1
|
Downie AT, Bennett WW, Wilkinson S, de Bruyn M, DiBattista JD. From land to sea: Environmental DNA is correlated with long-term water quality indicators in an urbanized estuary. MARINE POLLUTION BULLETIN 2024; 207:116887. [PMID: 39217873 DOI: 10.1016/j.marpolbul.2024.116887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 08/18/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Estuaries provide critical ecosystem services, and yet are increasingly under threat from urbanization. Non-invasive approaches to monitor biodiversity resident to or migrating through estuaries is critical to evaluate the holistic health of these ecosystems, often based entirely on water quality. In this study we compared tree of life metabarcoding (ToL-metabarcoding) biodiversity detections with measurements of physico-chemical variables (chlorophyll a, turbidity, total nitrogen, total phosphorous, dissolved oxygen) at eight sites of varying degrees of water quality in the Gold Coast Broadwater Estuary (Queensland, Australia). These sites were ranked according to an adapted Water Quality Index (WQI) score. Here, we detected 787 unique taxa, adding 137 new biodiversity records to the region, mostly micro-organisms such as bacteria, ciliates, diatoms, dinoflagellates, and cryptomonads. Sites with the lowest WQI were characterised by higher turbidity, lower dissolved oxygen, as well as higher total nitrogen and phosphorous, which correlated with an increased diversity of bacteria, ciliates, and green algae. Similarly, the composition of taxa was significantly different between sites with variable WQI values for most taxa but was less apparent for larger vertebrate groups. These findings suggest that rapid ToL-metabarcoding biodiversity detections, particularly for lower order taxonomic groups, can serve as valuable indicators of flora and fauna across the tree of life associated with dynamically shifting estuarine health along urbanized coastlines.
Collapse
Affiliation(s)
- Adam T Downie
- School of the Environment, The University of Queensland, St. Lucia, Queensland, Australia.
| | - William W Bennett
- School of Environment and Science, Griffith University, Southport, Queensland, Australia.
| | - Shaun Wilkinson
- Wilderlab NZ Ltd., Wellington, New Zealand; School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia.
| | - Mark de Bruyn
- School of Environment and Science, Griffith University, Southport, Queensland, Australia.
| | - Joseph D DiBattista
- School of Environment and Science, Griffith University, Southport, Queensland, Australia; Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.
| |
Collapse
|
2
|
Espinosa Prieto A, Hardion L, Debortoli N, Bournonville T, Mathot T, Marescaux J, Chanez E, Staentzel C, Beisel JN. A comparative analysis of eDNA metabarcoding and field surveys: Exploring freshwater plant communities in rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176200. [PMID: 39284450 DOI: 10.1016/j.scitotenv.2024.176200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/26/2024] [Accepted: 09/09/2024] [Indexed: 09/22/2024]
Abstract
While environmental DNA (eDNA) metabarcoding holds promise as a holistic approach to assess vegetation changes and community composition across diverse spatial and temporal scales, systematic investigations of its efficacy compared to conventional field surveys remain scarce in the literature. The present study explores the differences in plant diversity recovered from field surveys and captured with a multi-marker eDNA metabarcoding approach (two nrDNA ITS1 and ITS2, and two cpDNA rbcL and trnL) from river water samples. The eDNA metabarcoding approach retrieved 46 aquatic plants (hydrophytes and helophytes) and 245 terrestrial plants, compared to 24 and 127 species identified from field surveys. On average, eDNA samples collected immediately downstream of the survey sites recovered 43 % and 39 % of the aquatic and terrestrial species observed, respectively. Discrepancies were explained by differences in taxonomic resolution, the stochasticity of the retrieval of rare and elusive species, and the presence of reference sequences. We found a significant positive correlation between spatial and community distances at scales ranging from 2 to 9 km and identified turnover as the driving force of these differences. Metabarcoding demonstrated sensitivity to community changes and both approaches converge on a similar community structure. Interestingly, eDNA samples collected immediately upstream of the survey sites exhibited significant species overlap with the downstream samples (c. 100 m apart). Overall, our results demonstrate that within-site species mismatches between the methods are nonnegligible, and they question the use of eDNA for generating complete species lists at scales comparable to our field surveys (< 100-m transects). However, with adequate sampling and a multi-marker metabarcoding approach, eDNA has the potential to approximate catchment gamma diversity with less sampling effort than conventional surveys.
Collapse
Affiliation(s)
- Armando Espinosa Prieto
- University of Strasbourg, Laboratoire Image Ville Environnement, UMR 7362 CNRS, Strasbourg, France.
| | - Laurent Hardion
- University of Strasbourg, Laboratoire Image Ville Environnement, UMR 7362 CNRS, Strasbourg, France.
| | | | | | | | | | - Etienne Chanez
- University of Strasbourg, Laboratoire Image Ville Environnement, UMR 7362 CNRS, Strasbourg, France.
| | - Cybill Staentzel
- University of Strasbourg, Laboratoire Image Ville Environnement, UMR 7362 CNRS, Strasbourg, France; École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES), Strasbourg, France.
| | - Jean-Nicolas Beisel
- University of Strasbourg, Laboratoire Image Ville Environnement, UMR 7362 CNRS, Strasbourg, France; École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES), Strasbourg, France.
| |
Collapse
|
3
|
Espinosa Prieto A, Hardion L, Debortoli N, Beisel JN. Finding the perfect pairs: A matchmaking of plant markers and primers for multi-marker eDNA metabarcoding. Mol Ecol Resour 2024; 24:e13937. [PMID: 38363053 DOI: 10.1111/1755-0998.13937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/14/2023] [Accepted: 01/09/2024] [Indexed: 02/17/2024]
Abstract
As the scope of plant eDNA metabarcoding diversifies, so do the primers, markers and methods. A wealth of primers exists today, but their comparative evaluation is lacking behind. Similarly, multi-marker approaches are recommended but debates persist regarding barcode complementarity and optimal combinations. After a literature compilation of used primers, we compared in silico 102 primer pairs based on amplicon size, coverage and specificity, followed by an experimental evaluation of 15 primer pairs on a mock community sample covering 268 plant species and genera, and about 100 families. The analysis was done for the four most common plant metabarcoding markers, rbcL, trnL, ITS1 and ITS2 and their complementarity was assessed based on retrieved species. By focusing on existing primers, we identify common designs, promote alternatives and enhance prior-supported primers for immediate applications. The ITS2 was the best-performing marker for flowering vascular plants and was congruent to ITS1. However, the combined taxonomic breadth of ITS2 and rbcL surpassed any other combination, highlighting their high complementarity across Streptophyta. Overall, our study underscores the significance of comprehensive primer and barcode evaluations tailored to metabarcoding applications.
Collapse
Affiliation(s)
- Armando Espinosa Prieto
- University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France
| | - Laurent Hardion
- University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France
| | - Nicolas Debortoli
- Namur Molecular Tech, CHU UCL Namur, Yvoir, Belgium
- E-BIOM SA, Namur, Belgium
| | - Jean-Nicolas Beisel
- University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France
- École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES), Strasbourg, France
| |
Collapse
|
4
|
Nakai M, Masumoto T, Asaeda T, Rahman M. Improving the efficiency of adaptive management methods in multiple fishways using environmental DNA. PLoS One 2024; 19:e0301197. [PMID: 38557776 PMCID: PMC10984549 DOI: 10.1371/journal.pone.0301197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
Dams and weirs impede the continuity of rivers and transit of migratory fish. To overcome this obstacle, fishways are installed worldwide; however, management after installation is important. The Miyanaka Intake Dam has three fish ladders with different flow velocities and discharges and has been under adaptive management since 2012. Fish catch surveys, conducted as an adaptive management strategy, place a heavy burden on fish. Furthermore, a large number of investigators must be mobilized during the 30-day investigation period. Thus, a monitoring method using environmental DNA that exerts no burden on fish and requires only a few surveyors (to obtain water samples) and an in-house analyst was devised; however, its implementation in a fishway away from the point of analysis and with limited flow space and its effective water sampling frequency have not been reported. Therefore, in 2019, we started a trial aiming to evaluate the methods and application conditions of environmental DNA surveys for the continuous and long-term monitoring of various fish fauna upstream and downstream of the Miyanaka Intake Dam. To evaluate the fish fauna, the results of an environmental DNA survey (metabarcoding method) for 2019 to 2022 were compared to those of a catch survey in the fishway from 2012 to 2022. The results confirmed the use of environmental DNA surveys in evaluating the contribution of fishways to biodiversity under certain conditions and introduced a novel method for sample collection.
