Detection of a diverse marine fish fauna using environmental DNA from seawater samples (original) (raw)
Related papers
Scientific Reports, 2017
Effective marine management requires comprehensive data on the status of marine biodiversity. However, efficient methods that can document biodiversity in our oceans are currently lacking. Environmental DNA (eDNA) sourced from seawater offers a new avenue for investigating the biota in marine ecosystems. Here, we investigated the potential of eDNA to inform on the breadth of biodiversity present in a tropical marine environment. Directly sequencing eDNA from seawater using a shotgun approach resulted in only 0.34% of 22.3 million reads assigning to eukaryotes, highlighting the inefficiency of this method for assessing eukaryotic diversity. In contrast, using 'tree of life' (ToL) metabarcoding and 20-fold fewer sequencing reads, we could detect 287 families across the major divisions of eukaryotes. Our data also show that the best performing 'universal' PCR assay recovered only 44% of the eukaryotes identified across all assays, highlighting the need for multiple metabarcoding assays to catalogue biodiversity. Lastly, focusing on the fish genus Lethrinus, we recovered intra-and inter-specific haplotypes from seawater samples, illustrating that eDNA can be used to explore diversity beyond taxon identifications. Given the sensitivity and low cost of eDNA metabarcoding we advocate this approach be rapidly integrated into biomonitoring programs. Marine ecosystems are under increasing pressure from a variety of anthropogenic stressors, including climate change and fishing activities 1-4. Habitat degradation, overexploited fisheries, altered food web dynamics and shifts in community composition highlights the need for effective management of the marine biome in order to preserve and manage ocean resources sustainably into the future 4,5. A fundamental tool for providing data to support management of the marine environment is biomonitoring. By targeting indicator species or repeating surveys of specific sites, regular monitoring of the biota allows impacts affecting the abundance and/or alpha and beta diversity to be measured 6. However, current approaches to surveying conspicuous faunal elements (e.g. baited remote underwater video, transects, or diver tows) are dependent on suitable field conditions, a particular set of skills, and are limited to the narrow portion of biodiversity recorded. Indeed, community assemblage surveys are often restricted to a single taxonomic group such as fishes or corals, or even a subset of those groups 7,8. Considering the growing evidence that total biodiversity promotes healthy ecosystem functions and that sustaining biodiversity represents a practical framework for ecosystem-based management (EBM), there is a compelling need for more comprehensive approaches to monitoring marine biota 9-13. Recent advances in genomic technologies afford new opportunities across a broad range of applications in environmental science 14-18. One such application lies in the discovery that organisms leave traces of their DNA in the environment, including seawater, and when extracted, is collectively referred to as eDNA 19-21. Here, we refer to eDNA as all genetic material that is obtained directly from the environment as in Taberlet et al. 21 , which depending on sampling methodology, constitutes DNA from whole organisms (i.e. prokaryotes and microscopic
Revista de Biología Tropical, 2014
Genetic material (short DNA fragments) left behind by species in nonliving components of the environment (e.g. soil, sediment, or water) is defined as environmental DNA (eDNA). This DNA has been previously described as particulate DNA and has been used to detect and describe microbial communities in marine sediments since the mid-1980's and phytoplankton communities in the water column since the early-1990's. More recently, eDNA has been used to monitor invasive or endangered vertebrate and invertebrate species. While there is a steady increase in the applicability of eDNA as a monitoring tool, a variety of eDNA applications are emerging in fields such as forensics, population and community ecology, and taxonomy. This review provides scientist with an understanding of the methods underlying eDNA detection as well as applications, key methodological considerations, and emerging areas of interest for its use in ecology and conservation of freshwater and marine environments.
eDNA metabarcoding as a biomonitoring tool for marine protected areas
2020
Monitoring of marine protected areas (MPAs) is critical for marine ecosystem management, yet current protocols rely on SCUBA-based visual surveys that are costly and time consuming, limiting their scope and effectiveness. Environmental DNA (eDNA) metabarcoding is a promising alternative for marine ecosystem monitoring, but more direct comparisons to visual surveys are needed to understand the strengths and limitations of each approach. This study compares fish communities inside and outside the Scorpion State Marine Reserve off Santa Cruz Island, CA using eDNA metabarcoding and underwater visual census surveys. Results from eDNA captured 76% (19/25) of fish species and 95% (19/20) of fish genera observed during pairwise underwater visual census. Species missed by eDNA were due to the inability of MiFish 12S barcodes to differentiate species of rockfishes (Sebastes, n=4) or low site occupancy rates of crevice-dwelling Lythrypnus gobies. However, eDNA detected an additional 30 fish sp...
2018
The so called MONIS 3 project (see link below an also Annex to this document) reports the development of 22 species-specific eDNA-based test systems for monitoring and mapping of the occurrence of non-indigenous species in Danish marine waters. The development has been undertaken by the MONIS partnership and the species have been selected based on the outcome of the MONIS 2 project. It should be noted that the test systems are considered operational cf. the MONIS definition (see Chapter 1). It should also be noted that the 22 test systems have been applied in the MONIS 4 project (expected in December 2018), where monitoring of 16 Danish harbours have been carried out to map occurrence of nonindigenous marine species using both conventional methods (including the JHP-methods) and molecular methods (eDNA). Development of additional test systems is being planned and expected to be carried out in 2019 pending funding. The MONIS partnership encourages interested institutions, especially ...
