Skip to main content
SpringerLink
Log in

Methods and Techniques for Isolation, Enumeration and Characterization of Rhizosphere Microorganisms

  • Chapter
Microbial Activity in the Rhizoshere

Part of the book series: Soil Biology ((SOILBIOL,volume 7))

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Allen ON (1957) Experiments in soil bacteriology, 3rd revised edn. Burgess, Minneapolis, Minn

    Google Scholar 

  2. Alun AH, Vartdal F (1988) J Clin Microbiol 26:2572–2575 as cited in van Elsas et al. (1997), pp 279–309

    Google Scholar 

  3. Atlas RM, Bartha R (1998) Microbial ecology – fundamentals and applications. Addison-Wesley, Logman, California

    Google Scholar 

  4. Baker D (1990) Methods for the isolation, culture and characterization of the Frankiaciae: soil actinomycetes and symbionts of actinorrhizal plants. In: Labeda DP (ed) Isolation of biotechnological organisms from nature. McGraw-Hill, London, pp 213–236

    Google Scholar 

  5. Baker D, Torrey JG, Kidd JH (1979) Isolation by sucrose density fractionation and cultivation in vitro of actinomycetes from nitrogen fixing root nodules. Nature 218:76–78

    Google Scholar 

  6. Baty AM, Eastburn CC, Techkarnjanaruk S, Goodman AE, Geesey GG (2000) Spatial and temporal variations in chitinolytic gene expression and bacterial biomass production during chitin degradation. Appl Environ Microbiol 66:3574–3585

    CAS  PubMed  Google Scholar 

  7. Bloem J, Van Mullem DK, Bolhuis PR (1992) J Microbiol Methods 16:203 as cited in van Elsas et al. (1997), pp 279–309

    Article  Google Scholar 

  8. Bose RG (1963) A modified cellulose medium for isolation of cellulolytic fungi from infected material and soil. Nature Lond 198:505

    Google Scholar 

  9. Boulos L, Prevost M, Barbeau B, Coallier J, Desjardins R (1999) LIVE/DEAD BacLight: application of new rapid staining method for direct enumeration of viable and total bacteria in drinking water. J Microbiol Methods 37:77–86

    Article  CAS  PubMed  Google Scholar 

  10. Brand LE (1990) The isolation and culture of microalgae for biotechnological applications. In: Labeda DP (ed) Isolation of biotechnological organisms from nature. McGraw-Hill, London, pp 81–116

    Google Scholar 

  11. Burlage RS, Kuo C-T (1994) Living biosensors for the management and manipulation of microbial consortia. Ann Rev Microbiol 48:291–310

    CAS  Google Scholar 

  12. Byrd JJ, Colwell RR (1992) Microscopy analysis of environmental samples. In: Levin MA, Seider RJ, Rogul M (eds) Microbial ecology: principles, methods and applications. McGraw-Hill, New York, pp 93–112

    Google Scholar 

  13. Casida LR Jr (1968) Infrared colour photography. Selective demonstration of bacteria. Science 159:199

    PubMed  Google Scholar 

  14. Cavigelli MA, Robertson GP, Klug MJ (1995) Fatty acid methyl ester (FAME) profile as a measure of soil microbial community structure. Plant Soil 170:99–113

    Article  CAS  Google Scholar 

  15. Chalfie M (1995) Green fluorescent protein. Photochem Photobiol 62:651–656

    CAS  PubMed  Google Scholar 

  16. Couch JN (1954) The genus Actinoplanes and its relatives. T New York Acad Sci 16:315–318

    Google Scholar 

  17. Crook P, Carpenter CC, Klens PF (1950) The use of sodium propionate in isolating actinomycetes from soil. Science 112:656

    CAS  PubMed  Google Scholar 

  18. Dale B (1983) Collection, preparation and identification of dinoflagellate resting cysts. In: Taylor DL, Seliger HH (eds) Toxic dinoflagellate blooms. Elsevier/North-Holland, New York, pp 443–452

    Google Scholar 

  19. Damigi SM, Frederick LR, Bremner JM (1961) Effect of soil dispersion techniques on plate counts of fungi, bacteria and actinomycetes. Bacteriol Proc 61:53

    Google Scholar 

  20. Davey HM, Kell DB (1996) Flow cytometry and cell sorting of heterogeneous microbial populations: importance of single-cell analysis. Microbiol Rev 60:641–696

