Yuan Shen

Marine sequestration of carbon in bacterial metabolites

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.

Predicting Dissolved Lignin Phenol Concentrations in the Coastal Ocean from Chromophoric Dissolved Organic Matter (CDOM) Absorption Coefficients

Dissolved lignin is a well-established biomarker of terrigenous dissolved organic matter (DOM) in the ocean, and a chromophoric component of DOM. Although evidence suggests there is a strong linkage between lignin concentrations and chromophoric DOM (CDOM) absorption coefficients in coastal waters, the characteristics of this linkage and the existence of a relationship that is applicable across coastal oceans remain unclear. Here, 421 paired measurements of dissolved lignin concentrations (sum of 9 lignin phenols) and CDOM absorption coefficients (ag(λ)) were used to examine their relationship along the river-ocean continuum (0-37 salinity) and across contrasting coastal oceans (sub-tropical, temperate, high-latitude). Overall, lignin concentrations spanned four orders of magnitude and revealed a strong, non-linear relationship with ag(λ). The characteristics of the relationship (shape, wavelength dependency, lignin-composition dependency) and evidence from degradation indicators were all consistent with lignin being an important driver of CDOM variability in coastal oceans, and suggested physical mixing and long-term photodegradation were important in shaping the relationship. These observations were used to develop two simple empirical models for estimating lignin concentrations from ag(λ) with a +/- 20% error relative to measured values. The models are expected to be applicable in most coastal oceans influenced by terrigenous inputs.

Linkages among fluorescent dissolved organic matter, dissolved amino acids and lignin-derived phenols in a river-influenced ocean margin

Excitation emission matrix (EEM) fluorescence spectroscopy coupled with parallel factor analysis (PARAFAC) is commonly used to investigate the dynamics of dissolved organic matter (DOM). However, a lack of direct comparisons with known biomolecules makes it difficult to substantiate the molecular composition of specific fluorescent components. Here, coincident surface-water measurements of EEMs, dissolved lignin, and total dissolved amino acid (TDAA) acquired in the northern Gulf of Mexico were used to investigate the relationships between specific fluorescent components and DOM biomolecules. Two terrestrial humic-like components identified by EEM-PARAFAC using samples obtained from river to offshore waters were strongly linearly correlated with dissolved lignin concentrations. In addition, changes in terrestrial humic-like abundance were correlated with those in lignin phenol composition, suggesting such components are largely derived from lignin and its alteration products. By applying EEM-PARAFAC to offshore samples, two protein-like components were obtained. The tryptophan-like component was strongly correlated with TDAA concentrations, corroborating the suggested protein/peptide origin of this component. The ratios of tryptophan-like component to tyrosine-like component or dissolved organic carbon (DOC) concentrations were also correlated with DOC-normalized yields of TDAA, suggesting these proxies are useful indicators of the bioavailability of DOM in marine waters of the studied ecosystem.

Sources, Distributions, and Dynamics of Dissolved Organic Matter in the Canada and Makarov Basins

A comprehensive survey of dissolved organic carbon (DOC) and chromophoric dissolved organic matter (CDOM) was conducted in the Canada and Makarov Basins and adjacent seas during 2010-2012 to investigate the dynamics of dissolved organic matter (DOM) in the Arctic Ocean. Sources and distributions of DOM in polar surface waters were very heterogeneous and closely linked to hydrological conditions. Canada Basin surface waters had relatively low DOC concentrations (69±6 µmol L-1), CDOM absorption (a325: 0.32±0.07 m-1) and CDOM-derived lignin phenols (3±0.4 nmol L-1) and high spectral slope values (S275-295: 31.7±2.3 µm-1), indicating minor terrigenous inputs and evidence of photochemical alteration in the Beaufort Gyre. By contrast, surface waters of the Makarov Basin had elevated DOC (108±9 µmol L-1) and lignin phenol concentrations (15±3 nmol L-1), high a325 values (1.36±0.18 m-1) and low S275-295 values (22.8±0.8 µm-1), indicating pronounced Siberian river inputs associated with the Transpolar Drift and minor photochemical alteration. Observations near the Mendeleev Plain suggested limited interactions of the Transpolar Drift with Canada Basin waters, a scenario favoring export of Arctic DOM to the North Atlantic. The influence of sea-ice melt on DOM was region-dependent, resulting in an increase (Beaufort Sea), a decrease (Bering-Chukchi Seas), and negligible change (deep basins) in surface DOC concentrations and a325 values. Halocline structures differed between basins, and the Canada Basin upper halocline and Makarov Basin halocline were comparable in their average DOC (65-70 µmol L-1) and lignin phenol concentrations (3-4 nmol L-1) and S275-295 values (22.9-23.7 µm-1). Deep-water DOC concentrations decreased by 6-8 µmol L-1 with increasing depth, water mass age, nutrient concentrations, and apparent oxygen utilization. Maximal estimates of DOC degradation rates (0.036-0.039 µmol L-1 yr-1) in the deep Arctic were lower than those in other ocean basins, possibly due to low water temperatures. DOC concentrations in bottom waters (>2500 m; 46±2 µmol L-1) of the Canada and Makarov Basins were slightly lower than those reported for deep waters of the Eurasian Basin and Nordic Seas. Elevated a325 values (by 10-20%) were observed near the seafloor, indicating biological activity in Arctic basin sediments.

Bioavailable dissolved organic matter and biological hot spots during austral winter in Antarctic waters

Primary production and heterotrophic bacterial activity in the Antarctic Ocean are generally low during the austral winter. Organic carbon is considered to be a major factor limiting bacterial metabolism, but few studies have investigated the bioavailability of organic matter during winter. Herein, the chemical composition and bioavailability of dissolved organic matter (DOM) were investigated in surface (5–100 m) and mesopelagic (200–750 m) waters off the northwestern Antarctic Peninsula during August 2012. Concentrations of dissolved organic carbon (DOC) were low (42 ± 4 µmol L−1) and showed no apparent spatial patterns. By contrast, the composition of DOM exhibited significant spatial trends that reflected varying ecosystem productivity and water masses. Surface distributions of chlorophyll-a and particulate organic carbon depicted a southward decline in primary productivity from open waters (60.0°S–61.5°S) to ice-covered regions (61.5°S–62.5°S). This trend was evident from concentrations and DOC-normalized yields of dissolved amino acids in the surface waters, indicating decreasing DOM bioavailability with increasing latitude. A different pattern of DOM bioavailability was observed in the mesopelagic water masses, where amino acids indicated highly altered DOM in the Circumpolar Deep Water and bioavailable DOM in the Transitional Weddell Water. Depth distributions of amino acid yields and compositions revealed hot spots of elevated bioavailable DOM at ∼75 m relative to surrounding waters at most ice-free stations. Relatively low mole percentages of bacterially derived d-amino acids in hot spots were consistent with an algal source of bioavailable DOM. Overall, these results reveal the occurrence and spatial heterogeneity of bioavailable substrates in Antarctic waters during winter.

Mixing it up in the ocean carbon cycle and the removal of refractory dissolved organic carbon

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.