Microbial controls on DMSP degradation and DMS formation in the Sargasso Sea

Bacterial degradation of dimethylsulfoniopropionate (DMSP) represents one of the main sources of the climatically–active trace gas dimethylsulfide (DMS) in the upper ocean. Short-term enrichment studies to stimulate specific pathways of DMSP degradation in oligotrophic waters from the Sargasso Sea were used to explore regulatory connections between the different bacterial DMSP degradation steps and determine potential biological controls on DMS formation in the open ocean. Experiments were conducted with surface water at the BATS station in the western North Atlantic Ocean. We added selected organic substrates (25 nmol L^?1 final concentration) to induce different steps of DMSP degradation in the microbial community, and then measured DMSP dynamics (assimilation and turnover rates), DMS yields (using ³⁵sulfur-DMSP tracer), and bacterial production rates. In most treatments, the main fate of consumed S-DMSP was excretion as a non-volatile S product. ³⁵S-DMSP tracer turnover rates (accumulation + assimilation + excretion of transformed products as DMS or others) increased upon addition of DMSP and glucose, but not acrylate, methymercaptopropionate (MMPA), methanethiol, DMS or glycine betaine. DMS yields from ³⁵S-DMSP never exceeded 16 % except in a short term DMSP enrichment, for which the yield reached 45 % (±17 %). Results show that availability of non-sulfur containing labile C sources (glucose, acrylate) decreased bacterial DMS production while stimulating bacterial heterotrophic production, and suggest an influence of bacterial sulfur demand in controlling DMS-yielding pathways. However, regulatory effects on ³⁵S-DMSP fate were not consistent across all reduced sulfur compounds (i.e., methanethiol or MMPA), and may reflect alternate roles of DMSP as a bacterial energy source and osmolyte.     

Effect of iron on phytoplankton production in the Sargasso Sea

Addition of chelated iron at concentrations of 0.5, 1.0, 10 and 100μg Fe·l^?1 to Sargasso Sea phytoplankton assemblages did not affect the rate of photosynthesis during 4-h incubation experiments. In experiments with 72-h incubations, however, iron enhanced carbon assimilation. The enhancement was independent of iron concentration.     

Hydrogen production potential of fermentative microorganisms from the Sargasso Sea

Mounting evidence suggests that ammonia-oxidizing archaea (AOA) may play important roles in nitrogen cycling in geothermal environments. In this study, the diversity, distribution and ecological significance of AOA in terrestrial hot springs in Kamchatka (Far East Russia) were explored using amoA genes complemented by analysis of glycerol dialkyl glycerol tetraethers (GDGTs) of archaea. PCR amplification of functional genes (amoA) from AOA and ammonia-oxidizing bacteria (AOB) was performed on microbial mats/streamers and sediments collected from three hot springs (42°C to 87°C and pH 5.5-7.0). No amoA genes of AOB were detected. The amoA genes of AOA formed three distinct phylogenetic clusters with Cluster 3 representing the majority (～59%) of OTUs. Some of the sequences from Cluster 3 were closely related to those from acidic soil environments, which is consistent with the predominance of low pH (<7.0) in these hot springs. Species richness (estimated by Chao1) was more frequently higher at temperatures below 75°C than above it, indicating that AOA may be favored in the moderately high temperature environments. Quantitative PCR of 16S rRNA genes showed that crenarchaeota counted for up to 80% of total archaea. S-LIBSHUFF separated all samples into two phylogenetic groups. The profiles of GDGTs were well separated among the studied springs, suggesting a spatial patterning of archaeal lipid biomarkers. However, this patterning did not correlate significantly with variation in archaeal amoA, suggesting that AOA are not the predominant archaeal group in these springs producing the observed GDGTs.     

