Isolation and identification of natural endophytic rhizobia from rice (Oryza sativa L.) through rDNA PCR-RFLP and sequence analysis

Current Microbiology

Volumn 52, Issue 2, 2006, Pages 117-122

  Singh, Ramesh K ^a   Mishra, Ravi P N ^a   Jaiswal, Hemant K ^a   Kumar, Vinod ^a   Pandey, Shree P ^a,c   Rao, Sasi B ^b   Annapurna, Kannapali ^b  

^a BANARAS HINDU UNIVERSITY   (India)

^b INDIAN AGRICULTURAL RESEARCH INSTITUTE   (India)

^c MAX PLANCK INSTITUTE FOR CHEMICAL ECOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; RIBOSOME DNA;

ARTICLE; BACTERIAL CELL; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM COLONY; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; BACTERIUM ISOLATION; BINDING AFFINITY; BURKHOLDERIA CEPACIA COMPLEX; DNA SEQUENCE; GENE CONSTRUCT; GRAIN YIELD; GUS A REPORTER GENE; INOCULATION; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHASEOLUS VULGARIS; PLANT DISEASE; PLANT ROOT; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REPORTER GENE; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RICE; SEQUENCE ANALYSIS;

BURKHOLDERIA CEPACIA; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; PLANT ROOTS; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RHIZOBIUM LEGUMINOSARUM; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY;

BACTERIA (MICROORGANISMS); BURKHOLDERIA CEPACIA COMPLEX; ORYZA SATIVA; PHASEOLUS (ANGIOSPERM); PHASEOLUS VULGARIS; RHIZOBIUM LEGUMINOSARUM BV. PHASEOLI;

EID: 32944466695     PISSN: 03438651     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00284-005-0136-5     Document Type: Article

References (24)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programme. Nucleic Acids Res 25:3389-3402
2. Biswas JC, Ladha JK, Dazzo FB, Yanni YG, Rolfe BG (2000) Rhizobial inoculation influences seedling vigor and yield of rice. Agron J 92:880-886
3. Chaintreuil C, Giraud E, Prin Y, Lorquin J, Ba A, Gillis M, de Laudie P, Dreyfus B (2000) Photosynthetic bradyrhizobia are natural endophyte of the African wild rice Oryza breviligulata. Appl Environ Microbiol 66:543-544
4. Chen W-M, Laevens S, Lee T-M, Coenye T, DeVos P, Mergeay M, Vandamme P (2001) Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient. Int J Syst Evol Bacteriol 51:1729-1735
5. Coenye T, Vandamme P, Govan JRW, LiPuma JJ (2001) Taxonomy and identification of the Burkholderia cepacia complex. J Clin Microbiol 39:3427-3436
6. Fahraeus G (1957) The infection of clover root hairs by nodule bacteria studied by a simple glass slide technique. J Gen Microbiol 16:374-381
7. Laguerre G, Allard MR, Revoy F, Amarger N (1994) Rapid identification of rhizobia by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl Environ Microbiol 60:56-63
8. Lorenz MG (1998) Horizontal gene transfer among bacteria in soil by natural genetic transformation. In: Subba Rao NS, Dommergues YR (eds). Microbial interactions in agriculture and forestry, vol. 1. New Delhi, India: Oxford and IBH Publication, pp 19-44
9. Ludwig W, Amann R, Martinez-Romero E, Schonhuber W, Bauer S, Neef A, Schleifer K-H (1998) rRNA based identification and detection systems for rhizobia and other bacteria. Plant Soil 204:1-19
10. Matiru VN, Dakora FD (2004) Potential use of rhizobial bacteria as promoters of plant growth for increased yield in land races of African cereal crops. African J Biotechnol 3:1-7
11. Moulin L, Munive A, Dreyfus B, Boivin-Masson C (2001) Nodulation of legumes by members of the β-subclass of proteobacteria. Nature 411:948-950
12. Peng S, Biswas JC, Ladha JK, Gyaneshwar P, Chen Y (2002) Influences of rhizobial inoculation on photosynthesis and grain yield of rice. Agron J 94:925-929
13. Perrine FM, Prayitno J, Weinman JJ, Dazzo FB, Rolfe BG (2001) Rhizobium plasmids are involved in the inhibition or stimulation of rice growth and development. Aust J Plant Physiol 28:923-937
14. Reddy PM, Ladha JK, So RS, Hernandez RJ, Ramos MC, Angeles OR, Dazzo FB, de Bruijn FJ (1997) Rhizobial communication with rice roots: induction of phenotypic changes, mode of invasion and extent of colonization. Plant Soil 194:81-98
15. Sambrook J, Russell DW (2001) Molecular cloning: A laboratory manual (www.molecularcloning.com). Vol. 1, 3 ed. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press
16. Tan Z, Hurek T, Vinuesa P, Muller P, Ladha JK, Reinhold-Hurek B (2001) Specific detection of Bradyrhizobium and Rhizobium strains colonizing rice (Oryza sativa) roots by 16S-23S ribosomal DNA intergenic spacer-targeted PCR. Appl Environ Microbiol 67:3655-3664
17. Vandamme P, Goris J, Chen W-M, De Vos P, Willems A (2002) Burkholderia tuberum sp. nov. and Burkholderia phymatum sp. nov. nodulate the roots of tropical legumes. Syst Appl Microbiol 25:507-512
18. Vauterin L, Vauterin P (1992) Computer-aided objective comparison of electrophoresis patterns for grouping and identification of microorganisms. Eur Microbiol 1:37-41
19. Verma SC, Ladha JK, Tripathi AK (2001) Evaluation of plant growth promoting and colonization ability of endophytic diazotrophs from deep water rice. J Biotechnol 91:127-141
20. Verma SC, Chaudhari SP, Tripathi AK (2004) Phylogeny based on 16S rDNA and nifH sequences of Ralstonia taiwanensis strains isolated from nitrogen fixing nodules of Mimosa putida, in India. Can J Microbiol 50:313-322
21. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697-703
22. Yanni YG, Rizk RY, Corich V, Squartini A, Ninke K, Philip-Hollingsworth S, Orgambide G, de Bruijn FJ, Stoltzfus J, Buckley D, Schmidt TM, Mateos PF, Ladha JK, Dazzo FB (1997) Natural endophytic association between Rhizobium leguminosarum bv trifolii and rice roots and assessment of its potential to promote rice growth. Plant Soil 194:99-114
23. Yanni YG, Rizk RY, El-Fattah FKA, Squartini A, Corich V, Giacomini A, de Bruijn FJ, Rademaker JL, Maya-Flores J, Ostrom P, Vega-Hernandez M, Hollingsworth RI, Martinez-Molina E, Mateos P, Velazquez E, Wopereis J, Triplett E, Umali-Garcia M, Anarna JA, Rolfe BG, Ladha JK, Hills JH, Mujoo R, Ng KP, Dazzo FB (2001) The beneficial plant growth-promoting association of Rhizobium leguminosarum bv trifolii with rice plants. Aust J Plant Physiol 28:845-870
24. Zakhia F, Jeder H, Domergue O, Willems A, Cleyet-Marel J-C, Gillis M, Dreyfus B, De Lajudie P (2004) Characterization of wild Legume Nodulating Bacteria (LNB) in infra-arid zone of Tunisia. Syst Appl Microbiol 27:380-395