@article {pmid32974213, year = {2020}, author = {de Souza-Basqueira, M and Ribeiro, RM and de Oliveira, LC and Moreira, CHV and Martins, RCR and Franco, DC and Amado, PPP and Mayer, MPA and Sabino, EC}, title = {Gut Dysbiosis in Chagas Disease. A Possible Link to the Pathogenesis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {402}, pmid = {32974213}, issn = {2235-2988}, abstract = {Chagas disease is caused by the flagellate protozoan Trypanosoma cruzi. Cardiomyopathy and damage to gastrointestinal tissue are the main disease manifestations. There are data suggesting that the immune response to T. cruzi depends on the intestinal microbiota. We hypothesized that Chagas disease is associated with an altered gut microbiome and that these changes are related to the disease phenotype. The stool microbiome from 104 individuals, 73 with Chagas disease (30 with the cardiac, 11 with the digestive, and 32 with the indeterminate form), and 31 healthy controls was characterized using 16S rRNA amplification and sequencing. The QIIME (Quantitative Insights Into Microbial Ecology) platform was used to analyze the data. Alpha and beta diversity indexes did not indicate differences between the groups. However, the relative abundance of Verrucomicrobia, represented primarily by the genus Akkermansia, was significantly lower in the Chagas disease groups, especially the cardiac group, compared to the controls. Furthermore, differences in the relative abundances of Alistipes, Bilophila, and Dialister were observed between the groups. We conclude that T. cruzi infection results in changes in the gut microbiome that may play a role in the myocardial and intestinal inflammation seen in Chagas disease.}, }
@article {pmid32974121, year = {2020}, author = {Lee, NLY and Huang, D and Quek, ZBR and Lee, JN and Wainwright, BJ}, title = {Distinct fungal communities associated with different organs of the mangrove Sonneratia alba in the Malay Peninsula.}, journal = {IMA fungus}, volume = {11}, number = {}, pages = {17}, pmid = {32974121}, issn = {2210-6340}, abstract = {Mangrove forests are key tropical marine ecosystems that are rich in fungi, but our understanding of fungal communities associated with mangrove trees and their various organs remains limited because much of the diversity lies within the microbiome. In this study, we investigated the fungal communities associated with the mangrove tree Sonneratia alba throughout Peninsular Malaysia and Singapore. At each sampling location, we collected leaves, fruits, pneumatophores and sediment samples and performed amplicon sequencing of the ribosomal internal transcribed spacer 1 to characterise the associated communities. Results show distinct fungal communities at each sampled location with further differentiation according to the plant part. We find a significant distance decay of similarity, particularly for sediment samples due to the greater variability of sediment environments relative to the more stable fungal habitats provided by living plant organs. We are able to assign taxonomy to the majority of sequences from leaves and fruits, but a much larger portion of the sequences recovered from pneumatophores and sediment samples could not be identified. This pattern underscores the limited mycological research performed in marine environments and demonstrates the need for a concerted research effort on multiple species to fully characterise the coastal microbiome and its role in the functioning of marine ecosystems.}, }
@article {pmid32973727, year = {2020}, author = {Kuznecova, J and Šulčius, S and Vogts, A and Voss, M and Jürgens, K and Šimoliūnas, E}, title = {Nitrogen Flow in Diazotrophic Cyanobacterium Aphanizomenon flos-aquae Is Altered by Cyanophage Infection.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {2010}, pmid = {32973727}, issn = {1664-302X}, abstract = {Viruses can significantly influence cyanobacteria population dynamics and activity, and through this the biogeochemical cycling of major nutrients. However, surprisingly little attention has been given to understand how viral infections alter the ability of diazotrophic cyanobacteria for atmospheric nitrogen fixation and its release to the environment. This study addressed the importance of cyanophages for net 15N2 assimilation rate, expression of nitrogenase reductase gene (nifH) and changes in nitrogen enrichment (15N/14N) in the diazotrophic cyanobacterium Aphanizomenon flos-aquae during infection by the cyanophage vB_AphaS-CL131. We found that while the growth of A. flos-aquae was inhibited by cyanophage addition (decreased from 0.02 h-1 to 0.002 h-1), there were no significant differences in nitrogen fixation rates (control: 22.7 × 10-7 nmol N heterocyte-1; infected: 23.9 × 10-7 nmol N heterocyte-1) and nifH expression level (control: 0.6-1.6 transcripts heterocyte-1; infected: 0.7-1.1 transcripts heterocyte-1) between the infected and control A. flos-aquae cultures. This implies that cyanophage genome replication and progeny production within the vegetative cells does not interfere with the N2 fixation reactions in the heterocytes of these cyanobacteria. However, higher 15N enrichment at the poles of heterocytes of the infected A. flos-aquae, revealed by NanoSIMS analysis indicates the accumulation of fixed nitrogen in response to cyanophage addition. This suggests reduced nitrogen transport to vegetative cells and the alterations in the flow of fixed nitrogen within the filaments. In addition, we found that cyanophage lysis resulted in a substantial release of ammonium into culture medium. Cyanophage infection seems to substantially redirect N flow from cyanobacterial biomass to the production of N storage compounds and N release.}, }
@article {pmid32973299, year = {2020}, author = {Hernández-Del Amo, E and Dolinová, I and la Ramis-Jorba, G and Gich, F and Bañeras, L}, title = {Limited effect of radial oxygen loss on ammonia oxidizers in Typha angustifolia root hairs.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15694}, pmid = {32973299}, issn = {2045-2322}, support = {IF-UDG2013//Universitat de Girona/ ; }, abstract = {The benefits of plant-microbe interactions have been exploited extensively for nutrient removal. Radial oxygen loss in aquatic macrophytes potentially promotes nitrification and accelerates nitrogen removal through coupled nitrification-denitrification process. Nitrification is likely the limiting activity for an effective nitrogen removal in wetlands. In this work, we have quantified the effect of radial oxygen losses in Typha angustifolia plants in environments of contrasting salinities, including a temporary lagoon, a constructed wetland, and a river estuary. In all sites, radial oxygen diffusion occurred mainly at a narrow band, from 1 to 5 cm from the root tip, and were almost absent at the tip and basal sections of the root (> 5 cm). Root sections with active oxygen diffusion tended to show higher bacterial and archaeal densities in the rhizoplane according to 16S rRNA gene abundance data, except at higher salinities. Archaeal amoA /bacterial amoA gene ratios were highly variable among sites. Archaeal nitrifiers were only favoured over bacteria on the root surface of Typha collected from the constructed wetland. Collectively, radial oxygen loss had little effect on the nitrifying microbial community at the smaller scale (differences according to root-section), and observed differences were more likely related to prevailing physicochemical conditions of the studied environments or to long-term effects of the root microenvironment (root vs sediment comparisons).}, }
@article {pmid32970805, year = {2020}, author = {Sakarika, M and Sosa, DAT and Depoortere, M and Rottiers, H and Ganigué, R and Dewettinck, K and Rabaey, K}, title = {The type of microorganism and substrate determines the odor fingerprint of dried bacteria targeting microbial protein production.}, journal = {FEMS microbiology letters}, volume = {367}, number = {18}, pages = {}, doi = {10.1093/femsle/fnaa138}, pmid = {32970805}, issn = {1574-6968}, abstract = {The rapidly increasing demand for protein has led to the pursuit of new protein sources, among which microbial protein (MP) is one of the most promising. Although the nutritional properties of MP are important and often well-studied, the sensory properties of the microbial cells will in part determine the commercial success of the product and are much less investigated. Here we assessed the odor fingerprint of dried bacteria originating from pure cultures and enriched mixed microbial communities using an electronic nose (e-nose). The e-nose discriminated between the different MP sources, while the choice of culture and substrate substantially affected their volatile organic compound (VOC) profile. The most dominant odor descriptors (>20% of VOC peak area) were sweet, fruity and fishy, while the mixed cultures presented higher peak areas indicating potentially more intense aromas than the pure cultures. The e-nose can detect the suitability of new MP sources and determine their best end-use.}, }
@article {pmid32969526, year = {2020}, author = {Niemeier-Walsh, C and Ryan, PH and Meller, J and Ollberding, NJ and Adhikari, A and Indugula, R and Reponen, T}, title = {The mycobiomes and bacteriomes of sputum, saliva, and home dust.}, journal = {Indoor air}, volume = {}, number = {}, pages = {}, doi = {10.1111/ina.12750}, pmid = {32969526}, issn = {1600-0668}, support = {T42OH008432/OH/NIOSH CDC HHS/United States ; 5UL1TR001425-04/TR/NCATS NIH HHS/United States ; R21ES024807/ES/NIEHS NIH HHS/United States ; }, abstract = {Respiratory microbiome is an understudied area of research compared to other microbiomes of the human body. The respiratory tract is exposed to an array of environmental pollutants, including microbes. Yet, we know very little about the relationship between environmental and respiratory microbiome. The primary aim of our study was to compare the mycobiomes and bacteriomes between three sample types from the same participants, including home dust, saliva, and sputum. Samples were collected from 40 adolescents in a longitudinal cohort. We analyzed the samples using 16s bacterial rDNA and ITS fungal rDNA gene sequencing, as well as quantitative PCR with universal fungal and bacterial primers. Results showed that home dust had the greatest alpha diversity between the three sample types for both bacteria and fungi. Dust had the highest total fungal load and the lowest total bacterial load. Sputum had greater bacterial diversity than saliva, but saliva had greater fungal diversity than sputum. The distribution of major bacterial phyla differed between all sample types. However, the distribution of major fungal classes differed only between sputum and saliva. Future research should examine the biological significance of the taxa found in each sample type based on microbial ecology and associations with health effects.}, }
@article {pmid32968841, year = {2020}, author = {Zhao, D and Zhang, Z and Niu, H and Guo, H}, title = {Win by Quantity: a Striking Rickettsia-Bias Symbiont Community Revealed by Seasonal Tracking in the Whitefly Bemisia tabaci.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01607-5}, pmid = {32968841}, issn = {1432-184X}, support = {31701797//the National Natural Science Foundation of China/ ; BK20170598//the Natural Science Foundation of Jiangsu Province, China/ ; BE2010342//the Key Research and Development Program of Jiangsu Province, China/ ; }, abstract = {Maintaining an adaptive seasonality is a basic ecological requisite for cold-blooded organism insects which usually harbor various symbionts. However, how coexisting symbionts coordinate in insects during seasonal progress is still unknown. The whitefly Bemisia tabaci in China harbors the obligate symbiont Portiera that infects each individual, as well as various facultative symbionts. In this study, we investigated whitefly populations in cucumber and cotton fields from May to December 2019, aiming to reveal the fluctuations of symbiont infection frequencies, symbiont coordination in multiple infected individuals, and host plants effects on symbiont infections. The results indicated that the facultative symbionts Hamiltonella (H), Rickettsia (R), and Cardinium (C) exist in field whiteflies, with single (H) and double (HC and HR) infections occurring frequently. Infection frequencies of Hamiltonella (always 100%) and Cardinium (29.50-34.38%) remained steady during seasonal progression. Rickettsia infection frequency in the cucumber whitefly population decreased from 64.47% in summer to 35.29% in winter. Significantly lower Rickettsia infection frequency (15.55%) was identified in cotton whitefly populations and was not subject to seasonal fluctuation. Nevertheless, Rickettsia had a significantly quantitative advantage in the symbiont community of whitefly individuals and populations from both cucumber and cotton field all through the seasons. Moreover, higher Portiera and Hamiltonella densities were found in HC and HR whitefly than in H whitefly, suggesting these symbionts may contribute to producing nutrients for their symbiont partners. These results provide ample cues to further explore the interactions between coexisting symbionts, the coevolutionary relationship between symbionts and host symbiont-induced effects on host plant use.}, }
@article {pmid32967081, year = {2020}, author = {Ortiz, M and Bosch, J and Coclet, C and Johnson, J and Lebre, P and Salawu-Rotimi, A and Vikram, S and Makhalanyane, T and Cowan, D}, title = {Microbial Nitrogen Cycling in Antarctic Soils.}, journal = {Microorganisms}, volume = {8}, number = {9}, pages = {}, doi = {10.3390/microorganisms8091442}, pmid = {32967081}, issn = {2076-2607}, abstract = {The Antarctic continent is widely considered to be one of the most hostile biological habitats on Earth. Despite extreme environmental conditions, the ice-free areas of the continent, which constitute some 0.44% of the total continental land area, harbour substantial and diverse communities of macro-organisms and especially microorganisms, particularly in the more &quot;hospitable&quot; maritime regions. In the more extreme non-maritime regions, exemplified by the McMurdo Dry Valleys of South Victoria Land, nutrient cycling and ecosystem servicing processes in soils are largely driven by microbial communities. Nitrogen turnover is a cornerstone of ecosystem servicing. In Antarctic continental soils, specifically those lacking macrophytes, cold-active free-living diazotrophic microorganisms, particularly Cyanobacteria, are keystone taxa. The diazotrophs are complemented by heterotrophic bacterial and archaeal taxa which show the genetic capacity to perform elements of the entire N cycle, including nitrification processes such as the anammox reaction. Here, we review the current literature on nitrogen cycling genes, taxa, processes and rates from studies of Antarctic soils. In particular, we highlight the current gaps in our knowledge of the scale and contribution of these processes in south polar soils as critical data to underpin viable predictions of how such processes may alter under the impacts of future climate change.}, }
@article {pmid32963580, year = {2020}, author = {Floková, K and Shimels, M and Andreo Jimenez, B and Bardaro, N and Strnad, M and Novák, O and Bouwmeester, HJ}, title = {An improved strategy to analyse strigolactones in complex sample matrices using UHPLC-MS/MS.}, journal = {Plant methods}, volume = {16}, number = {}, pages = {125}, pmid = {32963580}, issn = {1746-4811}, abstract = {Background: Strigolactones represent the most recently described group of plant hormones involved in many aspects of plant growth regulation. Simultaneously, root exuded strigolactones mediate rhizosphere signaling towards beneficial arbuscular mycorrhizal fungi, but also attract parasitic plants. The seed germination of parasitic plants induced by host strigolactones leads to serious agricultural problems worldwide. More insight in these signaling molecules is hampered by their extremely low concentrations in complex soil and plant tissue matrices, as well as their instability. So far, the combination of tailored isolation-that would replace current unspecific, time-consuming and labour-intensive processing of large samples-and a highly sensitive method for the simultaneous profiling of a broad spectrum of strigolactones has not been reported.<br><br>Results: Depending on the sample matrix, two different strategies for the rapid extraction of the seven structurally similar strigolactones and highly efficient single-step pre-concentration on polymeric RP SPE sorbent were developed and validated. Compared to conventional methods, controlled temperature during the extraction and the addition of an organic modifier (acetonitrile, acetone) to the extraction solvent helped to tailor strigolactone isolation from low initial amounts of root tissue (150 mg fresh weight, FW) and root exudate (20 ml), which improved both strigolactone stability and sample purity. We have designed an efficient UHPLC separation with sensitive MS/MS detection for simultaneous analysis of seven natural strigolactones including their biosynthetic precursors-carlactone and carlactonoic acid. In combination with the optimized UHPLC-MS/MS method, attomolar detection limits were achieved. The new method allowed successful profiling of seven strigolactones in small exudate and root tissue samples of four different agriculturally important plant species-sorghum, rice, pea and tomato.<br><br>Conclusion: The established method provides efficient strigolactone extraction with aqueous mixtures of less nucleophilic organic solvents from small root tissue and root exudate samples, in combination with rapid single-step pre-concentration. This method improves strigolactone stability and eliminates the co-extraction and signal of matrix-associated contaminants during the final UHPLC-MS/MS analysis with an electrospray interface, which dramatically increases the overall sensitivity of the analysis. We show that the method can be applied to a variety of plant species.}, }
@article {pmid32963001, year = {2020}, author = {Dueholm, MS and Andersen, KS and McIlroy, SJ and Kristensen, JM and Yashiro, E and Karst, SM and Albertsen, M and Nielsen, PH}, title = {Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax).}, journal = {mBio}, volume = {11}, number = {5}, pages = {}, pmid = {32963001}, issn = {2150-7511}, abstract = {High-throughput 16S rRNA gene amplicon sequencing is an essential method for studying the diversity and dynamics of microbial communities. However, this method is presently hampered by the lack of high-identity reference sequences for many environmental microbes in the public 16S rRNA gene reference databases and by the absence of a systematic and comprehensive taxonomy for the uncultured majority. Here, we demonstrate how high-throughput synthetic long-read sequencing can be applied to create ecosystem-specific full-length 16S rRNA gene amplicon sequence variant (FL-ASV) resolved reference databases that include high-identity references (>98.7% identity) for nearly all abundant bacteria (>0.01% relative abundance) using Danish wastewater treatment systems and anaerobic digesters as an example. In addition, we introduce a novel sequence identity-based approach for automated taxonomy assignment (AutoTax) that provides a complete seven-rank taxonomy for all reference sequences, using the SILVA taxonomy as a backbone, with stable placeholder names for unclassified taxa. The FL-ASVs are perfectly suited for the evaluation of taxonomic resolution and bias associated with primers commonly used for amplicon sequencing, allowing researchers to choose those that are ideal for their ecosystem. Reference databases processed with AutoTax greatly improves the classification of short-read 16S rRNA ASVs at the genus- and species-level, compared with the commonly used universal reference databases. Importantly, the placeholder names provide a way to explore the unclassified environmental taxa at different taxonomic ranks, which in combination with in situ analyses can be used to uncover their ecological roles.}, }
@article {pmid32962223, year = {2020}, author = {Rothman, JA and Cox-Foster, DL and Andrikopoulos, C and McFrederick, QS}, title = {Diet Breadth Affects Bacterial Identity but Not Diversity in the Pollen Provisions of Closely Related Polylectic and Oligolectic Bees.}, journal = {Insects}, volume = {11}, number = {9}, pages = {}, doi = {10.3390/insects11090645}, pmid = {32962223}, issn = {2075-4450}, support = {NNX15AP99A/NASA/NASA/United States ; 2018-67011- 28123//U.S. Department of Agriculture/ ; CA-R-ENT-5109-H//U.S. Department of Agriculture/ ; 1929572//National Science Foundation/ ; Pollinating Insect Research Unit Base Funds//U.S. Department of Agriculture/ ; }, abstract = {Mounting evidence suggests that microbes found in the pollen provisions of wild and solitary bees are important drivers of larval development. As these microbes are also known to be transmitted via the environment, most likely from flowers, the diet breadth of a bee may affect the diversity and identity of the microbes that occur in its pollen provisions. Here, we tested the hypothesis that, due to the importance of floral transmission of microbes, diet breadth affects pollen provision microbial community composition. We collected pollen provisions at four sites from the polylectic bee Osmia lignaria and the oligolectic bee Osmia ribifloris. We used high-throughput sequencing of the bacterial 16S rRNA gene to characterize the bacteria found in these provisions. We found minimal overlap in the specific bacterial variants in pollen provisions across the host species, even when the bees were constrained to foraging from the same flowers in cages at one site. Similarly, there was minimal overlap in the specific bacterial variants across sites, even within the same host species. Together, these findings highlight the importance of environmental transmission and host specific sorting influenced by diet breadth for microbes found in pollen provisions. Future studies addressing the functional consequences of this filtering, along with tests for differences between more species of oligoletic and polylectic bees will provide rich insights into the microbial ecology of solitary bees.}, }
@article {pmid32962069, year = {2020}, author = {Cold, F and Kousgaard, SJ and Halkjaer, SI and Petersen, AM and Nielsen, HL and Thorlacius-Ussing, O and Hansen, LH}, title = {Fecal Microbiota Transplantation in the Treatment of Chronic Pouchitis: A Systematic Review.}, journal = {Microorganisms}, volume = {8}, number = {9}, pages = {}, doi = {10.3390/microorganisms8091433}, pmid = {32962069}, issn = {2076-2607}, support = {7076-00129B//Danish Innovation Fund/ ; }, abstract = {The objective was to evaluate available literature on treatment of chronic pouchitis with fecal microbiota transplantation (FMT) focusing on clinical outcomes, safety, and different approaches to FMT preparation and delivery. A systematic review of electronic databases was conducted using Medline, EMBASE, and the Cochrane Central Register of Controlled Trials Library from inception through April 2020. Human studies of all study types reporting results of FMT to treat chronic pouchitis were included. Nine studies, reporting FMT treatment of 69 patients with chronic pouchitis were found eligible for the review. Most studies were case series and cohort studies rated as having fair to poor quality due to high risk of bias and small sample size. Only one randomized controlled trial was included, finding no beneficial effect of FMT. In total clinical response after FMT was reported in 14 (31.8%) out of 44 evaluated patients at various timepoints after FMT, and clinical remission in ten (22.7%) patients. Only minor self-limiting adverse events were reported. FMT varied greatly regarding preparation, length of treatment, and route of delivery. The effects of FMT on symptoms of chronic pouchitis are not established, though some studies show promising results. Future controlled well-designed studies are warranted.}, }
@article {pmid32962009, year = {2020}, author = {Pantanella, F and Lekunberri, I and Gagliardi, A and Venuto, G and Sànchez-Melsió, A and Fabiani, M and Balcázar, JL and Schippa, S and De Giusti, M and Borrego, C and Solimini, A}, title = {Effect of Urban Wastewater Discharge on the Abundance of Antibiotic Resistance Genes and Antibiotic-Resistant Escherichia coli in Two Italian Rivers.}, journal = {International journal of environmental research and public health}, volume = {17}, number = {18}, pages = {}, doi = {10.3390/ijerph17186813}, pmid = {32962009}, issn = {1660-4601}, support = {2014-W-MS-17//Joint Programming Initiative Water challenges for a changing world/ ; }, abstract = {BACKGROUND: Wastewater treatment plants (WWTPs) are microbial factories aimed to reduce the amount of nutrients and pathogenic microorganisms in the treated wastewater before its discharge into the environment. We studied the impact of urban WWTP effluents on the abundance of antibiotic resistance genes (ARGs) and antibiotic-resistant Escherichia coli (AR-E. coli) in the last stretch of two rivers (Arrone and Tiber) in Central Italy that differ in size and flow volume.<br><br>METHODS: Water samples were collected in three seasons upstream and downstream of the WWTP, at the WWTP outlet, and at sea sites near the river mouth, and analyzed for the abundance of ARGs by qPCR and AR-E. coli using cultivation followed by disk diffusion assays.<br><br>RESULTS: For all studied genes (16S rRNA, intI1, sul1, ermB, blaTEM, tetW and qnrS), absolute concentrations were significantly higher in the Tiber than in the Arrone at all sampling sites, despite their collection date, but the prevalence of target ARGs within bacterial communities in both rivers was similar. The absolute concentrations of most ARGs were also generally higher in the WWTP effluent with median levels between log 4 and log 6 copies per ml but did not show differences along the studied stretches of rivers. Statistically significant site effect was found for E. coli phenotypic resistance to tetracycline and ciprofloxacin in the Arrone but not in the Tiber.<br><br>CONCLUSIONS: In both rivers, diffuse or point pollution sources other than the studied WWTP effluents may account for the observed resistance pattern, although the Arrone appears as more sensitive to the wastewater impact considering its lower flow volume.}, }
@article {pmid32961710, year = {2020}, author = {Yacoub, A and Magnin, N and Gerbore, J and Haidar, R and Bruez, E and Compant, S and Guyoneaud, R and Rey, P}, title = {The Biocontrol Root-Oomycete, Pythium Oligandrum, Triggers Grapevine Resistance and Shifts in the Transcriptome of the Trunk Pathogenic Fungus, Phaeomoniella Chlamydospora.}, journal = {International journal of molecular sciences}, volume = {21}, number = {18}, pages = {}, doi = {10.3390/ijms21186876}, pmid = {32961710}, issn = {1422-0067}, abstract = {The worldwide increase in grapevine trunk diseases, mainly esca, represents a major threat for vineyard sustainability. Biocontrol of a pioneer fungus of esca, Phaeomoniella chlamydospora, was investigated here by deciphering the tripartite interaction between this trunk-esca pathogen, grapevine and the biocontrol-oomycete, Pythium oligandrum. When P. oligandrum colonizes grapevine roots, it was observed that the wood necroses caused by P. chlamydospora were significantly reduced. Transcriptomic analyses of plant and fungus responses were performed to determine the molecular events occurring, with the aim to relate P.chlamydospora degradation of wood to gene expression modulation. Following P. oligandrum-root colonization, major transcriptomic changes occurred both, in the grapevine-defense system and in the P. chlamydospore-virulence factors. Grapevine-defense was enhanced in response to P. chlamydospora attacks, with P. oligandrum acting as a plant-systemic resistance inducer, promoting jasmonic/ethylene signaling pathways and grapevine priming. P. chlamydospora pathogenicity genes, such as those related to secondary metabolite biosynthesis, carbohydrate-active enzymes and transcription regulators, were also affected in their expression. Shifts in grapevine responses and key-fungal functions were associated with the reduction of P. chlamydospora wood necroses. This study provides evidence of wood fungal pathogen transcriptional changes induced by a root biocontrol agent, P. oligandrum, in which there is no contact between the two microorganisms.}, }
@article {pmid32961324, year = {2020}, author = {de Souza, CM and Garcia, MT and de Barros, PP and Pedroso, LLC and da Costa Ward, RA and Strixino, JF and Melo, VMM and Junqueira, JC}, title = {Chitosan enhances the Antimicrobial Photodynamic Inactivation mediated by Photoditazine® against Streptococcus mutans.}, journal = {Photodiagnosis and photodynamic therapy}, volume = {}, number = {}, pages = {102001}, doi = {10.1016/j.pdpdt.2020.102001}, pmid = {32961324}, issn = {1873-1597}, abstract = {Chitosan (CS), a biopolymer with intrinsic antimicrobial activity, can increase antimicrobial photodynamic inactivation (aPDI). The aim of this study was to evaluate the capacity of CS to potentiate the efficacy of Photoditazine® (PDZ)-mediated aPDI of the cariogenic bacterium Streptococcus mutans. CS effectively augmented the effects of aPDI, with reductions of approximately 4.5 logs in both planktonic and biofilm states. The combined treatment was also capable of reducing the number of S. mutans cells and amount of extracellular matrix in biofilms formed on enamel surfaces, which were characterized using scanning electron microscopy analysis. Furthermore, CS increased the absorption of PDZ by S. mutans cells. The combination of CS with PDZ-mediated aPDI is hence a promising antimicrobial approach against S. mutans and may be useful to control dental caries.}, }
@article {pmid32960315, year = {2020}, author = {Sodhi, KK and Kumar, M and Singh, DK}, title = {Assessing the bacterial diversity and functional profiles of the River Yamuna using Illumina MiSeq sequencing.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-020-02045-0}, pmid = {32960315}, issn = {1432-072X}, abstract = {A small percentage of the total freshwater on Earth is represented by river water. Microbes have an essential role to play in the biogeochemical cycles, mineralization of organic water, along with xenobiotics degradation. Microbial dynamics are susceptible to environmental stressors which includes pollutants such as antibiotics, metals, and other degradants. River Yamuna is polluted extensively by domestic and industrial wastes. Xenobiotics, when released into the environment, can lead to water pollution. The present study evaluates the microbial diversity in Yamuna River (28°40'5.53'' N, 77°15'0.35'' E) along with the prediction of the metagenome function. In this context, the metagenomic DNA was extracted and sequencing was done on Illumina@MiSeq platform. The total number of OTUs picked was 41,994, out of which 74% were classified within the kingdom Bacteria. 35% of the OTUs were assigned to phylum Proteobacteria, followed by Bacteriodetes (22%), whereas 26% of OTUs were unassigned. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used to predict metagenomic functions using 16S rDNA as a marker. Metagenomic reads were assigned to the Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous (COG), and Gene Ontology (GO). Functional characterization reveals the presence of methyl-accepting chemotaxis protein which is an important adaptation for the microbes in the environment. The enzymes can be mapped for the bioremediation of xenobiotics. Information obtained from the amplicon sequencing of River Yamuna, collaborated with &quot;omic&quot; studies, may help in the design of bioremediation strategies and can be used for environmental clean-up of pollutants.}, }
@article {pmid32958725, year = {2020}, author = {Wünsch, D and Strijkstra, A and Wöhlbrand, L and Freese, HM and Scheve, S and Hinrichs, C and Trautwein, K and Maczka, M and Petersen, J and Schulz, S and Overmann, J and Rabus, R}, title = {Global Response of Phaeobacter inhibens DSM 17395 to Deletion of Its 262-kb Chromid Encoding Antibiotic Synthesis.}, journal = {Microbial physiology}, volume = {}, number = {}, pages = {1-16}, doi = {10.1159/000508591}, pmid = {32958725}, issn = {2673-1673}, abstract = {The marine alphaproteobacterium Phaeobacter inhibens DSM 17395, a member of the Roseobacter group, was recently shown to markedly enhance growth upon deletion of its 262-kb chromid encoding biosynthesis of tropodithietic acid (TDA). To scrutinize the metabolic/regulatory adaptations that underlie enhanced growth of the Δ262 mutant, its transcriptome and proteome compared to the wild type were investigated in process-controlled bioreactors with Casamino Acids as growth substrate. Genome resequencing revealed only few additional genetic changes (a heterogenic insertion, prophage activation, and several point mutations) between wild type and Δ262 mutant, albeit with no conceivable effect on the studied growth physiology. The abundances of the vast majority of transcripts and proteins involved in the catabolic network for complete substrate oxidation to CO2 were found to be unchanged, suggesting that the enhanced amino acid utilization of the Δ262 mutant did not require elevated synthesis of most enzymes of the catabolic network. Similarly, constituents of genetic information processing and cellular processes remained mostly unchanged. In contrast, 426 genes displayed differential expression, of which 410 were localized on the 3.2-Mb chromosome, 5 on the 65-kb chromid, and 11 on the 78-kb chromid. Notably, the branched-chain amino transferase IlvE acting on rapidly utilized Val, Ile, and Leu was upregulated. Moreover, the transportome was reconfigured, as evidenced from increased abundances of transcripts and proteins of several uptake systems for amino acids and inorganic nutrients (e.g., phosphate). Some components of the respiratory chain were also upregulated, which correlates with the higher respiration rates of the Δ262 mutant. Furthermore, chromosomally encoded transcripts and proteins that are peripherally related to TDA biosynthesis (e.g., the serine acyl transferase CysE) were strongly downregulated in the Δ262 mutant. Taken together, these observations reflect adaptations to enhanced growth as well as the functional interconnectivity of the replicons of P. inhibens DSM 17395.}, }
@article {pmid32957572, year = {2020}, author = {Wang, Q and Fu, S and Yang, Q and Hao, J and Zhou, C and Liu, Y}, title = {The Impact of Water Intrusion on Pathogenic Vibrio Species to Inland Brackish Waters of China.}, journal = {International journal of environmental research and public health}, volume = {17}, number = {18}, pages = {}, doi = {10.3390/ijerph17186781}, pmid = {32957572}, issn = {1660-4601}, support = {81903372//National Natural Science Foundation of China/ ; }, abstract = {The estuary is the ecological niche of pathogenic Vibrio spp. as it provides abundant organic and inorganic nutrients from seawater and rivers. However, little is known about the ecology of these Vibrio species in the inland brackish water area. In this study, their co-occurrence and relationships to key environmental constraints (salinity and temperature) in the Hun-Tai River of China were examined using the most probable number polymerase chain reaction (MPN-PCR) approach. We hereby report 2-year continuous surveillance based on six water indices of the Hun-Tai River. The results showed that seawater intrusion maximally reached inland as far as 26.5 km for the Hun-Tai River. Pathogenic Vibrio spp. were detected in 21.9% of the water samples. In particular, V. cholerae, V. parahaemolyticus, and V. vulnificus were isolated in 10 (10.4%), 20 (20.8.5%), and 2 (2.08%) samples, respectively. All V. parahaemolyticus strains were tdh gene negative, 10% were positive for the trh gene. Multi-locus sequence typing (MLST) divided V. parahaemolyticus strains into 12 sequence types (STs) for the Hun-Tai River. Five STs were respectively present in various locations along the Hun-Tai River. The PCR assay for detecting six virulence genes and Vibrio seventh pandemic island I and II revealed three genotypes in 12 V. cholerae isolates. The results of our study showed that seawater intrusion and salinity have profound effects on the distribution of pathogenic Vibrio spp. in the inland river, suggesting a potential health risk associated with the waters of the Hun-Tai River used for irrigation and drinking.}, }
@article {pmid32950135, year = {2020}, author = {Peruzy, MF and Aponte, M and Proroga, YTR and Capuano, F and Cristiano, D and Delibato, E and Houf, K and Murru, N}, title = {Yersinia enterocolitica detection in pork products: Evaluation of isolation protocols.}, journal = {Food microbiology}, volume = {92}, number = {}, pages = {103593}, doi = {10.1016/j.fm.2020.103593}, pmid = {32950135}, issn = {1095-9998}, abstract = {Conventional methods for Yersinia enterocolitica detection in food samples are generally considered inadequate. Problems arise from the presence of the so-called &quot;background flora&quot;, coupled to the low contamination level of the pathogen. Since, data on the microbial ecology occurring in competitive microflora are still lacking, MALDI TOF MS was used for strains 'identification after enrichment in PSB or ITC broths, and after plating on selective CIN medium at different incubation times. SYBR Green Real time PCR was used for the Y. enterocolitica strains' detection (4/O:3, 1A/O:5) in experimentally contaminated foods, as well as in naturally contaminated samples. A higher number of different bacterial genera (10 on CIN and 18 on PCA) was recorded after enrichment in PSB, whilst enrichment in ITC led to recovery of 6 and 10 genera on CIN and PCA, respectively. Yersiniaceae was the dominant family on the first day of incubation, but on the second day the percentage of isolation considerably decreased. By testing experimentally contaminated samples, substantial difficulties were encountered. The biotype 1A was always detected, whereas strain 4/O:3 proved to be poorly competitive. Based on the data, the enrichment media PSB and ITC, currently proposed for Y. enterocolitica detection, need to be improved to promote a successful pathogen's recovery.}, }
@article {pmid32949457, year = {2020}, author = {Hermans, SM and Buckley, HL and Curran-Cournane, F and Taylor, M and Lear, G}, title = {Temporal variation in soil bacterial communities can be confounded with spatial variation.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaa192}, pmid = {32949457}, issn = {1574-6941}, abstract = {Investigating temporal variation in soil bacterial communities advances our fundamental understanding of the causal processes driving biological variation, and how the composition of these important ecosystem members may change into the future. Despite this, temporal variation in soil bacteria remains understudied and the effects of spatial heterogeneity in bacterial communities on the detection of temporal changes is largely unknown. Using 16S rRNA gene amplicon sequencing, we evaluated temporal patterns in soil bacterial communities from indigenous forest and human-impacted sites sampled repeatedly over a five-year period. Temporal variation appeared to be greater when fewer spatial samples per site were analysed, as well as in human-impacted compared to indigenous sites (P <0.01 for both). The biggest portion of variation in bacterial community richness and composition was explained by soil physicochemical variables (13-24%) rather than spatial distance or sampling time (<1%). These results highlight the importance of adequate spatiotemporal replication when sampling soil communities for environmental monitoring, and the importance of conducting temporal research across a wide variety of land uses. This will ensure we have a true understanding of how bacterial communities change over space and time; the work presented here provides important considerations for how such research should be designed.}, }
@article {pmid32948906, year = {2020}, author = {Jeong, SY and Kim, TG}, title = {Spatial Variance of Species Distribution Predicts the Interspecies Interactions within a Microbial Metacommunity.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01603-9}, pmid = {32948906}, issn = {1432-184X}, support = {2018R1D1A1B07048872//Ministry of Education/ ; }, abstract = {Interspecies interactions have a profound influence on spatial distribution of coexisting microbial species. We explored whether spatial variance of species distribution (SVSD) predicts the degree of interspecies interactions within a microbial metacommunity. Simulations were used to determine the relationships from random, lake, soil, and biofilm metacommunity datasets (1,000 times). All of the bacterial datasets showed a negative correlation between the habitat breadth (inverse to SVSD) and the numbers of total, positive, and negative interspecies interactions (P < 0.05); the only exception was the relationship between habitat breadth and negative interactions in the biofilm dataset. The random dataset had no significant relationships (P > 0.05). We repeated the simulations to determine the degree of correlation and reproducibility (100 times). Habitat breadth was negatively correlated with the total and positive interactions in all of the real datasets (P < 0.05), and the negative relationships persisted across repetitions. Despite variability in the slope of total interactions, the slope values of positive interactions were similar for the real datasets (- 19.9, - 19.2, and - 25.8 for lake, soil, and biofilm, respectively). In conclusion, our results demonstrate the patterns of species interaction-distribution and show that interspecies interactions are positively correlated with the SVSD.}, }
@article {pmid32948905, year = {2020}, author = {Mars Brisbin, M and Conover, AE and Mitarai, S}, title = {Influence of Regional Oceanography and Hydrothermal Activity on Protist Diversity and Community Structure in the Okinawa Trough.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {746-761}, doi = {10.1007/s00248-020-01583-w}, pmid = {32948905}, issn = {1432-184X}, abstract = {Microbial eukaryotes (protists) contribute substantially to ecological functioning in marine ecosystems, but the relative importance of factors shaping protist diversity, such as environmental selection and dispersal, remains difficult to parse. Water masses of a back-arc basin with hydrothermal activity provide a unique opportunity for studying the effects of dispersal and environmental selection on protist communities. In this study, we used metabarcoding to characterize protist communities in the Okinawa Trough, a back-arc spreading basin containing at least twenty-five active hydrothermal vent fields. Water was sampled from four depths at fourteen stations spanning the length of the Okinawa Trough, including three sites influenced by nearby hydrothermal vent sites. While significant differences in community structure reflecting water depth were present, protist communities were mostly homogeneous horizontally. Protist communities in the bottom waters affected by hydrothermal activity were significantly different from communities in other bottom waters, suggesting that environmental factors can be especially important in shaping community composition under specific conditions. Amplicon sequence variants that were enriched in hydrothermally influenced bottom waters largely derived from cosmopolitan protists that were present, but rare, in other near-bottom samples, thus highlighting the importance of the rare biosphere.}, }
@article {pmid32948266, year = {2020}, author = {Morimoto, D and Šulčius, S and Tominaga, K and Yoshida, T}, title = {Predetermined clockwork microbial worlds: Current understanding of aquatic microbial diel response from model systems to complex environments.}, journal = {Advances in applied microbiology}, volume = {113}, number = {}, pages = {163-191}, doi = {10.1016/bs.aambs.2020.06.001}, pmid = {32948266}, issn = {0065-2164}, abstract = {In the photic zone of aquatic ecosystems, microorganisms with different metabolisms and their viruses form complex interactions and food webs. Within these interactions, phototrophic microorganisms such as eukaryotic microalgae and cyanobacteria interact directly with sunlight, and thereby generate circadian rhythms. Diel cycling originally generated in microbial phototrophs is directly transmitted toward heterotrophic microorganisms utilizing the photosynthetic products as they are excreted or exuded. Such diel cycling seems to be indirectly propagated toward heterotrophs as a result of complex biotic interactions. For example, cell death of phototrophic microorganisms induced by viral lysis and protistan grazing provides additional resources of dissolved organic matter to the microbial community, and so generates diel cycling in other heterotrophs with different nutrient dependencies. Likewise, differences in the diel transmitting pathway via complex interactions among heterotrophs, and between heterotrophs and their viruses, may also generate higher variation and time lag diel rhythms in different heterotrophic taxa. Thus, sunlight and photosynthesis not only contribute energy and carbon supply, but also directly or indirectly control diel cycling of the microbial community through complex interactions in the photic zone of aquatic ecosystems.}, }
@article {pmid32945836, year = {2020}, author = {Pajdak-Stós, A and Fiałkowski, W and Fiałkowska, E}, title = {Rotifers weaken the efficiency of the cyanobacterium defence against ciliate grazers.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaa189}, pmid = {32945836}, issn = {1574-6941}, abstract = {Cyanobacteria can protect themselves through limited dispersion and by increasing the compactness of the mucilage-covered cyanobacterial mat as well as by producing sheaths covering their trichomes. These features have been used in research to measure their degree of inducible defence. The influence of the rotifers Lecane inermis presence on the effectiveness of Phormidium sp. (Ph2) cyanobacterium defence was investigated. Experiments were conducted on the ciliates Pseudomicrothorax dubius and Furgasonia blochmanni, specialized in the ingestion of filamentous cyanobacteria. The most compact were cyanobacterial mats that were subjected exclusively to ciliates, and the most dispersed were mats in the presence of rotifers alone. The presence of rotifers feeding on cyanobacterial mucilage led to the decreased effectiveness of the defence in two ways, by increasing the dispersion of cyanobacterial trichomes, thus loosening the cyanobacterial mat, and through the ingestion of the exopolysaccharide material covering the trichomes. As a result, in the presence of rotifers and the high density of ciliates, almost all the trichomes were removed. Moreover, in comparison to the other treatments, a higher number of ciliates and rotifers remained active until the end of the experiments. This is the first report to show how rotifers can weaken the defence of cyanobacteria.}, }
@article {pmid32939928, year = {2020}, author = {Masetti, R and Zama, D and Leardini, D and Muratore, E and Turroni, S and Prete, A and Brigidi, P and Pession, A}, title = {The gut microbiome in pediatric patients undergoing allogeneic hematopoietic stem cell transplantation.}, journal = {Pediatric blood &amp; cancer}, volume = {}, number = {}, pages = {e28711}, doi = {10.1002/pbc.28711}, pmid = {32939928}, issn = {1545-5017}, abstract = {The gut microbiome (GM) has been associated with different clinical outcomes in the context of allogeneic hematopoietic stem cell transplantation (HSCT). Large multicenter cohort studies in adults have found significant correlations with overall survival, relapse, and incidence of complications. Moreover, GM is already a promising target for therapeutic interventions. However, few data are available in children, a population presenting unique features and challenges. During childhood, the GM evolves rapidly with large structural fluctuations, alongside with the maturation of the immune system. Furthermore, the HSCT procedure presents significant differences in children. These considerations underline the importance of a specific focus on the pediatric setting, and the role of GM and its age-dependent trajectory in influencing the immunity reconstitution and clinical outcomes. This review provides a comprehensive overview of the available evidence in the field of GM and pediatric HSCT, highlighting age-specific issues and discussing GM-based therapeutic approaches.}, }
@article {pmid32935184, year = {2020}, author = {He, Y and Zhou, Y and Weng, R and Wang, J and Chen, J and Huang, M}, title = {Responses of Ammonia-Oxidizing Archaea and Bacteria in Malodorous River Sediments to Different Remediation Techniques.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01597-4}, pmid = {32935184}, issn = {1432-184X}, support = {41877477//National Natural Science Foundation of China/ ; 18DZ1203806//Shanghai Science and Technology Development Funds/ ; 2017ZX07207001//National Science and Technology Major Project for Water Pollution Control and Treatment/ ; 2018ZX07208008//National Science and Technology Major Project for Water Pollution Control and Treatment/ ; }, abstract = {In this study, the joint use of high throughput sequencing, real-time quantitative PCR, and ammonia-oxidizing bacteria (AOB)-inhibiting allylthiourea was used to differentiate between the contributions of ammonia-oxidizing archaea (AOA) vs AOB to ammonia oxidation and ascertain how AOA and AOB responded to two widely used river remediation techniques (aeration and Ca(NO3)2 injection). Results showed that ammonia oxidation was largely attributed to ATU-sensitive AOB rather than AOA and Nitrosomonas was the predominant AOB-related genus (53.86%) in the malodorous river. The contribution of AOB to ammonia oxidation in the context of aeration and Ca(NO3)2 injection was 75.51 ± 2.77% and 60.19 ± 10.44%, respectively. The peak of AOB/AOA ratio and the marked increase of relative abundances of Nitrosomonas and Nitrosospira in aeration runs further demonstrated aeration favored the ammonia oxidation of AOB. Comparatively, Ca(NO3)2 injection could increase the ammonia oxidation contribution of AOA from 31.32 ± 6.06 to 39.81 ± 10.44% and was significantly correlated with Nitrosococcus of AOB (r = 0.796, p < 0.05), Candidatus_Nitrosopelagicus of AOA (r = 0.986, p < 0.01), and AOA Simpson diversity (r = - 0.791, p < 0.05). Moreover, Candidatus_Nitrosopelagicus was only present in Ca(NO3)2 runs. Taken together, Ca(NO3)2 was recognized as an important factor in mediating the growth and ecological niches of ammonia oxidizers.Graphical abstract.}, }
@article {pmid32935183, year = {2020}, author = {Phoma, BS and Makhalanyane, TP}, title = {Depth-Dependent Variables Shape Community Structure and Functionality in the Prince Edward Islands.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01589-4}, pmid = {32935183}, issn = {1432-184X}, abstract = {Physicochemical variables limit and control the distribution of microbial communities in all environments. In the oceans, this may significantly influence functional processes such the consumption of dissolved organic material and nutrient sequestration. Yet, the relative contributions of physical factors, such as water mass variability and depth, on functional processes are underexplored. We assessed microbial community structure and functionality in the Prince Edward Islands (PEIs) using 16S rRNA gene amplicon analysis and extracellular enzymatic activity assays, respectively. We found that depth and nutrients substantially drive the structural patterns of bacteria and archaea in this region. Shifts from epipelagic to bathypelagic zones were linked to decreases in the activities of several extracellular enzymes. These extracellular enzymatic activities were positively correlated with several phyla including several Alphaproteobacteria (including members of the SAR 11 clade and order Rhodospirillales) and Cyanobacteria. We show that depth-dependent variables may be essential drivers of community structure and functionality in the PEIs.}, }
@article {pmid32930890, year = {2020}, author = {Gupta, D and Guzman, MS and Bose, A}, title = {Extracellular electron uptake by autotrophic microbes: physiological, ecological, and evolutionary implications.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10295-020-02309-0}, pmid = {32930890}, issn = {1476-5535}, support = {MCB2021822//National Science Foundation/ ; 201563111//David and Lucile Packard Foundation/ ; DESC0014613//U.S. Department of Energy/ ; W911NF-18-1-0037//U.S. Department of Defense/ ; }, abstract = {Microbes exchange electrons with their extracellular environment via direct or indirect means. This exchange is bidirectional and supports essential microbial oxidation-reduction processes, such as respiration and photosynthesis. The microbial capacity to use electrons from insoluble electron donors, such as redox-active minerals, poised electrodes, or even other microbial cells is called extracellular electron uptake (EEU). Autotrophs with this capability can thrive in nutrient and soluble electron donor-deficient environments. As primary producers, autotrophic microbes capable of EEU greatly impact microbial ecology and play important roles in matter and energy flow in the biosphere. In this review, we discuss EEU-driven autotrophic metabolisms, their mechanism and physiology, and highlight their ecological, evolutionary, and biotechnological implications.}, }
@article {pmid32929739, year = {2020}, author = {Raymond, NS and Gómez-Muñoz, B and van der Bom, FJT and Nybroe, O and Jensen, LS and Müller-Stöver, DS and Oberson, A and Richardson, AE}, title = {Phosphate-solubilising microorganisms for improved crop productivity: a critical assessment.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.16924}, pmid = {32929739}, issn = {1469-8137}, abstract = {Phosphate-solubilising microorganisms (PSM) are often reported to have positive effects on crop productivity through enhanced phosphorus (P) nutrition. Our aim was to evaluate the validity of this concept. Most studies that report 'positive effects' of PSM on plant growth have been conducted under controlled conditions, whereas field experiments more frequently fail to demonstrate a positive response. Many studies have indicated that the mechanisms seen in vitro do not translate into improved crop P nutrition in complex soil-plant systems. Furthermore, associated mechanisms are often not rigorously assessed. We suggest that PSM do not mobilise sufficient P to change the crops' nutritional environment under field conditions. The current concept, in which PSM solubilise P 'for the plant' should thus be revised. Although PSM have the capacity to solubilise P to meet their own needs, it is the turnover of the microbial biomass that subsequently provides P to plants over a longer time. Therefore, the existing concept of PSM function is unlikely to deliver a reliable strategy for increasing crop P nutrition. A further mechanistic understanding is needed to determine how P mobilisation by PSM as a component of the whole soil community can be manipulated to become more effective for plant P nutrition.}, }
@article {pmid32925728, year = {2020}, author = {Berentsen, B and Nagaraja, BH and Teige, EP and Lied, GA and Lundervold, AJ and Lundervold, K and Steinsvik, EK and Hillestad, ER and Valeur, J and Brønstad, I and Gilja, OH and Osnes, B and Hatlebakk, JG and Haász, J and Labus, J and Gupta, A and Mayer, EA and Benitez-Páez, A and Sanz, Y and Lundervold, A and Hausken, T}, title = {Study protocol of the Bergen brain-gut-microbiota-axis study: A prospective case-report characterization and dietary intervention study to evaluate the effects of microbiota alterations on cognition and anatomical and functional brain connectivity in patients with irritable bowel syndrome.}, journal = {Medicine}, volume = {99}, number = {37}, pages = {e21950}, pmid = {32925728}, issn = {1536-5964}, mesh = {Adolescent ; Adult ; Aged ; Brain/microbiology/physiopathology ; Case-Control Studies ; Cognition/physiology ; Diet, Carbohydrate-Restricted/*methods ; Female ; Fermentation ; Gastrointestinal Microbiome/*physiology ; Humans ; Irritable Bowel Syndrome/*diet therapy/*microbiology/psychology ; Male ; Middle Aged ; Prospective Studies ; Young Adult ; }, abstract = {INTRODUCTION: Irritable bowel syndrome (IBS) is a common clinical label for medically unexplained gastrointestinal (GI) symptoms, recently described as a disturbance of the brain-gut-microbiota (BGM) axis. To gain a better understanding of the mechanisms underlying the poorly understood etiology of IBS, we have designed a multifaceted study that aim to stratify the complex interaction and dysfunction between the brain, the gut, and the microbiota in patients with IBS.<br><br>METHODS: Deep phenotyping data from patients with IBS (n = 100) and healthy age- (between 18 and 65) and gender-matched controls (n = 40) will be collected between May 2019 and December 2021. Psychometric tests, questionnaires, human biological tissue/samples (blood, faeces, saliva, and GI biopsies from antrum, duodenum, and sigmoid colon), assessment of gastric accommodation and emptying using transabdominal ultrasound, vagal activity, and functional and structural magnetic resonance imaging (MRI) of the brain, are included in the investigation of each participant. A subgroup of 60 patients with IBS-D will be further included in a 12-week low FODMAP dietary intervention-study to determine short and long-term effects of diet on GI symptoms, microbiota composition and functions, molecular GI signatures, cognitive, emotional and social functions, and structural and functional brain signatures. Deep machine learning, prediction tools, and big data analyses will be used for multivariate analyses allowing disease stratification and diagnostic biomarker detection.<br><br>DISCUSSION: To our knowledge, this is the first study to employ unsupervised machine learning techniques and incorporate systems-based interactions between the central and the peripheral components of the brain-gut-microbiota axis at the levels of the multiomics, microbiota profiles, and brain connectome of a cohort of 100 patients with IBS and matched controls; study long-term safety and efficacy of the low-FODMAP diet on changes in nutritional status, gut microbiota composition, and metabolites; and to investigate changes in the brain and gut connectome after 12 weeks strict low-FODMAP-diet in patients with IBS. However, there are also limitations to the study. As a restrictive diet, the low-FODMAP diet carries risks of nutritional inadequacy and may foster disordered eating patterns. Strict FODMAP restriction induces a potentially unfavourable gut microbiota, although the health effects are unknown.<br><br>TRIAL REGISTRATION NUMBER: NCT04296552 (ClinicalTrials.gov).}, }
@article {pmid32923720, year = {2020}, author = {Giongo, A and Dos Anjos Borges, LG and Marconatto, L and de Lara Palhano, P and Serbent, MP and Moreira-Silva, E and de Abreu Siqueira, T and Martinho, CT and Barili, R and Paz, LV and Moser, LI and De Marco Veríssimo, C and Ketzer, JMM and Medina-Silva, R}, title = {Adaption of microbial communities to the hostile environment in the Doce River after the collapse of two iron ore tailing dams.}, journal = {Heliyon}, volume = {6}, number = {8}, pages = {e04778}, pmid = {32923720}, issn = {2405-8440}, abstract = {In November 2015, two iron ore tailing dams collapsed in the city of Mariana, Brazil. The dams' collapse generated a wave of approximately 50 million m3 of a mixture of mining waste and water. It was a major environmental tragedy in Brazilian history, which damaged rivers, and cities 660 km away in the Doce River basin until it reached the ocean coast. Shortly after the incident, several reports informed that the concentration of metals in the water was above acceptable legal limits under Brazilian laws. Here the microbial communities in samples of water, mud, foam, and rhizosphere of Eichhornia from Doce River were analyzed for 16S and 18S rRNA-based amplicon sequencing, along with microbial isolation, chemical and mineralogical analyses. Samples were collected one month and thirteen months after the collapse. Prokaryotic communities from mud shifted drastically over time (33% Bray-Curtis similarity), while water samples were more similar (63% Bray-Curtis similarity) in the same period. After 12 months, mud samples remained with high levels of heavy metals and a reduction in the diversity of microeukaryotes was detected. Amoebozoans increased in mud samples, reaching 49% of microeukaryote abundance, with Discosea and Lobosa groups being the most abundant. The microbial communities' structure in mud samples changed adapting to the new environment condition. The characterization of microbial communities and metal-tolerant organisms from such impacted environments is essential for understanding the ecological consequences of massive anthropogenic impacts and strategies for the restoration of contaminated sites such as the Doce River.}, }
@article {pmid32923454, year = {2020}, author = {Ardern, Z and Neuhaus, K and Scherer, S}, title = {Are Antisense Proteins in Prokaryotes Functional?.}, journal = {Frontiers in molecular biosciences}, volume = {7}, number = {}, pages = {187}, pmid = {32923454}, issn = {2296-889X}, abstract = {Many prokaryotic RNAs are transcribed from loci outside of annotated protein coding genes. Across bacterial species hundreds of short open reading frames antisense to annotated genes show evidence of both transcription and translation, for instance in ribosome profiling data. Determining the functional fraction of these protein products awaits further research, including insights from studies of molecular interactions and detailed evolutionary analysis. There are multiple lines of evidence, however, that many of these newly discovered proteins are of use to the organism. Condition-specific phenotypes have been characterized for a few. These proteins should be added to genome annotations, and the methods for predicting them standardized. Evolutionary analysis of these typically young sequences also may provide important insights into gene evolution. This research should be prioritized for its exciting potential to uncover large numbers of novel proteins with extremely diverse potential practical uses, including applications in synthetic biology and responding to pathogens.}, }
@article {pmid32920672, year = {2020}, author = {Valverde, A and Cason, ED and Gómez-Arias, A and Bozkale, D and Govender, D and Riddell, E and Cowan, D}, title = {Pollution shapes the microbial communities in river water and sediments from the Olifants River catchment, South Africa.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-020-02035-2}, pmid = {32920672}, issn = {1432-072X}, abstract = {Human activities such as agriculture and mining are leading causes of water pollution worldwide. Individual contaminants are known to negatively affect microbial communities. However, the effect of multifaceted pollution on these communities is less well understood. We investigated, using next-generation sequencing of the 16S rRNA genes, the effects of multisource (i.e., fertilizer industry and mining) chronic pollution on bacterial and archaeal communities in water and sediments from the Olifants River catchment, South Africa. Water samples showed less microbial species diversity than sediments and both habitats displayed different microbial communities. Within each of these habitats, pollution had no effect on alpha diversity but shaped the microbial composition and taxonomy-based predicted functions. Certain prokaryotic taxa and functional groups were indicative of different degrees of pollution. Heterotrophic taxa (e.g., Flavobacterium sp.) and sulphur-oxidizing bacteria (i.e., Thiobacillus sp.) were indicators of pollution in water and sediments, respectively. Ultimately, this information could be used to develop microbial indicators of water quality degradation.}, }
@article {pmid32920671, year = {2020}, author = {Lee, JC and Whang, KS}, title = {Lysobacter telluris sp. nov., isolated from Korean rhizosphere soil.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-020-02032-5}, pmid = {32920671}, issn = {1432-072X}, abstract = {A Gram-stain-negative, aerobic, non-motile, non-spore-forming light-yellow-coloured rod-shaped bacterial strain, designated YJ15T, was isolated from soil at Bigeum island in Korea. Growth was observed at 10-37 °C (optimum, 28 °C), at pH 6.0-7.5 (optimum, pH 7.0) and in the absence of NaCl. Based on 16S rRNA gene sequence analysis, strain YJ15T was closely related to 'Lysobacter tongrenensis' YS037T (97.8%), Lysobacter pocheonensis Gsoil193T (96.5%) and Lysobacter daecheongensis Dae08T (95.8%) and phylogenetically grouped together with 'Lysobacter tongrenensis' YS037T, Lysobacter dokdonensis DS-58T and Lysobacter pocheonensis Gsoil 193T. The DNA-DNA relatedness between strain YJ15T and 'Lysobacter tongrenensis' KCTC 52206T was 12% and the phylogenomic analysis based on the whole genome sequence demonstrated that strain YJ20T formed a distinct phyletic line with Lysobacterlter dokdonensis DS-58T showing average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of 76.3 and 21.3%, respectively. The predominant ubiquinone was identified as Q-8, and polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unidentified aminolipids. The major fatty acids were iso-C17:1 ω9c, iso-C15:0, iso-C16:0 and iso-C17:0. The genomic DNA G + C content was 68.2 mol %. On the basis of phenotypic, chemotaxonomic properties and phylogenetic analyses in this study, strain YJ15T is considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter telluris sp. nov. is proposed. The type strain is YJ15T (= KACC 19552T = NBRC 113197T).}, }
@article {pmid32920663, year = {2020}, author = {Paz, C and Öpik, M and Bulascoschi, L and Bueno, CG and Galetti, M}, title = {Dispersal of Arbuscular Mycorrhizal Fungi: Evidence and Insights for Ecological Studies.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01582-x}, pmid = {32920663}, issn = {1432-184X}, support = {2018/16697-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2018/00212-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, abstract = {Dispersal is a critical ecological process that modulates gene flow and contributes to the maintenance of genetic and taxonomic diversity within ecosystems. Despite an increasing global understanding of the arbuscular mycorrhizal (AM) fungal diversity, distribution and prevalence in different biomes, we have largely ignored the main dispersal mechanisms of these organisms. To provide a geographical and scientific overview of the available data, we systematically searched for the direct evidence on the AM fungal dispersal agents (abiotic and biotic) and different propagule types (i.e. spores, extraradical hyphae or colonized root fragments). We show that the available data (37 articles) on AM fungal dispersal originates mostly from North America, from temperate ecosystems, from biotic dispersal agents (small mammals) and AM fungal spores as propagule type. Much lesser evidence exists from South American, Asian and African tropical systems and other dispersers such as large-bodied birds and mammals and non-spore propagule types. We did not find strong evidence that spore size varies across dispersal agents, but wind and large animals seem to be more efficient dispersers. However, the data is still too scarce to draw firm conclusions from this finding. We further discuss and propose critical research questions and potential approaches to advance the understanding of the ecology of AM fungi dispersal.}, }
@article {pmid32920539, year = {2020}, author = {Zhang, R and Weinbauer, MG and Peduzzi, P}, title = {Aquatic Viruses and Climate Change.}, journal = {Current issues in molecular biology}, volume = {41}, number = {}, pages = {357-380}, doi = {10.21775/cimb.041.357}, pmid = {32920539}, issn = {1467-3045}, abstract = {The viral component in aquatic systems clearly needs to be incorporated into future ocean and inland water climate models. Viruses have the potential to influence carbon and nutrient cycling in aquatic ecosystems significantly. Changing climate likely has both direct and indirect influence on virus-mediated processes, among them an impact on food webs, biogeochemical cycles and on the overall metabolic performance of whole ecosystems. Here we synthesise current knowledge on potential climate-related consequences for viral assemblages, virus-host interactions and virus functions, and in turn, viral processes contributing to climate change. There is a need to increase the accuracy of predictions of climate change impacts on virus- driven processes, particularly of those linked to biological production and biogeochemical cycles. Comprehension of the relationships between microbial/viral processes and global phenomena is essential to predict the influence on as well as the response of the biosphere to global change.}, }
@article {pmid32920408, year = {2020}, author = {Soh, YNA and Kunacheva, C and Menon, S and Webster, RD and Stuckey, DC}, title = {Comparison of soluble microbial product (SMP) production in full-scale anaerobic/aerobic industrial wastewater treatment and a laboratory based synthetic feed anaerobic membrane system.}, journal = {The Science of the total environment}, volume = {754}, number = {}, pages = {142173}, doi = {10.1016/j.scitotenv.2020.142173}, pmid = {32920408}, issn = {1879-1026}, abstract = {This study focused on the characterisation of soluble microbial products (SMPs) produced from a full-scale multi-stage (anaerobic/aerobic) industrial wastewater treatment plant, and contrasted them to the SMPs detected in the effluent of a lab-scale AnMBR treating synthetic wastewater to determine if there were any common solutes detected irrespective of the feed organics. Recently developed analytical methods using gas chromatography coupled mass spectrometry (GC-MS) and liquid chromatography coupled quadrupole-time-of-flight (LC-Q-ToF) for SMP characterisation in a wide molecular weight (MW) range of 30-2000 Da (Da) were applied. Samples collected from the Industrial Wastewater plant were the upflow anaerobic sludge blanket (UASB) influent and effluent, and aerobic membrane bioreactor (MBR) effluent before discharge. The GC-MS detected a spike in cyclooctasulphur in the UASB effluent, an indicator of shock-loading, which disappeared after the MBR process. Alkanes, acids and nitrogenous compounds were found to be the end-products from the GC-MS results, while LC-Q-ToF analysis revealed that eicosanoids, a group of cell-signalling molecules, were produced in the aerobic MBR, and made up 71% of its effluent. A comparison of the submerged anaerobic membrane bioreactor (SAMBR) and aerobic MBR effluents using GC-MS showed that there was only a small degree of similarity between the SMPs, comprising mainly long chain alkanes and phthalate. On the other hand, LC-Q-ToF showed a large contrast in compound composition, mostly having cell-signalling functions, which deepened our understanding of the different metabolic processes occurring in aerobic and anaerobic systems. These data could be useful for future work in various areas such as controlling quorum-sensing and biofilm formation, process optimisation and control, and microbial ecology.}, }
@article {pmid32920334, year = {2020}, author = {Candry, P and Radić, L and Favere, J and Carvajal-Arroyo, JM and Rabaey, K and Ganigué, R}, title = {Mildly acidic pH selects for chain elongation to caproic acid over alternative pathways during lactic acid fermentation.}, journal = {Water research}, volume = {186}, number = {}, pages = {116396}, doi = {10.1016/j.watres.2020.116396}, pmid = {32920334}, issn = {1879-2448}, abstract = {Carbohydrate-rich waste streams can be used for bioproduction of medium-chain carboxylic acids (MCCA) such as caproic acid. The carbohydrates in these streams can be converted to lactic acid as the initial fermentation product, which can then be fermented to MCCA by chain elongation. In this process, chain elongators compete for lactic acid with other bacterial groups that, for instance, ferment lactic acid to propionic and acetic acid. Understanding the drivers that control the competition between these two pathways is essential to maximizing MCCA production. This study aimed to investigate the competition between chain elongating and propionic acid producing organisms as a function of operational pH. Operation of long-term lactic acid fermenting reactors with varying pH values showed that pH values above 6 resulted in a propionic acid producing community dominated by Veillonella and Aminobacterium. At pH values below 6, the community moved towards chain elongation, with communities dominated by Caproiciproducens. Short-term incubations showed that rates of lactic acid consumption were strongly reduced at pH below 6 (7.7 ± 1.2 mM lactic acid·h-1 at pH 6.5; 0.74 ± 0.33 mM lactic acid·h-1 at pH 5.5). Similar to observations in long-term reactors, when a chain elongating community adapted to pH 5.5 was used for short-term incubations at pH 6.5, propionic acid was the dominant product. The results of this study show that pH below 6 stimulate lactic acid chain elongators through kinetic effects, and potentially improved energetics, providing a tool for microbial management of MCCA-producing systems.}, }
@article {pmid32919387, year = {2020}, author = {Casterline, BW and Paller, AS}, title = {Early development of the skin microbiome: therapeutic opportunities.}, journal = {Pediatric research}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41390-020-01146-2}, pmid = {32919387}, issn = {1530-0447}, abstract = {As human skin hosts a diverse microbiota in health and disease, there is an emerging consensus that dysregulated interactions between host and microbiome may contribute to chronic inflammatory disease of the skin. Neonatal skin is a unique habitat, structurally similar to the adult but with a different profile of metabolic substrates, environmental stressors, and immune activity. The surface is colonized within moments of birth with a bias toward maternal strains. Initial colonists are outcompeted as environmental exposures increase and host skin matures. Nonetheless, early life microbial acquisitions may have long-lasting effects on health through modulation of host immunity and competitive interactions between bacteria. Microbial ecology and its influence on health have been of interest to dermatologists for >50 years, and an explosion of recent interest in the microbiome has prompted ongoing investigations of several microbial therapeutics for dermatological disease. In this review, we consider how recent insight into the host and microbial factors driving development of the skin microbiome in early life offers new opportunities for therapeutic intervention. IMPACT: Advancement in understanding molecular mechanisms of bacterial competition opens new avenues of investigation into dermatological disease. Primary development of the skin microbiome is determined by immunological features of the cutaneous habitat. Understanding coordinated microbial and immunological development in the pediatric patient requires a multidisciplinary synthesis of primary literature.}, }
@article {pmid32919372, year = {2020}, author = {Frommeyer, B and Fiedler, AW and Oehler, SR and Hanson, BT and Loy, A and Franchini, P and Spiteller, D and Schleheck, D}, title = {Environmental and Intestinal Phylum Firmicutes Bacteria Metabolize the Plant Sugar Sulfoquinovose via a 6-Deoxy-6-sulfofructose Transaldolase Pathway.}, journal = {iScience}, volume = {23}, number = {9}, pages = {101510}, pmid = {32919372}, issn = {2589-0042}, abstract = {Bacterial degradation of the sugar sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) produced by plants, algae, and cyanobacteria, is an important component of the biogeochemical carbon and sulfur cycles. Here, we reveal a third biochemical pathway for primary SQ degradation in an aerobic Bacillus aryabhattai strain. An isomerase converts SQ to 6-deoxy-6-sulfofructose (SF). A novel transaldolase enzyme cleaves the SF to 3-sulfolactaldehyde (SLA), while the non-sulfonated C3-(glycerone)-moiety is transferred to an acceptor molecule, glyceraldehyde phosphate (GAP), yielding fructose-6-phosphate (F6P). Intestinal anaerobic bacteria such as Enterococcus gilvus, Clostridium symbiosum, and Eubacterium rectale strains also express transaldolase pathway gene clusters during fermentative growth with SQ. The now three known biochemical strategies for SQ catabolism reflect adaptations to the aerobic or anaerobic lifestyle of the different bacteria. The occurrence of these pathways in intestinal (family) Enterobacteriaceae and (phylum) Firmicutes strains further highlights a potential importance of metabolism of green-diet SQ by gut microbial communities to, ultimately, hydrogen sulfide.}, }
@article {pmid32918562, year = {2020}, author = {Ennis, NJ and Dharumaduri, D and Bryce, JG and Tisa, LS}, title = {Metagenome Across a Geochemical Gradient of Indian Stone Ruins Found at Historic Sites in Tamil Nadu, India.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01598-3}, pmid = {32918562}, issn = {1432-184X}, abstract = {Although stone surfaces seem unlikely to be habitable, they support microbial life. Life on these surfaces are subjected to many varying harsh conditions and require the inhabitants to exhibit resistance to environmental factors including UV irradiation, toxic metal exposure, and fluctuating temperatures and humidity. Here we report the effect of hosting stone geochemistry on the microbiome of stone ruins found in Tamil Nadu, India. The microbial communities found on the two lithologies, granite and granodiorite, hosted distinct populations of bacteria. Geochemical composition analysis of sampled stones revealed quartz mineral content as a major driver of microbial community structure, particularly promoting community richness and proportions of Cyanobacteria and Deinococcus-Thermus. Other geochemical parameters including ilmenite, albite, anorthite, and orthoclase components or elemental concentrations (Ti, Fe, Mn, Na, and K) also influenced community structure to a lesser degree than quartz. Core members of the stone microbiome community found on both lithologies were also identified and included Cyanobacteria (Chroococcidiopsaceae and Dapisostemonum CCIBt 3536), Rubrobacter, and Deinococcus. A cluster of taxa including Sphingomonas, Geodermatophilus, and Truepera were mostly found in the granodiorite samples. Community diversity correlated with quartz mineral content in these samples may indicate that the microbial communities that attach to quartz surfaces may be transient and regularly changing. This work has expanded our understanding of built-stone microbial community structure based on lithology and geochemistry.}, }
@article {pmid32918153, year = {2020}, author = {Sajjad, W and Ali, B and Bahadur, A and Ghimire, PS and Kang, S}, title = {Bacterial Diversity and Communities Structural Dynamics in Soil and Meltwater Runoff at the Frontier of Baishui Glacier No.1, China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01600-y}, pmid = {32918153}, issn = {1432-184X}, abstract = {Comprehensive knowledge of bacterial ecology mainly in supraglacial habitats is pivotal particularly at the frontier of accelerated glacier retreat. In this study, bacterial diversity and community composition in glacial soil and meltwater runoff at the frontier of Baishui Glacier No.1 were evaluated using high throughput sequencing. Significant variations in the physiochemical parameters formed an ecological gradient between soil and meltwater runoff. Based on the richness and evenness indexes, the bacterial diversity was relatively higher in soil compared with meltwater runoff. Hierarchical clustering and bi-plot ordination revealed that the taxonomic composition of soil samples was highly similar and significantly influenced by the ecological parameters than the meltwater runoff. The overall relative abundance trend of bacterial phyla and genera were greatly varied in soil and water samples. The relative abundance of Proteobacteria was higher in water runoff samples (40.5-87%) compared with soil samples (32-52.7%). Proteobacteria, Firmicutes, and a little part of Cyanobacteria occupied a major portion of water runoff while the soil was dominated by Acidobacteria (6-16.2%), Actinobacteria (5-16%), Bacteroidetes (0.5-8.8%), and Cyanobacteria (0.1-8.3%) besides Proteobacteria and Firmicutes. Higher numbers of biomarkers were found in soil group compared with the water group. The study area is diverse in terms of richness, while community structures are not evenly distributed. This study provides a preliminary understanding of the bacterial diversity and shifts in community structure in soil and meltwater runoff at the frontier of the glacial. The findings revealed that the environmental factors are a significantly strong determinant of bacterial community structures in such a closely linked ecosystem.}, }
@article {pmid32917751, year = {2020}, author = {Park, SJ and Andrei, AŞ and Bulzu, PA and Kavagutti, VS and Ghai, R and Mosier, AC}, title = {Expanded diversity and metabolic versatility of marine nitrite-oxidizing bacteria revealed by cultivation- and genomics-based approaches.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.01667-20}, pmid = {32917751}, issn = {1098-5336}, abstract = {Nitrite-oxidizing bacteria (NOB) are ubiquitous and abundant microorganisms that play key roles in global nitrogen and carbon biogeochemical cycling. Despite recent advances in understanding NOB physiology and taxonomy, there are currently very few cultured NOB or representative NOB genome sequences from marine environments. In this study, we employed enrichment culturing and genomic approaches in order to shed light on the phylogeny and metabolic capacity of marine NOB. We successfully enriched two marine NOB (designated MSP and DJ) and obtained a high-quality metagenome-assembled genome (MAG) from each organism. The maximum nitrite oxidation rates of the MSP and DJ enrichment cultures were 13.8 (0.1 mM nitrite as optimum) and 30.0 μM (0.3 mM nitrite) nitrite per day, respectively. Each enrichment culture exhibited different tolerance to varying nitrite and salt concentrations. Based on phylogenomic position and overall genome relatedness indices, both NOB MAGs were proposed as novel taxa within the Nitrospinota and Nitrospirota phyla. Functional predictions indicated that both NOB MAGs shared many highly conserve metabolic features with other NOB. Both NOB MAGs encoded proteins for hydrogen and organic compound metabolism and defense mechanisms for oxidative stress. Additionally, these organisms may have the genetic potential to produce cobalamin (an essential enzyme cofactor that is limiting in many environments) and thus may play an important role in recycling cobalamin in marine sediment. Overall, this study appreciably expands our understanding of the Nitrospinota and Nitrospirota phyla, and suggests that these NOB may play important biogeochemical roles in marine habitats.Importance Nitrification is a key process in the biogeochemical and global nitrogen cycle. Nitrite-oxidizing bacteria (NOB) perform the second step of aerobic nitrification (converting nitrite to nitrate), which is critical for transferring nitrogen to other organisms for assimilation or energy. Despite their ecological importance, there are few cultured or genomic representatives from marine systems. Here, we obtained two NOB (designated as MSP and DJ) enriched from marine sediments and estimated the physiological and genomic traits of these marine microbes. Both NOB enrichment cultures exhibit distinct responses to varying nitrite and salt concentrations. Genomic analyses suggest that these NOB are metabolically flexible (similar to other previously described NOB), and yet also have individual genomic differences that likely support distinct niche distribution. In conclusion, this study provides more insights into the ecological roles of NOB in marine environments.}, }
@article {pmid32917275, year = {2020}, author = {Modin, O and Liébana, R and Saheb-Alam, S and Wilén, BM and Suarez, C and Hermansson, M and Persson, F}, title = {Hill-based dissimilarity indices and null models for analysis of microbial community assembly.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {132}, pmid = {32917275}, issn = {2049-2618}, support = {2012-5167//Vetenskapsrådet/ ; 2013-627//Svenska Forskningsrådet Formas/ ; 2018-01423//Svenska Forskningsrådet Formas/ ; 2018-00622//Svenska Forskningsrådet Formas/ ; }, abstract = {BACKGROUND: High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases, and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.<br><br>RESULTS: Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.<br><br>CONCLUSIONS: Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines. Video Abstract.}, }
@article {pmid32916620, year = {2020}, author = {Lukumbuzya, M and Kristensen, JM and Kitzinger, K and Pommerening-Röser, A and Nielsen, PH and Wagner, M and Daims, H and Pjevac, P}, title = {A refined set of rRNA-targeted oligonucleotide probes for in situ detection and quantification of ammonia-oxidizing bacteria.}, journal = {Water research}, volume = {186}, number = {}, pages = {116372}, doi = {10.1016/j.watres.2020.116372}, pmid = {32916620}, issn = {1879-2448}, abstract = {Ammonia-oxidizing bacteria (AOB) of the betaproteobacterial genera Nitrosomonas and Nitrosospira are key nitrifying microorganisms in many natural and engineered ecosystems. Since many AOB remain uncultured, fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has been one of the most widely used approaches to study the community composition, abundance, and other features of AOB directly in environmental samples. However, the established and widely used AOB-specific 16S rRNA-targeted FISH probes were designed up to two decades ago, based on much smaller rRNA gene sequence datasets than available today. Several of these probes cover their target AOB lineages incompletely and suffer from a weak target specificity, which causes cross-hybridization of probes that should detect different AOB lineages. Here, a set of new highly specific 16S rRNA-targeted oligonucleotide probes was developed and experimentally evaluated that complements the existing probes and enables the specific detection and differentiation of the known, major phylogenetic clusters of betaproteobacterial AOB. The new probes were successfully applied to visualize and quantify AOB in activated sludge and biofilm samples from seven pilot- and full-scale wastewater treatment systems. Based on its improved target group coverage and specificity, the refined probe set will facilitate future in situ analyses of AOB.}, }
@article {pmid32915303, year = {2020}, author = {Chan, YF and Chiang, PW and Tandon, K and Rogozin, D and Degermendzhi, A and Zykov, V and Tang, SL}, title = {Spatiotemporal Changes in the Bacterial Community of the Meromictic Lake Uchum, Siberia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01592-9}, pmid = {32915303}, issn = {1432-184X}, support = {No. 19-05-00428//Российский Фонд Фундаментальных Исследований (РФФИ) (RU)/ ; No. 18-45-243002//Krasnoyarsk Regional Fund of Science/ ; 105-2923-B-001-001-MY3//Ministry of Science and Technology, Taiwan/ ; 108-2811-M-001-603//Ministry of Science and Technology, Taiwan/ ; }, abstract = {Lake Uchum is a newly defined meromictic lake in Siberia with clear seasonal changes in its mixolimnion. This study characterized the temporal dynamics and vertical profile of bacterial communities in oxic and anoxic zones of the lake across all four seasons: October (autumn), March (winter), May (spring), and August (summer). Bacterial richness and diversity in the anoxic zone varied widely between time points. Proteobacteria was the dominant bacterial phylum throughout the oxic and anoxic zones across all four seasons. Alphaproteobacteria (Loktanella) and Gammaproteobacteria (Aliidiomarina) exhibited the highest abundance in the oxic and anoxic zone, respectively. Furthermore, there was a successional shift in sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria in the anoxic zone across the seasons. The most dominant SRB, Desulfonatronovibrio sp., is likely one of the main producers of hydrogen sulfide (H2S) and typically accumulates the most H2S in winter. The representative anoxygenic phototrophic bacterial group in Lake Uchum was purple sulfur bacteria (PSB). PSB were dominant (60.76%) in summer, but only had 0.2-1.5% relative abundance from autumn to spring. Multivariate analysis revealed that the abundance of these SRB and PSB correlated to the concentration of H2S in Lake Uchum. Taken together, this study provides insights into the relationships between changes in bacterial community and environmental features in Lake Uchum.}, }
@article {pmid32914254, year = {2020}, author = {Chen, J and Xie, P and Yu, D and Xie, L and Zeng, C and Chen, J}, title = {Dynamic Change of Sedimental Microbial Community During Black Bloom-an In Situ Enclosure Simulation Study.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01561-2}, pmid = {32914254}, issn = {1432-184X}, support = {2012ZX07101-010//Major Science and Technology Program for Water Pollution Control and Treatment/ ; 2014FBZ02, 2014FB15//State Key Laboratory of Freshwater Ecology and Biotechnology/ ; 31901081//National Natural Science Foundation of China/ ; }, abstract = {Black bloom is a worldwide environmental problem. Sediment microbes play important roles in the process of black bloom. The dynamic change of sedimental microbial community and their potential link between taste and odor compounds during black bloom was investigated in an in situ black bloom enclosure simulation experiment. Through high-throughput sequencing and analysis, pronounced shifts of sedimental microbial community were observed on the 3rd and 7th day in the black bloom group. Microbes in Cyanobacteria, Verrucomicrobia, Planctomycetes, and Actinobacteria were obviously increased, while microbes from the phyla OP8, Chloroflexi, and Acidobacteria were decreased significantly. RDA analysis revealed that the concentrations of chlorophyll a (Chla), total phosphorus (TP), and turbidity (NTU) in the water and the TP, TN concentrations in the sediment were the main environmental factors that affect the microbial community in the sediment. Correlation analysis revealed that microbes Dechloromonas sp. (OTU003567 and OTU000093), Desulfococcus sp. (OTU000911), Chromatiaceae (OTU001222), and Methanosaeta sp. (OTU004809) were positively correlated with the taste and odor substances in the sediment, such as dimethyl sulfide (DMS), β-ionone, β-cyclocitral and geosmin. The sedimental microbial community gradually recovered in the late phase of black bloom, indicating the stability and self-recovery ability of the sedimental microbial community during black bloom. Noteworthily, we observed many possible pathogens increased significantly during the black bloom, which alerts us to keep away from contaminated sediment when black bloom occurred.}, }
@article {pmid32911871, year = {2020}, author = {Mbareche, H and Dumont-Leblond, N and Bilodeau, GJ and Duchaine, C}, title = {An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists.}, journal = {Life (Basel, Switzerland)}, volume = {10}, number = {9}, pages = {}, doi = {10.3390/life10090185}, pmid = {32911871}, issn = {2075-1729}, abstract = {High-throughput DNA sequencing (HTS) has changed our understanding of the microbial composition present in a wide range of environments. Applying HTS methods to air samples from different environments allows the identification and quantification (relative abundance) of the microorganisms present and gives a better understanding of human exposure to indoor and outdoor bioaerosols. To make full use of the avalanche of information made available by these sequences, repeated measurements must be taken, community composition described, error estimates made, correlations of microbiota with covariates (variables) must be examined, and increasingly sophisticated statistical tests must be conducted, all by using bioinformatics tools. Knowing which analysis to conduct and which tools to apply remains confusing for bioaerosol scientists, as a litany of tools and data resources are now available for characterizing microbial communities. The goal of this review paper is to offer a guided tour through the bioinformatics tools that are useful in studying the microbial ecology of bioaerosols. This work explains microbial ecology features like alpha and beta diversity, multivariate analyses, differential abundances, taxonomic analyses, visualization tools and statistical tests using bioinformatics tools for bioaerosol scientists new to the field. It illustrates and promotes the use of selected bioinformatic tools in the study of bioaerosols and serves as a good source for learning the &quot;dos and don'ts&quot; involved in conducting a precise microbial ecology study.}, }
@article {pmid32910439, year = {2020}, author = {Callewaert, C and Ravard Helffer, K and Lebaron, P}, title = {Skin Microbiome and its Interplay with the Environment.}, journal = {American journal of clinical dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s40257-020-00551-x}, pmid = {32910439}, issn = {1179-1888}, abstract = {Advances in sequencing, bioinformatics and analytics now allow the structure, function and interrelations of whole microbial communities to be studied in greater detail. Collaborative efforts and multidisciplinary studies, crossing the boundary between environmental and medical microbiology, have allowed specific environmental, animal and human microbiomes to be characterized. One of the main challenges for microbial ecology is to link the phylogenetic diversity of host-associated microbes to their functional roles within the community. Much remains to be learned on the way microbes colonize the skin of different living organisms and the way the skin microbiome reacts to the surrounding environment (air, water, etc.). In this review, we discuss examples of recent studies that have used modern technology to provide insights into microbial communities in water and on skin, such as those in natural resources (thermal spring water), large mammals (humpback whales) and humans (the skin microbiome). The results of these studies demonstrate how a greater understanding of the structure and functioning of microbiota, together with their interactions with the environment, may facilitate the discovery of new probiotics or postbiotics, provide indicators for the quality of the environment, and show how changes in lifestyle and living environment, such as urbanization, can impact on the skin microbiome and skin health and disease in humans.}, }
@article {pmid32909073, year = {2020}, author = {Mootapally, C and Mahajan, MS and Nathani, NM}, title = {Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01587-6}, pmid = {32909073}, issn = {1432-184X}, support = {PDF/2016/001239//Science and Engineering Research Board/ ; PDF/2016/000190//Science and Engineering Research Board/ ; }, abstract = {Plasmidomes have become the research area of interest for ecologists exploring bacteria rich ecosystems. Marine environments are among such niche that host a huge number of microbes and have a complex environment which pose the need to study these bacterial indicators of horizontal gene transfer events for survival and stability. The plasmid content of the metagenomics data from 8 sediment samples of the Gulfs of Kathiawar and an open Arabian Sea sample was screened. The reads corresponding to hits against the plasmid database were assembled and studied for diversity using Kraken and functional content using MG-RAST. The sequences were also checked for resistome and virulence factors. The replicon hosts were overall dominated by Proteobacteria, Firmicutes, and Actinobacteria while red algae specific to the Kutch samples. The genes encoded were dominant in the flagella motility and type VI secretion systems. Overall, results from the study confirmed that the plasmids encoded traits for metal, antibiotic, and phage resistance along with virulence systems, and these would be conferring benefit to the hosts. The study throws insights into the environmental role of the plasmidome in adaptation of the microbes in the studied sites to the environmental stresses.}, }
@article {pmid32906802, year = {2020}, author = {Nakai, R and Naganuma, T and Tazato, N and Morohoshi, S and Koide, T}, title = {Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage.}, journal = {Microorganisms}, volume = {8}, number = {9}, pages = {}, doi = {10.3390/microorganisms8091373}, pmid = {32906802}, issn = {2076-2607}, support = {KAKENHI Grant Number JP13J03441//Japan Society for the Promotion of Science/ ; KAKENHI Grant Number JP15H05620//Japan Society for the Promotion of Science/ ; KAKENHI Grant Number JP19H05683//Ministry of Education, Culture, Sports, Science and Technology/ ; KAKENHI Grant Number JP19H05679//Ministry of Education, Culture, Sports, Science and Technology/ ; KAKENHI Grant Number JP23570117//Japan Society for the Promotion of Science/ ; }, abstract = {Rhizobiales bacterium strain IZ6 is a novel filterable bacterium that was isolated from a suspension filtrate (<0.22 µm) of soil collected in Shimane Prefecture, western Japan. Additional closely related isolates were recovered from filterable fractions of terrestrial environmental samples collected from other places in Japan; the Gobi Desert, north-central China; and Svalbard, Arctic Norway. These findings indicate a wide distribution of this lineage. This study reports the cell variation and genomic structure of IZ6. When cultured at lower temperatures (4 °C and 15 °C), this strain contained ultra-small cells and cell-like particles in the filtrate. PacBio sequencing revealed that this chromosome (3,114,641 bp) contained 3150 protein-coding, 51 tRNA, and three rRNA genes. IZ6 showed low 16S rRNA gene sequence identity (<97%) and low average nucleotide identity (<76%) with its closest known relative, Flaviflagellibacter deserti. Unlike the methylotrophic bacteria and nitrogen-fixing bacteria in related genera, there were no genes that encoded enzymes for one-carbon-compound utilization and nitrogen fixation in the IZ6 genome; the genes related to nitrate and nitrite reductase are retained and those related to the cell membrane function tend to be slightly enriched in the genome. This genomic information helps elucidate the eco-physiological function of a phenotypically heterogeneous and diverse Rhizobiales group.}, }
@article {pmid32903459, year = {2020}, author = {Álvarez-Rodríguez, I and Arana, L and Ugarte-Uribe, B and Gómez-Rubio, E and Martín-Santamaría, S and Garbisu, C and Alkorta, I}, title = {Type IV Coupling Proteins as Potential Targets to Control the Dissemination of Antibiotic Resistance.}, journal = {Frontiers in molecular biosciences}, volume = {7}, number = {}, pages = {201}, pmid = {32903459}, issn = {2296-889X}, abstract = {The increase of infections caused by multidrug-resistant bacteria, together with the loss of effectiveness of currently available antibiotics, represents one of the most serious threats to public health worldwide. The loss of human lives and the economic costs associated to the problem of the dissemination of antibiotic resistance require immediate action. Bacteria, known by their great genetic plasticity, are capable not only of mutating their genes to adapt to disturbances and environmental changes but also of acquiring new genes that allow them to survive in hostile environments, such as in the presence of antibiotics. One of the major mechanisms responsible for the horizontal acquisition of new genes (e.g., antibiotic resistance genes) is bacterial conjugation, a process mediated by mobile genetic elements such as conjugative plasmids and integrative conjugative elements. Conjugative plasmids harboring antibiotic resistance genes can be transferred from a donor to a recipient bacterium in a process that requires physical contact. After conjugation, the recipient bacterium not only harbors the antibiotic resistance genes but it can also transfer the acquired plasmid to other bacteria, thus contributing to the spread of antibiotic resistance. Conjugative plasmids have genes that encode all the proteins necessary for the conjugation to take place, such as the type IV coupling proteins (T4CPs) present in all conjugative plasmids. Type VI coupling proteins constitute a heterogeneous family of hexameric ATPases that use energy from the ATP hydrolysis for plasmid transfer. Taking into account their essential role in bacterial conjugation, T4CPs are attractive targets for the inhibition of bacterial conjugation and, concomitantly, the limitation of antibiotic resistance dissemination. This review aims to compile present knowledge on T4CPs as a starting point for delving into their molecular structure and functioning in future studies. Likewise, the scientific literature on bacterial conjugation inhibitors has been reviewed here, in an attempt to elucidate the possibility of designing T4CP-inhibitors as a potential solution to the dissemination of multidrug-resistant bacteria.}, }
@article {pmid32903319, year = {2020}, author = {Møller, TE and van der Bilt, WGM and Roerdink, DL and Jørgensen, SL}, title = {Microbial Community Structure in Arctic Lake Sediments Reflect Variations in Holocene Climate Conditions.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1520}, pmid = {32903319}, issn = {1664-302X}, abstract = {The reconstruction of past climate variability using physical and geochemical parameters from lake sedimentary records is a well-established and widely used approach. These geological records are also known to contain large and active microbial communities, believed to be responsive to their surroundings at the time of deposition, and proceed to interact intimately with their physical and chemical environment for millennia after deposition. However, less is known about the potential legacy of past climate conditions on the contemporary microbial community structure. We analysed two Holocene-length (past 10 ka BP) sediment cores from the glacier-fed Ymer Lake, located in a highly climate-sensitive region on south-eastern Greenland. By combining physical proxies, solid as well as fluid geochemistry, and microbial population profiling in a comprehensive statistical framework, we show that the microbial community structure clusters according to established lithological units, and thus captures past environmental conditions and climatic transitions. Further, comparative analyses of the two sedimentary records indicates that the manifestation of regional climate depends on local settings such as water column depth, which ultimately constrains microbial variability in the deposited sediments. The strong coupling between physical and geochemical shifts in the lake and microbial variation highlights the potential of molecular microbiological data to strengthen and refine existing sedimentological classifications of past environmental conditions and transitions. Furthermore, this coupling implies that microbially controlled transformation and partitioning of geochemical species (e.g., manganese and sulphate) in Ymer lake today is still affected by climatic conditions that prevailed thousands of years back in time.}, }
@article {pmid32901388, year = {2020}, author = {González-Dominici, LI and Saati-Santamaría, Z and García-Fraile, P}, title = {Genome Analysis and Genomic Comparison of the Novel Species Arthrobacter ipsi Reveal Its Potential Protective Role in Its Bark Beetle Host.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01593-8}, pmid = {32901388}, issn = {1432-184X}, support = {19-09072S//Grantová Agentura České Republiky/ ; CLU-2018-04//Junta de Castilla y León (ES)/ ; }, abstract = {The pine engraver beetle, Ips acuminatus Gyll, is a bark beetle that causes important damages in Scots pine (Pinus sylvestris) forests and plantations. As almost all higher organisms, Ips acuminatus harbours a microbiome, although the role of most members of its microbiome is not well understood. As part of a work in which we analysed the bacterial diversity associated to Ips acuminatus, we isolated the strain Arthrobacter sp. IA7. In order to study its potential role within the bark beetle holobiont, we sequenced and explored its genome and performed a pan-genome analysis of the genus Arthrobacter, showing specific genes of strain IA7 that might be related with its particular role in its niche. Based on these investigations, we suggest several potential roles of the bacterium within the beetle. Analysis of genes related to secondary metabolism indicated potential antifungal capability, confirmed by the inhibition of several entomopathogenic fungal strains (Metarhizium anisopliae CCF0966, Lecanicillium muscarium CCF6041, L. muscarium CCF3297, Isaria fumosorosea CCF4401, I. farinosa CCF4808, Beauveria bassiana CCF4422 and B. brongniartii CCF1547). Phylogenetic analyses of the 16S rRNA gene, six concatenated housekeeping genes (tuf-secY-rpoB-recA-fusA-atpD) and genome sequences indicated that strain IA7 is closely related to A. globiformis NBRC 12137T but forms a new species within the genus Arthrobacter; this was confirmed by digital DNA-DNA hybridization (37.10%) and average nucleotide identity (ANIb) (88.9%). Based on phenotypic and genotypic features, we propose strain IA7T as the novel species Arthrobacter ipsi sp. nov. (type strain IA7T = CECT 30100T = LMG 31782T) and suggest its protective role for its host.}, }
