Metagenomic analysis using 16S ribosomal RNA genes of a bacterial community in an urban stream,the Tama River,Tokyo

In an effort to determine genus- or species-level taxonomic profiles and diversity of bacterial consortia in the Tama River around urban Tokyo, next-generation sequencing technology targeting a 16S ribosomal RNA (rRNA) gene amplicon was employed. Metagenomic analysis performed by an Ion Personal Genome Machine after sequentially filtering samples through 5-, 0.8- and 0.2-μm filters yielded 1.48 Gb of 16S sequences (average 2.38 M reads/sample). The results indicated that half of the bacterial sequences belonged to Proteobacteria, followed by Bacteroidetes, Actinobacteria and Cyanobacteria. Flavobacterium (Bacteroidetes), possibly including a potential fish pathogen, was the most numerous genera in the Tama River metagenome, and accounted for?~?16% of assigned 16S reads, followed by Mycobacterium. Other dominant bacterial genera including Zoogloea, Sediminibacterium, Hyphomicrobium, Sphingopyxis, Thiothrix and Lysobacter, were thought to be associated with waste water and sludge. MiSeq metagenomic analysis revealed that environmental factors, particularly water temperature, influenced the bacterial composition throughout the year, with a strong negative correlation observed for Proteobacteria and a positive correlation for Bacteroidetes. In terms of bacterial genera, Flavobacterium was positively correlated with temperature, while Polaromonas, Pseudomonas and Bradyrhizobium were negatively correlated with this, suggesting dynamic change in the free-living bacterial population throughout the year and versatile adaptation strategies in relation to environmental factors.     

Relationships between body size and secondary sexual characters,and sperm characters in male Dolly Varden char (Salvelinus malma)

In Salmonidae, subordinate males are exposed to higher risks of sperm competition than dominant males and thus are expected to improve the sperm characteristics (sperm concentrations, sperm velocity and sperm longevity). In this study, we investigated the relationships between body size and secondary sexual characters (breeding colour, hump height and snout length), and sperm characteristics of one‐year‐old (newly matured) Dolly Varden char. Small males displayed higher sperm concentrations than large males. Moreover, males with dull breeding colours, but not with lesser snout length and hump height, displayed an increased sperm velocity compared to males with bright colours, suggesting a trade‐off between sperm quantity and the investment in breeding colour. In addition, sperm longevity decreased as sperm swimming velocity increased. These findings indicate that small males with dull breeding colours improve the quantity and quality of their sperm to a great extent to enhance their chances of reproductive success.     

Experimental evidence of a pathogenic change caused by homologous recombination between endogenous and introduced dysfunctional Avr-Pita genes in Pyricularia oryzae

To provide experimental evidence that somatic homologous recombination (HR) is involved in the instability and diversification of the avirulence gene Avr-Pita in Pyricularia oryzae, we generated a dysfunctional Avr-Pita homolog and integrated it into strain Hoku-1 containing Avr-Pita. In the transformants, the occurrence of somatic HR events between Avr-Pita and the dysfunctional homolog was confirmed by PCR–RFLP. Germlings from conidia from the HR-positive transformants had lost the avirulence function, which enabled it to infect rice cultivar Yashiromochi containing the corresponding resistant gene Pi-ta. These results suggested that genetic mutation caused by somatic HR is one of the mechanisms responsible for virulence diversity.     

Distribution of boron in wood treated with aqueous and methanolic boric acid solutions

The distributions of boron in Japanese cedar (Cryptomeria japonica D. Don) sapwood blocks treated with aqueous or methanolic boric acid [B(OH)₃] solutions were explored through Raman spectroscopy and prompt gamma-ray analysis (PGA). B(OH)₃ was the sole boron species observed in Raman spectra of the wood blocks treated with either solution. Plots of weight gain of the treated wood blocks versus boron concentration in treatment solutions were found to be linear. The results indicated that the methanolic solution makes it possible to impregnate wood with much larger amounts of boron than the aqueous solution. PGA confirmed that B(OH)₃ was highly enriched near the end grains of the treated wood blocks. Raman measurements suggested that boron content in the bulk of the wood block is not as large as expected from the weight gain of the treated wood blocks when an ordinary air-drying method is used. It was concluded that the aqueous solution impregnates the cell walls of wood with boron more easily than the methanolic solution. Part of this report was presented at the 55th (Kyoto, March 2005) and 56th (Akita, August 2006) Annual Meetings of the Japan Wood Research Society. This article follows the previous rapid communication “Analysis of boron in wood treated with boric acid solutions using Doppler broadening method of prompt gamma-rays.” J Wood Sci (2006) 52:279–281     

Changes of decay and termite durabilities of Japanese larch (Larix leptolepis) wood due to high-temperature kiln drying processes

We investigated the effects of high-temperature drying schedules (120°–130°C) on decay and termite feeding of Japanese larch timbers. Thermogravimetric analysis was conducted to investigate changes of the wood components. Decay and termite feeding tests showed that specimens dried under high-temperature schedules were susceptible against a decaying fungus Fomitopsis palustris and attacks from termites Coptotermes formosanus and Reticulitermes speratus. These drying schedules changed chemical components, which were suggested by the thermal analytical result compared to the control sample. The results of this study indicated that the acceleration of termite feeding takes place even under temperatures that are comparatively lower than that used in our previous research in which 170°C steaming treatment was applied to Japanese larch wood. Decay durability against a brown rot fungus also decreased, possibly from production of low molecular weight fragments when hemicellulose decreased during the high-temperature drying processes.     