Picoeukaryotic sequences in the Sargasso Sea metagenome

Background  

With genome sequencing becoming more and more affordable, environmental shotgun sequencing of the microorganisms present in an environment generates a challenging amount of sequence data for the scientific community. These sequence data enable the diversity of the microbial world and the metabolic pathways within an environment to be investigated, a previously unthinkable achievement when using traditional approaches. DNA sequence data assembled from extracts of 0.8 μm filtered Sargasso seawater unveiled an unprecedented glimpse of marine prokaryotic diversity and gene content. Serendipitously, many sequences representing picoeukaryotes (cell size <2 μm) were also present within this dataset. We investigated the picoeukaryotic diversity of this database by searching sequences containing homologs of eight nuclear anchor genes that are well conserved throughout the eukaryotic lineage, as well as one chloroplastic and one mitochondrial gene.     

The microbial selenoproteome of the Sargasso Sea

Background  

Selenocysteine (Sec) is a rare amino acid which occurs in proteins in major domains of life. It is encoded by TGA, which also serves as the signal for termination of translation, precluding identification of selenoprotein genes by available annotation tools. Information on full sets of selenoproteins (selenoproteomes) is essential for understanding the biology of selenium. Herein, we characterized the selenoproteome of the largest microbial sequence dataset, the Sargasso Sea environmental genome project.     

Response of Sargasso Sea phytoplankton biomass, growth rates and primary production to seasonally varying physical forcing

The response of phytoplankton biomass, growth rates and primaryproduction to seasonally varying physical forcing was studiedat a station southeast of Bermuda over an 18 month period. Phytoplanktongrowth rates and primary production were measured using thepigment-labeling method, and phytoplankton biomass was calculatedfrom these measurements. Phytoplankton carbon biomass variedsystematically over the year. Highest values were observed duringthe winter and spring. Seasonal variations of chlorophyll (Chi)a in the surface layer could primarily be attributed to variationsin phytoplankton biomass and secondarily to photoacclimation.During the summer period, average values of carbon (C)/Chl ratios(g C g^–1 Chi) ranged from 160 at the surface to 33 atthe 1.6% light level, changes attributed to photoacclimationof the phytoplankton, consistent with the observation that phytoplanktonbiomass did not vary as a function of depth. Phytoplankton growthrates in the surface layer did not vary systematically overthe year, ranging from 0.15 to 0.45 day^–1, in spite ofseasonally varying concentrations of nitrate. Growth rates variedas a function of depth from average values of 0.3 day^–1in the surface layer to <0.1 day¹ at the 1.6% light level.Thus, the primary response of the phytoplankton community tonutrient enrichment during the winter period was an increasein phytoplankton biomass rather than an increase in growth rates.A simple nutrient-phyto-plankton-zooplankton model was usedto explore this phenomenon. The model demonstrated that theobserved response of the phytoplankton to nutrient enrichmentis only possible when phytoplankton growth is not severely limitedby nutrients.     

Vertical distribution of picoeukaryotic diversity in the Sargasso Sea

Eukaryotic molecular diversity within the picoplanktonic size-fraction has primarily been studied in marine surface waters. Here, the vertical distribution of picoeukaryotic diversity was investigated in the Sargasso Sea from euphotic to abyssal waters, using size-fractionated samples (< 2 microm). 18S rRNA gene clone libraries were used to generate sequences from euphotic zone samples (deep chlorophyll maximum to the surface); the permanent thermocline (500 m); and the pelagic deep-sea (3000 m). Euphotic zone and deep-sea data contrasted strongly, the former displaying greater diversity at the first-rank taxon level, based on 232 nearly full-length sequences. Deep-sea sequences belonged almost exclusively to the Alveolata and Radiolaria, while surface samples also contained known and putative photosynthetic groups, such as unique Chlorarachniophyta and Chrysophyceae sequences. Phylogenetic analyses placed most Alveolata and Stramenopile sequences within previously reported 'environmental' clades, i.e. clades within the Novel Alveolate groups I and II (NAI and NAII), or the novel Marine Stramenopiles (MAST). However, some deep-sea NAII formed distinct, bootstrap supported clades. Stramenopiles were recovered from the euphotic zone only, although many MAST are reportedly heterotrophic, making the observed distribution a point for further investigation. An unexpectedly high proportion of radiolarian sequences were recovered. From these, five environmental radiolarian clades, RAD-I to RAD-V, were identified. RAD-IV and RAD-V were composed of Taxopodida-like sequences, with the former solely containing Sargasso Sea sequences, although from all depth zones sampled. Our findings highlight the vast diversity of these protists, most of which remain uncultured and of unknown ecological function.     