@article {pmid32901387, year = {2020}, author = {Wu, C and Wei, X and Hu, Z and Liu, Y and Hu, Y and Qin, H and Chen, X and Wu, J and Ge, T and Zhran, M and Su, Y}, title = {Diazotrophic Community Variation Underlies Differences in Nitrogen Fixation Potential in Paddy Soils Across a Climatic Gradient in China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01591-w}, pmid = {32901387}, issn = {1432-184X}, support = {2017YFD0800104//National Key Research and Development program/ ; 41977100//National Natural Science Foundation of China/ ; 41771300//National Natural Science Foundation of China/ ; 2018WK4012//Hunan Province Base for Scientific and Technological Innovation Cooperation/ ; 2017QNCXTD_GTD//Youth Innovation Team Project of Institute of Subtropical Agriculture, Chinese Academy of Sciences/ ; 2019JJ10003//Natural Science Foundation of Hunan Province/ ; }, abstract = {Biological nitrogen (N2) fixation as a source of new N input into the soil by free-living diazotrophs is important for achieving sustainable rice agriculture. However, the dominant environmental drivers or factors influencing N2 fixation and the functional significance of the diazotroph community structure in paddy soil across a climatic gradient are not yet well understood. Thus, we characterized the diazotroph community and identified the ecological predictors of N2 fixation potential in four different climate zones (mid-temperate, warm-temperate, subtropical, and tropical paddy soils) in eastern China. Comprehensive nifH gene sequencing, functional activity detection, and correlation analysis with environmental factors were estimated. The potential nitrogenase activity (PNA) was highest in warm-temperate regions, where it was 6.2-, 2.9-, and 2.2-fold greater than in the tropical, subtropical, and mid-temperate regions, respectively; nifH gene abundance was significantly higher in warm-temperate and subtropical zones than in the tropical or mid-temperate zones. Diazotroph diversity was significantly higher in the tropical climate zone and significantly lower in the mid-temperate zone. Non-metric multidimensional scaling and canonical correlation analysis indicated that paddy soil diazotroph populations differed significantly among the four climate zones, mainly owing to differences in climate and soil pH. Structural equation models and automatic linear models revealed that climate and nutrients indirectly affected PNA by affecting soil pH and diazotroph community, respectively, while diazotroph community, C/P, and nifH gene abundance directly affected PNA. And C/P ratio, pH, and the diazotroph community structure were the main predictors of PNA in paddy soils. Collectively, the differences in diazotroph community structure have ecological significance, with important implications for the prediction of soil N2-fixing functions under climate change scenarios.}, }
@article {pmid32901386, year = {2020}, author = {Petrzik, K and Lukavský, J and Koloniuk, I}, title = {Novel Virus on Filamentous Arthronema africanum Cyanobacterium.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01599-2}, pmid = {32901386}, issn = {1432-184X}, support = {RVO60077344//institutional support/ ; RVO67985939//institutional support/ ; Biocirtech T01000048//Technologická Agentura České Republiky/ ; }, abstract = {Widely distributed in water environments and in soil, cyanobacteria are hosts of lysogenic or lytic bacterioviruses. A novel, probably lysogenic virus (phage) for which the name Arthronema africanum virus TR020 (Aa-TR020) is proposed, has been isolated from filamentous freshwater cyanobacterium Arthronema africanum. The virus formed turbid plaques on plate culture of A. africanum strain 1980/01 but not on other Arthronema strain and other bacterial species. The genome of Aa-TR020 is linear molecule of dsDNA, 44,805 bp in length with 216 bp long terminal repeats and with G + C content of 46%. Fifty-five genes organized on plus and minus strands were predicted there. The genome size, gene arrangement, and selected protein sequences showed relatedness to Phormidium virus Pf-WMP3 and other viruses known to infect cyanobacteria and classified in the family Podoviridae.}, }
@article {pmid32897365, year = {2020}, author = {Rodrigues, GR and Pinto, OHB and Schroeder, LF and Fernandes, GDR and Costa, OYA and Quirino, BF and Kuramae, EE and Barreto, CC}, title = {Unraveling the xylanolytic potential of Acidobacteria bacterium AB60 from Cerrado soils.}, journal = {FEMS microbiology letters}, volume = {367}, number = {18}, pages = {}, doi = {10.1093/femsle/fnaa149}, pmid = {32897365}, issn = {1574-6968}, abstract = {The presence of genes for glycosyl hydrolases in many Acidobacteria genomes indicates an important role in the degradation of plant cell wall material. Acidobacteria bacterium AB60 was obtained from Cerrado oligotrophic soil in Brazil, where this phylum is abundant. The 16S rRNA gene analyses showed that AB60 was closely related to the genera Occallatibacter and Telmatobacter. However, AB60 grew on xylan as carbon source, which was not observed in Occallatibacter species; but growth was not detected on medium containing carboxymethyl cellulose, as observed in Telmatobacter. Nevertheless, the genome analysis of AB60 revealed genes for the enzymes involved in cellulose as well as xylan degradation. In addition to enzymes involved in xylan degradation, α-l-rhamnosidase was detected in the cultures of AB60. Functional screening of a small-insert genomic library did not identify any clones capable of carboxymethyl cellulose degradation, but open reading frames coding α-l-arabinofuranosidase and α-l-rhamnosidase were present in clones showing xylan degradation halos. Both enzymes act on the lateral chains of heteropolymers such as pectin and some hemicelluloses. These results indicate that the hydrolysis of α-linked sugars may offer a metabolic niche for slow-growing Acidobacteria, allowing them to co-exist with other plant-degrading microbes that hydrolyze β-linked sugars from cellulose or hemicellulose backbones.}, }
@article {pmid32897356, year = {2020}, author = {Bandini, F and Misci, C and Taskin, E and Cocconcelli, PS and Puglisi, E}, title = {Biopolymers modulate microbial communities in municipal organic waste digestion.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {10}, pages = {}, doi = {10.1093/femsec/fiaa183}, pmid = {32897356}, issn = {1574-6941}, abstract = {The development of biopolymers has raised issues about their recalcitrance in the environment. Their disposal is mainly carried out with the organic fraction of municipal solid waste (OFMSW) through thermophilic anaerobic digestion and aerobic composting, bioprocesses aimed at turning organic matter into biogas and compost. However, the effects of biopolymers on OFMSW treatment, on the final compost and on the microbial communities involved are partly unexplored. In this study, the OFMSW treatment was reproduced on a laboratory-scale respecting real plant conditions and testing the impacts of mixing polylactic acid (PLA) and starch-based bioplastic (SBB) separately. The dynamics of bacterial, archaeal and fungal communities during the process was screened by high-throughput sequencing (HTS) of phylogenetic amplicons. Starch-based bioplastic showed a minor and heterogeneous microbial diversity between the anaerobic and aerobic phases. Contrariwise, PLA treatment resulted in wider and more diverse bacterial and fungal communities for the compost and the aerobic biofilm. Since the biodiversity in compost may play a crucial role in its stability and safety, the modulation of environmental microbial communities induced by higher concentrations of PLA in OFMSW treatment can pose relevant issues.}, }
@article {pmid32896070, year = {2020}, author = {Fei, C and Ochsenkühn, MA and Shibl, AA and Isaac, A and Wang, C and Amin, SA}, title = {Quorum sensing regulates 'swim-or-stick' lifestyle in the phycosphere.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15228}, pmid = {32896070}, issn = {1462-2920}, support = {AD179//New York University Abu Dhabi/ ; NA19NOS4780183//National Oceanic and Atmospheric Administration (NOAA)/ ; }, abstract = {Interactions between phytoplankton and bacteria play major roles in global biogeochemical cycles and oceanic nutrient fluxes. These interactions occur in the microenvironment surrounding phytoplankton cells, known as the phycosphere. Bacteria in the phycosphere use either chemotaxis or attachment to benefit from algal excretions. Both processes are regulated by quorum sensing (QS), a cell-cell signalling mechanism that uses small infochemicals to coordinate bacterial gene expression. However, the role of QS in regulating bacterial attachment in the phycosphere is not clear. Here, we isolated a Sulfitobacter pseudonitzschiae F5 and a Phaeobacter sp. F10 belonging to the marine Roseobacter group and an Alteromonas macleodii F12 belonging to Alteromonadaceae, from the microbial community of the ubiquitous diatom Asterionellopsis glacialis. We show that only the Roseobacter group isolates (diatom symbionts) can attach to diatom transparent exopolymeric particles. Despite all three bacteria possessing genes involved in motility, chemotaxis, and attachment, only S. pseudonitzschiae F5 and Phaeobacter sp. F10 possessed complete QS systems and could synthesize QS signals. Using UHPLC-MS/MS, we identified three QS molecules produced by both bacteria of which only 3-oxo-C16:1 -HSL strongly inhibited bacterial motility and stimulated attachment in the phycosphere. These findings suggest that QS signals enable colonization of the phycosphere by algal symbionts.}, }
@article {pmid32894355, year = {2020}, author = {He, W and Zhang, M and Jin, G and Sui, X and Zhang, T and Song, F}, title = {Effects of Nitrogen Deposition on Nitrogen-Mineralizing Enzyme Activity and Soil Microbial Community Structure in a Korean Pine Plantation.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01595-6}, pmid = {32894355}, issn = {1432-184X}, support = {31971527//National Natural Science Foundation of China/ ; TD2019C002//Natural Science Foudation of Heilongjiang Province/ ; }, abstract = {To predict the effects of nitrogen deposition on nitrogen-mineralizing enzyme activity and soil microbial community structure in artificial temperate forests in northern China, we studied the soil properties, nitrogen-mineralizing enzyme activity, and microbial community structure in the soil of a Korean pine plantation in which different concentrations (0, 20, 40, 80 kg N ha-1 year-1) of ammonium nitrate were applied for 5 consecutive years. The results showed that nitrogen addition at different concentrations did not significantly affect the soil pH. High nitrogen addition (80 kg N ha-1 year-1) significantly increased the soil organic matter, ammonium nitrogen, and nitrate nitrogen content in the Korean pine plantation, and ammonium nitrogen was the key factor that influenced the soil fungal community structure. The urease activity under the moderate nitrogen addition treatment (40 kg N ha-1 year-1) was significantly lower than that under the control (0 kg N ha-1 year-1), and the protease activity in the three treatments was also significantly lower than that in the control. There was no significant correlation between microbial community structure and the four mineralizing enzymes. After nitrogen addition at different concentrations, the Simpson and Shannon indexes of soil bacteria decreased significantly under low nitrogen addition (20 kg N ha-1 year-1), but the α-diversity index of soil fungi did not show significant differences under nitrogen addition. The microbial community composition was significantly changed by the different treatments. PLS-DA analysis showed that Tardiphaga was an important genus that made the greatest contribution to the differences in bacterial community composition among treatments, as was Taeniolella for fungal community composition. The low level of nitrogen addition inhibited nitrogen mineralization in the Korean pine plantation by reducing the relative abundances of Nitrosomonadaceae and Betaproteobacteriales and by reducing the abundances of symbiotrophic fungi. Berkelbacteria and Polyporales were bacteria and fungi, respectively, that changed significantly under the high nitrogen addition treatment (80 kg N ha-1 year-1). This study provides more data to support predictions of the changes in nitrogen-mineralizing enzyme activity and microbial community structure in artificial temperate forest soils in response to increased nitrogen deposition.}, }
@article {pmid32893477, year = {2020}, author = {Castledine, M and Padfield, D and Buckling, A}, title = {Experimental (co)evolution in a multi-species microbial community results in local maladaptation.}, journal = {Ecology letters}, volume = {}, number = {}, pages = {}, doi = {10.1111/ele.13599}, pmid = {32893477}, issn = {1461-0248}, support = {BB/T002522/1//NERC National Environmental research council/ ; NE/S000771/1//NERC National Environmental research council/ ; NE/P001130/1//NERC National Environmental research council/ ; }, abstract = {Interspecific coevolutionary interactions can result in rapid biotic adaptation, but most studies have focused only on species pairs. Here, we (co)evolved five microbial species in replicate polycultures and monocultures and quantified local adaptation. Specifically, growth rate assays were used to determine adaptations of each species' populations to (1) the presence of the other four species in general and (2) sympatric vs. allopatric communities. We found that species did not show an increase in net biotic adaptation:ancestral, polyculture- and monoculture-evolved populations did not have significantly different growth rates within communities. However, 4/5 species' growth rates were significantly lower within the community they evolved in relative to an allopatric community. 'Local maladaptation' suggests that species evolved increased competitive interactions to sympatric species' populations. This increased competition did not affect community stability or productivity. Our results suggest that (co)evolution within communities can increase competitive interactions that are specific to (co)evolved community members.}, }
@article {pmid32892232, year = {2020}, author = {Dwidar, M and Jang, H and Sangwan, N and Mun, W and Im, H and Yoon, S and Choi, S and Nam, D and Mitchell, RJ}, title = {Diffusible Signaling Factor, a Quorum-Sensing Molecule, Interferes with and Is Toxic Towards Bdellovibrio bacteriovorus 109J.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01585-8}, pmid = {32892232}, issn = {1432-184X}, support = {2020R1A2C2012158//National Research Foundation of Korea/ ; 2017M1A3A3A02016642//National Research Foundation of Korea/ ; }, abstract = {Bdellovibrio bacteriovorus 109J is a predatory bacterium which lives by predating on other Gram-negative bacteria to obtain the nutrients it needs for replication and survival. Here, we evaluated the effects two classes of bacterial signaling molecules (acyl homoserine lactones (AHLs) and diffusible signaling factor (DSF)) have on B. bacteriovorus 109J behavior and viability. While AHLs had a non-significant impact on predation rates, DSF considerably delayed predation and bdelloplast lysis. Subsequent experiments showed that 50 μM DSF also reduced the motility of attack-phase B. bacteriovorus 109J cells by 50% (38.2 ± 14.9 vs. 17 ± 8.9 μm/s). Transcriptomic analyses found that DSF caused genome-wide changes in B. bacteriovorus 109J gene expression patterns during both the attack and intraperiplasmic phases, including the significant downregulation of the flagellum assembly genes and numerous serine protease genes. While the former accounts for the reduced speeds observed, the latter was confirmed experimentally with 50 μM DSF completely blocking protease secretion from attack-phase cells. Additional experiments found that 30% of the total cellular ATP was released into the supernatant when B. bacteriovorus 109J was exposed to 200 μM DSF, implying that this QS molecule negatively impacts membrane integrity.}, }
@article {pmid32889760, year = {2020}, author = {Harrison, JG and John Calder, W and Shuman, B and Alex Buerkle, C}, title = {The quest for absolute abundance: The use of internal standards for DNA-based community ecology.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13247}, pmid = {32889760}, issn = {1755-0998}, support = {EPS-1655726//National Science Foundation/ ; }, abstract = {To characterize microbiomes and other ecological assemblages, ecologists routinely sequence and compare loci that differ among focal taxa. Counts of these sequences convey information regarding the occurrence and relative abundances of taxa, but provide no direct measure of their absolute abundances, due to the technical limitations of the sequencing process. The relative abundances in compositional data are inherently constrained and difficult to interpret. The incorporation of internal standards (ISDs; colloquially referred to as 'spike-ins') into DNA pools can ameliorate the problems posed by relative abundance data and allow absolute abundances to be approximated. Unfortunately, many laboratory and sampling biases cause ISDs to underperform or fail. Here, we discuss how careful deployment of ISDs can avoid these complications and be an integral component of well-designed studies seeking to characterize ecological assemblages via sequencing of DNA.}, }
@article {pmid32888042, year = {2020}, author = {Dickey, JR and Fordyce, JA and Lebeis, SL}, title = {Bacterial communities of the Salvia lyrata rhizosphere explained by spatial structure and sampling grain.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {846-858}, doi = {10.1007/s00248-020-01594-7}, pmid = {32888042}, issn = {1432-184X}, support = {DEB1638922//National Science Foundation (USA)/ ; }, abstract = {Advancements in molecular technology have reduced the constraints that the grain of observation, or the spatial resolution and volume of the sampling unit, has on the characterization of plant-associated microbiomes. With discrete ecological sampling and massive parallel sequencing, we can more precisely portray microbiome community assembly and microbial recruitment to host tissue over space and time. Here, we differentiate rarefied community richness and relative abundance in bacterial microbiomes of Salvia lyrata dependent on three spatial depths, which are discrete physical distances from the soil surface within the rhizosphere microhabitat as a proxy for the root system zones. To assess the impact of sampling grain on rarefied community richness and relative abundance, we evaluated the variation of these metrics between samples pooled prior to DNA extraction and samples pooled after sequencing. A distance-based redundancy analysis with the quantitative Jaccard distance revealed that rhizosphere microbiomes vary in richness between rhizosphere soil depths. At all orders of diversity, rarefied microbial richness was consistently lowest at the deepest samples taken (approximately 4 cm from soil surface) in comparison with other rhizosphere soil depths. We additionally show that finer grain sampling (i.e., three samples of equal volume pooled after sequencing) recovers greater microbial richness when using 16S rRNA gene sequencing to describe microbial communities found within the rhizosphere system. In summary, to further elucidate the extent host-specific microbiomes assemble within the rhizosphere, the grain at which bacterial communities are sampled should reflect and encompass fine-scale heterogeneity of the system.}, }
@article {pmid32887945, year = {2020}, author = {Gao, CH and Cao, H and Cai, P and Sørensen, SJ}, title = {The initial inoculation ratio regulates bacterial coculture interactions and metabolic capacity.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-020-00751-7}, pmid = {32887945}, issn = {1751-7370}, abstract = {Coculture is an important model system in microbial ecology studies. As a key experimental parameter, the initial inoculation ratio has a crucial impact on the results of the coculture system. However, such an effect has never been investigated under multiple niche conditions. In this study, we established a simple coculture system with two model bacteria in various carbon sources and investigated the influence of initial inoculum ratios of 1:1000 to 1000:1 on community structure, function, and bacterial interaction. We found that the final ratio of the cocultures with different initial inoculum ratios differed in approximately five-sixths of the carbon sources, suggesting that the final ratio is highly dependent on the initial inoculum ratio, while the carbon source preferences of bacteria could not predict the final ratio of cocultures. Furthermore, we found that the initial ratio could regulate the metabolic capacity of the coculture, as only cocultures with initial ratios of 1:1 and 1000:1 gained high capacity on 14 specific carbon sources. The underlying reason may be that the pattern of species interaction is changed by the initial ratio. In conclusion, we showed that the initial ratio can induce emergent properties in coculture. These findings suggest that the initial ratio not only impacts the reproducibility of coculture experiments but also can influence our understanding of generic microbial ecology.}, }
@article {pmid32887010, year = {2020}, author = {Oliveira, BB and Veigas, B and Carlos, FF and Sánchez-Melsió, A and Balcázar, JL and Borrego, CM and Baptista, PV}, title = {Water safety screening via multiplex LAMP-Au-nanoprobe integrated approach.}, journal = {The Science of the total environment}, volume = {741}, number = {}, pages = {140447}, doi = {10.1016/j.scitotenv.2020.140447}, pmid = {32887010}, issn = {1879-1026}, mesh = {*Escherichia coli ; Feces ; *Nucleic Acid Amplification Techniques ; Real-Time Polymerase Chain Reaction ; Sensitivity and Specificity ; }, abstract = {Contaminated water resources remain a major global concern regarding public health. The majority of water safety protocols include indicators of microbial contamination to evaluate the potential risk to public health and are key elements of quality guidelines. Among these, markers for total coliforms and fecal coliforms are strong indicators of co-contamination with other pathogens. Traditional methods, recurring to slow and cumbersome culture-based approaches, have been gradually replaced by molecular methods, capable of faster and more specific screening. These are usually PCR-based methods that may allow for multiple pathogen detection but require dedicated laboratory equipment, hindering the rapid on-site assessment. Here, we used a multiplex Loop-Mediated Isothermal Amplification (mLAMP) strategy for the amplification of two markers associated with the contamination by total and fecal coliforms (e.g. Escherichia coli) - lacZ and uidA genes, respectively - thus allowing for single tube multiplex detection. The mLAMP products were then subject to an Au-nanoprobe colorimetric detection assay for precise discrimination of targets. This approach was validated in 22 water samples that were also screened for the presence of lacZ and uidA using standard and quantitative PCR, with the capability for discriminating the contamination level, e.g. a semi-quantitative evaluation of water quality.}, }
@article {pmid32885507, year = {2020}, author = {Wall, CB and Egan, CP and Swift, SIO and Hynson, NA}, title = {Three decades post-reforestation has not led to the reassembly of arbuscular mycorrhizal fungal communities associated with remnant primary forests.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15624}, pmid = {32885507}, issn = {1365-294X}, support = {//W. M. Keck Foundation/ ; 1556856//National Science Foundation/ ; }, abstract = {The negative effects of deforestation can potentially be ameliorated through ecological restoration. However, reforestation alone may not reassemble the same ecological communities or functions as primary forests. In part, this failure may be owed to forest ecosystems inherently involving complex interactions among guilds of organisms. Plants, which structure forest food webs, rely on intimate associations with symbiotic microbes such as root-inhabiting mycorrhizal fungi. Here, we leverage a large-scale reforestation project on Hawai'i Island underway for over three decades to assess whether arbuscular mycorrhizal (AM) fungal communities have concurrently been restored. The reference ecosystem for this restoration project is a remnant montane native Hawaiian forest that provides critical habitat for endangered birds. We sampled soils from 12 plots within remnant and restored forest patches and characterized AM fungal communities using high-throughput amplicon sequencing. While some AM fungal community metrics were comparable between remnant and restored forest (e.g. species richness), other key characteristics were not. Specifically, community membership and the identity of AM fungal keystone species differed between the two habitat types, as well as the primary environmental factors influencing community composition. Remnant forest AM fungal communities were strongly associated with soil chemical properties, especially pH, while restored forest communities were influenced by the spatial proximity to remnant forests. We posit that combined, these differences in soil AM fungal communities could be negatively affecting the recruitment of native plant hosts and that future restoration efforts should consider plant-microbe interactions as an important facet of forest health.}, }
@article {pmid32884655, year = {2020}, author = {Duplouy, A and Minard, G and Saastamoinen, M}, title = {The gut bacterial community affects immunity but not metabolism in a specialist herbivorous butterfly.}, journal = {Ecology and evolution}, volume = {10}, number = {16}, pages = {8755-8769}, pmid = {32884655}, issn = {2045-7758}, abstract = {Plant tissues often lack essential nutritive elements and may contain a range of secondary toxic compounds. As nutritional imbalance in food intake may affect the performances of herbivores, the latter have evolved a variety of physiological mechanisms to cope with the challenges of digesting their plant-based diet. Some of these strategies involve living in association with symbiotic microbes that promote the digestion and detoxification of plant compounds or supply their host with essential nutrients missing from the plant diet. In Lepidoptera, a growing body of evidence has, however, recently challenged the idea that herbivores are nutritionally dependent on their gut microbial community. It is suggested that many of the herbivorous Lepidopteran species may not host a resident microbial community, but rather a transient one, acquired from their environment and diet. Studies directly testing these hypotheses are however scarce and come from an even more limited number of species.By coupling comparative metabarcoding, immune gene expression, and metabolomics analyses with experimental manipulation of the gut microbial community of prediapause larvae of the Glanville fritillary butterfly (Melitaea cinxia, L.), we tested whether the gut microbial community supports early larval growth and survival, or modulates metabolism or immunity during early stages of development.We successfully altered this microbiota through antibiotic treatments and consecutively restored it through fecal transplants from conspecifics. Our study suggests that although the microbiota is involved in the up-regulation of an antimicrobial peptide, it did not affect the life history traits or the metabolism of early instars larvae.This study confirms the poor impact of the microbiota on diverse life history traits of yet another Lepidoptera species. However, it also suggests that potential eco-evolutionary host-symbiont strategies that take place in the gut of herbivorous butterfly hosts might have been disregarded, particularly how the microbiota may affect the host immune system homeostasis.}, }
@article {pmid32882545, year = {2020}, author = {Li, L and Ning, D and Jeon, Y and Ryu, H and Santo Domingo, JW and Kang, DW and Kadudula, A and Seo, Y}, title = {Ecological insights into assembly processes and network structures of bacterial biofilms in full-scale biologically active carbon filters under ozone implementation.}, journal = {The Science of the total environment}, volume = {751}, number = {}, pages = {141409}, doi = {10.1016/j.scitotenv.2020.141409}, pmid = {32882545}, issn = {1879-1026}, abstract = {To address the adverse effects of harmful algal blooms, there are increased demands over the implementation of ozone coupled with biologically active carbon (BAC) filters in the drinking water treatment plants. Although the microbial biofilms are vital elements to support the proper performance of BAC filters, except for taxonomic affiliations, little is known about the assembly mechanisms of microbial communities in the full-scale BAC filters. This study aimed to examine how the assembly processes and their associated factors (e.g., influent characteristics, biological interactions) drive the temporal dynamics of bacterial communities in full-scale BAC filters, which underwent ozone implementation (five consecutive seasons from 2017 to 2018). The results revealed that along with the increase of bacterial taxonomic richness and evenness, stochastic processes became more crucial to determine the bacterial community assembly in the summer and autumn after ozone implementation (relative contribution: 61.23% and 83.75%, respectively). Moreover, their corresponding networks possessed simple network structures with lower modularity than other seasons, which implied lesser biological interactions among bacterial populations. The correlation between taxonomic and predicted functional diversities using functional redundancy index indicated that relatively high levels of bacterial functional redundancy (>0.83) were generally present in BAC filters. However, compared to other seasons, significantly higher degrees of functional redundancy existed in the summer and autumn after ozone implementation (0.85 ± 0.01 and 0.86 ± 0.01, respectively). Overall, this work improves our understanding of the microbial ecology of full-scale BAC filters by providing a conceptual framework that characterizes bacterial biofilm assembly processes relevant to performance optimization of full-scale BAC filters.}, }
@article {pmid32880700, year = {2020}, author = {Sabu, EA and Gonsalves, MJ and Sreepada, RA and Shivaramu, MS and Ramaiah, N}, title = {Evaluation of the Physiological Bacterial Groups in a Tropical Biosecured, Zero-Exchange System Growing Whiteleg Shrimp, Litopenaeus vannamei.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01575-w}, pmid = {32880700}, issn = {1432-184X}, support = {PSC 0206//Council of Scientific and Industrial Research, India/ ; }, abstract = {To elucidate the individual and multiple roles of physiological bacterial groups involved in biogeochemical cycles of carbon, nitrogen, phosphorus and sulfur, the changes in the abundance of aerobic bacteria (heterotrophs, methane oxidizers, ammonia oxidizers, sulfur oxidizers, phosphate solubilizers, phosphate accumulators) and anaerobic bacteria (total anaerobes, nitrate reducers, denitrifiers and sulfate reducers) were investigated in a biosecured, zero-exchange system stocked with whiteleg shrimp, Litopenaeus vannamei for one production cycle. Key water quality parameters during the 96-day production cycle fell within the normal range for L. vannamei culture. Results of Spearman's correlation matrix revealed that different sets of variables correlated at varying levels of significance of the interrelationships between bacterial abundances and water quality parameters. The three nitrogenous species (ammonia, nitrite and nitrate) strongly influenced the physiological bacterial groups' abundance. The strong relationship of bacterial groups with phytoplankton biomass and abundance clearly showed the trophic interconnections in nutrient exchange/recycling. Canonical correspondence analysis performed to assess the total variation revealed that the three dissolved nitrogen species followed by salinity, temperature, phytoplankton biomass and pH collectively accounted for as much as 82% of the total variation. In conclusion, the results of the study revealed that the major drivers that interweaved biogeochemical cycles are the three dissolved nitrogen species, which microbially mediated various aerobic-anaerobic assimilation/dissimilation processes in the pond ecosystem. Considering the pond microbial ecology becoming an important management tool where applied research could improve the economic and environmental sustainability of the aquaculture industry, the findings of the present study are practically relevant.}, }
@article {pmid32880699, year = {2020}, author = {Wei, J and Segraves, KA and Li, WZ and Yang, XK and Xue, HJ}, title = {Gut bacterial communities and their contribution to performance of specialist Altica flea beetles.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {946-959}, doi = {10.1007/s00248-020-01590-x}, pmid = {32880699}, issn = {1432-184X}, support = {31672334//National Natural Science Foundation of China/ ; }, abstract = {Host plant shifts are a common mode of speciation in herbivorous insects. Although insects can evolve adaptations to successfully incorporate a new host plant, it is becoming increasingly recognized that the gut bacterial community may play a significant role in allowing insects to detoxify novel plant chemical defenses. Here, we examined differences in gut bacterial communities between Altica flea beetle species that feed on phylogenetically unrelated host plants in sympatry. We surveyed the gut bacterial communities of three closely related flea beetles from multiple locations using 16S rRNA amplicon sequencing. The results showed that the beetle species shared a high proportion (80.7%) of operational taxonomic units. Alpha-diversity indicators suggested that gut bacterial diversity did not differ among host species, whereas geography had a significant effect on bacterial diversity. In contrast, analyses of beta-diversity showed significant differences in gut bacterial composition among beetle species when we used species composition and relative abundance metrics, but there was no difference in composition when species presence/absence and phylogenetic distance indices were used. Within host beetle species, gut bacterial composition varied significantly among sites. A metagenomic functionality analysis predicted that the gut microbes had functions involved in xenobiotic biodegradation and metabolism as well as metabolism of terpenoids and polyketides. These predictions, however, did not differ among beetle host species. Antibiotic curing experiments showed that development time was significantly prolonged, and there was a significant decline in body weight of newly emerged adults in beetles lacking gut bacteria, suggesting the beetles may receive a potential benefit from the gut microbe-insect interaction. On the whole, our results suggest that although the gut bacterial community did not show clear host-specific patterns among Altica species, spatiotemporal variability is an important determinant of gut bacterial communities. Furthermore, the similarity of communities among these beetle species suggests that microbial facilitation may not be a determinant of host plant shifts in Altica.}, }
@article {pmid32879989, year = {2020}, author = {Gonzalo, M and Deveau, A and Aigle, B}, title = {Inhibitions Dominate but Stimulations and Growth Rescues Are Not Rare Among Bacterial Isolates from Grains of Forest Soil.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {872-884}, doi = {10.1007/s00248-020-01579-6}, pmid = {32879989}, issn = {1432-184X}, support = {ANR-11-LABX 0002 01//ANR/ ; }, abstract = {Soil is a complex environment made of multiple microhabitats in which a wide variety of microorganisms co-exist and interact to form dynamic communities. While the abiotic factors that regulate the structure of these communities are now quite well documented, our knowledge of how bacteria interact with each other within these communities is still insufficient. Literature reveals so far contradictory results and is mainly focused on antagonistic interactions. To start filling this gap, we isolated 35 different bacterial isolates from grains of soil assuming that, at this scale, these bacteria would have been likely interacting in their natural habitat. We tested pairwise interactions between all isolates from each grain and scored positive and negative interactions. We compared the effects of simultaneous versus delayed co-inoculations, allowing or not to a strain to modify first its environment. One hundred fifty-seven interactions, either positive or negative, were recorded among the 525 possible one's. Members of the Bacillus subtilis, Pseudomonas and Streptomyces genera were responsible for most inhibitions, while positive interactions occurred between isolates of the Bacillales order and only in delayed inoculation conditions. Antagonist isolates had broad spectral abilities to acquire nutrients from organic and inorganic matter, while inhibited isolates tended to have little potentials. Despite an overall domination of antagonistic interactions (87%), a third of the isolates were able to stimulate or rescue the growth of other isolates, suggesting that cooperation between bacteria may be underestimated.}, }
@article {pmid32879459, year = {2020}, author = {Rubbens, P and Props, R and Kerckhof, FM and Boon, N and Waegeman, W}, title = {Cytometric fingerprints of gut microbiota predict Crohn's disease state.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-020-00762-4}, pmid = {32879459}, issn = {1751-7370}, support = {BOFSTA2015000501//Universiteit Gent (UGent)/ ; }, abstract = {Variations in the gut microbiome have been associated with changes in health state such as Crohn's disease (CD). Most surveys characterize the microbiome through analysis of the 16S rRNA gene. An alternative technology that can be used is flow cytometry. In this report, we reanalyzed a disease cohort that has been characterized by both technologies. Changes in microbial community structure are reflected in both types of data. We demonstrate that cytometric fingerprints can be used as a diagnostic tool in order to classify samples according to CD state. These results highlight the potential of flow cytometry to perform rapid diagnostics of microbiome-associated diseases.}, }
@article {pmid32879458, year = {2020}, author = {Mooshammer, M and Kitzinger, K and Schintlmeister, A and Ahmerkamp, S and Nielsen, JL and Nielsen, PH and Wagner, M}, title = {Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-020-00761-5}, pmid = {32879458}, issn = {1751-7370}, support = {EXC 309//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 294343//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: &quot;Ideas&quot; Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; W 1257//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; }, abstract = {Stable isotope probing (SIP) is a key tool for identifying the microorganisms catalyzing the turnover of specific substrates in the environment and to quantify their relative contributions to biogeochemical processes. However, SIP-based studies are subject to the uncertainties posed by cross-feeding, where microorganisms release isotopically labeled products, which are then used by other microorganisms, instead of incorporating the added tracer directly. Here, we introduce a SIP approach that has the potential to strongly reduce cross-feeding in complex microbial communities. In this approach, the microbial cells are exposed on a membrane filter to a continuous flow of medium containing isotopically labeled substrate. Thereby, metabolites and degradation products are constantly removed, preventing consumption of these secondary substrates. A nanoSIMS-based proof-of-concept experiment using nitrifiers in activated sludge and 13C-bicarbonate as an activity tracer showed that Flow-SIP significantly reduces cross-feeding and thus allows distinguishing primary consumers from other members of microbial food webs.}, }
@article {pmid32877326, year = {2020}, author = {Lee, HJ and Kim, SY and Whang, KS}, title = {Cellulomonas citrea sp. nov., isolated from paddy soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1099/ijsem.0.004409}, pmid = {32877326}, issn = {1466-5034}, abstract = {Two Gram-stain-positive, facultatively anaerobic, motile, aerobic, rod-shaped and non-spore-forming actinobacteria, strains AO-9T and AO-18, were isolated from paddy soil collected from Daejeon, Republic of Korea. Colonies were smooth, lemon-yellow and circular and 0.5-0.8×2.0-2.4 µm in diameter after 3 days of incubation at 28 °C on tryptic soy agar. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains AO-9T and AO-18 belonged to the genus Cellulomonas, showing the highest sequence similarities to Cellulomonas marina FXJ8.089T (96.6 %), Cellulomonas endophytica SYSUP0004T (96.5 %), Cellulomonas gelida DSM 20111T (96.2 %), Cellulomonas uda DSM 20107T (96.1 %), Cellulomonas rhizosphaerae NEAU-TCZ24T (96.1 %), Cellulomonas composti TR7-06T (96.0 %), Cellulomonas persica JCM 18111T (96.0 %) and less than 96 % to other closely related species. The DNA-DNA hybridization values between strains AO-9T and AO-18 were 87 %. The average nucleotide identity and digital DNA-DNA hybridization values between strain AO-9T and type strains of related species of the genus Cellulomonas were 84.0-85.8 % and 20.3-20.9 %, respectively. The major cellular fatty acids are anteiso-C15:0 (49.9 %), C14:0 (12.9 %) and iso-C14:0 (12.1 %). The predominant isoprenoid quinone was MK-9 (H4). The polar lipid profile consists of diphosphatidylglycerol, phosphatidylglycerol and one unidentified lipid. The DNA G+C content was 72.9 mol%. Based on its distinctive phenotypic, phylogenetic and chemotaxonomic characteristics, the two strains are considered to represent novel species of the genus Cellulomonas, for which the name Cellulomonas citrea sp. nov. is proposed. The type strain is AO-9T (=KACC 19069T=NBRC 112523T).}, }
@article {pmid32875141, year = {2020}, author = {Corbin, KD and Krajmalnik-Brown, R and Carnero, EA and Bock, C and Emerson, R and Rittmann, BE and Marcus, AK and Davis, T and Dirks, B and Ilhan, ZE and Champagne, C and Smith, SR}, title = {Integrative and quantitative bioenergetics: Design of a study to assess the impact of the gut microbiome on host energy balance.}, journal = {Contemporary clinical trials communications}, volume = {19}, number = {}, pages = {100646}, pmid = {32875141}, issn = {2451-8654}, abstract = {The literature is replete with clinical studies that characterize the structure, diversity, and function of the gut microbiome and correlate the results to different disease states, including obesity. Whether the microbiome has a direct impact on obesity has not been established. To address this gap, we asked whether the gut microbiome and its bioenergetics quantitatively change host energy balance. This paper describes the design of a randomized crossover clinical trial that combines outpatient feeding with precisely controlled metabolic phenotyping in an inpatient metabolic ward. The target population was healthy, weight-stable individuals, age 18-45 and with a body mass index ≤30 kg/m2. Our primary objective was to determine within-participant differences in energy balance after consuming a control Western Diet versus a Microbiome Enhancer Diet intervention specifically designed to optimize the gut microbiome for positive impacts on host energy balance. We assessed the complete energy-balance equation via whole-room calorimetry, quantified energy intake, fecal energy losses, and methane production. We implemented conditions of tight weight stability and balance between metabolizable energy intake and predicted energy expenditure. We explored key factors that modulate the balance between host and microbial nutrient accessibility by measuring enteroendocrine hormone profiles, appetite/satiety, gut transit and gastric emptying. By integrating these clinical measurements with future bioreactor experiments, gut microbial ecology analysis, and mathematical modeling, our goal is to describe initial cause-and-effect mechanisms of gut microbiome metabolism on host energy balance. Our innovative methods will enable subsequent studies on the interacting roles of diet, the gut microbiome, and human physiology.<br><br>Clinicaltrialsgov identifier: NCT02939703. The present study reference can be found here: https://clinicaltrials.gov/ct2/show/NCT02939703.}, }
@article {pmid32874778, year = {2020}, author = {Marchioro, GM and Glasl, B and Engelen, AH and Serrão, EA and Bourne, DG and Webster, NS and Frade, PR}, title = {Microbiome dynamics in the tissue and mucus of acroporid corals differ in relation to host and environmental parameters.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e9644}, pmid = {32874778}, issn = {2167-8359}, abstract = {Corals are associated with diverse microbial assemblages; however, the spatial-temporal dynamics of intra-species microbial interactions are poorly understood. The coral-associated microbial community varies substantially between tissue and mucus microhabitats; however, the factors controlling the occurrence, abundance, and distribution of microbial taxa over time have rarely been explored for different coral compartments simultaneously. Here, we test (1) differentiation in microbiome diversity and composition between coral compartments (surface mucus and tissue) of two Acropora hosts (A. tenuis and A. millepora) common along inshore reefs of the Great Barrier Reef, as well as (2) the potential linkage between shifts in individual coral microbiome families and underlying host and environmental parameters. Amplicon based 16S ribosomal RNA gene sequencing of 136 samples collected over 14 months, revealed significant differences in bacterial richness, diversity and community structure among mucus, tissue and the surrounding seawater. Seawater samples were dominated by members of the Synechococcaceae and Pelagibacteraceae bacterial families. The mucus microbiome of Acropora spp. was dominated by members of Flavobacteriaceae, Synechococcaceae and Rhodobacteraceae and the tissue was dominated by Endozoicimonaceae. Mucus microbiome in both Acropora species was primarily correlated with seawater parameters including levels of chlorophyll a, ammonium, particulate organic carbon and the sum of nitrate and nitrite. In contrast, the correlation of the tissue microbiome to the measured environmental (i.e., seawater parameters) and host health physiological factors differed between host species, suggesting host-specific modulation of the tissue-associated microbiome to intrinsic and extrinsic factors. Furthermore, the correlation between individual coral microbiome members and environmental factors provides novel insights into coral microbiome-by-environment dynamics and hence has potential implications for current reef restoration and management efforts (e.g. microbial monitoring and observatory programs).}, }
@article {pmid32873609, year = {2020}, author = {Kloosterman, AM and Shelton, KE and van Wezel, GP and Medema, MH and Mitchell, DA}, title = {RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery.}, journal = {mSystems}, volume = {5}, number = {5}, pages = {}, pmid = {32873609}, issn = {2379-5077}, support = {R01 AI144967/AI/NIAID NIH HHS/United States ; T32 GM070421/GM/NIGMS NIH HHS/United States ; }, abstract = {Many ribosomally synthesized and posttranslationally modified peptide classes (RiPPs) are reliant on a domain called the RiPP recognition element (RRE). The RRE binds specifically to a precursor peptide and directs the posttranslational modification enzymes to their substrates. Given its prevalence across various types of RiPP biosynthetic gene clusters (BGCs), the RRE could theoretically be used as a bioinformatic handle to identify novel classes of RiPPs. In addition, due to the high affinity and specificity of most RRE-precursor peptide complexes, a thorough understanding of the RRE domain could be exploited for biotechnological applications. However, sequence divergence of RREs across RiPP classes has precluded automated identification based solely on sequence similarity. Here, we introduce RRE-Finder, a new tool for identifying RRE domains with high sensitivity. RRE-Finder can be used in precision mode to confidently identify RREs in a class-specific manner or in exploratory mode to assist in the discovery of novel RiPP classes. RRE-Finder operating in precision mode on the UniProtKB protein database retrieved ∼25,000 high-confidence RREs spanning all characterized RRE-dependent RiPP classes, as well as several yet-uncharacterized RiPP classes that require future experimental confirmation. Finally, RRE-Finder was used in precision mode to explore a possible evolutionary origin of the RRE domain. The results suggest RREs originated from a co-opted DNA-binding transcriptional regulator domain. Altogether, RRE-Finder provides a powerful new method to probe RiPP biosynthetic diversity and delivers a rich data set of RRE sequences that will provide a foundation for deeper biochemical studies into this intriguing and versatile protein domain.IMPORTANCE Bioinformatics-powered discovery of novel ribosomal natural products (RiPPs) has historically been hindered by the lack of a common genetic feature across RiPP classes. Herein, we introduce RRE-Finder, a method for identifying RRE domains, which are present in a majority of prokaryotic RiPP biosynthetic gene clusters (BGCs). RRE-Finder identifies RRE domains 3,000 times faster than current methods, which rely on time-consuming secondary structure prediction. Depending on user goals, RRE-Finder can operate in precision mode to accurately identify RREs present in known RiPP classes or in exploratory mode to assist with novel RiPP discovery. Employing RRE-Finder on the UniProtKB database revealed several high-confidence RREs in novel RiPP-like clusters, suggesting that many new RiPP classes remain to be discovered.}, }
@article {pmid32873292, year = {2020}, author = {Zhu, L and Xu, F and Wan, W and Yu, B and Tang, L and Yang, Y and Du, Y and Chen, Z and Xu, H}, title = {Gut microbial characteristics of adult patients with allergy rhinitis.}, journal = {Microbial cell factories}, volume = {19}, number = {1}, pages = {171}, doi = {10.1186/s12934-020-01430-0}, pmid = {32873292}, issn = {1475-2859}, support = {81900541//National Natural Science Foundation of China/ ; 2019J05005//Natural Science Foundation of Fujian Province/ ; }, abstract = {BACKGROUND: Although recent studies have indicated that intestinal microbiota dweller are involved in the pathogenesis of allergy rhinitis (AR), the influence of gut microbiota on AR adult has not been fully elucidated yet. Hence, we carried out this study to uncover the distinctive bacterial taxa that differentiate allergy rhinitis patients from healthy individuals. Feces samples from thirty three AR patients and thirty one healthy individuals were analyzed by 16S rRNA gene sequencing.<br><br>RESULTS: Results showed that the bacterial diversity in AR group was significantly higher than that of the non-AR group. Bacterial communities between AR and non-AR group were significantly differentiated as revealed by Principal coordinates analysis (PCoA) and the variation within non-AR were higher than that of the counterpart. Firmicutes, Fusobacteria, Actinobacteria, Cyanobacteria and Chloroflexi were the significantly differed phyla taxa and the top significantly distinguished bacterial genus included Prevotella_9, Phascolarctobacterium, Roseburia, Megamonas, Alistipes, Lachnoclostridium and Fusobacterium. The higher network complexity in AR group were dominated by taxa belonging to Firmicutes. The predicted function, alpha linolenic acid metabolism and bacterial invasion of epithelial cells pathway were higher in non-AR group while gonadotropin-releasing hormone (GnRH) signaling pathway, Fc γ-R mediated phagocytosis and endocytosis were higher in AR patients. Although the bacterial diversity between moderate and severe AR patients showed no significant difference, the significant correlation between featured genus and total nasal symptom score or rhinoconjunctivitis quality of life questionnaire, such as Butyricicoccus and Eisenbergiella, revealed the potential to intervene the AR status by means of gut microbiota.<br><br>CONCLUSIONS: In conclusion, patients with allergy rhinitis had distinguished gut microbiota characteritics in comparison with healthy controls. The results suggest that gut microbiota might play crucial roles in influencing the course and different symptoms of AR. Trial registration ChiCTR, ChiCTR1900028613. Registered 29 December 2019, https://www.chictr.org.cn/showproj.aspx?proj=47650 .}, }
@article {pmid32870508, year = {2020}, author = {Kedia, S and Ghosh, TS and Jain, S and Desigamani, A and Kumar, A and Gupta, V and Bopanna, S and Yadav, DP and Goyal, S and Makharia, G and Travis, SPL and Das, B and Ahuja, V}, title = {Gut microbiome diversity in acute severe colitis is distinct from mild to moderate ulcerative colitis.}, journal = {Journal of gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jgh.15232}, pmid = {32870508}, issn = {1440-1746}, support = {//Intramural THSTI research funds/ ; //Scheme for Promotion of Academic and Research Collaboration (SPARC)/ ; }, abstract = {BACKGROUND AND AIM: Although the gut microbiome of patients with ulcerative colitis (UC) has been characterized, no study has characterized the gut microbiome in acute severe colitis (ASC). We compared the gut microbiome of patients with UC, ASC, and healthy controls (HCs).<br><br>METHODS: Patients with mild to moderate UC (n = 24), ASC (n = 19 with 21 episodes) and HCs (n = 50) were recruited prospectively. A 16SrDNA amplicon approach was used to explore gut microbial diversity and taxonomic repertoires. UC was diagnosed using European Crohn's and Colitis Organization guidelines, and ASC was diagnosed using Truelove and Witts' criteria.<br><br>RESULTS: The normalized alpha diversity was significantly lower in ASC than mild-moderately active UC (P < 0.05) or HC (P < 0.001). The gut microbiome in ASC was highly unstable, as characterized by high intracohort variation (analyzed using J-divergence measure), which was significantly greater than in UC or HC. On principal coordinate analysis, the microbiome of HC and UC were similar, with the ASC cohort being distinct from both. Comparison of ranked abundances identified four distinct clusters of genera (G1, G2, G3, and G4), with specific trends in their abundance across three groups: G1/G2A clusters had the least, whereas G3 had the highest abundance in the ASC cohort.<br><br>CONCLUSIONS: Gut microbial diversity is lower in ASC than mild-moderate UC or HCs. Gut microbiome composition is increasingly unstable in ASC, with a distinct abundance of specific genera varying between HCs and ASC. Mild-moderate UC lies within the spectrum.}, }
@article {pmid32862246, year = {2020}, author = {Starke, R and Pylro, VS and Morais, DK}, title = {16S rRNA Gene Copy Number Normalization Does Not Provide More Reliable Conclusions in Metataxonomic Surveys.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01586-7}, pmid = {32862246}, issn = {1432-184X}, support = {18-25706S//Grantová Agentura České Republiky/ ; 20-02022Y//Grantová Agentura České Republiky/ ; }, abstract = {Sequencing 16S rRNA gene amplicons is the gold standard to uncover the composition of prokaryotic communities. The presence of multiple copies of this gene makes the community abundance data distorted and gene copy normalization (GCN) necessary for correction. Even though GCN of 16S data provided a picture closer to the metagenome before, it should also be compared with communities of known composition due to the fact that library preparation is prone to methodological biases. Here, we process 16S rRNA gene amplicon data from eleven simple mock communities with DADA2 and estimate the impact of GCN. In all cases, the mock community composition derived from the 16S sequencing differs from those expected, and GCN fails to improve the classification for most of the analysed communities. Our approach provides empirical evidence that GCN does not improve the 16S target sequencing analyses in real scenarios. We therefore question the use of GCN for metataxonomic surveys until a more comprehensive catalogue of copy numbers becomes available.}, }
@article {pmid32861933, year = {2020}, author = {Uroosa,  and Kazmi, SSUH and Xu, G and Xu, H}, title = {Insights into the effects of harmful algal bloom on ecological quality status using body-size spectrum of biofilm-dwelling ciliates in marine ecosystems.}, journal = {Marine pollution bulletin}, volume = {160}, number = {}, pages = {111596}, doi = {10.1016/j.marpolbul.2020.111596}, pmid = {32861933}, issn = {1879-3363}, abstract = {The effects of two harmful algae Alexandrium tamarense and Gymnodinium catenatum on ecological quality status were identified using biofilm-dwelling ciliate assemblage as test organism communities. The body-size spectra of the test ciliates were observed at a gradient of cell concentrations of both algal species: 100 (control), followed by102, 103, 104 and 105 cells ml-1. The test ciliates showed clear variations in body-size spectra along the concentration gradients of both algal species. In terms of probability density, the ciliates generally peaked at low levels of algal concentrations (100-104 cells ml-1) in small size forms, followed by the forms with large sizes at the concentration of 105 cells ml-1 of both algal species. Bootstrapped-average analysis demonstrated a significant change in body-size spectrum when algal concentrations were higher than 104 cells ml-1. It is suggested that the body-size spectrum of the ciliates may be used to indicate the effects of harmful algal bloom.}, }
@article {pmid32860516, year = {2020}, author = {Virta, L and Soininen, J and Norkko, A}, title = {Biodiversity Loss Threatens the Current Functional Similarity of Beta Diversity in Benthic Diatom Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01576-9}, pmid = {32860516}, issn = {1432-184X}, support = {294853//Academy of Finland/ ; }, abstract = {The global biodiversity loss has increased the need to understand the effects of decreasing diversity, but our knowledge on how species loss will affect the functioning of communities and ecosystems is still very limited. Here, the levels of taxonomic and functional beta diversity and the effect of species loss on functional beta diversity were investigated in an estuary that provides a naturally steep environmental gradient. The study was conducted using diatoms that are among the most important microorganisms in all aquatic ecosystems and globally account for 40% of marine primary production. Along the estuary, the taxonomic beta diversity of diatom communities was high (Bray-Curtis taxonomic similarity 0.044) and strongly controlled by the environment, particularly wind exposure, salinity, and temperature. In contrast, the functional beta diversity was low (Bray-Curtis functional similarity 0.658) and much less controlled by the environment. Thus, the diatom communities stayed functionally almost similar despite large changes in species composition and environment. This may indicate that, through high taxonomic diversity and redundancy in functions, microorganisms provide an insurance effect against environmental change. However, when studying the effect of decreasing species richness on functional similarity of communities, simulated species loss to 45% of the current species richness decreased functional similarity significantly. This suggests that decreasing species richness may increase variability and reduce the stability and resilience of communities. These results highlight the importance of high taxonomic biodiversity for the stable functioning of benthic communities.}, }
@article {pmid32860076, year = {2020}, author = {Câmara, PEAS and Carvalho-Silva, M and Pinto, OHB and Amorim, ET and Henriques, DK and da Silva, TH and Pellizzari, F and Convey, P and Rosa, LH}, title = {Diversity and Ecology of Chlorophyta (Viridiplantae) Assemblages in Protected and Non-protected Sites in Deception Island (Antarctica, South Shetland Islands) Assessed Using an NGS Approach.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01584-9}, pmid = {32860076}, issn = {1432-184X}, support = {23/2018//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Assessment of the diversity of algal assemblages in Antarctica has until now largely relied on traditional microbiological culture approaches. Here we used DNA metabarcoding through high-throughput sequencing (HTS) to assess the uncultured algal diversity at two sites on Deception Island, Antarctica. The first was a relatively undisturbed site within an Antarctic Specially Protected Area (ASPA 140), and the second was a site heavily impacted by human visitation, the Whalers Bay historic site. We detected 65 distinct algal taxa, 50 from within ASPA 140 and 61 from Whalers Bay. Of these taxa, 46 were common to both sites, and 19 only occurred at one site. Algal richness was about six times greater than reported in previous studies using culture methods. A high proportion of DNA reads obtained was assigned to the highly invasive species Caulerpa webbiana at Whalers Bay, and the potentially pathogenic genus Desmodesmus was found at both sites. Our data demonstrate that important differences exist between these two protected and human-impacted sites on Deception Island in terms of algal diversity, richness, and abundance. The South Shetland Islands have experienced considerable effects of climate change in recent decades, while warming through geothermal activity on Deception Island itself makes this island one of the most vulnerable to colonization by non-native species. The detection of DNA of non-native taxa highlights concerns about how human impacts, which take place primarily through tourism and national research operations, may influence future biological colonization processes in Antarctica.}, }
@article {pmid32859925, year = {2020}, author = {Jurburg, SD and Konzack, M and Eisenhauer, N and Heintz-Buschart, A}, title = {The archives are half-empty: an assessment of the availability of microbial community sequencing data.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {474}, pmid = {32859925}, issn = {2399-3642}, support = {FZT 118//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {As DNA sequencing has become more popular, the public genetic repositories where sequences are archived have experienced explosive growth. These repositories now hold invaluable collections of sequences, e.g., for microbial ecology, but whether these data are reusable has not been evaluated. We assessed the availability and state of 16S rRNA gene amplicon sequences archived in public genetic repositories (SRA, EBI, and DDJ). We screened 26,927 publications in 17 microbiology journals, identifying 2015 16S rRNA gene sequencing studies. Of these, 7.2% had not made their data public at the time of analysis. Among a subset of 635 studies sequencing the same gene region, 40.3% contained data which was not available or not reusable, and an additional 25.5% contained faults in data formatting or data labeling, creating obstacles for data reuse. Our study reveals gaps in data availability, identifies major contributors to data loss, and offers suggestions for improving data archiving practices.}, }
@article {pmid32859275, year = {2020}, author = {Lu, J and Salzberg, SL}, title = {Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {124}, pmid = {32859275}, issn = {2049-2618}, abstract = {BACKGROUND: For decades, 16S ribosomal RNA sequencing has been the primary means for identifying the bacterial species present in a sample with unknown composition. One of the most widely used tools for this purpose today is the QIIME (Quantitative Insights Into Microbial Ecology) package. Recent results have shown that the newest release, QIIME 2, has higher accuracy than QIIME, MAPseq, and mothur when classifying bacterial genera from simulated human gut, ocean, and soil metagenomes, although QIIME 2 also proved to be the most computationally expensive. Kraken, first released in 2014, has been shown to provide exceptionally fast and accurate classification for shotgun metagenomics sequencing projects. Bracken, released in 2016, then provided users with the ability to accurately estimate species or genus relative abundances using Kraken classification results. Kraken 2, which matches the accuracy and speed of Kraken 1, now supports 16S rRNA databases, allowing for direct comparisons to QIIME and similar systems.<br><br>METHODS: For a comprehensive assessment of each tool, we compare the computational resources and speed of QIIME 2's q2-feature-classifier, Kraken 2, and Bracken in generating the three main 16S rRNA databases: Greengenes, SILVA, and RDP. For an evaluation of accuracy, we evaluated each tool using the same simulated 16S rRNA reads from human gut, ocean, and soil metagenomes that were previously used to compare QIIME, MAPseq, mothur, and QIIME 2. We evaluated accuracy based on the accuracy of the final genera read counts assigned by each tool. Finally, as Kraken 2 is the only tool providing per-read taxonomic assignments, we evaluate the sensitivity and precision of Kraken 2's per-read classifications.<br><br>RESULTS: For both the Greengenes and SILVA database, Kraken 2 and Bracken are up to 100 times faster at database generation. For classification, using the same data as previous studies, Kraken 2 and Bracken are up to 300 times faster, use 100x less RAM, and generate results that more accurate at 16S rRNA profiling than QIIME 2's q2-feature-classifier.<br><br>CONCLUSION: Kraken 2 and Bracken provide a very fast, efficient, and accurate solution for 16S rRNA metataxonomic data analysis. Video Abstract.}, }
@article {pmid32857837, year = {2020}, author = {Ho, A and Mendes, LW and Lee, HJ and Kaupper, T and Mo, Y and Poehlein, A and Bodelier, PLE and Jia, Z and Horn, MA}, title = {Response of a methane-driven interaction network to stressor intensification.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {10}, pages = {}, doi = {10.1093/femsec/fiaa180}, pmid = {32857837}, issn = {1574-6941}, abstract = {Microorganisms may reciprocally select for specific interacting partners, forming a network with interdependent relationships. The methanotrophic interaction network, comprising methanotrophs and non-methanotrophs, is thought to modulate methane oxidation and give rise to emergent properties beneficial for the methanotrophs. Therefore, microbial interaction may become relevant for community functioning under stress. However, empirical validation of the role and stressor-induced response of the interaction network remains scarce. Here, we determined the response of a complex methane-driven interaction network to a stepwise increase in NH4Cl-induced stress (0.5-4.75 g L-1, in 0.25-0.5 g L-1 increments) using enrichment of a naturally occurring complex community derived from a paddy soil in laboratory-scale incubations. Although ammonium and intermediates of ammonium oxidation are known to inhibit methane oxidation, methanotrophic activity was unexpectedly detected even in incubations with high ammonium levels, albeit rates were significantly reduced. Sequencing analysis of the 16S rRNA and pmoA genes consistently revealed divergent communities in the reference and stressed incubations. The 16S rRNA-based co-occurrence network analysis revealed that NH4Cl-induced stress intensification resulted in a less complex and modular network, likely driven by less stable interaction. Interestingly, the non-methanotrophs formed the key nodes, and appear to be relevant members of the community. Overall, stressor intensification unravels the interaction network, with adverse consequences for community functioning.}, }
@article {pmid32855435, year = {2020}, author = {Fodelianakis, S and Valenzuela-Cuevas, A and Barozzi, A and Daffonchio, D}, title = {Direct quantification of ecological drift at the population level in synthetic bacterial communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-020-00754-4}, pmid = {32855435}, issn = {1751-7370}, support = {Baseline fund to DD//King Abdullah University of Science and Technology (KAUST)/ ; OSR-2018-CARF-1973//King Abdullah University of Science and Technology (KAUST)/ ; Baseline fund to DD//King Abdullah University of Science and Technology (KAUST)/ ; OSR-2018-CARF-1973//King Abdullah University of Science and Technology (KAUST)/ ; Baseline fund to DD//King Abdullah University of Science and Technology (KAUST)/ ; OSR-2018-CARF-1973//King Abdullah University of Science and Technology (KAUST)/ ; }, abstract = {In community ecology, drift refers to random births and deaths in a population. In microbial ecology, drift is estimated indirectly via community snapshots but in this way, it is almost impossible to distinguish the effect of drift from the effect of other ecological processes. Controlled experiments where drift is quantified in isolation from other processes are still missing. Here we isolate and quantify drift in a series of controlled experiments on simplified and tractable bacterial communities. We detect drift arising randomly in the populations within the communities and resulting in a 1.4-2% increase in their growth rate variability on average. We further use our experimental findings to simulate complex microbial communities under various conditions of selection and dispersal. We find that the importance of drift increases under high selection and low dispersal, where it can lead to ~5% of species loss and to ~15% increase in β-diversity. The species extinct by drift are mainly rare, but they become increasingly less rare when selection increases, and dispersal decreases. Our results provide quantitative insights regarding the properties of drift in bacterial communities and suggest that it accounts for a consistent fraction of the observed stochasticity in natural surveys.}, }
@article {pmid32854141, year = {2020}, author = {Altinli, M and Lequime, S and Atyame, C and Justy, F and Weill, M and Sicard, M}, title = {Wolbachia modulates prevalence and viral load of Culex pipiens densoviruses in natural populations.}, journal = {Molecular ecology}, volume = {29}, number = {20}, pages = {4000-4013}, doi = {10.1111/mec.15609}, pmid = {32854141}, issn = {1365-294X}, support = {ANR-16-CE02-0006-01//Agence Nationale de la Recherche/ ; //Campus France/ ; }, abstract = {The inadequacy of standard mosquito control strategies calls for ecologically safe novel approaches, for example the use of biological agents such as the endosymbiotic α-proteobacteria Wolbachia or insect-specific viruses (ISVs). Understanding the ecological interactions between these &quot;biocontrol endosymbionts&quot; is thus a fundamental step. Wolbachia are transmitted vertically from mother to offspring and modify their hosts' phenotypes, including reproduction (e.g., cytoplasmic incompatibility) and survival (e.g., viral interference). In nature, Culex pipiens (sensu lato) mosquitoes are always found infected with genetically diverse Wolbachia called wPip that belong to five phylogenetic groups. In recent years, ISVs have also been discovered in these mosquito species, although their interactions with Wolbachia in nature are unknown. Here, we studied the interactions between a widely prevalent ISV, the Culex pipiens densovirus (CpDV, Densovirinae), and Wolbachia in northern Tunisian C. pipiens populations. We showed an influence of different Wolbachia groups on CpDV prevalence and a general positive correlation between Wolbachia and CpDV loads. By investigating the putative relationship between CpDV diversification and wPip groups in the different sites, we detected a signal linked to wPip groups in CpDV phylogeny in sites where all larvae were infected by the same wPip group. However, no such signal was detected where the wPip groups coexisted, suggesting CpDV horizontal transfer between hosts. Overall, our results provide good evidence for an ecological influence of Wolbachia on an ISV, CpDV, in natural populations and highlight the importance of integrating Wolbachia in our understanding of ISV ecology in nature.}, }
@article {pmid32853201, year = {2020}, author = {Buongiorno, J and Sipes, K and Wasmund, K and Loy, A and Lloyd, KG}, title = {Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0234839}, pmid = {32853201}, issn = {1932-6203}, mesh = {Arctic Regions ; Bacterial Proteins/genetics ; Estuaries ; Gammaproteobacteria/classification/*genetics/metabolism ; Genome, Bacterial ; Geologic Sediments/*microbiology ; Heat-Shock Proteins/genetics ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Svalbard ; Transcriptome ; }, abstract = {Distinct lineages of Gammaproteobacteria clade Woeseiales are globally distributed in marine sediments, based on metagenomic and 16S rRNA gene analysis. Yet little is known about why they are dominant or their ecological role in Arctic fjord sediments, where glacial retreat is rapidly imposing change. This study combined 16S rRNA gene analysis, metagenome-assembled genomes (MAGs), and genome-resolved metatranscriptomics uncovered the in situ abundance and transcriptional activity of Woeseiales with burial in four shallow sediment sites of Kongsfjorden and Van Keulenfjorden of Svalbard (79°N). We present five novel Woeseiales MAGs and show transcriptional evidence for metabolic plasticity during burial, including sulfur oxidation with reverse dissimilatory sulfite reductase (dsrAB) down to 4 cm depth and nitrite reduction down to 6 cm depth. A single stress protein, spore protein SP21 (hspA), had a tenfold higher mRNA abundance than any other transcript, and was a hundredfold higher on average than other transcripts. At three out of the four sites, SP21 transcript abundance increased with depth, while total mRNA abundance and richness decreased, indicating a shift in investment from metabolism and other cellular processes to build-up of spore protein SP21. The SP21 gene in MAGs was often flanked by genes involved in membrane-associated stress response. The ability of Woeseiales to shift from sulfur oxidation to nitrite reduction with burial into marine sediments with decreasing access to overlying oxic bottom waters, as well as enter into a dormant state dominated by SP21, may account for its ubiquity and high abundance in marine sediments worldwide, including those of the rapidly shifting Arctic.}, }
@article {pmid32852571, year = {2020}, author = {Hubert, J and Nesvorna, M and Green, SJ and Klimov, PB}, title = {Microbial Communities of Stored Product Mites: Variation by Species and Population.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01581-y}, pmid = {32852571}, issn = {1432-184X}, support = {GA19-09998S//Grantová Agentura České Republiky/ ; 19-14-00004//Russian Science Foundation/ ; }, abstract = {Arthropod-associated microorganisms are important because they affect host fitness, protect hosts from pathogens, and influence the host's ability to vector pathogens. Stored product mites (Astigmata) often establish large populations in various types of food items, damaging the food by direct feeding and introducing contaminants, including their own bodies, allergen-containing feces, and associated microorganisms. Here we access the microbial structure and abundance in rearing diets, eggs, feces fraction, and mite bodies of 16 mite populations belonging to three species (Carpoglyphus lactis, Acarus siro, and Tyrophagus putrescentiae) using quantitative PCR and 16S ribosomal RNA (rRNA) gene amplicon sequencing. The mite microbiomes had a complex structure dominated by the following bacterial taxa (OTUs): (a) intracellular symbionts of the genera Cardinium and Wolbachia in the mite bodies and eggs; (b) putative gut symbionts of the genera Solitalea, Bartonella, and Sodalis abundant in mite bodies and also present in mite feces; (c) feces-associated or environmental bacteria of the genera Bacillus, Staphylococcus, and Kocuria in the diet, mite bodies, and feces. Interestingly and counterintuitively, the differences between microbial communities in various conspecific mite populations were higher than those between different mite species. To explain some of these differences, we hypothesize that the intracellular bacterial symbionts can affect microbiome composition in mite bodies, causing differences between microbial profiles. Microbial profiles differed between various sample types, such as mite eggs, bodies, and the environment (spent growth medium-SPGM). Low bacterial abundances in eggs may result in stochastic effects in parent-offspring microbial transmission, except for the intracellular symbionts. Bacteria in the rearing diet had little effect on the microbial community structure in SPGM and mite bodies. Mite fitness was positively correlated with bacterial abundance in SPGM and negatively correlated with bacterial abundances in mite bodies. Our study demonstrates critical host-microbe interactions, affecting all stages of mite growth and leading to alteration of the environmental microbiome. Correlational evidence based on absolute quantitation of bacterial 16S rRNA gene copies suggests that mite-associated microorganisms are critical for modulating important pest properties of mites by altering population growth.}, }
@article {pmid32850972, year = {2020}, author = {Álvarez-Rodríguez, I and Ugarte-Uribe, B and de la Arada, I and Arrondo, JLR and Garbisu, C and Alkorta, I}, title = {Conjugative Coupling Proteins and the Role of Their Domains in Conjugation, Secondary Structure and in vivo Subcellular Location.}, journal = {Frontiers in molecular biosciences}, volume = {7}, number = {}, pages = {185}, pmid = {32850972}, issn = {2296-889X}, abstract = {Type IV Coupling Proteins (T4CPs) are essential elements in many type IV secretion systems (T4SSs). The members of this family display sequence, length, and domain architecture heterogeneity, being the conserved Nucleotide-Binding Domain the motif that defines them. In addition, most T4CPs contain a Transmembrane Domain (TMD) in the amino end and an All-Alpha Domain facing the cytoplasm. Additionally, a few T4CPs present a variable domain at the carboxyl end. The structural paradigm of this family is TrwBR388, the T4CP of conjugative plasmid R388. This protein has been widely studied, in particular the role of the TMD on the different characteristics of TrwBR388. To gain knowledge about T4CPs and their TMD, in this work a chimeric protein containing the TMD of TraJpKM101 and the cytosolic domain of TrwBR388 has been constructed. Additionally, one of the few T4CPs of mobilizable plasmids, MobBCloDF13 of mobilizable plasmid CloDF13, together with its TMD-less mutant MobBΔTMD have been studied. Mating studies showed that the chimeric protein is functional in vivo and that it exerted negative dominance against the native proteins TrwBR388 and TraJpKM101. Also, it was observed that the TMD of MobBCloDF13 is essential for the mobilization of CloDF13 plasmid. Analysis of the secondary structure components showed that the presence of a heterologous TMD alters the structure of the cytosolic domain in the chimeric protein. On the contrary, the absence of the TMD in MobBCloDF13 does not affect the secondary structure of its cytosolic domain. Subcellular localization studies showed that T4CPs have a unipolar or bipolar location, which is enhanced by the presence of the remaining proteins of the conjugative system. Unlike what has been described for TrwBR388, the TMD is not an essential element for the polar location of MobBCloDF13. The main conclusion is that the characteristics described for the paradigmatic TrwBR388 T4CP should not be ascribed to the whole T4CP family. Specifically, it has been proven that the mobilizable plasmid-related MobBCloDF13 presents different characteristics regarding the role of its TMD. This work will contribute to better understand the T4CP family, a key element in bacterial conjugation, the main mechanism responsible for antibiotic resistance spread.}, }
@article {pmid32850744, year = {2020}, author = {Song, C and Zhu, F and Carrión, VJ and Cordovez, V}, title = {Beyond Plant Microbiome Composition: Exploiting Microbial Functions and Plant Traits via Integrated Approaches.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {8}, number = {}, pages = {896}, pmid = {32850744}, issn = {2296-4185}, abstract = {Plants recruit specific microorganisms to live inside and outside their roots that provide essential functions for plant growth and health. The study of the microbial communities living in close association with plants helps in understanding the mechanisms involved in these beneficial interactions. Currently, most of the research in this field has been focusing on the description of the taxonomic composition of the microbiome. Therefore, a focus on the plant-associated microbiome functions is pivotal for the development of novel agricultural practices which, in turn, will increase plant fitness. Recent advances in microbiome research using model plant species started to shed light on the functions of specific microorganisms and the underlying mechanisms of plant-microbial interaction. Here, we review (1) microbiome-mediated functions associated with plant growth and protection, (2) insights from native and agricultural habitats that can be used to improve soil health and crop productivity, (3) current -omics and new approaches for studying the plant microbiome, and (4) challenges and future perspectives for exploiting the plant microbiome for beneficial outcomes. We posit that integrated approaches will help in translating fundamental knowledge into agricultural practices.}, }
@article {pmid32849473, year = {2020}, author = {Sedlacek, CJ}, title = {It Takes a Village: Discovering and Isolating the Nitrifiers.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1900}, pmid = {32849473}, issn = {1664-302X}, abstract = {It has been almost 150 years since Jean-Jacques Schloesing and Achille Müntz discovered that the process of nitrification, the oxidation of ammonium to nitrate, is a biological process carried out by microorganisms. In the following 15 years, numerous researchers independently contributed paradigm shifting discoveries that formed the foundation of nitrification and nitrification-related research. One of them was Sergei Winogradsky, whose major accomplishments include the discovery of both lithotrophy (in sulfur-oxidizing bacteria) and chemoautotrophy (in nitrifying bacteria). However, Winogradsky often receives most of the credit for many other foundational nitrification discoveries made by his contemporaries. This accumulation of credit over time is at least in part due to the increased attention, Winogradsky receives in the scientific literature and textbooks as a &quot;founder of microbiology&quot; and &quot;the founder of microbial ecology.&quot; Here, some light is shed on several other researchers who are often overlooked, but whose work was instrumental to the emerging field of nitrification and to the work of Winogradsky himself. Specifically, the discovery of the biological process of nitrification by Schloesing and Müntz, the isolation of the first nitrifier by Grace and Percy Frankland, and the observation that nitrification is carried out by two distinct groups of microorganisms by Robert Warington are highlighted. Finally, the more recent discoveries of the chemolithoautotrophic ammonia-oxidizing archaea and complete ammonia oxidizers are put into this historical context.}, }
@article {pmid32849470, year = {2020}, author = {Nagler, M and Podmirseg, SM and Mayr, M and Ascher-Jenull, J and Insam, H}, title = {Quantities of Intra- and Extracellular DNA Reveal Information About Activity and Physiological State of Methanogenic Archaea.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1894}, pmid = {32849470}, issn = {1664-302X}, abstract = {Although being a common aim of many microbial ecology studies, measuring individual physiological conditions of a microbial group or species within a complex consortium is still a challenge. Here, we propose a novel approach that is based on the quantification of sequentially extracted extracellular (exDNA) and intracellular DNA (iDNA) and reveals information about cell lysis and activity of methanogenic archaea within a biogas-producing microbial community. We monitored the methane production rates of differently treated batch anaerobic cultures and compared the concentrations of the alpha subunit of the methyl coenzyme M reductase gene of methanogenic archaea in extracellular and intracellular DNA fractions and in the classically extracted total DNA pool. Our results showed that this fine-tuned DNA approach coupled with the interpretation of the ratio between free exDNA and iDNA considerably improved microbial activity tracking compared to the classical extraction/quantification of total DNA. Additionally, it allowed to identify and quantify methanogenic populations that are inactive and those that are strongly influenced by cell lysis. We argue that despite the need of further studies, this method represents a novel approach to gain specific physiological information from a complex environmental sample and holds the potential to be applied to other microbes of interest.}, }
@article {pmid32849423, year = {2020}, author = {Moonga, HB and Schoustra, SE and van den Heuvel, J and Linnemann, AR and Samad, MS and Shindano, J and Smid, EJ}, title = {Composition and Diversity of Natural Bacterial Communities in Mabisi, a Traditionally Fermented Milk.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1816}, pmid = {32849423}, issn = {1664-302X}, abstract = {Many traditionally fermented milk products such as mabisi involve spontaneous fermentation, which can result in bacterial community composition variation due to selection pressure. The aim of this study was to determine the composition of bacterial communities in the different types of mabisi produced across Zambia and identify the factors that influence their composition. Samples of mabisi were collected across the country, and analyzed for pH and bacterial communities using 16S rRNA amplicon sequencing. We found that the bacterial community composition was dominated by members of two phyla, i.e., Firmicutes and Proteobacteria, from which the top 10 most abundant genera were Lactococcus, Lactobacillus, Streptococcus, Enterobacter, Citrobacter, Klebsiella, Kluyvera, Buttiauxella, Aeromonas, and Acinetobacter. The most dominant genus was Lactococcus, which was present in all types of mabisi produced from all regions. The mabisi products from traditional mabisi production regions (TMPRs) were dominated by lactic acid bacteria (LAB) whereas products from non-TMPRs were dominated by non-LAB species. Tonga mabisi, the most popular type of mabisi produced in non-TMPRs, had the most complex and diverse bacterial community composition compared to the other types, which included barotse, backslopping, creamy, and thick-tonga mabisi. Other factors that influenced bacterial community composition were geographical location, fermentation duration and pH while the type of fermentation container and producer did not. This study provides new insights that can be applied in starter culture development as well as microbial functionality studies.}, }
@article {pmid32849396, year = {2020}, author = {Huang, J and Yang, J and Jiang, H and Wu, G and Liu, W and Wang, B and Xiao, H and Han, J}, title = {Microbial Responses to Simulated Salinization and Desalinization in the Sediments of the Qinghai-Tibetan Lakes.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1772}, pmid = {32849396}, issn = {1664-302X}, abstract = {Uncovering microbial response to salinization or desalinization is of great importance to understanding of the influence of global climate change on lacustrine microbial ecology. In this study, to simulate salinization and desalinization, sediments from Erhai Lake (salinity 0.3-0.8 g/L) and Chaka Lake (salinity 299.3-350.7 g/L) on the Qinghai-Tibetan Plateau were transplanted into different lakes with a range of salinity of 0.3-299.3 g/L, followed by in situ incubation for 50 days and subsequent geochemical and microbial analyses. Desalinization was faster than salinization in the transplanted sediments. The salinity of the transplanted sediment increased and decreased in the salinization and desalinization simulation experiments, respectively. The TOC contents of the transplanted sediments were lower than that of their undisturbed counterparts in the salinization experiments, whereas they had a strong negative linear relationship with salinity in the desalinization experiments. Microbial diversity decreased in response to salinization and desalinization, and microbial community dissimilarity significantly (P < 0.01) increased with salinity differences between the transplanted sediments and their undisturbed counterparts. Microbial groups belonging to Gammaproteobacteria and Actinobacteria became abundant in salinization whereas Bacteroidetes and Chloroflexi became dominant in desalinization. Among the predicted microbial functions, hydrogenotrophic methanogenesis, methanogenesis through CO2 reduction with H2, nitrate/nitrogen respiration, and nitrification increased in salinization; in desalinization, enhancement was observed for respiration of sulfur compounds, sulfate respiration, sulfur respiration, thiosulfate respiration, hydrocarbon degradation, chemoheterotrophy, and fermentation, whereas depressing was found for aerobic ammonia oxidation, nitrate/nitrogen respiration, nitrification, nitrite respiration, manganese oxidation, aerobic chemoheterotrophy, and phototrophy. Such microbial variations could be explained by changes of transplantation, salinity, and covarying variables. In summary, salinization and desalinization had profound influence on the geochemistry, microbial community, and function in lakes.}, }
@article {pmid32849356, year = {2020}, author = {Arbour, TJ and Gilbert, B and Banfield, JF}, title = {Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1694}, pmid = {32849356}, issn = {1664-302X}, abstract = {Extracellular electron transfer (EET) between microbes and iron minerals, and syntrophically between species, is a widespread process affecting biogeochemical cycles and microbial ecology. The distribution of this capacity among microbial taxa, and the thermodynamic controls on EET in complex microbial communities, are not fully known. Microbial electrochemical cells (MXCs), in which electrodes serve as the electron acceptor or donor, provide a powerful approach to enrich for organisms capable of EET and to study their metabolism. We used MXCs coupled with genome-resolved metagenomics to investigate the capacity for EET in microorganisms present in a well-studied aquifer near Rifle, CO. Electroactive biofilms were established and maintained for almost 4 years on anodes poised mostly at -0.2 to -0.25 V vs. SHE, a range that mimics the redox potential of iron-oxide minerals, using acetate as the sole carbon source. Here we report the metagenomic characterization of anode-biofilm and planktonic microbial communities from samples collected at timepoints across the study period. From two biofilm and 26 planktonic samples we reconstructed draft-quality and near-complete genomes for 84 bacteria and 2 archaea that represent the majority of organisms present. A novel Geobacter sp. with at least 72 putative multiheme c-type cytochromes (MHCs) was the dominant electrode-attached organism. However, a diverse range of other electrode-associated organisms also harbored putative MHCs with at least 10 heme-binding motifs, as well as porin-cytochrome complexes and e-pili, including Actinobacteria, Ignavibacteria, Chloroflexi, Acidobacteria, Firmicutes, Beta- and Gammaproteobacteria. Our results identify a small subset of the thousands of organisms previously detected in the Rifle aquifer that may have the potential to mediate mineral redox transformations.}, }
@article {pmid32849338, year = {2020}, author = {Presley, GN and Zhang, J and Purvine, SO and Schilling, JS}, title = {Functional Genomics, Transcriptomics, and Proteomics Reveal Distinct Combat Strategies Between Lineages of Wood-Degrading Fungi With Redundant Wood Decay Mechanisms.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1646}, pmid = {32849338}, issn = {1664-302X}, abstract = {Wood-degrading fungi vary in their strategies for deconstructing wood, and their competitive successes shape the rate and fate of carbon released from wood, Earth's largest pool of aboveground terrestrial carbon. In this study, one-on-one interspecific interactions between two model brown rot (carbohydrate-selective) fungi, Gloeophyllum trabeum and Rhodonia (Postia) placenta, were studied on wood wafers where a clearly resolved interaction zone (IZ) could be generated, reproducibly. Comparative RNAseq and proteomics between the IZ and non-interacting hyphae of each species identified combative strategies for each fungus. Glycoside hydrolases were a relatively smaller portion of the interaction secretome compared to non-interacting hyphae. The interaction zone showed higher pectinase specific activity than all other sampling locations, and higher laminarinase specific activity (branched β-glucan proxy) was seen in the IZ secretome relative to equivalent hyphae in single-species cultures. Our efforts also identified two distinct competitive strategies in these two fungi with a shared nutritional mode (brown rot) but polyphyletic ancestral lineages. Gloeophyllum trabeum (Gloeophyllum clade) upregulated more secondary metabolite (SM) synthesis genes in response to a competitor than did R. placenta. R. placenta (Antrodia clade) upregulated a larger variety of uncharacterized oxidoreductases in interacting hyphae, suggesting that these may play a role in mediating competitor response in this fungus. Both species produced several hypothetical proteins exclusively in the interaction zone, leaving questions as to the function of these proteins. This work supports the existence of multiple interaction strategies among brown rot fungi and highlights the functional diversity among wood decay fungi.}, }
@article {pmid32849330, year = {2020}, author = {Floc'h, JB and Hamel, C and Lupwayi, N and Harker, KN and Hijri, M and St-Arnaud, M}, title = {Bacterial Communities of the Canola Rhizosphere: Network Analysis Reveals a Core Bacterium Shaping Microbial Interactions.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1587}, pmid = {32849330}, issn = {1664-302X}, abstract = {The rhizosphere hosts a complex web of prokaryotes interacting with one another that may modulate crucial functions related to plant growth and health. Identifying the key factors structuring the prokaryotic community of the plant rhizosphere is a necessary step toward the enhancement of plant production and crop yield with beneficial associative microorganisms. We used a long-term field experiment conducted at three locations in the Canadian prairies to verify that: (1) the level of cropping system diversity influences the α- and β-diversity of the prokaryotic community of canola (Brassica napus) rhizosphere; (2) the canola rhizosphere community has a stable prokaryotic core; and (3) some highly connected taxa of this community fit the description of hub-taxa. We sampled the rhizosphere of canola grown in monoculture, in a 2-phase rotation (canola-wheat), in a 3-phase rotation (pea-barley-canola), and in a highly diversified 6-phase rotation, five and eight years after cropping system establishment. We detected only one core bacterial Amplicon Sequence Variant (ASV) in the prokaryotic component of the microbiota of canola rhizosphere, a hub taxon identified as cf. Pseudarthrobacter sp. This ASV was also the only hub taxon found in the networks of interactions present in both years and at all three sites. We highlight a cohort of bacteria and archaea that were always connected with the core taxon in the network analyses.}, }
@article {pmid32846525, year = {2020}, author = {Jilani, H and Cilla, A and Barberá, R and Hamdi, M}, title = {Antiproliferative activity of green, black tea and olive leaves polyphenols subjected to biosorption and in vitro gastrointestinal digestion in Caco-2 cells.}, journal = {Food research international (Ottawa, Ont.)}, volume = {136}, number = {}, pages = {109317}, doi = {10.1016/j.foodres.2020.109317}, pmid = {32846525}, issn = {1873-7145}, abstract = {Olive (Olea europaea L.) leaves and tea (Camellia sinensis) are rich sources of bioactive compounds, especially polyphenols. Our previous studies have evidenced the potential use of Saccharomyces cerevisiae as a natural delivery system for these antioxidants and a means to improve their bioaccessibility in the human gut. In the present work, the antiproliferative effect of green tea (GT), black tea (BT) and olive leaves (OL) infusions and suspensions of S. cerevisiae were evaluated, for the first time, in human colon cancer cells (Caco-2) after biosorption and in vitro gastrointestinal digestion. The bioaccessible fractions (BF) were not overtly cytotoxic, not affecting cell viability. ROS and mitochondrial membrane potential changes (Δψm) values were reduced compared with control cells. Moreover, all the BF after biosorption induced a significant (p < 0.05) increase in cell proportions in S-phase. The arrest of the cell cycle was reversible without induction of apoptosis, suggesting that the biosorbed phenolics in both infusions and suspensions act as cytostatic agents.}, }
@article {pmid32845305, year = {2020}, author = {Imchen, M and Kumavath, R}, title = {Shotgun metagenomics reveals a heterogeneous prokaryotic community and a wide array of antibiotic resistance genes in mangrove sediment.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {10}, pages = {}, doi = {10.1093/femsec/fiaa173}, pmid = {32845305}, issn = {1574-6941}, abstract = {Saline tolerant mangrove forests partake in vital biogeochemical cycles. However, they are endangered due to deforestation as a result of urbanization. In this study, we have carried out a metagenomic snapshot of the mangrove ecosystem from five countries to assess its taxonomic, functional and antibiotic resistome structure. Chao1 alpha diversity varied significantly (P < 0.001) between the countries (Brazil, Saudi Arabia, China, India and Malaysia). All datasets were composed of 33 phyla dominated by eight major phyla covering >90% relative abundance. Comparative analysis of mangrove with terrestrial and marine ecosystems revealed the strongest heterogeneity in the mangrove microbial community. We also observed that the mangrove community shared similarities to both the terrestrial and marine microbiome, forming a link between the two contrasting ecosystems. The antibiotic resistant genes (ARG) resistome was comprised of nineteen level 3 classifications dominated by multidrug resistance efflux pumps (46.7 ± 4.3%) and BlaR1 family regulatory sensor-transducer disambiguation (25.2 ± 4.8%). ARG relative abundance was significantly higher in Asian countries and in human intervention datasets at a global scale. Our study shows that the mangrove microbial community and its antibiotic resistance are affected by geography as well as human intervention and are unique to the mangrove ecosystem. Understanding changes in the mangrove microbiome and its ARG is significant for sustainable development and public health.}, }
@article {pmid32845128, year = {2020}, author = {Ceron-Chafla, P and Kleerebezem, R and Rabaey, K and van Lier, JB and Lindeboom, REF}, title = {Direct and Indirect Effects of Increased CO2 Partial Pressure on the Bioenergetics of Syntrophic Propionate and Butyrate Conversion.}, journal = {Environmental science &amp; technology}, volume = {54}, number = {19}, pages = {12583-12592}, doi = {10.1021/acs.est.0c02022}, pmid = {32845128}, issn = {1520-5851}, abstract = {Simultaneous digestion and in situ biogas upgrading in high-pressure bioreactors will result in elevated CO2 partial pressure (pCO2). With the concomitant increase in dissolved CO2, microbial conversion processes may be affected beyond the impact of increased acidity. Elevated pCO2 was reported to affect the kinetics and thermodynamics of biochemical conversions because CO2 is an intermediate and end-product of the digestion process and modifies the carbonate equilibrium. Our results showed that increasing pCO2 from 0.3 to 8 bar in lab-scale batch reactors decreased the maximum substrate utilization rate (rsmax) for both syntrophic propionate and butyrate oxidation. These kinetic limitations are linked to an increased overall Gibbs free energy change (ΔGOverall) and a potential biochemical energy redistribution among syntrophic partners, which showed interdependence with hydrogen partial pressure (pH2). The bioenergetics analysis identified a moderate, direct impact of elevated pCO2 on propionate oxidation and a pH-mediated effect on butyrate oxidation. These constraints, combined with physiological limitations on growth exerted by increased acidity and inhibition due to higher concentrations of undissociated volatile fatty acids, help to explain the observed phenomena. Overall, this investigation sheds light on the role of elevated pCO2 in delicate biochemical syntrophic conversions by connecting kinetic, bioenergetic, and physiological effects.}, }
@article {pmid32844509, year = {2020}, author = {Zhu, X and Jackson, RD and DeLucia, EH and Tiedje, JM and Liang, C}, title = {The soil microbial carbon pump: From conceptual insights to empirical assessments.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.15319}, pmid = {32844509}, issn = {1365-2486}, support = {31930070//National Natural Science Foundation of China/ ; 41977051//National Natural Science Foundation of China/ ; GJTD-2019-10//K.C. Wong Education Foundation/ ; }, abstract = {The global soil carbon (C) pool is massive, so relatively small changes in soil organic carbon (SOC) stocks can significantly alter atmospheric C and global climate. The recently proposed concept of the soil microbial carbon pump (MCP) emphasizes the active role of soil microbes in SOC storage by integrating the continual microbial transformation of organic C from labile to persistent anabolic forms. However, the concept has not been evaluated with data. Here, we combine datasets, including microbial necromass biomarker amino sugars and SOC, from two long-term agricultural field studies conducted by large United States bioenergy research programs. We interrogate the soil MCP concept by investigating the asynchronous responses of microbial necromass and SOC to land-use change. Microbial necromass appeared to preferentially accumulate in soil and be the dominant contributor to SOC accrual in diversified perennial bioenergy crops. Specifically, ~92% of the additional SOC enhanced by plant diversity was estimated to be microbial necromass C, and >76% of the additional SOC enhanced by land-use transition from annual to perennial crops was estimated to be microbial necromass. This suggests that the soil MCP was stimulated in diversified perennial agroecosystems. We further delineate and suggest two parameters-soil MCP capacity and efficacy-reflecting the conversion of plant C into microbial necromass and the contribution of microbial necromass to SOC, respectively, that should serve as valuable metrics for future studies evaluating SOC storage under alternative management in changing climates.}, }
@article {pmid32843743, year = {2020}, author = {Khoruts, A and Staley, C and Sadowsky, MJ}, title = {Faecal microbiota transplantation for Clostridioides difficile: mechanisms and pharmacology.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41575-020-0350-4}, pmid = {32843743}, issn = {1759-5053}, abstract = {Faecal microbiota transplantation (FMT) has emerged as a remarkably successful treatment for recurrent Clostridioides difficile infection that cannot be cured with antibiotics alone. Understanding the complex biology and pathogenesis of C. difficile infection, which we discuss in this Perspective, is essential for understanding the potential mechanisms by which FMT cures this disease. Although FMT has already entered clinical practice, different microbiota-based products are currently in clinical trials and are vying for regulatory approval. However, all these therapeutics belong to an entirely new class of agents that require the development of a new branch of pharmacology. Characterization of microbiota therapeutics uses novel and rapidly evolving technologies and requires incorporation of microbial ecology concepts. Here, we consider FMT within a pharmacological framework, including its essential elements: formulation, pharmacokinetics and pharmacodynamics. From this viewpoint, multiple gaps in knowledge become apparent, identifying areas that require systematic research. This knowledge is needed to help clinical providers use microbiota therapeutics appropriately and to facilitate development of next-generation microbiota products with improved safety and efficacy. The discussion here is limited to FMT as a representative of microbiota therapeutics and recurrent C. difficile as the indication; however, consideration of the intrinsic basic principles is relevant to this entire class of microbiota-based therapeutics.}, }
