Spatial Structure and Distribution of Small Pelagic Fish in the Northwestern Mediterranean Sea

Understanding the ecological and anthropogenic drivers of population dynamics requires detailed studies on habitat selection and spatial distribution. Although small pelagic fish aggregate in large shoals and usually exhibit important spatial structure, their dynamics in time and space remain unpredictable and challenging. In the Gulf of Lions (north-western Mediterranean), sardine and anchovy biomasses have declined over the past 5 years causing an important fishery crisis while sprat abundance rose. Applying geostatistical tools on scientific acoustic surveys conducted in the Gulf of Lions, we investigated anchovy, sardine and sprat spatial distributions and structures over 10 years. Our results show that sardines and sprats were more coastal than anchovies. The spatial structure of the three species was fairly stable over time according to variogram outputs, while year-to-year variations in kriged maps highlighted substantial changes in their location. Support for the McCall''s basin hypothesis (covariation of both population density and presence area with biomass) was found only in sprats, the most variable of the three species. An innovative method to investigate species collocation at different scales revealed that globally the three species strongly overlap. Although species often co-occurred in terms of presence/absence, their biomass density differed at local scale, suggesting potential interspecific avoidance or different sensitivity to local environmental characteristics. Persistent favourable areas were finally detected, but their environmental characteristics remain to be determined.     

Draft Genome Sequence of the Marine Streptomyces sp. Strain AA1529, Isolated from the Yellow Sea

Here we report the draft genome sequence of a Streptomyces strain, AA1529, isolated from marine sediment from the Yellow Sea. Its genome contains a subset of unique genes and gene clusters that encode diverse secondary metabolites, suggesting great potential as a source for the discovery of novel gene clusters and bioactive compounds.     

Draft Genome Sequence of the Marine Actinomycete Streptomyces sulphureus L180, Isolated from Marine Sediment

Marine-derived actinobacteria are rich sources of valuable natural products and industrial enzymes for biotechnology applications. The marine-derived Streptomyces sulphureus strain L180 was isolated from the marine sediment in a sea cucumber farm at a depth of about 10 m in Dalian, China, and its 16S rRNA gene sequence was determined to have the highest identity to that of Streptomyces sulphureus NRRL B-1627(T) (99.65%). Here, we report the draft genome sequence of this strain.     

Structure of the Marine Siphovirus TW1: Evolution of Capsid-Stabilizing Proteins and Tail Spikes

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Genome Sequence of the Oligotrophic Marine Gammaproteobacterium HTCC2143, Isolated from the Oregon Coast

