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

Abstract

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

Seabed mining could come at a high price for a unique fauna

“…The results of this study suggest the potential of the molecular approach for biodiversity assessments of remote ecosystems. eDNA sequencing was sensitive enough to detect distinct communities between adjacent habitat types, as was previously shown for shallow water tropical habitats (Nguyen et al, 2020). Sessile taxa detected on nodules with eDNA were broadly consistent with previous inventories of species associated with this abyssal substrate type.…”

More Than Expected From Old Sponge Samples: A Natural Sampler DNA Metabarcoding Assessment of Marine Fish Diversity in Nha Trang Bay (Vietnam)

“…However, Jeunen et al (2019) demonstrated that eDNA was able to discriminate diverse marine habitats within a small spatial scale subject to tidal and water currents. Indeed, some studies have already shown that eDNA surveys are able to detect fine-scale community composition patterns in heterogeneous aquatic habitats (Port et al, 2016;O'Donnell et al, 2017;Pont et al, 2018;Bakker et al, 2019;Stat et al, 2019;Nguyen et al, 2020;Oka et al, 2020). In our study, the residency time and degradation rate of nsDNA in the sponge tissues is an important factor that can hamper the detection of community patterns.…”

“…Some recent studies have pointed out the differences between eDNA metabarcoding methods and visual or capture methods (Tkachenko et al, 2016;Yamamoto et al, 2017;Fujii et al, 2019;Stat et al, 2019). The main advantages of metabarcoding rely on its time efficiency (Yamamoto et al, 2017;Nguyen et al, 2020), its detection capability of eDNA signatures of fishes that cannot be observed during visual surveys (Nguyen et al, 2020) and the dispensable need of taxonomic expertise (DiBattista et al, 2017). In this sense, censuses made by different observers may not be comparable, while results from eDNA are more objective and, particularly, better suited for archiving and future reanalyses (the sequences remain in databases, visual observations are hardly archivable).…”

“…In this sense, censuses made by different observers may not be comparable, while results from eDNA are more objective and, particularly, better suited for archiving and future reanalyses (the sequences remain in databases, visual observations are hardly archivable). However, the main drawbacks of the eDNA approach lie on the accuracy of the results obtained, which are biased by the coverage of the reference database (Nguyen et al, 2020), the number of replicates (Yamamoto et al, 2017), the possible PCR inhibition (Fujii et al, 2019), and the differences in the species DNA shedding rates (Port et al, 2016).…”

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

“…In addition to the above six case studies conducted in various marine environments, MiFish eDNA metabarcoding has been applied to biodiversity monitoring at two coastal areas of eastern Java and Sulawesi Sea, Indonesia (Masengi et al 2019;Andriyono et al 2019); port and urban canal area in Osaka Bay, central Japan (Kamimura et al 2018); Innoshima, Seto Inland Sea, Japan (Sakamoto 2019); coastal waters off Zhoushan, China (Chen et al 2019(Chen et al , 2020; a harbor at Sloehaven, the Netherlands (Hoorn and Gittenberger 2019); Gulf of St. Laurence Bay, Canada (Afzali et al 2020); Caribbean bay in Panama (Nguyen et al 2020); and coastal waters along the South Africa by members of the von der Heyden Lab (https ://www.vonde rheyd enlab .com/envir onmen tal-dna-and-metab arcod ing.html).…”