Analysis of the potential functional diversity of the bacterial community in soil: A reproducible procedure using sole-carbon-source utilization profiles

European Journal of Soil Biology

Volumn 41, Issue 1-2, 2005, Pages 11-20

  Calbrix, Raphäl ^a   Laval, Karine ^a   Barray, Sylvie ^b  

^a ESITPA   (France)

^b UNIVERSITÉ DE ROUEN   (France)

Author keywords

Biolog; Centrifugation; Community level physiological profile (CLPP); Farming practice; Soil

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 26944438656     PISSN: 11645563     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ejsobi.2005.02.004     Document Type: Article

References (40)

1. E. Bååth, M. Diaz-Raviña, A. Frostegard, and C.D. Campbell Effect of metal-rich sludge amendments on the soil microbial community Appl. Environ. Microbiol. 64 1998 238 245
2. M.H. Beare, D.C. Coleman, D.A. Crossley Jr., P.F. Hendrix, and E.P. Odum A hierarchical approach to evaluating the significance of soil biodiversity to biogeochemical cycling Plant Soil 170 1995 5 22
3. D.A. Bossio, and K.M. Scow Impact of carbon and flooding on the metabolic diversity of microbial communities in soils Appl. Environ. Microbiol. 61 1995 4043 4050
4. J.S. Buyer, and L.E. Drinkwater Comparison of substrate utilisation assay and fatty acid analysis of soil microbial communities J. Microbiol. Methods 30 1997 3 11
5. C.D. Campbell, S.J. Grayston, and D.J. Hirst Use of rhizosphere carbon sources in sole carbon source test to discriminate soil microbial communities J. Microbiol. Methods 30 1997 33 41
6. A. Chatzinotas, R.A. Sandaa, W. Schronhuber, R. Amann, F.L. Daae, and V. Torsvik Analysis of broad-scale differences in microbial community composition of two pristine forest soils Syst. Appl. Microbiol. 21 1998 579 587
7. R.J. Ellis, I.P. Thompson, and M.J. Bailey Metabolic profiling as a means of characterizing plant-associated microbial communities FEMS Microbiol. Ecol. 16 1995 9 18
8. R.J. Ellis, B. Neish, M.W. Trett, J.G. Best, A.J. Weightman, P. Morgan, and J.C. Fry Comparison of microbial and meiofaunal community analyses for determining impact of heavy metal contamination J. Microbiol. Methods 45 2001 171 185
9. B. Engelen, K. Meinken, F. von Wintzingerode, H. Heuer, H.P. Malkomes, and H. Backhaus Monitoring impact of a pesticide treatment on bacterial soil communities by metabolic and genetic fingerprinting in addition to conventional testing procedures Appl. Environ. Microbiol. 64 1998 2814 2821
10. M. Gamo, and T. Shoji A method of profiling microbial communities based on a most-probable-number assay that use BIOLOG plates and multiple sole carbon sources Appl. Environ. Microbiol. 65 1999 4419 4424
11. J.L. Garland, and R.M. Lehman Dilution/extinction of community phenotypic characters to estimate relative structural diversity in mixed communities FEMS Microbiol. Ecol. 30 1999 333 343
12. J.L. Garland, and A.L. Mills Classification and characterisation of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilisation Appl. Environ. Microbiol. 57 1991 2351 2359
13. J.L. Garland, and A.L. Mills A community level physiological approach for studying microbial communities K. Ritz J. Dighton K.E. Giller Beyond the Biomass: Compositional and Functional Analysis of Soil Microbial Communities 1994 Wiley Chichester 77 83
14. E. Glimm, H. Heuer, B. Engelen, K. Smalla, and H. Backhaus Statistical comparisons of community catabolic profiles, J Microbiol. Methods 30 1997 71 80
15. E. Gomez, J. Garland, and M. Conti Reproducibility in the response of soil bacterial community-level physiological profiles from a land use intensification gradient Appl. Soil Ecol. 26 2004 21 30
16. W.L. Goodfriend Microbial community patterns of potential substrate utilisation: a comparison of salt marsh, sand dune, and sea water-irrigated agronomic systems Soil Biol. Biochem. 8-9 1998 1169 1176
17. S.J. Grayston, G.S. Griffith, J.L. Mawdsley, C.D. Campbell, and R.D. Bardgett Accounting for variability in soil microbial communities of temperate upland grassland ecosystems Soil Biol. Biochem. 33 2001 533 551
18. J.B. Guckert, G.J. Carr, T.D. Johnson, B.G. Hamm, D.H. Davidson, and Y. Kumagai Community analysis by Biolog: curve integration for statistical analysis of activated sludge microbial habitats J. Microbiol. Methods 27 1996 183 197
19. S.K. Haack, H. Garchow, M.J. Klug, and L.J. Forney Analysis of factors affecting the accuracy, reproducibility, and interpretation of microbial community carbon source utilisation patterns Appl. Environ. Microbiol. 61 1995 1458 1468
