Bacterial communities associated with nodal roots of rice plants along with the growth stages: Estimation by PCR-DGGE and sequence analyses

References

• Chelius , MK and Triplett , EW . 2001 . The diversity of archaea and bacteria in associalion wilh lhe rools of Zea may L . Microb. Ecol. , 41 : 252 – 263 .
   PubMed Web of Science ®Google Scholar
• Conale-Parola , E . 1992 . “ Free-living saccharolytic Spirochetes: the genus Spirochaeta ” . In The Prokaryotes , Edited by: Balows , A , Truper , HG , Dworkin , M , Harder , W and Schleifer , KH . 3524 – 3536 . New York : Springer-Verlag .
   Google Scholar
• De Leiji , FAAM , Whipps , JM and Lynch , JM . 1994 . The use of colony dcvclopment for the characterization of bacterial communities in soil and on roots . Microb. Ecol. , 27 : 81 – 97 .
   PubMed Web of Science ®Google Scholar
• Duineveld , BM , Rosado , AS , van Elsas , JD and van Veen , JA . 1998 . Analysis of the dynamics of bacterial communities in the rhizosphere of the chrysanthemum via denaturing gradient gel electrophoresis and substrate utilization patterns . Appl. Environ. Microbial. , 64 : 4950 – 4957 .
   PubMed Web of Science ®Google Scholar
• Gillis , M and De Ley , J . 1992 . “ The genera Chromobacterium and Janthinobacterium ” . In The Prokaryotes , Edited by: Balows , A , Truper , HG , Dworkin , M , Harder , W and Schleifer , KH . 2591 – 2600 . New York : Springer-Verlag .
   Google Scholar
• Hengstmann , U , Chin , KJ , Janssen , PH and Liesack , E . 1999 . Comparative phylogenetic assignment of environmental sequences of genes encoding 16S rRNA and numerically abundant culturable bacteria from an anoxic rice paddy soil . Appl. Environ. Microbial. , 65 : 5050 – 5058 .
   PubMed Web of Science ®Google Scholar
• Holmes , B . 1992 . “ The genera Flavobacterium, Spingobacterium, and Weeksella ” . In The Prokaryotes , Edited by: Balows , A , Truper , HG , Dworkin , M , Harder , W and Schleifer , KH . 3620 – 3630 . New York : Springer-Verlag .
   Google Scholar
• Hoshikawa , K . 1975 . The Growing Rice Plant-An Anatomical Monograph , 87 – 101 . Tokyo : Nobunkyo .
   Google Scholar
• Hurek , T , Egener , T and Reinhold-Hurek , B . 1997 . Divergence in nitrogenases of Azoarcus sp., proteobacteria of the 13 subclass . J. Bacterial. , 179 : 4172 – 4178 .
   PubMed Web of Science ®Google Scholar
• Ikenaga , M , Muraoka , Y , Toyota , K and Kimura , M . 2002 . Community structure of the microbiota associated with nodal roots of rice plants along with the growth stages: Estimation by PCR-RFLP analysis . Biol. Fertil. Soils , 36 : 397 – 404 .
   Web of Science ®Google Scholar
• Kaiser , O , Puhler , A and Selbitschka , W . 2001 . Phylogenetic analysis of microbial diversity in the rhizoplane of oilseed rape (Brassica napus cv. Westar) employing cultivation-dependent and cultivation-independent approaches . Microb. Ecol. , 42 : 136 – 149 .
   PubMed Web of Science ®Google Scholar
• Kanungo , PK , Patnaik , GK , Adhya , TK and Rao , YR . 1995 . Nitrogenase activity and nitrogen-fixing bacteria associated with root base and root tip of rice plants . Microbial. Res. , 150 : 173 – 177 .
   Google Scholar
• Kimura , M , Wada , H and Takai , Y . 1980 . The studies on the rhizosphere of paddy rice VII. Microbes on the rhizoplane of rice plants . Soil Sci. Plant Nutr. , 51 : 85 – 89 .
