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

Mills, D.K. and Entry, J.A. and Voss, J.D. and Gillevet, P.M. and Mathee, K. (2006) 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. Federation of European Microbiological Societies in Microbiology Ecology. 57:496-503.

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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 and irrigated mouldboard-ploughed
soils from Idaho were queried as to which hypervariable domains,
or combinations 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 combined V1 and V3
domains were the markers that could best distinguish the undisturbed natural
sagebrush communities from the mouldboard-ploughed microbial communities.
Bray–Curtis similarity and multidimensional scaling were found to be better
metrics to ordinate and cluster the LH-PCR community profiling data. The use/
misuse of traditional ecological indices such as diversity and evenness to study
microbial community profiles will remain a major point to consider when
performing metagenomic studies.

Item Type:	Article
NWISRL Publication Number:	1192
Subjects:	Mass Import - unclassified
Depositing User:	Dan Stieneke
Date Deposited:	20 Nov 2010 21:49
Last Modified:	01 Nov 2016 15:28
Item ID:	42
URI:	https://eprints.nwisrl.ars.usda.gov/id/eprint/42