This Article Full Text Full Text (PDF) Other Versions of this Article: AEM.00514-07v1 73/16/5276    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Reprints and Permissions Copyright Information Books from ASM Press MicrobeWorld Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Blackwood, C. B. Articles by Buyer, J. S. Search for Related Content PubMed PubMed Citation Articles by Blackwood, C. B. Articles by Buyer, J. S. Agricola Articles by Blackwood, C. B. Articles by Buyer, J. S.

 Previous Article  |  Next Article 

Applied and Environmental Microbiology, August 2007, p. 5276-5283, Vol. 73, No. 16
0099-2240/07/$08.00+0     doi:10.1128/AEM.00514-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Interpreting Ecological Diversity Indices Applied to Terminal Restriction Fragment Length Polymorphism Data: Insights from Simulated Microbial Communities

Department of Biological Sciences, Kent State University, Kent, Ohio 44242,¹ Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109-1048,² School of Natural Resources and Environment, University of Michigan, Ann Arbor, Michigan 48109-1041,³ Sustainable Agricultural Systems Laboratory, USDA-ARS, Beltsville Agricultural Research Center, Beltsville, Maryland 20705⁴

Received 6 March 2007/ Accepted 19 June 2007

Ecological diversity indices are frequently applied to molecular profiling methods, such as terminal restriction fragment length polymorphism (T-RFLP), in order to compare diversity among microbial communities. We performed simulations to determine whether diversity indices calculated from T-RFLP profiles could reflect the true diversity of the underlying communities despite potential analytical artifacts. These include multiple taxa generating the same terminal restriction fragment (TRF) and rare TRFs being excluded by a relative abundance (fluorescence) threshold. True community diversity was simulated using the lognormal species abundance distribution. Simulated T-RFLP profiles were generated by assigning each species a TRF size based on an empirical or modeled TRF size distribution. With a typical threshold (1%), the only consistently useful relationship was between Smith and Wilson evenness applied to T-RFLP data (TRF-E_var) and true Shannon diversity (H'), with correlations between 0.71 and 0.81. TRF-H' and true H' were well correlated in the simulations using the lowest number of species, but this correlation declined substantially in simulations using greater numbers of species, to the point where TRF-H' cannot be considered a useful statistic. The relationships between TRF diversity indices and true indices were sensitive to the relative abundance threshold, with greatly improved correlations observed using a 0.1% threshold, which was investigated for comparative purposes but is not possible to consistently achieve with current technology. In general, the use of diversity indices on T-RFLP data provides inaccurate estimates of true diversity in microbial communities (with the possible exception of TRF-E_var). We suggest that, where significant differences in T-RFLP diversity indices were found in previous work, these should be reinterpreted as a reflection of differences in community composition rather than a true difference in community diversity.

Published ahead of print on 29 June 2007.

This article has been cited by other articles:

• Fierer, N., Blackwood, C. B., Zak, D. R., Buyer, J. S. (2007). Tilting at Windmills: a Response to a Recent Critique of Terminal Restriction Fragment Length Polymorphism Data. Appl. Environ. Microbiol. 73: 8041-8042 [Full Text]