@article {pmid32843539, year = {2020}, author = {Santillan, E and Constancias, F and Wuertz, S}, title = {Press Disturbance Alters Community Structure and Assembly Mechanisms of Bacterial Taxa and Functional Genes in Mesocosm-Scale Bioreactors.}, journal = {mSystems}, volume = {5}, number = {4}, pages = {}, pmid = {32843539}, issn = {2379-5077}, abstract = {Press disturbances are of interest in microbial ecology, as they can drive microbial communities to alternative stable states. However, the effect of press disturbances in community assembly mechanisms, particularly with regard to taxa and functional genes at different levels of abundance (i.e., common and rare), remains largely unknown. Here, we tested the effect of a continuous alteration in substrate feeding scheme on the structure, function, and assembly of bacterial communities. Two sets of replicate 5-liter sequencing batch reactors were operated at two different organic carbon loads for a period of 74 days, following 53 days of acclimation after inoculation with sludge from a full-scale treatment plant. Temporal dynamics of community taxonomic and functional gene structure were derived from metagenomics and 16S rRNA gene metabarcoding data. Disturbed reactors exhibited different community function, structure, and assembly compared to undisturbed reactors. Bacterial taxa and functional genes showed dissimilar α-diversity and community assembly patterns. Deterministic assembly mechanisms were generally stronger in disturbed reactors and in common fractions compared to rare ones. Function quickly recovered after the disturbance was removed, but community structure did not. Our results highlight that functional gene data from metagenomics can indicate patterns of community assembly that differ from those obtained from taxon data. This study reveals how a joint evaluation of assembly mechanisms and community structure of bacterial taxa and functional genes as well as ecosystem function can unravel the response of complex microbial systems to a press disturbance.IMPORTANCE Ecosystem management must be viewed in the context of increasing frequencies and magnitudes of various disturbances that occur at different scales. This work provides a glimpse of the changes in assembly mechanisms found in microbial communities exposed to sustained changes in their environment. These mechanisms, deterministic or stochastic, can cause communities to reach a similar or variable composition and function. For a comprehensive view, we use a joint evaluation of temporal dynamics in assembly mechanisms and community structure for both bacterial taxa and their functional genes at different abundance levels, in both disturbed and undisturbed states. We further reverted the disturbance state to contrast recovery of function with community structure. Our findings are relevant, as very few studies have employed such an approach, while there is a need to assess the relative importance of assembly mechanisms for microbial communities across different spatial and temporal scales, environmental gradients, and types of disturbance.}, }
@article {pmid32842646, year = {2020}, author = {Finore, I and Vigneron, A and Vincent, WF and Leone, L and Di Donato, P and Schiano Moriello, A and Nicolaus, B and Poli, A}, title = {Novel Psychrophiles and Exopolymers from Permafrost Thaw Lake Sediments.}, journal = {Microorganisms}, volume = {8}, number = {9}, pages = {}, doi = {10.3390/microorganisms8091282}, pmid = {32842646}, issn = {2076-2607}, support = {UMI-MicroMeNu//Program Sentinel North financed by the Canada First Research Excellence Fund (CFREF); the Natural Sciences and Engineering Research Council of Canada (NSERC); the CNR (Italy)-Université Laval UMI-MicroMeNu program; the Fonds de Recherche du Québec-Nature/ ; }, abstract = {Thermokarst lakes are one of the most abundant types of microbial ecosystems in the circumpolar North. These shallow basins are formed by the thawing and collapse of ice-rich permafrost, with subsequent filling by snow and ice melt. Until now, permafrost thaw lakes have received little attention for isolation of microorganisms by culture-based analysis. The discovery of novel psychrophiles and their biomolecules makes these extreme environments suitable sources for the isolation of new strains, including for potential biotechnological applications. In this study, samples of bottom sediments were collected from three permafrost thaw lakes in subarctic Québec, Canada. Their diverse microbial communities were characterized by 16S rRNA gene amplicon analysis, and subsamples were cultured for the isolation of bacterial strains. Phenotypic and genetic characterization of the isolates revealed affinities to the genera Pseudomonas, Paenibacillus, Acinetobacter,Staphylococcus and Sphingomonas. The isolates were then evaluated for their production of extracellular enzymes and exopolymers. Enzymes of potential biotechnological interest included α and β-glucosidase, α and β-maltosidase, β-xylosidase and cellobiohydrolase. One isolate, Pseudomonas extremaustralis strain 2ASCA, also showed the capability to produce, in the loosely bound cell fraction, a levan-type polysaccharide with a yield of 613 mg/L of culture, suggesting its suitability as a candidate for eco-sustainable alternatives to commercial polymers.}, }
@article {pmid32841483, year = {2020}, author = {Mammola, S and Amorim, IR and Bichuette, ME and Borges, PAV and Cheeptham, N and Cooper, SJB and Culver, DC and Deharveng, L and Eme, D and Ferreira, RL and Fišer, C and Fišer, Ž and Fong, DW and Griebler, C and Jeffery, WR and Jugovic, J and Kowalko, JE and Lilley, TM and Malard, F and Manenti, R and Martínez, A and Meierhofer, MB and Niemiller, ML and Northup, DE and Pellegrini, TG and Pipan, T and Protas, M and Reboleira, ASPS and Venarsky, MP and Wynne, JJ and Zagmajster, M and Cardoso, P}, title = {Fundamental research questions in subterranean biology.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {}, number = {}, pages = {}, doi = {10.1111/brv.12642}, pmid = {32841483}, issn = {1469-185X}, support = {ANR-15-CE32-0005//Agence Nationale de la Recherche/ ; CF19-0609//Carlsbergfondet/ ; RDP 00092-18//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 745530//H2020 Marie Skłodowska-Curie Actions/ ; 882221//H2020 Marie Skłodowska-Curie Actions/ ; 678193//Horizon 2020 Framework Programme/ ; eLTER//Horizon 2020 Framework Programme/ ; N1-0069//Javna Agencija za Raziskovalno Dejavnost RS/ ; 15471//Villum Fonden/ ; }, abstract = {Five decades ago, a landmark paper in Science titled The Cave Environment heralded caves as ideal natural experimental laboratories in which to develop and address general questions in geology, ecology, biogeography, and evolutionary biology. Although the 'caves as laboratory' paradigm has since been advocated by subterranean biologists, there are few examples of studies that successfully translated their results into general principles. The contemporary era of big data, modelling tools, and revolutionary advances in genetics and (meta)genomics provides an opportunity to revisit unresolved questions and challenges, as well as examine promising new avenues of research in subterranean biology. Accordingly, we have developed a roadmap to guide future research endeavours in subterranean biology by adapting a well-established methodology of 'horizon scanning' to identify the highest priority research questions across six subject areas. Based on the expert opinion of 30 scientists from around the globe with complementary expertise and of different academic ages, we assembled an initial list of 258 fundamental questions concentrating on macroecology and microbial ecology, adaptation, evolution, and conservation. Subsequently, through online surveys, 130 subterranean biologists with various backgrounds assisted us in reducing our list to 50 top-priority questions. These research questions are broad in scope and ready to be addressed in the next decade. We believe this exercise will stimulate research towards a deeper understanding of subterranean biology and foster hypothesis-driven studies likely to resonate broadly from the traditional boundaries of this field.}, }
@article {pmid32840670, year = {2020}, author = {Nikouli, E and Meziti, A and Smeti, E and Antonopoulou, E and Mente, E and Kormas, KA}, title = {Gut Microbiota of Five Sympatrically Farmed Marine Fish Species in the Aegean Sea.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01580-z}, pmid = {32840670}, issn = {1432-184X}, abstract = {In this study, we hypothesized that sympatrically grown farmed fish, i.e. fish which experience similar environmental conditions and nutritionally similar diets, would have more convergent gut microbiota. Using a &quot;common garden&quot; approach, we identified the core microbiota and bacterial community structure differences between five fish species farmed in the same aquaculture site on the west coast of the Aegean Sea, Greece. The investigated individuals were at similar developmental stages and reared in adjacent (< 50 m) aquaculture cages; each cage had 15 kg fish m-3. The diets were nutritionally similar to support optimal growth for each fish species. DNA from the midgut of 3-6 individuals per fish species was extracted and sequenced for the V3-V4 region of the bacterial 16S rRNA. Only 3.9% of the total 181 operational taxonomic units (OTUs) were shared among all fish. Between 5 and 74 OTUs were unique to each fish species. Each of the investigated fish species had a distinct profile of dominant OTUs, i.e. cumulative relative abundance of ≥ 80%. Co-occurrence network analysis for each fish species showed that all networks were strongly dominated by positive correlations between the abundances of their OTUs. However, each fish species had different network characteristics suggesting the differential significance of the OTUs in each of the five fish species midgut. The results of the present study may provide evidence that adult fish farmed in the Mediterranean Sea have a rather divergent and species-specific gut microbiota profile, which are shaped independently of the similar environmental conditions under which they grow.}, }
@article {pmid32840024, year = {2020}, author = {Sizikov, S and Burgsdorf, I and Handley, KM and Lahyani, M and Haber, M and Steindler, L}, title = {Characterization of sponge-associated Verrucomicrobia: microcompartment-based sugar utilization and enhanced toxin-antitoxin modules as features of host-associated Opitutales.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15210}, pmid = {32840024}, issn = {1462-2920}, support = {1243/16//Israel Science Foundation/ ; }, abstract = {Bacteria of the phylum Verrucomicrobia are ubiquitous in marine environments and can be found as free-living organisms or as symbionts of eukaryotic hosts. Little is known about host-associated Verrucomicrobia in the marine environment. Here we reconstructed two genomes of symbiotic Verrucomicrobia from bacterial metagenomes derived from the Atlanto-Mediterranean sponge Petrosia ficiformis and three genomes from strains that we isolated from offshore seawater of the Eastern Mediterranean Sea. Phylogenomic analysis of these five strains indicated that they are all members of Verrucomicrobia subdivision 4, order Opitutales. We compared these novel sponge-associated and seawater-isolated genomes to closely related Verrucomicrobia. Genomic analysis revealed that Planctomycetes-Verrucomicrobia microcompartment gene clusters are enriched in the genomes of symbiotic Opitutales including sponge symbionts but not in free-living ones. We hypothesize that in sponge symbionts these microcompartments are used for degradation of l-fucose and l-rhamnose, which are components of algal and bacterial cell walls and therefore may be found at high concentrations in the sponge tissue. Furthermore, we observed an enrichment of toxin-antitoxin modules in symbiotic Opitutales. We suggest that, in sponges, verrucomicrobial symbionts utilize these modules as a defence mechanism against antimicrobial activity deriving from the abundant microbial community co-inhabiting the host.}, }
@article {pmid32839879, year = {2020}, author = {Noskov, YA and Kabilov, MR and Polenogova, OV and Yurchenko, YA and Belevich, OE and Yaroslavtseva, ON and Alikina, TY and Byvaltsev, AM and Rotskaya, UN and Morozova, VV and Glupov, VV and Kryukov, VY}, title = {A Neurotoxic Insecticide Promotes Fungal Infection in Aedes aegypti Larvae by Altering the Bacterial Community.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01567-w}, pmid = {32839879}, issn = {1432-184X}, support = {18-74-00090//Russian Science Foundation (RU)/ ; }, abstract = {Symbiotic bacteria have a significant impact on the formation of defensive mechanisms against fungal pathogens and insecticides. The microbiome of the mosquito Aedes aegypti has been well studied; however, there are no data on the influence of insecticides and pathogenic fungi on its structure. The fungus Metarhizium robertsii and a neurotoxic insecticide (avermectin complex) interact synergistically, and the colonization of larvae with hyphal bodies is observed after fungal and combined (conidia + avermectins) treatments. The changes in the bacterial communities (16S rRNA) of Ae. aegypti larvae under the influence of fungal infection, avermectin toxicosis, and their combination were studied. In addition, we studied the interactions between the fungus and the predominant cultivable bacteria in vitro and in vivo after the coinfection of the larvae. Avermectins increased the total bacterial load and diversity. The fungus decreased the diversity and insignificantly increased the bacterial load. Importantly, avermectins reduced the relative abundance of Microbacterium (Actinobacteria), which exhibited a strong antagonistic effect towards the fungus in in vitro and in vivo assays. The avermectin treatment led to an increased abundance of Chryseobacterium (Flavobacteria), which exerted a neutral effect on mycosis development. In addition, avermectin treatment led to an elevation of some subdominant bacteria (Pseudomonas) that interacted synergistically with the fungus. We suggest that avermectins change the bacterial community to favor the development of fungal infection.}, }
@article {pmid32836127, year = {2020}, author = {Li, X and Wang, T and Chang, SX and Jiang, X and Song, Y}, title = {Biochar increases soil microbial biomass but has variable effects on microbial diversity: A meta-analysis.}, journal = {The Science of the total environment}, volume = {749}, number = {}, pages = {141593}, doi = {10.1016/j.scitotenv.2020.141593}, pmid = {32836127}, issn = {1879-1026}, abstract = {Biochar has been extensively studied as a soil amendment for carbon sequestration and for improving soil quality; however, a systematic understanding of the responses of soil microbial biomass and diversity to biochar addition is lacking. Here, a meta-analysis of 999 paired data points from 194 studies shows that biochar increases microbial biomass but has variable effects on microbial diversity. Generally, the effects of biochar on microbial biomass are dependent on biochar properties, while that on microbial diversity is dependent on soil properties. The application of biochar, particularly that produced under low temperature and from nutrient-rich feedstocks, could better increase soil microbial biomass (based on phospholipid fatty acid analysis (MBCPLFA)) and diversity. The increases of total microbial biomass with biochar addition are greater in the field than in laboratory studies, in sandy than in clay soils, and when measured by fumigation-extraction (MBCFE) than by MBCPLFA. The bacterial biomass only significantly increases in laboratory studies and fungal biomass only in soils with pH ≤ 7.5 and soil organic carbon ≤30 g kg-1. The increases in total microbial diversity with biochar addition were greater in acidic and sandy soils with low soil organic carbon content and in laboratory incubation studies. In addition, long-term and low-rate addition of biochar always increases microbial diversity. To better guide the use of biochar as a soil amendment, we suggest that establishing long-term and field studies, using a standard method for measuring microbial communities, on different soil types should be our emphasis in future research.}, }
@article {pmid32835181, year = {2020}, author = {Kirubakaran, R and ArulJothi, KN and Revathi, S and Shameem, N and Parray, JA}, title = {Emerging priorities for microbial metagenome research.}, journal = {Bioresource technology reports}, volume = {11}, number = {}, pages = {100485}, pmid = {32835181}, issn = {2589-014X}, abstract = {Overwhelming anthropogenic activities lead to deterioration of natural resources and the environment. The microorganisms are considered desirable, due to their suitability for easy genetic manipulation and handling. With the aid of modern biotechnological techniques, the culturable microorganisms have been widely exploited for the benefit of mankind. Metagenomics, a powerful tool to access the abundant biodiversity of the environmental samples including the unculturable microbes, to determine microbial diversity and population structure, their ecological roles and expose novel genes of interest. This review focuses on the microbial adaptations to the adverse environmental conditions, metagenomic techniques employed towards microbial biotechnology. Metagenomic approach helps to understand microbial ecology and to identify useful microbial derivatives like antibiotics, toxins, and enzymes with diverse and enhanced function. It also summarizes the application of metagenomics in clinical diagnosis, improving microbial ecology, therapeutics, xenobiotic degradation and impact on agricultural crops.}, }
@article {pmid32834061, year = {2020}, author = {D'Abramo, F and Neumeyer, S}, title = {A historical and political epistemology of microbes.}, journal = {Centaurus; international magazine of the history of science and medicine}, volume = {62}, number = {2}, pages = {321-330}, pmid = {32834061}, issn = {0008-8994}, abstract = {This article traces the historical co-evolution of microbiology, bacteriology, and virology, framed within industrial and agricultural contexts, as well as their role in colonial and national history between the end of the 19th century and the first decades of the 20th century. The epistemology of germ theory, coupled with the economic interests of European colonies, has shaped the understanding of human-microbial relationships in a reductionist way. We explore a brief history of the medical and biological sciences, focusing on microbes and the difficulty of implementing germ theory outside of biology laboratories. Furthermore, we highlight the work of Lynn Margulis, who conceptualized microbes within their ecological contexts. Such research shows the active role microbes play in handling life-sustaining biological and biochemical processes. We outline how the industrial and technological advancements of the last two centuries not only impacted almost all human societies, but also changed the world on microbial, biological, and geological levels. The narration of these histories is a complex task, and depends on how national, international, and intergovernmental institutions (such as the World Health Organization) conceive of the selective environmental pressures exerted by industry and biotechnological companies.}, }
@article {pmid32832265, year = {2020}, author = {Li, X and Li, Z and He, Y and Li, P and Zhou, H and Zeng, N}, title = {Regional distribution of Christensenellaceae and its associations with metabolic syndrome based on a population-level analysis.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e9591}, pmid = {32832265}, issn = {2167-8359}, abstract = {The link between the gut microbiota and metabolic syndrome (MetS) has attracted widespread attention. Christensenellaceae was recently described as an important player in human health, while its distribution and relationship with MetS in Chinese population is still unknown. This study sought to observe the association between Christensenellaceae and metabolic indexes in a large sample of residents in South China. A total of 4,781 people from the GGMP project were included, and the fecal microbiota composition of these individuals was characterized by 16S rRNA sequencing and analyzed the relation between Christensenellaceae and metabolism using QIIME (Quantitative Insight Into Microbial Ecology, Version 1.9.1). The results demonstrated that microbial richness and diversity were increased in the group with a high abundance of Christensenellaceae, who showed a greater complexity of the co-occurrence network with other bacteria than residents who lacked Christensenellaceae. The enriched bacterial taxa were predominantly represented by Oscillospira, Ruminococcaceae, RF39, Rikenellaceae and Akkermansia as the Christensenellaceae abundance increased, while the abundances of Veillonella, Fusobacterium and Klebsiella were significantly reduced. Furthermore, Christensenellaceae was negatively correlated with the pathological features of MetS, such as obesity, hypertriglyceridemia and body mass index (BMI). We found reduced levels of lipid biosynthesis and energy metabolism pathways in people with a high abundance of Christensenellaceae, which may explain the negative relationship between body weight and Christensenellaceae. In conclusion, we found a negative correlation between Christensenellaceae and MetS in a large Chinese population and reported the geographical distribution of Christensenellaceae in the GGMP study. The association data from this population-level research support the investigation of strains within Christensenellaceae as potentially beneficial gut microbes.}, }
@article {pmid32830554, year = {2020}, author = {Van Hul, M and Karnik, K and Canene-Adams, K and De Souza, M and Van den Abbeele, P and Marzorati, M and Delzenne, NM and Everard, A and Cani, PD}, title = {Comparison of the effects of soluble corn fiber and fructooligosaccharides on metabolism, inflammation, and gut microbiome of high-fat diet-fed mice.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {319}, number = {4}, pages = {E779-E791}, doi = {10.1152/ajpendo.00108.2020}, pmid = {32830554}, issn = {1522-1555}, support = {Grant for Medical Research 2015//Funds Baillet Latour/ ; WELBIO-CR-2019C-02R,EOS program no.30770//Fonds De La Recherche Scientifique - FNRS (Belgian National Fund for Scientific Research)/ ; }, abstract = {Dietary fibers are essential components of a balanced diet and have beneficial effects on metabolic functions. To gain insight into their impact on host physiology and gut microbiota, we performed a direct comparison of two specific prebiotic fibers in mice. During an 8-wk follow up, mice fed a high-fat diet (HFD) were compared with mice on a normal diet (basal condition, controls) and to mice fed the HFD but treated with one of the following prebiotics: fructooligosaccharides (FOS) or soluble corn fiber (SCF). Both prebiotic fibers led to a similar reduction of body weight and fat mass, lower inflammation and improved metabolic parameters. However, these health benefits were the result of different actions of the fibers, as SCF impacted energy excretion, whereas FOS did not. Interestingly, both fibers had very distinct gut microbial signatures with different short-chain fatty acid profiles, indicating that they do not favor the growth of the same bacterial communities. Although the prebiotic potential of different fibers may seem physiologically equivalent, our data show that the underlying mechanisms of action are different, and this by targeting different gut microbes. Altogether, our data provide evidence that beneficial health effects of specific dietary fibers must be documented to be considered a prebiotic and that studies devoted to understanding how structures relate to specific microbiota modulation and metabolic effects are warranted.}, }
@article {pmid32830371, year = {2020}, author = {Mukherjee, I and Salcher, MM and Andrei, AȘ and Kavagutti, VS and Shabarova, T and Grujčić, V and Haber, M and Layoun, P and Hodoki, Y and Nakano, SI and Šimek, K and Ghai, R}, title = {A freshwater radiation of diplonemids.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15209}, pmid = {32830371}, issn = {1462-2920}, support = {MSM200961801//Akademie Věd České Republiky/ ; 17-04828S//Grant Agency of the Czech Republic/ ; 19-23469S//Grant Agency of the Czech Republic/ ; 20-12496X//Grant Agency of the Czech Republic/ ; 022/2019/P//Grant Agency of the University of South Bohemia/ ; 116/2019/P//Grant Agency of the University of South Bohemia/ ; JSPS-17-17//JSPS Bilateral Japanese-Czech Joint Research Project/ ; 310030_185108/SNSF_/Swiss National Science Foundation/Switzerland ; }, abstract = {Diplonemids are considered marine protists and have been reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Japanese deep freshwater lakes. However, their distribution and abundances in freshwater ecosystems remain unknown. We assessed abundance and diversity of diplonemids from several geographically distant deep freshwater lakes of the world by amplicon-sequencing, shotgun metagenomics and catalysed reporter deposition-fluorescent in situ hybridization (CARD-FISH). We found diplonemids in all the studied lakes, albeit with low abundances and diversity. We assembled long 18S rRNA sequences from freshwater diplonemids and showed that they form a new lineage distinct from the diverse marine clades. Freshwater diplonemids are a sister-group to a marine clade, which are mainly isolates from coastal and bay areas, suggesting a recent habitat transition from marine to freshwater habitats. Images of CARD-FISH targeted freshwater diplonemids suggest they feed on bacteria. Our analyses of 18S rRNA sequences retrieved from single-cell genomes of marine diplonemids show they encode multiple rRNA copies that may be very divergent from each other, suggesting that marine diplonemid abundance and diversity both have been overestimated. These results have wider implications on assessing eukaryotic abundances in natural habitats by using amplicon-sequencing alone.}, }
@article {pmid32829442, year = {2020}, author = {Cabrerizo, MJ and Marañón, E}, title = {Grazing Pressure Is Independent of Prey Size in a Generalist Herbivorous Protist: Insights from Experimental Temperature Gradients.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01578-7}, pmid = {32829442}, issn = {1432-184X}, support = {PGC2018-094553B-I00//Ministerio de Ciencia, Innovación y Universidades/ ; FJCI2017-32318//Ministerio de Ciencia, Innovación y Universidades/ ; }, abstract = {Grazing by herbivorous protists contributes to structuring plankton communities through its effect on the growth, biomass, and competitiveness of prey organisms and also impacts the transfer of primary production towards higher trophic levels. Previous evidence shows that heterotrophic processes (grazing rates, g) are more sensitive to temperature than autotrophic ones (phytoplankton growth rates, μ) and also that small cells tend to be more heavily predated than larger ones; however, it remains unresolved how the interplay between changes in temperature and cell size modulates grazing pressure (i.e., g:μ ratio). We addressed this problem by conducting an experiment with four phytoplankton populations, from pico- to microphytoplankton, over a 12 °C gradient and in the presence/absence of a generalist herbivorous protist, Oxyrrhis marina. We found that highest g rates coincided with highest μ rates, which corresponded to intermediate cell sizes. There were no significant differences in either μ or g between the smallest and largest cell sizes considered. The g:μ ratio was largely independent of cell size and C:N ratios, and its thermal dependence was low although species-specific differences were large. We suggest that the similar g:μ found could be the consequence that the energetic demand imposed by rising temperatures would be a more important issue than the mechanical constriction to ingestion derived from prey cell size. Despite the difficulty of quantifying μ and g in natural planktonic communities, we suggest that the g:μ ratio is a key response variable to evaluate thermal sensitivity of food webs because it gives a more integrative view of trophic functioning than both rates separately.}, }
@article {pmid32829441, year = {2020}, author = {Silveira, R and Silva, MRSS and de Roure Bandeira de Mello, T and Alvim, EACC and Marques, NCS and Kruger, RH and da Cunha Bustamante, MM}, title = {Bacteria and Archaea Communities in Cerrado Natural Pond Sediments.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01574-x}, pmid = {32829441}, issn = {1432-184X}, support = {process number 193.000.567/2009//Fundação de Apoio à Pesquisa do Distrito Federal/ ; }, abstract = {Natural ponds in the Brazilian Cerrado harbor high biodiversity but are still poorly studied, especially their microbial assemblage. The characterization of the microbial community in aquatic environments is fundamental for understanding its functioning, particularly under the increasing pressure posed by land conversion and climate change. Here, we aim to characterize the structure (abundance, richness, and diversity) and composition of the Bacteria and Archaea in the sediment of two natural ponds belonging to different basins that primarily differ in size and depth in the Cerrado. Sediment samples were collected in the dry and rainy seasons and the transition periods between both. The structure and composition of Bacteria and Archaea were assessed by 16S rRNA gene pyrosequencing. We identified 45 bacterial and four archaeal groups. Proteobacteria and Acidobacteria dominated the bacterial community, while Euryarchaeota and Thaumarchaeota dominated the archaeal community. Seasonal fluctuations in the relative abundance of microbial taxa were observed, but pond characteristics were more determinant to community composition differences. Microbial communities are highly diverse, and local variability could partially explain the microbial structure's main differences. Functional predictions based in 16S rRNA gene accessed with Tax4Fun indicated an enriched abundance of predicted methane metabolism in the deeper pond, where higher abundance of methanogenic archaea Methanocella, Methanosaeta, and Methanomicrobiaceae was detected. Our dataset encompasses the more comprehensive survey of prokaryotic microbes in Cerrado's aquatic environments. Here, we present basic and essential information about composition and diversity, for initial insights into the ecology of Bacteria and Archaea in these environments.}, }
@article {pmid32829154, year = {2020}, author = {Jamwal, R and Amit,  and Kumari, S and Balan, B and Kelly, S and Cannavan, A and Singh, DK}, title = {Rapid and non-destructive approach for the detection of fried mustard oil adulteration in pure mustard oil via ATR-FTIR spectroscopy-chemometrics.}, journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy}, volume = {244}, number = {}, pages = {118822}, doi = {10.1016/j.saa.2020.118822}, pmid = {32829154}, issn = {1873-3557}, abstract = {Attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy integrated with chemometrics was effectively applied for the rapid detection and accurate quantification of fried mustard oil (FMO) adulteration in pure mustard oil (PMO). PMO was adulterated with FMO in the range of 0.5-50% v/v. Principal component analysis (PCA) elucidated the studied adulteration using two components with an explained variance of 97%. The linear discriminant analysis (LDA) was adopted to classify the adulterated PMO samples with FMO. LDA model showed 100% accuracy initially, as well as when cross-validated. To enhance the overall quality of models, characteristic spectral regions were optimized, and principal component regression (PCR) and partial least square regression (PLS-R) models were constructed with high accuracy and precision. PLS-R model for the 2nd derivative of the optimized spectral region 1260-1080 cm-1 showed best results for prediction sample sets in terms of high R2 and residual predictive deviation (RPD) value of 0.999 and 31.91 with low root mean square error (RMSE) and relative prediction error (RE %) of 0.53% v/v and 3.37% respectively. Thus, the suggested method can detect up to 0.5% v/v of adulterated FMO in PMO in a short time interval.}, }
@article {pmid32829116, year = {2020}, author = {Sakarika, M and Candry, P and Depoortere, M and Ganigué, R and Rabaey, K}, title = {Impact of substrate and growth conditions on microbial protein production and composition.}, journal = {Bioresource technology}, volume = {317}, number = {}, pages = {124021}, doi = {10.1016/j.biortech.2020.124021}, pmid = {32829116}, issn = {1873-2976}, mesh = {Biomass ; *Carbon ; }, abstract = {Production of microbial protein (MP) from recovered resources - e.g. CO2-sourced formate and acetate - could provide protein while enabling CO2 capture. To assess the protein quality obtained from this process, pure cultures and enriched communities were selected and characterized kinetically, stoichiometrically and nutritionally. Growth on acetate resulted in up to 5.3 times higher maximum specific growth rate (μmax) than formate (i.e. 0.15-0.41 h-1 for acetate compared to 0.061-0.29 h-1 for formate at pH = 7). The protein content was a function of the growth phase, with the highest values during stationary phase, ranging between 18 and 82%CDW protein depending on the organism and substrate. The negative correlation between biomass productivity and protein content indicated a trade-off between production rate and product quality. The final product (i.e. dried MP) quality was in most cases superior to soybean and all cultures were rich in threonine, phenylalanine and tyrosine, regardless of the carbon source.}, }
@article {pmid32827977, year = {2020}, author = {Dai, H and Gao, J and Wang, S and Li, D and Wang, Z}, title = {The key active degrader, metabolic pathway and microbial ecology of triclosan biodegradation in an anoxic/oxic system.}, journal = {Bioresource technology}, volume = {317}, number = {}, pages = {124014}, doi = {10.1016/j.biortech.2020.124014}, pmid = {32827977}, issn = {1873-2976}, mesh = {Bacteria/genetics ; Biodegradation, Environmental ; Drug Resistance, Microbial ; Metabolic Networks and Pathways ; *Triclosan ; }, abstract = {A lab-scale anoxic/oxic (A/O) system was used to reveal the key active triclosan-degrading bacteria (TCS-DB) in this study. The results showed that TCS was mainly removed by metabolism of heterotrophic bacteria (accounting for about 62%), and the potential metabolic pathway was the break of ether bond in TCS formed 2,4-dichlorophenol, and further dechlorination formed phenol or other metabolic end products. DNA-based stable isotope probing (DNA-SIP) assay further revealed that Methylobacillus accounting for 20.75% in 13C sample was the key active TCS-DB. Furthermore, methylotrophy and methanol oxidation were found to be the potential metabolic routes of TCS degradation by functional annotation of prokaryotic taxa analysis. Interestingly, TCS accelerated the propagation of antibiotic resistance genes (fabI) and intI1 which positively correlated with several functional microorganisms (p < 0.05). This study contributes to comprehend the potential mechanism, metabolic pathway and microbial ecology of TCS biodegradation in A/O system.}, }
@article {pmid32827089, year = {2020}, author = {Maher, AMD and Asaiyah, M and Quinn, S and Burke, R and Wolff, H and Bode, HB and Griffin, CT}, title = {Competition and Co-existence of Two Photorhabdus Symbionts with a Nematode Host.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01573-y}, pmid = {32827089}, issn = {1432-184X}, support = {16/RI/3399/SFI_/Science Foundation Ireland/Ireland ; }, abstract = {Photorhabdus spp. (Enterobacteriales: Morganellaceae) occur exclusively as symbionts of Heterorhabditis nematodes for which they provide numerous services, including killing insects and providing nutrition and defence within the cadavers. Unusually, two species (Photorhabdus cinerea and Photorhabdus temperata) associate with a single population of Heterorhabditis downesi at a dune grassland site. Building on previous work, we investigated competition between these two Photorhabdus species both at the regional (between insects) and local (within insect) level by trait comparison and co-culture experiments. There was no difference between the species with respect to supporting nematode reproduction and protection of cadavers against invertebrate scavengers, but P. cinerea was superior to P. temperata in several traits: faster growth rate, greater antibacterial and antifungal activity and colonisation of a higher proportion of nematodes in co-culture. Moreover, where both bacterial symbionts colonised single nematode infective juveniles, P. cinerea tended to dominate in numbers. Differences between Photorhabdus species were detected in the suite of secondary metabolites produced: P. temperata produced several compounds not produced by P. cinerea including anthraquinone pigments. Bioluminescence emitted by P. temperata also tended to be brighter than that from P. cinerea. Bioluminescence and pigmentation may protect cadavers against scavengers that rely on sight. We conclude that while P. cinerea may show greater local level (within-cadaver) competitive success, co-existence of the two Photorhabdus species in the spatially heterogeneous environment of the dunes is favoured by differing specialisations in defence of the cadaver against differing locally important threats.}, }
@article {pmid32826215, year = {2020}, author = {Gofstein, TR and Perkins, M and Field, J and Leigh, MB}, title = {The Interactive Effects of Crude Oil and Corexit 9500 on their Biodegradation in Arctic Seawater.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.01194-20}, pmid = {32826215}, issn = {1098-5336}, abstract = {The risk of petroleum spills coupled with the potential application of chemical dispersants as a spill response strategy necessitates further understanding of the fate of oil and dispersants and their interactive effects during biodegradation. Using Arctic seawater mesocosms amended with either crude oil, Corexit 9500, or both together, we quantified the chemical losses of crude oil and Corexit 9500 and identified microbial taxa implicated in their biodegradation based on shifts in the microbial community structure over a 30-day time course. Chemical analyses included total petroleum hydrocarbons (TPH), n-alkanes, branched alkanes, and polycyclic aromatic hydrocarbons (PAHs) for oil loss and the surfactant components dioctyl sodium sulfosuccinate (DOSS), Span 80, Tween 80, Tween 85, and the DOSS metabolite ethylhexyl sulfosuccinate (EHSS) for Corexit loss. Changes to the microbial communities and identification of key taxa were determined by 16S rRNA gene amplicon sequencing. The nonionic surfactants of Corexit 9500 (Span 80, Tweens 80+85) biodegraded rapidly, dropping to below the limits of detection within 5 days and prior to any detectable initiation of oil biodegradation. This resulted in no observable suppression of petroleum biodegradation in the presence of Corexit compared to that of oil alone. In contrast, biodegradation of DOSS was delayed in the presence of oil, based on the prolonged presence of DOSS concentrations and accumulation of the degradation intermediate EHSS that did not occur in the absence of oil. Microbial analyses revealed that oil and Corexit enriched different overall microbial communities, with the presence of both resulting in a community composition that shifted from one more similar to that of Corexit-only, then shifting to reflect the oil-only community over time, in parallel with the degradation of predominantly Corexit and then oil components. Some microbial taxa (Oleispira,Pseudofulvibacter, Roseobacter) responded to either oil or Corexit, suggesting that some organisms may be capable of utilizing both substrates. Together, these findings reveal interactive effects of crude oil and Corexit 9500 on chemical losses and microbial communities as they biodegrade, providing further insight into their fate when co-present in the environment.Importance Chemical dispersants such as Corexit 9500 are commonly used in oil spill response and are currently under consideration for use in the Arctic, where their fate and effects have not been well studied. This research was performed to determine the interactive effects of the co-presence of crude oil and Corexit 9500 on the degradation of components from each mixture and the associated microbial community structure over time in Arctic seawater. These findings will help yield a better understanding on the biodegradability of dispersant components applied to an oil spill, the temporal microbial community response to dispersed oil, and the fundamental microbial ecology of organic contaminant biodegradation processes in the Arctic marine environment.}, }
@article {pmid32825355, year = {2020}, author = {Floyd, AS and Mott, BM and Maes, P and Copeland, DC and McFrederick, QS and Anderson, KE}, title = {Microbial Ecology of European Foul Brood Disease in the Honey Bee (Apis mellifera): Towards a Microbiome Understanding of Disease Susceptibility.}, journal = {Insects}, volume = {11}, number = {9}, pages = {}, doi = {10.3390/insects11090555}, pmid = {32825355}, issn = {2075-4450}, abstract = {European honey bees (Apis mellifera Linnaeus) are beneficial insects that provide essential pollination services for agriculture and ecosystems worldwide. Modern commercial beekeeping is plagued by a variety of pathogenic and environmental stressors often confounding attempts to understand colony loss. European foulbrood (EFB) is considered a larval-specific disease whose causative agent, Melissococcus plutonius, has received limited attention due to methodological challenges in the field and laboratory. Here, we improve the experimental and informational context of larval disease with the end goal of developing an EFB management strategy. We sequenced the bacterial microbiota associated with larval disease transmission, isolated a variety of M.plutonius strains, determined their virulence against larvae in vitro, and explored the potential for probiotic treatment of EFB disease. The larval microbiota was a low diversity environment similar to honey, while worker mouthparts and stored pollen contained significantly greater bacterial diversity. Virulence of M. plutonius against larvae varied markedly by strain and inoculant concentration. Our chosen probiotic, Parasaccharibacter apium strain C6, did not improve larval survival when introduced alone, or in combination with a virulent EFB strain. We discuss the importance of positive and negative controls for in vitro studies of the larval microbiome and disease.}, }
@article {pmid32824323, year = {2020}, author = {Rutere, C and Knoop, K and Posselt, M and Ho, A and Horn, MA}, title = {Ibuprofen Degradation and Associated Bacterial Communities in Hyporheic Zone Sediments.}, journal = {Microorganisms}, volume = {8}, number = {8}, pages = {}, pmid = {32824323}, issn = {2076-2607}, support = {641939//European Commission/ ; }, abstract = {Ibuprofen, a non-steroidal anti-inflammatory pain reliever, is among pharmaceutical residues of environmental concern ubiquitously detected in wastewater effluents and receiving rivers. Thus, ibuprofen removal potentials and associated bacteria in the hyporheic zone sediments of an impacted river were investigated. Microbially mediated ibuprofen degradation was determined in oxic sediment microcosms amended with ibuprofen (5, 40, 200, and 400 µM), or ibuprofen and acetate, relative to an un-amended control. Ibuprofen was removed by the original sediment microbial community as well as in ibuprofen-enrichments obtained by re-feeding of ibuprofen. Here, 1-, 2-, 3-hydroxy- and carboxy-ibuprofen were the primary transformation products. Quantitative real-time PCR analysis revealed a significantly higher 16S rRNA abundance in ibuprofen-amended relative to un-amended incubations. Time-resolved microbial community dynamics evaluated by 16S rRNA gene and 16S rRNA analyses revealed many new ibuprofen responsive taxa of the Acidobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Latescibacteria, and Proteobacteria. Two ibuprofen-degrading strains belonging to the genera Novosphingobium and Pseudomonas were isolated from the ibuprofen-enriched sediments, consuming 400 and 300 µM ibuprofen within three and eight days, respectively. The collective results indicated that the hyporheic zone sediments sustain an efficient biotic (micro-)pollutant degradation potential, and hitherto unknown microbial diversity associated with such (micro)pollutant removal.}, }
@article {pmid32823898, year = {2020}, author = {Francis, F and Jacquemyn, H and Delvigne, F and Lievens, B}, title = {From Diverse Origins to Specific Targets: Role of Microorganisms in Indirect Pest Biological Control.}, journal = {Insects}, volume = {11}, number = {8}, pages = {}, pmid = {32823898}, issn = {2075-4450}, abstract = {Integrated pest management (IPM) is today a widely accepted pest management strategy to select and use the most efficient control tactics and at the same time reduce over-dependence on chemical insecticides and their potentially negative environmental effects. One of the main pillars of IPM is biological control. While biological control programs of pest insects commonly rely on natural enemies such as predatory insects, parasitoids and microbial pathogens, there is increasing evidence that plant, soil and insect microbiomes can also be exploited to enhance plant defense against herbivores. In this mini-review, we illustrate how microorganisms from diverse origins can contribute to plant fitness, functional traits and indirect defense responses against pest insects, and therefore be indirectly used to improve biological pest control practices. Microorganisms in the rhizosphere, phyllosphere and endosphere have not only been shown to enhance plant growth and plant strength, but also promote plant defense against herbivores both above- and belowground by providing feeding deterrence or antibiosis. Also, herbivore associated molecular patterns may be induced by microorganisms that come from oral phytophagous insect secretions and elicit plant-specific responses to herbivore attacks. Furthermore, microorganisms that inhabit floral nectar and insect honeydew produce volatile organic compounds that attract beneficial insects like natural enemies, thereby providing indirect pest control. Given the multiple benefits of microorganisms to plants, we argue that future IPMs should consider and exploit the whole range of possibilities that microorganisms offer to enhance plant defense and increase attraction, fecundity and performance of natural enemies.}, }
@article {pmid32823755, year = {2020}, author = {Quijada, NM and Bodas, R and Lorenzo, JM and Schmitz-Esser, S and Rodríguez-Lázaro, D and Hernández, M}, title = {Dietary Supplementation with Sugar Beet Fructooligosaccharides and Garlic Residues Promotes Growth of Beneficial Bacteria and Increases Weight Gain in Neonatal Lambs.}, journal = {Biomolecules}, volume = {10}, number = {8}, pages = {}, pmid = {32823755}, issn = {2218-273X}, support = {IDMICRO//Consejería de Agricultura y Ganadería, Castilla y León/ ; }, abstract = {The proper development of the early gastrointestinal tract (GIT) microbiota is critical for newborn ruminants. This microbiota is susceptible to modification by diverse external factors (such as diet) that can lead to long-lasting results when occurring in young ruminants. Dietary supplementation with prebiotics, ingredients nondigestible and nonabsorbable by the host that stimulate the growth of beneficial GIT bacteria, has been applied worldwide as a potential approach in order to improve ruminant health and production yields. However, how prebiotics affect the GIT microbiota during ruminants' early life is still poorly understood. We investigated the effect of milk supplementation with a combination of two well-known prebiotics, fructooligosaccharides (FOS) from sugar beet and garlic residues (all together named as &quot;additive&quot;), exerted on preweaned lamb growth and the composition of their fecal microbiota, by using 16S rRNA gene amplicon high-throughput sequencing. The results showed a significant increase in the mean daily weight gain of lambs fed with the additive. Lamb fecal microbiota was also influenced by the additive intake, as additive-diet lambs showed lower bacterial diversity and were significantly more abundant in Bifidobacterium, Enterococcus, Lactobacillus and Veillonella. These bacteria have been previously reported to confer beneficial properties to the ruminant, including promotion of growth and health status, and our results showed that they were strongly linked to the additive intake and the increased weight gain of lambs. This study points out the combination of FOS from sugar beet and garlic residues as a potential prebiotic to be used in young ruminants' nutrition in order to improve production yields.}, }
@article {pmid32819450, year = {2020}, author = {Berg, G and Rybakova, D and Fischer, D and Cernava, T and Vergès, MC and Charles, T and Chen, X and Cocolin, L and Eversole, K and Corral, GH and Kazou, M and Kinkel, L and Lange, L and Lima, N and Loy, A and Macklin, JA and Maguin, E and Mauchline, T and McClure, R and Mitter, B and Ryan, M and Sarand, I and Smidt, H and Schelkle, B and Roume, H and Kiran, GS and Selvin, J and de Souza, RSC and van Overbeek, L and Singh, BK and Wagner, M and Walsh, A and Sessitsch, A and Schloter, M}, title = {Correction to: Microbiome definition re-visited: old concepts and new challenges.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {119}, pmid = {32819450}, issn = {2049-2618}, abstract = {An amendment to this paper has been published and can be accessed via the original article.}, }
@article {pmid32818149, year = {2020}, author = {Kaplan, F and Shapiro-Ilan, D and Schiller, KC}, title = {Dynamics of entomopathogenic nematode foraging and infectivity in microgravity.}, journal = {NPJ microgravity}, volume = {6}, number = {}, pages = {20}, pmid = {32818149}, issn = {2373-8065}, abstract = {Microgravity is a unique environment to elucidate host-parasite biology. Entomopathogenic nematodes (EPNs), model parasites, kill host insects with mutualistic bacteria and provide environmentally friendly pest control. It is unknown how microgravity affects a multistep insect invasion by parasites with mutualistic bacteria. EPNs respond directionally to electromagnetic cues and their sinusoidal locomotion is affected by various physical factors. Therefore, we expected microgravity to impact EPN functionality. Microgravity experiments during space flight on the International Space Station (ISS) indicated that EPNs successfully emerged from consumed insect host cadavers, moved through soil, found and infected bait insects in a manner equivalent to Earth controls. However, nematodes that developed entirely in space, from the egg stage, died upon return to Earth, unlike controls in microgravity and on Earth. This agricultural biocontrol experiment in space gives insight to long-term space flight for symbiotic organisms, parasite biology, and the potential for sustainable crop protection in space.}, }
@article {pmid32817104, year = {2020}, author = {Miller, JI and Techtmann, S and Joyner, D and Mahmoudi, N and Fortney, J and Fordyce, JA and GaraJayeva, N and Askerov, FS and Cravid, C and Kuijper, M and Pelz, O and Hazen, TC}, title = {Microbial Communities across Global Marine Basins Show Important Compositional Similarities by Depth.}, journal = {mBio}, volume = {11}, number = {4}, pages = {}, pmid = {32817104}, issn = {2150-7511}, abstract = {The environmental surveys following the 2010 Deepwater Horizon (DWH) spill identified a variety of hydrocarbon-degrading microorganisms, and laboratory studies with field-collected water samples then demonstrated faster-than-expected hydrocarbon biodegradation rates at 5°C. Knowledge about microbial community composition, diversity, and functional metabolic capabilities aids in understanding and predicting petroleum biodegradation by microbial communities in situ and is therefore an important component of the petroleum spill response decision-making process. This study investigates the taxonomic composition of microbial communities in six different global basins where petroleum and gas activities occur. Shallow-water communities were strikingly similar across basins, while deep-water communities tended to show subclusters by basin, with communities from the epipelagic, mesopelagic, and bathypelagic zones sometimes appearing within the same cluster. Microbial taxa that were enriched in the water column in the Gulf of Mexico following the DWH spill were found across marine basins. Several hydrocarbon-degrading genera (e.g., Actinobacteria, Pseudomonas, and Rhodobacteriacea) were common across all basins. Other genera such as Pseudoalteromonas and Oleibacter were highly enriched in specific basins.IMPORTANCE Marine microbial communities are a vital component of global carbon cycling, and numerous studies have shown that populations of petroleum-degrading bacteria are ubiquitous in the oceans. Few studies have attempted to distinguish all of the taxa that might contribute to petroleum biodegradation (including, e.g., heterotrophic and nondesignated microbes that respond positively to petroleum and microbes that grow on petroleum as the sole carbon source). This study quantifies the subpopulations of microorganisms that are expected to be involved in petroleum hydrocarbon biodegradation, which is important information during the decision-making process in the event of a petroleum spill accident.}, }
@article {pmid32816051, year = {2020}, author = {Zhang, Q and Campos, M and Larama, G and Acuña, JJ and Valenzuela, B and Solis, F and Zamorano, P and Araya, R and Sadowsky, MJ and Jorquera, MA}, title = {Composition and predicted functions of the bacterial community in spouting pool sediments from the El Tatio Geyser field in Chile.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-020-02020-9}, pmid = {32816051}, issn = {1432-072X}, support = {1201386//FONDECYT/ ; NSFC190012//CONICYT/ ; }, abstract = {The El Tatio Geyser Field (ETGF), located in Northern Chile, is the main geyser field in the southern hemisphere. Despite this, details of its microbial ecology are still unknown. Here, we briefly report on the composition and predicted functions of the bacterial community in spouting pool sediments from the ETGF as revealed by high-throughput sequencing of 16S rRNA genes. Results of this analysis showed that while there were differences in richness and diversity between samples, bacterial communities were primarily dominated by the phyla Proteobacteria, followed Firmicutes, Bacteroidetes, Acidobacteria, and Chloroflexi. Analyses of predicted functional activity indicated that the functions were mostly attributed to chemoheterotrophy and aerobic chemoheterotrophy, followed by sulfur (respiration of sulfur compounds and sulfate) and nitrogen (nitrate reduction, respiration of nitrogen and nitrate) cycling. Taken together, our results suggest a high diversity in taxonomy and predictive functions of bacterial communities in sediments from spouting pools. This study provides fundamentally important information on the structure and function predictive functions of microbiota communities in spouting pools. Moreover, since the ETGF is intensively visited and impacted by tens of thousands of tourists every year, our results can be used to help guide the design of sustainable conservation strategies.}, }
@article {pmid32816010, year = {2020}, author = {Vestrum, RI and Attramadal, KJK and Vadstein, O and Gundersen, MS and Bakke, I}, title = {Bacterial community assembly in Atlantic cod larvae (Gadus morhua): contributions of ecological processes and metacommunity structure.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {9}, pages = {}, pmid = {32816010}, issn = {1574-6941}, abstract = {Many studies demonstrate the importance of the commensal microbiomes to animal health and development. However, the initial community assembly process is poorly understood. It is unclear to what extent the hosts select for their commensal microbiota, whether stochastic processes contribute, and how environmental conditions affect the community assembly. We investigated community assembly in Atlantic cod larvae exposed to distinct microbial metacommunities. We aimed to quantify ecological processes influencing community assembly in cod larvae and to elucidate the complex relationship between the bacteria of the environment and the fish. Selection within the fish was the major determinant for community assembly, but drift resulted in inter-individual variation. The environmental bacterial communities were highly dissimilar from those associated with the fish. Still, differences in the environmental bacterial communities strongly influenced the fish communities. The most striking difference was an excessive dominance of a single OTU (Arcobacter) for larvae reared in two of the three systems. These larvae were exposed to environments with higher fractions of opportunistic bacteria, and we hypothesise that detrimental host-microbe interactions might have made the fish susceptible to Arcobacter colonisation. Despite strong selection within the host, this points to a possibility to steer the metacommunity towards mutualistic host-microbe interactions and improved fish health and survival.}, }
@article {pmid32815317, year = {2020}, author = {Nascimento Lemos, L and Manoharan, L and William Mendes, L and Monteiro Venturini, A and Satler Pylro, V and Tsai, SM}, title = {Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.12880}, pmid = {32815317}, issn = {1758-2229}, support = {//Brazilian Microbiome Project/ ; 140032/2015-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 161931/2015-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 2014/50320-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2015/13546-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2016/18215-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/09643-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/24037-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; //Coordination for the Improvement of Higher Education Personnel/ ; //National Council for Scientific and Technological Development/ ; //São Paulo Research Foundation/ ; }, abstract = {Soil microbiome is one of the most heterogeneous biological systems. State-of-the-art molecular approaches such as those based on single-amplified genomes (SAGs) and metagenome assembled-genomes (MAGs) are now improving our capacity for disentailing soil microbial-mediated processes. Here, we analysed publicly available datasets of soil microbial genomes and MAG's reconstructed from the Amazon's tropical soil (primary forest and pasture) and active layer of permafrost, aiming to evaluate their genome size. Our results suggest that the Candidate Phyla Radiation (CPR)/Patescibacteria phyla have genomes with an average size fourfold smaller than the mean identified in the RefSoil database, which lacks any representative of this phylum. Also, by analysing the potential metabolism of 888 soil microbial genomes, we show that CPR/Patescibacteria representatives share similar functional profiles, but different from other microbial phyla and are frequently neglected in the soil microbial surveys. Finally, we argue that the use of MAGs may be a better choice over SAGs to expand the soil microbial databases, like RefSoil.}, }
@article {pmid32814025, year = {2020}, author = {Alexander, M and Turnbaugh, PJ}, title = {Deconstructing Mechanisms of Diet-Microbiome-Immune Interactions.}, journal = {Immunity}, volume = {53}, number = {2}, pages = {264-276}, pmid = {32814025}, issn = {1097-4180}, support = {T32 AI060537/AI/NIAID NIH HHS/United States ; R21 CA227232/CA/NCI NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; F32 AI147456/AI/NIAID NIH HHS/United States ; R01 AR074500/AR/NIAMS NIH HHS/United States ; }, abstract = {Emerging evidence suggests that the effect of dietary intake on human health and disease is linked to both the immune system and the microbiota. Yet, we lack an integrated mechanistic model for how these three complex systems relate, limiting our ability to understand and treat chronic and infectious disease. Here, we review recent findings at the interface of microbiology, immunology, and nutrition, with an emphasis on experimentally tractable models and hypothesis-driven mechanistic work. We outline emerging mechanistic concepts and generalizable approaches to bridge the gap between microbial ecology and molecular mechanism. These set the stage for a new era of precision human nutrition informed by a deep and comprehensive knowledge of the diverse cell types in and on the human body.}, }
@article {pmid32812858, year = {2020}, author = {Lee, JC and Whang, KS}, title = {Agriterribacter humi gen. nov., sp. nov., a novel bacterium of the family Chitinophagaceae isolated from soil of a farming field.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {9}, pages = {5123-5130}, doi = {10.1099/ijsem.0.004397}, pmid = {32812858}, issn = {1466-5034}, abstract = {A Gram-stain-negative bacterium, designated strain YJ03T, was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ03T was found to be an aerobic, non-motile and non-spore-forming bacterium which can grow at 10-33 °C (optimum, 25-28 °C), at pH 6.6-9.5 (optimum, pH 7.0-7.5) and at salinities of 0-1.0 % (w/v) NaCl (optimum, 0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ03T with the closely related relatives were in the range 93.9-92.2 %, and the results of phylogenomic analysis indicated that strain YJ03T was clearly separated from species of the genera in the family Chitinophagaceae, showing average nucleotide identity values of 68.8-64.3 %. The predominant isoprenoid quinone was identified as MK-7 and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and an unidentified fatty acid with an equivalent chain-length of 13.565. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, four unidentified aminolipids and six unidentified lipids. The G+C content of the genome was determined to be 41.8 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences in this study, strain YJ03T is considered to represent a novel species of a new genus in the family Chitinophagaceae, for which the name Agriterribacter humi gen. nov., sp. nov., is proposed. The type strain of Agriterribacter humi is YJ03T (=KACC 19548T=NBRC 113195T).}, }
@article {pmid32807105, year = {2020}, author = {Kabwe, MH and Vikram, S and Mulaudzi, K and Jansson, JK and Makhalanyane, TP}, title = {The gut mycobiota of rural and urban individuals is shaped by geography.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {257}, pmid = {32807105}, issn = {1471-2180}, abstract = {BACKGROUND: Understanding the structure and drivers of gut microbiota remains a major ecological endeavour. Recent studies have shown that several factors including diet, lifestyle and geography may substantially shape the human gut microbiota. However, most of these studies have focused on the more abundant bacterial component and comparatively less is known regarding fungi in the human gut. This knowledge deficit is especially true for rural and urban African populations. Therefore, we assessed the structure and drivers of rural and urban gut mycobiota.<br><br>RESULTS: Our participants (n = 100) were balanced by geography and sex. The mycobiota of these geographically separated cohorts was characterized using amplicon analysis of the Internal Transcribed Spacer (ITS) gene. We further assessed biomarker species specific to rural and urban cohorts. In addition to phyla which have been shown to be ubiquitous constituents of gut microbiota, Pichia were key constituents of the mycobiota. We found that geographic location was a major driver of gut mycobiota. Other factors such as smoking where also determined gut mycobiota albeit to a lower extent, as explained by the small proportion of total variation. Linear discriminant and the linear discriminant analysis effect size analysis revealed several distinct urban and rural biomarkers.<br><br>CONCLUSIONS: Together, our analysis reveals distinct community structure in urban and rural South African individuals. Geography was shown to be a key driver of rural and urban gut mycobiota.}, }
@article {pmid32806693, year = {2020}, author = {Martin-Rivilla, H and Gutierrez-Mañero, FJ and Gradillas, A and P Navarro, MO and Andrade, G and Lucas, JA}, title = {Identifying the Compounds of the Metabolic Elicitors of Pseudomonas fluorescens N 21.4 Responsible for Their Ability to Induce Plant Resistance.}, journal = {Plants (Basel, Switzerland)}, volume = {9}, number = {8}, pages = {}, pmid = {32806693}, issn = {2223-7747}, support = {AGL-2013-45189-R//Ministerio de Economía y Competitividad of Spain/ ; }, abstract = {In this work, the metabolic elicitors extracted from the beneficial rhizobacterium Pseudomonas fluorescens N 21.4 were sequentially fragmented by vacuum liquid chromatography to isolate, purify and identify the compounds responsible for the extraordinary capacities of this strain to induce systemic resistance and to elicit secondary defensive metabolism in diverse plant species. To check if the fractions sequentially obtained were able to increase the synthesis of isoflavones and if, therefore, they still maintained the eliciting capacity of the live strain, rapid and controlled experiments were done with soybean seeds. The optimal action concentration of the fractions was established and all of them elicited isoflavone secondary metabolism-the fractions that had been extracted with n-hexane being more effective. The purest fraction was the one with the highest eliciting capacity and was also tested in Arabidopsis thaliana seedlings to induce systemic resistance against the pathogen Pseudomonas syringae pv. tomato DC 3000. This fraction was then analyzed by UHPLC/ESI-QTOF-MS, and an alkaloid, two amino lipids, three arylalkylamines and a terpenoid were tentatively identified. These identified compounds could be part of commercial plant inoculants of biological and sustainable origin to be applied in crops, due to their potential to enhance the plant immune response and since many of them have putative antibiotic and/or antifungal potential.}, }
@article {pmid32804245, year = {2020}, author = {Wei, X and Chi, Z and Liu, GL and Hu, Z and Chi, ZM}, title = {The Genome-Wide Mutation Shows the Importance of Cell Wall Integrity in Growth of the Psychrophilic Yeast Metschnikowia australis W7-5 at Different Temperatures.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01577-8}, pmid = {32804245}, issn = {1432-184X}, support = {31970058//Major Research Plan/ ; }, abstract = {In this study, it was found that a Cre/loxP system could be successfully used as a tool for editing the genome of the psychrophilic yeast Metschnikowia australis W7-5 isolated from Antarctica. The deletion and over-expression of the TPS1 gene for trehalose biosynthesis, the GSY gene for glycogen biosynthesis, and the GPD1 and GPP genes for glycerol biosynthesis had no influence on cell growth of the mutants and transformants compared to cell growth of their wild-type strain M. australis W7-5, indicating that trehalose, glycogen, and glycerol had no function in growth of the psychrophilic yeast at different temperatures. However, removal of the SLT2 gene encoding the mitogen-activated protein kinase in the cell wall integrity (CWI) signaling pathway and the SWI4 and SWI6 genes encoding the transcriptional activators Swi4/6 had the crucial influence on cell growth of the psychrophilic yeast at the low temperature, especially at 25 °C and expression of the genes related to cell wall and lipid biosynthesis. Therefore, the cell wall could play an important role in growth of the psychrophilic yeast at different temperatures and biosynthesis of cell wall was actively regulated by the CWI signaling pathway. This was the first time to show that the genome of the psychrophilic yeast was successfully edited and the molecular evidences were obtained to elucidate mechanisms of low temperature growth of the psychrophilic yeast from Antarctica.}, }
@article {pmid32804239, year = {2020}, author = {Andras, JP and Rodriguez-Reillo, WG and Truchon, A and Blanchard, JL and Pierce, EA and Ballantine, KA}, title = {Rewilding the small stuff: the effect of ecological restoration on prokaryotic communities of peatland soils.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {10}, pages = {}, doi = {10.1093/femsec/fiaa144}, pmid = {32804239}, issn = {1574-6941}, abstract = {To investigate the effect that restoration has on the microbiome of wetland soils, we used 16S amplicon sequencing to characterize the soil prokaryotic communities of retired cranberry farms that were restored to approximate the peat wetlands they once were. For comparison, we also surveyed the soil communities of active cranberry farms, retired cranberry farms and natural peat wetlands that were never farmed. Our results show that the prokaryotic communities of active cranberry farms are distinct from those of natural peat wetlands. Moreover, 4 years after restoration, the prokaryotic community structure of restored cranberry farms had shifted, resulting in a community more similar to natural peat wetlands than to active farms. Meanwhile, the prokaryotic communities of retired cranberry farms remained similar to those of active farms. The observed differences in community structure across site types corresponded with significant differences in inferred capacity for denitrification, methanotrophy and methanogenesis, and community composition was also correlated with previously published patterns of denitrification and carbon sequestration measured from the same soil samples. Taken together, these results suggest that ecological restoration efforts have the potential to restore ecosystem functions of soils and that they do so by 'rewilding' the communities of resident soil microbes.}, }
@article {pmid32803365, year = {2020}, 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 = {Correction to: Titanium Ions Inhibit the Bacteria in Vase Solutions of Freshly Cut Gerbera jamesonii and Extend the Flower Longevity.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {960}, doi = {10.1007/s00248-020-01572-z}, pmid = {32803365}, issn = {1432-184X}, abstract = {We request that the following corrections be made in our article.}, }
@article {pmid32803364, year = {2020}, author = {Berlow, M and Phillips, JN and Derryberry, EP}, title = {Effects of Urbanization and Landscape on Gut Microbiomes in White-Crowned Sparrows.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01569-8}, pmid = {32803364}, issn = {1432-184X}, abstract = {Habitats are changing rapidly around the globe and urbanization is one of the primary drivers. Urbanization changes food availability, environmental stressors, and the prevalence of disease for many species. These changes can lead to divergence in phenotypic traits, including behavioral, physiological, and morphological features between urban and rural populations. Recent research highlights that urbanization is also changing the gut microbial communities found in a diverse group of host species. These changes have not been uniform, leaving uncertainty as to how urban habitats are shaping gut microbial communities. To better understand these effects, we investigated the gut bacterial communities of White-Crowned Sparrow (Zonotrichia leucophrys) populations along an urbanization gradient in the San Francisco Bay area. We examined how gut bacterial communities vary with the local environment and host morphological characteristics. We found direct effects of environmental factors, including urban noise levels and territory land cover, as well as indirect effects through body size and condition, on alpha and beta diversity of gut microbial communities. We also found that urban and rural birds' microbiomes differed in which variables predicted their diversity, with urban communities driven by host morphology, and rural communities driven by environmental factors. Elucidating these effects provides a better understanding of how urbanization affects wild avian physiology.}, }
@article {pmid32803363, year = {2020}, author = {Cai, Y and Zhou, X and Shi, L and Jia, Z}, title = {Atmospheric Methane Oxidizers Are Dominated by Upland Soil Cluster Alpha in 20 Forest Soils of China.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {859-871}, doi = {10.1007/s00248-020-01570-1}, pmid = {32803363}, issn = {1432-184X}, support = {41401294//National Natural Science Foundation of China/ ; 41877062//National Natural Science Foundation of China/ ; 91751204//National Natural Science Foundation of China/ ; 2019311//Youth Innovation Promotion Association, CAS/ ; }, abstract = {Upland soil clusters alpha and gamma (USCα and USCγ) are considered a major biological sink of atmospheric methane and are often detected in forest and grassland soils. These clusters are phylogenetically classified using the particulate methane monooxygenase gene pmoA because of the difficulty of cultivation. Recent studies have established a direct link of pmoA genes to 16S rRNA genes based on their isolated strain or draft genomes. However, whether the results of pmoA-based assays could be largely represented by 16S rRNA gene sequencing in upland soils remains unclear. In this study, we collected 20 forest soils across China and compared methane-oxidizing bacterial (MOB) communities by high-throughput sequencing of 16S rRNA and pmoA genes using different primer sets. The results showed that 16S rRNA gene sequencing and the semi-nested polymerase chain reaction (PCR) of the pmoA gene (A189/A682r nested with a mixture of mb661 and A650) consistently revealed the dominance of USCα (accounting for more than 50% of the total MOB) in 12 forest soils. A189f/A682r successfully amplified pmoA genes (mainly RA14 of USCα) in only three forest soils. A189f/mb661 could amplify USCα (mainly JR1) in several forest soils but showed a strong preferential amplification of Methylocystis and many other type I MOB groups. A189f/A650 almost exclusively amplified USCα (mainly JR1) and largely discriminated against Methylocystis and most of the other MOB groups. The semi-nested PCR approach weakened the bias of A189f/mb661 and A189f/A650 for JR1 and balanced the coverage of all USCα members. The canonical correspondence analysis indicated that soil NH4+-N and pH were the main environmental factors affecting the MOB community of Chinese forest soils. The RA14 of the USCα group prefers to live in soils with low pH, low temperature, low elevation, high precipitation, and rich in nitrogen. JR1's preferences for temperature and elevation were opposite to RA14. Our study suggests that combining the deep sequencing of 16S rRNA and pmoA genes to characterize MOB in forest soils is the best choice.}, }
@article {pmid32803362, year = {2020}, author = {Zilius, M and Samuiloviene, A and Stanislauskienė, R and Broman, E and Bonaglia, S and Meškys, R and Zaiko, A}, title = {Depicting Temporal, Functional, and Phylogenetic Patterns in Estuarine Diazotrophic Communities from Environmental DNA and RNA.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01562-1}, pmid = {32803362}, issn = {1432-184X}, support = {P-MIP-17-126//Lietuvos Mokslo Taryba/ ; }, abstract = {Seasonally nitrogen-limited and phosphorus-replete temperate coastal waters generally host dense and diverse diazotrophic communities. Despite numerous studies in marine systems, little is known about diazotrophs and their functioning in oligohaline estuarine environments. Here we applied a combination of nifH transcript and metagenomic shotgun sequencing approaches to investigate temporal shifts in taxonomic composition and nifH activity of size-fractionated diazotrophic communities in a shallow and mostly freshwater coastal lagoon. Patterns in active nifH phylotypes exhibited a clear seasonal succession, which reflected their different tolerances to temperature change and nitrogen (N) availability. Thus, in spring, heterotrophic diazotrophs (Proteobacteria) dominated the nifH phylotypes, while increasing water temperature and depletion of inorganic N fostered heterocystous Cyanobacteria in summer. Metagenomic data demonstrated four main N-cycling pathways and three of them with a clear seasonal pattern: denitrification (spring) → N2 fixation (summer) → assimilative NO3- reduction (fall), with NH4+ uptake into cells occurring across all seasons. Although a substantial denitrification signal was observed in spring, it could have originated from the re-suspended benthic rather than planktonic community. Our results contribute to a better understanding of the realized genetic potential of pelagic N2 fixation and its seasonal dynamics in oligohaline estuarine ecosystems, which are natural coastal biogeochemical reactors.}, }
@article {pmid32801177, year = {2020}, author = {Pilgrim, J and Siozios, S and Baylis, M and Hurst, GDD}, title = {Tissue Tropisms and Transstadial Transmission of a Rickettsia Endosymbiont in the Highland Midge, Culicoides impunctatus (Diptera: Ceratopogonidae).}, journal = {Applied and environmental microbiology}, volume = {86}, number = {20}, pages = {}, doi = {10.1128/AEM.01492-20}, pmid = {32801177}, issn = {1098-5336}, abstract = {Rickettsia is a genus of intracellular bacteria which can manipulate host reproduction and alter sensitivity to natural enemy attack in a diverse range of arthropods. The maintenance of Rickettsia endosymbionts in insect populations can be achieved through both vertical and horizontal transmission routes. For example, the presence of the symbiont in the follicle cells and salivary glands of Bemisia whiteflies allows Belli group Rickettsia transmission via the germ line and plants, respectively. However, the transmission routes of other Rickettsia bacteria, such as those in the Torix group of the genus, remain underexplored. Through fluorescence in situ hybridization (FISH) and transmission electron microscopy (TEM) screening, this study describes the pattern of Torix Rickettsia tissue tropisms in the highland midge, Culicoides impunctatus (Diptera: Ceratopogonidae). Of note is the high intensity of infection of the ovarian suspensory ligament, suggestive of a novel germ line targeting strategy. Additionally, localization of the symbiont in tissues of several developmental stages suggests transstadial transmission is a major route for ensuring maintenance of Rickettsia within C. impunctatus populations. Aside from providing insights into transmission strategies, the presence of Rickettsia bacteria in the fat body of larvae indicates potential host fitness and vector capacity impacts to be investigated in the future.IMPORTANCE Microbial symbionts of disease vectors have garnered recent attention due to their ability to alter vectorial capacity. Their consideration as a means of arbovirus control depends on symbiont vertical transmission, which leads to spread of the bacteria through a population. Previous work has identified a Rickettsia symbiont present in several species of biting midges (Culicoides spp.), which transmit bluetongue and Schmallenberg arboviruses. However, symbiont transmission strategies and host effects remain underexplored. In this study, we describe the presence of Rickettsia in the ovarian suspensory ligament of Culicoides impunctatus Infection of this organ suggests the connective tissue surrounding developing eggs is important for ensuring vertical transmission of the symbiont in midges and possibly other insects. Additionally, our results indicate Rickettsia localization in the fat body of Culicoides impunctatus As the arboviruses spread by midges often replicate in the fat body, this location implies possible symbiont-virus interactions to be further investigated.}, }
@article {pmid32801031, year = {2020}, author = {Hodges, JK and Sasaki, GY and Bruno, RS}, title = {Anti-inflammatory activities of green tea catechins along the gut-liver axis in nonalcoholic fatty liver disease: lessons learned from preclinical and human studies.}, journal = {The Journal of nutritional biochemistry}, volume = {85}, number = {}, pages = {108478}, doi = {10.1016/j.jnutbio.2020.108478}, pmid = {32801031}, issn = {1873-4847}, abstract = {Nonalcoholic fatty liver disease (NAFLD), which is the most prevalent hepatic disorder worldwide, affecting 25% of the general population, describes a spectrum of progressive liver conditions ranging from relatively benign liver steatosis and advancing to nonalcoholic steatohepatitis (NASH), fibrosis, and cirrhosis. Hallmark features of NASH are fatty hepatocytes and inflammatory cell infiltrates in association with increased activation of hepatic nuclear factor kappa-B (NFκB) that exacerbates liver injury. Because no pharmacological treatments exist for NAFLD, emphasis has been placed on dietary approaches to manage NASH risk. Anti-inflammatory bioactivities of catechin-rich green tea extract (GTE) have been well-studied, especially in preclinical models that have detailed its effects on inflammatory responses downstream of NFκB activation. This review will therefore discuss the experimental evidence that has advanced an understanding of the mechanisms by which GTE, either directly through its catechins or potentially indirectly through microbiota-derived metabolites, limits NFκB activation and NASH-associated liver injury. Specifically, it will describe the hepatic-level benefits of GTE that attenuate intracellular redox distress and pro-inflammatory signaling from extracellular receptors that otherwise activate NFκB. In addition, it will discuss the anti-inflammatory activities of GTE on gut barrier function as well as prebiotic and antimicrobial effects on gut microbial ecology that help to limit the translocation of gut-derived endotoxins (e.g. lipopolysaccharides) to the liver where they otherwise upregulate NFκB activation by Toll-like receptor-4 signaling. This summary is therefore expected to advance research translation of the hepatic- and intestinal-level benefits of GTE and its catechins to help manage NAFLD-associated morbidity.}, }
@article {pmid32800221, year = {2020}, author = {Yadav, R and Rajput, V and Gohil, K and Khairnar, K and Dharne, M}, title = {Comprehensive metagenomic insights into a unique mass gathering and bathing event reveals transient influence on a riverine ecosystem.}, journal = {Ecotoxicology and environmental safety}, volume = {202}, number = {}, pages = {110938}, doi = {10.1016/j.ecoenv.2020.110938}, pmid = {32800221}, issn = {1090-2414}, mesh = {Drug Resistance, Microbial ; Ecosystem ; *Environmental Monitoring ; Humans ; India ; Metagenome ; Microbiota ; Rivers/*chemistry ; Water Pollution/*statistics &amp; numerical data ; Water Quality ; }, abstract = {The religious mass gathering and bathing can pose a multitude of significant public health challenges and lead to severe alterations in the river microbial ecology. The Pandharpur Wari is an annual pilgrimage of Maharashtra, India, where millions of devotees carry the footprints of the saint-poets and pay their obeisance to Lord Vitthal on the 11th day of moon's waxing phase (Ashadi Ekadashi). As a part of the ritual, the engrossed devotees, walk over 250 km, take a first holy dip in a sacred river Indrayani at Alandi and secondly in Bhima River at Pandharpur. The MinION-based shotgun metagenomic approach was employed to examine the impact of spiritual mass bathing on environmental changes (concerning the river microbial community structure and functions); and public health aspects (in terms of changes in the pathogenic potential and antibiotic resistance). The analysis of bathing and post-bathing samples of both the rivers revealed alterations in the alpha and beta diversity, indicating significant spatiotemporal variations in the overall microbial structure and function. Furthermore, the analysis revealed up to 80% of differences in the abundance of virulence genes between the bathing and post bathing samples. We observed parallel increase of priority skin and enteric pathogens (ranging from 11% to 80%) such as Acinetobacter baumannii, Staphylococcus aureus, Streptococcus pyogenes, Mycobacterium tuberculosis, and Pseudomonas aeruginosa during the bathing event. Moreover, we observed a significant increase in the antibiotic resistance in the bathing samples of Bhima and Indrayani rivers respectively. Altogether, this is the first comprehensive metagenomic study unravelling the influence of religious mass-bathing on the riverine ecosystem.}, }
@article {pmid32798895, year = {2020}, author = {Rabaey, K and Vandekerckhove, T and de Walle, AV and Sedlak, DL}, title = {The third route: Using extreme decentralization to create resilient urban water systems.}, journal = {Water research}, volume = {185}, number = {}, pages = {116276}, doi = {10.1016/j.watres.2020.116276}, pmid = {32798895}, issn = {1879-2448}, abstract = {For much of the world's urban population, centralized treatment plants and pipe networks built in the nineteenth and twentieth centuries provide homes with water and a means of disposing of the resulting wastewater. Due to the real or perceived inability of existing systems to deliver safe and palatable water, many users apply additional treatment prior to consumption. Where piped water supply is lacking, drinking water is obtained through water vendors at considerable cost. Despite economic inefficiencies and public health risks inherent in these two water supply systems, the high sunk costs of existing water infrastructure along with low returns on investment and the inflexible nature of the institutions involved in water provision have slowed down the diffusion of alternative approaches that may prove to be less expensive, more adaptable and safer than the current system. We advocate a third, complementary route: household-based personalized water systems. Initially, relatively affluent people expecting more functionality and sustainability from water systems will invest in personalized water systems that allow them to tailor their water to their personal preferences. This approach will tap into the tremendous creativity-base of individual users and entrepreneurs, facilitating the type of co-creation that accelerated the rapid development of consumer electronics. Competition among manufacturers and economies of scale that accrue as these systems become more popular will lead to rapid innovation that drives down costs, improves performance and expands access. These solutions complement emerging approaches for sanitation and resource recovery that do not rely upon sewers for the management of human waste.}, }
@article {pmid32795675, year = {2020}, author = {Fernández-Murga, ML and Olivares, M and Sanz, Y}, title = {Bifidobacterium pseudocatenulatum CECT 7765 reverses the adverse effects of diet-induced obesity through the gut-bone axis.}, journal = {Bone}, volume = {141}, number = {}, pages = {115580}, doi = {10.1016/j.bone.2020.115580}, pmid = {32795675}, issn = {1873-2763}, abstract = {Obesity and the associated chronic metabolic diseases (e.g., type-2 diabetes) adversely affect bone metabolism and health. Gut microbiota is considered to be involved in the pathophysiology of obesity and also represents a therapeutic target. This study has investigated the contribution of diet-induced obesity to alterations in bone health and metabolism and whether these could be restored by oral administration of Bifidobacterium pseudocatenulatum CECT 7765. To do so, adult male wild-type C57BL-6 mice were fed either a standard or high-fat diet (HFD), supplemented or not with B. pseudocatenulatum CECT 7765 (109 CFU/day) for 14 weeks. Effects on bone mass density (BMD), bone mineral content, bone remodeling, bone structure and gene expression were assessed. In HFD-fed mice, bone microstructural properties at the distal femur showed deteriorated trabecular architecture in bone volumetric fraction, trabecular number and trabecular pattern factor. Besides, the HFD reduced the volumetric bone mineral density in the trabecular bone, but not in the cortical bone. All these bone microstructural alterations found in obese mice were reversed by B. pseudocatenulatum CECT 7765. Administration of the bacterium increased (p < .05) the Wnt/β-catenin pathway gene expression, which could mediate effects on BMD. Bifidobacterium pseudocatenulatum CECT 7765 supplementation increased (p < .05) serum osteocalcin (OC, bone formation parameter), and decreased serum C-terminal telopeptide (CTX) (p < .01) and parathormone (PTH) (p < .05) (both bone resorption parameters). It also altered the microstructure of the femur. In summary, HFD interfered with the normal bone homeostasis leading to increased bone loss. In obese mice, B. pseudocatenulatum CECT 7765 lowered bone mass loss and enhanced BMD by decreasing bone resorption and increasing bone formation.}, }
@article {pmid32795263, year = {2020}, author = {Puente-Sánchez, F and García-García, N and Tamames, J}, title = {SQMtools: automated processing and visual analysis of 'omics data with R and anvi'o.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {358}, pmid = {32795263}, issn = {1471-2105}, support = {CTM2016-80095-C2-1-R//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; PID2019-110011RB-C31//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; IJC2018-035180-I//Ministerio de Ciencia, Innovación y Universidades/ ; SEV-2013-0347-17-2//Ministerio de Ciencia, Innovación y Universidades/ ; }, mesh = {Computational Biology/*methods ; Contig Mapping ; Databases, Factual ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Software ; }, abstract = {BACKGROUND: The dramatic decrease in sequencing costs over the last decade has boosted the adoption of high-throughput sequencing applications as a standard tool for the analysis of environmental microbial communities. Nowadays even small research groups can easily obtain raw sequencing data. After that, however, non-specialists are faced with the double challenge of choosing among an ever-increasing array of analysis methodologies, and navigating the vast amounts of results returned by these approaches.<br><br>RESULTS: Here we present a workflow that relies on the SqueezeMeta software for the automated processing of raw reads into annotated contigs and reconstructed genomes (bins). A set of custom scripts seamlessly integrates the output into the anvi'o analysis platform, allowing filtering and visual exploration of the results. Furthermore, we provide a software package with utility functions to expose the SqueezeMeta results to the R analysis environment.<br><br>CONCLUSIONS: Altogether, our workflow allows non-expert users to go from raw sequencing reads to custom plots with only a few powerful, flexible and well-documented commands.}, }
@article {pmid32793165, year = {2020}, author = {Guyet, U and Nguyen, NA and Doré, H and Haguait, J and Pittera, J and Conan, M and Ratin, M and Corre, E and Le Corguillé, G and Brillet-Guéguen, L and Hoebeke, M and Six, C and Steglich, C and Siegel, A and Eveillard, D and Partensky, F and Garczarek, L}, title = {Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1707}, pmid = {32793165}, issn = {1664-302X}, abstract = {Understanding how microorganisms adjust their metabolism to maintain their ability to cope with short-term environmental variations constitutes one of the major current challenges in microbial ecology. Here, the best physiologically characterized marine Synechococcus strain, WH7803, was exposed to modulated light/dark cycles or acclimated to continuous high-light (HL) or low-light (LL), then shifted to various stress conditions, including low (LT) or high temperature (HT), HL and ultraviolet (UV) radiations. Physiological responses were analyzed by measuring time courses of photosystem (PS) II quantum yield, PSII repair rate, pigment ratios and global changes in gene expression. Previously published membrane lipid composition were also used for correlation analyses. These data revealed that cells previously acclimated to HL are better prepared than LL-acclimated cells to sustain an additional light or UV stress, but not a LT stress. Indeed, LT seems to induce a synergic effect with the HL treatment, as previously observed with oxidative stress. While all tested shift conditions induced the downregulation of many photosynthetic genes, notably those encoding PSI, cytochrome b6/f and phycobilisomes, UV stress proved to be more deleterious for PSII than the other treatments, and full recovery of damaged PSII from UV stress seemed to involve the neo-synthesis of a fairly large number of PSII subunits and not just the reassembly of pre-existing subunits after D1 replacement. In contrast, genes involved in glycogen degradation and carotenoid biosynthesis pathways were more particularly upregulated in response to LT. Altogether, these experiments allowed us to identify responses common to all stresses and those more specific to a given stress, thus highlighting genes potentially involved in niche acclimation of a key member of marine ecosystems. Our data also revealed important specific features of the stress responses compared to model freshwater cyanobacteria.}, }
@article {pmid32793158, year = {2020}, author = {Procopio, N and Ghignone, S and Voyron, S and Chiapello, M and Williams, A and Chamberlain, A and Mello, A and Buckley, M}, title = {Soil Fungal Communities Investigated by Metabarcoding Within Simulated Forensic Burial Contexts.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1686}, pmid = {32793158}, issn = {1664-302X}, support = {MR/S032878/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Decomposition of animal bodies in the burial environment plays a key role in the biochemistry of the soil, altering the balance of the local microbial populations present before the introduction of the carcass. Despite the growing number of studies on decomposition and soil bacterial populations, less is known on its effects on fungal communities. Shifts in the fungal populations at different post-mortem intervals (PMIs) could provide insights for PMI estimation and clarify the role that specific fungal taxa have at specific decomposition stages. In this study, we buried pig carcasses over a period of 1- to 6-months, and we sampled the soil in contact with each carcass at different PMIs. We performed metabarcoding analysis of the mycobiome targeting both the internal transcribed spacer (ITS) 1 and 2, to elucidate which one was more suitable for this purpose. Our results showed a decrease in the fungal taxonomic richness associated with increasing PMIs, and the alteration of the soil fungal signature even after 6 months post-burial, showing the inability of soil communities to restore their original composition within this timeframe. The results highlighted taxonomic trends associated with specific PMIs, such as the increase of the Mortierellomycota after 4- and 6-months and of Ascomycota particularly after 2 months, and the decrease of Basidiomycota from the first to the last time point. We have found a limited number of taxa specifically associated with the carrion and not present in the control soil, showing that the major contributors to the recorded changes are originated from the soil and were not introduced by the carrion. As this is the first study conducted on burial graves, it sets the baseline for additional studies to investigate the role of fungal communities on prolonged decomposition periods and to identify fungal biomarkers to improve the accuracy of PMI prediction for forensic applications.}, }
@article {pmid32793152, year = {2020}, author = {Lyu, Y and Su, C and Verbrugghe, A and Van de Wiele, T and Martos Martinez-Caja, A and Hesta, M}, title = {Past, Present, and Future of Gastrointestinal Microbiota Research in Cats.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1661}, pmid = {32793152}, issn = {1664-302X}, abstract = {The relationship between microbial community and host has profound effects on the health of animals. A balanced gastrointestinal (GI) microbial population provides nutritional and metabolic benefits to its host, regulates the immune system and various signaling molecules, protects the intestine from pathogen invasion, and promotes a healthy intestinal structure and an optimal intestinal function. With the fast development of next-generation sequencing, molecular techniques have become standard tools for microbiota research, having been used to demonstrate the complex intestinal ecosystem. Similarly to other mammals, the vast majority of GI microbiota in cats (over 99%) is composed of the predominant bacterial phyla Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Many nutritional and clinical studies have shown that cats' microbiota can be affected by several different factors including body condition, age, diet, and inflammatory diseases. All these factors have different size effects, and some of these may be very minor, and it is currently unknown how important these are. Further research is needed to determine the functional variations in the microbiome in disease states and in response to environmental and/or dietary modulations. Additionally, further studies are also needed to explain the intricate relationship between GI microbiota and the genetics and immunity of its host. This review summarizes past and present knowledge of the feline GI microbiota and looks into the future possibilities and challenges of the field.}, }
@article {pmid32790601, year = {2020}, author = {Lee, JC and Whang, KS}, title = {Agromyces humi sp. nov., actinobacterium isolated from farm soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {9}, pages = {5032-5039}, doi = {10.1099/ijsem.0.004376}, pmid = {32790601}, issn = {1466-5034}, abstract = {A Gram-stain-positive actinobacterial strain, designated ANK073T, was isolated from rhizosphere soil sampled at a spinach farming field in Shinan, Republic of Korea. Cells of strain ANK073T were found to be aerobic, non-motile, non-spore-forming rods which could grow at 20-40 °C (optimum, 30 °C), at pH 6.0-10.0 (optimum, pH 6.5-7.5) and at salinities of 0-4 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain ANK073T belongs to the genus Agromyces with high sequence similarities to Agromyces humatus CD5T (98.8 %), Agromyces tardus SJ-23T (98.5 %) and Agromyces iriomotensis IY07-20T (98.4 %). The phylogenetic analysis indicated that strain ANK073T formed a distinct phyletic line in the genus Agromyces and the results of DNA-DNA relatedness and phylogenomic analysis based on whole genome sequences demonstrated that strain ANK073T could be separated from its closest relatives in the genus Agromyces. The strain contained 2,4-diaminobutylic acid, glycine, d-glutamic acid and d-alanine in the peptidoglycan. The predominant menaquinones were identified as MK-12 and MK-11, and the major fatty acids were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C15:0. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genome was determined to be 70.2 mol%. On the basis of its phenotypic and chemotaxonomic properties and the results of phylogenetic and phylogenomic analyses, strain ANK073T is considered to represent a novel species in the genus Agromyces, for which the name Agromyces humi sp. nov. is proposed. The type strain is ANK073T (=KACC 18683T=NBRC 111825T).}, }
@article {pmid32789440, year = {2020}, author = {Kim, JW and Jeong, Y and Park, SJ and Jin, H and Lee, J and Ju, JH and Ji, GE and Park, SH}, title = {Influence of proton pump inhibitor or rebamipide use on gut microbiota of rheumatoid arthritis patients.}, journal = {Rheumatology (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/rheumatology/keaa316}, pmid = {32789440}, issn = {1462-0332}, abstract = {OBJECTIVE: Patients with RA commonly use gastrointestinal (GI) protective drugs for treatment and prevention of drug-associated GI injuries. However, how these drugs affect the gut microbiota in RA patients remains unknown. The objective of this study was to examine the gut microbiota of RA patients according to use of GI protective drugs such as proton pump inhibitors (PPIs), histamine 2-receptor antagonists and rebamipide.<br><br>METHODS: Faecal samples were obtained from 15 healthy controls and 32 RA patients who were receiving PPI, histamine 2-receptor antagonist or rebamipide. Bacterial DNA was extracted from the faecal samples and 16S rRNA sequencing was performed. Microbial composition and function were analysed using Quantitative Insights Into Microbial Ecology and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States.<br><br>RESULTS: RA patients exhibited reduced diversity and altered composition of the gut microbiota compared with healthy controls. The gut microbiota of RA patients receiving acid-suppressing drugs, particularly PPIs, was distinct from that of RA patients receiving rebamipide (PPI vs rebamipide, P = 0.005). Streptococcus was enriched in RA patients receiving PPI, while Clostridium bolteae was enriched in RA patients receiving rebamipide. The gut microbiota of PPI users was abundant with microbial functional pathway involved in the production of virulence factors. This featured microbial function was positively correlated with relative abundance of Streptococcus, the differentially abundant taxa of PPI users.<br><br>CONCLUSION: The gut microbiota of RA patients receiving PPIs was distinguishable from that of those receiving rebamipide. The enriched virulent function in the gut microbiota of PPI users suggests that inappropriate PPI use may be harmful in RA patients.}, }
@article {pmid32785735, year = {2020}, author = {Balan, B and Dhaulaniya, AS and Varma, DA and Sodhi, KK and Kumar, M and Tiwari, M and Singh, DK}, title = {Microbial biofilm ecology, in silico study of quorum sensing receptor-ligand interactions and biofilm mediated bioremediation.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00203-020-02012-9}, pmid = {32785735}, issn = {1432-072X}, abstract = {Biofilms are structured microbial communities of single or multiple populations in which microbial cells adhere to a surface and get embedded in extracellular polymeric substances (EPS). This review attempts to explain biofilm architecture, development phases, and forces that drive bacteria to promote biofilm mode of growth. Bacterial chemical communication, also known as Quorum sensing (QS), which involves the production, detection, and response to small molecules called autoinducers, is highlighted. The review also provides a brief outline of interspecies and intraspecies cell-cell communication. Additionally, we have performed docking studies using Discovery Studio 4.0, which has enabled our understanding of the prominent interactions between autoinducers and their receptors in different bacterial species while also scoring their interaction energies. Receptors, such as LuxN (Phosphoreceiver domain and RecA domain), LuxP, and LuxR, interacted with their ligands (AI-1, AI-2, and AHL) with a CDocker interaction energy of - 31.6083 kcal/mole; - 34.5821 kcal/mole, - 48.2226 kcal/mole and - 41.5885 kcal/mole, respectively. Since biofilms are ideal for the remediation of contaminants due to their high microbial biomass and their potential to immobilize pollutants, this article also provides an overview of biofilm-mediated bioremediation.}, }
