Asgard archaea capable of anaerobic hydrocarbon cycling

Seitz, Kiley W.; Dombrowski, Nina; Eme, Laura; Spang, Anja; Lombard, Jonathan; Sieber, Jessica R.; Teske, Andreas P.; Ettema, Thijs J.  G.; Baker, Brett J.

doi:10.1038/s41467-019-09364-x

Asgard archaea capable of anaerobic hydrocarbon cycling

Journal Article · Tue Apr 23 00:00:00 EDT 2019 · Nature Communications

DOI:https://doi.org/10.1038/s41467-019-09364-x· OSTI ID:1624145

Seitz, Kiley W. ^[1]; ^[2]; ^[3]; Spang, Anja ^[4]; Lombard, Jonathan ^[5]; Sieber, Jessica R. ^[6]; Teske, Andreas P. ^[7]; ^[8]; Baker, Brett J. ^[9]

Univ. of Texas, Austin, TX (United States). Dept. of Marine Science, Port Aransas, TX (United States); DOE/OSTI
Univ. of Texas, Austin, TX (United States). Dept. of Marine Science, Port Aransas, TX (United States); Univ. of Utrecht (Netherlands). Royal Netherlands Inst. of Sea Research (NIOZ)
Uppsala Univ. (Sweden). Dept. of Cell and Molecular Biology, Lab. of Molecular Biophysics; Centre National de la Recherche Scientifique (CNRS), Orsay (France). Unite d'Ecologie. Systematique et Evolution
Univ. of Utrecht (Netherlands). Royal Netherlands Inst. of Sea Research (NIOZ); Uppsala Univ. (Sweden). Dept. of Cell and Molecular Biology, Lab. of Molecular Biophysics
Uppsala Univ. (Sweden). Dept. of Cell and Molecular Biology, Lab. of Molecular Biophysics
Univ. of Minnesota, Duluth, MN (United States)
Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Marine Science
Uppsala Univ. (Sweden). Dept. of Cell and Molecular Biology, Lab. of Molecular Biophysics; Wageningen University, Wageningen (Netherlands). Dept. of Agrotechnology and Food Sciences. Lab. of Microbiology
Univ. of Texas, Austin, TX (United States). Dept. of Marine Science, Port Aransas, TX (United States)

Large reservoirs of natural gas in the oceanic subsurface sustain complex communities of anaerobic microbes, including archaeal lineages with potential to mediate oxidation of hydrocarbons such as methane and butane. Here we describe a previously unknown archaeal phylum, Helarchaeota, belonging to the Asgard superphylum and with the potential for hydrocarbon oxidation. We reconstruct Helarchaeota genomes from metagenomic data derived from hydrothermal deep-sea sediments in the hydrocarbon-rich Guaymas Basin. The genomes encode methyl-CoM reductase-like enzymes that are similar to those found in butane-oxidizing archaea, as well as several enzymes potentially involved in alkyl-CoA oxidation and the Wood-Ljungdahl pathway. We suggest that members of the Helarchaeota have the potential to activate and subsequently anaerobically oxidize hydrothermally generated short-chain hydrocarbons.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1624145

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 10; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (92)

Oceanic Methane Biogeochemistry Reeburgh, William S. ChemInform, Vol. 38, Issue 20 https://doi.org/10.1002/chin.200720267	journal	May 2007
Salinimonas marina sp. nov. Isolated from Jeju Island Marine Sediment Kim, Minji; Lee, Ki-Eun; Cha, In-Tae Current Microbiology, Vol. 78, Issue 8 https://doi.org/10.1007/s00284-021-02576-9	journal	June 2021
Complete genome analysis of a novel iflavirus from a leaf beetle, Aulacophora lewisii Ye, Zhuang-Xin; Li, Yue-Hong; Chen, Jian-Ping Archives of Virology, Vol. 166, Issue 1 https://doi.org/10.1007/s00705-020-04859-1	journal	October 2020
Biosorption of Cr(VI) by Halomonas sp. DK4, a halotolerant bacterium isolated from chrome electroplating sludge Kalola, Vidhi; Desai, Chirayu Environmental Science and Pollution Research, Vol. 27, Issue 22 https://doi.org/10.1007/s11356-019-05942-0	journal	July 2019
