Structural analysis of SNARE motifs from sea perch, Lateolabrax japonicus by computerized approaches

Three cDNA sequences encoding four SNARE (N-ethylmaleimide-sensitive fusion protein attachment protein receptors) motifs were cloned from sea perch, and the deduced peptide sequences were analyzed for structural prediction by using 14 different web servers and softwares. The "ionic layer" structure, the three dimensional extension and conformational characters of the SNARE 7S core complex by using bioinformatics approaches were compared respectively with those from mammalian X-ray crystallographic investigations. The result suggested that the formation and stabilization of fish SNARE core complex might be driven by hydrophobic association, hydrogen bond among R group of core amino acids and electrostatic attraction at molecular level. This revealed that the SNARE proteins interaction of the fish may share the same molecular mechanism with that of mammal, indicating the universality and solidity of SNARE core complex theory. This work is also an attempt to get the protein 3D structural information which appears to be similar to that obtained through X-ray crystallography, only by using computerized approaches. (C) 2007 Elsevier Ltd. All rights reserved.

Vertical distribution of bacterial and archaeal communities along discrete layers of a deep-sea cold sediment sample at the East Pacific Rise (similar to 13 degrees N)

The community structure and vertical distribution of prokaryotes in a deep-sea (ca. 3,191 m) cold sediment sample (ca. 43 cm long) collected at the East Pacific Rise (EPR) similar to 13 degrees N were studied with 16SrDNA-based molecular analyses. Total community DNA was extracted from each of four discrete layers EPRDS-1, -2, -3 and -4 (from top to bottom) and 16S rDNA were amplified by PCR. Cluster analysis of DGGE profiles revealed that the bacterial communities shifted sharply between EPRDS-1 and EPRDS-2 in similarity coefficient at merely 49%. Twenty-three sequences retrieved from DGGE bands fell into 11 groups based on BLAST and bootstrap analysis. The dominant groups in the bacterial communities were Chloroflexi, Gamma proteobacteria, Actinobacterium and unidentified bacteria, with their corresponding percentages varying along discrete layers. Pairwise Fst (F-statistics) values between the archaeal clone libraries indicated that the archaeal communities changed distinctly between EPRDS-2 and EPRDS-3. Sequences from the archaeal libraries were divided to eight groups. Crenarchaea Marine Group I (MGI) was prevalent in EPRDS-1 at 83%, while Uncultured Crenarchaea group II B (UCII B) abounded in EPRDS-4 at 61%. Our results revealed that the vertically stratified distribution of prokaryotic communities might be in response to the geochemical settings and suggested that the sampling area was influenced by hydrothermalism. The copresence of members related to hydrothermalism and cold deep-sea environments in the microbial community indicated that the area might be a transitional region from hydrothermal vents to cold deep-sea sediments.

Concurrence of cat and tet genes in multiple antibiotic-resistant bacteria isolated from a sea cucumber and sea urchin mariculture farm in China

A basic understanding of abundance and diversity of antibiotic-resistant microbes and their genetic determinants is necessary for finding a way to prevent and control the spread of antibiotic resistance. For this purpose, chloramphenicol and multiple antibiotic-resistant bacteria were screened from a mariculture farm in northern China. Both sea cucumber and sea urchin rearing ponds were populated with abundant antibiotic-resistant bacteria, especially marine vibrios. Sixty-five percent chloramphenicol-resistant isolates from sea cucumber harbored a cat gene, either cat IV or cat II, whereas 35% sea urchin isolates harbored a cat gene, actually cat II. The predominant resistance determinant cat IV gene mainly occurred in isolates related to Vibrio tasmaniensis or Pseudoalteromonas atlantica, and the cat II gene mainly occurred in Vibrio splendidus-like isolates. All the cat-positive isolates also harbored one or two of the tet genes, tet(D), tet(B), or tet(A). As no chloramphenicol-related antibiotic was ever used, coselection of the cat genes by other antibiotics, especially oxytetracycline, might be the cause of the high incidence of cat genes in the mariculture farm studied.

