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

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.

Fig. 1.

Dynamics of microbial populations during 27-h microcosm incubations. (A) Flow cytometric counts of microbial cells from control (○) and DOM-amended (●) treatments. Samples displayed in B highlighted in red. (B) Flow cytometry scatterplots from selected samples show little change in the distribution of cell size [as measured by forward scatter (FSC)] and DNA content (SYBR fluorescence) of control samples from beginning to end of the experiment, whereas most of the increase in cell numbers observed in the DOM-amended treatment can be attributed to the appearance of larger, high-DNA-content cells (circled in red). (C) Weighted neighbor-joining tree of selected SSU SSU rDNA sequences from proteobacterial type strains and the sequences obtained from flow cytometric sorting of the larger, higher-DNA-content population of cells present after DOM amendment. The sequences obtained from the flow-sorted population are restricted to three specific taxonomic clades: Rhodobacteraceae, Methylophaga, and Alteromonas.

Fig. 2.

Microbial community composition assessed by taxonomic classification of metagenomic and metatranscriptomic sequence reads. (A) SSU rRNA reads (outer ring) and non-rRNA reads (middle ring) from metatranscriptomic datasets as well as those reads from metagenomic datasets identified as SSU rDNA reads (center ring). Only taxonomic groups that represent >1% of total reads in at least one dataset have been included with all other groups binned together with unassigned reads. In some instances, reads can only be confidently assigned to broad class- and order-level taxonomic groups and are labeled as such. For mRNA datasets, some reads have no significant blast hits, the percentage of which is noted beside each sample. (B) Tracking the changes in community composition by comparing the difference between the DOM-amended treatment and control reveals distinct taxonomic groups responding at each time point. Only taxonomic groups showing more than ±2% change are plotted.

Fig. 3.

Diagram of representative dissimilatory and assimilatory methylotrophic pathways and enzymes that show increased transcript abundance following DOM amendment. A KEGG ortholog-based expression ratio comparing normalized abundances of reads present in the DOM-amended treatment with those from an untreated control at 2, 12, and 27 h following DOM addition. Asterisks mark those enzymes showing statistically significantly differences in transcript abundance relative to time and/or unamended control (SI Appendix, Table S7). H₄MPT, tetrahydromethanopterin; MFR, formylmethanofuran; H6P, hexulose-6-phosphate; F6P, fructose-6-phosphate; 6PGL, 6-phosphogluconolactone; 6PG, 6-phosphogluconate; KD, ketodeoxy; PEP, phosphoenolpyruvate; GAP, glyceraldehyde phosphate; E4P, erythrose-4-phosphate; X5P, xylulose-5-phosphate; S7P, sedoheptulose-5-phosphate; PRPP, phosphoribosyl diphosphate.