1
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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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2
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Qiu Z, Yuan L, Lian CA, Lin B, Chen J, Mu R, Qiao X, Zhang L, Xu Z, Fan L, Zhang Y, Wang S, Li J, Cao H, Li B, Chen B, Song C, Liu Y, Shi L, Tian Y, Ni J, Zhang T, Zhou J, Zhuang WQ, Yu K. BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis. Nat Commun 2024; 15:2179. [PMID: 38467684 PMCID: PMC10928208 DOI: 10.1038/s41467-024-46539-7] [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: 03/10/2023] [Accepted: 03/01/2024] [Indexed: 03/13/2024] Open
Abstract
Metagenomic binning is an essential technique for genome-resolved characterization of uncultured microorganisms in various ecosystems but hampered by the low efficiency of binning tools in adequately recovering metagenome-assembled genomes (MAGs). Here, we introduce BASALT (Binning Across a Series of Assemblies Toolkit) for binning and refinement of short- and long-read sequencing data. BASALT employs multiple binners with multiple thresholds to produce initial bins, then utilizes neural networks to identify core sequences to remove redundant bins and refine non-redundant bins. Using the same assemblies generated from Critical Assessment of Metagenome Interpretation (CAMI) datasets, BASALT produces up to twice as many MAGs as VAMB, DASTool, or metaWRAP. Processing assemblies from a lake sediment dataset, BASALT produces ~30% more MAGs than metaWRAP, including 21 unique class-level prokaryotic lineages. Functional annotations reveal that BASALT can retrieve 47.6% more non-redundant opening-reading frames than metaWRAP. These results highlight the robust handling of metagenomic sequencing data of BASALT.
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Affiliation(s)
- Zhiguang Qiu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
| | - Li Yuan
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
- School of Electronic and Computer Engineering, Peking University, Shenzhen, China
- Peng Cheng Laboratory, Shenzhen, China
| | - Chun-Ang Lian
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
| | - Bin Lin
- School of Electronic and Computer Engineering, Peking University, Shenzhen, China
| | - Jie Chen
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
- School of Electronic and Computer Engineering, Peking University, Shenzhen, China
- Peng Cheng Laboratory, Shenzhen, China
| | - Rong Mu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Xuejiao Qiao
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Liyu Zhang
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Zheng Xu
- Southern University of Sciences and Technology Yantian Hospital, Shenzhen, China
- Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Yunzeng Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, China
| | - Junyi Li
- School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China
| | - Huiluo Cao
- Department of Microbiology, University of Hong Kong, Hong Kong, China
| | - Bing Li
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Baowei Chen
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Chi Song
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Wuhan Benagen Technology Co., Ltd, Wuhan, China
| | - Yongxin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Lili Shi
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yonghong Tian
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
- School of Electronic and Computer Engineering, Peking University, Shenzhen, China
- Peng Cheng Laboratory, Shenzhen, China
| | - Jinren Ni
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, China
| | - Tong Zhang
- Department of Civil Engineering, University of Hong Kong, Hong Kong, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Wei-Qin Zhuang
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Auckland, Auckland, New Zealand
| | - Ke Yu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China.
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China.
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3
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Lu Z, Zhang S, Liu Y, Xia R, Li M. Origin of eukaryotic-like Vps23 shapes an ancient functional interplay between ESCRT and ubiquitin system in Asgard archaea. Cell Rep 2024; 43:113781. [PMID: 38358888 DOI: 10.1016/j.celrep.2024.113781] [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: 08/31/2023] [Revised: 01/08/2024] [Accepted: 01/25/2024] [Indexed: 02/17/2024] Open
Abstract
Functional interplay between the endosomal sorting complexes required for transport (ESCRT) and the ubiquitin system underlies the ubiquitin-dependent cargo-sorting pathway of the eukaryotic endomembrane system, yet its evolutionary origin remains unclear. Here, we show that a UEV-Vps23 protein family, which contains UEV and Vps23 domains, mediates an ancient ESCRT and ubiquitin system interplay in Asgard archaea. The UEV binds ubiquitin with high affinity, making the UEV-Vps23 a sensor for sorting ubiquitinated cargo. A steadiness box in the Vps23 domain undergoes ubiquitination through an Asgard E1, E2, and RING E3 cascade. The UEV-Vps23 switches between autoinhibited and active forms, regulating the ESCRT and ubiquitin system interplay. Furthermore, the shared sequence and structural homology among the UEV-Vps23, eukaryotic Vps23, and archaeal CdvA suggest a common evolutionary origin. Together, this work expands our understanding of the ancient ESCRT and ubiquitin system interplay that likely arose antedating divergent evolution between Asgard archaea and eukaryotes.
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Affiliation(s)
- Zhongyi Lu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Siyu Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Runyue Xia
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China.
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4
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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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5
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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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6
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Zheng J, Mallon J, Lammers A, Rados T, Litschel T, Moody ERR, Ramirez-Diaz DA, Schmid A, Williams TA, Bisson-Filho AW, Garner E. Salactin, a dynamically unstable actin homolog in Haloarchaea. mBio 2023; 14:e0227223. [PMID: 37966230 PMCID: PMC10746226 DOI: 10.1128/mbio.02272-23] [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: 08/25/2023] [Accepted: 10/05/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE Protein filaments play important roles in many biological processes. We discovered an actin homolog in halophilic archaea, which we call Salactin. Just like the filaments that segregate DNA in eukaryotes, Salactin grows out of the cell poles towards the middle, and then quickly depolymerizes, a behavior known as dynamic instability. Furthermore, we see that Salactin affects the distribution of DNA in daughter cells when cells are grown in low-phosphate media, suggesting Salactin filaments might be involved in segregating DNA when the cell has only a few copies of the chromosome.
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Affiliation(s)
- Jenny Zheng
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - John Mallon
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Alex Lammers
- Physiology Course, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
- Department of Biomedical Engineering, The Biological Design Center, Boston University, Boston, Massachusetts, USA
- The Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Theopi Rados
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Thomas Litschel
- Physiology Course, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Edmund R. R. Moody
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - Diego A. Ramirez-Diaz
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Amy Schmid
- Department of Biology, Duke University, Durham, North Carolina, USA
- Center for Genomics and Computational Biology, Duke University, Durham, North Carolina, USA
| | - Tom A. Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Alexandre W. Bisson-Filho
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Ethan Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
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7
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Bojanova DP, De Anda VY, Haghnegahdar MA, Teske AP, Ash JL, Young ED, Baker BJ, LaRowe DE, Amend JP. Well-hidden methanogenesis in deep, organic-rich sediments of Guaymas Basin. THE ISME JOURNAL 2023; 17:1828-1838. [PMID: 37596411 PMCID: PMC10579335 DOI: 10.1038/s41396-023-01485-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/06/2023] [Accepted: 07/24/2023] [Indexed: 08/20/2023]
Abstract
Deep marine sediments (>1mbsf) harbor ~26% of microbial biomass and are the largest reservoir of methane on Earth. Yet, the deep subsurface biosphere and controls on its contribution to methane production remain underexplored. Here, we use a multidisciplinary approach to examine methanogenesis in sediments (down to 295 mbsf) from sites with varying degrees of thermal alteration (none, past, current) at Guaymas Basin (Gulf of California) for the first time. Traditional (13C/12C and D/H) and multiply substituted (13CH3D and 12CH2D2) methane isotope measurements reveal significant proportions of microbial methane at all sites, with the largest signal at the site with past alteration. With depth, relative microbial methane decreases at differing rates between sites. Gibbs energy calculations confirm methanogenesis is exergonic in Guaymas sediments, with methylotrophic pathways consistently yielding more energy than the canonical hydrogenotrophic and acetoclastic pathways. Yet, metagenomic sequencing and cultivation attempts indicate that methanogens are present in low abundance. We find only one methyl-coenzyme M (mcrA) sequence within the entire sequencing dataset. Also, we identify a wide diversity of methyltransferases (mtaB, mttB), but only a few sequences phylogenetically cluster with methylotrophic methanogens. Our results suggest that the microbial methane in the Guaymas subsurface was produced over geologic time by relatively small methanogen populations, which have been variably influenced by thermal sediment alteration. Higher resolution metagenomic sampling may clarify the modern methanogen community. This study highlights the importance of using a multidisciplinary approach to capture microbial influences in dynamic, deep subsurface settings like Guaymas Basin.
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Affiliation(s)
- Diana P Bojanova
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Valerie Y De Anda
- Department of Marine Science, University of Texas at Austin, Austin, TX, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Andreas P Teske
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Jeanine L Ash
- Earth, Environmental, and Planetary Sciences, Rice University, Houston, TX, USA
| | - Edward D Young
- Earth, Planetary, and Space Sciences, University of California - Los Angeles, Los Angeles, CA, USA
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin, Austin, TX, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Douglas E LaRowe
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Jan P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA.
