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Rasmussen AN, Tolar BB, Bargar JR, Boye K, Francis CA. Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA. mSystems 2024:e0031424. [PMID: 38940520 DOI: 10.1128/msystems.00314-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/06/2024] [Indexed: 06/29/2024] Open
Abstract
We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling-particularly methane-cycling-microorganisms in montane riparian floodplain sediments. We generated 1,233 MAGs (>50% completeness and <10% contamination) from 50- to 150-cm depth below the sediment surface capturing the transition between oxic, unsaturated sediments and anoxic, saturated sediments in the Slate River (SR) floodplain (Crested Butte, CO, USA). We recovered genomes of putative methanogens, methanotrophs, and methylotrophs (n = 57). Methanogens, found only in deep, anoxic depths at SR, originate from three different clades (Methanoregulaceae, Methanotrichaceae, and Methanomassiliicoccales), each with a different methanogenesis pathway; putative methanotrophic MAGs originate from within the Archaea (Candidatus Methanoperedens) in anoxic depths and uncultured bacteria (Ca. Binatia) in oxic depths. Genomes for canonical aerobic methanotrophs were not recovered. Ca. Methanoperedens were exceptionally abundant (~1,400× coverage, >50% abundance in the MAG library) in one sample that also contained aceticlastic methanogens, indicating a potential C1/methane-cycling hotspot. Ca. Methylomirabilis MAGs from SR encode pathways for methylotrophy but do not harbor methane monooxygenase or nitrogen reduction genes. Comparative genomic analysis supports that one clade within the Ca. Methylomirabilis genus is not methanotrophic. The genetic potential for methylotrophy was widespread, with over 10% and 19% of SR MAGs encoding a methanol dehydrogenase or substrate-specific methyltransferase, respectively. MAGs from uncultured Thermoplasmata archaea in the Ca. Gimiplasmatales (UBA10834) contain pathways that may allow for anaerobic methylotrophic acetogenesis. Overall, MAGs from SR floodplain sediments reveal a potential for methane production and consumption in the system and a robust potential for methylotrophy.IMPORTANCEThe cycling of carbon by microorganisms in subsurface environments is of particular relevance in the face of global climate change. Riparian floodplain sediments contain high organic carbon that can be degraded into C1 compounds such as methane, methanol, and methylamines, the fate of which depends on the microbial metabolisms present as well as the hydrological conditions and availability of oxygen. In the present study, we generated over 1,000 MAGs from subsurface sediments from a montane river floodplain and recovered genomes for microorganisms that are capable of producing and consuming methane and other C1 compounds, highlighting a robust potential for C1 cycling in subsurface sediments both with and without oxygen. Archaea from the Ca. Methanoperedens genus were exceptionally abundant in one sample, indicating a potential C1/methane-cycling hotspot in the Slate River floodplain system.
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Affiliation(s)
- Anna N Rasmussen
- Department of Earth System Science, Stanford University, Stanford, California, USA
- SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Bradley B Tolar
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - John R Bargar
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kristin Boye
- SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Christopher A Francis
- Department of Earth System Science, Stanford University, Stanford, California, USA
- Oceans Department, Stanford University, Stanford, California, USA
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Liu R, Cai R, Wang M, Zhang J, Zhang H, Li C, Sun C. Metagenomic insights into Heimdallarchaeia clades from the deep-sea cold seep and hydrothermal vent. ENVIRONMENTAL MICROBIOME 2024; 19:43. [PMID: 38909236 PMCID: PMC11193907 DOI: 10.1186/s40793-024-00585-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 06/18/2024] [Indexed: 06/24/2024]
Abstract
Heimdallarchaeia is a class of the Asgardarchaeota, are the most probable candidates for the archaeal protoeukaryote ancestor that have been identified to date. However, little is known about their life habits regardless of their ubiquitous distribution in diverse habitats, which is especially true for Heimdallarchaeia from deep-sea environments. In this study, we obtained 13 metagenome-assembled genomes (MAGs) of Heimdallarchaeia from the deep-sea cold seep and hydrothermal vent. These MAGs belonged to orders o_Heimdallarchaeales and o_JABLTI01, and most of them (9 MAGs) come from the family f_Heimdallarchaeaceae according to genome taxonomy database (GTDB). These are enriched for common eukaryote-specific signatures. Our results show that these Heimdallarchaeia have the metabolic potential to reduce sulfate (assimilatory) and nitrate (dissimilatory) to sulfide and ammonia, respectively, suggesting a previously unappreciated role in biogeochemical cycling. Furthermore, we find that they could perform both TCA and rTCA pathways coupled with pyruvate metabolism for energy conservation, fix CO2 and generate organic compounds through an atypical Wood-Ljungdahl pathway. In addition, many genes closely associated with bacteriochlorophyll and carotenoid biosynthesis, and oxygen-dependent metabolic pathways are identified in these Heimdallarchaeia MAGs, suggesting a potential light-utilization by pigments and microoxic lifestyle. Taken together, our results indicate that Heimdallarchaeia possess a mixotrophic lifestyle, which may give them more flexibility to adapt to the harsh deep-sea conditions.
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Affiliation(s)
- Rui Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Ruining Cai
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Minxiao Wang
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jing Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Huan Zhang
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Chaolun Li
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
| | - Chaomin Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
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Li Y, Wang T, Jing H, Xiao Y. Evolutionary ecology of denitrifying methanotrophic NC10 bacteria in the deep-sea biosphere. Mol Ecol 2024; 33:e17372. [PMID: 38709214 DOI: 10.1111/mec.17372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/02/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024]
Abstract
The NC10 phylum links anaerobic methane oxidation to nitrite denitrification through a unique O2-producing intra-aerobic methanotrophic pathway. Although numerous amplicon-based studies revealed the distribution of this phylum, comprehensive genomic insights and niche characterization in deep-sea environments were still largely unknown. In this study, we extensively surveyed the NC10 bacteria across diverse deep-sea environments, including waters, sediments, cold seeps, biofilms, rocky substrates, and subseafloor aquifers. We then reconstructed and analysed 38 metagenome-assembled genomes (MAGs), and revealed the extensive distribution of NC10 bacteria and their intense selective pressure in these harsh environments. Isotopic analyses combined with gene expression profiling confirmed that active nitrite-dependent anaerobic methane oxidation (n-DAMO) occurs within deep-sea sediments. In addition, the identification of the Wood-Ljungdahl (WL) and 3-hydroxypropionate/4-hydroxybutyrat (3HB/4HP) pathways in these MAGs suggests their capability for carbon fixation as chemoautotrophs in these deep-sea environments. Indeed, we found that for their survival in the oligotrophic deep-sea biosphere, NC10 bacteria encode two branches of the WL pathway, utilizing acetyl-CoA from the carbonyl branch for citric acid cycle-based energy production and methane from the methyl branch for n-DAMO. The observed low ratios of non-synonymous substitutions to synonymous substitutions (pN/pS) in n-DAMO-related genes across these habitats suggest a pronounced purifying selection that is critical for the survival of NC10 bacteria in oligotrophic deep-sea environments. These findings not only advance our understanding of the evolutionary adaptations of NC10 bacteria but also underscore the intricate coupling between the carbon and nitrogen cycles within deep-sea ecosystems, driven by this bacterial phylum.
