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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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2
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Lynes MM, Jay ZJ, Kohtz AJ, Hatzenpichler R. Methylotrophic methanogenesis in the Archaeoglobi revealed by cultivation of Ca. Methanoglobus hypatiae from a Yellowstone hot spring. THE ISME JOURNAL 2024; 18:wrae026. [PMID: 38452205 PMCID: PMC10945360 DOI: 10.1093/ismejo/wrae026] [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: 11/13/2023] [Revised: 01/09/2024] [Accepted: 02/08/2024] [Indexed: 03/09/2024]
Abstract
Over the past decade, environmental metagenomics and polymerase chain reaction-based marker gene surveys have revealed that several lineages beyond just a few well-established groups within the Euryarchaeota superphylum harbor the genetic potential for methanogenesis. One of these groups are the Archaeoglobi, a class of thermophilic Euryarchaeota that have long been considered to live non-methanogenic lifestyles. Here, we enriched Candidatus Methanoglobus hypatiae, a methanogen affiliated with the family Archaeoglobaceae, from a hot spring in Yellowstone National Park. The enrichment is sediment-free, grows at 64-70°C and a pH of 7.8, and produces methane from mono-, di-, and tri-methylamine. Ca. M. hypatiae is represented by a 1.62 Mb metagenome-assembled genome with an estimated completeness of 100% and accounts for up to 67% of cells in the culture according to fluorescence in situ hybridization. Via genome-resolved metatranscriptomics and stable isotope tracing, we demonstrate that Ca. M. hypatiae expresses methylotrophic methanogenesis and energy-conserving pathways for reducing monomethylamine to methane. The detection of Archaeoglobi populations related to Ca. M. hypatiae in 36 geochemically diverse geothermal sites within Yellowstone National Park, as revealed through the examination of previously published gene amplicon datasets, implies a previously underestimated contribution to anaerobic carbon cycling in extreme ecosystems.
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Affiliation(s)
- Mackenzie M Lynes
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, Thermal Biology Institute, Montana State University, Bozeman, MT 59717, United States
| | - Zackary J Jay
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, Thermal Biology Institute, Montana State University, Bozeman, MT 59717, United States
| | - Anthony J Kohtz
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, Thermal Biology Institute, Montana State University, Bozeman, MT 59717, United States
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, Thermal Biology Institute, Montana State University, Bozeman, MT 59717, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, United States
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3
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Vulcano F, Hribovšek P, Denny EO, Steen IH, Stokke R. Potential for homoacetogenesis via the Wood-Ljungdahl pathway in Korarchaeia lineages from marine hydrothermal vents. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:698-707. [PMID: 37218095 PMCID: PMC10667645 DOI: 10.1111/1758-2229.13168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 05/05/2023] [Indexed: 05/24/2023]
Abstract
The Wood-Ljungdahl pathway (WLP) is a key metabolic component of acetogenic bacteria where it acts as an electron sink. In Archaea, despite traditionally being linked to methanogenesis, the pathway has been found in several Thermoproteota and Asgardarchaeota lineages. In Bathyarchaeia and Lokiarchaeia, its presence has been linked to a homoacetogenic metabolism. Genomic evidence from marine hydrothermal genomes suggests that lineages of Korarchaeia could also encode the WLP. In this study, we reconstructed 50 Korarchaeia genomes from marine hydrothermal vents along the Arctic Mid-Ocean Ridge, substantially expanding the Korarchaeia class with several taxonomically novel genomes. We identified a complete WLP in several deep-branching lineages, showing that the presence of the WLP is conserved at the root of the Korarchaeia. No methyl-CoM reductases were encoded by genomes with the WLP, indicating that the WLP is not linked to methanogenesis. By assessing the distribution of hydrogenases and membrane complexes for energy conservation, we show that the WLP is likely used as an electron sink in a fermentative homoacetogenic metabolism. Our study confirms previous hypotheses that the WLP has evolved independently from the methanogenic metabolism in Archaea, perhaps due to its propensity to be combined with heterotrophic fermentative metabolisms.