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
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8
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Mara P, Zhou YL, Teske A, Morono Y, Beaudoin D, Edgcomb V. Microbial gene expression in Guaymas Basin subsurface sediments responds to hydrothermal stress and energy limitation. THE ISME JOURNAL 2023; 17:1907-1919. [PMID: 37658181 PMCID: PMC10579382 DOI: 10.1038/s41396-023-01492-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 09/03/2023]
Abstract
Analyses of gene expression of subsurface bacteria and archaea provide insights into their physiological adaptations to in situ subsurface conditions. We examined patterns of expressed genes in hydrothermally heated subseafloor sediments with distinct geochemical and thermal regimes in Guaymas Basin, Gulf of California, Mexico. RNA recovery and cell counts declined with sediment depth, however, we obtained metatranscriptomes from eight sites at depths spanning between 0.8 and 101.9 m below seafloor. We describe the metabolic potential of sediment microorganisms, and discuss expressed genes involved in tRNA, mRNA, and rRNA modifications that enable physiological flexibility of bacteria and archaea in the hydrothermal subsurface. Microbial taxa in hydrothermally influenced settings like Guaymas Basin may particularly depend on these catalytic RNA functions since they modulate the activity of cells under elevated temperatures and steep geochemical gradients. Expressed genes for DNA repair, protein maintenance and circadian rhythm were also identified. The concerted interaction of many of these genes may be crucial for microorganisms to survive and to thrive in the Guaymas Basin subsurface biosphere.
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Affiliation(s)
- Paraskevi Mara
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Ying-Li Zhou
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Andreas Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Yuki Morono
- Kochi Institute for Core Sample Research, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Monobe, Nankoku, Kochi, Japan
| | - David Beaudoin
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Virginia Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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9
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Vogt C, Song Z, Richnow HH, Musat F. Carbon and hydrogen stable isotope fractionation due to monooxygenation of short-chain alkanes by butane monooxygenase of Thauera butanivorans Bu-B1211. Front Microbiol 2023; 14:1250308. [PMID: 37817750 PMCID: PMC10560718 DOI: 10.3389/fmicb.2023.1250308] [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: 09/07/2023] [Indexed: 10/12/2023] Open
Abstract
Multi element compound-specific stable isotope analysis (ME-CSIA) is a tool to assess (bio)chemical reactions of molecules in the environment based on their isotopic fingerprints. To that effect, ME-CSIA concepts are initially developed with laboratory model experiments to determine the isotope fractionation factors specific for distinct (bio)chemical reactions. Here, we determined for the first time the carbon and hydrogen isotope fractionation factors for the monooxygenation of the short-chain alkanes ethane, propane, and butane. As model organism we used Thauera butanivorans strain Bu-B1211 which employs a non-haem iron monooxygenase (butane monooxygenase) to activate alkanes. Monooxygenation of alkanes was associated with strong carbon and hydrogen isotope effects: εbulkC = -2.95 ± 0.5 ‰ for ethane, -2.68 ± 0.1 ‰ for propane, -1.19 ± 0.18 ‰ for butane; εbulkH = -56.3 ± 15 ‰ for ethane, -40.5 ± 2.3 ‰ for propane, -14.6 ± 3.6 ‰ for butane. This resulted in lambda (Λ ≈ εHbulk/εCbulk) values of 16.2 ± 3.7 for ethane, 13.2 ± 0.7 for propane, and 11.4 ± 2.8 for butane. The results show that ME-CSIA can be used to track the occurrence and impact of monooxygenase-dependent aerobic processes converting short-chain alkanes in natural settings like marine and terrestrial seeps, gas reservoirs, and other geological formations impacted by natural gas.
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Affiliation(s)
- Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
| | - Zhiyong Song
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
| | - Florin Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research–UFZ, Leipzig, Germany
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
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10
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Aparici-Carratalá D, Esclapez J, Bautista V, Bonete MJ, Camacho M. Archaea: current and potential biotechnological applications. Res Microbiol 2023; 174:104080. [PMID: 37196775 DOI: 10.1016/j.resmic.2023.104080] [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: 01/29/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
Archaea are microorganisms with great ability to colonize some of the most inhospitable environments in nature, managing to survive in places with extreme characteristics for most microorganisms. Its proteins and enzymes are stable and can act under extreme conditions in which other proteins and enzymes would degrade. These attributes make them ideal candidates for use in a wide range of biotechnological applications. This review describes the most important applications, both current and potential, that archaea present in Biotechnology, classifying them according to the sector to which the application is directed. It also analyzes the advantages and disadvantages of its use.
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Affiliation(s)
- David Aparici-Carratalá
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, Alicante, 03690, Spain.
| | - Julia Esclapez
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, Alicante, 03690, Spain.
| | - Vanesa Bautista
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, Alicante, 03690, Spain.
| | - María-José Bonete
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, Alicante, 03690, Spain.
| | - Mónica Camacho
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, Alicante, 03690, Spain.
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11
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Padilla-Vaca F, de la Mora J, García-Contreras R, Ramírez-Prado JH, Alva-Murillo N, Fonseca-Yepez S, Serna-Gutiérrez I, Moreno-Galván CL, Montufar-Rodríguez JM, Vicente-Gómez M, Rangel-Serrano Á, Vargas-Maya NI, Franco B. Two-Component System Sensor Kinases from Asgardian Archaea May Be Witnesses to Eukaryotic Cell Evolution. Molecules 2023; 28:5042. [PMID: 37446705 DOI: 10.3390/molecules28135042] [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: 03/30/2023] [Revised: 06/22/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
The signal transduction paradigm in bacteria involves two-component systems (TCSs). Asgardarchaeota are archaea that may have originated the current eukaryotic lifeforms. Most research on these archaea has focused on eukaryotic-like features, such as genes involved in phagocytosis, cytoskeleton structure, and vesicle trafficking. However, little attention has been given to specific prokaryotic features. Here, the sequence and predicted structural features of TCS sensor kinases analyzed from two metagenome assemblies and a genomic assembly from cultured Asgardian archaea are presented. The homology of the sensor kinases suggests the grouping of Lokiarchaeum closer to bacterial homologs. In contrast, one group from a Lokiarchaeum and a meta-genome assembly from Candidatus Heimdallarchaeum suggest the presence of a set of kinases separated from the typical bacterial TCS sensor kinases. AtoS and ArcB homologs were found in meta-genome assemblies along with defined domains for other well-characterized sensor kinases, suggesting the close link between these organisms and bacteria that may have resulted in the metabolic link to the establishment of symbiosis. Several kinases are predicted to be cytoplasmic; some contain several PAS domains. The data shown here suggest that TCS kinases in Asgardian bacteria are witnesses to the transition from bacteria to eukaryotic organisms.
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Affiliation(s)
- Felipe Padilla-Vaca
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
| | - Javier de la Mora
- Departamento de Genética Molecular, Instituto de Fisiologia Celular, Universidad Nacional Autonoma de Mexico, Circuito Exterior s/n, Mexico City 04510, Mexico
| | - Rodolfo García-Contreras
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | | | - Nayeli Alva-Murillo
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
| | - Sofia Fonseca-Yepez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
| | - Isaac Serna-Gutiérrez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
| | - Carolina Lisette Moreno-Galván
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
| | - José Manolo Montufar-Rodríguez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
| | - Marcos Vicente-Gómez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
| | - Ángeles Rangel-Serrano
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
| | - Naurú Idalia Vargas-Maya
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
| | - Bernardo Franco
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Mexico
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12
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Tanabe TS, Grosser M, Hahn L, Kümpel C, Hartenfels H, Vtulkin E, Flegler W, Dahl C. Identification of a novel lipoic acid biosynthesis pathway reveals the complex evolution of lipoate assembly in prokaryotes. PLoS Biol 2023; 21:e3002177. [PMID: 37368881 DOI: 10.1371/journal.pbio.3002177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Lipoic acid is an essential biomolecule found in all domains of life and is involved in central carbon metabolism and dissimilatory sulfur oxidation. The machineries for lipoate assembly in mitochondria and chloroplasts of higher eukaryotes, as well as in the apicoplasts of some protozoa, are all of prokaryotic origin. Here, we provide experimental evidence for a novel lipoate assembly pathway in bacteria based on a sLpl(AB) lipoate:protein ligase, which attaches octanoate or lipoate to apo-proteins, and 2 radical SAM proteins, LipS1 and LipS2, which work together as lipoyl synthase and insert 2 sulfur atoms. Extensive homology searches combined with genomic context analyses allowed us to precisely distinguish between the new and established pathways and map them on the tree of life. This not only revealed a much wider distribution of lipoate biogenesis systems than expected, in particular, the novel sLpl(AB)-LipS1/S2 pathway, and indicated a highly modular nature of the enzymes involved, with unforeseen combinations, but also provided a new framework for the evolution of lipoate assembly. Our results show that dedicated machineries for both de novo lipoate biogenesis and scavenging from the environment were implemented early in evolution and that their distribution in the 2 prokaryotic domains was shaped by a complex network of horizontal gene transfers, acquisition of additional genes, fusions, and losses. Our large-scale phylogenetic analyses identify the bipartite archaeal LplAB ligase as the ancestor of the bacterial sLpl(AB) proteins, which were obtained by horizontal gene transfer. LipS1/S2 have a more complex evolutionary history with multiple of such events but probably also originated in the domain archaea.
