Comparison of species composition between morphology, bulk DNA
and eDNA datasets
Morphological identification of the four samples yielded a total of 57
macrobenthos species. In addition, juveniles of Ophiura,Echinoidea, Ophelia , Nephtys , Phoronis ,Pontocrates , Spio, Magelona , Cirratulidae, Glycera ,Lanice as well as specimens belonging to Nemertea, Oligochaeta
and Anthozoa were identified to the respective order, genus or phylum. A
detailed list of all taxa and their abundance in each location is
presented in ESM Table 5. The number of morphological species was
highest in Location 120, where 39 species were identified, and decreased
over Locations 330, 840 and ZVL (13, 10 and 3, respectively) (ESM Fig
4). For six morphologically identified species (Capitella minima,
Caulleriella alata, Mediomastus fragilis, Pseudopolydora pulchra,
Spirobranchus lamarckii and Tanaissus liljeborgi ), no COI
sequence was present in our reference COI database. For the bulk DNA
datasets, all primer sets except primer set D showed the same decreasing
trend in species numbers from Location 120, over 330, 840 and ZVL (ESM
Fig 4). For the eDNA samples from the ethanol preservative, primer sets
B and D identified very low species numbers, and for all primer sets the
decreasing trend in species numbers was less clear compared to the bulk
DNA dataset. Bulk DNA generally detected a higher number of species than
the eDNA samples from the ethanol preservative (52, 37, 37, 25 and 44
species for bulk DNA and 45, 13, 22, 4 and 46 species for eDNA from the
ethanol preservative with primer sets A, B, C, D and E, respectively).
The biggest discrepancy between primer sets was situated in the number
of species detected for the most diverse sample 120B (ESM Fig 4).
Of the 57 species that were identified morphologically, primer set A was
able to pick up the highest number of species (Fig 3): 34 and 23 of the
morphological species were detected in the bulk DNA and in the eDNA from
the ethanol preservative, respectively. All primer sets missed a
substantial portion of the morphologically identified species: 21, 34,
33, 40 and 25 species of the 57 morphological species were only found in
the morphological dataset, for primer sets A, B, C, D and E respectively
(Fig 3). The number of morphological species detected in the bulk DNA
samples (34, 23, 24, 17 and 28 for primer sets A, B, C, D and E
respectively) was substantially higher than the number of morphological
species detected in the eDNA samples from the ethanol preservative (23,
7, 9, 3 and 22 for primer sets A, B, C, D and E, respectively). Primer
sets A and E clearly outperformed the detection of the morphological
species in the eDNA from the ethanol preservative.