1
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Cai W, MacDonald B, Korabik M, Gradin I, Neave EF, Harper LR, Kenchington E, Riesgo A, Whoriskey FG, Mariani S. Biofouling sponges as natural eDNA samplers for marine vertebrate biodiversity monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174148. [PMID: 38906285 DOI: 10.1016/j.scitotenv.2024.174148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
Environmental DNA (eDNA) analysis has now become a core approach in marine biodiversity research, which typically involves the collection of water or sediment samples. Yet, recently, filter-feeding organisms have received much attention for their potential role as natural eDNA samplers. While the indiscriminate use of living organisms as 'sampling tools' might in some cases raise conservation concerns, there are instances in which highly abundant sessile organisms may become a nuisance as biofouling on artificial marine structures. Here we demonstrate how a sea sponge species that colonizes the moorings of the world's largest curtain of hydroacoustic receivers can become a powerful natural collector of fish biodiversity information. By sequencing eDNA extracted from Vazella pourtalesii retrieved from moorings during routine biofouling maintenance, we detected 23 species of marine fish and mammals, compared to 19 and 15 species revealed by surface and bottom water eDNA respectively, and 28 species captured by groundfish survey in the surrounding area, which are more ecologically impactful and involve higher additional costs. Sponge-based species inventories proved at least as informative as those obtained by traditional survey methods, and are also able to detect seasonal differences in fish assemblages. We conclude that opportunistic sampling of marine sponge biofouling may become an efficient way to document and monitor biodiversity in our rapidly changing oceans.
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Affiliation(s)
- Wang Cai
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK; Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Barry MacDonald
- Ocean and Ecosystem Sciences Division, Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS B2Y 4A2, Canada
| | - Michelle Korabik
- Ocean and Ecosystem Sciences Division, Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS B2Y 4A2, Canada
| | - Iago Gradin
- Ocean Tracking Network, Dalhousie University, 1355 Oxford St., Halifax, NS B3H 4R2, Canada
| | - Erika F Neave
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK; Department of Life Sciences, Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK
| | - Lynsey R Harper
- The Freshwater Biological Association, The Hedley Wing, YMCA North Campus, Lakeside, Newby Bridge, Cumbria LA12 8BD, UK
| | - Ellen Kenchington
- Ocean and Ecosystem Sciences Division, Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS B2Y 4A2, Canada
| | - Ana Riesgo
- Department of Life Sciences, Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK; Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC), Calle José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Frederick G Whoriskey
- Ocean Tracking Network, Dalhousie University, 1355 Oxford St., Halifax, NS B3H 4R2, Canada
| | - Stefano Mariani
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK.
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2
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Bhendarkar M, Rodriguez-Ezpeleta N. Exploring uncharted territory: new frontiers in environmental DNA for tropical fisheries management. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:617. [PMID: 38874640 DOI: 10.1007/s10661-024-12788-8] [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: 11/07/2023] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
Tropical ecosystems host a significant share of global fish diversity contributing substantially to the global fisheries sector. Yet their sustainable management is challenging due to their complexity, diverse life history traits of tropical fishes, and varied fishing techniques involved. Traditional monitoring techniques are often costly, labour-intensive, and/or difficult to apply in inaccessible sites. These limitations call for the adoption of innovative, sensitive, and cost-effective monitoring solutions, especially in a scenario of climate change. Environmental DNA (eDNA) emerges as a potential game changer for biodiversity monitoring and conservation, especially in aquatic ecosystems. However, its utility in tropical settings remains underexplored, primarily due to a series of challenges, including the need for a comprehensive barcode reference library, an understanding of eDNA behaviour in tropical aquatic environments, standardized procedures, and supportive biomonitoring policies. Despite these challenges, the potential of eDNA for sensitive species detection across varied habitats is evident, and its global use is accelerating in biodiversity conservation efforts. This review takes an in-depth look at the current state and prospects of eDNA-based monitoring in tropical fisheries management research. Additionally, a SWOT analysis is used to underscore the opportunities and threats, with the aim of bridging the knowledge gaps and guiding the more extensive and effective use of eDNA-based monitoring in tropical fisheries management. Although the discussion applies worldwide, some specific experiences and insights from Indian tropical fisheries are shared to illustrate the practical application and challenges of employing eDNA in a tropical context.
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Affiliation(s)
- Mukesh Bhendarkar
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), 48395, Sukarrieta, Bizkaia, Spain.
- ICAR-National Institute of Abiotic Stress Management, Baramati, 413 115, Maharashtra, India.
| | - Naiara Rodriguez-Ezpeleta
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), 48395, Sukarrieta, Bizkaia, Spain
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Yoshida T, Yamazaki A, Kawato M, Fujiwara Y. Rapid, contamination-less, and efficient environmental DNA filtration system. MethodsX 2024; 12:102621. [PMID: 38439931 PMCID: PMC10909735 DOI: 10.1016/j.mex.2024.102621] [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: 01/09/2024] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
Due to the sporadic distribution and trace amount of environmental DNA (eDNA) in deep-sea water, in the context of biodiversity monitoring, large volumes of filtration and multiple filtration replicates are required for eDNA metabarcoding. To address issues tied to the use of multiple filtration devices and large filtration volumes (e.g., contamination, time consumption, etc.), we have developed two systems for simple, rapid, and contamination-less filtration simultaneously that allow for the processing of multiple sample replicates from large volumes of water. First, the water from a Niskin bottle was filtered directly using a solenoid pump. Second, the pumped deep-sea water, using the siphon effect, was directly filtered by a filtration device driven by water pressure. This system can process 24 replicates simultaneously without the need for expensive equipment and active driving force. Compared with conventional filtering methods, e.g., peristaltic pumps, the proposed systems reduce filtration time, minimizing contamination, and enabling the simultaneous acquisition of multiple replicates. Overall, the systems presented here provide an effective approach for eDNA metabarcoding analysis, particularly for the filtration of large volumes of water containing small amounts of eDNA, such as deep-sea water. •The present systems reduce filtration time and contamination without water having to be transferred.•Simultaneous multiple replicates improve the efficiency and reliability of biodiversity assessments.
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Affiliation(s)
- Takao Yoshida
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Aya Yamazaki
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Masaru Kawato
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yoshihiro Fujiwara
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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4
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Blackman R, Couton M, Keck F, Kirschner D, Carraro L, Cereghetti E, Perrelet K, Bossart R, Brantschen J, Zhang Y, Altermatt F. Environmental DNA: The next chapter. Mol Ecol 2024; 33:e17355. [PMID: 38624076 DOI: 10.1111/mec.17355] [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: 02/01/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dynamics of target species. Its scope thereafter broadened, uncovering previously unrecorded biodiversity via metabarcoding in both well-studied and understudied ecosystems across all taxonomic groups. The application of eDNA rapidly became an established part of biodiversity research, and a research field by its own. Here, we revisit key expectations made in a land-mark special issue on eDNA in Molecular Ecology in 2012 to frame the development in six key areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour of DNA in the environment and (6) reference database development. We pinpoint the success of eDNA, yet also discuss shortfalls and expectations not met, highlighting areas of research priority and identify the unexpected developments. In parallel, our retrospective couples a screening of the peer-reviewed literature with a survey of eDNA users including academics, end-users and commercial providers, in which we address the priority areas to focus research efforts to advance the field of eDNA. With the rapid and ever-increasing pace of new technical advances, the future of eDNA looks bright, yet successful applications and best practices must become more interdisciplinary to reach its full potential. Our retrospect gives the tools and expectations towards concretely moving the field forward.