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Affiliation(s)
- Francesca Vulcano
- Department of Biological Sciences, Centre for Deep Sea ResearchUniversity of BergenBergenNorway
| | - Petra Hribovšek
- Department of Biological Sciences, Centre for Deep Sea ResearchUniversity of BergenBergenNorway
- Department of Earth Science, Centre for Deep Sea ResearchUniversity of BergenBergenNorway
| | - Emily Olesin Denny
- Department of Biological Sciences, Centre for Deep Sea ResearchUniversity of BergenBergenNorway
- Department of Informatics, Computational Biological UnitUniversity of BergenBergenNorway
| | - Ida H. Steen
- Department of Biological Sciences, Centre for Deep Sea ResearchUniversity of BergenBergenNorway
| | - Runar Stokke
- Department of Biological Sciences, Centre for Deep Sea ResearchUniversity of BergenBergenNorway
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4
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Pan J, Zhang X, Xu W, Liu Y, Liu L, Luo Z, Li M. Wood-Ljungdahl pathway found in novel marine Korarchaeota groups illuminates their evolutionary history. mSystems 2023; 8:e0030523. [PMID: 37458475 PMCID: PMC10469681 DOI: 10.1128/msystems.00305-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/29/2023] [Indexed: 07/22/2023] Open
Abstract
Korarchaeota, due to its rarity in common environments, is one of the archaeal phyla that has received the least attention from researchers. It was previously thought to consist solely of strict thermophiles. However, our study provides genetic evidence for the presence of korarchaeal members in temperate subsurface seawater. Furthermore, a systematic reclassification of the Korarchaeota based on 16S rRNA genes and genomes has revealed three novel marine groups (Kor-6 to Kor-8) at the root of the Korarchaeota branch. Kor-6 contains microbes that are present in moderate temperatures. All three novel marine phyla possess genes for the Wood-Ljungdahl pathway, and Kor-7 and Kor-8 possess fewer genes encoding oxygen resistance traits than other korarchaeal groups, suggesting a distinct lifestyle for these novel phyla. Our results, together with estimations of Korarchaeota divergence times, suggest that oxygen availability may be one of the important factors that have influenced the evolution of Korarchaeota. IMPORTANCE Korarchaeota were previously thought to inhabit exclusively high-temperature environments. However, our study provides genetic evidence for their unexpected presence in temperate marine waters. Through analysis of publicly available korarchaeal reference data, we have systematically reclassified Korarchaeota and identified the existence of three previously unknown marine groups (Kor-6, Kor-7, and Kor-8) at the root of the Korarchaeota branch. Comparative analysis of their gene content revealed that these novel groups exhibit a lifestyle distinct from other Korarchaeota. Specifically, they have the ability to fix carbon exclusively via the Wood-Ljungdahl (WL) pathway, and the genomes within Kor-7 and Kor-8 contain few genes encoding antioxidant enzymes, indicating their strictly anaerobic lifestyle. Further studies suggest that the genes related to methane metabolism and the WL pathway may have been inherited from a common ancestor of the Korarchaeota and that oxygen availability may be one of the important evolutionary factors that shaped the diversification of this archaeal phylum.
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Affiliation(s)
- Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Xbiome Biotech Co. Ltd., Shenzhen, Guangdong, China
| | - Xinxu Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Lirui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
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Gulay A, Fournier G, Smets BF, Girguis PR. Proterozoic Acquisition of Archaeal Genes for Extracellular Electron Transfer: A Metabolic Adaptation of Aerobic Ammonia-Oxidizing Bacteria to Oxygen Limitation. Mol Biol Evol 2023; 40:msad161. [PMID: 37440531 PMCID: PMC10415592 DOI: 10.1093/molbev/msad161] [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: 03/03/2023] [Revised: 06/09/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023] Open
Abstract
Many aerobic microbes can utilize alternative electron acceptors under oxygen-limited conditions. In some cases, this is mediated by extracellular electron transfer (or EET), wherein electrons are transferred to extracellular oxidants such as iron oxide and manganese oxide minerals. Here, we show that an ammonia-oxidizer previously known to be strictly aerobic, Nitrosomonas communis, may have been able to utilize a poised electrode to maintain metabolic activity in anoxic conditions. The presence and activity of multiheme cytochromes in N. communis further suggest a capacity for EET. Molecular clock analysis shows that the ancestors of β-proteobacterial ammonia oxidizers appeared after Earth's atmospheric oxygenation when the oxygen levels were >10-4pO2 (present atmospheric level [PAL]), consistent with aerobic origins. Equally important, phylogenetic reconciliations of gene and species trees show that the multiheme c-type EET proteins in Nitrosomonas and Nitrosospira lineages were likely acquired by gene transfer from γ-proteobacteria when the oxygen levels were between 0.1 and 1 pO2 (PAL). These results suggest that β-proteobacterial EET evolved during the Proterozoic when oxygen limitation was widespread, but oxidized minerals were abundant.
