Little samplers, big fleet: eDNA metabarcoding from commercial trawlers enhances ocean monitoring

Maiello, Giulia; Talarico, Lorenzo; Carpentieri, Paolo; Angelis, Flavio De; Franceschini, Simone; Harper, Lynsey R.; Neave, Erika F.; Rickards, Olga; Sbrana, Alice; Shum, Peter; Veltre, Virginia; Mariani, Stefano; Russo, Tommaso

doi:10.1016/j.fishres.2022.106259

Cited by 37 publications

(34 citation statements)

References 37 publications

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“…Like in other eDNA studies metabarcoding fish diversity in the Mediterranean Sea by using Tele02 primers (Aglieri et al, 2021;Maiello et al, 2022), a high number of taxa was detected, and an elevated taxonomic resolution was achieved. In addition to bony fishes, three species of cartilaginous fishes were identified, indicating the applicability of this marker to simultaneously detect Actinopterygii and Chondrichthyes.…”

Section: Discussionmentioning

confidence: 60%

Environmental DNA metabarcoding reveals spatial and seasonal patterns in the fish community in the Venice Lagoon

et al. 2022

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Environmental DNA (eDNA) is an emerging tool for assessing biodiversity and understanding spatial and temporal community patterns and processes, directly from DNA sequencing of environmental samples such as air, water, and sediments. We applied eDNA methods to monitor bony fish communities, detecting as well locally allochthonous species, and to reveal seasonal patterns at two sites in the Venice Lagoon. We analyzed 17 water samples collected over 12 months at two ecologically distinct sites by using available primers for teleosts and High Throughput Illumina sequencing. We identified 1,289 amplicon sequence variants (ASVs) assigned to 62 fish taxa. Most of the species known to inhabit or to enter the Venice Lagoon were detected, with eDNA data reflecting differences in fish communities between the internal (freshwater associated) and the external (sea associated) part of the lagoon. Moreover, seasonal trends of migration have been portrayed, highlighting the most involved species and disclosing possible clashes between migration events and the temporary interruption of sea-lagoon connectivity due to MOSE (MOdulo Sperimentale Elettromeccanico). Of interest, the first-time detection of Oceanic puffer (Lagocephalus lagocephalus) DNA in the Venice Lagoon provides evidence of the further northward expansion of this species in the high Adriatic Sea. eDNA successfully profiled fish communities by season and habitat in the Venice Lagoon. Our results support routine application of eDNA to monitor potential ecological consequences of MOSE closures in this World Heritage site.

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Section: Discussionmentioning

confidence: 60%

Environmental DNA metabarcoding reveals spatial and seasonal patterns in the fish community in the Venice Lagoon

et al. 2022

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“…Using eDNA, we confirmed the detection of all fish species that were housed in the aquarium, but also obtained sequences from six fish that were not present in the mesocosm. Such observations are not unusual for eDNA studies (see Maiello et al, 2022) as sensitive eDNA assays can also capture ‘legacy’ signal from external sources; here, most likely, from the untreated marine inflow water (Nguyen et al, 2020), as all six fishes are common occurrences in the Otago Harbour. Interestingly, between all treatments, the visually most abundant and active fish ( Latris lineata ) was detected in only 3 of the overall 60 samples.…”

Section: Discussionmentioning

confidence: 94%

“…This study explored the application of passive eDNA capture (Bessey, Gao, et al, 2022; Bessey, Neil Jarman, et al, 2021; Kirtane et al, 2020; Maiello et al, 2022; Verdier et al, 2021) using a range of sampling substrates. In addition, we combined our tests of passive samplers with a novel in‐field nucleic acid extraction technology, the PDQeX extractor (Boykin et al, 2019; Stanton et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

“…Kirtane et al (2020) found that bigger pore sizes increase absorbency and therefore enhance eDNA capture. Maiello et al (2022) successfully investigated a similar adsorbing material in the form of simple and low‐cost rolls of gauze encapsulated in hollow perforated spherical probes designed to be dragged during deep sea trawling. Our net substrate, originally used to attach the passive samplers to the frame, detected the largest numbers of overall taxa compared to all other treatments, most likely due to its rough texture.…”

