Dissolved Organic Matter Remineralization Research Articles

Metaexoproteomics Reveals Microbial Behavior in the Ocean's Interior.

The proteins present in the extracellular environment of cells, named the “exoproteome,” are critical for microbial survival, growth, and interaction with their surroundings. However, little is known about microbial exoproteomes in natural marine environments. Here, we used a metaproteomic approach to characterize the exoprotein profiles (10 kDa-0.2 μm) throughout a water column in the South China Sea. Viruses, together with Alpha- and Gammaproteobacteria were the predominant contributors. However, the exoprotein-producing microbial communities varied with depth: SAR11 in the shallow waters, Pseudomonadales and Nitrososphaeria in the mesopelagic layer, and Alteromonadales, Rhizobiales, and Betaproteobacteria in the bathypelagic layer. Besides viral and unknown proteins, diverse transporters contributed substantially to the exoproteomes and varied vertically in their microbial origins, but presented similar patterns in their predicted substrate identities throughout the water column. Other microbial metabolic processes subject to vertical zonation included proteolysis, the oxidation of ammonia, nitrite and carbon monoxide, C1 metabolism, and the degradation of sulfur-containing dissolved organic matter (DOM). Our metaexoproteomic study provides insights into the depth-variable trends in the in situ ecological traits of the marine microbial community hidden in the non-cellular world, including nutrient cycling, niche partitioning and DOM remineralization.

DOM degradation by light and microbes along the Yukon River-coastal ocean continuum

The Arctic is experiencing rapid warming, resulting in fundamental shifts in hydrologic connectivity and carbon cycling. Dissolved organic matter (DOM) is a significant component of the Arctic and global carbon cycle, and significant perturbations to DOM cycling are expected with Arctic warming. The impact of photochemical and microbial degradation, and their interactive effects, on DOM composition and remineralization have been documented in Arctic soils and rivers. However, the role of microbes, sunlight and their interactions on Arctic DOM alteration and remineralization in the coastal ocean has not been considered, particularly during the spring freshet when DOM loads are high, photoexposure can be quite limited and residence time within river networks is low. Here, we collected DOM samples along a salinity gradient in the Yukon River delta, plume and coastal ocean during peak river discharge immediately after spring freshet and explored the role of UV exposure, microbial transformations and interactive effects on DOM quantity and composition. Our results show: (1) photochemical alteration of DOM significantly shifts processing pathways of terrestrial DOM, including increasing relative humification of DOM by microbes by > 10%; (2) microbes produce humic-like material that is not optically distinguishable from terrestrial humics; and (3) size-fractionation of the microbial community indicates a size-dependent role for DOM remineralization and humification of DOM observed through modeled PARAFAC components of fluorescent DOM, either through direct or community effects. Field observations indicate apparent conservative mixing along the salinity gradient; however, changing photochemical and microbial alteration of DOM with increasing salinity indicate changing DOM composition likely due to microbial activity. Finally, our findings show potential for rapid transformation of DOM in the coastal ocean from photochemical and microbial alteration, with microbes responsible for the majority of dissolved organic matter remineralization.

Migratory Zooplankton Excreta and Its Influence on Prokaryotic Communities

Particulate organic matter (POM) (fecal pellets) from zooplankton has been demonstrated to be an important nutrient source for the pelagic prokaryotic community. Significantly less is known about the chemical composition of the dissolved organic matter (DOM) produced by these eukaryotes and its influence on pelagic ecosystem structure. Zooplankton migrators, which daily transport surface-derived compounds to depth, may act as important vectors of limiting nutrients for mesopelagic microbial communities. In this role, zooplankton may increase the DOM remineralization rate by heterotrophic prokaryotes through the creation of nutrient rich “hot spots” that could potentially increase niche diversity. To explore these interactions, we collected the migratory copepodPleuromamma xiphiasfrom the northwestern Sargasso Sea and sampled its excreta after 12–16 h of incubation. We measured bulk dissolved organic carbon (DOC), dissolved free amino acids (DFAA) via high performance liquid chromatography and dissolved targeted metabolites via quantitative mass spectrometry (UPLC-ESI-MSMS) to quantify organic zooplankton excreta production and characterize its composition. We observed production of labile DOM, including amino acids, vitamins, and nucleosides. Additionally, we harvested a portion of the excreta and subsequently used it as the growth medium for mesopelagic (200 m) bacterioplankton dilution cultures. In zooplankton excreta treatments we observed a four-fold increase in bacterioplankton cell densities that reached stationary growth phase after five days of dark incubation. Analyses of 16S rRNA gene amplicons suggested a shift from oligotrophs typical of open ocean and mesopelagic prokaryotic communities to more copiotrophic bacterial lineages in the presence of zooplankton excreta. These results support the hypothesis that zooplankton and prokaryotes are engaged in complex and indirect ecological interactions, broadening our understanding of the microbial loop.