Chemistry of submarine hydrothermal solutions at Guaymas Basin, Gulf of California Von Damm, K. L.; Edmond, J. M.; Measures, C. I. Geochimica et Cosmochimica Acta, Vol. 49, Issue 11 https://doi.org/10.1016/0016-7037(85)90223-6	journal	November 1985
Hydrocarbons in surface sediments from a Guaymas Basin hydrothermal vent site Bazylinski, Dennis A.; Farrington, John W.; Jannasch, Holger W. Organic Geochemistry, Vol. 12, Issue 6 https://doi.org/10.1016/0146-6380(88)90146-5	journal	January 1988
Spatial heterogeneity and underlying geochemistry of phylogenetically diverse orange and white Beggiatoa mats in Guaymas Basin hydrothermal sediments McKay, Luke J.; MacGregor, Barbara J.; Biddle, Jennifer F. Deep Sea Research Part I: Oceanographic Research Papers, Vol. 67 https://doi.org/10.1016/j.dsr.2012.04.011	journal	September 2012
Phylogenomics: the beginning of incongruence? Jeffroy, O.; Brinkmann, H.; Delsuc, F. Trends in Genetics, Vol. 22, Issue 4 https://doi.org/10.1016/j.tig.2006.02.003	journal	April 2006
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/s0022-2836(05)80360-2	journal	October 1990
Complex archaea that bridge the gap between prokaryotes and eukaryotes Spang, Anja; Saw, Jimmy H.; Jørgensen, Steffen L. Nature, Vol. 521, Issue 7551 https://doi.org/10.1038/nature14447	journal	May 2015
Thermophilic archaea activate butane via alkyl-coenzyme M formation Laso-Pérez, Rafael; Wegener, Gunter; Knittel, Katrin Nature, Vol. 539, Issue 7629 https://doi.org/10.1038/nature20152	journal	October 2016
Asgard archaea illuminate the origin of eukaryotic cellular complexity Zaremba-Niedzwiedzka, Katarzyna; Caceres, Eva F.; Saw, Jimmy H. Nature, Vol. 541, Issue 7637 https://doi.org/10.1038/nature21031	journal	January 2017
Binning metagenomic contigs by coverage and composition Alneberg, Johannes; Bjarnason, Brynjar Smári; de Bruijn, Ino Nature Methods, Vol. 11, Issue 11 https://doi.org/10.1038/nmeth.3103	journal	September 2014
Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota Vanwonterghem, Inka; Evans, Paul N.; Parks, Donovan H. Nature Microbiology, Vol. 1, Issue 12 https://doi.org/10.1038/nmicrobiol.2016.170	journal	October 2016
Methanogenic archaea: ecologically relevant differences in energy conservation Thauer, Rudolf K.; Kaster, Anne-Kristin; Seedorf, Henning Nature Reviews Microbiology, Vol. 6, Issue 8 https://doi.org/10.1038/nrmicro1931	journal	June 2008
Commensal Pseudomonas protect Arabidopsis thaliana from a coexisting pathogen via multiple lineage-dependent mechanisms Shalev, Or; Ashkenazy, Haim; Neumann, Manuela The ISME Journal, Vol. 16, Issue 5 https://doi.org/10.1038/s41396-021-01168-6	journal	December 2021
Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments Dombrowski, Nina; Teske, Andreas P.; Baker, Brett J. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07418-0	journal	November 2018
Full-length transcriptome analysis of multiple organs and identification of adaptive genes and pathways in Mikania micrantha Ruan, Xiaoxian; Wang, Zhen; Su, Yingjuan Scientific Reports, Vol. 12, Issue 1 https://doi.org/10.1038/s41598-022-07198-0	journal	February 2022
The origin of the eukaryotic cell: A genomic investigation Hartman, H.; Fedorov, A. Proceedings of the National Academy of Sciences, Vol. 99, Issue 3 https://doi.org/10.1073/pnas.032658599	journal	January 2002
Tracking microbial habitats in subseafloor sediments Teske, Andreas P. Proceedings of the National Academy of Sciences, Vol. 109, Issue 42 https://doi.org/10.1073/pnas.1215867109	journal	October 2012
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses Capella-Gutierrez, S.; Silla-Martinez, J. M.; Gabaldon, T. Bioinformatics, Vol. 25, Issue 15 https://doi.org/10.1093/bioinformatics/btp348	journal	June 2009