Section: Discussionmentioning

confidence: 99%

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Moving environmental DNA (eDNA) technologies from benchtop to the field using passive sampling and PDQeX extraction

et al. 2022

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Environmental DNA (eDNA) metabarcoding has shown great promise as an effective, non‐invasive monitoring method for marine biomes. However, long filtration times and the need for state‐of‐the‐art laboratories are restricting sample replication and in situ species detections. Methodological innovations, such as passive filtration and self‐contained DNA extraction protocols, have the potential to alleviate these issues. We explored the implementation of passive sampling and a self‐contained DNA extraction protocol by comparing fish diversity obtained from active filtration (1 L; 0.45 μm cellulose nitrate [CN] filters) to five passive substrates, including 0.45 μm CN filters, 5 μm nylon filters, 0.45 μm positively charged nylon filters, artificial sponges, and fishing net. Fish diversity was then compared between the PDQeX Nucleic Acid Extractor and the conventional Qiagen DNeasy Blood & Tissue protocol. Experiments were conducted in both a controlled mesocosm and in situ at the Portobello Marine Laboratory, New Zealand. No significant differences in fish diversity were observed among active filtration and more porous passive materials (artificial sponges and fishing net) for both the mesocosm and harbor waters. For the in situ comparison, all passive filter membranes detected a significantly lower number of fish species, resulting from partial sample drop‐out. While no significant differences in fish eDNA signal diversity were observed between either DNA extraction methods in the mesocosm, the PDQeX system was less effective at detecting fish for the in situ comparison. Our results demonstrate that a passive sampling approach using porous substrates can be effectively implemented to capture eDNA from seawater, eliminating vacuum filtration processing. The large variation in efficiency observed among the five substrate types, however, warrants further optimization of the passive sampling approach for routine eDNA applications. The PDQeX system can extract high‐abundance DNA in a mesocosm with further optimization to detect low‐abundance eDNA from the marine environment.

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“…With the impossibility to sample individuals from SPSPA, metabarcoding emerges as the solution to survey and monitor SPSPA fish diversity. This approach is becoming a well-established tool for monitoring fishes not only from water samples ( Miya, 2022 ), but also from various types of samples such as air ( Lynggaard et al, 2022 ), sediment ( Ip et al, 2021 ), bottom trawl fishing vessels ( Maiello et al, 2022 ), and feces ( Creer et al, 2016 ; Jarman et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Saint Peter and Saint Paul Archipelago barcoded: Fish diversity in the remoteness and DNA barcodes reference library for metabarcoding monitoring

2022

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In order to monitor the effects of anthropogenic pressures in ecosystems, molecular techniques can be used to characterize species composition. Among molecular markers capable of identifying species, the cytochrome c oxidase I ( COI ) is the most used. However, new possibilities of biodiversity profiling have become possible, in which molecular fragments of medium and short-length can now be analyzed in metabarcoding studies. Here, a survey of fishes from the Saint Peter and Saint Paul Archipelago was barcoded using the COI marker, which allowed the identification of 21 species. This paved the way to further investigate the fish biodiversity of the archipelago, transitioning from barcoding to metabarcoding analysis. As preparatory steps for future metabarcoding studies, the first extensive COI library of fishes listed for these islands was constructed and includes new data generated in this survey as well as previously available data, resulting in a final database with 9,183 sequences from 169 species and 63 families of fish. A new primer specifically designed for those fishes was tested in silico to amplify a region of 262 bp. The new approach should guarantee a reliable surveillance of the archipelago and can be used to generate policies that will enhance the archipelago’s protection.

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Little samplers, big fleet: eDNA metabarcoding from commercial trawlers enhances ocean monitoring

Cited by 37 publications

References 37 publications

Environmental DNA metabarcoding reveals spatial and seasonal patterns in the fish community in the Venice Lagoon

Environmental DNA metabarcoding reveals spatial and seasonal patterns in the fish community in the Venice Lagoon

Moving environmental DNA (eDNA) technologies from benchtop to the field using passive sampling and PDQeX extraction

Saint Peter and Saint Paul Archipelago barcoded: Fish diversity in the remoteness and DNA barcodes reference library for metabarcoding monitoring

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