Collapse
Affiliation(s)
- Masahiko Nakai
- Japan International Consultants for Transportation Co., Ltd, Tokyo, Japan
| | - Taku Masumoto
- Energy Planning Department, East Japan Railway Company, Tokyo, Japan
| | | | | |
Collapse
|
5
|
Diaz-Suarez A, Noreikiene K, Kahar S, Ozerov MY, Gross R, Kisand V, Vasemägi A. DNA metabarcoding reveals spatial and temporal variation of fish eye fluke communities in lake ecosystems. Int J Parasitol 2024; 54:33-46. [PMID: 37633409 DOI: 10.1016/j.ijpara.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 08/28/2023]
Abstract
Eye flukes (Diplostomidae) are diverse and abundant trematode parasites that form multi-species communities in fish with negative effects on host fitness and survival. However, the environmental factors and host-related characteristics that determine species diversity, composition, and coexistence in such communities remain poorly understood. Here, we developed a cost-effective cox1 region-specific DNA metabarcoding approach to characterize parasitic diplostomid communities in two common fish species (Eurasian perch and common roach) collected from seven temperate lakes in Estonia. We found considerable inter- and intra-lake, as well as inter-host species, variation in diplostomid communities. Sympatric host species characterization revealed that parasite communities were typically more diverse in roach than perch. Additionally, we detected five positive and two negative diplostomid species associations in roach, whereas only a single negative association was observed in perch. These results indicate that diplostomid communities in temperate lakes are complex and dynamic systems exhibiting both spatial and temporal heterogeneity. They are influenced by various environmental factors and by host-parasite and inter-parasite interactions. We expect that the described methodology facilitates ecological and biodiversity research of diplostomid parasites. It is also adaptable to other parasite groups where it could serve to improve current understanding of diversity, distribution, and interspecies interactions of other understudied taxa.
Collapse
Affiliation(s)
- Alfonso Diaz-Suarez
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia.
| | - Kristina Noreikiene
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia. https://twitter.com/snaudale
| | - Siim Kahar
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia
| | - Mikhail Y Ozerov
- Biodiversity Unit, University of Turku, 20014 Turku, Finland; Department of Biology, University of Turku, 20014 Turku, Finland; Department of Aquatic Resources, Swedish University of Agricultural Sciences, Stångholmsvägen 2, 17893 Drottningholm, Sweden
| | - Riho Gross
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia
| | - Veljo Kisand
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia
| | - Anti Vasemägi
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia; Department of Aquatic Resources, Swedish University of Agricultural Sciences, Stångholmsvägen 2, 17893 Drottningholm, Sweden
| |
Collapse
|
6
|
Giusti A, Malloggi C, Magagna G, Filipello V, Armani A. Is the metabarcoding ripe enough to be applied to the authentication of foodstuff of animal origin? A systematic review. Compr Rev Food Sci Food Saf 2024; 23:e13256. [PMID: 38284609 DOI: 10.1111/1541-4337.13256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/25/2023] [Accepted: 10/02/2023] [Indexed: 01/30/2024]
Abstract
Food authentication using molecular techniques is of great importance to fight food fraud. Metabarcoding, based on the next-generation sequencing (NGS) technologies, allowing large-scale taxonomic identification of complex samples via massive parallel sequencing of fragments (called DNA barcodes) simultaneously, has become increasingly popular in many scientific fields. A systematic review to answer the question "Is the metabarcoding ripe enough to be applied to the authentication of foodstuff of animal origin?" is presented. The inclusion criteria were focused on the selection of scientific papers (SPs) only applying metabarcoding to foodstuff of animal origin collected on the market. The 23 included SPs were first analyzed with respect to the metabarcoding phases: library preparation (target genes, primer pairs, and fragment length), sequencing (NGS platforms), and final data analysis (bioinformatic pipelines). Given the importance of primer selection, the taxonomic coverage of the used primers was also evaluated. In addition, the SPs were scored based on the use of quality control measures (procedural blanks, positive controls, replicates, curated databases, and thresholds to filter the data). A lack of standardized protocols, especially with respect to the target barcode/s and the universal primer/s, and the infrequent application of the quality control measures, leads to answer that metabarcoding is not ripe enough for authenticating foodstuff of animal origin. However, the observed trend of the SP quality improvement over the years is encouraging. Concluding, a proper protocol standardization would allow a wider use of metabarcoding by both official and private laboratories, enabling this method to become the primary for the authentication of foodstuffs of animal origin.
Collapse
Affiliation(s)
- Alice Giusti
- FishLab, Department of Veterinary Sciences, University of Pisa, Pisa, Italy
| | - Chiara Malloggi
- FishLab, Department of Veterinary Sciences, University of Pisa, Pisa, Italy
| | - Giulia Magagna
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Virginia Filipello
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Andrea Armani
- FishLab, Department of Veterinary Sciences, University of Pisa, Pisa, Italy
| |
Collapse
|
7
|
Alexander JB, Marnane MJ, Elsdon TS, Bunce M, Sitaworawet P, Songploy S, Chaiyakul S, Harvey ES. Using environmental DNA to better inform decision making around decommissioning alternatives for offshore oil and gas infrastructure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:165991. [PMID: 37536600 DOI: 10.1016/j.scitotenv.2023.165991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
Artificial reefs are being utilised globally to aid in natural resource management, conservation, restoration or the creation of unique marine habitats. There is discussion around the optimal construction materials and designs for artificial reefs, the influences these have on biological communities, and the resulting ecological and social benefits. This discussion also includes the ecological value of repurposed marine infrastructure, such as decommissioned oil and gas platforms. Platforms often have an operational life spanning multiple decades, over which time they can develop extensive and unique community assemblages. The creation of artificial reefs by repurposing oil and gas platforms can have ecological, economic and sociological merit. However, with >12,000 platforms requiring decommissioning globally, there is the need for holistic assessment of biological communities associated with these platforms to inform the potential outcomes of different decommissioning options. We use environmental DNA metabarcoding (eDNA) of water, bio-foul and sediment samples to census broad eukaryotic diversity at eight platforms in the Gulf of Thailand (GoT) and five nearby soft sediment habitat locations. We sampled three target depths at sites (shallow, mid, deep) and detected 430 taxa at platforms, with higher diversity in shallow (near-surface) samples (313 taxa), compared to mid (30 m collection depth; 261 taxa) and deep (50 m; 273 taxa). Three percent of taxa were shared among all depths at platforms with distinct assembles at each depth. Introduced species are an ongoing risk for platforms, however the eDNA detected no known introduced species. While the eDNA data provide broad taxon coverage and significant assemblage patterns, ongoing sampling innovation, assay design and local reference material still require development to obtain the maximum benefit of the technique. This study highlights the versatility and scalability of eDNA metabarcoding to holistically census marine infrastructure and inform the management and potential conservation of extant communities.
Collapse
Affiliation(s)
- Jason B Alexander
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia.
| | | | - Travis S Elsdon
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia; Chevron Technical Center, Perth, Western Australia, Australia
| | - Michael Bunce
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia; Department of Conservation, New Zealand
| | | | - Se Songploy
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | - Sarin Chaiyakul
- Chevron Thailand Exploration and Production, Bangkok, Thailand
| | - Euan S Harvey
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| |
Collapse
|
8
|
Liao Y, Miao X, Wang R, Zhang R, Li H, Lin L. First pelagic fish biodiversity assessment of Cosmonaut Sea based on environmental DNA. MARINE ENVIRONMENTAL RESEARCH 2023; 192:106225. [PMID: 37866974 DOI: 10.1016/j.marenvres.2023.106225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/22/2023] [Accepted: 10/09/2023] [Indexed: 10/24/2023]
Abstract
The Cosmonaut Sea is a typical marginal sea in East Antarctica that has not yet been greatly impacted by climate change. As one of the least explored areas in the Southern Ocean, our knowledge regarding its fish taxonomy and diversity has been sparse. eDNA metabarcoding, as an emerging and promising tool for marine biodiversity research and monitoring, has been widely used across taxa and habitats. During the 38th Chinese Antarctic Research Expedition (CHINARE-38), we collected seawater and surface sediment samples from 38 stations in the Cosmonaut Sea and performed the first, to our knowledge, eDNA analysis of fish biodiversity in the Southern Ocean based on the molecular markers of 12S rRNA and 16S rRNA. There were 48 fish species detected by the two markers in total, with 30 and 34 species detected by the 12S rRNA and 16S rRNA marker, respectively. This was more than the trawling results (19 species) and historical survey records (16 species, "BROKE-West" cruise). With some nonsignificant differences between the Gunnerus Ridge and the Oceanic Area of Enderby Land, the Cosmonaut Sea had a richer fish biodiversity in this research compared with previous studies, and its overall composition and distribution patterns were consistent with what we know in East Antarctica. We also found that the eDNA composition of fish in the Cosmonaut Sea might be related to some environmental factors. Our study demonstrated that the use of the eDNA technique for Antarctic fish biodiversity research is likely to yield more information with less sampling effort than traditional methods. In the context of climate change, the eDNA approach will provide a novel and powerful tool that is complementary to traditional methods for polar ecology research.