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Affiliation(s)
- Rosetta Blackman
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Marjorie Couton
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - François Keck
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Dominik Kirschner
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, Ecosystems and Landscape Evolution, ETH Zürich, Zürich, Switzerland
- Department of Landscape Dynamics & Ecology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Luca Carraro
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Eva Cereghetti
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Kilian Perrelet
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- Department of Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Urban Water Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Raphael Bossart
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Jeanine Brantschen
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Yan Zhang
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
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5
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Li W, Hou X, Zhu Y, Du J, Xu C, Yang J, Li Y. eDNA Metabarcoding Reveals the Species-Area Relationship of Amphibians on the Zhoushan Archipelago. Animals (Basel) 2024; 14:1519. [PMID: 38891566 PMCID: PMC11171295 DOI: 10.3390/ani14111519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024] Open
Abstract
The species-area relationship is important for understanding species diversity patterns at spatial scales, but few studies have examined the relationship using environmental DNA (eDNA) techniques. We investigated amphibian diversity on 21 islands of the Zhoushan Archipelago and nearby mainland areas in China using the combination of eDNA metabarcoding and the traditional line transect method (TLTM) and identified the species-area relationship for amphibians on the islands. The mean detection probability of eDNA is 0.54, while the mean detection probability of TLTM is 0.24. The eDNA metabarcoding detected eight amphibian species on the islands and nine species in the mainland areas, compared with seven species on the islands and nine species in the mainland areas that were identified by TLTM. Amphibian richness on the islands increased with island area and habitat diversity. The species-area relationship for amphibians in the archipelago was formulated as the power function (S = 0.47A0.21) or exponential function (S = 2.59 + 2.41 (logA)). Our results suggested that eDNA metabarcoding is more sensitive for the detection of amphibian species. The combined use of eDNA metabarcoding and the traditional line transect method may optimize the survey results for amphibians.
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Affiliation(s)
- Wenhao Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianglei Hou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunlong Zhu
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiacong Du
- School of Life Sciences, Hebei University, Baoding 071002, China
| | - Chunxia Xu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingyuan Yang
- Shengnongjia National Park Administration, Huibei Provincial Key Laboratory on Conservation Biology of the Shennongjia Golden Snub-Nosed Monkey, Shennongjia 442421, China
| | - Yiming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, Hebei University, Baoding 071002, China
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6
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Bell KL, Campos M, Hoffmann BD, Encinas-Viso F, Hunter GC, Webber BL. Environmental DNA methods for biosecurity and invasion biology in terrestrial ecosystems: Progress, pitfalls, and prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171810. [PMID: 38513869 DOI: 10.1016/j.scitotenv.2024.171810] [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: 12/21/2023] [Revised: 03/13/2024] [Accepted: 03/16/2024] [Indexed: 03/23/2024]
Abstract
Analysis of environmental DNA (eDNA) enables indirect detection of species without the need to directly observe and sample them. For biosecurity and invasion biology, eDNA-based methods are useful to address biological invasions at all phases, from detecting arrivals to confirming eradication of past invasions. We conducted a systematic review of the literature and found that in biosecurity and invasion biology, eDNA has primarily been used to detect new incursions and monitor spread in marine and freshwater ecosystems, with much slower uptake in terrestrial ecosystems, reflecting a broader trend common to the usage of eDNA tools. In terrestrial ecosystems, eDNA research has mostly focussed on the use of eDNA metabarcoding to characterise biodiversity, rather than targeting biosecurity threats or non-native populations. We discuss how eDNA-based methods are being applied to terrestrial ecosystems for biosecurity and managing non-native populations at each phase of the invasion continuum: transport, introduction, establishment, and spread; across different management options: containment, control, and eradication; and for detecting the impact of non-native organisms. Finally, we address some of the current technical issues and caveats of eDNA-based methods, particularly for terrestrial ecosystems, and how these might be solved. As eDNA-based methods improve, they will play an increasingly important role in the early detection and adaptive management of biological invasions, and the implementation of effective biosecurity controls.
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Affiliation(s)
- Karen L Bell
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; School of Biological Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.
| | - Mariana Campos
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; Harry Butler Institute, Murdoch University, Murdoch, Western Australia 6150, Australia
| | | | - Francisco Encinas-Viso
- CSIRO Centre of Australian National Biodiversity Research, Black Mountain, Australian Capital Territory 2601, Australia
| | - Gavin C Hunter
- CSIRO Health & Biosecurity, Black Mountain, Australian Capital Territory 2601, Australia
| | - Bruce L Webber
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; School of Biological Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
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7
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Green ME, Hardesty BD, Deagle BE, Wilcox C. Environmental DNA as a tool to reconstruct catch composition for longline fisheries vessels. Sci Rep 2024; 14:10188. [PMID: 38702492 PMCID: PMC11068744 DOI: 10.1038/s41598-024-60917-7] [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: 12/20/2023] [Accepted: 04/29/2024] [Indexed: 05/06/2024] Open
Abstract
Global wild-capture fisheries are a large and diverse sector requiring various tools for fisheries-dependant data collection and effective Monitoring, Control and Surveillance (MCS). Here we present a novel protocol to collect eDNA from brine tanks onboard commercial longline vessels to reconstruct catch composition. We collected samples from nine vessels operating out of the Eastern Tuna Billfish Fishery, Australia, validating eDNA results with reliable catch data consisting of seven target and bycatch species. Environmental DNA was highly effective for detecting species retained on vessels without contamination or false positives. For four vessels, logbook data and eDNA were consistent with detections of all species. The remaining vessels detected all species except for rare catches of short-billed spearfish (Tetrapturus angustirostris). Similarities between rank abundance distributions of catch and eDNA reads were observed with logbook data mirrored when eDNA sequences were organised into rank order abundance. The method was effective at identifying highly abundant taxa retained in brine tanks- tuna (Thunnus spp.), swordfish (Xiphias gladius), marlin (Kajijia audax), and Atlantic Pomfret (Brama brama). Further research is required to validate how eDNA and other molecular monitoring tools can be scaled and applied to provide solutions for monitoring challenges in the fisheries sector.
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Affiliation(s)
- M E Green
- Institute for Marine and Antactic Studies, University of Tasmania, Private Bag 49, Hobart, TAS, 7001, Australia.
- Centre for Marine Socioecology, University of Tasmania, Private Bag 49, Hobart, TAS, 7001, Australia.
| | - B D Hardesty
- CSIRO Environment, Castray Esplanade, Hobart, TAS, 7001, Australia
| | - B E Deagle
- CSIRO Australian National Fish Collection, Castray Esplanade, Hobart, TAS, 7001, Australia
| | - C Wilcox
- Wilco Analytics, 93 Carlton Beach Road, Dodges Ferry, TAS, 7173, Australia
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Wilcox TM, Kronenberger JA, Young MK, Mason DH, Franklin TW, Schwartz MK. The unknown unknown: A framework for assessing environmental DNA assay specificity against unsampled taxa. Mol Ecol Resour 2024; 24:e13932. [PMID: 38263813 DOI: 10.1111/1755-0998.13932] [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: 02/23/2023] [Revised: 12/21/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
Taxon-specific quantitative PCR (qPCR) assays are commonly used for environmental DNA sampling-based inference of animal presence. These assays require thorough validation to ensure that amplification truly indicates detection of the target taxon, but a thorough validation is difficult when there are potentially many non-target taxa, some of which may have incomplete taxonomies. Here, we use a previously published, quantitative model of cross-amplification risk to describe a framework for assessing qPCR assay specificity when there is missing information and it is not possible to assess assay specificity for each individual non-target confamilial. In this framework, we predict assay specificity against unsampled taxa (non-target taxa without sequence data available) using the sequence information that is available for other confamilials. We demonstrate this framework using four case study assays for: (1) An endemic, freshwater arthropod (meltwater stonefly; Lednia tumana), (2) a globally distributed, marine ascidian (Didemnum perlucidum), (3) a continentally distributed freshwater crustacean (virile crayfish; Faxonius virilis, deanae and nais species complex) and (4) a globally distributed freshwater teleost (common carp; Cyprinus carpio and its close relative C. rubrofuscus). We tested the robustness of our approach to missing information by simulating application of our framework for all possible subsamples of 20-all non-target taxa. Our results suggest that the modelling framework results in estimates which are largely concordant with observed levels of cross-amplification risk using all available sequence data, even when there are high levels of data missingness. We explore potential limitations and extensions of this approach for assessing assay specificity and provide users with an R Markdown template for generating reproducible reports to support their own assay validation efforts.
