Extracellular hydrolytic enzyme screening of culturable heterotrophic bacteria from deep-sea sediments of the Southern Okinawa Trough

The Southern Okinawa Trough is an area of focused sedimentation due to particulate matter export from the shelf of the East China Sea and the island of Taiwan. In order to understand the geomicrobiological characteristics of this unique sedimentary environment, bacterial cultivations were carried out for an 8.61 m CASQ core sediment sample. A total of 98 heterotrophic bacterial isolates were characterized based on 16S rRNA gene phylogenetic analysis. These isolates can be grouped into four bacterial divisions, including 13 genera and more than 20 species. Bacteria of the gamma-Proteobacteria lineage, especially those from the Halomonas ( 27 isolates) and Psychrobacter ( 20 isolates) groups, dominate in the culturable bacteria assemblage. They also have the broadest distribution along the depth of the sediment. More than 72.4% of the isolates showed extracellular hydrolytic enzyme activities, such as amylases, proteases, lipases and Dnases, and nearly 59.2% were cold-adapted exoenzyme-producers. Several Halomonas strains show almost all the tested hydrolases activities. The wide distribution of exoenzyme activities in the isolates may indicate their important ecological role of element biogeochemical cycling in the studied deep-sea sedimentary environment.

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.

Petroleum System in Deepwater Basins of the Northern South China Sea

The northern South China Sea margin has experienced a rifting stage and a post-rifting stage during the Cenozoic. In the rifting stage, the margin received lacustrine and shallow marine facies sediments. In the post-rifting thermal subsidence, the margin accumulated shallow marine facies and hemipelagic deposits, and the deepwater basins formed. Petroleum systems of deepwater setting have been imaged from seismic data and drill wells. Two kinds of source rocks including Paleogene lacustrine black shale and Oligocene-Early Miocene mudstone were developed in the deepwater basin of the South China Sea. The deepwater reservoirs are characterized by the deep sea channel rill, mass flow complexes and drowned reef carbonate platform. Profitable capping rocks on the top are mudstones with huge thickness in the post-rifting stage. Meanwhile, the faults developed during the rifting stage provide a migration path favourable for the formation of reservoirs. The analysis of seismic and drilling data suggests that the joint structural and stratigraphic traps could form giant hydrocarbon fields and hydrocarbon reservoirs including syn-rifting graben subaqueous delta, deepwater submarine fan sandstone and reef carbonate reservoirs.

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.

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.

Radiolarian distribution in surface sediments of the northern and central South China Sea

Radiolarian distribution in surface sediments of 104 stations from northern and central South China Sea show that the abundance and diversity of radiolarians increase with the water depth and are related to radiolarian concentrations from the water column, diminished terrigenous input, variability in calcareous shell content and the rate of silica and carbonate dissolution in the deep sea. According to the appearances of individual species in surface sediments at particular depths, seven faunal boundaries distribution are recognized at water depths of 100, 450, 650, 1000, 1200, 1400 and 2500 m. Four radiolarian assemblages in the sediments were identified by applying clustering procedures. Geographic distributions of these four assemblages coincide with present-day hydrologic features of the surface waters in this area.

Diversity of Both the Cultivable Protease-Producing Bacteria and Their Extracellular Proteases in the Sediments of the South China Sea

Protease-producing bacteria are known to play an important role in degrading sedimentary particular organic nitrogen, and yet, their diversity and extracellular proteases remain largely unknown. In this paper, the diversity of the cultivable protease-producing bacteria and their extracellular proteases in the sediments of the South China Sea was investigated. The richness of the cultivable protease-producing bacteria reached 10(6) cells/g in all sediment samples. Analysis of the 16S rRNA gene sequences revealed that the predominant cultivated protease-producing bacteria are Gammaproteobacteria affiliated with the genera Pseudoalteromonas, Alteromonas, Marinobacter, Idiomarina, Halomonas, Vibrio, Shewanella, Pseudomonas, and Rheinheimera, with Alteromonas (34.6%) and Pseudoalteromonas (28.2%) as the predominant groups. Inhibitor analysis showed that nearly all the extracellular proteases from the bacteria are serine proteases or metalloproteases. Moreover, these proteases have different hydrolytic ability to different proteins, reflecting they may belong to different kinds of serine proteases or metalloproteases. To our knowledge, this study represents the first report of the diversity of bacterial proteases in deep-sea sediments.