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Affiliation(s)
- Arda Gulay
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Environmental and Resource Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Greg Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Barth F Smets
- Department of Environmental and Resource Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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Feehan B, Ran Q, Dorman V, Rumback K, Pogranichniy S, Ward K, Goodband R, Niederwerder MC, Lee STM. Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea. Anim Microbiome 2023; 5:35. [PMID: 37461084 DOI: 10.1186/s42523-023-00256-6] [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: 01/16/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focusing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea dynamics, including detection and methanogenic functions, while assessing global, temporal and host distribution of our novel archaeal metagenome-assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1-156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, MAG taxonomic assignment and functional annotation. MAGs were utilized in downstream phylogenetic analysis for global, temporal and host distribution in addition to methanogenic functional potential determination. RESULTS We generated 1130 non-redundant MAGs, representing 588 unique taxa at the species level, with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in archaea of monogastric hosts which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further improve our understanding of microbiome development and functions.
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Affiliation(s)
- Brandi Feehan
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Qinghong Ran
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Victoria Dorman
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Kourtney Rumback
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Sophia Pogranichniy
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Kaitlyn Ward
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Robert Goodband
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, 66506, USA
| | | | - Sonny T M Lee
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA.
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Řezanka T, Kyselová L, Murphy DJ. Archaeal lipids. Prog Lipid Res 2023; 91:101237. [PMID: 37236370 DOI: 10.1016/j.plipres.2023.101237] [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: 01/06/2023] [Revised: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023]
Abstract
The major archaeal membrane glycerolipids are distinguished from those of bacteria and eukaryotes by the contrasting stereochemistry of their glycerol backbones, and by the use of ether-linked isoprenoid-based alkyl chains rather than ester-linked fatty acyl chains for their hydrophobic moieties. These fascinating compounds play important roles in the extremophile lifestyles of many species, but are also present in the growing numbers of recently discovered mesophilic archaea. The past decade has witnessed significant advances in our understanding of archaea in general and their lipids in particular. Much of the new information has come from the ability to screen large microbial populations via environmental metagenomics, which has revolutionised our understanding of the extent of archaeal biodiversity that is coupled with a strict conservation of their membrane lipid compositions. Significant additional progress has come from new culturing and analytical techniques that are gradually enabling archaeal physiology and biochemistry to be studied in real time. These studies are beginning to shed light on the much-discussed and still-controversial process of eukaryogenesis, which probably involved both bacterial and archaeal progenitors. Puzzlingly, although eukaryotes retain many attributes of their putative archaeal ancestors, their lipid compositions only reflect their bacterial progenitors. Finally, elucidation of archaeal lipids and their metabolic pathways have revealed potentially interesting applications that have opened up new frontiers for biotechnological exploitation of these organisms. This review is concerned with the analysis, structure, function, evolution and biotechnology of archaeal lipids and their associated metabolic pathways.
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Affiliation(s)
- Tomáš Řezanka
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 142 00 Prague, Czech Republic
| | - Lucie Kyselová
- Research Institute of Brewing and Malting, Lípová 511, 120 44 Prague, Czech Republic
| | - Denis J Murphy
- School of Applied Sciences, University of South Wales, Pontypridd, CF37 1DL, United Kingdom.
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Wang J, Qu YN, Evans PN, Guo Q, Zhou F, Nie M, Jin Q, Zhang Y, Zhai X, Zhou M, Yu Z, Fu QL, Xie YG, Hedlund BP, Li WJ, Hua ZS, Wang Z, Wang Y. Evidence for nontraditional mcr-containing archaea contributing to biological methanogenesis in geothermal springs. SCIENCE ADVANCES 2023; 9:eadg6004. [PMID: 37379385 DOI: 10.1126/sciadv.adg6004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/24/2023] [Indexed: 06/30/2023]
Abstract
Recent discoveries of methyl-coenzyme M reductase-encoding genes (mcr) in uncultured archaea beyond traditional euryarchaeotal methanogens have reshaped our view of methanogenesis. However, whether any of these nontraditional archaea perform methanogenesis remains elusive. Here, we report field and microcosm experiments based on 13C-tracer labeling and genome-resolved metagenomics and metatranscriptomics, revealing that nontraditional archaea are predominant active methane producers in two geothermal springs. Archaeoglobales performed methanogenesis from methanol and may exhibit adaptability in using methylotrophic and hydrogenotrophic pathways based on temperature/substrate availability. A five-year field survey found Candidatus Nezhaarchaeota to be the predominant mcr-containing archaea inhabiting the springs; genomic inference and mcr expression under methanogenic conditions strongly suggested that this lineage mediated hydrogenotrophic methanogenesis in situ. Methanogenesis was temperature-sensitive , with a preference for methylotrophic over hydrogenotrophic pathways when incubation temperatures increased from 65° to 75°C. This study demonstrates an anoxic ecosystem wherein methanogenesis is primarily driven by archaea beyond known methanogens, highlighting diverse nontraditional mcr-containing archaea as previously unrecognized methane sources.