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Affiliation(s)
- Yingdong Li
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
| | - Ting Wang
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
| | - Yao Xiao
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
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Musat F, Kjeldsen KU, Rotaru AE, Chen SC, Musat N. Archaea oxidizing alkanes through alkyl-coenzyme M reductases. Curr Opin Microbiol 2024; 79:102486. [PMID: 38733792 DOI: 10.1016/j.mib.2024.102486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024]
Abstract
This review synthesizes recent discoveries of novel archaea clades capable of oxidizing higher alkanes, from volatile ones like ethane to longer-chain alkanes like hexadecane. These archaea, termed anaerobic multicarbon alkane-oxidizing archaea (ANKA), initiate alkane oxidation using alkyl-coenzyme M reductases, enzymes similar to the methyl-coenzyme M reductases of methanogenic and anaerobic methanotrophic archaea (ANME). The polyphyletic alkane-oxidizing archaea group (ALOX), encompassing ANME and ANKA, harbors increasingly complex alkane degradation pathways, correlated with the alkane chain length. We discuss the evolutionary trajectory of these pathways emphasizing metabolic innovations and the acquisition of metabolic modules via lateral gene transfer. Additionally, we explore the mechanisms by which archaea couple alkane oxidation with the reduction of electron acceptors, including electron transfer to partner sulfate-reducing bacteria (SRB). The phylogenetic and functional constraints that shape ALOX-SRB associations are also discussed. We conclude by highlighting the research needs in this emerging research field and its potential applications in biotechnology.
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Affiliation(s)
- Florin Musat
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark; Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania.
| | - Kasper U Kjeldsen
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark
| | - Amelia E Rotaru
- Department of Biology, Nordic Center for Earth Evolution, University of Southern Denmark, Odense, Denmark
| | - Song-Can Chen
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna A-1030, Austria
| | - Niculina Musat
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark
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Xie F, Zhao S, Zhan X, Zhou Y, Li Y, Zhu W, Pope PB, Attwood GT, Jin W, Mao S. Unraveling the phylogenomic diversity of Methanomassiliicoccales and implications for mitigating ruminant methane emissions. Genome Biol 2024; 25:32. [PMID: 38263062 PMCID: PMC10804542 DOI: 10.1186/s13059-024-03167-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 01/07/2024] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Methanomassiliicoccales are a recently identified order of methanogens that are diverse across global environments particularly the gastrointestinal tracts of animals; however, their metabolic capacities are defined via a limited number of cultured strains. RESULTS Here, we profile and analyze 243 Methanomassiliicoccales genomes assembled from cultured representatives and uncultured metagenomes recovered from various biomes, including the gastrointestinal tracts of different animal species. Our analyses reveal the presence of numerous undefined genera and genetic variability in metabolic capabilities within Methanomassiliicoccales lineages, which is essential for adaptation to their ecological niches. In particular, gastrointestinal tract Methanomassiliicoccales demonstrate the presence of co-diversified members with their hosts over evolutionary timescales and likely originated in the natural environment. We highlight the presence of diverse clades of vitamin transporter BtuC proteins that distinguish Methanomassiliicoccales from other archaeal orders and likely provide a competitive advantage in efficiently handling B12. Furthermore, genome-centric metatranscriptomic analysis of ruminants with varying methane yields reveal elevated expression of select Methanomassiliicoccales genera in low methane animals and suggest that B12 exchanges could enable them to occupy ecological niches that possibly alter the direction of H2 utilization. CONCLUSIONS We provide a comprehensive and updated account of divergent Methanomassiliicoccales lineages, drawing from numerous uncultured genomes obtained from various habitats. We also highlight their unique metabolic capabilities involving B12, which could serve as promising targets for mitigating ruminant methane emissions by altering H2 flow.
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Affiliation(s)
- Fei Xie
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Shengwei Zhao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaoxiu Zhan
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yang Zhou
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yin Li
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Weiyun Zhu
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Phillip B Pope
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Graeme T Attwood
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Wei Jin
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
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Benito Merino D, Lipp JS, Borrel G, Boetius A, Wegener G. Anaerobic hexadecane degradation by a thermophilic Hadarchaeon from Guaymas Basin. THE ISME JOURNAL 2024; 18:wrad004. [PMID: 38365230 PMCID: PMC10811742 DOI: 10.1093/ismejo/wrad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 11/06/2023] [Indexed: 02/18/2024]
Abstract
Hadarchaeota inhabit subsurface and hydrothermally heated environments, but previous to this study, they had not been cultured. Based on metagenome-assembled genomes, most Hadarchaeota are heterotrophs that grow on sugars and amino acids, or oxidize carbon monoxide or reduce nitrite to ammonium. A few other metagenome-assembled genomes encode alkyl-coenzyme M reductases (Acrs), β-oxidation, and Wood-Ljungdahl pathways, pointing toward multicarbon alkane metabolism. To identify the organisms involved in thermophilic oil degradation, we established anaerobic sulfate-reducing hexadecane-degrading cultures from hydrothermally heated sediments of the Guaymas Basin. Cultures at 70°C were enriched in one Hadarchaeon that we propose as Candidatus Cerberiarchaeum oleivorans. Genomic and chemical analyses indicate that Ca. C. oleivorans uses an Acr to activate hexadecane to hexadecyl-coenzyme M. A β-oxidation pathway and a tetrahydromethanopterin methyl branch Wood-Ljungdahl (mWL) pathway allow the complete oxidation of hexadecane to CO2. Our results suggest a syntrophic lifestyle with sulfate reducers, as Ca. C. oleivorans lacks a sulfate respiration pathway. Comparative genomics show that Acr, mWL, and β-oxidation are restricted to one family of Hadarchaeota, which we propose as Ca. Cerberiarchaeaceae. Phylogenetic analyses further indicate that the mWL pathway is basal to all Hadarchaeota. By contrast, the carbon monoxide dehydrogenase/acetyl-coenzyme A synthase complex in Ca. Cerberiarchaeaceae was horizontally acquired from Bathyarchaeia. The Acr and β-oxidation genes of Ca. Cerberiarchaeaceae are highly similar to those of other alkane-oxidizing archaea such as Ca. Methanoliparia and Ca. Helarchaeales. Our results support the use of Acrs in the degradation of petroleum alkanes and suggest a role of Hadarchaeota in oil-rich environments.
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Affiliation(s)
- David Benito Merino
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Klagenfurter Straße 2, 428359, Bremen, Germany
| | - Julius S Lipp
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, 28359, Bremen, Germany
| | - Guillaume Borrel
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
| | - Antje Boetius
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, 28359, Bremen, Germany
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, 28359, Bremen, Germany
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Liu S, Hu R, Peng N, Zhou Z, Chen R, He Z, Wang C. Phylogenetic and ecophysiological novelty of subsurface mercury methylators in mangrove sediments. THE ISME JOURNAL 2023; 17:2313-2325. [PMID: 37880540 PMCID: PMC10689504 DOI: 10.1038/s41396-023-01544-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023]
Abstract
Mangrove sediment is a crucial component in the global mercury (Hg) cycling and acts as a hotspot for methylmercury (MeHg) production. Early evidence has documented the ubiquity of well-studied Hg methylators in mangrove superficial sediments; however, their diversity and metabolic adaptation in the more anoxic and highly reduced subsurface sediments are lacking. Through MeHg biogeochemical assay and metagenomic sequencing, we found that mangrove subsurface sediments (20-100 cm) showed a less hgcA gene abundance but higher diversity of Hg methylators than superficial sediments (0-20 cm). Regional-scale investigation of mangrove subsurface sediments spanning over 1500 km demonstrated a prevalence and family-level novelty of Hg-methylating microbial lineages (i.e., those affiliated to Anaerolineae, Phycisphaerae, and Desulfobacterales). We proposed the candidate phylum Zixibacteria lineage with sulfate-reducing capacity as a currently understudied Hg methylator across anoxic environments. Unlike other Hg methylators, the Zixibacteria lineage does not use the Wood-Ljungdahl pathway but has unique capabilities of performing methionine synthesis to donate methyl groups. The absence of cobalamin biosynthesis pathway suggests that this Hg-methylating lineage may depend on its syntrophic partners (i.e., Syntrophobacterales members) for energy in subsurface sediments. Our results expand the diversity of subsurface Hg methylators and uncover their unique ecophysiological adaptations in mangrove sediments.
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Affiliation(s)
- Songfeng Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Nenglong Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhengyuan Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Ruihan Chen
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China.
