BradleyShipleyBeaulieu2006

Référence

Bradley, R.L., Shipley, B. and Beaulieu, C. (2006) Refining numerical approaches for analyzing soil microbial community catabolic profiles based on carbon source utilization patterns. Soil Biology and Biochemistry, 38(3):629-632.

Résumé

Despite several limitations, community level catabolic profiles (CLCPs) based on carbon source utilization patterns are extensively used in ecological surveys to study the functional diversity of soil microbial communities. Our paper discusses two ways by which numerical approaches currently applied to CLCP data may be refined. First, we discuss the negative relationship between the sensitivity of a functional diversity index (Df) and the number of catabolic reactions used to calculate this index. Consequently, we propose that Df be based on specific subsets of substrates to describe the diversity among functional subgroups of the soil microbial community. Secondly, we discuss the current lack of a proper inferential test of significance for testing treatment effects on CLCPs. Permutation multivariate analysis of variance (PMANOVA) is thus proposed as a robust statistical alternative for comparing treatment effects on multiple response variables that are not independent. For illustrative purposes, we have compared the sensitivity of principal component analysis (PCA) with that of PMANOVA, performed on the same CLCP data set. © 2005 Elsevier Ltd. All rights reserved.

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@ARTICLE { BradleyShipleyBeaulieu2006,
    AUTHOR = { Bradley, R.L. and Shipley, B. and Beaulieu, C. },
    TITLE = { Refining numerical approaches for analyzing soil microbial community catabolic profiles based on carbon source utilization patterns },
    JOURNAL = { Soil Biology and Biochemistry },
    YEAR = { 2006 },
    VOLUME = { 38 },
    PAGES = { 629-632 },
    NUMBER = { 3 },
    NOTE = { 00380717 (ISSN) Cited By (since 1996): 1 Export Date: 26 April 2007 Source: Scopus CODEN: SBIOA doi: 10.1016/j.soilbio.2005.07.002 Language of Original Document: English Correspondence Address: Bradley, R.L.; De?partement de Biologie; Universite? de Sherbrooke Sherbrooke, Que. J1K 2R1, Canada; email: robert.bradley@usherbrooke.ca References: Bradley, R.L., Titus, B.D., Hogg, K., Does shelterwood harvesting have less impact on forest floor nutrient availability and microbial properties than clearcutting? (2001) Biology \& Fertility of Soils, 34, pp. 162-169; Degens, B.P., Harris, J.A., Development of a physiological approach to measuring the catabolic diversity of soil microbial communities (1997) Soil Biology \& Biochemistry, 29, pp. 1309-1320; Derry, A.M., Staddon, W.J., Trevors, J.T., Functional diversity and community structure of microorganisms in uncontaminated and creosote-contaminated soils as determined by sole-carbon-source-utilization (1998) World Journal of Microbiology \& Biotechnology, 14, pp. 571-578; Garland, J.L., Mills, A.L., Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization (1991) Applied and Environmental Microbiology, 57, pp. 2351-2359; Good, P., (1994) Permutation Tests. A Practical Guide to Resampling Methods for Testing Hypotheses, , Springer, NY; Goodfriend, W.L., Microbial community patterns of potential substrate utilization: A comparison of salt marsh, sand dune, and seawater-irrigated agronomic systems (1998) Soil Biology \& Biochemistry, 30, pp. 1169-1176; Hitzl, W., Henrich, M., Kessel, M., Insam, H., Application of multivariate analysis of variance and related techniques in soil studies with substrate utilization (1997) Journal of Microbiological Methods, 30, pp. 81-89; Legendre, P., Anderson, M.J., Distance-based redundancy analysis: Testing multi-species responses in multi-factorial ecological experiments (1999) Ecological Monographs, 69, pp. 1-24; Muyzer, G., Structure, function and dynamics of microbial communities: The molecular biological approach (1998) Advances in Molecular Ecology, 306, pp. 87-117; Pesarin, F., (2001) Multivariate Permutation Tests with Applications in Biostatistics, , John Wiley \& Sons, New York, NY; Smalla, K., Wachtendorf, U., Heuer, H., Liu, W., Forney, L., Analysis of BIOLOG GN substrate utilization patterns by microbial communities (1998) Applied and Environmental Microbiology, 64, pp. 1220-1225; Staddon, W.J., Duchesne, L.C., Trevors, J.T., Impact of clear-cutting and prescribed burning on microbial diversity and community structure in a jack pine (Pinus Banksiana Lamb.) clear-cut using BIOLOG gram-negative microtiter plates (1998) World Journal of Microbiology \& Biotechnology, 14, pp. 119-123; Staddon, W.J., Trevors, J.T., Duchesne, L.C., Colombo, C.A., Soil microbial diversity and community structure across a climatic gradient in western Canada (1998) Biodiversity \& Conservation, 7, pp. 1081-1092; Zak, J.C., Willig, M.R., Moorhead, D.L., Wildman, H.G., Functional diversity of microbial communities: A quantitative approach (1994) Soil Biology \& Biochemistry, 26, pp. 1101-1108. },
    ABSTRACT = { Despite several limitations, community level catabolic profiles (CLCPs) based on carbon source utilization patterns are extensively used in ecological surveys to study the functional diversity of soil microbial communities. Our paper discusses two ways by which numerical approaches currently applied to CLCP data may be refined. First, we discuss the negative relationship between the sensitivity of a functional diversity index (Df) and the number of catabolic reactions used to calculate this index. Consequently, we propose that Df be based on specific subsets of substrates to describe the diversity among functional subgroups of the soil microbial community. Secondly, we discuss the current lack of a proper inferential test of significance for testing treatment effects on CLCPs. Permutation multivariate analysis of variance (PMANOVA) is thus proposed as a robust statistical alternative for comparing treatment effects on multiple response variables that are not independent. For illustrative purposes, we have compared the sensitivity of principal component analysis (PCA) with that of PMANOVA, performed on the same CLCP data set. © 2005 Elsevier Ltd. All rights reserved. },
    KEYWORDS = { Biolog microtiter plates Carbon source utilization pattern Community level catabolic profile Functional diversity index Functional subgroups PCA PMANOVA. },
    OWNER = { brugerolles },
    TIMESTAMP = { 2007.12.05 },
}

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