{"doi":"10.1111/1758-2229.12417","title":"Low genome content diversity of marine planktonic Thaumarchaeota","abstract":"<jats:title>Summary</jats:title>\n                  <jats:p>\n                    Members of Thaumarchaeota are responsible for much of the ammonia oxidation occurring in the ocean. Recent studies showed that marine Thaumarchaeota have versatile metabolic capabilities, but sequencing additional genomes has not significantly increased the gene content ascribed to this group. We used the assembly‐free\n                    <jats:italic>\n                      d\n                      <jats:sub>N</jats:sub>\n                    </jats:italic>\n                    pipeline software in combination with phylogenetic analyses to interrogate shotgun metagenomic data sets to gain a better understanding of the genomic diversity of Thaumarchaeota populations. The program confidently assigned ∼3,000 paired‐end reads to Thaumarchaeota, independent of homologies to any known Thaumarchaeota genome sequence. Only 2% of these reads potentially harbor new genes that were absent from the genome of ‘\n                    <jats:italic>Candidatus</jats:italic>\n                    Nitrosopumilus maritimus’ str. SCM1, even though this strain was isolated from a marine aquarium rather than directly from the ocean. One of these novel genes encode proteins associated with the CRISPR/Cas system, Cas1, suggesting that phage defense through CRISPR may be also present in planktonic Thaumarchaeota lineages. Our results suggest that marine Thaumarchaeota populations have very low diversity in genome content, which is corroborated using computer simulation analyses of two bacterial lineages with known genome content diversity.\n                  </jats:p>","journal":"Environmental Microbiology Reports","year":2016,"id":660988,"datarank":0.26876392038420827,"base_score":1.791759469228055,"endowment":1.791759469228055,"self_citation_contribution":0.26876392038420827,"citation_network_contribution":0.0,"self_endowment_contribution":0.26876392038420827,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":5,"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":311461,"name":"Ying Sun","orcid":"0000-0002-3027-7727","position":1,"is_corresponding":false},{"id":94786,"name":"James T. Hollibaugh","orcid":"0000-0001-8037-160X","position":2,"is_corresponding":false},{"id":78384,"name":"Mary Ann Moran","orcid":"0000-0002-0702-8167","position":3,"is_corresponding":false},{"id":1725479,"name":"Haiwei Luo","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Low genome content diversity of marine planktonic Thaumarchaeota","abstract":"<jats:title>Summary</jats:title>\n                  <jats:p>\n                    Members of Thaumarchaeota are responsible for much of the ammonia oxidation occurring in the ocean. Recent studies showed that marine Thaumarchaeota have versatile metabolic capabilities, but sequencing additional genomes has not significantly increased the gene content ascribed to this group. We used the assembly‐free\n                    <jats:italic>\n                      d\n                      <jats:sub>N</jats:sub>\n                    </jats:italic>\n                    pipeline software in combination with phylogenetic analyses to interrogate shotgun metagenomic data sets to gain a better understanding of the genomic diversity of Thaumarchaeota populations. The program confidently assigned ∼3,000 paired‐end reads to Thaumarchaeota, independent of homologies to any known Thaumarchaeota genome sequence. Only 2% of these reads potentially harbor new genes that were absent from the genome of ‘\n                    <jats:italic>Candidatus</jats:italic>\n                    Nitrosopumilus maritimus’ str. SCM1, even though this strain was isolated from a marine aquarium rather than directly from the ocean. One of these novel genes encode proteins associated with the CRISPR/Cas system, Cas1, suggesting that phage defense through CRISPR may be also present in planktonic Thaumarchaeota lineages. Our results suggest that marine Thaumarchaeota populations have very low diversity in genome content, which is corroborated using computer simulation analyses of two bacterial lineages with known genome content diversity.\n                  </jats:p>","is_dataset_classified":null,"base_score":1.791759469228055,"endowment":1.791759469228055,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"27120311","pmcid":null,"openalex_id":"https://openalex.org/W2368138360","authors":[],"funders":[{"funder_name":"Chinese University of Hong Kong","grant_id":"4930062","title":null},{"funder_name":"Chinese University of Hong Kong","grant_id":"4053105","title":null},{"funder_name":"Chinese University of Hong Kong","grant_id":"4441555","title":null},{"funder_name":"Gordon and Betty Moore Foundation","grant_id":"GBMF538.01","title":null}],"total_grants":4,"fwci":0.5559,"citation_percentile":0.72131218,"influential_citations":0,"citation_trend":[{"year":2017,"count":1},{"year":2019,"count":1},{"year":2022,"count":1},{"year":2024,"count":2}],"oa_status":"closed","license":"http://onlinelibrary.wiley.com/termsAndConditions#am","oa_locations":[{"url":"https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1758-2229.12417","host_type":"publisher"},{"url":"https://onlinelibrary.wiley.com/doi/pdf/10.1111/1758-2229.12417","host_type":"publisher"},{"url":"https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1758-2229.12417","host_type":"publisher"},{"url":"https://sfamjournals.onlinelibrary.wiley.com/doi/am-pdf/10.1111/1758-2229.12417","host_type":"publisher"},{"url":"https://sfamjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1758-2229.12417","host_type":"publisher"},{"url":"https://doi.org/10.1111/1758-2229.12417","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/27120311","host_type":"repository"}],"fields_of_study":["Microbial Community Ecology and Physiology","Genomics and Phylogenetic Studies","Protist diversity and phylogeny","Archaea","Computational Biology","Genetic Variation","Genome, Archaeal","Phylogeny","Seawater"],"mesh_terms":["Archaea","Phylogeny","Seawater","Genetic Variation","Computational Biology","Genome, Archaeal"],"keywords":["Thaumarchaeota","Biology","Metagenomics","Genome","Archaea","CRISPR","Genetics","Gene","Whole genome sequencing","Phylogenetic diversity","Bacterial genome size","Evolutionary biology","Computational biology","Phylogenetic tree"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life below water"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-12T10:13:40.435115Z","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":[]}