Faculty Profiles - MURASE, Jun

Papers - MURASE, Jun

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Effect of Zinc Application on Maize Dry Matter, Zinc Uptake, and Soil Microbial Community Grown Under Different Paddy Soil pH Open Access

Khongchiu, P; Murase, J; Wongkaew, A; Sajjaphan, K; Kumdee, O; Rakpenthai, A; Nakasathien, S

AGRONOMY-BASEL Vol. 16 ( 1 ) 2025.12

Fertilization turns a rubber plantation from sink to methane source

Epron, D; Chotiphan, R; Wang, ZX; Duangngam, O; Shibata, M; Paul, SK; Mochidome, T; Sathornkich, J; Azuma, WA; Murase, J; Nouvellon, Y; Kasemsap, P; Sajjaphan, K

BIOGEOSCIENCES Vol. 22 ( 15 ) page： 4013 - 4033 2025.8

Zinc Application Enhances Biomass Production, Grain Yield, and Zinc Uptake in Hybrid Maize Cultivated in Paddy Soil

Khongchiu, P; Wongkaew, A; Murase, J; Sajjaphan, K; Rakpenthai, A; Kumdee, O; Nakasathien, S

AGRONOMY-BASEL Vol. 15 ( 7 ) 2025.6

Methane oxidation potential of soils in a rubber plantation in Thailand affected by fertilization

Murase, J; Sajjaphan, K; Dechjiraratthanasiri, C; Duangngam, O; Chotiphan, R; Rattanapichai, W; Azuma, W; Shibata, M; Kasemsap, P; Epron, D

SOIL Vol. 11 ( 1 ) page： 457 - 466 2025.6

Multicriteria assessment of recently implemented conservation agriculture cropping systems across farmers' plots in northwestern Cambodia

Pheap, S; Thoumazeau, A; Murase, J; Seng, V; Sarthou, JP; Sar, V; Kimbo, L; Kheam, S; Chan, P; Srean, P; Leang, S; Hok, L; Tivet, F

FARMING SYSTEM Vol. 3 ( 2 ) 2025.4

Trophic modulation of endophytes by rhizosphere protists

Asiloglu, R; Bodur, SO; Samuel, SO; Aycan, M; Murase, J; Harada, N

ISME JOURNAL Vol. 18 ( 1 ) 2024.12

Protists: the hidden ecosystem players in a wetland rice field soil (Feb, 10.1007/s00374-023-01705-9, 2023)

Murase, J; Asiloglu, R

BIOLOGY AND FERTILITY OF SOILS Vol. 60 ( 2 ) page： 255 - 255 2024.2

Conversion from natural coniferous forests to cedar plantations increase soil nitrogen cycling through changing microbial community structures Open Access

Sawada, K; Inagaki, Y; Sugihara, S; Kunito, T; Murase, J; Toyota, K; Funakawa, S

APPLIED SOIL ECOLOGY Vol. 191 2023.11

Bacteriovory of enteric bacteria by soil isolated amoeba depends on both temperature and salinity Open Access

Das, S; Meyer, I; Alaguvel, V; Ghazaryan, L; Murase, J; Shnerb, N; Gillor, O

GEODERMA Vol. 439 2023.11

Type-specific quantification of particulate methane monooxygenase gene of methane-oxidizing bacteria at the oxic-anoxic interface of a surface paddy soil by digital PCR Open Access

Shinjo, R; Oe, F; Nakagawa, K; Murase, J; Asakawa, S; Watanabe, T

ENVIRONMENTAL MICROBIOLOGY REPORTS Vol. 15 ( 5 ) page： 392 - 403 2023.10

Arctic Plant Responses to Summer Climates and Flooding Events: A Study of Carbon and Nitrogen-Related Larch Growth and Ecosystem Parameters in Northeastern Siberia Open Access

Liang, MC; Sugimoto, A; Tei, S; Takano, S; Morozumi, T; Shingubara, R; Murase, J; Maximov, TC

JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES Vol. 128 ( 10 ) 2023.10

Arctic Plant Responses to Summer Climates and Flooding Events: A Study of Carbon and Nitrogen-Related Larch Growth and Ecosystem Parameters in Northeastern Siberia Reviewed International coauthorship Open Access

Liang, Maochang Sugimoto, Atsuko Tei, Shunsuke Takano, Shinya Morozumi, Tomoki Shingubara, Ryo Murase, Jun Maximov, Trofim C.

