Molecular weight fractionation of dissolved organic matter (DOM) released by phytoplankton

The application of an ultrafiltration procedure for fractionation of molecular weight of dissolved organic matter (DOM) extracellularly released by phytoplankton is described. Seven ultrafiltration membranes Diaflo (Amicon Corp. USA), with range 500--300,000 molecular weight (MW), were used for separation of different molecular weight compounds released by phytoplankton in Rhode River estuary of Chesapeake Bay, and their composition was determined. Percentage of extracellular release of DOM by phytoplankton varied from 3.92--68.07% of total carbon fixed in photosynthesis. The composition of algal extracellular products varied with different phytoplankton populations. However, two fractions of molecular weight compounds dominated in the composition of DOM released, i.e. a low molecular weight fraction of less than 1,000 MW and the fraction between 10,000--30,000 MW. The ultrafiltration procedure is effective for studying the composition of DOM released by phytoplankton in natural waters.     

Shifts in bacterial community composition associated with increased carbon cycling in a mosaic of phytoplankton blooms

Marine microbes have a pivotal role in the marine biogeochemical cycle of carbon, because they regulate the turnover of dissolved organic matter (DOM), one of the largest carbon reservoirs on Earth. Microbial communities and DOM are both highly diverse components of the ocean system, yet the role of microbial diversity for carbon processing remains thus far poorly understood. We report here results from an exploration of a mosaic of phytoplankton blooms induced by large-scale natural iron fertilization in the Southern Ocean. We show that in this unique ecosystem where concentrations of DOM are lowest in the global ocean, a patchwork of blooms is associated with diverse and distinct bacterial communities. By using on-board continuous cultures, we identify preferences in the degradation of DOM of different reactivity for taxa associated with contrasting blooms. We used the spatial and temporal variability provided by this natural laboratory to demonstrate that the magnitude of bacterial production is linked to the extent of compositional changes. Our results suggest that partitioning of the DOM resource could be a mechanism that structures bacterial communities with a positive feedback on carbon cycling. Our study, focused on bacterial carbon processing, highlights the potential role of diversity as a driving force for the cycling of biogeochemical elements.     

Cascading influence of inorganic nitrogen sources on DOM production,composition, lability and microbial community structure in the open ocean

Nitrogen frequently limits oceanic photosynthesis and the availability of inorganic nitrogen sources in the surface oceans is shifting with global change. We evaluated the potential for abrupt increases in inorganic N sources to induce cascading effects on dissolved organic matter (DOM) and microbial communities in the surface ocean. We collected water from 5 m depth in the central North Pacific and amended duplicate 20 liter polycarbonate carboys with nitrate or ammonium, tracking planktonic carbon fixation, DOM production, DOM composition and microbial community structure responses over 1 week relative to controls. Both nitrogen sources stimulated bulk phytoplankton, bacterial and DOM production and enriched Synechococcus and Flavobacteriaceae; ammonium enriched for oligotrophic Actinobacteria OM1 and Gammaproteobacteria KI89A clades while nitrate enriched Gammaproteobacteria SAR86, SAR92 and OM60 clades. DOM resulting from both N enrichments was more labile and stimulated growth of copiotrophic Gammaproteobacteria (Alteromonadaceae and Oceanospirillaceae) and Alphaproteobacteria (Rhodobacteraceae and Hyphomonadaceae) in weeklong dark incubations relative to controls. Our study illustrates how nitrogen pulses may have direct and cascading effects on DOM composition and microbial community dynamics in the open ocean.     

