Isolation and Staining Reveal the Presence of Extracellular DNA in Marine Gel Particles.

Marine gel particles (MGP) are amorphous hydrogel exudates from bacteria and microalgae that are ubiquitous in the oceans, but their biochemical composition and function are poorly understood. While dynamic ecological interactions between marine microorganisms and MGPs may result in the secretion and mixing of bacterial extracellular polymeric substances (EPS) such as nucleic acids, compositional studies currently are limited to the identification of acidic polysaccharides and proteins in transparent exopolymer particles (TEP) and Coomassie stainable particles (CSP). Previous studies targeted MGPs isolated by filtration. We developed a new way of isolating MGPs from seawater in liquid suspension and applied it to identify extracellular DNA (eDNA) in North Sea surface seawater. Seawater was filtered onto polycarbonate (PC) filters with gentle vacuum filtration, and then the filtered particles were gently resuspended in a smaller volume of sterile seawater. The resulting MGPs ranged in size from 0.4 to 100 µm in diameter. eDNA was detected by fluorescent microscopy using YOYO-1 (for eDNA), with Nile red (targeting cell membranes) as a counterstain. TOTO-3 was also used to stain eDNA, with ConA to localise glycoproteins and SYTO-9 for the live/dead staining of cells. Confocal laser scanning microscopy (CLSM) revealed the presence of proteins and polysaccharides. We found eDNA to be universally associated with MGPs. To further elucidate the role of eDNA, we established a model experimental MGP system using bacterial EPS from Pseudoalteromonas atlantica that also contained eDNA. Our results clearly demonstrate the occurrence of eDNA in MGPs, and should aid furthering our understanding of the micro-scale dynamics and fate of MGPs that underly the large-scale processes of carbon cycling and sedimentation in the ocean.

Photochemical oxidation of dimethylsulphide to dimethylsulphoxide in estuarine and coastal waters.

Dimethylsulphide (DMS) photo-oxidation and dimethylsulphoxide (DMSO) photoproduction were estimated in 26 laboratory irradiations of coastal samples from NE England (Tyne estuary) and W Scotland (Loch Linnhe and River Nant at Taynuilt). Pseudo-first order rate constants of DMS photo-oxidation (0.038 h-1 to 0.345 h-1) and DMSO photo-production (0.017 h-1 to 0.283 h-1) varied by one order of magnitude and were lowest in the coastal North Sea. Estuarine samples (salinity S < 30) had a mean DMSO yield of 96 ± 16% (n = 14), consistent with 1:1 M conversion via photosensitised oxidation by singlet oxygen. Photochemical rate constants were strongly correlated with coloured dissolved organic matter (CDOM) absorption coefficients at 350 nm, a350. Variations in a350 explained 61% (R2 = 0.61, n = 26) and 73% (R2 = 0.73, n = 17) of the variability in DMS photo-oxidation and DMSO production, respectively. However, CDOM normalised photochemical rate constants increased strongly towards coastal waters exhibiting lowest CDOM absorbance, indicating water samples of marine character (S > 30) to be most reactive with respect to DMS photo-oxidation. Estimates of water column averaged DMS photo-oxidation rate constants, obtained by scaling to mean daily irradiance (July, NE England) and mid-UV underwater irradiance, were 0.012 d-1, 0.019 d-1, and 0.017 d-1 for upper estuary (S < 20), lower estuary (20 < S < 30) and coastal waters (S > 30), at the lower end of previous observations. Comparing our water column averaged DMS photo-oxidation rate constants with estimated DMS losses via air-sea gas exchange and previously reported biological consumption implies that DMS photochemical removal is of only minor importance in our study area.

Nitrous oxide as a function of oxygen and archaeal gene abundance in the North Pacific.

Oceanic oxygen minimum zones are strong sources of the potent greenhouse gas N2O but its microbial source is unclear. We characterized an exponential response in N2O production to decreasing oxygen between 1 and 30 µmol O2 l-1 within and below the oxycline using 15NO2-, a relationship that held along a 550 km offshore transect in the North Pacific. Differences in the overall magnitude of N2O production were accounted for by archaeal functional gene abundance. A one-dimensional (1D) model, parameterized with our experimentally derived exponential terms, accurately reproduces N2O profiles in the top 350 m of water column and, together with a strong 45N2O signature indicated neither canonical nor nitrifier-denitrification production while statistical modelling supported production by archaea, possibly via hybrid N2O formation. Further, with just archaeal N2O production, we could balance high-resolution estimates of sea-to-air N2O exchange. Hence, a significant source of N2O, previously described as leakage from bacterial ammonium oxidation, is better described by low-oxygen archaeal production at the oxygen minimum zone's margins.

Response of copepods to elevated pCO2 and environmental copper as co-stressors--a multigenerational study.

