Forestry and Fisheries Research Council

Tokyo, Japan

Forestry and Fisheries Research Council

Tokyo, Japan
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Niwa S.,Hokkaido University | Toyota A.,Hokkaido University | Toyota A.,Kagawa University | Kishimoto T.,Japan Wildlife Research Center | And 33 more authors.
Ecological Research | Year: 2016

This data paper reports census data of ground-dwelling beetle and other fauna of the forest floor environment; collections were made from a network of 22 forest sites in Japan. To our knowledge, this represents the largest dataset for long-term monitoring of a ground-dwelling beetle community and other taxa in a ground environment in forests, which covers a broad climatic range in the temperate zone and is freely available. The network forms part of the Monitoring Sites 1000 Project launched by the Ministry of the Environment, Japan. It covers subalpine, cool- and warm-temperate and subtropical climatic zones and the four major forest types of Japan. Thirty-three permanent plots usually 1 ha in size were established in old-growth, secondary natural and a few plantation forests. Censuses of the ground-dwelling beetle community were conducted using pitfall trapping and forest floor environment monitoring every year from 2004 to the present. During the initial 9 years of the census (2004–2012), 59,762 beetle individuals (including 3182 larvae) of more than 314 species were recorded. This dataset includes taxonomy and biomass of each beetle individual and each taxonomic group of other invertebrates coincidently captured in pitfall trapping. The dataset also includes data related to ground coverage by forest floor vegetation, dry mass of the accumulated organic litter layer, and carbon and nitrogen contents and cellulose decomposition rate in organic layer and surface mineral soil. The data could be used to investigate geographical patterns and intra- and inter-annual dynamics of individual body mass, populations and community structures of ground-dwelling beetles, and their relationships with the forest floor environment. Furthermore, the data could be analyzed with other open datasets related to tree community dynamics and litter fall continuously measured in the same study plots. This dataset also provides information related to the distribution and average body mass of each beetle species. © 2016, The Ecological Society of Japan.


Akagi S.,Japan National Agriculture and Food Research Organization | Matsukawa K.,Japan National Agriculture and Food Research Organization | Matsukawa K.,Kochi University | Mizutani E.,Japan National Agriculture and Food Research Organization | And 5 more authors.
Journal of Reproduction and Development | Year: 2011

We examined the effects of treatment with histone deacetylase inhibitors (HDACi), trichostatin A (TSA) and scriptaid (SCR), on the blastocyst formation rate in bovine somatic cell nuclear transferred (SCNT) embryos derived from fibroblast cells. Three fibroblast cell lines (L1, L2 and L3) were used as somatic cell donors to produce SCNT embryos (L1, L2 and L3 embryos, respectively). In Experiment 1, we compared the in vitro developmental competence of L1 embryos treated with various concentrations of TSA for different time periods following chemical activation. Embryos treated with 5 nM TSA for 20 h showed a significantly increased blastocyst formation rate compared with untreated controls. In Experiment 2, we examined the effect of TSA (5 nM) treatment of L1, L2 and L3 embryos as well as the effect of treatment of L1, L2 and L3 embryos with various concentrations of SCR on in vitro developmental competence. It was found that 5 nM TSA treatment significantly increased the blastocyst formation rate in L1 and L3 embryos but did not have an influence on the development of L2 embryos. On the other hand, 5 nM SCR treatment significantly increased the blastocyst formation rates of L1 and L2 embryos compared with controls. However, there was no significant increase in the blastocyst formation rate of L3 embryos when they were treated with SCR. In Experiment 3, acetylation of H4K12 was examined in donor cells and pronuclear-stage L1, L2 and L3 embryos treated with 5 nM TSA or 5 nM SCR by immunostaining. The level of H4K12 acetylation was different among donor cells. The staining intensities in the TSA-treated L1 and L3 embryos and SCR-treated L2 embryos were significantly higher than those of untreated embryos. These results suggest that HDACi treatment of bovine SCNT embryos improves the blastocyst formation rate; however, the optimal treatment conditions may differ among donor cell lines. © 2011 by the Society for Reproduction and Development.


