Commercial DNA extraction kits impact observed microbial community composition in permafrost samples.

The total community genomic DNA (g DNA) from permafrost was extracted using four commercial DNA extraction kits. The g DNAs were compared using quantitative real-time PCR (q PCR) targeting 16 S r RNA genes and bacterial diversity analyses obtained via 454 pyrosequencing of the 16 S r RNA ( V3 region) amplified in single or nested PCR. The Fast DNA^® SPIN ( FDS) Kit provided the highest g DNA yields and 16 S r RNA gene concentrations, followed by Mo Bio Power Soil^® ( PS) and Mo Bio Power Lyzer™ ( PL) kits. The lowest g DNA yields and 16 S r RNA gene concentrations were from the Meta- G- Nome™ ( MGN) DNA Isolation Kit. Bacterial phyla identified in all DNA extracts were similar to that found in other soils and were dominated by Actinobacteria, Firmicutes, Gemmatimonadetes, Proteobacteria, and Acidobacteria. Weighted Uni Frac and statistical analyses indicated that bacterial community compositions derived from FDS, PS, and PL extracts were similar to each other. However, the bacterial community structure from the MGN extracts differed from other kits exhibiting higher proportions of easily lysed β- and γ- Proteobacteria and lower proportions of Actinobacteria and Methylocystaceae important in carbon cycling. These results indicate that g DNA yields differ between the extraction kits, but reproducible bacterial community structure analysis may be accomplished using g DNAs from the three bead-beating lysis extraction kits. [ABSTRACT FROM AUTHOR]