Fish eDNA detections in ports mirror fishing fleet activities and highlight the spread of non-indigenous species in the Mediterranean Sea

Aglieri, Giorgio; Quattrocchi, Federico; Mariani, Stefano; Baillie, Charles; Spatafora, Davide; Franco, Antonio; Turco, Gabriele; Tolone, Marco; Gerlando, Rosalia Di; Milazzo, Marco

doi:10.1016/j.marpolbul.2023.114792

Cited by 6 publications

(9 citation statements)

References 79 publications

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“…Among the 150 animal NIS recorded in the French Mediterranean waters (Massé et al., 2023), only 19 are present in our metazoa reference database. With a better taxonomic resolution, we would be able to better assign MOTU to NIS, an important issue here since seaports are recognized as primary steppingstones for NIS introductions and spread (Aglieri et al., 2023; Andrés et al., 2023; Darling et al., 2020; Rey et al., 2020), recreational shipping seaports included (Ferrario et al., 2017; Ulman et al., 2017). To address these limits, it is essential to complete genetic reference databases.…”

Section: Discussionmentioning

confidence: 99%

“…However, artificial structures may also act as corridors for opportunistic species offering new dispersal pathways for previously separated populations to extend their distribution and facilitate gene flow (Alter et al., 2021; Sammarco et al., 2004; Touchard et al., 2023). Additionally, seaports are stepping stones for non‐indigenous species (NIS) introductions and expansions, spreading from one seaport to another (Aglieri et al., 2023; Andrés et al., 2023; Darling et al., 2020; Rey et al., 2020).…”

Section: Introductionmentioning

confidence: 99%

“…This deficit of biomonitoring may partly come from the inherent difficulty to sample or detect species in seaports given regulations and water turbidity preventing both fishing and visual surveys. As an alternative, environmental DNA (eDNA) metabarcoding has the potential to bypass accessibility and visibility issues (Cheang et al., 2020; Ip et al., 2021; Sigsgaard et al., 2016) and is a promising tool to monitor seaport biodiversity (Aglieri et al., 2023; Rey et al., 2020). Defined as free or adsorbed DNA molecules released by organisms, eDNA can be extracted from environmental samples and then sequenced with appropriate markers (Miya, 2022; Taberlet et al., 2012).…”

Section: Introductionmentioning

confidence: 99%

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The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves

Macé,

Mouillot,

Dalongeville

et al. 2024

Molecular Ecology

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Coastal areas host a major part of marine biodiversity but are seriously threatened by ever‐increasing human pressures. Transforming natural coastlines into urban seascapes through habitat artificialization may result in loss of biodiversity and key ecosystem functions. Yet, the extent to which seaports differ from nearby natural habitats and marine reserves across the whole Tree of Life is still unknown. This study aimed to assess the level of α and β‐diversity between seaports and reserves, and whether these biodiversity patterns are conserved across taxa and evolutionary lineages. For that, we used environmental DNA (eDNA) metabarcoding to survey six seaports on the French Mediterranean coast and four strictly no‐take marine reserves nearby. By targeting four different groups—prokaryotes, eukaryotes, metazoans and fish—with appropriate markers, we provide a holistic view of biodiversity on contrasted habitats. In the absence of comprehensive reference databases, we used bioinformatic pipelines to gather similar sequences into molecular operational taxonomic units (MOTUs). In contrast to our expectations, we obtained no difference in MOTU richness (α‐diversity) between habitats except for prokaryotes and threatened fishes with higher diversity in reserves than in seaports. However, we observed a marked dissimilarity (β‐diversity) between seaports and reserves for all taxa. Surprisingly, this biodiversity signature of seaports was preserved across the Tree of Life, up to the order. This result reveals that seaports and nearby marine reserves share few taxa and evolutionary lineages along urbanized coasts and suggests major differences in terms of ecosystem functioning between both habitats.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves

Macé,

Mouillot,

Dalongeville

et al. 2024

Molecular Ecology

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“…In this study, following evidence obtained from a wider survey focused on elasmobranchs' catches by fishers in the Central Mediterranean Sea, we combined Local Expert Knowledge (LEK), Baited Underwater Video systems (BRUVs), and opportunistic catch reports (OCR) by longliners to identify important areas for early life stages of the Shortfin Mako in the Pelagie archipelago, a recognized hotspot for threatened shark species (Cattano et al, 2021;2023) and one of the most fishery exploited areas in the Mediterranean (Jarboui et al…”

Section: Introductionmentioning

confidence: 99%

“…The use of non-extractive sampling methods, such as Baited Remote Underwater Video or eDNA surveys (e.g. Aglieri et al 2021Aglieri et al , 2023Cattano et al 2021), should be promoted especially in studies focusing on species at risk of extinction, such as many pelagic shark species. This aspect is of particular importance since the shortfin mako is included in different international conventions and recommendations implemented by the General Fishery Commission for the Mediterranean (GFCM) and European Union (EU) that include a ban on targeted fishing and landings.…”

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confidence: 99%

Multiple interannual records of young-of-the-year identify an important area for the protection of the shortfin mako, Isurus oxyrinchus

Cattano,

Gambardella,

Grancagnolo

et al. 2023

Marine Environmental Research

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Nanopore environmental DNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries

Maggini,

Jacobsen,

Urban

et al. 2024

Environmental DNA

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Bycatch and discards, representing unwanted catches, undermine sustainable fisheries and hinder the conservation of vulnerable and endangered species. To effectively monitor bycatch and enhance the effectiveness of management measures while promoting sustainable fishing practices, reliable data is essential. Here, we explore the use of Nanopore metabarcoding to analyze the catch composition in demersal bottom fisheries. We collected eDNA samples directly from an onboard catch holding tank (catch water) for 10 fishing hauls from a fishing vessel operating in the Skagerrak (North‐East Atlantic). The approach involved sequencing a combination of long (~2 kb) and short (~170–313 bp) mitochondrial amplicons and was validated by analyzing a fishery‐related mock community sample and fishing haul replicates. Overall, the detection rate accuracy was 95% for landed species, and replicates obtained from the same fishing haul showed consistent results, validating the robustness of this approach. The detection rate accuracy for all caught species observed on board (including the non‐landed fraction) was 81%. Undetected species were always limited to species in low abundance, but may also be attributed to problems with identifying closely related species due to the impact of sequencing errors and limited diagnostic variation in the genetic regions used. In the future, such biases may be reduced by using additional markers to increase species discrimination power and applying newly available technological advantages in flow cell chemistry to improve sequencing accuracy. In conclusion, this study demonstrates the effectiveness of Nanopore eDNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries, including catches of non‐commercial and threatened and vulnerable species, without disrupting fishing activities. Incorporating eDNA analysis of catch water may therefore help facilitate effective monitoring, leading to better‐informed fisheries management, biodiversity conservation efforts, and the implementation of relevant legislation such as the EU landing obligation.

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Fish eDNA detections in ports mirror fishing fleet activities and highlight the spread of non-indigenous species in the Mediterranean Sea

Cited by 6 publications

References 79 publications

The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves

The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves

Multiple interannual records of young-of-the-year identify an important area for the protection of the shortfin mako, Isurus oxyrinchus

Nanopore environmental DNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries

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