Genetic and functional diversity of fluorescent Pseudomonas from rhizospheric soils of wheat crop

Journal of Basic Microbiology

Volumn 54, Issue 5, 2014, Pages 425-437

  Yadav, Subhash ^a   Yadav, Shivani ^a   Kaushik, Rajeev ^b   Saxena, Anil K ^b   Arora, Dilip K ^a  

^a ICAR NATIONAL BUREAU OF AGRICULTURALLY IMPORTANT MICROORGANISMS   (India)

^b INDIAN AGRICULTURAL RESEARCH INSTITUTE   (India)

Author keywords

ARDRA; Fluorescent Pseudomonas; Plant Growth Promotion; RFLP

Indexed keywords

PSEUDOMONAS; TRITICUM AESTIVUM;

1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE; BACTERIAL DNA; DNA DIRECTED RNA POLYMERASE; INDOLE DERIVATIVE; LYASE; PHOSPHATE; RIBOSOME DNA; RNA 16S; RNA POLYMERASE BETA SUBUNIT; SIDEROPHORE;

BIODIVERSITY; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; FLUORESCENCE; GENETICS; INDIA; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; MOLECULAR TYPING; PHYLOGENY; PSEUDOMONAS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RHIZOSPHERE; WHEAT;

BIODIVERSITY; CARBON-CARBON LYASES; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; DNA-DIRECTED RNA POLYMERASES; FLUORESCENCE; INDIA; INDOLES; MOLECULAR SEQUENCE DATA; MOLECULAR TYPING; PHOSPHATES; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; PSEUDOMONAS; RHIZOSPHERE; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SIDEROPHORES; SOIL MICROBIOLOGY; TRITICUM;

EID: 84900516746     PISSN: 0233111X     EISSN: 15214028     Source Type: Journal    
DOI: 10.1002/jobm.201200384     Document Type: Article

References (47)

