Faculty Profiles - ASAKAWA, Susumu

Papers - ASAKAWA, Susumu

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

Guanghua Wang, Jun Murase, Katsutoshi Taki, Yoshinori Ohashi, Nanako Yoshikawa, Susumu Asakawa, Makoto Kimura

Biol. Fertil. Soils Vol. 45 page： 521 - 529 2009.5

原生生物や線虫から見た土壌生態系の解明と活用 Reviewed Open Access

橋本知義・浅川晋・村瀬潤・島野智之・高橋忠夫・岡田浩明・佐藤恵利華・豊田剛己

日本土壌肥料学雑誌 Vol. 80 ( 2 ) page： 201 - 206 2009.4

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

Vita Ratri Cahyani, Jun Murase, Eiji Ishibashi, Susumu Asakawa, Makoto Kimura

Soil Sci. Plant Nutr. Vol. 55 page： 264 - 270 2009.4

Phylogenetic positions of Mn2+-oxidizing bacteria and fungi isolated from Mn nodules in rice field subsoils Reviewed International coauthorship

Vita Ratri Cahyani, Jun Murase, Eiji Ishibashi, Susumu Asakawa, Makoto Kimura

Biol. Fertil. Soils Vol. 45 page： 337 - 346 2009.3

Comparison of g23 gene sequence diversity between Novosphingobium and Sphingomonas phages and phage communities in the floodwater of a Japanese paddy field Reviewed

Natsuko Nakayama, Susumu Asakawa, Makoto Kimura

Soil Biol. Biochem. Vol. 41 page： 179 - 185 2009.2

*Distinct members of a stable methanogenic archaeal community transcribe mcrA genes under flooded and drained conditions in Japanese paddy field soil Reviewed

Takeshi Watanabe, Makoto Kimura, Susumu Asakawa

Soil Biol. Biochem. Vol. 41 page： 276 - 285 2009.2

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

The composition and succession of methanogenic archaea in a Japanese paddy field were investigated
during an annual cycle by analyses of methyl-coenzyme M reductase a subunit (mcrA) genes and their
mRNA transcripts, which encode a key enzyme for methanogenesis. The paddy field was managed with
a double-cropping cultivation, i.e. rice grown in summer under a flooded condition and wheat cultivated
in winter under a drained condition. The mcrA genes and their transcripts were amplified from genomic
DNA and total RNA extracted from soil samples, respectively. Numbers of the mcrA genes estimated by
the most probable number-PCR showed little variation among the samples, whereas those of the transcripts
and the transcripts/mcrA gene ratios increased in the late period of the rice cultivation under
flooded condition. In addition, band patterns of denaturing gradient gel electrophoresis of the mcrA gene
PCR products were similar among the samples, while those from the transcripts were different between
the samples under flooded and drained conditions. Methanogenic activities of the paddy soils were
higher under flooded conditions than drained conditions. Clones belonging to Methanomicrobiales,
Methanosarcinales, Methanocellales (Rice cluster I), mrtA cluster (isoenzyme genes) and Methanobacteriaceae
were detected in the soils by the clone library analysis. However, the relative proportions
in the libraries from the transcripts were completely different, i.e. transcripts derived from members of
unidentified Methanosarcinales and Rice cluster I were predominantly detected in the soils under
flooded and drained conditions, respectively. These results suggested that distinct members in a wellestablished
methanogenic archaeal community transcribed mcrA genes and contributed to methane
production corresponding to soil conditions.

DOI： 10.1016/j.soilbio.2008.10.025

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 International coauthorship

Takeshi Watanabe, Vita Ratri Cahyani, Jun Murase, Eiji Ishibashi, Makoto Kimura, Susumu Asakawa

Soil Sci. Plant Nutr. Vol. 55 page： 73 - 79 2009.2

Morphology, host range and phylogenetic diversity of Sphingomonas phages in the floodwater of a Japanese paddy field Reviewed

Natsuko Nakayama, Takashi Tsuge, Susumu Asakawa, Makoto Kimura

Soil Sci. Plant Nutr. Vol. 55 page： 53 - 64 2009.2

Survey of major capsid genes (g23) of T4-type bacteriophagesin rice fields in Northeast China Reviewed International coauthorship

Guanghua Wang, Jian Jin, Susumu Asakawa, Makoto Kimura

Soil Biol. Biochem. Vol. 41 page： 423 - 427 2009.2

Frequency of phage-infected bacterial cells in the floodwater of a Japanese paddy field Reviewed

Natsuko Nakayama, Susumu Asakawa, Makoto Kimura

Soil Biol. Biochem. Vol. 41 page： 186 - 191 2009.2

Survey of major capsid genes (g23) of T4-type bacteriophages in Japanese paddy field soils Reviewed International coauthorship

Guanghua Wang, Motoki Hayashi, Masato Saito, Kazunari Tsuchiya , Susumu Asakawa, Makoto Kimura

Soil Biol. Biochem. Vol. 41 page： 13 - 20 2009.1

部門別進歩総説，第３部門　土壌生物，土壌生物 Reviewed

浅川晋・鮫島玲子・齋藤明広・橋本知義

日本土壌肥料学雑誌 Vol. 76 ( 6(部門別進歩総説特集号) ) page： 557 - 560 2008.12

*Identification of the gene for disaggregatase from Methanosarcina mazei Reviewed