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Affiliation(s)
- Jiajia Wang
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Yan-Ni Qu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
- 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 510275, China
| | - Paul N Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4072, QLD, Australia
| | - Qinghai Guo
- MOE Key Laboratory of Groundwater Quality and Health, State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Fengwu Zhou
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
- College of Geography Science, Nanjing Normal University, Nanjing 210023, China
| | - Ming Nie
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Fudan University, Shanghai 200433, China
| | - Qusheng Jin
- Department of Earth Sciences, University of Oregon, Eugene, OR 97403, USA
| | - Yan Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiangmei Zhai
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Ming Zhou
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Zhiguo Yu
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Qing-Long Fu
- MOE Key Laboratory of Groundwater Quality and Health, State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Yuan-Guo Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, 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 510275, China
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Zimeng Wang
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Fudan University, Shanghai 200433, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Yanxin Wang
- MOE Key Laboratory of Groundwater Quality and Health, State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
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9
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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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Lynes MM, Krukenberg V, Jay ZJ, Kohtz AJ, Gobrogge CA, Spietz RL, Hatzenpichler R. Diversity and function of methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments. ISME COMMUNICATIONS 2023; 3:22. [PMID: 36949220 PMCID: PMC10033731 DOI: 10.1038/s43705-023-00225-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/17/2023] [Accepted: 02/28/2023] [Indexed: 03/24/2023]
Abstract
Metagenomic studies on geothermal environments have been central in recent discoveries on the diversity of archaeal methane and alkane metabolism. Here, we investigated methanogenic populations inhabiting terrestrial geothermal features in Yellowstone National Park (YNP) by combining amplicon sequencing with metagenomics and mesocosm experiments. Detection of methyl-coenzyme M reductase subunit A (mcrA) gene amplicons demonstrated a wide diversity of Mcr-encoding archaea inhabit geothermal features with differing physicochemical regimes across YNP. From three selected hot springs we recovered twelve Mcr-encoding metagenome assembled genomes (MAGs) affiliated with lineages of cultured methanogens as well as Candidatus (Ca.) Methanomethylicia, Ca. Hadesarchaeia, and Archaeoglobi. These MAGs encoded the potential for hydrogenotrophic, aceticlastic, hydrogen-dependent methylotrophic methanogenesis, or anaerobic short-chain alkane oxidation. While Mcr-encoding archaea represent minor fractions of the microbial community of hot springs, mesocosm experiments with methanogenic precursors resulted in the stimulation of methanogenic activity and the enrichment of lineages affiliated with Methanosaeta and Methanothermobacter as well as with uncultured Mcr-encoding archaea including Ca. Korarchaeia, Ca. Nezhaarchaeia, and Archaeoglobi. We revealed that diverse Mcr-encoding archaea with the metabolic potential to produce methane from different precursors persist in the geothermal environments of YNP and can be enriched under methanogenic conditions. This study highlights the importance of combining environmental metagenomics with laboratory-based experiments to expand our understanding of uncultured Mcr-encoding archaea and their potential impact on microbial carbon transformations in geothermal environments and beyond.
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Affiliation(s)
- Mackenzie M Lynes
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | - Viola Krukenberg
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA.
| | - Zackary J Jay
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | - Anthony J Kohtz
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | | | - Rachel L Spietz
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA.
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
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11
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Bueno de Mesquita CP, Wu D, Tringe SG. Methyl-Based Methanogenesis: an Ecological and Genomic Review. Microbiol Mol Biol Rev 2023; 87:e0002422. [PMID: 36692297 PMCID: PMC10029344 DOI: 10.1128/mmbr.00024-22] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Methyl-based methanogenesis is one of three broad categories of archaeal anaerobic methanogenesis, including both the methyl dismutation (methylotrophic) pathway and the methyl-reducing (also known as hydrogen-dependent methylotrophic) pathway. Methyl-based methanogenesis is increasingly recognized as an important source of methane in a variety of environments. Here, we provide an overview of methyl-based methanogenesis research, including the conditions under which methyl-based methanogenesis can be a dominant source of methane emissions, experimental methods for distinguishing different pathways of methane production, molecular details of the biochemical pathways involved, and the genes and organisms involved in these processes. We also identify the current gaps in knowledge and present a genomic and metagenomic survey of methyl-based methanogenesis genes, highlighting the diversity of methyl-based methanogens at multiple taxonomic levels and the widespread distribution of known methyl-based methanogenesis genes and families across different environments.
