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.

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.

Manganese abnormity in holocene Sediments of the Bohai Sea

Manganese abnormity has been observed in the Holocene sediments of the mud area of Bohai Sea. On the basis of grain size, chemical composition, heavy mineral content and accelerator mass spectrometry (AMS) C-14 dating of foraminifer, relationships between manganese abnormity and sedimentation rates, material source, hydrodynamic conditions are probed. Manganese abnormity occurred during the Middle Holocene when sea level and sedimentation rates were higher than those at present. Sedimentary hiatus was not observed when material sources and hydrodynamic conditions were quite similar. Compared with the former period, the latter period showed a decrease in reduction environment and an inclination toward oxidation environment with high manganese content, whereas provenance and hydrodynamic conditions showed only a slight change. From the above observations, it can be concluded that correlation among manganese abnormity, material source, and hydrodynamic conditions is not obvious. Redox environment seems to be the key factor for manganese enrichment, which is mainly related to marine authigenic process.

Simulating a typhoon storm surge in the East Sea of China using a coupled model

A coupled numerical model with a 2' x 2' resolution grid has been developed and used to simulate five typical typhoon storm surges (5612, 7413, 7910, 8114, and 9711) in the East Sea of China. Three main driving forces have been considered in this coupled model: wave radiation stress, combined wave-current bottom shear stress and wave-state-dependent surface wind stress. This model has then been compared with in situ measurements of the storm set-up. The effect of different driving force components on the total storm surge has also been investigated. This study has found that the coupled model with high resolution is capable of simulating the five typical typhoons better than the uncoupled models, and that the wave-dependent surface wind stress plays an important role in typhoon storm surge-wave coupling in this area and can increase the storm set-up by 1 m. The study of the five typhoon cases has shown that the general coupling effects could increase storm set-up by 20-32%. Thus, it is suggested that to predict typhoon storm surges in the East Sea of China, a storm surge-wave coupled model be adopted. (C) 2008 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.

Improvement of different source function expressions in SWAN model for the Bohai Sea

The simulating wave nearshore (SWAN) wave model has been widely used in coastal areas, lakes and estuaries. However, we found a poor agreement between modeling results and measurements in analyzing the chosen four typical cases when we used the default parameters of the source function formulas of the SWAN to make wave simulation for the Bohai Sea. Also, it was found that at the same wind process the simulated results of two wind generation expressions (Komen, Janssen) demonstrated a large difference. Further study showed that the proportionality coefficient alpha in linear growth term of wave growth source function plays an unperceived role in the process of wave development. Based on experiments and analysis, we thought that the coefficient alpha should change rather than be a constant. Therefore, the coefficient alpha changing with the variation of friction velocity U (*) was introduced into the linear growth term of wave growth source function. Four weather processes were adopted to validate the improvement in the linear growth term. The results from the improved coefficient alpha agree much better with the measurements than those from the default constant coefficient alpha. Furthermore, the large differences of results between Komen wind generation expression and Janssen wind generation expression were eliminated. We also experimented with the four weather processes to test the new white-capping mechanisms based on the cumulative steepness method. It was found that the parameters of the new white-capping mechanisms are not suitable for the Bohai Sea, but Alkyon's white-capping mechanisms can be applicable to the Bohai Sea after amendments, demonstrating that this improvement of parameter alpha can improve the simulated results of the Bohai Sea.

The statistic inversion algorithms of water constituents for the Huanghai Sea and the East China Sea

A group of statistical algorithms are proposed for the inversion of the three major components of Case-H waters in the coastal area of the Huanghai Sea and the East China Sea. The algorithms are based on the in situ data collected in the spring of 2003 with strict quality assurance according to NASA ocean bio-optic protocols. These algorithms are the first ones with quantitative confidence that can be applied for the area. The average relative error of the inversed and in situ measured components' concentrations are: Chl-a about 37%, total suspended matter (TSM) about 25%, respectively. This preliminary result is quite satisfactory for Case-H waters, although some aspects in the model need further study. The sensitivity of the input error of 5% to remote sensing reflectance (Rrs) is also analyzed and it shows the algorithms are quite stable. The algorithms show a large difference with Tassan's local SeaWiFS algorithms for different waters, except for the Chl-a algorithm.

On the western boundary currents in the Philippine Sea

In this study we describe the velocity structure and transport of the North Equatorial Current (NEC), the Kuroshio, and the Mindanao Current (MC) using repeated hydrographic sections near the Philippine coast. A most striking feature of the current system in the region is the undercurrent structure below the surface flow. Both the Luzon Undercurrent and the Mindanao Undercurrent appear to be permanent phenomena. The present data set also provides an estimate of the mean circulation diagram (relative to 1500 dbar) that involves a NEC transport of 41 Sverdrups (Sv), a Kuroshio transport of 14 Sv, and a MC transport of 27 Sv, inducing a mass balance better than 1 Sv within the region enclosed by stations. The circulation diagram is insensitive to vertical displacements of the reference level within the depth range between 1500 and 2500 dbar. Transport fluctuations are, in general, consistent with earlier observations; that is, the NEC and the Kuroshio vary in the same phase with a seasonal signal superimposed with interannual variations, and the transport of the MC is dominated by a quasi-biennial oscillation. Dynamic height distributions are also examined to explore the dynamics of the current system.