Geochemical character and material source of sediments in the eastern Philippine Sea

Based upon analyses of grain-size, rare earth element (REE) compositions, elemental occurrence phases of REE, and U-series isotopic dating, the sediment characteristics and material sources of the study area were examined for the recently formed deep-sea clays in the eastern Philippine Sea. The analytical results are summarized as follows. (1) Low accumulation rate, poor sorting and roundness, and high contents of grains coarser than fine silt indicate relatively low sediment input, with localized material source without long distance transport. (2) The REE Contents are relatively high. Shale-normalized patterns of REE indicate weak enrichment in heavy REE (HREE), Ce-passive anomaly, and Eu-positive anomaly. (3) Elemental occurrence phases of REE between the sediments with and without crust are similar. REE mainly concentrate in residual phase and then in ferromanganese oxide phase. The light REE (LREE) enrichment, Ce-positive anomaly, and Eu-positive anomaly occur in residual phase. Ferromanganese oxide phase shows the characteristics of relatively high HREE content and Ce-passive anomaly. (4) There are differences in each above mentioned aspect between the sediments with and without ferromanganese crust. (5) Synthesizing the above characteristics and source discriminant analysis, the study sediments are deduced to mainly result from the alteration of local and nearby volcanic materials. Continental materials transported by wind and/or river (ocean) flows also have minor contributions.

Mineral provinces and material provenance of the surficial sediments near the Zhongsha Islands in the South China Sea

Characteristics and distribution patterns of elastic minerals (0.063 similar to 0.125 mm) in bottom sediments represent a significant indicator for the identification of the origin of sediment. One hundred and fourteen surface sediment samples, which were collected from the area near the Zhongsha Islands in the South China Sea, were analysed to identify the mineral suites and their distributions in the study area. The area can be divided into three mineral provinces: ( I) a province of biogenic minerals, which mainly originate from the Zhongsha Atoll; ( H) a province of volcanogenic minerals, which are mainly derived from local basaltic seamounts and small-scale volcanoes that are probably erupting, with some influences from the island-are volcanic region around the South China Sea; and (II) a mixed mineral province whose material source includes biogenic minerals, volcanogenic minerals and terrigenous minerals; the last province can be subdivided into a mixed mineral sub-province of the northeastern part of the study area, in which terrigenous minerals are mainly derived from China's Mainland and do not exceed 17 degrees N, and a mixed mineral sub-province of the southeastern part of the study area, in which terrigenous minerals are derived from Kalimantan and Indochina Peninsula and might be further transported into the deep sea basin through submarine canyons.

Characteristics and flux of settling particulate matter in neritic waters: The southern Yellow Sea and the East China Sea

The typology and flux of settling particulate matter (SPM) were investigated based on sediment trap sampling at six typical stations in the Yellow Sea and the East China Sea. The settling particulate matter in the neritic seas was sorted into three categories, lithogenic particles, living organisms, and particle aggregates. The mass of individual organisms is an important portion of particulate matter in the neritic waters. The aggregates contain six types, mucus aggregates, fecal pellets, diatom aggregates, silicoflagellate aggregates, tintinnids, and miscellaneous aggregates, of which the silicoflagellate aggregates and tintinnids are the most abundant in the Yellow Sea and the East China Sea. High particle fluxes, such as 215 to 874 g m(-2). day(-1) SPM in the bottom layer, were found at three stations where the water was well mixed, and the maximum flux was detected in the boundary area between the Yellow Sea and the East China Sea, where a wide nepheloid layer was present. Hence, particle flux in neritic waters can be easily shifted by water turbulence. The net vertical flux (123 to 961 mg C day(-1)), the contribution of lateral advection to resuspension flux (5 to 76%), and the particulate organic carbon export ratio (18 to 60%) were estimated for the other three stations where the water was stratified. The highest values were all found in the upwelling area off the Zhejiang coast, suggesting that the area of high productivity provides a high net vertical flux of SPM. (C) 2010 Elsevier Ltd. All rights reserved.