    CAS  PubMed  Google Scholar 

  21. Domsch KH, Gams W, Anderson TH (1980) Compendium of soil fungi. Academic Press, London

    Google Scholar 

  22. Dye M (1994) J Microbiol Methods 19:235 as cited in van Elsas et al. (1977), pp 279–309

    Article  Google Scholar 

  23. Eader K (1995) Gas chromatographic analysis of fatty acid methyl esters. J Chromatogr B Biomed Appl 671:113–131

    Google Scholar 

  24. El-Nakeeb MA, Levchevalier HA (1963) Selective isolation of aerobic actinomycetes. Appl Microbiol 11:75–77

    CAS  PubMed  Google Scholar 

  25. Franzmann PD, Patterson BM, Powers TR, Nichols PD, Davis GB (1996) Microbial biomass in shallow, urban aquifer contaminated with aromatic hydrocarbons: analysis of phospholipids fatty acid content and composition. J Appl Bacteriol 80:617–625

    CAS  PubMed  Google Scholar 

  26. Gause GF, Preobrazhenskaya TP, Kudrina ES, Blinov NO, Ryabova ID, Sveshnikova MA (1957) Problems in the classification of antagonistic Actinomycetes. Medgiz, Moscow

    Google Scholar 

  27. Gerdman JW, Nicolson TH (1963) Spores of mycorrhizal Endogone species extracted from soil by wet sieving and decanting. Trans Br Mycol Soc 46:235–244

    Google Scholar 

  28. Hadrys H, Balik M, Schierwater B (1992) Applications of random amplified polymorphic DNA (RAPD) in molecular ecology. Mol Ecol 1:55–63

    CAS  PubMed  Google Scholar 

  29. Hall CAS, Day JW Jr (1977) Systems and models: terms and basic principles. In: Hall CAS, Day JW Jr (eds) Ecosystems modeling in theory and practice. Wiley, New York,pp 5–36

    Google Scholar 

  30. Hansen JF, Thingstad TF, Goksoyr J (1974) Evaluation of hyphal length and fungal biomass in soil by membrane filter technique. Oikos 25:102

    Google Scholar 

  31. Harley JL, Waid JS (1955) A method for studying active mycelia on living roots and other surfaces in the soil. Trans Br Mycol Soc 38:104–118

    Google Scholar 

  32. Hartmann A, Abmus B, Kirchhof G, Schloter M (1997) Direct approaches for studying soil microbes. In: van Elsas JD et al., pp 279–309

    Google Scholar 

  33. Heckman JR, Strick J (1996) Teaching plant soil relationships with colour images of rhizosphere pH. J Nat Res Life Sci Edu 25:13–17

    Google Scholar 

  34. Hirsch CF, Cristensen DL (1983) Novel method for selective isolation of actinomycetes. Appl Environ Microbiol 46:925–929

    CAS  PubMed  Google Scholar 

  35. Horwath WR, Paul EA (1994) Microbial biomass. In: Weaver RW, Angle JS, Bottomley PS (eds) Methods of soil analysis. Part 2. Microbiological and biochemical properties. Soil Sci Soc Am, Madison, WI, pp 753–773

    Google Scholar 

  36. Hoshaw RW, Rosowski JR (1973) Methods for microscopic algae. In: Stein JR (ed) Handbook of phycological methods. Cambridge University Press, New York, pp 53–68

    Google Scholar 

  37. Hsu SC, Lockwood JL (1975) Powdered chitin agar as a selective medium for enumeration of actinomycetes in water and soil. Appl Microbiol 29:422–426

    CAS  PubMed  Google Scholar 

  38. Hurst CJ, Knudsen GR, McInerney MJ, Stetzenbach LD, Watter MV (1997) Manual of environmental microbiology. Am Soc Microbiol Press, Washington, DC

    Google Scholar 

  39. Jenkins WR (1964) A rapid centrifugal-floatation for separating nematodes from soil. Pl Dis Rep 48:692

    Google Scholar 

  40. Jenkinson DS (1976) The effects of biocidal treatments on metabolism in soil. Part IV. The decomposition of fumigated organisms in soil. Soil Biol Biochem 11:193–199

    Google Scholar 

  41. Johnson LF, Curl EA (1972) Methods for research on ecology of soil-borne plant pathogens. Burgess, Minneapolis, Minn

    Google Scholar 

  42. Johnson LF, Curl EA, Bond JH, Fribourg HA (1959) Microorganisms in the plant rhizosphere. In: Johnson LF, Curl EA (eds) Methods for studying soil microflora – plant disease relationships. Burgess, Minneapolis, Minn, pp 29–37

