Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon

Abstract

Coastal ocean bacterioplankton control the flow of dissolved organic carbon (DOC) from terrestrial and oceanic sources into the marine food web, and regulate the release of inorganic carbon to atmospheric and offshore reservoirs. While the fate of the chemically complex coastal DOC reservoir has long been recognized as a critical feature of the global carbon budget, it has been problematic to identify both the compounds that serve as major conduits for carbon flux and the roles of individual bacterioplankton taxa in mediating that flux. Here we analyse random libraries of expressed genes from a coastal bacterial community to identify sequences representing DOC-transporting proteins. Predicted substrates of expressed transporter genes indicated that carboxylic acids, compatible solutes, polyamines and lipids may be key components of the biologically labile DOC pool in coastal waters, in addition to canonical bacterial substrates such as amino acids, oligopeptides and carbohydrates. Half of the expressed DOC transporter sequences in this coastal ocean appeared to originate from just eight taxa: Roseobacter, SAR11, Flavobacteriales and five orders of γ-Proteobacteria. While all major taxa expressed transporter genes for some DOC components (e.g. amino acids), there were indications of specialization within the bacterioplankton community for others (e.g. carbohydrates, carboxylic acids and polyamines). Experimental manipulations of the natural DOC pool that increased the concentration of phytoplankton- or vascular plant-derived compounds invoked a readily measured response in bacterial transporter gene expression. This highly resolved view of the potential for carbon flux into heterotrophic bacterioplankton cells identifies possible bioreactive components of the coastal DOC pool and highlights differing ecological roles in carbon turnover for the resident bacterial taxa.

Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate

“…Although abundant in 16S rRNA amplicon libraries (assuming no major biases in PCR amplifications), this group appears to have low per-cell levels of gene expression and did not show a rapid transcriptional response (that is, within the 30 min incubation) to DMSP addition (Figure 4). This finding is consistent with previous marine metatranscrioptomic studies Poretsky et al, 2009Poretsky et al, , 2010 and suggests that SAR11 members may not exhibit substantial transcriptional responses to substrate supply, at least on short time Supplementary Table S2. The C or D at the end of the category names refers to the Control or DMSP libraries, respectively.…”

“…Sequences unidentified in RefSeq but with similarity to sequences in the GOS metagenome accounted for 9% of total reads (Supplementary Table S1). An average of 17% of sequences remained unidentified, possibly representing unknown genes, poorly conserved regions of known genes (Poretsky et al, 2010) or small RNAs with regulatory functions (Shi et al, 2009). In general, functional assignments of transcripts in control versus experimental treatments indicated that bacterioplankton activity was stimulated within 30 min of DMSP addition.…”

“…To this point, metatranscriptomic analyses have shown community expression patterns over diel cycles or under enhanced CO 2 concentrations, as well as identified taxon-specific metabolic processes (Frias-Lopez et al, 2008;Gilbert et al, 2008;Hewson et al, 2009;Poretsky et al, 2009). The technique is particularly amenable to experimental manipulations designed to test hypotheses about complex microbial communities (Gilbert et al, 2008;Moran, 2008Moran, , 2009Poretsky et al, 2010).…”

Metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage

“…There is no evidence in the metatranscriptome that heterotrophy had a significant role in the nutrition of this MG1C population. MG1C reads were not assigned to COGs for transporters of organic compounds (Supplementary Tables 3 and 4), in contrast to the high proportion of reads in the Bacteria metatranscriptome that were assigned to transporters (B20% of the Bacteria reads assigned to the top 50 COGs, Gifford unpublished data) or found previously in a Bacteria-dominated metatranscriptome retrieved from a near-by site (Poretsky et al, 2010). Also, the ratio of MG1C amoA genes to MG1C 16S rRNA genes in these samples was 0.51 ( Figure 1b).…”

High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use

“…The advent of 16S rRNA sequencing and environmental genomics has revolutionized microbial ecology by identifying the genetic diversity (Rappé et al, 1997) and functional potential (DeLong et al, 2006) of a community without the need for cultivation. In particular, the comparative 'omics' strategy, relying on sequence comparisons to infer biogeochemical activity (Beja et al, 2001;Treusch et al, 2005;Poretsky et al, 2010), has been enormously fruitful in providing information about ecosystem function for entire microbial communities. Yet it is clear that although molecular surveys that describe the natural history of complex microbial systems can intimate which functions specific microorganisms or populations may perform, hypothesis-driven manipulative experiments are a critical follow-up step to enable quantitative associations between function and identity.…”