Collapse
Affiliation(s)
- Yuzhuo Liao
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China; College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Xing Miao
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Rui Wang
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Ran Zhang
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Hai Li
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
| | - Longshan Lin
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
| |
Collapse
|
9
|
Takahashi M, Saccò M, Kestel JH, Nester G, Campbell MA, van der Heyde M, Heydenrych MJ, Juszkiewicz DJ, Nevill P, Dawkins KL, Bessey C, Fernandes K, Miller H, Power M, Mousavi-Derazmahalleh M, Newton JP, White NE, Richards ZT, Allentoft ME. Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162322. [PMID: 36801404 DOI: 10.1016/j.scitotenv.2023.162322] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species and community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this is only possible with an in-depth overview of the technological advancements and a discussion of the pros and cons of available methods. We therefore conducted a systematic literature review of 407 peer-reviewed papers on aquatic eDNA published between 2012 and 2021. We observed a gradual increase in the annual number of publications from four (2012) to 28 (2018), followed by a rapid growth to 124 publications in 2021. This was mirrored by a tremendous diversification of methods in all aspects of the eDNA workflow. For example, in 2012 only freezing was applied to preserve filter samples, whereas we recorded 12 different preservation methods in the 2021 literature. Despite an ongoing standardisation debate in the eDNA community, the field is seemingly moving fast in the opposite direction and we discuss the reasons and implications. Moreover, by compiling the largest PCR-primer database to date, we provide information on 522 and 141 published species-specific and metabarcoding primers targeting a wide range of aquatic organisms. This works as a user-friendly 'distillation' of primer information that was hitherto scattered across hundreds of papers, but the list also reflects which taxa are commonly studied with eDNA technology in aquatic environments such as fish and amphibians, and reveals that groups such as corals, plankton and algae are under-studied. Efforts to improve sampling and extraction methods, primer specificity and reference databases are crucial to capture these ecologically important taxa in future eDNA biomonitoring surveys. In a rapidly diversifying field, this review synthetises aquatic eDNA procedures and can guide eDNA users towards best practice.
Collapse
Affiliation(s)
- Miwa Takahashi
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, Western Australia, Australia.
| | - Mattia Saccò
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia.
| | - Joshua H Kestel
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Georgia Nester
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Matthew A Campbell
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Mieke van der Heyde
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Matthew J Heydenrych
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Jarman Laboratory, Indian Ocean Marine Research Centre, School of Biological Sciences, University of Western Australia, Australia
| | - David J Juszkiewicz
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Kathryn L Dawkins
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Cindy Bessey
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Oceans and Atmosphere, Crawley, Western Australia, Australia
| | - Kristen Fernandes
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Haylea Miller
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, Western Australia, Australia
| | - Matthew Power
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Mahsa Mousavi-Derazmahalleh
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Joshua P Newton
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Zoe T Richards
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
10
|
Pont D, Meulenbroek P, Bammer V, Dejean T, Erős T, Jean P, Lenhardt M, Nagel C, Pekarik L, Schabuss M, Stoeckle BC, Stoica E, Zornig H, Weigand A, Valentini A. Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR. Mol Ecol Resour 2023; 23:396-409. [PMID: 36151931 DOI: 10.1111/1755-0998.13715] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 07/21/2022] [Accepted: 09/15/2022] [Indexed: 01/04/2023]
Abstract
Environmental DNA (eDNA) metabarcoding is an effective method for studying fish communities but allows only an estimation of relative species abundance (density/biomass). Here, we combine metabarcoding with an estimation of the total abundance of eDNA amplified by our universal marker (teleo) using a quantitative (q)PCR approach to infer the absolute abundance of fish species. We carried out a 2850-km eDNA survey within the Danube catchment using a spatial integrative sampling protocol coupled with traditional electrofishing for fish biomass and density estimation. Total fish eDNA concentrations and total fish abundance were highly correlated. The correlation between eDNA concentrations per taxon and absolute specific abundance was of comparable strength when all sites were pooled and remained significant when the sites were considered separately. Furthermore, a nonlinear mixed model showed that species richness was underestimated when the amount of teleo-DNA extracted from a sample was below a threshold of 0.65 × 106 copies of eDNA. This result, combined with the decrease in teleo-DNA concentration by several orders of magnitude with river size, highlights the need to increase sampling effort in large rivers. Our results provide a comprehensive description of longitudinal changes in fish communities and underline our combined metabarcoding/qPCR approach for biomonitoring and bioassessment surveys when a rough estimate of absolute species abundance is sufficient.
Collapse
Affiliation(s)
- Didier Pont
- Institute of Hydrobiology and Aquatic Ecosystem Management, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Paul Meulenbroek
- Institute of Hydrobiology and Aquatic Ecosystem Management, University of Natural Resources and Life Sciences, Vienna, Austria
- WasserCluster Lunz -Biologische Station GmbH, Lunz am See, Austria
| | - Vincenz Bammer
- Bundesamt für Wasserwirtschaft, Institut für Gewässerökologie und Fischereiwirtschaft, Abteilung Gewässerökologie, Mondsee, Austria
| | | | - Tibor Erős
- Balaton Limnological Research Institute, Eötvös Lor'and Research Network (ELKH), Tihany, Hungary
| | | | - Mirjana Lenhardt
- Institute for Multidisciplinary Research, Institute for Biological Research "Siniša Stanković," National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Christoffer Nagel
- Technical University of Munich, Chair of Aquatic Systems Biology, Freising-Weihenstephan, Germany
| | - Ladislav Pekarik
- Plant Science and Biodiversity Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Bernhard C Stoeckle
- Technical University of Munich, Chair of Aquatic Systems Biology, Freising-Weihenstephan, Germany
| | - Elena Stoica
- National Institute for Marine Research and Development "Grigore Antipa,", Constanţa, Romania
| | - Horst Zornig
- PRO FISCH OG Ecological Consultants, Vienna, Austria
| | | | | |
Collapse
|
11
|
Tsuji S, Inui R, Nakao R, Miyazono S, Saito M, Kono T, Akamatsu Y. Quantitative environmental DNA metabarcoding shows high potential as a novel approach to quantitatively assess fish community. Sci Rep 2022; 12:21524. [PMID: 36513686 PMCID: PMC9747787 DOI: 10.1038/s41598-022-25274-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
The simultaneous conservation of species richness and evenness is important to effectively reduce biodiversity loss and keep ecosystem health. Environmental DNA (eDNA) metabarcoding has been used as a powerful tool for identifying community composition, but it does not necessarily provide quantitative information due to several methodological limitations. Thus, the quantification of eDNA through metabarcoding is an important frontier of eDNA-based biomonitoring. Particularly, the qMiSeq approach has recently been developed as a quantitative metabarcoding method and has attracted much attention due to its usefulness. The aim here was to evaluate the performance of the qMiSeq approach as a quantitative monitoring tool for fish communities by comparing the quantified eDNA concentrations with the results of fish capture surveys. The eDNA water sampling and the capture surveys using the electrical shocker were conducted at a total of 21 sites in four rivers in Japan. As a result, we found significant positive relationships between the eDNA concentrations of each species quantified by qMiSeq and both the abundance and biomass of each captured taxon at each site. Furthermore, for seven out of eleven taxa, a significant positive relationship was observed between quantified DNA concentrations by sample and the abundance and/or biomass. In total, our results demonstrated that eDNA metabarcoding with the qMiSeq approach is a suitable and useful tool for quantitative monitoring of fish communities. Due to the simplicity of the eDNA analysis, the eDNA metabarcoding with qMiSeq approach would promote further growth of quantitative monitoring of biodiversity.