DendroPy: a Python library for phylogenetic computing Sukumaran, J.; Holder, M. T. Bioinformatics, Vol. 26, Issue 12 https://doi.org/10.1093/bioinformatics/btq228	journal	April 2010
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes Pruesse, Elmar; Peplies, Jörg; Glöckner, Frank Oliver Bioinformatics, Vol. 28, Issue 14 https://doi.org/10.1093/bioinformatics/bts252	journal	May 2012
InterProScan 5: genome-scale protein function classification Jones, P.; Binns, D.; Chang, H. -Y. Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu031	journal	January 2014
Distinct form I, II, III, and IV Rubisco proteins from the three kingdoms of life provide clues about Rubisco evolution and structure/function relationships Tabita, F. R.; Satagopan, S.; Hanson, T. E. Journal of Experimental Botany, Vol. 59, Issue 7 https://doi.org/10.1093/jxb/erm361	journal	June 2007
A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process Lartillot, Nicolas; Philippe, Hervé Molecular Biology and Evolution, Vol. 21, Issue 6 https://doi.org/10.1093/molbev/msh112	journal	June 2004
MEROPS: the peptidase database Rawlings, N. D. Nucleic Acids Research, Vol. 34, Issue 90001 https://doi.org/10.1093/nar/gkj089	journal	January 2006
KAAS: an automatic genome annotation and pathway reconstruction server Moriya, Y.; Itoh, M.; Okuda, S. Nucleic Acids Research, Vol. 35, Issue S2, p. W182-W185 https://doi.org/10.1093/nar/gkm321	journal	May 2007
IMG: the integrated microbial genomes database and comparative analysis system Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1044	journal	December 2011
Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads Brown, Matthew W.; Sharpe, Susan C.; Silberman, Jeffrey D. Proceedings of the Royal Society B: Biological Sciences, Vol. 280, Issue 1769 https://doi.org/10.1098/rspb.2013.1755	journal	October 2013
Environmental controls on intragroup diversity of the uncultured benthic archaea of the miscellaneous Crenarchaeotal group lineage naturally enriched in anoxic sediments of the White Oak River estuary (North Carolina, USA) : MCG intragroup diversity in estuary sediments Lazar, Cassandre Sara; Biddle, Jennifer F.; Meador, Travis B. Environmental Microbiology, Vol. 17, Issue 7 https://doi.org/10.1111/1462-2920.12659	journal	January 2015
Thermal and geochemical influences on microbial biogeography in the hydrothermal sediments of Guaymas Basin, Gulf of California: Investigation of microbial ecology in hydrothermal sediments McKay, Luke; Klokman, Vincent W.; Mendlovitz, Howard P. Environmental Microbiology Reports, Vol. 8, Issue 1 https://doi.org/10.1111/1758-2229.12365	journal	January 2016
F420H2: quinone oxidoreductase from Archaeoglobus fulgidus. Characterization of a membrane-bound multisubunit complex containing FAD and iron-sulfur clusters Kunow, Jasper; Linder, Dietmar; Stetter, Karl O. European Journal of Biochemistry, Vol. 223, Issue 2 https://doi.org/10.1111/j.1432-1033.1994.tb19019.x	journal	July 1994
Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics Evans, P. N.; Parks, D. H.; Chadwick, G. L. Science, Vol. 350, Issue 6259 https://doi.org/10.1126/science.aac7745	journal	October 2015
Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life Spang, Anja; Caceres, Eva F.; Ettema, Thijs J. G. Science, Vol. 357, Issue 6351 https://doi.org/10.1126/science.aaf3883	journal	August 2017
Methane and other Hydrocarbon Gases in Marine Sediment Claypool, G. E.; Kvenvolden, K. A. Annual Review of Earth and Planetary Sciences, Vol. 11, Issue 1 https://doi.org/10.1146/annurev.ea.11.050183.001503	journal	May 1983
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
