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.     

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.     

A multiphysics and multiscale software environment for modeling astrophysical systems

We present MUSE, a software framework for combining existing computational tools for different astrophysical domains into a single multiphysics, multiscale application. MUSE facilitates the coupling of existing codes written in different languages by providing inter-language tools and by specifying an interface between each module and the framework that represents a balance between generality and computational efficiency. This approach allows scientists to use combinations of codes to solve highly coupled problems without the need to write new codes for other domains or significantly alter their existing codes. MUSE currently incorporates the domains of stellar dynamics, stellar evolution and stellar hydrodynamics for studying generalized stellar systems. We have now reached a “Noah’s Ark” milestone, with (at least) two available numerical solvers for each domain. MUSE can treat multiscale and multiphysics systems in which the time- and size-scales are well separated, like simulating the evolution of planetary systems, small stellar associations, dense stellar clusters, galaxies and galactic nuclei. In this paper we describe three examples calculated using MUSE: the merger of two galaxies, the merger of two evolving stars, and a hybrid N-body simulation. In addition, we demonstrate an implementation of MUSE on a distributed computer which may also include special-purpose hardware, such as GRAPEs or GPUs, to accelerate computations. The current MUSE code base is publicly available as open source at http://muse.li.     

Magma-hydrothermal system interaction inferred from volcanic gas measurements obtained during 2003–2008 at Meakandake volcano,Hokkaido, Japan

Phreatic eruptions occurred at the Meakandake volcano in 1988, 1996, 1998, 2006, and 2008. We conducted geochemical surveillance that included measurements of temperature, SO₂ emission rates, and volcanic gas composition from 2003 to 2008 at the Nakamachineshiri (NM), Northwest (NW), and Akanuma (AK) fumarolic areas, and the 96–1 vent, where historical eruptions had occurred. The elemental compositions of the gases discharged from the different areas are similar compared with the large variations observed in volcanic gases discharged from subduction zones. All the gases showed high apparent equilibrium temperatures, suggesting that all these gases originated from a common magmatic gas. The gases discharged from each area also exhibited different characteristics, which are probably the results of differences in the conditions of meteoric water mixing, quenching of chemical reactions, and vapor-liquid separation. The highest apparent equilibrium temperatures (about 500°C) were observed in the case of NW fumarolic gases, despite the low outlet temperature of about 100°C at these fumaroles. Since the NW fumaroles were formed as a result of the 2006 phreatic eruption, the high-temperature gas supply to the NW fumarole suggests that the phreatic eruption was caused by the ascent of high-temperature magmatic gases. The temperatures, compositions, and emission rates of the NM and 96–1 gases did not show any appreciable change after the 2006 eruption, indicating that each fumarolic system had a separate magmatic-hydrothermal system. The temperatures, compositions, and emission rates of the NM fumarolic gases were apparently constant, and these fumaroles are inferred to be formed by the evaporation of a hydrothermal system with a constant temperature of about 300°C. The 96–1 gas compositions showed large changes during continuous temperature decrease from 390° to 190°C occurred from 2003 to 2008, but the sulfur gas emission rates were almost constant at about four tons/day. At the 96–1 vent, the SO₂/H₂S ratio decreased, while the H₂/H₂O ratio remained almost constant; this was probably caused by the rock-buffer controlled chemical reaction during the temperature decrease.     

Characteristics and regional classification of the copepod community in Ariake Bay with note on comparison with 3 decades ago

Ariake Bay, Kyushu Island, has recently exhibited environmental degradation in the form of red tides and anoxic bottom water. To determine the characteristics and regional classification of the copepod community, zooplankton surveys were made throughout the bay in three cruises each in October 2004, January 2005 and March 2009 by vertical tows of a 0.1-mm-mesh plankton net. Oithona davisae was the most abundant in January and March, and Microsetella norvegica in October. Cluster analysis revealed that the copepod community from each cruise was generally separated into the inner to eastern-middle region and the western-middle to mouth region. A SIMPER analysis revealed that dissimilarity between the groups and similarity within each group were mainly due to the dominant species, but the similarities within the outer-region group in January and March were mostly contributed by Paracalanus parvus s.l. A non-metric multidimensional scaling with bubble plots of environmental variables and a BIOENV analysis showed that transparency was more different between the two groups than temperature and salinity. As compared with two similarly sized, eutrophic bays (Tokyo and Osaka Bays), Ariake Bay differs from Tokyo Bay in the dominance of M. norvegica and from Osaka Bay in the high abundance of O. davisae even in the colder season. The dominant species and the regional classification of the copepod community in the bay were similar to those in the studies in the 1970s, suggesting that the copepod community has not notably changed during the last 3 decades.     

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.     

