Improved biodiversity detection using a large-volume environmental DNA sampler with in situ filtration and implications for marine eDNA sampling strategies

Metabarcoding analysis of environmental DNA samples is a promising new
tool for marine biodiversity and conservation. Typically, seawater samples
are obtained using Niskin bottles and filtered to collect eDNA. However,
standard sample volumes are small relative to the scale of the
environment, conventional collection strategies are limited, and the
filtration process is time consuming. To overcome these limitations, we
developed a new large – volume eDNA sampler with in situ filtration,
capable of taking up to 12 samples per deployment. We conducted three
deployments of our sampler on the robotic vehicle Mesobot in the Flower
Garden Banks National Marine Sanctuary in the northwestern Gulf of Mexico
and collected samples from 20 to 400 m depth. We compared the large volume
(~40 – 60 liters) samples collected by Mesobot with small volume (~2
liters) samples collected using the conventional CTD rosette – mounted
Niskin bottle approach. We sequenced the V9 region of 18S rRNA, which
detects a broad range of invertebrate taxa, and found that while both
methods detected biodiversity changes associated with depth, our large
volume samples detected approximately 66% more taxa than the CTD small
volume samples. We found that the fraction of the eDNA signal originating
from metazoans relative to the total eDNA signal decreased with sampling
depth, indicating that larger volume samples may be especially important
for detecting metazoans in mesopelagic and deep ocean environments. We
also noted substantial variability in biological replicates from both the
large volume Mesobot and small volume CTD sample sets. Both of the sample
sets also identified taxa that the other did not – although the number of
unique taxa associated with the Mesobot samples was almost four times
larger than those from the CTD samples. Large volume eDNA sampling with in
situ filtration, particularly when coupled with robotic platforms, has
great potential for marine biodiversity surveys, and we discuss practical
methodological and sampling considerations for future applications.