Bacterioplankton metabolism of phytoplankton lysates across a cyclone‐anticyclone eddy dipole impacts the cycling of semi‐labile organic matter in the photic zone

AbstractMesoscale eddies, prominent physical processes in the stratified ocean gyres, affect community composition and metabolic rates of both phytoplankton and heterotrophic bacterioplankton (free‐living bacterial and archaeal) communities. We hypothesized that in situ differences in organic matter production would predispose bacterioplankton communities from cyclonic vs. anticyclonic eddies toward metabolic capabilities better suited to utilizing dissolved organic matter (DOM) from the phytoplankton groups commonly associated with each eddy polarity. To test this, we established dilution batch‐culture bioassay incubations along a cyclone to anticyclone spatial transect in the North Pacific Subtropical Gyre. Unamended incubations, to assess spatial variability in ambient DOM bioavailability, and incubations amended with lysates of phytoplankton cultures were established and community growth and metabolic responses were assessed. Over timescales of days, lysate type was more influential than incubation origin: Prochlorococcus lysate was rapidly remineralized, while Emiliania huxleyi lysate was efficiently incorporated into biomass and developed a unique community of copiotrophic bacteria. Over timescales of 1 week to 1 month, eddy effects were indirectly apparent in their potential to promote metabolic processes related to DOM production and consumption. Surface lysate incubations showed priming of ambient DOM, that is, the remineralization of DOM, which was otherwise not bioavailable, in the presence of labile substrates. Some incubations originating from the deep chlorophyll maximum demonstrated signatures of chemoautotrophy fueled by nitrification, coincident with eddy‐driven isopycnal uplift. We conclude that eddy polarity itself does not determine community‐level bacterioplankton metabolic capabilities; however, mesoscale processes may indirectly affect slower, semi‐labile organic matter processing in the oligotrophic ocean.

Immobilization of relic anthropogenic dissolved organic matter from alpine rivers in the Himalayan-Tibetan Plateau in winter

The Tibetan Plateau is a critical ecosystem that sensitively responds to ongoing glacier shrinkage and permafrost thaw. Dissolved organic matter (DOM) in Tibetan Alpine rivers plays pivotal roles in the biogeochemical cycling of elements and nutrients at regional and even global scales, impacting water quality, downstream environments, and climate. However, little is known about the characteristics and dynamics of DOM in these watersheds. We investigated five major Himalayan rivers in the southern Tibetan Plateau, utilizing bulk dissolved organic carbon (DOC), optical properties, and molecular formulas. We found extremely low DOC and fluorescent DOM (FDOM) levels in the rivers (average DOC: 0.25–0.87 mg L−1, FDOM: 0.02–0.05 RU) with a highly degraded molecular signature, which was enriched with heteroatomic molecular formulas (S-containing: 58–72%, N-containing: 61–86%) and condensed aromatics (31–39% vs. ∼11% in world major rivers). Further, 81–99% of the condensed aromatics was identified as dissolved black nitrogen (DBN) with multiple nitrogen atoms, typical for grassy biomass combustion. The findings highlighted potentially fast DOM remineralization leading to the release of CO2 and enriched apparently anthropogenic condensed aromatics and heteroatomic formulas in what have been considered pristine Tibetan rivers. These findings should be considered in future biogeochemical models and ecosystem management.

Ultrahigh resolution mass spectrometric differentiation of dissolved organic matter isolated by coupled reverse osmosis-electrodialysis from various major oceanic water masses

A high-recovery technique of dissolved organic matter (DOM) isolation – reverse osmosis coupled with electrodialysis (RO/ED) – was used to isolate DOM from the North Atlantic Senegal-Mauritanian upwelling area surface water (5m), North Atlantic oxygen minimum water (415m) and deep water (3000m), North Pacific subtropical gyre surface water (5m), and North Pacific intermediate water (674m) and deep water (3500m). Samples were characterized by ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry with electrospray ionization (ESI FTICR-MS). RO/ED isolated DOM samples share a significant number of common formulas accounting for 54–79% of formulas in each sample. Total dissolved carbohydrate (TCHO) concentrations in RO/ED isolated DOM were specifically measured using a colorimetric method, and were found to have higher contribution to DOC than estimated by FTICR-MS data. Percentages of TCHO-C in DOC are in the range of 3.7–19.6% in all samples, with the North Pacific deep (3500m) water having the lowest % and the North Atlantic upwelling core surface water having the highest %. Principal component analysis (PCA) using the relative magnitudes of MS peaks facilitated identification of specific peaks that are enriched in different samples. Peaks enriched in surface samples have higher H/C values than peaks enriched in deep samples, in both the North Atlantic DOM and the North Pacific DOM. This enrichment pattern is likely due to the selective photo-degradation of aromatic compounds and the bio-production of aliphatic and carbohydrate-like compounds in surface waters, and the selective bio-degradation of aliphatic and carbohydrate-like compounds with increasing depth. In further support of a photo-degraded signature for DOM in surface waters, photo-resistant and photo-produced molecular formulas were present in the highest numbers in the surface North Pacific subtropical gyre DOM. Peaks enriched in the North Pacific intermediate and deep DOM have significantly higher O/C values than the North Atlantic oxygen minimum layer and deep DOM, for both CHO formula compounds and CHON formula compounds. This difference in O/C values observed for the deep Pacific vs. Atlantic suggests oxidation of DOM, possibly via microbial activity during the ageing of DOM or the preferential remineralization of DOM from sinking particles at depth in the Pacific.

