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    Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure

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    Huber_ForLibrary.pdf (514.9Kb)
    Date
    2008-07
    Author
    Huber, Julie A.  Concept link
    Morrison, Hilary G.  Concept link
    Huse, Susan M.  Concept link
    Neal, Phillip R.  Concept link
    Sogin, Mitchell L.  Concept link
    Mark Welch, David B.  Concept link
    Metadata
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    Citable URI
    https://hdl.handle.net/1912/2722
    As published
    https://doi.org/10.1111/j.1462-2920.2008.01857.x
    Abstract
    PCR-based surveys of microbial communities commonly use regions of the small subunit ribosomal RNA (SSU rRNA) gene to determine taxonomic membership and estimate total diversity. Here we show that the length of the target amplicon has a significant effect on assessments of microbial richness and community membership. Using OTU- and taxonomy-based tools, we compared the V6 hypervariable region of the bacterial SSU rRNA gene of three amplicon libraries of ca. 100 base pair (bp), 400bp, and 1000bp from each of two hydrothermal vent fluid samples. We found that the smallest amplicon libraries contained more unique sequences, higher diversity estimates, and a different community structure than the other two libraries from each sample. We hypothesize that a combination of polymerase dissociation, cloning bias, and mis-priming due to secondary structure accounts for the differences. While this relationship is not linear, it is clear that the smallest amplicon libraries contained more different types of sequences, and accordingly, more diverse members of the community. Because divergent and lower abundant taxa can be more readily detected with smaller amplicons, they may provide better assessments of total community diversity and taxonomic membership than longer amplicons in molecular studies of microbial communities.
    Description
    Author Posting. © The Authors, 2009. This is the author's version of the work. It is posted here by permission of Society for Applied Microbiology and Blackwell Publishing for personal use, not for redistribution. The definitive version was published in Environmental Microbiology 11 (2009): 1292-1302, doi:10.1111/j.1462-2920.2008.01857.x.
    Collections
    • Josephine Bay Paul Center in Comparative Molecular Biology and Evolution
    Suggested Citation
    Preprint: Huber, Julie A., Morrison, Hilary G., Huse, Susan M., Neal, Phillip R., Sogin, Mitchell L., Mark Welch, David B., "Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure", 2008-07, https://doi.org/10.1111/j.1462-2920.2008.01857.x, https://hdl.handle.net/1912/2722
     
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