    Google Scholar 

  43. Karwowski J (1986) The selective isolation of Micromonospora from soil by cesium chloride density gradient ultracentrifugation. J Ind Microbiol 1:181–186

    Article  Google Scholar 

  44. Kepner RL Jr, Pratt JR (1994) Use of fluorochromes for direct enumeration of total bacteria in environmental samples: past and present. Microbiol Rev 58:603–615

    CAS  PubMed  Google Scholar 

  45. King JD, White DC (1977) Muramic acid as a measure of microbial biomass in estuarine and marine samples. Appl Environ Microbiol 33:777–783

    CAS  PubMed  Google Scholar 

  46. King JMH, DiGrazia PM, Applegate B, Burlage R, Sanseverino J, Dunbar P, Larimer F, Sayler GS (1990) Bioluminescent reporter plasmid for naphthalene exposure and biodegradation. Science 249:778–791

    CAS  Google Scholar 

  47. King RJ, Short KA, Seidler RJ (1991) Assay for detection and enumeration of genetically engineered microorganisms which is based on the activity of a deregulated 2,4-dichlorophenoxyacetate monooxygenase. Appl Environ Microbiol 57:1790–1792

    CAS  PubMed  Google Scholar 

  48. Kogure K, Simidu U, Taga N (1984) Arch Hydrobiol 102:117 as cited in van Elsas JD et al. (1997), pp 279–309

    Google Scholar 

  49. Kuster E, Williums ST (1964) Selective media for the isolation of streptomycetes. Nature 202:928–929

    Google Scholar 

  50. Labeda DP, Shearer MC (1990) Isolation of actinomycetes for biotechnological applications. In: Labeda DP (ed) Isolation of biotechnological organisms from nature. McGraw-Hill, London, pp 1–20

    Google Scholar 

  51. Lawrence CH (1956) A method of isolating actinomycetes from scabby potato tissue and soil with minimal contamination. Can J Bot 34:44

    Google Scholar 

  52. Ledingham RJ, Chinn SHF (1955) A flotation method for obtaining spores of Helmithosporium sativum from soil. Can J Bot 33:298–303

    Google Scholar 

  53. Lee C, Russel NJ, White GF (1995) Rapid screening of bacterial phenotypes capable of biodegrading anionic sulfactants – development and validation of microtitre plate method. Microbiol 141:2801–2810

    Google Scholar 

  54. Lindgren PB, Fredrick R, Govindarajan AG, Panopoulas NJ, Staskawicz BJ, Lindow SE (1989) An ice nucleation reporter gene system: Identification of inducible pathogenicity genes in Pseudomonas syringae pv. phaseolicola. EMBO J 8:1291–1301

    CAS  PubMed  Google Scholar 

  55. Lunge VR, Ikuta N, Fonseca ASK, Hirigoyen D, Stoll M, Bonatto S (1994) Identification and interrelationship analysis of Bradyrhizobium japonicum strains by restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD). World J Microbiol Biotech 10:648–652

    CAS  Google Scholar 

  56. Makkar NS, Cross T (1982) Actinoplanets in soil and on plant litter from fresh water habitats. J Appl Bacteriol 52:209–218

    Google Scholar 

  57. Massol-Deya AR, Weller L, Rias-Hernandez J, Zhou Z, Hickey RF, Tiedje JM (1997) Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in ground water. Appl Environ Microbiol 63:270–276

    CAS  PubMed  Google Scholar 

  58. Mavingui P, Berge O, Heulin TR (1990) Symbiosis 9:215–221 as cited in van Elsas et al. (1997), pp 279–309

    Google Scholar 

  59. Menzies JD (1957) A dipper technique for serial dilutions of soil microbial analysis. Soil Sci Soc Am Proc 21:660

    Google Scholar 

  60. Meyer-Reil LA (1978) Autoradiography and epifluorescent microscopy combined for the determination of number and spectrum of actively metabolizing bacteria in natural waters. Appl Environ Microbiol 36:506–512

    CAS  PubMed  Google Scholar 

  61. Minderman G (1956) The preparation of microtome sections unaltered soil for the study of soil microorganisms in situ. Plant Soil 8:42

    Article  Google Scholar 

  62. Muyzer G, deWaal ED, Vitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700

    CAS  PubMed  Google Scholar 

  63. Nicholas DP, Parkinson D, Burges NA (1965) Studies on fungi in podzol. II. Application of the soil-sectioning technique to study of amounts of fungal mycelium in the soil. J Soil Sci 16:258

