Physical protection of extracellular and intracellular DNA in soil aggregates against simulated natural oxidative processes

Abstract

The combined action of physical protection and chemical stabilisation is the main factor regulating the persistence of soil organic matter (SOM). In particular, physical protection refers to the compartmentalization of SOM and microbial biomass within aggregates. Thus, we have investigated the role of (macro-, meso- and micro-) soil aggregates in the protection of SOM and extracellular and intracellular DNA (eDNA vs iDNA) from oxidative stress by treating aggregates with Low Temperature Ashing (LTA) for different durations (0, 5, 24 and 48 h). DNA (exDNA vs iDNA) was sequentially extracted from the different aggregate size classes, and qualitatively (agarose gel electrophoresis) and quantitatively (fluorimetry; spectrophotometry) analysed, discriminating between double stranded (ds) and single stranded (ss) DNA. In addition, comparative PCR-DGGE (exDNA vs iDNA) was performed to assess the bacterial, fungal and archaeal communities of the different aggregate size classes. The use of LTA enabled to determine the amount of physically protected DNA in different aggregate sizes, evidencing the potential involvement of both exDNA and iDNA in the formation of the aggregates. Our results also provided insights into the important role of soil aggregates in protecting the genetic information of the autochthonous soil microbiota. The PCoA of bacterial, archaeal and fungal DGGE patterns displayed contrasting results. While fungal and archaeal fingerprinting patterns revealed direct relationships with aggregate sizes and LTA treatment, the bacterial community was not affected by these factors. This suggests a selective action of the size of aggregates on the dominant soil microbial community members. Our findings indicate that aggregates provide a protective habitat for the soil microbial community against environmental stress conditions, such as oxidative stress. Further, the specific protection of the soil microbiota (bacteria vs archaea vs fungi) is directly correlated to the size distribution of the microbial community and the aggregate size classes.