Environmental DNA illuminates the dark diversity of sharks

Boussarie, Germain; Bakker, Judith; Wangensteen, Owen S.; Mariani, Stefano; Bonnin, Lucas; Juhel, Jean‐Baptiste; Kiszka, Jérémy J.; Kulbicki, Michel; Manel, Stéphanie; Robbins, William D.; Vigliola, Laurent; Mouillot, David

doi:10.1126/sciadv.aap9661

Cited by 251 publications

(227 citation statements)

References 55 publications

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“…Nonetheless, the Leray‐XT primer set was capable of detecting 54 teleost and 6 elasmobranch species. The use of a combination of multiple metabarcoding markers is essential to guarantee sufficient sequencing depth for capturing all the main components of eukaryotic diversity, including the better known metazoans groups upon which most conservation initiatives are based (Boussarie et al, ). Of course, the use of a single marker will significantly reduce operational costs, but a universal COI approach from aqueous eDNA samples, in the fashion of what is presented here, will always inevitably emphasize the micro‐eukaryotic component.…”

Section: Discussionmentioning

confidence: 99%

“…There are many potential benefits that whole‐community metabarcoding of eukaryotic marine eDNA, using multiple or even single‐assay approaches, could bring to biodiversity assessment and monitoring, such as using direct measurements of biodiversity, instead of relying on biodiversity indicators (Aylagas, Borja, Irigoien, & Rodríguez‐Ezpeleta, ; Djurhuus et al, ; Lindenmayer & Likens, ; Rees, Maddison, Middleditch, Patmore, & Gough, ). Environmental DNA analysis can also be used for the detection of “hidden diversity,” without a priori knowledge of the composition of species assemblages in a particular water body (Boussarie et al, ; Lindeque, Parry, Harmer, Somerfield, & Atkinson, ). As such, eDNA can be a powerful tool in the early detection of alien species (Zaiko, Samuiloviene, Ardura, & Garcia‐Vazquez, ) and of community changes in response to environmental disturbances or regime shifts (Bik, Halanych, Sharma, & Thomas, ; Bucklin, Lindeque, Rodriguez‐Ezpeleta, Albaina, & Lehtiniemi, ).…”

Section: Introductionmentioning

confidence: 99%

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Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

Bakker

Wangensteen

Baillie

et al. 2019

Ecology and Evolution

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Our understanding of marine communities and their functions in an ecosystem relies on the ability to detect and monitor species distributions and abundances. Currently, the use of environmental DNA (eDNA) metabarcoding is increasingly being applied for the rapid assessment and monitoring of aquatic species. Most eDNA metabarcoding studies have either focussed on the simultaneous identification of a few specific taxa/groups or have been limited in geographical scope. Here, we employed eDNA metabarcoding to compare beta diversity patterns of complex pelagic marine communities in tropical coastal shelf habitats spanning the whole Caribbean Sea. We screened 68 water samples using a universal eukaryotic COI barcode region and detected highly diverse communities, which varied significantly among locations, and proved good descriptors of habitat type and environmental conditions. Less than 15% of eukaryotic taxa were assigned to metazoans, most DNA sequences belonged to a variety of planktonic “protists,” with over 50% of taxa unassigned at the phylum level, suggesting that the sampled communities host an astonishing amount of micro‐eukaryotic diversity yet undescribed or absent from COI reference databases. Although such a predominance of micro‐eukaryotes severely reduces the efficiency of universal COI markers to investigate vertebrate and other metazoans from aqueous eDNA, the study contributes to the advancement of rapid biomonitoring methods and brings us closer to a full inventory of extant marine biodiversity.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

Bakker

Wangensteen

Baillie

et al. 2019

Ecology and Evolution

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“…The presence of a target species can be estimated by detecting the eDNA in water samples instead of locating or capturing individuals (Lodge et al, ). These advantages have enabled noninvasive, quick, and wide‐ranging assessments of the presence/absence of species and their biodiversity and abundance in freshwater (Balasingham, Walter, Mandrak, & Heath, ; Bista et al, ; Deiner, Fronhofer, Mächler, Walser, & Altermatt, ; Fukumoto, Ushimaru, & Minamoto, ; Yamanaka & Minamoto, ) and marine environments (Boussarie et al, ; Lacoursière‐Roussel et al, ; Sigsgaard et al, ; Thomsen, Kielgast, Iversen, Møller, et al, ; Thomsen, Kielgast, Iversen, Wiuf, et al, ; Yamamoto et al, ).…”

