Habitability analyses of aquatic bacteria

Habitability is defined as an ability of an organism to inhabit different environments. Habitability of organisms, however, cannot be inferred from analyses such as a whole genome or community structures. A recently developed database, the MetaMetaDB, gives us information from what kind of environments one particular 16S rRNA sequence data has ever been obtained, and thus enables us to infer the habitability of the bacterium in question. In order to check the applicability of this database to study the habitability of aquatic bacteria, samples collected at two Naka River stations, one estuarine station from Naka River Estuary, two coastal stations at Oarai in Ibaraki Prefecture, Japan and one station in the Kuroshio Current of the western North Pacific were examined. The phylotypes were tracked against the MetaMetaDB and it was reasonably found that the low-salinity stations were dominated by sequences with “freshwater and groundwater”, “human” and “wastewater” habitat identities, while the high-salinity stations were dominated by those with a “marine” identity. The phylotypes of low-salinity stations with a particular habitat identity were absent or rare in the high-salinity stations and vice versa. The MetaMetaDB also showed that sequences of Cyanobacteria or related phylogenetic groups may be present in the human gut, as well as the probable distribution of the relatives (ancestors/descendants/siblings) of some bacteria. These overall findings proved that the MetaMetaDB is useful as a new tool to infer microbial habitability and it gives us new information on the possible origin and ecology of microorganisms in the environments.     

User expectations for multibeam echo sounders backscatter strength data-looking back into the future

With the ability of multibeam echo sounders (MBES) to measure backscatter strength (BS) as a function of true angle of insonification across the seafloor, came a new recognition of the potential of backscatter measurements to remotely characterize the properties of the seafloor. Advances in transducer design, digital electronics, signal processing capabilities, navigation, and graphic display devices, have improved the resolution and particularly the dynamic range available to sonar and processing software manufacturers. Alongside these improvements the expectations of what the data can deliver has also grown. In this paper, we identify these user-expectations and explore how MBES backscatter is utilized by different communities involved in marine seabed research at present, and the aspirations that these communities have for the data in the future. The results presented here are based on a user survey conducted by the GeoHab (Marine Geological and Biological Habitat Mapping) association. This paper summarises the different processing procedures employed to extract useful information from MBES backscatter data and the various intentions for which the user community collect the data. We show how a range of backscatter output products are generated from the different processing procedures, and how these results are taken up by different scientific disciplines, and also identify common constraints in handling MBES BS data. Finally, we outline our expectations for the future of this unique and important data source for seafloor mapping and characterisation.     

Population Genetic Structure of Rock Bream (<Emphasis Type="Italic">Oplegnathus fasciatus</Emphasis> Temminck &amp; Schlegel, 1884) Revealed by mtDNA COI Sequence in Korea and China

The rock bream, Oplegnathus fasciatus, is a common rocky reef game fish in East Asia and recently has become an aquaculture species. Despite its commercial importance, the population genetic structure of this fish species remains poorly understood. In this study, 163 specimens were collected from 6 localities along the coastal waters of Korea and China and their genetic variation was analyzed with mtDNA COI sequences. A total of 34 polymorphic sites were detected which determined 30 haplotypes. The genetic pattern reveals a low level of nucleotide diversity (0.04 ± 0.003) but a high level of haplotype diversity (0.83 ± 0.02). The 30 haplotypes are divided into two major genealogical clades: one that consists of only Zhoushan (ZS, East China Sea) specific haplotypes from the southern East China Sea and the other that consists of the remaining haplotypes from the northern East China Sea, Yellow Sea, Korea Strait, and East Sea/Sea of Japan. The two clades are separated by approximately 330~435 kyBP. Analyses of AMOVA and F_st show a significant population differentiation between the ZS sample and the other ones, corroborating separation of the two genealogical clades. Larval dispersal and the fresh Yangtze River plume are invoked as the main determining factors for this population genetic structure of O. fasciatus. Neutrality tests and mismatch distribution analyses indicate late Pleistocene population expansion along the coastal waters of Korea and China approximately 133–183 kyBP during which there were periodic cycles of glaciations and deglaciations. Such population information needs to be taken into account when stock enhancement and conservation measures are implemented for this fisheries species.     

