Ferries and Environmental DNA: Underway Sampling From Commercial Vessels Provides New Opportunities for Systematic Genetic Surveys of Marine Biodiversity

Abstract

Marine environmental DNA (eDNA) is an important tool for biodiversity research and monitoring but challenges remain in scaling surveys over large spatial areas, and increasing the frequency of sampling in remote locations at reasonable cost. Here we demonstrate the feasibility of sampling from commercial vessels (Mediterranean ferries) while underway, as a strategy to facilitate replicable, systematic marine eDNA surveys in locations that would normally be challenging and expensive for researchers to access. Sixteen eDNA samples were collected from four fixed sampling stations, and in response to four cetacean sightings, across three cruises undertaken along the 300 km ferry route between Livorno (Tuscany) and Golfo Aranci (Sardinia) in the Ligurian/Tyrrhenian Seas, June-July 2018. Using 12SrDNA and 16SrDNA metabarcoding markers, we recovered diverse marine vertebrate Molecular Operational Taxonomic Units (MOTUs) from teleost fish, elasmobranchs, and cetaceans. We detected sample heterogeneity consistent with previously known variation in species occurrences, including putative species spawning peaks associated with specific sea surface temperature ranges, and increased night time abundance of bathypelagic species known to undertake diel migrations through the water column. We suggest commercial vessel based marine eDNA sampling using the global shipping network has potential to facilitate broad-scale biodiversity monitoring in the world’s oceans.

Using Environmental DNA to Detect Whales and Dolphins in the New York Bight

“…To this end, we encourage the cetacean research community to develop a research agenda that takes advantage of ongoing visual and acoustic survey work around the world, targeting a diversity of species and conditions. While there are still important challenges to be addressed regarding how to implement eDNA surveys for marine mammals across very large geographic regions, possible solutions include sampling from commercial vessels (e.g., ferries; Valsecchi et al, 2021), as part of large-scale marine biodiversity surveys (Closek et al, 2019) or using autonomous underwater vehicles or stationary monitoring devices (Yamahara et al, 2019;Hansen et al, 2020). Given the scale of renewable energy development on both coasts of the US, eDNA could contribute to a range of monitoring efforts.…”

A species-specific qPCR assay provides novel insight into range expansion of the Mediterranean monk seal (Monachus monachus) by means of eDNA analysis

“…The expected-positive eDNA control samples were not only used to assess the detection capability of the assays developed (quality control) but also, as term of comparison of the intensity of the molecular signal (quantitative control) when evaluating surveillance eDNA samples. We also tested the molecular assays on two Mediterranean marine eDNA samples (Categories 4 and 5), collected as part of previous (Valsecchi et al 2021) and ongoing projects, from areas where monk seals are considered to be extremely rare but not impossible to be found, as suggested by a few recent sightings (Supplementary Figure S1) some of which were proximal to our sampling sites, but the eDNA samples had been collected month to years previously. For each sampling event, sampling time was recorded (Supplementary Table S1): 20 (41.7%) out of 48 samples were collected during night-time.…”

“…Category 5 Mediterranean offshore eDNA samples. These samples were collected in the summers of 2018 (n = 16) and 2019 (n = 20) from the Northern Tyrrhenian Sea as part of an ongoing project ("MeD for Med") from marine water samples collected from operating ferries (Valsecchi et al 2021). The route surveyed was the Livorno-Golfo Aranci run by Corsica Sardinia Ferries.…”

“…For each sampling station 8-12 L of seawater were collected and stored in the Bag-in-Box Sampling System (BiBSS: Valsecchi et al 2021). Once in the laboratory (or on board the ferry for Category 5 samples), the contents of the water bags were aliquoted and filtered through 3 cellulose nitrate membranes using the Sartorius Monitor Biosart™ 100, thereby us producing 3 sample replicates for each eDNA sample collected (filters A, B and C).…”

“…Secondly, failing to amplify DNA in replicates of a positive sample may be due to the extremely low concentration of the target molecule. Some studies suggest that marine vertebrate DNA accounts for only 0.004% of the eDNA retrieved from marine samples (Stat et al 2017) and, although metabarcode vs barcode data are difficult to compare, it is noteworthy that in a DNA metabarcoding analysis on a subset of the same ferry samples (only from 2018), using the MarVer1 and MarVer3 universal primer pairs, over 90% of the reads were attributed to bony fish and no reads were attributed to the monk seal (Valsecchi et al 2021). Indeed, this figure decreased more than one order of magnitude when considering the incidence of rare vertebrates like marine mammals.…”