Distinct protistan assemblages characterize the euphotic zone and deep sea (2500 m) of the western North Atlantic (Sargasso Sea and Gulf Stream)

Protistan diversity was characterized at three locations in the western North Atlantic (Sargasso Sea and Gulf Stream) by sequencing 18S rRNA genes in samples from euphotic (< or = 125 m) and bathypelagic depths (2500 m). A total of 923 partial-length protistan sequences were analysed, revealing 324 distinct operational taxonomic units (OTUs) determined by an automated OTU-calling program set to 95% sequence similarity. Most OTUs were comprised of only one or two sequences suggesting a large but rare pool of protistan diversity. Many OTUs from both depth strata were associated with recently described novel alveolate and stramenopile lineages while many OTUs from the bathypelagic were affiliated with Acantharea, Polycystinea and Euglenozoa and were not observed in euphotic zone libraries. Protistan assemblages from the euphotic zone and the deep sea were largely composed of distinct OTUs; only 28 of the 324 protistan OTUs were detected in both shallow and deep sea clone libraries. The diversity of protistan assemblages in the deep sea was distinctly lower than the diversity of euphotic zone assemblages. Protistan assemblages from the Gulf Stream were the most diverse for either depth strata. Overall, protistan assemblages from different stations but comparable depths were more similar than the assemblages from different depths at the same station. These data suggest that particular groups of protistan OTUs formed distinct 'shallow' and 'deep-sea' assemblages across widely spaced oceanic locales.     

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.     

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.     

Diel activity of littoral and epipelagic teleost fishes in the Mediterranean Sea

Reviews in Fish Biology and Fisheries - Diel activity patterns are an important aspect of behavioural ecology, yet summarising works on diel activity patterns of fishes are lacking for several...     

Distribution of cephalopods in the upper epipelagic northwestern Bering Sea in autumn

In the northwestern Bering Sea in autumn, the epipelagic cephalopod community was represented by the boreal fauna, and was found to be composed of three families and nine species of the order Teuthida: Gonatidae (Berryteuthis magister, Boreoteuthis borealis, Gonatopsis japonicus, Gonatus madokai, Gonatus kamtschaticus, Gonatus onyx, and Gonatus pyros), Chiroteuthidae (Chiroteuthis calyx) and Onychoteuthidae (Onychoteuthis borealijaponica). Two pelagic gonatid species (B. borealis and G. kamtschaticus) dominated the cephalopod community in the upper 50 m. The distribution patterns of B. borealis and G. onyx were associated with diel vertical migrations of these squid. The distribution of two distinct size groups of G. kamtschaticus suggested ontogenetic migration of larger squid to deeper layers, and adds to previous data suggesting that this species may be a heterogeneous assemblage. Demersal B. magister rarely occurred in the surface waters. The occurrence of maturing O. borealijaponica in the southern marine area indicated that these were occasional seasonal migrants from the ocean. The occurrence of juvenile C. calyx suggested that these squid may conduct vertical forage migrations from deep waters to the surface layers.     

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).     

Vertical segregation of holoplanktonic molluscs in the epipelagic layer, southern Gulf of Mexico

The small-scale vertical distribution of five genera of holoplanktonic molluscs inhabiting the upper oceanic layer (0–105 m) was analysed to test whether evident distribution patterns could be attributed to habitat partitioning. Zooplankton samples were taken over neritic waters during the day and night using a 505-μm multiple closing net at five levels (0–6, 6–12, 12–18, 45–55 and 95–105 m) of the water column. Flowmeters were placed in each net to estimate the amount of filtered water. From the 55,654 identifiable specimens of holoplanktonic molluscs, only 6.2 % were in juvenile stage, and Cavolinia, Diacavolinia, Diacria, Oxygyrus and Clio were the most abundant genera. Adults of these genera comprised 3 % of the total abundance. The abundance data were examined using a spatial segregation index, and its significance was tested with null model methods based on Monte Carlo randomizations. Results indicated that adults showed a much more overlapped distribution in the water column than the in the earlier stages. Indeed, juveniles of Cavolinia, Diacavolinia and Oxygyrus were mainly found in the 0–18-m layer, whereas Diacria and Clio were recorded in the 45–105-m stratum. Null model arguments revealed a significant vertical segregation among them. Potential ecological factors involve preferential spawning areas of adults, avoidance of competition for feeding and spatial resources, use of visual capabilities in searching prey, brood protection and avoidance of strong turbulence conditions.     

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.     

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.     

Community differentiation of bacterioplankton in the epipelagic layer in the South China Sea

The South China Sea (SCS) is the largest marginal sea in the western tropical Pacific Ocean and is characterized by complex physicochemical environments. To date, the biogeographic patterns of the microbial communities have rarely been reported at a basin scale in the SCS. In this study, the bacterial assemblages inhabiting the epipelagic zone across 110°E to 119°E along 14°N latitude were uncovered. The vertical stratification of both bacterial taxa and their potential functions were revealed. These results suggest that the water depth‐specific environment is a driver of the vertical bacterioplankton distribution. Moreover, the bacterial communities were different between the eastern stations and the western stations, where the environmental conditions were distinct. However, the mesoscale eddy did not show an obvious effect on the bacterial community due to the large distance between the sampling site and the center of the eddy. In addition to the water depth and longitudinal location of the samples, the heterogeneity of the phosphate and salinity concentrations also significantly contributed to the variance in the epipelagic bacterial community in the SCS. To the best of our knowledge, this study is the first to report that the variability in epipelagic bacterioplankton is driven by the physicochemical environment at the basin scale in the SCS. Our results emphasize that the ecological significance of bacterioplankton can be better understood by considering the relationship between the biogeographic distribution of bacteria and the oceanic dynamics processes.     

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.     

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.     

Eggs of pelagic fish from the Sargasso Sea with special reference to Anguilliformes

Pelagic fish eggs from IKMT hauls, taken during the 1979 Sargasso Sea Expedition, were sorted and classified according to structural aspects. 13 types were distinguished, one of them classified as exocoetid, two of them as anguilliform. One of the anguilliform egg types could be determined as belonging toDerichthys serpentinus.     

In situ nitrogen fixation associated with seagrasses in the Gulf of Elat (Red Sea)

In situ nitrogen fixation associated with the seagrass Halophila stipulacea, at the northern Gulf of Elat (Red Sea), is eight to ten times higher than that of nearby plant-free areas. A daily cycle of nitrogen fixation is evident, with rates during the day being seven times greater than during the night. Removal of seagrass leaves only from a patch within a seagrass bed gradually decreases nitrogen fixation activity, reaching the rates of plant-free areas after ten hours. A method devised for the in situ measurement of nitrogen fixation rates using belljars is described in detail. Nitrogen fixation rates in situ are higher than in the laboratory and lack the lag period typical to laboratory measurements. In laboratory experiments using intact plant samples, glucose enhances nitrogen fixation rates both in light and dark. Photosystem II inhibitor (3-3,4-dichloro-phenyl-1,1-dimethylurea) doubles nitrogen fixation rates in light. Both field and laboratory results indicate that light is essential for nitrogen fixation activity in the H. stipulacea bed possibly through its effect on cyanobacterial population that occupy the aerobic niches of the phyllosphere and on photosynthetic Rhodospirillacean bacteria that inhabit the anaerobic ones. Nitrogen fixation rates evident in H. stipulacea beds in situ account for a considerable portion of the biomass production by the seagrasses. The dependence of high nitrogenase activity by the diazotrophs on the presence of the seagrasses indicates the great importance of the seagrass community to the nitrogen cycle in its highly oligotrophic surroundings of the Gulf of Elat.     

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     

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.