Abstract
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.