{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,5]],"date-time":"2026-07-05T13:14:33Z","timestamp":1783257273701,"version":"3.54.6"},"reference-count":75,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T00:00:00Z","timestamp":1780444800000},"content-version":"vor","delay-in-days":153,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100018554","name":"Science and Technology Program of Gansu Province","doi-asserted-by":"publisher","award":["25JRRA405"],"award-info":[{"award-number":["25JRRA405"]}],"id":[{"id":"10.13039\/501100018554","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["42277114"],"award-info":[{"award-number":["42277114"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Upland Soil Cluster Gamma (USC\u03b3) is a key high-affinity aerobic methanotroph driving atmospheric methane oxidation in grassland soils; however, it has never been obtained in pure culture, and its metabolic processes remain largely unknown. Here, we reconstructed a USC\u03b3 metagenome-assembled genome (MAG) containing the complete pmoA gene from desert grassland soil in northwestern China, designated USC_AKS. At the site, USC\u03b3 accounted for 9.83% of the microbial community in the 10\u201320\u00a0cm layer. BLASTn of its 16S rRNA gene against the NCBI database (excluding uncultured\/environmental sequences) showed 93.03% similarity to the non-methanotroph Thioalkalivibrio sulfidiphilus HL-EbGr7 (order Chromatiales). The closest match among named species was an uncultured bacterium (JN672117) at 97.86% similarity. Its pmoA shares 96.18% similarity with the original USC\u03b3-defining sequence. Phylogenomic analysis placed USC_AKS and seven other USC\u03b3 MAGs into a monophyletic group of three subclades, distantly related to culturable Type I methanotrophs. Their genomic average nucleotide identity values are all below 95%, confirming eight distinct species. Like other USC\u03b3 MAGs, USC_AKS encodes a complete pmoCAB operon, an XoxF-type methanol dehydrogenase, and enzymes for formaldehyde oxidation to CO2. However, it lacks key ribulose monophosphate (RuMP) cycle genes encoding 3-hexulose-6-phosphate synthase (hps) and 6-phospho-3-hexulose isomerase (phi). The serine cycle also appears incomplete, as these MAGs lack hpr, the gene encoding hydroxypyruvate reductase. Moreover, none encode Rubisco, ruling out the Calvin\u2013Benson\u2013Bassham CO2-fixation pathway. Consequently, the metabolic characteristics of USC\u03b3\u2014particularly its carbon assimilation pathway\u2014remain enigmatic, and obtaining pure cultures or enriched consortia is likely the only route to resolving this mystery.<\/jats:p>","DOI":"10.1093\/ismeco\/ycag151","type":"journal-article","created":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T11:24:17Z","timestamp":1780313057000},"source":"Crossref","is-referenced-by-count":0,"title":["Molecular insights into atmospheric methane-oxidizing USC\u03b3 from desert grassland soil based on metagenome-assembled genome analysis"],"prefix":"10.1093","volume":"6","author":[{"given":"Yufang","family":"Wang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences , Nanjing, Jiangsu Province 211135 ,","place":["P.R. China"]},{"name":"Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences , Lanzhou, Gansu Province 730000 ,","place":["P.R. China"]},{"name":"State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University , Lanzhou, Gansu Province 730020 ,","place":["P.R. China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4924-8819","authenticated-orcid":false,"given":"Yuanfeng","family":"Cai","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences , Nanjing, Jiangsu Province 211135 ,","place":["P.R. China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zechen","family":"Peng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University , Lanzhou, Gansu Province 730020 ,","place":["P.R. China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fujiang","family":"Hou","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University , Lanzhou, Gansu Province 730020 ,","place":["P.R. China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhongjun","family":"Jia","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences , Nanjing, Jiangsu Province 211135 ,","place":["P.R. China"]},{"name":"Northeast Institute of Geography and Agroecology, Chinese Academy of Science , Changchun, Jinlin Province 130102 \u00a0","place":["P.R. China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,6,3]]},"reference":[{"key":"2026070508165484200_ref1","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1128\/mr.60.2.439-471.1996","article-title":"Methanotrophic bacteria","volume":"60","author":"Hanson","year":"1996","journal-title":"Microbiol Rev"},{"key":"2026070508165484200_ref2","doi-asserted-by":"publisher","first-page":"6703","DOI":"10.1128\/AEM.69.11.6703-6714.2003","article-title":"Diversity and activity of methanotrophic bacteria in different upland soils","volume":"69","author":"Knief","year":"2003","journal-title":"Appl Environ Microbiol"},{"key":"2026070508165484200_ref3","doi-asserted-by":"publisher","first-page":"1150","DOI":"10.1111\/j.1462-2920.2005.00791.x","article-title":"Abundance and activity of uncultured methanotrophic bacteria involved in the consumption of atmospheric methane in two forest 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