Effects of soil preservation for biodiversity monitoring using environmental DNA

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 guideline for best practices so far. Here, we assessed the impact of four methods of soil sample preservation that can be conveniently used also in metabarcoding studies targeting remote or difficult to access areas. Tested methods include: 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 ideal 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, but MOTUs richness was similar across preservation methods if rare taxa were not considered. All the approaches were able to identify differences in community structure among habitats, 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.

Environmental DNA for biomonitoring

“…The last two papers in this section provide examples of metabarcoding optimizations aiming at improving its effectiveness in biomonitoring surveys. Guerrieri et al ( 2021 ) show how soil preservation methods can affect estimates of taxonomic richness and community composition. The authors propose guidelines for optimizing soil preservation conditions in agreement with the objectives and practical constraints of the research project.…”

All together now: Limitations and recommendations for the simultaneous analysis of all eukaryotic soil sequences

“…Empirical studies have shown how sample size (Wiesel et al, 2014), extraction method (Griffiths et al, 2018), and the primers used (Schenk et al, 2019) influence diversity estimates in isolated nematode communities, but less is known about how these procedures affect the diversity estimates of other groups of soil fauna (Marquina et al, 2019). One exception is the effect of DNA extraction and storage on diversity assessments, which has received considerable attention (Delmont et al, 2011; Guerrieri et al, 2020; İnceoǧlu et al, 2010; Zinger et al, 2016). Benchmarking is a formidable challenge, but it is necessary for soil eukaryotic biodiversity assessments.…”

Effects of soil preservation for biodiversity monitoring using environmental DNA

“…A total of 6.3, 7.9 and 25.7 million reads were obtained from the Bact02, Fung02 and Euka02 libraries, respectively. After read assembly, quality filtering, spurious sequence and contaminant removal, 481,411, 2,511,721 and 13,232,441 good-quality sequences remained, consisted of 660 (Bact02), 1,075 (Fung02) and 3,611 (Euka02) unique sequences (i.e., MOTUs) (Guerrieri et al, 2020).…”