Naoki Osumi, Yoshihiro Kakehashi, Shiho Matsumoto, Kazunari Nagaoka, Junich Sakai, Kiyotaka Miyashita, Makoto Kimura, Susumu Asakawa

Archaea Vol. 2 page： 185 - 191 2008.12

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal)

The gene sequences encoding disaggregatase
(Dag), the enzyme responsible for dispersion of cell aggregates
of Methanosarcina mazei to single cells, were determined
for three strains of M. mazei (S-6T, LYC and TMA). The
dag genes of the three strains were 3234 bp in length and had almost
the same sequences with 97% amino acid sequence identities.
Dagwas predicted to comprise 1077 amino acid residues
and to have a molecular mass of 120 kDa containing three repeats
of the DNRLRE domain in the C terminus, which is specific
to the genus Methanosarcina and may be responsible for
structural organization and cell wall function. Recombinant
Dag was overexpressed in Escherichia coli and preparations
of the expressed protein exhibited enzymatic activity. The
RT-PCR analysis showed that dagwas transcribed tomRNAin
M. mazei LYC and indicated that the gene was expressed in
vivo. This is the first time the gene involved in the morphological
change of Methanosarcina spp. from aggregate to single
cells has been identified.

DOI： 10.1155/2008/949458

Bacterial communities in iron mottles in the plow pan layer of a Japanese rice field: estimation using PCR-DGGE and sequencing analyses Reviewed International coauthorship Open Access

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

Soil Sci.Plant Nutr. Vol. 54 page： 711 - 717 2008.10

Distribution of Archaea in Japanese patients with periodontitis and humoral immune response to the components Reviewed Open Access

Kokoro Yamabe, Hiroshi Maeda, Susumu Kokeguchi, Ichiro Tanimoto, Norihiro Sonoi, Susumu Asakawa, Shogo Takashiba

FEMS Microbiol. Lett. Vol. 287 page： 69 - 75 2008.10

水田における微生物の機能と群集構造 Invited

浅川晋

バイオサイエンスとインダストリー Vol. 66 ( 9 ) page： 482 - 487 2008.9

白鳥神社と水田農業（追補）ー愛知県旧作手村（現新城市作手地区）の白鳥神社と水田稲作の関わりについてー

浅川晋，木村眞人，小野信一

農業と科学 Vol. 598 page： 11 - 14 2008.6

*Comparison of bacterial community structures at main habitats in paddy field ecosystem based on DGGE analysis Reviewed

Susumu Asakawa and Makoto Kimura

Soil Biol. Biochem. Vol. 40 page： 1322 - 1329 2008.6

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

Bacterial communities at different habitats in a Japanese paddy field ecosystem were compared to understand the bacterial world in the
ecosystem as a whole by analyzing data of the denaturing gradient gel electrophoresis (DGGE) band patterns and the sequenced DGGE
bands. The habitats were floodwater, percolating water, microcrustacean inhabiting in floodwater, plow layer soil, rice roots, rice straw
and rice straw compost incorporated in soil, rice straw placed on the soil surface, plant residues in paddy fields, and rice straw under
composting process. Phylotype (band) richness, diversity, evenness, and stability of the bacterial communities at the respective habitats
were evaluated based on the DGGE profile data. Phylotype richness was greater near plant residues, rice straw buried in soil and rice
straw placed on soil surface, while it was smaller at microcrustacean and rice straw compost buried in soil. The samples from plow layer
soil and rice straw compost buried in soil showed considerably higher index values for diversity, evenness, and stability, while those from
rice straw placed on soil surface and microcrustacean had lower values of the indices than other habitats. Sequences of totally 250 DGGE
bands were assigned to phyla or classes. Distribution of bacterial members to phylogenetic taxa was different among the respective
habitats. Inhabitants in plow layer soil were most widely distributed among the groups (nine phyla: Proteobacteria, Chloroflexi,
Chlorobi, Verrucomicrobia, Acidobacteria, Nitrospira, candidate division OP10, Cyanobacteria, and Actinobacteria), while those in
floodwater and microcrustacean were restricted to only three phyla (Proteobacteria, Bacteroidetes, and Actinobacteria). Proteobacteria
and Bacteroidetes were found at all the habitats and the habitats except for plow layer soil, respectively, whereas abundant members
belonged to Chloroflexi and Actinobacteria in plow layer soil. ``Comprehensive mapping'' of DGGE f

DOI： 10.1016/j.soilbio.2007.09.024

Novel capsid genes (g23) of T4-type bacteriophages in a Japanese paddy field Reviewed

Takeshi Fujii, Natsuko Nakayama, Mizuhiko Nishida, Hiroyuki Sekiya, Naoto Kato, Susumu Asakawa, and Makoto Kimura

Soil Biol. Biochem. Vol. 40 page： 1049 - 1059 2008.5

Cyanobacterial communities of rice straw left on the soil surface of a paddy field Reviewed

Naoko Asari, Rie Ishihara, Yasunori Nakajima, Makoto Kimura, and Susumu Asakawa

Biol. Fertil. Soils Vol. 44 page： 605 - 612 2008.4

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Papers - ASAKAWA, Susumu