Effect of temperature on the methyl chloride production rate in a marine phytoplankton, <Emphasis Type="Italic">Phaeodactylum tricornutum</Emphasis>

Methyl halides such as methyl chloride (CH₃Cl) are known to be important carriers of halogen from the ocean to the atmosphere, and the halogens they release into the stratosphere by photolysis catalyze ozone depletion. Marine phytoplankton have been reported as a source of CH₃Cl, but the effects of environmental temperature on the CH₃Cl production by phytoplankton have not been investigated. In this study, we investigated the effects of temperature on the production of CH₃Cl in the culture of a marine diatom, Phaeodactylum tricornutum CCMP 630, incubated at 10, 15, 20, 25, and 30 °C. CH₃Cl concentrations in cultured samples were determined using purge and trap gas chromatograph–mass spectrometry. Phytoplankton growth was monitored by measuring the chlorophyll a concentrations. CH₃Cl production was observed for several weeks at four different temperatures ranging from 10 to 25 °C. The CH₃Cl production from P. tricornutum was increased with increasing temperature from 10 to 25 °C, and the maximum production rate for CH₃Cl was 0.21~0.26 μmol (g chlorophyll a)^?1 d^?1 at 25 °C, which was several times higher than that at 10 °C (~0.03 μmol (g chlorophyll a)^?1 d^?1). The Arrhenius equation was successfully used to characterize the effects of temperature on the production rates of CH₃Cl in the culture of P. tricornutum. Our results suggest that water temperature directly affects CH₃Cl production derived from P. tricornutum and that water temperature would be a significant factor for estimating the emissions of CH₃Cl from marine environments.     

Magmatic fluids of Tatun volcanic group,Taiwan

Two distinctive magmatic fluids were recognized in the Tatun volcanic group (TVG), Taiwan. One is a relatively reduced fluid represented by the fumarolic gases at Hsiao-you-ken (HYK) geothermal field. Another is an oxidized fluid containing high concentrations of HCl represented by the fumarolic gases at Da-you-ken (DYK). An intermediate gas was recognized at Gung-tze-ping (GTP) and She-hung-ping (SHP). The fumarolic gases at HYK and GTP possess the features of so-called primary steam generated on mixing of magmatic gas and meteoric groundwater. The fumarolic gases at DYK are a simple mixture between magmatic gas and water vapor of meteoric origin. The CO₂/H₂O molar ratio of the magmatic component in the fumarolic gases at DYK was estimated to be 0.018, meanwhile it was estimated to be 0.027 for the fumarolic gases at HYK and GTP, suggesting the magma beneath DYK is depleted in volatiles relative to the magma beneath HYK and GTP. The estimated CO₂/H₂O ratio for the magmatic component is comparable to that of some active volcanoes in Japan, suggesting the enrichment of volatiles in the magmas beneath TVG.     

Study of the effect of water-soluble fractions of heavy-oil on coastal marine organisms using enclosed ecosystems,mesocosms

Mesocosm facilities composed of 4 experimental and 2 reservoir tanks (1.5 m in diameter, 3.0 m in depth and 5 tons in capacity) made of FRP plastics, were constructed in the concrete fish rearing pond in the Fisheries Laboratory, The University of Tokyo. The water-soluble fraction of Rank A heavy residual oil was formed by mixing 500 g of the oil with 10 l of seawater, which was introduced to the 5000 l-capacity tanks. Experimental Run 4 was conducted from May 31 to June 7, 2000. Oil concentrations in the tanks were 4.5 microg/l called LOW, and 13.5 microg/l, called HIGH tank. Bacterial growth rates very quickly accelerated in the HIGH tank just after the loading of oil which corresponded with a high increase of bacterial cells in the same tank after 2 days. Later, bacterial numbers in HIGH tank rapidly decreased, corresponding with the rapid increase of heterotrophic nano-flagellates and virus numbers on the same day. Sediment traps were deployed at the bottom of the experimental tanks, and were periodically retrieved. These samples were observed both under light microscope and epi-fluorescent microscope with UV-excitation. It was observed that the main components of the vertical flux were amorphous suspended matter, mostly originating from dead phytoplankton and living diatoms. It was further observed from the pictures that vertical transport of oil emulsions were probably conducted after adsorption to amorphous suspended matter and living diatoms, and were settling in the sediment traps at the bottom of the tanks. This means that the main force which drives the soluble fraction of oil into bottom sediment would be vertical flux of such amorphous suspended particles and phytoplankton. Further incubation of the samples revealed that the oil emulsions were degraded by the activity of autochtonous bacteria in the sediment in aerobic condition.     

The electromagnetic pickup of submicron-sized dust above Enceladus’s northern hemisphere

As the saturnian magnetoplasma sweeps past Enceladus, it experiences both a decrease in electron content and sharp slowdown in the northern hemisphere region within ～5 Enceladus Radii (R_e). This slowdown is observed by Cassini in regions not obviously associated with the southern directed plume-originating ions. We suggest herein that the decrease in northern hemisphere electron content and plasma slowdown could both be related to the presence of fine dust grains that are being accelerated by the Lorentz force created within the saturnian magnetic field system.