@article {pmid32784779, year = {2020}, author = {Kumar, H and Jang, YN and Kim, K and Park, J and Jung, MW and Park, JE}, title = {Compositional and Functional Characteristics of Swine Slurry Microbes through 16S rRNA Metagenomic Sequencing Approach.}, journal = {Animals : an open access journal from MDPI}, volume = {10}, number = {8}, pages = {}, pmid = {32784779}, issn = {2076-2615}, support = {PJ01252102//Rural Development Administration/ ; }, abstract = {Traditionally slurry is used as source of nitrogen, phosphorous, and potassium in bio fertilizers to improve crop production. However, poorly managed slurry causes a hazardous effect to the environment by producing greenhouse gases, causing the eutrophication of water bodies, and polluting the groundwater. It has been largely reported that the microbial presence in slurry causing a diverse effect on its storage and disposal system. However, the diversity of bacterial populations in pig slurries remains largely unexplored. Here we report the bacterial diversity present in the slurry from slurry pits, and the effect of storage time on bacterial population. We collected 42 samples from three different pig slurry pits, as three replicates from each one until the 14th week. We used the 16S rRNA, Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) protocols for the metagenomic downstream analysis. Taxonomic annotation using the Greengenes metagenomic database indicated that on an average 76.2% Firmicutes, 14.4% Bacteroidetes, 4.9% Proteobacteria, etc. microbial populations were present. Comparative microbial analysis showed that the population of Firmicutes decreased from the first to the 14th week, whereas the population of Bacteroidetes increased from the first to the 14th week. Through principal coordinate analysis (PCoA), (linear discriminant analysis effect size (LEfSe), and Pearson's correlation analysis, we found microbial biomarkers according to the storage time point. All bacterial populations were well clustered according to the early, middle, and last weeks of storage. LEfSe showed that Actinobacteria, Lachnospiraceae, Ruminococcaceae, and Bacteroidia are dominantly present in first, seventh, ninth, and 14th week, respectively. Lachnospiraceae and Ruminococcaceae are ubiquitous gastrointestinal non-pathogenic bacteria. KEGG pathways, such as membrane transport, carbohydrate and amino acid metabolism, genetic replication and repair, were significant among all samples. Such a KEGG pathway may indicate the association between the host organism's metabolic activity and the microbes present in the gastro intestinal tract (GIT).}, }
@article {pmid32783779, year = {2020}, author = {Belibasakis, GN and Manoil, D}, title = {Microbial Community-Driven Etiopathogenesis of Peri-Implantitis.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {22034520949851}, doi = {10.1177/0022034520949851}, pmid = {32783779}, issn = {1544-0591}, abstract = {Osseointegrated dental implants are a revolutionary tool in the armament of reconstructive dentistry, employed to replace missing teeth and restore masticatory, occlusal, and esthetic functions. Like natural teeth, the orally exposed part of dental implants offers a pristine nonshedding surface for salivary pellicle-mediated microbial adhesion and biofilm formation. In early colonization stages, these bacterial communities closely resemble those of healthy periodontal sites, with lower diversity. Because the peri-implant tissues are more susceptible to endogenous oral infections, understanding of the ecological triggers that underpin the microbial pathogenesis of peri-implantitis is central to developing improved prevention, diagnosis, and therapeutic strategies. The advent of next-generation sequencing (NGS) technologies, notably applied to 16S ribosomal RNA gene amplicons, has enabled the comprehensive taxonomic characterization of peri-implant bacterial communities in health and disease, revealing a differentially abundant microbiota between these 2 states, or with periodontitis. With that, the peri-implant niche is highlighted as a distinct ecosystem that shapes its individual resident microbial community. Shifts from health to disease include an increase in diversity and a gradual depletion of commensals, along with an enrichment of classical and emerging periodontal pathogens. Metatranscriptomic profiling revealed similarities in the virulence characteristics of microbial communities from peri-implantitis and periodontitis, nonetheless with some distinctive pathways and interbacterial networks. Deeper functional assessment of the physiology and virulence of the well-characterized microbial communities of the peri-implant niche will elucidate further the etiopathogenic mechanisms and drivers of the disease.}, }
@article {pmid32780919, year = {2020}, author = {Robles-Vera, I and de la Visitación, N and Toral, M and Sánchez, M and Romero, M and Gómez-Guzmán, M and Yang, T and Izquierdo-García, JL and Guerra-Hernández, E and Ruiz-Cabello, J and Raizada, MK and Pérez-Vizcaíno, F and Jiménez, R and Duarte, J}, title = {Probiotic Bifidobacterium breve prevents DOCA-salt hypertension.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {}, number = {}, pages = {}, doi = {10.1096/fj.202001532R}, pmid = {32780919}, issn = {1530-6860}, support = {SAF2017-84894-R//Ministerio de Economía, Industria y Competitividad, Gobierno de España (Ministeri d'Economia, Indústria i Competitivitat)/ ; HL102033//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; CTS164//Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía (Ministry of Economy, Innovation, Science and Employment, Government of Andalucia)/ ; }, abstract = {Many probiotics that affect gut microbial ecology have been shown to produce beneficial effects on renin-angiotensin-dependent rodent models and human hypertension. We hypothesized that Bifidobacterium breve CECT7263 (BFM) would attenuate hypertension in deoxycorticosterone acetate (DOCA)-salt rats, a renin-independent model of hypertension. Rats were randomly divided into five groups: control, DOCA-salt, treated DOCA-salt-BFM, treated DOCA-salt-butyrate, and treated DOCA-salt-acetate, for 5 weeks. BFM prevented the increase in systolic blood pressure, cardiac weight, and renal damage induced by DOCA-salt. BFM increased acetate-producing bacterial population and gut acetate levels, improved colonic integrity, normalized endotoxemia, plasma trimethylamine (TMA) levels, and restored the Th17 and Treg content in mesenteric lymph nodes and aorta. Furthermore, BFM improved nitric oxide-dependent vasorelaxation induced by acetylcholine in aortic rings and reduced NADPH oxidase activity in DOCA-salt animals. These protective effects were mimicked by acetate, but not by butyrate supplementation. These data demonstrate that BFM induces changes in gut microbiota linked with attenuation of endothelial dysfunction and increase in blood pressure in this low-renin form of hypertension. These beneficial effects seem to be mediated by increased acetate and reduced TMA production by gut microbiota, thus, improving gut integrity and restoring Th17/Tregs polarization and endotoxemia.}, }
@article {pmid32780840, year = {2020}, author = {Looby, CI and Martin, PH}, title = {Diversity and function of soil microbes on montane gradients: the state of knowledge in a changing world.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {9}, pages = {}, doi = {10.1093/femsec/fiaa122}, pmid = {32780840}, issn = {1574-6941}, abstract = {Mountains have a long history in the study of diversity. Like macroscopic taxa, soil microbes are hypothesized to be strongly structured by montane gradients, and recently there has been important progress in understanding how microbes are shaped by these conditions. Here, we summarize this literature and synthesize patterns of microbial diversity on mountains. Unlike flora and fauna that often display a mid-elevation peak in diversity, we found a decline (34% of the time) or no trend (33%) in total microbial diversity with increasing elevation. Diversity of functional groups also varied with elevation (e.g. saprotrophic fungi declined 83% of the time). Most studies (82%) found that climate and soils (especially pH) were the primary mechanisms driving shifts in composition, and drivers differed across taxa-fungi were mostly determined by climate, while bacteria (48%) and archaea (71%) were structured primarily by soils. We hypothesize that the central role of soils-which can vary independently of other abiotic and geographic gradients-in structuring microbial communities weakens diversity patterns expected on montane gradients. Moving forward, we need improved cross-study comparability of microbial diversity indices (i.e. standardizing sequencing) and more geographic replication using experiments to broaden our knowledge of microbial biogeography on global gradients.}, }
@article {pmid32778917, year = {2020}, author = {Gamez, RM and Ramirez, S and Montes, M and Cardinale, M}, title = {Complementary Dynamics of Banana Root Colonization by the Plant Growth-Promoting Rhizobacteria Bacillus amyloliquefaciens Bs006 and Pseudomonas palleroniana Ps006 at Spatial and Temporal Scales.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {656-668}, pmid = {32778917}, issn = {1432-184X}, support = {Public resources from Ministerio de Agricultura y Desarrollo Rural [Ministry of Agriculture and Rural Development] (MADR)//Corporación Colombiana de Investigación Agropecuaria - Agrosavia/ ; }, abstract = {Banana (Musa acuminata) growth for commercial purposes requires high amounts of chemical fertilizers, generating high costs and deleterious effects on the environment. In a previous study, we demonstrated that two plant growth-promoting rhizobacteria (PGPR), Bacillus amyloliquefaciens Bs006 and Pseudomonas palleroniana Ps006, isolated in Colombia, could partially replace chemical fertilizers for banana seedling growth. In a second work, the effects of the two inoculants on banana transcripts were found to occur at different times, earlier for Bs006 and later for Ps006. This leads to the hypothesis that the two rhizobacteria have different colonization dynamics. Accordingly, the aim of this work was to analyze the dynamics of root colonization of the two PGPR, Bs006 and Ps006, on banana growth over a time frame of 30 days. We used fluorescence in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM), followed by three-dimensional reconstruction and quantitative image analysis. Bacillus amyloliquefaciens Bs006 abundantly colonized banana roots earlier (from 1 to 48 h), ectophytically on the rhizoplane, and then decreased. Pseudomonas palleroniana Ps006 was initially scarce, but after 96 h it increased dramatically and became clearly endophytic. Here we identify and discuss the potential genetic factors responsible for this complementary behavior. This information is crucial for optimizing the formulation of an effective biofertilizer for banana and its inoculation strategy.}, }
@article {pmid32771820, year = {2020}, author = {Elhalis, H and Cox, J and Frank, D and Zhao, J}, title = {The crucial role of yeasts in the wet fermentation of coffee beans and quality.}, journal = {International journal of food microbiology}, volume = {333}, number = {}, pages = {108796}, doi = {10.1016/j.ijfoodmicro.2020.108796}, pmid = {32771820}, issn = {1879-3460}, abstract = {The objective of this study was to investigate the role of yeasts in the wet fermentation of coffee beans and their contribution to coffee quality using a novel approach. Natamycin (300 ppm) was added to the fermentation mass to suppress yeast growth and their metabolic activities, and the resultant microbial ecology, bean chemistry and sensory quality were analyzed and compared to non-treated spontaneous fermentation we reported previously. The yeast community was dominated by Hanseniaspora uvarum and Pichia kudriavzevii and grew to a maximum population of about 5.5 log CFU/g in the absence of Natamycin, while when Natamycin was added yeasts were suppressed. The major bacterial species in both the spontaneous and yeast-suppressed fermentations included the lactic acid bacteria Leuconostoc mesenteroides and Lactococcus lactis, the acetic acid bacteria Gluconobacter cerinus and Acetobacter persici and the Enterobacteriaceae Enterobacter, Citrobacter and Erwinia. For both fermentations, the mucilage layers were completely degraded by the end of the process and the absence of yeast activities had no significant impact on mucilage degradation. During fermentation, reducing sugars were consumed while lactic acid was accumulated inside the beans, and its concentration was significantly higher in the spontaneous fermentation (3 times) than that where yeasts were suppressed by Natamycin. Glycerol was detected with a concentration of 0.08% in the absence of Natamycin and was not identified when Natamycin was added. Green beans fermented with yeast growth contained a higher amount of isoamyl alcohol (21 times), ethanol (3.7 times), acetaldehyde (8 times), and ethyl acetate (25 times) compared to beans fermented in the absence of yeast activities, which remained higher in the former after roasting. Beans fermented without yeast activities had a mild fruity aroma, and lower sensory scores of fragrances (7.0), flavor (6.5), acidity (6.3), body (7.0) and overall score (6.5) compared to the former. These findings demonstrated the crucial roles of yeasts in wet fermentation of coffee beans and for producing high quality coffee.}, }
@article {pmid32770272, year = {2020}, author = {Thongprem, P and Davison, HR and Thompson, DJ and Lorenzo-Carballa, MO and Hurst, GDD}, title = {Incidence and Diversity of Torix Rickettsia-Odonata Symbioses.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01568-9}, pmid = {32770272}, issn = {1432-184X}, support = {CGL2008-02799//Ministerio de Ciencia e Innovación/ ; }, abstract = {Heritable microbes are an important component of invertebrate biology, acting both as beneficial symbionts and reproductive parasites. Whilst most previous research has focussed on the 'Wolbachia pandemic', recent work has emphasised the importance of other microbial symbionts. In this study, we present a survey of odonates (dragonflies and damselflies) for torix group Rickettsia, following previous research indicating that this clade can be common in other aquatic insect groups. PCR assays were used to screen a broad range of odonates from two continents and revealed 8 of 76 species tested were infected with Rickettsia. We then conducted further deeper screening of UK representatives of the Coenagrionidae damselfly family, revealing 6 of 8 UK coenagrionid species to be positive for torix Rickettsia. Analysis of Rickettsia gene sequences supported multiple establishments of symbiosis in the group. Some strains were shared between UK coenagrionid species that shared mtDNA barcodes, indicating a likely route for mitochondrial introgression between sister species. There was also evidence of coinfecting Rickettsia strains in two species. FISH analysis indicated Rickettsia were observed in the ovarioles, consistent with heritable symbiosis. We conclude that torix Rickettsia represent an important associate of odonates, being found in a broad range of species from both Europe and South America. There is evidence that coinfection can occur, vertical transmission is likely, and that symbiont movement following hybridisation may underpin the lack of 'barcoding gap' between well-established species pairs in the genus. Future work should establish the biological significance of the symbioses observed.}, }
@article {pmid32770154, year = {2020}, author = {Cichocki, N and Hübschmann, T and Schattenberg, F and Kerckhof, FM and Overmann, J and Müller, S}, title = {Bacterial mock communities as standards for reproducible cytometric microbiome analysis.}, journal = {Nature protocols}, volume = {15}, number = {9}, pages = {2788-2812}, doi = {10.1038/s41596-020-0362-0}, pmid = {32770154}, issn = {1750-2799}, mesh = {Bacteria/*cytology ; Computational Biology ; Cytological Techniques/*standards ; *Microbiota ; Reference Standards ; Reproducibility of Results ; }, abstract = {Flow cytometry has recently established itself as a tool to track short-term dynamics in microbial community assembly and link those dynamics with ecological parameters. However, instrumental configurations of commercial cytometers and variability introduced through differential handling of the cells and instruments frequently cause data set variability at the single-cell level. This is especially pronounced with microorganisms, which are in the lower range of optical resolution. Although alignment beads are valuable to generally minimize instrumental noise and align overall machine settings, an artificial microbial cytometric mock community (mCMC) is mandatory for validating lab workflows and enabling comparison of data between experiments, thus representing a necessary reference standard for the reproducible cytometric characterization of microbial communities, especially in long-term studies. In this study, the mock community consisted of two Gram-positive and two Gram-negative bacterial strains, which can be assembled with respective subsets of cells, including spores, in any selected ratio or concentration. The preparation of the four strains takes a maximum of 5 d, and the stains are storable with either PFA/ethanol fixation at -20 °C or drying at 4 °C for at least 6 months. Starting from this stock, an mCMC can be assembled within 1 h. Fluorescence staining methods are presented and representatively applied with two high-resolution cell sorters and three benchtop flow cytometers. Benchmarked data sets allow the use of bioinformatic evaluation procedures to decode community behavior or convey qualified cell sorting decisions for subsequent high-resolution sequencing or proteomic routines.}, }
@article {pmid32770005, year = {2020}, author = {Yang, S and Lv, Y and Liu, X and Wang, Y and Fan, Q and Yang, Z and Boon, N and Wang, F and Xiao, X and Zhang, Y}, title = {Genomic and enzymatic evidence of acetogenesis by anaerobic methanotrophic archaea.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {3941}, pmid = {32770005}, issn = {2041-1723}, mesh = {Acetates/*metabolism ; Anaerobiosis ; Archaea/*enzymology/genetics ; Bacterial Proteins/genetics/*metabolism ; Carbon Cycle/physiology ; Coenzyme A Ligases/genetics/*metabolism ; Genome, Archaeal ; Geologic Sediments/microbiology ; Metabolic Networks and Pathways/genetics ; Methane/*metabolism ; Oxidation-Reduction ; Seawater/microbiology ; }, abstract = {Anaerobic oxidation of methane (AOM) mediated by anaerobic methanotrophic archaea (ANME) is the primary process that provides energy to cold seep ecosystems by converting methane into inorganic carbon. Notably, cold seep ecosystems are dominated by highly divergent heterotrophic microorganisms. The role of the AOM process in supporting heterotrophic population remains unknown. We investigate the acetogenic capacity of ANME-2a in a simulated cold seep ecosystem using high-pressure biotechnology, where both AOM activity and acetate production are detected. The production of acetate from methane is confirmed by isotope-labeling experiments. A complete archaeal acetogenesis pathway is identified in the ANME-2a genome, and apparent acetogenic activity of the key enzymes ADP-forming acetate-CoA ligase and acetyl-CoA synthetase is demonstrated. Here, we propose a modified model of carbon cycling in cold seeps: during AOM process, methane can be converted into organic carbon, such as acetate, which further fuels the heterotrophic community in the ecosystem.}, }
@article {pmid32767092, year = {2020}, author = {Greer, JA and Swei, A and Vredenburg, VT and Zink, AG}, title = {Parental Care Alters the Egg Microbiome of Maritime Earwigs.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {920-934}, doi = {10.1007/s00248-020-01558-x}, pmid = {32767092}, issn = {1432-184X}, support = {IOS-1258133//National Science Foundation/ ; DBI-1427772//National Science Foundation/ ; DEB-1745411//National Science Foundation/ ; DEB-175037//National Science Foundation/ ; R25-GM059298//Foundation for the National Institutes of Health/ ; }, abstract = {Recruitment of beneficial microbes to protect offspring, often reducing the energetic costs of care, is now recognized as an important component of parental care in many animals. Studies on earwigs (order Dermaptera) have revealed that removal of females from egg tending increases mortality of eggs due to fungal infections, possibly caused by changes in the bacterial microbiome on the egg surface. We used a controlled female-removal experiment to evaluate whether female nest attendance in the maritime earwig, Anisolabis maritima, influences the bacterial microbiome on the egg surface. Further, we analyzed the microbiomes of mothers and their eggs to determine if there are a core set of bacteria transferred to eggs through female care. Microbiomes were analyzed using 16S rRNA bacterial DNA sequencing, revealing that bacterial operational taxonomic unit (OTU) richness and diversity were both significantly higher for female attended versus unattended eggs. The core microbiome of adult females contained bacteria which have the potential to carry anti-fungal characteristics; these bacteria were found in higher presence and relative abundance on eggs where females were allowed to provide care. These results demonstrate that female egg attendance significantly impacts the bacterial microbiome of A. maritima eggs, and identifies specific bacteria within the egg microbiome that should be investigated further for beneficial anti-fungal properties in this system.}, }
@article {pmid32767091, year = {2020}, author = {Vargas, S and Leiva, L and Wörheide, G}, title = {Short-Term Exposure to High-Temperature Water Causes a Shift in the Microbiome of the Common Aquarium Sponge Lendenfeldia chondrodes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01556-z}, pmid = {32767091}, issn = {1432-184X}, abstract = {Marine sponges harbor diverse microbiomes that contribute to their energetic and metabolic needs. Although numerous studies on sponge microbial diversity exist, relatively few focused on sponge microbial community changes under different sources of environmental stress. In this study, we assess the impact of elevated seawater temperature on the microbiome of cultured Lendenfeldia chondrodes, a coral reef sponge commonly found in marine aquaria. Lendenfeldia chondrodes exhibits high thermal tolerance showing no evidence of tissue damage or bleaching at 5 °C above control water temperature (26 °C). High-throughput sequencing of the bacterial 16S rRNA V4 region revealed a response of the microbiome of L. chondrodes to short-term exposure to elevated seawater temperature. Shifts in abundance and richness of the dominant bacterial phyla found in the microbiome of this species, namely Proteobacteria, Cyanobacteria, Planctomycetes, and Bacteroidetes, characterized this response. The observed resilience of L. chondrodes and the responsiveness of its microbiome to short-term increases in seawater temperature suggest that this holobiont may be capable of acclimating to anthropogenic-driven sublethal environmental stress via a re-accommodation of its associated bacterial community. This sheds a new light on the potential for resilience of some sponges to increasing surface seawater temperatures and associated projected regime shifts in coral reefs.}, }
@article {pmid32765428, year = {2020}, author = {Zhang, H and Sekar, R and Visser, PM}, title = {Editorial: Microbial Ecology in Reservoirs and Lakes.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1348}, pmid = {32765428}, issn = {1664-302X}, }
@article {pmid32763579, year = {2020}, author = {Gong, L and Wang, J and Abbas, T and Zhang, Q and Cai, M and Tahir, M and Wu, D and Di, H}, title = {Immobilization of exchangeable Cd in soil using mixed amendment and its effect on soil microbial communities under paddy upland rotation system.}, journal = {Chemosphere}, volume = {262}, number = {}, pages = {127828}, doi = {10.1016/j.chemosphere.2020.127828}, pmid = {32763579}, issn = {1879-1298}, abstract = {Cadmium (Cd) pollution is a widespread environmental problem that decreases crop production, destroys the microbial ecology of soil, and poses a severe risk to human health. Organo-chemical amendment is a cost-effective, eco-friendly, and community-acceptable widely applied an in situ technique for metal-contaminated farmland. In this study, we mixed lime, zeolite, calcium magnesium phosphate fertilizer, and biochar in a mixture ratio of 71:23:5:1 to form a mixed amendment. Field and laboratory experiments were conducted to study the effects of the mixed amendment on soil exchangeable Cd content, plant Cd accumulation, and soil microbial community. It was found that the application of 0.5% mixed amendment decreased exchangeable soil Cd by more than 85% and 64% in wheat and rice season, respectively, compared with control (CK), without increasing pH. Moreover, the application of 0.5% mixed amendment decreased Cd accumulation in grains by 22.9% and 41.2% in wheat and rice season, respectively, compared to CK. The result of phospholipid fatty acids (PLFAs) shows that the level of soil microbial diversity and species richness under mixed amendment treatments were higher than in lime treatment, indicating more copiotrophic conditions and faster rate of nutrient turnover in mixed amendment than pure lime treatment. Hence, it concluded that the mixed amendment has a strong effect on fixing exchangeable soil Cd and reducing the accumulation of Cd in crops. Finally, it was observed that the mixed amendment improved the soil microbial community structure and accelerate the rate of nutrient turnover by microbes under this favorable condition comparative to individual treatments.}, }
@article {pmid32761502, year = {2020}, author = {Herrmann, M and Geesink, P and Richter, R and Küsel, K}, title = {Canopy Position Has a Stronger Effect than Tree Species Identity on Phyllosphere Bacterial Diversity in a Floodplain Hardwood Forest.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01565-y}, pmid = {32761502}, issn = {1432-184X}, support = {FZT 118//Deutsche Forschungsgemeinschaft/ ; CRC1076 AquaDiva//Deutsche Forschungsgemeinschaft/ ; }, abstract = {The phyllosphere is a challenging microbial habitat in which microorganisms can flourish on organic carbon released by plant leaves but are also exposed to harsh environmental conditions. Here, we assessed the relative importance of canopy position-top, mid, and bottom at a height between 31 and 20 m-and tree species identity for shaping the phyllosphere microbiome in a floodplain hardwood forest. Leaf material was sampled from three tree species-maple (Acer pseudoplatanus L.), oak (Quercus robur L.), and linden (Tilia cordata MILL.)-at the Leipzig canopy crane facility (Germany). Estimated bacterial species richness (Chao1) and bacterial abundances approximated by quantitative PCR of 16S rRNA genes exhibited clear vertical trends with a strong increase from the top to the mid and bottom position of the canopy. Thirty operational taxonomic units (OTUs) formed the core microbiome, which accounted for 77% of all sequence reads. These core OTUs showed contrasting trends in their vertical distribution within the canopy, pointing to different ecological preferences and tolerance to presumably more extreme conditions at the top position of the canopy. Co-occurrence analysis revealed distinct tree species-specific OTU networks, and 55-57% of the OTUs were unique to each tree species. Overall, the phyllosphere microbiome harbored surprisingly high fractions of Actinobacteria of up to 66%. Our results clearly demonstrate strong effects of the position in the canopy on phyllosphere bacterial communities in a floodplain hardwood forest and-in contrast to other temperate or tropical forests-a strong predominance of Actinobacteria.}, }
@article {pmid32761501, year = {2020}, author = {Dos Passos, JH and Maia, LC and de Assis, DMA and da Silva, JA and Oehl, F and da Silva, IR}, title = {Arbuscular Mycorrhizal Fungal Community Structure in the Rhizosphere of Three Plant Species of Crystalline and Sedimentary Areas in the Brazilian Dry Forest.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01557-y}, pmid = {32761501}, issn = {1432-184X}, support = {420.129/2018-9; 307.129/2015-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 100.900/2018-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; Financie Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; IBPG-0010-2.03/18//Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco/ ; APV-0014-2.03/19//Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco/ ; }, abstract = {The Brazilian dry forest (Caatinga) is located in one of the world's largest tropical semiarid regions, and it occurs on two large geological environments named the crystalline and sedimentary basins. In order to determine the structure and the main drivers of the composition of communities of arbuscular mycorrhizal fungi (AMF) in the Caatinga, we collected soil samples from the rhizosphere of Jatropha mollissima, J. mutabilis, and Mimosa tenuiflora, species that occur in crystalline and sedimentary areas. Ninety-six AMF taxa were identified from soils collected directly in the field and trap cultures. Acaulospora, Glomus, and Rhizoglomus represented almost 49% of the taxon richness. The composition of the AMF communities differed between the crystalline and sedimentary areas and between the rhizospheres of the three plant species. Coarse sand, total sand, natural clay, calcium, soil particles density, flocculation, pH, and base saturation were the principal edaphic variables related to the distribution of these organisms. We registered nine and 17 AMF species classified as indicators, for the geological environments and plant species, respectively. Glomerospores of Glomerales predominated in crystalline basins, whereas glomerospores of Gigasporales prevailed in sedimentary areas; among the plant species, lower number of glomerospores of Archaeosporales and Glomerales was recorded in the rhizosphere of J. mollissima. The results show that the AMF community composition is shaped by geological environments and plant hosts. In addition, soil characteristics, mainly physical attributes, significantly influence the structure of Glomeromycota communities occurring in areas of the Brazilian semiarid.}, }
@article {pmid32760678, year = {2020}, author = {Celis Ramírez, AM and Amézquita, A and Cardona Jaramillo, JEC and Matiz-Cerón, LF and Andrade-Martínez, JS and Triana, S and Mantilla, MJ and Restrepo, S and Barrios, AFG and de Cock, H}, title = {Analysis of Malassezia Lipidome Disclosed Differences Among the Species and Reveals Presence of Unusual Yeast Lipids.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {338}, pmid = {32760678}, issn = {2235-2988}, abstract = {Malassezia yeasts are lipid dependent and part of the human and animal skin microbiome. However, they are also associated with a variety of dermatological conditions and even cause systemic infections. How these yeasts can live as commensals on the skin and switch to a pathogenic stage has long been a matter of debate. Lipids are important cellular molecules, and understanding the lipid metabolism and composition of Malassezia species is crucial to comprehending their biology and host-microbe interaction. Here, we investigated the lipid composition of Malassezia strains grown to the stationary phase in a complex Dixon medium broth. In this study, we perform a lipidomic analysis of a subset of species; in addition, we conducted a gene prediction analysis for the detection of lipid metabolic proteins. We identified 18 lipid classes and 428 lipidic compounds. The most commonly found lipids were triglycerides (TAG), sterol (CH), diglycerides (DG), fatty acids (FAs), phosphatidylcholine (PC), phosphatidylethanolamine (PE), ceramides, cholesteryl ester (CE), sphingomyelin (SM), acylcarnitine, and lysophospholipids. Particularly, we found a low content of CEs in Malassezia furfur, atypical M. furfur, and Malassezia pachydermatis and undetectable traces of these components in Malassezia globosa, Malassezia restricta, and Malassezia sympodialis. Remarkably, uncommon lipids in yeast, like diacylglyceryltrimethylhomoserine and FA esters of hydroxyl FAs, were found in a variable concentration in these Malassezia species. The latter are bioactive lipids recently reported to have antidiabetic and anti-inflammatory properties. The results obtained can be used to discriminate different Malassezia species and offer a new overview of the lipid composition of these yeasts. We could confirm the presence and the absence of certain lipid-biosynthesis genes in specific species. Further analyses are necessary to continue disclosing the complex lipidome of Malassezia species and the impact of the lipid metabolism in connection with the host interaction.}, }
@article {pmid32760379, year = {2020}, author = {Podar, PT and Yang, Z and Björnsdóttir, SH and Podar, M}, title = {Comparative Analysis of Microbial Diversity Across Temperature Gradients in Hot Springs From Yellowstone and Iceland.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1625}, pmid = {32760379}, issn = {1664-302X}, abstract = {Geothermal hot springs are a natural setting to study microbial adaptation to a wide range of temperatures reaching up to boiling. Temperature gradients lead to distinct microbial communities that inhabit their optimum niches. We sampled three alkaline, high temperature (80-100°C) hot springs in Yellowstone and Iceland that had cooling outflows and whose microbial communities had not been studied previously. The microbial composition in sediments and mats was determined by DNA sequencing of rRNA gene amplicons. Over three dozen phyla of Archaea and Bacteria were identified, representing over 1700 distinct organisms. We observed a significant non-linear reduction in the number of microbial taxa as the temperature increased from warm (38°C) to boiling. At high taxonomic levels, the community structure was similar between the Yellowstone and Iceland hot springs. We identified potential endemism at the genus level, especially in thermophilic phototrophs, which may have been potentially driven by distinct environmental conditions and dispersal limitations.}, }
@article {pmid32757814, year = {2020}, author = {Zhu, Y and Guo, J}, title = {Impact of dichlorprop on soil microbial community structure and diversity during its enantioselective biodegradation in agricultural soils.}, journal = {Journal of environmental science and health. Part. B, Pesticides, food contaminants, and agricultural wastes}, volume = {}, number = {}, pages = {1-9}, doi = {10.1080/03601234.2020.1802186}, pmid = {32757814}, issn = {1532-4109}, abstract = {Enantioselective biodegradation of racemic dichlorprop in two soils was investigated in the laboratory. Chiral separation of racemic dichlorprop was achieved by using HPLC with Phenomenex Lux Amylose-2. The first-order kinetic model fitted well the dissipation data of racemic dichlorprop and its pure R- and S-enantiomers. S-dichlorprop was preferentially degraded in both soils and enantioselectivity was affected by soil pH. The half-lives (DT50) of S-dichlorprop were 8.22 days in soil A and 8.06 days in soil D, while R-dichlorprop was more persistent with DT50 of 12.93 days in soil A and 12.38 days in soil D, respectively. Dichlorprop dissipated faster in soil D with lower organic matter content. In sterilized soils, neglected dissipation was observed and enantiomer fraction values remained constant, indicating that the enantioselective degradation was mainly controlled by soil microorganisms. Soil microbial community structure and diversity was assessed by Illumina MiSeq sequencing of 16S rRNA genes from dichlorprop and no dichlorprop contaminated microcosms. Compared with controls, dichlorprop application had no significant effect on microbial community structures at phylum level, but increased bacterial diversity and dichlorprop degradation related taxa in both soils. S-dichlorprop preferential degradation might be attributed to the S-enantiomer preferred degraders in the family of Sphingomonadaceae.}, }
@article {pmid32757488, year = {2020}, author = {Xu, Y and Tandon, R and Ancheta, C and Arroyo, P and Gilbert, JA and Stephens, B and Kelley, ST}, title = {Quantitative profiling of built environment bacterial and fungal communities reveals dynamic material dependent growth patterns and microbial interactions.}, journal = {Indoor air}, volume = {}, number = {}, pages = {}, doi = {10.1111/ina.12727}, pmid = {32757488}, issn = {1600-0668}, support = {F32 GM020013/GM/NIGMS NIH HHS/United States ; R01 HD095412/HD/NICHD NIH HHS/United States ; //Alfred P. Sloan Foundation/ ; }, abstract = {Indoor microbial communities vary in composition and diversity depending on material type, moisture levels, and occupancy. In this study, we integrated bacterial cell counting, fungal biomass estimation, and fluorescence-assisted cell sorting (FACS) with amplicon sequencing of bacterial (16S rRNA) and fungal (ITS) communities to investigate the influence of wetting on medium density fiberboard (MDF) and gypsum wallboard. Surface samples were collected longitudinally from wetted materials maintained at high relative humidity (~95%). Bacterial and fungal growth patterns were strongly time-dependent and material-specific. Fungal growth phenotypes differed between materials: spores dominated MDF surfaces while fungi transitioned from spores to hyphae on gypsum. FACS confirmed that most of the bacterial cells were intact (viable) on both materials over the course of the study. Integrated cell count and biomass data (quantitative profiling) revealed that small changes in relative abundance often resulted from large changes in absolute abundance, while negative correlations in relative abundances were explained by rapid growth of only one group of bacteria or fungi. Comparisons of bacterial-bacterial and fungal-bacterial networks suggested a top-down control of fungi on bacterial growth, possibly via antibiotic production. In conclusion, quantitative profiling provides novel insights into microbial growth dynamics on building materials with potential implications for human health.}, }
@article {pmid32756341, year = {2020}, author = {Sierra, MA and Li, Q and Pushalkar, S and Paul, B and Sandoval, TA and Kamer, AR and Corby, P and Guo, Y and Ruff, RR and Alekseyenko, AV and Li, X and Saxena, D}, title = {The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community.}, journal = {Genes}, volume = {11}, number = {8}, pages = {}, pmid = {32756341}, issn = {2073-4425}, support = {CA206105/NH/NIH HHS/United States ; DE025992/NH/NIH HHS/United States ; DE027074/NH/NIH HHS/United States ; NYU Mega grant initiative//New York University/ ; }, abstract = {There is currently no criterion to select appropriate bioinformatics tools and reference databases for analysis of 16S rRNA amplicon data in the human oral microbiome. Our study aims to determine the influence of multiple tools and reference databases on α-diversity measurements and β-diversity comparisons analyzing the human oral microbiome. We compared the results of taxonomical classification by Greengenes, the Human Oral Microbiome Database (HOMD), National Center for Biotechnology Information (NCBI) 16S, SILVA, and the Ribosomal Database Project (RDP) using Quantitative Insights Into Microbial Ecology (QIIME) and the Divisive Amplicon Denoising Algorithm (DADA2). There were 15 phyla present in all of the analyses, four phyla exclusive to certain databases, and different numbers of genera were identified in each database. Common genera found in the oral microbiome, such as Veillonella, Rothia, and Prevotella, are annotated by all databases; however, less common genera, such as Bulleidia and Paludibacter, are only annotated by large databases, such as Greengenes. Our results indicate that using different reference databases in 16S rRNA amplicon data analysis could lead to different taxonomic compositions, especially at genus level. There are a variety of databases available, but there are no defined criteria for data curation and validation of annotations, which can affect the accuracy and reproducibility of results, making it difficult to compare data across studies.}, }
@article {pmid32754956, year = {2020}, author = {Morimoto, D and Šulčius, S and Yoshida, T}, title = {Viruses of freshwater bloom-forming cyanobacteria: genomic features, infection strategies and coexistence with the host.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.12872}, pmid = {32754956}, issn = {1758-2229}, support = {//Bilateral Open Partnership Joint Research Project/ ; 16H06437//JSPS Scientific Research on Innovative Areas/ ; 203143100025//The Canon Foundation/ ; //Research Council of Lithuania/ ; S-MIP-17-28//Japan Society for the Promotion of Science/ ; 17H03850//Japan Society for the Promotion of Science/ ; }, abstract = {Freshwater bloom-forming cyanobacteria densely grow in the aquatic environments, leading to an increase in the viral-contact rate. They possess numerous antiviral genes, as well as cell differentiation- and physiological performance-related genes, owing to genome expansion. Their genomic features and unique lifestyles suggest that they coexist with cyanoviruses in ways different from marine cyanobacteria. Furthermore, genome contents of isolated freshwater bloom-forming cyanobacterial viruses have little in common with those of marine cyanoviruses studied to date. They lack the marine cyanoviral hallmark genes that sustain photosynthetic activity and redirect host metabolism to viral reproduction; therefore, they are predicted to share metabolisms and precursor pools with host cyanobacteria to ensure efficient viral reproduction and avoid nutrient deficiencies and antiviral response. Additionally, cyanovirus-cyanobacteria coexistence strategies may change as bloom density increases. Diverse genotypic populations of cyanoviruses and hosts coexist and fluctuate under high viral-contact rate conditions, leading to their rapid coevolution through antiviral responses. The ancestral and newly evolved genotypes coexist, thereby expanding the diversity levels of host and viral populations. Bottleneck events occurring due to season-related decreases in bloom-forming species abundance provide each genotype within cyanobacterial population an equal chance to increase in prevalence during the next bloom and enhance further diversification.}, }
@article {pmid32751149, year = {2020}, author = {Marsaux, B and Van den Abbeele, P and Ghyselinck, J and Prioult, G and Marzorati, M and Bogićević, B}, title = {Synbiotic Effect of Bifidobacterium lactis CNCM I-3446 and Bovine Milk-Derived Oligosaccharides on Infant Gut Microbiota.}, journal = {Nutrients}, volume = {12}, number = {8}, pages = {}, pmid = {32751149}, issn = {2072-6643}, abstract = {BACKGROUND: This study evaluated the impact of Bifidobacterium animalis ssp. lactis CNCM I-3446, Bovine Milk-derived OligoSaccharides (BMOS) and their combination on infant gut microbiota in vitro. In addition, a novel strategy consisting of preculturing B. lactis with BMOS to further enhance their potential synbiotic effects was assessed.<br><br>METHOD: Short-term fecal batch fermentations (48 h) were used to assess the microbial composition and activity modulated by BMOS alone, B. lactis grown on BMOS or dextrose alone, or their combinations on different three-month-old infant microbiota.<br><br>RESULTS: BMOS alone significantly induced acetate and lactate production (leading to pH decrease) and stimulated bifidobacterial growth in 10 donors. A further in-depth study on two different donors proved B. lactis ability to colonize the infant microbiota, regardless of the competitiveness of the environment. BMOS further enhanced this engraftment, suggesting a strong synbiotic effect. This was also observed at the microbiota activity level, especially in a donor containing low initial levels of bifidobacteria. In this donor, preculturing B. lactis with BMOS strengthened further the early modulation of microbiota activity observed after 6 h.<br><br>CONCLUSION: This study demonstrated the strong synbiotic effect of BMOS and B. lactis on the infant gut microbiota, and suggests a strategy to improve its effectiveness in an otherwise low-Bifidobacterium microbiota.}, }
@article {pmid32748335, year = {2020}, author = {Maal-Bared, R}, title = {Operational impacts of heavy metals on activated sludge systems: the need for improved monitoring.}, journal = {Environmental monitoring and assessment}, volume = {192}, number = {9}, pages = {560}, doi = {10.1007/s10661-020-08529-2}, pmid = {32748335}, issn = {1573-2959}, mesh = {Environmental Monitoring ; Metals, Heavy/*analysis ; *Microbiota ; Sewage ; Waste Water/analysis ; }, abstract = {Biological nutrient removal is highly reliant on maintaining a heterogeneous, balanced, and metabolically active microbial community that can adapt to the fluctuating composition of influent wastewater and encompassing environmental conditions. Maintaining this balance can be challenging in municipal wastewater systems that sporadically receive wastewater from industrial facilities due to the impact of heavy metals and other contaminants on the microbial ecology of the activated sludge. A thorough understanding of the impacts of heavy metals on activated sludge and of practical monitoring options is needed to support decision-making at the wastewater utility level. This paper is divided into two parts. In the first part, the review explains what happens when heavy metals interact with activated sludge systems by highlighting biosorption and bioaccumulation processes, and when an activated sludge system switches from bioaccumulation to toxic shock. Here, it also summarizes the impacts of heavy metal exposure on plant performance. In the second part, the review summarizes practical approaches that can be used at the plant outside the realm of traditional toxicological bioassays testing to determine the possible impacts of influent heavy metal concentrations on the BNR process. These approaches include the following: monitoring operational parameters for major shifts; respirometry; microscopy; ATP; chemical analyses of heavy metals with a focus on synergistic impacts and inhibitory limits; and other novel approaches, such as EPS chemical analyses, molecular techniques, and quorum sensing.}, }
@article {pmid32747713, year = {2020}, author = {Pieper, R and Dadi, TH and Pieper, L and Vahjen, W and Franke, A and Reinert, K and Zentek, J}, title = {Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire.}, journal = {The ISME journal}, volume = {14}, number = {11}, pages = {2783-2793}, doi = {10.1038/s41396-020-0730-3}, pmid = {32747713}, issn = {1751-7370}, abstract = {Despite a well-documented effect of high dietary zinc oxide on the pig intestinal microbiota composition less is it yet known about changes in microbial functional properties or the effect of organic zinc sources. Forty weaning piglets in four groups were fed diets supplemented with 40 or 110 ppm zinc as zinc oxide, 110 ppm as Zn-Lysinate, or 2500 ppm as zinc oxide. Host zinc homeostasis, intestinal zinc fractions, and ileal nutrient digestibility were determined as main nutritional and physiological factors putatively driving colon microbial ecology. Metagenomic sequencing of colon microbiota revealed only clear differences at genus level for the group receiving 2500 ppm zinc oxide. However, a clear group differentiation according to dietary zinc concentration and source was observed at species level. Functional analysis revealed significant differences in genes related to stress response, mineral, and carbohydrate metabolism. Taxonomic and functional gene differences were accompanied with clear effects in microbial metabolite concentration. Finally, a selection of certain antibiotic resistance genes by dietary zinc was observed. This study sheds further light onto the consequences of concentration and chemical form of dietary zinc on microbial ecology measures and the resistome in the porcine colon.}, }
@article {pmid32747679, year = {2020}, author = {Hach, PF and Marchant, HK and Krupke, A and Riedel, T and Meier, DV and Lavik, G and Holtappels, M and Dittmar, T and Kuypers, MMM}, title = {Rapid microbial diversification of dissolved organic matter in oceanic surface waters leads to carbon sequestration.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {13025}, pmid = {32747679}, issn = {2045-2322}, support = {EXC-2077-390741603//Deutsche Forschungsgemeinschaft/ ; }, abstract = {The pool of dissolved organic matter (DOM) in the deep ocean represents one of the largest carbon sinks on the planet. In recent years, studies have shown that most of this pool is recalcitrant, because individual compounds are present at low concentrations and because certain compounds seem resistant to microbial degradation. The formation of the diverse and recalcitrant deep ocean DOM pool has been attributed to repeated and successive processing of DOM by microorganisms over time scales of weeks to years. Little is known however, about the transformation and cycling that labile DOM undergoes in the first hours upon its release from phytoplankton. Here we provide direct experimental evidence showing that within hours of labile DOM release, its breakdown and recombination with ambient DOM leads to the formation of a diverse array of new molecules in oligotrophic North Atlantic surface waters. Furthermore, our results reveal a preferential breakdown of N and P containing molecules versus those containing only carbon. Hence, we show the preferential breakdown and molecular diversification are the crucial first steps in the eventual formation of carbon rich DOM that is resistant to microbial remineralization.}, }
@article {pmid32747621, year = {2020}, author = {Guerra, CA and Heintz-Buschart, A and Sikorski, J and Chatzinotas, A and Guerrero-Ramírez, N and Cesarz, S and Beaumelle, L and Rillig, MC and Maestre, FT and Delgado-Baquerizo, M and Buscot, F and Overmann, J and Patoine, G and Phillips, HRP and Winter, M and Wubet, T and Küsel, K and Bardgett, RD and Cameron, EK and Cowan, D and Grebenc, T and Marín, C and Orgiazzi, A and Singh, BK and Wall, DH and Eisenhauer, N}, title = {Blind spots in global soil biodiversity and ecosystem function research.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {3870}, pmid = {32747621}, issn = {2041-1723}, mesh = {Animals ; Bacteria/classification/metabolism ; *Biodiversity ; Biomass ; Climate ; *Ecosystem ; Fungi/classification/metabolism ; Geography ; Hydrogen-Ion Concentration ; Nematoda/classification/metabolism ; Oligochaeta/classification/metabolism ; Soil/chemistry/*parasitology ; *Soil Microbiology ; Temperature ; }, abstract = {Soils harbor a substantial fraction of the world's biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil taxa and ecosystem functioning data across soil macroecological studies and 17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research.}, }
@article {pmid32744986, year = {2020}, author = {Siebert, A and Huptas, C and Wenning, M and Scherer, S and Doll, EV}, title = {Fundicoccus ignavus gen. nov., sp. nov., a novel genus of the family Aerococcaceae isolated from bulk tank milk.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {8}, pages = {4774-4781}, doi = {10.1099/ijsem.0.004344}, pmid = {32744986}, issn = {1466-5034}, mesh = {Aerococcaceae/*classification/isolation &amp; purification ; Animals ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Glycolipids/chemistry ; Milk/*microbiology ; Peptidoglycan/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Three strains of a Gram-stain-positive, catalase-negative, facultative anaerobic, and coccoid species were isolated from German bulk tank milk. Phylogenetic analyses based on the 16S rRNA gene sequences indicated that the three strains (WS4937T, WS4759 and WS5303) constitute an independent phylogenetic lineage within the family Aerococcaceae with Facklamia hominis CCUG 36813T (93.7-94.1 %) and Eremococcus coleocola M1831/95/2T (93.5 %) as most closely related type species. The unclassified strains demonstrated variable growth with 6.5 % (w/v) NaCl and tolerated pH 6.5-9.5. Growth was observed from 12 to 39 °C. Their cell-wall peptidoglycan belongs to the A1α type (l-Lys-direct) consisting of alanine, glutamic acid and lysine. The predominant fatty acids were C16 : 1 ω9c, C16 : 0 and C18 : 1 ω9c and in the polar lipids profile three glycolipids, a phospholipid, phosphatidylglycerol, phosphoglycolipid and diphosphatidylglycerol were found. The G+C content of strain WS4937T was 37.4 mol% with a genome size of ~3.0 Mb. Based on phylogenetic, phylogenomic and biochemical characterizations, the isolates can be demarcated from all other genera of the family Aerococcaceae and, therefore, the novel genus Fundicoccus gen. nov. is proposed. The type species of the novel genus is Fundicoccus ignavus gen. nov., sp. nov. WS4937T (=DSM 109652T=LMG 31441T).}, }
@article {pmid32742267, year = {2020}, author = {Breitenwieser, F and Doll, EV and Clavel, T and Scherer, S and Wenning, M}, title = {Complementary Use of Cultivation and High-Throughput Amplicon Sequencing Reveals High Biodiversity Within Raw Milk Microbiota.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1557}, pmid = {32742267}, issn = {1664-302X}, abstract = {Raw milk microbiota are complex communities with a significant impact on the hygienic, sensory and technological quality of milk products. However, there is a lack of knowledge on factors determining their composition. In the present study, four bulk tank milk samples of two farms at two different time points were analyzed in detail for their microbiota using cultivation and 16S rRNA amplicon sequencing. Diversity in samples from the first time point was assessed via cultivation of 500 aerobic mesophilic bacterial isolates in each sample. A high biodiversity of 70 and 110 species per sample was determined, of which 25-28% corresponded to yet unknown taxa. The isolates were dominated by Gram-positive members of the genera Staphylococcus, Corynebacterium, Streptococcus, or Janibacter, whilst Chryseobacterium and Acinetobacter were most abundant among the Gram-negative taxa. At the second time point, samples of the same farms were analyzed via both cultivation (1,500 individual colonies each) and high-throughput 16S rRNA gene amplicon sequencing. The latter revealed a threefold higher biodiversity at the genus level, as anaerobic or fastidious species were also detected. However, cultivation identified genera not captured by sequencing, indicating that both approaches are complementary. Using amplicon sequencing, the relative abundance of a few genera was distorted, which seems to be an artifact of sample preparation. Therefore, attention needs to be paid to the library preparation procedure with special emphasis on cell lysis and PCR.}, }
@article {pmid32740757, year = {2020}, author = {Bose, T and Wingfield, MJ and Roux, J and Vivas, M and Burgess, TI}, title = {Phytophthora Species Associated with Roots of Native and Non-native Trees in Natural and Managed Forests.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01563-0}, pmid = {32740757}, issn = {1432-184X}, abstract = {Roots act as a biological filter that exclusively allows only a portion of the soil-associated microbial diversity to infect the plant. This microbial diversity includes organisms both beneficial and detrimental to plants. Phytophthora species are among the most important groups of detrimental microbes that cause various soil-borne plant diseases. We used a metabarcoding approach with Phytophthora-specific primers to compare the diversity and richness of Phytophthora species associated with roots of native and non-native trees, using different types of soil inocula collected from native and managed forests. Specifically, we analysed (1) roots of two non-native tree species (Eucalyptus grandis and Acacia mearnsii) and native trees, (2) roots of two non-native tree species from an in vivo plant baiting trial, (3) roots collected from the field versus those from the baiting trial, and (4) roots and soil samples collected from the field. The origin of the soil and the interaction between root and soil significantly influenced Phytophthora species richness. Moreover, species richness and community composition were significantly different between the field root samples and field soil samples with a higher number of Phytophthora species in the soil than in the roots. The results also revealed a substantial and previously undetected diversity of Phytophthora species from South Africa.}, }
@article {pmid32740714, year = {2020}, author = {Xian, L and Wan, T and Cao, Y and Sun, J and Wu, T and Apudo, AA and Li, W and Liu, F}, title = {Structural Variability and Functional Prediction in the Epiphytic Bacteria Assemblies of Myriophyllum spicatum.}, journal = {Current microbiology}, volume = {77}, number = {11}, pages = {3582-3594}, doi = {10.1007/s00284-020-02139-4}, pmid = {32740714}, issn = {1432-0991}, support = {31370262//National Natural Science Foundation of China/ ; 31670368//National Natural Science Foundation of China/ ; 31670369//National Natural Science Foundation of China/ ; 31500296//National Natural Science Foundation of China/ ; 2016YFA0601001//National Key R &amp; D Program of China/ ; }, abstract = {The underlying principles influencing bacteria community assembly have long been of interest in the field of microbial ecology. Environmental heterogeneity is believed to be important in controlling the uniqueness and variability of communities. However, little is known about the influence of the host macrophytes on epiphytic bacteria assembly. In this study, we used two contrasting artificial water environments (eutrophic and oligotrophic) for reciprocal transplant experiment of Myriophyllum spicatum to examine the colonization of epiphytic bacteria accompanied with plants growth. Comparative analysis addressed a higher species diversity in epiphytic bacteria than in bacterioplankton, and the highest microbiome richness in sediment. Our data revealed that the organization of epiphytic bacterial community was affected by both plant status (i.e. branch number, net photosynthesis rate etc.) and water bodies (i.e. total phosphate, total nitrogen, pH etc.). Moreover, plant status effected the assembly in priority to water. 16S rRNA gene sequencing further indicated that the epiphytic assemblies were motivated by functionalization and interplay with hosts as a whole. The results complemented new evidences for the 'lottery process' in the epiphytic bacteria assembly traits and shed insights into the assembly patterns referring to functional adaptation across epiphytic bacteria and macrophytes.}, }
@article {pmid32739699, year = {2020}, author = {De Paepe, J and De Paepe, K and Gòdia, F and Rabaey, K and Vlaeminck, SE and Clauwaert, P}, title = {Bio-electrochemical COD removal for energy-efficient, maximum and robust nitrogen recovery from urine through membrane aerated nitrification.}, journal = {Water research}, volume = {185}, number = {}, pages = {116223}, doi = {10.1016/j.watres.2020.116223}, pmid = {32739699}, issn = {1879-2448}, abstract = {Resource recovery from source-separated urine can shorten nutrient cycles on Earth and is essential in regenerative life support systems for deep-space exploration. In this study, a robust two-stage, energy-efficient, gravity-independent urine treatment system was developed to transform fresh real human urine into a stable nutrient solution. In the first stage, up to 85% of the COD was removed in a microbial electrolysis cell (MEC), converting part of the energy in organic compounds (27-46%) into hydrogen gas and enabling full nitrogen recovery by preventing nitrogen losses through denitrification in the second stage. Besides COD removal, all urea was hydrolysed in the MEC, resulting in a stream rich in ammoniacal nitrogen and alkalinity, and low in COD. This stream was fed into a membrane-aerated biofilm reactor (MABR) in order to convert the volatile and toxic ammoniacal nitrogen to non-volatile nitrate by nitrification. Bio-electrochemical pre-treatment allowed to recover all nitrogen as nitrate in the MABR at a bulk-phase dissolved oxygen level below 0.1 mg O2 L-1. In contrast, feeding the MABR directly with raw urine (omitting the first stage), at the same nitrogen loading rate, resulted in nitrogen loss (18%) due to denitrification. The MEC and MABR were characterised by very distinct and diverse microbial communities. While (strictly) anaerobic genera, such as Geobacter (electroactive bacteria), Thiopseudomonas, a Lentimicrobiaceae member, Alcaligenes and Proteiniphilum prevailed in the MEC, the MABR was dominated by aerobic genera, including Nitrosomonas (a known ammonium oxidiser), Moheibacter and Gordonia. The two-stage approach yielded a stable nitrate-rich, COD-low nutrient solution, suitable for plant and microalgae cultivation.}, }
@article {pmid32737846, year = {2020}, author = {Adeleke, BS and Babalola, OO}, title = {The endosphere microbial communities, a great promise in agriculture.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10123-020-00140-2}, pmid = {32737846}, issn = {1618-1905}, support = {123634//National Research Foundation/ ; }, abstract = {Agricultural food production and sustainability need intensification to address the current global food supply to meet human demand. The continuous human population increase and other anthropogenic activities threaten food security. Agrochemical inputs have long been used in conventional agricultural systems to boost crop productivity, but they are disadvantageous to a safe environment. Towards developing environmentally friendly agriculture, efforts are being directed in exploring biological resources from soil and plant microbes. The survival of the rhizosphere and endosphere microbiota is influenced by biotic and abiotic factors. Plant microbiota live interdependently with the host plants. Endophytes are regarded as colonizer microbes inhabiting and establishing microbial communities within the plant tissue. Their activities are varied and include fixing atmospheric nitrogen, solubilizing phosphate, synthesis of siderophores, secretion of metabolite-like compounds containing active biocontrol agents in the control of phytopathogens, and induced systemic resistance that stimulates plant response to withstand stress. Exploring beneficial endophyte resources in the formulation of bio-inoculants, such as biofertilizers, as an alternative to agrochemicals (fertilizers and pesticides) in developing environmentally friendly agriculture and for incorporation into crop breeding and disease control program is promising. Therefore, in this review, endosphere microbial ecology, associating environmental factors, and their roles that contribute to their effectiveness in promoting plant growth for maximum agricultural crop productivity were highlighted.}, }
@article {pmid32737539, year = {2020}, author = {Takamatsu, T and Arai, H and Abe, N and Nakai, M and Kunimi, Y and Inoue, MN}, title = {Coexistence of Two Male-Killers and Their Impact on the Development of Oriental Tea Tortrix Homona magnanima.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01566-x}, pmid = {32737539}, issn = {1432-184X}, support = {24580076//Japan Society for the Promotion of Science/ ; 19J13123//Japan Society for the Promotion of Science/ ; }, abstract = {Male-killing, the death of male offspring induced by maternally transmitted microbes, is classified as early, or late, male-killing. The primary advantage afforded by early male-killing, which typically occurs during embryogenesis, is the reallocation of resources to females, that would have otherwise been consumed by males. Meanwhile, the key advantage of late male-killing, which typically occurs during late larval development, is the maximized potential for horizontal transmission. To date, no studies have reported on the associated developmental and physiological effects of host coinfection with early and late male-killers, which may have a significant impact on the population dynamics of the male-killers. Here we used a lepidopteran tea pest Homona magnanima as a model, which is a unique system wherein an early male-killer (a Spiroplasma bacterium) and a late male-killer (an RNA virus) can coexist in nature. An artificially established matriline, coinfected with both Spiroplasma and RNA virus, exhibited embryonic death (early male-killing) as seen in the host line singly infected with Spiroplasma. Moreover, the coinfected line also exhibited developmental retardation and low pupal weight similar to the host line singly infected with the RNA virus. A series of field surveys revealed that Spiroplasma-RNA virus coinfection occurs in nature at a low frequency. Hence, although the two male-killers are capable of coexisting within the H. magnanima population independently, high associated fitness cost appears to limit the prevalence of male-killer coinfection in the field host population.}, }
@article {pmid32737538, year = {2020}, author = {Stone, BWG and Jackson, CR}, title = {Seasonal Patterns Contribute More Towards Phyllosphere Bacterial Community Structure than Short-Term Perturbations.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01564-z}, pmid = {32737538}, issn = {1432-184X}, abstract = {Phyllosphere microorganisms are sensitive to fluctuations in wind, temperature, solar radiation, and rain. However, recent explorations of patterns in phyllosphere communities across time often focus on seasonal shifts and leaf senescence without measuring the contribution of environmental drivers and leaf traits. Here, we focus on the effects of rain on the phyllosphere bacterial community of the wetland macrophyte broadleaf cattail (Typha latifolia) across an entire year, specifically targeting days before and 1, 3, and 5 days after rain events. To isolate the contribution of precipitation from other factors, we covered a subset of plants to shield them from rainfall. We used targeted Illumina sequencing of the V4 region of the bacterial 16S rRNA gene to characterize phyllosphere community composition. Rain events did not have a detectable effect on phyllosphere community richness or evenness regardless of whether the leaves were covered from rain or not, suggesting that foliar microbial communities are robust to such disturbances. While climatic and leaf-based variables effectively modeled seasonal trends in phyllosphere diversity and composition, they provided more limited explanatory value at shorter time scales. These findings underscore the dominance of long-term seasonal patterns related to climatic variation as the main factor influencing the phyllosphere community.}, }
@article {pmid32733460, year = {2020}, author = {Saresella, M and Marventano, I and Barone, M and La Rosa, F and Piancone, F and Mendozzi, L and d'Arma, A and Rossi, V and Pugnetti, L and Roda, G and Casagni, E and Cas, MD and Paroni, R and Brigidi, P and Turroni, S and Clerici, M}, title = {Alterations in Circulating Fatty Acid Are Associated With Gut Microbiota Dysbiosis and Inflammation in Multiple Sclerosis.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {1390}, pmid = {32733460}, issn = {1664-3224}, abstract = {Background: Butyric acid (BA) is a short-chain fatty acid (SCFA) with anti-inflammatory properties, which promotes intestinal barrier function. Medium-chain fatty acids (MCFA), including caproic acid (CA), promote TH1 and TH17 differentiation, thus supporting inflammation. Aim: Since most SCFAs are absorbed in the cecum and colon, the measurement of BA in peripheral blood could provide information on the health status of the intestinal ecosystem. Additionally, given the different immunomodulatory properties of BA and CA the evaluation of their serum concentration, as well as their ratio could be as a simple and rapid biomarker of disease activity and/or treatment efficacy in MS. Methods: We evaluated serum BA and CA concentrations, immune parameters, intestinal barrier integrity and the gut microbiota composition in patients with multiple sclerosis (MS) comparing result to those obtained in healthy controls. Results: In MS, the concentration of BA was reduced and that of CA was increased. Concurrently, the microbiota was depleted of BA producers while it was enriched in mucin-degrading, pro-inflammatory components. The reduced serum concentration of BA seen in MS patients correlated with alterations of the barrier permeability, as evidenced by the higher plasma concentrations of lipopolysaccharide and intestinal fatty acid-binding protein, and inflammation. Specifically, CA was positively associated with CD4+/IFNγ+ T lymphocytes, and the BA/CA ratio correlated positively with CD4+/CD25high/Foxp3+ and negatively with CD4+/IFNγ+ T lymphocytes. Conclusion: The gut microbiota dysbiosis found in MS is possibly associated with alterations of the SCFA/MCFA ratio and of the intestinal barrier; this could explain the chronic inflammation that characterizes this disease. SCFA and MCFA quantification could be a simple biomarker to evaluate the efficacy of therapeutic and rehabilitation procedures in MS.}, }
@article {pmid32733417, year = {2020}, author = {Dove, NC and Rogers, TJ and Leppanen, C and Simberloff, D and Fordyce, JA and Brown, VA and LeBude, AV and Ranney, TG and Cregger, MA}, title = {Microbiome Variation Across Two Hemlock Species With Hemlock Woolly Adelgid Infestation.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1528}, pmid = {32733417}, issn = {1664-302X}, abstract = {The hemlock woolly adelgid (Adelges tsugae, HWA), an invasive insect, is devastating native hemlock populations in eastern North America, and management outcomes have so far had limited success. While many plant microbiomes influence and even support plant immune responses to insect herbivory, relatively little is known about the hemlock microbiome and its interactions with pathogens or herbivores such as HWA. Using 16S rRNA and ITS gene amplicon sequencing, we characterized the needle, branch, root, and rhizosphere microbiome of two hemlock species, Tsuga canadensis and T. sieboldii, that displayed low and high levels of HWA populations. We found that both archaeal/bacterial and fungal needle communities, as well as the archaeal/bacterial branch and root communities, varied in composition in both hemlock species relative to HWA population levels. While host species and plant-associated habitats explained a greater proportion of the variance in the microbiome than did HWA population level, high HWA populations were associated with enrichment of 100 likely fungal pathogen sequence variants across the four plant-associated habitats (e.g., needle, branch, root, rhizosphere) compared to trees with lower HWA populations. This work contributes to a growing body of literature linking plant pathogens and pests with the changes in the associated plant microbiome and host health. Furthermore, this work demonstrates the need to further investigate plant microbiome effects across multiple plant tissues to understand their influences on host health.}, }
@article {pmid32728091, year = {2020}, author = {Gulati, S and Ballhausen, MB and Kulkarni, P and Grosch, R and Garbeva, P}, title = {A non-invasive soil-based setup to study tomato root volatiles released by healthy and infected roots.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12704}, pmid = {32728091}, issn = {2045-2322}, support = {F. No. 29-1/2009-EQR/Edn (Pt. III)//Indian Council of Agricultural Research (ICAR)/ ; }, abstract = {The role of root exudates in mediating plant-microbe interactions has been well documented. However, the function of volatile organic compounds (VOCs) emitted by plant roots has only recently begun to attract attention. This newly recognized relevance of belowground VOCs has so far mostly been tested using systems limited to a two-compartment Petri-dish design. Furthermore, many of the plant-microbe interaction studies have only investigated the effects of microbial VOCs on plant growth. Here, we go two steps further. First we investigated the volatile profile of healthy and pathogen (Fusarium oxysporum) infected tomato roots grown in soil. We then used a unique soil-based olfactometer-choice assay to compare the migration pattern of four beneficial bacteria (Bacillus spp.) towards the roots of the tomato plants. We demonstrate that the blend of root-emitted VOCs differs between healthy and diseased plants. Our results show that VOCs are involved in attracting bacteria to plant roots.}, }
@article {pmid32727863, year = {2020}, author = {Salcher, MM and Andrei, AŞ and Bulzu, PA and Keresztes, ZG and Banciu, HL and Ghai, R}, title = {Visualization of Lokiarchaeia and Heimdallarchaeia (Asgardarchaeota) by Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition (CARD-FISH).}, journal = {mSphere}, volume = {5}, number = {4}, pages = {}, pmid = {32727863}, issn = {2379-5042}, abstract = {Metagenome-assembled genomes (MAGs) of Asgardarchaeota have been recovered from a variety of habitats, broadening their environmental distribution and providing access to the genetic makeup of this archaeal lineage. The recent success in cultivating the first representative of Lokiarchaeia was a breakthrough in science at large and gave rise to new hypotheses about the evolution of eukaryotes. Despite their singular phylogenetic position at the base of the eukaryotic tree of life, the morphology of these bewildering organisms remains a mystery, except for the report of an unusual morphology with long, branching protrusions of the cultivated Lokiarchaeion strain &quot;Candidatus Prometheoarchaeum syntrophicum&quot; MK-D1. In order to visualize this elusive group, we applied a combination of fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) and epifluorescence microscopy on coastal hypersaline sediment samples, using specifically designed CARD-FISH probes for Heimdallarchaeia and Lokiarchaeia lineages, and provide the first visual evidence for Heimdallarchaeia and new images of a lineage of Lokiarchaeia that is different from the cultured representative. Here, we show that while Heimdallarchaeia are characterized by a uniform cellular morphology typified by a centralized DNA localization, Lokiarchaeia display a plethora of shapes and sizes that likely reflect their broad phylogenetic diversity and ecological distribution.IMPORTANCE Asgardarchaeota are considered to be the closest relatives to modern eukaryotes. These enigmatic microbes have been mainly studied using metagenome-assembled genomes (MAGs). Only very recently, a first member of Lokiarchaeia was isolated and characterized in detail; it featured a striking morphology with long, branching protrusions. In order to visualize additional members of the phylum Asgardarchaeota, we applied a fluorescence in situ hybridization technique and epifluorescence microscopy on coastal hypersaline sediment samples, using specifically designed probes for Heimdallarchaeia and Lokiarchaeia lineages. We provide the first visual evidence for Heimdallarchaeia that are characterized by a uniform cellular morphology typified by an apparently centralized DNA localization. Further, we provide new images of a lineage of Lokiarchaeia that is different from the cultured representative and with multiple morphologies, ranging from small ovoid cells to long filaments. This diversity in observed cell shapes is likely owing to the large phylogenetic diversity within Asgardarchaeota, the vast majority of which remain uncultured.}, }
@article {pmid32727027, year = {2020}, author = {Pédron, J and Guyon, L and Lecomte, A and Blottière, L and Chandeysson, C and Rochelle-Newall, E and Raynaud, X and Berge, O and Barny, MA}, title = {Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa.}, journal = {Microorganisms}, volume = {8}, number = {8}, pages = {}, pmid = {32727027}, issn = {2076-2607}, support = {Ec2co-CARTOBACTER//Centre National de la Recherche Scientifique/ ; CE32-2017-SPREE//Agence Nationale de la Recherche/ ; }, abstract = {To compare environmental and culture-derived microbial communities, we performed 16S metabarcoding of uncultured samples and their culture-derived bacterial lawns. Microbial communities were obtained from freshwater river samples representative of an anthropization gradient along a river stream. Their culture-derived bacterial lawns were obtained by growing aliquots of the samples on a broad range medium and on two different semi-selective media. The V3-V4 16S rRNA region was amplified and sequenced. The bacterial diversity of water samples decreased from the upper to lower stream sampling sites and, as expected, these differences were mostly suppressed by the culture step. Overall, the diversity of cultured-derived bacterial communities reflected selectivity of each tested medium. Comparison of treatments indicated that the culture selected both detected and rare undetected environmental species. Accurate detection of rare environmental bacteria of the Pectobacterium genus by 16S metabarcoding of the culture lawn was demonstrated. Interestingly, for abundant taxa, such as those of the Pseudomonas genus, the culture/environment ratio varied between sampled sites, indicating the difficulty of comparing cultured-derived taxa abundance between environmental sites. Finally, our study also highlighted media specificity and complementarity: bacterial communities grown on the two selective media, while selecting a small set of specific species, were mostly a subset of the bacterial community observed on the broad range medium.}, }
@article {pmid32723798, year = {2020}, author = {Xu, L and Xiang, M and Zhu, W and Zhang, M and Chen, H and Huang, J and Chen, Y and Chang, Q and Jiang, J and Zhu, L}, title = {The Behavior of Amphibians Shapes Their Symbiotic Microbiomes.}, journal = {mSystems}, volume = {5}, number = {4}, pages = {}, pmid = {32723798}, issn = {2379-5077}, abstract = {Seasonal dynamics in symbiotic microbiomes have been investigated in a number of vertebrates and are mainly caused by changes in the diet (in the gut microbiome) or the living environment (in the skin microbiome). Most amphibian microbiome studies focus on the skin, whereas internal microbiome structure and dynamics are often overlooked. The present study investigated the seasonal dynamics in three types of symbiotic microbiomes (the skin, stomach, and gut) across four wild frog species, belonging to different families, in May and October. The frogs harbored more water source microbes in May than in October. On the contrary, the frogs harbored more soil source microbes in October than in May. The frog species investigated tend to live in a water environment in May to maintain body surface humidity at high environmental temperatures and to breed. In October, these four species prefer to live on the land, as the environmental temperature decreases, to prepare for hibernation in caves or under stones. Thus, seasonal changes in the wild amphibian symbiotic microbiome may be caused by the difference in microbe transmission from their living environment due to specific behaviors. This study demonstrated that the behavior and living environment of wild amphibians shape their symbiotic microbiome externally (on the skin) and internally (in the stomach and gut). We revealed the potential association between specific behaviors in poikilothermic animals and host symbiotic microbiomes.IMPORTANCE Understanding the interactions between host behavior and microbiome dynamics remains an outstanding priority in the field of microbial ecology. Here, we provide the reader with a simple example of how the behavior and living environment of wild amphibians shape their symbiotic microbiome externally (on the skin) and internally (in the stomach and gut).}, }
@article {pmid32723791, year = {2020}, author = {Malli Mohan, GB and Parker, CW and Urbaniak, C and Singh, NK and Hood, A and Minich, JJ and Knight, R and Rucker, M and Venkateswaran, K}, title = {Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation.}, journal = {mSystems}, volume = {5}, number = {4}, pages = {}, pmid = {32723791}, issn = {2379-5077}, abstract = {Microbial contamination during long-term confinements of space exploration presents potential risks for both crew members and spacecraft life support systems. A novel swab kit was used to sample various surfaces from a submerged, closed, analog habitat to characterize the microbial populations. Samples were collected from various locations across the habitat which were constructed from various surface materials (linoleum, dry wall, particle board, glass, and metal), and microbial populations were examined by culture, quantitative PCR (qPCR), microbiome 16S rRNA gene sequencing, and shotgun metagenomics. Propidium monoazide (PMA)-treated samples identified the viable/intact microbial population of the habitat. The cultivable microbial population ranged from below the detection limit to 106 CFU/sample, and their identity was characterized using Sanger sequencing. Both 16S rRNA amplicon and shotgun sequencing were used to characterize the microbial dynamics, community profiles, and functional attributes (metabolism, virulence, and antimicrobial resistance). The 16S rRNA amplicon sequencing revealed abundance of viable (after PMA treatment) Actinobacteria (Brevibacterium, Nesternkonia, Mycobacterium, Pseudonocardia, and Corynebacterium), Firmicutes (Virgibacillus, Staphylococcus, and Oceanobacillus), and Proteobacteria (especially Acinetobacter) on linoleum, dry wall, and particle board (LDP) surfaces, while members of Firmicutes (Leuconostocaceae) and Proteobacteria (Enterobacteriaceae) were high on the glass/metal surfaces. Nonmetric multidimensional scaling determined from both 16S rRNA and metagenomic analyses revealed differential microbial species on LDP surfaces and glass/metal surfaces. The shotgun metagenomic sequencing of samples after PMA treatment showed bacterial predominance of viable Brevibacterium (53.6%), Brachybacterium (7.8%), Pseudonocardia (9.9%), Mycobacterium (3.7%), and Staphylococcus (2.1%), while fungal analyses revealed Aspergillus and Penicillium dominance.IMPORTANCE This study provides the first assessment of monitoring cultivable and viable microorganisms on surfaces within a submerged, closed, analog habitat. The results of the analyses presented herein suggest that the surface material plays a role in microbial community structure, as the microbial populations differed between LDP and metal/glass surfaces. The metal/glass surfaces had less-complex community, lower bioburden, and more closely resembled the controls. These results indicated that material choice is crucial when building closed habitats, even if they are simply analogs. Finally, while a few species were associated with previously cultivated isolates from the International Space Station and MIR spacecraft, the majority of the microbial ecology of the submerged analog habitat differs greatly from that of previously studied analog habitats.}, }
@article {pmid32721842, year = {2020}, author = {Pascual-Benito, M and Ballesté, E and Monleón-Getino, T and Urmeneta, J and Blanch, AR and García-Aljaro, C and Lucena, F}, title = {Impact of treated sewage effluent on the bacterial community composition in an intermittent mediterranean stream.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {266}, number = {Pt 1}, pages = {115254}, doi = {10.1016/j.envpol.2020.115254}, pmid = {32721842}, issn = {1873-6424}, mesh = {Bacteria/genetics ; Humans ; *Microbiota ; RNA, Ribosomal, 16S ; *Sewage ; Waste Water ; }, abstract = {Water quality monitoring is essential to safeguard human and environmental health. The advent of next-generation sequencing techniques in recent years, which allow a more in-depth study of environmental microbial communities in the environment, could broaden the perspective of water quality monitoring to include impact of faecal pollution bacteria on ecosystem. In this study, 16 S rRNA amplicon sequencing was used to evaluate the impact of wastewater treatment plant (WWTP) effluent on autochthonous microbial communities of a temporary Mediterranean stream characterized by high flow seasonality (from 0.02 m3/s in winter to 0.006 m3/s in summer). Seven sampling campaigns were performed under different temperatures and streamflow conditions (winter and summer). Water samples were collected upstream (Upper) of the WWTP, the secondary effluent (EF) discharge and 75 m (P75) and 1000 m (P1000) downstream of the WWTP. A total of 5,593,724 sequences were obtained, giving rise to 20,650 amplicon sequence variants (ASV), which were further analysed and classified into phylum, class, family and genus. Each sample presented different distribution and abundance of taxa. Although taxon distribution and abundance differed in each sample, the microbial community structure of P75 resembled that of EF samples, and Upper and P1000 samples mostly clustered together. Alpha diversity showed the highest values for Upper and P1000 samples and presented seasonal differences, being higher in winter conditions of high streamflow and low temperature. Our results suggest the microbial ecology re-establishment, since autochthonous bacterial communities were able to recover from the impact of the WWTP effluent in 1 km. Alpha diversity results indicates a possible influence of environmental factors on the bacterial community structure. This study shows the potential of next-generation sequencing techniques as useful tools in water quality monitoring and management within the climate change scenario.}, }
@article {pmid32720097, year = {2020}, author = {Zou, P and Yang, Q and Wang, H and Xie, G and Cao, Z and Chen, X and Gao, W and Huang, J}, title = {In vitro disinfection efficacy and clinical protective effects of common disinfectants against acute hepatopancreatic necrosis disease (AHPND)-causing Vibrio isolates in Pacific white shrimp Penaeus vannamei.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {58}, number = {8}, pages = {675-686}, doi = {10.1007/s12275-020-9537-1}, pmid = {32720097}, issn = {1976-3794}, abstract = {Acute hepatopancreatic necrosis disease (AHPND) is one of the most significant bacterial diseases in global shrimp culture, causing severe economic losses. In the present study, we carried out in vitro antimicrobial tests to investigate the disinfection efficacy of 14 common disinfectants toward different AHPND-causing Vibrio spp., including eight isolates of V. parahaemolyticus, four isolates of V. campbellii, and one isolate of V. owensii. Polyhexamethylene biguanidine hydrochloride (PHMB) was revealed to possess the strongest inhibitory activity. Through analyzing and evaluating the results of antimicrobial tests and acute toxicity test, we selected PHMB and hydrogen peroxide (H2O2) for further clinical protection test. Clinical manifestations indicated that both PHMB (2 mg/L and 4 mg/L) and H2O2 (12 mg/L) could effectively protect juvenile Penaeus vannamei from the infection of V. parahaemolyticus isolate Vp362 at 106 CFU/ml, and the survival rate was over 80%. When the bacterial concentration was reduced to 105 CFU/ml, 104 CFU/ml, and 103 CFU/ml, the survival rate after treated by 1 mg/L PHMB was 64.44%, 93.33%, and 100%, respectively. According to the results, PHMB and H2O2 showed a lower toxicity while a better protection activity, particularly against a lower concentration of the pathogens. Therefore, these two disinfectants are proved to be promising disinfectants that can be applied to prevent and control AHPND in shrimp culture. Moreover, the methods of this study also provided valuable information for the prevention of other important bacterial diseases and suggested a reliable means for screening potential drugs in aquaculture.}, }
@article {pmid32719667, year = {2020}, author = {Geelhoed, JS and van de Velde, SJ and Meysman, FJR}, title = {Quantification of Cable Bacteria in Marine Sediments via qPCR.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1506}, pmid = {32719667}, issn = {1664-302X}, abstract = {Cable bacteria (Deltaproteobacteria, Desulfobulbaceae) are long filamentous sulfur-oxidizing bacteria that generate long-distance electric currents running through the bacterial filaments. This way, they couple the oxidation of sulfide in deeper sediment layers to the reduction of oxygen or nitrate near the sediment-water interface. Cable bacteria are found in a wide range of aquatic sediments, but an accurate procedure to assess their abundance is lacking. We developed a qPCR approach that quantifies cable bacteria in relation to other bacteria within the family Desulfobulbaceae. Primer sets targeting cable bacteria, Desulfobulbaceae and the total bacterial community were applied in qPCR with DNA extracted from marine sediment incubations. Amplicon sequencing of the 16S rRNA gene V4 region confirmed that cable bacteria were accurately enumerated by qPCR, and suggested novel diversity of cable bacteria. The conjoint quantification of current densities and cell densities revealed that individual filaments carry a mean current of ∼110 pA and have a cell specific oxygen consumption rate of 69 fmol O2 cell-1 day-1. Overall, the qPCR method enables a better quantitative assessment of cable bacteria abundance, providing new metabolic insights at filament and cell level, and improving our understanding of the microbial ecology of electrogenic sediments.}, }
@article {pmid32719401, year = {2020}, author = {Huber, P and Metz, S and Unrein, F and Mayora, G and Sarmento, H and Devercelli, M}, title = {Environmental heterogeneity determines the ecological processes that govern bacterial metacommunity assembly in a floodplain river system.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-020-0723-2}, pmid = {32719401}, issn = {1751-7370}, support = {PICT 2016-0465//Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)/ ; }, abstract = {How diversity is structured has been a central goal of microbial ecology. In freshwater ecosystems, selection has been found to be the main driver shaping bacterial communities. However, its relative importance compared with other processes (dispersal, drift, diversification) may depend on spatial heterogeneity and the dispersal rates within a metacommunity. Still, a decrease in the role of selection is expected with increasing dispersal homogenization. Here, we investigate the main ecological processes modulating bacterial assembly in contrasting scenarios of environmental heterogeneity. We carried out a spatiotemporal survey in the floodplain system of the Paraná River. The bacterioplankton metacommunity was studied using both statistical inferences based on phylogenetic and taxa turnover as well as co-occurrence networks. We found that selection was the main process determining community assembly even at both extremes of environmental heterogeneity and homogeneity, challenging the general view that the strength of selection is weakened due to dispersal homogenization. The ecological processes acting on the community also determined the connectedness of bacterial networks associations. Heterogeneous selection promoted more interconnected networks increasing β-diversity. Finally, spatiotemporal heterogeneity was an important factor determining the number and identity of the most highly connected taxa in the system. Integrating all these empirical evidences, we propose a new conceptual model that elucidates how the environmental heterogeneity determines the action of the ecological processes shaping the bacterial metacommunity.}, }
@article {pmid32717345, year = {2020}, author = {Ahlawat, S and Asha,  and Sharma, KK}, title = {Immunological co-ordination between gut and lungs in SARS-CoV-2 infection.}, journal = {Virus research}, volume = {286}, number = {}, pages = {198103}, doi = {10.1016/j.virusres.2020.198103}, pmid = {32717345}, issn = {1872-7492}, mesh = {Antibodies, Monoclonal/therapeutic use ; Antiviral Agents/therapeutic use ; Betacoronavirus/immunology/*pathogenicity ; Coronavirus Infections/drug therapy/*immunology/microbiology/virology ; Cytokine Release Syndrome/drug therapy/*immunology/microbiology/virology ; Cytokines/antagonists &amp; inhibitors/genetics/immunology ; Dysbiosis/drug therapy/*immunology/microbiology/virology ; Gastrointestinal Microbiome/immunology ; Gastrointestinal Tract/drug effects/*immunology/microbiology/virology ; Gene Expression ; Host-Pathogen Interactions/immunology ; Humans ; Inflammatory Bowel Diseases/drug therapy/*immunology/microbiology/virology ; Lung/drug effects/*immunology/microbiology/virology ; Pandemics ; Peptidyl-Dipeptidase A/genetics/immunology ; Pneumonia, Viral/drug therapy/*immunology/microbiology/virology ; Receptors, Virus/genetics/immunology ; }, abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into a major pandemic called coronavirus disease 2019 (COVID-19) that has created unprecedented global health emergencies, and emerged as a serious threat due to its strong ability for human-to-human transmission. The reports indicate the ability of SARS-CoV-2 to affect almost any organ due to the presence of a receptor known as angiotensin converting enzyme 2 (ACE2) across the body. ACE2 receptor is majorly expressed in the brush border of gut enterocytes along with the ciliated cells and alveolar epithelial type II cells in the lungs. The amino acid transport function of ACE2 has been linked to gut microbial ecology in gastrointestinal (GI) tract, thereby suggesting that COVID-19 may, to some level, be linked to the enteric microbiota. The significant number of COVID-19 patients shows extra-pulmonary symptoms in the GI tract. Many subsequent studies revealed viral RNA of SARS-CoV-2 in fecal samples of COVID-19 patients. This presents a new challenge in the diagnosis and control of COVID-19 infection with a caution for proper sanitation and hygiene. Here, we aim to discuss the immunological co-ordination between gut and lungs that facilitates SARS-CoV-2 to infect and multiply in the inflammatory bowel disease (IBD) and non-IBD patients.}, }
@article {pmid32710789, year = {2020}, author = {Zhang, QF and Laanbroek, HJ}, title = {Tannins from senescent Rhizophora mangle mangrove leaves have a distinctive effect on prokaryotic and eukaryotic communities in a Distichlis spicata salt marsh soil.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {9}, pages = {}, doi = {10.1093/femsec/fiaa148}, pmid = {32710789}, issn = {1574-6941}, abstract = {Due to climate warming, tannin-rich Rhizophora mangle migrates into tannin-poor salt marshes, where the tannins interfere with the biogeochemistry in the soil. Changes in biogeochemistry are likely associated with changes in microbial communities. This was studied in microcosms filled with salt marsh soil and amended with leaf powder, crude condensed tannins, purified condensed tannins (PCT), all from senescent R. mangle leaves, or with tannic acid. Size and composition of the microbial communities were determined by denaturing gradient gel electrophoresis, high-throughput sequencing and real-time PCR based on the 16S and 18S rRNA genes. Compared with the control, the 16S rRNA gene abundance was lowered by PCT, while the 18S rRNA gene abundance was enhanced by all treatments. The treatments also affected the composition of the 16S rRNA and 18S rRNA gene assemblies, but the effects on the 18S rRNA gene were greater. The composition of the 18S rRNA gene, but not of the 16S rRNA gene, was significantly correlated with the mineralization of carbon, nitrogen and phosphorus. Distinctive microbial groups emerged during the different treatments. This study revealed that migration of mangroves may affect both the prokaryotic and the eukaryotic communities in salt marsh soils, but that the effects on the eukaryotes will likely be greater.}, }
@article {pmid32710756, year = {2020}, author = {Pedrinho, A and Mendes, LW and Merloti, LF and Andreote, FD and Tsai, SM}, title = {The natural recovery of soil microbial community and nitrogen functions after pasture abandonment in the Amazon region.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {9}, pages = {}, doi = {10.1093/femsec/fiaa149}, pmid = {32710756}, issn = {1574-6941}, abstract = {We assessed the impacts of forest-to-pasture conversion on the dynamic of soil microbial communities, especially those involved in the N-cycle, and their potential functions, using DNA-metagenomic sequencing coupled with the quantification of marker genes for N-cycling. We also evaluated whether the community's dynamic was reestablished with secondary forest growth. In general, the microbial community structure was influenced by changes in soil chemical properties. Aluminum and nitrate significantly correlated to community structure and with 12 out of 21 microbial phyla. The N-related microbial groups and their potential functions were also affected by land-use change, with pasture being clearly different from primary and secondary forest systems. The microbial community analysis demonstrated that forest-to-pasture conversion increased the abundance of different microbial groups related to nitrogen fixation, including Bacteroidetes, Chloroflexi and Firmicutes. In contrast, after pasture abandonment and with the secondary forest regeneration, there was an increase in the abundance of Proteobacteria taxa and denitrification genes. Our multi-analytical approach indicated that the secondary forest presented some signs of resilience, suggesting that the N-related microbial groups and their potential functions can be recovered over time with implications for future ecological restoration programs.}, }
@article {pmid32710182, year = {2020}, author = {Luzzi, G and Brinks, E and Fritsche, J and Franz, CMAP}, title = {Microbial composition of sweetness-enhanced yoghurt during fermentation and storage.}, journal = {AMB Express}, volume = {10}, number = {1}, pages = {131}, pmid = {32710182}, issn = {2191-0855}, support = {2819107616//Bundesanstalt für Landwirtschaft und Ernährung/ ; }, abstract = {The reformulation of dairy products to contain less added sugar can contribute to reducing sugar consumption, thereby reducing the risk of non-communicable diseases. The objective of this study was to investigate the microbial ecology of reformulated yoghurt, which was produced using bi-enzymatic modification of lactose to increase its sweetness by a factor of 2-3. Ultimately, this reformulation strategy could reduce the amount of added sugar needed for equal sweetness of the end product. The bi-enzymatic modification relied on utilisation of a β-galactosidase enzyme to convert the milk sugar lactose to galactose and glucose, followed by the enzymatic conversion of the glucose moiety to fructose using a glucose isomerase. The microbial ecology of reformulated yoghurt produced with two mixed starter culture preparations containing either Streptococcus (S.) thermophilus and Lactobacillus (Lb.) delbrueckii or S. thermophilus, Lb. acidophilus and Bifidobacterium sp. strains, was analysed during fermentation and cool storage using 16S rRNA based metagenomics. None of the yoghurt samples showed a significant difference in microbial composition between sweetness-enhanced and regular milk at all sampling time points during manufacture and storage of yoghurt. However, a significant difference between the microbiota of inoculated milk before and after fermentation was observed. In both types of yoghurt, the starter culture genera dominated the microbial ecology at the end of fermentation as expected, reducing the possibility of growth of potentially pathogenic or spoilage bacteria possibly resulting from a changed carbohydrate spectrum.}, }
@article {pmid32709974, year = {2020}, author = {Daebeler, A and Kitzinger, K and Koch, H and Herbold, CW and Steinfeder, M and Schwarz, J and Zechmeister, T and Karst, SM and Albertsen, M and Nielsen, PH and Wagner, M and Daims, H}, title = {Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-020-0724-1}, pmid = {32709974}, issn = {1751-7370}, support = {T938//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P25231-B21//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P27319-B21//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; }, abstract = {Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high pH. Nitrospira distribution, diversity, and ecophysiology were studied in hypo- and subsaline (1.3-12.8 g salt/l), highly alkaline (pH 8.9-10.3) lakes by amplicon sequencing, metagenomics, and cultivation-based approaches. Surprisingly, not only were Nitrospira populations detected, but they were also considerably diverse with presence of members from Nitrospira lineages I, II and IV. Furthermore, the ability of Nitrospira enrichment cultures to oxidize nitrite at neutral to highly alkaline pH of 10.5 was demonstrated. Metagenomic analysis of a newly enriched Nitrospira lineage IV species, &quot;Candidatus Nitrospira alkalitolerans&quot;, revealed numerous adaptive features of this organism to its extreme environment. Among them were a sodium-dependent N-type ATPase and NADH:quinone oxidoreductase next to the proton-driven forms usually found in Nitrospira. Other functions aid in pH and cation homeostasis and osmotic stress defense. &quot;Ca. Nitrospira alkalitolerans&quot; also possesses group 2a and 3b [NiFe] hydrogenases, suggesting it can use hydrogen as alternative energy source. These results reveal how Nitrospira cope with strongly fluctuating pH and salinity conditions and expand our knowledge of nitrogen cycling in extreme habitats.}, }
@article {pmid32709258, year = {2020}, author = {Nobu, MK and Narihiro, T and Mei, R and Kamagata, Y and Lee, PKH and Lee, PH and McInerney, MJ and Liu, WT}, title = {Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {111}, pmid = {32709258}, issn = {2049-2618}, abstract = {BACKGROUND: Current understanding of the carbon cycle in methanogenic environments involves trophic interactions such as interspecies H2 transfer between organotrophs and methanogens. However, many metabolic processes are thermodynamically sensitive to H2 accumulation and can be inhibited by H2 produced from co-occurring metabolisms. Strategies for driving thermodynamically competing metabolisms in methanogenic environments remain unexplored.<br><br>RESULTS: To uncover how anaerobes combat this H2 conflict in situ, we employ metagenomics and metatranscriptomics to revisit a model ecosystem that has inspired many foundational discoveries in anaerobic ecology-methanogenic bioreactors. Through analysis of 17 anaerobic digesters, we recovered 1343 high-quality metagenome-assembled genomes and corresponding gene expression profiles for uncultured lineages spanning 66 phyla and reconstructed their metabolic capacities. We discovered that diverse uncultured populations can drive H2-sensitive metabolisms through (i) metabolic coupling with concurrent H2-tolerant catabolism, (ii) forgoing H2 generation in favor of interspecies transfer of formate and electrons (cytochrome- and pili-mediated) to avoid thermodynamic conflict, and (iii) integration of low-concentration O2 metabolism as an ancillary thermodynamics-enhancing electron sink. Archaeal populations support these processes through unique methanogenic metabolisms-highly favorable H2 oxidation driven by methyl-reducing methanogenesis and tripartite uptake of formate, electrons, and acetate.<br><br>CONCLUSION: Integration of omics and eco-thermodynamics revealed overlooked behavior and interactions of uncultured organisms, including coupling favorable and unfavorable metabolisms, shifting from H2 to formate transfer, respiring low-concentration O2, performing direct interspecies electron transfer, and interacting with high H2-affinity methanogenesis. These findings shed light on how microorganisms overcome a critical obstacle in methanogenic carbon cycles we had hitherto disregarded and provide foundational insight into anaerobic microbial ecology. Video Abstract.}, }
@article {pmid32708991, year = {2020}, author = {Swarte, JC and Eelderink, C and Douwes, RM and Said, MY and Hu, S and Post, A and Westerhuis, R and Bakker, SJL and Harmsen, HJM}, title = {Effect of High versus Low Dairy Consumption on the Gut Microbiome: Results of a Randomized, Cross-Over Study.}, journal = {Nutrients}, volume = {12}, number = {7}, pages = {}, pmid = {32708991}, issn = {2072-6643}, abstract = {The influence of dairy on the gut microbiome has not been studied extensively. We performed a randomized cross-over study to analyze the effect of high dairy intake on the gut microbiome. Subjects were randomly assigned to a high-dairy diet (HDD) (5-6 dairy portions per day) and a low-dairy diet (LDD) (≤1 dairy portion per day) for 6 weeks with a washout period of 4 weeks in between both diets. The gut microbiome was assessed using 16S rRNA gene sequencing. Compositionality and functionality of the gut microbiome was assessed using Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Stool consistency was evaluated using the Bristol stool chart. In total, 46 healthy overweight subjects (BMI range 25-30 kg/m2) completed both intervention periods. During the HDD, there was a significantly higher abundance of the genera Streptococcus, Leuconostoc, and Lactococcus, and the species Streptococcusthermophilus, Erysipelatoclostridiumramosum and Leuconostocmesenteroides (pFDR < 0.10). Furthermore, during the HDD, there was a significantly lower abundance of the genera Faecalibacterium and Bilophila, and the species Faecalibacteriumprausnitzii, Clostridiumaldenense, Acetivibrioethanolgignens, Bilophilawadsworthia and Lactococcuslactis (pFDR < 0.10). There were eight subjects who became constipated during the HDD and these subjects all had a lower abundance of F. prausnitzii. This is the first cross-over study in which the effect of an HDD compared to an LDD on the gut microbiome has been studied. An HDD led to a significantly different composition of the gut microbiome, with a particularly lower abundance of F. prausnitzii and a higher abundance of S. thermophilus. Constipation was observed in several subjects during the HDD. Predicted metabolic pathways were not significantly altered due to an HDD.}, }
