Particulate peptidoglycan in seawater determined by the silkworm larvae plasma (SLP) assay

Peptidoglycan (PG) is a biopolymer found exclusively in the cell wall of bacteria. Recent chemical analysis of particulate organic matter suggests that a major amount of the muramic acid, an amino sugar present only in PG, could not be accounted for in terms of bacterial cells (Benner and Kaiser, 2003); however, data on particulate PG is quite sparse. In the present study, conducted in 1996, the PG was examined at 5 sampling sites in the northwestern Pacific Ocean, and in natural seawater cultures. Particulate PG, which was concentrated using a 96-well filtration plate equipped with Durapore filters (pore size, 0.22 μm), was measured by the silkworm larvae plasma (SLP) assay. The PG concentration generally decreased with depth and correlated significantly with bacterial abundance throughout the entire water column. However, the ratio of particulate PG to bacterial abundance varied with depth. The average ratio was 0.61 ± 0.53 (average ± SD, n = 40) between 50 and 2000 m, which agreed with the bacterial cellular PG content from 0.63 to 1.1 fg cell⁻¹ obtained in seawater cultures. On the other hand, the ratios of PG to bacteria from the surface to 50 m (3.7 ± 2.6, n = 29) and below 2,000 m (2.1 ± 1.7, n = 7) were significantly higher than that between 50 and 2,000 m. These results may suggest that, in the surface and deep layers, a significant fraction of particulate PG was present in bacterial detritus, whereas this fraction was reduced in the middle layer.     

Detecting fluctuations of the Kuroshio axis south of Japan using TOPEX/POSEIDON altimeter data

Sea surface dynamic topography (SSDT) can be divided into temporal mean SSDT and fluctuation SSDT. The former is approximated with a climatological mean SSDT and the latter is derived from satellite altimetry data, to give an approximated total SSDT (called a composite SSDT). The method is applied to detecting fluctuations of the Kuroshio axis south of Japan using TOPEX/POSEIDON altimeter data from the first year mission in 1992–1993. The fluctuation SSDT averaged over a wide area south of Japan clearly shows an annual cycle with an amplitude of about 15 cm. Temporal changes of SSDT along a subsatellite track crossing the Kuroshio compare moderately well with those estimated from repeated hydrographic observations, although there is a discrepancy of unknown origin. The composite SSDT also compares well with SSDT estimated from the same hydrographic data. Horizontal distribution of the surface geostrophic velocity component normal to subsatellite tracks is derived every ten days from the composite SSDT. Most locations of estimated strong eastward geostrophic velocities coincide well with locations of the Kuroshio axis determined every 15 days fromin situ surface velocity measurements on various vessels; for example, a fairly large meander of the Kuroshio south of Honshu is clearly detected. It is concluded that the composite SSDT can be used reliably to detect fluctuations of the Kuroshio axis south of Japan.     

Nitrogen isotopic discrimination by water column nitrification in a shallow coastal environment

Temporal changes in nitrogen isotopic composition (δ¹⁵N) of the NO₃ ⁻ pool in the water column below the pycnocline in Ise Bay, Japan were investigated to evaluate the effect of nitrification on the change in the δ¹⁵N in the water column. The δ¹⁵N of NO₃ ⁻ in the lower layers varied from −8.5‰ in May to +8.4‰ in July in response to the development of seasonal hypoxia and conversion from NH₄ ⁺ to NO₃ ⁻. The significantly ¹⁵N-depleted NO₃ ⁻ in May most likely arose from nitrification in the water column. The calculated apparent isotopic discrimination for water column nitrification (ɛ_nit = δ¹⁵N_substrate − δ¹⁵N_product) was 24.5‰, which lies within the range of previous laboratory-based estimates. Though prominent deficits of NO₃ ⁻ from hypoxic bottom waters due to denitrification were revealed in July, the isotopic discrimination of denitrification in the sediments was low (ɛ_denit = ∼1‰). δ¹⁵N_NO3 in the hypoxic lower layer mainly reflects the isotopic effect of water column nitrification, given that water column nitrification is not directly linked with sedimentary denitrification and the effect of sedimentary denitrification on the change in δ¹⁵N_NO3 is relatively small.     