Journal of Geophysical Research: Biogeosciences Vol. 128 page： e2022JG007135 2023

Estimating Yield-Related Traits Using UAV-Derived Multispectral Images to Improve Rice Grain Yield Prediction Reviewed Open Access

Bascon Maria Victoria, Nakata Tomohiro, Shibata Satoshi, Takata Itsuki, Kobayashi Nanami, Kato Yusuke, Inoue Shun, Doi Kazuyuki, Murase Jun, Nishiuchi Shunsaku

AGRICULTURE-BASEL Vol. 12 ( 8 ) 2022.8

eDNA解析を利用した土壌微生物機能への太陽熱土壌消毒の影響評価法 Reviewed Open Access

浅川晋、村瀬潤、篠原陽子

日本土壌肥料学雑誌 Vol. 92 ( 6 ) page： 476 - 480 2021.12

土壌に関する政府間技術パネル(ITPS)作業グループ会合報告 Invited Open Access

村瀬　潤

日本土壌肥料学会誌 Vol. 92 ( 6 ) page： 501 - 502 2021.12

Soil texture and properties rather than irrigation water type shape the diversity and composition of soil microbial communities Reviewed International coauthorship

Obayomi Olabiyi, Seyoum Mitiku Mihiret, Ghazaryan Lusine, Tebbe Christoph C., Murase Jun, Bernstein Nirit, Gillor Osnat

APPLIED SOIL ECOLOGY Vol. 161 2021.5

Top-down effects of protists are greater than bottom-up effects of fertilisers on the formation of bacterial communities in a paddy field soil International coauthorship

Asiloglu Rasit, Kenya Kobayashi, Samuel Solomon Oloruntoba, Sevilir Bahar, Murase Jun, Suzuki Kazuki, Harada Naoki

Soil Biology and Biochemistry Vol. 156 2021.5

Effect of protists on rhizobacterial community composition and rice plant growth in a biochar amended soil Reviewed International coauthorship

Asiloglu Rasit, Sevilir Bahar, Samuel Solomon Oloruntoba, Aycan Murat, Akca Muhittin Onur, Suzuki Kazuki, Murase Jun, Turgay Oguz Can, Harada Naoki

BIOLOGY AND FERTILITY OF SOILS Vol. 57 ( 2 ) page： 293 - 304 2021.2

Biochar affects taxonomic and functional community composition of protists Reviewed International coauthorship

Asiloglu Rasit, Samuel Solomon Oloruntoba, Sevilir Bahar, Akca Muhittin Onur, Bozkurt Pinar Acar, Suzuki Kazuki, Murase Jun, Turgay Oguz Can, Harada Naoki

BIOLOGY AND FERTILITY OF SOILS Vol. 57 ( 1 ) page： 15 - 29 2021.1

Soil: the great connector of our lives now and beyond COVID-19 Reviewed International coauthorship Open Access

Poch Rosa M., dos Anjos Lucia H. C., Attia Rafla, Balks Megan, Benavides-Mendoza Adalberto, Bolanos-Benavides Martha M., Calzolari Costanza, Chabala Lydia M., de Ruiter Peter C., Francke-Campana Samuel, Prechac Fernando Garcia, Graber Ellen R., Halavatau Siosiva, Hassan Kutaiba M., Hien Edmond, Jin Ke, Khan Mohammad, Konyushkova Maria, Lobb David A., Moshia Matshwene E., Murase Jun, Nziguheba Generose, Patra Ashok K., Pierzynski Gary, Eugenio Natalia Rodriguez, Rojas Ronald Vargas

SOIL Vol. 6 ( 2 ) page： 541 - 547 2020.11

Susceptibility and resilience of the soil ciliate community to high temperatures Reviewed Open Access

Oshima Takaaki, Shinohara Yoko, Asakawa Susumu, Murase Jun

SOIL SCIENCE AND PLANT NUTRITION Vol. 66 ( 6 ) page： 870 - 877 2020.11

Involvement of microaerophilic iron-oxidizing bacteria in the iron-oxidizing process at the surface layer of flooded paddy field soil Reviewed

Nakagawa Koki, Murase Jun, Asakawa Susumu, Watanabe Takeshi

JOURNAL OF SOILS AND SEDIMENTS Vol. 20 ( 11 ) page： 4034 - 4041 2020.11

Protist-enhanced survival of a plant growth promoting rhizobacteria, Azospirillum sp. B510, and the growth of rice ( Oryza sativa L.) plants

Asiloglu Rasit, Shiroishi Keiko, Suzuki Kazuki, Turgay Oguz Can, Murase Jun, Harada Naoki

APPLIED SOIL ECOLOGY Vol. 154 page： 103599 2020.10

Methane oxidation potential of the arctic wetland soils of a taiga-tundra ecotone in northeastern Siberia Reviewed International coauthorship Open Access

Murase Jun, Sugimoto Atsuko, Shingubara Ryo, Liang Maochang, Morozumi Tomoki, Takano Shinya, Maximov Trofim C.

