Characterization of depth-related changes and site-specific differences of microbial communities in marine sediments using quinone profiles

ABSTRACT:   Respiratory quinone compositions were analyzed by a high-performance liquid chromatography to characterize the depth-related changes and site-specific differences of microbial communities in marine sediments. Two deep-sea sediment samples and one coastal sediment sample were investigated from three sites on the coast of Japan, Sagami Bay, Suruga Bay and Tokyo Bay. Although depth-related changes in microbial community structures were observed, site-specific differences appeared to have greater influence on overall community structures. A variety of quinone homologs was commonly identified at all sampling sites and depths examined, but a few minor quinone fractions, mainly derived from Actinobacteria , were detected only at specific sampling sites. Methylmenaquinone-7 (MMK-7) was the major component throughout the examined depths in Sagami Bay and Tokyo Bay. Most abundant quinone homologs changed with each depth in Suruga Bay. Menaquinone-6 (MK-6) predominated in the 0 to 2-cm layer (19%). Below 0–2 cm, the most abundant homolog in each sampling depth was phylloquinone (K₁; 13%, 4–6 cm), MK-8 (19%, 8–10 cm) and MK-7 (13%, 16–18 cm). The microbial respiratory quinone profiling method shown here, successfully demonstrates the usefulness of this approach to characterize microbial communities in marine sediments.     

Amorphous clay materials of towada ando soils

Towada Ando soils consisted of five soils—Towada-a (1,000 years old), Towada-b (2,000 years old), Chuseri (4,000 years old), Nanbu (8,600 years old), and Ninokura soils (10,000 years Amorphous clay materials of these soils taken at different localities were studied by the combined use of selective dissolution and differential infrared spectroscopy, X-ray analysis, electron microscopy, etc.

The main clay minerals of Towada-a soils, present-day soils, were montmorillonite-vermic-ulite chloritic intergrades and opaline silica, or these minerals and allophane in the humus horizons, and allophane in the non-humus ones. Towada-b soils overlain by the Towada-a soils showed the clay mineralogical constituents similar to those of Towada-a soils. However, allophane was one of the main clay minerals in all the humus horizons as well as non-humus ones. The main clay minerals of Chuseri soils were allophane and layer silicates consisting chiefly of chloritic intergrades and chlorite in the humus horizons, and allophane in the non-humus ones. Opaline silica was present in minor amounts in the humus horizons of Chuseri soils, but nearly absent in Nanbu and Ninokura soils.

There were remarkable differences in the clay mineralogical composition of Nanbu and Ninokura soils with differences of their environmental conditions. Allophane and imogolite Were dominant in the clay fractions of both humus and non-humus horizons of very shallowly buried Nanbu soil which was subjected to the strong leaching process. Allophane was the main clay mineral of deeply buried Nanbu and Ninokura soils which showed the absence of notable accumulation of bases and silica. On the contrary, halloysite with a small amount of siliceous amorphous material appeared in very deeply buried Nanbu and Ninokura soils where bases and silica were distinctly accumulated. The amounts of halloysite in the clay fractions were larger in the humus horizons than non-humus ones, and in Ninokura soil than Nanbu soil.

Soil age, soil organic matter, and depositional overburden of tephras were observed to be conspicuous among various factors relating to the weathering of amorphous clay materials in Towada Ando soils.     

Sites and processes of nutrient accumulation in the subsoil through water percolation from the plow layer in a submerged paddy soil microcosm

The leaching of nutrients from the plow layer by water percolation and their accumulation in the subsoil observed in a Japanese paddy field (Katoh et al. 2004: Soil Sci. Plant Nutr., 50, 721-729) were determined semi-quantitatively in a soil column experiment. Ca²⁺, Mg²⁺, K⁺, Mn²⁺, Fe²⁺, and phosphate in percolating water from the plow layer soil column were retained in the subsoil columns that were connected to the plow layer soil column. Fe²⁺, K⁺, and phosphate accumulated in the uppermost part of the subsoil. Accumulation of Fe²⁺ in the uppermost part of the subsoil was presmnably due to the cation exchange process with concomitant desorption of Ca²⁺. In contrast, Ca²⁺ and Mg²⁺ in percolating water from the plow layer soil colmnn accumulated once in the subsoil, and translocated downwards slowly with successive water percolation. Considerable amounts of inorganic carbon (IC) and dissolved organic carbon (DOC) in percolating water from the plow layer soil column were also retained in the subsoil columns. IC did not accumulate a gaseous form.     