Optimization and sensitivity study of a biogeochemistry ocean model using an implicit solver and in situ phosphate data

A new implicit method for obtaining equilibrium solutions and their sensitivity to changes in parameters is described and applied to an OCMIP‐2 type ocean‐biogeochemistry model. The method is used to optimize model parameters by minimizing the difference between the observed and simulated PO4 distribution. The optimized parameters include (1) the exponent α in the power law vertical profile for particulate organic matter (POM) fluxes, (2) the fraction σ of biological production allocated to dissolved organic matter (DOM) and (3) the rate constant κ for the remineralization of DOM. Global PO4 observations constrain σ and κ but not independently because their sensitivity patterns are highly correlated. In contrast, the sensitivity pattern for α is uncorrelated to those of the other parameters, allowing it to be independently constrained. We show that export production from POC is well constrained by the distribution of PO4 in an OCMIP‐2 type model, but that new production and export production from DOC are not well constrained. With the optimal parameter set (α = −1.0, σ = 0.74, and κ = 1.0 yrs−1) the fraction of the spatial PO4 variance captured by our model increases from 60% with the reference OCMIP‐2 parameters to 70%. Combined changes in σ and κ account for most of the improvements by reducing but not completely eliminating the nutrient trapping effect in the Eastern Equatorial Pacific and northern Indian Ocean that causes the model to over‐predict PO4 concentrations. Important remaining model‐data misfits in the deep North Atlantic where PO4 is over predicted and in the North Pacific where the model does not produce the observed sharp nutricline are likely attributable to deficiencies in ocean transport. The fact that the fraction of unexplained variance is large at the optimal parameter values highlights the importance of properly simulating physical transport for ocean biogeochemical modeling.

Using preformed nitrate to infer decadal changes in DOM remineralization in the subtropical North Pacific

The preformed nitrate distribution throughout the subtropical North Pacific is characterized by a negative anomaly between 100 m and the 25.4 σθ surface. Its presence indicates that nitrogen remineralization in the upper thermocline deviates significantly from Redfield stoichiometry. It has been previously suggested that this feature is created during the degradation of nitrogen‐poor dissolved organic matter (DOM) (Emerson and Hayward, 1995). Here we present evidence from two transects in the eastern subtropical North Pacific that degradation of DOM with a high C:N ratio is quantitatively responsible for negative preformed nitrate. We develop a simple isopycnal mass balance to determine preformed nitrate using apparent oxygen utilization (AOU), dissolved organic carbon (DOC), and dissolved organic nitrogen (DON) data. These results agree well with the traditional preformed nitrate calculation and indicate that the intensity of the anomaly is proportional to the magnitude of DOM remineralization and its C:N remineralization ratio. An analysis of preformed nitrate distributions in the eastern subtropical North Pacific between 1980 and 1997 reveals a significant increase in the negative anomaly. While a portion of this change may be attributable to a reduction in ventilation of the gyre, the majority of the signal is due to an increase in the magnitude and/or C:N ratio of DOM remineralization. This conclusion supports recent hypotheses that DOM production and cycling may have increased in this region in the past 2 decades as a result of changes in the phytoplankton community structure.

Distributions of TOP, TON and TOC in the North Pacific subtropical gyre: Implications for nutrient supply in the surface ocean and remineralization in the upper thermocline

