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Microbiome Jun 2021Gut microbiomes, such as the rumen, greatly influence host nutrition due to their feed energy-harvesting capacity. We investigated temporal ecological interactions...
BACKGROUND
Gut microbiomes, such as the rumen, greatly influence host nutrition due to their feed energy-harvesting capacity. We investigated temporal ecological interactions facilitating energy harvesting at the fresh perennial ryegrass (PRG)-biofilm interface in the rumen using an in sacco approach and prokaryotic metatranscriptomic profiling.
RESULTS
Network analysis identified two distinct sub-microbiomes primarily representing primary (≤ 4 h) and secondary (≥ 4 h) colonisation phases and the most transcriptionally active bacterial families (i.e Fibrobacteriaceae, Selemondaceae and Methanobacteriaceae) did not interact with either sub-microbiome, indicating non-cooperative behaviour. Conversely, Prevotellaceae had most transcriptional activity within the primary sub-microbiome (focussed on protein metabolism) and Lachnospiraceae within the secondary sub-microbiome (focussed on carbohydrate degradation). Putative keystone taxa, with low transcriptional activity, were identified within both sub-microbiomes, highlighting the important synergistic role of minor bacterial families; however, we hypothesise that they may be 'cheating' in order to capitalise on the energy-harvesting capacity of other microbes. In terms of chemical cues underlying transition from primary to secondary colonisation phases, we suggest that AI-2-based quorum sensing plays a role, based on LuxS gene expression data, coupled with changes in PRG chemistry.
CONCLUSIONS
In summary, we show that fresh PRG-attached prokaryotes are resilient and adapt quickly to changing niches. This study provides the first major insight into the complex temporal ecological interactions occurring at the plant-biofilm interface within the rumen. The study also provides valuable insights into potential plant breeding strategies for development of the utopian plant, allowing optimal sustainable production of ruminants. Video Abstract.
Topics: Animals; Gastrointestinal Microbiome; Humans; Lolium; Microbiota; Plant Breeding; Rumen
PubMed: 34154659
DOI: 10.1186/s40168-021-01087-w -
Nature Communications Jun 2021Most archaea divide by binary fission using an FtsZ-based system similar to that of bacteria, but they lack many of the divisome components described in model bacterial...
Most archaea divide by binary fission using an FtsZ-based system similar to that of bacteria, but they lack many of the divisome components described in model bacterial organisms. Notably, among the multiple factors that tether FtsZ to the membrane during bacterial cell constriction, archaea only possess SepF-like homologs. Here, we combine structural, cellular, and evolutionary analyses to demonstrate that SepF is the FtsZ anchor in the human-associated archaeon Methanobrevibacter smithii. 3D super-resolution microscopy and quantitative analysis of immunolabeled cells show that SepF transiently co-localizes with FtsZ at the septum and possibly primes the future division plane. M. smithii SepF binds to membranes and to FtsZ, inducing filament bundling. High-resolution crystal structures of archaeal SepF alone and in complex with the FtsZ C-terminal domain (FtsZ) reveal that SepF forms a dimer with a homodimerization interface driving a binding mode that is different from that previously reported in bacteria. Phylogenetic analyses of SepF and FtsZ from bacteria and archaea indicate that the two proteins may date back to the Last Universal Common Ancestor (LUCA), and we speculate that the archaeal mode of SepF/FtsZ interaction might reflect an ancestral feature. Our results provide insights into the mechanisms of archaeal cell division and pave the way for a better understanding of the processes underlying the divide between the two prokaryotic domains.
Topics: Archaeal Proteins; Bacterial Proteins; Cell Cycle; Cell Division; Conserved Sequence; Crystallography, X-Ray; Evolution, Molecular; Methanobrevibacter; Microscopy, Electron, Transmission; Models, Molecular; Phylogeny; Protein Binding; Protein Interaction Domains and Motifs; Protein Structure, Quaternary; Recombinant Proteins
PubMed: 34088904
DOI: 10.1038/s41467-021-23099-8 -
Environmental Pollution (Barking, Essex... Sep 2021Bacteria and archaea (prokaryotes) are vital components for maintaining healthy function of groundwater ecosystems. The prokaryotic community composition and associated...
