Microbial Decomposition of Extracellular DNA in Clay Soils

Abstract:

Genomic analysis of soil communities can only be useful in predicting ecosystem processes if the genetic data gathered is representative of the microbial community. Consequently, extracellular DNA (eDNA) represents a pool of unexpressed genetic information that may skew genomic analyses. To date, our understanding of the representation of eDNA in metagenomic data and its decomposition in soil is very limited. To address this deficit, we performed a laboratory experiment wherein soils were amended with eDNA and/or clay minerals in a full factorial design. Specifically, the decomposition of ¹³C labeled E. coli DNA was monitored over a 30-day period in control, Kaolinite-amended, and Montmorillonite-amended soils. The amount of added eDNA carbon (C) remaining in the soil declined exponentially over time, with the majority of decomposition occurring in the first two weeks. Kaolinite significantly decreased eDNA decomposition rates and retained a higher fraction of eDNA–C (~70% remaining) than unamended and Montmorillonite-soils (~40% remaining) after 30 days. Phylogenetic (16S rRNA) sequencing of DNA extracted over the course of the incubation period enabled detection of the added eDNA. The relative abundance of added E. coli DNA decreased ~10-100 fold over 30 days. These results indicate that while a significant fraction of eDNA-C remained in the soil, this carbon was likely no longer in the form of intact strands of DNA amenable to sequencing. In addition, the eDNA affected the composition of the bacterial community. Specifically, the relative abundance of Planctomycetes and TM7 were elevated in soils that received eDNA regardless of clay addition, suggesting these phyla may be particularly effective at degrading eDNA and using it for growth. In conclusion these results indicate that the representation of eDNA in metagenomic sequence data declines rapidly, likely due to fragmentation. However, a fraction of eDNA material was resistant to decomposition, suggesting a substantial amount of recalcitrant eDNA could accumulate over time.