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Misidentification of soil bacteria by fatty acid methyl ester (FAME) and BIOLOG analyses

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Abstract

 Fatty acid methyl ester (FAME) analysis is commonly used by soil scientists as a sole method for identifying soil bacteria. We observed discrepancies with this method for identifying certain species of bacteria. Therefore, we used carbon substrate oxidation patterns (BIOLOG) and some simple physical and chemical tests to determine the extent of these discrepancies. Identification with FAME profiles gave false positives for Arthrobacter globiformis, Micrococcus kristinae, and M. luteus, and identification with BIOLOG patterns gave a false positive identification for A. globiformis. A visual check and Gram stain are recommended when FAME analysis identifies soil isolates as M. kristinae or M. luteus, and an additional spore formation test is recommended when FAME and BIOLOG analyses identify isolates as A. globiformis.

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Authors and Affiliations

  1. Department of Crop and Soil Sciences, 3111 Plant Sciences, University of Georgia, Athens, GA 30602-7272, USA e-mail: pghartel@arches.uga.edu Tel.: +1-706-5420898 Fax: +1-706-5420914, , , , , , GE

    N. Oka, P. G. Hartel & O. Finlay-Moore

  2. Department of Agronomy, University of Maryland, College Park, MD 20742, USA, , , , , , US

    J. Gagliardi & J. S. Angle

  3. Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA, , , , , , US

    D. A. Zuberer

  4. Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19717-1303, USA, , , , , , US

    J. J. Fuhrmann

  5. Department of Crop and Soil Environmental Science, Clemson University, Clemson, SC 29634-0359, USA, , , , , , US

    H. D. Skipper

Authors
  1. N. Oka
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  2. P. G. Hartel
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  3. O. Finlay-Moore
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  4. J. Gagliardi
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  5. D. A. Zuberer
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  6. J. J. Fuhrmann
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  7. J. S. Angle
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  8. H. D. Skipper
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Received: 14 January 2000

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Oka, N., Hartel, P., Finlay-Moore, O. et al. Misidentification of soil bacteria by fatty acid methyl ester (FAME) and BIOLOG analyses. Biol Fertil Soils 32, 256–258 (2000). https://doi.org/10.1007/s003740000244

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  • DOI: https://doi.org/10.1007/s003740000244

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