Diversity
One of the most important causes of biodiversity loss are non-indigenous species (NIS), in particular invasive ones. The dispersion of NIS mainly depends on anthropogenic activities such as maritime traffic, which account for almost half of the total NIS introduction in the European seas, as reported by the European Environmental Agency. For this reason, NIS management measures are mainly focused on commercial ports (i.e., ballast water management and Marine Strategy Framework Directive monitoring), underestimating the role of marinas and tourist harbors; these host small vessels (<20 m), such as recreational, fishery, and sail ones without ballast waters, but are also responsible for NIS arrival and spread through the bilge water as well as from hull fouling. With the aim of paying attention to marinas and tourist harbors and validating an innovative molecular methodology for NIS surveillance and monitoring, in the present work, eDNA metabarcoding of cytochrome oxidase subunit I...
Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring
ABSTRACTAquatic environmental DNA (eDNA) surveys are transforming how we monitor marine ecosystems. The time-consuming pre-processing step of active filtration, however, remains a bottleneck. Hence, new approaches omitting active filtration are in great demand. One exciting prospect is to use the filtering power of invertebrates to collect eDNA. While proof-of-concept has been achieved, comparative studies between aquatic and filter feeder eDNA signals are lacking. Here, we investigated the differences among four eDNA sources (water; bivalves; sponges; and ethanol in which filter-feeding organisms were stored) along a vertical transect in Doubtful Sound, New Zealand using three metabarcoding primers (fish (16S); MiFish-E/U). While concurrent SCUBA diver observations validated eDNA results, laboratory trials corroborated in-field bivalve eDNA detection results. Combined, eDNA sources detected 59 vertebrates, while divers observed eight fish species. There were no significant differen...
Molecular Ecology, 2020
In the marine realm, biomonitoring using environmental DNA (eDNA) of benthic communities requires destructive direct sampling or the setting‐up of settlement structures. Comparatively much less effort is required to sample the water column, which can be accessed remotely. In this study we assess the feasibility of obtaining information from the eukaryotic benthic communities by sampling the adjacent water layer. We studied two different rocky‐substrate benthic communities with a technique based on quadrat sampling. We also took replicate water samples at four distances (0, 0.5, 1.5, and 20 m) from the benthic habitat. Using broad range primers to amplify a ca. 313 bp fragment of the cytochrome oxidase subunit I gene, we obtained a total of 3,543 molecular operational taxonomic units (MOTUs). The structure obtained in the two environments was markedly different, with Metazoa, Archaeplastida and Stramenopiles being the most diverse groups in benthic samples, and Hacrobia, Metazoa and ...
Critical considerations for the application of environmental DNA methods to detect aquatic species
Methods in Ecology and Evolution, 2016
Summary Species detection using environmental DNA (eDNA) has tremendous potential for contributing to the understanding of the ecology and conservation of aquatic species. Detecting species using eDNA methods, rather than directly sampling the organisms, can reduce impacts on sensitive species and increase the power of field surveys for rare and elusive species. The sensitivity of eDNA methods, however, requires a heightened awareness and attention to quality assurance and quality control protocols. Additionally, the interpretation of eDNA data demands careful consideration of multiple factors. As eDNA methods have grown in application, diverse approaches have been implemented to address these issues. With interest in eDNA continuing to expand, supportive guidelines for undertaking eDNA studies are greatly needed. Environmental DNA researchers from around the world have collaborated to produce this set of guidelines and considerations for implementing eDNA methods to detect aquatic ...
Frontiers in Marine Science
To enable successful management of marine bioinvasions, timely and robust scientific advice is required. This knowledge should inform managers and stakeholders on the magnitude of a pressure (rate of human-mediated introductions), the environmental state of an ecosystem (impacts of non-indigenous species), and the success of management response (prevention, eradication, mitigation). This advice often relies on baseline biodiversity information in the form of measureable parameters (metrics). This can be derived from conventional approaches such as visual surveys, but also by utilizing environmental DNA/RNA-based molecular techniques, which are increasingly being touted as promising tools for assessing biodiversity and detecting rare or invasive species. Depending on the stage of incursion, each approach has merits and limitations. In this review we assess the performance of biosecurity-relevant biodiversity parameters derived from eDNA/eRNA samples and discuss the results in relation to different stages of invasion and management applications. The overall performance of considered methods ranged between 42 and 90% based on defined criteria, with target-specific approaches scoring higher for respective biosecurity applications, followed by eDNA metabarcoding. Caveats are discussed along with avenues which may enhance these techniques and their successful uptake for marine biosecurity surveillance and management. To facilitate and encourage uptake of these techniques, there is a need for an international collaborative framework aimed at unifying molecular sampling and analysis methodologies. Improvement of quantitative capacity and cost-efficiency will also enhance their integration in biosecurity programmes.
Evaluating eDNA for Use within Marine Environmental Impact Assessments
Journal of Marine Science and Engineering, 2022
In this review, the use of environmental DNA (eDNA) within Environmental Impact Assessment (EIA) is evaluated. EIA documents provide information required by regulators to evaluate the potential impact of a development project. Currently eDNA is being incorporated into biodiversity assessments as a complementary method for detecting rare, endangered or invasive species. However, questions have been raised regarding the maturity of the field and the suitability of eDNA information as evidence for EIA. Several key issues are identified for eDNA information within a generic EIA framework for marine environments. First, it is challenging to define the sampling unit and optimal sampling strategy for eDNA with respect to the project area and potential impact receptor. Second, eDNA assay validation protocols are preliminary at this time. Third, there are statistical issues around the probability of obtaining both false positives (identification of taxa that are not present) and false negati...