Innovations to culturing the uncultured microbial majority

Nature Reviews Microbiology, Journal Year: 2020, Volume and Issue: 19(4), P. 225 - 240

Published: Oct. 22, 2020

Language: Английский

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Spatiotemporal dynamics of the archaeal community in coastal sediments: assembly process and co-occurrence relationship

The ISME Journal, Journal Year: 2020, Volume and Issue: 14(6), P. 1463 - 1478

Published: March 4, 2020

Studies of marine benthic archaeal communities are updating our view their taxonomic composition and metabolic versatility. However, large knowledge gaps remain with regard to community assembly processes inter taxa associations. Here, using 16S rRNA gene amplicon sequencing qPCR, we investigated the spatiotemporal dynamics, processes, co-occurrence relationships in 58 surface sediment samples collected both summer winter from across ~1500 km eastern Chinese marginal seas. Clear patterns dynamics structure were observed, a more pronounced spatial rather than seasonal variation. Accompanying geographic variation was significant distance-decay pattern varying contributions different clades, determined by relative abundance. In seasons, dispersal limitation most important process, explaining ~40% variation, followed homogeneous selection ecological drift, that made an approximately equal contribution (~30%). This meant stochasticity determinism had greater impact on assembly. Furthermore, observed seasonality patterns: closer inter-taxa connections summer, unmatched between relationship. These results demonstrate assembled under seasonal-consistent mechanism but changed over indicating complex dynamic coastal sediments

Language: Английский

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Methanotrophs: Discoveries, Environmental Relevance, and a Perspective on Current and Future Applications

Frontiers in Microbiology, Journal Year: 2021, Volume and Issue: 12

Published: May 14, 2021

Methane is the final product of anaerobic decomposition organic matter. The conversion matter to methane (methanogenesis) as a mechanism for energy conservation exclusively attributed archaeal domain. oxidized by methanotrophic microorganisms using oxygen or alternative terminal electron acceptors. Aerobic bacteria belong phyla Proteobacteria and Verrucomicrobia, while oxidation also mediated more recently discovered methanotrophs with representatives in both archaea domains. coupled reduction nitrate, nitrite, iron, manganese, sulfate, acceptors (e.g., humic substances) This review highlights relevance methanotrophy natural anthropogenically influenced ecosystems, emphasizing environmental conditions, distribution, function, co-existence, interactions, availability that likely play key role regulating their function. A systematic overview aspects ecology, physiology, metabolism, genomics crucial understand contribution mitigation efflux atmosphere. We give significance processes under microaerophilic conditions aerobic oxidizers. In context we emphasize current potential future applications from two different angles, namely wastewater treatment through application methanotrophs, biotechnological resource recovery waste streams. Finally, identify knowledge gaps may lead opportunities harness further benefits production valuable bioproducts enabling bio-based circular economy.

Language: Английский

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Environmental filtering drives distinct continental atlases of soil archaea between dryland and wetland agricultural ecosystems

Microbiome, Journal Year: 2019, Volume and Issue: 7(1)

Published: Feb. 1, 2019

Understanding the spatial distributions and ecological diversity of soil archaeal communities in agricultural ecosystems is crucial for improvements crop productivity. Here, we conducted a comprehensive, continental-scale survey adjacent pairs maize (dryland) rice (wetland) fields eastern China.We revealed consequential roles environmental filtering driving community assembly both fields. Rice fields, abundant with Euryarchaeota, had higher steeper distance-decay slopes than dominated by Thaumarchaeota. Dominant archaea showed distinct continental atlases niche differentiation between dryland wetland habitats, where they were associated pH mean annual temperature, respectively. After identifying their preferences, grouped dominant taxa into different clusters determined unique co-occurrence patterns within each cluster. Using this empirical dataset, built atlas to provide reliable estimates ecosystems.Environmental plays role wetland, contrasting strategies archaeal-driven nutrient cycling these two ecosystems. These findings improve our ability predict how respond changes manage provisioning ecosystem services.

Language: Английский

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Effect of extreme pH conditions on methanogenesis: Methanogen metabolism and community structure

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 877, P. 162702 - 162702

Published: March 9, 2023

Language: Английский

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Taxonomic and carbon metabolic diversification of Bathyarchaeia during its coevolution history with early Earth surface environment

Science Advances, Journal Year: 2023, Volume and Issue: 9(27)

Published: July 5, 2023

Bathyarchaeia, as one of the most abundant microorganisms on Earth, play vital roles in global carbon cycle. However, our understanding their origin, evolution, and ecological functions remains poorly constrained. Here, we present largest dataset Bathyarchaeia metagenome assembled genome to date reclassify into eight order-level units corresponding former subgroup system. Highly diversified versatile metabolisms were found among different orders, particularly atypical C1 metabolic pathways, indicating that represent overlooked important methylotrophs. Molecular dating results indicate diverged at ~3.3 billion years, followed by three major diversifications ~3.0, ~2.5, ~1.8 1.7 likely driven continental emergence, growth, intensive submarine volcanism, respectively. The lignin-degrading clade emerged ~300 million years perhaps contributed sharply decreased sequestration rate during Late Carboniferous period. evolutionary history potentially has been shaped geological forces, which, turn, affected Earth's surface environment.