We report measurements of total organic phosphorus, nitrogen, and carbon (TOP, TON, and TOC) along a meridional transect in the eastern subtropical North Pacific. In the surface waters, TOP and TON comprise 83% and 98% of the total dissolved phosphorus and nitrogen pools, respectively. Between the equatorial region and the subtropical gyre, there is a distinct gradient in surface TOP of about 0.25 μM, but very little gradient in TON. TOC increases by nearly 30 μM across the same region. Meridional advection of TOP along its gradient via Ekman transport can provide 40-80% of the phosphorus necessary to supply present estimates of particulate phosphorus export from the subtropical gyre. Mass balance requires an additional input of nitrogen to the surface waters to fuel particulate nitrogen export. This input is likely supported by nitrogen fixation. As dissolved organic matter (DOM) is degraded along isopycnals that outcrop within the subtropical gyre, TOP and TOC are consumed more rapidly than TON. TOC and TON contribute 70% and 20% to organic matter remineralization along these isopycnals, respectively, and the C:N ratio for remineralization is 30 ± 10. In contrast, along isopycnals that outcrop to the north of the gyre, both TOC and TON contribute 30% to organic matter remineralization and the C:N ratio is 8 ± 1. Our results suggest that excess TOC, produced within the surface waters of the subtropical gyre during nitrogen fixation, is highly labile and dominates respiration along shallow isopycnals. Preferential remineralization of TOC relative to TON within the gyre results in a negative preformed nitrate signal in the upper thermocline, and may establish a feedback between upper thermocline DOM remineralization and surface ocean DOM production that maintains nitrogen fixation in the surface waters.

Modeling bacterial utilization of dissolved organic matter: Optimization replaces Monod growth kinetics

A bioenergetic model has been developed to examine growth kinetics associated with bacterial utilization of dissolved organic matter (DOM), NH4+, and NO3‒. A set of 11 metabolic reactions are used to govern the incorporation, oxidation, and N remineralization of DOM and dissolved inorganic N associated with bacterial growth. For each reaction, free energies and electron transfer requirements are calculated based on the C, H, O, and N composition of the substrates and their concentration in the environment. From these reactions, an optimization problem is constructed in which bacterial growth rate is maximized subject to constraints on energetics, electron balances, substrate uptake kinetics, and bacterial C : N ratio. The optimization approach provides more information on bacterial growth kinetics than do the Monod‐type models that are typically used to describe bacterial growth. Simulations are run to examine bacterial C yield and growth rate, N remineralization or immobilization, and substrate preferences as resource concentrations and compositions are varied. Results from the model agree well with observations in the literature, which indicate that the premise of the model, that bacteria allocate resources to maximize growth rate, may be an accurate overall description of bacterial growth. Simulations indicate that bacterial growth rate and yield are strongly correlated to the oxidation state of the labile DOM, as determined from its bulk elemental composition. Furthermore, the model demonstrates that bacterial growth cannot always be explained by a single constraint (such as the C : N ratio of substrate), since several constraints are often active simultaneously and continuously change with environmental conditions.

Anomalous temperature dependence of resistivity in heavily doped germanium : Y. Otsuka, S. Ikehata, S. Kobayashi and W. Sasaki. Solid-St. Commun.20, 441 (1976)

A high-recovery technique of dissolved organic matter (DOM) isolation – reverse osmosis coupled with electrodialysis (RO/ED) – was used to isolate DOM from the North Atlantic Senegal-Mauritanian upwelling area surface water (5 m), North Atlantic oxygen minimum water (415 m) and deep water (3000 m), North Pacific subtropical gyre surface water (5 m), and North Pacific intermediate water (674 m) and deep water (3500 m). Samples were characterized by ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry with electrospray ionization (ESI FTICR-MS). RO/ED isolated DOM samples share a significant number of common formulas accounting for 54–79% of formulas in each sample. Total dissolved carbohydrate (TCHO) concentrations in RO/ED isolated DOM were specifically measured using a colorimetric method, and were found to have higher contribution to DOC than estimated by FTICR-MS data. Percentages of TCHO-C in DOC are in the range of 3.7–19.6% in all samples, with the North Pacific deep (3500 m) water having the lowest % and the North Atlantic upwelling core surface water having the highest %. Principal component analysis (PCA) using the relative magnitudes of MS peaks facilitated identification of specific peaks that are enriched in different samples. Peaks enriched in surface samples have higher H/C values than peaks enriched in deep samples, in both the North Atlantic DOM and the North Pacific DOM. This enrichment pattern is likely due to the selective photo-degradation of aromatic compounds and the bio-production of aliphatic and carbohydrate-like compounds in surface waters, and the selective bio-degradation of aliphatic and carbohydrate-like compounds with increasing depth. In further support of a photo-degraded signature for DOM in surface waters, photo-resistant and photo-produced molecular formulas were present in the highest numbers in the surface North Pacific subtropical gyre DOM. Peaks enriched in the North Pacific intermediate and deep DOM have significantly higher O/C values than the North Atlantic oxygen minimum layer and deep DOM, for both CHO formula compounds and CHON formula compounds. This difference in O/C values observed for the deep Pacific vs. Atlantic suggests oxidation of DOM, possibly via microbial activity during the ageing of DOM or the preferential remineralization of DOM from sinking particles at depth in the Pacific.