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Affiliation(s)
- Taylor M Wilcox
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - John A Kronenberger
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - Michael K Young
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - Daniel H Mason
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - Thomas W Franklin
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - Michael K Schwartz
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
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9
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Mu Y, Zhang J, Yang J, Wu J, Zhang Y, Yu H, Zhang X. Enhancing amphibian biomonitoring through eDNA metabarcoding. Mol Ecol Resour 2024; 24:e13931. [PMID: 38345249 DOI: 10.1111/1755-0998.13931] [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: 05/08/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 02/17/2024]
Abstract
Surveying biodiversity has taken a quantum leap with environmental DNA (eDNA) metabarcoding, an immensely powerful approach lauded for its efficiency, sensitivity, and non-invasiveness. This approach emerges as a game-changer for the elusive realm of endangered and rare species-think nocturnal, environmentally elusive amphibians. Here, we have established a framework for constructing a reliable metabarcoding pipeline for amphibians, covering primer design, performance evaluation, laboratory validation, and field validation processes. The Am250 primer, located on the mitochondrial 16S gene, was optimal for the eDNA monitoring of amphibians, which demonstrated higher taxonomic resolution, smaller species amplification bias, and more extraordinary detection ability compared to the other primers tested. Am250 primer exhibit an 83.8% species amplification rate and 75.4% accurate species identification rate for Chinese amphibians in the in silico PCR and successfully amplified all tested species of the standard samples in the in vitro assay. Furthermore, the field-based mesocosm experiment showed that DNA can still be detected by metabarcoding even days to weeks after organisms have been removed from the mesocosm. Moreover, field mesocosm findings indicate that eDNA metabarcoding primers exhibit different read abundances, which can affect the relative biomass of species. Thus, appropriate primers should be screened and evaluated by three experimental approaches: in silico PCR simulation, target DNA amplification, and mesocosm eDNA validation. The selection of a single primer set or multiple primers' combination should be based on the monitoring groups to improve the species detection rate and the credibility of results.
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Affiliation(s)
- Yawen Mu
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
- Jiangsu Provincial Environmental Monitoring Center, Nanjing, China
| | - Jingwen Zhang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
- School of Marine Science and Engineering, Nanjing Normal University, Nanjing, China
| | - Jun Wu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, China
| | - Yong Zhang
- Jiangsu Provincial Environmental Monitoring Center, Nanjing, China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
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10
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Clark AJ, Atkinson SR, Scarponi V, Cane T, Geraldi NR, Hendy IW, Shipway JR, Peck M. Cost-effort analysis of Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) in monitoring marine ecological communities. PeerJ 2024; 12:e17091. [PMID: 38708339 PMCID: PMC11067900 DOI: 10.7717/peerj.17091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/20/2024] [Indexed: 05/07/2024] Open
Abstract
Monitoring the diversity and distribution of species in an ecosystem is essential to assess the success of restoration strategies. Implementing biomonitoring methods, which provide a comprehensive assessment of species diversity and mitigate biases in data collection, holds significant importance in biodiversity research. Additionally, ensuring that these methods are cost-efficient and require minimal effort is crucial for effective environmental monitoring. In this study we compare the efficiency of species detection, the cost and the effort of two non-destructive sampling techniques: Baited Remote Underwater Video (BRUV) and environmental DNA (eDNA) metabarcoding to survey marine vertebrate species. Comparisons were conducted along the Sussex coast upon the introduction of the Nearshore Trawling Byelaw. This Byelaw aims to boost the recovery of the dense kelp beds and the associated biodiversity that existed in the 1980s. We show that overall BRUV surveys are more affordable than eDNA, however, eDNA detects almost three times as many species as BRUV. eDNA and BRUV surveys are comparable in terms of effort required for each method, unless eDNA analysis is carried out externally, in which case eDNA requires less effort for the lead researchers. Furthermore, we show that increased eDNA replication yields more informative results on community structure. We found that using both methods in conjunction provides a more complete view of biodiversity, with BRUV data supplementing eDNA monitoring by recording species missed by eDNA and by providing additional environmental and life history metrics. The results from this study will serve as a baseline of the marine vertebrate community in Sussex Bay allowing future biodiversity monitoring research projects to understand community structure as the ecosystem recovers following the removal of trawling fishing pressure. Although this study was regional, the findings presented herein have relevance to marine biodiversity and conservation monitoring programs around the globe.
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Affiliation(s)
- Alice J. Clark
- Department of Ecology & Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Sophie R. Atkinson
- Department of Ecology & Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Valentina Scarponi
- Department of Ecology & Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Tim Cane
- Department of Geography, University of Sussex, Brighton, United Kingdom
| | | | - Ian W. Hendy
- School of Biological Science, University of Portsmouth, Portsmouth, United Kingdom
| | - J. Reuben Shipway
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom
| | - Mika Peck
- Department of Ecology & Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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11
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Lin CP, Huang CH, Padgett T, Bucay MAC, Chen CW, Shen ZY, Chiu L, Tseng YC, Yu JK, Wang J, Wang MC, Hoh DZ. Environmental DNA-based biodiversity profiling along the Houdong River in north-eastern Taiwan. Biodivers Data J 2024; 12:e116921. [PMID: 38694844 PMCID: PMC11061556 DOI: 10.3897/bdj.12.e116921] [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: 12/06/2023] [Accepted: 04/03/2024] [Indexed: 05/04/2024] Open
Abstract
Background This paper describes two datasets: species occurrences, which were determined by environmental DNA (eDNA) metabarcoding and their associated DNA sequences, originating from a research project which was carried out along the Houdong River (), Jiaoxi Township, Yilan, Taiwan. The Houdong River begins at an elevation of 860 m and flows for approximately 9 km before it empties into the Pacific Ocean. Meandering through mountains, hills, plains and alluvial valleys, this short river system is representative of the fluvial systems in Taiwan. The primary objective of this study was to determine eukaryotic species occurrences in the riverine ecosystem through the use of the eDNA analysis. The second goal was, based on the current dataset, to establish a metabarcoding eDNA data template that will be useful and replicable for all users, particularly the Taiwan community. The species occurrence data are accessible at the Global Biodiversity Information Facility (GBIF) portal and its associated DNA sequences have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI, respectively. A total of 12 water samples from the study yielded an average of 1.5 million reads. The subsequent species identification from the collected samples resulted in the classification of 432 Operational Taxonomic Units (OTUs) out of a total of 2,734. Furthermore, a total of 1,356 occurrences with taxon matches in GBIF were documented (excluding 4,941 incertae sedis, accessed 05-12-2023). These data will be of substantial importance for future species and habitat monitoring within the short river, such as assessment of biodiversity patterns across different elevations, zonations and time periods and its correlation to water quality, land uses and anthropogenic activities. Further, these datasets will be of importance for regional ecological studies, in particular the freshwater ecosystem and its status in the current global change scenarios. New information The datasets are the first species diversity description of the Houdong River system using either eDNA or traditional monitoring processes.
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Affiliation(s)
- Chieh-Ping Lin
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, TaiwanGenome and Systems Biology Degree Program, Academia Sinica and National Taiwan UniversityTaipeiTaiwan
- Biodiversity Research Center, Academia Sinica, Taipei, TaiwanBiodiversity Research Center, Academia SinicaTaipeiTaiwan
| | - Chung-Hsin Huang
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- International Graduate Degree Program for Biodiversity, Tunghai University, Taichung, TaiwanInternational Graduate Degree Program for Biodiversity, Tunghai UniversityTaichungTaiwan
| | - Trevor Padgett
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- International Graduate Degree Program for Biodiversity, Tunghai University, Taichung, TaiwanInternational Graduate Degree Program for Biodiversity, Tunghai UniversityTaichungTaiwan
| | - Mark Angelo C. Bucay
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- Department of Life Science, National Taiwan Normal University, Taipei, TaiwanDepartment of Life Science, National Taiwan Normal UniversityTaipeiTaiwan
| | - Cheng-Wei Chen
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- Department of Life Science, National Taiwan Normal University, Taipei, TaiwanDepartment of Life Science, National Taiwan Normal UniversityTaipeiTaiwan
| | - Zong-Yu Shen
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- Department of Life Science, National Taiwan Normal University, Taipei, TaiwanDepartment of Life Science, National Taiwan Normal UniversityTaipeiTaiwan
| | - Ling Chiu
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, TaiwanMarine Research Station, Institute of Cellular and Organismic Biology, Academia SinicaYilanTaiwan
- Institute of Oceanography, National Taiwan University, Taipei, TaiwanInstitute of Oceanography, National Taiwan UniversityTaipeiTaiwan
| | - Yung-Che Tseng
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, TaiwanMarine Research Station, Institute of Cellular and Organismic Biology, Academia SinicaYilanTaiwan
| | - Jr-Kai Yu
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, TaiwanMarine Research Station, Institute of Cellular and Organismic Biology, Academia SinicaYilanTaiwan
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, TaiwanInstitute of Cellular and Organismic Biology, Academia SinicaTaipeiTaiwan
| | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei, TaiwanBiodiversity Research Center, Academia SinicaTaipeiTaiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
| | - Min-Chen Wang
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, TaiwanMarine Research Station, Institute of Cellular and Organismic Biology, Academia SinicaYilanTaiwan
- Zoological Institute, Christian-Albrechts University of Kiel, Kiel, GermanyZoological Institute, Christian-Albrechts University of KielKielGermany
| | - Daphne Z. Hoh
- Taiwan Biodiversity Information Facility, Biodiversity Research Centre, Academia Sinica, Taipei, TaiwanTaiwan Biodiversity Information Facility, Biodiversity Research Centre, Academia SinicaTaipeiTaiwan
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12
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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.