Collapse
Affiliation(s)
- Satsuki Tsuji
- grid.258799.80000 0004 0372 2033Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto, 606–8502 Japan ,grid.268397.10000 0001 0660 7960Graduate School of Science and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube, Yamaguchi, 755–8611 Japan
| | - Ryutei Inui
- grid.418051.90000 0000 8774 3245Faculty of Socio-Environmental Studies, Fukuoka Institute of Technology, Wajiro-Higashi, Higashi-Ku, Fukuoka, 811–0295 Japan
| | - Ryohei Nakao
- grid.268397.10000 0001 0660 7960Graduate School of Science and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube, Yamaguchi, 755–8611 Japan
| | - Seiji Miyazono
- grid.268397.10000 0001 0660 7960Graduate School of Science and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube, Yamaguchi, 755–8611 Japan
| | - Minoru Saito
- grid.268397.10000 0001 0660 7960Graduate School of Science and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube, Yamaguchi, 755–8611 Japan ,grid.452611.50000 0001 2107 8171Fisheries Division, Japan International Research Center for Agricultural Sciences, 1-1, Ohwashi, Tsukuba, Ibaraki 305–8686 Japan
| | - Takanori Kono
- grid.268397.10000 0001 0660 7960Graduate School of Science and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube, Yamaguchi, 755–8611 Japan ,grid.472015.50000 0000 9513 8387Aqua Restoration Research Center, Public Works Research Institute, National Research and Development Agency, Kawashima, Kasada-Machi, Kakamigahara, Gifu, 501–6021 Japan
| | - Yoshihisa Akamatsu
- grid.268397.10000 0001 0660 7960Graduate School of Science and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube, Yamaguchi, 755–8611 Japan
| |
Collapse
|
12
|
Environmental DNA (eDNA): Powerful Technique for Biodiversity Conservation. J Nat Conserv 2022. [DOI: 10.1016/j.jnc.2022.126325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
13
|
Littlefair JE, Rennie MD, Cristescu ME. Environmental nucleic acids: A field-based comparison for monitoring freshwater habitats using eDNA and eRNA. Mol Ecol Resour 2022; 22:2928-2940. [PMID: 35730338 PMCID: PMC9796649 DOI: 10.1111/1755-0998.13671] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 05/03/2022] [Accepted: 06/01/2022] [Indexed: 01/01/2023]
Abstract
Nucleic acids released by organisms and isolated from environmental substrates are increasingly being used for molecular biomonitoring. While environmental DNA (eDNA) has received much attention, the potential of environmental RNA as a biomonitoring tool remains under-explored. Several recent studies using paired DNA and RNA metabarcoding of bulk samples suggest that RNA might better reflect "metabolically active" parts of the community. However, such studies mainly capture organismal eDNA and eRNA. For larger eukaryotes, isolation of extra-organismal RNA will be important, but viability needs to be examined in a field-based setting. In this study we evaluate (a) whether extra-organismal eRNA release from macroeukaryotes can be detected given its supposedly rapid degradation, and (b) if the same field collection methods for eDNA can be applied to eRNA. We collected eDNA and eRNA from water in lakes where fish community composition is well documented, enabling a comparison between the two nucleic acids in two different seasons with monitoring using conventional methods. We found that eRNA is released from macroeukaryotes and can be filtered from water and metabarcoded in a similar manner as eDNA to reliably provide species composition information. eRNA had a small but significantly greater true positive rate than eDNA, indicating that it correctly detects more species known to exist in the lakes. Given relatively small differences between the two molecules in describing fish community composition, we conclude that if eRNA provides significant advantages in terms of lability, it is a strong candidate to add to the suite of molecular monitoring tools.
Collapse
Affiliation(s)
- Joanne E. Littlefair
- Department of BiologyMcGill UniversityMontréalQuebecCanada,Queen Mary University of LondonLondonUK
| | - Michael D. Rennie
- IISD Experimental Lakes AreaWinnipegManitobaCanada,Department of BiologyLakehead UniversityThunder BayOntarioCanada
| | | |
Collapse
|
14
|
Yao M, Zhang S, Lu Q, Chen X, Zhang SY, Kong Y, Zhao J. Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward. Mol Ecol 2022; 31:5132-5164. [PMID: 35972241 DOI: 10.1111/mec.16659] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 12/15/2022]
Abstract
Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.
Collapse
Affiliation(s)
- Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Shan Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Qi Lu
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Xiaoyu Chen
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Si-Yu Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Yueqiao Kong
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Jindong Zhao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| |
Collapse
|
15
|
Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary. PLoS One 2022; 17:e0266720. [PMID: 35714082 PMCID: PMC9205523 DOI: 10.1371/journal.pone.0266720] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 03/26/2022] [Indexed: 12/21/2022] Open
Abstract
Metabarcoding of environmental DNA is increasingly used for biodiversity assessments in aquatic communities. The efficiency and outcome of these efforts are dependent upon either de novo primer design or selecting an appropriate primer set from the dozens that have already been published. Unfortunately, there is a lack of studies that have directly compared the efficacy of different metabarcoding primers in marine and estuarine systems. Here we evaluate five commonly used primer sets designed to amplify rRNA barcoding genes in fishes and compare their performance using water samples collected from estuarine sites in the highly biodiverse Indian River Lagoon in Florida. Three of the five primer sets amplify a portion of the mitochondrial 12S gene (MiFish_12S, 171bp; Riaz_12S, 106 bp; Valentini_12S, 63 bp), one amplifies 219 bp of the mitochondrial 16S gene (Berry_16S), and the other amplifies 271 bp of the nuclear 18S gene (MacDonald_18S). The vast majority of the metabarcoding reads (> 99%) generated using the 18S primer set assigned to non-target (non-fish) taxa and therefore this primer set was omitted from most analyses. Using a conservative 99% similarity threshold for species level assignments, we detected a comparable number of species (55 and 49, respectively) and similarly high Shannon’s diversity values for the Riaz_12S and Berry_16S primer sets. Meanwhile, just 34 and 32 species were detected using the MiFish_12S and Valentini_12S primer sets, respectively. We were able to amplify both bony and cartilaginous fishes using the four primer sets with the vast majority of reads (>99%) assigned to the former. We detected the greatest number of elasmobranchs (six species) with the Riaz_12S primer set suggesting that it may be a suitable candidate set for the detection of sharks and rays. Of the total 76 fish species that were identified across all datasets, the combined three 12S primer sets detected 85.5% (65 species) while the combination of the Riaz_12S and Berry_16S primers detected 93.4% (71 species). These results highlight the importance of employing multiple primer sets as well as using primers that target different genomic regions. Moreover, our results suggest that the widely adopted MiFish_12S primers may not be the best choice, rather we found that the Riaz_12S primer set was the most effective for eDNA-based fish surveys in our system.
Collapse
|
16
|
Flück B, Mathon L, Manel S, Valentini A, Dejean T, Albouy C, Mouillot D, Thuiller W, Murienne J, Brosse S, Pellissier L. Applying convolutional neural networks to speed up environmental DNA annotation in a highly diverse ecosystem. Sci Rep 2022; 12:10247. [PMID: 35715444 PMCID: PMC9205931 DOI: 10.1038/s41598-022-13412-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/24/2022] [Indexed: 01/04/2023] Open
Abstract
High-throughput DNA sequencing is becoming an increasingly important tool to monitor and better understand biodiversity responses to environmental changes in a standardized and reproducible way. Environmental DNA (eDNA) from organisms can be captured in ecosystem samples and sequenced using metabarcoding, but processing large volumes of eDNA data and annotating sequences to recognized taxa remains computationally expensive. Speed and accuracy are two major bottlenecks in this critical step. Here, we evaluated the ability of convolutional neural networks (CNNs) to process short eDNA sequences and associate them with taxonomic labels. Using a unique eDNA data set collected in highly diverse Tropical South America, we compared the speed and accuracy of CNNs with that of a well-known bioinformatic pipeline (OBITools) in processing a small region (60 bp) of the 12S ribosomal DNA targeting freshwater fishes. We found that the taxonomic labels from the CNNs were comparable to those from OBITools, with high correlation levels for the composition of the regional fish fauna. The CNNs enabled the processing of raw fastq files at a rate of approximately 1 million sequences per minute, which was about 150 times faster than with OBITools. Given the good performance of CNNs in the highly diverse ecosystem considered here, the development of more elaborate CNNs promises fast deployment for future biodiversity inventories using eDNA.
Collapse
Affiliation(s)
- Benjamin Flück
- Department of Environmental System Science, ETH Zürich, 8092, Zurich, Switzerland.
- Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland.
| | - Laëtitia Mathon
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - Stéphanie Manel
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | | | | | - Camille Albouy
- DECOD (Ecosystem Dynamics and Sustainability), IFREMER, INRAE, Institut Agro - Agrocampus Ouest, Rue de l'Ile d'Yeu, BP21105, 44311, Nantes Cedex 3, France
| | - David Mouillot
- MARBEC, Univ. Montpellier,CNRS, IRD, Ifremer, Montpellier, France
- Institut Universitaire de France, IUF, 75231, Paris, France
| | - Wilfried Thuiller
- CNRS, LECA, Laboratoire d'Écologie Alpine, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, 38000, Grenoble, France
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité Biologique (UMR5174), CNRS, IRD, Université Paul Sabatier, Toulouse, France
| | - Sébastien Brosse
- Laboratoire Evolution et Diversité Biologique (UMR5174), CNRS, IRD, Université Paul Sabatier, Toulouse, France
| | - Loïc Pellissier
- Department of Environmental System Science, ETH Zürich, 8092, Zurich, Switzerland.
- Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland.
| |
Collapse
|
17
|
Egeter B, Veríssimo J, Lopes-Lima M, Chaves C, Pinto J, Riccardi N, Beja P, Fonseca NA. Speeding up the detection of invasive bivalve species using environmental DNA: a Nanopore and Illumina sequencing comparison. Mol Ecol Resour 2022; 22:2232-2247. [PMID: 35305077 DOI: 10.1111/1755-0998.13610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 02/09/2022] [Accepted: 03/02/2022] [Indexed: 11/30/2022]
Abstract
Traditional detection of aquatic invasive species via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindrances, but sample processing is often lengthy. More recently, portable nanopore sequencing technology has become available, which has the potential to make molecular detection of invasive species more widely accessible and substantially decrease sample turnaround times. However, nanopore-sequenced reads have a much higher error rate than those produced by Illumina platforms, which has so far hindered the adoption of this technology. We provide a detailed laboratory protocol and bioinformatic tools (msi package) to increase the reliability of nanopore sequencing to detect invasive species, and we test its application using invasive bivalves while comparing it with Illumina-based sequencing. We sampled water from sites with pre-existing bivalve occurrence and abundance data, and contrasting bivalve communities, in Italy and Portugal. Samples were extracted, amplified, and sequenced by the two platforms. The mean agreement between sequencing methods was 69% and the difference between methods was non-significant. The lack of detections of some species at some sites could be explained by their known low abundances. This is the first reported use of MinION to detect aquatic invasive species from eDNA samples.
Collapse
Affiliation(s)
- Bastian Egeter
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,NatureMetrics, Bakeham Lane, Egham, Surrey, TW20 9TY, U.K
| | - Joana Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Manuel Lopes-Lima
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,IUCN SSC Mollusc Specialist Group, c/o 219 Huntingdon Road, Cambridge, CB3 0DL, U.K
| | - Cátia Chaves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Joana Pinto
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | | | - Pedro Beja
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,CIBIO/InBIO, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Nuno A Fonseca
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| |
Collapse
|
18
|
Sakata MK, Kawata MU, Kurabayashi A, Kurita T, Nakamura M, Shirako T, Kakehashi R, Nishikawa K, Hossman MY, Nishijima T, Kabamoto J, Miya M, Minamoto T. Development and evaluation of PCR primers for environmental DNA (eDNA) metabarcoding of Amphibia. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.76534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Biodiversity monitoring is important for the conservation of natural ecosystems in general, but particularly for amphibians, whose populations are pronouncedly declining. However, amphibians’ ecological traits (e.g. nocturnal or aquatic) often prevent their precise monitoring. Environmental DNA (eDNA) metabarcoding – analysis of extra-organismal DNA released into the environment – allows the easy and effective monitoring of the biodiversity of aquatic organisms. Here, we developed and tested the utility of original PCR primer sets. First, we conducted in vitro PCR amplification tests with universal primer candidates using total DNA extracted from amphibian tissues. Five primer sets successfully amplified the target DNA fragments (partial 16S rRNA gene fragments of 160–311 bp) from all 16 taxa tested (from the three living amphibian orders Anura, Caudata and Gymnophiona). Next, we investigated the taxonomic resolution retrieved using each primer set. The results revealed that the universal primer set “Amph16S” had the highest resolution amongst the tested sets. Finally, we applied Amph16S to the water samples collected in the field and evaluated its detection capability by comparing the species detected using eDNA and physical survey (capture-based sampling and visual survey) in multiple agricultural ecosystems across Japan (160 sites in 10 areas). The eDNA metabarcoding with Amph16S detected twice as many species as the physical surveys (16 vs. 8 species, respectively), indicating the effectiveness of Amph16S in biodiversity monitoring and ecological research for amphibian communities.
Collapse
|
19
|
de Melo AA, Nunes R, Telles MPDC. Same information, new applications: revisiting primers for the avian COI gene and improving DNA barcoding identification. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00507-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
20
|
Feist SM, Lance RF. Advanced molecular-based surveillance of quagga and zebra mussels: A review of environmental DNA/RNA (eDNA/eRNA) studies and considerations for future directions. NEOBIOTA 2021. [DOI: 10.3897/neobiota.66.60751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sensitive methods, capable of rapidly and accurately detecting aquatic invasive species, are in demand. Molecular-based approaches, such as environmental DNA (eDNA) surveys, satisfy these requirements and have grown in popularity. As such, eDNA surveys could aid the effort to combat the colonisation and spread of two notoriously invasive freshwater mussel species, the quagga mussel (Dreissena rostriformis bugensis) and zebra mussel (D. polymorpha), through improved surveillance ability. Here, we provide a review of dreissenid eDNA literature (both grey and published), summarising efforts involved in the development of various assays for use in multiple different technologies (e.g. quantitative PCR, high-throughput sequencing and loop-mediated isothermal amplification) and sampling scenarios. We discuss important discoveries made along the way, including novel revelations involving environmental RNA (eRNA), as well as the advantages and limitations of available methods and instrumentation. In closing, we highlight critical remaining gaps, where further investigation could lead to advancements in dreissenid monitoring capacity.
Collapse
|
21
|
Impact of anthropogenic activities on changes of ichthyofauna in the middle and lower Xiang River. AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2021.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
22
|
Shu L, Ludwig A, Peng Z. Environmental DNA metabarcoding primers for freshwater fish detection and quantification: In silico and in tanks. Ecol Evol 2021; 11:8281-8294. [PMID: 34188886 PMCID: PMC8216916 DOI: 10.1002/ece3.7658] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 03/25/2021] [Accepted: 04/19/2021] [Indexed: 11/10/2022] Open
Abstract
Environmental DNA (eDNA) techniques refer to utilizing the organisms' DNA extracted from environment samples to genetically identify target species without capturing actual organisms. eDNA metabarcoding via high-throughput sequencing can simultaneously detect multiple fish species from a single water sample, which is a powerful tool for the qualitative detection and quantitative estimates of multiple fish species. However, sequence counts obtained from eDNA metabarcoding may be influenced by many factors, of which primer bias is one of the foremost causes of methodological error. The performance of 18 primer pairs for COI, cytb, 12S rRNA, and 16S rRNA mitochondrial genes, which are all frequently used in fish eDNA metabarcoding, were evaluated in the current study. The ribosomal gene markers performed better than the protein-coding gene markers during in silico screening, resulting in higher taxonomic coverage and appropriate barcode lengths. Four primer pairs-AcMDB07, MiFish-U, Ve16S1, and Ve16S3-designed for various regions of the 12S and 16S rRNA genes were screened for tank metabarcoding in a case study targeting six freshwater fish species. The four primer pairs were able to accurately detect all six species in different tanks, while only MiFish-U, Ve16S1, and Ve16S3 revealed a significant positive relationship between species biomass and read count for the pooled tank data. The positive relationship could not be found in all species within the tanks. Additionally, primer efficiency differed depending on the species while primer preferential species varied in different fish assemblages. This case study supports the potential for eDNA metabarcoding to assess species diversity in natural ecosystems and provides an alternative strategy to evaluate the performance of candidate primers before application of eDNA metabarcoding in natural ecosystems.
Collapse
Affiliation(s)
- Lu Shu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)School of Life SciencesSouthwest UniversityChongqingChina
| | - Arne Ludwig
- Department of Evolutionary GeneticsLeibniz‐Institute for Zoo and Wildlife ResearchBerlinGermany
- Albrecht Daniel Thaer‐InstituteFaculty of Life SciencesHumboldt University BerlinBerlinGermany
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)School of Life SciencesSouthwest UniversityChongqingChina
| |
Collapse
|
23
|
Bombin S, Wysor B, Lopez-Bautista JM. Assessment of littoral algal diversity from the northern Gulf of Mexico using environmental DNA metabarcoding. JOURNAL OF PHYCOLOGY 2021; 57:269-278. [PMID: 33107058 DOI: 10.1111/jpy.13087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
Traditional methods for algal biodiversity monitoring are costly and time inefficient because they rely on high-level taxonomic expertise to address species identity problems involving phenotypic plasticity and morphological convergence. These problems are exacerbated in regions such as the Gulf of Mexico, that has a limited history of phycological exploration, but that are economically important or threatened by numerous anthropogenic stressors. Given the high pace of disturbance to natural systems, there is a critical need for expedient and cost-effective tools for the study of benthic algal communities. Here we document the use of environmental DNA metabarcoding, using the partial LSU rDNA and 23S rDNA plastid molecular markers, to elucidate littoral algal diversity in the Northern Gulf of Mexico. We assigned 73.7% of algal OTUs to genus and 59.6% to species ranks. Our current study detected molecular signals for 35 algal/protist species with no previous reports in the Gulf of Mexico, thus providing an important, molecular-validated, baseline of species richness for this region. We also make several bioinformatic recommendations for the efficient use of high-throughput sequence data to assess biological communities.
