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United States Department of Agriculture

Agricultural Research Service

Title: An Assessment of the Hypervariable Domains of the 16s Rrna Genes for Their Value in Determining Microbial Community Diversity: the Paradox of Traditional Ecological Indices

Authors
item Mills, D - FLORIDA INT'L UNIVERSITY
item Entry, James
item Voss, Joshua - FLORIDA INT'L UNIVERSITY
item Gillevet, Patrick - GEORGE MASON UNIVERSITY
item Mathee, Kalai - FLORIDA INT'L UNIVERSITY

Submitted to: Federation of European Microbiological Societies Microbiology Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 2, 2005
Publication Date: September 1, 2006
Citation: Mills, D.K., Entry, J.A., Voss, J., Gillevet, P., Mathee, K. 2006. An assessment of the hypervariable domains of the 16SsrRNA genes for their value in determining microbial community diversity: The paradox of traditional ecological indices. Federation of European Microbiological Societies Microbiology Ecology. 57:496-503.

Interpretive Summary: Amplicon length heterogeneity-PCR (LH-PCR) was investigated for its ability to distinguish between microbial community patterns from the same soil type under different land management practices. Natural sagebrush (NSB) and irrigated moldboard plowed (IMP) soils from Idaho were queried as to which hypervariable domain or combination of 16S rRNA gene domains were the best molecular markers. Using standard ecological indices to measure richness, diversity and evenness, the combination of three domains, V1, V3 and V1+V2 or the combinedV1 and V3 domains were the markers that could best distinguish the undisturbed NSB communities from the IMP microbial communities. Bray-Curtis similarity and multi-dimensional scaling were found to be better metrics to map and cluster the LH-PCR community profiling data than traditional ecological indices. The use/misuse of indices that assess diversity and evenness to study microbial community profiles will remain a major point to consider when performing metagenomic studies.

Technical Abstract: Amplicon length heterogeneity-PCR (LH-PCR) was investigated for its ability to distinguish between microbial community patterns from the same soil type under different land management practices. Natural sagebrush (NSB) and irrigated moldboard plowed (IMP) soils from Idaho were queried as to which hypervariable domain or combination of 16S rRNA gene domains were the best molecular markers. Using standard ecological indices to measure richness, diversity and evenness, the combination of three domains, V1, V3 and V1+V2 or the combinedV1 and V3 domains were the markers that could best distinguish the undisturbed NSB communities from the IMP microbial communities. Bray-Curtis similarity and multi-dimensional scaling were found to be better metrics to map and cluster the LH-PCR community profiling data than traditional ecological indices. The use/misuse of indices that assess diversity and evenness to study microbial community profiles will remain a major point to consider when performing metagenomic studies.

Last Modified: 10/23/2014
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