Saunders JK, Fuchsman CA, McKay C, Rocap G. Complete arsenic-based respiratory cycle in the marine microbial communities of pelagic oxygen-deficient zones. Proc Natl Acad Sci USA. 2019;116:9925–30.
Callbeck CM, Lavik G, Ferdelman TG, Fuchs B, Gruber-Vodicka HR, Hach PF, et al. Oxygen minimum zone cryptic sulfur cycling sustained by offshore transport of key sulfur oxidizing bacteria. Nat Commun. 2018;9:1729.
Garcia-Robledo E, Padilla CC, Aldunate M, Stewart FJ, Ulloa O, Paulmier A, et al. Cryptic oxygen cycling in anoxic marine zones. Proc Natl Acad Sci USA. 2017;114:8319–24.
Sun X, Kop LFM, Lau MCY, Frank J, Jayakumar A, Lücker S, et al. Uncultured Nitrospina-like species are major nitrite oxidizing bacteria in oxygen minimum zones. ISME J. 2019;13:2391–402.
Tsementzi D, Wu J, Deutsch S, Nath S, Rodriguez-R LM, Burns AS, et al. SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature. 2016;536:179–83.
Thamdrup B, Steinsdóttir HGR, Bertagnolli AD, Padilla CC, Patin NV, Garcia-Robledo E, et al. Anaerobic methane oxidation is an important sink for methane in the ocean’s largest oxygen minimum zone. Limnol Oceanogr. 2019;64:2569–85.
Breitburg D, Levin LA, Oschlies A, Grégoire M, Chavez FP, Conley DJ, et al. Declining oxygen in the global ocean and coastal waters. Science. 2018;359:eaam7240.
Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, et al. Unusual biology across a group comprising more than 15% of domain Bacteria. Nature. 2015;523:208–U173.
Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, et al. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr Biol. 2015;25:690–701.
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.
Mylroie JE, Carew JL, Moore AI. Blue holes: definition and genesis. Carbonates Evaporates. 1995;10:225–33.
Canganella F, Bianconi G, Kato C, Gonzalez J. Microbial ecology of submerged marine caves and holes characterized by high levels of hydrogen sulphide. Rev Environ Sci Biotechnol. 2007;6:61–70.
Gischler E, Shinn EA, Oschmann W, Fiebig J, Buster NA. A 1500-year holocene caribbean climate archive from the blue hole, Lighthouse Reef, Belize. J Coast Res. 2008;246:1495–505.
Pohlman JW. The biogeochemistry of anchialine caves: progress and possibilities. Hydrobiologia. 2011;677:33–51.
Davis MC, Garey JR. Microbial function and hydrochemistry within a stratified anchialine sinkhole: A window into coastal aquifer interactions. Water. 2018;10:972–972.
Garman KM, Rubelmann H, Karlen DJ, Wu T, Garey JR. Comparison of an inactive submarine spring with an active nearshore anchialine spring in Florida. Hydrobiologia. 2011;677:65–87.
Gonzalez BC, Iliffe TM, Macalady JL, Schaperdoth I, Kakuk B. Microbial hotspots in anchialine blue holes: Initial discoveries from the Bahamas. Hydrobiologia. 2011;677:149–56.
Seymour JR, Humphreys WF, Mitchell JG. Stratification of the microbial community inhabiting an anchialine sinkhole. Aquat Microb Ecol. 2007;50:11–24.
Yao P, Wang XC, Bianchi TS, Yang ZS, Fu L, Zhang XH, et al. Carbon cycling in the world’s deepest blue hole. J Geophys Res. 2020;125:e2019JG005307.
He H, Fu L, Liu Q, Fu L, Bi N, Yang Z, et al. Community Structure, abundance and potential functions of bacteria and archaea in the Sansha Yongle blue hole, Xisha, South China Sea. Front Microbiol. 2019;10:2404–2404.
He P, Xie L, Zhang X, Li J, Lin X, Pu X, et al. Microbial diversity and metabolic potential in the stratified Sansha Yongle Blue Hole in the South China Sea. Sci Rep. 2020;10:5949–5949.
DeWitt D. Submarine springs and other Karst features in offshore waters of the Gulf of Mexico and Tampa Bay, Southwest Florida Water Management District. 2003.
Hu C, Muller-Karger FE, Swarzenski PW. Hurricanes, submarine groundwater discharge, and Florida’s red tides. Geophys Res Lett. 2006;33:L11601.