Collapse
Affiliation(s)
- Sergei Bombin
- Department of Biological Sciences, The University of Alabama, 1325 Science and Engineering Complex (SEC), 300 Hackberry Lane, Tuscaloosa, Alabama, 35487-0344, USA
| | - Brian Wysor
- Department of Biology, Marine Biology & Environmental Science, Roger Williams University, 1 Old Ferry Road, Bristol, Rhode Island, 02809, USA
| | - Juan M Lopez-Bautista
- Department of Biological Sciences, The University of Alabama, 1325 Science and Engineering Complex (SEC), 300 Hackberry Lane, Tuscaloosa, Alabama, 35487-0344, USA
| |
Collapse
|
24
|
Jo T, Tomita S, Kohmatsu Y, Osathanunkul M, Ushimaru A, Minamoto T. Seasonal monitoring of Hida salamander Hynobius kimurae using environmental DNA with a genus-specific primer set. ENDANGER SPECIES RES 2020. [DOI: 10.3354/esr01073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The diversity and the abundance of amphibians have dramatically declined globally over the past 30 years, and the monitoring and conservation of their habitats is essential. However, traditional methods such as bait trapping and mark-recapture are costly, and morphological identification usually requires a high level of taxonomic expertise. Here, seasonal surveillances of Hida salamanderHynobius kimuraewere performed by means of environmental DNA (eDNA) analysis withHynobius-specific primers and a species-specific TaqMan probe. Water sampling and visual surveys were conducted seasonally in a stream in Kyoto Prefecture, Japan. Detection rates of eDNA were then calculated by real-time PCR, and eDNA site occupancy probability was estimated by multi-scale occupancy modeling. The eDNA-based detection rate of Hida salamander was 76.7%, whereas the visual survey-based detection rate was 23.3%, and target eDNA was detected at almost all sites where the presence of target species was visually confirmed. Moreover, factors relating to the site- and sample-level occurrence probabilities of the target eDNA differed depending on the developmental stage of the target species. Our findings support previous studies showing that eDNA analysis enables an effective assessment of amphibian distributions without damaging the organisms or their habitat, and we compare for the first time the site occupancy probability of amphibian eDNA throughout the life cycle of an amphibian species. The present study contributes to the development of eDNA analysis as a tool for understanding the distribution and seasonal activity of amphibian species and will thus aid in the planning of conservation measures and habitat restoration for these species.
Collapse
Affiliation(s)
- T Jo
- Graduate School of Human Development and Environment, Kobe University, 3-11, Tsurukabuto, Nada-ku, Kobe City, Hyogo 657-8501, Japan
- Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - S Tomita
- Graduate School of Human Development and Environment, Kobe University, 3-11, Tsurukabuto, Nada-ku, Kobe City, Hyogo 657-8501, Japan
| | - Y Kohmatsu
- Ritsumeikan-Global Innovation Research Organization, 56-1, Tojiin-Kitamachi, Kita-ku, Kyoto City, Kyoto 603-8577, Japan
| | - M Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - A Ushimaru
- Graduate School of Human Development and Environment, Kobe University, 3-11, Tsurukabuto, Nada-ku, Kobe City, Hyogo 657-8501, Japan
| | - T Minamoto
- Graduate School of Human Development and Environment, Kobe University, 3-11, Tsurukabuto, Nada-ku, Kobe City, Hyogo 657-8501, Japan
| |
Collapse
|
25
|
Banchi E, Ametrano CG, Tordoni E, Stanković D, Ongaro S, Tretiach M, Pallavicini A, Muggia L. Environmental DNA assessment of airborne plant and fungal seasonal diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 738:140249. [PMID: 32806340 DOI: 10.1016/j.scitotenv.2020.140249] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/25/2020] [Accepted: 06/14/2020] [Indexed: 05/06/2023]
Abstract
Environmental DNA (eDNA) metabarcoding and metagenomics analyses can improve taxonomic resolution in biodiversity studies. Only recently, these techniques have been applied in aerobiology, to target bacteria, fungi and plants in airborne samples. Here, we present a nine-month aerobiological study applying eDNA metabarcoding in which we analyzed simultaneously airborne diversity and variation of fungi and plants across five locations in North and Central Italy. We correlated species composition with the ecological characteristics of the sites and the seasons. The most abundant taxa among all sites and seasons were the fungal genera Cladosporium, Alternaria, and Epicoccum and the plant genera Brassica, Corylus, Cupressus and Linum, the latter being much more variable among sites. PERMANOVA and indicator species analyses showed that the plant diversity from air samples is significantly correlated with seasons, while that of fungi varied according to the interaction between seasons and sites. The results consolidate the performance of a new eDNA metabarcoding pipeline for the simultaneous amplification and analysis of airborne plant and fungal particles. They also highlight the promising complementarity of this approach with more traditional biomonitoring frameworks and routine reports of air quality provided by environmental agencies.
Collapse
Affiliation(s)
- Elisa Banchi
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy; National Institute of Oceanography and Applied Geophysics - OGS, via Piccard 54, I-34151 Trieste, Italy
| | - Claudio G Ametrano
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy
| | - Enrico Tordoni
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy
| | - David Stanković
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy; Marine Biology Station, National Institute of Biology, Fornače 41, SLO-6330 Piran, Slovenia
| | - Silvia Ongaro
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy
| | - Mauro Tretiach
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy; National Institute of Oceanography and Applied Geophysics - OGS, via Piccard 54, I-34151 Trieste, Italy.
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy.
| |
Collapse
|
26
|
Zhang S, Zhao J, Yao M. A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13485] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shan Zhang
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
| | - Jindong Zhao
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
- State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Meng Yao
- School of Life Sciences Peking University Beijing China
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
| |
Collapse
|
27
|
Suter L, Polanowski AM, Clarke LJ, Kitchener JA, Deagle BE. Capturing open ocean biodiversity: Comparing environmental DNA metabarcoding to the continuous plankton recorder. Mol Ecol 2020; 30:3140-3157. [PMID: 32767849 DOI: 10.1111/mec.15587] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/24/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022]
Abstract
Environmental DNA (eDNA) metabarcoding is emerging as a novel, objective tool for monitoring marine metazoan biodiversity. Zooplankton biodiversity in the vast open ocean is currently monitored through continuous plankton recorder (CPR) surveys, using ship-based bulk plankton sampling and morphological identification. We assessed whether eDNA metabarcoding (2 L filtered seawater) could capture similar Southern Ocean zooplankton biodiversity as conventional CPR bulk sampling (~1,500 L filtered seawater per CPR sample). We directly compared eDNA metabarcoding with (a) conventional morphological CPR sampling and (b) bulk DNA metabarcoding of CPR collected plankton (two transects for each comparison, 40 and 44 paired samples, respectively). A metazoan-targeted cytochrome c oxidase I (COI) marker was used to characterize species-level diversity. In the 2 L seawater eDNA samples, this marker amplified large amounts of non-metazoan picoplanktonic algae, but eDNA metabarcoding still detected up to 1.6 times more zooplankton species than morphologically analysed bulk CPR samples. COI metabarcoding of bulk DNA samples mostly avoided nonmetazoan amplifications and recovered more zooplankton species than eDNA metabarcoding. However, eDNA metabarcoding detected roughly two thirds of metazoan species and identified similar taxa contributing to community differentiation across the subtropical front separating transects. We observed a diurnal pattern in eDNA data for copepods which perform diel vertical migrations, indicating a surprisingly short temporal eDNA signal. Compared to COI, a eukaryote-targeted 18S ribosomal RNA marker detected a higher proportion, but lower diversity, of metazoans in eDNA. With refinement and standardization of methodology, eDNA metabarcoding could become an efficient tool for monitoring open ocean biodiversity.