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Affiliation(s)
| | - Dongying Wu
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Susannah G. Tringe
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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12
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Proteome-wide 3D structure prediction provides insights into the ancestral metabolism of ancient archaea and bacteria. Nat Commun 2022; 13:7861. [PMID: 36543797 PMCID: PMC9772386 DOI: 10.1038/s41467-022-35523-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Ancestral metabolism has remained controversial due to a lack of evidence beyond sequence-based reconstructions. Although prebiotic chemists have provided hints that metabolism might originate from non-enzymatic protometabolic pathways, gaps between ancestral reconstruction and prebiotic processes mean there is much that is still unknown. Here, we apply proteome-wide 3D structure predictions and comparisons to investigate ancestorial metabolism of ancient bacteria and archaea, to provide information beyond sequence as a bridge to the prebiotic processes. We compare representative bacterial and archaeal strains, which reveal surprisingly similar physiological and metabolic characteristics via microbiological and biophysical experiments. Pairwise comparison of protein structures identify the conserved metabolic modules in bacteria and archaea, despite interference from overly variable sequences. The conserved modules (for example, middle of glycolysis, partial TCA, proton/sulfur respiration, building block biosynthesis) constitute the basic functions that possibly existed in the archaeal-bacterial common ancestor, which are remarkably consistent with the experimentally confirmed protometabolic pathways. These structure-based findings provide a new perspective to reconstructing the ancestral metabolism and understanding its origin, which suggests high-throughput protein 3D structure prediction is a promising approach, deserving broader application in future ancestral exploration.
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13
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Lyu Z, Rotaru AE, Pimentel M, Zhang CJ, Rittmann SKMR. Editorial: The methane moment - Cross-boundary significance of methanogens: Preface. Front Microbiol 2022; 13:1055494. [PMID: 36504803 PMCID: PMC9731359 DOI: 10.3389/fmicb.2022.1055494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Zhe Lyu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States,Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, United States,*Correspondence: Zhe Lyu
| | - Amelia-Elena Rotaru
- Nordic Center for Earth Evolution (NORDCEE), University of Southern Denmark, Odense, Denmark,Amelia-Elena Rotaru
| | - Mark Pimentel
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, United States,Mark Pimentel
| | - Cui-Jing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China,Cui-Jing Zhang
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria,Arkeon GmbH, Tulln a.d. Donau, Austria,Simon K.-M. R. Rittmann
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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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Shao N, Fan Y, Chou CW, Yavari S, Williams RV, Amster IJ, Brown SM, Drake IJ, Duin EC, Whitman WB, Liu Y. Expression of divergent methyl/alkyl coenzyme M reductases from uncultured archaea. Commun Biol 2022; 5:1113. [PMID: 36266535 PMCID: PMC9584954 DOI: 10.1038/s42003-022-04057-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/30/2022] [Indexed: 11/08/2022] Open
Abstract
Methanogens and anaerobic methane-oxidizing archaea (ANME) are important players in the global carbon cycle. Methyl-coenzyme M reductase (MCR) is a key enzyme in methane metabolism, catalyzing the last step in methanogenesis and the first step in anaerobic methane oxidation. Divergent mcr and mcr-like genes have recently been identified in uncultured archaeal lineages. However, the assembly and biochemistry of MCRs from uncultured archaea remain largely unknown. Here we present an approach to study MCRs from uncultured archaea by heterologous expression in a methanogen, Methanococcus maripaludis. Promoter, operon structure, and temperature were important determinants for MCR production. Both recombinant methanococcal and ANME-2 MCR assembled with the host MCR forming hybrid complexes, whereas tested ANME-1 MCR and ethyl-coenzyme M reductase only formed homogenous complexes. Together with structural modeling, this suggests that ANME-2 and methanogen MCRs are structurally similar and their reaction directions are likely regulated by thermodynamics rather than intrinsic structural differences.
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Affiliation(s)
- Nana Shao
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Yu Fan
- EMTEC IT, ExxonMobil Technical Computing Company, Annandale, NJ, USA
| | - Chau-Wen Chou
- Department of Chemistry, University of Georgia, Athens, GA, USA
| | - Shadi Yavari
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, USA
| | | | | | - Stuart M Brown
- Energy Sciences, ExxonMobil Technology & Engineering Company, Annandale, NJ, USA
| | - Ian J Drake
- Biomedical Sciences, ExxonMobil Technology & Engineering Company, Annandale, NJ, USA
| | - Evert C Duin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, USA
| | | | - Yuchen Liu
- Energy Sciences, ExxonMobil Technology & Engineering Company, Annandale, NJ, USA.
