DNA metabarcoding of trawling bycatch reveals diversity and distribution patterns of sharks and rays in the central Tyrrhenian Sea

Author:

Albonetti Linda12,Maiello Giulia34ORCID,Cariani Alessia1ORCID,Carpentieri Paolo5,Ferrari Alice1,Sbrana Alice24ORCID,Shum Peter6,Talarico Lorenzo27,Russo Tommaso2,Mariani Stefano6

Affiliation:

1. Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna , Via Sant’Alberto 163, 48123 Ravenna , Italy

2. CESTHA, Experimental Centre for Habitat Conservation , 48122, marina di Ravenna , Italy

3. Department of Biology, University of Rome Tor Vergata , Via della Ricerca Scientifica 1, 00133 Rome , Italy

4. PhD Program in Evolutionary Biology and Ecology, University of Rome Tor Vergata , Via della Ricerca Scientifica 1, 00133 Rome , Italy

5. General Fisheries Commission for the Mediterranean (GFCM)—Food and Agriculture Organization of the United Nations , 00193, Rome , Italy

6. School of Biological and Environmental Sciences, Liverpool John Moores University , L33AF, Liverpool , UK

7. Italian National Institute for Environmental Protection and Research (ISPRA) , 00144, Rome , Italy

Abstract

AbstractConservation and management of chondrichthyans are becoming increasingly important, as many species are particularly vulnerable to fishing activities, primarily as bycatch, which leads to incomplete catch reporting, potentially hiding the impact on these organisms. Here, we aimed at implementing an eDNA metabarcoding approach to reconstruct shark and ray bycatch composition from 24 hauls of a bottom trawl fishing vessel in the central Mediterranean. eDNA samples were collected through the passive filtration of seawater by simple gauze rolls encapsulated in a probe (the “metaprobe”), which already showed great efficiency in detecting marine species from trace DNA in the environment. To improve molecular taxonomic detection, we enhanced the 12S target marker reference library by generating sequences for 14 Mediterranean chondrichthyans previously unrepresented in public repositories. DNA metabarcoding data correctly identifies almost all bycaught species and detected five additional species not present in the net, highlighting the potential of this method to detect rare species. Chondrichthyan diversity showed significant association with some key environmental variables (depth and distance from the coast) and the fishing effort, which are known to influence demersal communities. As DNA metabarcoding progressively positions itself as a staple tool for biodiversity monitoring, we expect that its melding with opportunistic, fishery-dependent surveys could reveal additional distribution features of threatened and elusive megafauna.

Funder

Food and Agriculture Organization of the United Nations

Natural Environment Research Council

Publisher

Oxford University Press (OUP)

Subject

Ecology,Aquatic Science,Ecology, Evolution, Behavior and Systematics,Oceanography

Reference70 articles.

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