Microbial Ecology

, Volume 54, Issue 3, pp 452–459 | Cite as

Bacterial Diversity of East Calcutta Wet Land Area: Possible Identification of Potential Bacterial Population for Different Biotechnological Uses

  • Abhrajyoti Ghosh
  • Bhaswar Maity
  • Krishanu Chakrabarti
  • Dhrubajyoti Chattopadhyay
Article

Abstract

The extent of microbial diversity in nature is still largely unknown, suggesting that there might be many more useful products yet to be identified from soil microorganisms. This insight provides the scientific foundation for a renewed interest in examining soil microorganisms for novel commercially important products. This has led us to access the metabolic potential of soil microorganisms via cultivation strategy. Keeping this in mind, we have performed a culture-dependent survey of important soil bacterial community diversity in East Calcutta Wetland area (Dhapa Landfill Area). We describe isolation of 38 strains, their phenotypic and biochemical characterization, and finally molecular identification by direct sequencing of polymerase chain reaction (PCR)-amplified 16S rRNA gene products. We have isolated and identified strains able to fix nitrogen, produce extracellular enzymes like protease, cellulase, xylanase, and amylase, and solubilize inorganic phosphates. Some isolates can synthesize extracellular insecticidal toxins. We find a good correlation between biochemical and phenotypic behavior and the molecular study using 16S rRNA gene of the isolates. Furthermore, our findings clearly indicate the composition of cultivable soil bacteria in East Calcutta Wetland Area.

