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.

Diverse and Novel nifH and nifH-Like Gene Sequences in the Deep-Sea Methane Seep Sediments of the Okhotsk Sea

Diverse nifH and nifH-like gene sequences were obtained from the deep-sea surface sediments of the methane hydrate-bearing Okhotsk Sea. Some sequences formed novel families of the NifH or NifH-like proteins, of currently unresolved bacterial or archaeal origin. Comparison with other marine environments indicates environmental specificity of some of the sequences, either unique to the methane seep sediments of the Okhotsk Sea or to the general deep-sea methane seep sedimentary environments.

Wangia profunda gen. nov., sp nov., a novel marine bacterium of the family Flavobacteriaceae isolated from southern Okinawa Trough deep-sea sediment

An orange-pigmented, Gram-negative, nonmotile, strictly aerobic and oxidase- and catalase-positive bacterium (SM-A87(T)) was isolated from the deep-sea sediment of the southern Okinawa Trough area. The main fatty acids were i15 : 0, i17 : 0 3OH, i15 : 1 G, i17 : 1 omega 9c, 15 : 0, i15 : 0 3OH and summed feature 3 (comprising i-15 : 0 2OH and/or 16 : 1 omega 7c). MK-6 was the predominant respiratory quinone. DNA G+C content was 35.8 mol%. Flexirubin-type pigments were absent. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain SM-A87(T) formed a distinct lineage within the family Flavobacteriaceae, with < 93% sequence similarity to the nearest strain of genus Salegentibacter. Moreover, strain SM-A87(T) could be distinguished from the nearest phylogenetic neighbors by a number of chemotaxonomic and phenotypic properties. On the basis of polyphasic analyses, it is proposed that strain SM-A87(T) be classified in a novel genus and a new species in the family Flavobacteriaceae, designated Wangia profunda gen. nov., sp. nov. The type strain is SM-A87(T) (CCTCC AB 206139(T)=DSM 18752).

Myroides profundi sp nov., isolated from deep-sea sediment of the southern Okinawa Trough

A Gram-negative, nonmotile, aerobic and oxidase- and catalase-positive bacterium,, designated D25(T), was isolated from the deep-sea sediments of the southern Okinawa Trough area. Phylogenetic analyses of 16S rRNA gene sequences showed that strain D25(T), fell within the genus Myroides, with 99.2%, 96.0% and 93.4% sequence similarities to the only three recognized species of Myroides. However, the DNA-DNA similarity Value between strain D25(T) and its nearest neighbour Myroides odoratimimus JCM 7460(T) was only 49.9% ( < 70%). Several phenotypic properties could be used to distinguish strain D25(T) from other Myroides species. The main cellular fatty acids of strain D25(T) were iso-C-15:0, iso-C-17:1 omega 9C, iso-C(17:0)3-OH and Summed Feature 3 (comprising C-16:1 omega 7c and/or iso-C(15:0)2-OH). The major respiratory quinone was MK-6. The DNA G+C content was 33.0 mol%. The results of the polyphasic taxonomy analysis suggested that strain D251(T) represents a novel species of the genus Myroides, for which the name Myroides profundi sp. nov. is proposed. The type strain is D25(T) (=CCTCC M 208030(T) = DSM 19823(T)).

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.

Genetic model of the hydrate system in the fine grain sediments in the northern continental slope of South China Sea

Gas hydrate samples were obtained firstly in China by drilling on the northern margin of South China Sea (SCS). To understand the formation mechanism of this unique accumulation system, this paper discusses the factors controlling the formation of the system by accurate geophysical interpretation and geological analysis, based on the high precision 2-D and 3-D multichannel seismic data in the drilling area. There are three key factors controlling the accumulation of the gas hydrate system in fine grain sediment: (1) large volume of fluid bearing methane gas Joins the formation of gas hydrate. Active fluid flow in the northern South China Sea makes both thermal gas and/or biogenic gas migrate into shallow strata and form hydrate in the gas hydrate stability zone (GHSZ). The fluid flow includes mud diapir and gas chimney structure. They are commonly characterized by positive topographic relief, acoustic turbidity and push-down, and low reflection intensity on seismic profiles. The gas chimneys can reach to GHSZ, which favors the development of BSRs. It means that the active fluid flow has a close relationship with the formation and accumulation of gas hydrate. (2) The episodic process of fracture plays an important role in the generation of gas hydrate. It may provide the passage along which thermogenic or biogenic gas migrated into gas hydrate stability zone (GHSZ) upward. And it increases the pore space for the growth of hydrate crystal. (3) Submarine landslide induced the anomalous overpressure activity and development of fracture in the GHSZ. The formation model of high concentration gas hydrate in the drilling sea area was proposed on the basis of above analysis.

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.

Seismic characteristics of a reef carbonate reservoir and implications for hydrocarbon exploration in deepwater of the Qiongdongnan Basin, northern South China Sea