Modified Moving Particle Semi-implicit methods for the prediction of 2D wave impact pressure

As a gridless particle method, the MPS (Moving Particle Semi-implicit) method has proven useful in a wide variety of engineering applications including free-surface hydrodynamic flows. Despite its wide range of applicability, the MPS method suffers from some shortcomings such as non-conservation of momentum and spurious pressure fluctuation. By introducing new formulations for the pressure gradient and a new formulation of the source term of the Poisson Pressure Equation (PPE), and by allowing a slight compressibility, we have proposed modified MPS methods for the prediction of wave impact pressure on a coastal structure. The improved performance of the modified methods is shown through the simulation of numerous wave impact problems (including the impacts by a dam break flow, a flip-through and two cases of slightly-breaking waves) in comparison with the experimental data.     

Microbial responses using denaturing gradient gel electrophoresis to oil and chemical dispersant in enclosed ecosystems

Microbial responses to the addition of oil with or without a chemical dispersant were examined in mesocosm and microcosm experiments by using denaturing gradient gel electrophoresis of bacterial ribosomal DNA and direct cell counting. When a water-soluble fraction of oil was added to seawater, increases in cell density were observed in the first 24h, followed by a decrease in abundance and a change in bacterial species composition. After addition of an oil-dispersant mixture, increases in cell density and changes in community structure coincided, and the amount of bacteria remained high. These phenomena also occurred in response to addition of only dispersant. Our results suggest that the chemical dispersant may be used as a nutrient source by some bacterial groups and may directly or indirectly prevent the growth of other bacterial groups.     

Hysteresis and Surface Shear Stresses During Snow-Particle Aeolian Transportation

Boundary-Layer Meteorology - Surface shear stresses produced by wind and particle collision play a key role in aerodynamic entrainment and splash processes. The fluid shear stress at the surface...     

The succession of microbial community in the organic rich fish-farm sediment during bioremediation by introducing artificially mass-cultured colonies of a small polychaete, Capitella sp. I

We monitored seasonal changes of the abundance and composition of microorganisms in the fish-farm sediment in Kusuura Bay, Amakusa, Japan, using the quinone profiling technique, during bioremediation by introducing cultured colonies of polychaete, Capitella sp. I. In November 2004, approximately 9.2 million cultured worms were transferred to the fish-farm sediment, which increased rapidly, and reached 458.5 gWW/m(2) (528,000 indiv./m(2)) in March 2005. During this fast-increasing period of Capitella, the microbial quinone content of the surface sediment (0-2 cm) also increased markedly, and reached 237 micromol/m(2) in January 2005, although the water temperature decreased to the lowest levels in the year. Particularly, the mole fraction of ubiquinone-10 in total quinones in the sediment, indicating the presence of alpha subclass of Proteobacteria, increased by 9.3%. These facts suggest that the bacterial growth was enhanced markedly by the biological activities of worms in the sediment, and the bacteria played an important role in the decomposition of the organic matter in the sediment.     

Transport of oceanic nitrate from the continental shelf to the coastal basin in relation to the path of the Kuroshio

Hydrographic and biogeochemical observations were conducted along the longitudinal section from Ise Bay to the continental margin (southern coast of Japan) to investigate changes according to the Kuroshio path variations during the summer. The strength of the uplift of the cold deep water was influenced by the surface intrusion of the Kuroshio water to the shelf region. When the intrusion of the Kuroshio surface water to the shelf region was weak in 2006, the cold and NO₃⁻-rich shelf water intruded into the bottom layer in the bay from the shelf. This bottom intrusion was intensified by the large river discharge. The nitrogen isotope ratio (δ¹⁵N) of NO₃⁻ (4–5‰) in the bottom bay water was same as that in the deeper NO₃⁻ over the shelf, indicating the supply of new nitrogen to the bay. The warm and NO₃⁻-poor shelf water intruded into the middle layer via the mixing region at the bay mouth when the Kuroshio water distributed in the coastal areas off Ise Bay in 2005. The regenerated NO₃⁻ with isotopically light nitrogen (δ¹⁵N=−1‰) was supplied from the shelf to the bay. This NO₃⁻ is regenerated by the nitrification in the upper layer over the shelf. The contribution rate of regenerated NO₃⁻ over the shelf to the total NO₃⁻ in the subsurface chlorophyll maximum layer in the bay was estimated at 56% by a two-source mixing model coupled with the Rayleigh equation.