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.

Palaeoenvironmental changes from pollen record in deep sea core PC-1 from northern Okinawa Trough, East China Sea during the past 24 ka

A pollen record of core PC-1 from the northern Okinawa Trough, East China Sea (ECS), provides information on vegetation and climate changes since 24 cal. kaBP. A total of 103 samples were palynologically analyzed at 8 cm intervals with a time resolution of 230 a. Four pollen zones are recognized: zone I (812-715 cm, 24.2-21.1 cal. kaBP), zone II (715-451 cm, 21.1-15.2 cal. kaBP), zone III (451-251 cm, 15.2-10.8 cal. kaBP), zone IV (251-0 cm, 10.8-0.3 cal. kaBP), corresponding to Late MIS 3, Last Glacial Maximum (LGM), deglaciation and Holocene, respectively. The LGM is characterized by the dominance of herbs, mainly Artemisia, and high pollen influx, implying an open vegetation on the exposed continental shelf and a cool and dry climate. The deglaciation is a climate warming stage with Pinus percentage increased and Artemisia percentage decreased and a rapid sea-level rise. The Holocene is characterized by predominance of tree pollen with rapid increase in Castanea-Castanopsis indicating the development of mixed evergreen and deciduous broad-leaved forest and a warm, humid climate. Low pollen influx during the Holocene probably implies submergence of the continental shelf and retreat of the pollen source area. The vegetation indicated by pollen assemblage found in this upper zone is consistent with the present vegetation found in Kyushu, Japan. Originating from the humid mountain area of North Luzon of the Philippines, Tasmania and New Zealand, Phyllocladus with sporadic occurrence throughout PC-1 core probably suggests the influence of Palaeo-Kuroshio Current or intense summer monsoon. The observed changes in Pinus and Herbs percentage indicate fluctuations of the sea level, and high Pinus percentage corresponds to high sea level. Spectrum analysis of the pollen percentage record reveals many millennial-scale periodicities, such as periodicities of 6.8, 3.85 2.2, 1.6 ka.

Seismic stratigraphy of the Qiongdongnan deep sea channel system, northwest South China Sea

Based on more than 4000 km 2D seismic data and seismic stratigraphic analysis, we discussed the extent and formation mechanism of the Qiongdongnan deep sea channel. The Qiongdongnan deep sea channel is a large incised channel which extends from the east boundary of the Yinggehai Basin, through the whole Qiongdongnan and the Xisha trough, and terminates in the western part of the northwest subbasin of South China Sea. It is more than 570 km long and 4-8 km wide. The chaotic (or continuous) middle (or high) amplitude, middle (or high) continuity seismic facies of the channel reflect the different lithological distribution of the channel. The channel formed as a complex result of global sea level drop during early Pliocene, large scale of sediment supply to the Yinggehai Basin, inversion event of the Red River strike-slip fault, and tilted direction of the Qiongdongnan Basin. The large scale of sediment supply from Red River caused the shelf break of the Yinggehai Basin to move torwards the S and SE direction and developed large scale of prograding wedge from the Miocene, and the inversion of the Red River strike-slip fault induced the sediment slump which formed the Qiongdongnan deep sea channel.

Deep Fractionation of Clinopyroxene in the East Pacific Rise 13 degrees N: Evidence from High MgO MORB and Melt Inclusions

Mid-ocean ridge basalts (MORBs) from East Pacific Rise (EPR) 13 degrees N are analysed for major and trace elements, both of which show a continuous evolving trend. Positive MgO-Al2O3 and negative MgO-Sc relationships manifest the cotectic crystallization of plagioclase and olivine, which exist with the presence of plagioclase and olivine phenocrysts and the absence of clinopyroxene phenocrysts. However, the fractionation of clinopyroxene is proven by the positive correlation of MgO and CaO. Thus, MORB samples are believed to show a "clinopyroxene paradox". The highest magnesium-bearing MORB sample E13-3B (MgO = 9.52%) is modelled for isobaric crystallization with COMAGMAT at different pressures. Observed CaO/Al2O3 ratios can be derived from E13-3B only by fractional crystallization at pressure > 4 +/- 1 kbar, which necessitates clinopyroxene crystallization and is not consistent with cotectic crystallization of olivine plus plagioclase in the magma chamber (at pressure similar to 1 kbar). The initial compositions of the melt inclusions, which could represent potential parental magmas, are reconstructed by correcting for post-entrapment crystallization (PEC). The simulated crystallization of initial melt inclusions also produce observed CaO/Al2O3 ratios only at > 4 +/- 1 kbar, in which clinopyroxene takes part in crystallization. It is suggested that MORB magmas have experienced clinopyroxene fractionation in the lower crust, in and below the Moho transition zone. The MORB magmas have experienced transition from clinopyroxene+plagioclase+olivine crystallization at > 4 +/- 1 kbar to mainly olivine+plagioclase crystallization at < 1 kbar, which contributes to the explanation of the "clinopyroxene paradox".