Our analysis of approximately 40,000 km of multichannel 2-D seismic data, reef oil-field seismic data, and data from several boreholes led to the identification of two areas of reef carbonate reservoirs in deepwater areas (water depth >= 500 in) of the Qiongdongnan Basin (QDNB), northern South China Sea. High-resolution sequence stratigraphic analysis revealed that the transgressive and highstand system tracts of the mid-Miocene Meishan Formation in the Beijiao and Ledong-Lingshui Depressions developed reef carbonates. The seismic features of the reef carbonates in these two areas include chaotic bedding, intermittent internal reflections, chaotic or blank reflections, mounded reflections, and apparent amplitude anomalies, similar to the seismic characteristics of the LH11-1 reef reservoir in the Dongsha Uplift and Island Reef of the Salawati Basin, Indonesia, which house large oil fields. The impedance values of reefs in the Beijiao and Ledong-Lingshui Depressions are 8000-9000 g/cc x m/s. Impedance sections reveal that the impedance of the LH11-1 reef reservoir in the northern South China Sea is 800010000 g/cc x m/s, whereas that of pure limestone in BD23-1-1 is > 10000 g/cc x m/s. The mid-Miocene paleogeography of the Beijiao Depression was dominated by offshore and neritic environments, with only part of the southern Beijiao uplift emergent at that time. The input of terrigenous sediments was relatively minor in this area, meaning that terrigenous source areas were insignificant in terms of the Beijiao Depression: reef carbonates were probably widely distributed throughout the depression, as with the Ledong-Lingshui Depression. The combined geological and geophysical data indicate that shelf margin atolls were well developed in the Beijiao Depression, as in the Ledong-Lingshui Depression where small-scale patch or pinnacle reefs developed. These reef carbonates are promising reservoirs, representing important targets for deepwater hydrocarbon exploration. (C) 2008 Elsevier Ltd. All rights reserved.

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".

Gas seepage on the sea floor of Okinawa Trough Miyako Section

A marine geophysical survey was carried out, on the RN Science 1 of the Institute of Oceanography, Chinese Academy of Sciences (IOCAS), in 2000, at the Miyako Section of Okinawa Trough. Here we present seismic and acoustic evidence of a gas seep on the sea floor on the western part of the Okinawa Through, near the lower slope of the East China Sea Slope and discuss the possibility of related formation of gas hydrate. A gas column reflection was observed in echo-sounder data above a section where the sea floor reflector was missing, on both the echo-sounder and the seismic data for line H14. The seismic data also show an acoustic curtain reflection and a turbidity reflection at this section. These anomalies are the evidence of the existence of a gas seep, which occupies an area 2.2 km in diameter. Based on the acoustic curtain on line H14, we believe that the amount of gas contained in the sediments below the gas seep is larger than 1 % by volume of sediment. Tectonically, the gas seep developed in a small basin controlled by basement uplift in the north, south and east. The thickness of the sediment layer can be greater than 3.5 km. A mud diapir structure was found in layer D beneath the gas seep. Over-pressure may occur due to the large sediment thickness and also the tectonic basement uplift in the north, south, and east. The mud diapir could be the preferential pathway for methane-rich fluids. The acoustic curtain may indicate that free gas related to the gas seep can be formed on the sea floor. We also note that the layer above the acoustic curtain on profile H14 may contain gas hydrate.

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.

A comprehensive investigation of an offshore active fault in the Western Sagami Bay, central Japan

Offshore active faults, especially those in the deep sea, are very difficult to study because of the water and sedimentary cover. To characterize the nature and geometry of offshore active faults, a combination of methods must be employed. Generally, seismic profiling is used to map these faults, but often only fault-related folds rather than fracture planes are imaged. Multi-beam swath bathymetry provides information on the structure and growth history of a fault because movements of an active fault are reflected in the bottom morphology. Submersible and deep-tow surveys allow direct observations of deformations on the seafloor (including fracture zones and microstructures). In the deep sea, linearly aligned cold seep communities provide indirect evidence for active faults and the spatial migration of their activities. The Western Sagami Bay fault (WSBF) in the western Sagami Bay off central Japan is an active fault that has been studied in detail using the above methods. The bottom morphology, fractured breccias directly observed and photographed, seismic profiles, as well as distribution and migration of cold seep communities provide evidence for the nature and geometry of the fault. Focal mechanism solutions of selected earthquakes in the western Sagami Bay during the period from 1900 to 1995 show that the maximum compression trends NW-SE and the minimum stress axis strikes NE-SW, a stress pattern indicating a left-lateral strike-slip fault.

Flux and fate of Yangtze river sediment delivered to the East China Sea

Numerous cores and dating show the Yangtze River has accumulated about 1.16 x 10(12) t sediment in its delta plain and proximal subaqueous delta during Holocene. High-resolution seismic profiling and coring in the southern East China Sea during 2003 and 2004 cruises has revealed an elongated (similar to 800 km) distal subaqueous mud wedge extending from the Yangtze River mouth southward off the Zhejiang and Fujian coasts into the Taiwan Strait. Overlying what appears to be a transgressive sand layer, this distal clinoform thins offshore, from similar to 40 in thickness between the 20 and 30 m water depth to < 1-2 in between 60 and 90 m water depth, corresponding to an across shelf distance of less than 100 km. Total volume of this distal mud wedge is about 4.5 x 10(11) m(3), equivalent to similar to 5.4 x 10(11) t of sediment. Most of the sediment in this mud wedge comes from the Yangtze River, with some input presumably coming from local smaller rivers. Thus, the total Yangtze-derived sediments accumulated in its deltaic system and East China Sea inner shelf have amounted to about 1.7 x 10(12) t. Preliminary analyses suggest this longshore and across-shelf transported clinoform mainly formed in the past 7000 yrs after postglacial sea level reached its mid-Holocene highstand, and after re-intensification of the Chinese longshore current system. Sedimentation accumulation apparently increased around 2000 yrs BP, reflecting the evolution of the Yangtze estuary and increased land erosion due to human activities, such as fanning and deforestation. The southward-flowing China Coastal Current, the northward-flowing Taiwan Warm Current, and the Kuroshio Current appear to have played critical roles in transporting and trapping most of Yangtze-derived materials in the inner shelf, and hence preventing the sediment escape into the deep ocean. (c) 2006 Elsevier B.V. All rights reserved.