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 gamma-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.

Fig. 1

DOC-related transporter COGs expressed in a south-eastern US coastal bacterioplankton community. Two independent replicate samples (Coastal 1 = light green; Coastal 2 = dark green) were collected at night on 6 May 2007, processed for mRNA extraction and amplification, and sequenced using the 454 FLX system. COGs are shown if either of the replicate coastal samples had at least one sequence. COG functional descriptions are as follows: Amino Acids, general: COG0834, ABC-type amino acid transport/signal transduction systems, periplasmic component/domain; COG1115, Na+/alanine symporter; COG1126, ABC-type polar amino acid transport system, ATPase component; COG0765, ABC-type amino acid transport system, permease component; COG4597, ABC-type amino acid transport system, permease component; COG0531, Amino acid transporters; COG4215, ABC-type arginine transport system, permease component; COG4598, ABC-type histidine transport system, ATPase component; COG4525, ABC-type taurine transport system, ATPase component; COG0814, Amino acid permeases; COG3633, Na+/serine symporter; COG4160, ABC-type arginine/histidine transport system, permease component; Amino Acids, branched chain: COG0683, ABC-type branched-chain amino acid transport systems, periplasmic component; COG0559, Branched-chain amino acid ABC-type transport system, permease components; COG0410, ABC-type branched-chain amino acid transport systems, ATPase component; COG4177, ABC-type branched-chain amino acid transport system, permease component; COG0411, ABC-type branched-chain amino acid transport systems, ATPase component; COG1296, Predicted branched-chain amino acid permease (azaleucine resistance); Amino Acids, di- and oligo-peptides: COG0747, ABC-type dipeptide transport system, periplasmic component; COG0601, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components; COG1173, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components; COG4608, ABC-type oligopeptide transport system, ATPase component; COG0444, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component; COG4166, ABC-type oligopeptide transport system, periplasmic component; COG3104, Dipeptide/tripeptide permease; COG1124, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component; Polyamines: COG0687, Spermidine/putrescine-binding periplasmic protein; COG3842, ABC-type spermidine/putrescine transport systems, ATPase components; COG1176, ABC-type spermidine/putrescine transport system, permease component I; COG1177, ABC-type spermidine/putrescine transport system, permease component II; Lipids: COG1133, ABC-type long-chain fatty acid transport system, fused permease and ATPase components; COG0580, Glycerol uptake facilitator and related permeases (Major Intrinsic Protein Family); COG2067, Long-chain fatty acid transport protein; COG2867, Oligoketide cyclase/lipid transport protein; Nucleotides and Coenzymes: COG1972, Nucleoside permease; COG2233, Xanthine/uracil permeases; COG1953, Cytosine/uracil/thiamine/allantoin permeases; COG4143, ABC-type thiamine transport system, periplasmic component; COG4145, Na+/panthothenate symporter; COG3840, ABC-type thiamine transport system, ATPase component; COG3201, Nicotinamide mononucleotide transporter; COG5042, Purine nucleoside permease; Carbohydrates, general: COG1653, ABC-type sugar transport system, periplasmic component; COG1879, ABC-type sugar transport system, periplasmic component; COG3839, ABC-type sugar transport systems, ATPase components; COG1175, ABC-type sugar transport systems, permease components; COG0395, ABC-type sugar transport system, permease component; COG1129, ABC-type sugar transport system, ATPase component; COG2211, Na+/melibiose symporter and related transporters; COG0738, Fucose permease; COG1134, ABC-type polysaccharide/polyol phosphate transport system, ATPase component; COG1682, ABC-type polysaccharide/polyol phosphate export systems, permease component; COG2271, Sugar phosphate permease; COG5037, Gluconate transport-inducing protein; COG3822, ABC-type sugar transport system, auxiliary component; COG1762, Phosphotransferase system mannitol/fructose-specific IIA domain (Ntr-type); COG1925, Phosphotransferase system, HPr-related proteins; COG2213, Phosphotransferase system, mannitol-specific IIBC component; COG2893, Phosphotransferase system, mannose/fructose-specific component IIA; COG3730, Phosphotransferase system sorbitol-specific component IIC; COG3732, Phosphotransferase system sorbitol-specific component IIBC; Carbohydrates, pentoses: COG1172, Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components; COG4214, ABC-type xylose transport system, permease component; COG2182, Maltose-binding periplasmic proteins/domains; COG3833, ABC-type maltose transport systems, permease component; COG1455, Phosphotransferase system cellobiose-specific component IIC; Carboxylic Acids: COG4663, TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component; COG1593, TRAP-type C4-dicarboxylate transport system, large permease component; COG1638, TRAP-type C4-dicarboxylate transport system, periplasmic component; COG4664, TRAP-type mannitol/chloroaromatic compound transport system, large permease component; COG2358, TRAP-type uncharacterized transport system, periplasmic component; COG0471, Di- and tricarboxylate transporters; COG4666, TRAP-type uncharacterized transport system, fused permease components; COG1301, Na+/H+-dicarboxylate symporters; COG4665, TRAP-type mannitol/chloroaromatic compound transport system, small permease component; COG0651, Formate hydrogenlyase subunit 3/Multisubunit Na+/H+ antiporter, MnhD subunit; COG1620, l-lactate permease; COG3090, TRAP-type C4-dicarboxylate transport system, small permease component; COG1823, Predicted Na+/dicarboxylate symporter; COG5037, Gluconate transport-inducing protein; Compatible Solutes: COG2113, ABC-type proline/glycine betaine transport systems, periplasmic components; COG1292, Choline-glycine betaine transporter; COG4176, ABC-type proline/glycine betaine transport system, permease component; COG0591, Na+/proline symporter; COG4175, ABC-type proline/glycine betaine transport system, ATPase component; COG1125, ABC-type proline/glycine betaine transport systems, ATPase components; COG1174, ABC-type proline/glycine betaine transport systems, permease component.

