{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T07:02:15Z","timestamp":1788850935812,"version":"build-2803163510"},"reference-count":65,"publisher":"American Society for Microbiology","issue":"7","license":[{"start":{"date-parts":[[2024,7,23]],"date-time":"2024-07-23T00:00:00Z","timestamp":1721692800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,7,23]],"date-time":"2024-07-23T00:00:00Z","timestamp":1721692800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100001809","name":"MOST | National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["No. 42030412"],"award-info":[{"award-number":["No. 42030412"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100010823","name":"China Ocean Mineral Resources Research and Development Association","doi-asserted-by":"crossref","award":["No. DY135-B2-01 and DY-XZ-04"],"award-info":[{"award-number":["No. DY135-B2-01 and DY-XZ-04"]}],"id":[{"id":"10.13039\/501100010823","id-type":"DOI","asserted-by":"crossref"}]},{"name":"MOST | National High-tech Research and Development Program","award":["No. 2012AA092102"],"award-info":[{"award-number":["No. 2012AA092102"]}]},{"name":"The Scientific Research Foundation of Third Institute of Oceanography, MNR","award":["No. 2024003"],"award-info":[{"award-number":["No. 2024003"]}]},{"DOI":"10.13039\/501100001809","name":"The National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["No.42376125"],"award-info":[{"award-number":["No.42376125"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"the Scientific Research Foundation of Third Institute of Oceanography, MNR","award":["No. 2019021"],"award-info":[{"award-number":["No. 2019021"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSystems"],"published-print":{"date-parts":[[2024,7,23]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Mixotrophy is an important trophic strategy for bacterial survival in the ocean. However, the global relevance and identity of the major mixotrophic taxa remain largely elusive. Here, we combined phylogenetic, metagenomic, and metatranscriptomic analyses to characterize ubiquitous\n                      <jats:italic>Arcobacteraceae<\/jats:italic>\n                      based on our deep-sea\n                      <jats:italic>in situ<\/jats:italic>\n                      incubations and the global data. The phylogenomic tree of\n                      <jats:italic>Arcobacteraceae<\/jats:italic>\n                      is divided into three large clades, among which members of clades A and B are almost all from terrestrial environments, while those of clade C are widely distributed in various marine habitats in addition to some terrestrial origins. All clades harbor genes putatively involved in chitin degradation, sulfide oxidation, hydrogen oxidation, thiosulfate oxidation, denitrification, dissimilatory nitrate reduction to ammonium, microaerophilic respiration, and metal (iron\/manganese) reduction. Additionally, in clade C, more unique pathways were retrieved, including thiosulfate disproportionation, ethanol fermentation, methane oxidation, fatty acid oxidation, cobalamin synthesis, and dissimilatory reductions of sulfate, perchlorate, and arsenate. Within this clade, two mixotrophic Candidatus genera represented by UBA6211 and CAIJNA01 harbor genes putatively involved in the reverse tricarboxylic acid pathway for carbon fixation. Moreover, the metatranscriptomic data in deep-sea\n                      <jats:italic>in situ<\/jats:italic>\n                      incubations indicated that the latter genus is a mixotroph that conducts carbon fixation by coupling sulfur oxidation and denitrification and metabolizing organic matter. Furthermore, global metatranscriptomic data confirmed the ubiquitous distribution and global relevance of\n                      <jats:italic>Arcobacteraceae<\/jats:italic>\n                      in the expression of those corresponding genes across all oceanic regions and depths. Overall, these results highlight the contribution of previously unrecognized\n                      <jats:italic>Arcobacteraceae<\/jats:italic>\n                      to carbon, nitrogen, and sulfur cycling in global oceans.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        Marine microorganisms exert a profound influence on global carbon cycling and ecological relationships. Mixotrophy, characterized by the simultaneous utilization of both autotrophic and heterotrophic nutrition, has a significant impact on the global carbon cycling. This report characterizes a group of uncultivated bacteria\n                        <jats:italic>Arcobacteraceae<\/jats:italic>\n                        that thrived on the \u201chot time\u201d of bulky particulate organic matter and exhibited mixotrophic strategy during the\n                        <jats:italic>in situ<\/jats:italic>\n                        organic mineralization. Compared with clades A and B, more unique metabolic pathways were retrieved in clade C, including the reverse tricarboxylic acid pathway for carbon fixation, thiosulfate disproportionation, methane oxidation, and fatty acid oxidation. Global metatranscriptomic data from the Tara Oceans expeditions confirmed the ubiquitous distribution and extensive transcriptional activity of\n                        <jats:italic>Arcobacteraceae<\/jats:italic>\n                        with the expression of genes putatively involved in carbon fixation, methane oxidation, multiple sulfur compound oxidation, and denitrification across all oceanic regions and depths.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/msystems.00513-24","type":"journal-article","created":{"date-parts":[[2024,6,21]],"date-time":"2024-06-21T09:01:22Z","timestamp":1718960482000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":31,"title":["<i>Arcobacteraceae<\/i>\n                    are ubiquitous mixotrophic bacteria playing important roles in carbon, nitrogen, and sulfur cycling in global