INAUGURAL ARTICLE by a Recently Elected Academy Member:Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea

Abstract

Microbial activities drive most of Earth's biogeochemical cycles. Many processes and players involved in these planetary cycles, however, remain largely uncharacterized, due to the inherent complexity of microbial community processes in the environment. Cycling of organic carbon in ocean surface waters is no exception. Though marine dissolved organic matter (DOM) is one of the largest reservoirs of organic carbon on the planet (1), microbial activities that regulate DOM turnover remain poorly resolved (2). Marine DOM is an important substrate for heterotrophic bacterioplankton, which efficiently remineralize as much as 50% of total primary productivity through the microbial loop (3–6). Though some DOM is remineralized on short timescales of minutes to hours, a significant fraction escapes rapid removal. In marine surface waters, this semilabile DOM transiently accumulates to concentrations 2–3 times greater than are found in the deep sea (7), and represents a large inventory of dissolved carbon and nutrients that are potential substrates for marine microbes. Time-series analyses of semilabile DOM accumulation in temperate and subtropical upper ocean gyres show an annual cycle in DOC inventory with net accumulation following the onset of summertime stratification, and net removal following with deep winter mixing. In addition, multiyear time-series data suggest that surface-water DOM inventories have been increasing over the past 10–20 y (8). The ecological factors behind these seasonal and decadal DOC accumulations are largely unknown. Nutrient (N, P) amendments do not appear to result in a drawdown of DOC, and other factors such as the microbial community structure and the chemical composition of semilabile DOM have been invoked to explain the dynamics of the semilabile DOC reservoir (9, 10). Whatever the cause, the balance and timing of semilabile DOM remineralization are critical factors that influence the magnitude of DOM and carbon exported to the ocean's interior through vertical mixing. There are significant challenges associated with characterizing and quantifying complex, microbially influenced processes such as DOM cycling in the sea. These challenges include inherent phylogenetic and population diversity and variability, the complexities of microbial community metabolic properties and interactions, and those associated with measuring microbial assemblage activities and responses on appropriate temporal and spatial scales. Past approaches have included measuring the bulk response of microbial communities to nutrient addition (e.g., community substrate incorporation or respiration), following changes in total or functional group cell numbers by microscopy or flow cytometry, or monitoring changes in relative taxa abundance, typically using rRNA-based phylogenetic markers. A number of field experiments (9–13) have indicated that specific shifts in microbial community composition might be linked to surface-water carbon utilization. However, the pure compound nutrient additions (such as glucose) frequently used in such field experiments (9, 11, 14, 15) may not well approximate the environmentally relevant chemical mixtures or compound concentrations present in naturally occurring DOM. Though complications associated with direct experimentation on natural microbial communities limit our understanding of oceanic carbon cycling to some extent, significant insight into these processes have been recently reported. For example, Carlson et al. (10) showed differences among depth-stratified microbial communities that may be related to their ability to use semilabile DOM that accumulates in ocean surface waters. In addition, phylogenetic analyses of time-series samples have identified some taxonomic groups that appear to be responsive to deep-water mixing events, which may be relevant to organic carbon cycling dynamics (16, 17). To better define the processes and population dynamics associated with marine microbial DOM cycling in ocean surface waters, we performed controlled experiments using seawater microcosms amended with freshly prepared, naturally occurring DOM. High-molecular-weight DOM (HMWDOM, defined here as the size fraction >1,000 Da and <30,000 Da) was concentrated by ultrafiltration using a 1-nm membrane filter, followed by a second filtration step to remove viruses. Whole, unfiltered seawater was distributed into replicate microcosms (20 L each) that were incubated at in-situ temperatures and light intensities. The ambient concentration of dissolved organic carbon (DOC) in the unamended microcosms was 82 μM DOC, whereas the HMWDOM-amended microcosms contained 328 μM DOC, representing a 4-fold increase over ambient DOC concentration. Replicate control and experimental microcosms were sampled periodically over the course of a 27-h period. The responses of microbial community members to HMWDOM addition over time were followed using flow cytometric, metagenomic, and metatranscriptomic analytical techniques. HMWDOM-induced shifts in microbial cell numbers, community composition, functional gene content, and gene expression were observed at each time point, as indicated by changes in the DOM-treated microcosms relative to an unamended control. The data indicated rapid and specific HMWDOM-induced shifts in transcription, metabolic pathway expression, and microbial growth that appear to be associated with HMWDOM turnover in ocean surface waters.