Diversity and phylogeny of plant growth-promoting bacilli from moderately acidic soil

Journal of Basic Microbiology

Volumn 51, Issue 1, 2011, Pages 98-106

  Yadav, Subhash ^a   Kaushik, Rajeev ^a   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; Bacilli; Phylogeny; Plant growth promotion

Indexed keywords

ACID; BACTERIAL DNA; CARBON; RNA 16S;

ARTICLE; BACILLUS; CLASSIFICATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; INDIA; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; PHYLOGENY; RHIZOSPHERE; RICE; SOIL;

ACIDS; BACILLUS; CARBON; DNA, BACTERIAL; INDIA; ORYZA SATIVA; PHYLOGENY; RHIZOSPHERE; RNA, RIBOSOMAL, 16S; SOIL; SOIL MICROBIOLOGY;

BACILLI (CLASS); BACILLUS (BACTERIUM); BACILLUS AESTUARII; BACILLUS ARBUTINIVORANS; BACILLUS DRENTENSIS; BACILLUS HUMI; BACILLUS MEGATERIUM; BACILLUS NIACINI; BREVIBACTERIUM; BREVIBACTERIUM CASEI; POSIBACTERIA;

EID: 79951527018     PISSN: 0233111X     EISSN: 15214028     Source Type: Journal    
DOI: 10.1002/jobm.201000098     Document Type: Article

References (46)