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Affiliation(s)
- Tomohisa Sebastian Tanabe
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Martina Grosser
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Lea Hahn
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Carolin Kümpel
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Hanna Hartenfels
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Evelyn Vtulkin
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Wanda Flegler
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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13
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Eme L, Tamarit D, Caceres EF, Stairs CW, De Anda V, Schön ME, Seitz KW, Dombrowski N, Lewis WH, Homa F, Saw JH, Lombard J, Nunoura T, Li WJ, Hua ZS, Chen LX, Banfield JF, John ES, Reysenbach AL, Stott MB, Schramm A, Kjeldsen KU, Teske AP, Baker BJ, Ettema TJG. Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes. Nature 2023; 618:992-999. [PMID: 37316666 PMCID: PMC10307638 DOI: 10.1038/s41586-023-06186-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/10/2023] [Indexed: 06/16/2023]
Abstract
In the ongoing debates about eukaryogenesis-the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors-members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2-4. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.
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Affiliation(s)
- Laura Eme
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Laboratoire Écologie, Systématique, Évolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Daniel Tamarit
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Eva F Caceres
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Courtney W Stairs
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Biology, Lund University, Lund, Sweden
| | - Valerie De Anda
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX, USA
- Department of Integrative Biology, University of Texas Austin, Austin, TX, USA
| | - Max E Schön
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kiley W Seitz
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX, USA
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nina Dombrowski
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX, USA
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - William H Lewis
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Felix Homa
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Jimmy H Saw
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Jonathan Lombard
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - 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, PR 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, PR China
| | - Lin-Xing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - 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
| | - Emily St John
- Department of Biology, Portland State University, Portland, OR, USA
| | | | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Andreas Schramm
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Kasper U Kjeldsen
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Andreas P Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas, TX, USA
- Department of Integrative Biology, University of Texas Austin, Austin, TX, USA
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
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14
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López-García P, Moreira D. The symbiotic origin of the eukaryotic cell. C R Biol 2023; 346:55-73. [PMID: 37254790 DOI: 10.5802/crbiol.118] [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: 01/26/2023] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 06/01/2023]
Abstract
Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, the most accepted scenario involved the evolution of an independent lineage of proto-eukaryotes endowed with an endomembrane system, including a nuclear compartment, a developed cytoskeleton and phagocytosis, which engulfed the alphaproteobacterial ancestor of mitochondria. However, the recent discovery by metagenomic and cultural approaches of Asgard archaea, which harbour many genes in common with eukaryotes and are their closest relatives in phylogenomic trees, rather supports scenarios based on the symbiosis of one Asgard-like archaeon and one or more bacteria at the origin of the eukaryotic cell. Here, we review the recent discoveries that led to this conceptual shift, briefly evoking current models of eukaryogenesis and the challenges ahead to discriminate between them and to establish a detailed, plausible scenario that accounts for the evolution of eukaryotic traits from those of their prokaryotic ancestors.
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15
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Oren A, Göker M. Candidatus List. Lists of names of prokaryotic Candidatus phyla. Int J Syst Evol Microbiol 2023; 73. [PMID: 37159402 DOI: 10.1099/ijsem.0.005821] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
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16
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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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17
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Zhang C, Fang YX, Yin X, Lai H, Kuang Z, Zhang T, Xu XP, Wegener G, Wang JH, Dong X. The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules. MICROBIOME 2023; 11:37. [PMID: 36864529 PMCID: PMC9979476 DOI: 10.1186/s40168-023-01482-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/30/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Gas hydrate-bearing subseafloor sediments harbor a large number of microorganisms. Within these sediments, organic matter and upward-migrating methane are important carbon and energy sources fueling a light-independent biosphere. However, the type of metabolism that dominates the deep subseafloor of the gas hydrate zone is poorly constrained. Here we studied the microbial communities in gas hydrate-rich sediments up to 49 m below the seafloor recovered by drilling in the South China Sea. We focused on distinct geochemical conditions and performed metagenomic and metatranscriptomic analyses to characterize microbial communities and their role in carbon mineralization. RESULTS Comparative microbial community analysis revealed that samples above and in sulfate-methane interface (SMI) zones were clearly distinguished from those below the SMI. Chloroflexota were most abundant above the SMI, whereas Caldatribacteriota dominated below the SMI. Verrucomicrobiota, Bathyarchaeia, and Hadarchaeota were similarly present in both types of sediment. The genomic inventory and transcriptional activity suggest an important role in the fermentation of macromolecules. In contrast, sulfate reducers and methanogens that catalyze the consumption or production of commonly observed chemical compounds in sediments are rare. Methanotrophs and alkanotrophs that anaerobically grow on alkanes were also identified to be at low abundances. The ANME-1 group actively thrived in or slightly below the current SMI. Members from Heimdallarchaeia were found to encode the potential for anaerobic oxidation of short-chain hydrocarbons. CONCLUSIONS These findings indicate that the fermentation of macromolecules is the predominant energy source for microorganisms in deep subseafloor sediments that are experiencing upward methane fluxes. Video Abstract.
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Affiliation(s)
- Chuwen Zhang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Yun-Xin Fang
- Guangzhou Marine Geological Survey, China Geological Survey, Ministry of Natural Resources, Guangzhou, China
| | - Xiuran Yin
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Hongfei Lai
- Guangzhou Marine Geological Survey, China Geological Survey, Ministry of Natural Resources, Guangzhou, China
| | - Zenggui Kuang
- Guangzhou Marine Geological Survey, China Geological Survey, Ministry of Natural Resources, Guangzhou, China
| | - Tianxueyu Zhang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Xiang-Po Xu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Gunter Wegener
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jiang-Hai Wang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China.
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
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18
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Zhang CJ, Liu YR, Cha G, Liu Y, Zhou XQ, Lu Z, Pan J, Cai M, Li M. Potential for mercury methylation by Asgard archaea in mangrove sediments. THE ISME JOURNAL 2023; 17:478-485. [PMID: 36639538 PMCID: PMC9938162 DOI: 10.1038/s41396-023-01360-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/22/2022] [Accepted: 01/06/2023] [Indexed: 01/15/2023]
Abstract
Methylmercury (MeHg) is a potent neurotoxin that bioaccumulates along food chains. The conversion of MeHg from mercury (Hg) is mediated by a variety of anaerobic microorganisms carrying hgcAB genes. Mangrove sediments are potential hotspots of microbial Hg methylation; however, the microorganisms responsible for Hg methylation are poorly understood. Here, we conducted metagenomic and metatranscriptomic analyses to investigate the diversity and distribution of putative microbial Hg-methylators in mangrove ecosystems. The highest hgcA abundance and expression occurred in surface sediments in Shenzhen, where the highest MeHg concentration was also observed. We reconstructed 157 metagenome-assembled genomes (MAGs) carrying hgcA and identified several putative novel Hg-methylators, including one Asgard archaea (Lokiarchaeota). Further analysis of MAGs revealed that Deltaproteobacteria, Euryarchaeota, Bacteroidetes, Chloroflexi, and Lokiarchaeota were the most abundant and active Hg-methylating groups, implying their crucial role in MeHg production. By screening publicly available MAGs, 104 additional Asgard MAGs carrying hgcA genes were identified from a wide range of coast, marine, permafrost, and lake sediments. Protein homology modelling predicts that Lokiarchaeota HgcAB proteins contained the highly conserved amino acid sequences and folding structures required for Hg methylation. Phylogenetic tree revealed that hgcA genes from Asgard clustered with fused hgcAB genes, indicating a transitional stage of Asgard hgcA genes. Our findings thus suggest that Asgard archaea are potential novel Hg-methylating microorganisms and play an important role in hgcA evolution.
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Affiliation(s)
- Cui-Jing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
| | - Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Guihong Cha
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
| | - Xin-Quan Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zhongyi Lu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
| | - Mingwei Cai
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
- Chemical Biology Institute, Shenzhen Bay Laboratory, Shenzhen, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China.
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19
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Ponlachantra K, Suginta W, Robinson RC, Kitaoku Y. AlphaFold2: A versatile tool to predict the appearance of functional adaptations in evolution: Profilin interactions in uncultured Asgard archaea: Profilin interactions in uncultured Asgard archaea. Bioessays 2023; 45:e2200119. [PMID: 36461738 DOI: 10.1002/bies.202200119] [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: 06/17/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 12/05/2022]
Abstract
The release of AlphaFold2 (AF2), a deep-learning-aided, open-source protein structure prediction program, from DeepMind, opened a new era of molecular biology. The astonishing improvement in the accuracy of the structure predictions provides the opportunity to characterize protein systems from uncultured Asgard archaea, key organisms in evolutionary biology. Despite the accumulation in metagenomics-derived Asgard archaea eukaryotic-like protein sequences, limited structural and biochemical information have restricted the insight in their potential functions. In this review, we focus on profilin, an actin-dynamics regulating protein, which in eukaryotes, modulates actin polymerization through (1) direct actin interaction, (2) polyproline binding, and (3) phospholipid binding. We assess AF2-predicted profilin structures in their potential abilities to participate in these activities. We demonstrate that AF2 is a powerful new tool for understanding the emergence of biological functional traits in evolution.
