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.

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.

From offshore to onshore: multiple origins of shallow-water corals from deep-sea ancestors.

Shallow-water tropical reefs and the deep sea represent the two most diverse marine environments. Understanding the origin and diversification of this biodiversity is a major quest in ecology and evolution. The most prominent and well-supported explanation, articulated since the first explorations of the deep sea, holds that benthic marine fauna originated in shallow, onshore environments, and diversified into deeper waters. In contrast, evidence that groups of marine organisms originated in the deep sea is limited, and the possibility that deep-water taxa have contributed to the formation of shallow-water communities remains untested with phylogenetic methods. Here we show that stylasterid corals (Cnidaria: Hydrozoa: Stylasteridae)--the second most diverse group of hard corals--originated and diversified extensively in the deep sea, and subsequently invaded shallow waters. Our phylogenetic results show that deep-water stylasterid corals have invaded the shallow-water tropics three times, with one additional invasion of the shallow-water temperate zone. Our results also show that anti-predatory innovations arose in the deep sea, but were not involved in the shallow-water invasions. These findings are the first robust evidence that an important group of tropical shallow-water marine animals evolved from deep-water ancestors.

Seasonal Sedimentation Of Phytoplankton To The Deep-Sea Benthos

Until recently the deep sea was considered to be a particularly stable environment1, free from seasonal variations. However, atmospheric storms may cause periodicity in deep-ocean currents2 and nepheloid layers3 while seasonality in the particulate flux to the deep sea is known to occur in the Sargasso Sea4,5 and Panama Basin6. Evidence is presented here of a similar seasonal pulse of detrital material to bathyal and abyssal depths in temperate latitudes; this material seems to be derived directly from the surface primary production and to sink rapidly to the deep-sea benthos. Considerable sedimentation occurs soon after the spring bloom and continues throughout the early summer. This process acts as a pathway for the descent of carbon from the euphotic zone, providing a periodic food source for the deep pelagic and benthic communities.