title: Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea.
abstract: Marine dissolved organic matter (DOM) contains as much carbon as the Earth's atmosphere, and represents a critical component of the global carbon cycle. To better define microbial processes and activities associated with marine DOM cycling, we analyzed genomic and transcriptional responses of microbial communities to high-molecular-weight DOM (HMWDOM) addition. The cell density in the unamended control remained constant, with very few transcript categories exhibiting significant differences over time. In contrast, the DOM-amended microcosm doubled in cell numbers over 27 h, and a variety of HMWDOM-stimulated transcripts from different taxa were observed at all time points measured relative to the control. Transcripts significantly enriched in the HMWDOM treatment included those associated with two-component sensor systems, phosphate and nitrogen assimilation, chemotaxis, and motility. Transcripts from Idiomarina and Alteromonas spp., the most highly represented taxa at the early time points, included those encoding TonB-associated transporters, nitrogen assimilation genes, fatty acid catabolism genes, and TCA cycle enzymes. At the final time point, Methylophaga rRNA and non-rRNA transcripts dominated the HMWDOM-amended microcosm, and included gene transcripts associated with both assimilatory and dissimilatory single-carbon compound utilization. The data indicated specific resource partitioning of DOM by different bacterial species, which results in a temporal succession of taxa, metabolic pathways, and chemical transformations associated with HMWDOM turnover. These findings suggest that coordinated, cooperative activities of a variety of bacterial "specialists" may be critical in the cycling of marine DOM, emphasizing the importance of microbial community dynamics in the global carbon cycle.
authors.affiliation: Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Jay
authors.initials: J
authors.lastname: McCarren
authors.forename: Jamie W
authors.initials: JW
authors.lastname: Becker
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Repeta
authors.forename: Yanmei
authors.initials: Y
authors.lastname: Shi
authors.forename: Curtis R
authors.initials: CR
authors.lastname: Young
authors.forename: Rex R
authors.initials: RR
authors.lastname: Malmstrom
authors.forename: Sallie W
authors.initials: SW
authors.lastname: Chisholm
authors.forename: Edward F
authors.initials: EF
authors.lastname: DeLong
mesh_terms: D002244:Carbon / Q000378:metabolism; D030541:Databases, Genetic; D017753:Ecosystem; D020869:Gene Expression Profiling; D053858:Metabolic Networks and Pathways; D056186:Metagenomics; D008827:Microbiological Phenomena; D008954:Models, Biological; D008969:Molecular Sequence Data; D009930:Organic Chemicals / Q000378:metabolism; D012623:Seawater / Q000737:chemistry* / Q000382:microbiology*; D014871:Water Microbiology
chemical_list: D009930:Organic Chemicals; D002244:Carbon
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