Widely used tool for assessing microbial diversity and numbers in environmental

Widely used tool for assessing microbial diversity and numbers in environmental samples using PCR-based methods [1,3]. The ,1500 base pair (bp) full-length 16S rRNA gene sequence contains conserved regions that are flanked by hyper-variable regions, and it is the degree of variation within these hyper-variable regions that distinguishes between microbial taxa at various classification levels [4,5]. Therefore, taxa-specific 16S rRNA gene primer sets coupled with SYBR chemistry is the most cost-effective method to target and quantify the maximum number of microbes at a given classification level within a test sample reviewed in [6]. A recent report has shown that supercoiled plasmid DNA used to generate standard curves grossly overestimated the number of pcna gene copies by 8-fold using the microalgae eukaryotic system[7]. Lin et al. [8] reported a similar finding, with a 3-fold increase in the NK603/zSSIIb gene(s) using the eukaryotic system, maize. Interestingly, little attention has been paid to the effect of circularTable 1. List of primers used to amplify the 16S rRNA gene.Primer Cloning fD1 rP2 Arc8f Arc1492r qPCR 27f 338r Arc8f Arc344rTaxa/ Direction Domain Sequence (59-39)ReferenceForward Reverse Forward ReverseBacteriaAGAGTTTGATCCTGGCTCAG ACGGCTACCTTGTTACGACTT[5]Archaea TCCGGTTGATCCTGCC GGCTACCTTGTTACGACTT[13]Forward Reverse Forward ReverseBacteriaAGAGTTTGATCMTGGCTCAG GCTGCCTCCCGTAGGAGT[14]Archaea TCCGGTTGATCCTGCC TCGCGCCTGCTGCICCCCGT[15]doi:10.1371/journal.pone.0051931.tEffect of qPCR Standards on 16S Gene Estimatesplasmid standards in bacterial and archaeal systems which commonly have genomes and plasmids that are circular, although linear forms are found in some cases [9]. In industrial microbiology, 16S rRNA gene copies can be reported as a means of assessing the microbial abundance in a given sample [10], with the SIS-3 custom synthesis caveat that 16S rRNA gene numbers can vary by a log-fold per genome between different species [11]; so if this inherent variation is further amplified by as much as a log-fold due to overestimation by a circular standard, this could have important ramifications for the quantification of microbes of interest in many different industrial and medical settings. Therefore, the goal of this study was to test the feasibility of using a circular plasmid standard purified from transformed bacterial cells with no further preparation for 16S rRNA gene copy number estimates in bacterial and archaeal systems. We hypothesized that circular plasmids would yield similar gene estimates as their linearized counterparts and could therefore be used in lieu of, with the major advantage of minimal standard preparation for continual qPCR analyses. To test this hypothesis, gene estimates based on two circular plasmid standards (supercoiled and nicked circles) were compared to those of two linear standards, a SpeI-digested plasmid and a PCR amplicon, using two sets of taxa-specific 16S rRNA gene primers. One set of 12926553 primers targeted the bacterial 16S rRNA gene while the other set targeted the archaeal 16S rRNA gene. The ratio of estimated to predicted 16S rRNA gene copies were analyzed using sequenced bacterial and archaeal genomes and results PD 168393 web presented here demonstrated that circular plasmids did not lead to gross overestimates in 16S rRNA gene copies. Therefore, propagated plasmids suffice for prokaryotic 16S rRNA gene estimates and require less preparation than linearized or PCR-amplicon DNA for use as qPCR standards.Methods Genomic DNA.Widely used tool for assessing microbial diversity and numbers in environmental samples using PCR-based methods [1,3]. The ,1500 base pair (bp) full-length 16S rRNA gene sequence contains conserved regions that are flanked by hyper-variable regions, and it is the degree of variation within these hyper-variable regions that distinguishes between microbial taxa at various classification levels [4,5]. Therefore, taxa-specific 16S rRNA gene primer sets coupled with SYBR chemistry is the most cost-effective method to target and quantify the maximum number of microbes at a given classification level within a test sample reviewed in [6]. A recent report has shown that supercoiled plasmid DNA used to generate standard curves grossly overestimated the number of pcna gene copies by 8-fold using the microalgae eukaryotic system[7]. Lin et al. [8] reported a similar finding, with a 3-fold increase in the NK603/zSSIIb gene(s) using the eukaryotic system, maize. Interestingly, little attention has been paid to the effect of circularTable 1. List of primers used to amplify the 16S rRNA gene.Primer Cloning fD1 rP2 Arc8f Arc1492r qPCR 27f 338r Arc8f Arc344rTaxa/ Direction Domain Sequence (59-39)ReferenceForward Reverse Forward ReverseBacteriaAGAGTTTGATCCTGGCTCAG ACGGCTACCTTGTTACGACTT[5]Archaea TCCGGTTGATCCTGCC GGCTACCTTGTTACGACTT[13]Forward Reverse Forward ReverseBacteriaAGAGTTTGATCMTGGCTCAG GCTGCCTCCCGTAGGAGT[14]Archaea TCCGGTTGATCCTGCC TCGCGCCTGCTGCICCCCGT[15]doi:10.1371/journal.pone.0051931.tEffect of qPCR Standards on 16S Gene Estimatesplasmid standards in bacterial and archaeal systems which commonly have genomes and plasmids that are circular, although linear forms are found in some cases [9]. In industrial microbiology, 16S rRNA gene copies can be reported as a means of assessing the microbial abundance in a given sample [10], with the caveat that 16S rRNA gene numbers can vary by a log-fold per genome between different species [11]; so if this inherent variation is further amplified by as much as a log-fold due to overestimation by a circular standard, this could have important ramifications for the quantification of microbes of interest in many different industrial and medical settings. Therefore, the goal of this study was to test the feasibility of using a circular plasmid standard purified from transformed bacterial cells with no further preparation for 16S rRNA gene copy number estimates in bacterial and archaeal systems. We hypothesized that circular plasmids would yield similar gene estimates as their linearized counterparts and could therefore be used in lieu of, with the major advantage of minimal standard preparation for continual qPCR analyses. To test this hypothesis, gene estimates based on two circular plasmid standards (supercoiled and nicked circles) were compared to those of two linear standards, a SpeI-digested plasmid and a PCR amplicon, using two sets of taxa-specific 16S rRNA gene primers. One set of 12926553 primers targeted the bacterial 16S rRNA gene while the other set targeted the archaeal 16S rRNA gene. The ratio of estimated to predicted 16S rRNA gene copies were analyzed using sequenced bacterial and archaeal genomes and results presented here demonstrated that circular plasmids did not lead to gross overestimates in 16S rRNA gene copies. Therefore, propagated plasmids suffice for prokaryotic 16S rRNA gene estimates and require less preparation than linearized or PCR-amplicon DNA for use as qPCR standards.Methods Genomic DNA.