We examined the impacts of ocean acidification and copper as co-stressors on the reproduction and population level responses of the benthic copepod Tisbe battagliai across two generations. Naupliar production, growth, and cuticle elemental composition were determined for four pH values: 8.06 (control); 7.95; 7.82; 7.67, with copper addition to concentrations equivalent to those in benthic pore waters. An additive synergistic effect was observed; the decline in naupliar production was greater with added copper at decreasing pH than for decreasing pH alone. Naupliar production modelled for the two generations revealed a negative synergistic impact between ocean acidification and environmentally relevant copper concentrations. Conversely, copper addition enhanced copepod growth, with larger copepods produced at each pH compared to the impact of pH alone. Copepod digests revealed significantly reduced cuticle concentrations of sulphur, phosphorus and calcium under decreasing pH; further, copper uptake increased to toxic levels that lead to reduced naupliar production. These data suggest that ocean acidification will enhance copper bioavailability, resulting in larger, but less fecund individuals that may have an overall detrimental outcome for copepod populations.

Microbiology of aquatic surface microlayers.

Aquatic surface microlayers are unique microbial ecosystems found at the air-water interface of all open water bodies and are often referred to as the neuston. Unambiguous interpretation of the microbiology of aquatic surface microlayers relies on robust sampling, for which several methods are available. All have particular advantages and disadvantages that make them more or less suited to this task. A key feature of surface microlayers is their role in regulating air-water gas exchange, which affords them a central role in global biogeochemistry that is only now being fully appreciated. The microbial populations in surface microlayers can impact air-water gas exchange through specific biogeochemical processes mediated by particular microbial groups such as methanotrophs or through more general metabolic activity such as the balance of primary production vs. heterotrophy. There have been relatively few studies of surface microlayers that have utilized molecular ecology techniques. The emerging consensus view is that aquatic surface microlayers are aggregate-enriched biofilm environments containing complex microbial communities that are ecologically distinct from those present in the subsurface water immediately below. Future research should focus on unravelling the complex interactions between microbial diversity and the ecosystem function of surface microlayers in order to better understand the important but complex role of microorganisms in Earth system processes.

Dissolved organic carbon and bacterial populations in the gelatinous surface microlayer of a Norwegian fjord mesocosm.

The sea surface microlayer is the interfacial boundary layer between the marine environment and the troposphere. Surface microlayer samples were collected during a fjord mesocosm experiment to study microbial assemblage dynamics within the surface microlayer during a phytoplankton bloom. Transparent exopolymer particles were significantly enriched in the microlayer samples, supporting the concept of a gelatinous surface film. Dissolved organic carbon and bacterial cell numbers (determined by flow cytometry) were weakly enriched in the microlayer samples. However, the numbers of Bacteria 16S rRNA genes (determined by quantitative real-time PCR) were more variable, probably due to variable numbers of bacterial cells attached to particles. The enrichment of transparent exopolymer particles in the microlayer and the subsequent production of a gelatinous biofilm have implications on air-sea gas transfer and the partitioning of organic carbon in surface waters.

Relating carbon monoxide photoproduction to dissolved organic matter functionality.

Aqueous solutions of humic substances (HSs) and pure monomeric aromatics were irradiated to investigate the chemical controls upon carbon monoxide (CO) photoproduction from dissolved organic matter (DOM). HSs were isolated from lakes, rivers, marsh, and ocean. Inclusion of humic, fulvic, hydrophobic organic, and hydrophilic organic acid fractions from these environments provided samples diverse in source and isolation protocol. In spite of these major differences, HS absorption coefficients (a) and photoreactivities (a bleaching and CO production) were strongly dependent upon HS aromaticity (r2 > 0.90; n = 11), implying aromatic moieties are the principal chromophores and photoreactants within HSs, and by extension, DOM. Carbonyl carbon and CO photoproduction were not correlated, implying that carbonyl moieties are not quantitatively important in CO photoproduction. CO photoproduction efficiency of aqueous solutions of monomeric aromatic compounds that are common constituents of organic matter varied with the nature of ring substituents. Specifically, electron donating groups increased, while electron withdrawing groups decreased CO photoproductivity, supporting our conclusion that carbonyl substituents are not quantitatively important in CO photoproduction. Significantly, aromatic CO photoproduction efficiency spanned 3 orders of magnitude, indicating that variations in the CO apparent quantum yields of natural DOM may be related to variations in aromatic DOM substituent group chemistry.

Discriminatory classification of natural and anthropogenic waters in two U.K. estuaries.

