Data from: Tracking earthworm communities from soil DNA

Earthworms are known for their important role within the functioning of an
ecosystem, and their diversity can be used as an indicator of ecosystem
health. To date, earthworm diversity has been investigated through
conventional extraction methods such as handsorting, soil washing or the
application of a mustard solution. Such techniques are time-consuming and
often difficult to apply. We showed that combining DNA metabarcoding and
next generation sequencing facilitates the identification of earthworm
species from soil samples. The first step of our experiments was to create
a reference database of mitochondrial DNA (mtDNA) 16S gene for 14
earthworm species found in the French Alps. Using this database, we
designed two new primer pairs targeting very short and informative DNA
sequences (about 30 bp and 70 bp) that allow unambiguous species
identification. Finally, we analyzed extracellular DNA taken from soil
samples in two localities (two plots per locality, eight samples per
plot). The two short metabarcode regions led to the identification of a
total of eight earthworm species. The earthworm communities identified by
the DNA-based approach appeared to be well-differentiated between the two
localities, and are consistent with results derived from inventories
collected using the handsorting method. The possibility of assessing
earthworm communities from hundreds or even thousands of localities
through the use of extracellular soil DNA will undoubtedly stimulate
further ecological research on these organisms. Using the same DNA
extracts, our study also illustrates the potential of environmental DNA as
a tool to assess the diversity of other soil-dwelling animal taxa.