@article {pmid32706331, year = {2020}, author = {Pérez-Cobas, AE and Gomez-Valero, L and Buchrieser, C}, title = {Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses.}, journal = {Microbial genomics}, volume = {6}, number = {8}, pages = {}, doi = {10.1099/mgen.0.000409}, pmid = {32706331}, issn = {2057-5858}, abstract = {Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples. Whole-genome shotgun sequencing analyses the total DNA of a chosen sample to determine the presence of micro-organisms from all domains of life and their genomic content. Importantly, the whole-genome shotgun sequencing approach reveals the genomic diversity present, but can also give insights into the functional potential of the micro-organisms identified. The marker gene approach is based on the sequencing of a specific gene region. It allows one to describe the microbial composition based on the taxonomic groups present in the sample. It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge. Here we review the primary workflows and software used for both approaches and discuss the current challenges in the field.}, }
@article {pmid32705812, year = {2020}, author = {Mitiku, AA and Andeta, AF and Borremans, A and Lievens, B and Bossaert, S and Crauwels, S and Aernouts, B and Kechero, Y and Van Campenhout, L}, title = {Silage making of maize stover and banana pseudostem under South Ethiopian conditions: evolution of pH, dry matter and microbiological profile.}, journal = {Microbial biotechnology}, volume = {13}, number = {5}, pages = {1477-1488}, doi = {10.1111/1751-7915.13626}, pmid = {32705812}, issn = {1751-7915}, support = {AMU 2017IUC035A10//Flemish Interuniversity Council for University Development Cooperation (VLIR-UOS)/ ; }, abstract = {The study was conducted to evaluate the microbial dynamics during silage of maize stover and banana pseudostem in the environmental conditions of southern Ethiopia. To meet this objective, microsilos containing either maize stover or banana pseudostem, both with and without molasses, were prepared. Subsequently, samples were analysed on day 0, 7, 14, 30, 60 and 90 of the fermentation process. As a result, on day 7, all treatments except banana pseudostem without molasses showed a significant reduction in pH. It was also this silage type that supported the growth of Enterobacteriaceae longer than three other silage types, i.e. until 30 days. The yeasts and moulds and the Clostridum endospore counts also showed a reducing trend in early fermentation and afterwards remained constant until day 90. Illumina MiSeq sequencing revealed that Leuconostoc, Buttiauxella species and Enterobacteriaceae were the most abundant bacteria in the initial phases of the fermentation. Later on, Buttiauxella, Lactobacillus, Weissella and Bifidobacterium species were found to be dominant. In conclusion, silage of the two crop by-products is possible under South Ethiopian conditions. For banana pseudostem, the addition of molasses is crucial for a fast fermentation, in contrast to maize. Upscaling needs to be investigated for the two by-products.}, }
@article {pmid32705311, year = {2020}, author = {Mateus-Barros, E and de Melo, ML and Bagatini, IL and Caliman, A and Sarmento, H}, title = {Local and Geographic Factors Shape the Occupancy-Frequency Distribution of Freshwater Bacteria.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01560-3}, pmid = {32705311}, issn = {1432-184X}, support = {2014/14139-3//São Paulo Research Foundation - FAPESP/ ; 2011/50054-4//São Paulo Research Foundation - FAPESP/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES)/ ; 309514/2017-7//National Council for Scientific and Technological Development - CNPq/ ; }, abstract = {Species prevalence across the landscape is related to their local abundance, which is a result of deterministic and stochastic processes that select organisms capable of recolonizing sites where they were once extinct, a process known as the rescue effect. The occupancy-frequency distribution (OFD) describes these patterns and has been extensively used to understand organism's distribution but has been poorly tested on microorganisms. In order to test OFD on freshwater bacteria, we collected data from 60 shallow lakes distributed across a wide area in southeastern Brazil, to determine the bacterial operational taxonomic units (OTUs) that were present in all sites (core) and at only one site (satellite). Then, we analyzed the spatial abundance distributions of individual OTUs to understand the influence of local abundances on regional occupancy patterns. Finally, we tested the environmental factors that influenced occupancy and abundance. We found a significant bimodal OFD for freshwater bacteria using both OTUs (97% clustering) and amplicon sequence variants (ASVs, unique sequences), with 13 core OTUs and 1169 satellite OTUs, but only three core ASVs. Core organisms had a bimodal or gamma abundance distribution. The main driver of the core community was pH, while nutrients were key when the core community was excluded and the rest of the community (mild and satellite taxa) was considered. This study demonstrates the close relationship between local environmental conditions and the abundance and dispersion of microorganisms, which shapes their distribution across the landscape.}, }
@article {pmid32704052, year = {2020}, author = {González-Ramos, S and Paz-García, M and Fernández-García, V and Portune, KJ and Acosta-Medina, EF and Sanz, Y and Castrillo, A and Martín-Sanz, P and Obregon, MJ and Boscá, L}, title = {NOD1 deficiency promotes an imbalance of thyroid hormones and microbiota homeostasis in mice fed high fat diet.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12317}, pmid = {32704052}, issn = {2045-2322}, support = {SAF2017-82436R//Mineco/AEI/FEDER/EU/ ; AGL2017-88801-P//Mineco/AEI/FEDER/EU/ ; SAF2016-75004R//Mineco/AEI/FEDER/EU/ ; SAF2017-82436R//Mineco/AEI/FEDER/EU/ ; AGL2017-88801-P//Mineco/AEI/FEDER/EU/ ; SAF2016-75004R//Mineco/AEI/FEDER/EU/ ; SAF2017-82436R//Mineco/AEI/FEDER/EU/ ; AGL2017-88801-P//Mineco/AEI/FEDER/EU/ ; SAF2016-75004R//Mineco/AEI/FEDER/EU/ ; SAF2017-82436R//Mineco/AEI/FEDER/EU/ ; AGL2017-88801-P//Mineco/AEI/FEDER/EU/ ; SAF2016-75004R//Mineco/AEI/FEDER/EU/ ; SAF2017-82436R//Mineco/AEI/FEDER/EU/ ; AGL2017-88801-P//Mineco/AEI/FEDER/EU/ ; SAF2016-75004R//Mineco/AEI/FEDER/EU/ ; SAF2017-82436R//Mineco/AEI/FEDER/EU/ ; AGL2017-88801-P//Mineco/AEI/FEDER/EU/ ; SAF2016-75004R//Mineco/AEI/FEDER/EU/ ; S2017/BMD-3686//Consejería de Educación e Investigación/ ; S2017/BMD-3686//Consejería de Educación e Investigación/ ; CIVP18A3864//Fundación Ramón Areces/ ; CIVP18A3864//Fundación Ramón Areces/ ; CIVP18A3864//Fundación Ramón Areces/ ; CIBERcv CIBERehd//Instituto de Salud Carlos III/ ; CIBERcv CIBERehd//Instituto de Salud Carlos III/ ; }, abstract = {The contribution of the nucleotide-binding oligomerization domain protein NOD1 to obesity has been investigated in mice fed a high fat diet (HFD). Absence of NOD1 accelerates obesity as early as 2 weeks after feeding a HFD. The obesity was due to increases in abdominal and inguinal adipose tissues. Analysis of the resting energy expenditure showed an impaired function in NOD1-deficient animals, compatible with an alteration in thyroid hormone homeostasis. Interestingly, free thyroidal T4 increased in NOD1-deficient mice fed a HFD and the expression levels of UCP1 in brown adipose tissue were significantly lower in NOD1-deficient mice than in the wild type animals eating a HFD, thus contributing to the observed adiposity in NOD1-deficient mice. Feeding a HFD resulted in an alteration of the proinflammatory profile of these animals, with an increase in the infiltration of inflammatory cells in the liver and in the white adipose tissue, and an elevation of the circulating levels of TNF-α. In addition, alterations in the gut microbiota in NOD1-deficient mice correlate with increased vulnerability of their ecosystem to the HFD challenge and affect the immune-metabolic phenotype of obese mice. Together, the data are compatible with a protective function of NOD1 against low-grade inflammation and obesity under nutritional conditions enriched in saturated lipids. Moreover, one of the key players of this early obesity onset is a dysregulation in the metabolism and release of thyroid hormones leading to reduced energy expenditure, which represents a new role for these hormones in the metabolic actions controlled by NOD1.}, }
@article {pmid32702578, year = {2020}, author = {Zhang, Q and Chen, X and Zhang, Z and Luo, W and Wu, H and Zhang, L and Zhang, X and Zhao, T}, title = {Performance and microbial ecology of a novel moving bed biofilm reactor process inoculated with heterotrophic nitrification-aerobic denitrification bacteria for high ammonia nitrogen wastewater treatment.}, journal = {Bioresource technology}, volume = {315}, number = {}, pages = {123813}, doi = {10.1016/j.biortech.2020.123813}, pmid = {32702578}, issn = {1873-2976}, mesh = {Ammonia ; Biofilms ; Bioreactors ; Denitrification ; *Nitrification ; Nitrogen/analysis ; *Waste Water ; }, abstract = {To overcome long start-up time, poor ammonia tolerance and removal performance of traditional moving bed biofilm reactor (MBBR) inoculated with activated sludge for high-ammonia wastewater treatment, a novel MBBR based on heterotrophic nitrification-aerobic denitrification (HN-AD) was proposed. Start-up of MBBR was firstly performed via inoculated with HN-AD bacteria. Start-up time was shortened from 39 d to 15 d, NH4+ tolerance was enhanced from 200 mg/L to 1000 mg/L, and TN removal was increased from 30.4% to 80.7%. The carrier types and NH4+ concentration had significant effects on nitrogen removal and microbial ecology. When the NH4+ concentration was increased to 900 mg/L in MBBR using polyvinyl alcohol gel as carrier, the TN removal, the abundance of HN-AD bacteria Acinetobacter, Pseudomonas and Paracoccus, which played a key role in TN removal and ammonia tolerance, and the abundance of genes related to nitrogen removal were much higher than those of MBBR using kaldness.}, }
@article {pmid32699992, year = {2020}, author = {Hopkins, JR and Huffman, JM and Platt, WJ and Sikes, BA}, title = {Frequent fire slows microbial decomposition of newly deposited fine fuels in a pyrophilic ecosystem.}, journal = {Oecologia}, volume = {193}, number = {3}, pages = {631-643}, doi = {10.1007/s00442-020-04699-5}, pmid = {32699992}, issn = {1432-1939}, support = {DEB-1557000//National Science Foundation/ ; DEB-1556837//National Science Foundation/ ; 1451148//National Science Foundation/ ; }, mesh = {Ecosystem ; *Fires ; *Pinus ; Soil ; }, abstract = {Frequent fires maintain nearly 50% of terrestrial ecosystems, and drive ecosystem changes that govern future fires. Since fires are dependent on available plant or fine fuels, ecosystem processes that alter fine fuel loads like microbial decomposition are particularly important and could modify future fires. We hypothesized that variation in short-term fire history would influence fuel dynamics in such ecosystems. We predicted that frequent fires within a short-time period would slow microbial decomposition of new fine fuels. We expected that fire effects would differ based on dominant substrates and that fire history would also alter soil nutrient availability, indirectly slowing decomposition. We measured decomposition of newly deposited fine fuels in a Longleaf pine savanna, comparing plots that burned 0, 1, 2, or 3 times between 2014 and 2016, and which were located in either close proximity to or away from overstory pines (Longleaf pine, Pinus palustris). Microbial decomposition was slower in plots near longleaf pines and, as the numbers of fires increased, decomposition slowed. We then used structural equation modeling to assess pathways for these effects (number of fires, 2016 fuel/fire characteristics, and soil chemistry). Increased fire frequency was directly associated with decreased microbial decomposition. While increased fires decreased nutrient availability, changes in nutrients were not associated with decomposition. Our findings indicate that increasing numbers of fires over short-time intervals can slow microbial decomposition of newly deposited fine fuels. This could favor fine fuel accumulation and drive positive feedbacks on future fires.}, }
@article {pmid32698767, year = {2020}, author = {Taparia, T and Krijger, M and Haynes, E and Elphinstone, JG and Noble, R and van der Wolf, J}, title = {Molecular characterization of Pseudomonas from Agaricus bisporus caps reveal novel blotch pathogens in Western Europe.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {505}, pmid = {32698767}, issn = {1471-2164}, support = {KV1509-050//Dutch Ministry of Economic Affairs (NL)/ ; M063//Agriculture and Horticulture Development Board/ ; }, abstract = {BACKGROUND: Bacterial blotch is a group of economically important diseases affecting the cultivation of common button mushroom, Agaricus bisporus. Despite being studied for more than a century, the identity and nomenclature of blotch-causing Pseudomonas species is still unclear. This study aims to molecularly characterize the phylogenetic and phenotypic diversity of blotch pathogens in Western Europe.<br><br>METHODS: In this study, blotched mushrooms were sampled from farms across the Netherlands, United Kingdom and Belgium. Bacteria were isolated from symptomatic cap tissue and tested in pathogenicity assays on fresh caps and in pots. Whole genome sequences of pathogenic and non-pathogenic isolates were used to establish phylogeny via multi-locus sequence alignment (MLSA), average nucleotide identity (ANI) and in-silico DNA:DNA hybridization (DDH) analyses.<br><br>RESULTS: The known pathogens &quot;Pseudomonas gingeri&quot;, P. tolaasii, &quot;P. reactans&quot; and P. costantinii were recovered from blotched mushroom caps. Seven novel pathogens were also identified, namely, P. yamanorum, P. edaphica, P. salomonii and strains that clustered with Pseudomonas sp. NC02 in one genomic species, and three non-pseudomonads, i.e. Serratia liquefaciens, S. proteamaculans and a Pantoea sp. Insights on the pathogenicity and symptom severity of these blotch pathogens were also generated.<br><br>CONCLUSION: A detailed overview of genetic and regional diversity and the virulence of blotch pathogens in Western Europe, was obtained via the phylogenetic and phenotypic analyses. This information has implications in the study of symptomatic disease expression, development of diagnostic tools and design of localized strategies for disease management.}, }
@article {pmid32697840, year = {2020}, author = {Cary, C and Cowan, DA and McMinn, A and Häggblom, MM}, title = {Editorial: Thematic issue on polar and alpine microbiology.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {8}, pages = {}, doi = {10.1093/femsec/fiaa136}, pmid = {32697840}, issn = {1574-6941}, }
@article {pmid32696567, year = {2020}, author = {Kuranaga, T and Matsuda, K and Takaoka, M and Tachikawa, C and Sano, A and Itoh, K and Enomoto, A and Fujita, K and Abe, I and Wakimoto, T}, title = {Total Synthesis and Structural Revision of Kasumigamide, and Identification of a New Analogue.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {}, number = {}, pages = {}, doi = {10.1002/cbic.202000409}, pmid = {32696567}, issn = {1439-7633}, abstract = {Kasumigamide is an antialgal hybrid peptide-polyketide isolated from the freshwater cyanobacterium Microcystis aeruginosa (NIES-87). The biosynthetic gene cluster was identified from not only the cyanobacterium but also Candidatus &quot;Entotheonella&quot;, associated with the Japanese marine sponge Discodermia calyx . Therefore, kasumigamide is considered to play a key role in microbial ecology, regardless of the terrestrial and marine habitats. We now report the synthetic studies on this intriguing natural product, leading to the structural revision and the first total synthesis. During this study, a new analogue deoxykasumigamide was also isolated and structurally validated. The present study confirmed the presence of the unusual pathway in the biosynthesis of a hybrid peptide-polyketide natural product.}, }
@article {pmid32696239, year = {2020}, author = {Cassán, F and López, G and Nievas, S and Coniglio, A and Torres, D and Donadio, F and Molina, R and Mora, V}, title = {What Do We Know About the Publications Related with Azospirillum? A Metadata Analysis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01559-w}, pmid = {32696239}, issn = {1432-184X}, support = {PICT-2017-0572//FONCyT-MINCYT/ ; }, abstract = {Azospirillum is one of the most successful plant growth-promoting bacteria (PGPB) genera and it is considered a study model for plant-bacteria interactions. Because of that, a wide broad of topics has been boarded and discussed in a significant number of publications in the last four decades. Using the Scopus® database, we conducted a bibliographic search in order to analyze the number and type of publications, the authors responsible of these contributions, and the origin of the researchers, as well as the keywords and journals selected by the authors, among other related characteristics, with the aim to understand some less addressed details about the work done with Azospirillum worldwide since its discovery in 1925. Despite that the largest numbers of publications about this bacterium were obtained between the 1970 and 1980s, there is still a linear increase tendency in the number of published works. Understanding the mechanisms involved in the ability of these bacteria to promote growth in a wide broad of plant species under both laboratory and field conditions has been a preferential target for these published articles. This tendency could be considered a cause or consequence of the current increase in the number of commercial products formulated with Azospirillum around the world and a catalyzer for the increase of published articles along time.}, }
@article {pmid32694129, year = {2020}, author = {Wang, S and Xiong, W and Wang, Y and Nie, Y and Wu, Q and Xu, Y and Geisen, S}, title = {Temperature-Induced Annual Variation in Microbial Community Changes and Resulting Metabolome Shifts in a Controlled Fermentation System.}, journal = {mSystems}, volume = {5}, number = {4}, pages = {}, doi = {10.1128/mSystems.00555-20}, pmid = {32694129}, issn = {2379-5077}, abstract = {We are rapidly increasing our understanding on the spatial distribution of microbial communities. However, microbial functioning, as well as temporal differences and mechanisms causing microbial community shifts, remains comparably little explored. Here, using Chinese liquor fermentation as a model system containing a low microbial diversity, we studied temporal changes in microbial community structure and functioning. For that, we used high-throughput sequencing to analyze the composition of bacteria and fungi and analyzed the microbially derived metabolome throughout the fermentation process in all four seasons in both 2018 and 2019. We show that microbial communities and the metabolome changed throughout the fermentation process in each of the four seasons, with metabolome diversity increasing throughout the fermentation process. Across seasons, bacterial and fungal communities as well as the metabolome driven by 10 indicator microorganisms and six metabolites varied even more. Daily average temperature in the external surroundings was the primary determinant of the observed temporal microbial community and metabolome changes. Collectively, our work reveals critical insights into patterns and processes determining temporal changes of microbial community composition and functioning. We highlight the importance of linking taxonomic to functional changes in microbial ecology to enable predictions of human-relevant applications.IMPORTANCE We used Chinese liquor fermentation as a model system to show that microbiome composition changes more dramatically across seasons than throughout the fermentation process within seasons. These changes translate to differences in the metabolome as the ultimate functional outcome of microbial activity, suggesting that temporal changes in microbiome composition are translating into functional changes. This result is striking as it suggests that microbial functioning, despite controlled conditions in the fermentors, fluctuates over season along with external temperature differences, which threatens a reproducible food taste. As such, we believe that our study provides a stepping-stone into novel taxonomy-functional studies that promote future work in other systems and that also is relevant in applied settings to better control surrounding conditions in food production.}, }
@article {pmid32694124, year = {2020}, author = {Sieradzki, ET and Koch, BJ and Greenlon, A and Sachdeva, R and Malmstrom, RR and Mau, RL and Blazewicz, SJ and Firestone, MK and Hofmockel, KS and Schwartz, E and Hungate, BA and Pett-Ridge, J}, title = {Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design.}, journal = {mSystems}, volume = {5}, number = {4}, pages = {}, doi = {10.1128/mSystems.00151-20}, pmid = {32694124}, issn = {2379-5077}, abstract = {Quantitative stable isotope probing (qSIP) estimates isotope tracer incorporation into DNA of individual microbes and can link microbial biodiversity and biogeochemistry in complex communities. As with any quantitative estimation technique, qSIP involves measurement error, and a fuller understanding of error, precision, and statistical power benefits qSIP experimental design and data interpretation. We used several qSIP data sets-from soil and seawater microbiomes-to evaluate how variance in isotope incorporation estimates depends on organism abundance and resolution of the density fractionation scheme. We assessed statistical power for replicated qSIP studies, plus sensitivity and specificity for unreplicated designs. As a taxon's abundance increases, the variance of its weighted mean density declines. Nine fractions appear to be a reasonable trade-off between cost and precision for most qSIP applications. Increasing the number of density fractions beyond that reduces variance, although the magnitude of this benefit declines with additional fractions. Our analysis suggests that, if a taxon has an isotope enrichment of 10 atom% excess, there is a 60% chance that this will be detected as significantly different from zero (with alpha 0.1). With five replicates, isotope enrichment of 5 atom% could be detected with power (0.6) and alpha (0.1). Finally, we illustrate the importance of internal standards, which can help to calibrate per sample conversions of %GC to mean weighted density. These results should benefit researchers designing future SIP experiments and provide a useful reference for metagenomic SIP applications where both financial and computational limitations constrain experimental scope.IMPORTANCE One of the biggest challenges in microbial ecology is correlating the identity of microorganisms with the roles they fulfill in natural environmental systems. Studies of microbes in pure culture reveal much about their genomic content and potential functions but may not reflect an organism's activity within its natural community. Culture-independent studies supply a community-wide view of composition and function in the context of community interactions but often fail to link the two. Quantitative stable isotope probing (qSIP) is a method that can link the identity and functional activity of specific microbes within a naturally occurring community. Here, we explore how the resolution of density gradient fractionation affects the error and precision of qSIP results, how they may be improved via additional experimental replication, and discuss cost-benefit balanced scenarios for SIP experimental design.}, }
@article {pmid32691599, year = {2020}, author = {Elsayed, SS and Genta-Jouve, G and Carrión, VJ and Nibbering, PH and Siegler, MA and de Boer, W and Hankemeier, T and van Wezel, GP}, title = {Atypical Spirotetronate Polyketides Identified in the Underexplored Genus Streptacidiphilus.}, journal = {The Journal of organic chemistry}, volume = {85}, number = {16}, pages = {10648-10657}, pmid = {32691599}, issn = {1520-6904}, abstract = {More than half of all antibiotics and many other bioactive compounds are produced by the actinobacterial members of the genus Streptomyces. It is therefore surprising that virtually no natural products have been described for its sister genus Streptacidiphilus within Streptomycetaceae. Here, we describe an unusual family of spirotetronate polyketides, called streptaspironates, which are produced by Streptacidiphilus sp. P02-A3a, isolated from decaying pinewood. The characteristic structural and genetic features delineating spirotetronate polyketides could be identified in streptaspironates A (1) and B (2). Conversely, streptaspironate C (3) showed an unprecedented tetronate-less macrocycle-less structure, which was likely produced from an incomplete polyketide chain, together with an intriguing decarboxylation step, indicating a hypervariable biosynthetic machinery. Taken together, our work enriches the chemical space of actinobacterial natural products and shows the potential of Streptacidiphilus as producers of new compounds.}, }
@article {pmid32690378, year = {2020}, author = {Zhang, X and Fan, L and Wu, J and Xu, H and Leung, WY and Fu, K and Wu, J and Liu, K and Man, K and Yang, X and Han, J and Ren, J and Yu, J}, title = {Erratum to: &quot;Macrophage p38 alpha promotes nutritional steatohepatitis through M1 polarization (J Hepatol 2019; 71(1):163-174)&quot;.}, journal = {Journal of hepatology}, volume = {73}, number = {3}, pages = {742-743}, doi = {10.1016/j.jhep.2020.06.019}, pmid = {32690378}, issn = {1600-0641}, }
@article {pmid32688217, year = {2020}, author = {Dey, P and Olmstead, BD and Sasaki, GY and Vodovotz, Y and Yu, Z and Bruno, RS}, title = {Epigallocatechin gallate but not catechin prevents nonalcoholic steatohepatitis in mice similar to green tea extract while differentially affecting the gut microbiota.}, journal = {The Journal of nutritional biochemistry}, volume = {84}, number = {}, pages = {108455}, doi = {10.1016/j.jnutbio.2020.108455}, pmid = {32688217}, issn = {1873-4847}, abstract = {Catechin-rich green tea extract (GTE) protects against nonalcoholic steatohepatitis (NASH) by alleviating gut-derived endotoxin translocation and hepatic Toll-like receptor-4 (TLR4)-nuclear factor κB (NFκB) inflammation. We hypothesized that intact GTE would attenuate NASH-associated responses along the gut-liver axis to a greater extent than purified (-)-epigallocatechin gallate (EGCG) or (+)-catechin (CAT). Male C57BL/6J mice were fed a low-fat diet, a high-fat (HF) diet, or the HF diet with 2% GTE, 0.3% EGCG or 0.3% CAT for 8 weeks prior to assessing NASH relative to endotoxemia, hepatic and intestinal inflammation, intestinal tight junction proteins (TJPs) and gut microbial ecology. GTE prevented HF-induced obesity to a greater extent than EGCG and CAT, whereas GTE and EGCG more favorably attenuated insulin resistance. GTE, EGCG and CAT similarly attenuated serum alanine aminotransferase and serum endotoxin, but only GTE and EGCG fully alleviated HF-induced NASH. However, hepatic TLR4/NFκB inflammatory responses that were otherwise increased in HF mice were similarly attenuated by GTE, EGCG and CAT. Each treatment also similarly prevented the HF-induced loss in expression of intestinal TJPs and hypoxia inducible factor-1α and the otherwise increased levels of ileal and colonic TNFα mRNA and fecal calprotectin protein concentrations. Gut microbial diversity that was otherwise lowered in HF mice was maintained by GTE and CAT only. Further, microbial metabolic functions were more similar between GTE and CAT. Collectively, GTE catechins similarly protect against endotoxin-TLR4-NFκB inflammation in NASH, but EGCG and CAT exert differential prebiotic and antimicrobial activities suggesting that catechin-mediated shifts in microbiota composition are not entirely responsible for their benefits along the gut-liver axis.}, }
@article {pmid32688002, year = {2020}, author = {Zhou, WH and Wang, YT and Lian, ZH and Yang, TT and Zeng, QW and Feng, SW and Fang, Z and Shu, WS and Huang, LN and Ye, ZH and Liao, B and Li, JT}, title = {Revegetation approach and plant identity unequally affect structure, ecological network and function of soil microbial community in a highly acidified mine tailings pond.}, journal = {The Science of the total environment}, volume = {744}, number = {}, pages = {140793}, doi = {10.1016/j.scitotenv.2020.140793}, pmid = {32688002}, issn = {1879-1026}, mesh = {Biodegradation, Environmental ; *Microbiota ; Ponds ; Soil ; Soil Microbiology ; Soil Pollutants/*analysis ; }, abstract = {Owing to its sustainability and low cost, direct revegetation (DR) has been considered a promising alternative to capped revegetation (CR) for dealing with the serious environmental problem derived from various types of mine wastelands that are widespread in the world. However, a direct comparison of the performance of these two revegetation approaches for reclamation of extremely acidic mine wastelands and the underlying mechanisms is still lacking. To bridge this critical knowledge gap, we established 5000 m2 of vegetation on a highly acidified (pH < 3) Pb/Zn mine tailings pond employing both CR and DR schemes (2500 m2 for each scheme). We then profiled the structure, ecological network and function of soil microbial communities associated with two dominant plant species of the vegetations via high-throughput sequencing. Our results showed that CR and DR achieved a vegetation coverage of 59.7% and 90.5% within two years, respectively. This pattern was accompanied by higher concentrations of plant nutrients and lower acidification potentials in topsoils of the rhizospheres of the vegetation established by DR compared to those of CR. Revegetation approach, rather than plant identity, mostly affected the structure, ecological network and function of soil microbial community in the mine tailings pond. Rhizosphere soils of the vegetation established by DR generally had higher microbial diversity, higher relative abundances of dominant microbial phyla (e.g. Nitrospirae) that can aid plant uptake of nutrients, more complicated microbial interactive networks and more microbial genes responsible for nutrient cycling than those by CR. As the first report on a direct comparison of CR and DR schemes for reclamation of an extremely acidic mine wasteland, our study has important implications for not only the understanding of microbial ecology in revegetated mine wastelands but also the further development of sustainable revegetation schemes.}, }
@article {pmid32686214, year = {2020}, author = {Liu, D and Howell, K}, title = {Community succession of the grapevine fungal microbiome in the annual growth cycle.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15172}, pmid = {32686214}, issn = {1462-2920}, support = {//University of Melbourne/ ; AGW Ph1602//Wine Australia/ ; }, abstract = {Microbial ecology and activity in wine production influences grapevine health and productivity, conversion of sugar to ethanol during fermentation, wine aroma, wine quality and distinctiveness. Fungi in the vineyard ecosystem are not well described. Here, we characterized the spatial and temporal dynamics of fungal communities associated with the grapevine (grapes, flowers, leaves, and roots) and soils over an annual growth cycle in two vineyards to investigate the influences of grape habitat, plant developmental stage (flowering, fruit set, veraison, and harvest), vineyards, and climatic conditions. Fungi were influenced by both the grapevine habitat and plant development stage. The core microbiome was prioritized over space and time, and the identified core members drove seasonal community succession. The developmental stage of veraison, where the grapes undergo a dramatic change in metabolism and start accumulating sugar, coincided with a distinct shift in fungal communities. Co-occurrence networks showed strong correlations between the plant microbiome, the soil microbiome, and weather indices. Our study describes the complex ecological dynamics that occur in microbial assemblages over a growing season and highlight succession of the core community in vineyards.}, }
@article {pmid32685479, year = {2020}, author = {Li, Z and Ni, M and Yu, H and Wang, L and Zhou, X and Chen, T and Liu, G and Gao, Y}, title = {Gut Microbiota and Liver Fibrosis: One Potential Biomarker for Predicting Liver Fibrosis.}, journal = {BioMed research international}, volume = {2020}, number = {}, pages = {3905130}, pmid = {32685479}, issn = {2314-6141}, abstract = {Purpose: To investigate the relationship between gut microbiota and liver fibrosis and establish a microbiota biomarker for detecting and staging liver fibrosis.<br><br>Methods: 131 Wistar rats were used in our study, and liver fibrosis was induced by carbon tetrachloride. Stool samples were collected within 72 hours after the last administration. The V4 regions of 16S rRNA gene were amplified. The sequencing data was processed using the Quantitative Insights Into Microbial Ecology (QIIME version 1.9). The diversity, principal coordinate analysis (PCoA), nonmetric multidimensional scaling (NMDS), and linear discriminant analysis (LDA) effect size (LEfSe) were performed. Random-Forest classification was performed for discriminating the samples from different groups. Microbial function was assessed using the PICRUST.<br><br>Results: The Simpson in the control group was lower than that in the liver fibrosis group (p = 0.048) and differed significantly among different fibrosis stages (p = 0.047). The Chao1 index in the control group was higher than that in the liver fibrosis group (p < 0.001). NMDS analysis showed a marked difference between the control and liver fibrosis groups (p < 0.001). PCoA analysis indicated the different community composition between the control and liver fibrosis groups with variances of PC1 13.76% and PC2 5.89% and between different liver fibrosis stages with variances of PC1 10.51% and PC2 7.78%. LEfSe analysis showed alteration of gut microbiota in the liver fibrosis group. Biomarkers obtained from Random-Forest classification showed excellent diagnostic accuracy in prediction of liver fibrosis with AUROCs of 0.99. The AUROCs were 0.77~0.84 in prediction of stage F4. There were six increased and 17 decreased metabolic functions in the liver fibrosis group and 6 metabolic functions significantly differed among four liver fibrosis stages.<br><br>Conclusion: Gut microbiota is a potential biomarker for detecting and staging liver fibrosis with high diagnostic accuracies.}, }
@article {pmid32681284, year = {2020}, author = {Varasteh, T and Hamerski, L and Tschoeke, D and Lima, AS and Garcia, G and Cosenza, CAN and Thompson, C and Thompson, F}, title = {Conserved Pigment Profiles in Phylogenetically Diverse Symbiotic Bacteria Associated with the Corals Montastraea cavernosa and Mussismilia braziliensis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01551-4}, pmid = {32681284}, issn = {1432-184X}, abstract = {Pigmented bacterial symbionts play major roles in the health of coral holobionts. However, there is scarce knowledge on the diversity of these microbes for several coral species. To gain further insights into holobiont health, pigmented bacterial isolates of Fabibacter pacificus (Bacteroidetes; n = 4), Paracoccus marcusii (Alphaproteobacteria; n = 1), and Pseudoalteromonas shioyasakiensis (Gammaproteobacteria; n = 1) were obtained from the corals Mussismilia braziliensis and Montastraea cavernosa in Abrolhos Bank, Brazil. Cultures of these bacterial symbionts produced strong antioxidant activity (catalase, peroxidase, and oxidase). To explore these bacterial isolates further, we identified their major pigments by HPLC and mass spectrometry. The six phylogenetically diverse symbionts had similar pigment patterns and produced myxol and keto-carotene. In addition, similar carotenoid gene clusters were confirmed in the whole genome sequences of these symbionts, which reinforce their antioxidant potential. This study highlights the possible roles of bacterial symbionts in Montastraea and Mussismilia holobionts.}, }
@article {pmid32681144, year = {2020}, author = {Hylling, O and Carstens, AB and Kot, W and Hansen, M and Neve, H and Franz, CMAP and Johansen, A and Ellegaard-Jensen, L and Hansen, LH}, title = {Two novel bacteriophage genera from a groundwater reservoir highlight subsurface environments as underexplored biotopes in bacteriophage ecology.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {11879}, pmid = {32681144}, issn = {2045-2322}, support = {5157-00004B//Innovationsfonden/ ; 5157-00004B//Innovationsfonden/ ; 5157-00004B//Innovationsfonden/ ; AUFF-E-2017-7-21//Aarhus Universitets Forskningsfond/ ; }, abstract = {Although bacteriophages are central entities in bacterial ecology and population dynamics, there is currently no literature on the genomes of bacteriophages isolated from groundwater. Using a collection of bacterial isolates from an aquifer as hosts, this study isolated, sequenced and characterised two bacteriophages native to the groundwater reservoir. Host phylogenetic analyses revealed that the phages targeted B. mycoides and a novel Pseudomonas species. These results suggest that both bacteriophages represent new genera, highlighting that groundwater reservoirs, and probably other subsurface environments as well, are underexplored biotopes in terms of the presence and ecology of bacteriophages.}, }
@article {pmid32680791, year = {2020}, author = {Daisley, BA and Chmiel, JA and Pitek, AP and Thompson, GJ and Reid, G}, title = {Missing Microbes in Bees: How Systematic Depletion of Key Symbionts Erodes Immunity.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2020.06.006}, pmid = {32680791}, issn = {1878-4380}, abstract = {Pesticide exposure, infectious disease, and nutritional stress contribute to honey bee mortality and a high rate of colony loss. This realization has fueled a decades-long investigation into the single and combined effects of each stressor and their overall bearing on insect physiology. However, one element largely missing from this research effort has been the evaluation of underlying microbial communities in resisting environmental stressors and their influence on host immunity and disease tolerance. In humans, multigenerational bombardment by antibiotics is linked with many contemporary diseases. Here, we draw a parallel conclusion for the case in honey bees and suggest that chronic exposure to antimicrobial xenobiotics can systematically deplete honey bees of their microbes and hamper cross-generational preservation of host-adapted symbionts that are crucial to health.}, }
@article {pmid32679495, year = {2020}, author = {Moopantakath, J and Imchen, M and Siddhardha, B and Kumavath, R}, title = {16s rRNA metagenomic analysis reveals predominance of Crtl and CruF genes in Arabian Sea coast of India.}, journal = {The Science of the total environment}, volume = {743}, number = {}, pages = {140699}, doi = {10.1016/j.scitotenv.2020.140699}, pmid = {32679495}, issn = {1879-1026}, mesh = {Archaea/*genetics ; Bacteria/genetics ; Geologic Sediments ; India ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Microbial communities perform crucial biogeochemical cycles in distinct ecosystems. Halophilic microbial communities are enriched in the saline areas. Hence, haloarchaea have been primarily studied in salterns and marine biosystems with the aim to harness haloarcheal carotenoids biosynthesis. In this study, sediment from several distinct biosystems (mangrove, seashore, estuary, river, lake, salt pan and island) across the Arabian coastal region of India were collected and analyzed though 16s rRNA metagenomic and whole genome approach to elucidated the dominant representative genre, haloarcheal diversity, and the prevalence of Crtl and CruF genes. We found that the microbial diversity in mangrove sediment (794 OTUs) was highest and lowest in lake and river (558-560 OTUs). Moreover, the bacterial domain dominated in all biosystems (96.00-99.45%). Top 10 abundant genera were involved in biochemical cycles such as sulfur, methane, ammonia, hydrocarbon degradation, and antibiotics production. The Archaea was mainly composed of Haloarchaea, Methanobacteria, Methanococci, Methanomicrobia and Crenarchaeota. Carotenoid gene, Crtl, was observed in a major portion (abundance 60%; diversity 45%) of microbial community. Interestingly, we found that all species under haloarcheal class that were represented in fresh as well as marine biosystems encodes CruF gene (bacterioruberin carotenoid). Our study demonstrates the high microbial diversity in various ecosystems, enrichment of Crtl gene, and also shows that Crtl and CruF genes are highly abundant in haloarcheal genera. The finding of ecosystems specific Crtl and CruF encoding genera opens up a promising area in bioprospecting the carotenoid derivatives from the wide range of natural biosystems.}, }
@article {pmid32678322, year = {2020}, author = {Li, L and Wang, S and Wang, H and Sahu, SK and Marin, B and Li, H and Xu, Y and Liang, H and Li, Z and Cheng, S and Reder, T and Çebi, Z and Wittek, S and Petersen, M and Melkonian, B and Du, H and Yang, H and Wang, J and Wong, GK and Xu, X and Liu, X and Van de Peer, Y and Melkonian, M and Liu, H}, title = {Author Correction: The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {9}, pages = {1280}, doi = {10.1038/s41559-020-1268-5}, pmid = {32678322}, issn = {2397-334X}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32677880, year = {2020}, author = {Zhang, Q and Xu, J and Warren, A and Yang, R and Shen, Z and Yi, Z}, title = {Assessing the utility of Hsp90 gene for inferring evolutionary relationships within the ciliate subclass Hypotricha (Protista, Ciliophora).}, journal = {BMC evolutionary biology}, volume = {20}, number = {1}, pages = {86}, pmid = {32677880}, issn = {1471-2148}, support = {31772440//National Natural Science Foundation of China/International ; 31970486//National Natural Science Foundation of China/International ; 31672279//National Natural Science Foundation of China/International ; 2018SDKJ0406-1//Marine S&amp;T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao)/International ; GDOE(2019)A23//Guangdong MEPP Fund/International ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Ciliophora/classification/*genetics ; DNA, Ribosomal/genetics ; Databases, Genetic ; Databases, Protein ; *Evolution, Molecular ; HSP90 Heat-Shock Proteins/chemistry/*genetics ; Phylogeny ; }, abstract = {BACKGROUND: Although phylogenomic analyses are increasingly used to reveal evolutionary relationships among ciliates, relatively few nuclear protein-coding gene markers have been tested for their suitability as candidates for inferring phylogenies within this group. In this study, we investigate the utility of the heat-shock protein 90 gene (Hsp90) as a marker for inferring phylogenetic relationships among hypotrich ciliates.<br><br>RESULTS: A total of 87 novel Hsp90 gene sequences of 10 hypotrich species were generated. Of these, 85 were distinct sequences. Phylogenetic analyses based on these data showed that: (1) the Hsp90 gene amino acid trees are comparable to the small subunit rDNA tree for recovering phylogenetic relationships at the rank of class, but lack sufficient phylogenetic signal for inferring evolutionary relationships at the genus level; (2) Hsp90 gene paralogs are recent and therefore unlikely to pose a significant problem for recovering hypotrich clades; (3) definitions of some hypotrich orders and families need to be revised as their monophylies are not supported by various gene markers; (4) The order Sporadotrichida is paraphyletic, but the monophyly of the &quot;core&quot; Urostylida is supported; (5) both the subfamily Oxytrichinae and the genus Urosoma seem to be non-monophyletic, but monophyly of Urosoma is not rejected by AU tests.<br><br>CONCLUSIONS: Our results for the first time demonstrate that the Hsp90 gene is comparable to SSU rDNA for recovering phylogenetic relationships at the rank of class, and its paralogs are unlikely to pose a significant problem for recovering hypotrich clades. This study shows the value of careful gene marker selection for phylogenomic analyses of ciliates.}, }
@article {pmid32673982, year = {2020}, author = {Ali, M and Yue, D}, title = {Population dynamics of microbial species under high and low ammonia nitrogen in the alternate layer bioreactor landfill (ALBL) approach.}, journal = {Bioresource technology}, volume = {315}, number = {}, pages = {123787}, doi = {10.1016/j.biortech.2020.123787}, pmid = {32673982}, issn = {1873-2976}, mesh = {*Ammonia ; Bioreactors ; Ecosystem ; Methane ; Nitrogen ; Population Dynamics ; *Refuse Disposal ; Waste Disposal Facilities ; }, abstract = {Anaerobic landfill process is still believed to be a complex ecosystem due to the lack of knowledge on the functional activities of microbial species. This research sought to introduce a novel landfill bioreactor, named here as the alternate layer bioreactor landfill (ALBL) of fresh MSW (FW) and stabilized waste (CT) to avoid inhibitory conditions for the microbial species in anaerobic landfill. The stabilized waste layer in the bottom of landfill cell significantly changed microbial ecology of fresh MSW which in turn reduced the concentrations of NH4-N (29-31%) and VFAs (33-38%) in the ALBL approach, compared to fresh MSW disposal in sanitary landfill. The reduction of NH4-N favored early onset of methanogenesis within 6 weeks and methane (CH4) content of landfill gas increased from 11% to 40-50% (v/v), owing to the coexistence of Methanosarcinales (36-50%) and Methanomicrobiales (26-28%) archaea. The acetoclastic methanogenesis was achieved by reducing NH4-N toxicity in the ALBL.}, }
@article {pmid32670501, year = {2020}, author = {Khot, V and Strous, M and Hawley, AK}, title = {Computational approaches in viral ecology.}, journal = {Computational and structural biotechnology journal}, volume = {18}, number = {}, pages = {1605-1612}, pmid = {32670501}, issn = {2001-0370}, abstract = {Dynamic virus-host interactions play a critical role in regulating microbial community structure and function. Yet for decades prior to the genomics era, viruses were largely overlooked in microbial ecology research, as only low-throughput culture-based methods of discovering viruses were available. With the advent of metagenomics, culture-independent techniques have provided exciting opportunities to discover and study new viruses. Here, we review recently developed computational methods for identifying viral sequences, exploring viral diversity in environmental samples, and predicting hosts from metagenomic sequence data. Methods to analyze viruses in silico utilize unconventional approaches to tackle challenges unique to viruses, such as vast diversity, mosaic viral genomes, and the lack of universal marker genes. As the field of viral ecology expands exponentially, computational advances have become increasingly important to gain insight into the role viruses in diverse habitats.}, }
@article {pmid32666305, year = {2020}, author = {Castelli, L and Branchiccela, B and Garrido, M and Invernizzi, C and Porrini, M and Romero, H and Santos, E and Zunino, P and Antúnez, K}, title = {Impact of Nutritional Stress on Honeybee Gut Microbiota, Immunity, and Nosema ceranae Infection.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {908-919}, doi = {10.1007/s00248-020-01538-1}, pmid = {32666305}, issn = {1432-184X}, support = {CSIC 6406//Comisión Sectorial de Investigación Científica (UY)/ ; POS_NAC_2013_1_12228//Agencia Nacional de Investigación e Innovación/ ; }, abstract = {Honeybees are important pollinators, having an essential role in the ecology of natural and agricultural environments. Honeybee colony losses episodes reported worldwide and have been associated with different pests and pathogens, pesticide exposure, and nutritional stress. This nutritional stress is related to the increase in monoculture areas which leads to a reduction of pollen availability and diversity. In this study, we examined whether nutritional stress affects honeybee gut microbiota, bee immunity, and infection by Nosema ceranae, under laboratory conditions. Consumption of Eucalyptus grandis pollen was used as a nutritionally poor-quality diet to study nutritional stress, in contraposition to the consumption of polyfloral pollen. Honeybees feed with Eucalyptus grandis pollen showed a lower abundance of Lactobacillus mellifer and Lactobacillus apis (Firm-4 and Firm-5, respectively) and Bifidobacterium spp. and a higher abundance of Bartonella apis, than honeybees fed with polyfloral pollen. Besides the impact of nutritional stress on honeybee microbiota, it also decreased the expression levels of vitellogenin and genes associated to immunity (glucose oxidase, hymenoptaecin and lysozyme). Finally, Eucalyptus grandis pollen favored the multiplication of Nosema ceranae. These results show that nutritional stress impacts the honeybee gut microbiota, having consequences on honeybee immunity and pathogen development. Those results may be useful to understand the influence of modern agriculture on honeybee health.}, }
@article {pmid32666084, year = {2020}, author = {Zhang, T and Fukuda, K and Topp, E and Zhu, YG and Smalla, K and Tiedje, JM and Larsson, DGJ}, title = {Editorial: The Environmental Dimension of Antibiotic Resistance.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {8}, pages = {}, doi = {10.1093/femsec/fiaa130}, pmid = {32666084}, issn = {1574-6941}, }
@article {pmid32664604, year = {2020}, author = {Marzorati, M and Abbeele, PVD and Bubeck, SS and Bayne, T and Krishnan, K and Young, A and Mehta, D and DeSouza, A}, title = {Bacillus subtilis HU58 and Bacillus coagulans SC208 Probiotics Reduced the Effects of Antibiotic-Induced Gut Microbiome Dysbiosis in An M-SHIME® Model.}, journal = {Microorganisms}, volume = {8}, number = {7}, pages = {}, pmid = {32664604}, issn = {2076-2607}, abstract = {Benefits associated with probiotic use have been reported; however, the mechanisms behind these benefits are poorly understood. The effects of a probiotic formulation (MegaDuo™) containing Bacillus coagulans SC208 and Bacillus subtilis HU58 on intestinal permeability and immune markers was assessed using a combination of the in vitro gut model, the mucosal simulator of the human intestinal microbial ecosystem (M-SHIME®), and an in vitro inflammatory bowel disease-like Caco-2/THP1 co-culture model in both healthy and antibiotic-induced dysbiosis conditions. Established M-SHIME® proximal colon vessels were treated with/without clindamycin (1 week) and then with/without daily MegaDuo™ treatment (2 weeks). The mucosal and luminal microbial communities were sampled weekly. Suspensions were removed from the proximal colon vessels after 1 and 2 weeks of MegaDuo™ treatment and added to the co-culture system. Transepithelial resistance (membrane barrier function), cytokine/chemokine release, and NFκB activity were then measured. Under conditions of antibiotic-induced dysbiosis, suspensions from MegaDuo™ treated vessels showed reduced gut membrane barrier damage and decreased levels of TNFα and IL-6 compared with suspensions from untreated vessels; no appreciable differences were observed under healthy conditions. MegaDuo™ treatment had no effect on NFκB activity of THP1-Blue™ cells. The potential benefits of MegaDuo™ treatment appeared most evident after 2 weeks of treatment.}, }
@article {pmid32661888, year = {2020}, author = {Szczepańska, A and Kiewra, D and Plewa-Tutaj, K and Dyczko, D and Guz-Regner, K}, title = {Sensitivity of Ixodes ricinus (L., 1758) and Dermacentor reticulatus (Fabr., 1794) ticks to entomopathogenic fungi isolates: preliminary study.}, journal = {Parasitology research}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00436-020-06805-1}, pmid = {32661888}, issn = {1432-1955}, abstract = {Entomopathogenic fungi of the genus Beauveria and Metarhizium play an important role in controlling the population of arthropods. However, the data on their effectiveness against ticks focus mainly on species that do not occur in Europe. The aim of the study was to assess the effectiveness of entomopathogenic fungi against two of the most important tick species in Europe: Ixodes ricinus and Dermacentor reticulatus. In our study, the majority of tested entomopathogenic fungi strains showed potential efficacy against both tick species; however, D. reticulatus was less susceptible in comparison to I. ricinus. The observed mortality of ticks was up to 100% by using all commercial strains as well as three out of nine of the environmental strains. Among all tested fungi, the most effective against both tick species was environmental strain Metarhizium anisopliae LO4(1) with LC50 values: 2.6 × 103 cfu/ml-5.7 × 105 cfu/ml. Botanigard proved to be more effective than MET52 with LC50 values: 6.8 × 103 cfu/ml-3.3 × 106 cfu/ml. The conducted bioassays indicate the potential possibility of using the environmental isolates of entomopathogenic fungi, as well as commercial strains in control of local populations of I. ricinus and D. reticulatus; however, the possibility of using them in vivo requires more research.}, }
@article {pmid32659564, year = {2020}, author = {Ray, D and Leary, P and Livens, F and Gray, N and Morris, K and Law, KA and Fuller, AJ and Abrahamsen-Mills, L and Howe, J and Tierney, K and Muir, G and Law, GTW}, title = {Controls on anthropogenic radionuclide distribution in the Sellafield-impacted Eastern Irish Sea.}, journal = {The Science of the total environment}, volume = {743}, number = {}, pages = {140765}, doi = {10.1016/j.scitotenv.2020.140765}, pmid = {32659564}, issn = {1879-1026}, abstract = {Understanding anthropogenic radionuclide biogeochemistry and mobility in natural systems is key to improving the management of radioactively contaminated environments and radioactive wastes. Here, we describe the contemporary depth distribution and phase partitioning of 137Cs, Pu, and 241Am in two sediment cores taken from the Irish Sea (Site 1: the Irish Sea Mudpatch; Site 2: the Esk Estuary). Both sites are located ~10 km from the Sellafield nuclear site. Low-level aqueous radioactive waste has been discharged from the Sellafield site into the Irish Sea for >50 y. We compare the depth distribution of the radionuclides at each site to trends in sediment and porewater redox chemistry, using trace element abundance, microbial ecology, and sequential extractions, to better understand the relative importance of sediment biogeochemistry vs. physical controls on radionuclide distribution/post-depositional mobility in the sediments. We highlight that the distribution of 137Cs, Pu, and 241Am at both sites is largely controlled by physical mixing of the sediments, physical transport processes, and sediment accumulation. Interestingly, at the Esk Estuary, microbially-mediated redox processes (considered for Pu) do not appear to offer significant controls on Pu distribution, even over decadal timescales. We also highlight that the Irish Sea Mudpatch likely still acts as a source of historical pollution to other areas in the Irish Sea, despite ever decreasing levels of waste output from the Sellafield site.}, }
@article {pmid32658690, year = {2020}, author = {Bai, X and Zhong, X and Guo, C and Gui, Y and Xu, H}, title = {Colonization dynamics of protozoan communities in marine bioassessment surveys using two modified sampling systems.}, journal = {Marine pollution bulletin}, volume = {157}, number = {}, pages = {111325}, doi = {10.1016/j.marpolbul.2020.111325}, pmid = {32658690}, issn = {1879-3363}, mesh = {Biodiversity ; China ; *Ciliophora ; Ecosystem ; Environmental Monitoring ; Surveys and Questionnaires ; }, abstract = {Colonization dynamics of protozoan communities were investigated at a depth of 1 m in the coastal waters of the Yellow Sea, northern China from May to June 2019, using modified glass slide (mGS) and modified polyurethane foam unit (mPFU) systems. The colonization process and growth curves of protozoa were well fitted to the MacArthur-Wilson and logistic models in both systems, respectively. However, they showed significant differences in both colonization dynamics and biodiversity/functional parameters between the mGS and mPFU systems. The H' (species diversity), the G (colonization rate), and Amax (maximum abundance) were higher, while the value of T90% (the time for reaching 90% equilibrium species number) was lower in the mGS system than those in the mPFU system. Multivariate analyses demonstrated that protozoa showed different models of colonization dynamics in both systems. The results suggest that the mGS system might be more effective than the mPFU system in marine bioassessment surveys.}, }
@article {pmid32656607, year = {2020}, author = {Xie, XG and Zhao, YY and Yang, Y and Lu, F and Dai, CC}, title = {Endophytic Fungus Alleviates Soil Sickness in Peanut Crops by Improving the Carbon Metabolism and Rhizosphere Bacterial Diversity.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01555-0}, pmid = {32656607}, issn = {1432-184X}, support = {31870478//National Natural Science Foundation of China/ ; 17CXTD00014//Program for Jiangsu Excellent Scientific and Technological Innovation Team/ ; }, abstract = {Endophytic fungi can profoundly affect host productivity, but the underlying mechanisms of these effects are only partly understood. As the most important regulators of plant-soil feedback, root exudates can easily cause soil sickness in continuous monoculture systems by reducing certain microbes in the rhizosphere. In this study, exudates from roots colonized by the endophytic fungus Phomopsis liquidambaris significantly increased rhizosphere bacterial abundance, soil respiration, microbial biomass and enzyme activities in a long-term continuously cropped peanut soil. Further analysis revealed that P. liquidambaris-colonized root exudates clearly altered the carbon metabolism and rhizosphere bacterial diversity, which were closely correlated with changes in soil chemical properties caused by the exudates from the colonized roots. Finally, a synthetic root exudate experiment further confirmed that the root exudates derived from P. liquidambaris colonization can indeed play an important role in promoting peanut growth. Therefore, these results show that this endophytic fungus could improve the carbon metabolism and rhizosphere bacterial community in long-term monoculture soils via exudates from colonized roots, which contribute to the alleviation of soil sickness.}, }
@article {pmid32656252, year = {2020}, author = {Adhikari, B and Jun, SR and Kwon, YM and Kiess, AS and Adhikari, P}, title = {Effects of Housing Types on Cecal Microbiota of Two Different Strains of Laying Hens During the Late Production Phase.}, journal = {Frontiers in veterinary science}, volume = {7}, number = {}, pages = {331}, pmid = {32656252}, issn = {2297-1769}, abstract = {Due to animal welfare issues, European Union has banned the use of conventional cages (CC) and non-EU countries including the US are also under constant public pressure to restrict their use in egg production. Very limited information is available on the composition of the microbial community of hens raised in different housing environments. This study was conducted to determine the effects of CC and enriched colony cages (EC) on cecal microbiota of two commercial laying hen strains, Hy-Line W36 (W36) and Hy-Line Brown (HB) during the late production stage (53, 58, 67, and 72 weeks of age). Cecal microbiota was studied by analyzing 16S rRNA gene sequences with Quantitative Insights Into Microbial Ecology (QIIME) 2 ver. 2018.8. Differentially abundant taxa were identified by Linear discriminant analysis Effect Size (LEfSe) analysis (P < 0.05, LDA score > 2.0). At phylum level, Actinobacteria was significantly enriched in W36 at all time points while Synergistetes (53 weeks), Spirochaetes (58 weeks), and Synergistetes and Spirochaetes (67 weeks) were significantly higher in HB. At genus level, Bifidobacterium (at all time points) and butyric acid producing genera such as Butyricicoccus and Subdoligranulum (58 and 72 weeks) were significantly higher in W36 as compared to HB. Moreover, Proteobacteria (72 weeks) and its associated genus Campylobacter (67 and 72 weeks) were significantly enriched in EC as compared to CC. Alpha diversity was significantly higher in HB (at all time points) and in EC (67 weeks) as compared to W36 and CC, respectively. Similarly, there was a significant difference in community structure (beta diversity) between W36 and HB (all time points) as well as between EC and CC (67 weeks). The effect of housing and strains was not only seen at the bacterial composition and structure but also reflected at their functional level. Notably, KEGG metabolic pathways predicted to be involved in carbohydrates degradation and amino acids biosynthesis by PICRUSt analysis were significantly different between W36 and HB housed at CC and EC. In sum, cecal microbiota composition, diversities, and their functional pathways were affected by housing type which further varied between two commercial laying hen strains, HB and W36. This suggests that both housing and genetic strains of laying hens should be considered for selection of the alternative housing systems such as enriched colony cage.}, }
@article {pmid32655529, year = {2020}, author = {Benítez-Páez, A and Olivares, M and Szajewska, H and Pieścik-Lech, M and Polanco, I and Castillejo, G and Nuñez, M and Ribes-Koninckx, C and Korponay-Szabó, IR and Koletzko, S and Meijer, CR and Mearin, ML and Sanz, Y}, title = {Breast-Milk Microbiota Linked to Celiac Disease Development in Children: A Pilot Study From the PreventCD Cohort.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1335}, pmid = {32655529}, issn = {1664-302X}, abstract = {Celiac disease (CeD) is an immune-mediated disorder triggered by exposure to dietary gluten proteins in genetically predisposed individuals. In addition to the host genome, the microbiome has recently been linked to CeD risk and pathogenesis. To progress in our understanding of the role of breast milk microbiota profiles in CeD, we have analyzed samples from a sub-set of mothers (n = 49) included in the PreventCD project, whose children did or did not develop CeD. The results of the microbiota data analysis indicated that neither the BMI, HLA-DQ genotype, the CeD condition nor the gluten-free diet of the mothers could explain the human milk microbiota profiles. Nevertheless, we found that origin country, the offspring's birth date and, consequently, the milk sampling date influenced the abundance and prevalence of microbes in human milk, undergoing a transition from an anaerobic to a more aerobic microbiota, including potential pathogenic species. Furthermore, certain microbial species were more abundant in milk samples from mothers whose children went on to develop CeD compared to those that remained healthy. These included increases in facultative methylotrophs such as Methylobacterium komagatae and Methylocapsa palsarum as well as in species such as Bacteroides vulgatus, that consumes fucosylated-oligosaccharides present in human milk, and other breast-abscess associated species. Theoretically, these microbiota components could be vertically transmitted from mothers-to-infants during breastfeeding, thereby influencing CeD risk.}, }
@article {pmid32655525, year = {2020}, author = {Raes, EJ and Karsh, K and Kessler, AJ and Cook, PLM and Holmes, BH and van de Kamp, J and Bodrossy, L and Bissett, A}, title = {Can We Use Functional Genetics to Predict the Fate of Nitrogen in Estuaries?.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1261}, pmid = {32655525}, issn = {1664-302X}, abstract = {Increasing nitrogen (N) loads present a threat to estuaries, which are among the most heavily populated and perturbed parts of the world. N removal is largely mediated by the sediment microbial process of denitrification, in direct competition to dissimilatory nitrate reduction to ammonium (DNRA), which recycles nitrate to ammonium. Molecular proxies for N pathways are increasingly measured and analyzed, a major question in microbial ecology, however, is whether these proxies can add predictive power around the fate of N. We analyzed the diversity and community composition of sediment nirS and nrfA genes in 11 temperate estuaries, covering four types of land use in Australia, and analyzed how these might be used to predict N removal. Our data suggest that sediment microbiomes play a central role in controlling the magnitude of the individual N removal rates in the 11 estuaries. Inclusion, however, of relative gene abundances of 16S, nirS, nrfA, including their ratios did not improve physicochemical measurement-based regression models to predict rates of denitrification or DNRA. Co-occurrence network analyses of nirS showed a greater modularity and a lower number of keystone OTUs in pristine sites compared to urban estuaries, suggesting a higher degree of niche partitioning in pristine estuaries. The distinctive differences between the urban and pristine network structures suggest that the nirS gene could be a likely gene candidate to understand the mechanisms by which these denitrifying communities form and respond to anthropogenic pressures.}, }
@article {pmid32651453, year = {2020}, author = {Sauder, LA and Albertsen, M and Engel, K and Schwarz, J and Nielsen, PH and Wagner, M and Neufeld, JD}, title = {Correction: Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system.}, journal = {The ISME journal}, volume = {14}, number = {9}, pages = {2366}, doi = {10.1038/s41396-020-0714-3}, pmid = {32651453}, issn = {1751-7370}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32651355, year = {2020}, author = {Lian, Y and Yan, C and Lian, Y and Yang, R and Chen, Q and Ma, D and Lian, W and Liu, J and Luo, C and Ren, J and Xu, H}, title = {Long intergenic non-protein-coding RNA 01446 facilitates the proliferation and metastasis of gastric cancer cells through interacting with the histone lysine-specific demethylase LSD1.}, journal = {Cell death &amp; disease}, volume = {11}, number = {7}, pages = {522}, pmid = {32651355}, issn = {2041-4889}, support = {2019J01554//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/ ; }, abstract = {Growing evidences illustrated that long non-coding RNAs (lncRNAs) exhibited widespread effects on the progression of human cancers via various mechanisms. Long intergenic non-protein-coding RNA 01446 (LINC01446), a 3484-bp ncRNA, is known to locate at chromosome 7p12.1. However, its biological functions and specific action mechanism in gastric cancer (GC) are still unclear. In our study, LINC01446 was proved to be markedly upregulated in GC tissues relative to the normal tissues, and positively correlated with the poor survival of GC patients. The multivariate Cox regression model showed that LINC01446 functioned as an independent prognostic factor for the survival of GC patients. Functionally, LINC01446 facilitated the proliferation and metastasis of GC cells. Moreover, RNA-seq analysis demonstrated that LINC01446 knockdown primarily regulated the genes relating to the growth and migration of GC. Mechanistically, LINC01446 could widely interact with histone lysine-specific demethylase LSD1 and recruit LSD1 to the Ras-related dexamethasone-induced 1 (RASD1) promoter, thereby suppressing RASD1 transcription. Overall, these findings suggest that LINC01446/LSD1/RASD1 regulatory axis may provide bona fide targets for anti-GC therapies.}, }
@article {pmid32647153, year = {2020}, author = {Borrego, C and Sabater, S and Proia, L}, title = {Lifestyle preferences drive the structure and diversity of bacterial and archaeal communities in a small riverine reservoir.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {11288}, pmid = {32647153}, issn = {2045-2322}, abstract = {Spatial heterogeneity along river networks is interrupted by dams, affecting the transport, processing, and storage of organic matter, as well as the distribution of biota. We here investigated the structure of planktonic (free-living, FL), particle-attached (PA) and sediment-associated (SD) bacterial and archaeal communities within a small reservoir. We combined targeted-amplicon sequencing of bacterial and archaeal 16S rRNA genes in the DNA and RNA community fractions from FL, PA and SD, followed by imputed functional metagenomics, in order to unveil differences in their potential metabolic capabilities within the reservoir (tail, mid, and dam sections) and lifestyles (FL, PA, SD). Both bacterial and archaeal communities were structured according to their life-style preferences rather than to their location in the reservoir. Bacterial communities were richer and more diverse when attached to particles or inhabiting the sediment, while Archaea showed an opposing trend. Differences between PA and FL bacterial communities were consistent at functional level, the PA community showing higher potential capacity to degrade complex carbohydrates, aromatic compounds, and proteinaceous materials. Our results stressed that particle-attached prokaryotes were phylogenetically and metabolically distinct from their free-living counterparts, and that performed as hotspots for organic matter processing within the small reservoir.}, }
@article {pmid32638044, year = {2020}, author = {Lukoseviciute, L and Lebedeva, J and Kuisiene, N}, title = {Diversity of Polyketide Synthases and Nonribosomal Peptide Synthetases Revealed Through Metagenomic Analysis of a Deep Oligotrophic Cave.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01554-1}, pmid = {32638044}, issn = {1432-184X}, abstract = {Caves are considered to be extreme and challenging environments. It is believed that the ability of microorganisms to produce secondary metabolites enhances their survivability and adaptiveness in the energy-starved cave environment. Unfortunately, information on the genetic potential for the production of secondary metabolites, such as polyketides and nonribosomal peptides, is limited. In the present study, we aimed to identify and characterize genes responsible for the production of secondary metabolites in the microbial community of one of the deepest caves in the world, Krubera-Voronja Cave (43.4184 N 40.3083 E, Western Caucasus). The analysed sample materials included sediments, drinkable water from underground camps, soil and clay from the cave walls, speleothems and coloured spots from the cave walls. The type II polyketide synthases (PKSs) ketosynthases α and β and the adenylation domains of nonribosomal peptide synthetases (NRPSs) were investigated using a metagenomic approach. Taxonomic diversity analysis showed that most PKS sequences could be attributed to Actinobacteria followed by unclassified bacteria and Acidobacteria, while the NRPS sequences were more taxonomically diverse and could be assigned to Proteobacteria, Actinobacteria, Cyanobacteria, Firmicutes, Chloroflexi, etc. Only three putative metabolites could be predicted: an angucycline group polyketide, a massetolide A-like cyclic lipopeptide and a surfactin-like lipopeptide. The absolute majority of PKS and NRPS sequences showed low similarity with the sequences of the reference biosynthetic pathways, suggesting that these sequences could be involved in the production of novel secondary metabolites.}, }
@article {pmid32638043, year = {2020}, author = {Griffin, TW and Baer, JG and Ward, JE}, title = {Direct Comparison of Fecal and Gut Microbiota in the Blue Mussel (Mytilus edulis) Discourages Fecal Sampling as a Proxy for Resident Gut Community.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01553-2}, pmid = {32638043}, issn = {1432-184X}, support = {1559180//Directorate for Biological Sciences/ ; }, abstract = {Bivalves have ecological and economic importance but information regarding their associated microbiomes is lacking. As suspension feeders, bivalves capture and ingest a myriad of particles, and their digestive organs have a high throughput of particle-associated microbiota. To better understand the complement of transient and resident microbial communities, standard methods need to be developed. For example, fecal sampling could represent a convenient proxy for the gut microbiome and is simple, nondestructive, and allows for sampling of individuals through time. The goal of this study was to evaluate fecal sampling as a reliable proxy for gut microbiome assessment in the blue mussel (Mytilus edulis). Mussels were collected from the natural environment and placed into individual sterilized microcosms for 6 h to allow for fecal egestion. Feces and gut homogenates from the same individuals were sampled and subjected to 16S rRNA gene amplicon sequencing. Fecal communities of different mussels resembled each other but did not resemble gut communities. Fecal communities were significantly more diverse, in terms of amplicon sequence variant (ASV) richness and evenness, than gut communities. Results suggested a mostly transient nature for fecal microbiota. Nonetheless, mussels retained a distinct resident microbial community in their gut after fecal egestion that was dominated by ASVs belonging to Mycoplasma. The use of fecal sampling as a nondestructive substitute for direct sampling of the gut is strongly discouraged. Experiments that aim to study solely resident bivalve gut microbiota should employ an egestion period prior to gut sampling to allow time for voidance of transient microbes.}, }
@article {pmid32629308, year = {2020}, author = {Qi, Y and Beriot, N and Gort, G and Huerta Lwanga, E and Gooren, H and Yang, X and Geissen, V}, title = {Impact of plastic mulch film debris on soil physicochemical and hydrological properties.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {266}, number = {Pt 3}, pages = {115097}, doi = {10.1016/j.envpol.2020.115097}, pmid = {32629308}, issn = {1873-6424}, mesh = {Agriculture ; Ecosystem ; Hydrology ; Plastics ; *Soil ; *Soil Pollutants ; }, abstract = {The plastic mulch films used in agriculture are considered to be a major source of the plastic residues found in soil. Mulching with low-density polyethylene (LDPE) is widely practiced and the resulting macro- and microscopic plastic residues in agricultural soil have aroused concerns for years. Over the past decades, a variety of biodegradable (Bio) plastics have been developed in the hope of reducing plastic contamination of the terrestrial ecosystem. However, the impact of these Bio plastics in agroecosystems have not been sufficiently studied. Therefore, we investigated the impact of macro (around 5 mm) and micro (<1 mm) sized plastic debris from LDPE and one type of starch-based Bio mulch film on soil physicochemical and hydrological properties. We used environmentally relevant concentrations of plastics, ranging from 0 to 2% (w/w), identified by field studies and literature review. We studied the effects of the plastic residue on a sandy soil for one month in a laboratory experiment. The bulk density, porosity, saturated hydraulic conductivity, field capacity and soil water repellency were altered significantly in the presence of the four kinds of plastic debris, while pH, electrical conductivity and aggregate stability were not substantially affected. Overall, our research provides clear experimental evidence that microplastics affect soil properties. The type, size and content of plastic debris as well as the interactions between these three factors played complex roles in the variations of the measured soil parameters. Living in a plastic era, it is crucial to conduct further interdisciplinary studies in order to have a comprehensive understanding of plastic debris in soil and agroecosystems.}, }
@article {pmid32628807, year = {2020}, author = {Rejeb, IB and Dhen, N and Gargouri, M and Boulila, A}, title = {Chemical Composition, Antioxidant Potential and Enzymes Inhibitory Properties of Globe Artichoke By-Products.}, journal = {Chemistry &amp; biodiversity}, volume = {17}, number = {9}, pages = {e2000073}, doi = {10.1002/cbdv.202000073}, pmid = {32628807}, issn = {1612-1880}, abstract = {In this study, chemical composition and in vitro biological activities of artichoke by-products (leaves, floral stems and bracts) issued from two Tunisian varieties were evaluated. Analysis was performed by means of high-performance liquid chromatography with diode array detection coupled to electrospray ionization mass spectrometric (LC/DAD/ESI-MS). Total phenolic (TPC) and flavonoid (TFC) contents as well as the antioxidant activity conducted by three complementary methods, DPPH, ABTS and FRAP tests, were performed for each sample. Enzyme inhibitory effects against acetylcholinesterase, butyrylcholinesterase and α-amylase were also studied. Results showed that TPC and TFC varied according to variety as well as the plant part. Bracts presented the highest TPC values (10-15 mg GAE/g DW), while leaves were distinguished by the highest TFC values (52-58 mg EQ/g DW). In vitro assays showed that Violet d'Hyères bracts and Blanc d'Oran leaves present the most antioxidant activities (30.040 and 20.428 mgET/gDW, respectively, by the DPPH method). Leaves demonstrated the highest acetylcholinesterase and butyrylcholinesterase inhibitory effects. Moreover, all organs displayed a noticeable inhibition towards α-amylase. LC/DAD/MS analysis revealed that artichoke by-products are a potential source of biopharmaceuticals such as luteolin derivatives from leaves and mono/dicaffeoylquinic acids in the other parts. This research demonstrates that globe artichoke by-products, unexploited in our country, are a promising source of natural health promoting compounds with potential applications in the food and pharmaceutical industries.}, }
@article {pmid32628343, year = {2020}, author = {Aguilar, P and Sommaruga, R}, title = {The balance between deterministic and stochastic processes in structuring lake bacterioplankton community over time.}, journal = {Molecular ecology}, volume = {29}, number = {16}, pages = {3117-3130}, pmid = {32628343}, issn = {1365-294X}, support = {P24442-B25//Austrian Science Fund/ ; }, abstract = {One major goal in microbial ecology is to establish the importance of deterministic and stochastic processes for community assembly. This is relevant to explain and predict how diversity changes at different temporal scales. However, understanding of the relative quantitative contribution of these processes and particularly of how they may change over time is limited. Here, we assessed the importance of deterministic and stochastic processes based on the analysis of the bacterial microbiome in one alpine oligotrophic and in one subalpine mesotrophic lake, which were sampled over two consecutive years at different time scales. We found that in both lakes, homogeneous selection (i.e., a deterministic process) was the main assembly process at the annual scale and explained 66.7% of the bacterial community turnover, despite differences in diversity and temporal variability patterns between ecosystems. However, in the alpine lake, homogenizing dispersal (i.e., a stochastic process) was the most important assembly process at the short-term (daily and weekly) sampling scale and explained 55% of the community turnover. Alpha diversity differed between lakes, and seasonal stability of the bacterial community was more evident in the oligotrophic lake than in the mesotrophic one. Our results demonstrate how important forces that govern temporal changes in bacterial communities act at different time scales. Overall, our study validates on a quantitative basis, the importance and dominance of deterministic processes in structuring bacterial communities in freshwater environments over long time scales.}, }
@article {pmid32625179, year = {2020}, author = {Costa, OYA and Oguejiofor, C and Zühlke, D and Barreto, CC and Wünsche, C and Riedel, K and Kuramae, EE}, title = {Impact of Different Trace Elements on the Growth and Proteome of Two Strains of Granulicella, Class &quot;Acidobacteriia&quot;.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1227}, pmid = {32625179}, issn = {1664-302X}, abstract = {Acidobacteria represents one of the most dominant bacterial groups across diverse ecosystems. However, insight into their ecology and physiology has been hampered by difficulties in cultivating members of this phylum. Previous cultivation efforts have suggested an important role of trace elements for the proliferation of Acidobacteria, however, the impact of these metals on their growth and metabolism is not known. In order to gain insight into this relationship, we evaluated the effect of trace element solution SL10 on the growth of two strains (5B5 and WH15) of Acidobacteria belonging to the genus Granulicella and studied the proteomic responses to manganese (Mn). Granulicella species had highest growth with the addition of Mn, as well as higher tolerance to this metal compared to seven other metal salts. Variations in tolerance to metal salt concentrations suggests that Granulicella sp. strains possess different mechanisms to deal with metal ion homeostasis and stress. Furthermore, Granulicella sp. 5B5 might be more adapted to survive in an environment with higher concentration of several metal ions when compared to Granulicella sp. WH15. The proteomic profiles of both strains indicated that Mn was more important in enhancing enzymatic activity than to protein expression regulation. In the genomic analyses, we did not find the most common transcriptional regulation of Mn homeostasis, but we found candidate transporters that could be potentially involved in Mn homeostasis for Granulicella species. The presence of such transporters might be involved in tolerance to higher Mn concentrations, improving the adaptability of bacteria to metal enriched environments, such as the decaying wood-rich Mn environment from which these two Granulicella strains were isolated.}, }
@article {pmid32623832, year = {2020}, author = {Morvan, S and Meglouli, H and Lounès-Hadj Sahraoui, A and Hijri, M}, title = {Into the wild blueberry (Vaccinium angustifolium) rhizosphere microbiota.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15151}, pmid = {32623832}, issn = {1462-2920}, abstract = {The ability of wild blueberries to adapt to their harsh environment is believed to be closely related to their symbiosis with ericoid mycorrhizal fungi which produce enzymes capable of organic matter mineralization. Although some of these fungi have been identified and characterized, we still know little about the microbial ecology of wild blueberry. Our study aims to characterize the fungal and bacterial rhizosphere communities of Vaccinium angustifolium (the main species encountered in wild blueberry fields). Our results clearly show that the fungal order Helotiales was the most abundant taxon associated with V. angustifolium. Helotiales contains most of the known ericoid mycorrhizal fungi which are expected to dominate in such a biotope. Furthermore, we found the dominant bacterial order was the nitrogen-fixing Rhizobiales. The Bradyrhizobium genus whose members are known to form nodules with legumes, was among the ten most abundant genera in the bacterial communities. In addition, Bradyrhizobium and Roseiarcus sequences significantly correlated with higher leaf-nitrogen content. Overall our data documented fungal and bacterial community structure differences in three wild blueberry production fields. This article is protected by copyright. All rights reserved.}, }
@article {pmid32623497, year = {2020}, author = {Pereira, A and Ferreira, V}, title = {Invasion of Native Riparian Forests by Acacia Species Affects In-Stream Litter Decomposition and Associated Microbial Decomposers.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01552-3}, pmid = {32623497}, issn = {1432-184X}, support = {SFRH/BD/118069/2016//Fundação para a Ciência e a Tecnologia/ ; IF/00129/2014//Fundação para a Ciência e a Tecnologia/ ; UID/MAR/04292/2019//Fundação para a Ciência e a Tecnologia/ ; }, abstract = {The invasion of native riparian forests by exotic tree species can lead to profound changes in the ecological integrity of freshwater ecosystems. We assessed litter decomposition of native (Alnus glutinosa and Quercus robur) and invasive (Acacia melanoxylon and Acacia dealbata) tree species, and associated microbial activity and community structure, after being immersed for conditioning in 3 reference and 3 &quot;invaded&quot; streams in Serra da Lousã (central Portugal) and used in microcosms simulating stream conditions. Litter decomposition differed among species, in the order: Al. glutinosa > Q. robur > (Ac. melanoxylon ~ Ac. dealbata). Alnus glutinosa litter decomposed faster probably because it was soft and had high nitrogen concentration for decomposers. Quercus robur litter decomposed slower most likely because it was tough and had high polyphenol and low nitrogen concentrations. Acacia melanoxylon litter was the toughest and had a thick cuticle that likely acted as a physical barrier for microbial colonization. In Ac. dealbata, the small-sized leaflets and high lignin concentration may have limited microbial litter decomposition. Litter decomposition was faster in &quot;invaded&quot; streams, probably because they were N-limited and increases in nitrogen concentration in water, promoted by Acacia species invasion, stimulated microbial activity on litter. The aquatic hyphomycete community structure differed among litter species and between stream types, further suggesting that microbes were sensitive to litter characteristics and water nutrient concentrations. Overall, the invasion of native riparian forests by Acacia species may affect microbial decomposer activity, thus altering important stream ecosystem processes, such as litter decomposition and nutrient cycles.}, }
@article {pmid32622275, year = {2020}, author = {Seuntjens, D and Carvajal Arroyo, JM and Van Tendeloo, M and Chatzigiannidou, I and Molina, J and Nop, S and Boon, N and Vlaeminck, SE}, title = {Mainstream partial nitritation/anammox with integrated fixed-film activated sludge: Combined aeration and floc retention time control strategies limit nitrate production.}, journal = {Bioresource technology}, volume = {314}, number = {}, pages = {123711}, doi = {10.1016/j.biortech.2020.123711}, pmid = {32622275}, issn = {1873-2976}, mesh = {*Ammonium Compounds ; Bioreactors ; Nitrites ; Nitrogen ; Oxidation-Reduction ; *Sewage ; }, abstract = {Implementation of mainstream partial nitritation/anammox (PN/A) can lead to more sustainable and cost-effective sewage treatment. For mainstream PN/A reactor, an integrated fixed-film activated sludge (IFAS) was operated (26 °C). The effects of floccular aerobic sludge retention time (AerSRTfloc), a novel aeration strategy, and N-loading rate were tested to optimize the operational strategy. The best performance was observed with a low, but sufficient AerSRTfloc (~7d) and continuous aeration with two alternating dissolved oxygen setpoints: 10 min at 0.07-0.13 mg O2 L-1 and 5 min at 0.27-0.43 mg O2 L-1. Nitrogen removal rates were 122 ± 23 mg N L-1 d-1, and removal efficiencies 73 ± 13%. These conditions enabled flocs to act as nitrite sources while the carriers were nitrite sinks, with low abundance of nitrite oxidizing bacteria. The operational strategies in the source-sink framework can serve as a guideline for successful operation of mainstream PN/A reactors.}, }
@article {pmid32621211, year = {2020}, author = {Stricker, E and Crain, G and Rudgers, J and Sinsabaugh, R and Fernandes, V and Nelson, C and Giraldo-Silva, A and Garcia-Pichel, F and Belnap, J and Darrouzet-Nardi, A}, title = {What Could Explain δ13C Signatures in Biocrust Cyanobacteria of Drylands?.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01536-3}, pmid = {32621211}, issn = {1432-184X}, support = {1557135//Directorate for Biological Sciences/ ; 1557162//Directorate for Biological Sciences/ ; 1832194//Directorate for Biological Sciences/ ; 1655499//National Science Foundation/ ; }, abstract = {Dryland ecosystems are increasing in geographic extent and contribute greatly to interannual variability in global carbon dynamics. Disentangling interactions among dominant primary producers, including plants and autotrophic microbes, can help partition their contributions to dryland C dynamics. We measured the δ13C signatures of biological soil crust cyanobacteria and dominant plant species (C3 and C4) across a regional scale in the southwestern USA to determine if biocrust cyanobacteria were coupled to plant productivity (using plant-derived C mixotrophically), or independent of plant activity (and therefore purely autotrophic). Cyanobacterial assemblages located next to all C3 plants and one C4 species had consistently more negative δ13C (by 2‰) than the cyanobacteria collected from plant interspaces or adjacent to two C4Bouteloua grass species. The differences among cyanobacterial assemblages in δ13C could not be explained by cyanobacterial community composition, photosynthetic capacity, or any measured leaf or root characteristics (all slopes not different from zero). Thus, microsite differences in abiotic conditions near plants, rather than biotic interactions, remain a likely mechanism underlying the observed δ13C patterns to be tested experimentally.}, }
@article {pmid32621210, year = {2020}, author = {Hery, L and Guidez, A and Durand, AA and Delannay, C and Normandeau-Guimond, J and Reynaud, Y and Issaly, J and Goindin, D and Legrave, G and Gustave, J and Raffestin, S and Breurec, S and Constant, P and Dusfour, I and Guertin, C and Vega-Rúa, A}, title = {Natural Variation in Physicochemical Profiles and Bacterial Communities Associated with Aedes aegypti Breeding Sites and Larvae on Guadeloupe and French Guiana.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01544-3}, pmid = {32621210}, issn = {1432-184X}, support = {Grant ACIP 01-2016//Action Concertées Inter Pasteuriennes/ ; grant 2015-FED-192//Programme Opérationnel FEDER-Guadeloupe-Conseil Régional 2014-2020/ ; Stage-2018//Calmette &amp; Yersin/ ; 2017-2020//La Région Guadeloupe/ ; }, abstract = {Aedes aegypti develop in aquatic habitats in which mosquito larvae are exposed to physicochemical elements and microorganisms that may influence their life cycle and their ability to transmit arboviruses. Little is known about the natural bacterial communities associated with A. aegypti or their relation to the biotic and abiotic characteristics of their aquatic habitats. We characterized the physicochemical properties and bacterial microbiota of A. aegypti breeding sites and larvae on Guadeloupe and in French Guiana. In addition, we explored whether geographic location, the type of breeding site and physicochemical parameters influenced the microbiota associated with this mosquito species. We used large-scale 16S rRNA gene sequencing of 160 breeding sites and 147 pools of A. aegypti larvae and recorded 12 physicochemical parameters at the sampled breeding sites. Ordination plots and multiple linear regression were used to assess the influence of environmental factors on the bacterial microbiota of water and larvae. We found territory-specific differences in physicochemical properties (dissolved oxygen, conductivity) and the composition of bacterial communities in A. aegypti breeding sites that influenced the relative abundance of several bacteria genera (e.g., Methylobacterium, Roseoccocus) on the corresponding larvae. A significant fraction of the bacterial communities identified on larvae, dominated by Herbiconiux and Microvirga genera, were consistently enriched in mosquitoes regardless the location. In conclusion, territory-specific differences observed in the biotic and abiotic properties of A. aegypti breeding sites raise concern about the impact of these changes on pathogen transmission by different A. aegypti populations.}, }
@article {pmid32621209, year = {2020}, author = {Shahraki, AH and Chaganti, SR and Heath, DD}, title = {Diel Dynamics of Freshwater Bacterial Communities at Beaches in Lake Erie and Lake St. Clair, Windsor, Ontario.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01539-0}, pmid = {32621209}, issn = {1432-184X}, abstract = {Bacteria play a key role in freshwater biogeochemical cycling as well as water safety, but short-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We sampled four public beaches in southern Ontario, Canada; in June, July, and August (2016) over a 24-h (diel) cycle at 2-h intervals. Using high-throughput sequencing of 16S rRNA gene, we found substantial bi-hourly and day/night variation in the bacterial communities with considerable fluctuation in the relative abundance of Actinobacteria and Proteobacteria phyla. Moreover, relative abundance of Enterobacteriaceae (associated with potential health risk) was significantly high at night in some dial cycles. Diversity was significantly high at night across most of the diel sampling events. qPCR assays showed a substantial bi-hourly variation of Escherichia coli levels with a significant high level of E. coli at night hours in comparison with day hours and the lowest levels at noon and during the afternoon hours. Taken together, these findings highlighted a considerable short-term temporal variation of bacterial communities which helps better understanding of freshwater bacterial dynamics and their ecology. E. coli monitoring showed that multiple samples in different hours will provide more accurate picture of freshwater safety and human health risk. Graphical abstract.}, }
@article {pmid32620132, year = {2020}, author = {Wang, Y and Wang, K and Huang, L and Dong, P and Wang, S and Chen, H and Lu, Z and Hou, D and Zhang, D}, title = {Fine-scale succession patterns and assembly mechanisms of bacterial community of Litopenaeus vannamei larvae across the developmental cycle.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {106}, pmid = {32620132}, issn = {2049-2618}, support = {LY18C030002//Zhejiang Provincial Natural Science Foundation of China/ ; 31672658//National Natural Science Foundation of China/ ; 2017C110001//Agricultural Major Project of Ningbo, China/ ; LGN20C190008//Basic Public Welfare Research Project of Zhejiang Province/ ; }, abstract = {BACKGROUND: Microbiome assembly in early life may have a long-term impact on host health. Larval nursery is a crucial period that determines the success in culture of Litopenaeus vannamei, the most productive shrimp species in world aquaculture industry. However, the succession patterns and assembly mechanisms of larval shrimp bacterial community still lack characterization at a fine temporal scale. Here, using a high-frequency sampling strategy and 16S rRNA gene amplicon sequencing, we investigated dynamics of larval shrimp bacterial community and its relationship with bacterioplankton in the rearing water across the whole developmental cycle in a realistic aquaculture practice.<br><br>RESULTS: Alpha-diversity of larval shrimp bacteria showed a U-shaped pattern across the developmental cycle with the stages zoea and mysis as the valley. Correspondingly, the compositions of dominant bacterial taxa at the stages nauplius and early postlarvae were more complex than other stages. Remarkably, Rhodobacteraceae maintained the overwhelming dominance after the mouth opening of larvae (zoea I~early postlarvae). The taxonomic and phylogenetic compositions of larval bacterial community both showed stage-dependent patterns with higher rate of taxonomic turnover, suggesting that taxonomic turnover was mainly driven by temporal switching among closely related taxa (such as Rhodobacteraceae taxa). The assembly of larval bacteria was overall governed by neutral processes (dispersal among individuals and ecological drift) at all the stages, but bacterioplankton also had certain contribution during three sub-stages of zoea, when larval and water bacterial communities were most associated. Furthermore, the positive host selection for Rhodobacteraceae taxa from the rearing water during the zoea stage and its persistent dominance and large predicted contribution to metabolic potentials of organic matters at post-mouth opening stages suggest a crucial role of this family in larval microbiome and thus a potential source of probiotic candidates for shrimp larval nursery.<br><br>CONCLUSIONS: Our results reveal pronounced succession patterns and dynamic assembly processes of larval shrimp bacterial communities during the developmental cycle, highlighting the importance of the mouth opening stage from the perspective of microbial ecology. We also suggest the possibility and potential timing in microbial management of the rearing water for achieving the beneficial larval microbiota in the nursery practice. Video Abstract.}, }
@article {pmid32617619, year = {2020}, author = {Pinto, OHB and Costa, FS and Rodrigues, GR and da Costa, RA and da Rocha Fernandes, G and Júnior, ORP and Barreto, CC}, title = {Soil Acidobacteria Strain AB23 Resistance to Oxidative Stress Through Production of Carotenoids.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01548-z}, pmid = {32617619}, issn = {1432-184X}, support = {88881.062152/2014-01//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {Metagenomic studies revealed the prevalence of Acidobacteria in soils, but the physiological and ecological reasons for their success are not well understood. Many Acidobacteria exhibit carotenoid-related pigments, which may be involved in their tolerance of environmental stress. The aim of this work was to investigate the role of the orange pigments produced by Acidobacteria strain AB23 isolated from a savannah-like soil and to identify putative carotenoid genes in Acidobacteria genomes. Phylogenetic analysis revealed that strain AB23 belongs to the Occallatibacter genus from the class Acidobacteriia (subdivision 1). Strain AB23 produced carotenoids in the presence of light and vitamins; however, the growth rate and biomass decreased when cells were exposed to light. The presence of carotenoids resulted in tolerance to hydrogen peroxide. Comparative genomics revealed that all members of Acidobacteriia with available genomes possess the complete gene cluster for phytoene production. Some Acidobacteriia members have an additional gene cluster that may be involved in the production of colored carotenoids. Both colored and colorless carotenoids are involved in tolerance to oxidative stress. These results show that the presence of carotenoid genes is widespread among Acidobacteriia. Light and atmospheric oxygen stimulate carotenoid synthesis, but there are other natural sources of oxidative stress in soils. Tolerance to environmental oxidative stress provided by carotenoids may offer a competitive advantage for Acidobacteria in soils.}, }
@article {pmid32615432, year = {2020}, author = {Yang, L and Hou, K and Zhang, B and Ouyang, C and Lin, A and Xu, S and Ke, D and Fang, L and Chen, Q and Wu, J and Yan, C and Lian, Y and Jiang, T and He, J and Wang, H and Fu, Y and Xiao, C and Chen, Z}, title = {Preservation of the fecal samples at ambient temperature for microbiota analysis with a cost-effective and reliable stabilizer EffcGut.}, journal = {The Science of the total environment}, volume = {741}, number = {}, pages = {140423}, doi = {10.1016/j.scitotenv.2020.140423}, pmid = {32615432}, issn = {1879-1026}, mesh = {Cost-Benefit Analysis ; Feces ; Humans ; *Microbiota ; RNA, Ribosomal, 16S ; *Specimen Handling ; Temperature ; }, abstract = {With the increasing researches on the role of gut microbiota in human health and disease, appropriate storage method of fecal samples at ambient temperature would conveniently guarantee the precise and reliable microbiota results. Nevertheless, less choice of stabilizer that is cost-efficient and feasible to be used in longer preservation period obstructed the large-scale metagenomics studies. Here, we evaluated the efficacy of a guanidine isothiocyanate-based reagent method EffcGut and compared it with the other already used storage method by means of 16S rRNA gene sequencing technology. We found that guanidine isothiocyanate-based reagent method at ambient temperature was not inferior to OMNIgene·GUT OM-200 and it could retain the similar bacterial community as that of -80 °C within 24 weeks. Furthermore, bacterial diversity and community structure difference were compared among different sample fraction (supernatant, suspension and precipitate) preserved in EffcGut and -80 °C. We found that supernatant under the preservation of EffcGut retained the similar community structure and composition as that of the low temperature preservation method.}, }
@article {pmid32615392, year = {2020}, author = {Kassaian, N and Feizi, A and Rostami, S and Aminorroaya, A and Yaran, M and Amini, M}, title = {The effects of 6 mo of supplementation with probiotics and synbiotics on gut microbiota in the adults with prediabetes: A double blind randomized clinical trial.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {79-80}, number = {}, pages = {110854}, doi = {10.1016/j.nut.2020.110854}, pmid = {32615392}, issn = {1873-1244}, abstract = {OBJECTIVES: The evidence of 16S rRNA genes in the gut microbiota distinguished a higher Firmicutes-to-Bacteroidetes ratio in individuals who were obese and had diabetes than in a healthy cohort. So, it seems that the modulation of intestinal microbial ecology by pro-/pre-/synbiotics may contribute to the progression and prevention of metabolic diseases. The aim of this study was to assess the effects of probiotics and synbiotic supplementation on the modification of the intestinal microbiome in adults with prediabetes.<br><br>METHODS: In a randomized, double-blinded, placebo-controlled clinical trial, 120 patients with prediabetes were randomly assigned to consume 6 g/d of either a placebo containing maltodextrin (control) or multispecies probiotic or inulin-based synbiotic for 6 mo. Fecal samples were obtained at baseline and after 6 mo of supplementation. Dietary intake was assessed throughout the study (at baseline and after 3 and 6 mo). Total energy, macronutrients, and dietary fiber were calculated using a dietary program Nutritionist 4. DNA was extracted from fecal samples and the numbers of Clostridium perfringens (the represent of phylum Firmicutes), Bacteroides fragilis (the representative of Bacteroidetes) and Escherichia coli (as universal bacteria) were determined by quantitative real-time polymerase chain reactions (qPCR). The changes in the relative abundance of the two fecal bacteria before and after supplementation were analyzed and compared within and between groups.<br><br>RESULTS: There were no significant changes in dietary intake during the study. Six mo of supplementation with probiotics resulted in a statistically significant increase in the abundance of the B. fragilis-to-E.coli ratio (mean difference [MD] ± SE 0.47 ± 0.37, P = 0.04) and decrease of the relative proportion of Firmicutes-to-Bacteroidetes representatives (MD ± SE -118.8 ± 114.6, P = 0.02). Synbiotic had no significant effect on the changes in the bacteria. There were no significant differences between the three groups.<br><br>CONCLUSION: The results of this study suggest that manipulation of the human gut microbiome by using probiotics could provide a potential therapeutic approach in the prevention and management of obesity and metabolic disorders such as diabetes.}, }
@article {pmid32614521, year = {2020}, author = {Cheng, XS and Huo, YN and Fan, YY and Xiao, CX and Ouyang, XM and Liang, LY and Lin, Y and Wu, JF and Ren, JL and Guleng, B}, title = {Mindin serves as a tumour suppressor gene during colon cancer progression through MAPK/ERK signalling pathway in mice.}, journal = {Journal of cellular and molecular medicine}, volume = {24}, number = {15}, pages = {8391-8404}, pmid = {32614521}, issn = {1582-4934}, support = {81970460//National Natural Science Foundation of China/ ; 81770548//National Natural Science Foundation of China/ ; 81570496//National Natural Science Foundation of China/ ; 2015CB553800//973 programs/ ; }, abstract = {Mindin is important in broad spectrum of immune responses. On the other hand, we previously reported that mindin attenuated human colon cancer development by blocking angiogenesis through Egr-1-mediated regulation. However, the mice original mindin directly suppressed the syngenic colorectal cancer (CRC) growth in our recent study and we aimed to further define the role of mindin during CRC development in mice. We established the mouse syngeneic CRC CMT93 and CT26 WT cell lines with stable mindin knock-down or overexpression. These cells were also subcutaneously injected into C57BL/6 and BALB/c mice as well as established a colitis-associated colorectal cancer (CAC) mouse model treated with lentiviral-based overexpression and knocked-down of mindin. Furthermore, we generated mindin knockout mice using a CRISPR-Cas9 system with CAC model. Our data showed that overexpression of mindin suppressed cell proliferation in both of CMT93 and CT26 WT colon cancer cell lines, while the silencing of mindin promoted in vitro cell proliferation via the ERK and c-Fos pathways and cell cycle control. Moreover, the overexpression of mindin significantly suppressed in vivo tumour growth in both the subcutaneous transplantation and the AOM/DSS-induced CAC models. Consistently, the silencing of mindin reversed these in vivo observations. Expectedly, the tumour growth was promoted in the CAC model on mindin-deficient mice. Thus, mindin plays a direct tumour suppressive function during colon cancer progression and suggesting that mindin might be exploited as a therapeutic target for CRC.}, }