Geomorphology, sedimentary processes and development of the Zenisu deep-sea channel, northern Philippine Sea

The Zenisu deep-sea channel originates on the Izu-Ogasawara island arc, and disappears in the Shikoku Basin of the Philippine Sea. The geomorphology, sedimentary processes, and the development of the Zenisu deep-sea channel were investigated on the basis of swath bathymetry, side-scan sonar imagery, submersible observations, and seismic data. The deep-sea channel can be divided into three segments according to the downslope gradient and channel orientation. They are the Zenisu Canyon, the E-W fan channel, and the trough-axis channel. The sediment fill is characterized by turbidite and debrite deposition and blocky-hummocky avalanche deposits on the flanks of the Zenisu Ridge. In the Zenisu Canyon and the Zenisu deep-sea channel, sediment transport by turbidity currents generates sediment waves (dunes) observed during the Shinkai 6500 dive 371. The development of the Zenisu Canyon is controlled by a N-S shear fault, whereas the trough-axis channel is controlled by basin subsidence associated with the Zenisu Ridge. The E-W fan channel was probably affected by the E-W fault and the basement morphology.

Analysis on deep crustal structure along the onshore-offshore seismic profile across the Binhai (littoral) fault zone in northeastern South China Sea

The onshore-offshore deep seismic experiment was carried out for the first time and filled the blankness of the seismic surveys in the transition area between South China and northeastern South China Sea. The seismic data were analyzed and processed. The different seismic phases were identified and their travel time arrivals were modeled by ray-tracing to study the P-wave velocity crustal structure of this area. The crustal structure of this area is the continental crust. The crust thickness is gradually decreasing southward along the on-shore-offshore seismic line. The low-velocity layer (5.5 similar to 5.9 km (.) s(-1)) exists generally in the middle crust (about 10.0 similar to 18.0km)with about 2.5 similar to 4.0 km thickness, which is also thinning seaward. No obvious high-velocity layer appears in the lower crust. The Binhai (littoral) fault zone is a low velocity zone, which is located about 35km southeast to the Nan'ao station and corresponding to the gradient belt of gravity & magnetism anomalies. The depth of the fault zone is close to the Moho discontinuity. The littoral fault zone is a boundary between the normal continental crust of South China and the thinned continental crust of the sea area.

Two different proteases produced by a deep-sea psychrotrophic bacterial strain, Pseudoaltermonas sp SM9913

A psychrotrophic bacterial strain, Pseudoaltermonas sp. SM9913, was isolated from deep-sea sediment collected at 1,855 m depth. Two proteases produced by Pseudoaltermonas sp. SM9913 were purified, MPC-01 and MCP-02. MCP-01 is a serine protease with a molecular weight of 60.7 kDa. It is cold-adapted with an optimum temperature of 30-35degreesC. Its K-m and E-a for the hydrolysis of casein were 0.18% and 39.1 kJ mol(-1), respectively. It had low thermostability, and its activity was reduced by 73% after incubation at 40degreesC for 10 min. MCP-02 is a mesophilic metalloprotease with a molecular weight of 36 kDa. Its optimum temperature for the hydrolysis of casein was 50-55degreesC. The K-m and E-a of MCP-02 for the hydrolysis of casein were 0.36% and 59.3 kJ mol(-1), respectively. MCP-02 had high thermostability, and its activity was reduced by only 30.5% after incubation at 60degreesC for 10 min. At low temperatures, Pseudoaltermonas sp. SM9913 mainly produced the psychrophilic protease MCP-01.

