Soil environments Raw sequence reads

The structure and diversity of the microbial community are attractive biological and ecological research topics since microbes play important roles in these fields. Different DNA isolation protocols may introduce bias and affect the final results of next-generation sequencing. To establish and evaluate the impact of protocols for DNA isolation from environmental soils, we compared the results obtained by two researchers using two different DNA extraction kits: (1) MO BIO PowerSoil® DNA Isolation kit by researchers R (MO_R) and T (MO_T) and (2) NucleoSpin® Soil kit by researchers R (MN_R) and T (MN_T). Samples were collected from six different sites in Okinawa Island, Japan. For all sites, the differences between the results of the microbial composition analysis of bacteria, archaea, fungi, and other eukaryotes, as obtained by the two kits and by different researchers, were negligible. However, the MN kit provided a significantly higher yield of genomic DNA at all sites as compared to the MO kit (ANOVA; P <0.006), with both researchers. In addition, operational taxonomic units for some phyla and classes were not obtained in some cases: Micrarchaea of archaeal communities were detected only in the MN_T and MO_R analyses; the Armatimonadetes phylum of bacteria, only in MO_R and MO_T; and the WIM5 of the Amoebozoa phylum of eukaryotes, only in the MO_T analysis. Our results suggest that there is a possibility of handling bias; therefore, it is crucial that DNA extraction is performed in replicate by at least two technicians for thorough microbial analyses and to obtain accurate estimates of microbial diversity.