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Meene A, Gierse L, Schwaiger T, Karte C, Schröder C, Höper D, Wang H, Groß V, Wünsche C, Mücke P, Kreikemeyer B, Beer M, Becher D, Mettenleiter TC, Riedel K, Urich T. Archaeome structure and function of the intestinal tract in healthy and H1N1 infected swine. Front Microbiol 2023; 14:1250140. [PMID: 37779690 PMCID: PMC10534045 DOI: 10.3389/fmicb.2023.1250140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/21/2023] [Indexed: 10/03/2023] Open
Abstract
Background Methanogenic archaea represent a less investigated and likely underestimated part of the intestinal tract microbiome in swine. Aims/Methods This study aims to elucidate the archaeome structure and function in the porcine intestinal tract of healthy and H1N1 infected swine. We performed multi-omics analysis consisting of 16S rRNA gene profiling, metatranscriptomics and metaproteomics. Results and discussion We observed a significant increase from 0.48 to 4.50% of archaea in the intestinal tract microbiome along the ileum and colon, dominated by genera Methanobrevibacter and Methanosphaera. Furthermore, in feces of naïve and H1N1 infected swine, we observed significant but minor differences in the occurrence of archaeal phylotypes over the course of an infection experiment. Metatranscriptomic analysis of archaeal mRNAs revealed the major methanogenesis pathways of Methanobrevibacter and Methanosphaera to be hydrogenotrophic and methyl-reducing, respectively. Metaproteomics of archaeal peptides indicated some effects of the H1N1 infection on central metabolism of the gut archaea. Conclusions/Take home message Finally, this study provides the first multi-omics analysis and high-resolution insights into the structure and function of the porcine intestinal tract archaeome during a non-lethal Influenza A virus infection of the respiratory tract, demonstrating significant alterations in archaeal community composition and central metabolic functions.
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Affiliation(s)
- Alexander Meene
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Laurin Gierse
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | | | | | | | - Dirk Höper
- Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Haitao Wang
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Verena Groß
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christine Wünsche
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Pierre Mücke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Bernd Kreikemeyer
- Institute for Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Martin Beer
- Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | | | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
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Zehnle H, Laso-Pérez R, Lipp J, Riedel D, Benito Merino D, Teske A, Wegener G. Candidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes. Nat Microbiol 2023:10.1038/s41564-023-01400-3. [PMID: 37264141 DOI: 10.1038/s41564-023-01400-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/28/2023] [Indexed: 06/03/2023]
Abstract
Methanogenic and methanotrophic archaea produce and consume the greenhouse gas methane, respectively, using the reversible enzyme methyl-coenzyme M reductase (Mcr). Recently, Mcr variants that can activate multicarbon alkanes have been recovered from archaeal enrichment cultures. These enzymes, called alkyl-coenzyme M reductase (Acrs), are widespread in the environment but remain poorly understood. Here we produced anoxic cultures degrading mid-chain petroleum n-alkanes between pentane (C5) and tetradecane (C14) at 70 °C using oil-rich Guaymas Basin sediments. In these cultures, archaea of the genus Candidatus Alkanophaga activate the alkanes with Acrs and completely oxidize the alkyl groups to CO2. Ca. Alkanophaga form a deep-branching sister clade to the methanotrophs ANME-1 and are closely related to the short-chain alkane oxidizers Ca. Syntrophoarchaeum. Incapable of sulfate reduction, Ca. Alkanophaga shuttle electrons released from alkane oxidation to the sulfate-reducing Ca. Thermodesulfobacterium syntrophicum. These syntrophic consortia are potential key players in petroleum degradation in heated oil reservoirs.
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Affiliation(s)
- Hanna Zehnle
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
- Faculty of Geosciences, University of Bremen, Bremen, Germany.
| | - Rafael Laso-Pérez
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
- Biogeochemistry and Microbial Ecology Department, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | - Julius Lipp
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Dietmar Riedel
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - David Benito Merino
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Andreas Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
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10
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Yu T, Wu W, Liang W, Wang Y, Hou J, Chen Y, Elvert M, Hinrichs KU, Wang F. Anaerobic degradation of organic carbon supports uncultured microbial populations in estuarine sediments. MICROBIOME 2023; 11:81. [PMID: 37081504 PMCID: PMC10116835 DOI: 10.1186/s40168-023-01531-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND A large proportion of prokaryotic microbes in marine sediments remains uncultured, hindering our understanding of their ecological functions and metabolic features. Recent environmental metagenomic studies suggested that many of these uncultured microbes contribute to the degradation of organic matter, accompanied by acetogenesis, but the supporting experimental evidence is limited. RESULTS Estuarine sediments were incubated with different types of organic matters under anaerobic conditions, and the increase of uncultured bacterial populations was monitored. We found that (1) lignin stimulated the increase of uncultured bacteria within the class Dehalococcoidia. Their ability to metabolize lignin was further supported by the presence of genes associated with a nearly complete degradation pathway of phenolic monomers in the Dehalococcoidia metagenome-assembled genomes (MAGs). (2) The addition of cellulose stimulated the increase of bacteria in the phylum Ca. Fermentibacterota and family Fibrobacterales, a high copy number of genes encoding extracellular endoglucanase or/and 1,4-beta-cellobiosidase for cellulose decomposition and multiple sugar transporters were present in their MAGs. (3) Uncultured lineages in the order Bacteroidales and the family Leptospiraceae were enriched by the addition of casein and oleic acid, respectively, a high copy number of genes encoding extracellular peptidases, and the complete β-oxidation pathway were found in those MAGs of Bacteroidales and Leptospiraceae, respectively. (4) The growth of unclassified bacteria of the order Clostridiales was found after the addition of both casein and cellulose. Their MAGs contained multiple copies of genes for extracellular peptidases and endoglucanase. Additionally, 13C-labeled acetate was produced in the incubations when 13C-labeled dissolved inorganic carbon was provided. CONCLUSIONS Our results provide new insights into the roles of microorganisms during organic carbon degradation in anaerobic estuarine sediments and suggest that these macro and single molecular organic carbons support the persistence and increase of uncultivated bacteria. Acetogenesis is an additional important microbial process alongside organic carbon degradation. Video Abstract.
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Affiliation(s)
- Tiantian Yu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, China
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weichao Wu
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
- Faculty of Geosciences, University of Bremen, 28359, Bremen, Germany
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Wenyue Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yunru Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Marcus Elvert
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
- Faculty of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
- Faculty of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Fengping Wang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, China.
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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11
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Zhang X, Xia L, Liu J, Wang Z, Yang Y, Wu Y, Yang Q, Huang L, Shen P. Comparative Genomic Analysis of a Methylorubrum rhodesianum MB200 Isolated from Biogas Digesters Provided New Insights into the Carbon Metabolism of Methylotrophic Bacteria. Int J Mol Sci 2023; 24:ijms24087521. [PMID: 37108681 PMCID: PMC10138955 DOI: 10.3390/ijms24087521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Methylotrophic bacteria are widely distributed in nature and can be applied in bioconversion because of their ability to use one-carbon source. The aim of this study was to investigate the mechanism underlying utilization of high methanol content and other carbon sources by Methylorubrum rhodesianum strain MB200 via comparative genomics and analysis of carbon metabolism pathway. The genomic analysis revealed that the strain MB200 had a genome size of 5.7 Mb and two plasmids. Its genome was presented and compared with that of the 25 fully sequenced strains of Methylobacterium genus. Comparative genomics revealed that the Methylorubrum strains had closer collinearity, more shared orthogroups, and more conservative MDH cluster. The transcriptome analysis of the strain MB200 in the presence of various carbon sources revealed that a battery of genes was involved in the methanol metabolism. These genes are involved in the following functions: carbon fixation, electron transfer chain, ATP energy release, and resistance to oxidation. Particularly, the central carbon metabolism pathway of the strain MB200 was reconstructed to reflect the possible reality of the carbon metabolism, including ethanol metabolism. Partial propionate metabolism involved in ethyl malonyl-CoA (EMC) pathway might help to relieve the restriction of the serine cycle. In addition, the glycine cleavage system (GCS) was observed to participate in the central carbon metabolism pathway. The study revealed the coordination of several metabolic pathways, where various carbon sources could induce associated metabolic pathways. To the best of our knowledge, this is the first study providing a more comprehensive understanding of the central carbon metabolism in Methylorubrum. This study provided a reference for potential synthetic and industrial applications of this genus and its use as chassis cells.
