Extracellular DNA masks subtle bacterial responses to soil rewetting

A major goal in microbial ecology is to understand how microbial communities respond to environmental change. However, DNA-based sequencing used to characterize changes in microbial communities often includes extracellular DNA (exDNA) from dead cells, obscuring measurements of microbial responses, particularly to short-term disturbances. We assessed whether exDNA obscured bacterial responses to a soil drying-rewetting in two crop types (conventionally-tilled corn and perennial switchgrass). We quantified changes in bacterial abundance (16S rRNA gene copies), alpha diversity, and community composition in paired samples with exDNA included, and those in which it was removed using propidium monoazide (PMAxx). We found that paired samples (removed and not removed exDNA) were usually not significantly different from one another , but removing exDNA was necessary in our experiment to detect some significant changes over time , as soil was rewet. The importance depended on crop type. Specifically, in corn soil, we observed significant changes in bacterial abundance and community composition over time when exDNA was removed, but differences were no longer significant if exDNA was included. exDNA pools were also higher at the beginning of the experiment, after a long drought, and lower after rewetting, suggesting this pool is dynamic. We conclude that exDNA removal can increase statistical sensitivity to detect subtle disturbance-driven shifts in microbial abundance and composition, but removal may not change conclusions when treatment differences are large or statistical power is high. Future work could describe controls on the size and turnover of the exDNA pool, since when this pool is larger, removal may be more important.