in

Helarchaeota and co-occurring sulfate-reducing bacteria in subseafloor sediments from the Costa Rica Margin

  • 1.

    Kallmeyer J, Pockalny R, Adhikari RR, Smith DC, D’Hondt S. Global distribution of microbial abundance and biomass in subseafloor sediment. Proc Natl Acad Sci USA. 2012;109:16213–6.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 2.

    Lloyd KG, May MK, Kevorkian RT, Steen AD. Meta-analysis of quantification methods shows that Archaea and Bacteria have similar abundances in the subseafloor. Appl Environ Microbiol. 2013;79:7790–9.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 3.

    Hoshino T, Inagaki F. Abundance and distribution of Archaea in the subseafloor sedimentary biosphere. ISME J. 2019;13:227–31.

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 4.

    Lipp JS, Morono Y, Inagaki F, Hinrichs K-U. Significant contribution of Archaea to extant biomass in marine subsurface sediments. Nature. 2008;454:991–4.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 5.

    Vuillemin A, Wankel SD, Coskun ÖK, Magritsch T, Vargas S, Estes ER, et al. Archaea dominate oxic subseafloor communities over multimillion-year time scales. Sci Adv. 2019;5:eaaw4108.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 6.

    Zhao R, Hannisdal B, Mogollon JM, Jørgensen SL. Nitrifier abundance and diversity peak at deep redox transition zones. Sci Rep. 2019;9:8633.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 7.

    Hiraoka S, Hirai M, Matsui Y, Makabe A, Minegishi H, Tsuda M, et al. Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments. ISME J. 2020;14:740–56.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 8.

    Hoshino T, Doi H, Uramoto GI, Wörmer L, Adhikari RR, Xiao N, et al. Global diversity of microbial communities in marine sediment. Proc Natl Acad Sci. 2020;117:27587–97.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 9.

    Durbin AM, Teske A. Archaea in organic-lean and organic-rich marine subsurface sediments: an environmental gradient reflected in distinct phylogenetic lineages. Front Microbiol. 2012;3:168.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 10.

    Biddle JF, Lipp JS, Lever MA, Lloyd KG, Sørensen KB, Anderson R, et al. Heterotrophic archaea dominate sedimentary subsurface ecosystems off Peru. Proc Natl Acad Sci USA. 2006;103:3846–51.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 11.

    Lloyd KG, Schreiber L, Petersen DG, Kjeldsen KU, Lever MA, Steen AD, et al. Predominant archaea in marine sediments degrade detrital proteins. Nature. 2013;496:215–8.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 12.

    Yu T, Wu W, Liang W, Lever MA, Hinrichs K-U, Wang F. Growth of sedimentary Bathyarchaeota on lignin as an energy source. Proc Natl Acad Sci. 2018;115:6022–7.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 13.

    Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Bäckström D, Juzokaite L, Vancaester E, et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature. 2017;541:353–8.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 14.

    Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature. 2015;521:173–9.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 15.

    Spang A, Caceres EF, Ettema TJG. Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science. 2017;357:eaaf3883.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 16.

    Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–D596.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 17.

    Manoharan L, Kozlowski JA, Murdoch RW, Löffler FE, Sousa FL, Schleper C. Metagenomes from coastal marine sediments give insights into the ecological role and cellular features of Loki-and Thorarchaeota. mBio. 2019;10:e02039–02019.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 18.

    Imachi H, Nobu MK, Nakahara N, Morono Y, Ogawara M, Takaki Y, et al. Isolation of an archaeon at the prokaryote–eukaryote interface. Nature. 2020;577:519–25.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 19.

    Seitz KW, Dombrowski N, Eme L, Spang A, Lombard J, Sieber JR, et al. Asgard archaea capable of anaerobic hydrocarbon cycling. Nat Commun. 2019;10:1822.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 20.

    Farag IF, Zhao R, Biddle JF. “Sifarchaeota” a novel Asgard phylum from Costa Rican sediment capable of polysaccharide degradation and anaerobic methylotrophy. Appl Environ Microbiol. 2021;87:e02584–02520.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 21.

    Spang A, Stairs CW, Dombrowski N, Eme L, Lombard J, Caceres EF, et al. Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism. Nat Microbiol. 2019;4:1138–48.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 22.

    Laso-Pérez R, Wegener G, Knittel K, Widdel F, Harding KJ, Krukenberg V, et al. Thermophilic archaea activate butane via alkyl-coenzyme M formation. Nature. 2016;539:396–401.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 23.

    Chen S-C, Musat N, Lechtenfeld OJ, Paschke H, Schmidt M, Said N, et al. Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep. Nature. 2019;568:108–11.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 24.

    Wang Y, Wegener G, Hou J, Wang F, Xiao X. Expanding anaerobic alkane metabolism in the domain of Archaea. Nat Microbiol. 2019;4:595–602.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 25.