Collapse
Affiliation(s)
- Leonie Suter
- Australian Antarctic Division, Department of Agriculture, Water and the Environment, Kingston, Tas., Australia
| | - Andrea Maree Polanowski
- Australian Antarctic Division, Department of Agriculture, Water and the Environment, Kingston, Tas., Australia
| | - Laurence John Clarke
- Australian Antarctic Division, Department of Agriculture, Water and the Environment, Kingston, Tas., Australia.,Institute of Marine and Antarctic Studies, University of Tasmania, Hobart, Tas., Australia
| | - John Andrew Kitchener
- Australian Antarctic Division, Department of Agriculture, Water and the Environment, Kingston, Tas., Australia
| | - Bruce Emerson Deagle
- Australian Antarctic Division, Department of Agriculture, Water and the Environment, Kingston, Tas., Australia.,Commonwealth Scientific and Industrial Research Organisation, Battery Point, Tas., Australia
| |
Collapse
|
28
|
Shu L, Ludwig A, Peng Z. Standards for Methods Utilizing Environmental DNA for Detection of Fish Species. Genes (Basel) 2020; 11:E296. [PMID: 32168762 PMCID: PMC7140814 DOI: 10.3390/genes11030296] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/13/2020] [Accepted: 03/07/2020] [Indexed: 11/30/2022] Open
Abstract
Environmental DNA (eDNA) techniques are gaining attention as cost-effective, non-invasive strategies for acquiring information on fish and other aquatic organisms from water samples. Currently, eDNA approaches are used to detect specific fish species and determine fish community diversity. Various protocols used with eDNA methods for aquatic organism detection have been reported in different eDNA studies, but there are no general recommendations for fish detection. Herein, we reviewed 168 papers to supplement and highlight the key criteria for each step of eDNA technology in fish detection and provide general suggestions for eliminating detection errors. Although there is no unified recommendation for the application of diverse eDNA in detecting fish species, in most cases, 1 or 2 L surface water collection and eDNA capture on 0.7-μm glass fiber filters followed by extraction with a DNeasy Blood and Tissue Kit or PowerWater DNA Isolation Kit are useful for obtaining high-quality eDNA. Subsequently, species-specific quantitative polymerase chain reaction (qPCR) assays based on mitochondrial cytochrome b gene markers or eDNA metabarcoding based on both 12S and 16S rRNA markers via high-throughput sequencing can effectively detect target DNA or estimate species richness. Furthermore, detection errors can be minimized by mitigating contamination, negative control, PCR replication, and using multiple genetic markers. Our aim is to provide a useful strategy for fish eDNA technology that can be applied by researchers, advisors, and managers.
Collapse
Affiliation(s)
- Lu Shu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China;
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, 10315 Berlin, Germany
- Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt University Berlin, 10115 Berlin, Germany
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China;
| |
Collapse
|
29
|
Westfall KM, Therriault TW, Abbott CL. A new approach to molecular biosurveillance of invasive species using DNA metabarcoding. GLOBAL CHANGE BIOLOGY 2020; 26:1012-1022. [PMID: 31657513 DOI: 10.1111/gcb.14886] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 09/10/2019] [Accepted: 10/17/2019] [Indexed: 06/10/2023]
Abstract
Non-indigenous species (NIS) reach every corner of the world, at times wreaking havoc on ecosystems and costing the global economy billions of dollars. A rapid and accurate biosurveillance tool tailored to a particular biogeographic region is needed to detect NIS when they are first introduced into an area as traditional detection methods are expensive and require specialized expertise. Metabarcoding of environmental and community DNA meets those biosurveillance requirements; a novel tool tailored to the Northwest Pacific Ocean is presented here using an approach that could revolutionize early detection of NIS. Eight newly designed genetic markers for multiple gene regions were implemented to meet the stringent taxonomic requirements for the detection of NIS across four major marine phyla. The tool was considered highly successful because it identified 12 known NIS in the study area and a further seven species representing potential new records. Overall community composition detected here was statistically different between substrate types; zooplankton sampling accounted for significantly higher species richness than filtered sea water in most cases, but this was dominated by mollusk and arthropod species. Both substrate types sampled were required to identify the wide taxonomic breadth of known NIS in the study area. Intensive sampling is known to be paramount for the detection of rare species, including new incursions of NIS, thus it is recommended to include diverse DNA sampling protocols based on species' life-history characteristics for broad detection capacity. Application of a metabarcoding-based molecular biosurveillance tool optimized for biogeographic regions enables rapid and accurate early detection across a wide taxonomic range to allow quick implementation of eradication or control efforts and potentially mitigate some of the devastating effects of NIS worldwide.
Collapse
Affiliation(s)
| | - Thomas W Therriault
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC, Canada
| | - Cathryn L Abbott
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC, Canada
| |
Collapse
|
30
|
Elbrecht V, Braukmann TW, Ivanova NV, Prosser SW, Hajibabaei M, Wright M, Zakharov EV, Hebert PD, Steinke D. Validation of COI metabarcoding primers for terrestrial arthropods. PeerJ 2019; 7:e7745. [PMID: 31608170 PMCID: PMC6786254 DOI: 10.7717/peerj.7745] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 08/25/2019] [Indexed: 01/08/2023] Open
Abstract
Metabarcoding can rapidly determine the species composition of bulk samples and thus aids biodiversity and ecosystem assessment. However, it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been sufficiently evaluated. This study tests the performance of 36 primer sets on a mock community containing 374 insect species. Amplification success was assessed with gradient PCRs and the 21 most promising primer sets selected for metabarcoding. These 21 primer sets were also tested by metabarcoding a Malaise trap sample. We identified eight primer sets, mainly those including inosine and/or high degeneracy, that recovered more than 95% of the species in the mock community. Results from the Malaise trap sample were congruent with the mock community, but primer sets generating short amplicons produced potential false positives. Taxon recovery from both mock community and Malaise trap sample metabarcoding were used to select four primer sets for additional evaluation at different annealing temperatures (40-60 °C) using the mock community. The effect of temperature varied by primer pair but overall it only had a minor effect on taxon recovery. This study reveals the weak performance of some primer sets employed in past studies. It also demonstrates that certain primer sets can recover most taxa in a diverse species assemblage. Thus, based our experimental set up, there is no need to employ several primer sets targeting the same gene region. We identify several suitable primer sets for arthropod metabarcoding, and specifically recommend BF3 + BR2, as it is not affected by primer slippage and provides maximal taxonomic resolution. The fwhF2 + fwhR2n primer set amplifies a shorter fragment and is therefore ideal when targeting degraded DNA (e.g., from gut contents).
Collapse
Affiliation(s)
- Vasco Elbrecht
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Natalia V. Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Sean W.J. Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Michael Wright
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Paul D.N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| |
Collapse
|
31
|
Multiplex real-time PCR enables the simultaneous detection of environmental DNA from freshwater fishes: a case study of three exotic and three threatened native fishes in Japan. Biol Invasions 2019. [DOI: 10.1007/s10530-019-02102-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
32
|
Collins RA, Bakker J, Wangensteen OS, Soto AZ, Corrigan L, Sims DW, Genner MJ, Mariani S. Non‐specific amplification compromises environmental DNA metabarcoding with COI. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13276] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
| | - Judith Bakker
- Department of Biological Sciences Florida International University Miami FL USA
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
| | - Owen S. Wangensteen
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
- Norwegian College of Fishery Science, UiT The Arctic University of Norway Tromsø Norway
| | - Ana Z. Soto
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
| | - Laura Corrigan
- Environment Agency Tyneside House Newcastle upon Tyne UK
| | - David W. Sims
- The Laboratory Marine Biological Association of the United Kingdom Plymouth UK
- Ocean and Earth Science, National Oceanography Centre Southampton University of Southampton Southampton UK
| | | | - Stefano Mariani
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
- School of Natural Sciences & Psychology Liverpool John Moores University Liverpool UK
| |
Collapse
|
33
|
Jo T, Arimoto M, Murakami H, Masuda R, Minamoto T. Particle Size Distribution of Environmental DNA from the Nuclei of Marine Fish. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:9947-9956. [PMID: 31328917 DOI: 10.1021/acs.est.9b02833] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Environmental DNA (eDNA) analyses have enabled a more efficient surveillance of species distribution and composition than conventional methods. However, the characteristics and dynamics of eDNA (e.g., origin, state, transport, and fate) remain unknown. This is especially limited for the eDNA derived from nuclei (nu-eDNA), which has recently been used in eDNA analyses. Here, we compared the particle size distribution (PSD) of nu-eDNA from Japanese Jack Mackerel (Trachurus japonicus) with that of mt-eDNA (eDNA derived from mitochondria) reported in previous studies. We repeatedly sampled rearing water from the tanks under multiple temperatures and fish biomass levels, and quantified the copy numbers of size-fractioned nu-eDNA. We found that the concentration of nu-eDNA was higher than that of mt-eDNA at 3-10 μm size fraction. Moreover, at the 0.8-3 μm and 0.4-0.8 μm size fractions, eDNA concentrations of both types increased with higher temperature and their degradation tended to be suppressed. These results imply that the production of eDNA from large to small size fractions could buffer the degradation of small-sized eDNA, which could improve its persistence in water. Our findings will contribute to refine the difference between nu- and mt-eDNA properties, and assist eDNA analyses as an efficient tool for the conservation of aquatic species.