Strain HTCC2143 was isolated from Oregon Coast surface waters using dilution-to-extinction culturing. Here we present the genome of strain HTCC2143 from the BD1-7 clade of the oligotrophic marine Gammaproteobacteria group. The genome of HTCC2143 contains genes for carotenoid biosynthesis and proteorhodopsin and for proteins that have potential biotechnological significance: epoxide hydrolases, Baeyer-Villiger monooxygenases, and polyketide synthases.Strain HTCC2143 was sampled and isolated from surface waters (depth, 10 m) off the Coastal Pacific Ocean, Newport, OR (44°36′0N, 124°6′0W). In the course of dilution-to-extinction culture studies on coastal microbial communities, strain HTCC2143 was isolated in a pristine seawater-based medium (2). Phylogenetic analysis of 16S rRNA gene sequences placed strain HTCC2143 in the BD1-7 clade of the oligotrophic marine Gammaproteobacteria (OMG) group (2) and indicated that it is related to Dasania marina, isolated from Arctic marine sediment (3, 8). The HTCC2143 16S rRNA gene sequence is 95.3% similar to that of D. marina ({type:entrez-nucleotide,attrs:{text:AY771747,term_id:157384056,term_text:AY771747}}AY771747) and is 96.6% similar to that of environmental gene clone 20m-45 ({type:entrez-nucleotide,attrs:{text:GU061297,term_id:262072220,term_text:GU061297}}GU061297), taken from intertidal beach seawater of the Yellow Sea, South Korea. Other closer relatives of HTCC2143 included uncultured gammaproteobacterial clones from seafloor lava (clone P0X3b5B06 from Hawaii South Point X3, {type:entrez-nucleotide,attrs:{text:EU491383,term_id:169640639,term_text:EU491383}}EU491383; 96.3%) (9), deep-sea sediment (Ucp1554 from the South Atlantic Ocean, Cape Basin, {type:entrez-nucleotide,attrs:{text:AM997645,term_id:283475537,term_text:AM997645}}AM997645; 95.9%) (10), Yellow Sea sediment (95.8%; D8S-33, {type:entrez-nucleotide,attrs:{text:EU652559,term_id:186462116,term_text:EU652559}}EU652559), and Arctic sediment (from Kings Bay, Svalbard, Norway; clone SS1_B_07_55, {type:entrez-nucleotide,attrs:{text:EU050825,term_id:156453922,term_text:EU050825}}EU050825; 95.7%).Genomic DNA was prepared at Oregon State University and sequenced by the J. Craig Venter Institute. The finished contigs were automatically annotated with a system based on the program GenDB (5) and manually annotated as described in previous reports (7, 12). The annotation is available at http://bioinfo.cgrb.oregonstate.edu/microbes/. The draft genome of strain HTCC2143 comprises 3,925,629 bases and 3,662 predicted coding sequences with a G+C content of 47.0%. The genome of HTCC2143 was predicted to contain 40 tRNAs, 1 16S rRNA, 2 5S rRNAs, and 2 23S rRNA genes. Four genes for selenocysteine metabolism were found, including a selenophosphate-dependent tRNA 2-selenouridine synthase and an l-seryl-tRNA(Sec) selenium transferase (EC 2.9.1.1).Strain HTCC2143 had genes for a complete tricarboxylic acid cycle, glycolysis, a pentose phosphate pathway, and an Entner-Doudoroff pathway. Genes were present for a high-affinity phosphate transporter and a pho regulon for sensing of environmental inorganic phosphate availability, as well as genes from the NUDIX (nucleoside diphosphate linked to some other moiety X) hydrolase domain family (1) that reflects the metabolic complexity of prokaryotes (4). Genes for ammonium transporters, nitrate reductase, and sulfate reductase were also present in the HTCC2143 genome.Carotenoid and proteorhodopsin genes were also found in the genome, as well as genes for polyketide synthase modules and related proteins. Carotenoid and proteorhodopsin genes were reported previously from another member of the OMG group, strain HTCC2207, a SAR92 clade isolate (11). HTCC2143 also encoded two epoxide hydrolases, two cyclohexanone monooxygenases (CHMOs) and a cyclododecanone monooxygenase (CDMO). CDMOs and CHMOs are members of the Baeyer-Villiger monooxygenase (BVMO) family. BVMOs are “green” alternatives to the chemically mediated Baeyer-Villiger reactions that allow the conversion of ketones into esters or of cyclic ketones into lactones (6).This genome provides further evidence that dilution-to-extinction culturing methods that make use of low-nutrient media that are similar to the conditions of the natural environment can result in the isolation of novel, environmentally significant organisms with potential biotechnological value (13).     

Elucidation of Structure of Lipid A from the Marine Gram-Negative Bacterium Pseudoalteromonas haloplanktis ATCC 14393T

The chemical structure of lipid A, from the marine -proteobacterium Pseudoalteromonas haloplanktis 14393, a main product of lipopolysaccharide hydrolysis (1% AcOH), was determined using chemical methods and NMR spectroscopy. The lipid A was shown to be -1,6-glucosaminobiose 1,4-diphosphate acylated with two (R)-3-hydroxyalkanoic acid residues at C3 and C3 and amidated with one (R)-3-hydroxydodecanoyl and one (R)-3-dodecanoyloxydodecanoyl residue at N2 and N2, respectively.     