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Affiliation(s)
- Masahiko Nakai
- Japan International Consultants for Transportation Co., Ltd, Tokyo, Japan
| | - Taku Masumoto
- Energy Planning Department, East Japan Railway Company, Tokyo, Japan
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13
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Kawaguchi M, Aoki H, Kamo H, Miura K, Hiruta Y, Simizu S, Citterio D. Simplified capture, extraction, and amplification of cellular DNA from water samples. ANAL SCI 2024; 40:501-510. [PMID: 38142247 DOI: 10.1007/s44211-023-00482-7] [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: 10/28/2023] [Accepted: 11/27/2023] [Indexed: 12/25/2023]
Abstract
DNA analysis in water samples is attracting attention in various fields. However, conventional methods for DNA analysis require a work-intensive and time-consuming sample pre-treatment. In this study, a simplified pre-treatment method for analyzing DNA in water samples was evaluated. The process consists of filtration, DNA extraction, and amplification, which can be achieved within a short time. In the filtration process, two types of filters, firstly a tissue paper (Kimwipe) and then a glass filter (GF/F), were used in sequence. The first large pore size filter enabled a reduction in filtration time by removing large particulate matter impurities present in river water matrix. Cells spiked into 1 L of river water were recovered at more than 90% within approximately 5 min filtration time. Also, DNA was extracted from the captured cells directly on the surface of the filter in only 5 min. Thus, DNA collection and extraction from a water sample can be completed within about 10 min. Furthermore, PCR amplification was performed directly from DNA-attached filter sections, which greatly reduced the number of required pre-treatment steps. Finally, we succeeded in establishing a simple and fast on-site pre-treatment system by using a hand-driven syringe filtration method. This pre-treatment system is expected to offer the possibility for the future establishment of a rapid and easy DNA analysis method applicable to various types of water samples.
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Affiliation(s)
- Mai Kawaguchi
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Hiroshi Aoki
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan.
| | - Hiroki Kamo
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Kazuki Miura
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Yuki Hiruta
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Siro Simizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Daniel Citterio
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan.
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14
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Zeng Y, Chen Z, Cao J, Li S, Xia Z, Sun Y, Zhang J, He P. Revolutionizing early-stage green tide monitoring: eDNA metabarcoding insights into Ulva prolifera and microecology in the South Yellow Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169022. [PMID: 38043827 DOI: 10.1016/j.scitotenv.2023.169022] [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: 09/21/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
Green tides, characterized by excessive Ulva prolifera blooms, pose significant ecological and economic challenges, especially in the South Yellow Sea. We successfully employed 18S environmental DNA (eDNA) metabarcoding to detect Ulva prolifera micropropagules, confirming the technique's reliability and introducing a rapid green tide monitoring method. Our investigation revealed notable disparities in the eukaryotic microbial community composition within Ulva prolifera habitats across different regions. Particularly, during the early stages of the South Yellow Sea green tide outbreak, potential interactions emerged between Ulva prolifera micropropagules and certain previously undocumented microorganisms from neighboring waters. These findings enhance our comprehension of early-stage green tide ecosystem dynamics, underscoring the value of merging advanced molecular techniques with conventional ecological methods to gain a comprehensive understanding of the impact of green tide on the local ecosystem. Overall, our study advances our understanding of green tide dynamics, offering novel avenues for control, ecological restoration, and essential scientific support for sustainable marine conservation and management.
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Affiliation(s)
- Yinqing Zeng
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Zehua Chen
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Jiaxing Cao
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Shuang Li
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Zhangyi Xia
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Yuqing Sun
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Jianheng Zhang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China.
| | - Peimin He
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China.
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15
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Larsen L. Why citizen scientists are gathering DNA from hundreds of lakes - on the same day. Nature 2024; 626:934-935. [PMID: 38383651 DOI: 10.1038/d41586-024-00520-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
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16
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Rishan ST, Kline RJ, Rahman MS. New prospects of environmental RNA metabarcoding research in biological diversity, ecotoxicological monitoring, and detection of COVID-19: a critical review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:11406-11427. [PMID: 38183542 DOI: 10.1007/s11356-023-31776-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/26/2023] [Indexed: 01/08/2024]
Abstract
Ecosystems are multifaceted and complex systems and understanding their composition is crucial for the implementation of efficient conservation and management. Conventional approaches to biodiversity surveys can have limitations in detecting the complete range of species present. In contrast, the study of environmental RNA (eRNA) offers a non-invasive and comprehensive method for monitoring and evaluating biodiversity across different ecosystems. Similar to eDNA, the examination of genetic material found in environmental samples can identify and measure many species, including ones that pose challenges to traditional methods. However, eRNA is degraded quickly and therefore shows promise in detection of living organisms closer to their actual location than eDNA methods. This method provides a comprehensive perspective on the well-being of ecosystems, facilitating the development of focused conservation approaches to save at-risk species and uphold ecological equilibrium. Furthermore, eRNA has been recognized as a valuable method for the identification of COVID-19 in the environment, besides its established uses in biodiversity protection. The SARS-CoV-2 virus, which is accountable for the worldwide epidemic, releases RNA particles into the surrounding environment via human waste, providing insights into the feasibility of detecting it in wastewater and other samples taken from the environment. In this article, we critically reviewed the recent research activities that use the eRNA method, including its utilization in biodiversity conservation, ecological surveillance, and ecotoxicological monitoring as well as its innovative potential in identifying COVID-19. Through this review, the reader can understand the recent developments, prospects, and challenges of eRNA research in ecosystem management and biodiversity conservation.
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Affiliation(s)
- Sakib Tahmid Rishan
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Richard J Kline
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Md Saydur Rahman
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA.
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA.
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17
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Sun X, Guo N, Gao J, Xiao N. Using eDNA to survey amphibians: Methods, applications, and challenges. Biotechnol Bioeng 2024; 121:456-471. [PMID: 37986625 DOI: 10.1002/bit.28592] [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: 08/16/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/22/2023]
Abstract
In recent years, environmental DNA (eDNA) has received attention from biologists due to its sensitivity, convenience, labor and material efficiency, and lack of damage to organisms. The extensive application of eDNA has opened avenues for the monitoring and biodiversity assessment of amphibians, which are frequently small and difficult to observe in the field, in areas such as biodiversity survey assessment and detection of specific, rare and threatened, or alien invasive species. However, the accuracy of eDNA can be influenced by factors such as ambient temperature, pH, and false positives or false negatives, which makes eDNA an adjunctive tool rather than a replacement for traditional surveys. This review provides a concise overview of the eDNA method and its workflow, summarizes the differences between applying eDNA for detecting amphibians and other organisms, reviews the research progress in eDNA technology for amphibian monitoring, identifies factors influencing detection efficiency, and discusses the challenges and prospects of eDNA. It aims to serve as a reference for future research on the application of eDNA in amphibian detection.
