Plant Soil Environ., 2004, 50(4):141-148 | DOI: 10.17221/4074-PSE

Evaluation of functional diversity of soil microbial communities - a case study

J. Hofman, J. ©vihálek, I. Holoubek
Faculty of Science, Masaryk University in Brno, Czech Republic

In our case study, we measured the functional diversity of the microbial communities of twelve soils from the small natural area to assess if this assay is suitable for routine monitoring of soil biological quality. We found the BIOLOG assay meets especially practical benefits in routine monitoring of soils being simple and quick assay. However, we confirmed the ambiguity about the most appropriate analysis of the BIOLOG multivariate data and about the best parameter, which can be derived from the assay. The different analyses of the data were examined and various parameters derived from the BIOLOG assay were comparatively used to contribute to the discussion of how the data should be evaluated. We showed that not-normalized raw absorbances or trapezoid areas should be used for calculation of diversity index if the inoculum was standardized. There was no single answer to what parameter provided more correct results in the multivariate statistical analysis. Evaluating at least one not-normalized (e.g. trapezoid area) and one normalized parameter (e.g. absorbances read in fixed AWCD) was strongly suggested keeping in mind that they reveal different information.

Keywords: BIOLOG; soil microorganisms; soil monitoring; functional diversity

Published: April 30, 2004  Show citation

ACS AIP APA ASA Harvard Chicago IEEE ISO690 MLA NLM Turabian Vancouver
Hofman J, ©vihálek J, Holoubek I. Evaluation of functional diversity of soil microbial communities - a case study. Plant Soil Environ.. 2004;50(4):141-148. doi: 10.17221/4074-PSE.
Share...
Download citation
  • BibTeX (.bib)
  • Bookends (.ris)
  • EasyBib (.ris)
  • EndNote (.enw)
  • EndNote 8 (.xml)
  • ISI WoS (.isi)
  • Medlars (.medlars)
  • Mendeley (.ris)
  • MODS (.xml)
  • Papers (.ris)
  • RefWorks (.txt)
  • RefManager (.ris)
  • RIS (.ris)
  • MS Word (.xml)
  • Zotero (.ris)
    • Open full article

