E References

1.
Louca S, Hawley AK, Katsev S, Torres-Beltran M, Bhatia MP, Kheirandish S, Michiels CC, Capelle D, Lavik G, Doebeli M, Crowe SA, Hallam SJ. 2016. Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone. Proceedings of the National Academy of Sciences 113:E5925–E5933.
2.
Hawley AK, Brewer HM, Norbeck AD, Pa a-Toli L, Hallam SJ. 2014. Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes. Proceedings of the National Academy of Sciences 111:11395–11400.
3.
Morgan-Lang C, McLaughlin R, Armstrong Z, Zhang G, Chan K, Hallam SJ. 2020. TreeSAPP: The Tree-based Sensitive and Accurate Phylogenetic Profiler. Bioinformatics btaa588–.
4.
Letunic I, Bork P. 2019. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Research 47:gkz239–.
5.
Khadka R, Clothier L, Wang L, Lim CK, Klotz MG, Dunfield PF. 2018. Evolutionary History of Copper Membrane Monooxygenases. Frontiers in Microbiology 9:2493.
6.
Criscuolo A, Gribaldo S. 2010. BMGE (block mapping and gathering with entropy): A new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol 10.
7.
Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. 2019. GTDB-Tk: A toolkit to classify genomes with the genome taxonomy database. Bioinformatics.
8.
Hallam SJ, Mincer TJ, Schleper C, Preston CM, Roberts K, Richardson PM, DeLong EF. 2006. Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS biology 4:e95.
9.
10.
Oswald K, Graf JS, Littmann S, Tienken D, Brand A, Wehrli B, Albertsen M, Daims H, Wagner M, Kuypers MMM, Schubert CJ, Milucka J. 2017. Crenothrix are major methane consumers in stratified lakes. ISME Journal 11:2124–2140.
11.
Rochman FF, Kwon M, Khadka R, Tamas I, Lopez-Jauregui AA, Sheremet A, V. Smirnova A, Malmstrom RR, Yoon S, Woyke T, Dunfield PF, Verbeke TJ. 2020. Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria. ISME Journal 14:714–726.
12.
Wagner GP, Kin K, Lynch VJ. 2012. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory in Biosciences 131:281–285.
13.
Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv.
14.
Hallam SJ, Torres-Beltrán M, Hawley AK. 2017. Monitoring microbial responses to ocean deoxygenation in a model oxygen minimum zone. Scientific Data 4:170158.
15.
Torres-Beltrán M, Hawley AK, Capelle D, Zaikova E, Walsh DA, Mueller A, Scofield M, Payne C, Pakhomova L, Kheirandish S, Finke J, Bhatia M, Shevchuk O, Gies EA, Fairley D, Michiels C, Suttle CA, Whitney F, Crowe SA, Tortell PD, Hallam SJ. 2017. A compendium of geochemical information from the Saanich Inlet water column. Scientific Data 4:170159.
16.
Uritskiy GV, DiRuggiero J, Taylor J. 2018. MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome 6:158.
17.
Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120.
18.
Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. 2020. Using SPAdes De Novo Assembler. Current Protocols in Bioinformatics 70:e102.
19.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research 25:1043–1055.
20.
Tennessen K, Andersen E, Clingenpeel S, Rinke C, Lundberg DS, Han J, Dangl JL, Ivanova N, Woyke T, Kyrpides N, Pati A. 2016. ProDeGe: a computational protocol for fully automated decontamination of genomes. The ISME Journal 10:269–272.
21.
Hawley AK, Torres-Beltrán M, Zaikova E, Walsh DA, Mueller A, Scofield M, Kheirandish S, Payne C, Pakhomova L, Bhatia M, Shevchuk O, Gies EA, Fairley D, Malfatti SA, Norbeck AD, Brewer HM, Pasa-Tolic L, Rio TG del, Suttle CA, Tringe S, Hallam SJ. 2017. A compendium of multi-omic sequence information from the Saanich Inlet water column. Scientific Data 4:170160.
22.
Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. 2015. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31:1674–1676.
23.
Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, Wang Z. 2019. MetaBAT 2: An adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7:e7359.
24.
Wu Y-W, Tang Y-H, Tringe SG, Simmons BA, Singer SW. 2014. MaxBin: An automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome 2:1–18.
25.
Wu Y-W, Simmons BA, Singer SW. 2016. MaxBin 2.0: An automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32:605–607.
26.
Raghunathan A, Ferguson HR, Bornarth CJ, Song W, Driscoll M, Lasken RS. 2005. Genomic DNA amplification from a single bacterium. Applied and environmental microbiology 71:3342–3347.
27.
Rinke C, Lee J, Nath N, Goudeau D, Thompson B, Poulton N, Dmitrieff E, Malmstrom R, Stepanauskas R, Woyke T. 2014. Obtaining genomes from uncultivated environmental microorganisms using FACS-based single-cell genomics. Nat Protoc 9:1038–1048.
28.
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43.
29.
Swan BK, Martinez-Garcia M, Preston CM, Sczyrba A, Woyke T, Lamy D, Reinthaler T, Poulton NJ, Masland EDP, Gomez ML, Sieracki ME, DeLong EF, Herndl GJ, Stepanauskas R. 2011. Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333:1296–1300.
30.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. 2013. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res 41:D590–6.
31.
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. BLAST+: Architecture and applications. BMC Bioinformatics 10:421.
32.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477.