Morphological traits and community composition of bulk DNA and
eDNA from the ethanol preservative
A detailed comparison between communities recovered in bulk DNA and eDNA
from the ethanol preservative was conducted for primer set A. Both DNA
datasets detected more species than the morphology based identification
(69 species in bulk DNA, 64 in eDNA and 57 in morphology, ESM Fig 7).
Although community composition significantly differed between bulk DNA
and eDNA of the ethanol preservative (Table 2), 49 species were also
shared between the two types of sample (ESM Fig 7). Nevertheless, the
differences observed between the two sample types could be explained by
morphological traits of the macrobenthos species. The two biological
traits larval stage and life span did not result in significant terms
and were not included in the final model. The final model included fixed
effects of sample type, body size and body skeleton, as well as the two
way interaction terms sample type * body size and sample type * body
skeleton. The probability of detecting a species in bulk DNA or eDNA
from the ethanol preservative was differently affected by body size and
body skeleton as shown by the significant sample type * body size and
sample type * body skeleton interaction effects (Table 3). The
probability of detecting species in the bulk samples was overall high
(Fig 5), with no significant differences between body sizes and body
skeleton (all pairwise comparisons had p > 0.05). In
contrast, the probability of detecting species in the eDNA from the
ethanol preservative was significantly higher for soft bodied species
compared to species with chitine (p = 0.0001) or CaCO3 in their skeleton
(p = 0.0001). The probability of detecting species with small and medium
body sizes was significantly higher in bulk DNA samples than in the eDNA
samples from the ethanol preservative (body size 0-20: p <
0.0001; body size 21-100: p = 0.003; Fig 5), while the probability of
detecting species with large body sizes was not significantly different
between the two sample types (p = 0.18). The presence of body skeleton
had also a clear impact on the probability of species detection in the
two sample types: the probability of detecting species with chitine or
CaCO3 in their skeleton was significantly lower in the eDNA of the
ethanol preservative compared to the bulk DNA samples (p = 0.0002 and p
< 0.0001, respectively, Fig 5), while no significant
difference was observed between the two sample types for species with
soft body skeleton (p = 0.21).