    Laso-Pérez R, Hahn C, van Vliet DM, Tegetmeyer HE, Schubotz F, Smit NT, et al. Anaerobic degradation of non-methane alkanes by “Candidatus Methanoliparia” in hydrocarbon seeps of the Gulf of Mexico. mBio. 2019;10:e01814–01819.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 26.

    Krukenberg V, Harding K, Richter M, Glöckner FO, Gruber-Vodicka HR, Adam B, et al. Candidatus Desulfofervidus auxilii, a hydrogenotrophic sulfate‐reducing bacterium involved in the thermophilic anaerobic oxidation of methane. Environ Microbiol. 2016;18:3073–91.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 27.

    Martino A, Rhodes ME, León-Zayas R, Valente IE, Biddle JF, House CH. Microbial diversity in sub-seafloor sediments from the Costa Rica Margin. Geosciences. 2019;9:218.

    CAS 
    Article 

    Google Scholar 

  • 28.

    Farag IF, Biddle JF, Zhao R, Martino AJ, House CH, León-Zayas RI. Metabolic potentials of archaeal lineages resolved from metagenomes of deep Costa Rica sediments. ISME J. 2020;14:1345–58.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 29.

    Barry PH, de Moor JM, Giovannelli D, Schrenk M, Hummer DR, Lopez T, et al. Forearc carbon sink reduces long-term volatile recycling into the mantle. Nature. 2019;568:487–92.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 30.

    Expedition 334 Scientists. Site U1379. In Vannucchi, P, Ujiie, K, Stroncik, N, Malinverno, A, and the Expedition 334 Scientists, Proc IODP, 334: Tokyo (Integrated Ocean Drilling Program Management International, Inc) (2012).

  • 31.

    Formolo M, Nuzzo M, Torres M, Solomon E. Expedition I Gas geochemical results from IODP Expedition 334: Influence of subsurface structure and fluid flow on gas composition. In: Proceedings of AGU Fall Meeting Abstracts) 2011.

  • 32.

    Boyd JA, Woodcroft BJ, Tyson GW. GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes. Nucleic Acids Res. 2018;46:e59.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 33.

    Singleton CM, McCalley CK, Woodcroft BJ, Boyd JA, Evans PN, Hodgkins SB, et al. Methanotrophy across a natural permafrost thaw environment. ISME J. 2018;12:2544–58.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 34.

    Borrel G, Adam PS, McKay LJ, Chen LX, Sierra-García IN, Sieber C, et al. Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nat Microbiol. 2019;4:603–13.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 35.

    Hua Z-S, Wang YL, Evans PN, Qu YN, Goh KM, Rao YZ, et al. Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea. Nat Commun. 2019;10:1–11.

    Article 
    CAS 

    Google Scholar 

  • 36.

    Cai M, et al. Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation. Science China Life Sciences, (2020).

  • 37.

    Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J. 2017;11:2399–406.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 38.

    Hahn CJ, Laso-Pérez R, Vulcano F, Vaziourakis KM, Stokke R, Steen IH, et al. “Candidatus Ethanoperedens,” a thermophilic genus of Archaea mediating the anaerobic oxidation of ethane. mBio. 2020;11:e00600–00620.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 39.

    Rastogi S, Liberles DA. Subfunctionalization of duplicated genes as a transition state to neofunctionalization. BMC Evolut Biol. 2005;5:28.

    Article 
    CAS 

    Google Scholar 

  • 40.

    Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. A new view of the tree of life. Nat Microbiol. 2016;1:16048.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 41.

    Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 2020;36:1925–7.

    CAS 

    Google Scholar 

  • 42.

    Skennerton CT, Chourey K, Iyer R, Hettich RL, Tyson GW, Orphan VJ. Methane-fueled syntrophy through extracellular electron transfer: uncovering the genomic traits conserved within diverse bacterial partners of anaerobic methanotrophic archaea. mBio. 2017;8:e00530–00517.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 43.

    Beulig F, Røy H, McGlynn SE, Jørgensen BB. Cryptic CH4 cycling in the sulfate–methane transition of marine sediments apparently mediated by ANME-1 archaea. ISME J. 2019;13:250–62.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 44.

    Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018;36:996–1004.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 45.

    Dombrowski N, Teske AP, Baker BJ. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat Commun. 2018;9:4999.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 46.

    Dong X, Greening C, Rattray JE, Chakraborty A, Chuvochina M, Mayumi D, et al. Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments. Nat Commun. 2019;10:1816.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 47.

    Brown CT, Olm MR, Thomas BC, Banfield JF. Measurement of bacterial replication rates in microbial communities. Nat Biotechnol. 2016;34:1256–63.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 48.

    Greening C, Biswas A, Carere CR, Jackson CJ, Taylor MC, Stott MB, et al. Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival. ISME J. 2016;10:761–77.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 49.

