{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T22:05:11Z","timestamp":1790805911141,"version":"4.1.0"},"reference-count":56,"publisher":"American Society for Microbiology","issue":"6","license":[{"start":{"date-parts":[[2016,11,22]],"date-time":"2016-11-22T00:00:00Z","timestamp":1479772800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2016,12,30]],"date-time":"2016-12-30T00:00:00Z","timestamp":1483056000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["EF0424599"],"award-info":[{"award-number":["EF0424599"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000893","name":"Simons Foundation","doi-asserted-by":"publisher","award":["329108"],"award-info":[{"award-number":["329108"]}],"id":[{"id":"10.13039\/100000893","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000936","name":"the Gordon E. and Betty I. Moore Foundation","doi-asserted-by":"publisher","award":["GBMF3298"],"award-info":[{"award-number":["GBMF3298"]}],"id":[{"id":"10.13039\/100000936","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000936","name":"the Gordon E. and Betty I. Moore Foundation","doi-asserted-by":"publisher","award":["GBMF3777"],"award-info":[{"award-number":["GBMF3777"]}],"id":[{"id":"10.13039\/100000936","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mBio"],"published-print":{"date-parts":[[2016,12,30]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            The members of the OM43 clade of\n            <jats:italic>Betaproteobacteria<\/jats:italic>\n            are abundant coastal methylotrophs with a range of carbon-utilizing capabilities. However, their underlying transcriptional and metabolic responses to shifting conditions or different carbon substrates remain poorly understood. We examined the transcriptional dynamics of OM43 isolate NB0046 subjected to various inorganic nutrient, vitamin, and carbon substrate regimes over different growth phases to (i) develop a quantitative model of its mRNA content; (ii) identify transcriptional markers of physiological activity, nutritional state, and carbon and energy utilization; and (iii) identify pathways involved in methanol or naturally occurring dissolved organic matter (DOM) metabolism. Quantitative transcriptomics, achieved through addition of internal RNA standards, allowed for analyses on a transcripts-per-cell scale. This streamlined bacterium exhibited substantial shifts in total mRNA content (ranging from 1,800 to 17 transcripts cell\n            <jats:sup>\u22121<\/jats:sup>\n            in the exponential and deep stationary phases, respectively) and gene-specific transcript abundances (&gt;1,000-fold increases in some cases), depending on the growth phase and nutrient conditions. Carbon metabolism genes exhibited substantial dynamics, including those for ribulose monophosphate, tricarboxylic acid (TCA), and proteorhodopsin, as well as methanol dehydrogenase (\n            <jats:italic>xoxF<\/jats:italic>\n            ), which, while always the most abundant transcript, increased from 5 to 120 transcripts cell\n            <jats:sup>\u22121<\/jats:sup>\n            when cultures were nutrient and vitamin amended. In the DOM treatment, upregulation of TCA cycle, methylcitrate cycle, vitamin, and organic phosphorus genes suggested a metabolic route for this complex mixture of carbon substrates. The genome-wide inventory of transcript abundances produced here provides insight into a streamlined marine bacterium\u2019s regulation of carbon metabolism and energy flow, providing benchmarks for evaluating the activity of OM43 populations\n            <jats:italic>in situ<\/jats:italic>\n            .\n          <\/jats:p>\n          <jats:p>\n            <jats:bold>IMPORTANCE<\/jats:bold>\n            Bacteria exert a substantial influence on marine organic matter flux, yet the carbon components targeted by specific bacterial groups, as well as how those groups\u2019 metabolic activities change under different conditions, are not well understood. Gene expression studies of model organisms can identify these responses under defined conditions, which can then be compared to environmental transcriptomes to elucidate\n            <jats:italic>in situ<\/jats:italic>\n            activities. This integration, however, is limited by the data\u2019s relative nature. Here, we report the fully quantitative transcriptome of a marine bacterium, providing a genome-wide survey of cellular transcript abundances and how they change with different states of growth, nutrient conditions, and carbon substrates. The results revealed the dynamic metabolic strategies this methylotroph has for processing both simple one-carbon compounds and the complex multicarbon substrates of naturally derived marine organic matter and provide baseline quantitative data for identifying their\n            <jats:italic>in situ<\/jats:italic>\n            activities and impact on the marine carbon cycle.\n          <\/jats:p>","DOI":"10.1128\/mbio.01279-16","type":"journal-article","created":{"date-parts":[[2016,11,23]],"date-time":"2016-11-23T02:00:45Z","timestamp":1479866445000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":35,"title":["Quantitative Transcriptomics Reveals the Growth- and Nutrient-Dependent Response of a Streamlined Marine Methylotroph to Methanol and Naturally Occurring Dissolved Organic Matter"],"prefix":"10.1128","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3222-9681","authenticated-orcid":false,"given":"Scott M.","family":"Gifford","sequence":"first","affiliation":[{"name":"Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA"},{"name":"Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5308-1818","authenticated-orcid":false,"given":"Jamie W.","family":"Becker","sequence":"additional","affiliation":[{"name":"Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oscar A.","family":"Sosa","sequence":"additional","affiliation":[{"name":"Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA"},{"name":"Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, Hawaii, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel J.","family":"Repeta","sequence":"additional","affiliation":[{"name":"Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward F.","family":"DeLong","sequence":"additional","affiliation":[{"name":"Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA"},{"name":"Daniel K. 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