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Affiliation(s)
- Khongpon Ponlachantra
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Robert C Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.,Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan
| | - Yoshihito Kitaoku
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan
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20
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Mei R, Kaneko M, Imachi H, Nobu MK. The origin and evolution of methanogenesis and Archaea are intertwined. PNAS NEXUS 2023; 2:pgad023. [PMID: 36874274 PMCID: PMC9982363 DOI: 10.1093/pnasnexus/pgad023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/20/2023] [Indexed: 02/01/2023]
Abstract
Methanogenesis has been widely accepted as an ancient metabolism, but the precise evolutionary trajectory remains hotly debated. Disparate theories exist regarding its emergence time, ancestral form, and relationship with homologous metabolisms. Here, we report the phylogenies of anabolism-involved proteins responsible for cofactor biosynthesis, providing new evidence for the antiquity of methanogenesis. Revisiting the phylogenies of key catabolism-involved proteins further suggests that the last Archaea common ancestor (LACA) was capable of versatile H2-, CO2-, and methanol-utilizing methanogenesis. Based on phylogenetic analyses of the methyl/alkyl-S-CoM reductase family, we propose that, in contrast to current paradigms, substrate-specific functions emerged through parallel evolution traced back to a nonspecific ancestor, which likely originated from protein-free reactions as predicted from autocatalytic experiments using cofactor F430. After LACA, inheritance/loss/innovation centered around methanogenic lithoautotrophy coincided with ancient lifestyle divergence, which is clearly reflected by genomically predicted physiologies of extant archaea. Thus, methanogenesis is not only a hallmark metabolism of Archaea, but the key to resolve the enigmatic lifestyle that ancestral archaea took and the transition that led to physiologies prominent today.
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Affiliation(s)
- Ran Mei
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan
| | - Masanori Kaneko
- Institute for Geo-Resources and Environment, Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8567, Japan
| | - Hiroyuki Imachi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan.,Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
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21
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Eco-evolutionary modelling of microbial syntrophy indicates the robustness of cross-feeding over cross-facilitation. Sci Rep 2023; 13:907. [PMID: 36650168 PMCID: PMC9845244 DOI: 10.1038/s41598-023-27421-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 12/29/2022] [Indexed: 01/18/2023] Open
Abstract
Syntrophic cooperation among prokaryotes is ubiquitous and diverse. It relies on unilateral or mutual aid that may be both catalytic and metabolic in nature. Hypotheses of eukaryotic origins claim that mitochondrial endosymbiosis emerged from mutually beneficial syntrophy of archaeal and bacterial partners. However, there are no other examples of prokaryotic syntrophy leading to endosymbiosis. One potential reason is that when externalized products become public goods, they incite social conflict due to selfish mutants that may undermine any mutualistic interactions. To rigorously evaluate these arguments, here we construct a general mathematical framework of the ecology and evolution of different types of syntrophic partnerships. We do so both in a general microbial and in a eukaryogenetic context. Studying the case where partners cross-feed on each other's self-inhibiting waste, we show that cooperative partnerships will eventually dominate over selfish mutants. By contrast, systems where producers actively secrete enzymes that cross-facilitate their partners' resource consumption are not robust against cheaters over evolutionary time. We conclude that cross-facilitation is unlikely to provide an adequate syntrophic origin for endosymbiosis, but that cross-feeding mutualisms may indeed have played that role.
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22
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Vosseberg J, Stolker D, von der Dunk SHA, Snel B. Integrating Phylogenetics With Intron Positions Illuminates the Origin of the Complex Spliceosome. Mol Biol Evol 2023; 40:6985000. [PMID: 36631250 PMCID: PMC9887622 DOI: 10.1093/molbev/msad011] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/09/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023] Open
Abstract
Eukaryotic genes are characterized by the presence of introns that are removed from pre-mRNA by a spliceosome. This ribonucleoprotein complex is comprised of multiple RNA molecules and over a hundred proteins, which makes it one of the most complex molecular machines that originated during the prokaryote-to-eukaryote transition. Previous works have established that these introns and the spliceosomal core originated from self-splicing introns in prokaryotes. Yet, how the spliceosomal core expanded by recruiting many additional proteins remains largely elusive. In this study, we use phylogenetic analyses to infer the evolutionary history of 145 proteins that we could trace back to the spliceosome in the last eukaryotic common ancestor. We found that an overabundance of proteins derived from ribosome-related processes was added to the prokaryote-derived core. Extensive duplications of these proteins substantially increased the complexity of the emerging spliceosome. By comparing the intron positions between spliceosomal paralogs, we infer that most spliceosomal complexity postdates the spread of introns through the proto-eukaryotic genome. The reconstruction of early spliceosomal evolution provides insight into the driving forces behind the emergence of complexes with many proteins during eukaryogenesis.
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Affiliation(s)
- Julian Vosseberg
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands,Laboratory of Microbiology, Wageningen University & Research, 6700 EH Wageningen, the Netherlands
| | - Daan Stolker
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Samuel H A von der Dunk
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
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23
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Actin cytoskeleton and complex cell architecture in an Asgard archaeon. Nature 2023; 613:332-339. [PMID: 36544020 PMCID: PMC9834061 DOI: 10.1038/s41586-022-05550-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/10/2022] [Indexed: 12/24/2022]
Abstract
Asgard archaea are considered to be the closest known relatives of eukaryotes. Their genomes contain hundreds of eukaryotic signature proteins (ESPs), which inspired hypotheses on the evolution of the eukaryotic cell1-3. A role of ESPs in the formation of an elaborate cytoskeleton and complex cellular structures has been postulated4-6, but never visualized. Here we describe a highly enriched culture of 'Candidatus Lokiarchaeum ossiferum', a member of the Asgard phylum, which thrives anaerobically at 20 °C on organic carbon sources. It divides every 7-14 days, reaches cell densities of up to 5 × 107 cells per ml and has a significantly larger genome compared with the single previously cultivated Asgard strain7. ESPs represent 5% of its protein-coding genes, including four actin homologues. We imaged the enrichment culture using cryo-electron tomography, identifying 'Ca. L. ossiferum' cells on the basis of characteristic expansion segments of their ribosomes. Cells exhibited coccoid cell bodies and a network of branched protrusions with frequent constrictions. The cell envelope consists of a single membrane and complex surface structures. A long-range cytoskeleton extends throughout the cell bodies, protrusions and constrictions. The twisted double-stranded architecture of the filaments is consistent with F-actin. Immunostaining indicates that the filaments comprise Lokiactin-one of the most highly conserved ESPs in Asgard archaea. We propose that a complex actin-based cytoskeleton predated the emergence of the first eukaryotes and was a crucial feature in the evolution of the Asgard phylum by scaffolding elaborate cellular structures.
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24
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Zhou Z, St John E, Anantharaman K, Reysenbach AL. Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits. MICROBIOME 2022; 10:241. [PMID: 36572924 PMCID: PMC9793634 DOI: 10.1186/s40168-022-01424-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/11/2022] [Indexed: 05/16/2023]
Abstract
BACKGROUND When deep-sea hydrothermal fluids mix with cold oxygenated fluids, minerals precipitate out of solution and form hydrothermal deposits. These actively venting deep-sea hydrothermal deposits support a rich diversity of thermophilic microorganisms which are involved in a range of carbon, sulfur, nitrogen, and hydrogen metabolisms. Global patterns of thermophilic microbial diversity in deep-sea hydrothermal ecosystems have illustrated the strong connectivity between geological processes and microbial colonization, but little is known about the genomic diversity and physiological potential of these novel taxa. Here we explore this genomic diversity in 42 metagenomes from four deep-sea hydrothermal vent fields and a deep-sea volcano collected from 2004 to 2018 and document their potential implications in biogeochemical cycles. RESULTS Our dataset represents 3635 metagenome-assembled genomes encompassing 511 novel and recently identified genera from deep-sea hydrothermal settings. Some of the novel bacterial (107) and archaeal genera (30) that were recently reported from the deep-sea Brothers volcano were also detected at the deep-sea hydrothermal vent fields, while 99 bacterial and 54 archaeal genera were endemic to the deep-sea Brothers volcano deposits. We report some of the first examples of medium- (≥ 50% complete, ≤ 10% contaminated) to high-quality (> 90% complete, < 5% contaminated) MAGs from phyla and families never previously identified, or poorly sampled, from deep-sea hydrothermal environments. We greatly expand the novel diversity of Thermoproteia, Patescibacteria (Candidate Phyla Radiation, CPR), and Chloroflexota found at deep-sea hydrothermal vents and identify a small sampling of two potentially novel phyla, designated JALSQH01 and JALWCF01. Metabolic pathway analysis of metagenomes provides insights into the prevalent carbon, nitrogen, sulfur, and hydrogen metabolic processes across all sites and illustrates sulfur and nitrogen metabolic "handoffs" in community interactions. We confirm that Campylobacteria and Gammaproteobacteria occupy similar ecological guilds but their prevalence in a particular site is driven by shifts in the geochemical environment. CONCLUSION Our study of globally distributed hydrothermal vent deposits provides a significant expansion of microbial genomic diversity associated with hydrothermal vent deposits and highlights the metabolic adaptation of taxonomic guilds. Collectively, our results illustrate the importance of comparative biodiversity studies in establishing patterns of shared phylogenetic diversity and physiological ecology, while providing many targets for enrichment and cultivation of novel and endemic taxa. Video Abstract.
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Affiliation(s)
- Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Emily St John
- Center for Life in Extreme Environments, Biology Department, Portland State University, Portland, OR, 97201, USA
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Anna-Louise Reysenbach
- Center for Life in Extreme Environments, Biology Department, Portland State University, Portland, OR, 97201, USA.