Algae-bacteria interactions and their effects on aggregation and organic matter flux in the sea

Aggregation of algae, mainly of diatoms, is an important process in marine pelagic systems, often terminating phytoplankton blooms and leading to the sinking of particulate organic matter in the form of marine snow. This process has been studied extensively, but the specific role of heterotrophic bacteria has largely been neglected, mainly because field studies and most experimental work were performed under non-axenic conditions. We tested the hypothesis that algae-bacteria interactions are instrumental in aggregate dynamics and organic matter flux. A series of aggregation experiments has been carried out in rolling tanks with two marine diatoms typical of temperate regions (Skeletonema costatum and Thalassiosira rotula) in an axenic treatment and one inoculated with marine bacteria. Exponentially growing S. costatum and T. rotula exhibited distinctly different aggregation behavior. This was reflected by their strikingly different release of dissolved organic matter (DOM), transparent exopolymer particles (TEP) and protein-containing particles (CSP), as well as their bacterial biodegradability and recalcitrance. Cells of S. costatum aggregated only little and their bacterial colonization remained low. Dissolved organic matter, TEP and CSP released by this alga were largely consumed by free-living bacteria. In contrast, T. rotula aggregated rapidly and DOM, TEP and CSP released resisted bacterial consumption. Experiments conducted with T. rotula cultures in the stationary growth phase, however, showed rapid bacterial colonization and decomposition of algal cells. Our study highlights the importance of heterotrophic bacteria to control the development and aggregation of phytoplankton in marine systems.     

Ammonia-oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean

Ammonia-oxidizing archaea (AOA) constitute a considerable fraction of microbial biomass in the global ocean, comprising 20%–40% of the ocean's prokaryotic plankton. However, it remains enigmatic to what extent these chemolithoautotrophic archaea release dissolved organic carbon (DOC). A combination of targeted and untargeted metabolomics was used to characterize the exometabolomes of three model AOA strains of the Nitrosopumilus genus. Our results indicate that marine AOA exude a suite of organic compounds with potentially varying reactivities, dominated by nitrogen-containing compounds. A significant fraction of the released dissolved organic matter (DOM) consists of labile compounds, which typically limit prokaryotic heterotrophic activity in open ocean waters, including amino acids, thymidine and B vitamins. Amino acid release rates corresponded with ammonia oxidation activity and the three Nitrosopumilus strains predominantly released hydrophobic amino acids, potentially as a result of passive diffusion. Despite the low contribution of DOC released by AOA (~0.08%–1.05%) to the heterotrophic prokaryotic carbon demand, the release of physiologically relevant metabolites could be crucial for microbes that are auxotrophic for some of these compounds, including members of the globally abundant and ubiquitous SAR11 clade.     

Distribution of dissolved organic carbon and nitrogen in a coral reef

Dissolved organic matter (DOM) concentrations in a fringing coral reef were measured for both carbon and nitrogen with the analytical technique of high-temperature catalytic oxidation. Because of high precision of the analytical system, not only the concentrations of dissolved organic carbon and nitrogen (DOC and DON, respectively) but the C:N ratio was also determined from the distribution of DOC and DON concentrations. The observed concentrations of DOC and DON ranged 57–76 and 3.8–5.6 μmol l⁻¹, respectively. The C:N ratios of the DOM that was produced on the reef flat were very similar between seagrass- and coral-dominated areas; the C:N ratio was 10 on average. The C:N ratio of DOM was significantly higher than that of particulate organic matter (POM) that was produced on the reef flat. Production rates of DOC were measured on the reef flat during stagnant periods and accounted for 3–7% of the net primary production, depending on the sampling site. The production rate of DON was estimated to be 10–30% of the net uptake of dissolved inorganic N in the reef community. Considering that the DOM and POM concentrations were not correlated with each other, a major source of the reef-derived DOM may be the benthic community and not POM such as phytoplankton. It was concluded that a widely distributed benthic community in the coral reef released C-rich DOM to the overlying seawater, conserving N in the community.     