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Affiliation(s)
- Xiaoxuan Sun
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Ningning Guo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Jianan Gao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
- Collage of Forestry, Shanxi Agricultural University, Jinzhong, China
| | - Nengwen Xiao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
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18
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Vanderpool DD, Wilcox TM, Young MK, Pilgrim KL, Schwartz MK. Simultaneous species detection and discovery with environmental DNA metabarcoding: A freshwater mollusk case study. Ecol Evol 2024; 14:e11020. [PMID: 38371866 PMCID: PMC10870330 DOI: 10.1002/ece3.11020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/11/2023] [Accepted: 01/03/2024] [Indexed: 02/20/2024] Open
Abstract
Environmental DNA (eDNA) sampling is a powerful tool for rapidly characterizing biodiversity patterns for specious, cryptic taxa with incomplete taxonomies. One such group that are also of high conservation concern are North American freshwater gastropods. In particular, springsnails of the genus Pyrgulopsis (Family: Hydrobiidae) are prevalent throughout the western United States where >140 species have been described. Many of the described species are narrow endemics known from a single spring or locality, and it is believed that there are likely many additional species which have yet to be described. The distribution of these species across the landscape is of interest because habitat loss and degradation, climate change, groundwater mining, and pollution have resulted in springsnail imperilment rates as high as 92%. Determining distributions with conventional sampling methods is limited by the fact that these snails are often <5 mm in length with few distinguishing morphological characters, making them both difficult to detect and to identify. We developed an eDNA metabarcoding protocol that is both inexpensive and capable of rapid, accurate detection of all known Pyrgulopsis species. When compared with conventional collection techniques, our pipeline consistently resulted in detection at sites previously known to contain Pyrgulopsis springsnails and at a cost per site that is likely to be substantially less than the conventional sampling and individual barcoding that has been done historically. Additionally, because our method uses eDNA extracted from filtered water, it is non-destructive and suitable for the detection of endangered species where "no take" restrictions may be in effect. This effort represents both a tool which is immediately applicable to taxa of high conservation concern across western North America and a case study in the broader application of eDNA sampling for landscape assessments of cryptic taxa of conservation concern.
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Affiliation(s)
- Daniel D. Vanderpool
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
| | - Taylor M. Wilcox
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
| | - Michael K. Young
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
| | - Kristine L. Pilgrim
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
| | - Michael K. Schwartz
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
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19
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Krol L, Langezaal M, Budidarma L, Wassenaar D, Didaskalou EA, Trimbos K, Dellar M, van Bodegom PM, Geerling GW, Schrama M. Distribution of Culex pipiens life stages across urban green and grey spaces in Leiden, The Netherlands. Parasit Vectors 2024; 17:37. [PMID: 38287368 PMCID: PMC10826093 DOI: 10.1186/s13071-024-06120-z] [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: 09/25/2023] [Accepted: 01/03/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND There is an urgent need for cities to become more climate resilient; one of the key strategies is to include more green spaces in the urban environment. Currently, there is a worry that increasing green spaces might increase mosquito nuisance. As such, this study explores a comprehensive understanding of how mosquitoes utilise contrasting grey and green habitats at different life stages and which environmental factors could drive these distributions. METHODS We used a setup of six paired locations, park (green) vs. residential (grey) areas in a single model city (Leiden, The Netherlands), where we sampled the abundances of different mosquito life stages (eggs, larvae, adults) and the local microclimatic conditions. In this study, we focused on Culex pipiens s.l., which is the most common and abundant mosquito species in The Netherlands. RESULTS Our results show that while Cx. pipiens ovipositioning rates (number of egg rafts) and larval life stages were far more abundant in residential areas, adults were more abundant in parks. These results coincide with differences in the number of suitable larval habitats (higher in residential areas) and differences in microclimatic conditions (more amenable in parks). CONCLUSIONS These findings suggest that Cx. pipiens dispersal may be considerably more important than previously thought, where adult Cx. pipiens seek out the most suitable habitat for survival and breeding success. Our findings can inform more targeted and efficient strategies to mitigate and reduce mosquito nuisance while urban green spaces are increased, which make cities more climate resilient.
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Affiliation(s)
- Louie Krol
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands.
- Deltares, Daltonlaan 600, Utrecht, The Netherlands.
| | - Melissa Langezaal
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Lisa Budidarma
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Daan Wassenaar
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Emilie A Didaskalou
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Krijn Trimbos
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Martha Dellar
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
- Deltares, Daltonlaan 600, Utrecht, The Netherlands
| | - Peter M van Bodegom
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Gertjan W Geerling
- Deltares, Daltonlaan 600, Utrecht, The Netherlands
- Department of Environmental Science, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Maarten Schrama
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
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20
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Song L, Feng Z, Zhou Q, Wu X, Zhang L, Sun Y, Li R, Chen H, Yang F, Yu Y. Metagenomic analysis of healthy and diseased peri-implant microbiome under different periodontal conditions: a cross-sectional study. BMC Oral Health 2024; 24:105. [PMID: 38233815 PMCID: PMC10795403 DOI: 10.1186/s12903-023-03442-9] [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: 02/05/2023] [Accepted: 09/21/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Peri-implantitis is a polybacterial infection that can lead to the failure of dental implant rehabilitation. This study aimed to profile the microbiome of the peri-implant plaque and estimate the effect of periodontitis on it among 40 Chinese participants with dental implant prostheses and presenting with varying peri-implant and periodontal health states. METHODS Submucosal plaque samples were collected from four distinct clinical categories based on both their implant and periodontal health status at sampling point. Clinical examinations of dental implant and remaining teeth were carried out. Metagenomic analysis was then performed. RESULTS The microbiome of the peri-implantitis sites differed from that of healthy implant sites, both taxonomically and functionally. Moreover, the predominant species in peri-implantitis sites were slightly affected by the presence of periodontitis. T. forsythia, P. gingivalis, T. denticola, and P. endodontalis were consistently associated with peri-implantitis and inflammatory clinical parameters regardless of the presence of periodontitis. Prevotella spp. and P. endodontalis showed significant differences in the peri-implantitis cohorts under different periodontal conditions. The most distinguishing function between diseased and healthy implants is related to flagellar assembly, which plays an important role in epithelial cell invasion. CONCLUSIONS The composition of the peri-implant microbiome varied in the diseased and healthy states of implants and is affected by individual periodontal conditions. Based on their correlations with clinical parameters, certain species are associated with disease and healthy implants. Flagellar assembly may play a vital role in the process of peri-implantitis.
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Affiliation(s)
- Liang Song
- Department of Stomatology, Shanghai Fifth People's Hospital, Fudan University, 801 Heqing Road, Shanghai, 200240, China
| | - Ziying Feng
- Department of Stomatology, Shanghai Fifth People's Hospital, Fudan University, 801 Heqing Road, Shanghai, 200240, China
| | - Qianrong Zhou
- Department of Stomatology, Zhongshan Hospital of Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Xingwen Wu
- Department of Stomatology, Zhongshan Hospital of Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Limin Zhang
- Department of Stomatology, Shanghai Fifth People's Hospital, Fudan University, 801 Heqing Road, Shanghai, 200240, China
| | - Yang Sun
- Department of Stomatology, Zhongshan Hospital of Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Ruixue Li
- Department of Stomatology, Zhongshan Hospital of Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Huijuan Chen
- Department of Stomatology, Shanghai Fifth People's Hospital, Fudan University, 801 Heqing Road, Shanghai, 200240, China
| | - Fei Yang
- Department of Stomatology, Zhongshan Hospital of Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
| | - Youcheng Yu
- Department of Stomatology, Zhongshan Hospital of Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
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Zhang L, Zhou W, Jiao M, Xie T, Xie M, Li H, Suo A, Yue W, Ding D, He W. Use of passive sampling in environmental DNA metabarcoding technology: Monitoring of fish diversity in the Jiangmen coastal waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168298. [PMID: 37939943 DOI: 10.1016/j.scitotenv.2023.168298] [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: 04/28/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/10/2023]
Abstract
Environmental DNA (eDNA) metabarcoding technology is proving to be the most up-to-date and promising method for monitoring marine fish diversity. Fish eDNA is usually collected on a filter membrane after the filtration of water. Not only does this require the use of specialized equipment, but the amount of filtered water needed is also difficult to meet. The recently proposed passive eDNA collection method can expand the sampling scale, providing new perspectives for monitoring marine biodiversity. The role of collection methods in eDNA surveys, however, remains unclear. In this study, a low-cost custom framework with two types of filter membrane materials was used to conduct passive submersion samplings at the north and south ends of Shangchuan Island, Jiangmen, China. After defined periods of submersion, the filter membranes were recovered and eDNA extracted. Metabarcoding techniques were applied to detect fish species information in the eDNA samples. A total of 106 marine fish species from 27 orders, 53 families, and 92 genera, including one cartilaginous fish, were identified in the samples. The majority of fish detected by active filtration were also found in the passively collected samples, within the same location. Both sampling methods, therefore, showed similar species richness. Passive sampling was effective in identifying fish species diversity and provided a higher spatial resolution owing to the sample replicates. Passive sampling was also more sensitive in detecting species that differ significantly in abundance (biomarkers) between different sampling depths. When active filtration is not possible, or when large-scale sampling is the purpose of the study, passive sampling methods certainly provide a promising alternative. The findings of our study provide guidance for fish surveys and continuous bio-stereoscopic monitoring in coastal waters.
