Cho, B. C. & Azam, F. major role of bacteria in biogeochemical fluxes in the ocean´s interior. Nature 332, 441–443 (1988).
Google Scholar
Bar-On, Y. M., Phillips, R. & Milo, R. The biomass distribution on Earth. Proc. Natl Acad. Sci. USA 115, 6506–6511 (2018).
Aristegui, J., Gasol, J. M., Duarte, C. M. & Herndl, G. J. Microbial oceanography of the dark ocean’s pelagic realm. Limnol. Oceanogr. 54, 1501–1529 (2009).
Google Scholar
Baltar, F., Arístegui, J., Gasol, J. M., Lekunberri, I. & Herndl, G. J. Mesoscale eddies: hotspots of prokaryotic activity and differential community structure in the ocean. ISME J. 4, 975–988 (2010).
Google Scholar
Del Giorgio, P. A. & Duarte, C. M. Respiration in the open ocean. Nature 420, 379–384 (2002).
Google Scholar
Arístegui, J. et al. Oceanography: dissolved organic carbon support of respiration in the dark ocean. Science 298, 1967 (2002).
Google Scholar
Herndl, G. J. & Reinthaler, T. Microbial control of the dark end of the biological pump. Nat. Geosci. 6, 718–724 (2013).
Google Scholar
Baltar, F. et al. Significance of non-sinking particulate organic carbon and dark CO2 fixation to heterotrophic carbon demand in the mesopelagic northeast Atlantic. Geophys. Res. Lett. 37, L09602 (2010).
Google Scholar
Boyd, P. W., Claustre, H., Levy, M., Siegel, D. A. & Weber, T. Multi-faceted particle pumps drive carbon sequestration in the ocean. Nature 568, 327–335 (2019).
Google Scholar
Stukel, M. R., Song, H., Goericke, R. & Miller, A. J. The role of subduction and gravitational sinking in particle export, carbon sequestration, and the remineralization length scale in the California Current Ecosystem. Limnol. Oceanogr. 63, 363–383 (2018).
Google Scholar
Omand, M. M. et al. Eddy-driven subduction exports particulate organic carbon from the spring bloom. Science 348, 222–225 (2015).
Google Scholar
Jónasdóttir, S. H., Visser, A. W., Richardson, K. & Heath, M. R. Seasonal copepod lipid pump promotes carbon sequestration in the deep North Atlantic. Proc. Natl Acad. Sci. USA 112, 12122–12126 (2015).
Google Scholar
Dall’Olmo, G., Dingle, J., Polimene, L., Brewin, R. J. W. & Claustre, H. Substantial energy input to the mesopelagic ecosystem from the seasonal mixed-layer pump. Nat. Geosci. 9, 820–823 (2016).
Google Scholar
Herndl, G. J. et al. Contribution of archaea to total prokaryotic production in the deep Atlantic Ocean. Appl. Environ. Microbiol. 71, 2303–2309 (2005).
Google Scholar
Wuchter, C. et al. Archaeal nitrification in the ocean. Proc. Natl Acad. Sci. USA 103, 12317–12322 (2006).
Google Scholar
Reinthaler, T., van Aken, H. M. & Herndl, G. J. Major contribution of autotrophy to microbial carbon cycling in the deep North Atlantic’s interior. Deep Res. Part II Top. Stud. Oceanogr. 57, 1572–1580 (2010).
Google Scholar
Swan, B. K. et al. Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333, 1296–1300 (2011).
Google Scholar
Pachiadaki, M. G. et al. Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation. Science 358, 1046–1051 (2017).
Google Scholar
Hügler, M. & Sievert, S. M. Beyond the Calvin Cycle: autotrophic carbon fixation in the ocean. Ann. Rev. Mar. Sci. 3, 261–289 (2011).
Google Scholar
Sorokin, D. Y. Oxidation of inorganic sulfur compounds by obligately organotrophic bacteria. Microbiology 72, 641–653 (2003).
Google Scholar
Alonso-Sáez, L., Galand, P. E., Casamayor, E. O., Pedrós-Alió, C. & Bertilsson, S. High bicarbonate assimilation in the dark by Arctic bacteria. ISME J. 4, 1581–1590 (2010).
