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Original article

Phylogenetic distribution of bacteria isolated from the floodwater of a Japanese paddy field

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Pages 305-312 | Received 21 Feb 2005, Accepted 12 Jan 2006, Published online: 17 Dec 2010

REFERENCES

  • Rangaswami , G and Narayanaswami , R . 1965 . Studies on the microbial population of irrigation water in rice fields . IntRice CommNewsl , 14 : 35 – 42 .
  • Wakao , N . 1973 . Ecological studies on sulfate-reducing bacteria in paddy-field soil . BullInstAgrResTohoku Univ , 24 : 177 – 224 . (in Japanese with English summary)
  • Furusaka , C . 1978 . “ Microbiology in paddy soils ” . In Soil Sciences in Paddy Fields , Edited by: Kawaguchi , K . 201 – 227 . Tokyo : Kodansha . (in Japanese)
  • Suzuki , T . 1967 . Characteristics of microorganisms in paddy field soils . JARQ , 2 : 8 – 12 .
  • Matsuguchi , T , Bunharn , T and Somchai , P . 1976 . Flora and N2-fixing activities of free-living N2-fixing bacteria in Thai paddy fields . Soil Microorganisms , 18 : 7 – 19 . (in Japanese)
  • Okabe , A , Oike , H , Toyota , K and Kimura , M . 2000a . Comparison of phospholipid fatty acid composition in floodwater and plow layer soil during the rice cultivation period in a Japanese paddy field . Soil SciPlant Nutr , 46 : 893 – 904 .
  • Hengstmann , U , Chin , KJ , Janssen , PH and Liesack , W . 1999 . Comparative phylogenetic assignment of environmental sequences of genes encoding 16S rRNA and numerically abundant culturable bacteria from an anoxic rice paddy soil . ApplEnvironMicrobiol , 65 : 5050 – 5058 .
  • Amann , RI , Ludwig , W and Schleifer , KH . 1995 . Phylogenetic identification and in situ detection of individual microbial cells without cultivation . MicrobiolRev , 59 : 143 – 169 .
  • Zelles , L . 1997 . Phospholipid fatty acid profiles in selected members of soil microbial communities . Chemosphere , 35 : 275 – 294 .
  • Katayama , A and Fujie , K . 2000 . “ Characterization of soil microbiota with quinone profile ” . In Soil Biochemistry , Edited by: Bollag , JM and Stotzky , G . Vol. 10 , 303 – 347 . New York : Marcel Dekker .
  • Okabe , A , Toyota , K and Kimura , M . 2000b . Seasonal variations of phospholipid fatty acid composition in the floodwater of a Japanese paddy field under a long-term fertilizer trial . Soil SciPlant Nutr , 46 : 177 – 188 .
  • Shimizu , M , Nakajima , Y , Matsuya , K and Kimura , M . 2002 . Comparison of phospholipid fatty acid composition in percolating water, floodwater, and the plow layer soil during the rice cultivation period in a Japanese paddy field . Soil SciPlant Nutr , 48 : 595 – 600 .
  • Shibagaki-Shimizu , T , Nakayama , N , Nakajima , Y , Matsuya , K , Kimura , M and Asakawa , S . Phylogenetic study on a bacterial community in the floodwater of a Japanese paddy field estimated by sequencing 16S rDNA fragments after denaturing gradient gel electrophoresis . BiolFertilSoils , DOI: 10.1007/s00374-005-0041-x
  • Josephson , KL , Gerba , CP and Pepper , IL . 1993 . Polymerase chain reaction detection of nonviable bacterial pathogens . ApplEnvironMicrobiol , 59 : 3513 – 3515 .
  • Suzuki , MT and Giovannoni , SJ . 1996 . Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR . ApplEnvironMicrobiol , 62 : 625 – 630 .
  • Wang , GC and Wang , Y . 1997 . Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes . ApplEnvironMicrobiol , 63 : 4645 – 4650 .
  • Dunbar , J , Takala , S , Barns , SM , Davis , JA and Kuske , CR . 1999 . Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning . ApplEnvironMicrobiol , 65 : 1662 – 1669 .
  • Kurisu , F . 1999 . “ Microbial community structure analysis for the thermophilic contact oxidation process ” . Japan : University of Tokyo . (PhD thesis)
  • Society of American Bacteriologists . 1957 . Manual of Microbiological MethodSociety of American Bacteriologists , New York : McGraw Hill .