SOIL SCIENCE AND PLANT NUTRITION Vol. 66 ( 4 ) page： 645 - 652 2020.7

田んぼの中の原生生物たちの暮らし Invited Reviewed Open Access

村瀬　潤

土と微生物 Vol. 74 ( 1 ) page： 26 - 31 2020.4

Invention of Artificial Rice Field Soil: A Tool to Study the Effect of Soil Components on the Activity and Community of Microorganisms Involved in Anaerobic Organic Matter Decomposition Open Access

Maeda, Y; Mise, K; Iwasaki, W; Watanabe, A; Asakawa, S; Asiloglu, R; Murase, J

MICROBES AND ENVIRONMENTS Vol. 35 ( 4 ) 2020

Diversity of 2-MIB-Producing Cyanobacteria in Lake Ogawara: Microscopic and Molecular Ecological Approaches. Reviewed

Shizuka, K., Ikenaga, M., Murase, J., Nakayama, N., Kakino, W., Taruya, H., & Maie, N.

Aquatic Science Vol. 68 page： 9 - 23 2020

水田への魚類の遡上を促す遡上板の開発 Reviewed Open Access

皆川明子、若宮慎二、竹下邦明、佐川志朗、河口洋一、村瀬潤、都築隆禎、深澤洋二、江崎保男

応用生態工学 Vol. 23 ( 1 ) page： 79 - 84 2020

Usability of water surface reflectance for the determination of riverine dissolved methane during extreme flooding in northeastern Siberia Open Access

Morozumi, T; Shingubara, R; Murase, J; Nagai, S; Kobayashi, H; Takano, S; Tei, S; Fan, R; Maximov, TC; Sugimoto, A

POLAR SCIENCE Vol. 21 page： 186 - 194 2019.9

Multi-year effect of wetting on CH4 flux at taiga-tundra boundary in northeastern Siberia deduced from stable isotope ratios of CH4 Open Access

Shingubara Ryo, Sugimoto Atsuko, Murase Jun, Iwahana Go, Tei Shunsuke, Liang Maochang, Takano Shinya, Morozumi Tomoki, Maximov Trofim C.

BIOGEOSCIENCES Vol. 16 ( 3 ) page： 755 - 768 2019.2

Microhabitat segregation of heterotrophic protists in the rice (<i>Oryza sativa</i> L.) rhizosphere Open Access

Asiloglu, R; Murase, J

RHIZOSPHERE Vol. 4 page： 82 - 88 2017.12

Quest of Soil Protists in a New Era Open Access

Murase Jun

MICROBES AND ENVIRONMENTS Vol. 32 ( 2 ) page： 99 - 102 2017.6

Response of the protistan community of a rice field soil to different oxygen tensions (vol 92, fiw104, 2016) Open Access

Takenouchi Yuriko, Iwasaki Kazufumi, Murase Jun

FEMS MICROBIOLOGY ECOLOGY Vol. 93 ( 5 ) 2017.5

Fluctuations in the abundance of ammonia oxidizers and the contents of inorganic nitrogen in solarized soil Open Access

Yamagata Mina, Shinohara Yoko, Maesaka Masahiro, Murase Jun, Asakawa Susumu

SOIL SCIENCE AND PLANT NUTRITION Vol. 63 ( 5 ) page： 434 - 440 2017

Response of the protistan community of a rice field soil to different oxygen tensions Reviewed Open Access

Takenouchi, Y., Iwasaki, K., Murase, J.

FEMS Microbiology Ecology 2016

Active community structure of microeukaryotes in a rice (Oryza sativa L.) rhizosphere revealed by RNA-based PCR-DGGE Reviewed Open Access

Asiloglu, R., Murase, J.

Soil Science and Plant Nutrition Vol. 62 page： 440-446 2016

Impact of long-term fertilizer treatment on the microeukaryotic community structure of a rice field soil. Reviewed

Murase, J., Hida, A., Ogawa, K., Nonoyama, T., Yoshikawa, N., Imai, K.

