Faculty Profiles - MURASE, Jun

Papers - MURASE, Jun

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Changes in major capsid genes (g23) of T4-type bacteriophages with soil depth in two Japanese rice fields. Reviewed

Wang GH, Murase J, Taki K, Ohashi Y, Yoshikawa N, Asakawa S, Kimura M

Biol. Fert. Soils Vol. 45 page： 521-529 2009

Eukaryotic communities associated with the decomposition of rice straw compost in a Japanese rice paddy field estimated by DGGE analysis Reviewed

HatamotoM., Tanahashi T., Murase J., Matsuya M., Hayashi M., Kimura M., Asakawa S.

Bio. Fert. Soils Vol. 44 ( 3 ) page： 527-532 2008

Language：English Publishing type：Research paper (scientific journal)

To estimate the succession and phylogenetic composition of the eukaryotic communities responsible for the decomposition of rice straw compost under flooded conditions during the cultivation period of paddy rice, denaturing gradient gel electrophoresis (DGGE) analysis targeting 18S rDNA followed by sequencing was conducted in a Japanese paddy field. The eukaryotic communities in rice straw compost incorporated into the flooded paddy field were influenced by the mid-season drainage and mainly composed of fungi (Ascomycota, Zygomycota, and Chytridiomycota) and protozoa (Ciliophora, Euglyphida, and Dactylopodida), most of which existed continuously during the cultivation period of paddy rice. The results indicated that these eukaryotic members were associated with the decomposition of rice straw compost in paddy field soil directly or indirectly

*Selective grazing of methanotrophs by protozoa in a rice field soil. Reviewed

Murase,J. Frenzel,P.

FEMS Microbiol. Ecol. Vol. 65 page： 408-414 2008

Phyologenetic positions of Mn-oxidizing bacteria and fungi inhabiting Mn nodules in rice field subsoils. Reviewed

Vita Ratri Cahyani, Jun Murase, Akihiro Ikeda, Katsutoshi Taki, Susumu Asakawa, and Makoto Kimura

Bio. Fert. Soils page： 10.1007/s00374-008-0337-8. 2008

Bacterial communities in Fe mottles in the plow pan layer of a Japanese rice field: estimation using PCR-DGGE and sequencing analyses Reviewed

Vita Ratri Cahyani, Jun Murase, Eiji Ishibasi, Susumu Asakawa, and Makoto Kimura

Soil Sci. Plant Nutr. Vol. 54 ( 4 ) page： doi: 10.1111/j.1747-0765.2008.00291.x 2008

*A methane-driven microbial food web in a wetland rice soil. Reviewed

Murase, J., Frenzel,P.

Environ. Microbiol. Vol. 9 ( 12 ) page： 3025-3034 2007.12

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal)

Methane oxidation is a key process controlling methane emission from anoxic habitats into the atmosphere. Methanotrophs, responsible for aerobic methane oxidation, do not only oxidize but also assimilate methane. Once assimilated, methane carbon may be utilized by other organisms. Here we report on a microbial food web in a rice field soil driven by methane. A thin layer of water-saturated rice field soil was incubated under opposing gradients of oxygen and 13C-labelled methane. Bacterial and eukaryotic communities incorporating methane carbon were analysed by RNA-stable isotope probing (SIP). Terminal restriction fragment length polymorphism (T-RFLP) and cloning showed that methanotrophs were the most prominent group of bacteria incorporating methane carbon. In addition, a few Myxobacteria-related sequences were obtained from the heavy rRNA fraction. Denaturing gradient gel electrophoresis (DGGE) targeting 18S rRNA detected various groups of protists in the heavy rRNA fraction including naked amoeba (Lobosea and Heterolobosea), ciliates (Colpodea) and flagellates (Cercozoa). Incubation of soil under different methane concentrations in air resulted in the development of distinct protozoan communities. These results suggest that methane carbon is incorporated into non-methanotrophic pro- and microeukaryotes probably via grazing, and that methane oxidation is a shaping force of the microeukaryotic community depending on methane availability

*水田土壌の細菌群集の構造と機能に及ぼす原生動物の影響 Invited

村瀬　潤

土と微生物 Vol. 61 page： 65-68 2007

Bacterial communities in manganese nodules in rice field subsoils: estimation by PCR-DGGE and sequencing analyses. Reviewed

Cahyani, V.R., Murase,J., Ishibashi,E., Asakawa,S., Kimura,M.

Soil Sci. Plant Nutr. Vol. 53 page： 578-584 2007

Language：English Publishing type：Research paper (scientific journal)

The phylogenetic positions of bacterial communities in manganese (Mn) nodules from subsoils of two Japanese rice fields were estimated using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis followed by sequencing of 16S rDNA. The DGGE band patterns and sequencing analysis of characteristic DGGE bands revealed that the bacterial communities in Mn nodules were markedly different from those in the plow layer and subsoils. Three out of four common bands found in Mn nodules from two sites corresponded to Deltaproteobacteria and were characterized as sulfate-reducing and iron-reducing bacteria. The other DGGE bands of Mn nodules corresponded to sulfate and iron reducers (Deltaproteobacteria), methane-oxidizing bacteria (Gamma and Alphaproteobacteria), nitrite-oxidizing bacteria (Nitrospirae) and Actinobacteria. In addition, some DGGE bands of Mn nodules showed no clear affiliation to any known bacteria. The present study indicates that members involved in the reduction of Mn nodules dominate the bacterial communities in Mn nodules in rice field subsoils

Impact of protists on the activity and structure of the bacterialcommunity in a rice field soil Reviewed

Murase, J., Noll, M., Frenzel,P.

