A large part of the soil protist diversity is missed in metabarcoding studies based on 0.25 g of soil environmental DNA (eDNA) and universal primers due to ca. 80 % co-amplification of non-target plants, animals and fungi. To overcome this problem, enrichment of the substrate used for eDNA extraction is an easyly implemented option but its effect has not yet been tested. In this study, we evaluated the effect of a 150 µm mesh size filtration and sedimentation method to improve the recovery of protist eDNA, while reducing the co-extraction of plant, animal and fungal eDNA, using a set of contrasted forest and alpine soils from La Réunion, Japan, Spain and Switzerland. Biodiversity of the whole eukaryotic community was estimated with V4 18S rRNA metabarcoding and classical amplicon sequence variant calling. A 2-3-fold enrichment in shelled protists (Euglyphida, Arcellinida and Chrysophyceae) was observed at the sample level with the proposed method, with, at the same time, a 2-fold depletion of Fungi and a 3-fold depletion of Embryophyceae. Protist alpha diversity was slightly lower in filtered samples due to reduced coverage in Variosea and Sarcomonadea, but significant differences were observed in only one region. Beta diversity was mostly impacted by region and habitat, and explained the same variance in bulk soil and filtered samples. The increase resolution in the soil protist diversity provided by the filtration-sedimentation method is a strong argument to include it in the standard preparation of any future soil for protist eDNA metabarcoding studies.

Soils of mountain regions are estimated to contain large amounts of organic matter (OM), equivalent to stocks found in high-latitude boreal and tundra soils. Mountain environments are also experiencing profound changes in land management under the influence of socio-economic pressures as well as the need to adapt to climate change, which is occurring at a faster rate than in lowland areas. These anthropogenic impacts are expected to strongly affect soil OM storage. Most studies of land-use change have however focused on topsoil OM; whether similar trends will hold true for subsoil OM remains unknown. Using Rock-Eval pyrolysis as a proxy for soil OM dynamics, we showed that the hierarchy of controls on OM properties and transformations varied greatly with increasing soil depth. In the topsoil, OM properties were related to the nature of plant inputs, their degree of in-mixing with the mineral matrix and the occurrence of seasonal water saturation. In the subsoil however, the foremost predictors of OM properties were geochemical parameters. This shift in the nature of determinants of OM dynamics indicates that shallow and deep soil OM pools should respond differently to external forcings. Podzolic profiles showed the strongest decoupling of topsoil and subsoil OM properties. We focused on this soil type to specifically investigate the effects of land use on subsoil OM. We selected field sites from the Coastal Range of British Columbia, Canada and the Pennine Alps, Switzerland representing undisturbed and managed forest, shrubland and pasture. Samples were analyzed for organic C content, OM quality and reactive mineralogy. Results showed that herbaceous cover was associated with an increase in topsoil but not subsoil OM. In the subsoil, variations in OM content and properties were associated with changes in reactive Al and Fe mineral phases. Overall, our data indicate that organo-mineral and organo-metal interactions are of prime importance to OM accumulation in the subsoil, and that understanding the response of deep soil C stocks to land use change will require consideration of the geochemical and mineralogical environment. Our results further suggest that so-called reactive mineral phases may themselves be impacted by land use, in turn affecting deep soil C stabilization and destabilization processes.