    References

    1. Anderson J.P.E., Domsch K.H. (1978): A physiological method for the quantitative measurement of microbial biomass in soil. Soil Biol. Biochem., 10: 215-221. Go to original source...
    2. Atlas R.M., Horowitz A., Krichevsky M., Bej A.K. (1991): Response of microbial populations to environmental disturbance. Microbial Ecol., 22: 249-256. Go to original source... Go to PubMed...
    3. Campbell C.D., Grayston S.J., Hirst D.J. (1997): Use of rhizosphere carbon sources in sole carbon source tests to discriminate soil microbial communities. J. Microbiol. Meth., 30: 33-41. Go to original source...
    4. Cartwright C.D., Thompson I.P., Burns R.G. (2000): Degradation and impact of phthalate plasticizers on soil microbial communities. Environ. Toxicol. Chem., 19: 1253-1261. Go to original source...
    5. Choi K.H., Dobbs F.C. (1999): Comparison of two kind of Biolog microplates (GN and ECO) in their ability to distinguish among aquatic microbial communities. J. Microbiol. Meth., 36: 203-213. Go to original source... Go to PubMed...
    6. Forster J.C. (1995): Soil sampling, handling, storage and analysis. In: Alef K., Nannipieri P. (eds.): Methods in soil microbiology and biochemistry. London, Acad. Press: 49-123. Go to original source...
    7. Garland J.L. (1996): Analytical approaches to the characterization of samples of microbial communities using patterns of potential C source utilization. Soil Biol. Biochem., 28: 213-221. Go to original source...
    8. Garland J.L. (1997): Analysis and interpretation of community-level physiological profiles in microbial ecology. FEMS Microbiol. Ecol., 24: 289-300. Go to original source...
    9. Garland J.L., Mills A.L. (1991): Classification and characterization of heterothrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Appl. Environ. Microbiol., 57: 2351-2359. Go to original source... Go to PubMed...
    10. Garland J.L., Mills A.L. (1994): A community-level physiological approach for studying microbial communities. In: Ritz K., Dighton J., Giller K.E. (eds.): Beyond the biomass. Chichester, John Wiley & Sons: 77-83.
    11. Garland J.L., Mills A.L., Young J.S. (2001): Relative effectiveness of kinetic analysis vs single point readings for classifying environmental samples based on community-level physiological profiles (CLPP). Soil Biol Biochem., 33: 1059-1066. Go to original source... Go to PubMed...
    12. Guckert J.B., Carr G.J., Johnson T.D., Hamm B.G., Davidson D.H., Kumagai Y. (1996): Community analysis by Biolog: Curve integration for statistical analysis of activated sludge microbial habitats. J. Microbiol. Meth., 27: 183-197. Go to original source...
    13. Haack K.S., Garchow H., Klug J.M., Forney J.L. (1995): Analysis of factors affecting the accuracy, reproducibility and interpretation of microbial community carbon source utilization patterns. Appl. Environ. Microbiol., 61: 1458-1468. Go to original source... Go to PubMed...
    14. Hackett C.A., Griffiths B.S. (1997): Statistical analysis of the time-course of Biolog substrate utilization. J. Microbiol. Meth., 30: 63-69. Go to original source...
    15. Howard P.J.A. (1999): Analysis of inter-sample distance from BIOLOG plate data in Euclidean and simplex spaces. Soil Biol. Biochem., 31: 1323-1330. Go to original source...
    16. ISO 10381-6 (1993): Soil quality-Sampling-Part 6: Guidance on the collection, handling and storage of soil for the assessment of aerobic microbial processess in the laboratory. Int. Org. Stand. Geneve, Switzerland.
    17. ISO 14240-1 (1997): Soil quality - Determination of soil microbial biomass. Part 1: Subtrate-induced respiration method. Int. Org. Stand. Geneve, Switzerland.
    18. ISO 14240-2 (1997): Soil quality - Determination of soil microbial biomass - Part 2: Fumigation-extraction method. Int. Org. Stand. Geneve, Switzerland.
    19. Juck D., Charles T., Whyte L.G., Greer C.W. (2000): Polyphasic microbial community analysis of petroleum hydrocarbon-contaminated soils from two northern Canadian communities. FEMS Microbiol. Ecol., 33: 241-249. Go to original source... Go to PubMed...
    20. Kandeler E., Kampichler C., Horak O. (1996): Influence of heavy metals on the functional diversity of soil microbial communities. Biol. Fertil. Soils, 23: 299-306. Go to original source...
    21. Laine M.M., Haario H., Jorgensen K.S. (1997): Microbial functional activity during composting of chlorophenol-contaminated sawmill soil. J. Microbiol. Meth., 30: 21-32. Go to original source...
    22. Pennanen T., Perkiomaki J., Kiikkila O., Vanhala P., Neuvonen S., Fritze H. (1998): Prolonged, simulated acid rain and heavy metal deposition: separated and combined effects on forest soil microbial community structure. FEMS Microbiol. Ecol., 27: 291-300. Go to original source...
    23. Preston-Mafham J., Boddy L., Randerson P.F. (2002): Analysis of microbial community functional diversity using sole-carbon-source utilisation profiles - a critique. FEMS Microbiol. Ecol., 42: 1-14. Go to original source... Go to PubMed...
    24. Rutgers M., Breure A.M. (1999): Risk assessment, microbial communities, and pollution-induced community tolerance. Hum. Ecol. Risk Assess., 5: 661-670. Go to original source...
    25. StatSoft Inc. (2001): STATISTICA (data analysis software system), version 6. www.statsoft.com.
    26. Zak J.C., Willig M.R., Moorhead D.L., Wildman H.G. (1994): Functional diversity of microbial communities a quantitative approach. Soil Biol. Biochem., 26: 1101-1108. Go to original source...

    This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY NC 4.0), which permits non-comercial use, distribution, and reproduction in any medium, provided the original publication is properly cited. No use, distribution or reproduction is permitted which does not comply with these terms.


    Return to the content