    Google Scholar 

  64. Nikitin D (1973) Direct electron microscopic techniques for the observation of microorganisms in soil. Bull Ecol Res Com Stockholm 17:85–92

    Google Scholar 

  65. Nonomura H, Hayakawa M (1988) New methods for the selective isolation of soil actinomycetes. In: Okami Y, Beppu T, Ogawara H (eds) Biology of Actinomycetes 88. Japan Sci Soc Press, Tokyo, pp 288–293

    Google Scholar 

  66. Oades JM, Jenkinson DS (1979) Adenosine tri-phosphate content of the soil microbial biomass. Soil Biol Biochem 11:201–204

    CAS  Google Scholar 

  67. Overmann J, Coolen MJL, Tuschak C (1999) Specific detection of different phylogenetic groups of chemocline bacteria based on PCR and denaturing gradient gel electrophoresis of 16S rRNA fragments. Arch Microbiol 173:83–94

    Google Scholar 

  68. Palleroni NJ (1980) A chemotactic method for the isolation of Actinoplanaceae. Arch Microbiol 128:53–55

    Article  Google Scholar 

  69. Parkinson D (1957) New methods for the quantitative and qualitative study of fungi in the rhizosphere. Symposium, Methodes d'Etudes Microbiologiques du sol. Louvain, Belgium

    Google Scholar 

  70. Parkinson D (1973) Techniques for the study of soil fungi. Bull Ecol Res Com Stockholm 17:29–36

    Google Scholar 

  71. Parkinson D, Gray TRG, Williams ST (1971) Methods for studying the ecology of soil micro-organisms. IBP Handbook No 19. Blackwell, Oxford

    Google Scholar 

  72. Paul EA, Clark FE (1988) Soil microbiology and biochemistry. Academic Press, San Diego

    Google Scholar 

  73. Penrose DM, Glick BR (2003) Methods for isolating and characterizing ACC deaminase-containing plant growth promoting rhizobacteria. Physiol Plant 118:10–15

    Article  CAS  PubMed  Google Scholar 

  74. Petersen SO, Klug MJ (1994) Effects of sieving, storage and incubation temperature on the phospholipids fatty acid profile of soil community. Appl Environ Microbiol 60:2421–2430

    CAS  PubMed  Google Scholar 

  75. Phillips BJ, Kalpan W (1976) Effect of cetyl pyrididinium chloride on pathogenic fungi and Nocordia asteroides in sputum. J Clin Microbiol 3:272–276

    CAS  PubMed  Google Scholar 

  76. Prosser JI (1997) Mathematical modeling and statistical analysis. In: Burlage RS, Atlas R, Stahl D, Geesey G, Sayler G (eds) Techniques in microbial ecology. Oxford University Press, New York, pp 408–437

    Google Scholar 

  77. Robinson JA (1985) Determining microbial kinetic parameters using non-linear regression analysis. Adv Microb Ecol 8:61–114

    Google Scholar 

  78. Robinson JA (1986) Approaches and limits to modeling microbiological processes. In: Meguseu F, Gantar M (eds) Perspective in microbial ecology. Slovene Society of Microbiology, Ljubljana, Yugoslavia, pp 20–29

    Google Scholar 

  79. Rowbotham TJ, Cross T (1977) Ecology of Rhodocroccus coprophilus and associated actinomycetes in fresh water and agricultural habitats. J Gen Microbiol 100:231–240

    Google Scholar 

  80. Sharma PD, Fisher PJ, Webster J (1977) Critique of the chitin assay technique for estimation of fungal biomass. Trans Br Mycol Soc 69:479–483

    CAS  Google Scholar 

  81. Skinner FA, Passmore FM, Devanport RR (eds) (1980) Media and methods for growing yeasts. In: Biology and activities of yeasts. Academic Press, London, pp 260–301

    Google Scholar 

  82. Smit E, Leeflang P, Glandorph B, Van Elsas JD, Wernars K (1999) Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Appl Environ Microbiol 65:2614–2621

    CAS  PubMed  Google Scholar 

  83. Soderstrom DE (1977) Vital staining of fungi in pure cultures and in soil with fluorescein diacetate. Soil Biol Biochem 9:59–63

    Article  Google Scholar 

  84. Strugger S (1948) Fluorescence microscope examination of bacteria in soil. Can J Res 26:188–193

    Google Scholar 

  85. Throndsen J (1978) The dilution-culture method. In: Sournia A (ed) Phytoplankton manual UNESCO. Page Brothers, Paris, pp 218–224