Measurement of the maximum amount of water-extractable phosphorus in animal manure compost by continuous and sequential water extraction

Measuring the phosphorus (P) solubility in animal manure compost (AMC) is important to estimate both the risk of P loss from agricultural land and the P availability for crops in agriculture that use AMC as fertilizer. Water-extractable phosphorus (WEP) has most often been used to estimate P solubility in AMC. A single water extraction with a high ratio of compost to water is usually used to determine WEP, but in many cases, this may not evaluate the maximum WEP. In this study, we extracted the P included in AMC by using a continuous extraction method with a large amount of water, and tested this approach for 16 AMCs: four cattle manure composts, five swine manure composts, five layer (chicken) manure composts, and two broiler (chicken) litter composts. The P dissolution patterns were fitted to kinetic models, and the maximum WEP (WEP_max) was determined by the coefficient of the non-linear regression equation. The WEP_max values corresponded to the sum of H₂O- and sodium bicarbonate (NaHCO₃)-extractable P measured using the modified Hedley sequential extraction method. The result also suggests that the maximum amount of WEP from AMC can be estimated rapidly using a sequential extraction (the Hedley method) that has been widely used to characterize P in manure or AMC. The maximum water-extractable magnesium (Mg) (WEMg_max) was significantly positively correlated with WEP_max (r = 0.854, P < 0.01). This suggests that WEP_max in the AMCs is affected by water-soluble magnesium compounds.     

A weeding-duration model for Abies sachalinensis plantations in Hokkaido, northern Japan

I developed a weeding-duration model for Sakhalin fir (Abies sachalinensis (Fr. Schmidt) Masters) plantations that employs a generalized linear model. The number of years following planting that weeding is necessary is the response variable, and elevation, slope steepness, maximum snow depth, annual precipitation, geology, soil, site index, slope aspect, and vegetation type are explanatory variables. Among the explanatory variables, geology, soil, slope aspect, and vegetation type are categorical data. A Poisson distribution is assumed for the response variable, with a log-link function. Elevation, slope steepness, maximum snow depth, annual precipitation, site index, and vegetation type had a significant effect on weeding duration. Among the eight models with the smallest Akaike information criterion (AIC), I chose the model with no multicollinearity among the explanatory variables. The weeding-duration model includes site index, maximum snow depth, slope steepness (angle) and vegetation type as explanatory variables; elevation and annual precipitation were not included in the selected model because of multicol- linearity with maximum snow depth. This model is useful for cost-benefit analyses of afforestation or reforestation with Abies sachalinensis.     

Dynamic responses of nailed plywood-timber joints under a band-limited white-noise wave

In this study, dynamic tests of nailed plywood-timber joints are conducted under a band-limited white-noise wave using a uniaxial hydraulic shaking table. The principal results are as follows: dynamic responses of nailed plywood-timber joints under a band-limited white-noise wave are reasonably related to the static load-slip relationships and the dynamic responses under harmonic waves of them. When nailed plywood-timber joints are shaken under a composite wave of wide frequency range, they resonate transitionally with one of the frequency components one after another decreasing their equivalent resonant frequencies along their static load-slip curves. Nailed plywood-timber joints are in danger of ultimate failures even though the input maximum accelerations do not exceed their damage limits, if they are shaken for long times with or without intermittences. In this case, nailed plywood-timber joints are prone to fail in low-cyclic bending fatigue failure of nails. Nailed plywood-timber joints, on the other hand, are prone to fail in typical static failure modes when they are shaken under strong input maximum accelerations equivalent to their ultimate limits.     

