Importance of sample pre-treatments for the DNA-based characterization of microbiomes in cropland and forest soils

This study examined the effects of different common soil sample pre-treatments on the microbial community composition of cropland and forest soils from five sites. Pre-treatments included the analysis of fresh samples (without and after pre-incubation), dried and rewetted samples (with pre-incubation), and frozen and thawed samples (with pre-incubation). Regardless of pre-treatment, microbial communities remained distinguishable among sites and land uses. However, some prokaryotic phyla (Acidobacteriota, Actinobacteriota, and Thermoproteota) were found to be more sensitive to pretreatment than others (Bacteriodota, Firmicutes or Planctomycetota). Among fungi, Basidiomycota and Mucoromycota, which were predominant in forest soils, were also more affected than Ascomycota, which were dominant in arable soils. Interestingly, 2-mm sieves increased DNA yield during DNA extraction (except in dried soils), but resulted in a shift in species and reduced Shannon diversity. The results suggest that drying of soils, in particular, should be avoided when analyzing the soil microbial community. Preferably, fresh soils, or frozen samples should be used for the analyses. However, here it is sufficient to freeze the samples at -20°C after sampling, instead of freezing them directly in the field.

https://doi.org/10.1016/j.soilbio.2023.109077