Historical Changes in Marine Resources,Food-web Structure and Ecosystem Functioning in the Adriatic Sea,Mediterranean

The Mediterranean Sea has been strongly influenced by human activities for millennia. Although the environmental history of its surrounding terrestrial ecosystems has received considerable study, historical changes in its marine realm are less known. We used a multidisciplinary approach combining paleontological, archeological, historical, fisheries, and ecological data to reconstruct past changes in marine populations, habitats, and water quality in the Adriatic Sea. Then, we constructed binary food webs for different historical periods to analyze possible changes in food-web structure and functioning over time. Our results indicate that human activities have influenced marine resource abundance since at least Roman times and accelerated in the nineteenth and twentieth centuries. Today, 98% of traditional marine resources are depleted to less than 50% of former abundance, with large (>1 m) predators and consumers being most affected. With 37% of investigated species rare and 11% extirpated, diversity has shifted towards smaller, lower trophic-level species, further aggravated by more than 40 species invasions. Species providing habitat and filter functions have been reduced by 75%, contributing to the degradation of water quality and increased eutrophication. Increased exploitation and functional extinctions have altered and simplified food-web structure over time, especially by changing the proportions of top predators, intermediate consumers, and basal species. Moreover, simulations of species losses indicate that today’s ecosystems may be less robust to species extinctions than in the past. Our results illustrate the long-term and far-reaching consequences human activities can have on marine food webs and ecosystems.     

Genome Sequence of the Protease-Producing Bacterium Rheinheimera nanhaiensis E407-8T,Isolated from Deep-Sea Sediment of the South China Sea

The protease-producing bacterium E407-8^T was isolated from deep-sea sediment of the South China Sea and has been identified recently as representing a new species, Rheinheimera nanhaiensis. The draft genome of R. nanhaiensis E407-8^T consists of 3,987,205 bp and contains 3,730 predicated protein-coding genes, including 82 extracellular peptidase genes.     

Identification of Bacterial Strains Isolated from the Mediterranean Sea Exhibiting Different Abilities of Biofilm Formation

The Mediterranean Sea has rarely been investigated for the characterization of marine bacteria as compared to other marine environments such as the Atlantic or Pacific Ocean. Bacteria recovered from inert surfaces are poorly studied in these environments, when it has been shown that the community structure of attached bacteria can be dissimilar from that of planktonic bacteria present in the water column. The objectives of this study were to identify and characterize marine bacteria isolated from biofilms developed on inert surfaces immersed in the Mediterranean Sea and to evaluate their capacity to form a biofilm in vitro. Here, 13 marine bacterial strains have been isolated from different supports immersed in seawater in the Bay of Toulon (France). Phylogenetic analysis and different biological and physico-chemical properties have been investigated. Among the 13 strains recovered, 8 different genera and 12 different species were identified including 2 isolates of a novel bacterial species that we named Persicivirga mediterranea and whose genus had never been isolated from the Mediterranean Sea. Shewanella sp. and Pseudoalteromonas sp. were the most preponderant genera recovered in our conditions. The phenotypical characterization revealed that one isolate belonging to the Polaribacter genus differed from all the other ones by its hydrophobic properties and poor ability to form biofilms in vitro. Identifying and characterizing species isolated from seawater including from Mediterranean ecosystems could be helpful for example, to understand some aspects of bacterial biodiversity and to further study the mechanisms of biofilm (and biofouling) development in conditions approaching those of the marine environment.     

Genome sequences of six Pseudoalteromonas strains isolated from Arctic sea ice

Yu et al. (Polar Biol. 32:1539-1547, 2009) isolated 199 Pseudoalteromonas strains from Arctic sea ice. We sequenced the genomes of six of these strains, which are affiliated to different Pseudoalteromonas species based on 16S rRNA gene sequences, facilitating the study of physiology and adaptation of Arctic sea ice Pseudoalteromonas strains.     

The Phenolic Contents and Antimicrobial Activities of Some Marine Algae from the Mediterranean Sea (Algeria)

In this study, three marine algae collected from western coast of algerian mediteranean sea (Ulva lactuca, Dictyota dichotoma, and Corallina elongata) were tested using the agar-well diffusion method for their production of antibacterial and antifungal agents on various organisms that cause diseases of humans and plants (Eschirichia coli ATCC 25922, Staphylococcus aureus ATCC 25923, Salmonella sp, Candida albicans, and Penicillium sp.). The total phenol content and antimicrobial activity were determined using different crude seaweeds extracts (methanol, diethylether, and chloroform). The results show that the chloroform extracts of (Ulva lactuca and Corallina elongata) had the highest activity against E. coli and Salmonella sp. The methanol extract obtained from (Ulva lactuca, Dictyota dichotoma, and Corallina elongata) showed antifungal activity for Candida albicans. The results of the study revealed that the seaweeds from Algeria appear to have immense potential as a source of antibacterial and antifungal compounds; they can be used in treating diseases caused by these organisms.     