Diversity, abundance and distribution of amoA-encoding archaea in deep-sea methane seep sediments of the Okhotsk Sea

The authors would like to thank Jin Sun, Jian Sun, Liangliang Kong, Nianshuang Wang, Chunhui Wang, Linbao Zhang and Ying Zhang for their assistance in the project. This work was supported by China Ocean Mineral Resources R&D Association grants DYXM-115-02-2-20 and DYXM-115-02-2-6, Hi-Tech Research and Development Program of China grant 2007AA091903, China National Natural Science Foundation grant 40576069, National Basic Research Program of China grant 2009CB219506 and the Fundamental Research Funds for the Central Universities of China grant 09CX05005A. M. G. K. was funded by incentive funds provided by the UofL-EVPR office and the US National Science Foundation (EF-0412129).

Diversity and spatial distribution of amoA-encoding archaea in the deep-sea sediments of the tropical West Pacific Continental Margin

The ecological characteristics of the deep-sea amoA-encoding archaea (AEA) are largely unsolved. Our aim was to study the diversity, structure and distribution of the AEA community in the sediments of the tropical West Pacific Continental Margin, to develop a general view of the AEA biogeography in the deep-sea extreme environment. Archaeal amoA clone libraries were constructed. Diverse and novel amoA sequences were identified, with the Bohol Sea, Bashi Strait and Sibuyan Sea harbouring the highest and the Bicol Shelf the lowest AEA diversity. Phylogenetic and statistical analyses illustrate a heterogeneous distribution of the AEA community, probably caused by the differential distribution of the terrestrial or estuarine AEA in the various sampling sites. The deep-sea sedimentary environments potentially harbour diverse and novel AEA in the tropical West Pacific Continental Margin. The stations in the Philippine inland seas (including station 3043) may represent AEA assemblages with various terrestrial influences and the stations connected directly to the open Philippine Sea may represent marine environment-dominant AEA assemblages. Our study indicates the potential importance of geological and climatic events in the transport of terrestrial micro-organisms to the deep-sea sedimentary environments, almost totally neglected previously.

Diversity and spatial distribution of sediment ammonia-oxidizing crenarchaeota in response to estuarine and environmental gradients in the Changjiang Estuary and East China Sea

Ammonia-oxidizing archaea (AOA) have recently been found to be potentially important in nitrogen cycling in a variety of environments, such as terrestrial soils, wastewater treatment reactors, marine waters and sediments, and especially in estuaries, where high input of anthropogenic nitrogen is often experienced. The sedimentary AOA diversity, community structure and spatial distribution in the Changjiang Estuary and the adjacent East China Sea were studied. Multivariate statistical analysis indicated that the archaeal amoA genotype communities could be clustered according to sampling transects, and the station located in an estuarine mixing zone harboured a distinct AOA community. The distribution of AOA communities correlated significantly with the gradients of surface-water salinity and sediment sorting coefficient. The spatial distribution of putative soil-related AOA in certain sampling stations indicated a strong impact of the Changjiang freshwater discharge on the marine benthic microbial ecosystem. Besides freshwater, nutrients, organic matter and suspended particles, the Changjiang Diluted Water might also contribute to the transport of terrestrial archaea into the seawater and sediments along its flow path.