@article {pmid32613267, year = {2020}, author = {Douglas, AJ and Hug, LA and Katzenback, BA}, title = {Composition of the North American Wood Frog (Rana sylvatica) Bacterial Skin Microbiome and Seasonal Variation in Community Structure.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01550-5}, pmid = {32613267}, issn = {1432-184X}, support = {RGPIN-2017-04218//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {While a number of amphibian skin microbiomes have been characterized, it is unclear how these communities might vary in response to seasonal changes in the environment and the corresponding behaviors that many amphibians exhibit. Given recent studies demonstrating the importance of the skin microbiome in frog innate immune defense against pathogens, investigating how changes in the environment impact the microbial species present will provide a better understanding of conditions that may alter host susceptibility to pathogens in their environment. We sampled the bacterial skin microbiome of North American wood frogs (Rana sylvatica) from two breeding ponds in the spring, along with the bacterial community present in their vernal breeding pools, and frogs from the nearby forest floor in the summer and fall to determine whether community composition differs by sex, vernal pond site, or temporally across season (spring, summer, fall). Taxon relative abundance data reveals a profile of bacterial phyla similar to those previously described on anuran skin, with Proteobacteria, Bacteroidetes, and Actinobacteria dominating the wood frog skin microbiome. Our results indicate that sex had no significant effect on skin microbiota diversity; however, this may be due to our limited female frog sample size. Vernal pool site had a small but significant effect on skin microbiota, but skin-associated communities were more similar to each other than to the communities observed in the frogs' respective pond water. Across seasons, diversity analyses suggest that there are significant differences between the bacterial skin microbiome of frogs from spring and summer/fall groups while the average α-diversity per frog remained consistent. These results illustrate seasonal variation in wood frog skin microbiome structure and highlight the importance of considering temporal trends in an amphibian microbiome, particularly for species whose life history requires recurrent shifts in habitat and behavior.}, }
@article {pmid32610452, year = {2020}, author = {Van den Abbeele, P and Verstrepen, L and Ghyselinck, J and Albers, R and Marzorati, M and Mercenier, A}, title = {A Novel Non-Digestible, Carrot-Derived Polysaccharide (cRG-I) Selectively Modulates the Human Gut Microbiota while Promoting Gut Barrier Integrity: An Integrated in Vitro Approach.}, journal = {Nutrients}, volume = {12}, number = {7}, pages = {}, pmid = {32610452}, issn = {2072-6643}, support = {SMEi 811592//Horizon 2020/ ; Eurostars E! 10574-NIMF//European Commission/ ; }, abstract = {Modulation of the gut microbiome as a means to improve human health has recently gained increasing interest. In this study, it was investigated whether cRG-I, a carrot-derived pectic polysaccharide, enriched in rhamnogalacturonan-I (RG-I) classifies as a potential prebiotic ingredient using novel in vitro models. First, digestion methods involving α-amylase/brush border enzymes demonstrated the non-digestibility of cRG-I by host-derived enzymes versus digestible (starch/maltose) and non-digestible controls (inulin). Then, a recently developed short-term (48 h) colonic incubation strategy was applied and revealed that cRG-I fermentation increased levels of health-promoting short-chain fatty acids (SCFA; mainly acetate and propionate) and lactate comparable but not identical to the reference prebiotic inulin. Upon upgrading this fermentation model by inclusion of a simulated mucosal environment while applying quantitative 16S-targeted Illumina sequencing, cRG-I was additionally shown to specifically stimulate operational taxonomic units (OTUs) related to health-associated species such as Bifidobacterium longum, Bifidobacterium adolescentis, Bacteroides dorei, Bacteroides ovatus, Roseburia hominis, Faecalibacterium prausnitzii, and Eubacterium hallii. Finally, in a novel model to assess host-microbe interactions (Caco-2/peripheral blood mononuclear cells (PBMC) co-culture) fermented cRG-I increased barrier integrity while decreasing markers for inflammation. In conclusion, by using novel in vitro models, cRG-I was identified as a promising prebiotic candidate to proceed to clinical studies.}, }
@article {pmid32607236, year = {2020}, author = {Skarżyńska, E and Wilczyńska, P and Kiersztyn, B and Żytyńska-Daniluk, J and Jakimiuk, A and Lisowska-Myjak, B}, title = {Comparison of protease and aminopeptidase activities in meconium: A pilot study.}, journal = {Biomedical reports}, volume = {13}, number = {2}, pages = {7}, pmid = {32607236}, issn = {2049-9434}, abstract = {The successive accumulation of proteases and aminopeptidases in meconium are important physiological components of the intrauterine environment in which a fetus develops. The aim of the present study was to assess the changes in the activities of these enzymes in meconium of healthy infants, and to investigate whether there were any statistically significant associations between activity of the enzymes of interest and the mode of delivery. The activities of proteases and aminopeptidases were determined in meconium portions (n=110) using the substrates BODIPY FL casein and L-leucine-7-amido-4-methylcoumarin hydrochloride, respectively. Serial meconium samples (2-5 per neonate) were collected from healthy infants born vaginally (n=14), and by a cesarean section (n=16). Protease activity (104 RFU/h) was lower in the first meconium sample compared with the final sample from the same infant (3.99±2.03 vs. 5.76±2.24, respectively, mean ± standard deviation; P=0.004). Conversely, there was no significant difference in aminopeptidase activity (103 nM/l/h) between consecutive meconium samples (P=0.702). The ratios of the first-meconium sample enzyme activity to the last-meconium sample enzyme activity were lower for proteases compared with aminopeptidases (0.76±0.48 vs. 1.35±1.04, respectively mean ± standard deviation; P=0.014), and sustained in the infants born by a cesarean section (P=0.008). Spearman's correlation coefficient analysis between the first and last meconium samples showed the correlation increased in the infants born vaginally compared with the rest of the infants (proteases, R=0.618 vs. R=0.314; aminopeptidases, R=0.688 vs. R=0.566). Aminopeptidase activity did not exhibit any notable dynamic changes during meconium accumulation in the fetal intestine. In infants born vaginally compared with those born by a cesarean section, the activity of both proteases and aminopeptidases in the first meconium sample showed an improved correlation with the activity of the final meconium sample. This may suggest that in the intrauterine environment, during accumulation of meconium in the digestive tract of the fetus, the activity and/or levels of these enzymes and the substrates they catalyze were more stable in newborns born vaginally compared with infants born by caesarean section.}, }
@article {pmid32606027, year = {2020}, author = {Altamia, MA and Lin, Z and Trindade-Silva, AE and Uy, ID and Shipway, JR and Wilke, DV and Concepcion, GP and Distel, DL and Schmidt, EW and Haygood, MG}, title = {Secondary Metabolism in the Gill Microbiota of Shipworms (Teredinidae) as Revealed by Comparison of Metagenomes and Nearly Complete Symbiont Genomes.}, journal = {mSystems}, volume = {5}, number = {3}, pages = {}, pmid = {32606027}, issn = {2379-5077}, support = {U19 TW008163/TW/FIC NIH HHS/United States ; }, abstract = {Shipworms play critical roles in recycling wood in the sea. Symbiotic bacteria supply enzymes that the organisms need for nutrition and wood degradation. Some of these bacteria have been grown in pure culture and have the capacity to make many secondary metabolites. However, little is known about whether such secondary metabolite pathways are represented in the symbiont communities within their hosts. In addition, little has been reported about the patterns of host-symbiont co-occurrence. Here, we collected shipworms from the United States, the Philippines, and Brazil and cultivated symbiotic bacteria from their gills. We analyzed sequences from 22 shipworm gill metagenomes from seven shipworm species and from 23 cultivated symbiont isolates. Using (meta)genome sequencing, we demonstrate that the cultivated isolates represent all the major bacterial symbiont species and strains in shipworm gills. We show that the bacterial symbionts are distributed among shipworm hosts in consistent, predictable patterns. The symbiotic bacteria harbor many gene cluster families (GCFs) for biosynthesis of bioactive secondary metabolites, only <5% of which match previously described biosynthetic pathways. Because we were able to cultivate the symbionts and to sequence their genomes, we can definitively enumerate the biosynthetic pathways in these symbiont communities, showing that ∼150 of ∼200 total biosynthetic gene clusters (BGCs) present in the animal gill metagenomes are represented in our culture collection. Shipworm symbionts occur in suites that differ predictably across a wide taxonomic and geographic range of host species and collectively constitute an immense resource for the discovery of new biosynthetic pathways corresponding to bioactive secondary metabolites.IMPORTANCE We define a system in which the major symbionts that are important to host biology and to the production of secondary metabolites can be cultivated. We show that symbiotic bacteria that are critical to host nutrition and lifestyle also have an immense capacity to produce a multitude of diverse and likely novel bioactive secondary metabolites that could lead to the discovery of drugs and that these pathways are found within shipworm gills. We propose that, by shaping associated microbial communities within the host, the compounds support the ability of shipworms to degrade wood in marine environments. Because these symbionts can be cultivated and genetically manipulated, they provide a powerful model for understanding how secondary metabolism impacts microbial symbiosis.}, }
@article {pmid32605663, year = {2020}, author = {Berg, G and Rybakova, D and Fischer, D and Cernava, T and Vergès, MC and Charles, T and Chen, X and Cocolin, L and Eversole, K and Corral, GH and Kazou, M and Kinkel, L and Lange, L and Lima, N and Loy, A and Macklin, JA and Maguin, E and Mauchline, T and McClure, R and Mitter, B and Ryan, M and Sarand, I and Smidt, H and Schelkle, B and Roume, H and Kiran, GS and Selvin, J and Souza, RSC and van Overbeek, L and Singh, BK and Wagner, M and Walsh, A and Sessitsch, A and Schloter, M}, title = {Microbiome definition re-visited: old concepts and new challenges.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {103}, doi = {10.1186/s40168-020-00875-0}, pmid = {32605663}, issn = {2049-2618}, support = {European Union's Horizon 2020//Horizon 2020/ ; }, abstract = {The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term &quot;microbiome.&quot; Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract.}, }
@article {pmid32599485, year = {2020}, author = {Balan, B and Dhaulaniya, AS and Jamwal, R and Yadav, A and Kelly, S and Cannavan, A and Singh, DK}, title = {Rapid detection and quantification of sucrose adulteration in cow milk using Attenuated total reflectance-Fourier transform infrared spectroscopy coupled with multivariate analysis.}, journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy}, volume = {240}, number = {}, pages = {118628}, doi = {10.1016/j.saa.2020.118628}, pmid = {32599485}, issn = {1873-3557}, abstract = {Adulteration of milk to gain economic benefit has become a common practice in recent years. Sucrose is illegally added in milk to reconstitute its compositional requirement by improving the total solid contents. The present study is aimed to use FTIR spectroscopy in combination with multivariate chemometric modelling for the differentiation and quantification of sucrose in cow milk. Pure milk and adulterated milk spectra (0.5-7.5% w/v) were observed in the spectral region 4000-400 cm-1. Principal component analysis (PCA) was used for the discrimination of pure milk and adulterated milk. Soft independent modelling of class analogy (SIMCA) was able to classify test samples with a classification efficiency of 100%. Partial least square regression (PLS-R) and principle component regression (PCR) models were established for normal spectra, 1st derivative and 2nd derivative for the quantification of sucrose in milk. PLS-R model (normal spectra) in the combined wavenumber range of 1070-980 cm-1 showed the best prediction based on parameters like coefficient of determination (R2) (Cal: 0.996; Val: 0.993), RMSE (Cal: 0.15% w/v; Val: 0.20% w/v), RE% (Cal: 4.9% w/v; Val: 5.1% w/v) and RPD (13.40). This method has a detection level of 0.5% w/v sucrose adulteration.}, }
@article {pmid32595912, year = {2020}, author = {Hernández, M and Planells, P and Martínez, E and Mira, A and Carda-Diéguez, M}, title = {Microbiology of molar-incisor hypomineralization lesions. A pilot study.}, journal = {Journal of oral microbiology}, volume = {12}, number = {1}, pages = {1766166}, pmid = {32595912}, issn = {2000-2297}, abstract = {Objective: An insufficient mineralization (hypomineralization) in the teeth during the maturation stage of amelogenesis cause defects in 3-44% of children. Here, we describe for the first time the microbiota associated with these defects and compared it to healthy teeth within the same subjects. Methods: Supragingival dental plaque was sampled from healthy and affected teeth from 25 children with molar-incisor hypomineralization (MIH). Total DNA was extracted and the 16S rRNA gene was sequenced by Illumina sequencing in order to describe the bacterial composition. Results: We detected a higher bacterial diversity in MIH samples, suggesting better bacterial adhesion or higher number of niches in those surfaces. We found the genera Catonella, Fusobacterium, Campylobacter, Tannerella, Centipeda, Streptobacillus, Alloprevotella and Selenomonas associated with hypomineralized teeth, whereas Rothia and Lautropia were associated with healthy sites. Conclusion: The higher protein content of MIH-affected teeth could favour colonization by proteolytic microorganisms. The over-representation of bacteria associated with endodontic infections and periodontal pathologies suggests that, in addition to promote caries development, MIH could increase the risk of other oral diseases.}, }
@article {pmid32595184, year = {2020}, author = {Morono, Y and Kubota, K and Tsukagoshi, D and Terada, T}, title = {EDTA-FISH: A Simple and Effective Approach to Reduce Non-specific Adsorption of Probes in Fluorescence in situ Hybridization (FISH) for Environmental Samples.}, journal = {Microbes and environments}, volume = {35}, number = {3}, pages = {}, doi = {10.1264/jsme2.ME20062}, pmid = {32595184}, issn = {1347-4405}, abstract = {Fluorescence in situ hybridization (FISH) is a widely used molecular technique in microbial ecology. However, the non-specific adsorption of fluorescent probes and resulting high intensity of background signals from mineral particles hampers the specific detection of microbial cells in grain-rich environmental samples, such as subseafloor sediments. We herein demonstrated that a new buffer composition containing EDTA efficiently reduced the adsorption of probes without compromising the properties of the FISH-based probing of microbes. The inclusion of a high concentration of EDTA in the buffer in our protocol provides a simple and effective approach for reducing the background in FISH for environmental samples.}, }
@article {pmid32594248, year = {2020}, author = {Sugden, S and St Clair, CC and Stein, LY}, title = {Individual and Site-Specific Variation in a Biogeographical Profile of the Coyote Gastrointestinal Microbiota.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01547-0}, pmid = {32594248}, issn = {1432-184X}, support = {RGPIN-2017-05915//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2019-04399//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Most knowledge of the vertebrate gut microbiota comes from fecal samples; due to difficulties involved in sample collection, the upper intestinal microbiota is poorly understood in wild animals despite its potential to inform broad interpretations about host-gut microbe relationships under natural conditions. Here, we used 16S rRNA gene sequencing to characterize the microbiota of wild coyotes (Canis latrans) along the gastrointestinal tract, including samples from the duodenum, jejunum, ileum, caecum, ascending and descending colon, and feces. We used this intestinal profile to (1) quantify how intestinal site and individual identity interact to shape the microbiota in an uncontrolled setting, and (2) evaluate whether the fecal microbiota adequately represent other intestinal sites. Microbial communities in the large intestine were distinct from those in the small intestine, with higher diversity and a greater abundance of anaerobic taxa. Within each of the small and large intestine, individual identity explained significantly more among-sample variation than specific intestinal sites, revealing the importance of individual variation in the microbiota of free-living animals. Fecal samples were not an adequate proxy for studying upper intestinal environments, as they contained only half the amplicon sequence variants (ASVs) present in the small intestine at three- to four-fold higher abundances. Our study is a unique biogeographical investigation of the microbiota using free-living mammals rather than livestock or laboratory organisms and provides a foundational understanding of the gastrointestinal microbiota in a wild canid.}, }
@article {pmid32592942, year = {2020}, author = {Valencia, A and Ordonez, D and Wen, D and McKenna, AM and Chang, NB and Wanielista, MP}, title = {The interaction of dissolved organic nitrogen removal and microbial abundance in iron-filings based green environmental media for stormwater treatment.}, journal = {Environmental research}, volume = {188}, number = {}, pages = {109815}, doi = {10.1016/j.envres.2020.109815}, pmid = {32592942}, issn = {1096-0953}, abstract = {Nonpoint sources pollution from agricultural crop fields and urbanized regions oftentimes have elevated concentrations of dissolved organic nitrogen (DON) in stormwater runoff, which are difficult for microbial communities to decompose. The impact of elevated DON can be circumvented through the use of green sorption media, such as Biosorption Activated Media (BAM) and Iron-Filing Green Environmental Media (IFGEM), which, as integral parts of microbial ecology, can contribute to the decomposition of DON. To compare the fate, transport, and transformation of DON in green sorption media relative to natural soil (control), a series of fixed-bed columns, which contain natural soil, BAM, and two types of IFGEM, respectively, were constructed to compare nutrient removal efficiency under three distinct stormwater influent conditions containing nitrogen and phosphorus. The interactions among six microbial species, including ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, complete ammonia oxidation (comammox) bacteria, anaerobic ammonium oxidation (anammox) bacteria, dissimilatory nitrate reduction to ammonium bacteria, and iron-reducing bacteria, were further analyzed from microbial ecology perspectives to determine the DON impact on nutrient removal in BAM and IFGEM. Natural soil was only able to achieve adequate DON transformation at the influent condition of lower nutrient concentration. However, the two types of IFGEM showed satisfactory nutrient removals and achieved greater transformation of DON relative to BAM when treating stormwater in all three influent conditions.}, }
@article {pmid32591381, year = {2020}, author = {Luo, Y and Huang, Y and Xu, RX and Qian, B and Zhou, JW and Xia, XL}, title = {Primary and Secondary Succession Mediate the Accumulation of Biogenic Amines during Industrial Semidry Chinese Rice Wine Fermentation.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {17}, pages = {}, pmid = {32591381}, issn = {1098-5336}, abstract = {The use of exogenous functional microorganisms to regulate biogenic amine (BA) content is a common approach in fermentation systems. Here, to better understand the microbial traits of succession trajectories in resource-based and biotic interference systems, the BA-related primary and secondary succession were tracked during industrial semidry Chinese rice wine (CRW) fermentation. Dominant abundance and BA-associated microbial functionality based on phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) indicated that Citrobacter, Acinetobacter, Lactobacillus, Exiguobacterium, Bacillus, Pseudomonas, and Enterobacter spp. prominently contributed to the decarboxylase gene family in CRW. The expression levels of tyrosine decarboxylase (tyrDC), ornithine decarboxylase (odc), and agmatine deiminase (aguA) genes were assessed by quantitative PCR (qPCR). The transcription levels of these genes did not correlate with the BA formation rate during postfermentation, indicating that acidification and carbon source depletion upregulated the expression and microbes launch the dormancy strategy to respond to unfavorable conditions. Furthermore, microbial interference with CRW fermentation by Lactobacillus plantarum (ACBC271) and Staphylococcus xylosus (CGMCC1.8382) coinoculated at a ratio of 1:2 exhibited the best synergetic control of BA content. Spearman correlations revealed that Lactobacillus and Staphylococcus exhibited influence on BA-associated microbiota (|ρ| > 0), Exiguobacterium and Pseudomonas were strongly suppressed by Lactobacillus (ρ = -0.867 and ρ = -0.782, respectively; P < 0.05), and Staphylococcus showed the strongest inhibitory effect toward Lactobacillus (ρ = -0.115) and Citrobacter (ρ = -0.188) in the coinoculated 1:2 group. The high inhibitory effect of exogenous added strains on specific bacteria presented evidence for the obtained BA-associated contributors. Overall, this work provides important insight into the microbial traits that rely on resource usage and functional microbiota within food microbial ecology.IMPORTANCE Understanding the shifting patterns of substance usage and microbial interactions is a fundamental objective within microbiology and ecology. Analyses of primary and secondary microbial succession allow for determinations of taxonomic diversity, community traits, and functional transformations over time or after a disturbance. The kinetics of BA generation and the patterns of resource consumption, functional metagenome prediction, and microbial interactions were profiled to elucidate the equilibrium mechanism of microbial systems. Secondary succession after a disturbance triggers a change in resource usage, which in turn affects primary succession and metabolism. In this study, the functional potential of exogenous microorganisms under disturbance synergized with secondary succession strategies, including rebalancing and dormancy, which ultimately reduced BA accumulation. Thus, this succession system could facilitate the settling of essential issues with respect to microbial traits that rely on resource usage and microbial interactions that occur in natural ecosystems.}, }
@article {pmid32588072, year = {2020}, author = {Zhou, X and Wang, JT and Wang, WH and Tsui, CK and Cai, L}, title = {Changes in Bacterial and Fungal Microbiomes Associated with Tomatoes of Healthy and Infected by Fusarium oxysporum f. sp. lycopersici.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01535-4}, pmid = {32588072}, issn = {1432-184X}, support = {NSFC 31725001//National Natural Science Foundation of China/ ; QYZDB-SSW-SMC044//Key Research Program of Frontier Sciences,CAS/ ; }, abstract = {Fusarium wilt of tomato caused by the pathogen Fusarium oxysporum f. sp. lycopersici (Fol) is one of the most devastating soilborne diseases of tomato. To evaluate whether microbial community composition associated with Fol-infected tomato is different from healthy tomato, we analyzed the tomato-associated microbes in both healthy and Fol-infected tomato plants at both the taxonomic and functional levels; both bacterial and fungal communities have been characterized from bulk soil, rhizosphere, rhizoplane, and endosphere of tomatoes using metabarcoding and metagenomics approaches. The microbial community (bacteria and fungi) composition of healthy tomato was significantly different from that of diseased tomato, despite similar soil physicochemical characteristics. Both fungal and bacterial diversities were significantly higher in the tomato plants that remained healthy than in those that became diseased; microbial diversities were also negatively correlated with the concentration of Fol pathogen. Network analysis revealed the microbial community of healthy tomato formed a larger and more complex network than that of diseased tomato, probably providing a more stable community beneficial to plant health. Our findings also suggested that healthy tomato contained significantly greater microbial consortia, including some well-known biocontrol agents (BCAs), and enriched more functional genes than diseased tomato. The microbial taxa enriched in healthy tomato plants are recognized as potential suppressors of Fol pathogen invasion.}, }
@article {pmid32583006, year = {2020}, author = {Mapelli, F and Riva, V and Vergani, L and Choukrallah, R and Borin, S}, title = {Unveiling the Microbiota Diversity of the Xerophyte Argania spinosa L. Skeels Root System and Residuesphere.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {822-836}, doi = {10.1007/s00248-020-01543-4}, pmid = {32583006}, issn = {1432-184X}, support = {688320//Horizon 2020 Framework Programme (Research and Innovation)/ ; 20172TZHYX//MIUR-PRIN2017/ ; }, abstract = {The microbiota associated to xerophyte is a &quot;black box&quot; that might include microbes involved in plant adaptation to the extreme conditions that characterize their habitat, like water shortage. In this work, we studied the bacterial communities inhabiting the root system of Argania spinosa L. Skeels, a tree of high economic value and ecological relevance in Northern Africa. Illumina 16S rRNA gene sequencing and cultivation techniques were applied to unravel the bacterial microbiota's structure in environmental niches associated to argan plants (i.e., root endosphere, rhizosphere, root-surrounding soil), not associated to the plant (i.e., bulk soil), and indirectly influenced by the plant being partially composed by its leafy residue and the associated microbes (i.e., residuesphere). Illumina dataset indicated that the root system portions of A. spinosa hosted different bacterial communities according to their degree of association with the plant, enriching for taxa typical of the plant microbiome. Similar alpha- and beta-diversity trends were observed for the total microbiota and its cultivable fraction, which included 371 isolates. In particular, the residuesphere was the niche with the highest bacterial diversity. The Plant Growth Promotion (PGP) potential of 219 isolates was investigated in vitro, assessing several traits related to biofertilization and biocontrol, besides the production of exopolysaccharides. Most of the multivalent isolates showing the higher PGP score were identified in the residuesphere, suggesting it as a habitat that favor their proliferation. We hypothesized that these bacteria can contribute, in partnership with the argan root system, to the litter effect played by this tree in its native arid lands.}, }
@article {pmid32582085, year = {2020}, author = {Trego, AC and Galvin, E and Sweeney, C and Dunning, S and Murphy, C and Mills, S and Nzeteu, C and Quince, C and Connelly, S and Ijaz, UZ and Collins, G}, title = {Growth and Break-Up of Methanogenic Granules Suggests Mechanisms for Biofilm and Community Development.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1126}, pmid = {32582085}, issn = {1664-302X}, abstract = {Methanogenic sludge granules are densely packed, small, spherical biofilms found in anaerobic digesters used to treat industrial wastewaters, where they underpin efficient organic waste conversion and biogas production. Each granule theoretically houses representative microorganisms from all of the trophic groups implicated in the successive and interdependent reactions of the anaerobic digestion (AD) process. Information on exactly how methanogenic granules develop, and their eventual fate will be important for precision management of environmental biotechnologies. Granules from a full-scale bioreactor were size-separated into small (0.6-1 mm), medium (1-1.4 mm), and large (1.4-1.8 mm) size fractions. Twelve laboratory-scale bioreactors were operated using either small, medium, or large granules, or unfractionated sludge. After >50 days of operation, the granule size distribution in each of the small, medium, and large bioreactor sets had diversified beyond-to both bigger and smaller than-the size fraction used for inoculation. Interestingly, extra-small (XS; <0.6 mm) granules were observed, and retained in all of the bioreactors, suggesting the continuous nature of granulation, and/or the breakage of larger granules into XS bits. Moreover, evidence suggested that even granules with small diameters could break. &quot;New&quot; granules from each emerging size were analyzed by studying community structure based on high-throughput 16S rRNA gene sequencing. Methanobacterium, Aminobacterium, Propionibacteriaceae, and Desulfovibrio represented the majority of the community in new granules. H2-using, and not acetoclastic, methanogens appeared more important, and were associated with abundant syntrophic bacteria. Multivariate integration (MINT) analyses identified distinct discriminant taxa responsible for shaping the microbial communities in different-sized granules.}, }
@article {pmid32582065, year = {2020}, author = {Navarro, MOP and Dilarri, G and Simionato, AS and Grzegorczyk, K and Dealis, ML and Cano, BG and Barazetti, AR and Afonso, L and Chryssafidis, AL and Ferreira, H and Andrade, G}, title = {Determining the Targets of Fluopsin C Action on Gram-Negative and Gram-Positive Bacteria.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1076}, pmid = {32582065}, issn = {1664-302X}, abstract = {The antibiotic activity of metalloantibiotic compounds has been evaluated since the 90s, and many different modes of action were characterized. In the last decade, the effects of secondary metabolites produced by Pseudomonas aeruginosa LV strain, including a cupric compound identified as Fluopsin C, were tested against many pathogenic bacteria strains, proving their high antibiotic activity. In the present study, the bactericidal mechanisms of action of Fluopsin C and the semi-purified fraction F4A were elucidated. The results found in electron microscopy [scanning electron microscopy (SEM) and transmission electronic microscopy (TEM)] demonstrated that both Fluopsin C and F4A are affecting the cytoplasmatic membrane of Gram-positive and Gram-negative bacteria. These results were confirmed by fluorescence microscopy, where these bacteria presented permeabilization of their cytoplasmatic membranes after contact with the semi-purified fraction and pure compound. Using electronic and fluorescence microscopy, along with bacterial mutant strains with marked divisional septum, the membrane was defined as the primary target of Fluopsin C in the tested bacteria.}, }
@article {pmid32582043, year = {2020}, author = {Gill, AS and Purnell, K and Palmer, MI and Stein, J and McGuire, KL}, title = {Microbial Composition and Functional Diversity Differ Across Urban Green Infrastructure Types.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {912}, pmid = {32582043}, issn = {1664-302X}, abstract = {Functional and biogeographical properties of soil microbial communities in urban ecosystems are poorly understood despite their role in metabolic processes underlying valuable ecosystem services. The worldwide emergence of engineered habitats in urban landscapes-green roofs, bioswales, and other types of soil-based green infrastructure-highlights the importance of understanding how environmental changes affect the community assembly processes that shape urban microbial diversity and function. In this study we investigated (1) whether engineered green roofs and bioswales in New York City had distinct microbial community composition and trait-associated diversity compared to non-engineered soils in parks and tree pits, and (2) if these patterns were consistent with divergent community assembly processes associated with engineered specifications of green infrastructure habitats not present in conventional, non-engineered green infrastructure; specifically, tree pit and park lawn soils. We found that green roofs and bioswales each had distinct bacterial and fungal communities, but that community composition and diversity were not significantly associated with geographic distance, suggesting that the processes structuring these differences are related to aspects of the habitats themselves. Bioswales, and to a lesser extent green roofs, also contained increased functional potential compared to conventional GI soils, based on the diversity and abundance of taxa associated with nitrogen cycling, biodegradation, decomposition, and traits positively associated with plant growth. We discuss these results in the context of community assembly theory, concluding that urban soil microbial community composition and diversity in engineered habitats are driven largely by environmental filtering, whereas stochastic processes are more important among non-engineered soils.}, }
@article {pmid32580805, year = {2020}, author = {Garber, A and Hastie, PM and Farci, V and McGuinness, D and Bulmer, L and Alzahal, O and Murray, JMD}, title = {The effect of supplementing pony diets with yeast on 2. The faecal microbiome.}, journal = {Animal : an international journal of animal bioscience}, volume = {}, number = {}, pages = {1-10}, doi = {10.1017/S1751731120001512}, pmid = {32580805}, issn = {1751-732X}, abstract = {There is a need to develop feeding strategies to prevent the adverse effect of concentrate feeding in high-performance horses fed energy-dense diets aiming to maintain their health and welfare. The objective of this study is to determine the effect of a VistaEQ product containing 4% live yeast Saccharomyces cerevisiae (S. cerevisiae), with activity 5 × 108 colony-forming unit/g and fed 2 g/pony per day, on faecal microbial populations when supplemented with high-starch and high-fibre diets using Illumina next generation sequencing of the V3-V4 region of the 16S ribosomal RNA gene. The four treatments were allocated to eight mature Welsh section A pony geldings enrolled in a 4-period × 8 animal crossover design. Each 19-day experimental period consisted of an 18-day adaptation phase and a single collection day, followed by a 7-day wash out period. After DNA extraction from faeces and library preparation, α-diversity and linear discriminant analysis effect size were performed using 16S metagenomics pipeline in Quantitative Insights Into Microbial Ecology (QIIME™) and Galaxy/Hutlab. Differences between the groups were considered significant when linear discriminant analysis score was >2 corresponding to P < 0.05. The present study showed that S. cerevisiae used was able to induce positive changes in the equine microbiota when supplemented to a high-fibre diet: it increased relative abundance (RA) of Lachnospiraceae and Dehalobacteriaceae family members associated with a healthy core microbiome. Yeast supplementation also increased the RA of fibrolytic bacteria (Ruminococcus) when fed with a high-fibre diet and reduced the RA of lactate producing bacteria (Streptococcus) when a high-starch diet was fed. In addition, yeast increased the RA of acetic, succinic acid producing bacterial family (Succinivibrionaceae) and butyrate producing bacterial genus (Roseburia) when fed with high-starch and high-fibre diets, respectively. VistaEQ supplementation to equine diets can be potentially used to prevent acidosis and increase fibre digestibility. It may help to meet the energy requirements of performance horses while maintaining gut health.}, }
@article {pmid32577778, year = {2020}, author = {Huang, R and Zeng, J and Zhao, D and Yong, B and Yu, Z}, title = {Co-association of Two nir Denitrifiers Under the Influence of Emergent Macrophytes.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {809-821}, doi = {10.1007/s00248-020-01545-2}, pmid = {32577778}, issn = {1432-184X}, support = {31730013, 41621002, 41871096, and 31971478//National Natural Science Foundation of China/ ; 2018B43414, 2019B17814//Fundamental Research Funds for the Central Universities/ ; 2018M642147//China Postdoctoral Science Foundation/ ; 2017FY100300//Science &amp; Technology Basic Resources Investigation Program of China/ ; }, abstract = {Diverse microorganisms perform similar metabolic process in biogeochemical cycles, whereas they are found of highly genomic differentiation. Biotic interactions should be considered in any community survey of these functional groups, as they contribute to community assembly and ultimately alter ecosystem properties. Current knowledge has mainly been achieved based on functional community characterized by a single gene using co-occurrence network analysis. Biotic interactions between functionally equivalent microorganisms, however, have received much less attention. Herein, we propose the nirK- and nirS-type denitrifier communities represented by these two nitrite reductase (nir)-encoding genes, as model communities to investigate the potential interactions of two nir denitrifiers. We evaluated co-occurrence patterns and co-association network structures of nir denitrifier community from an emergent macrophyte-dominated riparian zone of highly active denitrification in Lake Taihu, China. We found a more segregated pattern in combined nir communities than in individual communities. Network analyses revealed a modularized structure of associating nir denitrifiers. An increased proportion of negative associations among combined communities relative to those of individual communities indicated potential interspecific competition between nirK and nirS denitrifiers. pH and NH4+-N were the most important factors driving co-occurrence and mutual exclusion between nirK and nirS denitrifiers. We also showed the topological importance of nirK denitrifiers acting as module hubs for constructing entire association networks. We revealed previously unexplored co-association relationships between nirK and nirS denitrifiers, which were previously neglected in network analyses of individual communities. Using nir denitrifier community as a model, these findings would be helpful for us to understand the biotic interactions and mechanisms underlying how functional groups co-exist in performing biogeochemical cycles.}, }
@article {pmid32576522, year = {2020}, author = {Lopetuso, LR and Quagliariello, A and Schiavoni, M and Petito, V and Russo, A and Reddel, S and Del Chierico, F and Ianiro, G and Scaldaferri, F and Neri, M and Cammarota, G and Putignani, L and Gasbarrini, A}, title = {Towards a disease-associated common trait of gut microbiota dysbiosis: The pivotal role of Akkermansia muciniphila.}, journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver}, volume = {52}, number = {9}, pages = {1002-1010}, doi = {10.1016/j.dld.2020.05.020}, pmid = {32576522}, issn = {1878-3562}, abstract = {BACKGROUND: Gut microbiota exerts a crucial role in gastrointestinal (GI) and extra-intestinal (EI) disorders. In this context, Akkermansia muciniphila is pivotal for the maintenance of host health and has been correlated with several disorders.<br><br>AIM: To explore the potential role of A. muciniphila as common dysbiotic marker linked to the disease status.<br><br>METHODS: A cohort of patients affected by GI and EI disorders was enrolled and compared to healthy controls (CTRLs). A targeted-metagenomics approach combined to unsupervised cluster and machine learning (ML) analyses provided microbiota signatures.<br><br>RESULTS: Microbiota composition was associated to disease phenotype, therapies, diet and anthropometric features, identifying phenotype and therapies as the most impacting variables on microbiota ecology. Unsupervised cluster analyses identified one cluster composed by the majority of patients. DESeq2 algorithm identified ten microbial discriminatory features of patients and CTRLs clusters. Among these microbes, Akkermansia muciniphila resulted the discriminating ML node between patients and CTRLs, independently of specific GI/EI disease or confounding effects. A. muciniphila decrease represented a transversal signature of gut microbiota alteration, showing also an inverse correlation with α-diversity.<br><br>CONCLUSION: Overall, A. muciniphila decline may have a crucial role in affecting microbial ecology and in discriminating patients from healthy subjects. Its grading may be considered as a gut dysbiosis feature associated to disease-related microbiota profile.}, }
@article {pmid32574158, year = {2020}, author = {Desai, C and Handley, SA and Rodgers, R and Rodriguez, C and Ordiz, MI and Manary, MJ and Holtz, LR}, title = {Growth velocity in children with Environmental Enteric Dysfunction is associated with specific bacterial and viral taxa of the gastrointestinal tract in Malawian children.}, journal = {PLoS neglected tropical diseases}, volume = {14}, number = {6}, pages = {e0008387}, pmid = {32574158}, issn = {1935-2735}, support = {R21 AI121939/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics/isolation &amp; purification/virology ; Bacteriophages/*classification/genetics/growth &amp; development/isolation &amp; purification ; Child, Preschool ; Female ; Gastrointestinal Diseases/microbiology/virology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology/*virology ; Growth Disorders/*microbiology/*virology ; Humans ; Infant ; Intestine, Small/microbiology/virology ; Malawi ; Male ; Microbial Viability ; Permeability ; RNA, Ribosomal, 16S ; }, abstract = {Environmental enteric dysfunction (EED) is characterized by diffuse villous atrophy of the small bowel. EED is strongly associated with stunting, a major public health problem linked to increased childhood morbidity and mortality. EED and subsequent stunting of linear growth are surmised to have microbial origins. To interrogate this relationship, we defined the comprehensive virome (eukaryotic virus and bacteriophage) and bacterial microbiome of a longitudinal cohort of rural Malawian children with extensive metadata and intestinal permeability testing at each time point. We found thirty bacterial taxa differentially associated with linear growth. We detected many eukaryotic viruses. Neither the total number of eukaryotic families nor a specific viral family was statistically associated with improved linear growth. We identified 3 differentially abundant bacteriophage among growth velocities. Interestingly, there was a positive correlation between bacteria and bacteriophage richness in children with subsequent adequate/moderate growth which children with subsequent poor growth lacked. This suggests that a disruption in the equilibrium between bacteria and bacteriophage communities might be associated with subsequent poor growth. Future studies of EED and stunting should include the evaluation of viral communities in addition to bacterial microbiota to understand the complete microbial ecology of these poorly understood entities.}, }
@article {pmid32572536, year = {2020}, author = {Díaz-García, L and Bugg, TDH and Jiménez, DJ}, title = {Exploring the Lignin Catabolism Potential of Soil-Derived Lignocellulolytic Microbial Consortia by a Gene-Centric Metagenomic Approach.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {885-896}, doi = {10.1007/s00248-020-01546-1}, pmid = {32572536}, issn = {1432-184X}, support = {PR.3.2018.5287//Universidad de Los Andes/ ; BB/P01738X/1//BBSRC/ ; }, abstract = {An exploration of the ligninolytic potential of lignocellulolytic microbial consortia can improve our understanding of the eco-enzymology of lignin conversion in nature. In this study, we aimed to detect enriched lignin-transforming enzymes on metagenomes from three soil-derived microbial consortia that were cultivated on &quot;pre-digested&quot; plant biomass (wheat straw, WS1-M; switchgrass, SG-M; and corn stover, CS-M). Of 60 selected enzyme-encoding genes putatively involved in lignin catabolism, 20 genes were significantly abundant in WS1-M, CS-M, and/or SG-M consortia compared with the initial forest soil inoculum metagenome (FS1). These genes could be involved in lignin oxidation (e.g., superoxide dismutases), oxidative stress responses (e.g., catalase/peroxidases), generation of protocatechuate (e.g., vanAB genes), catabolism of gentisate, catechol and 3-phenylpropionic acid (e.g., gentisate 1,2-dioxygenases, muconate cycloisomerases, and hcaAB genes), the beta-ketoadipate pathway (e.g., pcaIJ genes), and tolerance to lignocellulose-derived inhibitors (e.g., thymidylate synthases). The taxonomic affiliation of 22 selected lignin-transforming enzymes from WS1-M and CS-M consortia metagenomes revealed that Pseudomonadaceae, Alcaligenaceae, Sphingomonadaceae, Caulobacteraceae, Comamonadaceae, and Xanthomonadaceae are the key bacterial families in the catabolism of lignin. A predictive &quot;model&quot; was sketched out, where each microbial population has the potential to metabolize an array of aromatic compounds through different pathways, suggesting that lignin catabolism can follow a &quot;task division&quot; strategy. Here, we have established an association between functions and taxonomy, allowing a better understanding of lignin transformations in soil-derived lignocellulolytic microbial consortia, and pinpointing some bacterial taxa and catabolic genes as ligninolytic trait-markers.}, }
@article {pmid32572535, year = {2020}, author = {Cohen, H and McFrederick, QS and Philpott, SM}, title = {Environment Shapes the Microbiome of the Blue Orchard Bee, Osmia lignaria : RRH: Environmental Drivers of Bee Microbiome.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {897-907}, doi = {10.1007/s00248-020-01549-y}, pmid = {32572535}, issn = {1432-184X}, support = {2016-67019-25185//USDA-NIFA/ ; }, abstract = {Wild bees encounter environmental microbes while foraging. While environmental context affects bee diversity, little is known about it how affects the wild bee microbiome. We used field surveys in 17 urban gardens to examine whether and how variation in local and landscape habitat features shapes the microbiome of the solitary Blue Orchard Bee, Osmia lignaria. We installed O. lignaria cocoons at each site, allowed bees to emerge and forage, then collected them. We measured local features of gardens using vegetation transects and landscape features with GIS. We found that in microbiome composition between bee individuals varied by environmental features such as natural habitat, floral resources, and bee species richness. We also found that environmental features were associated with the abundance of bacterial groups important for bee health, such as Lactobacillus. Our study highlights complex interactions between environment context, bee species diversity, and the bee-associated microbes.}, }
@article {pmid32572534, year = {2020}, author = {Arce-Rodríguez, A and Puente-Sánchez, F and Avendaño, R and Libby, E and Mora-Amador, R and Rojas-Jimenez, K and Martínez, M and Pieper, DH and Chavarría, M}, title = {Microbial Community Structure Along a Horizontal Oxygen Gradient in a Costa Rican Volcanic Influenced Acid Rock Drainage System.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {793-808}, doi = {10.1007/s00248-020-01530-9}, pmid = {32572534}, issn = {1432-184X}, support = {VI 809-B6-524//Vicerrectoría de Investigación, Universidad de Costa Rica/ ; No FI-255B-17//The Costa Rican Ministry of Science, Technology and Telecommunication (MICITT) and Federal Ministry of Education and Research (BMBF)/ ; ERC250350-IPBSL//ERC grant IPBSL/ ; CTM2016-80095-C2-1-R//Spanish Economy and Competitiveness Ministry (MINECO)/ ; }, abstract = {We describe the geochemistry and microbial diversity of a pristine environment that resembles an acid rock drainage (ARD) but it is actually the result of hydrothermal and volcanic influences. We designate this environment, and other comparable sites, as volcanic influenced acid rock drainage (VARD) systems. The metal content and sulfuric acid in this ecosystem stem from the volcanic milieu and not from the product of pyrite oxidation. Based on the analysis of 16S rRNA gene amplicons, we report the microbial community structure in the pristine San Cayetano Costa Rican VARD environment (pH = 2.94-3.06, sulfate ~ 0.87-1.19 g L-1, iron ~ 35-61 mg L-1 (waters), and ~ 8-293 g kg-1 (sediments)). San Cayetano was found to be dominated by microorganisms involved in the geochemical cycling of iron, sulfur, and nitrogen; however, the identity and abundance of the species changed with the oxygen content (0.40-6.06 mg L-1) along the river course. The hypoxic source of San Cayetano is dominated by a putative anaerobic sulfate-reducing Deltaproteobacterium. Sulfur-oxidizing bacteria such as Acidithiobacillus or Sulfobacillus are found in smaller proportions with respect to typical ARD. In the oxic downstream, we identified aerobic iron-oxidizers (Leptospirillum, Acidithrix, Ferrovum) and heterotrophic bacteria (Burkholderiaceae bacterium, Trichococcus, Acidocella). Thermoplasmatales archaea closely related to environmental phylotypes found in other ARD niches were also observed throughout the entire ecosystem. Overall, our study shows the differences and similarities in the diversity and distribution of the microbial communities between an ARD and a VARD system at the source and along the oxygen gradient that establishes on the course of the river.}, }
@article {pmid32572216, year = {2020}, author = {Li, L and Wang, S and Wang, H and Sahu, SK and Marin, B and Li, H and Xu, Y and Liang, H and Li, Z and Cheng, S and Reder, T and Çebi, Z and Wittek, S and Petersen, M and Melkonian, B and Du, H and Yang, H and Wang, J and Wong, GK and Xu, X and Liu, X and Van de Peer, Y and Melkonian, M and Liu, H}, title = {The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {9}, pages = {1220-1231}, doi = {10.1038/s41559-020-1221-7}, pmid = {32572216}, issn = {2397-334X}, abstract = {Genome analysis of the pico-eukaryotic marine green alga Prasinoderma coloniale CCMP 1413 unveils the existence of a novel phylum within green plants (Viridiplantae), the Prasinodermophyta, which diverged before the split of Chlorophyta and Streptophyta. Structural features of the genome and gene family comparisons revealed an intermediate position of the P. coloniale genome (25.3 Mb) between the extremely compact, small genomes of picoplanktonic Mamiellophyceae (Chlorophyta) and the larger, more complex genomes of early-diverging streptophyte algae. Reconstruction of the minimal core genome of Viridiplantae allowed identification of an ancestral toolkit of transcription factors and flagellar proteins. Adaptations of P. coloniale to its deep-water, oligotrophic environment involved expansion of light-harvesting proteins, reduction of early light-induced proteins, evolution of a distinct type of C4 photosynthesis and carbon-concentrating mechanism, synthesis of the metal-complexing metabolite picolinic acid, and vitamin B1, B7 and B12 auxotrophy. The P. coloniale genome provides first insights into the dawn of green plant evolution.}, }
@article {pmid32572143, year = {2020}, author = {Ren, FR and Sun, X and Wang, TY and Yao, YL and Huang, YZ and Zhang, X and Luan, JB}, title = {Biotin provisioning by horizontally transferred genes from bacteria confers animal fitness benefits.}, journal = {The ISME journal}, volume = {14}, number = {10}, pages = {2542-2553}, pmid = {32572143}, issn = {1751-7370}, support = {31871967//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Insect symbionts are widespread in nature and lateral gene transfer is prevalent in insect symbiosis. However, the function of horizontally transferred genes (HTGs) in insect symbiosis remains speculative, including the mechanism that enables insects to feed on plant phloem deficient in B vitamins. Previously, we found there is redundancy in biotin synthesis pathways from both whitefly Bemisia tabaci and symbiotic Hamiltonella due to the presence of whitefly HTGs. Here, we demonstrate that elimination of Hamiltonella decreased biotin levels but elevated the expression of horizontally transferred biotin genes in whiteflies. HTGs proteins exhibit specific expression patterns in specialized insect cells called bacteriocytes housing symbionts. Complementation with whitefly HTGs rescued E. coli biotin gene knockout mutants. Furthermore, silencing whitefly HTGs in Hamiltonella-infected whiteflies reduced biotin levels and hindered adult survival and fecundity, which was partially rescued by biotin supplementation. Each of horizontally transferred biotin genes are conserved in various laboratory cultures and species of whiteflies with geographically diverse distributions, which shares an evolutionary origin. We provide the first experimental evidence that biotin synthesized through acquired HTGs is important in whiteflies and may be as well in other animals. Our findings suggest that B vitamin provisioning in animal-microbe symbiosis frequently evolved from bacterial symbionts to animal hosts through horizontal gene transfer events. This study will also shed light on how the animal genomes evolve through functional transfer of genes with bacterial origin in the wider contexts of microbial ecology.}, }
@article {pmid32568403, year = {2020}, author = {Toe, LC and Kerckhof, FM and De Bodt, J and Morel, FB and Ouedraogo, JB and Kolsteren, P and Van de Wiele, T}, title = {A prebiotic-enhanced lipid-based nutrient supplement (LNSp) increases Bifidobacterium relative abundance and enhances short-chain fatty acid production in simulated colonic microbiota from undernourished infants.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {7}, pages = {}, doi = {10.1093/femsec/fiaa105}, pmid = {32568403}, issn = {1574-6941}, abstract = {Undernutrition remains a public health problem in the developing world with an attributable under-five death proportion of 45%. Lower gut microbiota diversity and poor metabolic output are associated with undernutrition and new therapeutic paths may come from steering gut microbiota composition and functionality. Using a dynamic gut model, the Simulator of Human Intestinal Microbial Ecosystem (SHIME®), we investigated the effect of a lipid-based nutrient supplement enriched with prebiotics (LNSp), compared to LNS alone and control treatment, on the composition and metabolic functionality of fecal microbiota from three infants suffering from undernutrition. LNS elicited a significant increase in acetate and branched-chain fatty acid production, and a higher relative abundance of the genera Prevotella, Megasphaera, Acinetobacter, Acidaminococcus and Pseudomonas. In contrast, LNSp treatment resulted in a significant 9-fold increase in Bifidobacterium relative abundance and a decrease in that of potential pathogens and detrimental bacteria such as Enterobacteriaceae spp. and Bilophila sp. Moreover, the LNSp treatment resulted in a significantly higher production of acetate, butyrate and propionate, as compared to control and LNS. Our results suggest that provision of prebiotic-enhanced LNS to undernourished children could be a possible strategy to steer the microbiota toward a more beneficial composition and metabolic activity. Further in vivo investigations are needed to assess these effects and their repercussion on nutritional status.}, }
@article {pmid32562995, year = {2020}, author = {Rowles Iii, LS and Hossain, AI and Ramirez, I and Durst, NJ and Ward, PM and Kirisits, MJ and Araiza, I and Lawler, DF and Saleh, NB}, title = {Seasonal contamination of well-water in flood-prone colonias and other unincorporated U.S. communities.}, journal = {The Science of the total environment}, volume = {740}, number = {}, pages = {140111}, doi = {10.1016/j.scitotenv.2020.140111}, pmid = {32562995}, issn = {1879-1026}, mesh = {*Floods ; Humans ; Seasons ; Southwestern United States ; Texas ; United States ; Water Supply ; *Water Wells ; }, abstract = {Many of the six million residents of unincorporated communities in the United States depend on well-water to meet their needs. One group of unincorporated communities is the colonias, located primarily in several southwestern U.S. states. Texas is home to the largest number of these self-built communities, of mostly low-income families, lacking basic infrastructure. While some states have regulations that mandate minimum infrastructure for these communities, water and sewage systems are still lacking for many of their residents. Unprotected wells and self-built septic/cesspool systems serve as the primary infrastructure for many such colonias. This research was designed to probe how wells and septic/cesspool systems are influenced by heavy rainfall events. Such events are hypothesized to impact water quality with regard to human health. Inorganic and microbiological water quality of the wells in nine colonias located in Nueces County, Texas, were evaluated during dry and wet periods. Nueces County was selected as an example based on its flooding history and the fact that many colonias there depend entirely on well-water and septic/cesspool systems. The results demonstrate that well-water quality in these communities varies seasonally with respect to arsenic (up to 35 μg/L) and bacterial contamination (Escherichia coli), dependent on the amount of rainfall, which leaves this population vulnerable to health risks during both wet and dry periods. Microbial community analyses were also conducted on selected samples. To explore similar seasonal contamination of well-water, an analysis of unincorporated communities, flooding frequency, and arsenic contamination in wells was conducted by county throughout the United States. This nationwide analysis indicates that unincorporated communities elsewhere in the United States are likely experiencing comparable challenges for potable water access because of a confluence of socioeconomic, infrastructural, and policy realities.}, }
@article {pmid32561945, year = {2020}, author = {Rapp, D and Ross, CM and Maclean, P and Cave, VM and Brightwell, G}, title = {Investigation of On-Farm Transmission Routes for Contamination of Dairy Cows with Top 7 Escherichia coli O-Serogroups.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01542-5}, pmid = {32561945}, issn = {1432-184X}, abstract = {Shiga toxin-producing Escherichia coli (STEC) are foodborne bacterial pathogens, with cattle a significant reservoir for human infection. This study evaluated environmental reservoirs, intermediate hosts and key pathways that could drive the presence of Top 7 STEC (O157:H7, O26, O45, O103, O111, O121 and O145) on pasture-based dairy herds, using molecular and culture-based methods. A total of 235 composite environmental samples (including soil, bedding, pasture, stock drinking water, bird droppings and flies and faecal samples of dairy animals) were collected from two dairy farms, with four sampling events on each farm. Molecular detection revealed O26, O45, O103 and O121 as the most common O-serogroups, with the greatest occurrence in dairy animal faeces (> 91%), environments freshly contaminated with faeces (> 73%) and birds and flies (> 71%). STEC (79 isolates) were a minor population within the target O-serogroups in all sample types but were widespread in the farm environment in the summer samplings. Phylogenetic analysis of whole genome sequence data targeting single nucleotide polymorphisms revealed the presence of several clonal strains on a farm; a single STEC clonal strain could be found in several sample types concurrently, indicating the existence of more than one possible route for transmission to dairy animals and a high rate of transmission of STEC between dairy animals and wildlife. Overall, the findings improved the understanding of the ecology of the Top 7 STEC in open farm environments, which is required to develop on-farm intervention strategies controlling these zoonoses.}, }
@article {pmid32561944, year = {2020}, author = {Adomako, MO and Xue, W and Tang, M and Du, DL and Yu, FH}, title = {Synergistic Effects of Soil Microbes on Solidago canadensis Depend on Water and Nutrient Availability.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {837-845}, doi = {10.1007/s00248-020-01537-2}, pmid = {32561944}, issn = {1432-184X}, abstract = {Soil microbes may greatly affect plant growth. While plants are commonly associated with diverse communities of soil microbes, complementary roles of different microbial communities that may stimulate synergistic effects on plant growth are not adequately tested. Also, such synergistic effects may vary with environmental conditions such as soil nutrient and water availability. We conducted a greenhouse experiment with a widespread clonal plant Solidago canadensis. The experiment was a factorial design with four levels of soil microbial inoculation (fresh soil inocula from grasslands in northern and southern China that were expected to differ in soil microbial composition, a mixture of the two fresh soil inocula, and a sterilized mixed inoculum control), two levels of nutrient availability (low vs. high), and two levels of water supply (low vs. high, i.e., 1376 vs. 352 mm per year). Irrespective of water supply and nutrient availability, total, aboveground, and belowground mass of S. canadensis were generally higher when the plant grew in soil inoculated with a mixture of soil microbes from the south and north of China (in the mixed inoculum treatment) than when it grew in soil inoculated with soil microbes from only the north or the south or the sterilized control. Such effects of soil microbes on total and aboveground mass were stronger under high than under low nutrient availability and also under high than under low water supply. Our results suggest that interactions of different soil microbial communities can result in a synergistic effect on plant growth and such a synergistic effect depends on environmental conditions. The findings shed light on the importance of plant-microbe interactions during the spreading of some plant species in face of increased atmospheric nutrient deposition coupled with altered rainfall pattern due to global change.}, }
@article {pmid32561583, year = {2020}, author = {Henson, MW and Lanclos, VC and Pitre, DM and Weckhorst, JL and Lucchesi, AM and Cheng, C and Temperton, B and Thrash, JC}, title = {Expanding the Diversity of Bacterioplankton Isolates and Modeling Isolation Efficacy with Large-Scale Dilution-to-Extinction Cultivation.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {17}, pages = {}, pmid = {32561583}, issn = {1098-5336}, abstract = {Cultivated bacterioplankton representatives from diverse lineages and locations are essential for microbiology, but the large majority of taxa either remain uncultivated or lack isolates from diverse geographic locales. We paired large-scale dilution-to-extinction (DTE) cultivation with microbial community analysis and modeling to expand the phylogenetic and geographic diversity of cultivated bacterioplankton and to evaluate DTE cultivation success. Here, we report results from 17 DTE experiments totaling 7,820 individual incubations over 3 years, yielding 328 repeatably transferable isolates. Comparison of isolates to microbial community data for source waters indicated that we successfully isolated 5% of the observed bacterioplankton community throughout the study; 43% and 26% of our isolates matched operational taxonomic units and amplicon single-nucleotide variants, respectively, within the top 50 most abundant taxa. Isolates included those from previously uncultivated clades such as SAR11 LD12 and Actinobacteria acIV, as well as geographically novel members from other ecologically important groups like SAR11 subclade IIIa, SAR116, and others, providing isolates in eight putatively new genera and seven putatively new species. Using a newly developed DTE cultivation model, we evaluated taxon viability by comparing relative abundance with cultivation success. The model (i) revealed the minimum attempts required for successful isolation of taxa amenable to growth on our media and (ii) identified possible subpopulation viability variation in abundant taxa such as SAR11 that likely impacts cultivation success. By incorporating viability in experimental design, we can now statistically constrain the effort necessary for successful cultivation of specific taxa on a defined medium.IMPORTANCE Even before the coining of the term &quot;great plate count anomaly&quot; in the 1980s, scientists had noted the discrepancy between the number of microorganisms observed under the microscope and the number of colonies that grew on traditional agar media. New cultivation approaches have reduced this disparity, resulting in the isolation of some of the &quot;most wanted&quot; bacterial lineages. Nevertheless, the vast majority of microorganisms remain uncultured, hampering progress toward answering fundamental biological questions about many important microorganisms. Furthermore, few studies have evaluated the underlying factors influencing cultivation success, limiting our ability to improve cultivation efficacy. Our work details the use of dilution-to-extinction (DTE) cultivation to expand the phylogenetic and geographic diversity of available axenic cultures. We also provide a new model of the DTE approach that uses cultivation results and natural abundance information to predict taxon-specific viability and iteratively constrain DTE experimental design to improve cultivation success.}, }
@article {pmid32561582, year = {2020}, author = {Blackwell, N and Bryce, C and Straub, D and Kappler, A and Kleindienst, S}, title = {Genomic Insights into Two Novel Fe(II)-Oxidizing Zetaproteobacteria Isolates Reveal Lifestyle Adaption to Coastal Marine Sediments.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {17}, pages = {}, pmid = {32561582}, issn = {1098-5336}, abstract = {The discovery of the novel Zetaproteobacteria class greatly expanded our understanding of neutrophilic, microaerophilic microbial Fe(II) oxidation in marine environments. Despite molecular techniques demonstrating their global distribution, relatively few isolates exist, especially from low-Fe(II) environments. Furthermore, the Fe(II) oxidation pathways used by Zetaproteobacteria remain poorly understood. Here, we present the genomes (>99% genome completeness) of two Zetaproteobacteria, which are the only cultivated isolates originating from typical low-Fe [porewater Fe(II), 70 to 100 μM] coastal marine sediments. The two strains share <90% average nucleotide identity (ANI) with each other and <80% ANI with any other Zetaproteobacteria genome. The closest relatives were Mariprofundus aestuarium strain CP-5 and Mariprofundus ferrinatatus strain CP-8 (96 to 98% 16S rRNA gene sequence similarity). Fe(II) oxidation of strains KV and NF is most likely mediated by the putative Fe(II) oxidase Cyc2. Interestingly, the genome of strain KV also encodes a putative multicopper oxidase, PcoAB, which could play a role in Fe(II) oxidation, a pathway found only in two other Zetaproteobacteria genomes (Ghiorsea bivora TAG-1 and SCGC AB-602-C20). The strains show potential adaptations to fluctuating O2 concentrations, indicated by the presence of both cbb3- and aa3-type cytochrome c oxidases, which are adapted to low and high O2 concentrations, respectively. This is further supported by the presence of several oxidative-stress-related genes. In summary, our results reveal the potential Fe(II) oxidation pathways employed by these two novel chemolithoautotrophic Fe(II)-oxidizing species and the lifestyle adaptations which enable the Zetaproteobacteria to survive in coastal environments with low Fe(II) and regular redox fluctuations.IMPORTANCE Until recently, the importance and relevance of Zetaproteobacteria were mainly thought to be restricted to high-Fe(II) environments, such as deep-sea hydrothermal vents. The two novel Mariprofundus isolates presented here originate from typical low-Fe(II) coastal marine sediments. As well as being low in Fe(II), these environments are often subjected to fluctuating O2 concentrations and regular mixing by wave action and bioturbation. The discovery of two novel isolates highlights the importance of these organisms in such environments, as Fe(II) oxidation has been shown to impact nutrients and trace metals. Genome analysis of these two strains further supported their lifestyle adaptation and therefore their potential preference for coastal marine sediments, as genes necessary for surviving dynamic O2 concentrations and oxidative stress were identified. Furthermore, our analyses also expand our understanding of the poorly understood Fe(II) oxidation pathways used by neutrophilic, microaerophilic Fe(II) oxidizers.}, }
@article {pmid32561577, year = {2020}, author = {Onyango, SO and De Clercq, N and Beerens, K and Van Camp, J and Desmet, T and Van de Wiele, T}, title = {Oral Microbiota Display Profound Differential Metabolic Kinetics and Community Shifts upon Incubation with Sucrose, Trehalose, Kojibiose, and Xylitol.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {16}, pages = {}, pmid = {32561577}, issn = {1098-5336}, abstract = {This study compares the metabolic properties of kojibiose, trehalose, sucrose, and xylitol upon incubation with representative oral bacteria as monocultures or synthetic communities or with human salivary bacteria in a defined medium. Compared to sucrose and trehalose, kojibiose resisted metabolism during a 48-h incubation with monocultures, except for Actinomyces viscosus Incubations with Lactobacillus-based communities, as well as salivary bacteria, displayed kojibiose metabolism, yet to a lesser extent than sucrose and trehalose. Concurring with our in vitro findings, screening for carbohydrate-active enzymes revealed that only Lactobacillus spp. and A. viscosus possess enzymes from glycohydrolase (GH) families GH65 and GH15, respectively, which are associated with kojibiose metabolism. Donor-dependent differences in salivary microbiome composition were noted, and differences in pH drop during incubation indicated different rates of sugar metabolism. However, functional analysis indicated that lactate, acetate, and formate evenly dominated the metabolic profile for all sugars except for xylitol. 16S rRNA gene sequencing analysis and α-diversity markers revealed that a significant shift of the microbiome community by sugars was more pronounced in sucrose and trehalose than in kojibiose and xylitol. In Streptococcus spp., a taxon linked to cariogenesis dominated in sucrose (mean ± standard deviation, 91.8 ± 6.4%) and trehalose (55.9 ± 38.6%), representing a high diversity loss. In contrast, Streptococcus (5.1 ± 3.7%) was less abundant in kojibiose, which instead was dominated by Veillonella (26.8 ± 19.6%), while for xylitol, Neisseria (29.4 ± 19.1%) was most abundant. Overall, kojibiose and xylitol incubations stimulated cariogenic species less yet closely maintained an abundance of key phyla and genera of the salivary microbiome, suggesting that kojibiose has low cariogenic properties.IMPORTANCE This study provides a detailed scientific insight on the metabolism of a rare disaccharide, kojibiose, whose mass production has recently been made possible. While the resistance of kojibiose was established with monocultures, delayed utilization of kojibiose was observed with communities containing lactobacilli and A. viscosus as well as with complex communities of bacteria from human saliva. Kojibiose is, therefore, less metabolizable than sucrose and trehalose. Moreover, although conventional sugars cause distinct shifts in salivary microbial communities, our study has revealed that kojibiose is able to closely maintain the salivary microbiome composition, suggesting its low cariogenic properties. This study furthermore underscores the importance and relevance of microbial culture and ex vivo mixed cultures to study cariogenicity and substrate utilization; this is in sharp contrast with tests that solely rely on monocultures such as Streptococcus mutans, which clearly fail to capture complex interactions between oral microbiota.}, }
@article {pmid32558638, year = {2020}, author = {Prudence, SMM and Addington, E and Castaño-Espriu, L and Mark, DR and Pintor-Escobar, L and Russell, AH and McLean, TC}, title = {Advances in actinomycete research: an ActinoBase review of 2019.}, journal = {Microbiology (Reading, England)}, volume = {166}, number = {8}, pages = {683-694}, doi = {10.1099/mic.0.000944}, pmid = {32558638}, issn = {1465-2080}, abstract = {The actinomycetes are Gram-positive bacteria belonging to the order Actinomycetales within the phylum Actinobacteria. They include members with significant economic and medical importance, for example filamentous actinomycetes such as Streptomyces species, which have a propensity to produce a plethora of bioactive secondary metabolites and form symbioses with higher organisms, such as plants and insects. Studying these bacteria is challenging, but also fascinating and very rewarding. As a Microbiology Society initiative, members of the actinomycete research community have been developing a Wikipedia-style resource, called ActinoBase, the purpose of which is to aid in the study of these filamentous bacteria. This review will highlight 10 publications from 2019 that have been of special interest to the ActinoBase community, covering 4 major components of actinomycete research: (i) development and regulation; (ii) specialized metabolites; (iii) ecology and host interactions; and (iv) technology and methodology.}, }
@article {pmid32556417, year = {2020}, author = {Fuster, M and Billard, H and Mandart, M and Steiger, J and Sime-Ngando, T and Colombet, J}, title = {Trophic Conditions Influence Widespread Distribution of Aster-Like Nanoparticles Within Aquatic Environments.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {741-745}, doi = {10.1007/s00248-020-01541-6}, pmid = {32556417}, issn = {1432-184X}, abstract = {Aster-like nanoparticles (ALNs) are newly described femto-entities. Their ecology (e.g., geographic distribution, spatial dynamic, preferences, forcing factors) is still unknown. Here, we report that these entities, which have largely been ignored until now, can develop or maintain themselves in most aquatic environments in the Loire River catchment, France. We observed a significant influence of the trophic state on ALN ecological distributions. A positive relationship between prokaryotic abundance and ALN (r2 = 0.72, p < 0.01) has been identified, but its exact nature remains to be clarified. Combined with their ubiquitous distribution and high abundances (up to 7.9 × 106 ALNs mL-1) recorded in our samples, this probably makes ALNs an overlooked functional component in aquatic ecosystems.}, }
@article {pmid32556393, year = {2020}, author = {Carteron, A and Beigas, M and Joly, S and Turner, BL and Laliberté, E}, title = {Temperate Forests Dominated by Arbuscular or Ectomycorrhizal Fungi Are Characterized by Strong Shifts from Saprotrophic to Mycorrhizal Fungi with Increasing Soil Depth.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01540-7}, pmid = {32556393}, issn = {1432-184X}, support = {RGPIN-2014-06106, RGPIN-2019-04537//Natural Sciences and Engineering Research Council of Canada/ ; 2016-NC-188823//Fonds de Recherche du Québec - Nature et Technologies/ ; }, abstract = {In temperate and boreal forests, competition for soil resources between free-living saprotrophs and ectomycorrhizal (EcM) fungi has been suggested to restrict saprotrophic fungal dominance to the most superficial organic soil horizons in forests dominated by EcM trees. By contrast, lower niche overlap with arbuscular mycorrhizal (AM) fungi could allow fungal saprotrophs to maintain this dominance into deeper soil horizons in AM-dominated forests. Here we used a natural gradient of adjacent forest patches that were dominated by either AM or EcM trees, or a mixture of both to determine how fungal communities characterized with high-throughput amplicon sequencing change across organic and mineral soil horizons. We found a general shift from saprotrophic to mycorrhizal fungal dominance with increasing soil depth in all forest mycorrhizal types, especially in organic horizons. Vertical changes in soil chemistry, including pH, organic matter, exchangeable cations, and extractable phosphorus, coincided with shifts in fungal community composition. Although fungal communities and soil chemistry differed among adjacent forest mycorrhizal types, variations were stronger within a given soil profile, pointing to the importance of considering horizons when characterizing soil fungal communities. Our results also suggest that in temperate forests, vertical shifts from saprotrophic to mycorrhizal fungi within organic and mineral horizons occur similarly in both ectomycorrhizal and arbuscular mycorrhizal forests.}, }
@article {pmid32551196, year = {2020}, author = {Coil, DA and Neches, RY and Lang, JM and Jospin, G and Brown, WE and Cavalier, D and Hampton-Marcell, J and Gilbert, JA and Eisen, JA}, title = {Bacterial communities associated with cell phones and shoes.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e9235}, pmid = {32551196}, issn = {2167-8359}, abstract = {Background: Every human being carries with them a collection of microbes, a collection that is likely both unique to that person, but also dynamic as a result of significant flux with the surrounding environment. The interaction of the human microbiome (i.e., the microbes that are found directly in contact with a person in places such as the gut, mouth, and skin) and the microbiome of accessory objects (e.g., shoes, clothing, phones, jewelry) is of potential interest to both epidemiology and the developing field of microbial forensics. Therefore, the microbiome of personal accessories are of interest because they serve as both a microbial source and sink for an individual, they may provide information about the microbial exposure experienced by an individual, and they can be sampled non-invasively.<br><br>Findings: We report here a large-scale study of the microbiome found on cell phones and shoes. Cell phones serve as a potential source and sink for skin and oral microbiome, while shoes can act as sampling devices for microbial environmental experience. Using 16S rRNA gene sequencing, we characterized the microbiome of thousands of paired sets of cell phones and shoes from individuals at sporting events, museums, and other venues around the United States.<br><br>Conclusions: We place this data in the context of previous studies and demonstrate that the microbiome of phones and shoes are different. This difference is driven largely by the presence of &quot;environmental&quot; taxa (taxa from groups that tend to be found in places like soil) on shoes and human-associated taxa (taxa from groups that are abundant in the human microbiome) on phones. This large dataset also contains many novel taxa, highlighting the fact that much of microbial diversity remains uncharacterized, even on commonplace objects.}, }
@article {pmid32547588, year = {2020}, author = {Rantsiou, K and Giacosa, S and Pugliese, M and Englezos, V and Ferrocino, I and Río Segade, S and Monchiero, M and Gribaudo, I and Gambino, G and Gullino, ML and Rolle, L}, title = {Impact of Chemical and Alternative Fungicides Applied to Grapevine cv Nebbiolo on Microbial Ecology and Chemical-Physical Grape Characteristics at Harvest.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {700}, pmid = {32547588}, issn = {1664-462X}, abstract = {Viticulture is a cropping system in which treatment against fungal diseases (in particular powdery and downy mildews) can be extremely frequent. Accordingly, a reduction in antimicrobial treatments and the application of environmentally-friendly compounds are becoming increasingly important for a more sustainable viticulture. In addition to their effect against pathogens, the impact of these products on the quality of the grapes is very important for the oenological industries, but unfortunately at present few data are available. We evaluated the effect of the application of biocontrol products and resistance inducers in the vineyard on the mechanical properties, microbial ecology, technological and phenolic maturity of Vitis vinifera &quot;Nebbiolo&quot; grapes at harvest. The yield and vigor of vines were not influenced by the treatments, nor were the production of primary and secondary metabolites. However, the active ingredients influenced the mechanical properties of the skin (hardness and thickness). A significant hardening of the skin was detected when laminarin and chito-oligosaccharides were used, and sulfur induced a thickening of the skin with potential consequences for wine quality. Furthermore, the yeast community present on grape berries was influenced by the treatments. The abundance of Aureobasidium pullulans, the dominant species on the grape berry, changed in response to the compounds used. In addition, Alternaria sp. was reduced in some treatments with a potentially positive effect on the quality and the safety of the grapes. This study provides an overview of the effect of biocontrol products and resistance inducers on microbial ecology and &quot;Nebbiolo&quot; grape quality, contributing to the establishment of more sustainable and effective defense strategies in viticulture.}, }
@article {pmid32546676, year = {2020}, author = {Gulino, K and Rahman, J and Badri, M and Morton, J and Bonneau, R and Ghedin, E}, title = {Initial Mapping of the New York City Wastewater Virome.}, journal = {mSystems}, volume = {5}, number = {3}, pages = {}, pmid = {32546676}, issn = {2379-5077}, abstract = {Bacteriophages are abundant members of all microbiomes studied to date, influencing microbial communities through interactions with their bacterial hosts. Despite their functional importance and ubiquity, phages have been underexplored in urban environments compared to their bacterial counterparts. We profiled the viral communities in New York City (NYC) wastewater using metagenomic data collected in November 2014 from 14 wastewater treatment plants. We show that phages accounted for the largest viral component of the sewage samples and that specific virus communities were associated with local environmental conditions within boroughs. The vast majority of the virus sequences had no homology matches in public databases, forming an average of 1,700 unique virus clusters (putative genera). These new clusters contribute to elucidating the overwhelming proportion of data that frequently goes unidentified in viral metagenomic studies. We assigned potential hosts to these phages, which appear to infect a wide range of bacterial genera, often outside their presumed host. We determined that infection networks form a modular-nested pattern, indicating that phages include a range of host specificities, from generalists to specialists, with most interactions organized into distinct groups. We identified genes in viral contigs involved in carbon and sulfur cycling, suggesting functional importance of viruses in circulating pathways and gene functions in the wastewater environment. In addition, we identified virophage genes as well as a nearly complete novel virophage genome. These findings provide an understanding of phage abundance and diversity in NYC wastewater, previously uncharacterized, and further examine geographic patterns of phage-host association in urban environments.IMPORTANCE Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment.}, }
@article {pmid32540743, year = {2020}, author = {Cahill, N and Morris, D}, title = {Recreational waters - A potential transmission route for SARS-CoV-2 to humans?.}, journal = {The Science of the total environment}, volume = {740}, number = {}, pages = {140122}, doi = {10.1016/j.scitotenv.2020.140122}, pmid = {32540743}, issn = {1879-1026}, mesh = {*Betacoronavirus ; *Coronavirus Infections/transmission ; Humans ; Pandemics ; Pneumonia, Viral ; *Recreation ; *Water Microbiology ; }, abstract = {Coronavirus disease 2019 (COVID-19), the respiratory illness caused by the novel virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has lead to high morbidity and mortality rates worldwide, has been causing major public health concerns since first detected in late 2019. Following identification of novel pathogens, questions in relation to dissemination of the pathogen and transmission routes begin to emerge. This rapidly spreading SARS-CoV-2 virus has been detected in both faecal and wastewater samples across the globe, highlighting the potential for faecal-oral transmission of the virus. As a result, concerns regarding the transmission of the virus in the environment and the risk associated with contracting the virus in recreational waters, particularly where inadequately treated wastewater is discharged, have been emerging in recent weeks. This paper highlights the need for further research to be carried out to investigate the presence, infectivity and viability of this newly identified SARS-CoV-2 virus in wastewater effluent and receiving recreational waters.}, }
@article {pmid32540193, year = {2020}, author = {Candry, P and Ulcar, B and Petrognani, C and Rabaey, K and Ganigué, R}, title = {Ethanol:propionate ratio drives product selectivity in odd-chain elongation with Clostridium kluyveri and mixed communities.}, journal = {Bioresource technology}, volume = {313}, number = {}, pages = {123651}, doi = {10.1016/j.biortech.2020.123651}, pmid = {32540193}, issn = {1873-2976}, mesh = {Caproates ; *Clostridium kluyveri ; Ethanol ; Fermentation ; Propionates ; }, abstract = {Microbial production of valerate, a five-carbon carboxylate, can occur from propionate and ethanol through a process called odd-chain elongation. The generation of even-chain compounds in this process lowers product selectivity, forming a key challenge. This study investigated factors determining product selectivity during odd-chain elongation in an odd-chain elongating mixed community and the pure culture Clostridium kluyveri DSM555. Incubations at different ratios of ethanol:propionate showed that increasing ratios (from 0.5 to 7) lowered product specificity, as evidenced by a decrease in the odd:even product ratio from 5.5 to 1.5 for C. kluyveri and from 15 to 0.8 for the mixed community. The consistency of these observations with literature data suggests that control of ethanol:propionate ratio offers a robust tool for process control in odd-chain elongation, while the flexible metabolism can also have implications for efficient use of ethanol during even-chain elongation processes.}, }
@article {pmid32539984, year = {2020}, author = {Zagdoun, M and Coeuret, G and N'Dione, M and Champomier-Vergès, MC and Chaillou, S}, title = {Large microbiota survey reveals how the microbial ecology of cooked ham is shaped by different processing steps.}, journal = {Food microbiology}, volume = {91}, number = {}, pages = {103547}, doi = {10.1016/j.fm.2020.103547}, pmid = {32539984}, issn = {1095-9998}, abstract = {Cooked ham production involves numerous steps shaping the microbial communities of the final product, with consequences on spoilage metabolites production. To identify the main factors driving the ecology of ham and its spoilage, we designed a study encompassing five variables related to ham production: type of storage during meat transportation, churning speed, drain-off time, slicing line and O2 packaging permeability. About 200 samples from the same facility were obtained and characterized with respect to i) their microbiota based on gyrB amplicon sequencing ii) their production of spoilage-related metabolites based on E-Nose analysis and enzymatic assays. The slicing was the most critical step, shaping two general types of microbiota according to the slicing line: one dominated by Carnobacterium divergens and another one dominated by Leuconostoc carnosum and Serratia proteamaculans. Regarding metabolites production, L. carnosum was associated to d-lactic acid, ethanol and acetic acid production, whereas Serratia proteamaculans was associated to acetic acid production. This last species prevailed with highly O2-permeable packaging. Within a given slicing line, campaign-based variations were observed, with Lactobacillus sakei, Leuconostoc mesenteroides and Carnobacterium maltaromaticum prevalent in summer. L. sakei was associated with l-lactic acid production and C. maltaromaticum with formic and acetic acid productions.}, }
@article {pmid32539232, year = {2020}, author = {Hussan, JR and Hunter, PJ}, title = {Our natural &quot;makeup&quot; reveals more than it hides: Modeling the skin and its microbiome.}, journal = {Wiley interdisciplinary reviews. Systems biology and medicine}, volume = {}, number = {}, pages = {e1497}, doi = {10.1002/wsbm.1497}, pmid = {32539232}, issn = {1939-005X}, support = {//Aotearoa Foundation/ ; }, abstract = {Skin is our primary interface with the environment. A structurally and functionally complex organ that hosts a dynamic ecosystem of microbes, and synthesizes many compounds that affect our well-being and psychosocial interactions. It is a natural platform of signal exchange between internal organs, skin resident microbes, and the environment. These interactions have gained a great deal of attention due to the increased prevalence of atopic diseases, and the co-occurrence of multiple allergic diseases related to allergic sensitization in early life. Despite significant advances in experimentally characterizing the skin, its microbial ecology, and disease phenotypes, high-levels of variability in these characteristics even for the same clinical phenotype are observed. Addressing this variability and resolving the relevant biological processes requires a systems approach. This review presents some of our current understanding of the skin, skin-immune, skin-neuroendocrine, skin-microbiome interactions, and computer-based modeling approaches to simulate this ecosystem in the context of health and disease. The review highlights the need for a systems-based understanding of this sophisticated ecosystem. This article is categorized under: Models of Systems Properties and Processes > Organ, Tissue, and Physiological Models Laboratory Methods and Technologies > Metabolomics Physiology > Organismal Responses to Environment.}, }
@article {pmid32535638, year = {2020}, author = {Cardarelli, EL and Bargar, JR and Francis, CA}, title = {Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {778-792}, doi = {10.1007/s00248-020-01534-5}, pmid = {32535638}, issn = {1432-184X}, support = {DE-AC02-76SF00515//Office of Science/ ; DE-SC0019119//U.S. Department of Energy/ ; }, abstract = {Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.}, }
@article {pmid32529471, year = {2020}, author = {López-López, A and Mira, A}, title = {Shifts in Composition and Activity of Oral Biofilms After Fluoride Exposure.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {729-738}, doi = {10.1007/s00248-020-01531-8}, pmid = {32529471}, issn = {1432-184X}, support = {RTI 2018-102032-B-100//Ministerio de Ciencia y Tecnología/ ; }, abstract = {Oral diseases are biofilm-mediated diseases caused by imbalances in the ecology of resident microflora. Among them, dental caries (tooth decay) is considered the most common disease worldwide, and toothbrushing, which physically eliminates the oral biofilm, is the most widespread prevention strategy. Although it is well established that fluoride increases enamel resistance to acidic pH and promotes tooth remineralization, its effect on the biofilm bacterial communities' composition and metabolism is not fully understood. We have grown in vitro oral biofilms and used 16S rRNA Illumina sequencing to study the effect of fluoride on DNA- and RNA-based bacterial populations. In addition, a metatranscriptomic approach has also been performed, in which total RNA has been sequenced to study gene expression profiles in the presence/absence of 500 ppm sodium fluoride. Our data show a lower pH drop and a clear shift in total and metabolically active bacterial composition after fluoride exposure. Streptococcus oralis was the species most affected, with a 10-fold reduction in both DNA and RNA samples, whereas Rothia mucilaginosa underwent an 8-fold increase in the DNA and S. salivarius a 4- and 5-fold increase in the RNA and DNA samples, respectively. The metatranscriptomes indicated that fluoride exposure induced a dramatic shutdown of sugar metabolism, including significant under-expression of different sugar transporters, fucosidases, and a pyruvate oxidase, among others. The reduction in saccharolytic organisms and the inhibition of sugar fermentation pathways by fluoride may therefore be considered instrumental for the beneficial effect of fluoride-containing oral hygiene products.}, }
@article {pmid32525738, year = {2020}, author = {Aszalós, JM and Szabó, A and Megyes, M and Anda, D and Nagy, B and Borsodi, AK}, title = {Bacterial Diversity of a High-Altitude Permafrost Thaw Pond Located on Ojos del Salado (Dry Andes, Altiplano-Atacama Region).}, journal = {Astrobiology}, volume = {20}, number = {6}, pages = {754-765}, doi = {10.1089/ast.2018.2012}, pmid = {32525738}, issn = {1557-8070}, abstract = {Microbial ecology of permafrost, due to its ecological and astrobiological importance, has been in the focus of studies in past decades. Although permafrost is an ancient and stable environment, it is also subjected to current climate changes. Permafrost degradation often results in generation of thaw ponds, a phenomenon not only reported mainly from polar regions but also present in high-altitude permafrost environments. Our knowledge about microbial communities of thaw ponds in these unique, remote mountain habitats is sparse. This study presents the first culture collection and results of the next-generation DNA sequencing (NGS) analysis of bacterial communities inhabiting a high-altitude permafrost thaw pond. In February 2016, a permafrost thaw pond on the Ojos del Salado at 5900 m a.s.l. (meters above sea level) was sampled as part of the Hungarian Dry Andes Research Programme. A culture collection of 125 isolates was established, containing altogether 11 genera belonging to phyla Bacteroidetes, Actinobacteria, and Proteobacteria. Simplified bacterial communities with a high proportion of candidate and hitherto uncultured bacteria were revealed by Illumina MiSeq NGS. Water of the thaw pond was dominated by Bacteroidetes and Proteobacteria, while in the sediment of the lake and permafrost, members of Acidobacteria, Actinobacteria, Bacteroidetes, Patescibacteria, Proteobacteria, and Verrucomicrobia were abundant. This permafrost habitat can be interesting as a potential Mars analog.}, }
@article {pmid32525284, year = {2020}, author = {Verbeeck, K and De Vrieze, J and Pikaar, I and Verstraete, W and Rabaey, K}, title = {Assessing the potential for up-cycling recovered resources from anaerobic digestion through microbial protein production.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.13600}, pmid = {32525284}, issn = {1751-7915}, support = {//Agentschap Innoveren en Ondernemen/ ; //Fonds Wetenschappelijk Onderzoek/ ; }, abstract = {Anaerobic digesters produce biogas, a mixture of predominantly CH4 and CO2 , which is typically incinerated to recover electrical and/or thermal energy. In a context of circular economy, the CH4 and CO2 could be used as chemical feedstock in combination with ammonium from the digestate. Their combination into protein-rich bacterial, used as animal feed additive, could contribute to the ever growing global demand for nutritive protein sources and improve the overall nitrogen efficiency of the current agro- feed/food chain. In this concept, renewable CH4 and H2 can serve as carbon-neutral energy sources for the production of protein-rich cellular biomass, while assimilating and upgrading recovered ammonia from the digestate. This study evaluated the potential of producing sustainable high-quality protein additives in a decentralized way through coupling anaerobic digestion and microbial protein production using methanotrophic and hydrogenotrophic bacteria in an on-farm bioreactor. We show that a practical case digester handling liquid piggery manure, of which the energy content is supplemented for 30% with co-substrates, provides sufficient biogas to allow the subsequent microbial protein as feed production for about 37% of the number of pigs from which the manure was derived. Overall, producing microbial protein on the farm from available methane and ammonia liberated by anaerobic digesters treating manure appears economically and technically feasible within the current range of market prices existing for high-quality protein. The case of producing biomethane for grid injection and upgrading the CO2 with electrolytic hydrogen to microbial protein by means of hydrogen-oxidizing bacteria was also examined but found less attractive at the current production prices of renewable hydrogen. Our calculations show that this route is only of commercial interest if the protein value equals the value of high-value protein additives like fishmeal and if the avoided costs for nutrient removal from the digestate are taken into consideration.}, }
@article {pmid32523566, year = {2020}, author = {Taparia, T and Krijger, M and Hodgetts, J and Hendriks, M and Elphinstone, JG and van der Wolf, J}, title = {Six Multiplex TaqManTM-qPCR Assays for Quantitative Diagnostics of Pseudomonas Species Causative of Bacterial Blotch Diseases of Mushrooms.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {989}, pmid = {32523566}, issn = {1664-302X}, abstract = {Bacterial blotch is a group of economically important diseases of the common button mushroom (Agaricus bisporus). Once the pathogens are introduced to a farm, mesophilic growing conditions (that are optimum for mushroom production) result in severe and widespread secondary infections. Efficient, timely and quantitative detection of the pathogens is hence critical for the design of localized control strategies and prediction of disease risk. This study describes the development of real-time TaqManTM assays that allow molecular diagnosis of three currently prevalent bacterial blotch pathogens: &quot;Pseudomonas gingeri,&quot; Pseudomonas tolaasii and (as yet uncharacterized) Pseudomonas strains (belonging to Pseudomonas salomonii and Pseudomonas edaphica). For each pathogen, assays targeting specific DNA markers on two different loci, were developed for primary detection and secondary verification. All six developed assays showed high diagnostic specificity and sensitivity when tested against a panel of 63 Pseudomonas strains and 40 other plant pathogenic bacteria. The assays demonstrated good analytical performance indicated by linearity across calibration curve (>0.95), amplification efficiency (>90%) and magnitude of amplification signal (>2.1). The limits of detection were optimized for efficient quantification in bacterial cultures, symptomatic tissue, infected casing soil and water samples from mushroom farms. Each target assay was multiplexed with two additional assays. Xanthomonas campestris was detected as an extraction control, to account for loss of DNA during sample processing. And the total Pseudomonas population was detected, to quantify the proportion of pathogenic to beneficial Pseudomonas in the soil. This ratio is speculated to be an indicator for blotch outbreaks. The multiplexed assays were successfully validated and applied by routine testing of diseased mushrooms, peat sources, casing soils, and water from commercial production units.}, }
@article {pmid32518182, year = {2020}, author = {Topçuoğlu, BD and Lesniak, NA and Ruffin, MT and Wiens, J and Schloss, PD}, title = {A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems.}, journal = {mBio}, volume = {11}, number = {3}, pages = {}, pmid = {32518182}, issn = {2150-7511}, support = {R01 CA215574/CA/NCI NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; }, abstract = {Machine learning (ML) modeling of the human microbiome has the potential to identify microbial biomarkers and aid in the diagnosis of many diseases such as inflammatory bowel disease, diabetes, and colorectal cancer. Progress has been made toward developing ML models that predict health outcomes using bacterial abundances, but inconsistent adoption of training and evaluation methods call the validity of these models into question. Furthermore, there appears to be a preference by many researchers to favor increased model complexity over interpretability. To overcome these challenges, we trained seven models that used fecal 16S rRNA sequence data to predict the presence of colonic screen relevant neoplasias (SRNs) (n = 490 patients, 261 controls and 229 cases). We developed a reusable open-source pipeline to train, validate, and interpret ML models. To show the effect of model selection, we assessed the predictive performance, interpretability, and training time of L2-regularized logistic regression, L1- and L2-regularized support vector machines (SVM) with linear and radial basis function kernels, a decision tree, random forest, and gradient boosted trees (XGBoost). The random forest model performed best at detecting SRNs with an area under the receiver operating characteristic curve (AUROC) of 0.695 (interquartile range [IQR], 0.651 to 0.739) but was slow to train (83.2 h) and not inherently interpretable. Despite its simplicity, L2-regularized logistic regression followed random forest in predictive performance with an AUROC of 0.680 (IQR, 0.625 to 0.735), trained faster (12 min), and was inherently interpretable. Our analysis highlights the importance of choosing an ML approach based on the goal of the study, as the choice will inform expectations of performance and interpretability.IMPORTANCE Diagnosing diseases using machine learning (ML) is rapidly being adopted in microbiome studies. However, the estimated performance associated with these models is likely overoptimistic. Moreover, there is a trend toward using black box models without a discussion of the difficulty of interpreting such models when trying to identify microbial biomarkers of disease. This work represents a step toward developing more-reproducible ML practices in applying ML to microbiome research. We implement a rigorous pipeline and emphasize the importance of selecting ML models that reflect the goal of the study. These concepts are not particular to the study of human health but can also be applied to environmental microbiology studies.}, }
@article {pmid32515051, year = {2020}, author = {Koch, C and Kuchenbuch, A and Marosvölgyi, M and Weisshart, K and Harnisch, F}, title = {Label-Free Four-Dimensional Visualization of Anaerobically Growing Electroactive Biofilms.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {97}, number = {7}, pages = {737-741}, doi = {10.1002/cyto.a.24169}, pmid = {32515051}, issn = {1552-4930}, support = {Programme Renewable Energies//Helmholtz Association/ ; }, abstract = {Light sheet fluorescence microscopy (LSFM) allows nondestructive, label-free and in vivo imaging of large specimen, even at nontransparent surfaces. We show that LSFM can be applied for label-free analyses of prokaryotes on the example of electroactive biofilms. Biofilm growth is linked to the production of current serving as measure of metabolic activity in vivo by monitoring with high spatial and temporal resolution. After 35 h of exponential growth, a homogeneous biofilm with a thickness of 9 μm was formed. This was followed by a stratification of the biofilm including the formation of 3D structures over the next 100 h. Light reflection was sufficient to visualize the biofilm structure and development over time and the terminal morphology was confirmed using fluorescence staining. This proof of concept on using LSFM for investigation of biofilms opens the door for its application in the entire field of microbial ecology. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry.}, }