    Google Scholar 

  86. Timonin MI (1940) The interaction of higher plants and soil microorganisms. I. Microbial populations of rhizosphere of seedlings of certain cultivated plants. Can J Res 18:307–317

    Google Scholar 

  87. Trainor FR (1983) Survival of algae in soil after high temperature treatment. Phycologia 22:201–202

    Google Scholar 

  88. Tribe HT, Abu-Elsound SM (1979) Colonization of hair in soil-water cultures with special reference to the genera Pilimelia and Spirillospora (Actinomycetales). Nova Hedwigia 31:789–805

    Google Scholar 

  89. van Elsas JD, Trevoss JT, Wellington EMH (1997) Modern soil microbiology. Marcel Dekker, New York

    Google Scholar 

  90. van Elsas JD, Duarte GF, Keijzer-Wolters A, Smit E (2000) Analysis of dynamics of the fungal communities in soil via fungal-specific PCR of soil DNA followed by denaturing gradient gel electrophoresis. J Microbiol Methods 43:133–151

    PubMed  Google Scholar 

  91. Warcup JH (1951) Soil-steaming: a selective method for the isolation of Ascomycetes from soil. Trans Br Mycol Soc 34:515–518

    Google Scholar 

  92. Warcup JH (1955) On the origin of colonies of fungi on soil dilution plates. Trans Br Mycol Soc 38:298

    Google Scholar 

  93. Watson SW, Novitsky TJ, Quinby HL, Valoris FW (1977) Determination of bacterial numbers and biomass in marine environment. Appl Environ Microbiol 33:940–946

    CAS  PubMed  Google Scholar 

  94. Wellington EMH, Marsh P, Watts JEM, Burdon J (1997) Indirect approaches for studying soil microorganisms based on cell extraction and culturing. In: Van Elsas JD, Trevors JT, Wellington EMH (eds) Modern soil biology. Marcel Dekker

    Google Scholar 

  95. White DC (1995) Chemical ecology: possible link between macro and microbial ecology. Oikos 74:177–184

    Google Scholar 

  96. Williams ST, Vickers JC (1988) Detection of actinomycetes in the natural environment-Problems and perspectives. In: Okami Y, Beppu T, Ogawara H (eds) Biology of actinomycetes 88. Japan Sci Soc Press, Tokyo, pp 265–270

    Google Scholar 

  97. Wilson D, Forest HS (1957) An exploratory study of algae. Ecology 38:309–313

    Google Scholar 

  98. Woolmer PL (1994) Methods of soil analysis. Part 2. In: Weaver RW, Angle S, Bottomley P, Bezdicek D, Smith S, Tabatabai A, Wollum A (eds) Microbiological and biochemical properties. Soil Sci Soc Am, Madison, WI, p 60

    Google Scholar 

  99. Zukowski MM, Gaffney DF, Speck M, Kaffmann M, Findeli A, Wisecup A, Lecocq JP (1983) Chromogenic identification of genetic regulatory signals in Bacillus subtilis based on the expression of a cloned Pseudomonas gene. Proc Nat Acad Sci USA 80:1101–1105

    CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Botany, Osmania University, 500007, Hyderabad, India

    Nandanavanam Ranganayaki & Chakravarthula Manoharachary

  2. Department of Botany, University of Delhi, 237, DDA/SFS Mukherji Apartments, East Mukherji Nagar, 110009, Delhi, India

    Kolluru V. B. R. Tilak & Krishna G. Mukerji

Authors
  1. Nandanavanam Ranganayaki
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kolluru V. B. R. Tilak
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Chakravarthula Manoharachary
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Krishna G. Mukerji
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Botany, University of Delhi, 110007, Delhi, India

    K. G. Mukerji

  2. Department of Botany, Osmania University, 50007, Hyderabad, India

    C. Manoharachary

  3. Environmental Building Solutions Ltd., Galley Cottage, Galley Lane, MK17 9AA, Milton Keynes, United Kingdom

    Jagjit Singh

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Springer-Verlag

About this chapter

Cite this chapter

Ranganayaki, N., Tilak, K.V.B.R., Manoharachary, C., Mukerji, K.G. (2006). Methods and Techniques for Isolation, Enumeration and Characterization of Rhizosphere Microorganisms. In: Mukerji, K.G., Manoharachary, C., Singh, J. (eds) Microbial Activity in the Rhizoshere. Soil Biology, vol 7. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-29420-1_2

Download citation

Publish with us

Policies and ethics

Search

Navigation