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Affiliation(s)
- Xi Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Liqing Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Jianyi Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Zihao Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Yanni Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Yiting Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Qingshan Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Luodong Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Peihong Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530005, China
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12
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Bacterial origins of thymidylate metabolism in Asgard archaea and Eukarya. Nat Commun 2023; 14:838. [PMID: 36792581 PMCID: PMC9931769 DOI: 10.1038/s41467-023-36487-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/03/2023] [Indexed: 02/17/2023] Open
Abstract
Asgard archaea include the closest known archaeal relatives of eukaryotes. Here, we investigate the evolution and function of Asgard thymidylate synthases and other folate-dependent enzymes required for the biosynthesis of DNA, RNA, amino acids and vitamins, as well as syntrophic amino acid utilization. Phylogenies of Asgard folate-dependent enzymes are consistent with their horizontal transmission from various bacterial groups. We experimentally validate the functionality of thymidylate synthase ThyX of the cultured 'Candidatus Prometheoarchaeum syntrophicum'. The enzyme efficiently uses bacterial-like folates and is inhibited by mycobacterial ThyX inhibitors, even though the majority of experimentally tested archaea are known to use carbon carriers distinct from bacterial folates. Our phylogenetic analyses suggest that the eukaryotic thymidylate synthase, required for de novo DNA synthesis, is not closely related to archaeal enzymes and might have been transferred from bacteria to protoeukaryotes during eukaryogenesis. Altogether, our study suggests that the capacity of eukaryotic cells to duplicate their genetic material is a sum of archaeal (replisome) and bacterial (thymidylate synthase) characteristics. We also propose that recent prevalent lateral gene transfer from bacteria has markedly shaped the metabolism of Asgard archaea.
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13
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Boyd ES, Spietz RL, Kour M, Colman DR. A naturalist perspective of microbiology: Examples from methanogenic archaea. Environ Microbiol 2023; 25:184-198. [PMID: 36367391 DOI: 10.1111/1462-2920.16285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]
Abstract
Storytelling has been the primary means of knowledge transfer over human history. The effectiveness and reach of stories are improved when the message is appropriate for the target audience. Oftentimes, the stories that are most well received and recounted are those that have a clear purpose and that are told from a variety of perspectives that touch on the varied interests of the target audience. Whether scientists realize or not, they are accustomed to telling stories of their own scientific discoveries through the preparation of manuscripts, presentations, and lectures. Perhaps less frequently, scientists prepare review articles or book chapters that summarize a body of knowledge on a given subject matter, meant to be more holistic recounts of a body of literature. Yet, by necessity, such summaries are often still narrow in their scope and are told from the perspective of a particular discipline. In other words, interdisciplinary reviews or book chapters tend to be the rarity rather than the norm. Here, we advocate for and highlight the benefits of interdisciplinary perspectives on microbiological subjects.
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Affiliation(s)
- Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Rachel L Spietz
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Manjinder Kour
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
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14
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Adam PS, Kolyfetis GE, Bornemann TLV, Vorgias CE, Probst AJ. Genomic remnants of ancestral methanogenesis and hydrogenotrophy in Archaea drive anaerobic carbon cycling. SCIENCE ADVANCES 2022; 8:eabm9651. [PMID: 36332026 PMCID: PMC9635834 DOI: 10.1126/sciadv.abm9651] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 09/19/2022] [Indexed: 05/19/2023]
Abstract
Anaerobic methane metabolism is among the hallmarks of Archaea, originating very early in their evolution. Here, we show that the ancestor of methane metabolizers was an autotrophic CO2-reducing hydrogenotrophic methanogen that possessed the two main complexes, methyl-CoM reductase (Mcr) and tetrahydromethanopterin-CoM methyltransferase (Mtr), the anaplerotic hydrogenases Eha and Ehb, and a set of other genes collectively called "methanogenesis markers" but could not oxidize alkanes. Overturning recent inferences, we demonstrate that methyl-dependent hydrogenotrophic methanogenesis has emerged multiple times independently, either due to a loss of Mtr while Mcr is inherited vertically or from an ancient lateral acquisition of Mcr. Even if Mcr is lost, Mtr, Eha, Ehb, and the markers can persist, resulting in mixotrophic metabolisms centered around the Wood-Ljungdahl pathway. Through their methanogenesis remnants, Thorarchaeia and two newly reconstructed order-level lineages in Archaeoglobi and Bathyarchaeia act as metabolically versatile players in carbon cycling of anoxic environments across the globe.
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Affiliation(s)
- Panagiotis S. Adam
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Corresponding author.
| | - George E. Kolyfetis
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15784 Athens, Greece
| | - Till L. V. Bornemann
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Constantinos E. Vorgias
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15784 Athens, Greece
| | - Alexander J. Probst
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Research Center One Health Ruhr, Research Alliance Ruhr, Environmental Metagenomics, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
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15
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Kohtz AJ, Jay ZJ, Lynes MM, Krukenberg V, Hatzenpichler R. Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments. ISME COMMUNICATIONS 2022; 2:86. [PMID: 37938354 PMCID: PMC9723716 DOI: 10.1038/s43705-022-00175-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/03/2022] [Accepted: 09/08/2022] [Indexed: 11/09/2023]
Abstract
Geothermal environments, including terrestrial hot springs and deep-sea hydrothermal sediments, often contain many poorly understood lineages of archaea. Here, we recovered ten metagenome-assembled genomes (MAGs) from geothermal sediments and propose that they constitute a new archaeal class within the TACK superphylum, "Candidatus Culexarchaeia", named after the Culex Basin in Yellowstone National Park. Culexarchaeia harbor distinct sets of proteins involved in key cellular processes that are either phylogenetically divergent or are absent from other closely related TACK lineages, with a particular divergence in cell division and cytoskeletal proteins. Metabolic reconstruction revealed that Culexarchaeia have the capacity to metabolize a wide variety of organic and inorganic substrates. Notably, Culexarchaeia encode a unique modular, membrane associated, and energy conserving [NiFe]-hydrogenase complex that potentially interacts with heterodisulfide reductase (Hdr) subunits. Comparison of this [NiFe]-hydrogenase complex with similar complexes from other archaea suggests that interactions between membrane associated [NiFe]-hydrogenases and Hdr may be more widespread than previously appreciated in both methanogenic and non-methanogenic lifestyles. The analysis of Culexarchaeia further expands our understanding of the phylogenetic and functional diversity of lineages within the TACK superphylum and the ecology, physiology, and evolution of these organisms in extreme environments.
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Affiliation(s)
- Anthony J Kohtz
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Zackary J Jay
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Mackenzie M Lynes
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Viola Krukenberg
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA.
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
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16
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Pi HW, Lin JJ, Chen CA, Wang PH, Chiang YR, Huang CC, Young CC, Li WH. Origin and evolution of nitrogen fixation in prokaryotes. Mol Biol Evol 2022; 39:6673025. [PMID: 35993177 PMCID: PMC9447857 DOI: 10.1093/molbev/msac181] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The origin of nitrogen fixation is an important issue in evolutionary biology. While nitrogen is required by all living organisms, only a small fraction of bacteria and archaea can fix nitrogen. The prevailing view is that nitrogen fixation first evolved in archaea and was later transferred to bacteria. However, nitrogen-fixing (Nif) bacteria are far larger in number and far more diverse in ecological niches than Nif archaea. We, therefore, propose the bacteria-first hypothesis, which postulates that nitrogen fixation first evolved in bacteria and was later transferred to archaea. As >30,000 prokaryotic genomes have been sequenced, we conduct an in-depth comparison of the two hypotheses. We first identify the six genes involved in nitrogen fixation in all sequenced prokaryotic genomes and then reconstruct phylogenetic trees using the six Nif proteins individually or in combination. In each of these trees, the earliest lineages are bacterial Nif protein sequences and in the oldest clade (group) the archaeal sequences are all nested inside bacterial sequences, suggesting that the Nif proteins first evolved in bacteria. The bacteria-first hypothesis is further supported by the observation that the majority of Nif archaea carry the major bacterial Mo (molybdenum) transporter (ModABC) rather than the archaeal Mo transporter (WtpABC). Moreover, in our phylogeny of all available ModA and WtpA protein sequences, the earliest lineages are bacterial sequences while archaeal sequences are nested inside bacterial sequences. Furthermore, the bacteria-first hypothesis is supported by available isotopic data. In conclusion, our study strongly supports the bacteria-first hypothesis.