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25
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Spang A. Is an archaeon the ancestor of eukaryotes? Environ Microbiol 2022; 25:775-779. [PMID: 36562617 DOI: 10.1111/1462-2920.16323] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
The origin of complex cellular life is a key puzzle in evolutionary research, which has broad implications for various neighbouring scientific disciplines. Naturally, views on this topic vary widely depending on the world view and context from which this topic is approached. In the following, I will share my perspective about our current scientific knowledge on the origin of eukaryotic cells, that is, eukaryogenesis, from a biological point of view focusing on the question as to whether an archaeon was the ancestor of eukaryotes.
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Affiliation(s)
- Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, AB Den Burg, The Netherlands.,Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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26
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Allioux M, Yvenou S, Merkel A, Cozannet M, Aubé J, Pommellec J, Le Romancer M, Lavastre V, Guillaume D, Alain K. A metagenomic insight into the microbiomes of geothermal springs in the Subantarctic Kerguelen Islands. Sci Rep 2022; 12:22243. [PMID: 36564496 PMCID: PMC9789041 DOI: 10.1038/s41598-022-26299-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
The Kerguelen Islands, located in the southern part of the Indian Ocean, are very isolated geographically. The microbial diversity and communities present on the island, especially associated to geothermal springs, have never been analyzed with high-throughput sequencing methods. In this article, we performed the first metagenomics analysis of microorganisms present in Kerguelen hot springs. From four hot springs, we assembled metagenomes and recovered 42 metagenome-assembled genomes, mostly associated with new putative taxa based on phylogenomic analyses and overall genome relatedness indices. The 42 MAGs were studied in detail and showed putative affiliations to 13 new genomic species and 6 new genera of Bacteria or Archaea according to GTDB. Functional potential of MAGs suggests the presence of thermophiles and hyperthermophiles, as well as heterotrophs and primary producers possibly involved in the sulfur cycle, notably in the oxidation of sulfur compounds. This paper focused on only four of the dozens of hot springs in the Kerguelen Islands and should be considered as a preliminary study of the microorganisms inhabiting the hot springs of these isolated islands. These results show that more efforts should be made towards characterization of Kerguelen Islands ecosystems, as they represent a reservoir of unknown microbial lineages.
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Affiliation(s)
- Maxime Allioux
- Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, Unité Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, IUEM, Rue Dumont d'Urville, 29280, Plouzané, France
| | - Stéven Yvenou
- Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, Unité Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, IUEM, Rue Dumont d'Urville, 29280, Plouzané, France
| | - Alexander Merkel
- , Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Marc Cozannet
- Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, Unité Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, IUEM, Rue Dumont d'Urville, 29280, Plouzané, France
| | - Johanne Aubé
- Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, Unité Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, IUEM, Rue Dumont d'Urville, 29280, Plouzané, France
| | - Jolann Pommellec
- Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, Unité Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, IUEM, Rue Dumont d'Urville, 29280, Plouzané, France
| | - Marc Le Romancer
- UBO, UFR Sciences et Techniques, UR 7462, Laboratoire Géoarchitecture, Territoires, Urbanisation, Biodiversité, Environnement, Rennes, France
| | | | | | - Karine Alain
- Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, Unité Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, IUEM, Rue Dumont d'Urville, 29280, Plouzané, France.
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27
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Zhang X, Zhang C, Liu Y, Zhang R, Li M. Non-negligible roles of archaea in coastal carbon biogeochemical cycling. Trends Microbiol 2022; 31:586-600. [PMID: 36567186 DOI: 10.1016/j.tim.2022.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 12/25/2022]
Abstract
Coastal zones are among the world's most productive ecosystems. They store vast amounts of organic carbon, as 'blue carbon' reservoirs, and impact global climate change. Archaeal communities are integral components of coastal microbiomes but their ecological roles are often overlooked. However, archaeal diversity, metabolism, evolution, and interactions, revealed by recent studies using rapidly developing cutting-edge technologies, place archaea as important players in coastal carbon biogeochemical cycling. We here summarize the latest advances in the understanding of archaeal carbon cycling processes in coastal ecosystems, specifically, archaeal involvement in CO2 fixation, organic biopolymer transformation, and methane metabolism. We also showcase the potential to use of archaeal communities to increase carbon sequestration and reduce methane production, with implications for mitigating climate change.
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Affiliation(s)
- 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
| | - Cuijing 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
| | - 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
| | - Rui 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
| | - 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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28
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Gong X, Del Río ÁR, Xu L, Chen Z, Langwig MV, Su L, Sun M, Huerta-Cepas J, De Anda V, Baker BJ. New globally distributed bacterial phyla within the FCB superphylum. Nat Commun 2022; 13:7516. [PMID: 36473838 PMCID: PMC9727166 DOI: 10.1038/s41467-022-34388-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 10/24/2022] [Indexed: 12/12/2022] Open
Abstract
Microbes in marine sediments play crucial roles in global carbon and nutrient cycling. However, our understanding of microbial diversity and physiology on the ocean floor is limited. Here, we use phylogenomic analyses of thousands of metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments to identify 55 MAGs that are phylogenetically distinct from previously described bacterial phyla. We propose that these MAGs belong to 4 novel bacterial phyla (Blakebacterota, Orphanbacterota, Arandabacterota, and Joyebacterota) and a previously proposed phylum (AABM5-125-24), all of them within the FCB superphylum. Comparison of their rRNA genes with public databases reveals that these phyla are globally distributed in different habitats, including marine, freshwater, and terrestrial environments. Genomic analyses suggest these organisms are capable of mediating key steps in sedimentary biogeochemistry, including anaerobic degradation of polysaccharides and proteins, and respiration of sulfur and nitrogen. Interestingly, these genomes code for an unusually high proportion (~9% on average, up to 20% per genome) of protein families lacking representatives in public databases. Genes encoding hundreds of these protein families colocalize with genes predicted to be involved in sulfur reduction, nitrogen cycling, energy conservation, and degradation of organic compounds. Our findings advance our understanding of bacterial diversity, the ecological roles of these bacteria, and potential links between novel gene families and metabolic processes in the oceans.
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Affiliation(s)
- Xianzhe Gong
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong, 266237, China.
- Department of Marine Science, University of Texas at Austin, Port Aransas, TX, 78373, USA.
| | - Álvaro Rodríguez Del Río
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Le Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Zhiyi Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong, 266237, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Marguerite V Langwig
- Department of Marine Science, University of Texas at Austin, Port Aransas, TX, 78373, USA
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Lei Su
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Mingxue Sun
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Valerie De Anda
- Department of Marine Science, University of Texas at Austin, Port Aransas, TX, 78373, USA.
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin, Port Aransas, TX, 78373, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78701, USA.
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29
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Zhou Z, Liu Y, Anantharaman K, Li M. The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis. MLIFE 2022; 1:374-381. [PMID: 38818484 PMCID: PMC10989744 DOI: 10.1002/mlf2.12048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/13/2022] [Accepted: 11/13/2022] [Indexed: 06/01/2024]
Abstract
The division of organisms on the Tree of Life into either a three-domain (3D) tree or a two-domain (2D) tree has been disputed for a long time. Ever since the discovery of Archaea by Carl Woese in 1977 using 16S ribosomal RNA sequence as the evolutionary marker, there has been a great advance in our knowledge of not only the growing diversity of Archaea but also the evolutionary relationships between different lineages of living organisms. Here, we present this perspective to summarize the progress of archaeal diversity and changing notion of the Tree of Life. Meanwhile, we provide the latest progress in genomics/physiology-based discovery of Asgard archaeal lineages as the closest relative of Eukaryotes. Furthermore, we propose three major directions for future research on exploring the "next one" closest Eukaryote relative, deciphering the function of archaeal eukaryotic signature proteins and eukaryogenesis from both genomic and physiological aspects, and understanding the roles of horizontal gene transfer, viruses, and mobile elements in eukaryogenesis.
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Affiliation(s)
- Zhichao Zhou
- Department of BacteriologyUniversity of Wisconsin–MadisonMadisonWisconsinUSA
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced StudyShenzhen UniversityShenzhenChina
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced StudyShenzhen UniversityShenzhenChina
| | | | - Meng Li
- Archaeal Biology Center, Institute for Advanced StudyShenzhen UniversityShenzhenChina
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced StudyShenzhen UniversityShenzhenChina
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30
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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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31
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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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32
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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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33
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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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34
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Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily. THE ISME JOURNAL 2022; 16:1750-1764. [PMID: 35352015 PMCID: PMC9213671 DOI: 10.1038/s41396-022-01222-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/18/2022] [Accepted: 02/09/2022] [Indexed: 01/04/2023]
Abstract
Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physicochemical data and 16S rRNA gene amplicons to characterize the sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 30% of those currently known, showing the microbial community in Auka hydrothermal sediments is highly diverse. 16S rRNA gene amplicon screening of 224 sediment samples across the vent field indicates that the MAGs retrieved from a single site are representative of the microbial community in the vent field sediments. Metabolic reconstruction of a vent-specific, deeply branching clade within the Desulfobacterota suggests these organisms metabolize sulfur using novel octaheme cytochrome-c proteins related to hydroxylamine oxidoreductase. Community-wide comparison between Auka MAGs and MAGs from Guaymas Basin revealed a remarkable 20% species-level overlap, suggestive of long-distance species transfer over 400 km and subsequent sediment colonization. Optimal growth temperature prediction on the Auka MAGs, and thousands of reference genomes, shows that thermophily is a trait that has evolved frequently. Taken together, our Auka vent field results offer new perspectives on our understanding of hydrothermal vent microbiology.