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16
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Lv Z, Ding J, Wang H, Wan J, Chen Y, Liang L, Yu T, Wang Y, Wang F. Isolation of a Novel Thermophilic Methanogen and the Evolutionary History of the Class Methanobacteria. BIOLOGY 2022; 11:biology11101514. [PMID: 36290418 PMCID: PMC9598358 DOI: 10.3390/biology11101514] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022]
Abstract
Methanogens can produce methane in anaerobic environments via the methanogenesis pathway, and are regarded as one of the most ancient life forms on Earth. They are ubiquitously distributed across distinct ecosystems and are considered to have a thermophilic origin. In this study, we isolated, pure cultured, and completely sequenced a single methanogen strain DL9LZB001, from a hot spring at Tengchong in Southwest China. DL9LZB001 is a thermophilic and hydrogenotrophic methanogen with an optimum growth temperature of 65 °C. It is a putative novel species, which has been named Methanothermobacter tengchongensis-a Class I methanogen belonging to the class Methanobacteria. Comparative genomic and ancestral analyses indicate that the class Methanobacteria originated in a hyperthermal environment and then evolved to adapt to ambient temperatures. This study extends the understanding of methanogens living in geothermal niches, as well as the origin and evolutionary history of these organisms in ecosystems with different temperatures.
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Affiliation(s)
- Zhenbo Lv
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiaxin Ding
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Heng Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiaxin Wan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yifan Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lewen Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tiantian Yu
- 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
- Correspondence:
| | - 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 519000, China
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17
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Vulcano F, Hahn CJ, Roerdink D, Dahle H, Reeves EP, Wegener G, Steen IH, Stokke R. Phylogenetic and functional diverse ANME-1 thrive in Arctic hydrothermal vents. FEMS Microbiol Ecol 2022; 98:6747120. [PMID: 36190327 PMCID: PMC9576274 DOI: 10.1093/femsec/fiac117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 09/15/2022] [Accepted: 09/29/2022] [Indexed: 01/21/2023] Open
Abstract
The methane-rich areas, the Loki's Castle vent field and the Jan Mayen vent field at the Arctic Mid Ocean Ridge (AMOR), host abundant niches for anaerobic methane-oxidizers, which are predominantly filled by members of the ANME-1. In this study, we used a metagenomic-based approach that revealed the presence of phylogenetic and functional different ANME-1 subgroups at AMOR, with heterogeneous distribution. Based on a common analysis of ANME-1 genomes from AMOR and other geographic locations, we observed that AMOR subgroups clustered with a vent-specific ANME-1 group that occurs solely at vents, and with a generalist ANME-1 group, with a mixed environmental origin. Generalist ANME-1 are enriched in genes coding for stress response and defense strategies, suggesting functional diversity among AMOR subgroups. ANME-1 encode a conserved energy metabolism, indicating strong adaptation to sulfate-methane-rich sediments in marine systems, which does not however prevent global dispersion. A deep branching family named Ca. Veteromethanophagaceae was identified. The basal position of vent-related ANME-1 in phylogenomic trees suggests that ANME-1 originated at hydrothermal vents. The heterogeneous and variable physicochemical conditions present in diffuse venting areas of hydrothermal fields could have favored the diversification of ANME-1 into lineages that can tolerate geochemical and environmental variations.
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Affiliation(s)
- F Vulcano
- Corresponding author: Thormølens gate 53 A 5006 Bergen Postboks 7803 5020 Bergen. E-mail:
| | - C J Hahn
- Max-Plank Institute for Marine Microbiology, HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Bremen, 28359, Germany
| | - D Roerdink
- Department of Earth Science, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - H Dahle
- Computational Biological Unit, Department of Informatics, Department of Biological Sciences, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - E P Reeves
- Department of Earth Science, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - G Wegener
- Max-Plank Institute for Marine Microbiology, HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Bremen, 28359, Germany,MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, 28359, Germany,Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - I H Steen
- Department of Biological Sciences, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - R Stokke
- Corresponding author: Thormølens gate 53 A 5006 Bergen Postboks 7803 5020 Bergen. E-mail:
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18
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Ou YF, Dong HP, McIlroy SJ, Crowe SA, Hallam SJ, Han P, Kallmeyer J, Simister RL, Vuillemin A, Leu AO, Liu Z, Zheng YL, Sun QL, Liu M, Tyson GW, Hou LJ. Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis. THE ISME JOURNAL 2022; 16:2373-2387. [PMID: 35810262 PMCID: PMC9478090 DOI: 10.1038/s41396-022-01281-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 05/28/2023]
Abstract
Methane produced by methanogenic archaea has an important influence on Earth's changing climate. Methanogenic archaea are phylogenetically diverse and widespread in anoxic environments. These microorganisms can be divided into two subgroups based on whether or not they use b-type cytochromes for energy conservation. Methanogens with b-type cytochromes have a wider substrate range and higher growth yields than those without them. To date, methanogens with b-type cytochromes were found exclusively in the phylum "Ca. Halobacteriota" (formerly part of the phylum Euryarchaeota). Here, we present the discovery of metagenome-assembled genomes harboring methyl-coenzyme M reductase genes reconstructed from mesophilic anoxic sediments, together with the previously reported thermophilic "Ca. Methylarchaeum tengchongensis", representing a novel archaeal order, designated the "Ca. Methylarchaeales", of the phylum Thermoproteota (formerly the TACK superphylum). These microorganisms contain genes required for methyl-reducing methanogenesis and the Wood-Ljundahl pathway. Importantly, the genus "Ca. Methanotowutia" of the "Ca. Methylarchaeales" encode a cytochrome b-containing heterodisulfide reductase (HdrDE) and methanophenazine-reducing hydrogenase complex that have similar gene arrangements to those found in methanogenic Methanosarcinales. Our results indicate that members of the "Ca. Methylarchaeales" are methanogens with cytochromes and can conserve energy via membrane-bound electron transport chains. Phylogenetic and amalgamated likelihood estimation analyses indicate that methanogens with cytochrome b-containing electron transfer complexes likely evolved before diversification of Thermoproteota or "Ca. Halobacteriota" in the early Archean Eon. Surveys of public sequence databases suggest that members of the lineage are globally distributed in anoxic sediments and may be important players in the methane cycle.
