Soil filtration-sedimentation improves shelled protist discovery in
eukaryotic eDNA surveys
Abstract
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.