Release of dissolved organic matter by photosynthesizing algae in Lake Kinneret,Israel*

The incorporation of inorganic carbon in particulate and dissolved organic matter by natural populations of photosynthesizing algae has been studied in Lake Kinneret, Israel, from August 1972 to December 1973. The release of dissolved organic material was directly related to the rates of particulate productivity. However, the percentage of extracellular release (PER) of dissolved organic compounds showed an inverse relationship with chlorophyll a concentrations. Mean PER values (for the trophogenic layer) over the experimental period were 3·7%, and were lowest during the exponential growth phase of the annual dinoflagellate bloom (mean PER = 1·9%). Highest PER were measured in deep, light-limited samples (mean = 31·7%; s.d.· 21·9%). In a dense metalimnic layer of photosynthetic sulphur bacteria (Chlorobium phaeobacterioides), PER was not as extremely high as has been reported for a similar layer in Lake Wadolek, Poland. Although the amounts of dissolved organic matter released by phytoplankton in Lake Kinneret were low, they may have significance as growth modulators and as substrates for heterotrophic organism.     

Phytoplankton exudation: exploitation of the microbial loop as a defence against algal viruses

Healthy phytoplankton cells exude dissolved organic matter (DOM).In a model, DOM exudation is demonstrated to be a cost-effective,indirect, means of reducing virus infection, which can be amajor cause of phytoplankton mortality. Diffusion theoly showsthat, for a given biomass, small particles will have a muchhigher rate of wlsorption of solutes than will large ones. Thuscolloidal viruses are far more likely to come into contact withbacteria than with phytoplankton if the same biomasses are present.B can destroy viruses in a large proportion of contacts. Althoughflagellate protozoa have lower contact rates with viruses, theymay consume more of the viruses that they do encounter and theydeal with larger viruses particularly effectively. The exudedDOM supports bacterial growth, which in turn may support flagellates.Even fairly low levels of exudation can maintain the biomassof bacteria or small flagellates required to remove >50%of viruses before they have a chance to infect their host, atleast for larger phytoplankton. High rates of virus removalmay occur at the high exudation rates that are typical of lateblooms, It is concluded that healthy phytoplankton cells exudeDOM in order to remain healthy.     

Dissolved organic matter released by two marine heterotrophic bacterial strains and its bioavailability for natural prokaryotic communities

Marine heterotrophic prokaryotes (HP) play a key role in organic matter processing in the ocean; however, the view of HP as dissolved organic matter (DOM) sources remains underexplored. In this study, we quantified and optically characterized the DOM produced by two single marine bacterial strains. We then tested the availability of these DOM sources to in situ Mediterranean Sea HP communities. Two bacterial strains were used: Photobacterium angustum (a copiotrophic gammaproteobacterium) and Sphingopyxis alaskensis (an oligotrophic alphaproteobacterium). When cultivated on glucose as the sole carbon source, the two strains released from 7% to 23% of initial glucose as bacterial derived DOM (B-DOM), the quality of which (as enrichment in humic or protein-like substances) differed between strains. B-DOM induced significant growth and carbon consumption of natural HP communities, suggesting that it was partly labile. However, B-DOM consistently promoted lower prokaryotic growth efficiencies than in situ DOM. In addition, B-DOM changed HP exoenzymatic activities, enhancing aminopeptidase activity when degrading P. angustum DOM, and alkaline phosphatase activity when using S. alaskensis DOM, and promoted differences in HP diversity and composition. DOM produced by HP affects in situ prokaryotic metabolism and diversity, thus changing the pathways for DOM cycling (e.g. respiration over biomass production) in the ocean.     

Quantitative and qualitative analyses of dissolved organic matter released from Ecklonia cava Kjellman, in Oura Bay, Shimoda, Izu Peninsula, Japan