Google Scholar
Turner, J. T. Zooplankton fecal pellets, marine snow and sinking phytoplankton blooms. Aquat. Microb. Ecol. 27, 57–102 (2002).
Google Scholar
Ploug, H., Iversen, M. H. & Fischer, G. Ballast, sinking velocity, and apparent diffusivity within marine snow and zooplankton fecal pellets: implications for substrate turnover by attached bacteria. Limnol. Oceanogr. 53, 1878–1886 (2008).
Google Scholar
Agusti, S. et al. Ubiquitous healthy diatoms in the deep sea confirm deep carbon injection by the biological pump. Nat. Commun. 6, 7608 (2015).
Google Scholar
Smith, K. L., Ruhl, H. A., Huffard, C. L., Messié, M. & Kahru, M. Episodic organic carbon fluxes from surface ocean to abyssal depths during long-term monitoring in NE Pacific. Proc. Natl Acad. Sci. USA 115, 12235–12240 (2018).
Google Scholar
Salazar, G. et al. Global diversity and biogeography of deep-sea pelagic prokaryotes. ISME J. 10, 596–608 (2016).
Google Scholar
Mestre, M. et al. Sinking particles promote vertical connectivity in the ocean microbiome. Proc. Natl Acad. Sci. USA 115, E6799–E6807 (2018).
Google Scholar
Salazar, G. et al. Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes. Mol. Ecol. 24, 5692–5706 (2015).
Google Scholar
DeLong, E. F. et al. Community genomics among stratified microbial assemblages in the ocean’s interior. Science 311, 496–503 (2006).
Google Scholar
Martín-Cuadrado, A.-B. et al. Metagenomics of the deep mediterranean, a warm bathypelagic habitat. PLoS ONE 2, e914 (2007).
Google Scholar
Boeuf, D. et al. Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean. Proc. Natl Acad. Sci. USA 116, 11824–11832 (2019).
Google Scholar
Ganesh, S. et al. Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone. ISME J. 9, 2682–2696 (2015).
Google Scholar
Rusch, D. B. et al. The Sorcerer II global ocean sampling expedition: northwest Atlantic through eastern tropical pacific. PLoS Biol. 5, e77 (2007).
Google Scholar
Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015).
Google Scholar
Louca, S., Parfrey, L. W. & Doebeli, M. Decoupling function and taxonomy in the global ocean microbiome. Science 353, 1272–1277 (2016).
Google Scholar
Duarte, C. M. Seafaring in the 21St Century: the Malaspina 2010 circumnavigation expedition. Limnol. Oceanogr. Bull. 24, 11–14 (2015).
Google Scholar
Salazar, G. et al. Gene expression changes and community turnover differentially shape the global ocean metatranscriptome. Cell 179, 1068–1083.e21 (2019).
Google Scholar
Baltar, F. et al. Prokaryotic extracellular enzymatic activity in relation to biomass production and respiration in the meso- and bathypelagic waters of the (sub)tropical Atlantic. Environ. Microbiol 11, 1998–2014 (2009).
Google Scholar
Bergauer, K. et al. Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics. Proc. Natl Acad. Sci. USA 115, E400–E408 (2018).
Google Scholar
Zhao, Z., Baltar, F. & Herndl, G. J. Linking extracellular enzymes to phylogeny indicates a predominantly particle-associated lifestyle of deep-sea prokaryotes. Sci. Adv. 6, 1–11 (2020).
Google Scholar
Ruiz‐González, C. et al. Major imprint of surface plankton on deep ocean prokaryotic structure and activity. Mol. Ecol. 29, 1820–1838 (2020).
Pernice, M. C. et al. Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans. ISME J. 10, 945–958 (2016).
Google Scholar
Hingamp, P. et al. Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. ISME J. 7, 1678–1695 (2013).
Google Scholar
Kanehisa, M. & Goto, S. KEGG: Kyoto Encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30 (2000).
Google Scholar
Galperin, M. Y., Makarova, K. S., Wolf, Y. I. & Koonin, E. V. Expanded Microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 43, D261–D269 (2015).
