Karner MB, DeLong EF, Karl DM. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature. 2001;409:507–10.
Oton EV, Quince C, Nicol GW, Prosser JI, Gubry-Rangin C. Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota. ISME J. 2016;10:85–96.
Lin X, Handley KM, Gilbert JA, Kostka JE. Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat. ISME J. 2015;9:2740–4.
Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun. 2016;7:1–11.
Beam JP, Jay ZJ, Kozubal MA, Inskeep WP. Niche specialization of novel Thaumarchaeota to oxic and hypoxic acidic geothermal springs of Yellowstone National Park. ISME J. 2014;8:938–51.
Hua Z-S, Qu Y-N, Zhu Q, Zhou E-M, Qi Y-L, Yin Y-R, et al. Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nat Commun. 2018;9:208–11.
Weber EB, Lehtovirta-Morley LE, Prosser JI, Gubry-Rangin C, Laanbroek R. Ammonia oxidation is not required for growth of Group 1.1c soil Thaumarchaeota. FEMS Microbiol Ecol. 2015;91:fiv001 https://doi.org/10.1093/femsec/fiv001.
Ren M, Feng X, Huang Y, Wang H, Hu Z, Clingenpeel S, et al. Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution. ISME J. 2019;13:2150–61.
DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard N-U, et al. Community genomics among stratified microbial assemblages in the ocean’s interior. Science. 2006;311:496–503.
Barns SM, Delwiche CF, Palmer JD, Pace NR. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. PNAS. 1996;93:9188–93.
Mincer TJ, Church MJ, Taylor LT, Preston C, Karl DM, DeLong EF. Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Environ Microbiol. 2007;9:1162–75.
Martin-Cuadrado A-B, 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.
Agogué H, Brink M, Dinasquet J, Herndl GJ. Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic. Nature. 2008;456:788–91.
La Cono V, Smedile F, Ferrer M, Golyshin PN, Giuliano L, Yakimov MM. Genomic signatures of fifth autotrophic carbon assimilation pathway in bathypelagic Crenarchaeota. Micro Biotechnol. 2010;3:595–606.
Church MJ, Wai B, Karl DM, DeLong EF. Abundances of crenarchaeal amoA genes and transcripts in the Pacific Ocean. Environ Microbiol. 2010;12:679–88.
Tolar BB, King GM, Hollibaugh JT. An analysis of Thaumarchaeota populations from the Northern Gulf of Mexico. Front Microbiol. 2013;4:72 https://doi.org/10.3389/fmicb.2013.00072.
Tolar BB, Reji L, Smith JM, Blum M, Pennington JT, Chavez FP, et al. Time series assessment of Thaumarchaeota ecotypes in Monterey Bay reveals the importance of water column position in predicting distribution-environment relationships. Limnol Oceanogr. 2020. https://doi.org/10.1002/LNO.11436.
Bushnell B. BBTools software package. 2014. sourceforge.net/projects/bbmap/
Li H. BFC: correcting Illumina sequencing errors. Bioinformatics. 2015;31:2885–7.
Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31:1674–6.
Li D, Luo R, Liu C-M, Leung C-M, Ting H-F, Sadakane K, et al. MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods. 2016;102:3–11.
Kang D, Li F, Kirton ES, Thomas A, Egan RS, An H, et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019;7:e7359 https://doi.org/10.7717/peerj.7359
Wu Y-W, Tang Y-H, Tringe SG, Simmons BA, Singer SW. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome. 2014;2:26 https://doi.org/10.1186/2049-2618-2-26
Wu Y-W, Simmons BA, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Nucleic Acids Res. 2016;32:605–7. https://doi.org/10.1093/bioinformatics/btv638
Uritskiy GV, DiRuggiero J, Taylor J. MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome. 2018;6:1–13.
Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A, Lapidus A, et al. Assembling genomes and mini-metagenomes from highly chimeric reads. J Comput Biol. 2013;20:714–37.
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.
Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil P-A, et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018;36:996–1004.
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.
Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinforma. 2010;11:119.
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.
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.
Graham ED, Heidelberg JF, Tully BJ. Potential for primary productivity in a globally-distributed bacterial phototroph. ISME J. 2018;12:1861–6.
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2019. https://www.r-project.org/.