Soil Biology and Biochemistry Vol. 80 page： 237-243 2015

Impact of soil solarization on the ciliate community structure of a greenhouse soil. Reviewed

Murase, J., Shinohara, Y., Yokoe, K., Matsuda, R., Asakawa, S., Hashimoto, T.

Vol. 60 ( 4 ) page： 927-933 2015

Community structure of microeukaryotes in a rice rhizosphere revealed by DNA-based PCR-DGGE. Reviewed Open Access

Asiloglu, R., Honjo, H., Saka, N., Asakawa, S., Murase, J.

Soil Sci Plant Nutr Vol. 61 page： 761-768 2015

Impact of soil solarization on the ciliate community structure of a greenhouse soil. 61, 927-933 (2015) Reviewed

Yokoe, K., Maesaka, M., Murase, J., Asakawa, S

Soil Sci. Plant Nutr. Vol. 61 page： 641-652 2015

Abundance and composition of ammonia oxidizers in response to degradation of root cap cells of rice in soil microcosms. Reviewed

Li, Y., Watanabe, T., Murase, J., Asakawa, S., Kimura, M.

Journal of soils and sediments Vol. 14 page： 1587-1598 2014

Branched and isoprenoid glycerol dialkyl glycerol tetraethers in soils and lake/river sediments in Lake Biwa basin and implications for MBT/CBT proxies. Reviewed

Ajioka, T., Yamamoto, M., Murase, J.

Organic Geochemistry Vol. 73 page： 70-82 2014

Low nitrogen fertilization adapts rice root microbiome to low nutrient environment by changing biogeochemical functions. Reviewed Open Access

Ikeda, S., Sasaki, K., Okubo, T., Yamashita, A., Terasawa, K., Bao, Z., Liu, D., Watanabe, T., Murase, J., Asakawa, S., Eda, S., Mitsui, H., Sato, T., Minamisawa, K.

Microbes and Environments Vol. 29 page： 50-59 2014

Growth of hydrogenotrophic and acetoclastic methanogens on substrate from rice plant callus cells in anaerobic soil: an estimation to the role of slough-off root cap cells to their growth Reviewed

Li Y, Watanabe T, Murase J, Asakawa S, Kimura M

Vol. 59 page： 548-558 2013

Identification of the major capsid gene (g23) of T4-type bacteriophages that assimilate substrates from root cap cells under aerobic and anaerobic soil conditions using a DNA-SIP approach Reviewed

Li Y, Watanabe T, Murase J, Asakawa S, Kimura M

Vol. 63 page： 97-105 2013

安定同位体プロービング(SIP)法で探る水田土壌の物質動態と微生物 Invited Reviewed

村瀬　潤

　土と微生物　67, 39-46 (2013) Vol. 67 page： 39-46 2013

Growth of hydrogenotrophic and acetoclastic methanogens on substrate from rice plant callus cells in anaerobic soil: an estimation to the role of slough-off root cap cells to their growth. Reviewed

Li, Y., Watanabe, T., Murase, J., Asakawa, S., Kimura, M.

Soil Sci. Plant Nutr. Vol. 59 page： 548-558 2013

Growth of methanogens in an oxic soil microcosm: Elucidation by a DNA-SIP experiment using 13C-labeled dried rice callus. Reviewed

Li, Y, Lee CG, Watanabe T, Murase J, Asakawa S, Kimura M

Vol. 58 page： 37-44 2012

Phylogenetic diversity of microturbellarians in Japanese rice paddy fields, with special attention to the genus Stenostomum. Reviewed Open Access

Yamazaki, M, Murase, J, Asakawa, S, Kimura, M

Soil Science and Plant Nutrition Vol. 58 page： 11-23 2012

Incorporation of plant residue-derived carbon into the microeukaryotic community in a rice field soil revealed by DNA stable-isotope probing. Reviewed Open Access

Murase J, Shibata M, Lee CG, Watanabe T, Asakawa S, Kimura M

Vol. 79 page： 371-379 2012

北方湿地生態系からのメタン放出に及ぼす積雪の影響 Invited Reviewed Open Access

村瀬　潤

低温科学 Vol. 70 page： 131-136 2012

Identification of microbial communities that assimilate substrate from root cap cells in an aerobic soil using a DNA-SIP approach. Reviewed

Li, Y, Lee CG, Watanabe T, Murase J, Asakawa S, Kimura M

Soil Biology & Biochemistry Vol. 43 page： 1928-1935 2011

Assimilation of glucose-derived carbon into methanogenic archaea in soil under unflooded condition. Reviewed