Bacteria and archaea (prokaryotes) are vital components for maintaining healthy function of groundwater ecosystems. The prokaryotic community composition and associated putative functional processes were examined in a shallow sandy aquifer in a wet-dry tropical environment. The aquifer had a contaminated gradient of saline mine-water, which primarily consisted of elevated magnesium (Mg) and sulfate (SO), although other major ions and trace metals were also present. Groundwaters were sampled from piezometers, approximately 2 m in depth, located in the creek channel upstream and downstream of the mine-water influence. Sampling occurred during the dry-season when only subsurface water flow was present. Next generation sequencing was used to analyse the prokaryote assemblages using 16S rDNA and metabolic functions were predicted with FAPROTAX. Significant changes in community composition and functional processes were observed with exposure to mine-waters. Communities in the exposed sites had significantly lower relative abundance of methanotrophs such as Methylococcaceae and methanogens (Methanobacteriaceae), but higher abundance in Nitrososphaeraceae, associated with nitrification, indicating potentially important changes in the biogeochemistry of the exposed sites. The changes were most strongly correlated with concentrations of SO, Mg and Na. This knowledge allows an assessment of the risk of mine-water contamination to groundwater ecosystem function and aids mine-water management.
Topics: Archaea; Bacteria; Ecosystem; Groundwater; Water
PubMed: 34052601
DOI: 10.1016/j.envpol.2021.117318 -
Nature Jun 2021Loss of gut microbial diversity in industrial populations is associated with chronic diseases, underscoring the importance of studying our ancestral gut microbiome....
Loss of gut microbial diversity in industrial populations is associated with chronic diseases, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000-2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces.
Topics: Anti-Bacterial Agents; Bacteria; Biodiversity; Biological Evolution; Chronic Disease; Developed Countries; Developing Countries; Diet, Western; Feces; Gastrointestinal Microbiome; Genome, Bacterial; History, Ancient; Host Microbial Interactions; Humans; Industrial Development; Methanobrevibacter; Mexico; Sedentary Behavior; Southwestern United States; Species Specificity; Symbiosis
PubMed: 33981035
DOI: 10.1038/s41586-021-03532-0 -
Applied and Environmental Microbiology May 2021Hydrologic shifts due to climate change will affect the cycling of carbon (C) stored in boreal peatlands. Carbon cycling in these systems is carried out by...
Hydrologic shifts due to climate change will affect the cycling of carbon (C) stored in boreal peatlands. Carbon cycling in these systems is carried out by microorganisms and plants in close association. This study investigated the effects of experimentally manipulated water tables (lowered and raised) and plant functional groups on the peat and root microbiomes in a boreal rich fen. All samples were sequenced and processed for bacterial, archaeal (16S DNA genes; V4), and fungal (internal transcribed spacer 2 [ITS2]) DNA. Depth had a strong effect on microbial and fungal communities across all water table treatments. Bacterial and archaeal communities were most sensitive to the water table treatments, particularly at the 10- to 20-cm depth; this area coincides with the rhizosphere or rooting zone. Iron cyclers, particularly members of the family , were enriched around the roots of sedges, horsetails, and grasses. The fungal community was affected largely by plant functional group, especially cinquefoils. Fungal endophytes (particularly spp.) were enriched in sedge and grass roots, which may have underappreciated implications for organic matter breakdown and cycling. Fungal lignocellulose degraders were enriched in the lowered water table treatment. Our results were indicative of two main methanogen communities, a rooting zone community dominated by the archaeal family and a deep peat community dominated by the family . This study demonstrated that roots and the rooting zone in boreal fens support organisms likely capable of methanogenesis, iron cycling, and fungal endophytic association and are directly or indirectly affecting carbon cycling in these ecosystems. These taxa, which react to changes in the water table and associate with roots and, particularly, graminoids, may gain greater biogeochemical influence, as projected higher precipitation rates could lead to an increased abundance of sedges and grasses in boreal fens.
Topics: Alaska; Archaea; Bacteria; Carbon Cycle; Groundwater; Iron; Magnoliopsida; Methane; Microbiota; Plant Roots; Rhizosphere; Soil; Soil Microbiology
PubMed: 33811029
DOI: 10.1128/AEM.00241-21 -
International Journal of Molecular... Mar 2021In anaerobic bioreactors, the electrons produced during the oxidation of organic matter can potentially be used for the biological reduction of pharmaceuticals in...