Hidden Markov model speed heuristic and iterative HMM search procedure Johnson, L. Steven; Eddy, Sean R.; Portugaly, Elon BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-431	journal	August 2010
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments Criscuolo, Alexis; Gribaldo, Simonetta BMC Evolutionary Biology, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2148-10-210	journal	January 2010
Community-wide analysis of microbial genome sequence signatures Dick, Gregory J.; Andersson, Anders F.; Baker, Brett J. Genome Biology, Vol. 10, Issue 8 https://doi.org/10.1186/gb-2009-10-8-r85	journal	January 2009
Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments Dombrowski, Nina; Seitz, Kiley W.; Teske, Andreas P. Microbiome, Vol. 5, Issue 1 https://doi.org/10.1186/s40168-017-0322-2	journal	August 2017
Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction Kai-Uwe, Hinrichs,; W., Seitz, Kiley; S., Lazar, Cassandre The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/ymjj-1c73	text	January 2016
Microbial Communities in Methane- and Short Chain Alkane-Rich Hydrothermal Sediments of Guaymas Basin Dowell, Frederick; Cardman, Zena; Dasarathy, Srishti Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00017	journal	January 2016
Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales Makarova, Kira; Wolf, Yuri; Koonin, Eugene Life, Vol. 5, Issue 1 https://doi.org/10.3390/life5010818	journal	March 2015
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities Kang, Dongwan D.; Froula, Jeff; Egan, Rob PeerJ, Vol. 3 https://doi.org/10.7717/peerj.1165	journal	January 2015
Anvi’o: an advanced analysis and visualization platform for ‘omics data Eren, A. Murat; Esen, Özcan C.; Quince, Christopher PeerJ, Vol. 3 https://doi.org/10.7717/peerj.1319	journal	January 2015
PhyloSift: phylogenetic analysis of genomes and metagenomes Darling, Aaron E.; Jospin, Guillaume; Lowe, Eric PeerJ, Vol. 2 https://doi.org/10.7717/peerj.243	journal	January 2014
Occurrence, Classification, and Biological Function of Hydrogenases: An Overview Vignais, Paulette M.; Billoud, Bernard ChemInform, Vol. 38, Issue 50 https://doi.org/10.1002/chin.200750259	journal	December 2007
Molecular profiling of microbial community structure and their CAZymes via metagenomics, from Tsomgo lake in the Eastern Himalayas Rai, Aditi; Bhattacharjee, Arindam Archives of Microbiology, Vol. 203, Issue 6 https://doi.org/10.1007/s00203-021-02278-7	journal	April 2021
Complex Evolution of the Mismatch Repair System in Eukaryotes is Illuminated by Novel Archaeal Genomes Hofstatter, Paulo G.; Lahr, Daniel J. G. Journal of Molecular Evolution, Vol. 89, Issue 1-2 https://doi.org/10.1007/s00239-020-09979-5	journal	January 2021
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990
Classification and phylogeny of hydrogenases Vignais, P. FEMS Microbiology Reviews, Vol. 25, Issue 4 https://doi.org/10.1016/S0168-6445(01)00063-8	journal	August 2001
Occurrence, Classification, and Biological Function of Hydrogenases: An Overview Vignais, Paulette M.; Billoud, Bernard Chemical Reviews, Vol. 107, Issue 10, p. 4206-4272 https://doi.org/10.1021/cr050196r	journal	October 2007
Oceanic Methane Biogeochemistry Reeburgh, William S. Chemical Reviews, Vol. 107, Issue 2 https://doi.org/10.1021/cr050362v	journal	February 2007
Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction Seitz, Kiley W.; Lazar, Cassandre S.; Hinrichs, Kai-Uwe The ISME Journal, Vol. 10, Issue 7 https://doi.org/10.1038/ismej.2015.233	journal	January 2016
Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria Wegener, Gunter; Krukenberg, Viola; Riedel, Dietmar Nature, Vol. 526, Issue 7574 https://doi.org/10.1038/nature15733	journal	October 2015