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Affiliation(s)
- Hong Wei Pi
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529
| | - Jinn Jy Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529
| | - Chi An Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529.,Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| | - Po Hsiang Wang
- Graduate Institute of Environmental Engineering, National Central University, Taoyuan, Taiwan 32001.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan 145-0061
| | - Yin Ru Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529
| | - Chieh Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan 402
| | - Chiu Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan 402
| | - Wen Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529.,Department of Ecology and Evolution, University of Chicago, Chicago 60637, USA
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17
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Santos Correa S, Schultz J, Lauersen KJ, Soares Rosado A. Natural carbon fixation and advances in synthetic engineering for redesigning and creating new fixation pathways. J Adv Res 2022; 47:75-92. [PMID: 35918056 PMCID: PMC10173188 DOI: 10.1016/j.jare.2022.07.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/30/2022] [Accepted: 07/25/2022] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Autotrophic carbon fixation is the primary route through which organic carbon enters the biosphere, and it is a key step in the biogeochemical carbon cycle. The Calvin-Benson-Bassham pathway, which is predominantly found in plants, algae, and some bacteria (mainly cyanobacteria), was previously considered to be the sole carbon-fixation pathway. However, the discovery of a new carbon-fixation pathway in sulfurous green bacteria almost two decades ago encouraged further research on previously overlooked ancient carbon-fixation pathways in taxonomically and phylogenetically distinct microorganisms. AIM OF REVIEW In this review, we summarize the six known natural carbon-fixation pathways and outline the newly proposed additions to this list. We also discuss the recent achievements in synthetic carbon fixation and the importance of the metabolism of thermophilic microorganisms in this field. KEY SCIENTIFIC CONCEPTS OF REVIEW Currently, at least six carbon-fixation routes have been confirmed in Bacteria and Archaea. Other possible candidate routes have also been suggested on the basis of emerging "omics" data analyses, expanding our knowledge and stimulating discussions on the importance of these pathways in the way organisms acquire carbon. Notably, the currently known natural fixation routes cannot balance the excessive anthropogenic carbon emissions in a highly unbalanced global carbon cycle. Therefore, significant efforts have also been made to improve the existing carbon-fixation pathways and/or design new efficient in vitro and in vivo synthetic pathways.
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Affiliation(s)
- Sulamita Santos Correa
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Junia Schultz
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Kyle J Lauersen
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Alexandre Soares Rosado
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Bioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
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18
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Garcia PS, Gribaldo S, Borrel G. Diversity and Evolution of Methane-Related Pathways in Archaea. Annu Rev Microbiol 2022; 76:727-755. [PMID: 35759872 DOI: 10.1146/annurev-micro-041020-024935] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methane is one of the most important greenhouse gases on Earth and holds an important place in the global carbon cycle. Archaea are the only organisms that use methanogenesis to produce energy and rely on the methyl-coenzyme M reductase (Mcr) complex. Over the last decade, new results have significantly reshaped our view of the diversity of methane-related pathways in the Archaea. Many new lineages that synthesize or use methane have been identified across the whole archaeal tree, leading to a greatly expanded diversity of substrates and mechanisms. In this review, we present the state of the art of these advances and how they challenge established scenarios of the origin and evolution of methanogenesis, and we discuss the potential trajectories that may have led to this strikingly wide range of metabolisms.Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Pierre Simon Garcia
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
| | - Guillaume Borrel
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
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19
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Hu G, Guo L, Gao C, Song W, Liu L, Chen X. Synergistic Metabolism of Glucose and Formate Increases the Yield of Short-Chain Organic Acids in Escherichia coli. ACS Synth Biol 2022; 11:135-143. [PMID: 34979802 DOI: 10.1021/acssynbio.1c00289] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microbial cell factories using a single carbon source (e.g., sugars) have been used to produce a wide variety of chemicals. However, this process is often accompanied by stoichiometric constraints on carbons and redox cofactors. Here, a synthetic pathway was designed and constructed in Escherichia coli to synergistically use glucose and formate as mixed carbon sources. By optimizing this synthetic pathway via enzyme mining, protein engineering, and bioprocess approaches, the yield of pyruvate from glucose was enhanced to 94% of the theoretical glycolysis yield, reaching 1.88 mol/mol. Finally, the optimized synthetic pathway was integrated with a phosphite reductase-based NADH regeneration system in malate-producing E. coli, resulting in the conversion of glucose into l-malate with a high yield of up to 1.65 mol/mol. This synergistic carbon metabolism strategy can be used to establish carbon- and energy-efficient productive processes.
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Affiliation(s)
- Guipeng Hu
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Wei Song
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
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20
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Bornemann TLV, Adam PS, Turzynski V, Schreiber U, Figueroa-Gonzalez PA, Rahlff J, Köster D, Schmidt TC, Schunk R, Krauthausen B, Probst AJ. Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing. Nat Commun 2022; 13:284. [PMID: 35022403 PMCID: PMC8755723 DOI: 10.1038/s41467-021-27783-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 12/02/2021] [Indexed: 12/30/2022] Open
Abstract
Earth’s mantle releases 38.7 ± 2.9 Tg/yr CO2 along with other reduced and oxidized gases to the atmosphere shaping microbial metabolism at volcanic sites across the globe, yet little is known about its impact on microbial life under non-thermal conditions. Here, we perform comparative metagenomics coupled to geochemical measurements of deep subsurface fluids from a cold-water geyser driven by mantle degassing. Key organisms belonging to uncultivated Candidatus Altiarchaeum show a global biogeographic pattern and site-specific adaptations shaped by gene loss and inter-kingdom horizontal gene transfer. Comparison of the geyser community to 16 other publicly available deep subsurface sites demonstrate a conservation of chemolithoautotrophic metabolism across sites. In silico replication measures suggest a linear relationship of bacterial replication with ecosystems depth with the exception of impacted sites, which show near surface characteristics. Our results suggest that subsurface ecosystems affected by geological degassing are hotspots for microbial life in the deep biosphere. Geological degassing can impact subsurface metabolism. Here, the authors describe microbial communities from a cold-water geyser are described and compared with other deep subsurface sites, finding a key role for an uncultivated archaeon.
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Affiliation(s)
- Till L V Bornemann
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Panagiotis S Adam
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Victoria Turzynski
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Ulrich Schreiber
- Department of Geology, University Duisburg-Essen, Essen, Germany
| | | | - Janina Rahlff
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany.,Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linneaus University, Kalmar, Sweden
| | - Daniel Köster
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Torsten C Schmidt
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.,Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, Essen, Germany
| | | | - Bernhard Krauthausen
- Institute of Applied Geosciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Alexander J Probst
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany. .,Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, Essen, Germany.
