{"doi":"10.1073/pnas.0506625102","title":"Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean","abstract":"<jats:p>\n                    Nitrification, the microbial oxidation of ammonia to nitrite and nitrate, occurs in a wide variety of environments and plays a central role in the global nitrogen cycle. Catalyzed by the enzyme ammonia monooxygenase, the ability to oxidize ammonia was previously thought to be restricted to a few groups within the β- and γ-\n                    <jats:italic>Proteobacteria</jats:italic>\n                    . However, recent metagenomic studies have revealed the existence of unique ammonia monooxygenase α-subunit (amoA) genes derived from uncultivated, nonextremophilic Crenarchaeota. Here, we report molecular evidence for the widespread presence of ammonia-oxidizing archaea (AOA) in marine water columns and sediments. Using PCR primers designed to specifically target archaeal\n                    <jats:italic>amoA</jats:italic>\n                    , we find AOA to be pervasive in areas of the ocean that are critical for the global nitrogen cycle, including the base of the euphotic zone, suboxic water columns, and estuarine and coastal sediments. Diverse and distinct AOA communities are associated with each of these habitats, with little overlap between water columns and sediments. Within marine sediments, most AOA sequences are unique to individual sampling locations, whereas a small number of sequences are evidently cosmopolitan in distribution. Considering the abundance of nonextremophilic archaea in the ocean, our results suggest that AOA may play a significant, but previously unrecognized, role in the global nitrogen cycle.\n                  </jats:p>","journal":"Proceedings of the National Academy of Sciences","year":2005,"id":666783,"datarank":1.1680450503922308,"base_score":7.786967002614872,"endowment":7.786967002614872,"self_citation_contribution":1.1680450503922308,"citation_network_contribution":0.0,"self_endowment_contribution":1.1680450503922308,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":2408,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":299797,"name":"Kathryn J. Roberts","orcid":"0000-0003-1200-5362","position":1,"is_corresponding":false},{"id":630659,"name":"J. Michael Beman","orcid":"0000-0002-0655-4800","position":2,"is_corresponding":false},{"id":273604,"name":"Alyson E. Santoro","orcid":"0000-0003-2503-8219","position":3,"is_corresponding":false},{"id":94509,"name":"Brian B. Oakley","orcid":"0000-0003-2098-6439","position":4,"is_corresponding":false},{"id":1741244,"name":"Christopher A. Francis","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean","abstract":"<jats:p>\n                    Nitrification, the microbial oxidation of ammonia to nitrite and nitrate, occurs in a wide variety of environments and plays a central role in the global nitrogen cycle. Catalyzed by the enzyme ammonia monooxygenase, the ability to oxidize ammonia was previously thought to be restricted to a few groups within the β- and γ-\n                    <jats:italic>Proteobacteria</jats:italic>\n                    . However, recent metagenomic studies have revealed the existence of unique ammonia monooxygenase α-subunit (amoA) genes derived from uncultivated, nonextremophilic Crenarchaeota. Here, we report molecular evidence for the widespread presence of ammonia-oxidizing archaea (AOA) in marine water columns and sediments. Using PCR primers designed to specifically target archaeal\n                    <jats:italic>amoA</jats:italic>\n                    , we find AOA to be pervasive in areas of the ocean that are critical for the global nitrogen cycle, including the base of the euphotic zone, suboxic water columns, and estuarine and coastal sediments. Diverse and distinct AOA communities are associated with each of these habitats, with little overlap between water columns and sediments. Within marine sediments, most AOA sequences are unique to individual sampling locations, whereas a small number of sequences are evidently cosmopolitan in distribution. Considering the abundance of nonextremophilic archaea in the ocean, our results suggest that AOA may play a significant, but previously unrecognized, role in the global nitrogen cycle.\n                  </jats:p>","is_dataset_classified":null,"base_score":7.786967002614872,"endowment":7.786967002614872,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"16186488","pmcid":"PMC1253578","openalex_id":"https://openalex.org/W2159237163","authors":[],"funders":[],"total_grants":0,"fwci":45.9477,"citation_percentile":0.99969198,"influential_citations":0,"citation_trend":[{"year":2012,"count":120},{"year":2013,"count":152},{"year":2014,"count":170},{"year":2015,"count":139},{"year":2016,"count":132},{"year":2017,"count":145},{"year":2018,"count":141},{"year":2019,"count":147},{"year":2020,"count":131},{"year":2021,"count":137},{"year":2022,"count":163},{"year":2023,"count":127},{"year":2024,"count":114},{"year":2025,"count":97},{"year":2026,"count":59}],"oa_status":"closed","license":null,"oa_locations":[{"url":"https://pnas.org/doi/pdf/10.1073/pnas.0506625102","host_type":"publisher"},{"url":"https://doi.org/10.1073/pnas.0506625102","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/16186488","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1253578","host_type":"repository"}],"fields_of_study":["Microbial Community Ecology and Physiology","Wastewater Treatment and Nitrogen Removal","Genomics and Phylogenetic Studies","Base Sequence","Cloning, Molecular","Cluster Analysis","Crenarchaeota","DNA Primers","Genetic Variation","Geologic Sediments","Mediterranean Sea","Molecular Sequence Data","Oxidoreductases","Pacific Ocean","Phylogeny","Seawater","Sequence Analysis, DNA","Species Specificity"],"mesh_terms":["Base Sequence","Cloning, Molecular","Mediterranean Sea","Molecular Sequence Data","Oxidoreductases","Pacific Ocean","Phylogeny","Seawater","Species Specificity","Genetic Variation","Cluster Analysis","Sequence Analysis, DNA","DNA Primers","Geologic Sediments","Crenarchaeota"],"keywords":["Ammonia monooxygenase","Archaea","Thaumarchaeota","Crenarchaeota","Water column","Photic zone","Nitrification","Nitrogen cycle","Biology","Nitrate","Ecology","Environmental chemistry","Oceanography","Nitrogen","Chemistry","Bacteria","Paleontology","Geology","Nutrient"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life below water"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"gen"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-13T15:28:56.580507Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}