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms13219	journal	October 2016
Electron transfer in syntrophic communities of anaerobic bacteria and archaea Stams, Alfons J. M.; Plugge, Caroline M. Nature Reviews Microbiology, Vol. 7, Issue 8 https://doi.org/10.1038/nrmicro2166	journal	August 2009
Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences Yarza, Pablo; Yilmaz, Pelin; Pruesse, Elmar Nature Reviews Microbiology, Vol. 12, Issue 9 https://doi.org/10.1038/nrmicro3330	journal	August 2014
Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins Carim, Sean; Azadeh, Ashley L.; Kazakov, Alexey E. The ISME Journal, Vol. 15, Issue 8 https://doi.org/10.1038/s41396-021-00921-1	journal	March 2021
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy Sieber, Christian M. K.; Probst, Alexander J.; Sharrar, Allison Nature Microbiology, Vol. 3, Issue 7 https://doi.org/10.1038/s41564-018-0171-1	journal	May 2018
Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism Spang, Anja; Stairs, Courtney W.; Dombrowski, Nina Nature Microbiology, Vol. 4, Issue 7 https://doi.org/10.1038/s41564-019-0406-9	journal	April 2019
HydDB: A web tool for hydrogenase classification and analysis Søndergaard, Dan; Pedersen, Christian N. S.; Greening, Chris Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep34212	journal	September 2016
Genetic analysis of the archaeon Methanosarcina barkeri Fusaro reveals a central role for Ech hydrogenase and ferredoxin in methanogenesis and carbon fixation Meuer, J.; Kuettner, H. C.; Zhang, J. K. Proceedings of the National Academy of Sciences, Vol. 99, Issue 8 https://doi.org/10.1073/pnas.072615499	journal	April 2002
Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge Jorgensen, S. L.; Hannisdal, B.; Lanzen, A. Proceedings of the National Academy of Sciences, Vol. 109, Issue 42 https://doi.org/10.1073/pnas.1207574109	journal	October 2012
The Sequence Alignment/Map format and SAMtools Li, H.; Handsaker, B.; Wysoker, A. Bioinformatics, Vol. 25, Issue 16 https://doi.org/10.1093/bioinformatics/btp352	journal	June 2009
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data Kearse, M.; Moir, R.; Wilson, A. Bioinformatics, Vol. 28, Issue 12 https://doi.org/10.1093/bioinformatics/bts199	journal	April 2012
Prokka: rapid prokaryotic genome annotation Seemann, T. Bioinformatics, Vol. 30, Issue 14 https://doi.org/10.1093/bioinformatics/btu153	journal	March 2014
On Reduced Amino Acid Alphabets for Phylogenetic Inference Susko, E.; Roger, A. J. Molecular Biology and Evolution, Vol. 24, Issue 9 https://doi.org/10.1093/molbev/msm144	journal	May 2007
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability Katoh, K.; Standley, D. M. Molecular Biology and Evolution, Vol. 30, Issue 4 https://doi.org/10.1093/molbev/mst010	journal	January 2013
Ultrafast Approximation for Phylogenetic Bootstrap Minh, B. Q.; Nguyen, M. A. T.; von Haeseler, A. Molecular Biology and Evolution, Vol. 30, Issue 5 https://doi.org/10.1093/molbev/mst024	journal	February 2013
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies Nguyen, Lam-Tung; Schmidt, Heiko A.; von Haeseler, Arndt Molecular Biology and Evolution, Vol. 32, Issue 1 https://doi.org/10.1093/molbev/msu300	journal	November 2014
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A. Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402 https://doi.org/10.1093/nar/25.17.3389	journal	September 1997
MEROPS: the peptidase database Rawlings, N. D. Nucleic Acids Research, Vol. 32, Issue 90001 https://doi.org/10.1093/nar/gkh071	journal	January 2004
MEROPS: the peptidase database Rawlings, Neil D.; Barrett, Alan J.; Bateman, Alex Nucleic Acids Research, Vol. 38, Issue suppl_1 https://doi.org/10.1093/nar/gkp971	journal	November 2009