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Affiliation(s)
- Ya-Fei Ou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Hong-Po Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China.
| | - Simon J McIlroy
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Sean A Crowe
- Ecosystem Services, Commercialization Platforms, and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Ping Han
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Rachel L Simister
- Ecosystem Services, Commercialization Platforms, and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Aurele Vuillemin
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Andy O Leu
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Zhanfei Liu
- Marine Science Institute, The University of Texas at Austin, Port Aransas, TX, 78373, USA
| | - Yan-Ling Zheng
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Qian-Li Sun
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Li-Jun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China.
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19
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Benito Merino D, Zehnle H, Teske A, Wegener G. Deep-branching ANME-1c archaea grow at the upper temperature limit of anaerobic oxidation of methane. Front Microbiol 2022; 13:988871. [PMID: 36212815 PMCID: PMC9539880 DOI: 10.3389/fmicb.2022.988871] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/15/2022] [Indexed: 01/03/2023] Open
Abstract
In seafloor sediments, the anaerobic oxidation of methane (AOM) consumes most of the methane formed in anoxic layers, preventing this greenhouse gas from reaching the water column and finally the atmosphere. AOM is performed by syntrophic consortia of specific anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Cultures with diverse AOM partners exist at temperatures between 12°C and 60°C. Here, from hydrothermally heated sediments of the Guaymas Basin, we cultured deep-branching ANME-1c that grow in syntrophic consortia with Thermodesulfobacteria at 70°C. Like all ANME, ANME-1c oxidize methane using the methanogenesis pathway in reverse. As an uncommon feature, ANME-1c encode a nickel-iron hydrogenase. This hydrogenase has low expression during AOM and the partner Thermodesulfobacteria lack hydrogen-consuming hydrogenases. Therefore, it is unlikely that the partners exchange hydrogen during AOM. ANME-1c also does not consume hydrogen for methane formation, disputing a recent hypothesis on facultative methanogenesis. We hypothesize that the ANME-1c hydrogenase might have been present in the common ancestor of ANME-1 but lost its central metabolic function in ANME-1c archaea. For potential direct interspecies electron transfer (DIET), both partners encode and express genes coding for extracellular appendages and multiheme cytochromes. Thermodesulfobacteria encode and express an extracellular pentaheme cytochrome with high similarity to cytochromes of other syntrophic sulfate-reducing partner bacteria. ANME-1c might associate specifically to Thermodesulfobacteria, but their co-occurrence is so far only documented for heated sediments of the Gulf of California. However, in the deep seafloor, sulfate-methane interphases appear at temperatures up to 80°C, suggesting these as potential habitats for the partnership of ANME-1c and Thermodesulfobacteria.