   Google Scholar
• Kimura , M , Wada , H and Takai , Y . 1983 . Rice rhizosphere as an environment of mjcrobial growth . Soil Microorg. , 25 : 45 – 55 . (in Japanese)
   Google Scholar
• Kimura , M , Wada , H and Takai , Y . 1987 . Relationships between microbes on the rhizoplane of lice plants and deposition of iron oxide . Soil Sci. Plant Nutr. , 58 : 684 – 690 .
   Google Scholar
• Kimura , M , Wada , H and Takai , Y . 1989 . Microbial colonization and decomposition process in rice rhizoplane I. Microbial colonization associated with lateral root emergence . Soil Sci. Plant Nutr. , 35 : 63 – 70 .
   Web of Science ®Google Scholar
• Lüdemann , H , Arth , I and Liesack , W . 2000 . Spatial changes in the bacterial community structure along a vertical oxygen gradienl in flooded paddy soil cores . Appl. Environ. Microbial. , 66 : 754 – 762 .
   PubMed Web of Science ®Google Scholar
• Murakami , H , Kimura , M and Wada , H . 1990 . Microbial colonization and decomposition process in rice rhizoplane II. Decomposition of young and old roots . Soil Sci. Plant Nutr. , 36 : 441 – 450 .
   Web of Science ®Google Scholar
• Muraoka , Y , Hamakawa , E , Toyota , K and Kimura , M . 2000 . Observation of microbial colonization on the surface of rice roots along with their development and degradation . Soil Sci. Plant Nutr. , 46 : 491 – 502 .
   Web of Science ®Google Scholar
• Muyzer , G , De Waal , EC and Uitterlinden , AG . 1993 . Profiling of complex microbial populations by denaturing gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA . Appl. Environ. Microbial. , 59 : 695 – 700 .
   PubMed Web of Science ®Google Scholar
• Newman , EI and Watson , A . 1977 . Microbial abundance in the rhizosphere a computer model . Plant Soil , 48 : 17 – 56 .
   Web of Science ®Google Scholar
• Reichenbach , H . 1992 . “ The order Cytophagales ” . In The Prokaryotes , Edited by: Balows , A , Truper , HG , Dworkin , M , Harder , W and Schleifer , KH . 3631 – 3675 . New York : Springer-Verlag .
   Google Scholar
• Reichenbach , H and Dworkin , M . 1992 . “ The Myxobacteria ” . In The Prokaryotcs , Edited by: Balows , A , Truper , HG , Dworkin , M , Harder , W and Schleifer , KH . 3416 – 3487 . New York : Springer-Verlag .
   Google Scholar
• Shiomi , Y , Nishiyama , M , Onizuka , T and Marumoto , T . 1999 . Comparison of bacterial community structure in the rhizoplane of tomato plants grown in soils suppressive and conducive towards bacterial wilt . Appl. Environ. Microbial. , 65 : 3996 – 4001 .
   PubMed Web of Science ®Google Scholar
• Sims , GK and Dunigan , EP . 1984 . Diurnal and seasonal variations in nitrogenase activity (C2H2 reduction) of rice roots . Soil Biol. Biochem. , 16 : 15 – 18 .
   Web of Science ®Google Scholar
• Ueda , T , Suga , Y , Yahiro , N and Matsuguchi , T . 1995 . Remarkable N2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences . J. Bacterial. , 177 : 1414 – 1417 .
   PubMed Web of Science ®Google Scholar
• Umeda , T , Suga , Y , Yahiro , N and Matsuguchi , T . 1995 . Remarkable N2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences . J. Bacterial. , 177 : 1414 – 1417 .
   PubMed Web of Science ®Google Scholar
• Wind , T , Stubner , S and Conrad , R . 1999 . Sulfate-reducing bacteria in rice field soil and on rice roots . Syst. Appl. Microbial. , 22 : 269 – 279 .
   PubMed Web of Science ®Google Scholar
• Yang , CH and Crowley , DE . 2000 . Rhizosphere microbial community structure in relation to root location and plant iron nutritional status . Appl. Environ. Microbial. , 66 : 345 – 351 .
   PubMed Web of Science ®Google Scholar