Smith CG, Swarzenski PW. An investigation of submarine groundwater-borne nutrient fluxes to the west Florida shelf and recurrent harmful algal blooms. Limnol Oceanogr. 2012;57:471–85.
Vargo GA, Heil CA, Fanning KA, Dixon LK, Neely MB, Lester K, et al. Nutrient availability in support of Karenia brevis blooms on the central West Florida Shelf: What keeps Karenia blooming? Continental Shelf Res. 2008;28:73–98.
Walsh DA, Zaikova E, Howes CG, Song YC, Wright JJ, Tringe SG, et al. Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science. 2009;326:578–82.
Weisberg RH, Liu YG, Lembke C, Hu CM, Hubbard K, Garrett M. The coastal ocean circulation influence on the 2018 West Florida Shelf K. brevis Red Tide Bloom. J Geophys Res Oceans. 2019;124:2501–12.
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:D590–6.
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.
Rodriguez RLM, Gunturu S, Tiedje JM, Cole JR, Konstantinidis KT. Nonpareil 3: fast estimation of metagenomic coverage and sequence diversity. Msystems. 2018;3: e00039-18.
Baker BJ, De Anda V, Seitz KW, Dombrowski N, Santoro AE, Lloyd KG. Diversity, ecology and evolution of Archaea. Nat Microbiol. 2020;5:887–900.
Thiel V, Costas AMG, Fortney NW, Martinez JN, Tank M, Roden EE, et al. “Candidatus Thermonerobacter thiotrophicus,” a non-phototrophic member of the Bacteroidetes/Chlorobi with dissimilatory sulfur metabolism in hot spring mat communities. Front Microbiol. 2019;9:3159–3159.
Helly JJ, Levin LA. Global distribution of naturally occurring marine hypoxia on continental margins. Deep-Sea Res Part I. 2004;51:1159–68.
Xie LP, Wang BD, Pu XM, Xin M, He PQ, Li CX, et al. Hydrochemical properties and chemocline of the Sansha Yongle blue hole in the South China Sea. Sci Total Environ. 2019;649:1281–92.
Thamdrup B, Dalsgaard T, Revsbech NP. Widespread functional anoxia in the oxygen minimum zone of the Eastern South Pacific. Deep-Sea Res Part I. 2012;65:36–45.
Wyrtki K. The oxygen minima in relation to ocean circulation. Deep-Sea Res Oceanographic Abstr. 1962;9:11–23.
Ghosh W, Dam B. Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea. FEMS Microbiol Rev. 2009;33:999–1043.
Luther GW, Findlay AJ, MacDonald DJ, Owings SM, Hanson TE, Beinart RA, et al. Thermodynamics and kinetics of sulfide oxidation by oxygen: a look at inorganically controlled reactions and biologically mediated processes in the environment. Front Microbiol. 2011;2:1–9.
Houghton JL, Foustoukos DI, Flynn TM, Vetriani C, Bradley AS, Fike DA. Thiosulfate oxidation by Thiomicrospira thermophila: metabolic flexibility in response to ambient geochemistry. Environ Microbiol. 2016;18:3057–72.
Kelly DP, Shergill JK, Lu WP, Wood AP. Oxidative metabolism of inorganic sulfur compounds by bacteria. Antonie Van Leeuwenhoek Int J Gen Mol Microbiol. 1997;71:95–107.
Grimm F, Franz B, Dahl C. Thiosulfate and sulfur oxidation in purple sulfur bacteria. In: Dahl C, Friedrich C, editors. Microbial sulfur metabolism. Springer: Heidelberg, Germany; 2008. p. 101–16.
Zopfi J, Ferdelman TG, Fossing H. Distribution and fate of sulfur intermediates – sulfite, tetrathionate, thiosulfate, and elemental sulfur – in marine sediments. In: Amend JP, Edwards KJ, Lyons TW, editors. Sulfur biogeochemistry: past and present. The Geological Society of America: Boulder, Colorado; 2004. p. 97–116.
Wright JJ, Konwar KM, Hallam SJ. Microbial ecology of expanding oxygen minimum zones. Nat Rev Microbiol. 2012;10:381–94.
Bertagnolli AD, Stewart FJ. Microbial niches in marine oxygen minimum zones. Nat Rev Microbiol. 2018;16:723–9.