Fine-scale vertical distribution of bacteria in the East Pacific deep-sea sediments determined via 16S rRNA gene T-RFLP and clone library analyses

Although the deep-sea sediments harbor diverse and novel bacteria with important ecological and environmental functions, a comprehensive view of their community characteristics is still lacking, considering the vast area and volume of the deep-sea sedimentary environments. Sediment bacteria vertical distribution and community structure were studied of the E272 site in the East Pacific Ocean with the molecular methods of 16S rRNA gene T-RFLP (terminal restriction fragment length polymorphism) and clone library analyses. Layered distribution of the bacterial assemblages was detected by both methods, indicating that the shallow sediments (40 cm in depth) harbored a diverse and distinct bacterial composition with fine-scale spatial heterogeneity. Substantial bacterial diversity was detected and nine major bacterial lineages were obtained, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Nitrospirae, Planctomycetes, Proteobacteria, and the candidate divisions OP8 and TM6. Three subdivisions of the Proteobacteria presented in our libraries, including the alpha-, gamma- and delta-Proteobacteria. Most of our sequences have low similarity with known bacterial 16S rRNA genes, indicating that these sequences may represent as-yet-uncultivated novel bacteria. Most of our sequences were related to the GenBank nearest neighboring sequences retrieved from marine sediments, especially from deep-sea methane seep, gas hydrate or mud volcano environments. Several sequences were related to the sequences recovered from the deep-sea hydrothermal vent or basalt glasses-bearing sediments, indicating that our deep-sea sampling site might be influenced to certain degree by the nearby hydrothermal field of the East Pacific Rise at 13A degrees N.

Characterization of a homogeneous taxonomic group of marine magnetotactic cocci within a low tide zone in the China Sea

Magnetotactic bacteria are a heterologous group of motile prokaryotes, ubiquitous in aquatic habitats and cosmopolitan in distribution. Here, we studied the diversity of magnetotactic bacteria in a seawater pond within an intertidal zone at Huiquan Bay in the China Sea. The pond is composed of a permanently submerged part and a low tide subregion. The magnetotactic bacteria collected from the permanently submerged part display diversity in morphology and taxonomy. In contrast, we found a virtually homogenous population of ovoid-coccoid magnetotactic bacteria in the low tide subregion of the pond. They were bilophotrichously flagellated and exhibited polar magnetotactic behaviour. Almost all cells contained two chains of magnetosomes composed of magnetite crystals. Intriguingly, the combination of restriction fragment length polymorphism analysis (RFLP) and sequencing of cloned 16S rDNA genes from the low tide subregion samples as well as fluorescence in situ hybridization (FISH) revealed the presence of a homogenous population. Moreover, phylogenetic analysis indicated that the Qingdao Huiquan low tide magnetotactic bacteria belong to a new genus affiliated with the alpha-subclass of Proteobacteria. This finding suggests the adaptation of the magnetotactic bacterial population to the marine tide.

Close coupling between phytoplankton growth and microzooplankton grazing in the western South China Sea

We conducted 28 dilution experiments during August-September 2007 to investigate the coupling of growth and microzooplankton grazing rates among ultraphytoplankton populations and the phytoplankton community and their responses to habitat variability (open-ocean oligotrophy, eddy-induced upwelling, and the Mekong River plume) in the western South China Sea. At the community level, standing stocks, growth, and grazing rates were strongly and positively correlated, and were related to the higher abundance of larger phytoplankton cells (diatoms) at stations with elevated chlorophyll concentration. Phytoplankton growth rates were highest (> 2 d(-1)) within an eastward offshore jet at 13 degrees N and at a station influenced by the river plume. Among ultraphytoplankton populations, Prochlorococcus dominated the more oceanic and oligotrophic stations characterized by generally lower biomass and phytoplankton community growth, whereas Synechococcus became more important in mesotrophic areas (eddies, offshore jet, and river plume). The shift to Synechococcus dominance reflected, in part, its higher growth rates (0.87 +/- 0.45 d(-1)) compared to Prochlorococcus (0.65 +/- 0.29 d(-1)) or picophytoeukaryotes (0.54 +/- 0.50 d(-1)). However, close coupling of microbial mortality rates via common predators is seen to play a major role in driving the dominance transition as a replacement of Prochlorococcus, rather than an overprinting of its steady-state standing stock.