Release of dissolved organic matter (DOM) was studied on macroalga, Ecklonia cava Kjellman, by in situ field bag experiments, which were designed to keep the algal body under natural field condition, in Oura Bay, Shimoda, Izu Peninsula, Japan, from August 2003 to May 2005. The experiments were conducted 6 times in different seasons. The concentrations of dissolved organic carbon (DOC) in the experimental bag generally increased during the first 1-2 days, showing the release of DOC from algae. The daily release rates of DOC varied between 0.12 and 5.8 mgC per g (dry wt) of the algal blades per day. The seasonal variability of the DOC release rate was similar to those of the growth and the photosynthetic rates reported by the previous studies on E. cava in the same location. The fractions of the DOC release of the net primary production accounted for 18-62%. These contributions are comparable to other macroalgae in the previous studies (27-43%) using other macroalgae. Analysis of organic composition of DOM using gas chromatography (neutral aldose composition) and spectrometry (UV-visible and fluorescence) indicates that E. cava usually release extracellular products containing mucilaginous polysaccharides containing fucose as a main constituent and colored dissolved organic matter (CDOM). The release of these organic compounds is likely performed as the ordinary metabolism of brown algae. An exceptional release of a considerable amount of protein and carbohydrates mainly composed of mannose was found in June 2004, probably reflecting leakage of the intracellular material by an autolysis of the algal cells. The high DOM release rate in the present study suggests that macroalgae would be one of the important DOM producers in coastal regions.     

Constant release of photosynthate from marine phytoplankton.

The release rate of dissolved organic carbon (DOC) by unialgal cultures and natural phytoplankton assemblages was constant over a wide range of dissolved inorganic carbon concentrations. DOC release was not proportional to the particulate organic carbon production rate. We postulate that intracellular DOC, fated for release, exists either as a separate pool from that leading to particulate organic carbon production or that there is active metabolic control on one portion of a common pool.     

Instream release of dissolved organic matter from coarse and fine particulate organic matter of different origins

Dissolved organic matter (DOM), produced through leaching from particulate organic matter (POM), is an essential component of the carbon cycle in streams. The present study investigated the instream DOM release from POM, varying in size and chemical quality. We produced large and medium sized fine particulate organic matter (L-FPOM, 250–500 μm; M-FPOM, 100–250 μm) of defined quality by feeding five types of coarse particulate organic matter (CPOM) to shredding amphipods (Gammarus spp.). Microscopic observations showed that L-FPOM and M-FPOM mainly consisted of the fecal pellets of amphipods, and incompletely eaten plant fragments, respectively. DOM release experiments were conducted by exposing CPOM and M- and L-FPOM fractions in natural stream water over a two week period. For CPOM, the release of dissolved organic carbon (DOC) by leaching was highest during the first 6 h (3.64–23.9 mg C g C^?1 h^?1) and decreased rapidly afterwards. For M- and L-FPOM, the DOC release remained low during the entire study period (range: 0.008–0.15 mg C g C^?1 h^?1). Two-way ANOVA revealed that the DOC release rate significantly differed with POM source and size fraction, both at day 1 and after a week of exposure. Multiple regression analyses revealed a significant correlation of elemental contents and lignin content to DOC release rate after a week of exposure. Overall, the results indicated that DOC release rate of FPOM, on a carbon basis, is comparable to that of CPOM after leaching, while size and source of POM significantly affect DOC release rate.     

Chemical and seasonal controls on the dynamics of dissolved organic matter in a coniferous old-growth stand in the Pacific Northwest,USA

Soil organic matter (SOM) is the largest terrestrial C pool, and retention and release of dissolved organic matter (DOM) cause formation and loss of SOM. However, we lack information on how different sources of DOM affect its chemical composition, and how DOM chemical composition affects retention. We studied seasonal controls on DOM production and chemical controls on retention in soils of a temperate coniferous forest. The O horizon was not usually the dominant source for dissolved organic C (DOC) or N (DON) as has been reported for other sites. Rather, net production of both DOC and DON was often greater in the shallow mineral soil (0–10 cm) than in the O horizon. DOM production in the shallow mineral soil may be from root exudation as well as turnover of fine roots and microflora in the rhizosphere. In the field, the two acid fractions (hydrophobic and hydrophilic acids) dominated the soil solution at all depths. A major portion of net production and removal of total DOC within the soil column was explained by increases and decreases in these fractions, although a shift in chemical composition of DOM between the O and mineral soil horizons suggested different origins of DOM in these layers. A larger loss of the free amino fraction to deep soil water at this study site than at other sites suggested lower retention of labile DON. Field DOM removal measurements suggest that field-measured parameters may provide a good estimate for total DOM retained in mineral soil.     