Toma Y.,Ehime University | Oomori S.,Ehime University | Maruyama A.,Ehime University | Ueno H.,Ehime University | And 3 more authors.
Soil Science and Plant Nutrition | Year: 2016

Agricultural fields, including rice (Oryza sativa L.) paddy fields, constitute one of the major sources of atmospheric methane (CH4) and nitrous oxide (N2O). Organic matter application, such as straw and organic fertilizer, enhances CH4 emission from paddy fields. In addition, rice straw management after harvest regulates CH4 emissions in the growing season. The interaction of tillage times and organic fertilizer application on CH4 and N2O emissions is largely unknown. Therefore, we studied the effects of fallow-season tillage times and fertilizer types on CH4 and N2O emissions in paddy fields in Ehime, southwestern Japan. From November 2011 to October 2013, four treatments, two (autumn and spring) or one (spring) in the first year, or two (autumn and spring) or three (autumn, winter, and spring) in the second year times of tillage with chemical or organic fertilizer application, were established. Gas fluxes were measured by the closed-chamber method. Increasing the number of tillage times from one to two decreased succeeding CH4 emission and the emission factor for CH4 (EFCH4) in the rice-growing season, suggesting that the substrate for CH4 production was reduced by autumn and spring tillage in the fallow season. Higher EFCH4 [1.8–2.0 kg carbon (C) ha−1 d−1] was observed when more straw was applied (6.9–7.2 Mg ha−1) in the second year. Organic fertilizer application induced higher CH4 emission just after the application as basal and supplemental fertilizers, especially at a lower straw application rate. This indicated that EFCH4 in the organically managed fields should be determined individually. Organic fertilizer application with two tillage times induced N2O efflux during the rice-growing season in the second year, but N2O emissions were not affected by winter tillage. Although paddy fields can act as an N2O sink because of reduced soil conditions when straw application was high, application of organic C and nitrogen as fertilizer can enhance N2O production by the denitrification process during the growing season, especially in the ripening stage when soil anaerobic conditions became moderate. These results suggest that negative emission factors for N2O (EFN2O) can be applied, and EFN2O of organic fertilizer should be considered during the estimation of N2O emission in the paddy field. © 2015 Japanese Society of Soil Science and Plant Nutrition.


Tanaka J.,Forestry and Fisheries Research Council | Tanaka J.,Japan National Agriculture and Food Research Organization
Crop Science | Year: 2010

In recent decades, yield improvements of major autogamous crops have slowed. Contrastingly, the yield of maize (Zea mays L.) has continuously increased through breeding based on wide genetic diversity and recurrent selection. Recurrent selection is very powerful and is a suitable breeding system for outcrossing (allogamous) crops. To achieve recurrent selection of autogamous crops, some progress has been made in rice (Oryza sativa L.), sorghum [Sorghum bicolor (L.) Moench], and soybean [Glycine max (L.) Merr.] using genetic male sterility. However, this approach has not provided major improvements for the breeding of autogamous crops, because it is laborious or based on specific properties of the crops. To prevent this from becoming a bottleneck for the use of recurrent selection in autogamous crops, the author devised an efficient recurrent selection system based on transgenic male sterility, herbicide tolerance, and conditional lethality suitable for use with autogamous crops. This system offers three advantages. First, it can be applied on a large scale while permitting continuous recurrent selection. Second, the cultivars that are the final products of this breeding do not contain the transgenes introduced by this system. Third, the transgenic plants cannot produce pollen and therefore cannot cross naturally with cultivated crops or related wild species. This paper proposes an efficient recurrent selection for autogamous crops using transgenic male sterility. © Crop Science Society of America.


Ohdaira Y.,Akita | Sasaki R.,Forestry and Fisheries Research Council | Takeda H.,Japan National Agriculture and Food Research Organization
Japanese Journal of Crop Science | Year: 2013

