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Applied and Environmental Microbiology, April 2000, p. 1668-1675, Vol. 66, No. 4
0099-2240/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

Use of Length Heterogeneity PCR and Fatty Acid Methyl Ester Profiles To Characterize Microbial Communities in Soildagger

Nancy J. Ritchie, Mary E. Schutter, Richard P. Dick, and David D. Myrold*

Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon 97331-7306

Received 17 September 1999/Accepted 17 January 2000

In length heterogeneity PCR (LH-PCR) a fluorescently labeled primer is used to determine the relative amounts of amplified sequences originating from different microorganisms. Labeled fragments are separated by gel electrophoresis and detected by laser-induced fluorescence with an automated gene sequencer. We used LH-PCR to evaluate the composition of the soil microbial community. Four soils, which differed in terms of soil type and/or crop management practice, were studied. Previous data for microbial biomass, nitrogen and carbon contents, and nitrogen mineralization rates suggested that the microbial characteristics of these soils were different. One site received two different treatments: no-till and conventional till perennial ryegrass. The other sites were no-till continuous grass plots at separate locations with different soil types. Community composition was characterized by assessing the natural length heterogeneity in eubacterial sequences amplified from the 5' domain of the 16S rRNA gene and by determining fatty acid methyl ester (FAME) profiles. We found that LH-PCR results were reproducible. Both methods distinguished the three sites. The most abundant bacterial community members, based on cloned LH-PCR products, were members of the beta  subclass of the class Proteobacteria, the Cytophaga-Flexibacter-Bacteriodes group, and the high-G+C-content gram-positive bacterial group. Strong correlations were found between LH-PCR results and FAME results. We found that the LH-PCR method is an efficient, reliable, and highly reproducible method that should be a useful tool in future assessments of microbial community composition.

* Corresponding author. Mailing address: Department of Crop and Soil Science, Agric. Life Sci. Bldg., Rm 3017, Oregon State University, Corvallis, OR 97331-7306. Phone: (541) 737-5737. Fax: (541) 737-5725. E-mail: David.Myrold{at}orst.edu.

dagger Oregon Agricultural Experiment Station technical paper 11,614.

Applied and Environmental Microbiology, April 2000, p. 1668-1675, Vol. 66, No. 4
0099-2240/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.


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