Bioluminescence of colonial radiolaria in the western Sargasso Sea

Colonial radiolaria (Protozoa: Spumellarida) were a conspicuous feature in surface waters of the Sargasso Sea during the April (1985) Biowatt cruise. The abundance of colonies at the sea surface at one station was estimated to be 23 colonies · m⁻².Bioluminescence by colonial radiolaria, representing at least six taxa, was readily evoked by mechanical stimuli and measured by fast spectroscopy and photon-counting techniques. Light emission was deep blue in color (peak emissions between 443 and 456 nm) and spectral distributions were broad (average half bandwidth of 80 nm). Single flashes were 1–2 s in duration at ≈23 °C, with species-dependent kinetics which were not attributed to differences in colony morphology, since colonies similar in appearance could belong to different species (even families) and display different flash kinetics. Although the presence of dinoflagellate symbionts was confirmed by the presence of dinoflagellate marker pigments in the colonies, luminescence in the radiolaria examined most likely did not originate from symbiotic dinoflagellates because of (1) differences in the emission spectra, (2) unresponsiveness to low pH stimulation, (3) differences in flash kinetics and photon emission of light emission, and (4) lack of light inhibition.The quantal content of single flashes averaged 1 × 10⁹ photons flash⁻¹, and colonies were capable of prolonged light emission. The mean value of bioluminescence potential based on measurements of total mechanically stimulated bioluminescence was 1.2 × 10¹¹ photons · colony⁻¹. It is estimated that colonial radiolaria are capable of producing ≈2.8 × 10¹² photons · m⁻² of sea surface. However, this represented only 0.5% of in situ measured bioluminescence potential.     

Effect of UV- radiation on DMSP content and DMS formation of Phaeocystis antarctica

DMSP (dimethyl sulphonium propionate) contents produced by an Antarctic marine phytoplankton species, Phaeocystis antarctica (Prymnesiophyta), which were incubated under light conditions with radiations of different UV wavebands, were measured by gas chromatography after various exposure times. Full light (UV-B + UV-A + PAR) caused the strongest decrease in the production of DMSP in the alga. A marked depression of DMSP content was also observed with short UV-B and UV-A wavebands after 3 h. It was therefore hypothesised that DMSP production in Phaeocystis antarctica was inhibited by UV radiation. There was a negative correlation on change of DMSP contents under UV radiation. There was a negative correlation on change of DMSP contents under UV radiation with exposure times. The conversion rate of DMSP dissolved to DMS (dimethyl sulphide) was significantly increased with UV radiation. The possibility could not be excluded that a high concentration of free chemical radicals in seawater due to UV radiation resulted in an increase of DMSP cleavage in seawater. The oxidation of DMS in seawater due to UV-B radiation could result in a decrease of its flux to the atmosphere. The effect of UV radiation on DMSP production and oxidation of DMS may be an important factor in the variability of DMSP and the global flux of DMS from ocean to atmosphere. Received: 17 June 1996 / Accepted: 17 July 1997     

Distribution and Identification of Luminous Bacteria from the Sargasso Sea

Vibrio fischeri and Lucibacterium harveyi constituted 75 of the 83 luminous bacteria isolated from Sargasso Sea surface waters. Photobacterium leiognathi and Photobacterium phosphoreum constituted the remainder of the isolates. Luminescent bacteria were recovered at concentrations of 1 to 63 cells per 100 ml from water samples collected at depths of 160 to 320 m. Two water samples collected at the thermocline yielded larger numbers of viable, aerobic heterotrophic and luminous bacteria. Luminescent bacteria were not recovered from surface microlayer samples. The species distribution of the luminous bacteria reflected previously recognized growth patterns; i.e., L. harveyi and V. fischeri were predominant in the upper, warm waters (only one isolate of P. phosphoreum was obtained from surface tropical waters).     