Fig. 2

Taxon-specific expression patterns for DOC-related transporter genes. Left column: all DOC-related sequences in unmanipulated coastal seawater (pooled Coastal 1 and Coastal 2 samples). Middle and right columns: significantly enriched DOC-related sequences in coastal seawater amended with phytoplankton-derived DOC (middle) and vascular plant-derived DOC (right). Each point of the radar plot represents the per cent of transporter sequences assigned to a given taxon that was annotated for uptake of the indicated compound class. The number of DOC-related transcript sequences included in the analysis is indicated in the upper right of each plot.

Fig. 3

Transcripts assigned to selected major functional categories as a per cent of total COG assignments (COG J only; translation and ribosomal structure) or as a per cent of COG assignments after removal of COG J sequences (COG O, protein turnover and chaperones; COG L, DNA replication, recombination, and repair; COG D, cell division and chromosome partitioning). The ‘transporter’ category sums transporter-related sequences across major functional categories.

Fig. 4

M–A plots of pair-wise comparisons of transcript relative abundance in transporter-related COGs for the combined coastal sample versus phytoplankton-derived DOC (A) and vascular plant-derived DOC (B). M = log₂(transcript_E/transcript_C) and A = 0alf; log₂(transcript_E + transcript_C), where transcript_E and transcript_C are the per cent of transcripts assigned to a COG in experimentally manipulated and coastal treatments respectively. Grey squares indicate COGs that are significantly different between samples. See Fig. 2B for the pair-wise comparison between the two experimentally manipulated DOC pools.

Fig. 5

Taxonomic assignment of transporters by DOC compound class. Carbohydrate = transcripts assigned to the general carbohydrate category in Fig. 1; Amino acids = transcripts assigned to the general amino acid category in Fig. 1. Notations above each pie diagram = the number of transcripts included in the pie diagram (i.e. those assigned to one of the eight major taxa)/total transcripts (including minor groups and those not taxonomically assigned at the order level).