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35
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Medvedeva S, Sun J, Yutin N, Koonin EV, Nunoura T, Rinke C, Krupovic M. Three families of Asgard archaeal viruses identified in metagenome-assembled genomes. Nat Microbiol 2022; 7:962-973. [PMID: 35760839 PMCID: PMC11165672 DOI: 10.1038/s41564-022-01144-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 05/04/2022] [Indexed: 02/07/2023]
Abstract
Asgardarchaeota harbour many eukaryotic signature proteins and are widely considered to represent the closest archaeal relatives of eukaryotes. Whether similarities between Asgard archaea and eukaryotes extend to their viromes remains unknown. Here we present 20 metagenome-assembled genomes of Asgardarchaeota from deep-sea sediments of the basin off the Shimokita Peninsula, Japan. By combining a CRISPR spacer search of metagenomic sequences with phylogenomic analysis, we identify three family-level groups of viruses associated with Asgard archaea. The first group, verdandiviruses, includes tailed viruses of the class Caudoviricetes (realm Duplodnaviria); the second, skuldviruses, consists of viruses with predicted icosahedral capsids of the realm Varidnaviria; and the third group, wyrdviruses, is related to spindle-shaped viruses previously identified in other archaea. More than 90% of the proteins encoded by these viruses of Asgard archaea show no sequence similarity to proteins encoded by other known viruses. Nevertheless, all three proposed families consist of viruses typical of prokaryotes, providing no indication of specific evolutionary relationships between viruses infecting Asgard archaea and eukaryotes. Verdandiviruses and skuldviruses are likely to be lytic, whereas wyrdviruses potentially establish chronic infection and are released without host cell lysis. All three groups of viruses are predicted to play important roles in controlling Asgard archaea populations in deep-sea ecosystems.
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Affiliation(s)
- Sofia Medvedeva
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
- Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, Russia
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Evolutionary Biology of the Microbial Cell Unit, Paris, France
| | - Jiarui Sun
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France.
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36
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Abstract
Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.
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37
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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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38
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Hatano T, Palani S, Papatziamou D, Salzer R, Souza DP, Tamarit D, Makwana M, Potter A, Haig A, Xu W, Townsend D, Rochester D, Bellini D, Hussain HMA, Ettema TJG, Löwe J, Baum B, Robinson NP, Balasubramanian M. Asgard archaea shed light on the evolutionary origins of the eukaryotic ubiquitin-ESCRT machinery. Nat Commun 2022; 13:3398. [PMID: 35697693 PMCID: PMC9192718 DOI: 10.1038/s41467-022-30656-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 05/10/2022] [Indexed: 11/23/2022] Open
Abstract
The ESCRT machinery, comprising of multiple proteins and subcomplexes, is crucial for membrane remodelling in eukaryotic cells, in processes that include ubiquitin-mediated multivesicular body formation, membrane repair, cytokinetic abscission, and virus exit from host cells. This ESCRT system appears to have simpler, ancient origins, since many archaeal species possess homologues of ESCRT-III and Vps4, the components that execute the final membrane scission reaction, where they have been shown to play roles in cytokinesis, extracellular vesicle formation and viral egress. Remarkably, metagenome assemblies of Asgard archaea, the closest known living relatives of eukaryotes, were recently shown to encode homologues of the entire cascade involved in ubiquitin-mediated membrane remodelling, including ubiquitin itself, components of the ESCRT-I and ESCRT-II subcomplexes, and ESCRT-III and Vps4. Here, we explore the phylogeny, structure, and biochemistry of Asgard homologues of the ESCRT machinery and the associated ubiquitylation system. We provide evidence for the ESCRT-I and ESCRT-II subcomplexes being involved in ubiquitin-directed recruitment of ESCRT-III, as it is in eukaryotes. Taken together, our analyses suggest a pre-eukaryotic origin for the ubiquitin-coupled ESCRT system and a likely path of ESCRT evolution via a series of gene duplication and diversification events.
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Grants
- MC_U105184326 Medical Research Council
- MC_UP_1201/27 Medical Research Council
- 203276/Z/16/Z Wellcome Trust
- Wellcome Trust
- WT101885MA Wellcome Trust
- Wellcome Trust (Wellcome)
- Leverhulme Trust
- Svenska Forskningsrådet Formas (Swedish Research Council Formas)
- Above funding attributed to the authors as follows (from paper acknowledgements): Computational analysis was facilitated by resources provided by the Swedish National Infrastructure for Computing (SNIC) at the Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX), partially funded by the Swedish Research Council through grant agreement no. 2018-05973. We thank the Warwick Proteomics RTP for mass spectrometry. MKB was supported by the Wellcome Trust (WT101885MA) and the European Research Council (ERC-2014-ADG No. 671083). Work by the NR laboratory was supported by start-up funds from the Division of Biomedical and Life Sciences (BLS, Lancaster University) and a Leverhulme Research Project Grant (RPG-2019-297). NR would like to thank Johanna Syrjanen for performing trial expressions of the Odinarchaeota ESCRT proteins, and Joseph Maman for helpful discussion regarding the SEC-MALS. NR, WX and AP would like to thank Charley Lai and Siu-Kei Yau for assistance with initial Odinarchaeota ESCRT protein purifications. DPS and BB would like to thank Chris Johnson at the MRC LMB Biophysics facility for performing the SEC-MALS assay on Heimdallarchaeotal Vps22. TH, HH, MB, RS, JL, D Tamarit, TE, DPS and BB received support from a Wellcome Trust collaborative award (203276/Z/16/Z). BB and DPS were supported by the MRC. D Tamarit was supported by the Swedish Research Council (International Postdoc grant 2018-06609).
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Affiliation(s)
- Tomoyuki Hatano
- Centre for Mechanochemical Cell Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Saravanan Palani
- Centre for Mechanochemical Cell Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Dimitra Papatziamou
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK
| | - Ralf Salzer
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Diorge P Souza
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Daniel Tamarit
- Laboratory of Microbiology, Wageningen University, 6708 WE, Wageningen, The Netherlands
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| | - Mehul Makwana
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK
| | - Antonia Potter
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK
| | - Alexandra Haig
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK
| | - Wenjue Xu
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK
| | - David Townsend
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK
| | - David Rochester
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK
| | - Dom Bellini
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Hamdi M A Hussain
- Centre for Mechanochemical Cell Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Buzz Baum
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
| | - Nicholas P Robinson
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK.
| | - Mohan Balasubramanian
- Centre for Mechanochemical Cell Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK.
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39
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Gophna U, Altman-Price N. Horizontal Gene Transfer in Archaea-From Mechanisms to Genome Evolution. Annu Rev Microbiol 2022; 76:481-502. [PMID: 35667126 DOI: 10.1146/annurev-micro-040820-124627] [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
Archaea remains the least-studied and least-characterized domain of life despite its significance not just to the ecology of our planet but also to the evolution of eukaryotes. It is therefore unsurprising that research into horizontal gene transfer (HGT) in archaea has lagged behind that of bacteria. Indeed, several archaeal lineages may owe their very existence to large-scale HGT events, and thus understanding both the molecular mechanisms and the evolutionary impact of HGT in archaea is highly important. Furthermore, some mechanisms of gene exchange, such as plasmids that transmit themselves via membrane vesicles and the formation of cytoplasmic bridges that allows transfer of both chromosomal and plasmid DNA, may be archaea specific. This review summarizes what we know about HGT in archaea, and the barriers that restrict it, highlighting exciting recent discoveries and pointing out opportunities for future research. 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)
- Uri Gophna
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; ,
| | - Neta Altman-Price
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; , .,Department of Natural and Life Sciences, The Open University of Israel, Raanana, Israel
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40
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Mkhondwane ST, Pullabhotla VSR. Cyclohexane oxidation using advanced oxidation processes with metals and metal oxides as catalysts: a review. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2021-0146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Selective oxidation of cyclohexane has gained substantial interest in the field of research due to the prominence of its products in industrial processes. Particularly, advanced oxidation processes (AOPs) constitute a positive technology for the oxidation of cyclohexane owing to their high oxidation potentials and environmental benign properties. This review entails to address the progress made in advanced oxidation of cyclohexane over nanostructured metals and metal oxides catalysts. The main focus is directed toward the photocatalysis, Fenton oxidation and ozonation as advanced oxidation processes. Mainly, the fundamental principles, prime factors of the AOPs in conjunction with metal and metal oxide catalysts and the mechanistic insight toward the oxidation of cyclohexane are highlighted. The affirmative effects of the metals and metal oxide catalysts mainly focusing on particle size, structure and elemental composition is stressed. Lastly, the advantages and disadvantages of the AOPs and the strategic approaches to counter the disadvantages are also clearly elucidated.