Environmental drivers of sardine (Sardina pilchardus) in the Catalan Sea (NW Mediterranean Sea)

In the area surrounding the Ebro Delta, similar to the rest of the north-western Mediterranean Sea, the sardine (Sardina pilchardus), one of the most exploited small pelagic fishes, has suffered a decreasing trend in abundance and biomass in the last decade, with low values in evidence since 2007. The dependence of this species on environmental factors makes it vulnerable to environmental changes; consequently, the abundance of the species is highly variable. Using segmented regression, we evaluated the presence of discontinuities in the temporal pattern of the seasonally adjusted landings per unit effort (LPUE), which was used as a proxy for abundance, between 2000 and 2013. The results suggested a sudden increase in mid-2005, followed by a sharp decrease starting in 2006. A generalized additive mixed model (GAMM), incorporating the linear correlation structure, was used to identify relationships between the seasonally adjusted LPUE and trends of the Western Mediterranean Oscillation index (WeMOI), sea surface temperature (SST), salinity (SAL) and the Zonal and Meridional Currents (ZC and MC, respectively). The variance inflation factors (VIFs) were calculated between all environmental variables to avoid high-dimensional collinearities. The final GAMM, selected using the Akaike information criterion, indicated that positive WeMOI values, which favour the productivity of the area, along with SAL (at ca. 38) and a northward-flowing MC, favoured LPUE. Our results, obtained by applying a method in which variation due to season, non-linearity, autocorrelation and collinearity of the covariates was taken into account, provided further evidence of the dependence of the sardine population upon specific hydrographic variables.     

Metabolism of DMSP, DMS and DMSO by the cultivable bacterial community associated with the DMSP-producing dinoflagellate Scrippsiella trochoidea

Bacterial species associated with the dimethylsulfoniopropionate (DMSP)-producing phytoplankton Scrippsiella trochoidea were cultured and identified, with the aim of establishing their ability to metabolise DMSP, dimethylsulfide (DMS) and dimethylsulfoxide (DMSO). Results demonstrate that of the cultivable bacteria only α-Proteobacteria were capable of producing DMS from DMSP. The concentration of DMSP was shown to affect the amount of DMS produced. Lower DMSP concentrations (1.5?μmol?dm^?3) were completely assimilated, whereas higher concentrations (10?μmol?dm^?3) resulted in increasing amounts of DMS being produced. By contrast to the restricted set of bacteria that metabolised DMSP,?~?70% of the bacterial isolates were able to ‘consume’ DMS. However, 98-100% of the DMS removed was accounted for as DMSO. Notably, a number of these bacteria would only oxidise DMS in the presence of glucose, including members of the γ-Proteobacteria and Bacteroidetes. The observations from this study, coupled with published field data, identify DMS oxidation to DMSO as a major transformation pathway for DMS, and we speculate that the fate of DMS and DMSP in the field are tightly coupled to the available carbon produced by phytoplankton.     

Occurrence of the pugnose pipefish Bryx dunckeri in the Sargasso Sea

Juvenile specimens of the pugnose pipefish, Bryx dunckeri, were collected during a multipurpose research survey conducted within the Sargasso Sea Subtropical Convergence Zone, extending the known distribution range of this species to include open ocean areas of the Western North Atlantic. Novel spatial data are of scientific interest as information on the distribution, population structure, and population size of this species is limited. Additionally, we present detailed photographs and morphological data on the collected specimens. The results are discussed in relation to the dispersal abilities and population structure in syngnathids.     

Studies on the small invertebrate plankton of the Sargasso Sea

During the German Eel Expedition in Spring 1979, the horizontal and vertical distribution of the invertebrate plankton was studied in the epipelagic zone of the western central Sargasso Sea, based on 55 µm and 100 µm mesh net samples. In the isothermal waters north of the thermal front, plankton biomass was on average 2–3 times higher than in the warmer stratified waters south of the front. With regard to the fraction of small invertebrates (nauplii and microcopepods) the differences in numerical abundance between the two areas were similar to those reported in the literature for other size ranges of organisms. No divergency was obvious in the plankton composition in terms of major taxonomic groups and size classes. In both parts of the area, organisms smaller than 400 µm, which form a fraction not quantitatively sampled by the conventional 200 µm or 300 µm mesh nets, accounted for 71–92 % of the total number of organisms in the 55 µm net samples and for more than 50 % in the 100 µm net samples. Average concentrations of the potential food supply for early larval fish stages in the upper 100 m appear to be comparable with values reported in the literature for areas well known for larval fish development, such as the California Current.     

