Effects of soil preservation for biodiversity monitoring using environmental DNA

Environmental DNA metabarcoding is becoming a key tool for biodiversity
monitoring over large geographical or taxonomic scales and for elusive
taxa like soil organisms. Increasing sample sizes and interest in remote
or extreme areas often require the preservation of soil samples and thus
deviations from optimal standardized protocols. However, we still ignore
the impact of different methods of soil sample preservation on the results
of metabarcoding studies and there is no guidelines for best practices so
far. Here, we assessed the impact of four methods of soil sample
preservation commonly used in metabarcoding studies (preservation at room
temperature for 6h, preservation at 4°C for three days, desiccation
immediately after sampling and preservation for 21 days, and desiccation
after 6h at room temperature and preservation for 21 days). For each
preservation method, we benchmarked resulting estimates of taxon diversity
and community composition of three different taxonomic groups (bacteria,
fungi and eukaryotes) in three different habitats (forest, river bank and
grassland) against results obtained under optimal conditions (i.e.
extraction of eDNA right after sampling). Overall, the different
preservation methods only marginally impaired results and only under
certain conditions. When rare taxa were considered, we detected small but
significant changes in MOTU richness of bacteria, fungi and eukaryotes
across treatments, while the exclusion of rare taxa led to robust results
across preservation methods. The differences in community structure among
habitats were evident for all treatments, and the communities retrieved
using the different preservation conditions were extremely similar. We
propose guidelines on the selection of the optimal soil sample
preservation conditions for metabarcoding studies, depending on the
practical constraints, costs and ultimate research goals.