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Affiliation(s)
- Li Zhang
- Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiguo Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Mengyu Jiao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tian Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Mujiao Xie
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Hanying Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anning Suo
- Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Weizhong Yue
- Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Dewen Ding
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 51145, China
| | - Weihong He
- Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
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22
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Holmes AE, Baerwald MR, Rodzen J, Schreier BM, Mahardja B, Finger AJ. Evaluating environmental DNA detection of a rare fish in turbid water using field and experimental approaches. PeerJ 2024; 12:e16453. [PMID: 38188170 PMCID: PMC10768661 DOI: 10.7717/peerj.16453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/23/2023] [Indexed: 01/09/2024] Open
Abstract
Detection sensitivity of aquatic species using environmental DNA (eDNA) generally decreases in turbid water but is poorly characterized. In this study, eDNA detection targeted delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish associated with turbid water. eDNA sampling in the field was first paired with a trawl survey. Species-specific detection using a Taqman qPCR assay showed concordance between the methods, but a weak eDNA signal. Informed by the results of field sampling, an experiment was designed to assess how turbidity and filtration methods influence detection of a rare target. Water from non-turbid (5 NTU) and turbid (50 NTU) estuarine sites was spiked with small volumes (0.5 and 1 mL) of water from a delta smelt tank to generate low eDNA concentrations. Samples were filtered using four filter types: cartridge filters (pore size 0.45 μm) and 47 mm filters (glass fiber, pore size 1.6 μm and polycarbonate, pore sizes 5 and 10 μm). Prefiltration was also tested as an addition to the filtration protocol for turbid water samples. eDNA copy numbers were analyzed using a censored data method for qPCR data. The assay limits and lack of PCR inhibition indicated an optimized assay. Glass fiber filters yielded the highest detection rates and eDNA copies in non-turbid and turbid water. Prefiltration improved detection in turbid water only when used with cartridge and polycarbonate filters. Statistical analysis identified turbidity as a significant effect on detection probability and eDNA copies detected; filter type and an interaction between filter type and prefilter were significant effects on eDNA copies detected, suggesting that particulate-filter interactions can affect detection sensitivity. Pilot experiments and transparent criteria for positive detection could improve eDNA surveys of rare species in turbid environments.
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Affiliation(s)
- Ann E. Holmes
- Genomic Variation Laboratory, University of California, Davis, Davis, California, United States
- Graduate Group in Ecology, University of California, Davis, Davis, California, United States
| | - Melinda R. Baerwald
- California Department of Water Resources, West Sacramento, California, United States
| | - Jeff Rodzen
- Genetics Research Laboratory, California Department of Fish and Wildlife, Sacramento, California, United States
| | - Brian M. Schreier
- California Department of Water Resources, West Sacramento, California, United States
| | - Brian Mahardja
- Bureau of Reclamation, US Department of the Interior, Sacramento, California, United States
| | - Amanda J. Finger
- Genomic Variation Laboratory, University of California, Davis, Davis, California, United States
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23
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Snyder ED, Tank JL, Brandão-Dias PFP, Bibby K, Shogren AJ, Bivins AW, Peters B, Curtis EM, Bolster D, Egan SP, Lamberti GA. Environmental DNA (eDNA) removal rates in streams differ by particle size under varying substrate and light conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166469. [PMID: 37633388 DOI: 10.1016/j.scitotenv.2023.166469] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/17/2023] [Accepted: 08/19/2023] [Indexed: 08/28/2023]
Abstract
The use of environmental DNA (eDNA) as a sampling tool offers insights into the detection of invasive and/or rare aquatic species and enables biodiversity assessment without traditional sampling approaches, which are often labor-intensive. However, our understanding of the environmental factors that impact eDNA removal (i.e., how rapidly eDNA is removed from the water column by the combination of decay and physical removal) in flowing waters is limited. This limitation constrains predictions about the location and density of target organisms after positive detection. To address this question, we spiked Common Carp (Cyprinus carpio) eDNA into recirculating mesocosms (n = 24) under varying light (shaded versus open) and benthic substrate conditions (no substrate, bare substrate, and biofilm-colonized substrate). We then collected water samples from each mesocosm at four time points (40 min, 6 h, 18 h, and 48 h), and sequentially filtered the samples through 10, 1.0, and 0.2 μm filters to quantify removal rates for different eDNA particle sizes under varying light and substrate conditions. Combining all size classes, total eDNA removal rates were higher for mesocosms with biofilm-colonized substrate compared to those with no substrate or bare (i.e., no biofilm) substrate, which is consistent with previous findings linking biofilm colonization with increased eDNA removal and degradation. Additionally, when biofilm was present, light availability increased eDNA removal; eDNA levels fell below detection after 6-18 h for open mesocosms versus 18-48 h for shaded mesocosms. Among size classes, larger particles (>10 μm) were removed faster than small particles (1.0-0.2 μm). These results suggest that changes in the distribution of eDNA size classes over time (e.g., with downstream transport) and with differing environmental conditions could be used to predict the location of target organisms in flowing waters, which will advance the use of eDNA as a tool for species monitoring and management.
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Affiliation(s)
- Elise D Snyder
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA.
| | - Jennifer L Tank
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA.
| | | | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall of Engineering, Notre Dame, IN 46556, USA.
| | - Arial J Shogren
- Department of Biological Sciences, The University of Alabama, Science and Engineering Complex,1325 Hackberry Ln, Tuscaloosa, AL 35401, USA.
| | - Aaron W Bivins
- Department of Civil and Environmental Engineering, Louisiana State University, 3255 Patrick F. Taylor Hall, Baton Rouge, LA 70803, USA.
| | - Brett Peters
- Environmental Change Initiative, University of Notre Dame, 721 Flanner Hall, Notre Dame, IN 46556, USA.
| | - Erik M Curtis
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA.
| | - Diogo Bolster
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA; Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall of Engineering, Notre Dame, IN 46556, USA.
| | - Scott P Egan
- Department of BioSciences, Rice University, 6100 Main St, Houston, TX 77005-1827, USA.
| | - Gary A Lamberti
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA.
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24
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Roth SA, Griffis-Kyle KL, Barnes MA. Batrachochytrium dendrobatidis in the Arid and Thermally Extreme Sonoran Desert. ECOHEALTH 2023; 20:370-380. [PMID: 38243042 DOI: 10.1007/s10393-023-01668-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 12/08/2023] [Indexed: 01/21/2024]
Abstract
Batrachochytrium dendrobatidis (Bd), the causative agent of the devastating global amphibian disease chytridiomycosis, was not projected to threaten amphibians in hot and arid regions due to its sensitivity to heat and desiccation. However, Bd is being detected more frequently than ever in hot and arid regions of Australia and the USA, challenging our current understanding of the environmental tolerances of the pathogen under natural conditions. We surveyed for Bd in an extremely hot and arid portion of the Sonoran Desert, where the pathogen is not projected to occur, and related presence and prevalence of the pathogen to local environmental conditions. We collected eDNA samples from isolated desert water sites including six tinajas and 13 catchments in June and August of 2020 and swabbed a total of 281 anurans of three species (red-spotted toad Anaxyrus punctatus, Couch's spadefoot Scaphiopus couchii, and the Sonoran Desert toad Incillius alvarius) across five catchments and six tinajas from June to September of 2020. Overall, Bd occurred at 68.4% of sites, despite extreme heat and aridity routinely exceeding tolerances established in laboratory studies. Average summer maximum air and water temperatures were 40.7°C and 30.7°C, respectively, and sites received an average of just 16.9 mm of precipitation throughout the summer monsoon season. Prevalence was low (5.7%) across species and life stage. Our results demonstrate that Bd is capable of persisting and infecting amphibians beyond its projected range, indicating a need to account for higher thermal tolerances when quantifying risk of Bd presence and infection.
