Bulk DNA samples detect more macrobenthos species than eDNA from
the ethanol preservative and are not affected by morphological traits of
the species
The characterization of macrobenthos communities by DNA metabarcoding
the ethanol preservative instead of bulk specimens would greatly speed
up processing time of samples in the laboratory since the decantation
and sorting step can be avoided. The use of the ethanol preservative to
reliably characterize macroinvertebrate diversity and composition has
been demonstrated for fresh water samples (Martins et al., 2019). Our
results show that the number of morphological species detected in the
ethanol preservative of each sample is lower compared to the bulk DNA
samples (ESM Fig 4), which has also been observed for insect communities
(Zenker, Specht, & Fonseca, 2020) and for freshwater benthic
communities (Hajibabaei et al., 2019). Substantial differences between
both sample types have been observed with almost no shared species
between bulk DNA and eDNA (Marquina, Esparza-Salas, et al., 2019). Our
results also show significant differences between communities from the
bulk and ethanol preservative (Table 2), but many species were detected
in both sample types. The 15 species that were exclusively detected in
the ethanol preservative were mainly pelagic species. In view of the low
read numbers allocated to these species (at most 153 reads) these DNA
molecules are most likely “contaminant” DNA molecules that were
absorbed to the organic debris. Our results show that morphological
traits of macrobenthos species can explain their detection in the eDNA
from the ethanol preservative. Species with soft body skeleton and large
body size showed higher probability of being detected in the eDNA
fraction, while these traits did not strongly impact the detection in
bulk DNA samples (Fig 5). The latter illustrates that mixing or grinding
the samples before DNA extraction greatly increases the detection of a
variety of species in bulk DNA samples.