In anaerobic bioreactors, the electrons produced during the oxidation of organic matter can potentially be used for the biological reduction of pharmaceuticals in wastewaters. Common electron transfer limitations benefit from the acceleration of reactions through utilization of redox mediators (RM). This work explores the potential of carbon nanomaterials (CNM) as RM on the anaerobic removal of ciprofloxacin (CIP). Pristine and tailored carbon nanotubes (CNT) were first tested for chemical reduction of CIP, and pristine CNT was found as the best material, so it was further utilized in biological anaerobic assays with anaerobic granular sludge (GS). In addition, magnetic CNT were prepared and also tested in biological assays, as they are easier to be recovered and reused. In biological tests with CNM, approximately 99% CIP removal was achieved, and the reaction rates increased ≈1.5-fold relatively to the control without CNM. In these experiments, CIP adsorption onto GS and CNM was above 90%. Despite, after applying three successive cycles of CIP addition, the catalytic properties of magnetic CNT were maintained while adsorption decreased to 29 ± 3.2%, as the result of CNM overload by CIP. The results suggest the combined occurrence of different mechanisms for CIP removal: adsorption on GS and/or CNM, and biological reduction or oxidation, which can be accelerated by the presence of CNM. After biological treatment with CNM, toxicity towards was evaluated, resulting in ≈ 46% detoxification of CIP solution, showing the advantages of combining biological treatment with CNM for CIP removal.
Topics: Adsorption; Aliivibrio fischeri; Anaerobiosis; Biodegradation, Environmental; Bioreactors; Ciprofloxacin; Electrons; Humans; Magnetite Nanoparticles; Methanobacterium; Methanobrevibacter; Methanosarcinales; Methanospirillum; Microbial Sensitivity Tests; Nanotubes, Carbon; Oxidation-Reduction; Sewage; Water Pollutants, Chemical
PubMed: 33805783
DOI: 10.3390/ijms22062932 -
The Science of the Total Environment Aug 2021Microbial community assembly mechanisms are pivotal for understanding the ecological functions of microorganisms in biogeochemical cycling in Earth's ecosystems, yet...
Microbial community assembly mechanisms are pivotal for understanding the ecological functions of microorganisms in biogeochemical cycling in Earth's ecosystems, yet rarely investigated in the context of deep terrestrial ecology. Here, the microbial communities in the production waters collected from water injection wells and oil production wells across eight oil reservoirs throughout northern China were determined and analyzed by proportional distribution analysis and null model analysis. A 'core' microbiota consisting of three bacterial genera, including Arcobacter, Pseudomonas and Acinetobacter, and eight archaeal genera, including Archaeoglobus, Methanobacterium, Methanothermobacter, unclassified Methanobacteriaceae, Methanomethylovorans, Methanoculleus, Methanosaeta and Methanolinea, was found to be present in all production water samples. Canonical correlation analysis reflected that the core archaea were significantly influenced by temperature and reservoir depth, while the core bacteria were affected by the combined impact of the core archaea and environmental factors. Thermodynamic calculations indicate that bioenergetic constraints are the driving force that governs the enrichment of two core archaeal guilds, aceticlastic methanogens versus hydrogenotrophic methanogens, in low- and high-temperature oil reservoirs, respectively. Collectively, our study indicates that microbial community structures in wells of oil reservoirs are structured by the thermodynamic window of opportunity, through which the core archaeal communities are accommodated directly followed by the deterministic recruiting of core bacterial genera, and then the stochastic selection of some other microbial members from local environments. Our study enhances the understanding of the microbial assembly mechanism in deep terrestrial habitats. Meanwhile, our findings will support the development of functional microbiota used for bioremediation and bioaugmentation in microbial enhanced oil recovery.
Topics: Archaea; Bacteria; China; Oil and Gas Fields; Phylogeny; RNA, Ribosomal, 16S
PubMed: 33794455
DOI: 10.1016/j.scitotenv.2021.146506 -
JBMR Plus Mar 2021Osteoporosis and its precursor osteopenia are common metabolic bone diseases in postmenopausal women. A growing body of evidence suggests that the gut microbiota is...
