## 3 Results
### Optimized Extraction Applied to Diverse Environmental Samples  
As NaOH extraction was a reliable method for obtaining bacterial DNA from the air samples, we tested whether this method was also applicable to other environmental samples (Table 3; Figure 4). The bacterial samples include soil; chicken cloacal swabs; food samples; laboratory surfaces; and pond water and sewage. Soil specimens, collected on the University of Arkansas campus, were suspended in 100 mM NaOH with or without 5% saline. The results in Table 3 show that the inclusion of 5% saline during the extraction resulted in increased Ct values (\(p\) = 0.02), and purification with paramagnetic beads gives superior amplification compared to direct dilution (\(p\) = 0.019). Chicken cloacal swabs, collected at the University of Arkansas Poultry Research farm, were extracted, followed by paramagnetic bead capture or direct dilution. Eight total swabs were individually processed, with four purified by paramagnetic bead capture and four directly diluted for triplicate qPCR-HRM for each swab extracted. Ct values from the paramagnetic purified extracts were lower but not significant (\(p\) = 0.13). NaOH extraction was applied to swabs from cheese slices and bread. While none of the swabs from bread gave specific amplification of bacterial 16S, the extracts from swabs from cheese purified with paramagnetic beads gave specific amplification, whereas no amplification resulted from direct dilution. This may result from PCR inhibitors, since alternative methods of DNA extraction from foods with high fat and protein content typically result in the release of significant amounts of PCR inhibitors [38], which may be removed during the paramagnetic bead capture. NaOH extractions from swab samples from four different laboratory surfaces were extracted with 100 mM NaOH followed by either paramagnetic bead capture for two or direct dilution for the other two prior to qPCR-HRM. All four samples gave specific 16S amplification, with paramagnetic bead capture somewhat lower. Sewage and pond water samples collected included the following: (a) incoming sewage from the Paul R. Noland Wastewater Treatment facility, and (b) pond water samples from Clarence Craft Park, both in Fayetteville, AR, USA. Pellets from these samples were resuspended in SPW and brought to 100 mM with NaOH. Separate aliquots of each sample were subjected to either direct dilution or paramagnetic bead capture prior to qPCR-HRM. The Ct values (Figure 4) for the sewage plant effluent were lower than for the pond water samples, and although paramagnetic bead capture gave lower Ct values than direct dilution, that was not always the case.  
\begin{table}
\begin{tabular}{c c c} \hline
**Sample** & **MB/Dil** & **qPCR-HRM Ct \(\pm\) SEM** \\ \hline Soil with 5\% saline & Dil & 30.4 \(\pm\) 0.04 \\  & MB & 31.2 \(\pm\) 0.3 \\ \hline Soil with H\({}_{2}\)O & Dil & 27.5 \(\pm\) 0.2 \\  & MB & 25.8 \(\pm\) 0.1 \\ \hline Four chicken cloacal swabs & Dil & 21.9 \(\pm\) 1.4 \\  & MB & 22.7 \(\pm\) 2.2 \\ \hline Cheese & Dil & NS \\  & MB & 19.6 \(\pm\) 0.07 \\ \hline   Bread & MB/Dil & NS \\ \hline Lab surface 1 & Dil & 30.4 \(\pm\) 0.1 \\ \hline Lab surface 2 & MB & 26.6 \(\pm\) 0.3 \\ \hline Lab surface 3 & Dil & 32.3 \(\pm\) 0.4 \\ \hline Lab surface 4 & MB & 29.8 \(\pm\) 0.