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21
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Thomas CM, Taib N, Gribaldo S, Borrel G. Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis. ISME COMMUNICATIONS 2021; 1:47. [PMID: 37938279 PMCID: PMC9723798 DOI: 10.1038/s43705-021-00050-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/08/2021] [Accepted: 08/26/2021] [Indexed: 05/15/2023]
Abstract
Other than the Methanobacteriales and Methanomassiliicoccales, the characteristics of archaea that inhabit the animal microbiome are largely unknown. Methanimicrococcus blatticola, a member of the Methanosarcinales, currently reunites two unique features within this order: it is a colonizer of the animal digestive tract and can only reduce methyl compounds with H2 for methanogenesis, a increasingly recognized metabolism in the archaea and whose origin remains debated. To understand the origin of these characteristics, we have carried out a large-scale comparative genomic analysis. We infer the loss of more than a thousand genes in M. blatticola, by far the largest genome reduction across all Methanosarcinales. These include numerous elements for sensing the environment and adapting to more stable gut conditions, as well as a significant remodeling of the cell surface components likely involved in host and gut microbiota interactions. Several of these modifications parallel those previously observed in phylogenetically distant archaea and bacteria from the animal microbiome, suggesting large-scale convergent mechanisms of adaptation to the gut. Strikingly, M. blatticola has lost almost all genes coding for the H4MPT methyl branch of the Wood-Ljungdahl pathway (to the exception of mer), a phenomenon never reported before in any member of Class I or Class II methanogens. The loss of this pathway illustrates one of the evolutionary processes that may have led to the emergence of methyl-reducing hydrogenotrophic methanogens, possibly linked to the colonization of organic-rich environments (including the animal gut) where both methyl compounds and hydrogen are abundant.
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Affiliation(s)
- Courtney M Thomas
- Department of Microbiology, UMR 2001, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Najwa Taib
- Department of Microbiology, UMR 2001, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
| | - Simonetta Gribaldo
- Department of Microbiology, UMR 2001, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
| | - Guillaume Borrel
- Department of Microbiology, UMR 2001, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France.
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22
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Grinter R, Greening C. Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea. FEMS Microbiol Rev 2021; 45:fuab021. [PMID: 33851978 PMCID: PMC8498797 DOI: 10.1093/femsre/fuab021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/11/2021] [Indexed: 12/11/2022] Open
Abstract
Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis and xenobiotic biodegradation. In the last 5 years, there has been much progress in understanding its distribution, biosynthesis, role and applications. Whereas F420 was previously thought to be confined to Actinobacteria and Euryarchaeota, new evidence indicates it is synthesized across the bacterial and archaeal domains, as a result of extensive horizontal and vertical biosynthetic gene transfer. F420 was thought to be synthesized through one biosynthetic pathway; however, recent advances have revealed variants of this pathway and have resolved their key biosynthetic steps. In parallel, new F420-dependent biosynthetic and metabolic processes have been discovered. These advances have enabled the heterologous production of F420 and identified enantioselective F420H2-dependent reductases for biocatalysis. New research has also helped resolve how microorganisms use F420 to influence human and environmental health, providing opportunities for tuberculosis treatment and methane mitigation. A total of 50 years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.
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Affiliation(s)
- Rhys Grinter
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Chris Greening
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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23
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Comparative Genomics Reveals Thermal Adaptation and a High Metabolic Diversity in " Candidatus Bathyarchaeia". mSystems 2021; 6:e0025221. [PMID: 34282939 PMCID: PMC8407382 DOI: 10.1128/msystems.00252-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
"Candidatus Bathyarchaeia" is a phylogenetically diverse and widely distributed lineage often in high abundance in anoxic submarine sediments; however, their evolution and ecological roles in terrestrial geothermal habitats are poorly understood. In the present study, 35 Ca. Bathyarchaeia metagenome-assembled genomes (MAGs) were recovered from hot spring sediments in Tibet and Yunnan, China. Phylogenetic analysis revealed all MAGs of Ca. Bathyarchaeia can be classified into 7 orders and 15 families. Among them, 4 families have been first discovered in the present study, significantly expanding the known diversity of Ca. Bathyarchaeia. Comparative genomics demonstrated Ca. Bathyarchaeia MAGs from thermal habitats to encode a large variety of genes related to carbohydrate degradation, which are likely a metabolic adaptation of these organisms to a lifestyle at high temperatures. At least two families are potential methanogens/alkanotrophs, indicating a potential for the catalysis of short-chain hydrocarbons. Three MAGs from Family-7.3 are identified as alkanotrophs due to the detection of an Mcr complex. Family-2 contains the largest number of genes relevant to alkyl-CoM transformation, indicating the potential for methylotrophic methanogenesis, although their evolutionary history suggests the ancestor of Ca. Bathyarchaeia was unable to metabolize alkanes. Subsequent lineages have acquired the ability via horizontal gene transfer. Overall, our study significantly expands our knowledge and understanding of the metabolic capabilities, habitat adaptations, and evolution of Ca. Bathyarchaeia in thermal environments. IMPORTANCE Ca. Bathyarchaeia MAGs from terrestrial hot spring habitats are poorly revealed, though they have been studied extensively in marine ecosystems. In this study, we uncovered the metabolic capabilities and ecological role of Ca. Bathyarchaeia in hot springs and give a comprehensive comparative analysis between thermal and nonthermal habitats to reveal the thermal adaptability of Ca. Bathyarchaeia. Also, we attempt to determine the evolutionary history of methane/alkane metabolism in Ca. Bathyarchaeia, since it appears to be the first archaea beyond Euryarchaeota which contains the mcrABG genes. The reclassification of Ca. Bathyarchaeia and significant genomic differences among different lineages largely expand our knowledge on these cosmopolitan archaea, which will be beneficial in guiding the future studies.
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24
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Devos DP. Reconciling Asgardarchaeota Phylogenetic Proximity to Eukaryotes and Planctomycetes Cellular Features in the Evolution of Life. Mol Biol Evol 2021; 38:3531-3542. [PMID: 34229349 PMCID: PMC8382908 DOI: 10.1093/molbev/msab186] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The relationship between the three domains of life—Archaea, Bacteria, and Eukarya—is one of Biology’s greatest mysteries. Current favored models imply two ancestral domains, Bacteria and Archaea, with eukaryotes originating within Archaea. This type of models has been supported by the recent description of the Asgardarchaeota, the closest prokaryotic relatives of eukaryotes. However, there are many problems associated with any scenarios implying that eukaryotes originated from within the Archaea, including genome mosaicism, phylogenies, the cellular organization of the Archaea, and their ancestral character. By contrast, all models of eukaryogenesis fail to consider two relevant discoveries: the detection of membrane coat proteins, and of phagocytosis-related processes in Planctomycetes, which are among the bacteria with the most developed endomembrane system. Consideration of these often overlooked features and others found in Planctomycetes and related bacteria suggest an evolutionary model based on a single ancestral domain. In this model, the proximity of Asgard and eukaryotes is not rejected but instead, Asgard are considered as diverging away from a common ancestor instead of on the way toward the eukaryotic ancestor. This model based on a single ancestral domain solves most of the ambiguities associated with the ones based on two ancestral domains. The single-domain model is better suited to explain the origin and evolution of all three domains of life, blurring the distinctions between them. Support for this model as well as the opportunities that it presents not only for reinterpreting previous results, but also for planning future experiments, are explored.
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Affiliation(s)
- Damien P Devos
- Centro Andaluz de Biología del Desarrollo (CABD) - CSIC, Junta de Andalucía, Universidad Pablo de Olavide, Carretera de Utrera Km 1, Seville, 41013, Spain
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25
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Wang Y, Wegener G, Williams TA, Xie R, Hou J, Tian C, Zhang Y, Wang F, Xiao X. A methylotrophic origin of methanogenesis and early divergence of anaerobic multicarbon alkane metabolism. SCIENCE ADVANCES 2021; 7:eabj1453. [PMID: 34215592 PMCID: PMC11057702 DOI: 10.1126/sciadv.abj1453] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/21/2021] [Indexed: 06/13/2023]
Abstract
Methanogens are considered as one of the earliest life forms on Earth, and together with anaerobic methane-oxidizing archaea, they have crucial effects on climate stability. However, the origin and evolution of anaerobic alkane metabolism in the domain Archaea remain controversial. Here, we present evidence that methylotrophic methanogenesis was the ancestral form of this metabolism. Carbon dioxide-reducing methanogenesis developed later through the evolution of tetrahydromethanopterin S-methyltransferase, which linked methanogenesis to the Wood-Ljungdahl pathway for energy conservation. Anaerobic multicarbon alkane metabolisms in Archaea also originated early, with genes coding for the activation of short-chain or even long-chain alkanes likely evolving from an ethane-metabolizing ancestor. These genes were likely horizontally transferred to multiple archaeal clades including Candidatus (Ca) Bathyarchaeia, Ca. Lokiarchaeia, Ca. Hadarchaeia, and the methanogenic Ca. Methanoliparia.