Collapse
Affiliation(s)
- Toshiaki Jo
- Graduate School of Human Development and Environment , Kobe University , 3-11 Tsurukabuto , Nada-ku, Kobe City , Hyogo 657-8501 , Japan
- Research Fellow of Japan Society for the Promotion of Science , 5-3-1 Kojimachi , Chiyoda-ku, Tokyo , 102-0083 , Japan
| | - Mio Arimoto
- Faculty of Human Development , Kobe University , 3-11 Tsurukabuto , Nada-ku, Kobe City , Hyogo 657-8501 , Japan
| | - Hiroaki Murakami
- Maizuru Fisheries Research Station, Field Science Education and Research Center , Kyoto University , Maizuru , Kyoto 625-0086 , Japan
| | - Reiji Masuda
- Maizuru Fisheries Research Station, Field Science Education and Research Center , Kyoto University , Maizuru , Kyoto 625-0086 , Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment , Kobe University , 3-11 Tsurukabuto , Nada-ku, Kobe City , Hyogo 657-8501 , Japan
| |
Collapse
|
34
|
Piper AM, Batovska J, Cogan NOI, Weiss J, Cunningham JP, Rodoni BC, Blacket MJ. Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance. Gigascience 2019; 8:giz092. [PMID: 31363753 PMCID: PMC6667344 DOI: 10.1093/gigascience/giz092] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 06/25/2019] [Accepted: 07/09/2019] [Indexed: 12/21/2022] Open
Abstract
Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well as track the population levels of established or endemic pests. Where these surveillance traps have low specificity and capture non-target endemic species in excess of the target pests, the need for extensive specimen sorting and identification creates a major diagnostic bottleneck. While the recent development of standardized molecular diagnostics has partly alleviated this requirement, the single specimen per reaction nature of these methods does not readily scale to the sheer number of insects trapped in surveillance programmes. Consequently, target lists are often restricted to a few high-priority pests, allowing unanticipated species to avoid detection and potentially establish populations. DNA metabarcoding has recently emerged as a method for conducting simultaneous, multi-species identification of complex mixed communities and may lend itself ideally to rapid diagnostics of bulk insect trap samples. Moreover, the high-throughput nature of recent sequencing platforms could enable the multiplexing of hundreds of diverse trap samples on a single flow cell, thereby providing the means to dramatically scale up insect surveillance in terms of both the quantity of traps that can be processed concurrently and number of pest species that can be targeted. In this review of the metabarcoding literature, we explore how DNA metabarcoding could be tailored to the detection of invasive insects in a surveillance context and highlight the unique technical and regulatory challenges that must be considered when implementing high-throughput sequencing technologies into sensitive diagnostic applications.
Collapse
Affiliation(s)
- Alexander M Piper
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Jana Batovska
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Noel O I Cogan
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - John Weiss
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - John Paul Cunningham
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - Brendan C Rodoni
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Mark J Blacket
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| |
Collapse
|
35
|
Unmack PJ, Adams M, Bylemans J, Hardy CM, Hammer MP, Georges A. Perspectives on the clonal persistence of presumed 'ghost' genomes in unisexual or allopolyploid taxa arising via hybridization. Sci Rep 2019; 9:4730. [PMID: 30894575 PMCID: PMC6426837 DOI: 10.1038/s41598-019-40865-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/20/2019] [Indexed: 01/19/2023] Open
Abstract
Although hybridization between non-sibling species rarely results in viable or fertile offspring, it occasionally produces self-perpetuating or sexually-parasitic lineages in which ancestral genomes are inherited clonally and thus may persist as ‘ghost species’ after ancestor extinction. Ghost species have been detected in animals and plants, for polyploid and diploid organisms, and across clonal, semi-clonal, and even sexual reproductive modes. Here we use a detailed investigation of the evolutionary and taxonomic status of a newly-discovered, putative ghost lineage (HX) in the fish genus Hypseleotris to provide perspectives on several important issues not previously explored by other studies on ghost species, but relevant to ongoing discussions about their detection, conservation, and artificial re-creation. Our comprehensive genetic (allozymes, mtDNA) and genomic (SNPs) datasets successfully identified a threatened sexual population of HX in one tiny portion of the extensive distribution displayed by two hemi-clonal HX-containing lineages. We also discuss what confidence should be placed on any assertion that an ancestral species is actually extinct, and how to assess whether any putative sexual ancestor represents a pure remnant, as shown here, or a naturally-occurring resurrection via the crossing of compatible clones or hemi-clones.
Collapse
Affiliation(s)
- P J Unmack
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.
| | - M Adams
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Department of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - J Bylemans
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - C M Hardy
- CSIRO Land and Water, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - M P Hammer
- Museum & Art Gallery of the Northern Territory, Darwin, Northern Territory, 0810, Australia
| | - A Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| |
Collapse
|
36
|
Bylemans J, Gleeson DM, Lintermans M, Hardy CM, Beitzel M, Gilligan DM, Furlan EM. Monitoring riverine fish communities through eDNA metabarcoding: determining optimal sampling strategies along an altitudinal and biodiversity gradient. METABARCODING AND METAGENOMICS 2018. [DOI: 10.3897/mbmg.2.30457] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Monitoring aquatic biodiversity through DNA extracted from environmental samples (eDNA) combined with high-throughput sequencing, commonly referred to as eDNA metabarcoding, is increasing in popularity within the scientific community. However, sampling strategies, laboratory protocols and analytical pipelines can influence the results of eDNA metabarcoding surveys. While the impact of laboratory protocols and analytical pipelines have been extensively studied, the importance of sampling strategies on eDNA metabarcoding surveys has not received the same attention. To avoid underestimating local biodiversity, adequate sampling strategies (i.e. sampling intensity and spatial sampling replication) need to be implemented. This study evaluated the impact of sampling strategies along an altitudinal and biodiversity gradient in the upper section of the Murrumbidgee River (Murray-Darling Basin, Australia). An eDNA metabarcoding survey was used to determine the local fish biodiversity and evaluate the influence of sampling intensity and spatial sampling replication on the biodiversity estimates. The results show that optimal eDNA sampling strategies varied between sites and indicate that river morphology, species richness and species abundance affect the optimal sampling intensity and spatial sampling replication needed to accurately assess the fish biodiversity. While the generality of the patterns will need to be confirmed through future studies, these findings provide a basis to guide future eDNA metabarcoding surveys in river systems.
Collapse
|
37
|
Stoeckle MY, Das Mishu M, Charlop-Powers Z. GoFish: A versatile nested PCR strategy for environmental DNA assays for marine vertebrates. PLoS One 2018; 13:e0198717. [PMID: 30533051 PMCID: PMC6289459 DOI: 10.1371/journal.pone.0198717] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 11/21/2018] [Indexed: 12/30/2022] Open
Abstract
Here we describe GoFish, a strategy for single-species environmental DNA (eDNA) presence/absence assays using nested PCR. The assays amplify a mitochondrial 12S rDNA segment with vertebrate metabarcoding primers, followed by nested PCR with M13-tailed, species-specific primers. Sanger sequencing confirms positives detected by gel electrophoresis. We first obtained 12S sequences from 77 fish specimens for 36 northwestern Atlantic taxa not well documented in GenBank. Using these and existing 12S records, we designed GoFish assays for 11 bony fish species common in the lower Hudson River estuary and tested seasonal abundance and habitat preference at two sites. Additional assays detected nine cartilaginous fish species and a marine mammal, bottlenose dolphin, in southern New York Bight. GoFish sensitivity was equivalent to Illumina MiSeq metabarcoding. Unlike quantitative PCR (qPCR), GoFish does not require tissues of target and related species for assay development and a basic thermal cycler is sufficient. Unlike Illumina metabarcoding, indexing and batching samples are unnecessary and advanced bioinformatics expertise is not needed. From water collection to Sanger sequencing results, the assay can be carried out in three days. The main limitations to this approach, which employs metabarcoding primers, are the same as for metabarcoding, namely, inability to distinguish species with shared target sequences and inconsistent amplification of rarer eDNA. In addition, the performance of the 20 assays reported here as compared to other single-species eDNA assays is not known. This approach will be a useful addition to current eDNA methods when analyzing presence/absence of known species, when turnaround time is important, and in educational settings.
Collapse
Affiliation(s)
- Mark Y. Stoeckle
- Program for the Human Environment, The Rockefeller University, New York, New York, United States of America
| | | | - Zachary Charlop-Powers
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, United States of America
| |
Collapse
|