Marine water environmental DNA metabarcoding provides a comprehensive fish diversity assessment and reveals spatial patterns in a large oceanic area

Fraija-Fernández, Natalia; Bouquieaux, Marie-Catherine; Rey, Anaïs; Mendibil, Iñaki; Cotano, Unai; Irigoien, Xabier; Santos, M.B.; Rodríguez-Ezpeleta, Naiara

doi:10.1101/864710

Cited by 19 publications

(35 citation statements)

References 67 publications

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“…Noticeable heterogeneity was observed among sites, and temporal samples at the same location, despite the study covering a relatively small geographic area (approximately 300 km transect length), and close sampling time intervals (3 collections spaced 15 days apart in June-July). Consistent with a previous study in the Bay of Biscay, (Fraija□Fernández et al, 2020), reads from anchovy ( Engraulis sp.) and sardine ( Sardina sp.)…”

Section: Discussionsupporting

confidence: 91%

Ferries and environmental DNA: underway sampling from commercial vessels provides new opportunities for systematic genetic surveys of marine biodiversity

Valsecchi

Arcangeli

Lombardi

et al. 2021

Preprint

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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 4 fixed sampling stations, and in response to 4 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 oceans.

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Section: Discussionsupporting

confidence: 91%

Ferries and environmental DNA: underway sampling from commercial vessels provides new opportunities for systematic genetic surveys of marine biodiversity

Valsecchi

Arcangeli

Lombardi

et al. 2021

Preprint

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“…Laboratory and bioinformatic analysis procedures for eDNA metabarcoding were performed as described in Fraija-Fernández et al (2020) and are detailed in Supplementary Information.…”

Section: Dna Extraction and Metabarcodingmentioning

confidence: 99%

“…Notwithstanding, applying eDNA metabarcoding still offers remarkable advantages for the study of deep-sea ecosystems: it surpasses the depth-related orographic limitations imposed to trawling, and provides i) a higher diversity detection capability (Fraija-Fernández et al 2020;Stoeckle et al 2020), facilitating the monitoring of threatened, invasive, elusive, and rare species (Jerde 2019;Bani et al 2020) -for instance, we detected here 6 fish species considered at least as vulnerable by the International Union for Conservation of Nature (IUCN ; Table S3)-, ii) a lower dependency on taxonomic expertise (Hansen et al 2018), iii) a reduction in costs (Jerde 2019;Bani et al 2020), and iv) a minimum habitat destruction and organism disturbance (Valentini et al 2016;Bani et al 2020).…”

Section: Considerations For Edna-based Studies In Oceanic Vertical Prmentioning

confidence: 99%

Vertical stratification of environmental DNA in the open ocean captures ecological patterns and behavior of deep-sea fishes

Canals

Mendibil

Santos

et al. 2021

Preprint

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The deep-sea remains among the most unknown ecosystems on Earth despite its relevant role in carbon sequestration and increasing threat due to interest by fishing and mining industries. This, together with the recent discovery that the upper layer of this ecosystem (mesopelagic zone) harbors about 90% of the fish biomass on Earth, claims for a deeper understanding of the deep-sea so that the foundations for a sustainable use of its resources can be established. The analysis of environmental DNA (eDNA) collected from the water column emerges as an alternative to traditional methods to acquire this elusive information, but its application to the deep ocean is still incipient. Here, we have amplified and sequenced the fish eDNA contained in vertical profile samples (from surface to 2000 m depth) collected during day and night-time throughout the Bay of Biscay. We found that eDNA-derived deep-sea fish richness and abundance follow a day-night pattern that is consistent with the diel migratory behavior of many mesopelagic species, and that eDNA can reveal species-specific distribution and movement through the water column. These results highlight the potential of eDNA-based studies to improve our knowledge on the species inhabiting the dark ocean before this still pristine ecosystem is exploited.

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“…Furthermore, eDNA‐derived compositional data can provide greater biological coverage to distinguish spatial and habitat variation, identify network associations, trophic structure, biological invasions and the presence of critically endangered species (Valentini et al., 2016). Whilst eDNA metabarcoding has demonstrated its applicability across small, yet highly sensitive, spatial (Jeunen et al., 2019; O’Donnell et al., 2017; Port et al., 2016; West et al., 2020) and temporal scales (Berry et al., 2019) in marine ecosystems, it is in a preliminary stage of being scaled up and tested across broader regional scales (Aglieri et al., 2020; Fraija‐Fernández et al., 2020).…”

Section: Introductionmentioning

confidence: 99%

Large‐scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north‐western Australia

West

Travers

Stat

et al. 2021

Diversity and Distributions

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Aim Environmental DNA (eDNA) metabarcoding has demonstrated its applicability as a highly sensitive biomonitoring tool across small spatial and temporal scales in marine ecosystems. However, it has rarely been tested across large spatial scales or biogeographical barriers. Here, we scale up marine eDNA metabarcoding, test its ability to detect a major marine biogeographic break and evaluate its use as a regional biomonitoring tool in Australia. Location North‐western Australia (NWA). Methods We applied metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes to 284 surface seawater eDNA samples collected from 71 mid‐shelf, inshore, coastal and nearshore estuarine sites over 700 km of the NWA coastline. Results Metabarcoding detected a wide range of bony fish (404 taxa), elasmobranchs (44) and aquatic reptiles (5). We detected bioregional and depth differentiation within inshore bony fish communities. These findings support the presence of a marine biogeographic break, which is purported to occur in the vicinity of Cape Leveque, demarcating the border between the Kimberley and Canning bioregions. Inshore bony fish and elasmobranch communities, as well as coastal bony fish assemblages, were additionally found to differ between the South and North Kimberley regions suggesting previously unrecognized subregional differentiation amongst these taxa. The overall compositional data have been used to update distribution information for a number of endangered, elusive and data‐deficient taxa, including sawfish (family: Pristidae), northern river shark (Glyphis garricki) and wedgefish (genus: Rhynchobatus). Main conclusions eDNA metabarcoding demonstrated a high level of sensitivity that was able to discern fine‐scale patterns across the large‐scale, remote and oceanographically complex region of North‐western Australia. Importantly, this study highlights the potential of integrating broad‐scale eDNA metabarcoding alongside other baseline surveys and long‐term monitoring approaches, which are crucial for the sustainable management and conservation of marine biodiversity in this unique marine region.

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Marine water environmental DNA metabarcoding provides a comprehensive fish diversity assessment and reveals spatial patterns in a large oceanic area

Abstract: 0Current methods for monitoring marine fish diversity mostly rely on trawling surveys, 1 1 which are invasive, costly and time-consuming. Moreover, these methods are selective,

Cited by 19 publications

References 67 publications

Ferries and environmental DNA: underway sampling from commercial vessels provides new opportunities for systematic genetic surveys of marine biodiversity

Ferries and environmental DNA: underway sampling from commercial vessels provides new opportunities for systematic genetic surveys of marine biodiversity

Vertical stratification of environmental DNA in the open ocean captures ecological patterns and behavior of deep-sea fishes

Large‐scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north‐western Australia

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