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

Proc Natl Acad Sci U S A. 2010 Sep 21;107(38):16420-7. doi: 10.1073/pnas.1010732107. Epub 2010 Aug 31.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Carbon / metabolism
  • Databases, Genetic
  • Ecosystem
  • Gene Expression Profiling
  • Metabolic Networks and Pathways
  • Metagenomics
  • Microbiological Phenomena*
  • Models, Biological
  • Molecular Sequence Data
  • Organic Chemicals / metabolism
  • Seawater / chemistry*
  • Seawater / microbiology*
  • Water Microbiology*

Substances

  • Organic Chemicals
  • Carbon

Associated data

  • GENBANK/HQ012268
  • GENBANK/HQ012269
  • GENBANK/HQ012270
  • GENBANK/HQ012271
  • GENBANK/HQ012272
  • GENBANK/HQ012273
  • GENBANK/HQ012274
  • GENBANK/HQ012275
  • GENBANK/HQ012276
  • GENBANK/HQ012277
  • GENBANK/HQ012278