References

  1. 1.
    Bakken, LR, Olsen, RA (1987) The relationship between cell size and viability of soil bacteria. Microb Ecol 13: 103–114CrossRefGoogle Scholar
  2. 2.
    Billi, D, Potts, M (2002) Life and death of dried prokaryotes. Res Microbial 153: 7–12CrossRefGoogle Scholar
  3. 3.
    Bintrim, SB, Donohue, TJ, Handelsman, J, Roberts, GP, Goodman, RM (1997) Molecular phylogeny of archaea from soil. Proc Natl Acad Sci USA 94: 277–282PubMedCrossRefGoogle Scholar
  4. 4.
    Boettger, EC (1989) Rapid determination of bacterial RNA sequences by direct sequencing of enzymatically amplified DNA. FEMS Microbiol Lett 65: 171–176CrossRefGoogle Scholar
  5. 5.
    Borneman, J, Skrouch, PW, O’Sullivan, KM, Palus, JA, Rumjanek, NG, Jansen, JL, Nienhuis, J, Triplett, EW (1996) Molecular diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 62: 1935–1943PubMedGoogle Scholar
  6. 6.
    Chandler, DP, Li, SM, Spadoni, CM, Drake, GR, Balkwill, DL, Fredrickson, JK, Brockman, FJ (1997) A molecular comparison of cultivated aerobic heterotropic bacteria and 16S rDNA clone derived from a deep subsurface sediment. FEMS Microbiol Ecol 23: 131–144CrossRefGoogle Scholar
  7. 7.
    Chin, KJ, Hahn, D, Hengstmann, U, Liesack, W, Janssen, PH (1999) Characterisation and identification of numerically abundant cultivable bacteria from the anoxic bulk soil of rice paddy microcosms. Appl Environ Microbiol 65: 5042–5049PubMedGoogle Scholar
  8. 8.
    Chowdhury, SP, Khanna, S, Verma, SC, Tripathi, AK (2004) Molecular diversity of tannic acid degrading bacteria isolated from tannery soil. J Appl Microbiol 97: 1210–1219PubMedCrossRefGoogle Scholar
  9. 9.
    Davison, J (1988) Plant beneficial bacteria. Biotechnology 6: 282–286CrossRefGoogle Scholar
  10. 10.
    De Fede, KL, Sexstone, AJ (2001) Differencial response of size fractionated soil bacteria in BIOLOG microtitre plates. Soil Biol Biochem 33: 1547–1554CrossRefGoogle Scholar
  11. 11.
    Edwards, U, Rogall, T, Bloecker, H, Emde, M, Bloecker, E (1989) Isolation and direct complete nucleotide determination of entire genes. Characterisation of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 17: 7843–7853PubMedCrossRefGoogle Scholar
  12. 12.
    Falsenstein, J (1985) Con.dence limits on phylogenetics: an approach using bootstrap. Evolution 39: 783–791CrossRefGoogle Scholar
  13. 13.
    Felske, A, Akkermans, ADL (1998) Special homogeneity of abundant bacterial 16S rRNA molecules in grassland soils. Microb Ecol 36: 31–36PubMedCrossRefGoogle Scholar
  14. 14.
    Fritze, D, Flossdorf, J, Claus, D (1990) Taxonomy of alkaliphilic Bacillus strains. Int J Syst Bacteriol 40: 92–97PubMedCrossRefGoogle Scholar
  15. 15.
    Gallardo-Lara, F, Nogales, R (1987) Effect of the amplification of town refuge compost on the soil plant system: a review. Biol Wastes 19: 35–62CrossRefGoogle Scholar
  16. 16.
    Garbeva, P, van Veen, JA, van Elsas1, JD (2003) Predominant Bacillus spp. in agricultural soil under different management regimes detected via PCR-DGGE. Microb Ecol 45: 302–316PubMedCrossRefGoogle Scholar
  17. 17.
    Head, IM, Saunders, JR, Pickup, RW (1998) Microbial evolution, diversity and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microb Ecol 23: 45–54Google Scholar
  18. 18.
    Hershberger, K, Barns, SM, Reysenbech, AL, Dawson, SC, Pace, NR (1996) Wide diversity of Crenarchaeota. Nature 384: 420PubMedCrossRefGoogle Scholar
  19. 19.
    Holtz, JD (1993) Bergey’s Manual of Determinative Bacteriology, 9th edn. Williams and Wilkins, BaltimoreGoogle Scholar
  20. 20.
    Lane, DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (Eds.) Nucleic Acid Techniques in Bacterial Systematics. John Wiley & Sons, New York NY, pp 115–175Google Scholar
  21. 21.
    Leisack, W, Jessen, PH, Rainey, FA, Ward-Rainey, N, Stackebrandt, E (1997) Microbial diversity in soil: the need for a combined approach using molecular and cultivation techniques. In: vanElsas, JD, Trevors JT, Wellington, EMH (Eds.) Modern Soil Microbiology. Marcel Dekker Inc., New York NY, pp 375–439Google Scholar
  22. 22.
    Lenke, H, Piper, DH, Bruhn, C, Knackmuss, HJ (1992) Degradation of 2,4-Dinitrophenol by two Rhodococcus erythropolis strains, HL24-1 and HL24-2. Appl Environ Microbiol 58: 2928–2932PubMedGoogle Scholar
  23. 23.
    Lodewyckx, C, Vangronsveld, J, Porteous, F, Moore, ERB, Taghavi, S, Mezgeay, M, van der, LD (2002) Endophytic bacteria and their potential application. Crit Rev Plant Sci 21(6): 583–606CrossRefGoogle Scholar
  24. 24.
    Macrae, A (2000) The use of 16S rDNA methods in soil microbial ecology. Braz J Microbiol 31: 77–82CrossRefGoogle Scholar
  25. 25.
    Nicholson, WL (2002) Roles of Bacillus endospores in the environment. Cell Mol Life Sci 59: 410–416PubMedCrossRefGoogle Scholar
  26. 26.
    Olaniya, MS, Sur, MS, Bhide, AD, Swarnakar, SN (1998) Heavy metals pollution of agricultural soil and vegetation due to application of solid waste—a case study. Indian J Environ Health 40(2): 160–168Google Scholar
  27. 27.
    Page, RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12: 357–358PubMedGoogle Scholar
  28. 28.
    Perucci, P (1990) Effect of the addition of municipal soil waste compost on microbiological biomass and enzyme activities in soil. Biol Fertil Soils 10: 221–226Google Scholar
  29. 29.
    Perucci, P (1992) Enzyme activity and microbial biomass in a field soil amended with municipal refuge. Biol Fertil Soils 14: 54–60CrossRefGoogle Scholar
  30. 30.
    Pikovskaya, RI (1948) Mobilisation of phosphorous in soil in connection with the vital activity of some microbial species. Microbiologia 17: 362–370Google Scholar
  31. 31.
    Sambrook, J, Russel, DW (2001) Molecular cloning: A laboratory manual. 3rd edn. CSH Laboratory Press, Cold Spring Harbor, New YorkGoogle Scholar
  32. 32.
    Schumacher, JD, Fakonssa, RM (1999) Degradation of acyclic molecules by Rhodococcus rubber CD4. Appl Microbiol Biotechnol 52: 85–90PubMedCrossRefGoogle Scholar
  33. 33.
    Sorger, GJ (1971) Effect of nitrogenase components from mutant and wild-type strains of Azotobacter on the dilution effect of Nitrogenase. Biochem J 122: 305–309PubMedGoogle Scholar
  34. 34.
    Sprent, JI, de Faria, SM (1988) Mechanisms of infection of plants by nitrogen fixing organisms. Plant Soil 110: 157–165CrossRefGoogle Scholar
  35. 35.
    Tapp, H, Stotzky, G (1995) Insecticidal activity of the toxins from Bacillus thuringensis subspecies kurstaki and tenebrionis adsorbed and bound on pure and soil clays. Appl Environ Microbiol 61: 1786–1790PubMedGoogle Scholar
  36. 36.
    Thompson, JD, Gibson, TJ, Plewniak, F, Jeanmougin, F, Higgins, DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24: 4876–4882CrossRefGoogle Scholar
  37. 37.
    Topp, E, Zhu, H, Nour, SM, Houot, S, Lewis, M, Cuppels, D (2000) Characterization of atrazine-degrading Pseudaminobacter sp. Isolated from Canadian and French agricultural soils. Appl Environ Microbiol 66: 2773–2782PubMedCrossRefGoogle Scholar
  38. 38.
    Whiteley, AS, O’Donnell, AG, Macnaughton, SI, Barer, MR (1996) Cytochemical colocalisation and quantitation of phenotypic and genotypic characteristics in individual bacterial cells. Appl Environ Microbiol 62: 1873–1879PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Abhrajyoti Ghosh
    • 1
    • 2
  • Bhaswar Maity
    • 3
  • Krishanu Chakrabarti
    • 2
  • Dhrubajyoti Chattopadhyay
    • 1
    • 2
  1. 1.Dr. B C Guha Centre for Genetic Engineering and BiotechnologyUniversity of CalcuttaCalcuttaIndia
  2. 2.Department of BiochemistryUniversity of CalcuttaCalcuttaIndia
  3. 3.The Center for Genomic Application, IGIB-IMM CollaborationNew DelhiIndia

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