Numerical simulation of principal tidal constituents in the South China Sea, Gulf of Tonkin and Gulf of Thailand

The principal tidal constituents M-2, S-2, K-1 and O-1 in the South China Sea, Gulf of Tonkin and Gulf of Thailand are simulated simultaneously using the numerical scheme of Kwok et al. (1995 Proceedings of the 1st Asian Computational Fluid Dynamics Conference, pp. 16-19). The average differences between the computed and observed harmonic constants are mostly within 5 cm and 10 degrees for amplitudes and phase-lags, respectively. The simulated tidal regimes in the present model are believed to be more accurate than the previous numerical results. Our studies confirm that a clockwise rotating M-2 amphidromic system lies in the southeast of the Gulf of Thailand and an S-2 amphidromic system at the near-shore area of the northeast South China Sea. The linear tidal energy equation developed by Garrett (1975 Deep-Sea Research 22, 23-35) is generalized to the nonlinear case. Based on the numerical results, the energy budgets in the South China Sea and its subareas, namely the Taiwan Strait, the Gulf of Tonkin, the Gulf of Thailand and the remaining area are investigated. The tidal motion in the Taiwan Strait is maintained mainly by the energy fluxes from the East China Sea for both semidiurnal and diurnal species and partially from the Luzon Strait for semidiurnal species. For the other parts of the South China Sea, the tidal motion is mainly maintained by the energy fluxes through the Luzon Strait. The energy inputs from the tide-generating force are negative for semidiurnal species and positive for diurnal species. (C) 1999 Elsevier Science Ltd. All rights reserved.

Characteristics of nitrogen forms in the surface sediments of southwestern Nansha Trough, South China Sea

The area of the southwestern Nansha Trough is one of the most productive areas of the southern South China Sea. It is a typical semi-deep sea area of transition from shoal to abyssal zone. To understand distributions and roles of nitrogen forms involved in biogeochemical cycling in this area, contents of nitrogen in four extractable forms: nitrogen in ion exchangeable form (IEF-N), nitrogen in weak acid extractable form (WAEF-N), nitrogen in strong alkali extractable form (SAEF-N) and nitrogen in strong oxidation extractable form (SOEF-N), as well as in total nitrogen content (TN) in surface sediments were determined from samples collected from the cruise in April-May 1999. The study area was divided into three regions (A, B and C) in terms of clay sediment (< 4 mu m) content at < 40%, 40%-60% and > 60%, respectively. Generally, region C was the richest in the nitrogen of all forms and region A the poorest, indicating that the finer the grain size is, the richer the contents of various nitrogen are. The burial efficiency of total nitrogen in surface sediments was 28.79%, indicating that more than 70% of nitrogen had been released and participated in biogeochemical recycling through sediment-water interface.

Main geochemical characteristics and key biogeochemical carbon processes in the East China Sea

Research related to carbon geochemistry and biogeochemistry in the East China Sea is reviewed in this paper. The East China Sea is an annual net sink for atmospheric CO, and a large net source of dissolved inorganic carbon to the ocean. The sea absorbs CO, from the atmosphere in spring and summer and releases it in autumn and winter. The East China Sea is a CO, sink in summer because Changjiang River freshwater flows into it. The net average sea-air interface carbon flux of the East China Sea is estimated to be about 4.3 X 10(6) t/y. Vertical carbon transport is mainly in the form of particulate organic carbon in spring; more than 98% of total carbon is transported in this form in surface water, and the number exceeds 68% in water near the bottom. In the southern East China Sea, the average particulate organic carbon inventory was about one-tenth that of the dissolved organic carbon. Research indicates that the southern Okinawa Trough is an important site for particulate organic carbon export from the shelf. The annual cross-shelf exports are estimated to be 414 and 106 Gmol/y for dissolved organic carbon and particulate organic carbon, respectively. Near-bottom transport could be the key process for shelf-to-deep sea export of biogenic and lithogenic particles.