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Title

Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities

AuthorsGonzález Grau, Juan Miguel ; Portillo Guisado, María del Carmen ; Belda-Ferre, Pedro; Mira, Alex
Issue DateJan-2012
PublisherPublic Library of Science
CitationPlos ONE 7 (1): e29973 (2012)
AbstractThe microbial world has been shown to hold an unimaginable diversity. The use of rRNA genes and PCR amplification to assess microbial community structure and diversity present biases that need to be analyzed in order to understand the risks involved in those estimates. Herein, we show that PCR amplification of specific sequence targets within a community depends on the fractions that those sequences represent to the total DNA template. Using quantitative, real-time, multiplex PCR and specific Taqman probes, the amplification of 16S rRNA genes from four bacterial species within a laboratory community were monitored. Results indicate that the relative amplification efficiency for each bacterial species is a nonlinear function of the fraction that each of those taxa represent within a community or multispecies DNA template. Consequently, the low-proportion taxa in a community are under-represented during PCR-based surveys and a large number of sequences might need to be processed to detect some of the bacterial taxa within the ‘rare biosphere’. The structure of microbial communities from PCR-based surveys is clearly biased against low abundant taxa which are required to decipher the complete extent of microbial diversity in nature.
Description11 pages, 6 figures, 4 tables, 49 references. Conceived and designed the experiments: JMG. Performed the experiments: MCP JMG PB-F AM. Analyzed the data: MCP JMG PB-F AM. Contributed reagents/materials/analysis tools: JMG AM. Wrote the paper: JMG.
Publisher version (URL)doi:10.1371/journal.pone.0029973
URIhttp://hdl.handle.net/10261/44320
E-ISSN1932-6203
Appears in Collections:(IRNAS) Artículos
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