Vertical distribution of bacterial and archaeal communities along discrete layers of a deep-sea cold sediment sample at the East Pacific Rise (similar to 13 degrees N)

The community structure and vertical distribution of prokaryotes in a deep-sea (ca. 3,191 m) cold sediment sample (ca. 43 cm long) collected at the East Pacific Rise (EPR) similar to 13 degrees N were studied with 16SrDNA-based molecular analyses. Total community DNA was extracted from each of four discrete layers EPRDS-1, -2, -3 and -4 (from top to bottom) and 16S rDNA were amplified by PCR. Cluster analysis of DGGE profiles revealed that the bacterial communities shifted sharply between EPRDS-1 and EPRDS-2 in similarity coefficient at merely 49%. Twenty-three sequences retrieved from DGGE bands fell into 11 groups based on BLAST and bootstrap analysis. The dominant groups in the bacterial communities were Chloroflexi, Gamma proteobacteria, Actinobacterium and unidentified bacteria, with their corresponding percentages varying along discrete layers. Pairwise Fst (F-statistics) values between the archaeal clone libraries indicated that the archaeal communities changed distinctly between EPRDS-2 and EPRDS-3. Sequences from the archaeal libraries were divided to eight groups. Crenarchaea Marine Group I (MGI) was prevalent in EPRDS-1 at 83%, while Uncultured Crenarchaea group II B (UCII B) abounded in EPRDS-4 at 61%. Our results revealed that the vertically stratified distribution of prokaryotic communities might be in response to the geochemical settings and suggested that the sampling area was influenced by hydrothermalism. The copresence of members related to hydrothermalism and cold deep-sea environments in the microbial community indicated that the area might be a transitional region from hydrothermal vents to cold deep-sea sediments.

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.

Impact of difference accuracy on computational properties of vertical grids for a nonhydrostatic model

Starting from nonhydrostatic Boussinesq approximation equations, a general method is introduced to deduce the dispersion relationships. A comparative investigation is performed on inertia-gravity wave with horizontal lengths of 100, 10 and 1 km. These are examined using the second-order central difference scheme and the fourth-order compact difference scheme on vertical grids that are currently available from the perspectives of frequency, horizontal and vertical component of group velocity. These findings are compared to analytical solutions. The obtained results suggest that whether for the second-order central difference scheme or for the fourth-order compact difference scheme, Charny-Phillips and Lorenz ( L) grids are suitable for studying waves at the above-mentioned horizontal scales; the Lorenz time-staggered and Charny-Phillips time staggered (CPTS) grids are applicable only to the horizontal scales of less than 10 km, and N grid ( unstaggered grid) is unsuitable for simulating waves at any horizontal scale. Furthermore, by using fourth-order compact difference scheme with higher difference precision, the errors of frequency and group velocity in horizontal and vertical directions produced on all vertical grids in describing the waves with horizontal lengths of 1, 10 and 100 km cannot inevitably be decreased. So in developing a numerical model, the higher-order finite difference scheme, like fourth-order compact difference scheme, should be avoided as much as possible, typically on L and CPTS grids, since it will not only take many efforts to design program but also make the calculated group velocity in horizontal and vertical directions even worse in accuracy.

Effect of low-frequency Rossby wave on thermal structure of the upper southwestern tropical Indian Ocean

We investigate the influence of low-frequency Rossby waves on the thermal structure of the upper southwestern tropical Indian Ocean (SWTIO) using Argo profiles, satellite altimetric data, sea surface temperature, wind field data and the theory of linear vertical normal mode decomposition. Our results show that the SWTIO is generally dominated by the first baroclinic mode motion. As strong downwelling Rossby waves reach the SWTIO, the contribution of the second baroclinic mode motion in this region can be increased mainly because of the reduction in the vertical stratification of the upper layer above thermocline, and the enhancement in the vertical stratification of the lower layer under thermocline also contributes to it. The vertical displacement of each isothermal is enlarged and the thermal structure of the upper level is modulated, which is indicative of strong vertical mixing. However, the cold Rossby waves increase the vertical stratification of the upper level, restricting the variability related to the second baroclinic mode. On the other hand, during decaying phase of warm Rossby waves, Ekman upwelling and advection processes associated with the surface cyclonic wind circulation can restrain the downwelling processes, carrying the relatively colder water to the near-surface, which results in an out-of-phase phenomenon between sea surface temperature anomaly (SSTA) and sea surface height anomaly (SSHA) in the SWTIO.

