Polymorphism analysis of Fagaceae and DNA-based identification ofFagus species grown in Japan based on therbcL gene

Fagaceae species in Japan were identified by restriction fragment length polymorphism (RFLP) and sequence comparison of a region ofrbcL. Of nine restriction endonucleases used for digestion, three (MspI,RsaI,HaeIII) produced different restriction patterns in Fagaceae. Digestion byMspI yielded four patterns: Fagus species,Castanea crenata, Pasania glabra, and others. Digestion byRsaI andHaeIII afforded two patterns:Fagus species and others. These facts indicate thatCastanea crenata andPasania glabra can be identified byMspI restriction patterns ofrbcL. Sequence comparison of a region of therbcL gene among 20 species of Fagaceae showed that: (1) they could be divided into seven groups; (2) there is a site mutation betweenFagus crenata andF. japonica. The latter indicates that the wood of both Fagus species are identifiable at the species level, which is not the case using conventional methods. This result indicates the possibility of wood identification based on DNA polymorphism in Fagaceae at the intrageneric level.Part of this paper was presented at the 46th annual meeting of the Japan Wood Research Society, Kumamoto, April 3–5, 1996 and the 47th annual meeting of the Japan Wood Research Society, Kochi, April 3–5, 1997     

Spatial–temporal variations in the composition of two <Emphasis Type="Italic">Zostera</Emphasis> species in a seagrass bed: implications for population management of a commercially exploited grass shrimp

We examined spatial and temporal variations in the species composition of two seagrass species, Zostera marina and Z. caespitosa, in a lagoon facing the Sea of Okhotsk. We also considered how those variations affected habitat quality for motile epifauna, especially for a commercial shrimp. A long-interval comparison between 1996 and 2013 showed that seagrass species composition in the lagoon did not vary, while their relative abundances did. A survey in 2012 revealed that the abundance of Z. caespitosa was affected by the abundance of Z. marina, water depth, and location in the lagoon. Although these seagrass species have similar aboveground morphology, differences in their fine structures were detected. Diversities of motile animals inhabiting the seagrass species were the same. Differences in seagrass utilization were observed when we focused on a commercial shrimp, Pandalus latirostris. This shrimp always preferred higher densities of shoots irrespective of the species and seasonally changed their preference for the number of leaves per shoot. They were therefore more abundant in Z. caespitosa, which had those structural characteristics. The results suggest that the management of shrimp resources could be improved by flexibly changing protected areas in accordance with the dynamics of seagrass distribution in the lagoon.     

Rice <Emphasis Type="Italic">terpene synthase 18</Emphasis> (<Emphasis Type="Italic">OsTPS18</Emphasis>) encodes a sesquiterpene synthase that produces an antibacterial (<Emphasis Type="Italic">E</Emphasis>)-nerolidol against a bacterial pathogen of rice

Plant volatile compounds, including terpenes, are known to be involved in the rice defense system. In the present analysis of a terpene synthase, OsTPS18, in rice, we found that OsTPS18 was localized in the cytoplasm and synthesized the sesquiterpenes (E)-nerolidol and (E)-β-farnesene. The amounts of (E)-nerolidol and (E)-β-farnesene increased after jasmonic acid (JA) treatment. (E)-Nerolidol had significant antibacterial activity against Xanthomonas oryzae pv. oryzae (Xoo). These results suggest that (E)-nerolidol plays an important role in JA-induced resistance against Xoo and that it functions as an antibacterial compound in rice.     

T4-type bacteriophage communities estimated from the major capsid genes (g23) in manganese nodules in Japanese paddy fields

The present study compared the capsid gene ( g23 ) of T4-type bacteriophages (phages) in Mn nodules with those in the plow layer soil and subsoils of two Japanese paddy fields by applying the primers MZIA1bis and MZIA6 to DNA extracts from the nodules and soils. The deduced amino acid sequences of the g23 genes in the Mn nodules were similar to those in the plow layer soil and in the subsoils. This result indicated that similar T4-type phage communities developed at these sites and that the diversity of T4-type phage communities was wide enough to cover those in the plow layer soil and in the subsoils. The majority of g23 clones formed several clusters with the clones and phages obtained from far-apart paddy fields, and the sequences of two clones were completely identical to a phage and a clone from other paddy fields at the nucleotide or amino acid level, indicating horizontal transfer of g23 genes between those paddy fields. A clone with a long nucleotide residue (686 bp) and a distribution remote from the other clones in the phylogenetic tree indicated that there were many uncharacterized, novel g23 genes in the paddy fields.     

Effects of sika deer (Cervus nippon) and dwarf bamboo (Sasamorpha borealis) on seedling emergence and survival in cool-temperate mixed forests in the Kyushu Mountains

Effects of sika deer (Cervus nippon) and dwarf bamboo (“sasa;” Sasamorpha borealis) on seedling emergence and survival were investigated in cool-temperate mixed forests in the Kyushu mountain range, Japan. We compared the effects of sika deer between two sites with different sika deer densities. One site (no-sasa forest) has sparse cover of S. borealis and a high density of sika deer, and the other site (sasa forest) has dense cover of S. borealis with a low density of sika deer. In the no-sasa forest, more seedlings emerged and the survival rate of the seedlings was higher compared with the sasa forest. Compared with the sasa forest, the canopy in the no-sasa forest was more open, the organic layer was shallower and drier, the mean daily soil temperature was higher, and soil temperature fluctuated more widely. Those environmental parameters did not differ between unfenced and fenced plots. The comparison between the sasa and no-sasa forests suggested that removal of S. borealis by sika deer had an indirect positive effect on seedling emergence and survival. However, the fenced-plot experiments indicated that sika deer inhibited seedling emergence and survival. These contradictory conclusions could result from the much larger negative effects of S. borealis on seedling emergence and survival compared with the effects of sika deer browsing.     

