{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T10:58:35Z","timestamp":1788346715960,"version":"build-2803163510"},"reference-count":93,"publisher":"American Society for Microbiology","issue":"9","license":[{"start":{"date-parts":[[2024,9,17]],"date-time":"2024-09-17T00:00:00Z","timestamp":1726531200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,9,17]],"date-time":"2024-09-17T00:00:00Z","timestamp":1726531200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"The development fund of South China Sea Institute of Oceanology of the Chinese Academy of Sciences","award":["SCSIO202205"],"award-info":[{"award-number":["SCSIO202205"]}]},{"name":"The National Key Research and Development Program of China","award":["2022YFC3105301"],"award-info":[{"award-number":["2022YFC3105301"]}]},{"name":"The Hong Kong Research and Development Grants Council","award":["16101318,16101622"],"award-info":[{"award-number":["16101318,16101622"]}]},{"name":"The Major Project of Basic and Applied Basic Research of Guangdong Province","award":["2019B030302004"],"award-info":[{"award-number":["2019B030302004"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSystems"],"published-print":{"date-parts":[[2024,9,17]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:sec>\n            <jats:title\/>\n            <jats:p>\n              Nitrogen (N)-fixing organisms, also known as diazotrophs, play a crucial role in N-limited ecosystems by controlling the production of bioavailable N. The carbon-dominated cold-seep ecosystems are inherently N-limited, making them hotspots of N fixation. However, the knowledge of diazotrophs in cold-seep ecosystems is limited compared to other marine ecosystems. In this study, we used multi-omics to investigate the diversity and catabolism of diazotrophs in deep-sea cold-seep bottom waters. Our findings showed that the relative abundance of diazotrophs in the bacterial community reached its highest level in the cold-seep bottom waters compared to the cold-seep upper waters and non-seep bottom waters. Remarkably, more than 98% of metatranscriptomic reads aligned on diazotrophs in cold-seep bottom waters belonged to the genus\n              <jats:italic>Sagittula<\/jats:italic>\n              , an alphaproteobacterium. Its metagenome-assembled genome, named Seep-BW-D1, contained catalytic genes (\n              <jats:italic>nifHDK<\/jats:italic>\n              ) for nitrogen fixation, and the\n              <jats:italic>nifH<\/jats:italic>\n              gene was actively transcribed\n              <jats:italic>in situ<\/jats:italic>\n              . Seep-BW-D1 also exhibited chemosynthetic capability to oxidize C1 compounds (methanol, formaldehyde, and formate) and thiosulfate (S\n              <jats:sub>2<\/jats:sub>\n              O\n              <jats:sub>3<\/jats:sub>\n              <jats:sup>2\u2212<\/jats:sup>\n              ). In addition, we observed abundant transcripts mapped to genes involved in the transport systems for acetate, spermidine\/putrescine, and pectin oligomers, suggesting that Seep-BW-D1 can utilize organics from the intermediates synthesized by methane-oxidizing microorganisms, decaying tissues from cold-seep benthic animals, and refractory pectin derived from upper photosynthetic ecosystems. Overall, our study corroborates that carbon-dominated cold-seep bottom waters select for diazotrophs and reveals the catabolism of a novel chemosynthetic alphaproteobacterial diazotroph in cold-seep bottom waters.\n            <\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>IMPORTANCE<\/jats:title>\n            <jats:p>\n              Bioavailable nitrogen (N) is a crucial element for cellular growth and division, and its production is controlled by diazotrophs. Marine diazotrophs contribute to nearly half of the global fixed N and perform N fixation in various marine ecosystems. While previous studies mainly focused on diazotrophs in the sunlit ocean and oxygen minimum zones, recent research has recognized cold-seep ecosystems as overlooked N-fixing hotspots because the seeping fluids in cold-seep ecosystems introduce abundant bioavailable carbon but little bioavailable N, making most cold seeps inherently N-limited. With thousands of cold-seep ecosystems detected at continental margins worldwide in the past decades, the significant role of cold seeps in marine N biogeochemical cycling is emphasized. However, the diazotrophs in cold-seep bottom waters remain poorly understood. Through multi-omics, this study identified a novel alphaproteobacterial chemoheterotroph belonging to\n              <jats:italic>Sagittula<\/jats:italic>\n              as one of the most active diazotrophs residing in cold-seep bottom waters and revealed its catabolism.\n            <\/jats:p>\n          <\/jats:sec>","DOI":"10.1128\/msystems.00176-24","type":"journal-article","created":{"date-parts":[[2024,8,6]],"date-time":"2024-08-06T13:00:31Z","timestamp":1722949231000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":3,"title":["Chemosynthetic alphaproteobacterial diazotrophs reside in deep-sea cold-seep bottom waters"],"prefix":"10.1128","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4874-3474","authenticated-orcid":false,"given":"Jiawei","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, 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