Amplification by PCR Artificially Reduces the Proportion of the Rare Biosphere in Microbial Communities 英文参考文献.docVIP
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Amplification by PCR Artificially Reduces the Proportion of the Rare Biosphere in Microbial Communities 英文参考文献
AmplificationbyPCRArtificiallyReducestheProportion
oftheRareBiosphereinMicrobialCommunities
JuanM.Gonzalez1*,MariaC.Portillo1,PedroBelda-Ferre2,AlexMira2
1Institute of Natural Resources and Agrobiology, Spanish Council for Research, IRNAS-CSIC, Sevilla, Spain, 2Genomics and Health Department, Center for Advanced
ResearchinPublicHealth(CSISP),Valencia,Spain
Abstract
Themicrobialworldhasbeenshowntoholdanunimaginablediversity.TheuseofrRNAgenesandPCRamplificationto
assessmicrobialcommunitystructureanddiversitypresentbiasesthatneedtobeanalyzedinordertounderstandtherisks
involved in those estimates. Herein, we show that PCR amplification of specific sequence targets within a community
dependsonthefractionsthatthosesequencesrepresenttothetotalDNAtemplate.Usingquantitative,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
structureofmicrobialcommunitiesfromPCR-basedsurveysisclearlybiasedagainstlowabundanttaxawhicharerequired
todecipherthecompleteextentofmicrobialdiversityinnature.
Citation: Gonzalez JM, Portillo MC, Belda-Ferre P, Mira A (2012) Amplification by PCR Artificially Reduces the Proportion of the Rare Biosphere in Microbial
Communities.PLoSONE7(1):e29973.doi:10.1371/journal.pone.0029973
Editor:JackAnthonyGilbert,ArgonneNationalLaboratory,UnitedStatesofAmerica
ReceivedAugust9,2011;AcceptedDecember9,2011;PublishedJanuary11,2012
Copyright: ? 2012 Gonzalez et al. This is an open-access article distributed under the terms of
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