The essential points for controlling the digestible protein content (DP) of rice grain at low levels in seed-protein mutant rice cultivars (SPMR) were investigated. A low-glutelin cultivar 'LGCsoft', a 26-kDa globulin-deficient low-glutelin cultivar 'LGC-Jun', and a normal-type cultivar 'Nihonmasari', were cultivated for 8-9 cropping seasons over a period of 4 years. Factors affecting seed protein composition and protein content in rice grain were analyzed. DP was affected by both the total protein content (TP) and the ratio of DP to TP in all cultivars. However, the effect of DP/TP on DP was greater in 'LGCsoft' and 'LGCJun' than in 'Nihonmasari'. A positive correlation between DP/TP and air temperature from 0 to 15 days after heading was observed in all cultivars. The highest correlation coefficient was observed from 0 to 10 days after heading in 'LGCsoft' and 'LGCJun', which was slightly earlier than in 'Nihonmasari'. Therefore, it is important to adjust the planting season to avoid high temperatures during the early ripening period for the cultivation of SPMR. TP affected DP more than DP/TP not only in 'Nihonmasari' but also in SPMR. A positive correlation was observed between TP and the nitrogen content of shoots at the heading stage, and a negative correlation was observed between TP and the percentage of ripened grains. These results indicate that shoot nitrogen status and percentage of ripened grains should be taken into account in planting and cultivation management plans.