Bacteria-organic matter coupling and its significance for oceanic carbon cycling

This paper synthesizes current ideas on the role of the microbial loop in carbon fluxes in the ocean and proposes some directions for future research. Organic matter flux into bacteria is highly variable, which can significantly influence the pathways of carbon flow in the ocean. A goal for future research is to elucidate the mechanistic bases of bacteria-organic matter coupling. This research should take into consideration the micrometer-scale distribution of bacteria and the composition, structure, and dynamics of the organic matter field in the bacterium's microhabitat. The ideas on the interactions of bacteria with the particulate organic phase need to be revised in view of recent findings of highly abundant, previously unknown particles ranging in size from nanometers to hundreds of micrometers. The hot-spots in the distribution of organic matter and remineralized nutrients can influence the rates as well as the direction of biogeochemical fluxes. Slow-to-degrade dissolved organic matter (DOM) may be produced because of loose bacteria-organic matter coupling resulting in DOM storage. Its use at a later time and place has profound implications for carbon fluxes and food web dynamics. A fundamental research need for the future is to understand the ecological interactions among the members of the microbial loop in an appropriate microhabitat context. While this goal was previously intractable, new molecular and optical techniques should make it possible to understand the biogeochemical activities of the microbial loop in terms of the ecology and evolution of pelagic microbial communities.     

The role of dissolved organic matter bioavailability in promoting phytoplankton blooms in Florida Bay

The clear, shallow, oligotrophic waters of Florida Bay are characterized by low phytoplankton biomass, yet periodic cyanobacteria and diatom blooms do occur. We hypothesized that allochthonous dissolved organic matter (DOM) was providing a subsidy to the system in the form of bound nutrients. Water from four bay sites was incubated under natural light and dark conditions with enrichments of either DOM ( > 1 kD, 2×DOM) or inorganic nutrients (N+P). Samples were analyzed for bacterial numbers, bacterial production, phytoplankton biomass, phytoplankton community structure, and production, nutrients, and alkaline phosphatase (AP) activity. The influence of 2×DOM enrichment on phytoplankton biomass developed slowly during the incubations and was relatively small compared to nutrient additions. Inorganic nutrient additions resulted in an ephemeral bloom characterized initially as cyanobacterial and brown algae but which changed to dinoflagellate and/or brown algae by day six. The DIN:TP ratio decreased 10-fold in the N+P treatments as the system progressed towards N limitation. This ratio did not change significantly for 2×DOM treatments. In addition, these experiments indicated that both autotrophic and heterotrophic microbial populations in Florida Bay may fluctuate in their limitation by organic and inorganic nutrient availability. Both N+P and 2×DOM enrichments revealed significant and positive response in bioavailability of dissolved organic carbon (BDOC). Potential BDOC ranged from 1.1 to 35.5%, with the most labile forms occurring in Whipray Basin. BDOC at all sites was stimulated by the 2×DOM addition. Except for Duck Key, BDOC at all sites was also stimulated by the addition of N+P. BDOC was lower in the dry season than in the wet season (5.56% vs. 16.86%). This may be explained by the distinct chemical characteristics of the DOM produced at different times of year. Thus, both the heterotrophic and autotrophic microbial communities in Florida Bay are modulated by bioavailability of DOM. This has ramifications for the fate of DOM from the Everglades inputs, implicating DOM bioavailability as a contributing factor in regulating the onset, persistence, and composition of phytoplankton blooms.     