Applied and Environmental Microbiology Vol. 72 ( 8 ) page： 5436-5444 2006.8

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal)

Flooded rice fields have become a model system for the study of soil microbial ecology. In Italian rice fields,
in particular, aspects from biogeochemistry to molecular ecology have been studied, but the impact of protistan
grazing on the structure and function of the prokaryotic community has not been examined yet. We compared
an untreated control soil with a -radiation-sterilized soil that had been reinoculated with a natural bacterial
assemblage. In order to verify that the observed effects were due to protistan grazing and did not result from
sterilization, we set up a third set of microcosms containing sterilized soil that had been reinoculated with
natural assemblage bacteria plus protists. The spatial and temporal changes in the protistan and prokaryotic
communities were examined by denaturing gradient gel electrophoresis (DGGE) and terminal restriction
fragment length polymorphism (T-RFLP) analysis, respectively, both based on the small-subunit gene. Sequences
retrieved from DGGE bands were preferentially affiliated with Cercozoa and other bacteriovorous
flagellates. Without protists, the level of total DNA increased with incubation time, indicating that the level of
the microbial biomass was elevated. Betaproteobacteria were preferentially preyed upon, while low-GC-content
gram-positive bacteria became more dominant under grazing pressure. The bacterial diversity detectable by
T-RFLP analysis was greater in the presence of protists. The level of extractable NH4
was lower and the level
of extractable SO4
2 was higher without protists, indicating that nitrogen mineralization and SO4
2 reduction
were stimulated by protists. Most of these effects were more obvious in the partially oxic surface layer (0 to 3
mm), but they could also be detected in the anoxic subsurface layer (10 to 13 mm). Our observations fit well
into the overall framework developed for protistan grazing, but with some modifications pertinent to the
wetland situation

土壌中の遺伝子・遺伝情報　何ができるのか、何が分かるのか９．土壌DNAの利用、新しい研究手法（その２）Stable Isotope Probing Invited Reviewed

村瀬　潤

日本土壌肥料学雑誌 Vol. 77 ( 2 ) page： 231-234 2006

*Incorporation of 13C-labeled rice straw carbon into microbial communities in submerged rice field soil and the percolating water. Reviewed

Vol. 38 page： 3483-3491 2006

Vertical Changes in Bacterial communities in percolating water of a Japanese paddy field as revealed by PCR-DGGE. Reviewed

Murase,J., Shimizu,M., Hayashi,M., Matsuya,K., and Kimura,M.

Soil Sci. Plant Nutr. Vol. 51 page： 821-829 2005

Inhibitory effect of light on methane oxidation in the pelagic water column of a mesotrophic lake (Lake Biwa, Japan). Reviewed

Murase,J. and Sugimoto,A.

Limnol. Oceanogr. Vol. 50 page： 1339-1343 2005

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal)

Methane oxidation was studied in mesotrophic lake water (Lake Biwa, Japan) under thermally stratified conditions. Methane oxidation rates at in situ concentrations were very low in lake water from the epilimnion and thermocline but were high in hypolimnetic water. Incubation under light conditions ranging from 4.1 to 57 mu mol photons m(-2) s(-1) resulted in decreased methane oxidation in hypolimnetic water. This inhibition was more severe as the light intensity increased. Addition of inorganic nitrogen (ammonium and nitrate) did not promote methane oxidation in the thermocline but inhibited it in the hypolimnion. Methane oxidation activity in the thermocline was observed after I month of incubation under dark conditions. Our results suggest that the inhibitory effect of light was bacteriostatic for the methanotrophic population. The different rates of methane oxidation between the hypolimnion and epilimnion/thermocline may explain the surface maximum of dissolved methane during the period of thermal stratification

Carbon cycling in rice field ecosystems in the context of input, decomposition and translocation of organic materials and the fates of their end products (CO2 and CH4). Reviewed

Kimura,M., Murase,J., and Lu,Y.

Soil Biol. Biochem. Vol. 36 page： 1399-1416 2005

Effect of rice straw amendment on dissolved organic and inorganic carbon, and cationic nutrients in percolating water from a flooded paddy soil: A microcosm experiment using 13C-enriched rice straw. Invited Reviewed

Katoh,M., Murase,J., Sugimoto,A., and Kimura,M.

Org. Geochem. Vol. 36 page： 803-811 2005

Bacterial community responsible for the decomposition of rice straw compost in a Japanese rice paddy field estimated by DGGE analysis of amplified 16S rDNA and 16S rRNA fragments. Reviewed

Tanahashi,T., Murase,J., Matsuya,K., Asakawa, S., and Kimura,M.

Soil Sci. Plant Nutr., 51, 351-360 (2005) Vol. 51 page： 351-360 2005

Dynamics of methane in a mesotrophic Lake Biwa, Japan. Invited Reviewed

Murase.J., Sakai,Y., Kametani,A., and Sugimoto,A.

Ecol. Res. Vol. 20 page： 377-385 2005

Analysis of communities of ammonia oxidizers, methanotrophs, and methanogens associated with microcrustaceans in the floodwater of a rice field microcosm. Reviewed

Niswati,A., Murase,J., Asakawa,S., and Kimura,M.

Soil Sci. Plant Nutr. Vol. 50 page： 447-455 2004

Linking microbial community dynamics to rhizosphere carbon flow in a wetland rice soil. Reviewed

Lu,Y., Murase,J., Watanabe,A., Sugimoto,A., and Kimura,M.

FEMS Microbiol. Ecol. Vol. 48 page： 179-186 2004

Microbial communities responsible for the decomposition of rice straw compost in a Japanese rice paddy field determined by phospholipid fatty acid (PLFA) analysis. Reviewed

Tanahashi,T., Murase,J., Matsuya,K., Asakawa,S., and Kimura,M.

Soil Sci. Plant Nutr., 50, 1229-1236 (2004) Vol. 50 page： 1229-1236 2004

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