Variability in Particle Mixing Rates in Sediments with Polymetallic Nodules in the Equatorial Eastern Pacific as Determined from Measurements of Excess <Superscript>210</Superscript>Pb

Radionuclide activities of ²¹⁰Pb and ²²⁶Ra were measured to determine bioturbation coefficients (D_b) in seven sediment cores from the Korean licensed block for polymetallic nodules in the Clarion–Clipperton Fracture Zone. Variability in D_b is considered in the context of the sedimentological, geochemical, and geotechnical properties of the sediments. D_b values in the studied cores were estimated using a steady-state diffusion model and varied over a wide range from 1.1 to 293 cm²/yr with corresponding mixing depths (L) of 26 to 144 cm. When excepting for spurious results obtained from cores where diffusive mixing does not apply, D_b values range from 1.1 to 9.0 cm²/yr with corresponding mixing depths (L) of 26 to 63 cm. Such wide variability in D_b and L values is exceptional in sites with water depths of ～5000 m and is attributed in this study to an uneven distribution of sediment layers with different shear strengths and total organic carbon (TOC) contents, caused by erosion events. The studied cores can be grouped into two categories based on lithologic associations: layers with high maximum shear strength (MSS) and low TOC content, showing a narrow range of D_b values (1.1–9.0 cm²/yr); and layers with low MSS and high TOC content, yielding much higher D_b values of over 30 cm²/yr. The distribution of different lithologies, and the resultant spatial variability in MSS and labile organic matter content, controls the presence and maximum burrowing depth of infauna by affecting their mobility and the availability of food. This study provides a unique case showing that shear strength, which relates to the degree of sediment consolidation, might be an important factor in controlling rates of bioturbation and sediment mixing depths.     

Wave-induced Maintenance of Suspended Sediment Concentration during Slack in a Tidal Channel on a Sheltered Macro-tidal Flat,Gangwha Island,Korea

A field campaign was conducted to better understand the influence of wave action, in terms of turbulence and bed shear stress, on sediment resuspension and transport processes on a protected tidal flat. An H-frame was deployed in a tidal channel south of Gangwha Island for 6 tidal cycles during November 2006 with instrumentation including an Acoustic Doppler Velocimeter, an Acoustic Backscatter System, and an Optical Backscatter Sensor. During calm conditions, the current-induced shear was dominant and responsible for suspending sediments during the accelerating phases of flood and ebb. During the high-tide slack, both bed shear stress and suspended sediment concentration were reduced. The sediment flux was directed landward due to the scour-lag effect over a tidal cycle. On the other hand, when waves were stronger, the wave-induced turbulence appeared to keep sediments in suspension even during the high-tide slack, while the current-induced shear remained dominant during the accelerating phases of flood and ebb. The sediment flux under strong waves was directed offshore due to the sustained high suspended sediment concentration during the high-tide slack. Although strong waves can induce offshore sediment flux, infrequent events with strong waves are unlikely to alter the long-term accretion of the protected southern Gangwha tidal flats.     

Free Vibration Analysis of Symmetrically Laminated Composite Plates on Elastic Foundation and Coupled with Stationary Fluid

Free vibration analysis of symmetrically laminated composite plates resting on Pasternak elastic support and coupled with an ideal, incompressible and inviscid fluid is the objective of the present work. The fluid domain is considered to be infinite in the length direction but bounded in the depth and width directions. In order to derive the eigenvalue equation, Rayleigh-Ritz method is applied for the fluid-plate-foundation system. The efficiency of the method is proved by comparison studies with those reported in the open literature. At the end, parametric studies are carried out to examine the impact of different parameters on the natural frequencies.     

Optimization Design of Minimum Total Resistance Hull Form Based on CFD Method

In order to reduce the resistance and improve the hydrodynamic performance of a ship, two hull form design methods are proposed based on the potential flow theory and viscous flow theory. The flow fields are meshed using body-fitted mesh and structured grids. The parameters of the hull modification function are the design variables. A three-dimensional modeling method is used to alter the geometry. The Non-Linear Programming (NLP) method is utilized to optimize a David Taylor Model Basin (DTMB) model 5415 ship under the constraints, including the displacement constraint. The optimization results show an effective reduction of the resistance. The two hull form design methods developed in this study can provide technical support and theoretical basis for designing green ships.     

Lateral Bearing Capacity of Modified Suction Caissons Determined by Using the Limit Equilibrium Method

The modified suction caisson (MSC) adds a short-skirted structure around the regular suction caissons to increase the lateral bearing capacity and limit the deflection. The MSC is suitable for acting as the offshore wind turbine foundation subjected to larger lateral loads compared with the imposed vertical loads. Determination of the lateral bearing capacity is a key issue for the MSC design. The formula estimating the lateral bearing capacity of the MSC was proposed in terms of the limit equilibrium method and was verified by the test results. Parametric studies on the lateral bearing capacity were also carried out. It was found that the lateral bearing capacity of the MSC increases with the increasing length and radius of the external skirt, and the lateral bearing capacity increases linearly with the increasing coefficient of subgrade reaction. The maximum lateral bearing capacity of the MSC is attained when the ratio of the radii of the internal compartment to the external skirt equals 0.82 and the ratio of the lengths of the external skirt to the internal compartment equals 0.48, provided that the steel usage of the MSC is kept constant.