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

Elena Valsecchi,Simon J Goodman,Roberto Lombardi,Paolo Galli,Ian M Carr,Elizabeth Boyse,Antonella Arcangeli

doi:10.3389/fmars.2021.704786

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.

Highlights

Environmental DNA is an important tool to support biodiversity research and monitoring but challenges remain on how to scale eDNA surveys for assessments over large spatial areas, and to make it feasible to increase the frequency of sampling in remote locations at reasonable cost (Pawlowski et al, 2018)
Scaling marine eDNA studies to support surveys over large spatial scales, or increasing the temporal frequency of sampling efforts is limited by logistical and financial constraints arising from the high costs and access to survey vessels for use offshore (Bani et al, 2020; Sigsgaard et al, 2020)
In principle this allows for transect based study designs, and facilitates temporal comparisons ranging from days to seasons and years for specific locations; (3) Easy diurnal sampling: commercial vessel scheduling allows for routine operation at night, which may not be feasible for smaller port-based research vessels that have operating restrictions during hours of darkness; (4) Synchronicity: different routes can be surveyed concurrently, allowing co-ordinated simultaneous sampling over ocean basins; (5) Linear sampling: sampling from vessels allows collection of eDNA over tracks of 3–4 km, which may be advantageous for some applications, by increasing the amount and diversity of eDNA recovered; (6) “Emission

Summary

Introduction

Environmental DNA (eDNA) is an important tool to support biodiversity research and monitoring but challenges remain on how to scale eDNA surveys for assessments over large spatial areas, and to make it feasible to increase the frequency of sampling in remote locations at reasonable cost (Pawlowski et al, 2018). Developing strategies to facilitate sampling in offshore pelagic environments could enhance the contribution of eDNA to large scale marine biodiversity surveys This is important for marine megafauna, where large distributions and dispersal capabilities of species mean that such taxa may have partial, low-resolution coverage from conventional techniques, while being a high priority for conservation planning due to their vulnerability and exposure to anthropogenic pressures (Hooker et al, 2011). Developing metabarcoding approaches to reliably detect marine mammal eDNA in assays targeting marine vertebrates communities would increase efficiency and the scaling up of ecosystem level surveys and monitoring (Foote et al, 2012; Baker et al, 2018; Székely et al, 2021)

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