Linking microbial metabolomics and carbon sequestration in the ocean via refractory organic molecules has been hampered by the chemical complexity of dissolved organic matter (DOM). Here, using bioassay experiments and ultra-high resolution metabolic profiling, we demonstrate that marine bacteria rapidly utilize simple organic molecules and produce exometabolites of remarkable molecular and structural diversity. Bacterial DOM is similar in chemical composition and structural complexity to naturally occurring DOM in sea water. An appreciable fraction of bacterial DOM has molecular and structural properties that are consistent with those of refractory molecules in the ocean, indicating a dominant role for bacteria in shaping the refractory nature of marine DOM. The rapid production of chemically complex and persistent molecules from simple biochemicals demonstrates a positive feedback between primary production and refractory DOM formation. It appears that carbon sequestration in diverse and structurally complex dissolved molecules that persist in the environment is largely driven by bacteria.

Dissolved organic matter (DOM) in groundwater influences water quality and fuels microbial metabolism, but its origins, bioavailability and chemical composition are poorly understood. The origins and concentrations of dissolved organic carbon (DOC) and bioavailable DOM were monitored during a long-term (2-year) study of groundwater in a fractured-rock aquifer in the Carolina slate belt. Surface precipitation was significantly correlated with groundwater concentrations of DOC, bioavailable DOM and chromophoric DOM, indicating strong hydrological connections between surface and ground waters. The physicochemical and biological processes shaping the concentrations and compositions of DOM during its passage through the soil column to the saturated zone are conceptualized in the regional chromatography model. The model provides a framework for linking hydrology with the processes affecting the transformation, remineralization and microbial production of DOM during passage through the soil column. Lignin-derived phenols were relatively depleted in groundwater DOM indicating substantial removal in the unsaturated zone, and optical properties of chromophoric DOM indicated lower molecular weight DOM in groundwater relative to surface water. The prevalence of glycine, γ-aminobutyric acid, and d-enantiomers of amino acids indicated the DOM was highly diagenetically altered. Bioassay experiments were used to establish DOC-normalized yields of amino acids as molecular indicators of DOM bioavailability in groundwater. A relatively small fraction (8 ± 4 %) of DOC in groundwater was bioavailable. The relatively high yields of specific d-enantiomers of amino acids indicated a substantial fraction (15–34 %) of groundwater DOC was of bacterial origin.

The global ocean sequesters a large amount of reduced carbon in dissolved organic molecules that can persist for centuries to millennia. The persistence of dissolved organic carbon (DOC) in the deep ocean has been attributed to inherently refractory molecules and to low concentrations of molecules, but the relative roles of molecular properties and molecular concentrations remain uncertain. We investigate both of these possibilities using bioassay experiments with unfiltered seawater collected from five depths (50–1500 m) at the Bermuda Atlantic Time‐Series Study site. The microbial utilization of compositionally distinct forms of seawater DOC at in situ and elevated concentrations was determined. Microbial utilization of in situ organic carbon ranged from 6% to 7% in surface waters to 0% in deep water after 180 d. Additions of surface plankton‐derived DOC (~18 μmol L⁻¹), which was enriched in amino acids and carbohydrates, revealed substantial (50–75%) removal of the added DOC at all depths within 7 d. In sharp contrast, additions of C‐18 isolated deep‐sea DOC (~20 μmol L⁻¹) showed insignificant or minimal utilization at all depths after 7 or 180 d, even when primed with labile substrates. These experiments demonstrate microbial communities from varying depths and environments in the ocean could rapidly utilize elevated concentrations of plankton‐derived DOC, whereas these same microbes failed to utilize elevated concentrations of C‐18 DOC. These results indicate molecular properties are the primary control on the microbial utilization of DOC in the ocean. Our findings imply a dynamic DOC reservoir with a flexible capacity for carbon sequestration in the global ocean.

A large quantity of reduced carbon is sequestered in the ocean as refractory dissolved molecules that persist through several circuits of global overturning circulation. Key aspects of the cycling of refractory dissolved organic carbon (DOC) remain unknown, making it challenging to predict how this large carbon reservoir will respond to climate change. Herein we investigate mechanisms that remove refractory DOC using bioassay experiments with DOC isolated from surface, mesopelagic and deep waters of the Atlantic Ocean. The isolated DOC was refractory to degradation by native microbial communities, even at elevated concentrations. However, when the refractory DOC was introduced to a series of novel environmental conditions, including addition of a labile substrate, a microbial community from coastal waters and exposure to solar radiation, a substantial fraction (7–13%) was removed within 1.5 years. Our results suggest that while refractory molecules can persist in the ocean for millennia, removal is rapid when they encounter their fate. The observed and projected climate-induced slowdown of global overturning circulation could reduce the exposure of refractory molecules to disparate removal processes. Assuming a constant rate of production, the reservoir size of refractory DOC could increase as overturning circulation slows, providing a negative feedback to rising atmospheric CO₂.

Dissolved organic carbon (DOC) and total dissolved amino acids (TDAA) were measured in high (Chukchi Sea) and low (Beaufort Sea) productivity regions of the western Arctic Ocean to investigate the composition and bioavailability of dissolved organic matter (DOM). Concentrations and DOC-normalized yields of TDAA in Chukchi surface waters were relatively high, indicating an accumulation of bioavailable DOM. High concentrations and yields of TDAA were also observed in the upper halocline of slope and basin waters, indicating off-shelf transport of bioavailable DOM from the Chukchi Sea. In contrast, concentrations and yields of TDAA in Beaufort surface waters were relatively low, indicting DOM was of limited bioavailability. Concentrations and yields of TDAA in the upper halocline of slope and basin waters were also low, suggesting the Beaufort is not a major source of bioavailable DOM to slope and basin waters. In shelf waters of both systems, elevated concentrations and yields of TDAA were often observed in waters with higher chlorophyll concentrations and productivity. Surface concentrations of DOC were similar (p > 0.05) in the two systems despite the contrasting productivity, but concentrations and yields of TDAA were significantly higher (p < 0.0001) in the Chukchi than in the Beaufort. Unlike bulk DOC, TDAA concentrations and yields reflect ecosystem productivity in the western Arctic. The occurrence of elevated bioavailable DOM concentrations in the Chukchi Sea implies an uncoupling between the biological production and utilization of DOM and has important implications for sustaining heterotrophic microbial growth and diversity in oligotrophic waters of the central Arctic basins.