The effects of spring-neap tide on the phytoplankton community development in the Jiaozhou Bay, China

The development of the phytoplankton community was studied in the Jiaozhou Bay during the spring to neap tide in August 2001, through three cruises and a 15 d continuous observation. This investigation indicates that diatom cell abundance increased sharply following the end of a spring tide, from 9 cells/cm(3) to a peak of 94 cells/cm(3). The dominant species composition and abundance show a quick species sequence from spring to neap tide, and the dominant species at the start phase is Skeletomena costatum, then changes to Chaetoceros curvisetus, finally it changes to Eucampia zodiacus. Silicate concentration increases during spring tide, as a result of nutrient replenishment from the water-sediment interface, its initial average concentration in neap tide is 1.39 mumol/dm(3) and reached the peak average concentration of 8.40 mumol/dm(3) in spring tide. But the nitrogen concentration dropped due to dilution by the low nitrogen seawater from the Huanghai Sea, its initial average concentration in neap tide is 67 mumol/dm(3) and decreased to the average concentration of 54 mumol/dm(3) in spring tide. The degree of silicon limitation was decreased and phytoplankton, especially diatoms, responds immediately after nutrient replenishment in the water column. Skeletonmea costatum, as one of the dominant species in the Jiaozhou Bay, shows a quicker response to nutrient availability than Eucampia zodiacus and Chaetoceros curvisetus. It is proposed that dominant species composition and water column stability synchronously determine the development of phytoplankton summer blooms in the Raozhou bay.

Grazing impact of copepods on phytoplankton in the Bohai Sea

During spring (April/May 1999) and autumn (September/October 1998) cruises in the Bohai Sea, China, copepods were the dominant components of mesozooplankton, the most abundant species being Calanus sinicus, Centropages mcmurrichi, Paracalanus parvus, Acartia bifilosa and Oithona similis. Pigment ingestion rates by three size classes of copepods (200-500, 500-1000 and > 1000 mum) were measured. In the south of the investigation area, gut pigment content (GPC), individual pigment-specific ingestion rates and grazing impacts on phytoplankton were lower in spring than in autumn. In the central area, GPC and individual pigment-specific ingestion rates were higher in spring than in autumn. The grazing impact on phytoplankton by the copepod assemblages was lower in spring than in autumn, however, because of the relatively smaller biomass in spring. In the western area where the Bohai Sea joins the Yellow Sea, GPC, individual pigment-specific ingestion rates and grazing impacts on phytoplankton were higher in spring than in autumn. Among the three size groups, the small-sized animals (200-500 mum) contributed more than 50% (range 38-98%) of the total copepod grazing during both cruises. The grazing impact on phytoplankton by copepods was equivalent to 11.9% (range 3.0-37.1%) of the chlorophyll-a standing stock and 53.3% (range 21.4-91.4%) of the primary production during the spring cruise. Grazing impact was equivalent to 6.3% (range 2.0-11.6%) of the chlorophyll-a standing stock and >100% (range 25.7-141.6%) of the primary production during the autumn cruise. The copepod community apparently consumed only a modest proportion of the standing stock of phytoplankton during spring and autumn blooms. They did, however, sometimes graze a significant proportion of daily primary production and hence were presumably able to limit the rate of further accumulation of phytoplankton, or even to prevent it. (C) 2003 Elsevier Ltd. All rights reserved.

Rapid changes in stocks of ciliate microzooplankton associated with a hurricane in the Bohai Sea (China)

The ciliate community in the Bohai Sea (China) was studied from 23 September to 7 October 1998. A hurricane struck the study area between the 2 grid station investigations; which were 6 d apart. The ciliate biomass decreased drastically after the hurricane. The surface ciliate biomass decreased from 0.2-12.3 to 0.02-2.8 mug C l(-1) and the water column ciliate biomass from 2-136 to 0.01-47 mg C m(-2). The ciliate biomass:chlorophyll ratios in the surface water were calculated to be 0.04 to 4.7 (1.41 on average) during the first grid investigation and 0.01 to 1.18 (0.26 on average) during the second grid investigation. Distinct patterns of temporal changes in ciliate abundances were found at different stations both before and after the hurricane.

