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microorganisms in the ocean, exerting primary control on nitrification and nitrogen oxides emission. Although united by a common physiology of chemoautotrophic growth on ammonia, a corresponding high genomic and habitat variability suggests tremendous adaptive capacity. Here, we compared 44 diverse AOA genomes, 37 from species cultivated from samples collected across diverse geographic locations and seven assembled from metagenomic sequences from the mesopelagic to hadopelagic zones of the deep ocean. Comparative analysis identified seven major marine AOA genotypic groups having gene content correlated with their distinctive biogeographies. Phosphorus and ammonia availabilities as well as hydrostatic pressure were identified as selective forces driving marine AOA genotypic and gene content variability in different oceanic regions. Notably, AOA methylphosphonate biosynthetic genes span diverse oceanic provinces, reinforcing their importance for methane production in the ocean. Together, our combined comparative physiological, genomic, and metagenomic analyses provide a comprehensive view of the biogeography of globally abundant AOA and their adaptive radiation into a vast range of marine and terrestrial habitats.<\/jats:p>","DOI":"10.1038\/s41396-020-0710-7","type":"journal-article","created":{"date-parts":[[2020,7,7]],"date-time":"2020-07-07T12:04:10Z","timestamp":1594123450000},"page":"2595-2609","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":117,"title":["Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea"],"prefix":"10.1093","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0895-0126","authenticated-orcid":false,"given":"Wei","family":"Qin","sequence":"first","affiliation":[{"name":"School of Oceanography, University of Washington , Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5281-3773","authenticated-orcid":false,"given":"Yue","family":"Zheng","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen, China"},{"name":"University of Chinese Academy of Sciences , Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1525-042X","authenticated-orcid":false,"given":"Feng","family":"Zhao","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen, China"},{"name":"University of Chinese Academy of Sciences , Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9899-7712","authenticated-orcid":false,"given":"Yulin","family":"Wang","sequence":"additional","affiliation":[{"name":"Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong , Hong Kong, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3748-6027","authenticated-orcid":false,"given":"Hidetoshi","family":"Urakawa","sequence":"additional","affiliation":[{"name":"Department of Ecology and Environmental Studies, Florida Gulf Coast University , Fort Myers, FL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Willm","family":"Martens-Habbena","sequence":"additional","affiliation":[{"name":"Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida , Davie, FL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haodong","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology , Shenzhen, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaowu","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University , Hong Kong, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinxu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University , Shenzhen, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tatsunori","family":"Nakagawa","sequence":"additional","affiliation":[{"name":"College of Bioresource Sciences, Nihon University , Fujisawa, Kanagawa, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel R","family":"Mende","sequence":"additional","affiliation":[{"name":"Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii , Honolulu, HI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annette","family":"Bollmann","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Miami University , Oxford, OH, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5673-5730","authenticated-orcid":false,"given":"Baozhan","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University , Nanjing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yao","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Marine Environmental Sciences and College of Ocean and Earth Sciences, Xiamen University , Xiamen, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3780-8102","authenticated-orcid":false,"given":"Shady A","family":"Amin","sequence":"additional","affiliation":[{"name":"Department of Biology, New York University Abu Dhabi , Abu Dhabi, UAE"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8747-6938","authenticated-orcid":false,"given":"Jeppe L","family":"Nielsen","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Bioscience, Aalborg University , Aalborg, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Koji","family":"Mori","sequence":"additional","affiliation":[{"name":"NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE) , Kisarazu, Chiba, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reiji","family":"Takahashi","sequence":"additional","affiliation":[{"name":"College of Bioresource Sciences, Nihon University , Fujisawa, Kanagawa, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7865-5101","authenticated-orcid":false,"given":"E","family":"Virginia Armbrust","sequence":"additional","affiliation":[{"name":"School of Oceanography, University of Washington , Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mari-K H","family":"Winkler","sequence":"additional","affiliation":[{"name":"Department of Civil and Environmental Engineering, University of Washington , Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3088-4965","authenticated-orcid":false,"given":"Edward F","family":"DeLong","sequence":"additional","affiliation":[{"name":"Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii , Honolulu, HI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8675-0758","authenticated-orcid":false,"given":"Meng","family":"Li","sequence":"additional","affiliation":[{"name":"Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University , Shenzhen, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Po-Heng","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Civil and Environmental Engineering, Imperial College London , London, UK"},{"name":"Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University , Hong Kong, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2014-0564","authenticated-orcid":false,"given":"Jizhong","family":"Zhou","sequence":"additional","affiliation":[{"name":"Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma , Norman, OK, USA"},{"name":"Earth and Environmental Sciences, Lawrence Berkeley National Laboratory , Berkeley, CA, USA"},{"name":"School of Environment, Tsinghua University , Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chuanlun","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology , Shenzhen, 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USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,7,7]]},"reference":[{"key":"2024011503444111600_CR1","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1038\/35054051","article-title":"Archaeal dominance in the mesopelagic zone of the Pacific Ocean","volume":"409","author":"Karner","year":"2001","journal-title":"Nature."},{"key":"2024011503444111600_CR2","doi-asserted-by":"crossref","first-page":"908","DOI":"10.1038\/ismej.2010.171","article-title":"Examining the global distribution of dominant archaeal populations in soil","volume":"5","author":"Bates","year":"2011","journal-title":"ISME J"},{"key":"2024011503444111600_CR3","doi-asserted-by":"crossref","first-page":"14683","DOI":"10.1073\/pnas.0506625102","article-title":"Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean","volume":"102","author":"Francis","year":"2005","journal-title":"Proc Natl Acad Sci 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