oceans"],"prefix":"10.1128","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2466-6881","authenticated-orcid":true,"given":"Jianyang","family":"Li","sequence":"first","affiliation":[{"name":"Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shizheng","family":"Xiang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yufei","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8568-2252","authenticated-orcid":true,"given":"Ruolin","family":"Cheng","sequence":"additional","affiliation":[{"name":"Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiliang","family":"Lai","sequence":"additional","affiliation":[{"name":"Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liping","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guizhen","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunming","family":"Dong","sequence":"additional","affiliation":[{"name":"Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4784-090X","authenticated-orcid":false,"given":"Zongze","family":"Shao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China"},{"name":"Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1203690"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01559-06"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-marine-010816-060617"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1111\/oik.03539"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1517118113"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aan8260"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41396-020-0662-y"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-023-01374-2"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1814860116"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0600756103"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature03911"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1038\/ngeo1921"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1912367117"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2017.37"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.dsr.2003.10.004"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1175309"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1038\/415493b"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.3354\/meps07972"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2017.163"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2009.02072.x"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","unstructured":"Li J Dong C Lai Q Huang Z Zhou D Gong L Wang G Shao Z. 2022. Unique deep-sea bacterial assemblages thriving on different organic matters delivered via in-situ incubators. In review. doi:10.21203\/rs.3.rs-1700182\/v3","DOI":"10.21203\/rs.3.rs-1700182\/v3"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2022.158714"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.68.1.316-325.2002"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.003101"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1289\/ehp.9430"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.1111\/zph.12215"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens11020244"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1903080116"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.watres.2019.115405"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.00864-22"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jare.2022.07.011"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.66.6.2491-2501.2000"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.1002\/lno.11759"},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.1002\/bit.260390806"},{"key":"e_1_3_4_36_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aar6329"},{"key":"e_1_3_4_37_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03456-9"},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","unstructured":"Borchert E Garc\u00eda-Moyano A Sanchez-Carrillo S Dahlgren TG Slaby BM Bjerga GEK Ferrer M Franzenburg S Hentschel U. 2020. Deciphering a marine bone degrading microbiome reveals a complex community effort. Microbiology. doi:10.1101\/2020.05.13.093005","DOI":"10.1101\/2020.05.13.093005"},{"key":"e_1_3_4_39_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.envint.2021.106776"},{"key":"e_1_3_4_40_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1720765115"},{"key":"e_1_3_4_41_2","doi-asserted-by":"publisher","DOI":"10.1007\/s12275-018-8014-6"},{"key":"e_1_3_4_42_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.00987"},{"key":"e_1_3_4_43_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.930601"},{"key":"e_1_3_4_44_2","doi-asserted-by":"publisher","DOI":"10.3390\/biology11040599"},{"key":"e_1_3_4_45_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41396-019-0455-3"},{"key":"e_1_3_4_46_2","doi-asserted-by":"publisher","DOI":"10.1002\/lno.10603"},{"key":"e_1_3_4_47_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-019-0527-1"},{"key":"e_1_3_4_48_2","doi-asserted-by":"publisher","DOI":"10.3390\/jmse11010224"},{"key":"e_1_3_4_49_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2016.12"},{"key":"e_1_3_4_50_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty560"},{"key":"e_1_3_4_51_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.213959.116"},{"key":"e_1_3_4_52_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-018-0541-1"},{"key":"e_1_3_4_53_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2017.126"},{"key":"e_1_3_4_54_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.186072.114"},{"key":"e_1_3_4_55_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz848"},{"key":"e_1_3_4_56_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-119"},{"key":"e_1_3_4_57_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm321"},{"key":"e_1_3_4_58_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msx148"},{"key":"e_1_3_4_59_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-021-01213-8"},{"key":"e_1_3_4_60_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh340"},{"key":"e_1_3_4_61_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp348"},{"key":"e_1_3_4_62_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu033"},{"key":"e_1_3_4_63_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad359"},{"key":"e_1_3_4_64_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac112"},{"key":"e_1_3_4_65_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_3_4_66_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt656"}],"container-title":["mSystems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msystems.00513-24","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msystems.00513-24","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,23]],"date-time":"2024-07-23T09:18:45Z","timestamp":1721726325000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/msystems.00513-24"}},"subtitle":[],"editor":[{"given":"Thomas J.","family":"Sharpton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,7,23]]},"references-count":65,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2024,7,23]]}},"alternative-id":["10.1128\/msystems.00513-24"],"URL":"https:\/\/doi.org\/10.1128\/msystems.00513-24","relation":{},"ISSN":["2379-5077"],"issn-type":[{"value":"2379-5077","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,7,23]]},"assertion":[{"value":"2024-04-08","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-05-14","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-06-21","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00513-24"}}