Open AccessAn assessment of the hypervariable domains of the 16S rRNA genes for their value in determining microbial community diversity: the paradox of traditional ecological indices
Author(s) -
Mills DeEtta K.,
Entry James A.,
Voss Joshua D.,
Gillevet Patrick M.,
Mathee Kalai
Publication year - 2006
Publication title -
fems microbiology ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.377
H-Index - 155
eISSN - 1574-6941
pISSN - 0168-6496
DOI - 10.1111/j.1574-6941.2006.00135.x
Subject(s) - biology , species evenness , hypervariable region , ecology , species richness , metagenomics , microbial population biology , community structure , amplicon , polymerase chain reaction , genetics , gene , bacteria
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.