The present results have elucidated for the first time a unique mechanism involved in acquiring specific symbiotic bacteria, which is a characteristic shared by diverse stink bugs, a kind of pest insect, and are expected to lead to the development of a new method for controlling pest insects by inhibiting the establishment of gut symbiosis. The results will be published online in a US academic journal, Proceedings of the National Academy of Sciences, on September 1, 2015. Almost all "pest insects" such as agricultural pests that damage crops, sanitary pests that transmit pathogenic microorganisms, and household pests such as termites that damage wooden houses, commonly possess symbiotic bacteria in their bodies. These bacteria play a role in supplying the nutrients necessary for growth, living, and breeding, and/or assist in digestion of food materials. Since the symbiotic bacteria could be a new target for controlling pest insects, various research has focused on elucidating the mechanism(s) for establishment of the symbiotic associations. With regard to stink bugs (Hemiptera: Heteroneura), more than 40,000 species in the world and 1,500 species or so in Japan are known, many of which are serious agricultural pests. Few studies have thoroughly examined such a large number of species, their ecological aspects are not well understood, and therefore the pest insects are difficult to control, damaging various agricultural crops such as rice and soybean; a method of controlling them is demanded. Many of the plant sap-sucking stink bugs harbor symbiotic bacteria in their gut, which play an important role in supplying nutrients, adapting to plant hosts, and retaining insecticide resistance. Although knowledge has been accumulated regarding the function and evolution of symbiotic bacteria, the mechanism for establishment of the specific gut symbiosis in the stink bugs is not well understood. AIST discovered that the bean bug Riptortus pedestris, a serious pest of soybean, has a unique system of gut symbiosis. Although symbiotic bacteria are transmitted directly from mother to offspring in most insects, in the bean bug, a new symbiotic relationship is established for respective generations by their nymph's oral ingestion of symbiotic bacteria called Burkholderia which inhabit environmental soil. Since Burkholderia are easy to cultivate and can be genetically modified, they have attracted research interest to elucidate the genetic background involved in the symbiotic association. With respect to the gut symbiotic system of the bean bug, AIST has achieved research results such as "Discovery of Symbiotic Bacteria Mediating Insecticide Resistance to Pest" and "Novel Biological Function of Polyester in Insect-Bacterium Symbiosis." Hokkaido University has a cooperative graduate school with AIST, under which research of the bean bug has been conducted with graduate students, and has advanced development of excellent human resources such as a Hokkaido University graduate student winning the Best Poster Award of an international conference (Hokkaido University press release on September 25, 2014). The present research has been conducted by Tsubasa Ohbayashi and others, who are Hokkaido University graduate students, under the mentorship of Yoshitomo Kikuchi (Senior Researcher) of AIST. This research was supported by the "Program for the Promotion of Agriculture, Forestry and Fisheries Industry and Food Industry Science and Technology Research" of the Agriculture, Forestry and Fisheries Research Council of the Ministry of Agriculture, Forestry and Fisheries, and the "Endowed Courses Subsidy" of the Institute for Fermentation, Osaka. The bean bug has a large number of sac-like tissues in the posterior half part of the gastrointestinal tract (Fig. 1), where Burkholderia colonize symbiotically. The researchers have called this gastrointestinal tract region, where a large number of sac-like tissues develop, a "symbiotic organ." In addition, as the gastrointestinal tract becomes very narrow near the middle (the site located anterior to the symbiotic organ), the researchers named this site "constricted region" (Fig. 1) in this research. The constricted region was described in previous studies, but its function was unknown. First, in order to clarify the food flow in the gastrointestinal tract of the bean bug, the researchers observed the flow path of the contents of the gastrointestinal tract after feeding bean bugs with various food dyes. They found that, even though the dye reached the constricted region, the dye never flowed beyond the constricted region into the symbiotic organ (Fig. 2), indicating that the inflow of food was extremely restricted at this constricted region of the gastrointestinal tract. Next, the researchers orally inoculated bean bug nymphs having no Burkholderia symbiont with both a food dye and Burkholderia labeled by green fluorescent protein (GFP), and found that the food dye stopped at the constricted region and only Burkholderia passed through the region and enter into the symbiotic organ (Fig. 3A). Furthermore, in bean bug nymphs fed with both the GFP-labeled Burkholderia and red fluorescent protein (RFP)-labeled E. coli, whereas the E. coli stopped at the constricted region, only the Burkholderia passed through it and reached the symbiotic organ (Fig. 3B). Besides E. coli, in bean bug nymphs orally inoculated with Pseudomonas putida and Bacillus subtilis that are typical soil bacteria, neither of the bacteria infected the symbiotic organ. Based on these findings, the researchers conclude that the bean bug has sophisticated bacterium-screening machinery in its gastrointestinal tract, which allows symbiotic bacteria specifically to pass through while restricting the inflow of substances. Based on the fact that the food dyes were detected in the Malpighian tubule and feces, it is considered that all the digestion and absorption of food materials is accomplished before the constricted region and the dye absorbed into body fluid was gathered in the Malpighian tubule and excreted. In short, the gastrointestinal tract of bean bugs has two functionally distinct parts, an "anterior part to digest and absorb feed" and a "posterior part to harbor symbiotic bacteria," with the constricted region in the middle of it. Although the restriction of feed inflow half way through the gastrointestinal tract like this has not been reported in the case of ordinary animals, it is likely to be related to the fact that bean bugs feed on plant sap, which is easy to digest and absorb. Second, in order to elucidate the mechanism by which Burkholderia pass through the constricted region, the researchers produced transposon-generating mutants of Burkholderia and screened mutant strains that cannot colonize in the gut symbiotic organ. The results revealed that the non-motility strains having transposon-insertions in flagella formation genes could not pass through the constricted region. This strongly suggests that Burkholderia pass through the constricted region by flagellar mortality. A number of stink bug species, which are crop-damaging pest insects, possess gut symbiotic bacteria, as shown in the bean bug. Observation of the gastrointestinal tract of stink bug species of diverse taxonomic groups revealed that there was a constricted region near the middle of the gastrointestinal tract as is the case with the bean bug. The stink bug species were fed with a food dye to confirm the flow path, revealing that the dye stopped at the constricted region and never flowed into the symbiotic organ in all of the species investigated (Fig. 4). Based on these results, it is considered that the gastrointestinal tract has two functionally distinct parts, an "anterior part to digest and absorb feed" and a "posterior part to harbor symbiotic bacteria" and symbiotic bacteria are screened through the constricted region in the stink bug species, which seems to be a common feature among diverse stink bug species. The researchers intend to analyze expressed genes and proteins in the constricted region that is the bacteria-screening organ, focusing on the bean bug, and try to reveal the genetic basis of the sophisticated gut screening of symbiotic bacteria. Since the symbiont screening by the constricted region is a common mechanism in most stink bug species, a kind of pest insect, elucidation of the genetic basis could lead to the development of a new pest control technology for preventing infection and colonization of symbiotic bacteria. From this viewpoint, the researchers will pursue their research. Explore further: Bean bugs found to harbor bacteria that keep them safe from an insecticide


Ishikawa S.,Japan National Institute for Agro - Environmental Sciences | Ishimaru Y.,University of Tokyo | Ishimaru Y.,Tohoku University | Igura M.,Japan National Institute for Agro - Environmental Sciences | And 9 more authors.
Proceedings of the National Academy of Sciences of the United States of America | Year: 2012

