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Applied and Environmental Microbiology, April 2009, p. 2495-2505, Vol. 75, No. 8
0099-2240/09/$08.00+0     doi:10.1128/AEM.02409-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Quantitative Community Fingerprinting Methods for Estimating the Abundance of Operational Taxonomic Units in Natural Microbial Communities{triangledown}

Alban Ramette*

Microbial Habitat Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany

Received 21 October 2008/ Accepted 2 February 2009

Molecular fingerprinting techniques offer great promise for analyzing changes in microbial community structure, especially when dealing with large number of samples. However, a serious limitation has been the lack of quantification offered by such techniques since the relative abundances of the identified operational taxonomic units (OTUs) in the original samples are not measured. A quantitative fingerprinting approach designated "qfingerprinting" is proposed here. This method involves serial dilutions of the sample of interest and further systematic fingerprinting of all dilution series. Using the ultimate dilutions for which OTU are still PCR amplifiable and taking into account peak size inaccuracy and peak reproducibility, the relative abundance of each OTU is then simultaneously determined over a scale spanning several orders of magnitude. The approach was illustrated by using a quantitative version of automated ribosomal intergenic spacer analysis (ARISA), here called qARISA. After validating the concept with a synthetic mixture of known DNA targets, qfingerprinting was applied to well-studied marine sediment samples to examine specific changes in OTU abundance associated with sediment depth. The new strategy represents a major advance for the detailed quantitative description of specific OTUs within complex communities. Further ecological applications of the new strategy are also proposed.

* Mailing address: Microbial Habitat Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany. Phone: (49) 421 2028 863. Fax: (49) 421 2028 870. E-mail: aramette{at}mpi-bremen.de

{triangledown} Published ahead of print on 6 February 2009.

Applied and Environmental Microbiology, April 2009, p. 2495-2505, Vol. 75, No. 8
0099-2240/09/$08.00+0     doi:10.1128/AEM.02409-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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