Sedimentary processes and development of the Zenisu deep-sea channel, Philippine Sea

Zenisu deep-sea channel originated from a volcanic arc region, Izu-Ogasawara Island Arc, and vanished in the Shikoku Basin of the Philippine Sea. According to the swath bathymetry, the deep-sea channel can be divided into three,segments. They are Zenisu canyon, E-W fan channel and trough-axis channel. A lot of volcanic detritus were deposited in the Zenisu Trough via the deep-sea channel because it originated from volcanic arc settings. On the basis of the swath bathymetry, submersible and seismic reflection data, the deposits are characterized by turbidite and debrite deposits as those in the other major deep-sea channels. Erosion or few sediments were observed in the Zenisu canyon, whereas a lot of turbidites and debrites occurred in the E-W channel and trough axis channel. Cold seep communities, active fault and fluid flow were discovered along the lower slope of the Zenisu Ridge. Vertical sedimentary sequences in the Zenisu Trough consist of the four post-rift sequence units of the Shikoku Basin, among which Units A and B are two turbidite units. The development of Zenisu canyon is controlled by the N-S shear fault, the E-W fan channel is related to the E-W shear fault, and the trough-axis channel is related to the subsidence of central basin.

NONLINEAR GRAVITY-WAVES IN DEEP-WATER

In consideration of the problem on the boundary condition of nonlinear free water wave, coordinate transform is used to handle the free boundary. Supposing the solution form be the traveling wave, the ordinary differential equations of the one-order autonomous system with two variables are caused, then expanding the nonlinear terms at the equilibrium point with the Taylor expansion, we obtained the solution to traveling wave. The linear approximate equation near the equilibrium point is the small amplitude wave. A new nonlinear periodic traveling wave and nonlinear dispersion relation are shown when expanding to the second-order terms. A conclusion that the expansion of dispersion relation does not contain any odd-power terms of wave steepness and because of the nonlinear effort an oscillate structure is produced in the vertical direction is drawn.

Seasonal variations in growth and clearance rate of the Zhikong scallop Chlamys farreri suspended in the deep water of Haizhou Bay, China

The growth and survival of the Zhikong scallop Chlamys farreri suspended in deep water of Haizhou Bay were studied from July 2007 to June 2008, and the biodeposition method was used to estimate the clearance rate of C. farreri under field conditions. Results showed that the scallop grew fast during all the culture time, with the exception of summer. The condition index of the scallop increased with time and reached the highest value in spring of the second year. The survival of scallops was 60.8 +/- A 3.9% at the end of this study, mortality occurring mainly during the summer and autumn of the first year. The clearance rate fluctuated obviously with season,with the highest value in September 2007, and the lowest value in March 2008. Factors accounting for variations in growth and clearance rate of scallops are also discussed.

Survival, growth and immune activity of scallop Chlamys farreri cultured at different depths in Haizhou Bay (Yellow Sea, China) during hot season

Survival, growth and immune response of the scallop, Chlamys farreri, cultured in lantern nets at five different depths (2, 5, 10, 15, and 20 m below the sea surface) were studied in Haizhou Bay during the hot season (summer and autumn) of 2007. Survival and growth rates were quantified bimonthly. Immune activities in hemolymph (superoxide dismutase (SOD) and acid phosphatase (ACP)) were measured to evaluate the health of scallops at the end of the study. Environmental parameters at the five depths were also monitored during the experiment. Mortalities mainly occurred during summer. Survival of scallops suspended at 15 m (78.0%) and 20 m (86.7%) was significantly higher than at 2 m (62.9%), 5 m (60.8%) or 10 m (66.8%) at the end of the study. Mean shell height grew significantly faster at 10 m (205.0 mu m/d) and 20 m (236.9 mu m/d) than at 2, 5 or 15 m in summer (July 9 to September 1); however, shell growth rate at 20 m was significantly lower than at the other four depths in autumn (September 2 to November 6). In contrast to summer, scallops at 5 m grew faster (262.9 mu m/d) during autumn. The growth of soft tissue at different depths showed a similar trend to the shell. Growth rates of shell height and soft tissue were faster in autumn than in summer, with the exception of shell height at 20 m. SOD activity of scallops increased with depth, and ACP activity was significantly higher at 15 and 20 m than at other depths, which suggests that scallops were healthier near the bottom. Factors explaining the depth-related mortality and growth of scallops are also discussed. We conclude that the mass mortality of scallop, C. farreri, during summer can be prevented by moving the culture area to deeper water and yield can be maximized by suspending the scallops in deep water during summer and then transferring them to shallow water in autumn.

