He qPCR reactions. These results were not unexpected, as the efficiencies were not consistently different for eukaryotic 
gene amplification [7].Comparison of Microbial 16S rRNA Gene Copies Based on Standard CurvesWhile Hou et al. [7] found no consistent difference between amplification efficiencies between circular and linear curves, they did however find that standard 58-49-1 curves based on the circular plasmids overestimated the number of gene copies in their eukaryotic system by approximately 8-fold. Therefore, using two bacterial and two archaeal genomes we asked if either circular plasmid conformation caused the same degree of inflation. Genomic DNA samples were assayed at three dilutions: 1:10, 1:50, and 1:100, each in triplicate. This range was deemed appropriate as DNA extracted from environmental samples mayEffect of qPCR Standards on 16S Gene EstimatesFigure 4. Comparison of expected and estimated 16S rRNA gene copies in archaeal DNA samples. Expected 22948146 archaeal 16S rRNA gene copies were calculated based on one and two 16S copies per genome for (a) A. fulgidus and (b) M. jannaschii, respectively. Black bars = predicted 16S copies. White bars = estimated 16S copies based on supercoiled plasmid standard. Grey bars = estimated 16S copies based on nicked circular plasmid standard. Black and white striped bars = estimated 16S copies based on linearized plasmid standard. Black and gray striped bars = estimated 16S copies based on amplicon standard. Data shown are representative of two experiments. Data are the average (n = 3) and error bars are 61 standard deviation among replicates. doi:10.1371/journal.pone.0051931.gcontain inhibitors to the qPCR reaction in the DNA preparations at stock concentration reviewed in [18]. The estimated number of bacterial 16S rRNA gene copies, based on the four standard curves, was MedChemExpress 57773-65-6 compared to predicted 16S rRNA gene copy numbers (Figure 3 and Table 4). For both bacterial genomes, gene estimates derived from nicked circles and linearized plasmids were indistinguishable from one another. For both archaeal genomes, estimates derived from both linear and circular standard curves approached 1 (Figure 4 and Table 4). Note that the A. fulgidus 16S rRNA gene sequence was used as the standard for the archaeal qPCR reactions and was expected to be a precise match. Interestingly, both circular plasmids provided the best estimates for the archaeal 16S rRNA gene. Taken together, these results demonstrate than no single standard conformation performed the best in all instances. Importantly, estimates using the supercoiled standard never approached the 8-fold overestimates noted for eukaryotic systems.DiscussionPropagated plasmid DNA containing a gene sequence of interest is likely 
the most common form used to generate standards for the quantitative analysis of gene copies [19] due to its ease of preparation. In most instances the form of the standard is not reported and only recently has it come into question. A recent study [7] compared the precision of gene estimates in eukaryotic systems based on linear versus circular standards, but this effect of the conformation of the DNA standard was only tested in eukaryotic systems. It was concluded that supercoiled plasmids led to approximately 8-fold overestimates relative to its linearized counterpart and suggested that these findings be tested in systems whose target DNA is itself circular [7]. Therefore, the goal of this study was to determine if circular plasmids led to sim.He qPCR reactions. These results were not unexpected, as the efficiencies were not consistently different for eukaryotic gene amplification [7].Comparison of Microbial 16S rRNA Gene Copies Based on Standard CurvesWhile Hou et al. [7] found no consistent difference between amplification efficiencies between circular and linear curves, they did however find that standard curves based on the circular plasmids overestimated the number of gene copies in their eukaryotic system by approximately 8-fold. Therefore, using two bacterial and two archaeal genomes we asked if either circular plasmid conformation caused the same degree of inflation. Genomic DNA samples were assayed at three dilutions: 1:10, 1:50, and 1:100, each in triplicate. This range was deemed appropriate as DNA extracted from environmental samples mayEffect of qPCR Standards on 16S Gene EstimatesFigure 4. Comparison of expected and estimated 16S rRNA gene copies in archaeal DNA samples. Expected 22948146 archaeal 16S rRNA gene copies were calculated based on one and two 16S copies per genome for (a) A. fulgidus and (b) M. jannaschii, respectively. Black bars = predicted 16S copies. White bars = estimated 16S copies based on supercoiled plasmid standard. Grey bars = estimated 16S copies based on nicked circular plasmid standard. Black and white striped bars = estimated 16S copies based on linearized plasmid standard. Black and gray striped bars = estimated 16S copies based on amplicon standard. Data shown are representative of two experiments. Data are the average (n = 3) and error bars are 61 standard deviation among replicates. doi:10.1371/journal.pone.0051931.gcontain inhibitors to the qPCR reaction in the DNA preparations at stock concentration reviewed in [18]. The estimated number of bacterial 16S rRNA gene copies, based on the four standard curves, was compared to predicted 16S rRNA gene copy numbers (Figure 3 and Table 4). For both bacterial genomes, gene estimates derived from nicked circles and linearized plasmids were indistinguishable from one another. For both archaeal genomes, estimates derived from both linear and circular standard curves approached 1 (Figure 4 and Table 4). Note that the A. fulgidus 16S rRNA gene sequence was used as the standard for the archaeal qPCR reactions and was expected to be a precise match. Interestingly, both circular plasmids provided the best estimates for the archaeal 16S rRNA gene. Taken together, these results demonstrate than no single standard conformation performed the best in all instances. Importantly, estimates using the supercoiled standard never approached the 8-fold overestimates noted for eukaryotic systems.DiscussionPropagated plasmid DNA containing a gene sequence of interest is likely the most common form used to generate standards for the quantitative analysis of gene copies [19] due to its ease of preparation. In most instances the form of the standard is not reported and only recently has it come into question. A recent study [7] compared the precision of gene estimates in eukaryotic systems based on linear versus circular standards, but this effect of the conformation of the DNA standard was only tested in eukaryotic systems. It was concluded that supercoiled plasmids led to approximately 8-fold overestimates relative to its linearized counterpart and suggested that these findings be tested in systems whose target DNA is itself circular [7]. Therefore, the goal of this study was to determine if circular plasmids led to sim.