Google Scholar
El-Gebali, S. et al. The Pfam protein families database in 2019. Nucleic Acids Res. 47, D427–D432 (2019).
Google Scholar
Allen, L. Z. et al. Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic. ISME J. 6, 1403–1414 (2012).
Google Scholar
López-Pérez, M., Kimes, N. E., Haro-Moreno, J. M. & Rodríguez-Valera, F. Not all particles are equal: the selective enrichment of particle-associated bacteria from the mediterranean sea. Front. Microbiol. 7, 996 (2016).
Google Scholar
Smith, M. W., Zeigler Allen, L., Allen, A. E., Herfort, L. & Simon, H. M. Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem. Front. Microbiol. 4, 120 (2013).
Google Scholar
Könneke, M. et al. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437, 543–546 (2005).
Google Scholar
Alonso-Saez, L. et al. Role for urea in nitrification by polar marine Archaea. Proc. Natl Acad. Sci. USA 109, 17989–17994 (2012).
Google Scholar
Cordero, P. R. F. et al. Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival. ISME J. 13, 2868–2881 (2019).
Google Scholar
Anantharaman, K., Breier, J. A., Sheik, C. S. & Dick, G. J. Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria. Proc. Natl Acad. Sci. USA 110, 330–335 (2013).
Google Scholar
Brazelton, W. J., Nelson, B. & Schrenk, M. O. Metagenomic evidence for H2 oxidation and H2 production by serpentinite-hosted subsurface microbial communities. Front. Microbiol. 2, 268 (2012).
Google Scholar
Ragsdale, S. W. Life with carbon monoxide. Crit. Rev. Biochem. Mol. Biol. 39, 165–195 (2004).
Google Scholar
Weber, C. F. & King, G. M. Physiological, ecological, and phylogenetic characterization of Stappia, a marine CO-oxidizing bacterial genus. Appl. Environ. Microbiol. 73, 1266–1276 (2007).
Google Scholar
Martín-Cuadrado, A. B., Ghai, R., Gonzaga, A. & Rodríguez-Valera, F. CO dehydrogenase genes found in metagenomic fosmid clones from the deep Mediterranean Sea. Appl. Environ. Microbiol. 75, 7436–7444 (2009).
Google Scholar
Einsle, O. et al. Structure of cytochrome c nitrite reductase. Nature 400, 476–480 (1999).
Google Scholar
Harborne, N. R., Griffiths, L., Busby, S. J. W. & Cole, J. A. Transcriptional control, translation and function of the products of the five open reading frames of the Escherichia coli nir operon. Mol. Microbiol. 6, 2805–2813 (1992).
Google Scholar
Bianchi, D., Weber, T. S., Kiko, R. & Deutsch, C. Global niche of marine anaerobic metabolisms expanded by particle microenvironments. Nat. Geosci. 11, 263–268 (2018).
Google Scholar
Bowers, R. M. et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat. Biotechnol. 35, 725–731 (2017).
Google Scholar
Delmont, T. O. et al. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat. Microbiol. 3, 804–813 (2018).
Google Scholar
Tully, B. J., Sachdeva, R., Graham, E. D. & Heidelberg, J. F. 290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology. PeerJ 5, e3558 (2017).
Google Scholar
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).
Google Scholar
Huber, H. et al. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417, 63–67 (2002).
Google Scholar
Sharma, G., Khatri, I. & Subramanian, S. Complete genome of the starch-degrading myxobacteria Sandaracinus amylolyticus DSM 53668T. Genome Biol. Evol. 8, 2520–2529 (2016).
Google Scholar
Mohr, K. Diversity of myxobacteria—we only see the tip of the iceberg. Microorganisms 6, 84 (2018).
Google Scholar
Farnelid, H. et al. Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria. PLoS ONE 6, e19223 (2011).
Google Scholar
Moisander, P. H. et al. Chasing after non-cyanobacterial nitrogen fixation in marine pelagic environments. Front. Microbiol. 8, 1736 (2017).