Responses of a coastal phytoplankton community to increased nutrient input from the Changjiang (Yangtze) River

Nutrient input from the Changjiang River (Yangtze River) has been increasing dramatically since the 1960s. At the mouth of the Changjiang River, the nitrate concentration has increased about three-fold in 40 years, from 20.5 mu mol/L in the 1960s to 59.1 mu mol/L in the 1980s and to 80.6 mu mol/L in 1990-2004. Phosphate concentration increased by a factor of 30%, from 0.59 mu mol/L in the 1980s to 0.77 mu mol/L in 1990-2004. The increasing nitrate input has arisen mostly from the mid and lower reaches of the Changjiang River, where the river meets one of the most strongly developed agriculture areas in China. Responses of the coastal phytoplankton community to the increasing nutrient inputs are also seen in the available monitoring data. First, a trend of increasing phytoplankton standing stock from 1984 to 2002 appeared in the Changjiang River estuary and adjacent coastal waters, especially in late spring. Secondly, the proportion of diatoms in the whole phytoplankton community showed a decreasing trend from about 85% in 1984 to about 60% in 2000. Finally, red tides/harmful algal blooms increased dramatically in this area in terms of both number and scale. About 30-80 red tide events were recorded each year from 2000 to 2005 in the East China Sea. The scale of some blooms has been in excess of 10,000 km(2). (c) 2008 Elsevier Ltd. All rights reserved.

Changes in nitrogen and phosphorus and their effects on phytoplankton in the Bohai Sea

Systematic studies of the changes in dissolved inorganic nitrogen (DIN) and dissolved inorganic phosphorus (DIP) and their effects on phytoplankton over the last 30 years in the Bohai Sea are presented. The amount of sewage disposal, use of fertilizer and the Huanghe River runoff were found to have a significant influence on the DIN or DIP concentrations in the Bohai Sea over the last 30 years. Moreover, the changes in DIN and DIP resulted in changes in the limiting nutrients of phytoplankton in the Bohai Sea from nitrogen in the early 1980s to nitrogen-phosphorus in the late 1980s, and then to phosphorus after the 1990s. In addition, changes in nitrogen and phosphorus had a significant effect on the phytoplankton community structure. The half saturation constant (K (s)) was used to evaluate the effect of nutrients on the phytoplankton community structure in the Bohai Sea over the last 30 years. Cell abundance percentages of dominant phytoplankton species with high K (s) values for phosphorus and low K (s) values for nitrogen have decreased since the 1980s, while those of dominant phytoplankton species with low K (s) values for phosphorus and high K (s) values for nitrogen increased during this period.

Impact of microzooplankton and Calanus sinicus (Brodsky, 1962) on phytoplankton in the Yellow Sea during early summer

Dilution incubations and Calanus sinicus addition incubations were simultaneously conducted at five stations in the Yellow Sea in June of 2004 to evaluate the impact of microzooplankton and Calanus sinicus on phytoplankton based on the Chlorophyll a (Chl-a) levels. The Chl-a growth rates (k) ranged from 0.60-1.67 d(-1), while microzooplankton grazed the Chl-a at rates (g) of 0.29-0.62 d(t-1). The addition of C. sinicus enhanced the Chl-a growth rate (Z) by 0.004-0.037 d(-1) ind.(-1) L. C. sinicus abundance ranged from 84.1-160.9 ind. m(-3), which occupied 90.7%-99.1% of the copepod (> 500 mu m) population. The in-situ increase in phytoplankton by C. sinicus community was estimated to be 0.000 4-0.005 9 d(-1). These results showed that microzooplankton were the main grazers of phytoplankton, while C. sinicus induced a slight increase in the levels of phytoplankton.