Hawley AK, Brewer HM, Norbeck AD, Pasǎ-Tolić L, Hallam SJ. Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes. Proc Natl Acad Sci USA. 2014;111:11395–400.
Anantharaman K, Hausmann B, Jungbluth SP, Kantor RS, Lavy A, Warren LA, et al. Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. ISME J. 2018;12:1715–28.
Murillo AA, Ramírez-Flandes S, DeLong EF, Ulloa O. Enhanced metabolic versatility of planktonic sulfur-oxidizing gamma-proteobacteria in an oxygen-deficient coastal ecosystem. Front Mar Sci. 2014;1:1–13.
Shah V, Chang BX, Morris RM. Cultivation of a chemoautotroph from the SUP05 clade of marine bacteria that produces nitrite and consumes ammonium. ISME J. 2017;11:263–71.
Wirsen CO, Sievert SM, Cavanaugh CM, Molyneaux SJ, Ahmad A, Taylor LT, et al. Characterization of an autotrophic sulfide-oxidizing marine Arcobacter sp. that produces filamentous sulfur. Appl Environ Microbiol. 2002;68:316–25.
Luther GW, Glazer BT, Hohmann L, Popp JI, Tailefert M, Rozan TF, et al. Sulfur speciation monitored in situ with solid state gold amalgam voltammetric microelectrodes: polysulfides as a special case in sediments, microbial mats and hydrothermal vent waters. J Environ Monit. 2001;3:61–6.
Rozan TF, Theberge SM, Luther G. Quantifying elemental sulfur (S0), bisulfide (HS-) and polysulfides (S(x)2-) using a voltammetric method. Analyt Chim Acta. 2000;415:175–84.
Sievert SM, Wieringa EBA, Wirsen CO, Taylor CD. Growth and mechanism of filamentous-sulfur formation by Candidatus Arcobacter sulfidicus in opposing oxygen-sulfide gradients. Environ Microbiol. 2007;9:271–6.
Moussard H, Corre E, Cambon-Bonavita MA, Fouquet Y, Jeanthon C. Novel uncultured Epsilonproteobacteria dominate a filamentous sulphur mat from the 13 degrees N hydrothermal vent field, East Pacific Rise. FEMS Microbiol Ecol. 2006;58:449–63.
Heylen K, Vanparys B, Wittebolle L, Verstraete W, Boon N, De PV. Cultivation of denitrifying bacteria: optimization of isolation conditions and diversity study. Appl Environ Microbiol. 2006;72:2637–43.
Taillefert M, Bono AB, Luther GW. Reactivity of freshly formed Fe(III) in synthetic solutions and (pore)waters: voltammetric evidence of an aging process. Environ Sci Technol. 2000;34:2169–77.
Barco RA, Emerson D, Sylvan JB, Orcutt BN, Jacobson Meyers ME, Ramírez GA, et al. New insight into microbial iron oxidation as revealed by the proteomic profile of an obligate iron-oxidizing chemolithoautotroph. Appl Environ Microbiol. 2015;81:5927–37.
Garber AI, Nealson KH, Okamoto A, McAllister SM, Chan CS, Barco RA, et al. FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genome and metagenome assemblies. Front Microbiol. 2020;11:37.
Canfield DE, Stewart FJ, Thamdrup B, De Brabandere L, Dalsgaard T, Delong EF, et al. A cryptic sulfur cycle in oxygen-minimum-zone waters off the Chilean Coast. Science. 2010;330:1375–8.
Ding J, Zhang Y, Wang H, Jian H, Leng H, Xiao X. Microbial community structure of deep-sea hydrothermal vents on the ultraslow spreading Southwest Indian Ridge. Front Microbiol. 2017;8:1012.
Leon-Zayas R, Peoples L, Biddle JF, Podell S, Novotny M, Cameron J, et al. The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the candidate superphylum Parcubacteria (OD1). Environ Microbiol. 2017;19:2769–84.
Liu X, Li M, Castelle CJ, Probst AJ, Zhou Z, Pan J, et al. Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages. Microbiome. 2018;6:102–102.
Ortiz-Alvarez R, Casamayor EO. High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes. Environ Microbiol Rep. 2016;8:210–7.
Suominen S, Dombrowski N, Damste JSS, Villanueva L. A diverse uncultivated microbial community is responsible for organic matter degradation in the Black Sea sulphidic zone. Environ Microbiol. 2021. https://doi.org/10.1111/1462-2920.14902.