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41
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Lemaire ON, Wagner T. A Structural View of Alkyl-Coenzyme M Reductases, the First Step of Alkane Anaerobic Oxidation Catalyzed by Archaea. Biochemistry 2022; 61:805-821. [PMID: 35500274 PMCID: PMC9118554 DOI: 10.1021/acs.biochem.2c00135] [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] [Indexed: 11/28/2022]
Abstract
![]()
Microbial anaerobic
oxidation of alkanes intrigues the scientific
community by way of its impact on the global carbon cycle, and its
biotechnological applications. Archaea are proposed to degrade short-
and long-chain alkanes to CO2 by reversing methanogenesis,
a theoretically reversible process. The pathway would start with alkane
activation, an endergonic step catalyzed by methyl-coenzyme M reductase
(MCR) homologues that would generate alkyl-thiols carried by coenzyme
M. While the methane-generating MCR found in methanogens has been
well characterized, the enzymatic activity of the putative alkane-fixing
counterparts has not been validated so far. Such an absence of biochemical
investigations contrasts with the current explosion of metagenomics
data, which draws new potential alkane-oxidizing pathways in various
archaeal phyla. Therefore, validating the physiological function of
these putative alkane-fixing machines and investigating how their
structures, catalytic mechanisms, and cofactors vary depending on
the targeted alkane have become urgent needs. The first structural
insights into the methane- and ethane-capturing MCRs highlighted unsuspected
differences and proposed some explanations for their substrate specificity.
This Perspective reviews the current physiological, biochemical, and
structural knowledge of alkyl-CoM reductases and offers fresh ideas
about the expected mechanistic and chemical differences among members
of this broad family. We conclude with the challenges of the investigation
of these particular enzymes, which might one day generate biofuels
for our modern society.
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Affiliation(s)
- Olivier N Lemaire
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Tristan Wagner
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
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Genomic Evidence for the Recycling of Complex Organic Carbon by Novel
Thermoplasmatota
Clades in Deep-Sea Sediments. mSystems 2022; 7:e0007722. [PMID: 35430893 PMCID: PMC9239135 DOI: 10.1128/msystems.00077-22] [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] [Indexed: 12/03/2022] Open
Abstract
Thermoplasmatota have been widely reported in a variety of ecosystems, but their distribution and ecological role in marine sediments are still elusive. Here, we obtained four draft genomes affiliated with the former RBG-16-68-12 clade, which is now considered a new order, “Candidatus Yaplasmales,” of the Thermoplasmatota phylum in sediments from the South China Sea. The phylogenetic trees based on the 16S rRNA genes and draft genomes showed that “Ca. Yaplasmales” archaea are composed of three clades: A, B, and C. Among them, clades A and B are abundantly distributed (up to 10.86%) in the marine anoxic sediment layers (>10-cm depth) of six of eight cores from 1,200- to 3,400-m depths. Metabolic pathway reconstructions indicated that all clades of “Ca. Yaplasmales” have the capacity for alkane degradation by predicted alkyl-succinate synthase. Clade A of “Ca. Yaplasmales” might be mixotrophic microorganisms for the identification of the complete Wood-Ljungdahl pathway and putative genes involved in the degradation of aromatic and halogenated organic compounds. Clades B and C were likely heterotrophic, especially with the potential capacity of the spermidine/putrescine and aromatic compound degradation, as suggested by a significant negative correlation between the concentrations of aromatic compounds and the relative abundances of clade B. The sulfide-quinone oxidoreductase and pyrophosphate-energized membrane proton pump were encoded by all genomes of “Ca. Yaplasmales,” serving as adaptive strategies for energy production. These findings suggest that “Ca. Yaplasmales” might synergistically transform benthic pollutant and detrital organic matter, possibly playing a vital role in the marine and terrestrial sedimentary carbon cycle. IMPORTANCE Deep oceans receive large amounts of complex organic carbon and anthropogenic pollutants. The deep-sea sediments of the continental slopes serve as the biggest carbon sink on Earth. Particulate organic carbons and detrital proteins accumulate in the sediment. The microbially mediated recycling of complex organic carbon is still largely unknown, which is an important question for carbon budget in global oceans and maintenance of the deep-sea ecosystem. In this study, we report the prevalence (up to 10.86% of the microbial community) of archaea from a novel order of Thermoplasmatota, “Ca. Yaplasmales,” in six of eight cores from 1,200- to 3,400-m depths in the South China Sea. We provide genomic evidence of “Ca. Yaplasmales” in the anaerobic microbial degradation of alkanes, aliphatic and monoaromatic hydrocarbons, and halogenated organic compounds. Our study identifies the key archaeal players in anoxic marine sediments, which are probably critical in recycling the complex organic carbon in global oceans.
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Xie R, Wang Y, Huang D, Hou J, Li L, Hu H, Zhao X, Wang F. Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes. SCIENCE CHINA. LIFE SCIENCES 2022; 65:818-829. [PMID: 34378142 DOI: 10.1007/s11427-021-1969-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
The hypothesis that eukaryotes originated from within the domain Archaea has been strongly supported by recent phylogenomic analyses placing Heimdallarchaeota-Wukongarchaeota branch from the Asgard superphylum as the closest known archaeal sister-group to eukaryotes. However, our understanding is still limited in terms of the relationship between eukaryotes and archaea, as well as the evolution and ecological functions of the Asgard archaea. Here, we describe three previously unknown phylum-level Asgard archaeal lineages, tentatively named Sigyn-, Freyr- and Njordarchaeota. Additional members in Wukongarchaeota and Baldrarchaeota from distinct environments are also reported here, further expanding their ecological roles and metabolic capacities. Comprehensive phylogenomic analyses further supported the origin of eukaryotes within Asgard archaea and a new lineage Njordarchaeota was supposed as the known closest branch with the eukaryotic nuclear host lineage. Metabolic reconstruction suggests that Njordarchaeota may have a heterotrophic lifestyle with capability of peptides and amino acids utilization, while Sigynarchaeota and Freyrarchaeota also have the potentials to fix inorganic carbon via the Wood-Ljungdahl pathway and degrade organic matters. Additionally, the Ack/Pta pathway for homoacetogenesis and de novo anaerobic cobalamin biosynthesis pathway were found in Freyrarchaeota and Wukongrarchaeota, respectively. Some previously unidentified eukaryotic signature proteins for intracellular membrane trafficking system, and the homologue of mu/sigma subunit of adaptor protein complex, were identified in Freyrarchaeota. This study expands the Asgard superphylum, sheds new light on the evolution of eukaryotes and improves our understanding of ecological functions of the Asgard archaea.
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Affiliation(s)
- Ruize Xie
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Danyue Huang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liuyang Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Haining Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoxiao Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fengping Wang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China.
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China.
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44
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Diverse methylotrophic methanogenic archaea cause high methane emissions from seagrass meadows. Proc Natl Acad Sci U S A 2022; 119:2106628119. [PMID: 35165204 PMCID: PMC8892325 DOI: 10.1073/pnas.2106628119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2021] [Indexed: 11/18/2022] Open
Abstract
Marine coastlines colonized by seagrasses are a net source of methane to the atmosphere. However, methane emissions from these environments are still poorly constrained, and the underlying processes and responsible microorganisms remain largely unknown. Here, we investigated methane turnover in seagrass meadows of Posidonia oceanica in the Mediterranean Sea. The underlying sediments exhibited median net fluxes of methane into the water column of ca. 106 µmol CH4 ⋅ m-2 ⋅ d-1 Our data show that this methane production was sustained by methylated compounds produced by the plant, rather than by fermentation of buried organic carbon. Interestingly, methane production was maintained long after the living plant died off, likely due to the persistence of methylated compounds, such as choline, betaines, and dimethylsulfoniopropionate, in detached plant leaves and rhizomes. We recovered multiple mcrA gene sequences, encoding for methyl-coenzyme M reductase (Mcr), the key methanogenic enzyme, from the seagrass sediments. Most retrieved mcrA gene sequences were affiliated with a clade of divergent Mcr and belonged to the uncultured Candidatus Helarchaeota of the Asgard superphylum, suggesting a possible involvement of these divergent Mcr in methane metabolism. Taken together, our findings identify the mechanisms controlling methane emissions from these important blue carbon ecosystems.
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45
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Da Cunha V, Gaïa M, Forterre P. The expanding Asgard archaea and their elusive relationships with Eukarya. MLIFE 2022; 1:3-12. [PMID: 38818326 PMCID: PMC10989751 DOI: 10.1002/mlf2.12012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/25/2022] [Accepted: 02/10/2022] [Indexed: 06/01/2024]
Abstract
The discovery of Asgard archaea and the exploration of their diversity over the last 6 years have deeply impacted the scientific community working on eukaryogenesis, rejuvenating an intense debate on the topology of the universal tree of life (uTol). Here, we discuss how this debate is impacted by two recent publications that expand the number of Asgard lineages and eukaryotic signature proteins (ESPs). We discuss some of the main difficulties that can impair the phylogenetic reconstructions of the uTol and suggest that the debate about its topology is not settled. We notably hypothesize the existence of horizontal gene transfers between ancestral Asgards and proto-eukaryotes that could result in the observed abnormal behaviors of some Asgard ESPs and universal marker proteins. This hypothesis is relevant regardless of the scenario considered regarding eukaryogenesis. It implies that the Asgards were already diversified before the last eukaryotic common ancestor and shared the same biotopes with proto-eukaryotes. We suggest that some Asgards might be still living in symbiosis today with modern Eukarya.
