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Factors governing extracellular DNA degradation dynamics in soil

Sirois, Sara Hope, Buckley, Daniel H.
Environmental microbiology reports 2019 v.11 no.2 pp. 173-184
DNA, agricultural management, forest soils, habitats, high-throughput nucleotide sequencing, meadow soils, microbial communities, no-tillage, quantitative polymerase chain reaction, soil ecology, soil organic carbon, soil water, temperature
We examined the impacts of soil moisture, temperature, agricultural management and habitat type on the degradation dynamics of eDNA in soils. Synthetic eDNA was added to soil microcosms, and its disappearance over time was measured using both high‐throughput sequencing and qPCR. The synthetic eDNA was degraded rapidly, but a small fraction remained detectable throughout the experiments (39–80 days). The eDNA degradation rate was positively correlated with moisture and temperature, but negatively correlated with soil organic carbon content. End‐point stabilization of eDNA was highest at low moisture and temperature, but exhibited no relationship with soil organic carbon. Tilled soils had higher rates of degradation and less stabilization than no‐till soils. Among different habitats we observed that forest soils had the slowest degradation rate, and meadow soils had the greatest stabilization of eDNA. While eDNA was detectable by qPCR in all treatments across all time‐points, it became inconsistently detectable with high‐throughput gene sequencing in less than 1 week. We conclude that eDNA degradation and stabilization dynamics vary with moisture, temperature and habitat characteristics, that small amounts of eDNA may persist in soils indefinitely, and that the ability of persistent eDNA to impact microbial community estimates depends on method sensitivity and experimental objectives.