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Affiliation(s)
- Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, BS8 1TH Bristol, UK
| | - Ruize Xie
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen Tian
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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26
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De Anda V, Chen LX, Dombrowski N, Hua ZS, Jiang HC, Banfield JF, Li WJ, Baker BJ. Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways. Nat Commun 2021; 12:2404. [PMID: 33893309 PMCID: PMC8065059 DOI: 10.1038/s41467-021-22736-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 03/18/2021] [Indexed: 02/02/2023] Open
Abstract
Geothermal environments, such as hot springs and hydrothermal vents, are hotspots for carbon cycling and contain many poorly described microbial taxa. Here, we reconstructed 15 archaeal metagenome-assembled genomes (MAGs) from terrestrial hot spring sediments in China and deep-sea hydrothermal vent sediments in Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct group within the TACK superphylum, and thus we propose their classification as a new phylum, 'Brockarchaeota', named after Thomas Brock for his seminal research in hot springs. Based on the MAG sequence information, we infer that some Brockarchaeota are uniquely capable of mediating non-methanogenic anaerobic methylotrophy, via the tetrahydrofolate methyl branch of the Wood-Ljungdahl pathway and reductive glycine pathway. The hydrothermal vent genotypes appear to be obligate fermenters of plant-derived polysaccharides that rely mostly on substrate-level phosphorylation, as they seem to lack most respiratory complexes. In contrast, hot spring lineages have alternate pathways to increase their ATP yield, including anaerobic methylotrophy of methanol and trimethylamine, and potentially use geothermally derived mercury, arsenic, or hydrogen. Their broad distribution and their apparent anaerobic metabolic versatility indicate that Brockarchaeota may occupy previously overlooked roles in anaerobic carbon cycling.
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Affiliation(s)
- Valerie De Anda
- Department of Marine Science, University of Texas Austin, Port Aransas, TX, 78373, USA
| | - Lin-Xing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Nina Dombrowski
- Department of Marine Science, University of Texas Austin, Port Aransas, TX, 78373, USA
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Den Burg, Netherlands
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, PR China
| | - Hong-Chen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, People's Republic of China.
| | - Brett J Baker
- Department of Marine Science, University of Texas Austin, Port Aransas, TX, 78373, USA.
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27
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Wang Y, Wegener G, Williams TA, Xie R, Hou J, Wang F, Xiao X. A methylotrophic origin of methanogenesis and early divergence of anaerobic multicarbon alkane metabolism. SCIENCE ADVANCES 2021; 7:eabd7180. [PMID: 33568477 PMCID: PMC7875538 DOI: 10.1126/sciadv.abd7180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/23/2020] [Indexed: 05/17/2023]
Abstract
Methanogens are considered as one of the earliest life forms on Earth, and together with anaerobic methane-oxidizing archaea, they have crucial effects on climate stability. Yet, the origin and evolution of anaerobic alkane metabolism in the domain Archaea remain controversial. Here, we show that methanogenesis was already present in the common ancestor of Euryarchaeota, TACK archaea, and Asgard archaea likely in the late Hadean or early Archean eon and that the ancestral methanogen was dependent on methylated compounds and hydrogen. Carbon dioxide-reducing methanogenesis developed later through the evolution of tetrahydromethanopterin S-methyltransferase, which linked methanogenesis to the Wood-Ljungdahl pathway for energy conservation. Multicarbon alkane metabolisms in Archaea also originated early, with genes coding for the activation of short- or even long-chain alkanes likely evolving from an ethane-metabolizing ancestor. These genes were likely horizontally transferred to multiple archaeal clades including Candidatus (Ca) Bathyarchaeota, Ca. Helarchaeota, Ca Hadesarchaeota, and the methanogenic Ca. Methanoliparia.
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Affiliation(s)
- Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, BS8 1TH Bristol, UK
| | - Ruize Xie
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean & Civil Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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28
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Ślesak I, Ślesak H. The activity of RubisCO and energy demands for its biosynthesis. Comparative studies with CO 2-reductases. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153337. [PMID: 33421837 DOI: 10.1016/j.jplph.2020.153337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/14/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
Most CO2 on Earth is fixed into organic matter via reactions catalysed by enzymes called carboxylases. CO2-fixation via carboxylases occurs in the Calvin-Benson-Bassham (CBB) cycle, and the crucial role in this cycle is played by RubisCO (D-ribulose 1,5-bisphosphate carboxylase/oxygenase). CO2 can also be fixed by pathways, where a reduction of CO2 to formate or carbon monoxide (CO) occurs. The latter reactions are performed by so-called CO2-reductases e.g. formate dehydrogenase (FDH), carbon-monooxide (CO) dehydrogenase (CODH), and crotonyl-CoA reductase/carboxylase (CCR). In general, a simple model of enzymatic activity based only on a turnover rate of an enzyme for an appropriate substrate (kcat) is insufficient. Based on estimated metabolic costs of each amino acid, the average energetic costs of amino acid biosynthesis (Eaa), and the total costs (ET) for selected CO2-fixing enzymes were analyzed concerning 1) kcat for CO2 (kC), and 2) specificity factor (Srel) for RubisCO. A comparison of Eaa and ET to their kC showed that CODH and FDHs do not need to be more efficient enzymes in CO2 capturing pathways than some forms of RubisCO. CCR was the only both low-cost and highly active CO2-fixing enzyme. The obtained results showed also that there exists an evolutionarily conserved trade-off between Srel of RubisCOs and the energetic demands needed for their biosynthesis. Phylogenetic analysis demonstrated that RubisCO, CODH, FDH, and CCR are enzymes formed as a result of parallel evolution. Moreover, the kinetic parameters (kC) of CO2-fixing enzymes were plausibly optimized already at the early stages of life evolution on Earth.
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Affiliation(s)
- Ireneusz Ślesak
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Kraków, Poland.
| | - Halina Ślesak
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland
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29
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Raggi L, García-Guevara F, Godoy-Lozano EE, Martínez-Santana A, Escobar-Zepeda A, Gutierrez-Rios RM, Loza A, Merino E, Sanchez-Flores A, Licea-Navarro A, Pardo-Lopez L, Segovia L, Juarez K. Metagenomic Profiling and Microbial Metabolic Potential of Perdido Fold Belt (NW) and Campeche Knolls (SE) in the Gulf of Mexico. Front Microbiol 2020; 11:1825. [PMID: 32903729 PMCID: PMC7438803 DOI: 10.3389/fmicb.2020.01825] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/10/2020] [Indexed: 01/04/2023] Open
Abstract
The Gulf of Mexico (GoM) is a particular environment that is continuously exposed to hydrocarbon compounds that may influence the microbial community composition. We carried out a metagenomic assessment of the bacterial community to get an overall view of this geographical zone. We analyzed both taxonomic and metabolic markers profiles to explain how the indigenous GoM microorganims participate in the biogeochemical cycling. Two geographically distant regions in the GoM, one in the north-west (NW) and one in the south-east (SE) of the GoM were analyzed and showed differences in their microbial composition and metabolic potential. These differences provide evidence the delicate equilibrium that sustains microbial communities and biogeochemical cycles. Based on the taxonomy and gene groups, the NW are more oxic sediments than SE ones, which have anaerobic conditions. Both water and sediments show the expected sulfur, nitrogen, and hydrocarbon metabolism genes, with particularly high diversity of the hydrocarbon-degrading ones. Accordingly, many of the assigned genera were associated with hydrocarbon degradation processes, Nitrospira and Sva0081 were the most abundant in sediments, while Vibrio, Alteromonas, and Alcanivorax were mostly detected in water samples. This basal-state analysis presents the GoM as a potential source of aerobic and anaerobic hydrocarbon degradation genes important for the ecological dynamics of hydrocarbons and the potential use for water and sediment bioremediation processes.