Distribution ofSargassum natans and some of its epibionts in the Sargasso Sea

Sargassum was collected during the Sargasso Sea Eel Expedition in Spring 1979. On average, the morphological form typeSargassum natans (I) made up 85 % of the total wet weight of the samples. South of the thermal front, larger amounts of weeds were observed. Here, the bladder size ofS. natans (I) was significantly smaller (surface 47±7 mm²) than in the northern part (surface: 64±15 mm²), while phylloids showed no differences. The composition and density of some epibionts were examined.Membranipora tuberculata (Bryozoa),Clytia noliformis (Hydrozoa) and the calcarious algae Melobesia sp. (Rhodophyta) were studied quantitatively according to different features at 17 stations.M. tuberculata was the most abundant epibiont followed byC. noliformis. Compared with these species, "Melobesia sp." occurred in considerably lower quantities.M. tuberculata showed a preference for bladders rather than phylloids;C. noliformis was found more frequently on phylloids than on bladders. "Melobesia sp." did not show any preference. Frequency and abundance of these epibionts were higher north of the thermal front than south of this front. North of the frontS. natans (I) was less abundant but bladders were larger.     

Characterization of a DMSP-degrading bacterial isolate from the Sargasso Sea

A bacterium which cleaves dimethylsulfoniopropionate (DMSP) to form dimethylsulfide (DMS) was isolated from surface Sargasso Sea water by a DMSP enrichment technique. The isolate, here designated LFR, is a Gram-negative, obligately aerobic, rod-shaped, carotenoid-containing bacterium with a DNA G+C content of 70%. Sequencing and comparison of its 16S ribosomal ribonucleic acid (rRNA) with that of known eubacteria revealed highest similarity (91% unrestricted sequence similarity) to Roseobacter denitrificans (formerly Erythrobacter species strain OCh114), an aerobic, bacteriochlorophyll-containing marine representative of the -Proteobacteria. However, physiological differences between the two bacteria, and the current lack of other characterized close relatives, preclude assignment of strain LFR to the Roseobacter genus. Screening of fifteen characterized marine bacteria revealed only one, Pseudomonas doudoroffii, capable of degrading DMSP to DMS. Strain LFR is deposited with the American Type Culture Collection (ATCC 51258) and 16S rRNA sequence data are available under GenBank accession number 15345.Contribution no. 8337 of the Woods Hole Oceanographic Institution     

Macroscale patterns of the biological cycling of dimethylsulfoniopropionate (DMSP) and dimethylsulfide (DMS) in the Northwest Atlantic

The influence of the seasonal development of microplankton communities on the cycling of dimethylsulfide (DMS) and its precursor dimethylsulfoniopropionate (DMSP) was investigated along a South–North gradient (36–59^°N) in the Northwest (NW) Atlantic Ocean. Three surveys allowed the sampling of surface mixed layer (SML) waters at stations extending from the subtropical gyre to the Greenland Current during May, July and October 2003. Pools and transformation rates of DMSP and DMS were quantified and related to prevailing physical and biochemical conditions, phytoplankton abundance and taxonomic composition, as well as bacterioplankton abundance and leucine uptake. The South–North progression of the diatom bloom, a prominent feature in the NW Atlantic, did not influence the production of DMS whereas conditions in the N Atlantic Drift lead to a persistent bloom of DMSP-rich flagellate-dominated phytoplankton community and high net DMS production rates. Macroscale patterns of the observed variables were further explored using principal component analysis (PCA). The first axis of the PCA showed a strong association between the spatio-temporal distribution of DMSP and the abundance of several phytoplankton groups including dinoflagellates and prymnesiophytes, as well as with microbial-mediated DMSP_d consumption and yields and rates of the conversion of DMSP into DMS. The second axis revealed a strong association between concentrations of DMS and SML depth and photosynthetically active radiation, a result supporting the prominent role of solar radiation as a driver of DMS dynamics.