Identification of a silicatein(-related) protease in the giant spicules of the deep-sea hexactinellid Monorhaphis chuni

Silicateins, members of the cathepsin L family, are enzymes that have been shown to be involved in the biosynthesis/condensation of biosilica in spicules from Demospongiae (phylum Porifera), e. g. Tethya aurantium and Suberites domuncula. The class Hexactinellida also forms spicules from this inorganic material. This class of sponges includes species that form the largest biogenic silica structures on earth. The giant basal spicules from the hexactinellids Monorhaphis chuni and Monorhaphis intermedia can reach lengths of up to 3 m and diameters of 10 mm. The giant spicules as well as the tauactines consist of a biosilica shell that surrounds the axial canal, which harbours the axial filament, in regular concentric, lamellar layers, suggesting an appositional growth of the spicules. The lamellae contain 27 kDa proteins, which undergo post-translational modification (phosphorylation), while total spicule extracts contain additional 70 kDa proteins. The 27 kDa proteins cross-reacted with anti-silicatein antibodies. The extracts of spicules from the hexactinellid Monorhaphis displayed proteolytic activity like the silicateins from the demosponge S. domuncula. Since the proteolytic activity in spicule extracts from both classes of sponge could be sensitively inhibited by E-64 (a specific cysteine proteinase inhibitor), we used a labelled E-64 sample as a probe to identify the protein that bound to this inhibitor on a blot. The experiments revealed that the labelled E-64 selectively recognized the 27 kDa protein. Our data strongly suggest that silicatein(-related) molecules are also present in Hexactinellida. These new results are considered to also be of impact for applied biotechnological studies.

Deep-sea pontoniines (Decapoda : Palaemonidae) from the philippine "PANGLAO 2005" expedition, with descriptions of four new species

Ten species belonging to three genera of the subfamily Pontoniinae were colleted by the deep-sea expedition "PANGLAO 2005" in the Philippines, including four new species of the genus Periclimenes, i.e., P. boucheti n. sp., P. leptunguis n. sp., P. ngi n. sp., and P. panglaonis sp. nov., and one newly recorded species from the Philippines, Periclimenes laccadivensis. They are reported with color photographs except one species, Plesiopontonia monodi. The possible synonymy of Periclimenes foresti and P. granuloides is discussed.

Seasonal regulations of energetics, serum concentrations of leptin, and uncoupling protein 1 content of brown adipose tissue in root voles (Microtus oeconomus) from the Qinghai-Tibetan plateau

Survival of small mammals in winter requires proper adjustments in physiology, behavior and morphology. The present study was designed to examine the changes in serum leptin concentration and the molecular basis of thermogenesis in seasonally acclimatized root voles (Microtus oeconomus) from the Qinghai-Tibetan plateau. In January root voles had lower body mass and body fat mass coupled with higher nonshivering thermogenesis (NST) capacity. Consistently, cytochrome c oxidase activity and mitochondrial uncoupling protein-1 (UCP1) protein contents in brown adipose tissues were higher in January as compared to that in July. Circulating level of serum leptin was significantly lower in winter and higher in July. Correlation analysis showed that serum leptin levels were positively related with body mass and body fat mass while negatively correlated with UCP1 protein contents. Together, these data provided further evidence for our previous findings that root voles from the Qinghai-Tibetan plateau mainly depend on higher NST coupled with lower body mass to enhance winter survival. Further, fat deposition was significantly mobilized in cold winter and leptin was potentially involved in the regulation of body mass and thermogenesis in root voles. Serum leptin might act as a starvation signal in winter and satiety signal in summer.