    Shimoyama T, Kato S, Ishii SI, Watanabe K. Flagellum mediates symbiosis. Science. 2009;323:1574–1574.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 50.

    Valentine DL, Reeburgh WS. New perspectives on anaerobic methane oxidation: minireview. Environ Microbiol. 2000;2:477–84.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 51.

    Vannucchi P, Ujiie K, Stroncik N, the IESP. IODP Expedition 334: An investigation of the sedimentary record, fluid flow and state of stress on top of the seismogenic zone of an erosive subduction margin. Sci Dril. 2013;15:23–30.

    Article 

    Google Scholar 

  • 52.

    Torres ME, Muratli JM, Solomon EA Data report: minor element concentrations in pore fluids from the CRISP-A transect drilled during Expedition 334. In: Proceeding sof IODP | Volume) 2014.

  • 53.

    Riedinger N, Torres ME, Screaton E, Solomon EA, Kutterolf S, Schindlbeck‐Belo J, et al. Interplay of subduction tectonics, sedimentation, and carbon cycling. Geochem, Geophys, Geosyst. 2019;20:4939–55.

    CAS 
    Article 

    Google Scholar 

  • 54.

    Andrews S. FastQC: a quality control tool for high throughput sequence data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ 2010.

  • 55.

    Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 56.

    Gruber-Vodicka HR, Seah BKB, Pruesse E. phyloFlash: rapid small-subunit rRNA profiling and targeted assembly from metagenomes. mSystems. 2020;5:e00920–00920.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 57.

    Li DH, Liu CM, Luo RB, Sadakane K, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31:1674–6.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 58.

    Wu YW, Simmons BA, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2016;32:605–7.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 59.

    Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 60.

    Seah BK, Gruber-Vodicka HR. gbtools: interactive visualization of metagenome bins in R. Front. Microbiol. 2015;6:1451.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 61.

    Bushnell B. BBMap: a fast, accurate, splice-aware aligner. Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US) (2014).

  • 62.

    Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 63.

    Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.

    CAS 
    Article 

    Google Scholar 

  • 64.

    Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 2016;44:D286–D293.

    CAS 
    Article 

    Google Scholar 

  • 65.

    Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol. 2016;428:726–31.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 66.

    Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Research. 2011;40:D109–D114.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 67.

    Garcia PS, Jauffrit F, Grangeasse C. Brochier-Armanet C. GeneSpy, a user-friendly and flexible genomic context visualizer. Bioinformatics. 2018;35:329–31.

    Article 
    CAS 

    Google Scholar 

  • 68.

    Badalamenti JP, Summers ZM, Chan CH, Gralnick JA, Bond DR. Isolation and genomic characterization of ‘Desulfuromonas soudanensis WTL’, a metal-and electrode-respiring bacterium from anoxic deep subsurface brine. Front Microbiol. 2016;7:913.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 69.

    Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 2010;11:119.

    Article 
    CAS 

    Google Scholar 

  • 70.

    Hernsdorf AW, Amano Y, Miyakawa K, Ise K, Suzuki Y, Anantharaman K, et al. Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments. ISME J. 2017;11:1915–29.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 71.

    Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9:5114.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 72.

    Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 73.

    Sorek R, Zhu YW, Creevey CJ, Francino MP, Bork P, Rubin EM. Genome-wide experimental determination of barriers to horizontal gene transfer. Science. 2007;318:1449–52.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 74.

    Campbell JH, O’Donoghue P, Campbell AG, Schwientek P, Sczyrba A, Woyke T, et al. UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proc Natl Acad Sci USA. 2013;110:5540–5.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 75.

    Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, et al. Anvi’o: an advanced analysis and visualization platformfor ‘omics data. PeerJ. 2015;3:e1319.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 76.

    Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 77.

    Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–3.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 78.

    Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evolut. 2015;32:268–74.

    CAS 
    Article 

    Google Scholar 

  • 79.

    Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14:587–9.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 80.

    Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evolut. 2018;35:518–22.

    CAS 
    Article 

    Google Scholar 

  • 81.

    Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–402.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 82.

    Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evolut. 2013;30:772–80.

    CAS 
    Article 

    Google Scholar 

  • 83.

    Okonechnikov K, Golosova O, Fursov M, Team U. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics. 2012;28:1166–7.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 84.

    Matheus Carnevali PB, Schulz F, Castelle CJ, Kantor RS, Shih PM, Sharon I, et al. Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. Nat Commun. 2019;10:463.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 85.

    Kessler AJ, Chen YJ, Waite DW, Hutchinson T, Koh S, Popa ME, et al. Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments. Nat Microbiol. 2019;4:1014–23.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 86.

    R Development Core Team. R: a language and environment for statistical computing.). R foundation for statistical computing, Vienna, Austria (2011).


  • Source: Ecology - nature.com

    Imagining the distant past — and finding keys to the future

    Salmon going viral