Osteoporosis and its precursor osteopenia are common metabolic bone diseases in postmenopausal women. A growing body of evidence suggests that the gut microbiota is involved in the regulation of bone metabolism; however, there are few studies examining how gut microbiomes in osteoporosis and osteopenia may differ from those in healthy individuals. The aim of this study was to characterize the diversity, composition, and functional gene potential of the gut microbiota of healthy, osteopenic, and osteoporotic women. Body composition, bone density, and fecal metagenomes were analyzed in 86 postmenopausal women. The women were classified as healthy, osteopenic, or osteoporotic based on -scores. The taxonomic and functional gene compositions of the microbiome were analyzed using shotgun metagenomic sequencing. Both osteoporotic and osteopenic taxonomic compositions were found to be significantly different from healthy participants. Linear discriminant-analysis effect-size analyses identified that healthy participants had more unclassified and methanogenic archaea () than in both osteoporotic and osteopenic participants. was found to be more abundant in osteoporosis and osteopenia groups. Some KEGG pathways, including carbohydrate metabolism, biosynthesis of secondary metabolites, and cyanoamino acid metabolism, were found to be more abundant in both osteoporosis and osteopenia. These results show that osteoporosis and osteopenia alter the gut microbiome of postmenopausal women and identify potential microbial taxonomic and functional pathways that may be involved in this disease. © 2020 The Authors. published by Wiley Periodicals LLC. on behalf of American Society for Bone and Mineral Research.
PubMed: 33778322
DOI: 10.1002/jbm4.10452 -
Archaea (Vancouver, B.C.) 2021Electromethanogenesis refers to the bioelectrochemical synthesis of methane from CO by biocathodes. In an electromethanogenic system using thermophilic microorganisms,...
Electromethanogenesis refers to the bioelectrochemical synthesis of methane from CO by biocathodes. In an electromethanogenic system using thermophilic microorganisms, metagenomic analysis along with quantitative real-time polymerase chain reaction and fluorescence hybridization revealed that the biocathode microbiota was dominated by the methanogen sp. strain EMTCatA1 and the actinobacterium sp. strain EMTCatB1. RNA sequencing was used to compare the transcriptome profiles of each strain at the methane-producing biocathodes with those in an open circuit and with the methanogenesis inhibitor 2-bromoethanesulfonate (BrES). For the methanogen, genes related to hydrogenotrophic methanogenesis were highly expressed in a manner similar to those observed under H-limited conditions. For the actinobacterium, the expression profiles of genes encoding multiheme c-type cytochromes and membrane-bound oxidoreductases suggested that the actinobacterium directly takes up electrons from the electrode. In both strains, various stress-related genes were commonly induced in the open-circuit biocathodes and biocathodes with BrES. This study provides a molecular inventory of the dominant species of an electromethanogenic biocathode with functional insights and therefore represents the first multiomics characterization of an electromethanogenic biocathode.
Topics: Euryarchaeota; In Situ Hybridization, Fluorescence; Methane; Methanobacteriaceae; Microbiota
PubMed: 33746613
DOI: 10.1155/2021/8865133 -
Nature Chemical Biology May 2021YcaO enzymes catalyze several post-translational modifications on peptide substrates, including thioamidation, which substitutes an amide oxygen with sulfur. Most...
YcaO enzymes catalyze several post-translational modifications on peptide substrates, including thioamidation, which substitutes an amide oxygen with sulfur. Most predicted thioamide-forming YcaO enzymes are encoded adjacent to TfuA, which when present, is required for thioamidation. While activation of the peptide amide backbone is well established for YcaO enzymes, the function of TfuA has remained enigmatic. Here we characterize the TfuA protein involved in methyl-coenzyme M reductase thioamidation and demonstrate that TfuA catalyzes the hydrolysis of thiocarboxylated ThiS (ThiS-COSH), a proteinaceous sulfur donor, and enhances the affinity of YcaO toward the thioamidation substrate. We also report a crystal structure of a TfuA, which displays a new protein fold. Our structural and mutational analyses of TfuA have uncovered conserved binding interfaces with YcaO and ThiS in addition to revealing a hydrolase-like active site featuring a Ser-Lys catalytic pair.
Topics: Archaeal Proteins; Binding Sites; Cloning, Molecular; Crystallography, X-Ray; Escherichia coli; Euryarchaeota; Gene Expression; Genetic Vectors; Histidine; Kinetics; Mannose-Binding Lectin; Methanobacteriaceae; Methanocaldococcus; Models, Molecular; Mutation; Oligopeptides; Oxidoreductases; Peptides; Protein Binding; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand; Protein Interaction Domains and Motifs; Protein Processing, Post-Translational; Recombinant Fusion Proteins; Substrate Specificity; Thioamides
PubMed: 33707784
DOI: 10.1038/s41589-021-00771-0