Annual cycle of carbon, nitrogen and phosphorus in the Bohai Sea: A model study

The annual cycle of nutrient-phytoplankton dynamics in Bohai Sea (BS) is simulated using a coupled physical-biological model in this study. By comparison, the modeled seasonal variations of nutrients and primary productivity agree with observations rather well. Although the annual cycles of chlorophyll a and primary production are both characterized by a double-peak configuration, a structural difference is still apparent: the phytoplankton biomass reaches the highest value in spring while summer is characterized by the most productivity in the BS, which can be ascribed to the combined impact of seawater temperature and zooplankton-grazing pressure on the growth of algae. Based on the validated simulations, the annual budgets of carbon, nitrogen and phosphorus are estimated, and are about 0.82 mt C surplus, 39 kt N deficit and 12kt P surplus, respectively, implying that the BS ecosystem is somewhat nitrogen limited. The contribution of two external nutrient sources, namely river discharges and resuspended sediments, to the growth of algae is also examined numerically, and it is found that the influence of river-borne nutrients mainly concentrates in estuaries, whereas the reduction of sediment-borne nutrients may significantly inhibit the onset of algae bloom in the whole BS. (c) 2007 Elsevier Ltd. All rights reserved.

Annual cycle of stratification and tidal fronts in the Bohai Sea: A model study

In general, competition between buoyancy mechanisms and mixing dynamics largely determines the water column structure in a shelf sea. A three dimensional baroclinic ocean model forced by surface heat fluxes and the 2.5 order Mellor-Yamada turbulence scheme is used to simulate the annual cycle of the temperature in the Bohai Sea. The difference between the sea surface temperature (SST) and sea bottom temperature (SBT) is used to examine the evolution of its vertical stratification. It is found that the water column is well-mixed from October to March and that the seasonal thermocline appears in April, peaks in July and then weakens afterwards, closely following the heat budget. In addition, the Loder parameter based on the topography and tidal current amplitude is also computed in order to examine tidal fronts in the BS, which are evident in summer months when the wind stirring mechanism is weak.

A new empirical model for retrieving sea surface salinity in L band

Sea surface salinity is a key physical parameter in ocean science. It is important in the ocean remote sensing to retrieve sea surface salinity by the microwave probe technology. Based on the in situ measurement data and remote sensing data of the Yellow Sea, we have built a new empirical model in this paper, which can be used to retrieve sea surface salinity of the Yellow Sea by means of the brightness temperature of the sea water at L-band. In this model, the influence of the roughness of the sea surface is considered, and the retrieved result is in good agreement with the in situ measurement data, where the mean absolute error of the retrieved sea surface salinity is about 0.288 psu. This result shows that our model has greater retrieval precision compared with similar models.

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.

Persistent organic pollutant residues in the sediments and mollusks from the Bohai Sea coastal areas, North China: An overview

The Bohai Sea costal area is one of the most developed zones of China and the sewage water from populous and developed cities, including Beijing, Tianjin. Qinhuangdao and Dalian is discharged into the Bohai Sea. Additionally, its semi-enclosed characteristic restricts water exchange, which leads to high accumulation of pollutants in the environment. This overview presents the residues of 6 classes of Persistent Organic Pollutants (POPs). including PAHs, DDTs. HCHs, PCBs and PCDD/Fs. in the sediments and mollusks of the Bohai Sea through analyzing previous literatures. In the sediments. the highest PAH concentrations were detected in the vicinities of Qinhuangdao, while the northeast corner of the Bohai Bay possessed the highest levels of DDTs and PCBs. The investigations on HCHs and PCDD/Fs distributions on the whole sea scale have not been reported. In mollusks, PAH concentrations were in the same order of magnitude in the whole Bohai Sea, so were DDTs. HCHs and PCBs, while the outlier maximum values of PCDDs and PCDFs occurred in Yingkou. In general, the POPs residues in mollusks collected from Shandong Province were higher than the other areas. The compositions of DDTs, HCHs and PCBs in sediments indicated their recent usage. By comparing POP concentrations in sediments with the recommended criterions, it was shown that some individual PAH compounds occasionally associated with adverse biological effects in the vicinities of the Liaodong Bay and Qinhuangdao, and the Liaohe River Estuary were heavily contaminated with DDTs, but PCBs were all below the thresholds. In order to reveal the transference and transformation of POPs in the environment, further studies concerning with their behavior, fate and bioaccumulation in the different trophic levels should be programmed. Moreover, laws and regulations should be enforced to ban the illegal usage of POPs-containing pesticides to guarantee health of the environment and human. (C) 2008 Elsevier Ltd. All rights reserved.