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Affiliation(s)
- Sadie A Roth
- Department of Natural Resources Management, Texas Tech University, 2500 Broadway, Lubbock, TX, 79409, USA.
| | - Kerry L Griffis-Kyle
- Department of Natural Resources Management, Texas Tech University, 2500 Broadway, Lubbock, TX, 79409, USA
| | - Matthew A Barnes
- Department of Natural Resources Management, Texas Tech University, 2500 Broadway, Lubbock, TX, 79409, USA
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25
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Baletaud F, Lecellier G, Gilbert A, Mathon L, Côme JM, Dejean T, Dumas M, Fiat S, Vigliola L. Comparing Seamounts and Coral Reefs with eDNA and BRUVS Reveals Oases and Refuges on Shallow Seamounts. BIOLOGY 2023; 12:1446. [PMID: 37998045 PMCID: PMC10669620 DOI: 10.3390/biology12111446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023]
Abstract
Seamounts are the least known ocean biome. Considered biodiversity hotspots, biomass oases, and refuges for megafauna, large gaps exist in their real diversity relative to other ecosystems like coral reefs. Using environmental DNA metabarcoding (eDNA) and baited video (BRUVS), we compared fish assemblages across five environments of different depths: coral reefs (15 m), shallow seamounts (50 m), continental slopes (150 m), intermediate seamounts (250 m), and deep seamounts (500 m). We modeled assemblages using 12 environmental variables and found depth to be the main driver of fish diversity and biomass, although other variables like human accessibility were important. Boosted Regression Trees (BRT) revealed a strong negative effect of depth on species richness, segregating coral reefs from deep-sea environments. Surprisingly, BRT showed a hump-shaped effect of depth on fish biomass, with significantly lower biomass on coral reefs than in shallowest deep-sea environments. Biomass of large predators like sharks was three times higher on shallow seamounts (50 m) than on coral reefs. The five studied environments showed quite distinct assemblages. However, species shared between coral reefs and deeper-sea environments were dominated by highly mobile large predators. Our results suggest that seamounts are no diversity hotspots for fish. However, we show that shallower seamounts form biomass oases and refuges for threatened megafauna, suggesting that priority should be given to their protection.
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Affiliation(s)
- Florian Baletaud
- ENTROPIE, Institut de Recherche pour le Développement (IRD), UR, UNC, IFREMER, CNRS, Centre IRD de Nouméa, 98848 Noumea, New Caledonia, France; (F.B.); (G.L.); (L.M.); (M.D.); (S.F.)
- GINGER SOPRONER, 98000 Noumea, New Caledonia, France;
- GINGER BURGEAP, 69000 Lyon, France;
- MARBEC, University of Montpellier, CNRS, IFREMER, 34000 Montpellier, France
| | - Gaël Lecellier
- ENTROPIE, Institut de Recherche pour le Développement (IRD), UR, UNC, IFREMER, CNRS, Centre IRD de Nouméa, 98848 Noumea, New Caledonia, France; (F.B.); (G.L.); (L.M.); (M.D.); (S.F.)
- ISEA, University of New Caledonia, 98800 Noumea, New Caledonia, France
| | | | - Laëtitia Mathon
- ENTROPIE, Institut de Recherche pour le Développement (IRD), UR, UNC, IFREMER, CNRS, Centre IRD de Nouméa, 98848 Noumea, New Caledonia, France; (F.B.); (G.L.); (L.M.); (M.D.); (S.F.)
- CEFE, University of Montpellier, CNRS, EPHE-PSL, IRD, 34000 Montpellier, France
| | | | | | - Mahé Dumas
- ENTROPIE, Institut de Recherche pour le Développement (IRD), UR, UNC, IFREMER, CNRS, Centre IRD de Nouméa, 98848 Noumea, New Caledonia, France; (F.B.); (G.L.); (L.M.); (M.D.); (S.F.)
| | - Sylvie Fiat
- ENTROPIE, Institut de Recherche pour le Développement (IRD), UR, UNC, IFREMER, CNRS, Centre IRD de Nouméa, 98848 Noumea, New Caledonia, France; (F.B.); (G.L.); (L.M.); (M.D.); (S.F.)
| | - Laurent Vigliola
- ENTROPIE, Institut de Recherche pour le Développement (IRD), UR, UNC, IFREMER, CNRS, Centre IRD de Nouméa, 98848 Noumea, New Caledonia, France; (F.B.); (G.L.); (L.M.); (M.D.); (S.F.)
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26
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Casabella-Herrero G, Martín-Torrijos L, Diéguez-Uribeondo J. eDNA monitoring as a tool for evaluating the reintroduction of Austropotamobius pallipes after a crayfish plague outbreak. J Invertebr Pathol 2023; 201:108026. [PMID: 38007177 DOI: 10.1016/j.jip.2023.108026] [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: 04/26/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 11/27/2023]
Abstract
The crayfish plague, a severe disease caused by the oomycete Aphanomyces astaci, is responsible for most population declines of susceptible crayfish in Europe. This pathogen has been devastating native populations of Austropotamobius pallipes since the 1970s in the Iberian Peninsula. In this study, we report a massive mortality event in one of the most important Spanish populations of A. pallipes. We aimed to: (i) identify the cause of the mortality, and (ii) evaluate the reintroduction viability of the species. Over the course of six months, we used environmental DNA (eDNA) and traditional trap-based methods to detect the presence of A. astaci or of native or invasive crayfish in order to evaluate the reintroduction viability of A. pallipes to the affected population. We did not capture any live crayfish or detect the presence of A. astaci in the reservoir water during the six months following the mass mortality event. Our analyses indicated that it was feasible to initiate a reintroduction program at the site, which will continue to be monitored for three to five years and will help improve the conservation status of A. pallipes.
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Affiliation(s)
| | - Laura Martín-Torrijos
- Mycology Department, Real Jardín Botánico-CSIC, Plaza Murillo 2, 28014 Madrid, Spain.
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27
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Shen Y, Zhang Y, Cheng R, Wang W, Duan C, Liu Z, Chen Q, Li Y, Wang M, Luo Y. Diversity and spatiotemporal dynamics of fish communities in the Chongqing section of the upper Yangtze River based on eDNA metabarcoding. Ecol Evol 2023; 13:e10681. [PMID: 37953986 PMCID: PMC10636638 DOI: 10.1002/ece3.10681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 09/28/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023] Open
Abstract
Fish diversity plays a critical role in maintaining the balance of water ecosystems, especially in the Chongqing section of the National Nature Reserve for Rare and Endemic Fishes in the upper Yangtze River, which serves as an important habitat for rare and endemic fish, as well as an important channel for the replenishment of fishery resources in the Three Gorges Reservoir. Under a 10-year ban on fishing in the Yangtze River basin, we investigate fish diversity and seasonal variation in the Reserve by using environmental DNA (eDNA) metabarcoding. We found fishes belonging to 85 genera, 24 families, and 8 orders in the Reserve. A comparison of eDNA metabarcoding results with the diversity of a recent fish catch revealed that eDNA metabarcoding not only enables rapid and efficient fish monitoring but also has a high sensitivity. Furthermore, the study demonstrates that eDNA metabarcoding can be used as a tool for monitoring seasonal variations of fish composition in freshwater ecosystems. The alpha and beta diversity analysis both showed compositional differences in the fish community in accordance with seasonal variations. In addition, changes in eDNA relative sequence abundance and the detection of fish species at different sampling sites may reflect shifts in habitat use and distribution. Thus, we provide detailed seasonal data on fish diversity in the Chongqing section of the Reserve. This will contribute to conservation and to the understanding of fish diversity and community dynamics in the Chongqing section of the Reserve.