Exopolymer production as a function of cell permeability and death in a diatom (Thalassiosira weissflogii) and a cyanobacterium (Synechococcus elongatus)

Exopolymer particles are found throughout the ocean and play a significant biogeochemical role in carbon cycling. Transparent exopolymer particles (TEP) are composed of acid polysaccharides, and Coomassie staining particles (CSP) are proteins. TEPs have been extensively studied in the ocean, while CSP have been largely overlooked. The objective of this research was to determine the role of stress and cell permeability in the formation of TEP and CSP. The diatom Thalassiosira weissflogii and cyanobacterium Synechococcus elongatus were grown in batch cultures and exposed to hydrogen peroxide (0, 10, and 100 μM) as an environmental stressor. There was no correlation between TEP and CSP concentrations, indicating that they are different populations of particles rather than different chemical components of the same particles. CSP concentrations were not affected by hydrogen peroxide concentration and did not correlate with indicators of stress and cell death. In contrast, TEP concentrations in both taxa were correlated with a decrease in the effective quantum yield of photosystem II, increased activity of caspase‐like enzymes, and an increase in the proportion of the population with permeable cell membranes, indicating that TEP production was associated with the process of cell death. These data show that different environmental factors and physiological processes affected the production of TEP and CSP by phytoplankton. TEP and CSP are separate populations of exopolymer particles with potentially different biogeochemical roles in the ocean.     

Sorption of hydrophobic organic contaminants and trace metals on phytoplankton and implications for toxicity assessment

The partitioning of trace metals and hydrophobic organic contaminants to phytoplankton determines their toxicity as well as their fate and transport in aquatic ecosystems. Accurate impact assessments, therefore, depend on a good understanding of the factors regulating the sorption of these compounds to biotic particles. The accumulation of chlorinated organic compounds in phytoplankton is generally considered as being due solely to physical sorption, described by reversible equilibrium models based on Langmuir or Freundlich isotherms. On the other hand, the uptake of trace metals is a two phase process: a fast sorption component viewed as an ionexchange or a covalent bonding process with cell surface ligands, followed by an intracellular transport phase that is dependent on cellular metabolic activity. The uptake of inorganic and hydrophobic organic pollutants and their bioaccumulation are influenced in a complex manner by duration of exposure and cell density, by environmental factors such as pH, the concentration of cations and of dissolved and colloidal organic matter, as well as by phytoplankton physiological condition. High concentrations of H⁺, Ca²⁺, and Mg²⁺ ions will reduce trace metal sorption by directly competing for uptake sites on the cell's surface, whereas the presence of dissolved organic carbon such as natural and synthetic chelators and phytoplankton exudates will reduce the bioavailability of both trace metals and hydrophobic organic contaminants. Thus, the impact of toxic contaminants on phytoplankton may be determined as much by the factors influencing uptake and partitioning as by the potency of the toxicants and interspecies differences in sensitivity. Recommendations for improving toxicity assessments are presented.     

Photo-biochemical transformation of dissolved organic matter on the surface of the coastal East Antarctic ice sheet

Recent studies have highlighted the composition and complexity of dissolved organic matter (DOM) in glacial environments. Climate-induced changes to glacier runoff are projected to be an important source of DOM to coastal ecosystems. Photochemical and microbial (termed photo-biochemical) degradation of DOM would determine its fate on the glacier surface and in recipient coastal ecosystems. In order to understand the molecular imprints of photo-biochemical alteration of DOM, in situ field experiments were conducted over a period of 35 days in a coastal Antarctic site and DOM molecularly characterised using ultrahigh-resolution mass spectrometry. We show that the biogeochemistry of DOM is highly complex and intimately connected with microbial and photochemical processes operating individually or in combination. Photo-biochemical processes resulted in shifts in the nitrogen, sulfur, and phosphorous content of the DOM. These processes are also an important mechanism for transforming refractory DOM, like dissolved black carbon and carboxylic rich alicyclic molecules from the snow surface. This study is unique, as it provides new molecular-level information on compounds that comprise the photo- and bio-labile, photo- and bio-refractory, as well as photo- and bio-produced fractions of the supraglacial DOM pool. These insights into the interactions between microbes, light, and specific components of the DOM pool highlight the need for studies focused on the biogeochemistry of supraglacial carbon and its response to a changing climate.