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res. 2013;42:D206–14.
Elbourne LDH, Tetu SG, Hassan KA, Paulsen IT. TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life. Nucleic Acids Res. 2016;45:D320–4.
Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ. 2015;3:e1319 https://doi.org/10.7717/peerj.1319
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–3.
Price MN, Dehal PS, Arkin AP. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE. 2010;5:e9490 https://doi.org/10.1371/journal.pone.0009490
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Katoh K, Misawa K, Kuma KI, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059–66.
Jaffe AL, Castelle CJ, Dupont CL, Banfield JF. Lateral gene transfer shapes the distribution of RuBisCO among Candidate Phyla Radiation Bacteria and DPANN Archaea. Mol Biol Evol. 2019;36:435–46.
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;9:1–8.
Parks DH, Rinke C, Chuvochina M, Chaumeil P-A, Woodcroft BenJ, Evans PN, et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol. 2017;2:1533–42.
Reji L, Tolar BB, Smith JM, Chavez FP, Francis CA. Differential co-occurrence relationships shaping ecotype diversification within Thaumarchaeota populations in the coastal ocean water column. ISME J. 2019;13:1144–58.
Reji L, Tolar BB, Smith JM, Chavez FP, Francis CA. Depth distributions of nitrite reductase (nirK) gene variants reveal spatial dynamics of thaumarchaeal ecotype populations in coastal Monterey Bay. Environ Microbiol. 2019;21:4032–45. https://doi.org/10.1111/1462-2920.14753
Langmead Ben, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.
Parada AE, Needham DM, Fuhrman JA. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol. 2015;18:1403–14.
Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. PNAS. 2005;102:2567–72.
Könneke M, Schubert DM, Brown PC, Hügler M, Standfest S, Schwander T, et al. Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation. PNAS. 2014;111:8239–44.
Kerou M, Offre P, Valledor L, Abby SS, Melcher M, Nagler M, et al. Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers. PNAS. 2016;113:E7937–46. https://doi.org/10.1073/pnas.1601212113
Mall A, Sobotta J, Huber C, Tschirner C, Kowarschik S, Bacnik K, et al. Reversibility of citrate synthase allows autotrophic growth of a thermophilic bacterium. Science. 2018;359:563–7.
Edgren T, Nordlund S. The fixABCX genes in Rhodospirillum rubrum encode a putative membrane complex participating in electron transfer to nitrogenase. J Bacteriol. 2004;186:2052–60.
Bartossek R, Spang A, Weidler G, Lanzen A, Schleper C. Metagenomic analysis of ammonia-oxidizing archaea affiliated with the soil group. Front Microbiol. 2012;3:208.
Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. PNAS. 2005;102:14683–8.
Anthony C. The quinoprotein dehydrogenases for methanol and glucose. Arch Biochem Biophys. 2004;428:2–9.
Erb TJ, Zarzycki J.A short history of RubisCO: the rise and fall (?) of Nature’spredominant CO2 fixing enzyme. Curr Opin Biotechnol. 2018;49:100–7.
Wrighton KC, Castelle CJ, Varaljay VA, Satagopan S, Brown CT, Wilkins MJ, et al. RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria. ISME J. 2016;10:2702–14.
Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, et al. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science. 2012;337:1661–5.
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.
Herbold CW, Lehtovirta-Morley LE, Jung M-Y, Jehmlich N, Hausmann B, Han P, et al. Ammonia-oxidising archaea living at low pH: Insights from comparative genomics. Environ Microbiol. 2017;19:4939–52.
Sato T, Atomi H, Imanaka T. Archaeal type III RuBisCOs function in a pathway for AMP metabolism. Science. 2007;315:1003–6.
Aono R, Sato T, Imanaka T, Atomi H. A pentose bisphosphate pathway for nucleoside degradation in Archaea. Nat Chem Biol. 2015;11:355–60.
Kono T, Mehrotra S, Endo C, Kizu N, Matusda M, Kimura H, et al. A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea. Nat Commun. 2017;8:1–12.
Falb M, Müller K, Königsmaier L, Oberwinkler T, Horn P, Gronau von S, et al. Metabolism of halophilic archaea. Extremophiles. 2008;12:177–96.
Source: Ecology - nature.com