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Affiliation(s)
- David Benito Merino
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Hanna Zehnle
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Andreas Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - 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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20
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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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21
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Wegener G, Laso-Pérez R, Orphan VJ, Boetius A. Anaerobic Degradation of Alkanes by Marine Archaea. Annu Rev Microbiol 2022; 76:553-577. [PMID: 35917471 DOI: 10.1146/annurev-micro-111021-045911] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alkanes are saturated apolar hydrocarbons that range from its simplest form, methane, to high-molecular-weight compounds. Although alkanes were once considered biologically recalcitrant under anaerobic conditions, microbiological investigations have now identified several microbial taxa that can anaerobically degrade alkanes. Here we review recent discoveries in the anaerobic oxidation of alkanes with a specific focus on archaea that use specific methyl coenzyme M reductases to activate their substrates. Our understanding of the diversity of uncultured alkane-oxidizing archaea has expanded through the use of environmental metagenomics and enrichment cultures of syntrophic methane-, ethane-, propane-, and butane-oxidizing marine archaea with sulfate-reducing bacteria. A recently cultured group of archaea directly couples long-chain alkane degradation with methane formation, expanding the range of substrates used for methanogenesis. This article summarizes the rapidly growing knowledge of the diversity, physiology, and habitat distribution of alkane-degrading archaea. 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)
- Gunter Wegener
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rafael Laso-Pérez
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany.,Current affiliation: Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Victoria J Orphan
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Division of Geological and Planetary Sciences and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Antje Boetius
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany.,Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany;
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22
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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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23
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Steinsdóttir HGR, Gómez Ramírez E, Mhatre S, Schauberger C, Bertagnolli AD, Pratte ZA, Stewart FJ, Thamdrup B, Bristow LA. Anaerobic methane oxidation in a coastal oxygen minimum zone: spatial and temporal dynamics. Environ Microbiol 2022; 24:2361-2379. [PMID: 35415879 PMCID: PMC9323439 DOI: 10.1111/1462-2920.16003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 11/28/2022]
Abstract
Coastal waters are a major source of marine methane to the atmosphere. Particularly high concentrations of this potent greenhouse gas are found in anoxic waters, but it remains unclear if and to what extent anaerobic methanotrophs mitigate the methane flux. Here we investigate the long-term dynamics in methanotrophic activity and the methanotroph community in the coastal oxygen minimum zone (OMZ) of Golfo Dulce, Costa Rica, combining biogeochemical analyses, experimental incubations, and 16S rRNA gene sequencing over three consecutive years. Our results demonstrate a stable redox zonation across the years with high concentrations of methane (up to 1.7 μmol L-1 ) in anoxic bottom waters. However, we also measured high activities of anaerobic methane oxidation in the OMZ core (rate constant, k, averaging 30 yr-1 in 2018 and 8 yr-1 in 2019-2020). The OPU3 and Deep Sea-1 clades of the Methylococcales were implicated as conveyors of the activity, peaking in relative abundance 5-25 m below the oxic-anoxic interface and in the deep anoxic water, respectively. Although their genetic capacity for anaerobic methane oxidation remains unexplored, their sustained high relative abundance indicates an adaptation of these clades to the anoxic, methane-rich OMZ environment, allowing them to play major roles in mitigating methane fluxes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Eddy Gómez Ramírez
- CIMAR, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Snehit Mhatre
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | | | - Anthony D Bertagnolli
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana
| | - Zoe A Pratte
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana
| | - Frank J Stewart
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana.,School of Biological Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA
| | - Bo Thamdrup
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Laura A Bristow
- Department of Biology, University of Southern Denmark, Odense, Denmark
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24
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Wang Y, Xie R, Hou J, Lv Z, Li L, Hu Y, Huang H, Wang F. The late Archaean to early Proterozoic origin and evolution of anaerobic methane-oxidizing archaea. MLIFE 2022; 1:96-100. [PMID: 38818328 PMCID: PMC10989977 DOI: 10.1002/mlf2.12013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/19/2022] [Indexed: 06/01/2024]
Abstract
Microorganisms, called anaerobic methane-oxidizing archaea (ANME), can reduce a large amount of greenhouse gas methane and therefore have the potential to cool the Earth. We collected nearly all ANMEs genomes in public databases and performed a comprehensive comparative genomic analysis and molecular dating. Our results show that ANMEs originated in the late Archaean to early Proterozoic eon. During this period of time, our planet Earth was experiencing the Great Oxygenation Event and Huronian Glaciation, a dramatic drop in the Earth's surface temperature. This suggests that the emergence of ANMEs may contribute to the reduction of methane at that time, which is an unappreciated potential cause that led to the Huronian Glaciation.
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Affiliation(s)
- Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ruize Xie
- School of OceanographyShanghai Jiao Tong UniversityShanghaiChina
| | - Jialin Hou
- School of OceanographyShanghai Jiao Tong UniversityShanghaiChina
| | - Zhenbo Lv
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Liuyang Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Yaoxun Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Hungchia Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Fengping Wang
- School of OceanographyShanghai Jiao Tong UniversityShanghaiChina
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)ZhuhaiChina
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25
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Hedlund BP, Zhang C, Wang F, Rinke C, Martin WF. Editorial: Ecology, Metabolism and Evolution of Archaea-Perspectives From Proceedings of the International Workshop on Geo-Omics of Archaea. Front Microbiol 2022; 12:827229. [PMID: 35126338 PMCID: PMC8816317 DOI: 10.3389/fmicb.2021.827229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Brian P. Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Oceanography, Shanghai JiaoTong University, Shanghai, China
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - William F. Martin
- Institute for Molecular Evolution, University of Dusseldorf Medical School, Düsseldorf, Germany
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26
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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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