20. H. Heuer, and K. Smalla Evaluation of community-level catabolic profiling using BIOLOG GN Microplates to study microbial community changes in potato phyllosphere J. Microbiol. Methods 30 1997 49 61
21. W. Hitzl, M. Henrich, M. Kessel, and H. Insam Application of multivariate analysis of variance and related techniques in soil studies with substrate utilisation tests J. Microbiol. Methods 30 1997 81 89
22. D. Juck, T. Charles, L.G. Whyte, and C.W. Greer Polyphasic microbial community analysis of petroleum hydrocarbon-contaminated soils from two northern Canadian communities FEMS Microbiol. Ecol. 33 2000 241 249
23. B.P. Knight, S.P. McGrath, and A.M. Chaudri Biomass carbon measurements and substrate utilization patterns of microbial populations from soils amended with cadmium, copper, or zinc Appl. Environ. Microbiol. 63 1997 39 43
24. A. Konopka, L. Oliver, and R.F. Turco Jr. The use of carbon substrate utilisation patterns in environmental and ecological microbiology Microb. Ecol. 3 1998 103 115
25. T. Lawley, and C. Bell Kinetic analysis of Biolog community profiles to detect changes in inoculum density and species diversity of river bacterial communities Can. J. Microbiol. 44 1998 588 597
26. K. Lawlor, B.P. Knight, V.L. Barbosa-Jefferson, P.W. Lane, A.K. Lilley, G.I. Paton, S.P. McGrath, S.M. O'Flaherty, and P.R. Hirsch Comparison of methods to investigate microbial populations in soils under different agricultural management FEMS Microbiol. Ecol. 33 2000 129 137
27. C. Mayr, A. Winding, and N.B. Hendriksen Community level physiological profile of soil bacteria unaffected by extraction method J. Microbiol. Methods 36 1999 29 33
28. 2 alters community-level physiological profiles and enzyme activities in alpine grassland J. Microbiol. Methods 36 1999 35 43
29. C.E. Morris, M. Badin, O. Berge, P. Frey-Klett, N. Fromin, H. Girardin, M.H. Guinebretìre, P. Lebaron, J.M. Thíry, and M. Troussellier Microbial biodiversity: approaches to experimental design and hypothesis testing in primary scientific literature from 1975 to 1999 Microbiol. Mol. Biol. Rev. 66 2002 592 616
30. S. O'Connell, R.D. Lawson, M.E. Watwood, and R.M. Lehman BASIC program for reduction of data from community-level physiological profiling using Biolog microplates: rationale and critical interpretation of data J. Microbiol. Methods 40 2000 213 220
31. R.A. Olsen, and L.R. Bakken Viability of soil bacteria: optimization of plate counting technique and comparison between total counts and plate counts within different size groups Microb. Ecol. 13 1987 59 74
32. J. Preston-Mafham, L. Boddy, and P.F. Randerson Analysis of microbial community functional diversity using sole-carbon-source utilisation profiles - a critique FEMS Microbiol. Ecol. 42 2002 1 14
33. O. Priha, S.J. Grayston, T. Pennanen, and A. Smolander Microbial activities related to C and N cycling and microbial community structure in the rhizospheres of Pinus sylvestris, Picea abies and Betula pendula in an organic and mineral soil FEMS Microbiol. Ecol. 30 1999 187 199
34. K. Smalla, U. Wachtendorf, H. Heuer, W.T. Liu, and L. Forney Analysis of BIOLOG GN substrate utilisation patterns by microbial communities Appl. Environ. Microbiol. 64 1998 1220 1225
35. V. Torsvik, J. Goksøyr, and F.L. Daae High diversity in DNA of soil bacteria Appl. Environ. Microbiol. 56 1990 782 787
36. M. Wairiu, and R. Lal Soil organic carbon in relation to cultivation and topsoil removal on sloping lands of Kolombangara, Solomon Islands Soil Till. Res. 70 2003 19 27
37. A. Walker, M. Jurado-Exposito, G.D. Bending, and V.J.R. Smith Spatial variability in the degradation rate of isoproturon in soil Environ. Pollut. 111 2001 407 415
38. A. Winding Fingerprinting bacterial soil communities using Biolog microtitre plates K. Ritz J. Dighton K.E. Giller Beyond the Biomass: Compositional and Functional Analysis of Soil Microbial Communities 1994 Wiley Chichester 85 94
39. L. Wünsche, L. Brüggemann, and W. Babel Determination of substrate utilisation patterns of soil microbial communities: an approach to assess population changes after hydrocarbon pollution FEMS Microbiol. Ecol. 17 1995 295 306
40. J.C. Zak, M.R. Willig, D.L. Moorhead, and H.G. Wildman Functional diversity of microbial communities: a quantitative approach Soil Biol. Biochem. 26 1994 1101 1108