Immunohistochemical observations of vitellin synthesis and accumulation processes in ovary of Ezo abalone <Emphasis Type="Italic">Haliotis discus hannai</Emphasis>

Ovarian follicle cells are the site of yolk protein synthesis in the Ezo abalone Haliotis discus hannai. In this study, histological observations of ovarian follicle cells were conducted in H. discus hannai by immunocytochemical and in situ hybridization methods focusing on their function of yolk protein synthesis. An antibody raised against purified yolk protein (vitellin, Vn) recognized yolk granules in oocytes, and ovarian follicle cells adjacent to the oocytes under yolk accumulation were stained positively with both anti-Vn antibody and an antisense probe for vitellogenin (the precursor for vitellin, Vtg) mRNA. These results indicate that the abalone Vtg gene is transcribed and translated in the ovarian follicle cells. In oocytes in the early phase of yolk accumulation, positive reactions with the antibody appeared first in the stalk part, and the follicle cells adjacent to the stalk were also stained positively. These observations imply local transport of yolk protein from the follicle cells to the oocyte through an extracellular space around the oocyte stalk. Ovarian follicle cells changed their morphological characteristics and reactivity to the antibody in close relation to the stages of the adjacent oocyte, which suggests the presence of functional interactions between follicle cells and oocytes in the course of yolk protein synthesis and accumulation.     

Oocyte maturation and active motility of spermatozoa are triggered by retinoic acid in pen shell <Emphasis Type="Italic">Atrina pectinata</Emphasis>

For recovery of the declining population of pen shells in the wild, the production of pen shell juveniles for transplantation or aquaculture is underway in Japan. For more stable juvenile production, artificial fertilization methods for pen shells are needed, but methods to induce oocyte maturation (meiosis resumption) used in other bivalves, which make oocytes fertilizable, were ineffective for pen shells. Here, we report evidence showing that retinoic acid (RA) has strong activity in inducing oocyte maturation and activating sperm motility in pen shells. Treatment of fully developed oocytes with 1.0 μM all-trans-RA (at-RA) induced germinal vesicle breakdown, a typical morphological sign of oocyte maturation, but 1.0 μM at-retinol and at-retinal, 2 mM ammonia, and 1.0 μM serotonin were ineffective. Treatment with at-RA for 30 min was sufficient for oocyte maturation and was more potent than its isomers, 9-cis- and 13-cis-RA. Parallel results were obtained for sperm motility activation. Oocyte responsiveness to at-RA increased during the final stage of ovary development. Artificial fertilization was successful only with the oocytes treated with at-RA, and fertilized eggs developed to D-shaped (veliger) larvae without apparent morphological abnormalities. These results indicate the possible application of RA for the artificial fertilization of pen shells.     

Itokawa dust particles: a direct link between S-type asteroids and ordinary chondrites

The Hayabusa spacecraft successfully recovered dust particles from the surface of near-Earth asteroid 25143 Itokawa. Synchrotron-radiation x-ray diffraction and transmission and scanning electron microscope analyses indicate that the mineralogy and mineral chemistry of the Itokawa dust particles are identical to those of thermally metamorphosed LL chondrites, consistent with spectroscopic observations made from Earth and by the Hayabusa spacecraft. Our results directly demonstrate that ordinary chondrites, the most abundant meteorites found on Earth, come from S-type asteroids. Mineral chemistry indicates that the majority of regolith surface particles suffered long-term thermal annealing and subsequent impact shock, suggesting that Itokawa is an asteroid made of reassembled pieces of the interior portions of a once larger asteroid.     

A Spontaneous Oligodendroglioma in the Lumbar Portion of the Spinal Cord in a Young BrlHan:WIST@Jcl (GALAS) Rat

Oligodendroglioma is a rare tumor originating from oligodendrocytes found mainly in the cerebrum in aged rats. Only a few reports have shown spontaneous occurrence of this tumor in the spinal cord, and no report has mentioned its occurrence in young rats. We encountered a case of spontaneous oligodendroglioma in the lumbar portion of the spinal cord in a young (9 weeks old) female BrlHan:WIST@Jcl (GALAS) rat. Here we report the detailed histopathological and immunohistochemical characteristics of this case. No clinical signs, no gross lesions at necropsy, and no specific changes in hematology or blood biochemistry were observed. The tumor was located in the dorsal funiculus in the lumbar portion of the spinal cord and widely spread to the dorsal root nerve. The neoplastic cells showed a sheet-like growth pattern and had small round nuclei, clear cytoplasm and distinct cell borders that resulted in a honeycomb pattern. No mitotic figures or other histological lesions were observed. The neoplastic cells were positively stained for Olig2 and PCNA. The present case was considered to be a low-grade oligodendroglioma based on the histological and immunohistochemical features. To our knowledge, our case is considered to be extremely rare and the first report in a young rat.