@article {pmid32514926, year = {2020}, author = {McGee, CF}, title = {The effects of silver nanoparticles on the microbial nitrogen cycle: a review of the known risks.}, journal = {Environmental science and pollution research international}, volume = {27}, number = {25}, pages = {31061-31073}, doi = {10.1007/s11356-020-09548-9}, pmid = {32514926}, issn = {1614-7499}, mesh = {*Metal Nanoparticles ; Nitrogen Cycle ; Sewage ; Silver/*analysis ; Soil ; }, abstract = {The nitrogen cycle is an integral biogeochemical function for maintaining healthy environments. Nitrogen is a key nutrient that must be continuously replenished through recycling mechanisms to sustain ecosystems, disruption to which can result in compromised ecosystem functioning. Certain stages in the microbial conversion of nitrogen compounds are performed by a limited range of micro-organisms making these key functional species in ecosystems. The growing industrial use of silver nanoparticles (AgNPs) potentially poses significant risks for microbial nitrogen cycling species. AgNPs possess potent antimicrobial properties and are expected to reach a range of natural environments through several routes of exposure. Certain functional nitrogen cycling microbes have been shown to be highly susceptible to AgNP toxicity. The current literature indicates that AgNPs can negatively affect certain nitrogen fixing, nitrifying and denitrifying microbes in vitro. In vivo studies investigating the effect of AgNPs on nitrogen cycling microbial communities and nitrogen transformation rates in soil, sediment and sludge environments have also indicated disruption of these functional processes. This review provides a comprehensive description of the current state of knowledge regarding the toxicity of AgNPs to nitrogen cycling communities. The aim of the review is to highlight the most susceptible stages in the nitrogen cycle and the implications for the affected ecosystems.}, }
@article {pmid32514604, year = {2020}, author = {Ruan, Y and Wang, T and Guo, S and Ling, N and Shen, Q}, title = {Plant Grafting Shapes Complexity and Co-occurrence of Rhizobacterial Assemblages.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {643-655}, doi = {10.1007/s00248-020-01532-7}, pmid = {32514604}, issn = {1432-184X}, support = {IRT_17R56//Innovative Research Team Development Plan of the Ministry of Education of China/ ; KYT201802//Fundamental Research Funds for the Central Universities/ ; 31772398//National Nature Science Foundation of China/ ; }, abstract = {Grafting is a basic technique which is widely used to increase yield and enhance biotic and abiotic stress tolerance in plant production. The diversity and interactions of rhizobacterial assemblages shaped by grafting are important for the growth of their hosts but remain poorly understood. To test the hypothesis that plant grafting shapes complexity and co-occurrence of rhizobacterial assemblage, four types of plants, including ungrafted bottle gourd (B), ungrafted watermelon (W), grafted watermelon with bottle gourd rootstock (W/B), and grafted bottle gourd with watermelon rootstock (B/W), were cultivated in two soil types in a greenhouse, and the rhizosphere bacterial communities were analyzed by 16S rRNA gene high-throughput sequencing. Both the soil type and grafting significantly influenced the bacterial community composition. Grafting increased bacterial within-sample diversity in both soils. Core enriched operational taxonomic units (OTUs) in the W/B rhizosphere compared with the other three treatments (B, W, and B/W) were mainly affiliated with Alphaproteobacteria, Deltaproteobacteria, and Bacteroidetes, which are likely related to methanol oxidation, methylotrophy, fermentation, and ureolysis. Co-occurrence network analysis proved that grafting increased network complexity, including the number of nodes, edges, and modules. Moreover, grafting strengthened the structural robustness of the network in the rhizosphere, while ungrafted watermelon had the lowest network robustness. Homogeneous selection played a predominant role in bacterial community assembly, and the contribution of dispersal limitation was increased in grafted watermelon with bottle gourd rootstock. Grafting increased the diversity and transformed the network topology of the bacterial community, which indicated that grafting could improve species coexistence in the watermelon rhizosphere.}, }
@article {pmid32514073, year = {2020}, author = {Murray, AE and Freudenstein, J and Gribaldo, S and Hatzenpichler, R and Hugenholtz, P and Kämpfer, P and Konstantinidis, KT and Lane, CE and Papke, RT and Parks, DH and Rossello-Mora, R and Stott, MB and Sutcliffe, IC and Thrash, JC and Venter, SN and Whitman, WB and Acinas, SG and Amann, RI and Anantharaman, K and Armengaud, J and Baker, BJ and Barco, RA and Bode, HB and Boyd, ES and Brady, CL and Carini, P and Chain, PSG and Colman, DR and DeAngelis, KM and de Los Rios, MA and Estrada-de Los Santos, P and Dunlap, CA and Eisen, JA and Emerson, D and Ettema, TJG and Eveillard, D and Girguis, PR and Hentschel, U and Hollibaugh, JT and Hug, LA and Inskeep, WP and Ivanova, EP and Klenk, HP and Li, WJ and Lloyd, KG and Löffler, FE and Makhalanyane, TP and Moser, DP and Nunoura, T and Palmer, M and Parro, V and Pedrós-Alió, C and Probst, AJ and Smits, THM and Steen, AD and Steenkamp, ET and Spang, A and Stewart, FJ and Tiedje, JM and Vandamme, P and Wagner, M and Wang, FP and Hedlund, BP and Reysenbach, AL}, title = {Roadmap for naming uncultivated Archaea and Bacteria.}, journal = {Nature microbiology}, volume = {5}, number = {8}, pages = {987-994}, pmid = {32514073}, issn = {2058-5276}, support = {DEB-1841658//National Science Foundation (NSF)/ ; }, abstract = {The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.}, }
@article {pmid32512474, year = {2020}, author = {Di Cesare, A and Pjevac, P and Eckert, E and Curkov, N and Miko Šparica, M and Corno, G and Orlić, S}, title = {The role of metal contamination in shaping microbial communities in heavily polluted marine sediments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {265}, number = {Pt B}, pages = {114823}, doi = {10.1016/j.envpol.2020.114823}, pmid = {32512474}, issn = {1873-6424}, mesh = {Croatia ; Environmental Monitoring ; Environmental Pollution ; Geologic Sediments ; Metals, Heavy/*analysis ; *Microbiota ; Water Pollutants, Chemical/*analysis ; }, abstract = {Microorganisms in coastal sediments are fundamental for ecosystem functioning, and regulate processes relevant in global biogeochemical cycles. Still, our understanding of the effects anthropogenic perturbation and pollution can have on microbial communities in marine sediments is limited. We surveyed the microbial diversity, and the occurrence and abundance of metal and antibiotic resistance genes is sediments collected from the Pula Bay (Croatia), one of the most significantly polluted sites along the Croatian coast. With a collection of 14 samples from the bay area, we were able to generate a detailed status quo picture of a site that only recently started a cleaning and remediation process (closing of sewage pipes and reduction of industrial activity). The concentrations of heavy metals in Pula Bay sediments are significantly higher than in pristine sediments from the Adriatic Sea, and in some cases, manifold exceed international sediment quality guidelines. While the sedimentary concentrations of heavy metals did significantly influence the abundance of the tested metal resistance genes, no strong effect of heavy metal pollution on the overall microbial community composition was observed. Like in many other marine sediments, Gammaproteobacteria, Bacteroidota and Desulfobacterota dominated the microbial community composition in most samples, and community assembly was primarily driven by water column depth and nutrient (carbon and nitrogen) availability, regardless of the degree of heavy metal pollution.}, }
@article {pmid32511085, year = {2020}, author = {Gurney, J and Azimi, S and Brown, SP and Diggle, SP}, title = {Combinatorial quorum sensing in Pseudomonas aeruginosa allows for novel cheating strategies.}, journal = {Microbiology (Reading, England)}, volume = {166}, number = {8}, pages = {777-784}, doi = {10.1099/mic.0.000941}, pmid = {32511085}, issn = {1465-2080}, abstract = {In the opportunistic pathogen Pseudomonas aeruginosa, quorum sensing (QS) is a social trait that is exploitable by non-cooperating cheats. Previously it has been shown that by linking QS to the production of both public and private goods, cheats can be prevented from invading populations of cooperators and this was described by Dandekar et al. (Science 2012;338:264-266) as 'a metabolic incentive to cooperate'. We hypothesized that P. aeruginosa could evolve novel cheating strategies to circumvent private goods metabolism by rewiring its combinatorial response to two QS signals (3O-C12-HSL and C4-HSL). We performed a selection experiment that cycled P. aeruginosa between public and private goods growth media and evolved an isolate that rewired its control of cooperative protease expression from a synergistic (AND-gate) response to dual-signal input to a 3O-C12-HSL-only response. We show that this isolate circumvents metabolic incentives to cooperate and acts as a combinatorial signalling cheat, with higher fitness in competition with its ancestor. Our results show three important principles: first, combinatorial QS allows for diverse social strategies to emerge; second, restrictions levied by private goods are not sufficient to explain the maintenance of cooperation in natural populations; and third, modifying combinatorial QS responses could result in important physiological outcomes in bacterial populations.}, }
@article {pmid32510910, year = {2020}, author = {Iddins, BO and Waugh, MH and Robbins, T and Cunningham, J and Graham, DE and Finn, MT}, title = {Antimicrobial Silver Touch Surfaces in an Occupational Medicine Clinic.}, journal = {Journal of occupational and environmental medicine}, volume = {62}, number = {6}, pages = {e287-e288}, pmid = {32510910}, issn = {1536-5948}, }
@article {pmid32510000, year = {2020}, author = {Chopra, S and Kumar, D}, title = {Ibuprofen as an emerging organic contaminant in environment, distribution and remediation.}, journal = {Heliyon}, volume = {6}, number = {6}, pages = {e04087}, pmid = {32510000}, issn = {2405-8440}, abstract = {Pharmaceutical and personal care products (PPCPs) are the one of sub-class under emerging organic contaminants (EOCs). Ibuprofen is the world's third most consumable drug. This drug enters into our water system through human pharmaceutical use. It attracts the attention of environmentalist on the basis of risk associated, presence and transformation in the environment. The detection and removal are the two key area where we need to focus. The concentration of such compounds in waterbodies detected through conventional and also by the advanced methods. This review we described the available technologies including chemical, physical and biological methods, etc used the for removal of Ibuprofen. The pure culture based method, mixed culture approach and activated sludge culture approach focused and pathway of degradation of ibuprofen was deciphered by using the various methods of structure determination. The various degradation methods used for Ibuprofen are discussed. The advanced methods coupled with physical, chemical, biological, chemical methods like ozonolysis, oxidation and adsorption, nanotechnology based methods, nanocatalysis and use of nonosensors to detect the presence of small amount in waterbodies can enhance the future degradation of this drug. It is necessary to develop the new detection methods to enhance the detection of such pollutants. With the developments in new detection methods based on GC-MS//MS, HPLC, LC/MS and nanotechnology based sensors makes easier detection of these compounds which can detect even very minute amount with great sensitivity and in less time. Also, the isolation and characterization of more potent microbial strains and nano-photocatalysis will significantly increase the future degradation of such harmful compounds from the environment.}, }
@article {pmid32508155, year = {2020}, author = {Mercer, KE and Yeruva, L and Pack, L and Graham, JL and Stanhope, KL and Chintapalli, SV and Wankhade, UD and Shankar, K and Havel, PJ and Adams, SH and Piccolo, BD}, title = {Xenometabolite signatures in the UC Davis type 2 diabetes mellitus rat model revealed using a metabolomics platform enriched with microbe-derived metabolites.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {319}, number = {2}, pages = {G157-G169}, pmid = {32508155}, issn = {1522-1547}, support = {6026-51000-010-05S//U.S. Department of Agriculture (USDA)/International ; R01HL091333//HHS | NIH | National Heart, Lung, and Blood Institute (NHBLI)/International ; R01HL107256//HHS | NIH | National Heart, Lung, and Blood Institute (NHBLI)/International ; RO1HL121324//HHS | NIH | National Heart, Lung, and Blood Institute (NHBLI)/International ; U24DK092933//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/International ; RC1DK087307//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/International ; R01DK095060//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/International ; }, abstract = {The gut microbiome has the potential to create or modify xenometabolites (i.e., nonhost-derived metabolites) through de novo synthesis or modification of exogenous and endogenous compounds. While there are isolated examples of xenometabolites influencing host health and disease, wide-scale characterization of these metabolites remains limited. We developed a metabolomics platform (&quot;XenoScan&quot;) using liquid chromatography-mass spectrometry to characterize a range of known and suspected xenometabolites and their derivatives. This assay currently applies authentic standards for 190 molecules, enriched for metabolites of microbial origin. As a proof-of-principle, we characterized the cecal content xenometabolomics profile in adult male lean Sprague-Dawley (LSD) and University of California, Davis type 2 diabetes mellitus (UCD-T2DM) rats at different stages of diabetes. These results were correlated to specific bacterial species generated via shotgun metagenomic sequencing. UCD-T2DM rats had a unique xenometabolite profile compared with LSD rats, regardless of diabetes status, suggesting that at least some of the variation is associated with host genetics. Furthermore, modeling approaches revealed that several xenometabolites discriminated UCD-T2DM rats at early stages of diabetes versus those at 3 mo postdiabetes onset. Several xenometabolite hubs correlated with specific bacterial species in both LSD and UCD-T2DM rats. For example, indole-3-propionic acid negatively correlated with species within the Oscillibacter genus in UCD-T2DM rats considered to be prediabetic or recently diagnosed diabetic, in contrast to gluconic acid and trimethylamine, which were positively correlated with Oscillibacter species. The application of a xenometabolite-enriched metabolomics assay in relevant milieus will enable rapid identification of a wide variety of gut-derived metabolites, their derivatives, and their potential biochemical origins of xenometabolites in relationship to host gastrointestinal microbial ecology.NEW &amp; NOTEWORTHY We debut a liquid chromatography-mass spectrometry (LC/MS) platform called the XenoScan, which is a metabolomics platform for xenometabolites (nonself-originating metabolites). This assay has 190 in-house standards with the majority enriched for microbe-derived metabolites. As a proof-of-principle, we used the XenoScan to discriminate genetic differences from cecal samples associated with different rat lineages, in addition to characterizing diabetes progression in rat model of type 2 diabetes. Complementing microbial sequencing data with xenometabolites uncovered novel microbial metabolism in targeted organisms.}, }
@article {pmid32504423, year = {2020}, author = {Lacalle, RG and Garbisu, C and Becerril, JM}, title = {Effects of the application of an organic amendment and nanoscale zero-valent iron particles on soil Cr(VI) remediation.}, journal = {Environmental science and pollution research international}, volume = {27}, number = {25}, pages = {31726-31736}, doi = {10.1007/s11356-020-09449-x}, pmid = {32504423}, issn = {1614-7499}, support = {AGL2015-64481-C2-1-R//Ministerio de Economía y Competitividad/ ; AGL2016-76592-R//Ministerio de Economía y Competitividad/ ; GV IT1018-16//Eusko Jaurlaritza/ ; PhytoSUDOE-SOE1/P5/E0189//Interreg/ ; }, mesh = {Chromium/analysis ; *Environmental Restoration and Remediation ; Iron ; Soil ; Soil Pollutants/*analysis ; }, abstract = {Chromium is considered an environmental pollutant of much concern whose toxicity depends, to a great extent, on its valence state, with Cr(VI) being more soluble, bioavailable, and toxic, compared to Cr(III). Nanoremediation is a promising strategy for the remediation of metal pollutants by changing their valence state. However, among other aspects, its effectiveness for soil remediation is seriously hampered by the interaction of nanoparticles with soil organic matter. In this study, soil was (i) amended with two doses of a municipal solid organic waste and (ii) artificially polluted with 300 mg Cr(VI) kg-1 DW soil. After a period of aging, a nanoremediation treatment with nanoscale zero-valent iron particles (1 g nZVI kg-1 DW soil) was applied. The efficiency of the remediation treatment was assessed in terms of Cr(VI) immobilization and recovery of soil health. The presence of the organic amendment caused (i) a decrease of redox potential, (ii) Cr(VI) immobilization via its reduction to Cr(III), (iii) a stimulation of soil microbial communities, and (iv) an improvement of soil health, compared to unamended soil. By contrast, nZVI did not have any impact on Cr(VI) immobilization nor on soil health. It was concluded that, unlike the presence of the organic amendment, nanoremediation with nZVI was not a valid option for soils polluted with Cr(VI) under our experimental conditions.}, }
@article {pmid32503635, year = {2020}, author = {Tao, X and Feng, J and Yang, Y and Wang, G and Tian, R and Fan, F and Ning, D and Bates, CT and Hale, L and Yuan, MM and Wu, L and Gao, Q and Lei, J and Schuur, EAG and Yu, J and Bracho, R and Luo, Y and Konstantinidis, KT and Johnston, ER and Cole, JR and Penton, CR and Tiedje, JM and Zhou, J}, title = {Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {84}, pmid = {32503635}, issn = {2049-2618}, support = {DE-SC0004601//U.S. Department of Energy/ ; DE-SC0010715//U.S. Department of Energy/ ; 41430856//National Natural Science Foundation of China/ ; 41877048//National Natural Science Foundation of China/ ; 41825016//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: In a warmer world, microbial decomposition of previously frozen organic carbon (C) is one of the most likely positive climate feedbacks of permafrost regions to the atmosphere. However, mechanistic understanding of microbial mediation on chemically recalcitrant C instability is limited; thus, it is crucial to identify and evaluate active decomposers of chemically recalcitrant C, which is essential for predicting C-cycle feedbacks and their relative strength of influence on climate change. Using stable isotope probing of the active layer of Arctic tundra soils after depleting soil labile C through a 975-day laboratory incubation, the identity of microbial decomposers of lignin and, their responses to warming were revealed.<br><br>RESULTS: The β-Proteobacteria genus Burkholderia accounted for 95.1% of total abundance of potential lignin decomposers. Consistently, Burkholderia isolated from our tundra soils could grow with lignin as the sole C source. A 2.2 °C increase of warming considerably increased total abundance and functional capacities of all potential lignin decomposers. In addition to Burkholderia, α-Proteobacteria capable of lignin decomposition (e.g. Bradyrhizobium and Methylobacterium genera) were stimulated by warming by 82-fold. Those community changes collectively doubled the priming effect, i.e., decomposition of existing C after fresh C input to soil. Consequently, warming aggravates soil C instability, as verified by microbially enabled climate-C modeling.<br><br>CONCLUSIONS: Our findings are alarming, which demonstrate that accelerated C decomposition under warming conditions will make tundra soils a larger biospheric C source than anticipated. Video Abstract.}, }
@article {pmid32502166, year = {2020}, author = {Lu, GS and LaRowe, DE and Fike, DA and Druschel, GK and Gilhooly, WP and Price, RE and Amend, JP}, title = {Bioenergetic characterization of a shallow-sea hydrothermal vent system: Milos Island, Greece.}, journal = {PloS one}, volume = {15}, number = {6}, pages = {e0234175}, pmid = {32502166}, issn = {1932-6203}, mesh = {*Energy Metabolism ; Greece ; *Hydrothermal Vents/microbiology ; Islands ; Thermodynamics ; }, abstract = {Shallow-sea hydrothermal systems, like their deep-sea and terrestrial counterparts, can serve as relatively accessible portals into the microbial ecology of subsurface environments. In this study, we determined the chemical composition of 47 sediment porewater samples along a transect from a diffuse shallow-sea hydrothermal vent to a non-thermal background area in Paleochori Bay, Milos Island, Greece. These geochemical data were combined with thermodynamic calculations to quantify potential sources of energy that may support in situ chemolithotrophy. The Gibbs energies (ΔGr) of 730 redox reactions involving 23 inorganic H-, O-, C-, N-, S-, Fe-, Mn-, and As-bearing compounds were calculated. Of these reactions, 379 were exergonic at one or more sampling locations. The greatest energy yields were from anaerobic CO oxidation with NO2- (-136 to -162 kJ/mol e-), followed by reactions in which the electron acceptor/donor pairs were O2/CO, NO3-/CO, and NO2-/H2S. When expressed as energy densities (where the concentration of the limiting reactant is taken into account), a different set of redox reactions are the most exergonic: in sediments affected by hydrothermal input, sulfide oxidation with a range of electron acceptors or nitrite reduction with different electron donors provide 85~245 J per kg of sediment, whereas in sediments less affected or unaffected by hydrothermal input, various S0 oxidation reactions and aerobic respiration reactions with several different electron donors are most energy-yielding (80~95 J per kg of sediment). A model that considers seawater mixing with hydrothermal fluids revealed that there is up to ~50 times more energy available for microorganisms that can use S0 or H2S as electron donors and NO2- or O2 as electron acceptors compared to other reactions. In addition to revealing likely metabolic pathways in the near-surface and subsurface mixing zones, thermodynamic calculations like these can help guide novel microbial cultivation efforts to isolate new species.}, }
@article {pmid32501785, year = {2020}, author = {Lee, JC and Whang, KS}, title = {Sphingomonas segetis sp. nov., isolated from spinach farming field soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {6}, pages = {3905-3911}, doi = {10.1099/ijsem.0.004257}, pmid = {32501785}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; *Farms ; Fatty Acids/chemistry ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; Pigmentation ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil Microbiology ; Spermidine/chemistry ; Sphingomonas/*classification ; Spinacia oleracea ; Ubiquinone/analogs &amp; derivatives/chemistry ; }, abstract = {A Gram-stain-negative bacterium, designated strain YJ09T, was isolated from spinach farming field soil at Shinan in the Republic of Korea. Cells of strain YJ09T were found to be strictly aerobic, non-motile, non-spore-forming creamy-yellow rods which can grow at 20-37 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0) and at salinities of 0-0.5 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain YJ09T belongs to the genus Sphingomonas with high sequence similarities to Sphingomonas parvus GP20-2 T (98.0 %), Sphingomonas agri HKS-06T (97.7 %) and Sphingomonas lutea JS5T (97.4 %). The results of phylogenetic analysis indicated that strain YJ09T formed a distinct phyletic line in the genus Sphingomonas and the results of DNA-DNA relatedness studies demonstrated that strain YJ09T could be separated from its closest relatives in the genus Sphingomonas. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified glycolipids, an unidentified phospholipid and sphingoglycolipid. The predominant ubiquinone and polyamine components were Q-10 and spermidine, respectively. The major fatty acids were C18:1 ω7c, C16 : 0 and C16:1 ω7c and/or iso-C15 : 0 2-OH. The DNA G+C content of this novel isolate was 65.9 mol%. On the basis of phenotypic, chemotaxonomic properties and phylogenetic analyses in this study, strain YJ09T is considered to represent a novel species in the genus Sphingomonas, for which the name Sphingomonas segetis sp. nov. is proposed. The type strain is YJ09T (=KACC 19551T=NBRC 113247T).}, }
@article {pmid32500958, year = {2020}, author = {Kundu, K and Weber, N and Griebler, C and Elsner, M}, title = {Phenotypic heterogeneity as key factor for growth and survival under oligotrophic conditions.}, journal = {Environmental microbiology}, volume = {22}, number = {8}, pages = {3339-3356}, doi = {10.1111/1462-2920.15106}, pmid = {32500958}, issn = {1462-2920}, abstract = {Productivity-poor oligotrophic environments are plentiful on earth. Yet it is not well understood how organisms maintain population sizes under these extreme conditions. Most scenarios consider the adaptation of a single microorganism (isogenic) at the cellular level, which increases their fitness in such an environment. However, in oligotrophic environments, the adaptation of microorganisms at population level - that is, the ability of living cells to differentiate into subtypes with specialized attributes leading to the coexistence of different phenotypes in isogenic populations - remains a little-explored area of microbiology research. In this study, we performed experiments to demonstrate that an isogenic population differentiated to two subpopulations under low energy-flux in chemostats. Fluorescence cytometry and turnover rates revealed that these subpopulations differ in their nucleic acid content and metabolic activity. A mechanistic modelling framework for the dynamic adaptation of microorganisms with the consideration of their ability to switch between different phenotypes was experimentally calibrated and validated. Simulation of hypothetical scenarios suggests that responsive diversification upon a change in energy availability offers a competitive advantage over homogenous adaptation for maintaining viability and metabolic activity with time.}, }
@article {pmid32500269, year = {2020}, author = {Yang, Y and Liu, W and Zhang, Z and Grossart, HP and Gadd, GM}, title = {Microplastics provide new microbial niches in aquatic environments.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {15}, pages = {6501-6511}, doi = {10.1007/s00253-020-10704-x}, pmid = {32500269}, issn = {1432-0614}, support = {2015282 and 2017388//Chinese Academy of Sciences/ ; }, abstract = {Microplastics in the biosphere are currently of great environmental concern because of their potential toxicity for aquatic biota and human health and association with pathogenic microbiota. Microplastics can occur in high abundance in all aquatic environments, including oceans, rivers and lakes. Recent findings have highlighted the role of microplastics as important vectors for microorganisms, which can form fully developed biofilms on this artificial substrate. Microplastics therefore provide new microbial niches in the aquatic environment, and the developing biofilms may significantly differ in microbial composition compared to natural free-living or particle-associated microbial populations in the surrounding water. In this article, we discuss the composition and ecological function of the microbial communities found in microplastic biofilms. The potential factors that influence the richness and diversity of such microbial microplastic communities are also evaluated. Microbe-microbe and microbe-substrate interactions in microplastic biofilms have been little studied and are not well understood. Multiomics tools together with morphological, physiological and biochemical analyses should be combined to provide a more comprehensive overview on the ecological role of microplastic biofilms. These new microbial niches have so far unknown consequences for microbial ecology and environmental processes in aquatic ecosystems. More knowledge is required on the microbial community composition of microplastic biofilms and their ecological functions in order to better evaluate consequences for the environment and animal health, including humans, especially since the worldwide abundance of microplastics is predicted to dramatically increase. Key Points • Bacteria are mainly studied in community analyses: fungi are neglected. • Microbial colonization of microplastics depends on substrate, location and time. • Community ecology is a promising approach to investigate microbial colonization. • Biodegradable plastics, and ecological roles of microplastic biofilms, need analysis.}, }
@article {pmid32499774, year = {2020}, author = {Hallin, S and Bodelier, PLE}, title = {Grand Challenges in Terrestrial Microbiology: Moving on From a Decade of Progress in Microbial Biogeochemistry.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {981}, pmid = {32499774}, issn = {1664-302X}, }
@article {pmid32499764, year = {2020}, author = {Liu, W and Graham, EB and Zhong, L and Zhang, J and Li, S and Lin, X and Feng, Y}, title = {Long-Term Stochasticity Combines With Short-Term Variability in Assembly Processes to Underlie Rice Paddy Sustainability.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {873}, pmid = {32499764}, issn = {1664-302X}, abstract = {Revealing temporal patterns of community assembly processes is important for understanding how microorganisms underlie the sustainability of agroecosystem. The ancient terraced rice paddies at Longji provide an ideal platform to study temporal dynamics of agroecosystem sustainability due to their chronosequential records of soil physicochemistry and well-archived microbial information along 630-year rice cultivation. We used statistical null models to evaluate microbial assembly processes along the soil chronosequences of Longji rice paddies through time. Stochastic and deterministic assembly processes jointly governed microbial community composition within successional eras (less than 250 years), and within-era determinism was mainly driven by soil fertility and redox conditions alone or in combination. Conversely, across successional eras (i.e., over 300 years), stochasticity linearly increased with increasing duration between eras and was eventually predominant for the whole 630 years. We suggest that the impact of stochasticity vs. determinism on assembly is timescale-dependent, and we propose that the importance of stochastic assembly of microbial community at longer timescales is due to the gradual changes in soil properties under long-term rice cultivation, which in turn contribute to the sustainability of paddy ecosystem by maintaining a diverse community of microorganisms with multi-functional traits. In total, our results indicate that knowledge on the timescales at which assembly processes govern microbial community composition is key to understanding the ecological mechanisms generating agroecosystem sustainability.}, }
@article {pmid32498175, year = {2020}, author = {Benidire, L and El Khalloufi, F and Oufdou, K and Barakat, M and Tulumello, J and Ortet, P and Heulin, T and Achouak, W}, title = {Phytobeneficial bacteria improve saline stress tolerance in Vicia faba and modulate microbial interaction network.}, journal = {The Science of the total environment}, volume = {729}, number = {}, pages = {139020}, doi = {10.1016/j.scitotenv.2020.139020}, pmid = {32498175}, issn = {1879-1026}, mesh = {Bacteria ; Humans ; Microbial Consortia ; Microbial Interactions ; Plant Roots ; RNA, Ribosomal, 16S ; Soil Microbiology ; *Vicia faba ; }, abstract = {Increased global warming, caused by climate change and human activities, will seriously hinder plant development, such as increasing salt concentrations in soils, which will limit water availability for plants. To ensure optimal plant growth under such changing conditions, microorganisms that improve plant growth and health must be integrated into agricultural practices. In the present work, we examined the fate of Vicia faba microbiota structure and interaction network upon inoculation with plant-nodulating rhizobia (Rhizobium leguminosarum RhOF125) and non-nodulating strains (Paenibacillus mucilaginosus BLA7 and Ensifer meliloti RhOL1) in the presence (or absence) of saline stress. Inoculated strains significantly improved plant tolerance to saline stress, suggesting either a direct or indirect effect on the plant response to such stress. To determine the structure of microbiota associated with V. faba, samples of the root-adhering soil (RAS), and the root tissues (RT) of seedlings inoculated (or not) with equal population size of RhOF125, BLA7 and RhOL1 strains and grown in the presence (or absence) of salt, were used to profile the microbial composition by 16S rRNA gene sequencing. The inoculation did not show a significant impact on the composition of the RT microbiota or RAS microbiota. The saline stress shifted the RAS microbiota composition, which correlated with a decrease in Enterobacteriaceae and an increase in Sphingobacterium, Chryseobacterium, Stenotrophomonas, Agrobacterium and Sinorhizobium. When the microbiota of roots and RAS are considered together, the interaction networks for each treatment are quite different and display different key populations involved in community assembly. These findings indicate that upon seed inoculation, community interaction networks rather than their composition may contribute to helping plants to better tolerate environmental stresses. The way microbial populations interfere with each other can have an impact on their functions and thus on their ability to express the genes required to help plants tolerate stresses.}, }
@article {pmid32497654, year = {2020}, author = {Nardello, LCL and Amado, PPP and Franco, DC and Cazares, RXR and Nogales, CG and Mayer, MPA and Karygianni, L and Thurnheer, T and Pinheiro, ET}, title = {Next-Generation Sequencing to Assess Potentially Active Bacteria in Endodontic Infections.}, journal = {Journal of endodontics}, volume = {46}, number = {8}, pages = {1105-1112}, doi = {10.1016/j.joen.2020.05.004}, pmid = {32497654}, issn = {1878-3554}, mesh = {Actinobacteria ; Bacteria ; *Bacterial Infections ; Clostridiales ; DNA, Bacterial ; *High-Throughput Nucleotide Sequencing ; Humans ; RNA, Ribosomal, 16S ; }, abstract = {INTRODUCTION: Because active bacteria present a higher abundance of ribosomal RNA (rRNA) than DNA (rRNA gene), the rRNA/DNA ratio of next-generation sequencing (NGS) data was measured to search for active bacteria in endodontic infections.<br><br>METHODS: Paired complementary DNA and DNA samples from 5 root canals of teeth with apical periodontitis were subjected to polymerase chain reaction with bar-coded primers amplifying the 16S rRNA gene hypervariable regions V4-V5. High-throughput sequencing was performed using MiSeq (Illumina, San Deigo, CA), and data were analyzed using Quantitative Insights Into Microbial Ecology and Human Oral Microbiome Database. Statistical analysis was performed for relative abundance of bacteria in the DNA- and rRNA-based NGS data using the Mann-Whitney test, whereas differences in the diversity and richness indexes were assessed using a nonparametric 2-sample t test (P < .05). For bacterial taxa detected in both approaches, the rRNA/DNA ratios were calculated by dividing the average abundance of individual species in the respective analysis.<br><br>RESULTS: Although no significant difference was found in the indexes of bacterial richness and diversity, the relative abundance of bacterial members varied in both analyses. Comparing rRNA with DNA data, there was a significant decrease in the relative abundance of Firmicutes (P < .05). The bacterial taxa Bacteroidales [G-2] bacterium HMT 274, Porphyromonas endodontalis, Tannerella forsythia, Alloprevotella tannerae, Prevotella intermedia, Pseudoramibacter alactolyticus, Olsenella sp. HMT 809, Olsenella sp. HMT 939, Olsenella uli, and Fusobacterium nucleatum subsp. animalis were both dominant (DNA ≥ 1%) and active (rRNA/DNA ≥ 1).<br><br>CONCLUSIONS: The integrated DNA- and rRNA-based NGS strategy was particularly important to disclose the activity of as-yet-uncultivated or difficult-to-culture bacteria in endodontic infections.}, }
@article {pmid32497185, year = {2020}, author = {Van den Abbeele, P and Duysburgh, C and Rakebrandt, M and Marzorati, M}, title = {Dried yeast cell walls high in beta-glucan and mannan-oligosaccharides positively affect microbial composition and activity in the canine gastrointestinal tract in vitro.}, journal = {Journal of animal science}, volume = {98}, number = {6}, pages = {}, pmid = {32497185}, issn = {1525-3163}, abstract = {The outer cell wall of yeast is characterized by high levels of β-glucans and mannan-oligosaccharides (MOS), which have been linked with beneficial effects on intestinal health and immune status in dogs. In this study, a standardized in vitro simulation of the canine gastrointestinal tract (Simulator of the Canine Intestinal Microbial Ecosystem; SCIME) was used to evaluate the effect of a Saccharomyces cerevisiae-based product, consisting of 27.5% β-glucans and 22.5% MOS, on the activity (as assessed by measurement of fermentative metabolites) and composition (as assessed by 16S-targeted Illumina sequencing) of canine intestinal microbiota. The S. cerevisiae-based product was tested at three different dosages, i.e., 0.5, 1.0, and 2.0 g/d. A dose-dependent fermentation pattern was observed along the entire length of the colon, as shown by the increased production of the health-related acetate, propionate, and butyrate for the three concentrations tested (0.5, 1.0, and 2.0 g/d). A consistent finding for all three tested concentrations was the increased propionate production (P < 0.05) in the simulated proximal and distal colon. These changes in terms of fermentative metabolites could be linked to specific microbial alterations at the family level, such as the specific stimulation of the propionate-producing families Porphyromonadaceae and Prevotellaceae upon in vitro exposure to the S. cerevisiae-based product. Other consistent changes in community composition upon repeated exposure included the decrease in the Enterobacteriaceae and the Fusobacteriaceae families, which both contain several potentially opportunistic pathogens. Altogether, the generated data support a possible health-promoting role of a product high in β-glucans and MOS when supplemented to the dogs' diet.}, }
@article {pmid32494840, year = {2020}, author = {Xiong, J and Li, X and Yan, M and Lu, J and Qiu, Q and Chen, J}, title = {Comparable Ecological Processes Govern the Temporal Succession of Gut Bacteria and Microeukaryotes as Shrimp Aged.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {935-945}, doi = {10.1007/s00248-020-01533-6}, pmid = {32494840}, issn = {1432-184X}, support = {31872693//the National Natural Science Foundation of China/ ; LR19C030001//Natural Science Fund for Distinguished Young Scholars of Zhejiang Province/ ; 2015C110018//Technology Innovation Team of Ningbo/ ; }, abstract = {Understanding the rules that govern the successions of gut microbiota is prerequisite for testing general ecological theories and sustaining a desirable microbiota. However, the ignorance of microeukaryotes raises the question of whether gut microeukaryotes are assembled according to the same rules as bacteria. We tracked the shrimp gut bacterial and microeukaryotic communities by a longitudinal dense sampling. The successions of both domains were significantly correlated with host age, with relatively stable microeukaryotic communities in adult shrimp. Gut microeukaryotes exhibited significantly higher turnover rate, but fewer transient species, lower proportion of temporal generalists, and narrower habitat niche breadth than bacteria. The γ-diversity partitioning analysis revealed that the successions of gut microbiotas were primarily ascribed to the high dissimilarity as shrimp aged ([Formula: see text]IntraTimes), whereas the relative importance of [Formula: see text]IntraTimes was significantly higher for microeukaryotes than that for bacteria. Compared with contrasting ecological processes in governing free-living bacteria and microeukaryotes, the ecological patterns were comparable between host-associated gut counterparts. However, the gut microeukaryotes were governed more strongly by deterministic selection relative to nestedness compared with the gut bacteria, which supports the &quot;size-plasticity&quot; hypothesis. Our results highlight the importance of independently interpreting free-living and host-associated meta-communities for a comprehensive understanding of the processes that govern microbial successions.}, }
@article {pmid32493970, year = {2020}, author = {Monteiro, DA and Fonseca, EDS and Rodrigues, RAR and da Silva, JJN and da Silva, EP and Balieiro, FC and Alves, BJR and Rachid, CTCDC}, title = {Structural and functional shifts of soil prokaryotic community due to Eucalyptus plantation and rotation phase.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {9075}, doi = {10.1038/s41598-020-66004-x}, pmid = {32493970}, issn = {2045-2322}, abstract = {Agriculture, forestry and other land uses are currently the second highest source of anthropogenic greenhouse gases (GHGs) emissions. In soil, these gases derive from microbial activity, during carbon (C) and nitrogen (N) cycling. To investigate how Eucalyptus land use and growth period impact the microbial community, GHG fluxes and inorganic N levels, and if there is a link among these variables, we monitored three adjacent areas for 9 months: a recently planted Eucalyptus area, fully developed Eucalyptus forest (final of rotation) and native forest. We assessed the microbial community using 16S rRNA gene sequencing and qPCR of key genes involved in C and N cycles. No considerable differences in GHG flux were evident among the areas, but logging considerably increased inorganic N levels. Eucalyptus areas displayed richer and more diverse communities, with selection for specific groups. Land use influenced communities more extensively than the time of sampling or growth phase, although all were significant modulators. Several microbial groups and genes shifted temporally, and inorganic N levels shaped several of these changes. No correlations among microbial groups or genes and GHG were found, suggesting no link among these variables in this short-rotation Eucalyptus study.}, }
@article {pmid32488484, year = {2020}, author = {Semiatizki, A and Weiss, B and Bagim, S and Rohkin-Shalom, S and Kaltenpoth, M and Chiel, E}, title = {Effects, interactions, and localization of Rickettsia and Wolbachia in the house fly parasitoid, Spalangia endius.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {718-728}, doi = {10.1007/s00248-020-01520-x}, pmid = {32488484}, issn = {1432-184X}, support = {435/18//Planning and Budgeting Committee of the Council for Higher Education of Israel/ ; CoG 819585/ERC_/European Research Council/International ; }, abstract = {Many insect species harbor facultative microbial symbionts that affect their biology in diverse ways. Here, we studied the effects, interactions, and localization of two bacterial symbionts-Wolbachia and Rickettsia-in the parasitoid Spalangia endius. We crossed between four S. endius colonies-Wolbachia only (W), Rickettsia only (R), both (WR), and none (aposymbiotic, APS) (16 possible crosses) and found that Wolbachia induces incomplete cytoplasmic incompatibility (CI), both when the males are W or WR. Rickettsia did not cause reproductive manipulations and did not rescue the Wolbachia-induced CI. However, when R females were crossed with W or WR males, significantly less offspring were produced compared with that of control crosses. In non-CI crosses, the presence of Wolbachia in males caused a significant reduction in offspring numbers. Females' developmental time was significantly prolonged in the R colony, with adults starting to emerge one day later than the other colonies. Other fitness parameters did not differ significantly between the colonies. Using fluorescence in situ hybridization microscopy in females, we found that Wolbachia is localized alongside Rickettsia inside oocytes, follicle cells, and nurse cells in the ovaries. However, Rickettsia is distributed also in muscle cells all over the body, in ganglia, and even in the brain.}, }
@article {pmid32488483, year = {2020}, author = {Hejduková, E and Elster, J and Nedbalová, L}, title = {Annual Cycle of Freshwater Diatoms in the High Arctic Revealed by Multiparameter Fluorescent Staining.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {559-572}, doi = {10.1007/s00248-020-01521-w}, pmid = {32488483}, issn = {1432-184X}, support = {20217//Grantová Agentura, Univerzita Karlova/ ; LM2015078//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; }, abstract = {Diatoms (Bacillariophyceae) are important primary producers in a wide range of hydro-terrestrial habitats in polar regions that are characterized by many extreme environmental conditions. Nevertheless, how they survive periods of drought and/or freeze remains unknown. A general strategy of microorganisms to overcome adverse conditions is dormancy, but morphologically distinct diatom resting stages are rare. This study aimed to evaluate the annual cycle of freshwater diatoms in the High Arctic (Central Spitsbergen) and provide an insight into their physiological cell status variability. The diversity and viability of diatom cells were studied in samples collected five times at four study sites, tracing the key events for survival (summer vegetative season, autumn dry-freezing, winter freezing, spring melting, summer vegetative season [again]). For viability evaluation, a multiparameter fluorescent staining was used in combination with light microscopy and allowed to reveal the physiological status at a single-cell level. The proportions of the cell categories were seasonally and locality dependent. The results suggested that a significant portion of vegetative cells survive winter and provide an inoculum for the following vegetative season. The ice thickness significantly influenced spring survival. The thicker the ice layer was, the more dead cells and fewer other stages were observed. The influence of the average week max-min temperature differences in autumn and winter was not proven.}, }
@article {pmid32485888, year = {2020}, author = {Aliyu, H and Mohr, T and Cowan, D and de Maayer, P and Neumann, A}, title = {Time-Course Transcriptome of Parageobacillus thermoglucosidasius DSM 6285 Grown in the Presence of Carbon Monoxide and Air.}, journal = {International journal of molecular sciences}, volume = {21}, number = {11}, pages = {}, pmid = {32485888}, issn = {1422-0067}, abstract = {Parageobacillus thermoglucosidasius is a metabolically versatile, facultatively anaerobic thermophile belonging to the family Bacillaceae. Previous studies have shown that this bacterium harbours co-localised genes coding for a carbon monoxide (CO) dehydrogenase (CODH) and Ni-Fe hydrogenase (Phc) complex and oxidises CO and produces hydrogen (H2) gas via the water-gas shift (WGS) reaction. To elucidate the genetic events culminating in the WGS reaction, P. thermoglucosidasius DSM 6285 was cultivated under an initial gas atmosphere of 50% CO and 50% air and total RNA was extracted at ~8 (aerobic phase), 20 (anaerobic phase), 27 and 44 (early and late hydrogenogenic phases) hours post inoculation. The rRNA-depleted fraction was sequenced using Illumina NextSeq, v2.5, 1x75bp chemistry. Differential expression revealed that at 8 vs 20, 20 vs 27 and 27 vs 44 hours post inoculation, 2190, 2118 and 231 transcripts were differentially (FDR < 0.05) expressed. Cluster analysis revealed 26 distinct gene expression trajectories across the four time points. Of these, two similar clusters, showing overexpression at 20 relative to 8 hours and depletion at 27 and 44 hours, harboured the CODH and Phc transcripts, suggesting possible regulation by O2. The transition between aerobic respiration and anaerobic growth was marked by initial metabolic deterioration, as reflected by up-regulation of transcripts linked to sporulation and down-regulation of transcripts linked to flagellar assembly and metabolism. However, the transcriptome and growth profiles revealed the reversal of this trend during the hydrogenogenic phase.}, }
@article {pmid32483324, year = {2020}, author = {van Bergeijk, DA and Terlouw, BR and Medema, MH and van Wezel, GP}, title = {Ecology and genomics of Actinobacteria: new concepts for natural product discovery.}, journal = {Nature reviews. Microbiology}, volume = {18}, number = {10}, pages = {546-558}, doi = {10.1038/s41579-020-0379-y}, pmid = {32483324}, issn = {1740-1534}, abstract = {Actinobacteria constitute a highly diverse bacterial phylum with an unrivalled metabolic versatility. They produce most of the clinically used antibiotics and a plethora of other natural products with medical or agricultural applications. Modern 'omics'-based technologies have revealed that the genomic potential of Actinobacteria greatly outmatches the known chemical space. In this Review, we argue that combining insights into actinobacterial ecology with state-of-the-art computational approaches holds great promise to unlock this unexplored reservoir of actinobacterial metabolism. This enables the identification of small molecules and other stimuli that elicit the induction of poorly expressed biosynthetic gene clusters, which should help reinvigorate screening efforts for their precious bioactive natural products.}, }
@article {pmid32482859, year = {2020}, author = {Roach, TNF and Little, M and Arts, MGI and Huckeba, J and Haas, AF and George, EE and Quinn, RA and Cobián-Güemes, AG and Naliboff, DS and Silveira, CB and Vermeij, MJA and Kelly, LW and Dorrestein, PC and Rohwer, F}, title = {A multiomic analysis of in situ coral-turf algal interactions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {24}, pages = {13588-13595}, pmid = {32482859}, issn = {1091-6490}, mesh = {Animals ; Anthozoa/chemistry/*metabolism/microbiology/parasitology ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Chlorophyta/chemistry/*metabolism ; Coral Reefs ; Ecosystem ; Metagenomics ; Microbiota ; }, abstract = {Viruses, microbes, and host macroorganisms form ecological units called holobionts. Here, a combination of metagenomic sequencing, metabolomic profiling, and epifluorescence microscopy was used to investigate how the different components of the holobiont including bacteria, viruses, and their associated metabolites mediate ecological interactions between corals and turf algae. The data demonstrate that there was a microbial assemblage unique to the coral-turf algae interface displaying higher microbial abundances and larger microbial cells. This was consistent with previous studies showing that turf algae exudates feed interface and coral-associated microbial communities, often at the detriment of the coral. Further supporting this hypothesis, when the metabolites were assigned a nominal oxidation state of carbon (NOSC), we found that the turf algal metabolites were significantly more reduced (i.e., have higher potential energy) compared to the corals and interfaces. The algae feeding hypothesis was further supported when the ecological outcomes of interactions (e.g., whether coral was winning or losing) were considered. For example, coral holobionts losing the competition with turf algae had higher Bacteroidetes-to-Firmicutes ratios and an elevated abundance of genes involved in bacterial growth and division. These changes were similar to trends observed in the obese human gut microbiome, where overfeeding of the microbiome creates a dysbiosis detrimental to the long-term health of the metazoan host. Together these results show that there are specific biogeochemical changes at coral-turf algal interfaces that predict the competitive outcomes between holobionts and are consistent with algal exudates feeding coral-associated microbes.}, }
@article {pmid32482164, year = {2020}, author = {Costa, OYA and de Hollander, M and Pijl, A and Liu, B and Kuramae, EE}, title = {Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {76}, pmid = {32482164}, issn = {2049-2618}, support = {729.004.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 202496/2015-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {BACKGROUND: Cultivation-independent methods, including metagenomics, are tools for the exploration and discovery of biotechnological compounds produced by microbes in natural environments. Glycoside hydrolases (GHs) enzymes are extremely desired and important in the industry of production for goods and biofuel and removal of problematic biofilms and exopolysaccharide (EPS). Biofilms and EPS are complex, requiring a wide range of enzymes for a complete degradation. The aim of this study was to identify potential GH microbial producers and GH genes with biotechnological potential, using EPS-complex structure (WH15EPS) of Acidobacteria Granulicella sp. strain WH15 as an enrichment factor, in cultivation-independent and cultivation-dependent methods. We performed stable isotope probing (SIP) combined with metagenomics on topsoil litter amended with WH15EPS and coupled solid culture-EPS amended medium with metagenomics.<br><br>RESULTS: SIP metagenome analysis of the soil litter demonstrated that phyla Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes were the most abundant in WH15EPS amended and unamended treatments. The enrichment cultures in solid culture medium coupled to metagenomics demonstrated an enrichment in Proteobacteria, and the metagenome assembly of this enrichment cultures resulted in 4 metagenome-assembled genomes (MAGs) of microbes with low identity (42-86%) to known microorganisms. Among all carbohydrate-active enzymes (CAZymes) retrieved genes, glycoside transferase (GT) was the most abundant family, either in culture-independent or culture-based metagenome datasets. Within the glycoside hydrolases (GHs), GH13 was the most abundant family in both metagenome datasets. In the &quot;heavy&quot; fraction of the culture-independent metagenome SIP dataset, GH109 (α-N-acetylgalactosaminidases), GH117 (agarases), GH50 (agarases), GH32 (invertases and inulinases), GH17 (endoglucanases), and GH71 (mutanases) families were more abundant in comparison with the controls. Those GH families are affiliated to microorganism that are probably capable to degrade WH15EPS and potentially applicable for biofilm deconstruction. Subsequent in culture-based metagenome, the assembled 4 MAGs (unclassified Proteobacteria) also contained GH families of interest, involving mannosidases, lysozymes, galactosidases, and chitinases.<br><br>CONCLUSIONS: We demonstrated that functional diversity induced by the presence of WH15EPS in both culture-independent and culture-dependent approaches was enriched in GHs, such as amylases and endoglucanases that could be applied in chemical, pharmaceutical, and food industrial sectors. Furthermore, WH15EPS may be used for the investigation and isolation of yet unknown taxa, such as unclassified Proteobacteria and Planctomycetes, increasing the number of current cultured bacterial representatives with potential biotechnological traits. Video Abstract.}, }
@article {pmid32477286, year = {2020}, author = {Bagnoud, A and Pramateftaki, P and Bogard, MJ and Battin, TJ and Peter, H}, title = {Microbial Ecology of Methanotrophy in Streams Along a Gradient of CH4 Availability.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {771}, pmid = {32477286}, issn = {1664-302X}, abstract = {Despite the recognition of streams and rivers as sources of methane (CH4) to the atmosphere, the role of CH4 oxidation (MOX) in these ecosystems remains poorly understood to date. Here, we measured the kinetics of MOX in stream sediments of 14 sites to resolve the ecophysiology of CH4 oxidizing bacteria (MOB) communities. The streams cover a gradient of land cover and associated physicochemical parameter and differed in stream- and porewater CH4 concentrations. Michealis-Menten kinetic parameter of MOX, maximum reaction velocity (Vmax), and CH4 concentration at half Vmax (KS) increased with CH4 supply. KS values in the micromolar range matched the CH4 concentrations measured in shallow stream sediments and indicate that MOX is mostly driven by low-affinity MOB. 16S rRNA gene sequencing identified MOB classified as Methylococcaceae and particularly Crenothrix. Their relative abundance correlated with pmoA gene counts and MOX rates, underscoring their pivotal role as CH4 oxidizers in stream sediments. Building on the concept of enterotypes, we identify two distinct groups of co-occurring MOB. While there was no taxonomic difference among the members of each cluster, one cluster contained abundant and common MOB, whereas the other cluster contained rare operational taxonomic units (OTUs) specific to a subset of streams. These integrated analyses of changes in MOB community structure, gene abundance, and the corresponding ecosystem process contribute to a better understanding of the distal controls on MOX in streams.}, }
@article {pmid32475802, year = {2020}, author = {Zhang, Z and van Kleunen, M and Becks, L and Thakur, MP}, title = {Towards a General Understanding of Bacterial Interactions.}, journal = {Trends in microbiology}, volume = {28}, number = {10}, pages = {783-785}, doi = {10.1016/j.tim.2020.05.010}, pmid = {32475802}, issn = {1878-4380}, abstract = {Understanding the general rules of microbial interactions is central for advancing microbial ecology. Recent studies show that interaction range, interaction strength, and community context determine bacterial interactions and the coexistence and evolution of bacteria. We highlight how these factors could contribute to a general understanding of bacterial interactions.}, }
@article {pmid32474660, year = {2020}, author = {Musonerimana, S and Bez, C and Licastro, D and Habarugira, G and Bigirimana, J and Venturi, V}, title = {Pathobiomes Revealed that Pseudomonas fuscovaginae and Sarocladium oryzae Are Independently Associated with Rice Sheath Rot.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {627-642}, doi = {10.1007/s00248-020-01529-2}, pmid = {32474660}, issn = {1432-184X}, abstract = {Rice sheath rot has been mainly associated with the bacterial pathogen Pseudomonas fuscovaginae and in some cases to the fungal pathogen Sarocladium oryzae; it is yet unclear if they are part of a complex disease. The bacterial and fungal community associated with rice sheath rot symptomatic and asymptomatic rice plants was determined/studied with the main aim to shed light on the pathogen(s) causing rice sheath rot. Plant samples were collected from different rice varieties in two locations (highland and lowland) in two rice-growing seasons (wet and dry season) in Burundi. Our results showed that the bacterial Pseudomonas genus was prevalent in highland in both rice-growing seasons and was not affected by rice plant varieties. Pseudomonas sequence reads displayed a significant high similarity to Pseudomonas fuscovaginae indicating that it is the causal agent of rice sheath rot as previously reported. The fungal Sarocladium genus was on the other hand prevalent in lowland only in the wet season; the sequence reads were most significantly similar to Sarocladium oryzae. These studies showed that plant microbiome analysis is very useful in determining the microorganisms involved in a plant disease. P. fuscovaginae and S. oryzae were prevalent in symptomatic samples in highland and lowland respectively being present independently and hence are not part of a complex disease. The significant presence of other bacterial and fungal taxa in symptomatic samples is also discussed possibly making this disease more complex. Finally, we also report the microbial communities that are associated with the plant sheath in symptomatic and asymptomatic plants from the same rice fields.}, }
@article {pmid32474659, year = {2020}, author = {Liu, RR and Tian, Y and Zhou, EM and Xiong, MJ and Xiao, M and Li, WJ}, title = {Distinct Expression of the Two NO-Forming Nitrite Reductases in Thermus antranikianii DSM 12462T Improved Environmental Adaptability.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {614-626}, doi = {10.1007/s00248-020-01528-3}, pmid = {32474659}, issn = {1432-184X}, support = {91951205//National Natural Science Foundation of China/ ; 31970122//National Natural Science Foundation of China/ ; 31470139//National Natural Science Foundation of China/ ; 31600298//National Natural Science Foundation of China/ ; 2018B020206001//Guangdong Province Science and Technology Innovation Strategy Special Fund/ ; }, abstract = {Hot spring ecosystems are analogous to some thermal environments on the early Earth and represent ideal models to understand life forms and element cycling on the early Earth. Denitrification, an important component of biogeochemical nitrogen cycle, is highly active in hot springs. Nitrite (NO2-) reduction to nitric oxide (NO) is the significant and rate-limiting pathway in denitrification and is catalyzed by two types of nitrite reductases, encoded by nirS and nirK genes. NirS and NirK were originally considered incompatible in most denitrifying organisms, although a few strains have been reported to possess both genes. Herein, we report the functional division of nirS and nirK in Thermus, a thermophilic genus widespread in thermal ecosystems. Transcriptional levels of nirS and nirK coexisting in Thermus antranikianii DSM 12462T were measured to assess the effects of nitrite, oxygen, and stimulation time. Thirty-nine Thermus strains were used to analyze the phylogeny and distribution of nirS and nirK; six representative strains were used to assess the denitrification phenotype. The results showed that both genes were actively transcribed and expressed independently in T. antranikianii DSM 12462T. Strains with both nirS and nirK had a wider range of nitrite adaptation and revealed nir-related physiological adaptations in Thermus: nirK facilitated adaptation to rapid changes and extended the adaptation range of nitrite under oxygen-limited conditions, while nirS expression was higher under oxic and relatively stable conditions.}, }
@article {pmid32471167, year = {2020}, author = {Su, L and Zhang, L and Nie, D and Kuramae, EE and Shen, B and Shen, Q}, title = {Bacterial Tomato Pathogen Ralstonia solanacearum Invasion Modulates Rhizosphere Compounds and Facilitates the Cascade Effect of Fungal Pathogen Fusarium solani.}, journal = {Microorganisms}, volume = {8}, number = {6}, pages = {}, pmid = {32471167}, issn = {2076-2607}, support = {41571242//Chinese Natural Science Fund Program/ ; }, abstract = {Soil-borne pathogen invasions can significantly change the microbial communities of the host rhizosphere. However, whether bacterial Ralstonia solanacearum pathogen invasion influences the abundance of fungal pathogens remains unclear. In this study, we combined high-throughput sequencing, qPCR, liquid chromatography and soil culture experiments to analyze the rhizosphere fungal composition, co-occurrence of fungal communities, copy numbers of functional genes, contents of phenolic acids and their associations in healthy and bacterial wilt-diseased tomato plants. We found that R. solanacearum invasion increased the abundance of the soil-borne pathogen Fusarium solani. The concentrations of three phenolic acids in the rhizosphere soil of bacterial wilt-diseased tomato plants were significantly higher than those in the rhizosphere soil of healthy tomato plants. In addition, the increased concentrations of phenolic acids significantly stimulated F. solani growth in the soil. Furthermore, a simple fungal network with fewer links, nodes and hubs (highly connected nodes) was found in the diseased tomato plant rhizosphere. These results indicate that once the symptom of bacterial wilt disease is observed in tomato, the roots of the wilt-diseased tomato plants need to be removed in a timely manner to prevent the enrichment of other fungal soil-borne pathogens. These findings provide some ecological clues for the mixed co-occurrence of bacterial wilt disease and other fungal soil-borne diseases.}, }
@article {pmid32470594, year = {2020}, author = {Capson-Tojo, G and Batstone, DJ and Grassino, M and Vlaeminck, SE and Puyol, D and Verstraete, W and Kleerebezem, R and Oehmen, A and Ghimire, A and Pikaar, I and Lema, JM and Hülsen, T}, title = {Purple phototrophic bacteria for resource recovery: Challenges and opportunities.}, journal = {Biotechnology advances}, volume = {43}, number = {}, pages = {107567}, doi = {10.1016/j.biotechadv.2020.107567}, pmid = {32470594}, issn = {1873-1899}, abstract = {Sustainable development is driving a rapid focus shift in the wastewater and organic waste treatment sectors, from a &quot;removal and disposal&quot; approach towards the recovery and reuse of water, energy and materials (e.g. carbon or nutrients). Purple phototrophic bacteria (PPB) are receiving increasing attention due to their capability of growing photoheterotrophically under anaerobic conditions. Using light as energy source, PPB can simultaneously assimilate carbon and nutrients at high efficiencies (with biomass yields close to unity (1 g CODbiomass·g CODremoved-1)), facilitating the maximum recovery of these resources as different value-added products. The effective use of infrared light enables selective PPB enrichment in non-sterile conditions, without competition with other phototrophs such as microalgae if ultraviolet-visible wavelengths are filtered. This review reunites results systematically gathered from over 177 scientific articles, aiming at producing generalized conclusions. The most critical aspects of PPB-based production and valorisation processes are addressed, including: (i) the identification of the main challenges and potentials of different growth strategies, (ii) a critical analysis of the production of value-added compounds, (iii) a comparison of the different value-added products, (iv) insights into the general challenges and opportunities and (v) recommendations for future research and development towards practical implementation. To date, most of the work has not been executed under real-life conditions, relevant for full-scale application. With the savings in wastewater discharge due to removal of organics, nitrogen and phosphorus as an important economic driver, priorities must go to using PPB-enriched cultures and real waste matrices. The costs associated with artificial illumination, followed by centrifugal harvesting/dewatering and drying, are estimated to be 1.9, 0.3-2.2 and 0.1-0.3 $·kgdry biomass-1. At present, these costs are likely to exceed revenues. Future research efforts must be carried out outdoors, using sunlight as energy source. The growth of bulk biomass on relatively clean wastewater streams (e.g. from food processing) and its utilization as a protein-rich feed (e.g. to replace fishmeal, 1.5-2.0 $·kg-1) appears as a promising valorisation route.}, }
@article {pmid32469071, year = {2020}, author = {Rampal, R and Wari, N and Singh, AK and Das, U and Bopanna, S and Gupta, V and Nayak, B and Velapandian, T and Kedia, S and Kumar, D and Awasthi, A and Ahuja, V}, title = {Retinoic Acid Is Elevated in the Mucosa of Patients With Active Ulcerative Colitis and Displays a Proinflammatory Role by Augmenting IL-17 and IFNγ Production.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izaa121}, pmid = {32469071}, issn = {1536-4844}, abstract = {BACKGROUND: All-trans retinoic acid (RA) plays a crucial role in promoting Foxp3+ Treg generation while reciprocally inhibiting Th1/Th17 generation. Our previous research highlighted that in the face of inflammatory conditions, RA plays a contrary role where it aggravates intestinal inflammation by promoting interferon (IFN) γ and interleukin (IL)-17 differentiation in vitro.<br><br>METHODS: In this study we translated our in vitro results into a clinical setting where we estimated mucosal and serum RA levels along with the immunophenotypic profile (IL-17, IFNγ, Foxp3, IL-10) in adaptive (CD4, CD8) and innate-like T cells (mucosal associated invariant T cells and γδ T cells) in patients with ulcerative colitis in remission or with active inflammation.<br><br>RESULTS: This is the first study to estimate RA levels in the human gut and shows that patients with active disease had increased mucosal RA levels as compared with patients in remission (4.0 vs 2.5 ng/mL; P < 0.01) and control patients (3.4 vs 0.8 ng/mL; P < 0.0001). This effect was accompanied by significantly elevated IL-17 and IFNγ in tissue CD4+, CD8+, mucosal associated invariant T+ cells, and γδ + T cells. Moreover, the raised RA levels in patients with active disease showed a positive correlation with proinflammatory cytokines (IL-17, IFNγ) and a negative correlation with IL-10. We also found that RA negatively correlated with IL-9, thereby reinstating our previous finding that RA inhibits Th9 differentiation.<br><br>CONCLUSIONS: These data confirm our previous in vitro results that in the presence of inflammation, RA plays a crucial role in maintaining gut inflammation by upregulating proinflammatory markers.}, }
@article {pmid32468160, year = {2020}, author = {Tschoeke, D and Salazar, VW and Vidal, L and Campeão, M and Swings, J and Thompson, F and Thompson, C}, title = {Unlocking the Genomic Taxonomy of the Prochlorococcus Collective.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {546-558}, doi = {10.1007/s00248-020-01526-5}, pmid = {32468160}, issn = {1432-184X}, abstract = {Prochlorococcus is the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on the Prochlorococcus collective (PC) is based on the assumption that it comprises one single genus comprising the species Prochlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC. Novel genomic data for the PC prompted us to revisit this group, applying the current methods used in genomic taxonomy. As a result, we were able to distinguish the five genera: Prochlorococcus, Eurycolium, Prolificoccus, Thaumococcus, and Riococcus. The novel genera have distinct genomic and ecological attributes.}, }
@article {pmid32466615, year = {2020}, author = {Van den Abbeele, P and Ghyselinck, J and Marzorati, M and Villar, A and Zangara, A and Smidt, CR and Risco, E}, title = {In Vitro Evaluation of Prebiotic Properties of a Commercial Artichoke Inflorescence Extract Revealed Bifidogenic Effects.}, journal = {Nutrients}, volume = {12}, number = {6}, pages = {}, pmid = {32466615}, issn = {2072-6643}, abstract = {: Background: Prebiotics used as a dietary supplement, stimulate health-related gut microbiota (e.g., bifidobacteria, lactobacilli, etc.). This study evaluated potential prebiotic effects of an artichoke aqueous dry extract (AADE) using in vitro gut model based on the Simulator of Human Intestinal Microbial Ecosystem (SHIME®).<br><br>METHODS: Short-term colonic fermentations (48 h) of AADE, fructo-oligosaccharides (FOS), and a blank were performed. Microbial metabolites were assessed at 0, 6, 24, and 48 h of colonic incubation via measuring pH, gas pressure, lactate, ammonium, and short-chain fatty acids (SCFAs) levels. Community composition was assessed via targeted qPCRs.<br><br>RESULTS: After 24 and 48 h of incubation, bifidobacteria levels increased 25-fold with AADE (p < 0.05) and >100-fold with FOS (p < 0.05) compared to blank. Lactobacillus spp. levels only tended to increase with AADE, whereas they increased 10-fold with FOS. At 6 h, pH decreased with AADE and FOS and remained stable until 48 h; however, gas pressure increased significantly till the end of study. Acetate, propionate, and total SCFA production increased significantly with both at all time-points. Lactate levels initially increased but branched SCFA and ammonium levels remained low till 48 h.<br><br>CONCLUSION: AADE displayed prebiotic potential by exerting bifidogenic effects that stimulated production of health-related microbial metabolites, which is potentially due to inulin in AADE.}, }
@article {pmid32466517, year = {2020}, author = {Jia, X and Dini-Andreote, F and Falcão Salles, J}, title = {Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data.}, journal = {Microorganisms}, volume = {8}, number = {6}, pages = {}, pmid = {32466517}, issn = {2076-2607}, abstract = {Quantifying which assembly processes structure microbiomes can assist prediction, manipulation, and engineering of community outcomes. However, the relative importance of these processes might depend on whether DNA or RNA are used, as they differ in stability. We hypothesized that. RNA-inferred community responses to (a)biotic fluctuations are faster than those inferred by DNA; the relative influence of variable selection is stronger in RNA-inferred communities (environmental factors are spatiotemporally heterogeneous), whereas homogeneous selection largely influences DNA-inferred communities (environmental filters are constant). To test these hypotheses, we characterized soil bacterial communities by sequencing both 16S rRNA amplicons from the extracted DNA and RNA transcripts across distinct stages of soil primary succession and quantified the relative influence of each assembly process using ecological null model analysis. Our results revealed that variations in α-diversity and temporal turnover were higher in RNA- than in DNA-inferred communities across successional stages, albeit there was a similar community composition; in line with our hypotheses, the assembly of RNA-inferred community was more closely associated with environmental variability (variable selection) than using the standard DNA-based approach, which was largely influenced by homogeneous selection. This study illustrates the need for benchmarking approaches to properly elucidate how community assembly processes structure microbial communities.}, }
@article {pmid32462391, year = {2020}, author = {Möhlmann, TWR and Vogels, CBF and Göertz, GP and Pijlman, GP and Ter Braak, CJF and Te Beest, DE and Hendriks, M and Nijhuis, EH and Warris, S and Drolet, BS and van Overbeek, L and Koenraadt, CJM}, title = {Impact of Gut Bacteria on the Infection and Transmission of Pathogenic Arboviruses by Biting Midges and Mosquitoes.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {703-717}, pmid = {32462391}, issn = {1432-184X}, support = {Rubicon 019.181EN.004//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; Global One Health strategic programme//Wageningen University/ ; }, abstract = {Tripartite interactions among insect vectors, midgut bacteria, and viruses may determine the ability of insects to transmit pathogenic arboviruses. Here, we investigated the impact of gut bacteria on the susceptibility of Culicoides nubeculosus and Culicoides sonorensis biting midges for Schmallenberg virus, and of Aedes aegypti mosquitoes for Zika and chikungunya viruses. Gut bacteria were manipulated by treating the adult insects with antibiotics. The gut bacterial communities were investigated using Illumina MiSeq sequencing of 16S rRNA, and susceptibility to arbovirus infection was tested by feeding insects with an infectious blood meal. Antibiotic treatment led to changes in gut bacteria for all insects. Interestingly, the gut bacterial composition of untreated Ae. aegypti and C. nubeculosus showed Asaia as the dominant genus, which was drastically reduced after antibiotic treatment. Furthermore, antibiotic treatment resulted in relatively more Delftia bacteria in both biting midge species, but not in mosquitoes. Antibiotic treatment and subsequent changes in gut bacterial communities were associated with a significant, 1.8-fold increased infection rate of C. nubeculosus with Schmallenberg virus, but not for C. sonorensis. We did not find any changes in infection rates for Ae. aegypti mosquitoes with Zika or chikungunya virus. We conclude that resident gut bacteria may dampen arbovirus transmission in biting midges, but not so in mosquitoes. Use of antimicrobial compounds at livestock farms might therefore have an unexpected contradictory effect on the health of animals, by increasing the transmission of viral pathogens by biting midges.}, }
@article {pmid32462390, year = {2020}, author = {Yang, M and Shi, J and Wang, B and Xiao, J and Li, W and Liu, CQ}, title = {Control of Hydraulic Load on Bacterioplankton Diversity in Cascade Hydropower Reservoirs, Southwest China.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {537-545}, doi = {10.1007/s00248-020-01523-8}, pmid = {32462390}, issn = {1432-184X}, support = {2016YFA0601001//the National Key R &amp; D Program of China/ ; U1612441//Innovative Research Group Project of the National Natural Science Foundation of China (CN)/ ; }, abstract = {Hydroelectric reservoirs are highly regulated ecosystems, where the understanding on bacterioplankton has been very limited so far. In view of significant changes in river hydrological conditions by dam construction, hydraulic load (i.e., the ratio of mean water depth to water retention time) was assumed to control bacterioplankton diversity in cascading hydropower reservoirs. To evaluate this hypothesis, we investigated bacterioplankton composition and diversity using high-throughput sequencing and related environmental variables in eleven reservoirs on the Wujiang River, Southwest China. Our results showed a decrease of bacterioplankton diversity index with an increase of reservoir hydraulic load. This is because hydraulic load governs dissolved oxygen variation in the water column, which is a key factor shaping bacterioplankton composition in these hydroelectric reservoirs. In contrast, bacterioplankton abundance was mainly affected by nutrient-related environmental factors. Therefore, from a hydrological perspective, hydraulic load is a decisive factor for the bacterioplankton diversity in the hydroelectric reservoirs. This study can improve the understanding of reservoir bacterial ecology, and the empirical relationship between hydraulic load and bacterioplankton diversity index will help to quantitatively evaluate ecological effects of river damming.}, }
@article {pmid32461136, year = {2020}, author = {Flanagan, E and Lamport, D and Brennan, L and Burnet, P and Calabrese, V and Cunnane, SC and de Wilde, MC and Dye, L and Farrimond, JA and Emerson Lombardo, N and Hartmann, T and Hartung, T and Kalliomäki, M and Kuhnle, GG and La Fata, G and Sala-Vila, A and Samieri, C and Smith, AD and Spencer, JPE and Thuret, S and Tuohy, K and Turroni, S and Vanden Berghe, W and Verkuijl, M and Verzijden, K and Yannakoulia, M and Geurts, L and Vauzour, D}, title = {Nutrition and the ageing brain: Moving towards clinical applications.}, journal = {Ageing research reviews}, volume = {62}, number = {}, pages = {101079}, doi = {10.1016/j.arr.2020.101079}, pmid = {32461136}, issn = {1872-9649}, abstract = {The global increases in life expectancy and population have resulted in a growing ageing population and with it a growing number of people living with age-related neurodegenerative conditions and dementia, shifting focus towards methods of prevention, with lifestyle approaches such as nutrition representing a promising avenue for further development. This overview summarises the main themes discussed during the 3rd Symposium on &quot;Nutrition for the Ageing Brain: Moving Towards Clinical Applications&quot; held in Madrid in August 2018, enlarged with the current state of knowledge on how nutrition influences healthy ageing and gives recommendations regarding how the critical field of nutrition and neurodegeneration research should move forward into the future. Specific nutrients are discussed as well as the impact of multi-nutrient and whole diet approaches, showing particular promise to combatting the growing burden of age-related cognitive decline. The emergence of new avenues for exploring the role of diet in healthy ageing, such as the impact of the gut microbiome and development of new techniques (imaging measures of brain metabolism, metabolomics, biomarkers) are enabling researchers to approach finding answers to these questions. But the translation of these findings into clinical and public health contexts remains an obstacle due to significant shortcomings in nutrition research or pressure on the scientific community to communicate recommendations to the general public in a convincing and accessible way. Some promising programs exist but further investigation to improve our understanding of the mechanisms by which nutrition can improve brain health across the human lifespan is still required.}, }
@article {pmid32460826, year = {2020}, author = {Roelofs, D and Zwaenepoel, A and Sistermans, T and Nap, J and Kampfraath, AA and Van de Peer, Y and Ellers, J and Kraaijeveld, K}, title = {Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {57}, pmid = {32460826}, issn = {1741-7007}, support = {PhD fellowship//Fonds Wetenschappelijk Onderzoek/ ; 15494//Stichting voor de Technische Wetenschappen/ ; NWA StartImpulse//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, abstract = {BACKGROUND: Gene duplication events play an important role in the evolution and adaptation of organisms. Duplicated genes can arise through different mechanisms, including whole-genome duplications (WGDs). Recently, WGD was suggested to be an important driver of evolution, also in hexapod animals.<br><br>RESULTS: Here, we analyzed 20 high-quality hexapod genomes using whole-paranome distributions of estimated synonymous distances (KS), patterns of within-genome co-linearity, and phylogenomic gene tree-species tree reconciliation methods. We observe an abundance of gene duplicates in the majority of these hexapod genomes, yet we find little evidence for WGD. The majority of gene duplicates seem to have originated through small-scale gene duplication processes. We did detect segmental duplications in six genomes, but these lacked the within-genome co-linearity signature typically associated with WGD, and the age of these duplications did not coincide with particular peaks in KS distributions. Furthermore, statistical gene tree-species tree reconciliation failed to support all but one of the previously hypothesized WGDs.<br><br>CONCLUSIONS: Our analyses therefore provide very limited evidence for WGD having played a significant role in the evolution of hexapods and suggest that alternative mechanisms drive gene duplication events in this group of animals. For instance, we propose that, along with small-scale gene duplication events, episodes of increased transposable element activity could have been an important source for gene duplicates in hexapods.}, }
@article {pmid32460009, year = {2020}, author = {De Boeck, I and van den Broek, MFL and Allonsius, CN and Spacova, I and Wittouck, S and Martens, K and Wuyts, S and Cauwenberghs, E and Jokicevic, K and Vandenheuvel, D and Eilers, T and Lemarcq, M and De Rudder, C and Thys, S and Timmermans, JP and Vroegop, AV and Verplaetse, A and Van de Wiele, T and Kiekens, F and Hellings, PW and Vanderveken, OM and Lebeer, S}, title = {Lactobacilli Have a Niche in the Human Nose.}, journal = {Cell reports}, volume = {31}, number = {8}, pages = {107674}, doi = {10.1016/j.celrep.2020.107674}, pmid = {32460009}, issn = {2211-1247}, abstract = {Although an increasing number of beneficial microbiome members are characterized for the human gut and vagina, beneficial microbes are underexplored for the human upper respiratory tract (URT). In this study, we demonstrate that taxa from the beneficial Lactobacillus genus complex are more prevalent in the healthy URT than in patients with chronic rhinosinusitis (CRS). Several URT-specific isolates are cultured, characterized, and further explored for their genetic and functional properties related to adaptation to the URT. Catalase genes are found in the identified lactobacilli, which is a unique feature within this mostly facultative anaerobic genus. Moreover, one of our isolated strains, Lactobacillus casei AMBR2, contains fimbriae that enable strong adherence to URT epithelium, inhibit the growth and virulence of several URT pathogens, and successfully colonize nasal epithelium of healthy volunteers. This study thus demonstrates that specific lactobacilli are adapted to the URT and could have a beneficial keystone function in this habitat.}, }
@article {pmid32456625, year = {2020}, author = {Alderliesten, JB and Duxbury, SJN and Zwart, MP and de Visser, JAGM and Stegeman, A and Fischer, EAJ}, title = {Effect of donor-recipient relatedness on the plasmid conjugation frequency: a meta-analysis.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {135}, pmid = {32456625}, issn = {1471-2180}, support = {50-54100-98-1 19//ZonMw/ ; }, abstract = {BACKGROUND: Conjugation plays a major role in the transmission of plasmids encoding antibiotic resistance genes in both clinical and general settings. The conjugation efficiency is influenced by many biotic and abiotic factors, one of which is the taxonomic relatedness between donor and recipient bacteria. A comprehensive overview of the influence of donor-recipient relatedness on conjugation is still lacking, but such an overview is important to quantitatively assess the risk of plasmid transfer and the effect of interventions which limit the spread of antibiotic resistance, and to obtain parameter values for conjugation in mathematical models. Therefore, we performed a meta-analysis on reported conjugation frequencies from Escherichia coli donors to various recipient species.<br><br>RESULTS: Thirty-two studies reporting 313 conjugation frequencies for liquid broth matings and 270 conjugation frequencies for filter matings were included in our meta-analysis. The reported conjugation frequencies varied over 11 orders of magnitude. Decreasing taxonomic relatedness between donor and recipient bacteria, when adjusted for confounding factors, was associated with a lower conjugation frequency in liquid matings. The mean conjugation frequency for bacteria of the same order, the same class, and other classes was 10, 20, and 789 times lower than the mean conjugation frequency within the same species, respectively. This association between relatedness and conjugation frequency was not found for filter matings. The conjugation frequency was furthermore found to be influenced by temperature in both types of mating experiments, and in addition by plasmid incompatibility group in liquid matings, and by recipient origin and mating time in filter matings.<br><br>CONCLUSIONS: In our meta-analysis, taxonomic relatedness is limiting conjugation in liquid matings, but not in filter matings, suggesting that taxonomic relatedness is not a limiting factor for conjugation in environments where bacteria are fixed in space.}, }
@article {pmid32455626, year = {2020}, author = {Xu, J and Bu, F and Zhu, W and Luo, G and Xie, L}, title = {Microbial Consortiums of Hydrogenotrophic Methanogenic Mixed Cultures in Lab-Scale Ex-Situ Biogas Upgrading Systems under Different Conditions of Temperature, pH and CO.}, journal = {Microorganisms}, volume = {8}, number = {5}, pages = {}, pmid = {32455626}, issn = {2076-2607}, support = {51678424 and 51378373//National Natural Science Foundation of China/ ; }, abstract = {In this study, hydrogenotrophic methanogenic mixed cultures taken from 13 lab-scale ex-situ biogas upgrading systems under different temperature (20-70 °C), pH (6.0-8.5), and CO (0-10%, v/v) variables were systematically investigated. High-throughput 16S rRNA gene sequencing was used to identify the microbial consortia, and statistical analyses were conducted to reveal the microbial diversity, the core functional microbes, and their correlative relationships with tested variables. Overall, bacterial community was more complex than the archaea community in all mixed cultures. Hydrogenotrophic methanogens Methanothermobacter, Methanobacterium, and Methanomassiliicoccus, and putative syntrophic acetate-oxidizing bacterium Coprothermobacter and Caldanaerobacter were found to predominate, but the core functional microbes varied under different conditions. Multivariable sensitivity analysis indicated that temperature (p < 0.01) was the crucial variable to determine the microbial consortium structures in hydrogenotrophic methanogenic mixed cultures. pH (0.01 < p < 0.05) significantly interfered with the relative abundance of dominant archaea. Although CO did not affect community (p > 0.1), some potential CO-utilizing syntrophic metabolisms might be enhanced. Understanding of microbial consortia in the hydrogenotrophic methanogenic mixed cultures related to environmental variables was a great advance to reveal the microbial ecology in microbial biogas upgrading process.}, }
@article {pmid32454384, year = {2020}, author = {Zhang, H and Zhang, B and Wang, S and Chen, J and Jiang, B and Xing, Y}, title = {Spatiotemporal vanadium distribution in soils with microbial community dynamics at vanadium smelting site.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {265}, number = {Pt A}, pages = {114782}, doi = {10.1016/j.envpol.2020.114782}, pmid = {32454384}, issn = {1873-6424}, mesh = {China ; Environmental Monitoring ; *Microbiota ; Soil ; Soil Pollutants/*analysis ; Vanadium/analysis ; }, abstract = {Whereas the adverse effects of vanadium released from smelting activities on soil microbial ecology have been widely recognized, little is known about spatiotemporal vanadium distribution and microbial community dynamics in typical contaminated sites. This study describes vanadium contents associated with health risk and microbial responses in both topsoil and subsoil during four consecutive seasons around an ongoing-production smelter in Panzhihua, China. Higher levels of vanadium concentration exceeding soil background value in China (82 mg/kg) were found close to the smelter. Vanadium concentrations decreased generally with the increase in distance to the smelter and depth below surface, as soil vanadium pollution is induced mainly by atmospheric deposition of vanadium bearing dust during smelting. Residual fraction was the predominated vanadium form in soils, with pronounced increase in bioavailable vanadium during rainfall period due to frequent drought-rewetting process. Topsoil close to the smelter exhibited significant contamination, inducing high probability of adverse health effects. Spatiotemporal vanadium distribution creates filtering effects on soil microorganisms, promoting metal tolerant genera in topsoil (e.g. Microvirga) and subsoil (e.g. Bacillus, Geobacter), which is the key in maintaining the community structure by promoting cooperative relation with other taxa. Our results reveal spatiotemporal vanadium distribution in soils at site scale with potential health risk and microbial responses, which is helpful in identifying severe contamination and implementing bioremediation.}, }
@article {pmid32454291, year = {2020}, author = {Lourenço, KS and Suleiman, AKA and Pijl, A and Cantarella, H and Kuramae, EE}, title = {Dynamics and resilience of soil mycobiome under multiple organic and inorganic pulse disturbances.}, journal = {The Science of the total environment}, volume = {733}, number = {}, pages = {139173}, doi = {10.1016/j.scitotenv.2020.139173}, pmid = {32454291}, issn = {1879-1026}, mesh = {Fertilizers/analysis ; Fungi ; *Mycobiome ; Soil ; Soil Microbiology ; }, abstract = {Disturbances in soil can cause short-term soil changes, consequently changes in microbial community what may result in long-lasting ecological effects. Here, we evaluate how multiple pulse disturbances effect the dynamics and resilience of fungal community, and the co-occurrence of fungal and bacterial communities in a 389 days field experiment. We used soil under sugarcane cultivation as soil ecosystem model, and organic residue (vinasse - by-product of sugarcane ethanol production) combined or not with inorganic (organic residue applied 30 days before or together with mineral N fertilizer) amendments as disturbances. Application of organic residue alone as a single disturbance or 30 days prior to a second disturbance with mineral N resulted in similar changes in the fungal community. The simultaneous application of organic and mineral N as a single pulse disturbance had the greatest impact on the fungal community. Organic amendment increased the abundance of saprotrophs, fungal species capable of denitrification, and fungi described to have copiotrophic and oligotrophic lifestyles. Furthermore, the changes in the fungal community were not correlated with the changes in the bacterial community. The fungal community was neither resistant nor resilient to organic and inorganic disturbances over the one-year sampling period. Our findings provide insights on the immediate and delayed responses of the fungal community over one year to disturbance by organic and inorganic amendments.}, }
@article {pmid32451559, year = {2020}, author = {Nettles, R and Ricks, KD and Koide, RT}, title = {The Dynamics of Interacting Bacterial and Fungal Communities of the Mouse Colon Following Antibiotics.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {573-592}, doi = {10.1007/s00248-020-01525-6}, pmid = {32451559}, issn = {1432-184X}, support = {2011-67009-20072//National Institute of Food and Agriculture/ ; }, abstract = {We tested two hypotheses concerning the dynamics of intestinal microbial communities of young mice following antibiotic-induced disturbance. The first is that disturbance of the bacterial community causes disturbance of the fungal community. Our results were consistent with that hypothesis. Antibiotics significantly altered bacterial community structure. Antibiotics also altered fungal community structure, significantly increasing the relative abundance of Candida lusitaniae, a known pathogen, while simultaneously significantly decreasing the relative abundances of several other common fungal species. The result was a temporary decrease in fungal diversity. Moreover, bacterial load was negatively correlated with the relative abundances of Candida lusitaniae and Candida parapsilosis, while it was positively correlated with the relative abundances of many other fungal species. Our second hypothesis is that control mice serve as a source of probiotics capable of invading intestines of mice with disturbed microbial communities and restoring pre-antibiotic bacterial and fungal communities. However, we found that control mice did not restore disturbed microbial communities. Instead, mice with disturbed microbial communities induced disturbance in control mice, consistent with the hypothesis that antibiotic-induced disturbance represents an alternate stable state that is easier to achieve than to correct. Our results indicate the occurrence of significant interactions among intestinal bacteria and fungi and suggest that the stimulation of certain bacterial groups may potentially be useful in countering the dominance of fungal pathogens such as Candida spp. However, the stability of disturbed microbial communities could complicate recovery.}, }
@article {pmid32451471, year = {2020}, author = {Sichert, A and Corzett, CH and Schechter, MS and Unfried, F and Markert, S and Becher, D and Fernandez-Guerra, A and Liebeke, M and Schweder, T and Polz, MF and Hehemann, JH}, title = {Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan.}, journal = {Nature microbiology}, volume = {5}, number = {8}, pages = {1026-1039}, doi = {10.1038/s41564-020-0720-2}, pmid = {32451471}, issn = {2058-5276}, support = {HE 7217/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; BE 3869/4-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHW 595/10-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DE-SC0008743//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; }, abstract = {Brown algae are important players in the global carbon cycle by fixing carbon dioxide into 1 Gt of biomass annually, yet the fate of fucoidan-their major cell wall polysaccharide-remains poorly understood. Microbial degradation of fucoidans is slower than that of other polysaccharides, suggesting that fucoidans are more recalcitrant and may sequester carbon in the ocean. This may be due to the complex, branched and highly sulfated structure of fucoidans, which also varies among species of brown algae. Here, we show that 'Lentimonas' sp. CC4, belonging to the Verrucomicrobia, acquired a remarkably complex machinery for the degradation of six different fucoidans. The strain accumulated 284 putative fucoidanases, including glycoside hydrolases, sulfatases and carbohydrate esterases, which are primarily located on a 0.89-megabase pair plasmid. Proteomics reveals that these enzymes assemble into substrate-specific pathways requiring about 100 enzymes per fucoidan from different species of brown algae. These enzymes depolymerize fucoidan into fucose, which is metabolized in a proteome-costly bacterial microcompartment that spatially constrains the metabolism of the toxic intermediate lactaldehyde. Marine metagenomes and microbial genomes show that Verrucomicrobia including 'Lentimonas' are abundant and highly specialized degraders of fucoidans and other complex polysaccharides. Overall, the complexity of the pathways underscores why fucoidans are probably recalcitrant and more slowly degraded, since only highly specialized organisms can effectively degrade them in the ocean.}, }
@article {pmid32446079, year = {2020}, author = {Schröer, L and De Kock, T and Cnudde, V and Boon, N}, title = {Differential colonization of microbial communities inhabiting Lede stone in the urban and rural environment.}, journal = {The Science of the total environment}, volume = {733}, number = {}, pages = {139339}, doi = {10.1016/j.scitotenv.2020.139339}, pmid = {32446079}, issn = {1879-1026}, mesh = {Archaea ; Belgium ; High-Throughput Nucleotide Sequencing ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {Air pollution is one of the main actors of stone deterioration. It influences not only the material itself but also prokaryotes colonizing rocks. Prokaryotes can affect rock substrates and biological colonization will most likely become relatively more important during the course of the 21st century. Therefore, it is necessary to understand the effects of air pollution on biological colonization and on the impact of this colonization on rock weathering. For this reason, we studied the prokaryotic community of Lede stone from two deteriorated monuments in Belgium: one in the urban and one in the rural environment. This research conducts 16S rRNA gene Next Generation Sequencing combined with an isolation campaign. It revealed diverse and complex prokaryotic communities with more specialized bacteria present in the urban environment, while archaea were barely detected. Some genera could cause biodeterioration but the isolates did not produce a significant amount of acid. Soluble salts analysis revealed an important effect of salts on the prokaryotic community. Colour measurements at least indicate that a main effect of prokaryotes might be on the aesthetics: In the countryside prokaryotic communities seemed to discolour Lede stone, while pollution most likely blackened building stones in the urban environment.}, }
@article {pmid32445418, year = {2020}, author = {Spielmann, J and Ahmadi, H and Scheepers, M and Weber, M and Nitsche, S and Carnol, M and Bosman, B and Kroymann, J and Motte, P and Clemens, S and Hanikenne, M}, title = {The two copies of the zinc and cadmium ZIP6 transporter of Arabidopsis halleri have distinct effects on cadmium tolerance.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.13806}, pmid = {32445418}, issn = {1365-3040}, support = {IAP no. P7/44//Belgian Federal Science Policy Office/ ; SPP1529 ADAPTOMICS//Deutsche Forschungsgemeinschaft/ ; Cl152/9-1//Deutsche Forschungsgemeinschaft/ ; Cl152/9-2//Deutsche Forschungsgemeinschaft/ ; PDR-T.0206.13, MIS-F.4511.16, CDR J.0009.17//Fonds De La Recherche Scientifique - FNRS/ ; PDR T0120.18//Fonds De La Recherche Scientifique - FNRS/ ; //Fonds pour la Formation à la Recherche dans l'Industrie et dans l'Agriculture/ ; SFRD-12/03//University of Liège/ ; }, abstract = {Plants have the ability to colonize highly diverse environments. The zinc and cadmium hyperaccumulator Arabidopsis halleri has adapted to establish populations on soils covering an extreme range of metal availabilities. The A. halleri ZIP6 gene presents several hallmarks of hyperaccumulation candidate genes: it is constitutively highly expressed in roots and shoots and is associated with a zinc accumulation quantitative trait locus. Here, we show that AhZIP6 is duplicated in the A. halleri genome. The two copies are expressed mainly in the vasculature in both A. halleri and Arabidopsis thaliana, indicative of conserved cis regulation, and acquired partial organ specialization. Yeast complementation assays determined that AhZIP6 is a zinc and cadmium transporter. AhZIP6 silencing in A. halleri or expression in A. thaliana alters cadmium tolerance, but has no impact on zinc and cadmium accumulation. AhZIP6-silenced plants display reduced cadmium uptake upon short-term exposure, adding AhZIP6 to the limited number of Cd transporters supported by in planta evidence. Altogether, our data suggest that AhZIP6 is key to fine-tune metal homeostasis in specific cell types. This study additionally highlights the distinct fates of duplicated genes in A. halleri.}, }
@article {pmid32444696, year = {2020}, author = {Zhang, R and Li, Y and Yan, W and Wang, Y and Cai, L and Luo, T and Li, H and Weinbauer, MG and Jiao, N}, title = {Viral control of biomass and diversity of bacterioplankton in the deep sea.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {256}, doi = {10.1038/s42003-020-0974-5}, pmid = {32444696}, issn = {2399-3642}, support = {91951209//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41706154//National Natural Science Foundation of China (National Science Foundation of China)/ ; DY135-E2-1-04//China Ocean Mineral Resources Research and Development Association (China Ocean Mineral Resources R&amp;D Association)/ ; QNLM2016ORP0303//Qingdao National Laboratory for Marine Science and Technology (QNLM)/ ; }, abstract = {Viral abundance in deep-sea environments is high. However, the biological, ecological and biogeochemical roles of viruses in the deep sea are under debate. In the present study, microcosm incubations of deep-sea bacterioplankton (2,000 m deep) with normal and reduced pressure of viral lysis were conducted in the western Pacific Ocean. We observed a negative effect of viruses on prokaryotic abundance, indicating the top-down control of bacterioplankton by virioplankton in the deep-sea. The decreased bacterial diversity and a different bacterial community structure with diluted viruses indicate that viruses are sustaining a diverse microbial community in deep-sea environments. Network analysis showed that relieving viral pressure decreased the complexity and clustering coefficients but increased the proportion of positive correlations for the potentially active bacterial community, which suggests that viruses impact deep-sea bacterioplankton interactions. Our study provides experimental evidences of the crucial role of viruses in microbial ecology and biogeochemistry in deep-sea ecosystems.}, }
@article {pmid32444671, year = {2020}, author = {van Tilburg Bernardes, E and Pettersen, VK and Gutierrez, MW and Laforest-Lapointe, I and Jendzjowsky, NG and Cavin, JB and Vicentini, FA and Keenan, CM and Ramay, HR and Samara, J and MacNaughton, WK and Wilson, RJA and Kelly, MM and McCoy, KD and Sharkey, KA and Arrieta, MC}, title = {Intestinal fungi are causally implicated in microbiome assembly and immune development in mice.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2577}, doi = {10.1038/s41467-020-16431-1}, pmid = {32444671}, issn = {2041-1723}, support = {//CIHR/Canada ; }, mesh = {Animals ; Bacterial Physiological Phenomena ; Colitis/chemically induced/microbiology ; Dextran Sulfate/toxicity ; Feces/microbiology ; Female ; Fungi/isolation &amp; purification/*physiology ; Gastrointestinal Microbiome/immunology/*physiology ; Germ-Free Life ; Humans ; Immune System/*growth &amp; development ; Inflammation/chemically induced/microbiology ; Intestines/*microbiology ; Metabolome ; Mice, Inbred C57BL ; Ovalbumin/toxicity ; }, abstract = {The gut microbiome consists of a multi-kingdom microbial community. Whilst the role of bacteria as causal contributors governing host physiological development is well established, the role of fungi remains to be determined. Here, we use germ-free mice colonized with defined species of bacteria, fungi, or both to differentiate the causal role of fungi on microbiome assembly, immune development, susceptibility to colitis, and airway inflammation. Fungal colonization promotes major shifts in bacterial microbiome ecology, and has an independent effect on innate and adaptive immune development in young mice. While exclusive fungal colonization is insufficient to elicit overt dextran sulfate sodium-induced colitis, bacterial and fungal co-colonization increase colonic inflammation. Ovalbumin-induced airway inflammation reveals that bacterial, but not fungal colonization is necessary to decrease airway inflammation, yet fungi selectively promotes macrophage infiltration in the airway. Together, our findings demonstrate a causal role for fungi in microbial ecology and host immune functionality, and therefore prompt the inclusion of fungi in therapeutic approaches aimed at modulating early life microbiomes.}, }