1. 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.
2. Ash, C., Farrow, J.A.E., Wallbanks, S., Collins, M.D., 1991. Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small subunit-rRNA sequences. Lett. Appl. Microbiol., 13, 202-206.
3. Ash, C., Collins, M.D., 1992. Comparative analysis of 23S rRNA gene sequences of Bacillus anthracis and emetic Bacillus cereus determined by PCR-direct sequencing. FEMS Microbiol. Lett., 94, 75-80.
4. Bakker, A.W., Schippers, B., 1987. Microbial cyanide production in the rhizosphere in relation to potato yield reduction and Pseudomonas spp.-mediated plant growth stimulation. Soil Biol. Biochem., 19, 451-457.
5. 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.
6. Ettoumi, B., Raddadi, N., Borin, S., Daffonchio, D. et al., 2009. Diversity and phylogeny of culturable spore-forming bacilli isolated from marine sediments. J. Basic Microbiol., 49, S13-S23.
7. Bloemberg, G.V., Lugtenberg, B.J.J., 2001. Molecular basis of plant growth promotion and biocontrol by rhizobacteria. Curr. Opin. Plant Biol., 4, 343-350.
8. Brannen, P.M., Backman, P.A., 1993. Cotton colonization by Bacillus subtilis inoculants to augment seedling disease control and promote season-long root health. In: Proceedings of the Beltwide Cotton Production Research Conference, pp. 194-196.
9. Broadbent, P., Baker, K.F., Franks, N., Holland, J., 1977. Effect of Bacillus spp. on increased growth of seedlings in steamed and non-treated soil. Phytopathol., 67, 1027-1034.
10. 3 test).
11. Matthies, C., Erhard, H.P., Drake, H.L., 1997. Effects of pH on the comparative culturability of fungi and bacteria from acidic and less acidic forest soils. J. Basic Microbiol., 37, 335-343.
12. 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.
13. Ahmad, F., Ahmad, I., Khan, M.S., 2008. Screening of free-living rhizospheric bacteria for their multiple plant growth promoting activities. Microbiol. Res., 163, 173-181.
14. Felsenstein, J., 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol., 17, 368-376.
15. Garbeva, P., van Veen, J.A., van Elsas, J.D., 2003. Predominant Bacillus sp. in agricultural soil under different management regimes detected via PCR-DGGE. Microb. Ecol., 45, 302-316.
16. Gardener, B.B.M., 2004. Ecology of Bacillus and Paenibacillus sp. in agricultural systems. (Ed.), Symposium: The Nature and Application of Biocontrol Microbes: Bacillus sp. Phytopathol. (pp. 1252-1258).
17. Glickmann, E., Dessaux, Y., 1995. A critical examination of the specificity of the Salkowski reagent for indolic compounds produced by phytopathogenic bacteria. Appl. Environ. Microbiol., 61, 793-796.
18. 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.
19. Hameeda, B., Harini, G., Rupela, O.P., Wani, S.P. et al., 2008. Growth promotion of maize by phosphate solubilizing bacteria isolated from composts and macrofauna. Microbiol. Res., 163, 234-242.
20. Jaccard, P., 1912. The distribution of the flora in the alpine zone. New Phytol., 11, 37-50.
21. Heyrman, J., Verbeeren, J., Schumann, P., Devos, J. et al., 2004. Brevibacterium picturae sp. nov., isolated from a damaged mural painting at the Saint-Catherine chapel (Castle Herberstein, Austria). Int. J. Syst. Evol. Microbiol., 54, 1537-1541.
22. Kanekar, P.P., Nilegaonkar, S.S., Sarnaik, S.S., Kelkar, A.S., 2002. Optimization of protease activity of alkaliphilic bacteria isolated from an alkaline lake in India. Bioresource Technol., 85, 87-93.
23. Kloepper, J.W., Hume, D.J., Scher, F.M., Singleton, C. et al., 1988. Plant growth-promoting rhizobacteria on canola (rapeseed). Plant Disease, 72, 42-46.
24. Lifshitz, R., Kloepper, J.W., Kozlowski, M., Simonson, C. et al., 1987. Growth promotion of canola (rapeseed) seedlings by a strain of Pseudomonas putida under gnotobiotic conditions. Can. J. Microbiol., 33, 390-395.
25. Mehta, S., Nautiyal, C.S., 2001. An efficient method for qualitative screening of phosphate solubilizing bacteria. Curr. Microbiol., 43, 51-56.
26. Wilson, M.K., Abergel, R.J., Raymond, K.N., Arceneaux, J.E.L. et al., 2006. Siderophores of Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis. Biochem. Biophys. Res. Commun., 348, 320-325.
27. Nautiyal, C.S., Bhadauria, S., Kumar, P., Lal, H. et al., 2000. Stress induced phosphate solubilization in bacteria isolated from alkaline soils. FEMS Microbiol. Lett., 182, 291-296.
28. 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.
29. Pospiech, A., Neumann, B., 1995. A versatile quick-prep of genomic DNA from gram positive bacteria. Trends Genet., 11, 217-218.
30. Reese, E.T., Mandels, M., 1963. Enzymatic hydrolysis of cellulose and its derivatives. Methods in Carbohydrate Chem., 3, 139-143.
31. Rodriguez, H., Fraga, R., 1999. Phosphate solubilizing bacteria and their role in plant growth promotion. Biotechnol. Adv., 17, 319-339.
32. Rozycki, H., Dahm, H., Strzelczyk, E., Li, C.Y., 1999. Diazotrophic bacteria in root-free soil and in the root zone of pine (Pinus sylvestris L.) and oak (Quercus robur L.). Appl. Soil Ecol., 12, 239-250.
33. Saitou, N., Nei, M., 1987. The neighbour joining method a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
34. Schippers, B., 1988. Biological control of pathogens with rhizobacteria. Philosophical Transactions of the Royal Society, B318, 283-293.
35. Schwyn, B., Neilands, J.B., 1987. Universal chemical assay for the detection and determination of siderophores. Anal. Biochem., 160, 47-56.
36. Seshadri, S., Ignacimuthu, S., Vadivelu, M., Lakshminarasimhan, C., 2007. Inorganic phosphate solubilization by two insect pathogenic Bacillus sp. Dev. Plant. Soil Sci., 102, 351-355.
37. Porwal, S., Lal, S., Cheema, S., Kalia, V.C., 2009. Phylogeny in aid of the present and novel microbial lineages: Diversity in Bacillus. PLoS ONE 4(2): e4438.
38. 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.
39. Stackebrandt, E., Swiderski, J., 2002. From phylogeny to systematics: The dissection of the genus Bacillus. In: Berkeley, R., Heyndrickx, M., Logan, N.A., De Vos, P. (eds.), Applications and Systematics of Bacillus and Relatives. Oxford: Blackwell.
40. 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.
41. 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, 4673-4680.
42. Timmusk, S., Wagner, E.G.H., 1999. The plant-growth-promoting rhizobacterium Paenibacillus polymyxa induces changes in Arabidopsis thaliana gene expression: A possible connection between biotic and abiotic stress response. Mol. Plant-Microbe Interact., 12, 951-959.
43. 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.
44. Vessey, J.K., 2003. Plant growth promoting rhizobacteria as biofertilizers. Plant Soil, 255, 571-586.
45. Weller, D.M., 1988. Biological control of soilborne plant pathogens in the rhizosphere with bacteria. Annu. Rev. Phytophath., 26, 379-407.
46. Yim, W.-J., Poonguzhali, S., Madhaiyan, M., Palaniappan, P. et al., 2009. Characterisation of plant-growth promoting diazotrophic bacteria isolated from field grown Chinese cabbage under different fertilization conditions. J. Microbiol., 47, 147-155.