Watanabe T, Wang G, Taki K, Lee CG, Murase J, Asakawa S, Kimura M

Applied Soil Ecology Vol. 48 page： 201-209 2011

A new thermophilic heterolobosean amoeba, Fumarolamoeba ceborucoi, gen. nov., sp. nov., isolated near a fumarole at a volcano in Mexico. Reviewed

Johan F. De Jonckheere JF, Murase J, Opperdoes FR

Vol. 50 page： 43-50 2011

Bacterial populations assimilating carbon from ¹³C-labeled plant residue in soil: analysis by a DNA-SIP approach. Reviewed

Lee CG, Watanabe T, Sato Y, Murase J, Asakawa S, Kimura M

Vol. 43 page： 814-822 2011

Strain-specific incorporation of methanotrophic biomass into eukaryotic grazers in a rice field soil revealed by PLFA-SIP. Reviewed

FEMS Microbiology Ecology Vol. 75 page： 284-290 2011

Unique viral capsid assembly protein gene (g20) of cyanophages in the floodwater of a Japanese paddy field. Reviewed

Wang GH, Murase J, Asakawa S, Kimura M

Biol. Fert. Soils Vol. 46 page： 93-102 2010

Isolation of a new heterolobosean amoeba from a rice field soil: Vrihiamoeba italica gen. nov., sp. nov. Reviewed

Murase J, Kawasaki M, De Jonckheere JF

Eur. J. Protistol. Vol. 46 page： 164-170 2010

Isolation of a new heterolobosean amoeba from a rice field soil: Vrihiamoeba italica gen. nov., sp. nov. Reviewed

Murase J, Kawasaki M, De Jonckheere JF

European Jouranal of Protistology Vol. 46 page： 164-170 2010

Low diversity of T4-type bacteriophages in applied rice straw, plant residues and rice roots in Japanese rice soils: Estimation from major capsid gene (g23) composition. Reviewed

Fujihara S, Murase J, Tun CC, Matsuyama T, Ikenaga M, Asakawa S, Kimura M

Soil Science and Plant Nutrition Vol. 56 page： 800-812 2010

Novel cyanophage photosynthetic gene psbA in the floodwater of a Japanese rice field. Reviewed Open Access

Wang GH, Murase J, Asakawa S, Kimura M

FEMS Microbiol. Ecol. Vol. 70 page： 79-86 2009

Methanogenic archaeal communities developed in paddy fields in the Kojima Bay polder, estimated by denaturing gradient gel electrophoresis, real-time PCR and sequencing analyses. Reviewed

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

Soil Sci. Plant Nutr. Vol. 55 page： 73-79 2009

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

Cahyani, V.R., Murase, J., Ikeda, A., Taki, K., Asakawa, S., Kimura,M

Biol. Fertil. Soils Vol. 45 page： 337-346 2009

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

Cahyani VR, Murase J, Ishibashi E, Asakawa S, Kimura M

Soil Sci. Plant Nutr. Vol. 55 page： 468-477 2009

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

DOI： 10.1007/s00374-007-0239-1

*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 Open Access

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

DOI： 10.1111/j.1462-2920.2007.01414.x

*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 Open Access

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 Open Access

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

DOI： 10.4319/lo.2005.50.4.1339

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

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

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

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

Soil Sci. Plant Nutr. Vol. 50 page： 731-738 2004

Nutrient leaching from the plow layer by water percolation and accumulation in the subsoil in an irrigated paddy field. Reviewed

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

Soil Sci. Plant Nutr. Vol. 50 page： 721-729 2004

Biotic and abiotic methane releases from Lake Biwa sediment slurry. Reviewed

Dan,J., Kumai,T., Sugimoto,A., and Murase,J.

Limnology Vol. 5 page： 149-154 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

Effect of application of rice straw and compost on the community structure of bacteria associated with microcrustaceans in the floodwater of a paddy field microcosm. Reviewed

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

Soil Sci. Plant Nutr. Vol. 49 page： 191-200 2003

Adsorption as a methane storage process in natural lake sediment. Reviewed Open Access

Sugimoto,A., Dan,J., Kumai,T., and Murase,J.

Geophys. Res. Lett. Vol. 30 page： doi:10.1029/2003GL018162 2003

Molecular analysis of β-proteobacterial ammonia oxidizer populations in surface layers of a submerged paddy soil microcosm. Reviewed

Murase,J., Itoh,K., Kano,M., and Kimura,M.