Incidence of Plasmids in Marine Vibrio spp. Isolated from an Oil Field in the Northwestern Gulf of Mexico

Presumptive marine Vibrio spp. were collected from an operational oil field and control site located in the northwestern Gulf of Mexico. Of 440 isolates analyzed for the presence of extrachromosomal deoxyribonucleic acid elements or plasmids by using the cleared lysate and agarose gel techniques, 31% showed distinct plasmid bands on agarose gels. A majority of the plasmids detected were estimated to have molecular masses of 10 × 10⁶ or less. Multiple plasmids were observed in approximately half of the plasmid-containing strains. A number of isolates contained plasmids with similar banding and mobility patterns. The oil field area had noticeably more plasmid-containing strains (35 versus 23% in the control site) and a greater number of plasmids per plasmid-containing strain (an average of 2.5 plasmids, versus 1.5 in the control site). Oil field discharges might have resulted in increased plasmid incidence and diversity.     

Photoacclimation of Prochlorococcus sp. (Prochlorophyta) Strains Isolated from the North Atlantic and the Mediterranean Sea

Two Atlantic (SARG and NATL1) strains and one Mediterranean (MED) strain of Prochlorococcus sp., a recently discovered marine, free-living prochlorophyte, were grown over a range of "white" irradiances (lg) and under low blue light to examine their photoacclimation capacity. All three strains contained divinyl (DV) chlorophylls (Chl) a and b, both distinguishable from "normal" Chls by their red-shifted blue absorption maximum, a Chl c-like pigment at low concentration, zeaxanthin, and [alpha]-carotene. The presence of two phaeophytin b peaks in acidified extracts from both Atlantic strains grown at high lg suggests that these strains also had a normal Chl b-like pigment. In these strains, the total Chl b to DV-Chl a molar ratio decreased from about 1 at 7.5 [mu]mol quanta m-2 s-1 to 0.4 to 0.5 at 133 [mu]mol quanta m-2 s-1. In contrast, the MED strain always had a low DV-Chl b to DV-Chl a molar ratio, ranging between 0.13 at low lg and 0.08 at high lg. The discrepancies between the Atlantic and MED strains could result from differences either in the number of light-harvesting complexes (LHC) II per photosystem II or in the Chl b-binding capacity of the apoproteins constituting LHC II. Photosynthesis was saturated at approximately 5 fg C(fg Chl)-1 h-1 or 6 fg C cell-1 h-1, and growth was saturated at approximately 0.45 d-1 for both MED and SARG strains at 18[deg]C, but saturating irradiances differed between strains. Atlantic strains exhibited increased light-saturated rates and quantum yield for carbon fixation under blue light.     

Pelagibacterium nitratireducens sp.nov., A Marine Alphaproteobacterium Isolated from the East China Sea

A Gram-negative, rod-shaped, non-spore-forming aerobic bacterium, motile with a single polar flagellum, strain JLT2005^T, was isolated from surface seawater collected from the East China Sea and formed ivory white colonies on a rich organic medium. The strain was positive for catalase, oxidase, and urease. It grew in the presence of 0–12 % (w/v) NaCl (optimum 5 %), at 20–35 °C (optimum 25 °C), or at pH 6–10 (optimum pH 9). The major fatty acids (>10 %) were C_18:1ω7c, C_19:0ω8c cyclo, C_16:0, and C_18:0. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and five unidentified glycolipids. Ubiquinone-10 and Ubiquinone-11 were present as the major quinones. The DNA G+C content was 74.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain JLT2005^T belongs to the genus Pelagibacterium in the family Hyphomicrobiaceae, class Alphaproteobacteria. The closest neighbors were Pelagibacterium halotolerans B2^T (98.7 % similarity) and Pelagibacterium luteolum 1_C16_27^T (97.1 % similarity). DNA–DNA relatedness values of strain JLT2005^T with P. halotolerans B2^T and with P. luteolum 1_C16_27^T were 31.6 and 25 %. Evidence from genotypic, chemotaxonomic, and phenotypic data shows that strain JLT2005^T represents a novel species of the genus Pelagibacterium, for which the name Pelagibacterium nitratireducens sp. nov is proposed. The type strain is JLT2005^T (=CGMCC 1.10829^T =JCM 17767^T).     