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Affiliation(s)
- Luciana Raggi
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,CONACYT-Laboratorio de Biotecnología Acuícola, Instituto de Investigaciones Agropecuarias y Forestales, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | | | - E Ernestina Godoy-Lozano
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Centro de Investigación Sobre Enfermedades Infecciosas, Departamento de Bioinformática en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | | | | | | | - Antonio Loza
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Enrique Merino
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexei Licea-Navarro
- Laboratorio de Inmunología Molecular y Biotoxinas, Departamento de Innovación Biomedica, CICESE, Ensenada, Mexico
| | - Liliana Pardo-Lopez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Lorenzo Segovia
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Katy Juarez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Merino N, Kawai M, Boyd ES, Colman DR, McGlynn SE, Nealson KH, Kurokawa K, Hongoh Y. Single-Cell Genomics of Novel Actinobacteria With the Wood-Ljungdahl Pathway Discovered in a Serpentinizing System. Front Microbiol 2020; 11:1031. [PMID: 32655506 PMCID: PMC7325909 DOI: 10.3389/fmicb.2020.01031] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/27/2020] [Indexed: 01/04/2023] Open
Abstract
Serpentinite-hosted systems represent modern-day analogs of early Earth environments. In these systems, water-rock interactions generate highly alkaline and reducing fluids that can contain hydrogen, methane, and low-molecular-weight hydrocarbons-potent reductants capable of fueling microbial metabolism. In this study, we investigated the microbiota of Hakuba Happo hot springs (∼50°C; pH∼10.5-11), located in Nagano (Japan), which are impacted by the serpentinization process. Analysis of the 16S rRNA gene amplicon sequences revealed that the bacterial community comprises Nitrospirae (47%), "Parcubacteria" (19%), Deinococcus-Thermus (16%), and Actinobacteria (9%), among others. Notably, only 57 amplicon sequence variants (ASV) were detected, and fifteen of these accounted for 90% of the amplicons. Among the abundant ASVs, an early-branching, uncultivated actinobacterial clade identified as RBG-16-55-12 in the SILVA database was detected. Ten single-cell genomes (average pairwise nucleotide identity: 0.98-1.00; estimated completeness: 33-93%; estimated genome size: ∼2.3 Mb) that affiliated with this clade were obtained. Taxonomic classification using single copy genes indicates that the genomes belong to the actinobacterial class-level clade UBA1414 in the Genome Taxonomy Database. Based on metabolic pathway predictions, these actinobacteria are anaerobes, capable of glycolysis, dissimilatory nitrate reduction and CO2 fixation via the Wood-Ljungdahl (WL) pathway. Several other genomes within UBA1414 and two related class-level clades also encode the WL pathway, which has not yet been reported for the Actinobacteria phylum. For the Hakuba actinobacterium, the energy metabolism related to the WL pathway is likely supported by a combination of the Rnf complex, group 3b and 3d [NiFe]-hydrogenases, [FeFe]-hydrogenases, and V-type (H+/Na+ pump) ATPase. The genomes also harbor a form IV ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) complex, also known as a RubisCO-like protein, and contain signatures of interactions with viruses, including clustered regularly interspaced short palindromic repeat (CRISPR) regions and several phage integrases. This is the first report and detailed genome analysis of a bacterium within the Actinobacteria phylum capable of utilizing the WL pathway. The Hakuba actinobacterium is a member of the clade UBA1414/RBG-16-55-12, formerly within the group "OPB41." We propose to name this bacterium 'Candidatus Hakubanella thermoalkaliphilus.'
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Affiliation(s)
- Nancy Merino
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States.,Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Mikihiko Kawai
- School of Life Sciences and Technology, Tokyo Institute of Technology, Tokyo, Japan.,Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan.,Blue Marble Space Institute of Science, Seattle, WA, United States
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Ken Kurokawa
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Department of Informatics, National Institute of Genetics, Shizuoka, Japan
| | - Yuichi Hongoh
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,School of Life Sciences and Technology, Tokyo Institute of Technology, Tokyo, Japan
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Diversity, ecology and evolution of Archaea. Nat Microbiol 2020; 5:887-900. [PMID: 32367054 DOI: 10.1038/s41564-020-0715-z] [Citation(s) in RCA: 194] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 03/30/2020] [Indexed: 12/23/2022]
Abstract
Compared to bacteria, our knowledge of archaeal biology is limited. Historically, microbiologists have mostly relied on culturing and single-gene diversity surveys to understand Archaea in nature. However, only six of the 27 currently proposed archaeal phyla have cultured representatives. Advances in genomic sequencing and computational approaches are revolutionizing our understanding of Archaea. The recovery of genomes belonging to uncultured groups from the environment has resulted in the description of several new phyla, many of which are globally distributed and are among the predominant organisms on the planet. In this Review, we discuss how these genomes, together with long-term enrichment studies and elegant in situ measurements, are providing insights into the metabolic capabilities of the Archaea. We also debate how such studies reveal how important Archaea are in mediating an array of ecological processes, including global carbon and nutrient cycles, and how this increase in archaeal diversity has expanded our view of the tree of life and early archaeal evolution, and has provided new insights into the origin of eukaryotes.
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Methylofuran is a prosthetic group of the formyltransferase/hydrolase complex and shuttles one-carbon units between two active sites. Proc Natl Acad Sci U S A 2019; 116:25583-25590. [PMID: 31776258 PMCID: PMC6926001 DOI: 10.1073/pnas.1911595116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Methylotrophs play a crucial role in the global carbon cycle as they oxidize reduced one-carbon compounds such as methanol or methane to CO2. The step-wise conversion of these substrates generally takes place while the one-carbon units are bound to diffusible carrier molecules. However, our crystal structure of the formyltransferase/hydrolase complex from Methylorubrum extorquens demonstrates that the one-carbon carrier methylofuran tightly binds to the enzyme via its extended and branched polyglutamate chain. A swinging motion of the coenzyme then shuttles one-carbon units between the two active sites of the enzyme complex over a distance of 50 Å. The structure further highlights how the bacterial formate generation system relates to the archaeal CO2 fixation system. Methylotrophy, the ability of microorganisms to grow on reduced one-carbon substrates such as methane or methanol, is a feature of various bacterial species. The prevailing oxidation pathway depends on tetrahydromethanopterin (H4MPT) and methylofuran (MYFR), an analog of methanofuran from methanogenic archaea. Formyltransferase/hydrolase complex (Fhc) generates formate from formyl-H4MPT in two consecutive reactions where MYFR acts as a carrier of one-carbon units. Recently, we chemically characterized MYFR from the model methylotroph Methylorubrum extorquens and identified an unusually long polyglutamate side chain of up to 24 glutamates. Here, we report on the crystal structure of Fhc to investigate the function of the polyglutamate side chain in MYFR and the relatedness of the enzyme complex with the orthologous enzymes in archaea. We identified MYFR as a prosthetic group that is tightly, but noncovalently, bound to Fhc. Surprisingly, the structure of Fhc together with MYFR revealed that the polyglutamate side chain of MYFR is branched and contains glutamates with amide bonds at both their α- and γ-carboxyl groups. This negatively charged and branched polyglutamate side chain interacts with a cluster of conserved positively charged residues of Fhc, allowing for strong interactions. The MYFR binding site is located equidistantly from the active site of the formyltransferase (FhcD) and metallo-hydrolase (FhcA). The polyglutamate serves therefore an additional function as a swinging linker to shuttle the one-carbon carrying amine between the two active sites, thereby likely increasing overall catalysis while decreasing the need for high intracellular MYFR concentrations.
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