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Affiliation(s)
- Violette Da Cunha
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayGif‐sur‐YvetteFrance
| | - Morgan Gaïa
- Génomique Métabolique, Génoscope, Institut François Jacob, CEA, CNRSUniv. Evry, Université Paris‐SaclayEvryFrance
| | - Patrick Forterre
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayGif‐sur‐YvetteFrance
- Département de Microbiologie, Institut PasteurParisFrance
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46
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Spang A, Mahendrarajah TA, Offre P, Stairs CW. Evolving perspective on the origin and diversification of cellular life and the virosphere. Genome Biol Evol 2022; 14:6537539. [PMID: 35218347 PMCID: PMC9169541 DOI: 10.1093/gbe/evac034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 11/14/2022] Open
Abstract
The tree of life (TOL) is a powerful framework to depict the evolutionary history of cellular organisms through time, from our microbial origins to the diversification of multicellular eukaryotes that shape the visible biosphere today. During the past decades, our perception of the TOL has fundamentally changed, in part, due to profound methodological advances, which allowed a more objective approach to studying organismal and viral diversity and led to the discovery of major new branches in the TOL as well as viral lineages. Phylogenetic and comparative genomics analyses of these data have, among others, revolutionized our understanding of the deep roots and diversity of microbial life, the origin of the eukaryotic cell, eukaryotic diversity, as well as the origin, and diversification of viruses. In this review, we provide an overview of some of the recent discoveries on the evolutionary history of cellular organisms and their viruses and discuss a variety of complementary techniques that we consider crucial for making further progress in our understanding of the TOL and its interconnection with the virosphere.
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Affiliation(s)
- Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, The Netherlands and 1790 AB Den Burg.,Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden SE-75123, Uppsala
| | - Tara A Mahendrarajah
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, The Netherlands and 1790 AB Den Burg
| | - Pierre Offre
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, The Netherlands and 1790 AB Den Burg
| | - Courtney W Stairs
- Department of Biology, Lund University, Sweden Sölvegatan 35, 223 62 Lund
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47
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Vigneron A, Cruaud P, Lovejoy C, Vincent WF. Genomic evidence of functional diversity in DPANN archaea, from oxic species to anoxic vampiristic consortia. ISME COMMUNICATIONS 2022; 2:4. [PMID: 37938653 PMCID: PMC9723730 DOI: 10.1038/s43705-022-00088-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/15/2021] [Accepted: 01/07/2022] [Indexed: 04/26/2023]
Abstract
DPANN archaea account for half of the archaeal diversity of the biosphere, but with few cultivated representatives, their metabolic potential and environmental functions are poorly understood. The extreme geochemical and environmental conditions in meromictic ice-capped Lake A, in the Canadian High Arctic, provided an isolated, stratified model ecosystem to resolve the distribution and metabolism of uncultured aquatic DPANN archaea living across extreme redox and salinity gradients, from freshwater oxygenated conditions, to saline, anoxic, sulfidic waters. We recovered 28 metagenome-assembled genomes (MAGs) of DPANN archaea that provided genetic insights into their ecological function. Thiosulfate oxidation potential was detected in aerobic Woesearchaeota, whereas diverse metabolic functions were identified in anaerobic DPANN archaea, including degradation and fermentation of cellular compounds, and sulfide and polysulfide reduction. We also found evidence for "vampiristic" metabolism in several MAGs, with genes coding for pore-forming toxins, peptidoglycan degradation, and RNA scavenging. The vampiristic MAGs co-occurred with other DPANNs having complementary metabolic capacities, leading to the possibility that DPANN form interspecific consortia that recycle microbial carbon, nutrients and complex molecules through a DPANN archaeal shunt, adding hidden novel complexity to anaerobic microbial food webs.
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Affiliation(s)
- Adrien Vigneron
- Département de Biologie, Université Laval, Québec, QC, Canada.
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, Canada.
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.
- Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada.
| | - Perrine Cruaud
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, QC, Canada
| | - Connie Lovejoy
- Département de Biologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada
- Québec Océan, Université Laval, Québec, QC, Canada
| | - Warwick F Vincent
- Département de Biologie, Université Laval, Québec, QC, Canada
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada
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48
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Unique mobile elements and scalable gene flow at the prokaryote-eukaryote boundary revealed by circularized Asgard archaea genomes. Nat Microbiol 2022; 7:200-212. [PMID: 35027677 PMCID: PMC8813620 DOI: 10.1038/s41564-021-01039-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/29/2021] [Indexed: 12/22/2022]
Abstract
Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to an Asgard archaea clade phylogenetically closest to eukaryotes. These genomes reveal diverse mobile elements, including an integrative viral genome that bidirectionally replicates in a circular form and aloposons, transposons that encode the 5,000 amino acid-sized proteins Otus and Ephialtes. Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. The number of archaea- and bacteria-related genes follow strikingly different scaling laws in Asgard archaea, exhibiting a genome size-dependent ratio and a functional division resembling the bacteria- and archaea-derived gene repertoire across eukaryotes. Bacterial gene import has thus likely been a continuous process unaltered by eukaryogenesis and scaled up through genome expansion. Our data further highlight the importance of viewing eukaryogenesis in a pan-Asgard context, which led to the proposal of a conceptual framework, that is, the Heimdall nucleation–decentralized innovation–hierarchical import model that accounts for the emergence of eukaryotic complexity. The recovery of two circularized genomes of the Heimdallarchaeum species from hydrothermal vent enrichment cultures reveals that these Asgard archaea carry diverse mobile genetic elements, such as an integrative viral genome and aloposons. These mobile genetic elements contain several bacteria- and phage-derived genes, modulating the shuffling of information between bacteria and archaea, and potentially influencing eukaryogenesis.
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49
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Mukai T, Amikura K, Fu X, Söll D, Crnković A. Indirect Routes to Aminoacyl-tRNA: The Diversity of Prokaryotic Cysteine Encoding Systems. Front Genet 2022; 12:794509. [PMID: 35047015 PMCID: PMC8762117 DOI: 10.3389/fgene.2021.794509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/18/2021] [Indexed: 01/23/2023] Open
Abstract
Universally present aminoacyl-tRNA synthetases (aaRSs) stringently recognize their cognate tRNAs and acylate them with one of the proteinogenic amino acids. However, some organisms possess aaRSs that deviate from the accurate translation of the genetic code and exhibit relaxed specificity toward their tRNA and/or amino acid substrates. Typically, these aaRSs are part of an indirect pathway in which multiple enzymes participate in the formation of the correct aminoacyl-tRNA product. The indirect cysteine (Cys)-tRNA pathway, originally thought to be restricted to methanogenic archaea, uses the unique O-phosphoseryl-tRNA synthetase (SepRS), which acylates the non-proteinogenic amino acid O-phosphoserine (Sep) onto tRNACys. Together with Sep-tRNA:Cys-tRNA synthase (SepCysS) and the adapter protein SepCysE, SepRS forms a transsulfursome complex responsible for shuttling Sep-tRNACys to SepCysS for conversion of the tRNA-bound Sep to Cys. Here, we report a comprehensive bioinformatic analysis of the diversity of indirect Cys encoding systems. These systems are present in more diverse groups of bacteria and archaea than previously known. Given the occurrence and distribution of some genes consistently flanking SepRS, it is likely that this gene was part of an ancient operon that suffered a gradual loss of its original components. Newly identified bacterial SepRS sequences strengthen the suggestion that this lineage of enzymes may not rely on the m1G37 identity determinant in tRNA. Some bacterial SepRSs possess an N-terminal fusion resembling a threonyl-tRNA synthetase editing domain, which interestingly is frequently observed in the vicinity of archaeal SepCysS genes. We also found several highly degenerate SepRS genes that likely have altered amino acid specificity. Cross-analysis of selenocysteine (Sec)-utilizing traits confirmed the co-occurrence of SepCysE and the Sec-utilizing machinery in archaea, but also identified an unusual O-phosphoseryl-tRNASec kinase fusion with an archaeal Sec elongation factor in some lineages, where it may serve in place of SepCysE to prevent crosstalk between the two minor aminoacylation systems. These results shed new light on the variations in SepRS and SepCysS enzymes that may reflect adaptation to lifestyle and habitat, and provide new information on the evolution of the genetic code.
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Affiliation(s)
- Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Kazuaki Amikura
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Xian Fu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
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50
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Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species. Nature 2022; 601:257-262. [PMID: 34937940 DOI: 10.1038/s41586-021-04235-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 11/10/2021] [Indexed: 11/08/2022]
Abstract
The methanogenic degradation of oil hydrocarbons can proceed through syntrophic partnerships of hydrocarbon-degrading bacteria and methanogenic archaea1-3. However, recent culture-independent studies have suggested that the archaeon 'Candidatus Methanoliparum' alone can combine the degradation of long-chain alkanes with methanogenesis4,5. Here we cultured Ca. Methanoliparum from a subsurface oil reservoir. Molecular analyses revealed that Ca. Methanoliparum contains and overexpresses genes encoding alkyl-coenzyme M reductases and methyl-coenzyme M reductases, the marker genes for archaeal multicarbon alkane and methane metabolism. Incubation experiments with different substrates and mass spectrometric detection of coenzyme-M-bound intermediates confirm that Ca. Methanoliparum thrives not only on a variety of long-chain alkanes, but also on n-alkylcyclohexanes and n-alkylbenzenes with long n-alkyl (C≥13) moieties. By contrast, short-chain alkanes (such as ethane to octane) or aromatics with short alkyl chains (C≤12) were not consumed. The wide distribution of Ca. Methanoliparum4-6 in oil-rich environments indicates that this alkylotrophic methanogen may have a crucial role in the transformation of hydrocarbons into methane.
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