Zehr, J. P., Weitz, J. S. & Joint, I. How microbes survive in the open ocean. Science 357, 646–647 (2017).
Google Scholar
Zehr, J. P. & Capone, D. G. Changing perspectives in marine nitrogen fixation. Science 368, eaay9514 (2020).
Google Scholar
Hewson, I. et al. Characteristics of diazotrophs in surface to abyssopelagic waters of the Sargasso Sea. Aquat. Microb. Ecol. 46, 15–30 (2007).
Google Scholar
Hamersley, M. R. et al. Nitrogen fixation within the water column associated with two hypoxic basins in the Southern California Bight. Aquat. Microb. Ecol. 63, 193–205 (2011).
Google Scholar
Farnelid, H. et al. Diverse diazotrophs are present on sinking particles in the North Pacific Subtropical Gyre. ISME J. 13, 170–182 (2019).
Google Scholar
Sorokin, D. Y., Tourova, T. P. & Muyzer, G. Citreicella thiooxidans gen. nov., sp. nov., a novel lithoheterotrophic sulfur-oxidizing bacterium from the Black Sea. Syst. Appl. Microbiol. 28, 679–687 (2005).
Google Scholar
Tiirola, M. A., Männistö, M. K., Puhakka, J. A. & Kulomaa, M. S. Isolation and characterization of Novosphingobium sp. strain MT1, a dominant polychlorophenol-degrading strain in a groundwater bioremediation system. Appl. Environ. Microbiol. 68, 173–180 (2002).
Google Scholar
Yuan, J., Lai, Q., Zheng, T. & Shao, Z. Novosphingobium indicum sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from a deep-sea environment. Int. J. Syst. Evol. Microbiol. 59, 2084–2088 (2009).
Google Scholar
Addison, S. L., Foote, S. M., Reid, N. M. & Lloyd-Jones, G. Novosphingobium nitrogenifigens sp. nov., a polyhydroxyalkanoate-accumulating diazotroph isolated from a New Zealand pulp and paper wastewater. Int. J. Syst. Evol. Microbiol 57, 2467–2471 (2007).
Google Scholar
Kim, S. H. et al. Ketobacter alkanivorans gen. nov., sp. nov., an n-alkane-degrading bacterium isolated from seawater. Int. J. Syst. Evol. Microbiol. 68, 2258–2264 (2018).
Google Scholar
Tully, B. J., Graham, E. D. & Heidelberg, J. F. The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. Sci. Data 5, 170203 (2018).
Google Scholar
Teira, E., Lebaron, P., Van Aken, H. & Herndl, G. J. Distribution and activity of bacteria and archaea in the deep water masses of the North Atlantic. Limnol. Oceanogr. 51, 2131–2144 (2006).
Google Scholar
Yakimov, M. M. et al. Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep waters (Central Mediterranean Sea). ISME J. 5, 945–961 (2011).
Google Scholar
La Cono, V. et al. Contribution of bicarbonate assimilation to carbon pool dynamics in the deep Mediterranean Sea and cultivation of actively nitrifying and CO2-fixing bathypelagic prokaryotic consortia. Front. Microbiol. 9, 3 (2018).
Google Scholar
Zarzycki, J., Brecht, V., Müller, M. & Fuchs, G. Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus. Proc. Natl Acad. Sci. USA 106, 21317–21322 (2009).
Google Scholar
Landry, Z., Swan, B. K., Herndl, G. J., Stepanauskas, R. & Giovannoni, S. J. SAR202 genomes from the dark ocean predict pathways for the oxidation of recalcitrant dissolved organic matter. mBio 8, 1e00413-17–19e00413-17 (2017).
Google Scholar
Mehrshad, M., Rodríguez-Valera, F., Amoozegar, M. A., López-García, P. & Ghai, R. The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling. ISME J. 12, 655–668 (2018).
Google Scholar
Tabita, F. R., Satagopan, S., Hanson, T. E., Kreel, N. E. & Scott, S. S. Distinct form I, II, III, and IV Rubisco proteins from the three kingdoms of life provide clues about Rubisco evolution and structure/function relationships. J. Exp. Bot. 59, 1515–1524 (2008).
