Using vertebrate environmental DNA from seawater in biomonitoring of marine habitats

Sigsgaard, Eva Egelyng; Torquato, Felipe; Frøslev, Tobias Guldberg; Moore, Alec B. M.; Sorensen, Johan Molgard; Range, Pedro; Ben‐Hamadou, Radhouane; Bach, Steffen; Møller, Peter Rask; Thomsen, Philip Francis

doi:10.1111/cobi.13437

Cited by 87 publications

(96 citation statements)

References 43 publications

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“…Interestingly, the similar patterns of fish community composition uncovered by the two methods were driven by different pools of fish species. This suggests that eDNA can unveil distribution patterns of fish taxa (as well as invertebrates) previously missed or underreported by visual methods, consistent with other eDNA fish studies 69 . Our results also indicate that habitat and wave exposure drive the distribution of diversity across various taxonomic groups.…”

Section: Discussionsupporting

confidence: 85%

Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape

Nguyen

Shen

Seemann

et al. 2020

Sci Rep

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Accurate, rapid, and comprehensive biodiversity assessments are critical for investigating ecological processes and supporting conservation efforts. Environmental DNA (eDNA) surveys show promise as a way to effectively characterize fine-scale patterns of community composition. We tested whether a single PCR survey of eDNA in seawater using a broad metazoan primer could identify differences in community composition between five adjacent habitats at 19 sites across a tropical Caribbean bay in Panama. We paired this effort with visual fish surveys to compare methods for a conspicuous taxonomic group. eDNA revealed a tremendous diversity of animals (8,586 operational taxonomic units), including many small taxa that would be undetected in traditional in situ surveys. Fish comprised only 0.07% of the taxa detected by a broad COI primer, yet included 43 species not observed in the visual survey. eDNA revealed significant differences in fish and invertebrate community composition across adjacent habitats and areas of the bay driven in part by taxa known to be habitat-specialists or tolerant to wave action. Our results demonstrate the ability of broad eDNA surveys to identify biodiversity patterns in the ocean. Coastal regions make up less than 10% of the Earth's surface but their ecosystems contribute disproportionately to the globe's primary productivity, biodiversity, and ecosystem services 1-4. Coral reefs alone are thought to be home to 25% or more of described marine species 5. Human activities such as coastal development, exploitative fishing practices, and eutrophication, however, have resulted in the widespread decline of commercially-important fisheries, the loss of important habitat-forming species, and biological invasions 6-8. The accelerating pace of changes in the structure and function of coastal ecosystems due to these impacts makes it urgently important to develop methods for efficient and effective biomonitoring to support management, conservation, and basic science initiatives 9. Systematic survey data are especially fundamental in understanding the link between biodiversity and the health and functioning of marine ecosystems 10-12. At its core, biomonitoring requires the reliable identification of species that are present in an environment, and answers if, how, and why populations of these species change over time. Yet, it still remains a challenge to capture the full taxonomic diversity of ecosystems in a repeatable way to identify trends through time and patterns across space 13. Traditional marine biodiversity surveying methods, such as visual surveys by divers, are often expensive, invasive, require taxonomic expertise, are limited by visibility or habitat complexity, and miss cryptic diversity, including most invertebrates 14-16. As a result, such traditional

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Section: Discussionsupporting

confidence: 85%

Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape

Nguyen

Shen

Seemann

et al. 2020

Sci Rep

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“…Marine ecosystems comprise extremely diverse habitats, horizontally ranging from coastal to oceanic areas in terms of distance from land, geographically extending from polar to equatorial regions, and vertically ranging from the surface to deep waters exceeding a depth of 10 km. Here, we introduce those case studies using MiFish eDNA metabarcoding conducted in the inner bay along the coast of Sea of Japan (Yamamoto et al 2017), oceanic sites in Monterey Bay, southern California (Andruszkiewicz et al 2017b), various coastal habitats off Qatar, Arabian Gulf (Sigsgaard et al 2019), and a coral-reef lagoon in Okinawa Island, southern Japan (Oka et al 2020). Additionally, we introduce a case study using sponges (phylum Poriphera) as eDNA samplers, comparing results from MiFish metabarcoding between the Antarctic and Mediterranean waters (Mariani et al 2019).…”