Reconstruction of vertical thermal structure from several subsurface temperatures in the China Seas and adjacent waters

Empirical Orthogonal Function (EOF) analysis is used in this study to generate main eigenvector fields of historical temperature for the China Seas (here referring to Chinese marine territories) and adjacent waters from 1930 to 2002 (510 143 profiles). A good temperature profile is reconstructed based on several subsurface in situ temperature observations and the thermocline was estimated using the model. The results show that: 1) For the study area, the former four principal components can explain 95% of the overall variance, and the vertical distribution of temperature is most stable using the in situ temperature observations near the surface. 2) The model verifications based on the observed CTD data from the East China Sea (ECS), South China Sea (SCS) and the areas around Taiwan Island show that the reconstructed profiles have high correlation with the observed ones with the confidence level > 95%, especially to describe the characteristics of the thermocline well. The average errors between the reconstructed and observed profiles in these three areas are 0.69A degrees C, 0.52A degrees C and 1.18A degrees C respectively. It also shows the model RMS error is less than or close to the climatological error. The statistical model can be used to well estimate the temperature profile vertical structure. 3) Comparing the thermocline characteristics between the reconstructed and observed profiles, the results in the ECS show that the average absolute errors are 1.5m, 1.4 m and 0.17A degrees C/m, and the average relative errors are 24.7%, 8.9% and 22.6% for the upper, lower thermocline boundaries and the gradient, respectively. Although the relative errors are obvious, the absolute error is small. In the SCS, the average absolute errors are 4.1 m, 27.7 m and 0.007A degrees C/m, and the average relative errors are 16.1%, 16.8% and 9.5% for the upper, lower thermocline boundaries and the gradient, respectively. The average relative errors are all < 20%. Although the average absolute error of the lower thermocline boundary is considerable, but contrast to the spatial scale of average depth of the lower thermocline boundary (165 m), the average relative error is small (16.8%). Therefore the model can be used to well estimate the thermocline.

A unified criterion for initiation of sediment motion and inception of sheet flow under water waves

A unified criterion is developed for initiation of non-cohesive sediment motion and inception of sheet flow under water waves over a horizontal bed of sediment based on presently available experimental data. The unified threshold criterion is of the single form, U-o = 2 pi C[1 + 5(T-R/T)(2)](-1/4), where U-o is the onset velocity of sediment motion or sheet flow, T is wave period, and C and T-R are the coefficients. It is found that for a given sediment, U-o initially increases sharply with wave period, then gradually approaches the maximum onset velocity U-o = 2 pi C and becomes independent of T when T is larger. The unified criterion can also be extended to define sediment initial motion and sheet flow under irregular waves provided the significant wave orbital velocity and period of irregular waves are introduced in this unified criterion.

Numerical modeling of water wave interaction with a soft mud bed

A vertical 2-D numerical model is presented for simulating the interaction between water waves and a soft mud bed. Taking into account nonlinear rheology, a semi-empirical rheological model is applied to this water-mud model, reflecting the combined visco-elasto-plastic properties of soft mud under such oscillatory external forces as water waves. In order to increase the resolution of the flow in the neighborhood of both sides of the inter-surface, a logarithmic grid in the vertical direction is employed for numerical treatment. Model verifications are given through comparisons between the calculated and the measured mud mass transport velocities as well as wave height changes.

Numerical wave flume study on wave motion around submerged plates

Nonlinear interaction between surface waves and a submerged horizontal plate is investigated in the absorbed numerical wave flume developed based on the volume of fluid (VOF) method. The governing equations of the numerical model are the continuity equation and the Reynolds-Averaged Navier-Stokes (RANS) equations with the k-epsilon turbulence equations. Incident waves are generated by an absorbing wave-maker that eliminates the waves reflected from structures. Results are obtained for a range of parameters, with consideration of the condition under which the reflection coefficient becomes maximal and the transmission coefficient minimal. Wave breaking over the plate, vortex shedding downwave, and pulsating flow below the plate are observed. Time-averaged hydrodynamic force reveals a negative drift force. All these characteristics provide a reference for construction of submerged plate breakwaters.

Ship-board measurements and estimations of air-sea fluxes in the western tropical Pacific during TOGA COARE

Direct air-sea flux measurements were made on RN Kexue #1 at 40 degrees S, 156 degrees E during the Tropical Ocean Global Atmosphere (TOGA) Coupled Ocean-Atmospheric Response Experiment (COARE) Intensive Observation Period (IOP). An array of six accelerometers was used to measure the motion of the anchored ship, and a sonic anemometer and Lyman-alpha hygrometer were used to measure the turbulent wind vector and specific humidity. The contamination of the turbulent wind components by ship motion was largely removed by an improvement of a procedure due to Shao based on the acceleration signals. The scheme of the wind correction for ship motion is briefly outlined. Results are presented from data for the best wind direction relative to the ship to minimize flow distortion effects. Both the time series and the power spectra of the sonic-measured wind components show swell-induced ship motion contamination, which is largely removed by the accelerometer correction scheme, There was less contamination in the longitudinal wind component than in the vertical and transverse components. The spectral characteristics of the surface-layer turbulence properties are compared with those from previous land and ocean results, Momentum and latent heat fluxes were calculated by eddy correlation and compared to those estimated by the inertial dissipation method and the TOGA COARE bulk formula. The estimations of wind stress determined by eddy correlation are smaller than those from the TOGA COARE bulk formula, especially for higher wind speeds, while those from the bulk formula and inertial dissipation technique are generally in agreement. The estimations of latent heal flux from the three different methods are in reasonable agreement. The effect of the correction for ship motion on latent heat fluxes is not as large as on momentum fluxes.