Marine molluscs and fish as biomarkers of pollution stress in littoral regions of the Red Sea, Mediterranean Sea and North Sea

The intensive development of industry and urban structures along the seashores of the world, as well as the immense increase in marine transportation and other activities, has resulted in the deposition of thousands of new chemicals and organic compounds, endangering the existence of organisms and ecosystems. The conventional single biomarker methods used in ecological assessment studies cannot provide an adequate base for environmental health assessment, management and sustainability planning. The present study uses a set of novel biochemical, physiological, cytogenetic and morphological methods to characterize the state of health of selected molluscs and fish along the shores of the German North Sea, as well as the Israeli Mediterranean and Red Sea. The methods include measurement of activity of multixenobiotic resistance-mediated transporter (MXRtr) and the system of active transport of organic anions (SATOA) as indicators of antixenobiotic defence; glutathione S-transferase (GST) activity as an indicator of biotransformation of xenobiotics; DNA unwinding as a marker of genotoxicity; micronucleus test for clastogenicity; levels of phagocytosis for immunotoxicity; cholinesterase (ChE) activity and level of catecholamines as indicators of neurotoxicity; permeability of external epithelia to anionic hydrophilic probe, intralysosomal accumulation of cationic amphiphilic probe and activity of non-specific esterases as indicators of cell/tissue viability. Complete histopathological examination was used for diagnostics of environmental pathology. The obtained data show that the activity of the defensive pumps, MXRtr and SATOA in the studied organisms was significantly higher in the surface epithelia of molluscs from a polluted site than that of the same species from control, unpolluted stations, providing clear evidence of response to stress. Enhanced frequency of DNA lesions (alkaline and acidic DNA unwinding) and micronucleus-containing cells was significantly higher in samples from polluted sites in comparison to those from the clean sites that exhibited genotoxic and clastogenic activity of the pollutants. In all the studied molluscs a negative correlation was found between the MXRtr levels of activity and the frequency of micronucleus-containing hemocytes. The expression of this was in accordance with the level of pollution. The complete histopathological examination demonstrates significantly higher frequencies of pathological alterations in organs of animals from polluted sites. A strong negative correlation was found between the frequency of these alterations and MXRtr activity in the same specimens. In addition to these parameters, a decrease in the viability was noted in molluscs from the polluted sites, but ChE activities remained similar at most sites. The methods applied in our study unmasked numerous early cryptic responses and negative alterations of health in populations of marine biota sampled from the polluted sites. This demonstrates that genotoxic, clastogenic and pathogenic xenobiotics are present and act in the studied sites and this knowledge can provide a reliable base for consideration for sustainable development. Received: 2 March 1999 / Received in revised form: 2 August 1999 / Accepted: 3 August 1999     

Complete Genome Sequence of a Coxsackievirus B3 Isolated from a Sichuan Snub-Nosed Monkey

Coxsackievirus B3 (CVB3) is an enterovirus in the family Picornaviridae that is significant to human health, being associated with myocarditis, aseptic meningitis, and pancreatitis, among other conditions. In addition to humans, Sichuan snub-nosed monkeys can be infected and killed by CVB3. Here, we report the first complete genome sequence of a novel coxsackievirus B3 strain, SSM-CVB3, which was isolated from a deceased Sichuan snub-nosed monkey with severe myocarditis. Our findings may aid in understanding the evolutionary characteristics and molecular pathogenesis of this virus.     

New Data on Scleractinians from the Northwestern Sea of Japan

three species of scleractinians, individual caryophyllids Caryophyllia alaskensis, C. japonica, and the colonial dendrophyllid Dendrophyllia arbuscula were described for the first time for the Sea of Japan. The findings of these corals in different areas of Peter the Great Bay, Sea of Japan, allow us to expand their geographic range and the depth range of their distribution. The depth of inhabitation reached 1280 m for C. alaskensis and up to 15–3 m deep for D. arbuscula.