The ability to distinguish water inputs from both natural and anthropogenic sources was investigated in the complex environment of an urban estuary (Tyne) and a relatively pristine estuary (Tweed). We used a data set from a total of 11 estuarine transects, comprising measurements of bulk dissolved organic matter (dissolved organic carbon and nitrogen), dissolved nitrogen (total dissolved nitrogen, ammonium, nitrate+nitrite and dissolved organic nitrogen), optical absorbance measurements (a350, S290-350) and fluorescence excitation emission matrix measurements (fluorophores A, H, B and T intensity and A and H emission wavelength maxima). In order to investigate trends within the numerous parameters measured, multivariate statistics were employed. Principal components analyses showed 63.4% of the variability in the total data set can be explained by two sets of components and 74.9% of the variability by the spectrophotometric measurements alone. In both analyses the first component correlated to the mixing of terrestrial and marine waters and the second component was correlated to sources of pollution such as domestic sewage. Within the data set, river flow and terrestrially derived DOM were significantly correlated, and situations with high river input showed an increase in terrestrial signature in the estuary. Discriminant analyses were also carried out and indicated that 59.8% (total data set) and 53.3% (solely spectrophotometric data) of the samples can be correctly classified into their respective groups (water categories) assigned on the basis of salinity and sampling location. Overall the results clearly show the potential of spectrophotometric techniques to discriminate distinct water categories with different DOM characteristics. In particular, measurement of the fluorophore H emission maxima, the spectral slope parameter, S290-350, and fluorophores T and B intensity enabled discrimination of DOM from riverine, estuarine, marine, and sewage affected water categories. The results presented here indicate the ability of spectrophotometric data alone to distinguish between marine, anthropogenic and terrestrial DOM and distinguish terrestrial DOM from different catchments (Tyne vs. Tweed). With current advances in the in-situ deployment of absorbance and fluorescence spectroscopy it is anticipated that multivariate statistics will gain importance as a cost effective, powerful and diagnostic approach to assessing the distributions of water types and their associated DOM characteristics and fluxes at the land-ocean interface.

Evaluating the sources and fate of anthropogenic dissolved inorganic nitrogen (DIN) in two contrasting North Sea estuaries.

Nitrogen isotope ratios (delta(15)N) were used to help elucidate the sources and fate of ammonium (NH(4)(+)) and nitrate (NO(3)(-)) in two northeastern English estuaries. The dominant feature of NH(4)(+) in the heavily urbanised Tyne estuary was a plume arising from a single point source; a large sewage works. Although NH(4)(+) concentrations (ranging from 30-150 microM) near the sewage outfall varied considerably between surveys, the sewage-derived delta(15)N-NH(4)(+) signature was remarkably constant (+10.6+/-0.5 per thousand) and could be tracked across the estuary. As indirectly supported by (15)N-depleted delta(15)N-NO(3)(-) values observed close to the mouth of the Tyne, this sewage-derived NH(4)(+) was thought to initiate lower estuarine and coastal zone nitrification. In the more rural Tweed, NH(4)(+) concentrations were low (<7 microM) compared to those in the Tyne and delta(15)N-NH(4)(+) values were consistent with mixing between riverine and marine sources. The dominant form of dissolved inorganic nitrogen (DIN) in the Tweed was agricultural soil-derived NO(3)(-). A decrease in riverine NO(3)(-) flux during the summer coinciding with an increase in delta(15)N-NO(3)(-) values was mainly attributed to enhanced watershed nutrient processing. In the Tyne, where agricultural inputs are less important compared to the Tweed, light delta(15)N-NO(3)(-) (ca. 0 per thousand) detected in the estuary during one winter survey pointed to a larger contribution from precipitation-derived NO(3)(-) during high river discharge. Regardless of the dominant sources, in both estuaries most of the variability in DIN concentrations and delta(15)N values was explained by simple end-member mixing models, implying very little estuarine processing.

Bacterial diversity in the bacterioneuston (sea surface microlayer): the bacterioneuston through the looking glass.

The bacterioneuston is defined as the community of bacteria present within the neuston or sea surface microlayer. Bacteria within this layer were sampled using a membrane filter technique and bacterial diversity was compared with that in the underlying pelagic coastal seawater using molecular ecological techniques. 16S rRNA gene libraries of approximately 500 clones were constructed from both bacterioneuston and the pelagic water samples and representative clones from each library were sequenced for comparison of bacterial diversity. The bacterioneuston was found to have a significantly lower bacterial diversity than the pelagic seawater, with only nine clone types (ecotaxa) as opposed to 46 ecotaxa in the pelagic seawater library. Surprisingly, the bacterioneuston clone library was dominated by 16S rRNA gene sequences affiliated to two groups of organisms, Vibrio spp. which accounted for over 68% of clones and Pseudoalteromonas spp. accounting for 21% of the library. The dominance of these two 16S rRNA gene sequence types within the bacterioneuston clone library was confirmed in a subsequent gene probing experiment. 16S rRNA gene probes specific for these groups of bacteria were designed and used to probe new libraries of 1000 clones from both the bacterioneuston and pelagic seawater DNA samples. This revealed that 57% of clones from the bacterioneuston library hybridized to a Vibrio sp.-specific 16S rRNA gene probe and 32% hybridized to a Pseudoalteromonas sp.-specific 16S rRNA gene probe. In contrast, the pelagic seawater library resulted in only 13% and 8% of 16S rRNA gene clones hybridizing to the Vibrio sp. and Pseudoalteromonas sp. probes respectively. Results from this study suggest that the bacterioneuston contains a distinct population of bacteria and warrants further detailed study at the molecular level.