STUDY ON THE FORMATIONAL MECHANISM OF THE NORTHERN YELLOW (HUANGHAI) SEA COLD WATER MASS .2. DISCUSSION ON THE SOLUTION OF THE MODEL

The theoretical solution of the model of the Northern Yellow (Huanghai) Sea Cold Water Mass (NYSCWM) reveals that the NYSCWM is mainly formed through the continuous temperature increase of the overwintered water body above the Northern Yellow Sea Depression (NYSD) after spring when heat is continuously conducted from the sea surface to the deeper layer. In the NYSCWM's growing period, (June-July), nonlinear vertical convection and advection effects continuously increase, and are gradually balanced by the heat diffusion effect as the temperature increases from the surface to the bottom, which leads to the formation of an intensive thermocline and lateral front. Meanwhile, the three-dimensional circulation correspondingly occurs. In the NYSCWM's entire growing period, the horizontal circulation is always in the cyclonic motion, while the vertical circulation passes through a transition from a period with the cold centre as downwelling to a period with the cold centre as upwelling.

Submesoscale activity over the shelf of the northern South China Sea in summer: simulation with an embedded model

We applied a primitive equation ocean model to simulate submesoscale activities and processes over the shelf of the northern South China Sea (NSCS) with a one-way nesting technology for downscaling. The temperature and density fields showed that submesoscale activities were ubiquitous in the NSCS shelf. The vertical velocity was considerably enhanced in submesoscale processes and could reach an average of 58 m per day in the subsurface. At this point, the mixed layer depth also was deepened along the front, and the surface kinetic energy also increased with the intense vertical movement induced by submesoscale activity. Thus, submesoscale stirring/mixing is important for tracers, such as temperature, salinity, nutrients, dissolved organic, and inorganic carbon. This result may have implication for climate and biogeochemical investigations.

Vertical structure and evolution of the Luzon Warm Eddy

Eddies are frequently observed in the northeastern South China Sea (SCS). However, there have been few studies on vertical structure and temporal-spatial evolution of these eddies. We analyzed the seasonal Luzon Warm Eddy (LWE) based on Argo float data and the merged data products of satellite altimeters of Topex/Poseidon, Jason-1 and European Research Satellites. The analysis shows that the LWE extends vertically to more than 500 m water depth, with a higher temperature anomaly of 5A degrees C and lower salinity anomaly of 0.5 near the thermocline. The current speeds of the LWE are stronger in its uppermost 200 m, with a maximum speed of 0.6 m/s. Sometimes the LWE incorporates mixed waters from the Kuroshio Current and the SCS, and thus has higher thermohaline characteristics than local marine waters. Time series of eddy kinematic parameters show that the radii and shape of the LWE vary during propagation, and its eddy kinetic energy follows a normal distribution. In addition, we used the empirical orthogonal function (EOF) here to analyze seasonal characteristics of the LWE. The results suggest that the LWE generally forms in July, intensifies in August and September, separates from the coast of Luzon in October and propagates westward, and weakens in December and disappears in February. The LWE's westward migration is approximately along 19A degrees N latitude from northwest of Luzon to southeast of Hainan, with a mean speed of 6.6 cm/s.

Diel vertical migration of zooplankton following optimal food intake under predation

A model is developed to investigate the trade-offs between benefits and costs involved in zooplanktonic diel vertical migration (DVM) strategies. The 'venturous revenue' (VR) is used as the criterion for optimal trade-offs. It is a function of environmental factors and the age of zooplankter. During vertical migration, animals are assumed to check instantaneously the variations of environmental parameters and thereby select the optimal behavioral strategy to maximize the value of VR, i.e. taking up as much food as possible with a certain risk of mortality. The model is run on a diel time scale (24 h) in four possible scenarios during the animal's life history. The results show that zooplankton can perform normal DVM balancing optimal food intake against predation risk, with the profile of DVM largely modified by the age of zooplankter.

Control mechanisms of diel vertical migration: Theoretical assumptions

We explore control mechanisms underlying the vertical migration of zooplankton in the water column under the predator-avoidance hypothesis. Two groups of assumptions in which the organisms are assumed to migrate vertically in order to minimize realized or effective predation pressure (type-I) and to minimize changes in realized or effective predation pressure (type-II), respectively, are investigated. Realized predation pressure is defined as the product of light intensity and relative predation abundance and the part of realized predation pressure that really affects organisms is termed as effective predation pressure. Although both types of assumptions can lead to the migration of zooplankton to avoid the mortality from predators, only the mechanisms based on type-II assumptions permit zooplankton to undergo a normal diel vertical migration (morning descent and evening ascent). The assumption of minimizing changes in realized predation pressure is based on consideration of DVM induction only by light intensity and predators. The assumption of minimizing changes in effective predation pressure takes into account, apart from light and predators also the effects of food and temperature. The latter assumption results in the same expression of migration velocity as the former one when both food and temperature are constant over water depth. A significant characteristic of the two type-II assumptions is that the relative change in light intensity plays a primary role in determining the migration velocity. The photoresponse is modified by other environmental variables: predation pressure, food and temperature. Both light and predation pressure are necessary for organisms to undertake DVM. We analyse the effect of each single variable. The modification of the phototaxis of migratory organisms depends on the vertical distribution of these variables. (C) 2001 Academic Press.