Comparison of the amount of thiotrophic symbionts in the deep-sea mussel <Emphasis Type="Italic">Bathymodiolus septemdierum</Emphasis> under different sulfide levels using fluorescent in situ hybridization

Various invertebrates inhabiting hydrothermal vents harbor thiotrophic endosymbionts that provide the host with nutrients and are possibly involved in the detoxification of harmful sulfides. In this study, we first determined the partial 16S rRNA gene sequence of the thiotrophic symbiont of the deep-sea mussel Bathymodiolus septemdierum, a dominant species at hydrothermal vents in the Izu–Ogasawara (Bonin) area. We then designed a new probe, Bsob692, for fluorescent in situ hybridization (FISH) using regions completely conserved among thiotrophic symbionts of all bathymodiolin mussels and established the protocol for FISH to compare the distribution and amount of the symbiont using an image analysis program that is commercially available. We compared fluorescent intensity in the gill of the mussels collected at different sites and found a higher intensity in specimens collected from a site with higher sulfide concentration. We also compared mussels reared in the presence and absence of sulfide and found that the former had a higher fluorescent intensity.     

Bacterial community incorporating carbon derived from plant residue in an anoxic non-rhizosphere soil estimated by DNA-SIP analysis

Purpose

Plant residues are one of the main sources of soil organic matter in paddy fields, and elucidation of the bacterial communities decomposing plant residues was important to understand their function and roles, as the microbial decomposition of plant residues is linked to soil fertility. We conducted a DNA stable isotope probing (SIP) experiment to elucidate the bacterial community assimilating 13-carbon (¹³C) derived from plant residue under an anoxic soil condition. In addition, we compared the bacterial community with that under the oxic soil condition, which was elucidated in our previous study (Lee et al. in Soil Biol Biochem 43:814–822, 2011).

Materials and methods

We used the ¹³C-labeled dried rice callus cells as a model of rice plant residue. A paddy field soil was incubated with unlabeled and ¹³C-labeled callus cells. DNA extracted from the soils was subjected to buoyant density gradient centrifugation to fractionate ¹³C-enriched DNA. Then, polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) analysis of bacterial 16S rDNA band patterns and band sequencing method were used to evaluate bacterial community.

Results and discussion

DGGE analysis showed that the band patterns in the ¹³C-enriched fractions were distinctly changed over time, while the changes in the community structure before fractionation were minor. Sequencing of the ¹³C-labeled DGGE bands revealed that Clostridia were a major group in the bacterial communities incorporating the callus-derived carbon although Gram-negative bacteria, and Actinobacteria also participated in the carbon flow from the callus under the anoxic condition. The proportion of Gram-negative bacteria and Actinobacteria increased on 14 days after the onset of incubation, suggesting that the callus was decomposed by diverse bacterial members on this phase. When the bacterial groups incorporating the ¹³C were compared between under anoxic and oxic soil conditions, the composition was largely different under the two opposite conditions. However, some members of Gram-negative bacteria were commonly found under the anoxic and oxic soil conditions.

Conclusions

The majority of bacterial members assimilating the callus carbon was Clostridia in the soil under anoxic conditions. However, several Gram-negative bacterial members, such as Acidobacteria, Bacteroidetes, and Proteobacteria, also participated in the decomposition of callus under anoxic soil conditions. Our study showed that carbon flow into the diverse bacterial members during the callus decomposition and the distinctiveness of the bacterial communities was formed under the anoxic and oxic soil conditions.

     

Effects of muscle type on beef taste‐traits assessed by an electric sensing system

To assess the role of muscle fiber type in beef taste‐traits, we analyzed cooked meats from bovine masseter, diaphragm, psoas major, longissimus thoracis, and semitendinosus muscles with an electric taste sensing system (INSENT SA402B). The system is composed of five taste sensors of polymer membranes fixing different lipids. The sensors, CT0, CA0, AAE, C00 and AE1 are designed to respond to the individual tastes of salty, sour, umami, bitter and astringent, respectively. The system found significant differences in the converted outputs of CA0 (cvCA0), C00 (cvC00) and AE1 (cvAE1) among the bovine muscles. The slow‐type muscles (masseter and diaphragm) showed lower cvCA0, higher cvC00, and higher cvAE1 than did the fast‐type muscles (psoas major, longissimus thoracis, and semitendinosus). Lactic acid content was different among muscle types and was highly related to the cvCA0 output and pH. carbonyl compounds and free fatty acids were higher in the slow‐type muscles. Free fatty acids were major components causing the difference in the C00 output among the muscle types. Iron content was also different among the muscle types and related to the cvC00 and cvAE1 outputs. These results suggested that the muscle fiber type affects the beef taste characteristics.