Stem water transport of Lithocarpus edulis, an evergreen oak with radial-porous wood

The stem water conducting system of an evergreen broad-leaved oak, Lithocarpus edulis (Mak.) Nakai, was investigated. Evergreen broad-leaved oaks (Lithocarpus, Castanopsis, Cyclobalanopsis, Quercus) belonging to the Quercoideae are a major component of Asian monsoon forests, and are characterized by the possession of radial-porous wood. A characteristic of radial-porous wood is the development of aggregate rays between radially oriented files of vessels. We measured the distribution of vessel lumen diameters in a stem cross section and calculated the theoretical water conductivity of the wood. The radial profile of the heat pulse velocity (HPV) was measured for an intact whole tree under field conditions and compared with the theoretical distribution of water conductivity. Soft X-ray photographs of frozen stem sections indicated that most of the vessel lumina were filled with water, including those of vessels more than 20 years old. Even when vessels were relatively wide (lumen diameters > 100 microm), cavitation was negligible. The rate of water uptake from the cut stem base correlated closely with HPV (r = 0.96), and HPV closely reflected the mean volume flow per stem sectional area (SFVS) around the sensor probes. However, the ray tissue sharply inhibited heat transfer, and the positioning of the probes strongly affected the absolute value of HPV. It was also found that HPV more closely reflected the mean sap flow velocity in the vessels than did SFVS.     

Ophiostomatoid fungi associated with bark beetles onAbies veitchii in wave-regenerated forests

Relationships between tree mortality and bark beetle infestation onAbies veitchii at the wave-regenerated forest in Mt. Asahi, Okuchichibu area were investigated. Most of the firs with green needles and newly developed current year’s shoots in the dieback zone were heavily infested by bark beetles before the death of the trees. After heavy infestation of beetles, about half of the infested firs died within the year, and the other half died in the next year. When the species composition of bark beetles and associated ophiostomatoid fungi were investigated in Mt. Asahi and also at a typical wave-regenerated forest in Mt. Shimagare, Yatsugatake area,Cryphalus montanus andC. piceae were dominant beetle species for Mt. Asahi and Mt. Shimagare, respectively.Ophiostoma subalpinum andO. europhioides were dominant fungal species at both wave-generated forests. BecauseO. subalpinum was detected more frequently from deeper areas of sapwood thanO. europhioides, it was suggested that the fungal species may accelerate the death of stressed firs in wave-regenerated forests. Contribution No. 169, Laboratory of Plant Parasitic Mycology, Institute of Agriculture and Forestry, University of Tsukuba.     

Comparison of morphological and DNA-based techniques for stomach content analyses in juvenile chum salmon <Emphasis Type="Italic">Oncorhynchus keta</Emphasis>: a case study on diet richness of juvenile fishes

To identify the stomach contents of marine organisms, morphological observations are commonly conducted. However, the results obtained by this traditional method are frequently biased, as it is difficult to detect partially digested, soft-bodied organisms. To resolve this, recent studies have used DNA-based (DNA barcoding) analyses to examine the diet breadth of marine organisms. Here, we compared the prey richness of juvenile fishes using morphological observations and DNA-based analyses, with a focus on juvenile chum salmon Oncorhynchus keta. A higher number of prey taxa were successfully identified using DNA-based analyses than morphological observations. However, we also noticed several shortcomings of the DNA-based analyses, as reported in other diet-analysis studies that used molecular techniques. For example, the degree of digestion among prey taxa might have resulted in differential sensitivity to DNA detection. Additionally, several prey taxa could not be precisely identified, as the sequence data for some of the targeted organismal groups are unavailable in public gene databases. Remarkably, it is also possible that DNA-based analyses detected secondary prey, and therefore, the richness of prey taxa was likely overestimated. Thus, dietary analyses of juvenile fishes need to be carefully conducted, considering the respective advantages and disadvantages of DNA-based and morphological techniques.     

A method for visualizing cesium ions adsorbed on wood charcoal using SEM–EDX

A new method based on scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM–EDX) was developed for visualizing the distribution of cesium ions (Cs⁺) adsorbed by Japanese cedar charcoal. After being soaked in saturated aqueous CsCl solutions, wood charcoal and regular wood samples were embedded in resin, and thin sections of sample were prepared for the Cs⁺ observations. The Cs⁺ ions on charcoal could be seen in EDX mapping images and also in line profiles with enough contrast to identify differences between the various carbonized cell wall regions. On the other hand, Cs⁺ could not be observed in the EDX mapping images of wood samples, despite having been soaked in a saturated aqueous CsCl solution. These results indicate that Cs⁺ adsorbed on charcoal can be visualized using this method, but not Cs⁺ in wood. Additionally, oxygen detected on the charcoal by EDX can be regarded as an indicator of the presence of surface functional groups.