Soil aggregates: Protective hot spots for microbes under extreme environmental conditions.

Soil aggregates, the basic structural unit of soil, provide special microhabitats and are assumed to protect both soil organic matter and microbiota against negative effects of harsh environmental conditions. Challenging to assess this protective effect on soil microbiota and soil DNA, we have calibrated in laboratory three different sizes of aggregates (0.5-1mm, 500-100µm and <100µm), obtained by dry sieving from 2 mm sieved fraction from a forest soil. In order to simulate extreme conditions, each fraction of aggregates was subjected to 1) Low Temperature Ashing (LTA) by oxygen plasma treatment and 2) high temperature by oven drying at 250°C, both at various time period of exposure (0, 5, 20 and 48 hours). Aggregate protection-effects on soil microbiota were evaluated in terms of microbial biomass (double strand DNA) and microbial community structure (Bacteria, Archaea and Fungi). To accurately assess the effect of oxidation and high temperature on soil DNA, we analytically discriminated between the extracellular (eDNA) and intracellular (iDNA) fraction of the soil metagenome, by sequential extraction and comparative genetic fingerprinting (Polymerase Chain Reaction and Denaturing Gradient Gel Electrophoresis) of eDNA and iDNA. The performed fine-tuning DNA analyses provided clear evidences about the protective effect of aggregates not only on the microbial cells of all domains (iDNA) but also on the soil extracellular DNA, this latter with important evolutionary implication (genetic exchange by natural transformation). Clear differences were observed between the type of treatment (oxidation, temperature), duration of treatment, and pore sizes. Microbiota was much more affected by high temperature than by oxidation (LTA), and the protection was negatively correlated with the duration of the treatment.