Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 107; no. 38; pp. 16420 - 16427
• Main Authors: McCarren, Jay, Becker, Jamie W., Repeta, Daniel J., Shi, Yanmei, Young, Curtis R., Malmstrom, Rex R., Chisholm, Sallie W., DeLong, Edward F.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 21.09.2010; National Acad Sciences
• Series: Inaugural Article
• Subjects: Alteromonadaceae; Alteromonas; Bacteria; Biological Sciences; Carbon - metabolism; Carbon cycle; Cells; Complementary DNA; Databases, Genetic; Ecosystem; Enzymes; Gene Expression Profiling; Genes; Idiomarina; Metabolic Networks and Pathways; Metabolism; Metagenomics; Methylophaga; Microbiological Phenomena; Microbiology; Microcosms; Models, Biological; Molecular Sequence Data; Organic Chemicals - metabolism; Sea water; Seawater - chemistry; Seawater - microbiology; Taxa; Taxonomy; Water Microbiology
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1010732107

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.