@article {pmid32441612, year = {2020}, author = {Murrell, JC and McGenity, TJ and Crombie, AT}, title = {Microbial metabolism of isoprene: a much-neglected climate-active gas.}, journal = {Microbiology (Reading, England)}, volume = {166}, number = {7}, pages = {600-613}, doi = {10.1099/mic.0.000931}, pmid = {32441612}, issn = {1465-2080}, abstract = {The climate-active gas isoprene is the major volatile produced by a variety of trees and is released into the atmosphere in enormous quantities, on a par with global emissions of methane. While isoprene production in plants and its effect on atmospheric chemistry have received considerable attention, research into the biological isoprene sink has been neglected until recently. Here, we review current knowledge on the sources and sinks of isoprene and outline its environmental effects. Focusing on degradation by microbes, many of which are able to use isoprene as the sole source of carbon and energy, we review recent studies characterizing novel isoprene degraders isolated from soils, marine sediments and in association with plants. We describe the development and use of molecular methods to identify, quantify and genetically characterize isoprene-degrading strains in environmental samples. Finally, this review identifies research imperatives for the further study of the environmental impact, ecology, regulation and biochemistry of this interesting group of microbes.}, }
@article {pmid32440700, year = {2020}, author = {Des Marteaux, LE and Kullik, SA and Habash, M and Schmidt, JM}, title = {Terrestrial Isopods Porcellio scaber and Oniscus asellus (Crustacea: Isopoda) Increase Bacterial Abundance and Modify Microbial Community Structure in Leaf Litter Microcosms: a Short-Term Decomposition Study.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {690-702}, doi = {10.1007/s00248-020-01527-4}, pmid = {32440700}, issn = {1432-184X}, abstract = {Invasive terrestrial isopods are likely to have altered leaf litter decomposition processes in North American forests, but the mechanisms underlying these alterations and the degree to which they differ among isopod species are poorly characterized. Using mixed-deciduous leaf litter microcosms, we quantified the effects of two common, invasive isopods (Oniscus asellus and Porcellio scaber) on short-term leaf litter decomposition and microbial community structure and function. Microcosms containing ground litter and a microbial inoculant were exposed to one of the two isopod species or no isopods for 21 days. Mass loss was then quantified as the change in litter dry mass after leaching, and microbial respiration was quantified as the mass of CO2 absorbed by soda lime. Litter leachates were plated on agar to quantify culturable bacterial and fungal abundance, and denaturing gradient gel electrophoresis of amplified leachate microbial DNA was used to characterize shifts in microbial community structure. Isopod presence increased litter mass loss by a modest ~ 6%, but did not affect litter microbial respiration. Bacterial abundance increased significantly in the presence of isopods, while fungal abundance was either unchanged or reduced. Overall litter microbial species richness was reduced by isopods, with O. asellus specifically reducing fungal abundance and diversity. Isopods modified the microbial community structure by suppressing four bacterial and one fungal species, while promoting growth of four other bacterial species (two unique to each isopod species) and two fungal species (one which was unique to O. asellus).}, }
@article {pmid32440699, year = {2020}, author = {Grimes, DJ}, title = {The Vibrios: Scavengers, Symbionts, and Pathogens from the Sea.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {501-506}, doi = {10.1007/s00248-020-01524-7}, pmid = {32440699}, issn = {1432-184X}, abstract = {Bacteria belonging to the genus Vibrio are major carbon cycle drivers in marine and estuarine environments. As is the case for most carbon cycle participants, the vibrios metabolize degradable compounds such as sugars and amino acids; they can also degrade some more recalcitrant compounds including hydrocarbons and lignins. Several vibrios are symbionts and even fewer are pathogenic for animals, including humans and marine animals and plants. This paper reviews Vibrio ecology, metabolism, and survival, and it also discusses select vibrios-V. alginolyticus, V. cholerae, V. coralliilyticus, V. cortegadensis, V. fischeri, V. harveyi, V. harveyi var. carahariae, V. ordalii, V. parahaemolyticus, and V. vulnificus.}, }
@article {pmid32440698, year = {2020}, author = {Torralba, MG and Kuelbs, C and Moncera, KJ and Roby, R and Nelson, KE}, title = {Characterizing Microbial Signatures on Sculptures and Paintings of Similar Provenance.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-020-01504-x}, pmid = {32440698}, issn = {1432-184X}, abstract = {The preservation of artwork challenges museums, collectors, and art enthusiasts. Currently, reducing moisture, adjusting the type of lighting, and preventing the formation of mold are primary methods to preserving and preventing deterioration. Other methods such as ones based in detailed knowledge of molecular biology such as microbial community characterization using polymerase chain reaction (PCR) and sequencing have yet to be explored. Such molecular biology approaches are essential to explore as some environmental bacteria are capable of oxidizing nonpolar chemical substances rich in hydrocarbons such as oil-based paints. Using 16S rDNA Illumina Sequencing, we demonstrate a novel finding that there are differing bacterial communities for artwork from roughly the same era when comparing paintings on wood, paintings on canvases, and sculptures made of stone and marble. We also demonstrate that there are specific genera such as Aeromonas known for having oxidase positive strains, present on paintings on wood and paintings on canvas that could potentially be responsible for deterioration and fading as such organisms produce water or hydrogen peroxide as a byproduct of cytochrome c oxidase activity. The advantages of these genomics-based approaches to characterizing the microbial population on deteriorating artwork provides immense potential by identifying potentially damaging species that may not be detected using conventional methods in addition to addressing challenges to identification, restoration, and preservation efforts.}, }
@article {pmid32440491, year = {2020}, author = {Zheng, P and Li, Y and Wu, J and Zhang, H and Huang, Y and Tan, X and Pan, J and Duan, J and Liang, W and Yin, B and Deng, F and Perry, SW and Wong, ML and Licinio, J and Wei, H and Yu, G and Xie, P}, title = {Erratum: Perturbed Microbial Ecology in Myasthenia Gravis: Evidence from the Gut Microbiome and Fecal Metabolome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {7}, number = {10}, pages = {2001296}, doi = {10.1002/advs.202001296}, pmid = {32440491}, issn = {2198-3844}, abstract = {[This corrects the article DOI: 10.1002/advs.201901441.].}, }
@article {pmid32439665, year = {2020}, author = {Kirchner, N and Cano-Prieto, C and van der Voort, M and Raaijmakers, JM and Gross, H}, title = {Draft Genome Sequence of Lipopeptide-Producing Strain Pseudomonas fluorescens DSM 11579 and Comparative Genomics with Pseudomonas sp. Strain SH-C52, a Closely Related Lipopeptide-Producing Strain.}, journal = {Microbiology resource announcements}, volume = {9}, number = {21}, pages = {}, pmid = {32439665}, issn = {2576-098X}, abstract = {Pseudomonas fluorescens DSM 11579 is known to be a producer of the lipopeptides brabantamide and thanamycin. Its draft genome gives insight into the complete secondary metabolite production capacity of the strain and builds the basis for a comparative study with Pseudomonas sp. strain SH-C52, a lipopeptide-producing strain involved in natural disease-suppressive soils.}, }
@article {pmid32438141, year = {2020}, author = {Hooban, B and Joyce, A and Fitzhenry, K and Chique, C and Morris, D}, title = {The role of the natural aquatic environment in the dissemination of extended spectrum beta-lactamase and carbapenemase encoding genes: A scoping review.}, journal = {Water research}, volume = {180}, number = {}, pages = {115880}, doi = {10.1016/j.watres.2020.115880}, pmid = {32438141}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; Bacterial Proteins ; Drug Resistance, Microbial ; *Genes, Bacterial ; *beta-Lactamases ; }, abstract = {The natural aquatic environment is a significant contributor to the development and circulation of clinically significant antibiotic resistance genes (ARGs). The potential for the aquatic environment to act as a reservoir for ARG accumulation in areas receiving anthropogenic contamination has been thoroughly researched. However, the emergence of novel ARGs in the absence of external influences, as well as the capacity of environmental bacteria to disseminate ARGs via mobile genetic elements remain relatively unchallenged. In order to address these knowledge gaps, this scoping literature review was established focusing on the detection of two important and readily mobile ARGs, namely, extended spectrum beta-lactamase (ESBL) and carbapenemase genes. This review included 41 studies from 19 different countries. A range of different water bodies including rivers (n = 26), seawaters (n = 6) and lakes (n = 3), amongst others, were analysed in the included studies. ESBL genes were reported in 29/41 (70.7%) studies, while carbapenemase genes were reported in 13/41 (31.7%), including joint reporting in 9 studies. The occurrence of mobile genetic elements was evaluated, which included the detection of integrons (n = 22), plasmids (n = 18), insertion sequences (n = 4) and transposons (n = 3). The ability of environmental bacteria to successfully transfer resistance genes via conjugation was also examined in 11 of the included studies. The findings of this scoping review expose the presence of clinically significant ARGs in the natural aquatic environment and highlights the potential ability of environmental isolates to disseminate these genes among different bacterial species. As such, the results presented demonstrate how anthropogenic point discharges may not act as the sole contributor to the development and spread of clinically significant antibiotic resistances. A number of critical knowledge gaps in current research were also identified. Key highlights include the limited number of studies focusing on antibiotic resistance in uncontaminated aquatic environments as well as the lack of standardisation among methodologies of reviewed investigations.}, }
@article {pmid32436568, year = {2020}, author = {Van Landuyt, J and Cimmino, L and Dumolin, C and Chatzigiannidou, I and Taveirne, F and Mattelin, V and Zhang, Y and Vandamme, P and Scoma, A and Williamson, A and Boon, N}, title = {Microbial enrichment, functional characterization and isolation from a cold seep yield piezotolerant obligate hydrocarbon degraders.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {9}, pages = {}, doi = {10.1093/femsec/fiaa097}, pmid = {32436568}, issn = {1574-6941}, abstract = {Deep-sea environments can become contaminated with petroleum hydrocarbons. The effects of hydrostatic pressure (HP) in the deep sea on microbial oil degradation are poorly understood. Here, we performed long-term enrichments (100 days) from a natural cold seep while providing optimal conditions to sustain high hydrocarbon degradation rates. Through enrichments performed at increased HP and ambient pressure (AP) and by using control enrichments with marine broth, we demonstrated that both pressure and carbon source can have a big impact on the community structure. In contrast to previous studies, hydrocarbonoclastic operational taxonomic units (OTUs) remained dominant at both AP and increased HP, suggesting piezotolerance of these OTUs over the tested pressure range. Twenty-three isolates were obtained after isolation and dereplication. After recultivation at increased HP, an Alcanivorax sp. showed promising piezotolerance in axenic culture. Furthermore, preliminary co-cultivation tests indicated synergistic growth between some isolates, which shows promise for future synthetic community construction. Overall, more insights into the effect of increased HP on oil-degrading communities were obtained as well as several interesting isolates, e.g. a piezotolerant hydrocarbonoclastic bacterium for future deep-sea bioaugmentation investigation.}, }
@article {pmid32436040, year = {2020}, author = {Rocha, KF and Kuramae, EE and Borges, BMF and Leite, MFA and Rosolem, CA}, title = {Microbial N-cycling gene abundance is affected by cover crop specie and development stage in an integrated cropping system.}, journal = {Archives of microbiology}, volume = {202}, number = {7}, pages = {2005-2012}, doi = {10.1007/s00203-020-01910-2}, pmid = {32436040}, issn = {1432-072X}, support = {2015/50305-8//FAPESP/ ; BB/N013201/1//BBRSC/ ; }, mesh = {*Agriculture ; Ammonia/metabolism ; Archaea/genetics ; Bacteria/genetics ; Crops, Agricultural/*microbiology ; Nitrification ; Nitrogen/metabolism ; Nitrogen Cycle/*genetics ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Zea mays ; }, abstract = {Grasses of the Urochloa genus have been widely used in crop-livestock integration systems or as cover crops in no-till systems such as in rotation with maize. Some species of Urochloa have mechanisms to reduce nitrification. However, the responses of microbial functions in crop-rotation systems with grasses and its consequence on soil N dynamics are not well-understood. In this study, the soil nitrification potential and the abundance of ammonifying microorganisms, total bacteria and total archaea (16S rRNA gene), nitrogen-fixing bacteria (NFB, nifH), ammonia-oxidizing bacteria (AOB, amoA) and archaea (AOA, amoA) were assessed in soil cultivated with ruzigrass (Urochloa ruziziensis), palisade grass (Urochloa brizantha) and Guinea grass (Panicum maximum). The abundance of ammonifying microorganisms was not affected by ruzigrass. Ruzigrass increased the soil nitrification potential compared with palisade and Guinea grass. Ruzigrass increased the abundance of N-fixing microorganisms at the middle and late growth stages. The abundances of nitrifying microorganisms and N-fixers in soil were positively correlated with the soil N-NH4+ content. Thus, biological nitrogen fixation might be an important input of N in systems of rotational production of maize with forage grasses. The abundance of microorganisms related to ammonification, nitrification and nitrogen fixing and ammonia-oxidizing archea was related to the development stage of the forage grass.}, }
@article {pmid32434844, year = {2020}, author = {Minich, JJ and Petrus, S and Michael, JD and Michael, TP and Knight, R and Allen, EE}, title = {Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus.}, journal = {mSphere}, volume = {5}, number = {3}, pages = {}, pmid = {32434844}, issn = {2379-5042}, support = {P01 ES021921/ES/NIEHS NIH HHS/United States ; }, abstract = {Changing ocean conditions driven by anthropogenic activities may have a negative impact on fisheries by increasing stress and disease. To understand how environment and host biology drives mucosal microbiomes in a marine fish, we surveyed five body sites (gill, skin, digesta, gastrointestinal tract [GI], and pyloric ceca) from 229 Pacific chub mackerel, Scomber japonicus, collected across 38 time points spanning 1 year from the Scripps Institution of Oceanography Pier (La Jolla, CA). Mucosal sites had unique microbial communities significantly different from the surrounding seawater and sediment communities with over 10 times more total diversity than seawater. The external surfaces of skin and gill were more similar to seawater, while digesta was more similar to sediment. Alpha and beta diversity of the skin and gill was explained by environmental and biological factors, specifically, sea surface temperature, chlorophyll a, and fish age, consistent with an exposure gradient relationship. We verified that seasonal microbial changes were not confounded by regional migration of chub mackerel subpopulations by nanopore sequencing a 14,769-bp region of the 16,568-bp mitochondria across all temporal fish specimens. A cosmopolitan pathogen, Photobacterium damselae, was prevalent across multiple body sites all year but highest in the skin, GI, and digesta between June and September, when the ocean is warmest. The longitudinal fish microbiome study evaluates the extent to which the environment and host biology drives mucosal microbial ecology and establishes a baseline for long-term surveys linking environment stressors to mucosal health of wild marine fish.IMPORTANCE Pacific chub mackerel, Scomber japonicus, are one of the largest and most economically important fisheries in the world. The fish is harvested for both human consumption and fish meal. Changing ocean conditions driven by anthropogenic stressors like climate change may negatively impact fisheries. One mechanism for this is through disease. As waters warm and chemistry changes, the microbial communities associated with fish may change. In this study, we performed a holistic analysis of all mucosal sites on the fish over a 1-year time series to explore seasonal variation and to understand the environmental drivers of the microbiome. Understanding seasonality in the fish microbiome is also applicable to aquaculture production for producers to better understand and predict when disease outbreaks may occur based on changing environmental conditions in the ocean.}, }
@article {pmid32432525, year = {2020}, author = {Jakubovics, NS and Shi, W}, title = {A New Era for the Oral Microbiome.}, journal = {Journal of dental research}, volume = {99}, number = {6}, pages = {595-596}, doi = {10.1177/0022034520918536}, pmid = {32432525}, issn = {1544-0591}, }
@article {pmid32430405, year = {2020}, author = {Fu, X and Li, Y and Yuan, Q and Cai, GH and Deng, Y and Zhang, X and Norbäck, D and Sun, Y}, title = {Continental-Scale Microbiome Study Reveals Different Environmental Characteristics Determining Microbial Richness, Composition, and Quantity in Hotel Rooms.}, journal = {mSystems}, volume = {5}, number = {3}, pages = {}, pmid = {32430405}, issn = {2379-5077}, abstract = {Culture-independent microbiome surveys have been conducted in homes, hospitals, schools, kindergartens and vehicles for public transport, revealing diverse microbial distributions in built environments. However, microbiome composition and the associated environmental characteristics have not been characterized in hotel environments. We presented here the first continental-scale microbiome study of hotel rooms (n = 68) spanning Asia and Europe. Bacterial and fungal communities were described by amplicon sequencing of the 16S rRNA gene and internal transcribed spacer (ITS) region and quantitative PCR. Similar numbers of bacterial (4,344) and fungal (4,555) operational taxonomic units were identified in the same sequencing depth, but most fungal taxa showed a restricted distribution compared to bacterial taxa. Aerobic, ubiquitous bacteria dominated the hotel microbiome with compositional similarity to previous samples from building and human nasopharynx environments. The abundance of Aspergillus was negatively correlated with latitude and accounted for ∼80% of the total fungal load in seven low-latitude hotels. We calculated the association between hotel microbiome and 16 indoor and outdoor environmental characteristics. Fungal composition and absolute quantity showed concordant associations with the same environmental characteristics, including latitude, quality of the interior, proximity to the sea, and visible mold, while fungal richness was negatively associated with heavy traffic (95% confidence interval [CI] = -127.05 to -0.25) and wall-to-wall carpet (95% CI = -47.60 to -3.82). Bacterial compositional variation was associated with latitude, quality of the interior, and floor type, while bacterial richness was negatively associated with recent redecoration (95% CI -179.00 to -44.55) and mechanical ventilation (95% CI = -136.71 to -5.12).IMPORTANCE This is the first microbiome study to characterize the microbiome data and associated environmental characteristics in hotel environments. In this study, we found concordant variation between fungal compositional variation and absolute quantity and discordant variation between community variation/quantity and richness. Our study can be used to promote hotel hygiene standards and provide resource information for future microbiome and exposure studies associated with health effects in hotel rooms.}, }
@article {pmid32426533, year = {2020}, author = {Venturini, AM and Nakamura, FM and Gontijo, JB and da França, AG and Yoshiura, CA and Mandro, JA and Tsai, SM}, title = {Robust DNA protocols for tropical soils.}, journal = {Heliyon}, volume = {6}, number = {5}, pages = {e03830}, pmid = {32426533}, issn = {2405-8440}, abstract = {Studies in the Amazon are being intensified to evaluate the alterations in the microbial communities of soils and sediments in the face of increasing deforestation and land-use changes in the region. However, since these environments present highly heterogeneous physicochemical properties, including contaminants that hinder nucleic acids isolation and downstream techniques, the development of best molecular practices is crucial. This work aimed to optimize standard protocols for DNA extraction and gene quantification by quantitative real-time PCR (qPCR) based on natural and anthropogenic soils and sediments (primary forest, pasture, Amazonian Dark Earth, and várzea, a seasonally flooded area) of the Eastern Amazon. Our modified extraction protocol increased the fluorometric DNA concentration by 48%, reaching twice the original amount for most of the pasture and várzea samples, and the 260/280 purity ratio by 15% to values between 1.8 to 2.0, considered ideal for DNA. The addition of bovine serum albumin in the qPCR reaction improved the quantification of the 16S rRNA genes of Archaea and Bacteria and its precision among technical replicates, as well as allowed their detection in previously non-amplifiable samples. It is concluded that the changes made in the protocols improved the parameters of the DNA samples and their amplification, thus increasing the reliability of microbial communities' analysis and its ecological interpretations.}, }
@article {pmid32425165, year = {2020}, author = {Oliveira, BG and Mendes, LW and Smyth, EM and Tsai, SM and Feigl, BJ and Mackie, RI}, title = {Assessment of microbial diversity associated with CH4 emission from sugarcane vinasse storage and transportation systems.}, journal = {Journal of environmental management}, volume = {269}, number = {}, pages = {110748}, doi = {10.1016/j.jenvman.2020.110748}, pmid = {32425165}, issn = {1095-8630}, mesh = {Brazil ; *Greenhouse Gases ; Methane ; RNA, Ribosomal, 16S ; *Saccharum ; }, abstract = {Sugarcane bioethanol has favorable energy and greenhouse gas balance, although the production process generates several residues including vinasse, which deserves attention because of its significant methane (CH4) emission during storage and transportation stages. Considering that CH4 emissions are dependent on the structure and abundance of microbial communities, we hypothesized that different vinasse transportation systems would harbor different microbial community composition, resulting in distinct CH4 patterns. To test this hypothesis, we used high-throughput 16S rRNA sequencing with real-time PCR to evaluate the composition and abundance of microorganisms in the two main systems of vinasse storage and transportation (i.e. open channels and tanks systems) in Brazil. Our results showed higher microbial diversity and CH4 emissions in channel system, especially in the uncoated section. Significant differences in microbial community structure, diversity, and abundance between the uncoated/coated open channel and tanks indicated a clear selection at taxonomic and functional levels, especially in relation to CH4 production. These responses included higher methanogens diversity in the uncoated section of the channel and are in agreement with the methanogen abundance determined by mcrA and mba genes copy number (1.5 × 107 and 4.3 × 1010) and subsequent positive correlation with CH4 emissions (R2 = 0.8). The most representative methanogen genus across the samples was Methanobrevibacter. The results observed herein shows that the use of the coating in the bottom of channels and tanks prevent the growth and development of a methanogen-related community. We concluded that the improvements in vinasse storage and transportation systems would significantly change the microbial community and reduce CH4 emissions, thereby making bioethanol a greener biofuel.}, }
@article {pmid32424717, year = {2020}, author = {Grajal-Puche, A and Murray, CM and Kearley, M and Merchant, M and Nix, C and Warner, JK and Walker, DM}, title = {Microbial Assemblage Dynamics Within the American Alligator Nesting Ecosystem: a Comparative Approach Across Ecological Scales.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {603-613}, doi = {10.1007/s00248-020-01522-9}, pmid = {32424717}, issn = {1432-184X}, abstract = {Understanding the ecological processes that shape species assemblage patterns is central to community ecology. The effects of ecological processes on assemblage patterns are scale-dependent. We used metabarcoding and shotgun sequencing to determine bacterial taxonomic and functional assemblage patterns among varying defined focal scales (micro-, meso-, and macroscale) within the American alligator (Alligator mississippiensis) nesting microbiome. We correlate bacterial assemblage patterns among eight nesting compartments within and proximal to alligator nests (micro-), across 18 nests (meso-), and between 4 geographic sampling sites (macro-), to determine which ecological processes may drive bacterial assemblage patterns within the nesting environment. Among all focal scales, bacterial taxonomic and functional richness (α-diversity) did not statistically differ. In contrast, bacterial assemblage structure (β-diversity) was unique across all focal scales, whereas functional pathways were redundant within nests and across geographic sites. Considering these observed scale-based patterns, taxonomic bacterial composition may be governed by unique environmental filters and dispersal limitations relative to microbial functional attributes within the alligator nesting environment. These results advance pattern-process dynamics within the field of microbial community ecology and describe processes influencing the American alligator nest microbiome.}, }
@article {pmid32419297, year = {2020}, author = {Xing, J and Jia, X and Wang, H and Ma, B and Falcão Salles, J and Xu, J}, title = {The legacy of bacterial invasions on soil native communities.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15086}, pmid = {32419297}, issn = {1462-2920}, support = {B17039//Higher Education Discipline Innovation Project/ ; //KNAW-CSC/ ; 2016YFD0800207//National Key Research and Development Program of China/ ; 41721001//National Natural Science Foundation of China/ ; }, abstract = {Soil microbial communities are often not resistant to the impact caused by microbial invasions, both in terms of structure and functionality, but it remains unclear whether these changes persist over time. Here, we used three strains of Escherichia coli O157:H7 (E. coli O157:H7), a species used for modelling bacterial invasions, to evaluate the resilience of the bacterial communities from four Chinese soils to invasion. The impact of E. coli O157:H7 strains on soil native communities was tracked for 120 days by analysing bacterial community composition as well as their metabolic potential. We showed that soil native communities were not resistant to invasion, as demonstrated by a decline in bacterial diversity and shifts in bacterial composition in all treatments. The resilience of native bacterial communities (diversity and composition) was inversely correlated with invader's persistence in soils (R2 = 0.487, p < 0.001). Microbial invasions also impacted the functionality of the soil communities (niche breadth and community niche), the degree of resilience being dependent on soil or native community diversity. Collectively, our results indicate that bacteria invasions can potentially leave a footprint in the structure and functionality of soil communities, indicating the need of assessing the legacy of introducing exotic species in soil environments.}, }
@article {pmid32417556, year = {2020}, author = {Gallego, S and Barkay, T and Fahrenfeld, NL}, title = {Tagging the vanA gene in wastewater microbial communities for cell sorting and taxonomy of vanA carrying cells.}, journal = {The Science of the total environment}, volume = {732}, number = {}, pages = {138865}, doi = {10.1016/j.scitotenv.2020.138865}, pmid = {32417556}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Bacterial Proteins ; Carbon-Oxygen Ligases ; In Situ Hybridization, Fluorescence ; Microbial Sensitivity Tests ; *Microbiota ; Phylogeny ; Waste Water ; }, abstract = {Failure to understand the microbial ecology driving the proliferation of antibiotic resistance in the environment prevents us from developing strategies to limit the spread of antibiotic resistant infectious disease. In this study, we developed for the first time a tyramide signal amplification-fluorescence in situ hybridization-fluorescence-activated cell sorting protocol (TSA-FISH-FACS) for the characterization of all vanA carrying bacteria in wastewater samples. Firstly, we validated the TSA-FISH protocol through microscopy in pure cultures and wastewater influent. Then, samples were sorted and quantified by FACS and qPCR. Significantly higher percentage tagging of cells was detected in vanA carrying pure cultures and wastewater samples spiked with vanA carrying cells as compared to vanA negative Gram positive strains and non-spiked wastewater samples respectively. qPCR analysis targeting vanZ, a regulating gene in the vanA cluster, showed its relative abundance was significantly greater in Enterococcus faecium ATCC 700221-spiked and positively sorted samples compared to the E. faecium spiked and negatively sorted samples. Phylogenetic analysis was then performed. Although further efforts are needed to overcome technical problems, we have, for the first time, demonstrated sorting bacterial-cells carrying antibiotic resistance genes from wastewater samples through a TSA-FISH-FACS protocol and provided insight into the microbial ecology of vancomycin resistant bacteria. Future potential applications using this approach will include the separation of members of an environmental microbial community (cultured and hard-to-culture) to allow for metagenomics on single cells or, in the case of clumping, targeting a smaller portion of the community with a priori knowledge that the target gene is present.}, }
@article {pmid32415330, year = {2020}, author = {Pajares, S and Varona-Cordero, F and Hernández-Becerril, DU}, title = {Spatial Distribution Patterns of Bacterioplankton in the Oxygen Minimum Zone of the Tropical Mexican Pacific.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {519-536}, doi = {10.1007/s00248-020-01508-7}, pmid = {32415330}, issn = {1432-184X}, support = {PAPIIT-IA201617//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; }, abstract = {Microbial communities within oxygen minimum zones (OMZs) are crucial drivers of marine biogeochemical cycles; however, we still lack an understanding of how these communities are distributed across an OMZ. We explored vertical (from 5 to 500 m depth) and horizontal (coast to open ocean) distribution of bacterioplankton and its relationships with the main oceanographic conditions in three transects of the tropical Mexican Pacific OMZ. The distribution of the microbial diversity and the main clades changed along the transition from oxygen-rich surface water to the OMZ core, demonstrating the sensitivity of key bacterial groups to deoxygenation. The euphotic zone was dominated by Synechococcales, followed by Flavobacteriales, Verrucomicrobiales, Rhodobacterales, SAR86, and Cellvibrionales, whereas the OMZ core was dominated by SAR11, followed by SAR406, SAR324, SAR202, UBA10353 marine group, Thiomicrospirales and Nitrospinales. The marked environmental gradients along the water column also supported a high potential for niche partitioning among OMZ microorganisms. Additionally, in the OMZ core, bacterial assemblages from the same water mass were more similar to each other than those from another water mass. There were also important differences between coastal and open-ocean communities: Flavobacteriales, Verrucomicrobiales, Rhodobacterales, SAR86, and Cellvibrionales were more abundant in coastal areas, while Synechococcales, SAR406, SAR324, SAR202, UBA10353 marine group, and Thiomicrospirales were more abundant in the open ocean. Our results suggest a biogeographic structure of the bacterioplankton in this OMZ region, with limited community mixing across water masses, except in upwelling events, and little dispersion of the community by currents in the euphotic zone.}, }
@article {pmid32414800, year = {2020}, author = {Jiang, W and Wang, Y and Luo, J and Chen, X and Zeng, Y and Li, X and Feng, Z and Zhang, L}, title = {Antimicrobial Peptide GH12 Prevents Dental Caries by Regulating Dental Plaque Microbiota.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {14}, pages = {}, pmid = {32414800}, issn = {1098-5336}, abstract = {Due to the complex microecology and microenvironment of dental plaque, novel caries prevention strategies require modulating the microbial communities ecologically and reducing the cariogenic properties effectively. Antimicrobial peptide GH12 reduced the lactic acid production and exopolysaccharide (EPS) synthesis of a Streptococcus mutans biofilm and a three-species biofilm in vitro in previous studies. However, the anticaries effects and microecological effects of GH12 remained to be investigated in a complex biofilm model in vitro and an animal caries model in vivo In the present study, GH12 at 64 mg/liter showed the most effective inhibition of lactic acid production, EPS synthesis, pH decline, and biofilm integrity of human dental plaque-derived multispecies biofilms in vitro, and GH12 at 64 mg/liter was therefore chosen for use in subsequent in vitro and in vivo assays. When treated with 64-mg/liter GH12, the dental plaque-derived multispecies biofilms sampled from healthy volunteers maintained its microbial diversity and showed a microbial community structure similar to that of the control group. In the rat caries model with a caries-promoting diet, 64-mg/liter GH12 regulated the microbiota of dental plaque, in which the abundance of caries-associated bacteria was decreased and the abundance of commensal bacteria was increased. In addition, 64-mg/liter GH12 significantly reduced the caries scores of sulcal and smooth surface caries in all locations. In conclusion, GH12 inhibited the cariogenic properties of dental plaque without perturbing the dental plaque microbiota of healthy individuals and GH12 regulated the dysbiotic microbial ecology and arrested caries development under cariogenic conditions.IMPORTANCE The anticaries effects and microecological regulation effects of the antimicrobial peptide GH12 were evaluated systematically in vitro and in vivo GH12 inhibited the cariogenic virulence of dental plaque without overintervening in the microbial ecology of healthy individuals in vitro GH12 regulated the microbial ecology of dental plaque to a certain extent in vivo under cariogenic conditions, increased the proportion of commensal bacteria, and decreased the abundance of caries-associated bacteria. GH12 significantly suppressed the incidence and severity of dental caries in vivo This study thus describes an alternative antimicrobial therapy for dental caries.}, }
@article {pmid32414048, year = {2020}, author = {Kuramae, EE and Derksen, S and Schlemper, TR and Dimitrov, MR and Costa, OYA and Silveira, APDD}, title = {Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics.}, journal = {Microorganisms}, volume = {8}, number = {5}, pages = {}, pmid = {32414048}, issn = {2076-2607}, support = {729.004.013//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 456420/2013-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Bacteria from the genera Paraburkholderia and Herbaspirillum can promote the growth of Sorghum bicolor, but the underlying mechanisms are not yet known. In a pot experiment, sorghum plants grown on sterilized substrate were inoculated with Paraburkholderia tropica strain IAC/BECa 135 and Herbaspirillumfrisingense strain IAC/BECa 152 under phosphate-deficient conditions. These strains significantly increased Sorghum bicolor cultivar SRN-39 root and shoot biomass. Shotgun metagenomic analysis of the rhizosphere revealed successful colonization by both strains; however, the incidence of colonization was higher in plants inoculated with P. tropica strain IAC/BECa 135 than in those inoculated with H. frisingense strain IAC/BECa 152. Conversely, plants inoculated with H. frisingense strain IAC/BECa 152 showed the highest increase in biomass. Genomic analysis of the two inoculants implied a high degree of rhizosphere fitness of P. tropica strain IAC/BECa 135 through environmental signal processing, biofilm formation, and nutrient acquisition. Both genomes contained genes related to plant growth-promoting bacterial (PGPB) traits, including genes related to indole-3-acetate (IAA) synthesis, nitrogen fixation, nodulation, siderophore production, and phosphate solubilization, although the P. tropica strain IAC/BECa 135 genome contained a slightly more extensive repertoire. This study provides evidence that complementary mechanisms of growth promotion in Sorghum might occur, i.e., that P. tropica strain IAC/BECa 135 acts in the rhizosphere and increases the availability of nutrients, while H. frisingense strain IAC/BECa 152 influences plant hormone signaling. While the functional and taxonomic profiles of the rhizobiomes were similar in all treatments, significant differences in plant biomass were observed, indicating that the rhizobiome and the endophytic microbial community may play equally important roles in the complicated plant-microbial interplay underlying increased host plant growth.}, }
@article {pmid32413640, year = {2020}, author = {Barbosa, RG and Sleutels, T and Verstraete, W and Boon, N}, title = {Hydrogen oxidizing bacteria are capable of removing orthophosphate to ultra-low concentrations in a fed batch reactor configuration.}, journal = {Bioresource technology}, volume = {311}, number = {}, pages = {123494}, doi = {10.1016/j.biortech.2020.123494}, pmid = {32413640}, issn = {1873-2976}, mesh = {Bacteria ; Bioreactors ; *Hydrogen ; Oxidation-Reduction ; *Phosphates ; Phosphorus ; }, abstract = {This paper proposes the use of hydrogen oxidizing bacteria (HOB) for the removal of orthophosphate from surface water as treatment step to prevent cyanobacterial blooms. To be effective as an orthophosphate removal strategy, an efficient transfer of hydrogen to the HOB is essential. A trickling filter was selected for this purpose. Using this system, a removal rate of 11.32 ± 0.43 mg PO4-3-P/L.d was achieved. The HOB biomass, developed on the trickling filter, is composed of 1.25% phosphorus on dry matter, which suggests that the orthophosphate removal principle is based on HOB growth. Cyanobacterial growth assays of the untreated and treated water showed that Synechocystis sp was only able to grow in the untreated water. Orthophosphate was removed to average residual values of 0.008 mg/L. In this proof of principle study, it is shown that HOB are able to remove orthophosphate from water to concentrations that prevent cyanobacterial growth.}, }
@article {pmid32410366, year = {2020}, author = {Durán-Viseras, A and Andrei, AŞ and Vera-Gargallo, B and Ghai, R and Sánchez-Porro, C and Ventosa, A}, title = {Culturomics-based genomics sheds light on the ecology of the new haloarchaeal genus Halosegnis.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15082}, pmid = {32410366}, issn = {1462-2920}, support = {MSM200961801//Akademie Věd České Republiky/ ; BIO-213//Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía/ ; US-1263771//Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía/ ; 17-04828 S//Grantová Agentura České Republiky/ ; CGL2017-83385-P//Secretaría de Estado de Investigación, Desarrollo e Innovación/ ; }, abstract = {The development of culture-independent techniques has revolutionized our understanding of microbial ecology, especially through the illustration of the vast gap between the environmentally abundant microbial diversity and that accessible through cultivation. However, culture-based approaches are not only crucial for understanding the evolutionary, metabolic and ecological milieu of microbial diversity but also for the development of novel biotechnological applications. In this study, we used a culturomics-based approach in order to isolate novel microbial taxa from hypersaline environments (i.e. Isla Cristina and Isla Bacuta salterns in Huelva, Spain). We managed to obtain axenic cultures of four haloarchaeal strains that belong to a new haloarchaeal genus and to obtain their genomic sequences. The phylogenomic and phylogenetic analyses (together with AAI, ANI and digital DDH indices) showed that the isolates constitute two new species, for which we propose the names Halosegnis longus sp. nov. and Halosegnis rubeus sp. nov. The genomic-based metabolic reconstructions indicated that members of this new haloarchaeal genus have photoheterotrophic aerobic lifestyle with a typical salt-in signature. 16S rRNA gene sequence reads abundance profiles and genomic recruitment analyses revealed that the Halosegnis genus has a worldwide geographical distribution, reaching high abundance (up to 8%) in habitats with intermediate salinities.}, }
@article {pmid32410293, year = {2020}, author = {Qureshi, SS and Kedo, M and Berthrong, ST}, title = {Gender-neutral bathroom surfaces recolonized by microbes more quickly than single-gender bathrooms.}, journal = {Letters in applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/lam.13316}, pmid = {32410293}, issn = {1472-765X}, support = {//Butler University's Center for High Achievement and Scholarly Engagement Honors Program/ ; }, abstract = {As humans become increasingly urban and spend more time inside the built environment, there will be increased interactions between humans and shared public surface microbiomes. Recent cultural changes in the United States have led to increased numbers of gender-neutral bathrooms. Given that bathroom surfaces are frequently sanitized, we used this increased availability of gender-neutral bathrooms to examine how single-gender or gender-neutral surfaces are recolonized with microbes. Given that male and female microbiomes vary, we hypothesized that rates of recolonization would differ between male, female and gender-neutral bathroom surfaces. We collected swabs from common hand-contacted surfaces in bathrooms and cultured microbes on selective and rich media to determine microbial abundance after cleaning. Recolonization was dominated by Gram-positive bacteria and was slowest on male, intermediate on female and fastest on gender-neutral surfaces. These results imply that gender-neutral surfaces approach normal climax microbial communities more quickly than single-gender bathrooms.}, }
@article {pmid32409544, year = {2020}, author = {Šimoliūnienė, M and Tumėnas, D and Kvederavičiūtė, K and Meškys, R and Šulčius, S and Šimoliūnas, E}, title = {Complete Genome Sequence of Bacillus cereus Bacteriophage vB_BceS_KLEB30-3S.}, journal = {Microbiology resource announcements}, volume = {9}, number = {20}, pages = {}, pmid = {32409544}, issn = {2576-098X}, abstract = {In this study, we present the genomic characterization of the temperate bacteriophage vB_BceS_KLEB30-3S (KLEB30-3S), which was induced from Bacillus cereus strain KR3M-30, isolated from a gypsum karst lake ecosystem in Lithuania. The 37,134-bp genome of KLEB30-3S contains 58 predicted protein-encoding genes and no tRNA genes.}, }
@article {pmid32409535, year = {2020}, author = {Köstlbacher, S and Michels, S and Siegl, A and Schulz, F and Domman, D and Jongwutiwes, S and Putaporntip, C and Horn, M and Collingro, A}, title = {Draft Genome Sequences of Chlamydiales Bacterium STE3 and Neochlamydia sp. Strain AcF84, Endosymbionts of Acanthamoeba spp.}, journal = {Microbiology resource announcements}, volume = {9}, number = {20}, pages = {}, pmid = {32409535}, issn = {2576-098X}, abstract = {Chlamydiales bacterium STE3 and Neochlamydia sp. strain AcF84 are obligate intracellular symbionts of Acanthamoeba spp. isolated from the biofilm of a littoral cave wall and gills from striped tiger leaf fish, respectively. We report the draft genome sequences of these two environmental chlamydiae affiliated with the family Parachlamydiaceae.}, }
@article {pmid32405432, year = {2020}, author = {Zwart, MP and Elena, SF}, title = {Modeling multipartite virus evolution: the genome formula facilitates rapid adaptation to heterogeneous environments†.}, journal = {Virus evolution}, volume = {6}, number = {1}, pages = {veaa022}, pmid = {32405432}, issn = {2057-1577}, abstract = {Multipartite viruses have two or more genome segments, and package different segments into different particle types. Although multipartition is thought to have a cost for virus transmission, its benefits are not clear. Recent experimental work has shown that the equilibrium frequency of viral genome segments, the setpoint genome formula (SGF), can be unbalanced and host-species dependent. These observations have reinvigorated the hypothesis that changes in genome-segment frequencies can lead to changes in virus-gene expression that might be adaptive. Here we explore this hypothesis by developing models of bipartite virus infection, leading to a threefold contribution. First, we show that the SGF depends on the cellular multiplicity of infection (MOI), when the requirements for infection clash with optimizing the SGF for virus-particle yield per cell. Second, we find that convergence on the SGF is very rapid, often occurring within a few cellular rounds of infection. Low and intermediate MOIs lead to faster convergence on the SGF. For low MOIs, this effect occurs because of the requirements for infection, whereas for intermediate MOIs this effect is also due to the high levels of variation generated in the genome formula (GF). Third, we explored the conditions under which a bipartite virus could outcompete a monopartite one. As the heterogeneity between environments and specificity of gene-expression requirements for each environment increased, the bipartite virus was more likely to outcompete the monopartite virus. Under some conditions, changes in the GF helped to exclude the monopartite competitor, highlighting the versatility of the GF. Our results show the inextricable relationship between MOI and the SGF, and suggest that under some conditions, the cost of multipartition can be outweighed by its benefits for the rapid tuning of viral gene expression.}, }
@article {pmid32404904, year = {2020}, author = {Pascual-García, A and Bell, T}, title = {Community-level signatures of ecological succession in natural bacterial communities.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2386}, pmid = {32404904}, issn = {2041-1723}, mesh = {Bacteria/classification/genetics/*growth &amp; development ; *Biodiversity ; *Biota ; DNA, Bacterial/genetics ; Ecosystem ; Metagenome/genetics ; Microbiota ; Phylogeny ; Population Dynamics ; RNA, Ribosomal, 16S/*genetics ; Stochastic Processes ; }, abstract = {A central goal in microbial ecology is to simplify the extraordinary biodiversity that inhabits natural environments into ecologically coherent units. We profiled (16S rRNA sequencing) > 700 semi-aquatic bacterial communities while measuring their functional capacity when grown in laboratory conditions. This approach allowed us to investigate the relationship between composition and function excluding confounding environmental factors. Simulated data allowed us to reject the hypothesis that stochastic processes were responsible for community assembly, suggesting that niche effects prevailed. Consistent with this idea we identified six distinct community classes that contained samples collected from distant locations. Structural equation models showed there was a functional signature associated with each community class. We obtained a more mechanistic understanding of the classes using metagenomic predictions (PiCRUST). This approach allowed us to show that the classes contained distinct genetic repertoires reflecting community-level ecological strategies. The ecological strategies resemble the classical distinction between r- and K-strategists, suggesting that bacterial community assembly may be explained by simple ecological mechanisms.}, }
@article {pmid32402266, year = {2020}, author = {Mahú, I and Barateiro, A and Rial-Pensado, E and Martinéz-Sánchez, N and Vaz, SH and Cal, PMSD and Jenkins, B and Rodrigues, T and Cordeiro, C and Costa, MF and Mendes, R and Seixas, E and Pereira, MMA and Kubasova, N and Gres, V and Morris, I and Temporão, C and Olivares, M and Sanz, Y and Koulman, A and Corzana, F and Sebastião, AM and López, M and Bernardes, GJL and Domingos, AI}, title = {Brain-Sparing Sympathofacilitators Mitigate Obesity without Adverse Cardiovascular Effects.}, journal = {Cell metabolism}, volume = {31}, number = {6}, pages = {1120-1135.e7}, doi = {10.1016/j.cmet.2020.04.013}, pmid = {32402266}, issn = {1932-7420}, abstract = {Anti-obesity drugs in the amphetamine (AMPH) class act in the brain to reduce appetite and increase locomotion. They are also characterized by adverse cardiovascular effects with origin that, despite absence of any in vivo evidence, is attributed to a direct sympathomimetic action in the heart. Here, we show that the cardiac side effects of AMPH originate from the brain and can be circumvented by PEGylation (PEGyAMPH) to exclude its central action. PEGyAMPH does not enter the brain and facilitates SNS activity via theβ2-adrenoceptor, protecting mice against obesity by increasing lipolysis and thermogenesis, coupled to higher heat dissipation, which acts as an energy sink to increase energy expenditure without altering food intake or locomotor activity. Thus, we provide proof-of-principle for a novel class of exclusively peripheral anti-obesity sympathofacilitators that are devoid of any cardiovascular and brain-related side effects.}, }
@article {pmid32399630, year = {2020}, author = {Brunel, C and Da Silva, AF and Gros, R}, title = {Environmental Drivers of Microbial Functioning in Mediterranean Forest Soils.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {669-681}, doi = {10.1007/s00248-020-01518-5}, pmid = {32399630}, issn = {1432-184X}, abstract = {Mediterranean forests own distinct characteristics resulting from climate, soil, and vegetation that affect soil microbial communities' assembly and their associated functions. We initiated a multi-scalar analysis of environmental drivers of soil functioning to (1) identify pertinent factorial scales and (2) determine the relative importance of soil, vegetation, and geoclimate influences in shaping soil microbial functions across the French Mediterranean forests. Soil samples (0-15 cm) were collected from 60 forest sites and soil physicochemical and microbiological properties were assessed across different factorial scales i.e., bioclimates, slope exposures, and forest stands. Patterns in microbial catabolic potential (i.e., extracellular enzymes and microbial respiration) and carbon (C) source utilization (i.e., catabolic-level physiological profiling) were partitioned between vegetation cover, soil characteristics, and geoclimate components. Our results reveal that the catabolic potential of soil microbes was strongly influenced by the forest stands and mainly relied on ammonium and nitrate contents. In contrast, variation in C source utilization was mainly explained by vegetation cover. Soil metabolic capacities of microorganisms and resulting C dynamics were largely constrained by climate parameters, which suggests potentially important consequences for soil C storage. Our study revealed diverse structuration patterns between the catabolic potential and the carbon source utilization of soil microbial communities, and gives insights into the underlying mechanisms of soil microbial functioning in Mediterranean forests.}, }
@article {pmid32398103, year = {2020}, author = {Mohr, AE and Jäger, R and Carpenter, KC and Kerksick, CM and Purpura, M and Townsend, JR and West, NP and Black, K and Gleeson, M and Pyne, DB and Wells, SD and Arent, SM and Kreider, RB and Campbell, BI and Bannock, L and Scheiman, J and Wissent, CJ and Pane, M and Kalman, DS and Pugh, JN and Ortega-Santos, CP and Ter Haar, JA and Arciero, PJ and Antonio, J}, title = {The athletic gut microbiota.}, journal = {Journal of the International Society of Sports Nutrition}, volume = {17}, number = {1}, pages = {24}, pmid = {32398103}, issn = {1550-2783}, mesh = {Athletic Performance/*physiology ; *Diet ; Exercise/*physiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Sports Nutritional Physiological Phenomena ; }, abstract = {The microorganisms in the gastrointestinal tract play a significant role in nutrient uptake, vitamin synthesis, energy harvest, inflammatory modulation, and host immune response, collectively contributing to human health. Important factors such as age, birth method, antibiotic use, and diet have been established as formative factors that shape the gut microbiota. Yet, less described is the role that exercise plays, particularly how associated factors and stressors, such as sport/exercise-specific diet, environment, and their interactions, may influence the gut microbiota. In particular, high-level athletes offer remarkable physiology and metabolism (including muscular strength/power, aerobic capacity, energy expenditure, and heat production) compared to sedentary individuals, and provide unique insight in gut microbiota research. In addition, the gut microbiota with its ability to harvest energy, modulate the immune system, and influence gastrointestinal health, likely plays an important role in athlete health, wellbeing, and sports performance. Therefore, understanding the mechanisms in which the gut microbiota could play in the role of influencing athletic performance is of considerable interest to athletes who work to improve their results in competition as well as reduce recovery time during training. Ultimately this research is expected to extend beyond athletics as understanding optimal fitness has applications for overall health and wellness in larger communities. Therefore, the purpose of this narrative review is to summarize current knowledge of the athletic gut microbiota and the factors that shape it. Exercise, associated dietary factors, and the athletic classification promote a more &quot;health-associated&quot; gut microbiota. Such features include a higher abundance of health-promoting bacterial species, increased microbial diversity, functional metabolic capacity, and microbial-associated metabolites, stimulation of bacterial abundance that can modulate mucosal immunity, and improved gastrointestinal barrier function.}, }
@article {pmid32397606, year = {2020}, author = {Colquhoun, C and Duncan, M and Grant, G}, title = {Inflammatory Bowel Diseases: Host-Microbial-Environmental Interactions in Dysbiosis.}, journal = {Diseases (Basel, Switzerland)}, volume = {8}, number = {2}, pages = {}, pmid = {32397606}, issn = {2079-9721}, abstract = {Crohn's Disease (CD) and Ulcerative Colitis (UC) are world-wide health problems in which intestinal dysbiosis or adverse functional changes in the microbiome are causative or exacerbating factors. The reduced abundance and diversity of the microbiome may be a result of a lack of exposure to vital commensal microbes or overexposure to competitive pathobionts during early life. Alternatively, many commensal bacteria may not find a suitable intestinal niche or fail to proliferate or function in a protective/competitive manner if they do colonize. Bacteria express a range of factors, such as fimbriae, flagella, and secretory compounds that enable them to attach to the gut, modulate metabolism, and outcompete other species. However, the host also releases factors, such as secretory IgA, antimicrobial factors, hormones, and mucins, which can prevent or regulate bacterial interactions with the gut or disable the bacterium. The delicate balance between these competing host and bacteria factors dictates whether a bacterium can colonize, proliferate or function in the intestine. Impaired functioning of NOD2 in Paneth cells and disrupted colonic mucus production are exacerbating features of CD and UC, respectively, that contribute to dysbiosis. This review evaluates the roles of these and other the host, bacterial and environmental factors in inflammatory bowel diseases.}, }
@article {pmid32396806, year = {2020}, author = {Herren, CM}, title = {Disruption of cross-feeding interactions by invading taxa can cause invasional meltdown in microbial communities.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1927}, pages = {20192945}, pmid = {32396806}, issn = {1471-2954}, mesh = {Biota ; *Ecosystem ; *Introduced Species ; *Microbiota ; }, abstract = {The strength of biotic interactions within an ecological community affects the susceptibility of the community to invasion by introduced taxa. In microbial communities, cross-feeding is a widespread type of biotic interaction that has the potential to affect community assembly and stability. Yet, there is little understanding of how the presence of cross-feeding within a community affects invasion risk. Here, I develop a metabolite-explicit model where native microbial taxa interact through both cross-feeding and competition for metabolites. I use this model to study how the strength of biotic interactions, especially cross-feeding, influence whether an introduced taxon can join the community. I found that stronger cross-feeding and competition led to much lower invasion risk, as both types of biotic interactions lead to greater metabolite scarcity for the invader. I also evaluated the impact of a successful invader on community composition and structure. The effect of invaders on the native community was greatest at intermediate levels of cross-feeding; at this 'critical' level of cross-feeding, successful invaders generally cause decreased diversity, decreased productivity, greater metabolite availability, and decreased quantities of metabolites exchanged among taxa. Furthermore, these changes resulting from a successful primary invader made communities further susceptible to future invaders. The increase in invasion risk was greatest when the network of metabolite exchange between taxa was minimally redundant. Thus, this model demonstrates a case of invasional meltdown that is mediated by initial invaders disrupting the metabolite exchange networks of the native community.}, }
@article {pmid32394640, year = {2020}, author = {Paula, CCP and Bichuette, ME and Seleghim, MHR}, title = {Nutrient availability in tropical caves influences the dynamics of microbial biomass.}, journal = {MicrobiologyOpen}, volume = {9}, number = {7}, pages = {e1044}, pmid = {32394640}, issn = {2045-8827}, support = {2015/24763-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, abstract = {Few studies have evaluated the trophic level in tropical caves, and none related the microbial biomass dynamics in the immobilization of carbon and nitrogen. Here, four tropical caves of Terra Ronca State Park, Brazil, were studied: Angélica, São Bernardo, Terra Ronca I, and Terra Ronca II caves. Physical, chemical, and microbiological parameters (microbial biomass and respiration) were estimated in the dry and wet seasons. São Bernardo, Terra Ronca I, and Terra Ronca II caves presented higher nitrogen and microbial biomass nitrogen (MBN) values in the wet season than in the dry season. On the other hand, the Angélica cave showed larger amounts of nitrogen and lower MBN values in the dry season. These results indicate that caves can be adjusted in two ecological theories known as &quot;stoichiometric decomposition&quot; and &quot;microbial nitrogen mining&quot;-to the effects of nutrient availability on organic matter decomposition. The caves studied showed different environmental dynamics in relation to organic matter decomposition, which allows them to be considered unique and possess specific characteristics. Microbial biomass dynamics can be an important parameter to evaluate the availability of nutrients and ecological dynamics of the trophic network in subterranean environments.}, }
@article {pmid32393397, year = {2020}, author = {Koh, H and Zhao, N}, title = {A powerful microbial group association test based on the higher criticism analysis for sparse microbial association signals.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {63}, pmid = {32393397}, issn = {2049-2618}, support = {P30 AI094189/AI/NIAID NIH HHS/United States ; U24 OD023382/OD/NIH HHS/United States ; }, abstract = {BACKGROUND: In human microbiome studies, it is crucial to evaluate the association between microbial group (e.g., community or clade) composition and a host phenotype of interest. In response, a number of microbial group association tests have been proposed, which account for the unique features of the microbiome data (e.g., high-dimensionality, compositionality, phylogenetic relationship). These tests generally fall in the class of aggregation tests which amplify the overall group association by combining all the underlying microbial association signals, and, therefore, they are powerful when many microbial species are associated with a given host phenotype (i.e., low sparsity). However, in practice, the microbial association signals can be highly sparse, and this is especially the situation where we have a difficulty to discover the microbial group association.<br><br>METHODS: Here, we introduce a powerful microbial group association test for sparse microbial association signals, namely, microbiome higher criticism analysis (MiHC). MiHC is a data-driven omnibus test taken in a search space spanned by tailoring the higher criticism test to incorporate phylogenetic information and/or modulate sparsity levels and including the Simes test for excessively high sparsity levels. Therefore, MiHC robustly adapts to diverse phylogenetic relevance and sparsity levels.<br><br>RESULTS: Our simulations show that MiHC maintains a high power at different phylogenetic relevance and sparsity levels with correct type I error controls. We also apply MiHC to four real microbiome datasets to test the association between respiratory tract microbiome and smoking status, the association between the infant's gut microbiome and delivery mode, the association between the gut microbiome and type 1 diabetes status, and the association between the gut microbiome and human immunodeficiency virus status.<br><br>CONCLUSIONS: In practice, the true underlying association pattern on the extent of phylogenetic relevance and sparsity is usually unknown. Therefore, MiHC can be a useful analytic tool because of its high adaptivity to diverse phylogenetic relevance and sparsity levels. MiHC can be implemented in the R computing environment using our software package freely available at https://github.com/hk1785/MiHC.}, }
@article {pmid32392181, year = {2020}, author = {He, J and Xu, S and Zhang, B and Xiao, C and Chen, Z and Si, F and Fu, J and Lin, X and Zheng, G and Yu, G and Chen, J}, title = {Gut microbiota and metabolite alterations associated with reduced bone mineral density or bone metabolic indexes in postmenopausal osteoporosis.}, journal = {Aging}, volume = {12}, number = {9}, pages = {8583-8604}, pmid = {32392181}, issn = {1945-4589}, abstract = {Reduced bone mineral density (BMD) is associated with an altered microbiota in senile osteoporosis. However, the relationship among gut microbiota, BMD and bone metabolic indexes remains unknown in postmenopausal osteoporosis. In this study, fecal microbiota profiles for 106 postmenopausal individuals with osteopenia (n=33) or osteoporosis (n=42) or with normal BMD (n=31) were determined. An integrated 16S rRNA gene sequencing and LC-MS-based metabolomics approach was applied to explore the association of estrogen-reduced osteoporosis with the gut microbiota and fecal metabolic phenotype. Adjustments were made using several statistical models for potential confounding variables identified from the literature. The results demonstrated decreased bacterial richness and diversity in postmenopausal osteoporosis. Additionally, showed significant differences in abundance levels among phyla and genera in the gut microbial community were found. Moreover, postmenopausal osteopenia-enriched N-acetylmannosamine correlated negatively with BMD, and distinguishing metabolites were closely associated with gut bacterial variation. Both serum procollagen type I N propeptide (P1NP) and C-terminal telopeptide of type I collagen (CTX-1) correlated positively with osteopenia-enriched Allisonella, Klebsiella and Megasphaera. However, we did not find a significant correlation between bacterial diversity and estrogen. These observations will lead to a better understanding of the relationship between bone homeostasis and the microbiota in postmenopausal osteoporosis.}, }
@article {pmid32391569, year = {2020}, author = {Young, JN and Schmidt, K}, title = {It's what's inside that matters: physiological adaptations of high-latitude marine microalgae to environmental change.}, journal = {The New phytologist}, volume = {227}, number = {5}, pages = {1307-1318}, doi = {10.1111/nph.16648}, pmid = {32391569}, issn = {1469-8137}, support = {//University of Washington: Innovation Award/ ; 1744645//National Science Foundation/ ; 561645//Simons Foundation: Early Career Investigator in Marine Microbial Ecology and Evolution Awards/ ; }, abstract = {Marine microalgae within seawater and sea ice fuel high-latitude ecosystems and drive biogeochemical cycles through the fixation and export of carbon, uptake of nutrients, and production and release of oxygen and organic compounds. High-latitude marine environments are characterized by cold temperatures, dark winters and a strong seasonal cycle. Within this environment a number of diverse and dynamic habitats exist, particularly in association with the formation and melt of sea ice, with distinct microalgal communities that transition with the season. Algal physiology is a crucial component, both responding to the dynamic environment and in turn influencing its immediate physicochemical environment. As high-latitude oceans shift into new climate regimes the analysis of seasonal responses may provide insights into how microalgae will respond to long-term environmental change. This review discusses recent developments in our understanding of how the physiology of high-latitude marine microalgae is regulated over a polar seasonal cycle, with a focus on ice-associated (sympagic) algae. In particular, physiologies that impact larger scale processes will be explored, with an aim to improve our understanding of current and future ecosystems and biogeochemical cycles.}, }
@article {pmid32391139, year = {2019}, author = {Obolski, U and Perez, PN and Villabona-Arenas, CJ and Thézé, J and Faria, NR and Lourenço, J}, title = {MVSE: An R-package that estimates a climate-driven mosquito-borne viral suitability index.}, journal = {Methods in ecology and evolution}, volume = {10}, number = {8}, pages = {1357-1370}, pmid = {32391139}, issn = {2041-210X}, abstract = {Viruses, such as dengue, Zika, yellow fever and chikungunya, depend on mosquitoes for transmission. Their epidemics typically present periodic patterns, linked to the underlying mosquito population dynamics, which are known to be driven by natural climate fluctuations. Understanding how climate dictates the timing and potential of viral transmission is essential for preparedness of public health systems and design of control strategies. While various alternative approaches have been proposed to estimate local transmission potential of such viruses, few open-source, ready to use and freely available software tools exist.We developed the Mosquito-borne Viral Suitability Estimator (MVSE) software package for the R programming environment. MVSE estimates the index P, a novel suitability index based on a climate-driven mathematical expression for the basic reproductive number of mosquito-borne viruses. By accounting for local humidity and temperature, as well as viral, vector and human priors, the index P can be estimated for specific host and viral species in different regions of the globe.We describe the background theory, empirical support and biological interpretation of the index P. Using real-world examples spanning multiple epidemiological contexts, we further demonstrate MVSE's basic functionality, research and educational potentials.}, }
@article {pmid32390961, year = {2020}, author = {Samad, MS and Lee, HJ and Cerbin, S and Meima-Franke, M and Bodelier, PLE}, title = {Niche Differentiation of Host-Associated Pelagic Microbes and Their Potential Contribution to Biogeochemical Cycling in Artificially Warmed Lakes.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {582}, pmid = {32390961}, issn = {1664-302X}, abstract = {It has been proposed that zooplankton-associated microbes provide numerous beneficial services to their &quot;host&quot;. However, there is still a lack of understanding concerning the effect of temperature on the zooplankton microbiome. Furthermore, it is unclear to what extent the zooplankton microbiome differs from free-living and particle-associated (PA) microbes. Here, we explicitly addressed these issues by investigating (1) the differences in free-living, PA, and zooplankton associated microbes and (2) the impact of temperature on these microbes in the water column of a series of lakes artificially warmed by two power plants. High-throughput amplicon sequencing of the 16S rRNA gene showed that diversity and composition of the bacterial community associated to zooplankton, PA, and bacterioplankton varied significantly from one another, grouping in different clusters indicating niche differentiation of pelagic microbes. From the abiotic parameters measured, temperature significantly affected the diversity and composition of all analyzed microbiomes. Two phyla (e.g., Proteobacteria and Bacteroidetes) dominated in zooplankton microbiomes whereas Actinobacteria was the dominant phylum in the bacterioplankton. The microbial species richness and diversity was lower in zooplankton compared to bacterioplankton and PA. Surprisingly, genera of methane-oxidizing bacteria, methylotrophs and nitrifiers (e.g., Nitrobacter) significantly associated with the microbiome of zooplankton and PA. Our study clearly demonstrates niche differentiation of pelagic microbes and their potential link to biogeochemical cycling in freshwater systems.}, }
@article {pmid32389289, year = {2020}, author = {Araújo, CAS and Ferreira, PC and Pupin, B and Dias, LP and Avalos, J and Edwards, J and Hallsworth, JE and Rangel, DEN}, title = {Osmotolerance as a determinant of microbial ecology: A study of phylogenetically diverse fungi.}, journal = {Fungal biology}, volume = {124}, number = {5}, pages = {273-288}, doi = {10.1016/j.funbio.2019.09.001}, pmid = {32389289}, issn = {1878-6146}, abstract = {Osmotic stress induced by high solute concentration can prevent fungal metabolism and growth due to alterations in properties of the cytosol, changes in turgor, and the energy required to synthesize and retain compatible solutes. We used germination to quantify tolerance/sensitivity to the osmolyte KCl (0.1-4.5 M, in 0.1 M increments) for 71 strains (40 species) of ecologically diverse fungi. These include 11 saprotrophic species (17 strains, including two xerophilic species), five mycoparasitic species (five strains), six plant-pathogenic species (13 strains), and 19 entomopathogenic species (36 strains). A dendrogram obtained from cluster analyses, based on KCl inhibitory concentrations 50 % and 90 % calculated by Probit Analysis, revealed three groups of fungal isolates accordingly to their osmotolerance. The most-osmotolerant group (Group 3) contained the majority of saprotrophic fungi, and Aspergillus niger (F19) was the most tolerant. The highly xerophilic Aspergillus montevidense and Aspergillus pseudoglaucus were the second- and third-most tolerant species, respectively. All Aspergillus and Cladosporium species belonged to Group 3, followed by the entomopathogens Colletotrichum fioriniae, Simplicillium lanosoniveum, and Trichothecium roseum. Group 2 exhibited a moderate osmotolerance, and included plant-pathogens such as Colletotrichum and Fusarium, mycoparasites such as Clonostachys spp, some saprotrophs such as Mucor and Penicillium spp., and some entomopathogens such as Isaria, Lecanicillium, Mariannaea, Simplicillium, and Torrubiella. Group 1 contained the osmo-sensitive strains: the rest of the entomopathogens and the mycoparasitic Gliocladium and Trichoderma. Although stress tolerance did not correlate with their primary ecological niche, classification of these 71 fungal strains was more closely aligned with their ecology than with their phylogenetic relatedness. We discuss the implications for both microbial ecology and fungal taxonomy.}, }
@article {pmid32388577, year = {2020}, author = {Seward, J and Carson, MA and Lamit, LJ and Basiliko, N and Yavitt, JB and Lilleskov, E and Schadt, CW and Smith, DS and Mclaughlin, J and Mykytczuk, N and Willims-Johnson, S and Roulet, N and Moore, T and Harris, L and Bräuer, S}, title = {Peatland Microbial Community Composition Is Driven by a Natural Climate Gradient.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {593-602}, doi = {10.1007/s00248-020-01510-z}, pmid = {32388577}, issn = {1432-184X}, abstract = {Peatlands are important players in climate change-biosphere feedbacks via long-term net carbon (C) accumulation in soil organic matter and as potential net C sources including the potent greenhouse gas methane (CH4). Interactions of climate, site-hydrology, plant community, and groundwater chemical factors influence peatland development and functioning, including C dioxide (CO2) and CH4 fluxes, but the role of microbial community composition is not well understood. To assess microbial functional and taxonomic dissimilarities, we used high throughput sequencing of the small subunit ribosomal DNA (SSU rDNA) to determine bacterial and archaeal community composition in soils from twenty North American peatlands. Targeted DNA metabarcoding showed that although Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla on average, intermediate and rich fens hosted greater diversity and taxonomic richness, as well as an array of candidate phyla when compared with acidic and nutrient-poor poor fens and bogs. Moreover, pH was revealed to be the strongest predictor of microbial community structure across sites. Predictive metagenome content (PICRUSt) showed increases in specific genes, such as purine/pyrimidine and amino-acid metabolism in mid-latitude peatlands from 38 to 45° N, suggesting a shift toward utilization of microbial biomass over utilization of initial plant biomass in these microbial communities. Overall, there appears to be noticeable differences in community structure between peatland classes, as well as differences in microbial metabolic activity between latitudes. These findings are in line with a predicted increase in the decomposition and accelerated C turnover, and suggest that peatlands north of 37° latitude may be particularly vulnerable to climate change.}, }
@article {pmid32388576, year = {2020}, author = {Gnanasekaran, G}, title = {Correction to: Disappearance of Quorum Sensing in Burkholderia Glumae During Experimental Evolution.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {739}, doi = {10.1007/s00248-020-01516-7}, pmid = {32388576}, issn = {1432-184X}, abstract = {Following the publication of this article [ 1 ], authors Jae Yun Lim and Ingyu Hwang have stated that they were not aware of, nor were they involved in the drafting, submission, or revision of this manuscript.}, }
@article {pmid32385877, year = {2020}, author = {Loos, BG and Van Dyke, TE}, title = {The role of inflammation and genetics in periodontal disease.}, journal = {Periodontology 2000}, volume = {83}, number = {1}, pages = {26-39}, pmid = {32385877}, issn = {1600-0757}, mesh = {Genome-Wide Association Study ; *Gingivitis ; Humans ; Inflammation ; *Periodontal Diseases ; *Periodontitis ; }, abstract = {Periodontitis is a complex disease: (a) various causative factors play a role simultaneously and interact with each other; and (b) the disease is episodic in nature, and bursts of disease activity can be recognized, ie, the disease develops and cycles in a nonlinear fashion. We recognize that various causative factors determine the immune blueprint and, consequently, the immune fitness of a subject. Normally, the host lives in a state of homeostasis or symbiosis with the oral microbiome; however, disturbances in homeostatic balance can occur, because of an aberrant host response (inherited and/or acquired during life). This imbalance results from hyper- or hyporesponsiveness and/or lack of sufficient resolution of inflammation, which in turn is responsible for much of the disease destruction seen in periodontitis. The control of this destruction by anti-inflammatory processes and proresolution processes limits the destruction to the tissues surrounding the teeth. The local inflammatory processes can also become systemic, which in turn affect organs such as the heart. Gingival inflammation also elicits changes in the ecology of the subgingival environment providing optimal conditions for the outgrowth of gram-negative, anaerobic species, which become pathobionts and can propagate periodontal inflammation and can further negatively impact immune fitness. The factors that determine immune fitness are often the same factors that determine the response to the resident biofilm, and are clustered as follows: (a) genetic and epigenetic factors; (b) lifestyle factors, such as smoking, diet, and psychosocial conditions; (c) comorbidities, such as diabetes; and (d) local and dental factors, as well as randomly determined factors (stochasticity). Of critical importance are the pathobionts in a dysbiotic biofilm that drive the viscious cycle. Focusing on genetic factors, currently variants in at least 65 genes have been suggested as being associated with periodontitis based on genome-wide association studies and candidate gene case control studies. These studies have found pleiotropy between periodontitis and cardiovascular diseases. Most of these studies point to potential pathways in the pathogenesis of periodontal disease. Also, most contribute to a small portion of the total risk profile of periodontitis, often limited to specific racial and ethnic groups. To date, 4 genetic loci are shared between atherosclerotic cardiovascular diseases and periodontitis, ie, CDKN2B-AS1(ANRIL), a conserved noncoding element within CAMTA1 upstream of VAMP3, PLG, and a haplotype block at the VAMP8 locus. The shared genes suggest that periodontitis is not causally related to atherosclerotic diseases, but rather both conditions are sequelae of similar (the same?) aberrant inflammatory pathways. In addition to variations in genomic sequences, epigenetic modifications of DNA can affect the genetic blueprint of the host responses. This emerging field will yield new valuable information about susceptibility to periodontitis and subsequent persisting inflammatory reactions in periodontitis. Further studies are required to verify and expand our knowledge base before final cause and effect conclusions about the role of inflammation and genetic factors in periodontitis can be made.}, }
@article {pmid32385616, year = {2020}, author = {Cockburn, CF and Gregory, BRB and Nasser, NA and Patterson, RT}, title = {Intra-Lake Arcellinida (Testate Lobose Amoebae) Response to Winter De-icing Contamination in an Eastern Canada Road-Side &quot;Salt Belt&quot; Lake.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {366-383}, doi = {10.1007/s00248-020-01513-w}, pmid = {32385616}, issn = {1432-184X}, abstract = {Salt contamination of lakes, due to the application of winter de-icing salts on roads, presents a significant environmental challenge in the &quot;salt belt&quot; region of eastern North America. The research reported here presents the first deployment of a previously published proxy tool based on Arcellinida (testate lobose amoebae) for monitoring road salt contamination. The research was conducted at Silver Lake in Eastern Ontario, a 4-km-long lake with the heavily traveled Trans-Canada Highway (HWY 7) transiting the entire southern shore. The lake showed elevated conductivity (297-310 μS/cm) and sub-brackish conditions (0.14-0.15 ppt). Sodium levels were also elevated near the roadside (median Na = 1020 ppm). Cluster analysis and nonmetric multidimensional scaling results revealed four distinct Arcellinida assemblages: &quot;Stressed Cool Water Assemblage (SCWA),&quot; &quot;Deep Cold Water Assemblage (DCWA),&quot; both from below the 8-m thermocline, and the shallower water &quot;Shallow Water Assemblage 1 (SWA-1)&quot; and &quot;Shallow Water Assemblage 2 (SWA-2)&quot;. Redundancy analysis showed a minor response of Arcellinida to road salt contamination in shallower areas of the lake, with confounding variables significantly impacting assemblage distribution, particularly beneath the thermocline (e.g., water temperature, water depth, sediment runoff from catchment [Ti], sediment geochemistry [Ca, S]). The results of this study indicate that the trophic structure of the lake has to date only been modestly impacted by the cumulative nature of road salt contamination. Nonetheless, the Silver Lake results should be considered of concern and warrant continued arcellinidan biomonitoring to gauge the ongoing and long-term effects of road salt on its ecosystem.}, }
@article {pmid32385615, year = {2020}, author = {Vences, A and Abushattal, S and Matanza, XM and Dubert, J and Uzun, E and Ogut, H and Osorio, CR}, title = {Highly Transferable pAQU-Related Plasmids Encoding Multidrug Resistance Are Widespread in the Human and Fish Pathogen Photobacterium damselae subsp. damselae in Aquaculture Areas in the Black Sea.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {507-518}, doi = {10.1007/s00248-020-01519-4}, pmid = {32385615}, issn = {1432-184X}, support = {AGL2016-79738-R//Agencia Estatal de Investigación/ ; AGL2016-79738-R//FEDER/ ; ED431C 2018/18//Secretaria Xeral de Investigación e Desenvolvemento, Xunta de Galicia/ ; }, abstract = {The marine bacterium Photobacterium damselae subsp. damselae is a pathogen that causes disease in diverse marine animals, and is also a serious opportunistic human pathogen that can cause fatal infections. Strains of this pathogen isolated from diseased European sea bass in aquaculture facilities in the Turkish coast of the Black Sea were found to exhibit reduced sensitivity to multiple antimicrobials. Selected representative strains were subjected to complete genome sequencing and plasmid characterization. It was found that multidrug resistant (MDR) isolates harboured large conjugative plasmids sharing part of their sequence backbone with pAQU-group plasmids, hitherto reported exclusively in China and Japan. Four new pAQU-group versions of plasmids were identified in the present study, containing distinct combinations of the resistance determinants tetB, floR, sul2, qnrVC, dfrA and strAB. Conjugative transfer of pPHDD2-OG2, a representative plasmid of 170,998 bp, occurred at high frequencies (2.2 × 10-2 transconjugants per donor cell), to E. coli and to pathogenic P. damselae subsp. damselae and subsp. piscicida strains. Upon transfer, pPHDD2-OG2 conferred reduced susceptibility to a number of antimicrobials to the recipient strains. Comparative genomics analysis of host strains suggested that these MDR plasmids of the pAQU-group were acquired by different genetic lineages of Pdd. This study provides evidence that P. damselae subsp. damselae isolated from diseased fish constitute a reservoir for conjugative MDR pAQU-group plasmids in the Mediterranean basin, and have the potential to spread to diverse bacterial species.}, }
@article {pmid32385111, year = {2020}, author = {Glaub, A and Huptas, C and Neuhaus, K and Ardern, Z}, title = {Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data.}, journal = {The Journal of biological chemistry}, volume = {295}, number = {27}, pages = {8999-9011}, pmid = {32385111}, issn = {1083-351X}, abstract = {Ribosome profiling (RIBO-Seq) has improved our understanding of bacterial translation, including finding many unannotated genes. However, protocols for RIBO-Seq and corresponding data analysis are not yet standardized. Here, we analyzed 48 RIBO-Seq samples from nine studies of Escherichia coli K12 grown in lysogeny broth medium and particularly focused on the size-selection step. We show that for conventional expression analysis, a size range between 22 and 30 nucleotides is sufficient to obtain protein-coding fragments, which has the advantage of removing many unwanted rRNA and tRNA reads. More specific analyses may require longer reads and a corresponding improvement in rRNA/tRNA depletion. There is no consensus about the appropriate sequencing depth for RIBO-Seq experiments in prokaryotes, and studies vary significantly in total read number. Our analysis suggests that 20 million reads that are not mapping to rRNA/tRNA are required for global detection of translated annotated genes. We also highlight the influence of drug-induced ribosome stalling, which causes bias at translation start sites. The resulting accumulation of reads at the start site may be especially useful for detecting weakly expressed genes. As different methods suit different questions, it may not be possible to produce a &quot;one-size-fits-all&quot; ribosome profiling data set. Therefore, experiments should be carefully designed in light of the scientific questions of interest. We propose some basic characteristics that should be reported with any new RIBO-Seq data sets. Careful attention to the factors discussed should improve prokaryotic gene detection and the comparability of ribosome profiling data sets.}, }
@article {pmid32384669, year = {2020}, author = {Kazou, M and Tzamourani, A and Panagou, EZ and Tsakalidou, E}, title = {Unraveling the Microbiota of Natural Black cv. Kalamata Fermented Olives through 16S and ITS Metataxonomic Analysis.}, journal = {Microorganisms}, volume = {8}, number = {5}, pages = {}, pmid = {32384669}, issn = {2076-2607}, support = {2018ΣΕ01300000//Greek national funds through the Public Investments Program (PIP) of General Secretariat for Research &amp; Technology (GSRT), under the Emblematic Action &quot;The Olive Road&quot;/ ; }, abstract = {Kalamata natural black olives are one of the most economically important Greek varieties. The microbial ecology of table olives is highly influenced by the co-existence of bacteria and yeasts/fungi, as well as the physicochemical parameters throughout the fermentation. Therefore, the aim of this study was the identification of bacterial and yeast/fungal microbiota of both olives and brines obtained from 29 cv. Kalamata olive samples industrially fermented in the two main producing geographical regions of Greece, namely Aitoloakarnania and Messinia/Lakonia. The potential microbial biogeography association between certain taxa and geographical area was also assessed. The dominant bacterial family identified in olive and brine samples from both regions was Lactobacillaceae, presenting, however, higher average abundances in the samples from Aitoloakarnania compared to Messinia/Lakonia. At the genus level, Lactobacillus, Celerinatantimonas, Propionibacterium and Pseudomonas were the most abundant. In addition, the yeasts/fungal communities were less diverse compared to those of bacteria, with Pichiaceae being the dominant family and Pichia, Ogataea, and Saccharomyces being the most abundant genera. To the best of our knowledge, this is the first report on the microbiota of both olives and brines of cv. Kalamata black olives fermented on an industrial scale between two geographical regions of Greece using metagenomics analysis.}, }
@article {pmid32382073, year = {2020}, author = {Floudas, D and Bentzer, J and Ahrén, D and Johansson, T and Persson, P and Tunlid, A}, title = {Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi.}, journal = {The ISME journal}, volume = {14}, number = {8}, pages = {2046-2059}, pmid = {32382073}, issn = {1751-7370}, support = {2013.0073//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; P4151, A.Tunlid_16_01//Science for Life Laboratory (SciLifeLab)/ ; }, abstract = {Litter decomposing Agaricales play key role in terrestrial carbon cycling, but little is known about their decomposition mechanisms. We assembled datasets of 42 gene families involved in plant-cell-wall decomposition from seven newly sequenced litter decomposers and 35 other Agaricomycotina members, mostly white-rot and brown-rot species. Using sequence similarity and phylogenetics, we split the families into phylogroups and compared their gene composition across nutritional strategies. Subsequently, we used Raman spectroscopy to examine the ability of litter decomposers, white-rot fungi, and brown-rot fungi to decompose crystalline cellulose. Both litter decomposers and white-rot fungi share the enzymatic cellulose decomposition, whereas brown-rot fungi possess a distinct mechanism that disrupts cellulose crystallinity. However, litter decomposers and white-rot fungi differ with respect to hemicellulose and lignin degradation phylogroups, suggesting adaptation of the former group to the litter environment. Litter decomposers show high phylogroup diversity, which is indicative of high functional versatility within the group, whereas a set of white-rot species shows adaptation to bulk-wood decomposition. In both groups, we detected species that have unique characteristics associated with hitherto unknown adaptations to diverse wood and litter substrates. Our results suggest that the terms white-rot fungi and litter decomposers mask a much larger functional diversity.}, }
@article {pmid32379897, year = {2020}, author = {Hicks, LC and Leizeaga, A and Rousk, K and Michelsen, A and Rousk, J}, title = {Simulated rhizosphere deposits induce microbial N-mining that may accelerate shrubification in the subarctic.}, journal = {Ecology}, volume = {}, number = {}, pages = {e03094}, doi = {10.1002/ecy.3094}, pmid = {32379897}, issn = {1939-9170}, support = {20150561//The Crafoord Foundation/ ; 2018-01315//The Swedish Research Council Formas/ ; KAW 2017.0171//The Knut and Alice Wallenberg Foundation/ ; CTS16: 385//Carl Tryggers Foundation/ ; }, abstract = {Climate change is exposing high-latitude systems to warming and a shift towards more shrub-dominated plant communities, resulting in increased leaf-litter inputs at the soil surface, and more labile root-derived organic matter (OM) input in the soil profile. Labile OM can stimulate the mineralization of soil organic matter (SOM); a phenomenon termed &quot;priming.&quot; In N-poor subarctic soils, it is hypothesized that microorganisms may &quot;prime&quot; SOM in order to acquire N (microbial N-mining). Increased leaf-litter inputs with a high C/N ratio might further exacerbate microbial N demand, and increase the susceptibility of N-poor soils to N-mining. We investigated the N-control of SOM mineralization by amending soils from climate change-simulation treatments in the subarctic (+1.1°C warming, birch litter addition, willow litter addition, and fungal sporocarp addition) with labile OM either in the form of glucose (labile C; equivalent to 400 µg C/g fresh [fwt] soil) or alanine (labile C + N; equivalent to 400 µg C and 157 µg N/g fwt soil), to simulate rhizosphere inputs. Surprisingly, we found that despite 5 yr of simulated climate change treatments, there were no significant effects of the field-treatments on microbial process rates, community structure or responses to labile OM. Glucose primed the mineralization of both C and N from SOM, but gross mineralization of N was stimulated more than that of C, suggesting that microbial SOM use increased in magnitude and shifted to components richer in N (i.e., selective microbial N-mining). The addition of alanine also resulted in priming of both C and N mineralization, but the N mineralization stimulated by alanine was greater than that stimulated by glucose, indicating strong N-mining even when a source of labile OM including N was supplied. Microbial carbon use efficiency was reduced in response to both labile OM inputs. Overall, these findings suggest that shrub expansion could fundamentally alter biogeochemical cycling in the subarctic, yielding more N available for plant uptake in these N-limited soils, thus driving positive plant-soil feedbacks.}, }
@article {pmid32377220, year = {2020}, author = {Masteling, R and Voorhoeve, L and IJsselmuiden, J and Dini-Andreote, F and de Boer, W and Raaijmakers, JM}, title = {DiSCount: computer vision for automated quantification of Striga seed germination.}, journal = {Plant methods}, volume = {16}, number = {}, pages = {60}, pmid = {32377220}, issn = {1746-4811}, abstract = {Background: Plant parasitic weeds belonging to the genus Striga are a major threat for food production in Sub-Saharan Africa and Southeast Asia. The parasite's life cycle starts with the induction of seed germination by host plant-derived signals, followed by parasite attachment, infection, outgrowth, flowering, reproduction, seed set and dispersal. Given the small seed size of the parasite (< 200 μm), quantification of the impact of new control measures that interfere with seed germination relies on manual, labour-intensive counting of seed batches under the microscope. Hence, there is a need for high-throughput assays that allow for large-scale screening of compounds or microorganisms that adversely affect Striga seed germination.<br><br>Results: Here, we introduce DiSCount (Digital Striga Counter): a computer vision tool for automated quantification of total and germinated Striga seed numbers in standard glass fibre filter assays. We developed the software using a machine learning approach trained with a dataset of 98 manually annotated images. Then, we validated and tested the model against a total dataset of 188 manually counted images. The results showed that DiSCount has an average error of 3.38 percentage points per image compared to the manually counted dataset. Most importantly, DiSCount achieves a 100 to 3000-fold speed increase in image analysis when compared to manual analysis, with an inference time of approximately 3 s per image on a single CPU and 0.1 s on a GPU.<br><br>Conclusions: DiSCount is accurate and efficient in quantifying total and germinated Striga seeds in a standardized germination assay. This automated computer vision tool enables for high-throughput, large-scale screening of chemical compound libraries and biological control agents of this devastating parasitic weed. The complete software and manual are hosted at https://gitlab.com/lodewijk-track32/discount_paper and the archived version is available at Zenodo with the DOI 10.5281/zenodo.3627138. The dataset used for testing is available at Zenodo with the DOI 10.5281/zenodo.3403956.}, }
@article {pmid32375874, year = {2020}, author = {Rifkin, RF and Vikram, S and Ramond, JB and Rey-Iglesia, A and Brand, TB and Porraz, G and Val, A and Hall, G and Woodborne, S and Le Bailly, M and Potgieter, M and Underdown, SJ and Koopman, JE and Cowan, DA and Van de Peer, Y and Willerslev, E and Hansen, AJ}, title = {Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the 'ancestral' sub-Saharan African intestinal microbiome.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {62}, pmid = {32375874}, issn = {2049-2618}, abstract = {BACKGROUND: The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen.<br><br>METHODS: Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM.<br><br>RESULTS: Our results indicate that the distal IM of the Neolithic 'Middle Iron Age' (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Ötzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to 'Western' diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants.<br><br>CONCLUSIONS: Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000 years ago. Video Abtract.}, }
@article {pmid32373631, year = {2020}, author = {Zannoni, A and Pietra, M and Gaspardo, A and Accorsi, PA and Barone, M and Turroni, S and Laghi, L and Zhu, C and Brigidi, P and Forni, M}, title = {Non-invasive Assessment of Fecal Stress Biomarkers in Hunting Dogs During Exercise and at Rest.}, journal = {Frontiers in veterinary science}, volume = {7}, number = {}, pages = {126}, pmid = {32373631}, issn = {2297-1769}, abstract = {Intense exercise causes to organisms to have oxidative stress and inflammation at the gastrointestinal (GI) level. The reduction in intestinal blood flow and the exercise-linked thermal damage to the intestinal mucosa can cause intestinal barrier disruption, followed by an inflammatory response. Furthermore, the adaptation to exercise may affect the gut microbiota and the metabolome of the biofluids. The aim of the present research was to evaluate the presence of a GI derangement in hunting dogs through a non-invasive sampling as a consequence of a period of intense exercise in comparison with samples collected at rest. The study included nine dogs that underwent the same training regime for hunting wild boar. In order to counterbalance physiological variations, multiple-day replicates were collected and pooled at each experimental point for each dog. The samples were collected immediately at rest before the training (T0), after 60 days of training (T1), after 60 days of hunting wild boar (T2), and finally, at 60 days of rest after hunting (T3). A number of potential stress markers were evaluated: fecal cortisol metabolites (FCMs) as a major indicator of altered physiological states, immunoglobulin A (IgA) as an indicator of intestinal immune protection, and total antioxidant activity [total antioxidant capacity (TAC)]. Since stool samples contain exfoliated cells, we investigated also the presence of some transcripts involved in GI permeability [occludin (OCLN), protease-activated receptor-2 (PAR-2)] and in the inflammatory mechanism [interleukin (IL)-8, IL-6, IL-1b, tumor necrosis factor alpha (TNFα), calprotectin (CALP), heme oxygenase-1 (HO-1)]. Finally, the metabolome and the microbiota profiles were analyzed. No variation in FCM and IgA content and no differences in OCLN and CALP gene expression between rest and training were observed. On the contrary, an increase in PAR-2 and HO-1 transcripts, a reduction in total antioxidant activity, and a different profile of microbiota and metabolomics data were observed. Collectively, the data in the present study indicated that physical exercise in our model could be considered a mild stressor stimulus.}, }
@article {pmid32373155, year = {2020}, author = {Coenen, AR and Hu, SK and Luo, E and Muratore, D and Weitz, JS}, title = {A Primer for Microbiome Time-Series Analysis.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {310}, pmid = {32373155}, issn = {1664-8021}, abstract = {Time-series can provide critical insights into the structure and function of microbial communities. The analysis of temporal data warrants statistical considerations, distinct from comparative microbiome studies, to address ecological questions. This primer identifies unique challenges and approaches for analyzing microbiome time-series. In doing so, we focus on (1) identifying compositionally similar samples, (2) inferring putative interactions among populations, and (3) detecting periodic signals. We connect theory, code and data via a series of hands-on modules with a motivating biological question centered on marine microbial ecology. The topics of the modules include characterizing shifts in community structure and activity, identifying expression levels with a diel periodic signal, and identifying putative interactions within a complex community. Modules are presented as self-contained, open-access, interactive tutorials in R and Matlab. Throughout, we highlight statistical considerations for dealing with autocorrelated and compositional data, with an eye to improving the robustness of inferences from microbiome time-series. In doing so, we hope that this primer helps to broaden the use of time-series analytic methods within the microbial ecology research community.}, }
@article {pmid32371471, year = {2020}, author = {Bezuidt, OKI and Lebre, PH and Pierneef, R and León-Sobrino, C and Adriaenssens, EM and Cowan, DA and Van de Peer, Y and Makhalanyane, TP}, title = {Phages Actively Challenge Niche Communities in Antarctic Soils.}, journal = {mSystems}, volume = {5}, number = {3}, pages = {}, pmid = {32371471}, issn = {2379-5077}, abstract = {By modulating the structure, diversity, and trophic outputs of microbial communities, phages play crucial roles in many biomes. In oligotrophic polar deserts, the effects of katabatic winds, constrained nutrients, and low water availability are known to limit microbial activity. Although phages may substantially govern trophic interactions in cold deserts, relatively little is known regarding the precise ecological mechanisms. Here, we provide the first evidence of widespread antiphage innate immunity in Antarctic environments using metagenomic sequence data from hypolith communities as model systems. In particular, immunity systems such as DISARM and BREX are shown to be dominant systems in these communities. Additionally, we show a direct correlation between the CRISPR-Cas adaptive immunity and the metavirome of hypolith communities, suggesting the existence of dynamic host-phage interactions. In addition to providing the first exploration of immune systems in cold deserts, our results suggest that phages actively challenge niche communities in Antarctic polar deserts. We provide evidence suggesting that the regulatory role played by phages in this system is an important determinant of bacterial host interactions in this environment.IMPORTANCE In Antarctic environments, the combination of both abiotic and biotic stressors results in simple trophic levels dominated by microbiomes. Although the past two decades have revealed substantial insights regarding the diversity and structure of microbiomes, we lack mechanistic insights regarding community interactions and how phages may affect these. By providing the first evidence of widespread antiphage innate immunity, we shed light on phage-host dynamics in Antarctic niche communities. Our analyses reveal several antiphage defense systems, including DISARM and BREX, which appear to dominate in cold desert niche communities. In contrast, our analyses revealed that genes which encode antiphage adaptive immunity were underrepresented in these communities, suggesting lower infection frequencies in cold edaphic environments. We propose that by actively challenging niche communities, phages play crucial roles in the diversification of Antarctic communities.}, }
@article {pmid32367214, year = {2020}, author = {Muñoz-Leal, S and Ramirez, DG and Luz, HR and Faccini, JLH and Labruna, MB}, title = {&quot;Candidatus Borrelia ibitipoquensis,&quot; a Borrelia valaisiana-Related Genospecies Characterized from Ixodes paranaensis in Brazil.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {682-689}, doi = {10.1007/s00248-020-01512-x}, pmid = {32367214}, issn = {1432-184X}, support = {150961/2017-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 2018/02521-1 and 2019/17960-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {Borrelia burgdorferi sensu lato (Bbsl) spirochetes include the agents of Lyme borreliosis in temperate regions of the Northern Hemisphere, and merge their transmission cycles mainly with ticks of the Ixodes ricinus complex. Twenty genospecies compose Bbsl currently, and with the exception of Borrelia chilensis, and Borrelia garinii, all have been described only for North America, Europe, North Africa, and Asia. Here, we collected specimens of Ixodes paranaensis, a tick associated with swifts in a Brazilian natural park from the state of Minas Gerais, and performed a molecular characterization of 11 borrelial genes. Based on comparisons of inter and intraspecific genetic divergences, and Bayesian phylogenetic trees inferred for 16S rRNA, flaB, p66, and concatenated clpA, clpX, pepX, pyrG, recG, nifS rlpB, and uvrA genes, we demonstrate the occurrence of a new genospecies of Bbsl. &quot;Candidatus Borrelia ibitipoquensis&quot; Ip37 is closely related to Borrelia sp. Am501, and Borrelia valaisiana, a spirochete transmitted by ticks of the I. ricinus complex in Eurasia that uses birds as reservoirs. In a