  • Muyzer , G , Waal , ECD and Uitterlinden , AG . 1993 . Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA . ApplEnvironMicrobiol , 59 : 695 – 700 .
  • Kimura , M , Shibagaki , T , Nakajima , Y , Matuya , K and Ikenaga , M . 2002 . Community structure of the microbiota in the floodwater of a Japanese paddy field estimated by restriction fragment length polymorphism and denaturing gradient gel electrophoresis pattern analyses . BiolFertilSoils , 36 : 306 – 312 .
  • Collins , MD and Bradbury , JF . 1992 . “ The genera Agromyces, Aureobacterium, Clavibacter, Curtobacterium, and Microbacterium ” . In The Prokaryotes: A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications , 2nd edn , Edited by: Balows , A , Trüper , HG , Dworkin , M , Harder , W and Schleifer , KH . Vol. 2 , 1355 – 1368 . New York : Springer-Verlag .
  • Jones , D and Keddie , RM . 1992 . “ The genus Arthrobacter ” . In The Prokaryotes: A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications , 2nd edn , Edited by: Balows , A , Trüper , HG , Dworkin , M , Harder , W and Schleifer , KH . Vol. 2 , 1283 – 1299 . New York : Springer-Verlag .
  • Smith , NR , Gordon , RE and Clark , FE . 1952 . Aerobic spore-forming bacteria , Monograph No.16 US Department of Agriculture .
  • Holmes , B . 1992 . “ The genera Flavobacterium, Sphingobacterium, and Weeksella ” . In The Prokaryotes: A Handbook on the Biology of bacteria: Ecophysiology, Isolation, Identification, Applications 2nd edn , Edited by: Balows , A , Trüper , HG , Dworkin , M , Harder , W and Schleifer , KH . Vol. 4 , 3620 – 3630 . New York : Springer-Verlag .
  • Balkwill , DL , Fredrickson , JK and Romine , MF . 2003 . “ Sphingomonasand related genera ” . In The Prokaryotes , 3rd edn , Edited by: Dworkin , M . New York : Springer-Verlag . release 3.14., http://141.150.157.117:8080/prokPUB/chaprender/jsp/showchap.jsp?chapnum=314
  • Janda , JM . 2002 . “ New members of the family Enterobacteriaceae ” . In The Prokaryotes , 3rd edn , Edited by: Dworkin , M . New York : Springer-Verlag . release 39, http://141.150.157.117:8080/prokPUB/chaprender/jsp/showchap.jsp?chapnum=375
  • Palleroni , NJ . 1992 . “ Introduction to the family Pseudomonadaceae ” . In The Prokaryotes: A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications , 2nd edn , Edited by: Balows , A , Trüper , HG , Dworkin , M , Harder , W and Schleifer , KH . Vol. 3 , 3074 – 3085 . New York : Springer-Verlag .
  • Towner , K . 1992 . “ The genus Acinetobacter ” . In The Prokaryotes: A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications , 2nd edn , Edited by: Balows , A , Trüper , HG , Dworkin , M , Harder , W and Schleifer , KH . Vol. 4 , 3137 – 3143 . New York : Springer-Verlag .
  • Sugano , A , Tsuchimoto , H , Tun , CC , Asakawa , S and Kimura , M . 2005 . Succession and phylogenetic profile of eubacterial communities in rice straw incorporated into a rice field: Estimation by PCR-DGGE analysis . Soil SciPlant Nutr , 51 : 51 – 60 .
  • Ikenaga , M , Asakawa , S , Muraoka , Y and Kimura , M . 2003 . Bacterial communities associated with nodal roots of rice plants along with the growth stages: Estimation by PCR-DGGE and sequence analyses . Soil Sci Plant Nutr , 49 : 591 – 602 .
  • Niswati , A , Murase , J and Kimura , M . 2005 . Comparison of bacterial communities associated with microcrustaceans from the floodwater of a paddy field microcosm: Estimation based on DGGE pattern and sequence analyses . Soil SciPlant Nutr , 51 : 281 – 290 .
  • Murase , J , Shimizu , M , Hayashi , M , Matsuya , K and Kimura , M . 2005 . Vertical changes in bacterial communities in percolating water of a Japanese paddy field as revealed by PCR-DGGE . Soil SciPlant Nutr , 51 : 83 – 90 .
  • Present addresses: Home, 151-1, Kitanominami, Gifu 501-2516, Japan.
  • Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei 184-8588, Japan.

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