dbCAN: a web resource for automated carbohydrate-active enzyme annotation Yin, Yanbin; Mao, Xizeng; Yang, Jincai Nucleic Acids Research, Vol. 40, Issue W1 https://doi.org/10.1093/nar/gks479	journal	May 2012
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0 Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent Systematic Biology, Vol. 59, Issue 3 https://doi.org/10.1093/sysbio/syq010	journal	March 2010
Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation Wang, Huai-Chun; Minh, Bui Quang; Susko, Edward Systematic Biology, Vol. 67, Issue 2 https://doi.org/10.1093/sysbio/syx068	journal	August 2017
Improvement of molecular phylogenetic inference and the phylogeny of Bilateria Lartillot, Nicolas; Philippe, Hervé Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 363, Issue 1496 https://doi.org/10.1098/rstb.2007.2236	journal	January 2008
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T. Genome Research, Vol. 25, Issue 7 https://doi.org/10.1101/gr.186072.114	journal	May 2015
Candidatus Desulfofervidus auxilii, a hydrogenotrophic sulfate-reducing bacterium involved in the thermophilic anaerobic oxidation of methane : The partner bacterium in thermophilic methanotrophy Krukenberg, Viola; Harding, Katie; Richter, Michael Environmental Microbiology, Vol. 18, Issue 9 https://doi.org/10.1111/1462-2920.13283	journal	April 2016
Classification and phylogeny of hydrogenases Vignais, Paulette M.; Billoud, Bernard; Meyer, Jacques FEMS Microbiology Reviews, Vol. 25, Issue 4, p. 455-501 https://doi.org/10.1111/j.1574-6976.2001.tb00587.x	journal	August 2001
Draft Genome Sequence of Comamonas aquatilis Strain LK (= CSUR P6418 = CECT 9772), Isolated from the Planarian Schmidtea mediterranea Kangale, Luis Johnson; Levasseur, Anthony; Raoult, Didier Microbiology Resource Announcements, Vol. 10, Issue 5 https://doi.org/10.1128/mra.00297-20	journal	February 2021
Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis Vu, Nga T. T.; Zenger, Kyall R.; Guppy, Jarrod L. BMC Genomics, Vol. 21, Issue 1 https://doi.org/10.1186/s12864-020-07084-x	journal	September 2020
Microbial Communities in Methane- and Short Chain Alkane-Rich Hydrothermal Sediments of Guaymas Basin J., McKay, Luke; S., Lipp, Julius; Srishti, Dasarathy, The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/a9p6-1x29	text	January 2016
Biosphere frontiers of subsurface life in the sedimented hydrothermal system of Guaymas Basin V., Callaghan, Amy; E., LaRowe, Douglas; Andreas, Teske, The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/xcf8-0055	text	January 2014
Quantitative and phylogenetic study of the Deep Sea Archaeal Group in sediments of the Arctic mid-ocean spreading ridge Jørgensen, Steffen L.; Thorseth, Ingunn H.; Pedersen, Rolf B. Frontiers in Microbiology, Vol. 4 https://doi.org/10.3389/fmicb.2013.00299	journal	January 2013
Biosphere frontiers of subsurface life in the sedimented hydrothermal system of Guaymas Basin Teske, Andreas; Callaghan, Amy V.; LaRowe, Douglas E. Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00362	journal	July 2014
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0 Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent ETH Zurich https://doi.org/10.3929/ethz-b-000025281	text	January 2010
Quantitative and phylogenetic study of the Deep Sea Archaeal Group in sediments of the Arctic mid-ocean spreading ridge Jørgensen, Steffen L.; Thorseth, Ingunn H.; Pedersen, Rolf B. ETH Zurich https://doi.org/10.3929/ethz-b-000073031	text	January 2013
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0 Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent Oxford University Press https://doi.org/10.5167/uzh-155669	text	January 2010
Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments Dombrowski, Nina; Seitz, Kiley; Teske, Andreas Figshare https://doi.org/10.6084/m9.figshare.c.3861700.v1	collection	January 2017

Cited By (16)

Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea Hua, Zheng-Shuang; Wang, Yu-Lin; Evans, Paul N. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12574-y	journal	October 2019
Asgard archaeon rises from the mud Hofer, Ursula Nature Reviews Microbiology, Vol. 18, Issue 3 https://doi.org/10.1038/s41579-020-0334-y	journal	January 2020
Diversity and evolution of B-family DNA polymerases Kazlauskas, Darius; Krupovic, Mart; Guglielmini, Julien Nucleic Acids Research, Vol. 48, Issue 18 https://doi.org/10.1093/nar/gkaa760	journal	September 2020
Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki - and Thorarchaeota Manoharan, Lokeshwaran; Kozlowski, Jessica A.; Murdoch, Robert W. mBio, Vol. 10, Issue 5 https://doi.org/10.1128/mbio.02039-19	journal	October 2019
Design of targeted primers based on 16S rRNA sequences in meta-transcriptomic datasets and identification of a novel taxonomic group in the Asgard archaea Zhang, Ru-Yi; Zou, Bin; Yan, Yong-Wei BMC Microbiology, Vol. 20, Issue 1 https://doi.org/10.1186/s12866-020-1707-0	journal	February 2020
10 Years of Extreme Microbiology: An Interim Reflection and Future Prospects Teske, Andreas Frontiers in Microbiology, Vol. 11 https://doi.org/10.3389/fmicb.2020.00131	journal	February 2020
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives Ambrosino, Luca; Tangherlini, Michael; Colantuono, Chiara Marine Drugs, Vol. 17, Issue 10 https://doi.org/10.3390/md17100576	journal	October 2019
Metal-dependent anaerobic methane oxidation in marine sediment: Insights from marine settings and other systems Liang, Lewen; Wang, Yinzhao; Sivan, Orit Science China Life Sciences, Vol. 62, Issue 10 https://doi.org/10.1007/s11427-018-9554-5	journal	June 2019
Meet the relatives of our cellular ancestor Schleper, Christa; Sousa, Filipa L. Nature, Vol. 577, Issue 7791 https://doi.org/10.1038/d41586-020-00039-y	journal	January 2020
Eukaryogenesis, a syntrophy affair López-García, Purificación; Moreira, David Nature Microbiology, Vol. 4, Issue 7 https://doi.org/10.1038/s41564-019-0495-5	journal	June 2019
Metabolic activity analyses demonstrate that Lokiarchaeon exhibits homoacetogenesis in sulfidic marine sediments Orsi, William D.; Vuillemin, Aurèle; Rodriguez, Paula Nature Microbiology, Vol. 5, Issue 2 https://doi.org/10.1038/s41564-019-0630-3	journal	December 2019
Isolation of an archaeon at the prokaryote–eukaryote interface Imachi, Hiroyuki; Nobu, Masaru K.; Nakahara, Nozomi Nature, Vol. 577, Issue 7791 https://doi.org/10.1038/s41586-019-1916-6	journal	January 2020
Methylotrophic methanogens everywhere — physiology and ecology of novel players in global methane cycling Söllinger, Andrea; Urich, Tim Biochemical Society Transactions, Vol. 47, Issue 6 https://doi.org/10.1042/bst20180565	journal	December 2019
Contrasting bacterial and archaeal distributions reflecting different geochemical processes in a sediment core from the Pearl River Estuary Wang, Wenxiu; Tao, Jianchang; Liu, Haodong AMB Express, Vol. 10, Issue 1 https://doi.org/10.1186/s13568-020-0950-y	journal	January 2020
Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments Zhang, Cui-Jing; Pan, Jie; Liu, Yang Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-00876-z	journal	June 2020
Functional interactions between posttranslationally modified amino acids of methyl-coenzyme M reductase in Methanosarcina acetivorans Nayak, Dipti D.; Liu, Andi; Agrawal, Neha PLOS Biology, Vol. 18, Issue 2 https://doi.org/10.1371/journal.pbio.3000507	journal	February 2020