Coastal ocean ecosystems process dissolved organic carbon (DOC) from both terrestrial and marine sources, making these complex and productive systems critical to our understanding of the global carbon cycle (Hedges et al., 1997). Bacterial processing of coastal DOC remains a significant conceptual and analytical challenge, however. Thousands of compounds make up the DOC pool, each with different biological turnover rates (Cherrier and Bauer, 2004) and many of which no longer resemble the parent biomolecules from which they were formed (Ogawa et al., 2001). This complex DOC pool is processed by a diverse community of heterotrophic bacterioplankton composed of hundreds of different taxa (Giovannoni and Stingl, 2005) with varying ecological strategies for the uptake and metabolism of organic carbon (Cottrell and Kirchman, 2000; Mou et al., 2008).
Several methodologies can provide insights into biological turnover of DOC in marine waters. Approaches that track changes in substrate concentrations over time (Raymond and Bauer, 2000), or use radiotracers to estimate turnover rates (i.e. the fraction of a compound transformed per unit time) (Wright, 1978; Zubkov et al., 2008) can measure fluxes of individual components of DOC into bacterioplankton cells. These studies show important roles for amino acids and monosaccharides (usually glucose) in bacterially mediated DOC turnover; together, these two compound classes can account for ∼40% of total carbon assimilation by bacterial cells (Kirchman, 2003). Approaches measuring DOC uptake at the single-cell level (e.g. Ouverney and Fuhrman, 1999; Cottrell and Kirchman, 2000; Mou et al., 2007) show that most marine bacterioplankton are capable of transporting amino acids and glucose (Malmstrom et al., 2005) and that phylum- or class-level taxonomic groupings exhibit differential uptake of DOC components, including amino acids, glucose, dimethylsulfoniopropionate, glycine betaine and vanillic acid (Cottrell and Kirchman, 2000; Malmstrom et al., 2005; Alonso and Pernthaler, 2006; Mou et al., 2008). These methodologies are typically limited, however, to a small number of compounds whose importance as a bacterial substrate must be assumed a priori. Thus further work is needed to assemble a comprehensive understanding of the compounds that act as primary conduits for carbon flow in coastal waters, and how these pipelines for DOC processing fluctuate on a spatial and temporal basis.
Here we use a complementary methodology based on functional metagenomics that surveys the DOC pool to identify potentially bioreactive components as well as the taxa that may be responsible for their turnover. We assembled large-scale libraries of mRNA sequences from a coastal bacterioplankton community, identified transcripts involved in the transport of DOC, and analysed the predicted substrates and taxonomic origin of these transporter sequences. Although it cannot furnish quantitative measures of flux, transporter gene expression analysis provides insight into potential uptake of organic compounds by bacterioplankton, including substrates that are in low concentration but high demand (and therefore difficult to assess by direct chemical measures of DOC) and those not presupposed to be important conduits for DOC turnover. Using this functional metagenomics approach, we generate hypotheses about the bioreactive components of south-eastern US coastal DOC and the taxonomic identities and substrate preferences of the bacterial taxa controlling DOC flux.