Soil Sci. Plant Nutr. Vol. 49 page： 909-913 2003

Sources of dissolved methane in Lake Biwa. Reviewed

Murase,J., Sakai,Y., Sugimoto,A., Okubo,K., and Sakamoto,M.

Limnology Vol. 4 page： 91-99 2003

第2編第2章2.2自然特性

村瀬潤

2002.3

Resuspension of bottom sediment by an internal wave in Lake Biwa Reviewed

Sakai,Y., Murase,J., Sugimoto,A., Okubo,K., and Nakayama,E.

Lakes Reserv. Vol. 7 page： 339-344 2002

Comparison of microbial communities in percolating water from plow layer and subsoil layer estimated by phospholipid fatty acid (PLFA) analysis. Reviewed

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

Soil Sci. Plant Nutr. Vol. 48 page： 877-881 2002

Uptake of carbon and nitrogen through roots of rice and corn plants, grown in soils treated with 13C and 15N dual-labeled cattle manure compost. Reviewed Open Access

Yamamuro,S., Ueno,H., Yamada,H., Takahashi,Y., Shiga,Y., Miyahara,S., Shimonihara,T., Murase,J., Yanai,J., and Nishida,M.

Soil Sci. Plant Nutr. Vol. 48 page： 787-795 2002

沿岸帯を観るキーワード　－その多面的多様性－ Invited Reviewed

村瀬　潤・野崎健太郎・山田佳裕

陸水学雑誌 Vol. 63 page： 269-270 2002

Seasonal and spatial variations of methane production in mesotrophic lake sediments (Lake Biwa, Japan).

Murase,J. and Sugimoto,A.:

Verh.Int. Ver. Limnol. Vol. 28 page： 971-974 2002

Spatial distribution of methane in the Lake Biwa sediments and its carbon isotopic compositions Open Access

Jun MURASE & Atsuko SUGIMOTO

Geochemical Journal Vol. 35 page： 257-263 2001.8

Horizontal distribution of carbon and nitrogen and their isotopic compositions in the surface sediment of Lake Biwa

"Murase,J. and Sakamoto,M"

Limnology Vol. 1 page： 177-184 2000.1

琵琶湖堆積物の生元素の空間的分布

村瀬潤

1998.1

"Anaerobic reoxidation of Mn2+, Fe2+, S0 and S2- in submerged paddy soils."

"Murase,J. and Kimura,M.:"

Biol.Fert.Soil. Vol. 25 page： 302-306 1997.1

Anaerobic reoxidation of Mn²⁺, Fe²⁺, S⁰ and S^2- in submerged poddy soils.

Biology Fertility Soil Vol. 25 page： 302-306 1997

Methane production and its fate in paddy fields. IX. Methane flux distribution and decomposition of methane in the subsoil during the growth period of rice plants.

"Murase,J. and Kimura,M."

Soil Sci. Plant Nutr. Vol. 42(1) page： 187-190 1996.1

Utilization of the feces sludge from the swine farm for rice production in the problem soils in Thailand.

"Murase,J., Korpraditskul,R., Osotsapar,Y., and Korpraditskul,V"

J. ISSAAS Vol. 2 page： 54-71 1996.1

Methane production and its fate in paddy fields. (]G0009[) Methane flux distribution and decompostition of methane in the subsoil during the growth period of rice plants

Soil Science and Plant Nutrition Vol. 42 ( 1 ) page： 187-190 1996

Utilization of the faces sludge from the swine Farm for rice production in the problem soils in Thailand

Journal of International Society for Southeast Asian Agricultural Sciences(J. ISSAAS) Vol. 2 page： 54-71 1996

Methane production and its fate in paddy fields. IV. Sources of microorganisms and substrates responsible for anaerobic methane oxidation in subsoil. Reviewed

Soil Science and Plant Nutrition Vol. 40 ( 1 ) page： 57-61 1994

Methane production and its fate in paddy fields. (]G0006[) Anaerobic oxidation of methane in plow layer soil

Soil Science and Plant Nutrition Vol. 40 ( 3 ) page： 505-514 1994

Methane production and Its fate in paddy fields. (]G0007[) Electron Acceptors responsible for anaerobic methane oxidation

Soil Science and Plant Nutrition Vol. 40 ( 4 ) page： 647-654 1994

Methane production and its fate in paddy fields. (]G0003[). Effects of percolation on methane flux distribution to the atmosphere and the subsoil

Soil Science and Plant Nutrition Vol. 39 ( 1 ) page： 63-70 1993

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