Section: Introductionmentioning

confidence: 99%

Effect of water temperature and fish biomass on environmental DNA shedding, degradation, and size distribution

Murakami

Yamamoto

et al. 2019

Ecology and Evolution

205

263

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Environmental DNA (eDNA) analysis has successfully detected organisms in various aquatic environments. However, there is little basic information on eDNA, including the eDNA shedding and degradation processes. This study focused on water temperature and fish biomass and showed that eDNA shedding, degradation, and size distribution varied depending on water temperature and fish biomass. The tank experiments consisted of four temperature levels and three fish biomass levels. The total eDNA and size‐fractioned eDNA from Japanese Jack Mackerels (Trachurus japonicus) were quantified before and after removing the fish. The results showed that the eDNA shedding rate increased at higher water temperature and larger fish biomass, and the eDNA decay rate also increased at higher temperature and fish biomass. In addition, the small‐sized eDNA fractions were proportionally larger at higher temperatures, and these proportions varied among fish biomass. After removing the fish from the tanks, the percentage of eDNA temporally decreased when the eDNA size fraction was >10 µm, while the smaller size fractions increased. These results have the potential to make the use of eDNA analysis more widespread in the future.

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“…The emergence of environmental DNA (eDNA) metabarcoding, an innovative detection technique profiling multispecies genetic material in an environmental sample, is revolutionising our approach to noninvasive, efficient, whole‐ecosystem surveying (Bista et al, 2017; Port et al, 2016; Stat et al, 2017). After widespread global testing, this technique has demonstrated its ability to detect a wide variety of biota from aquatic ecosystems, including dark diversity—taxa that are not easily identified using observation‐based approaches (Boussarie et al, 2018; Jerde, Mahon, Chadderton, & Lodge, 2011; Vörös, Márton, Schmidt, Gál, & Jelić, 2017). As such, eDNA metabarcoding is anticipated to become a key tool in marine biodiversity discovery and monitoring, as recently outlined in a decadal plan for taxonomy and biosystematics in Australia and New Zealand (Taxonomy Decadal Plan Working Group, 2018).…”

Section: Introductionmentioning

confidence: 99%

eDNA metabarcoding survey reveals fine‐scale coral reef community variation across a remote, tropical island ecosystem

et al. 2020

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Environmental DNA (eDNA) metabarcoding, a technique for retrieving multispecies DNA from environmental samples, can detect a diverse array of marine species from filtered seawater samples. There is a growing potential to integrate eDNA alongside existing monitoring methods in order to establish or improve the assessment of species diversity. Remote island reefs are increasingly vulnerable to climate‐related threats and as such there is a pressing need for cost‐effective whole‐ecosystem surveying to baseline biodiversity, study assemblage changes and ultimately develop sustainable management plans. We investigated the utility of eDNA metabarcoding as a high‐resolution, multitrophic biomonitoring tool at the Cocos (Keeling) Islands, Australia (CKI)—a remote tropical coral reef atoll situated within the eastern Indian Ocean. Metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes, as well as the 18S rRNA nuclear gene, were applied to 252 surface seawater samples collected from 42 sites within a 140 km2 area. Our assays successfully detected a wide range of bony fish and elasmobranchs (244 taxa), crustaceans (88), molluscs (37) and echinoderms (7). Assemblage composition varied significantly between sites, reflecting habitat partitioning across the island ecosystem and demonstrating the localisation of eDNA signals, despite extensive tidal and oceanic movements. In addition, we document putative new occurrence records for 46 taxa and compare the efficiency of our eDNA approach to visual survey techniques at CKI. Our study demonstrates the utility of a multimarker metabarcoding approach in capturing multitrophic biodiversity across an entire coral reef atoll and sets an important baseline for ongoing monitoring and management.

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Environmental DNA illuminates the dark diversity of sharks

Abstract: Environmental DNA reveals unsuspected shark diversity and calls for monitoring and protection of residual populations.

Cited by 251 publications

References 55 publications

Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

Effect of water temperature and fish biomass on environmental DNA shedding, degradation, and size distribution

eDNA metabarcoding survey reveals fine‐scale coral reef community variation across a remote, tropical island ecosystem

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