Castelle CJ, Banfield JF. Major new microbial groups expand diversity and alter our understanding of the tree of life. Cell. 2018;172:1181–97.
Dombrowski N, Lee JH, Williams TA, Offre P, Spang A. Genomic diversity, lifestyles and evolutionary origins of DPANN archaea. FEMS Microbiol Lett. 2019;366:fnz008.
Tian RM, Ning DL, He ZL, Zhang P, Spencer SJ, Gao SH, et al. Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity. Microbiome. 2020;8:51.
Vigneron A, Cruaud P, Langlois V, Lovejoy C, Culley AI, Vincent WF. Ultra-small and abundant: Candidate phyla radiation bacteria are potential catalysts of carbon transformation in a thermokarst lake ecosystem. Limnol Oceanogr Lett. 2020;5:212–20.
Beam JP, Becraft ED, Brown JM, Schulz F, Jarett JK, Bezuidt O, et al. Ancestral absence of electron transport chains in Patescibacteria and DPANN. Front Microbiol. 2020;11:1848.
Luef B, Frischkorn KR, Wrighton KC, Holman HYN, Birarda G, Thomas BC, et al. Diverse uncultivated ultra-small bacterial cells in groundwater. Nat Commun. 2015;6:6372.
Wrighton KC, Castelle CJ, Wilkins MJ, Hug LA, Sharon I, Thomas BC, et al. Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer. ISME J. 2014;8:1452–63.
Konstantinidis KT, Tiedje JM. Trends between gene content and genome size in prokaryotic species with larger genomes. Proc Natl Acad Sci USA. 2004;101:3160–5.
Moya A, Pereto J, Gil R, Latorre A. Learning how to live together: genomic insights into prokaryote-animal symbioses. Nat Rev Genet. 2008;9:218–29.
Moran NA, Plague GR. Genomic changes following host restriction in bacteria. Curr Opin Genet Dev. 2004;14:627–33.
Chaudhury P, Quax TEF, Albers SV. Versatile cell surface structures of archaea. Mol Microbiol. 2018;107:298–311.
Pohlschroder M, Esquivel RN. Archaeal type IV pili and their involvement in biofilm formation. Front Microbiol. 2015;6:190.
Aylward FO, Santoro AE. Heterotrophic Thaumarchaea with small genomes are widespread in the dark ocean. mSystems. 2020;5:e00415–20.
Reji L, Francis CA. Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage. ISME J. 2020;14:2105–15.
Santoro AE, Richter RA, Dupont CL. Planktonic marine Archaea. Annu Rev Mar Sci. 2019;11:131–58.
Rinke C, Rubino F, Messer LF, Youssef N, Parks DH, Chuvochina M, et al. A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). ISME J. 2019;13:663–75.
Pereira O, Hochart C, Auguet JC, Debroas D, Galand PE. Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean. Microbiol Open. 2019;8:e00852.
Martin-Cuadrado AB, Garcia-Heredia I, Moltó AG, López-Úbeda R, Kimes N, López-García P, et al. A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum. ISME J. 2015;9:1619–34.
Martin-Cuadrado AB, Rodriguez-Valera F, Moreira D, Alba JC, Ivars-Martínez E, Henn MR, et al. Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions. ISME J. 2008;2:865–86.
Moreira D, Rodríguez-Valera F, López-García P. Analysis of a genome fragment of a deep-sea uncultivated Group II euryarchaeote containing 16S rDNA, a spectinomycin-like operon and several energy metabolism genes. Environ Microbiol. 2004;6:959–69.
Sforna MC, Philippot P, Somogyi A, Van Zuilen MA, Medjoubi K, Schoepp-Cothenet B, et al. Evidence for arsenic metabolism and cycling by microorganisms 2.7 billion years ago. Nat Geosci. 2014;7:811–5.
Meheust R, Burstein D, Castelle CJ, Banfield JF. The distinction of CPR bacteria from other bacteria based on protein family content. Nat Commun. 2019;10:4173.
Luther GW, Glazer BT, Ma S, Trouwborst RE, Moore TS, Metzger E, et al. Use of voltammetric solid-state (micro)electrodes for studying biogeochemical processes: laboratory measurements to real time measurements with an in situ electrochemical analyzer (ISEA). Mar Chem. 2008;108:221–35.