Google Scholar
Carter, M. S. et al. Functional assignment of multiple catabolic pathways for D-apiose. Nat. Chem. Biol. 14, 696–705 (2018).
Google Scholar
Yelton, A. P. et al. Global genetic capacity for mixotrophy in marine picocyanobacteria. ISME J. 10, 2946–2957 (2016).
Google Scholar
Buesseler, K. O. et al. An assessment of the use of sediment traps for estimating upper ocean particle fluxes. J. Mar. Res. 65, 345–416 (2007).
Google Scholar
Crump, B. C., Armbrust, E. V. & Baross, J. A. Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia River, Its Estuary, and the Adjacent Coastal Ocean. Appl. Environ. Microbiol. 65, 3192–3204 (1999).
Google Scholar
Ghiglione, J. F., Conan, P. & Pujo-Pay, M. Diversity of total and active free-living vs. particle-attached bacteria in the euphotic zone of the NW Mediterranean Sea. FEMS Microbiol. Lett. 299, 9–21 (2009).
Google Scholar
Logares, R. et al. Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. Environ. Microbiol. 16, 2659–2671 (2014).
Google Scholar
Huntemann, M. et al. The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4). Stand. Genom. Sci. 11, 1–5 (2016).
Google Scholar
Oksanen, J. et al. vegan: community ecology package. https://cran.r-project.org/package=vegan (2019).
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/ (2020).
Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).
Google Scholar
Suzek, B. E., Wang, Y., Huang, H., McGarvey, P. B. & Wu, C. H. UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics 31, 926–932 (2015).
Google Scholar
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2014).
Google Scholar
Federhen, S. The NCBI Taxonomy database. Nucleic Acids Res. 40, 136–143 (2012).
Google Scholar
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).
Google Scholar
Guillou, L. et al. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 41, 597–604 (2013).
Google Scholar
Yutin, N., Wolf, Y. I., Raoult, D. & Koonin, E. V. Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution. Virol. J. 6, 223 (2009).
Google Scholar
Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
Google Scholar
Brum, J. R. et al. Patterns and ecological drivers of ocean viral communities. Science 348, 1261498 (2015).
Google Scholar
Roux, S. et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537, 689–693 (2016).
Google Scholar
Anderson, M. J. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 26, 32–46 (2008).
Google Scholar
Li, D. et al. MEGAHIT v1.0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods 102, 3–11 (2016).
Google Scholar
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Google Scholar
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Google Scholar
Kang, D. D., Froula, J., Egan, R. & Wang, Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3, e1165 (2015).
Google Scholar
Huang, X. & Madan, A. CAP3: a DNA sequence assembly program resource 868 genome research. Genome Res. 9, 868–877 (1999).
Letunic, I. & Bork, P. Interactive tree of life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 47, W256–W259 (2019).
Google Scholar
Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925–1927 (2019).
Google Scholar
Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).
Google Scholar
Aramaki, T. et al. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36, 2251–2252 (2020).
Google Scholar
Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).
Bushnell, B.BBMap. 1. Bushnell, B. BBMap. https://sourceforge.net/projects/bbmap/ (2018).
Caro-Quintero, A. & Konstantinidis, K. T. Bacterial species may exist, metagenomics reveal. Environ. Microbiol. 14, 347–355 (2012).
Google Scholar
Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).
Jaffe, A. L., Castelle, C. J., Dupont, C. L. & Banfield, J. F. Lateral gene transfer shapes the distribution of RuBisCO among candidate phyla radiation bacteria and DPANN archaea. Mol. Biol. Evol. 36, 435–446 (2019).
Google Scholar
Aylward, F. O. & Santoro, A. E. Heterotrophic Thaumarchaea with small genomes are widespread in the dark ocean. mSystems 5, e00415-20 (2020).
Google Scholar
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26, 1641–1650 (2009).
Google Scholar
Alves, R. J. E., Minh, B. Q., Urich, T., Von Haeseler, A. & Schleper, C. Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes. Nat. Commun. 9, 1–17 (2018).
Google Scholar
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Google Scholar
Source: Ecology - nature.com
