Opportunistic diver-assisted eDNA sampling unpicks fine-scale ecological and conservation signals in tropical reef fishes

Maiello, G, Burgos-Rubio, V, Allen, L, Neave, EF, Bonne, R, Theresine, P and Mariani, S ORCID: 0000-0002-5329-0553 (2025) Opportunistic diver-assisted eDNA sampling unpicks fine-scale ecological and conservation signals in tropical reef fishes. Global Ecology and Conservation, 62. ISSN 2351-9894

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Abstract

Coral reefs are emblematic ecosystems of astonishing biological diversity and significant economic value for many countries, yet they are increasingly vulnerable to direct and indirect human-related threats, such as heavy tourism and global warming. To assess the biodiversity status, track assemblage changes and forecast future trends of these megadiverse ecosystems, there is pressing need for accurate, rapid and comprehensive assessments of fish communities. Here, we employed a versatile low-tech passive environmental DNA collector, the ‘metaprobe’, in association with the recreational activity of SCUBA divers to collect eDNA data from reefs in the Seychelles archipelago and assess both the taxonomic and functional fish diversity of the area. Using a fish-specific 12S marker on eDNA metaprobe samples collected during 18 dives, we detected 174 fish taxa (eight elasmobranchs and 166 teleosts), corresponding to 112 unique functional entities and including iconic tropical reef taxa, endangered elasmobranchs and commercially valuable species. Despite the geographic proximity of dive sites, we identified ecological patterns of fish composition and community structure influenced by both the presence of marine protected areas (MPAs) and the type of predominant substrate (i.e., coral vs rocky). Ecological differences between MPA/non-MPA and coral/rocky habitats involved both taxonomic and functional fish community elements. In both cases, protected areas and coral habitats consistently exhibited significantly higher fish diversity. We argue that simple, inexpensive eDNA-based collection tools in association with recreational activities, such as SCUBA diving, provide a promising approach for upscaling ecological data collection and expanding biodiversity monitoring, while engaging and empowering the public.

Item Type:	Article
Uncontrolled Keywords:	Environmental DNA; Coral reefs; Functional ecology; Marine protected areas; Fish communities; 4101 Climate Change Impacts and Adaptation; 31 Biological Sciences; 3103 Ecology; 4104 Environmental Management; 41 Environmental Sciences; 15 Life on Land; 14 Life Below Water; 0502 Environmental Science and Management; 0602 Ecology; 3103 Ecology; 4104 Environmental management
Subjects:	Q Science > QH Natural history > QH301 Biology Q Science > QL Zoology
Divisions:	Biological and Environmental Sciences (from Sep 19)
Publisher:	Elsevier
Date of acceptance:	11 September 2025
Date of first compliant Open Access:	10 June 2026
Date Deposited:	10 Jun 2026 12:54
Last Modified:	10 Jun 2026 12:54
DOI or ID number:	10.1016/j.gecco.2025.e03850
URI:	https://researchonline.ljmu.ac.uk/id/eprint/28801

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