Section: Marine Fish Communitymentioning

confidence: 99%

“…Moreover, biodiversity monitoring of macroorganisms such as fishery resources is laborious, costly, and time consuming, often relying on direct capture of specimens through various kinds of netting, trapping, or fishing (Thomsen et al 2012;Evans et al 2017;Oka et al 2020). These capture-based sampling methods are both invasive and destructive, and subsequent morphological identification of specimens based on taxonomic expertise is also required (Thomsen and Willerslev 2015;Andruszkiewicz et al 2017b;Sigsgaard et al 2019), which is increasingly scarce and declining in availability (Hopkins and Freckleton 2002). Additionally, sampling feasibility heavily depends on weather and water conditions.…”

Section: Introductionmentioning

confidence: 99%

MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples

2020

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We reviewed the current methodology and practices of the DNA metabarcoding approach using a universal PCR primer pair MiFish, which co-amplifies a short fragment of fish DNA (approx. 170 bp from the mitochondrial 12S rRNA gene) across a wide variety of taxa. This method has mostly been applied to biodiversity monitoring using environmental DNA (eDNA) shed from fish and, coupled with next-generation sequencing technologies, has enabled massively parallel sequencing of several hundred eDNA samples simultaneously. Since the publication of its technical outline in 2015, this method has been widely used in various aquatic environments in and around the six continents, and MiFish primers have demonstrably outperformed other competing primers. Here, we outline the technical progress in this method over the last 5 years and highlight some case studies on marine, freshwater, and estuarine fish communities. Additionally, we discuss various applications of MiFish metabarcoding to non-fish organisms, single-species detection systems, quantitative biodiversity monitoring, and bulk DNA samples other than eDNA. By recognizing the MiFish eDNA metabarcoding strengths and limitations, we argue that this method is useful for ecosystem conservation strategies and the sustainable use of fishery resources in “ecosystem-based fishery management” through continuous biodiversity monitoring at multiple sites.

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“…As species-area accumulation curves in community surveys 43, 44 , increasing the sample size would increase the detectability of species by eDNA metabarcoding 20,45 .…”

Section: Study Lakes and Sampling Sitesmentioning

confidence: 99%

Effects of species traits and ecosystem characteristics on species detection by eDNA metabarcoding in lake fish communities

Doi¹,

Matsuoka²,

Matsuzaki³

et al. 2020

Preprint

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Although environmental DNA (eDNA) metabarcoding is acknowledged to be an exceptionally useful and powerful tool for monitoring surveys, it has limited applicability, particularly for nationwide surveys. To evaluate the performance of eDNA metabarcoding in broad-scale monitoring, we examined the effects of species ecological/biological traits and ecosystem characteristics on species detection rates and the consequences for community analysis. We conducted eDNA metabarcoding on fish communities in 18 Japanese lakes on a country-wide scale. By comparing species records, we found that certain species traits, including body size, body shape, saltwater tolerance, and habitat preferences, influenced eDNA detection. We also found that the proportion of species detected decreased significantly with an increase in lake surface area, owing to an ecosystem-size effect on species detection. We conclude that species traits, including habitat preferences and body size, and ecosystem size should be taken into consideration when assessing the performance of eDNA metabarcoding in broad-scale monitoring.

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Using vertebrate environmental DNA from seawater in biomonitoring of marine habitats

Abstract: Article impact statement: Environmental DNA provides habitat-characteristic molecular signatures and can be used efficiently to map marine biodiversity at large spatial scales.

Cited by 87 publications

References 43 publications

Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape

Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape

MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples

Effects of species traits and ecosystem characteristics on species detection by eDNA metabarcoding in lake fish communities

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