Rice (Oryza sativa L.) grain is amajor dietary source of cadmium(Cd), which is toxic to humans, but no practical technique exists to substantially reduce Cd contamination. Carbon ion-beamirradiation produced three rice mutants with <0.05 mg Cd·kg-1 in the grain compared with a mean of 1.73 mg Cd·kg-1 in the parent, Koshihikari. We identified the gene responsible for reduced Cd uptake and developed a strategy for marker-assisted selection of low-Cd cultivars. Sequence analysis revealed that these mutants have different mutations of the same gene (OsNRAMP5), which encodes a natural resistance-associated macrophage protein. Functional analysis revealed that the defective transporter protein encoded by the mutant osnramp5 greatly decreases Cd uptake by roots, resulting in decreased Cd in the straw and grain. In addition, we developed DNA markers to facilitate marker-assisted selection of cultivars carrying osnramp5. When grown in Cd-contaminated paddy fields, the mutants have nearly undetectable Cd in their grains and exhibit no agriculturally or economically adverse traits. Because mutants produced by ion-beam radiation are not transgenic plants, they are likely to be accepted by consumers and thus represent a practical choice for rice production worldwide.


Yamashita S.,Japan Forestry and Forest Products Research Institute | Yamashita S.,Tokushima University | Masuya H.,Japan Forestry and Forest Products Research Institute | Abe S.,Japan Forestry and Forest Products Research Institute | And 3 more authors.
PLoS ONE | Year: 2015

We examined the relationship between the community structure of wood-decaying fungi, detected by high-throughput sequencing, and the decomposition rate using 13 years of data from a forest dynamics plot. For molecular analysis and wood density measurements, drill dust samples were collected from logs and stumps of Fagus and Quercus in the plot. Regression using a negative exponential model between wood density and time since death revealed that the decomposition rate of Fagus was greater than that of Quercus. The residual between the expected value obtained from the regression curve and the observed wood density was used as a decomposition rate index. Principal component analysis showed that the fungal community compositions of both Fagus and Quercus changed with time since death. Principal component analysis axis scores were used as an index of fungal community composition. A structural equation model for each wood genus was used to assess the effect of fungal community structure traits on the decomposition rate and how the fungal community structure was determined by the traits of coarse woody debris. Results of the structural equation model suggested that the decomposition rate of Fagus was affected by two fungal community composition components: one that was affected by time since death and another that was not affected by the traits of coarse woody debris. In contrast, the decomposition rate of Quercus was not affected by coarse woody debris traits or fungal community structure. These findings suggest that, in the case of Fagus coarse woody debris, the fungal community structure is related to the decomposition process of its host substrate. Because fungal community structure is affected partly by the decay stage and wood density of its substrate, these factors influence each other. Further research on interactive effects is needed to improve our understanding of the relationship between fungal community structure and the woody debris decomposition process. © 2015 Yamashita et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Fittipaldi N.,University of Montréal | Xu J.,Chinese National Institute for Communicable Disease Control and Prevention | Lacouture S.,University of Montréal | Tharavichitkul P.,Chiang Mai University | And 4 more authors.
Emerging Infectious Diseases | Year: 2011

We performed multilocus sequence typing of 64 North American Streptococcus suis serotype 2 porcine isolates. Strains were sequence type (ST) 28 (51%), ST25 (44%), and ST1 (5%). We identified nonrandom associations between STs and expression of the virulence markers suilysin (SLY), muramidase-relased protein (MRP), and extracellular factor (EF). Expression of pili encoded by the srtF and srtG pilus clusters was also nonrandomly associated with STs. ST1 strains were SLY+ EF+ MRP+ srtF pilus+ srtG pilus-. ST25 strains were SLY- EF- MRP- srtF pilus- srtG pilus+, and most ST28 strains were SLY- MRP+ EF- srtF pilus+ srtG pilus+. ST28 isolates proved essentially nonvirulent in a mouse infection model; ST25 strains showed moderate virulence and ST1 isolates were highly virulent. ST1 is responsible for a high proportion of S. suis disease in humans worldwide. Its presence in North America indicates that potential zoonotic S. suis outbreaks in this continent cannot be disregarded.

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