Brendel PJ, Luther GW. Development of a gold amalgam voltammetric microelectrode for the determination of dissolved Fe, Mn, O2, and S(-II) in porewaters of marine and freshwater sediments. Environ Sci Technol. 1995;29:751–61.
Arar EJ, Collins GB. Method 445.0 in vitro determination of chlorophyll a and pheophytin a in marine and freshwater algae by fluorescence. Washington, DC: U.S. Environmental Protection Agency; 1997.
Bran+Luebbe/Seal. Ammonia in water and seawater, in Method No G-171-96. 2005. Norderstedt, Germany.
Bran+Luebbe/Seal. Nitrate and nitrite in water and seawater; total nitrogen in persulfate digests, in Metho No G-172-96. 2010. Norderstedt, Germany.
Solórzano L, Sharp JH. Determination of total dissolved nitrogen in natural waters. Limnol Oceanogr. 1980;25:751–4.
Solórzano L, Sharp JH. Determination of total dissolved phosphorus and particulate phosphorus in natural waters. Limnol Oceanogr. 1980;25:754–8.
Dickson AG, Sabine CL, Christian JR. Guide to best practices for ocean CO2 measurements. PICES Special Publication 3. 2007.
Murphy J, Riley JP. A modified single solution method for the determination of phosphate in natural waters. Analy Chim Acta. 1962;27:31–6.
Stookey LL. Ferrozine—a new spectrophotometric reagent for iron. Anal Chem. 1970;42:779–81.
Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, et al. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012;9:676–82.
Padilla CC, Bertagnolli AD, Bristow LA, Sarode N, Glass JB, Thamdrup B, et al. Metagenomic binning recovers a transcriptionally active gammaproteobacterium linking methanotrophy to partial denitrification in an anoxic oxygen minimum zone. Front Mar Sci. 2017;4:23–23.
Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq illumina sequencing platform. Appl Environ Microbiol. 2013;79:5112–20.
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37:852–7.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550–550.
McMurdie PJ, Holmes S. Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8:e61217–e61217.
McMurdie PJ, Holmes S. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol. 2014;10:e1003531.
Willis AD, Martin BD. DivNet: estimating diversity in networked communities. bioRxiv. 2018. Available from https://www.biorxiv.org/content/10.1101/305045v1.
Wickham H. Elegant graphics for data analysis. New York: Springer-Verlag; 2016.
Oksanen J, Blanchet F, Friendly M, Kindt R, Legendre P, Mcglinn D, et al. vegan: Community Ecology package, in R package version 2.5-5. 2019. https://cran.r-project.org/package=vegan.
Nayfach S, Pollard KS. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biol. 2015;16:51–51.
Nayfach S, Bradley PH, Wyman SK, Laurent TJ, Williams A, Eisen JA, et al. Automated and accurate estimation of gene family abundance from shotgun metagenomes. PLoS Comput Biol. 2015;11:e1004573.
Nayfach S, Pollard KS. Toward accurate and quantitative comparative metagenomics. Cell. 2016;166:1103–16.
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. MetaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27:824–34.
Li D, Liu CM, Luo R, 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.
Mikheenko A, Saveliev V, Gurevich A. MetaQUAST: evaluation of metagenome assemblies. Bioinformatics. 2016;32:1088–90.
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.
Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119–119.
James BT, Luczak BB, Girgis HZ. MeShClust: an intelligent tool for clustering DNA sequences. Nucleic Acids Res. 2018;46:e83.
Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M, Goto S, et al. KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics. 2019;36:2251–2.
Boratyn GM, Thierry-Mieg J, Thierry-Mieg D, Busby B, Madden TL. Magic-BLAST, an accurate RNA-seq aligner for long and short reads. BMC Bioinformatics. 2019;20:405–405.
Dunivin TK, Yeh SY, Shade A. A global survey of arsenic-related genes in soil microbiomes. BMC Biol. 2019;17:45–45.
Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol. 2019;20:257.
Lu J, Breitwieser FP, Thielen P, Salzberg SL. Bracken: estimating species abundance in metagenomics data. PeerJ Comput Sci. 2017;3:e104.
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.
Olm MR, Brown CT, Brooks B, Banfield JF. DRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017;11:2864–8.
Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 2019;36:1925–7.
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.
Letunic I, Bork P. Interactive Tree of Life (iTOL) v4: Recent updates and new developments. Nucleic Acids Res. 2019;47:p. W256–9.
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