Language: Английский

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Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution

The ISME Journal, Journal Year: 2019, Volume and Issue: 13(9), P. 2150 - 2161

Published: April 25, 2019

Language: Английский

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Genomic and transcriptomic insights into the ecology and metabolism of benthic archaeal cosmopolitan, Thermoprofundales (MBG-D archaea)

The ISME Journal, Journal Year: 2018, Volume and Issue: 13(4), P. 885 - 901

Published: Dec. 4, 2018

Abstract Marine Benthic Group D (MBG-D) archaea, discovered by 16S rRNA gene survey decades ago, are ecologically important, yet understudied and uncultured sedimentary archaea. In this study, a comprehensive meta-analysis based on the genes of MBG-D archaea showed that one most frequently found archaeal lineages in global sediment with widespread distribution high abundance, including 16 subgroups total. Interestingly, some show significant segregations toward salinity methane seeps. Co-occurrence analyses indicate non-random association Lokiarchaeota (in both saline freshwater sediments) Hadesarchaea, suggesting potential interactions among these groups. Meanwhile, four nearly complete metagenome-assembled genomes (MAGs) corresponding metatranscriptomes reconstructed from mangrove intertidal mudflat sediments, we provide insights metabolic potentials ecological functions appear to be capable transporting assimilating peptides generating acetate ethanol through fermentation. Metatranscriptomic analysis suggests expression for amino acid utilization peptidases, especially M09B-type extracellular peptidase (collagenase) showing levels all MAGs. Beyond heterotrophic central carbon metabolism, include might encode two autotrophic pathways: Wood–Ljundahl (WL) pathways using H4MPT H4folate as C1 carriers, an incomplete dicarboxylate/4-hydroxybutyrate cycle alternative bypasses pyruvate malate/oxaloacetate during dicarboxylation. These findings reveal important ubiquitous benthic group specific mixotrophic metabolisms, so proposed name Thermoprofundales new Order within Class Thermoplasmata. Globally, other synergistically transform organic matter, possibly playing vital role cycle.

Language: Английский

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Methylotrophic methanogens everywhere — physiology and ecology of novel players in global methane cycling

Biochemical Society Transactions, Journal Year: 2019, Volume and Issue: 47(6), P. 1895 - 1907

Published: Dec. 10, 2019

Research on methanogenic Archaea has experienced a revival, with many novel lineages of methanogens recently being found through cultivation and suggested via metagenomics approaches, respectively. Most these comprise (potentially) capable methanogenesis from methylated compounds, pathway that had previously received comparably little attention. In this review, we provide an overview new focus the Methanomassiliicoccales. These lack Wood–Ljungdahl employ hydrogen-dependent methylotrophic fundamentally different traditional methanogens. Several archaeal candidate identified metagenomics, such as Ca. Verstraetearchaeota Methanofastidiosa, encode genes for similar to Thus, latter are emerging model system physiological, biochemical ecological studies Methanomassiliicoccales occur in large variety anoxic habitats including wetlands animal intestinal tracts, i.e. major natural anthropogenic sources methane emissions, Especially ruminant animals, they likely among producers. Taken together, (hydrogen-dependent) much more diverse widespread than thought. Considering role potent greenhouse gas, resolving nature broad range putative assessing their emitting environments pressing issues future research

Language: Английский

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Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments

Frontiers in Microbiology, Journal Year: 2021, Volume and Issue: 12

Published: Feb. 18, 2021

Large amounts of methane, a potent greenhouse gas, are produced in anoxic sediments by methanogenic archaea. Nonetheless, over 90% the methane is oxidized via sulfate-dependent anaerobic oxidation (S-AOM) sulfate-methane transition zone (SMTZ) consortia methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Coastal systems account for majority total marine emissions typically have lower sulfate concentrations, hence S-AOM less significant. However, alternative electron acceptors such as metal oxides or nitrate could be used AOM instead sulfate. The availability determined redox zonation sediment, which may vary due to changes oxygen type rate organic matter inputs. Additionally, eutrophication climate change can affect microbiome, biogeochemical zonation, cycling coastal sediments. This review summarizes current knowledge on processes microorganisms involved factors influencing from these systems. In eutrophic areas, inputs key driver bottom water hypoxia. Global warming reduce solubility surface waters, enhancing column stratification, increasing primary production, favoring methanogenesis. ANME notoriously slow growers not able effectively oxidize upon rapid sedimentation shoaling SMTZ. settings, ANME-2d ( Methanoperedenaceae ) ANME-2a couple iron- and/or manganese reduction AOM, while NC10 Methylomirabilota nitrite reduction. Ultimately, aerobic methanotrophs upper millimeters sediment column. role mitigating sediments, including exact pathways involved, still underexplored, controlling unclear. Further studies needed order understand driving methane-cycling identify responsible microorganisms. Integration microbial geochemical expected lead more accurate predictions zones future.

Language: Английский

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