1. Van Peer, R., Schippers, B., 1989. Plant growth responses to bacterization with selected Pseudomonas spp. strains and rhizosphere microbial development in hydroponic cultures. Can. J. Microbiol., 35, 456-463.
2. Thomashow, L.S., Weller, D.M., Bonsall, R.F., Pierson, L.S., 1990. Production of the antibiotic phenazine-1-carboxylic acid by fluorescent Pseudomonas species in the rhizosphere of wheat. Appl. Environ. Microbiol., 56, 908-912.
3. Compant, S., Duffy, B., Nowak, J., Clement, C. et al., 2005. Use of plant growth-promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl. Environ. Microbiol., 71, 4951-4959.
4. Lugtenberg, B.J.J., De Weger, A.L., Bennet, J.W., 1991. Microbial stimulation of plant growth and protection from disease. Curr. Op. Biotechnol., 2, 457-464.
5. Haas, D., Defago, G., 2005. Biological control of soil-borne pathogens by fluorescent pseudomonads. Nature Reviews Microbiol., 3, 307-319.
6. Dahllof, I., Baillie, H., Kjelleberg, S., 2000. rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl. Environ. Microbiol., 66, 3376-3380.
7. Hasegawa, M., Hashimoto, T., 1993. Ribosomal RNA trees misleading? Nature, 361, 23-23.
8. De Vos, D., Bouton, C., Sarniguet, A., De Vos, P. et al., 1998. Sequence diversity of the oprI Gene, coding for major outer membrane lipoprotein I, among rRNA group I pseudomonads. J. Bacteriol., 180, 6551-6556.
9. Widmer, F., Seidler, R.J., Gillevet, P.M., Watrud, L.S. et al., 1998. A highly selective PCR protocol for detecting 16S rRNA genes of the genus Pseudomonas (sensu stricto) in environmental samples. Appl. Environ. Microbiol., 64, 2545-2553.
10. Tayeb, L.A., Ageron, E., Grimont, F., Grimont, P.A.D., 2005. Molecular phylogeny of the genus Pseudomonas based on rpoB sequences and application for the identification of isolates. Res. Microbiol., 156, 763-773.
11. Yamamoto, S., Kasai, H., Arnold, D.L., Jackson, R.W. et al., 2000. Phylogeny of the genus Pseudomonas: Intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology, 146, 2385-2394.
12. Mollet, C., Drancourt, M., Raoult, D., 1997. rpoB sequence analysis as a novel basis of bacterial identification. Mol. Microbiol., 26, 1005-1011.
13. Borodin, A.M., Danilkovich, A.V., Allikmets, R.L., Rostapshov, V.M. et al., 1988. Nucleotide sequence of the rpoB gene coding for the beta-subunit of RNA polymerase in Pseudomonas putida. Dokl. Biochem., 302, 1261-1265.
14. Mollet, C., Drancourt, M., Raoult, D., 1998. Determination of Coxiella burnetii rpoB sequence and its use for phylogenetic analysis. Gene, 207, 97-103.
15. Qi, Y., Patra, G., Liang, X., Williams, L.E. et al., 2001. Utilization of rpoB gene as a specific chromosomal marker for real-time PCR detection of Bacillus anthracis. Appl. Environ. Microbiol., 67, 3720-3727.
16. Pospiech, A., Neumann, B., 1995. A versatile quick-prep of genomic DNA from gram positive bacteria. Trends Genet., 11, 217-218.
17. Glickmann, E., Dessaux, Y., 1995. A critical examination of the specificity of the salkowski reagent for indolic compound produced by phytopathogenic bacteria. Appl. Environ. Microbiol., 61, 793-796.
18. Mehta, S., Nautiyal, C.S., 2001. An efficient method for qualitative screening of phosphate solubilizing bacteria. Curr. Microbiol., 43, 51-56.
19. Schwyn, B., Neilands, J.B., 1987. Universal chemical assay for the detection and determination of siderophores. Anal. Biochem., 160, 47-56.
20. Glick, B.R., Penrose, D.M., Li, J., 1998. A model for the lowering of plant ethylene concentrations by plant growth promoting bacteria. J. Theor. Biol., 190, 63-68.
21. Edwards, U., Rogall, T., Blocker, H., Emde, M. et al., 1989. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res., 17, 7843-7853.
22. Jaccard, P., 1912. The distribution of the flora in the alpine zone. New Phytol., 11, 37-50.
23. Nei, M., Li, W.H., 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA, 76, 5269-5273.
24. Saitou, N., Nei, M., 1987. The neighbour joining method a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
25. Tamura, K., Dudley, J., Nei, M., Kumar, S., 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.2. Mol. Biol. Evol., 24, 1596-1599.
26. Felsenstein, J., 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol., 17, 368-376.
27. Shannon, C.E., Weaver, W., 1949. The Mathematical Theory of Communication, University of Illinois Press, Urbana.
28. Margalef, R., 1958. Information theory in ecology. Gen. Syst., 3, 36-71.
29. Pielou, E.C., 1969. An Introduction to Mathematical Ecology, Wiley, London.
30. Thompson, J.D., Higgins, D.G., Gibson, T.J., 1994. CLUSTAL W: improving sensitivity of progressive multiple sequence alignments through sequence weighing, position specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-7680.
31. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J. et al., 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
32. Rodriguez, H., Fraga, R., 1999. Phosphate solubilizing bacteria and their role in plant growth promotion. Biotechnol. Adv., 17, 319-339.
33. Gulati, A., Rahi, P., Vyas, P., 2008. Characterization of phosphate-solubilizing fluorescent pseudomonads from the rhizosphere of Seabuckthorn growing in the Cold Deserts of Himalayas. Curr. Microbiol., 56, 73-79.
34. Meyer, J.M., Geoffroy, V.A., Baida, N., Gardan, L. et al., 2002. Siderophore typing, a powerful tool for the identification of fluorescent and nonfluorescent pseudomonads. Appl. Environ. Microbiol., 68, 2745-2753.
35. Essen, S.A., Johnsson, A., Bylund, D., Pedersen, K. et al., 2007. Siderophore production by Pseudomonas stutzeri under aerobic and anaerobic conditions. Appl. Environ. Microbiol., 73, 5857-5864.
36. Wandersman, C., Delepelaire, P., 2004. Bacterial iron sources: from siderophores to hemophores. Annu. Rev. Microbiol., 58, 611-647.
37. Kloepper, J.W., Leong, J., Teintze, M., Schroth, M.N., 1980. Enhanced plant growth by siderophores produced by plant growth-promoting rhizobacteria. Nature, 286, 885-886.
38. Patten, C.L., Glick, B.R., 2002. Role of Pseudomonas putida indoleacetic acid in development of the host plant root system. Appl. Environ. Microbiol., 68, 3795-3801.
39. Cattelan, A.J., Hartel, P.G., Fuhrmann, J.J., 1999. Screening for plant growth-promoting rhizobacteria to promote early soybean growth. Soil Sci. Soc. Am. J., 63, 1670-1680.
40. Lwin, K.M., Han, M.M., Myint, M., Oo, Z.K., 2008. Screening of indole-3-acetic acid (IAA) producing plant growth promoting rhizobacteria (Pseudomonas sp. and Azotobacter sp.) and study on the IAA productivity of the best IAA producer strain GMSARN International Conference on Sustainable Development: Issues and Prospects for the GMS 12-14 November 2008.
41. Gravel, V.G., Antoun, H., Tweddell, R.J., 2007. Growth stimulation and fruit yield improvement of greenhouse tomato plants by inoculation with Pseudomonas putida or Trichoderma atroviride: possible role of indole acetic acid (IAA). Soil Biol. Biochem., 39, 1968-1977.
42. Beneduzi, A., Peres, D., da Costa, P.B., Zanettini, M.H.B. et al., 2008. Genetic and phenotypic diversity of plant-growth-promoting bacilli isolated from wheat fields in southern Brazil. Res. Microbiol., 159, 244-250.
43. Gupta, A., Saxena, A.K., Murali, G., Tilak, K.V.B.R., 1998. Effect of plant growth promoting rhizobacteria on competitive ability of introduced Bradyrhizobium sp. (Vigna) for nodulation. J. Sci. Ind. Res., 57, 720-725.
44. Garland, J.L., Mills, A.L., 1991. Classification and characterization of heterotrophic microbial communities on the basis of patterns of community level sole-carbon-source utilization. Appl. Environ. Microbiol., 57, 2351-2359.
45. Dawson, S.L., Fry, J.C., Dancer, B.N., 2002. A comparative evaluation of five typing techniques for determining the diversity of fluorescent pseudomonads. J. Microbiol. Methods, 50, 9-22.
46. Kim, B.J., Lee, S.H., Lyu, M.A., Kim, S.J. et al., 1999. Identification of mycobacterial species by comparative sequence analysis of the RNA polymerase gene (rpoB). J. Clin. Microbiol., 37, 1714-1720.
47. Husan, D.H., Bryant, D., 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol., 23, 254-267.