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Affiliation(s)
- Yanjun Shen
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Yufeng Zhang
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Ruli Cheng
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Wei Wang
- Chongqing Rare and Endemic Fish National Nature Reserve Management OfficeChongqingChina
| | - Cong Duan
- Chongqing Rare and Endemic Fish National Nature Reserve Management OfficeChongqingChina
| | - Zhihao Liu
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Qiliang Chen
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Yingwen Li
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Meng Wang
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Yang Luo
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
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28
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Corral-Lou A, Doadrio I. Environmental DNA metabarcoding of water samples as a tool for monitoring Iberian freshwater fish composition. PLoS One 2023; 18:e0283088. [PMID: 37903086 PMCID: PMC10615313 DOI: 10.1371/journal.pone.0283088] [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: 04/21/2022] [Accepted: 03/01/2023] [Indexed: 11/01/2023] Open
Abstract
Environmental DNA (eDNA) metabarcoding has been increasingly used to monitor the community assemblages of a wide variety of organisms. Here, we test the efficacy of eDNA metabarcoding to assess the composition of Iberian freshwater fishes, one of the most endangered groups of vertebrates in Spain. For this purpose, we sampled 12 sampling sites throughout one of Spain's largest basins, the Duero, which is home to approximately 70% of the genera and 30% of the primary freshwater fish in Spain. We sampled these sampling sites in the summer by using electrofishing, a traditional sampling method, and eDNA metabarcoding of river water samples using the mitochondrial 12S rRNA gene (12S) as a marker. We also resampled four of these sampling sites in autumn by eDNA. We compared the results obtained through eDNA metabarcoding with those of electrofishing surveys (ones conducted for the present study and past ones) and assessed the suitability of 12S as an eDNA metabarcoding marker for this group of freshwater fishes. We found that the 12S fragment, analysed for 25 Iberian species, showed sufficient taxonomic resolution to be useful for eDNA approaches, and even showed population-level differences in the studied populations across the tissue samples for Achondrostoma arcasii. In most cases, a greater number of species was detected through eDNA metabarcoding than through electrofishing. Based on our results, eDNA metabarcoding is a powerful tool to study the freshwater fish composition in the Iberian Peninsula and to unmask cryptic diversity. However, we highlight the need to generate a local genetic database for 12S gene for such studies and to interpret the results with caution when studying only mitochondrial DNA. Finally, our survey shows that the high detection sensitivity of eDNA metabarcoding and the non-invasiveness of this method allows it to act as a detection system for species of low abundance, such as early invasive species or species in population decline, two key aspects of conservation management of Spanish freshwater fishes.
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Affiliation(s)
- Andrea Corral-Lou
- Biodiversity and Evolutionary Biology Department, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, Madrid, Spain
- Consultores en Biología de la Conservación S.L., Daoiz, Madrid, Spain
| | - Ignacio Doadrio
- Biodiversity and Evolutionary Biology Department, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, Madrid, Spain
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29
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Waters T, Gold Z, Obaza A, Ambrose RF, Eagle RA. Environmental DNA metabarcoding reveals distinct fish assemblages supported by seagrass (Zostera marina and Zostera pacifica) beds in different geographic settings in Southern California. PLoS One 2023; 18:e0286228. [PMID: 37796915 PMCID: PMC10553302 DOI: 10.1371/journal.pone.0286228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023] Open
Abstract
Seagrass beds are disappearing at a record pace despite their known value to our oceans and coastal communities. Simultaneously, our coastlines are under the constant pressure of climate change which is impacting their chemical, physical and biological characteristics. It is thus pertinent to evaluate and record habitat use so we can understand how these different environments contribute to local biodiversity. This study evaluates the assemblages of fish found at five Zostera beds in Southern California using environmental DNA (eDNA) metabarcoding. eDNA is a powerful biodiversity monitoring tool that offers key advantages to conventional monitoring. Results from our eDNA study found 78 species of fish that inhabit these five beds around Southern California representing embayment, open coastal mainland and open coastal island settings. While each bed had the same average number of species found throughout the year, the composition of these fish assemblages was strongly site dependent. There were 35 fish that were found at both open coast and embayment seagrass beds, while embayment seagrass sites had 20 unique fish and open coast sites had 23 unique fish. These results demonstrate that seagrass fish assemblages are heterogenous based on their geographic positioning and that marine managers must take this into account for holistic conservation and restoration efforts.
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Affiliation(s)
- Tanner Waters
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA, United States of America
- Center for Diverse Leadership in Science, University of California, Los Angeles, CA, United States of America
| | - Zachary Gold
- NOAA Pacific Marine Environmental Laboratory, Seattle, WA, United States of America
| | - Adam Obaza
- Paua Marine Research Group, Long Beach, CA, United States of America
| | - Richard F. Ambrose
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA, United States of America
- Department of Environmental Health Sciences, Jonathan and Karen Fielding School of Public Health, University of California, Los Angeles, CA, United States of America
| | - Robert A. Eagle
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA, United States of America
- Center for Diverse Leadership in Science, University of California, Los Angeles, CA, United States of America
- Atmospheric and Oceanic Sciences Department, University of California, Los Angeles, CA, United States of America
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30
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Rees HC, Measures GH, Kane SD, Maddison BC. Quantitative PCR (qPCR) assay for the specific detection of the Chinese mystery snail (Cipangopaludina chinensis) in the UK. PLoS One 2023; 18:e0292163. [PMID: 37796948 PMCID: PMC10553251 DOI: 10.1371/journal.pone.0292163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/13/2023] [Indexed: 10/07/2023] Open
Abstract
Cipangopaludina chinensis Gray 1833 is an East Asian freshwater snail and invasive species in many parts of the world (Global Invasive Species Database, 2022). Within the UK, it was first found at the Pevensey Levels, Sussex, and has since been reported at a second site at Southampton Common, Hampshire. Both sites are designated as Sites of Special Scientific Interest (SSSI) for their wildlife importance. Although the impacts of this species within the UK have not yet been investigated several exotic parasites of the snail have been reported and research suggests that its presence can negatively impact native snail species. This is especially important at the Pevensey Levels due to the presence of the rare freshwater mollusc Anisus vorticulus (Little Whirlpool Rams's-horn snail). Here, we have developed a qPCR-based eDNA assay for the detection of C. chinensis and compared water samples tested for eDNA with results from manual survey of the ditches at the Pevensey Levels. Our eDNA analysis exhibited an overall observed percentage agreement of 80% with a kappa coefficient of agreement between manual and eDNA surveys of 0.59 (95% CI 0.31 to 0.88). Some samples which were qPCR negative for C. chinensis were positive by manual survey, and vice versa revealing the potential for improved overall detection rates when using a combination of manual and eDNA methodologies. eDNA analysis can therefore augment manual survey techniques for C. chinensis as a relatively quick and inexpensive tool for collecting presence and distribution data that could be used to inform further manual surveys and control measures within the ditches.
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Affiliation(s)
- Helen C. Rees
- Biotechnology, RSK ADAS Ltd, Nottingham, United Kingdom
| | - Gavin H. Measures
- Species Recovery and Reintroductions Team, Natural England, Peterborough, United Kingdom
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Zhang M, Zou Y, Xiao S, Hou J. Environmental DNA metabarcoding serves as a promising method for aquatic species monitoring and management: A review focused on its workflow, applications, challenges and prospects. MARINE POLLUTION BULLETIN 2023; 194:115430. [PMID: 37647798 DOI: 10.1016/j.marpolbul.2023.115430] [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: 04/23/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023]
Abstract
Marine and freshwater biodiversity is under threat from both natural and manmade causes. Biological monitoring is currently a top priority for biodiversity protection. Given present limitations, traditional biological monitoring methods may not achieve the proposed monitoring aims. Environmental DNA metabarcoding technology reflects species information by capturing and extracting DNA from environmental samples, using molecular biology techniques to sequence and analyze the DNA, and comparing the obtained information with existing reference libraries to obtain species identification. However, its practical application has highlighted several limitations. This paper summarizes the main steps in the environmental application of eDNA metabarcoding technology in aquatic ecosystems, including the discovery of unknown species, the detection of invasive species, and evaluations of biodiversity. At present, with the rapid development of big data and artificial intelligence, certain advanced technologies and devices can be combined with environmental DNA metabarcoding technology to promote further development of aquatic species monitoring and management.
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Affiliation(s)
- Miaolian Zhang
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Yingtong Zou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shan Xiao
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Jing Hou
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
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Reji Chacko M, Altermatt F, Fopp F, Guisan A, Keggin T, Lyet A, Rey PL, Richards E, Valentini A, Waldock C, Pellissier L. Catchment-based sampling of river eDNA integrates terrestrial and aquatic biodiversity of alpine landscapes. Oecologia 2023; 202:699-713. [PMID: 37558733 PMCID: PMC10475001 DOI: 10.1007/s00442-023-05428-4] [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: 11/04/2022] [Accepted: 07/22/2023] [Indexed: 08/11/2023]
Abstract
Monitoring of terrestrial and aquatic species assemblages at large spatial scales based on environmental DNA (eDNA) has the potential to enable evidence-based environmental policymaking. The spatial coverage of eDNA-based studies varies substantially, and the ability of eDNA metabarcoding to capture regional biodiversity remains to be assessed; thus, questions about best practices in the sampling design of entire landscapes remain open. We tested the extent to which eDNA sampling can capture the diversity of a region with highly heterogeneous habitat patches across a wide elevation gradient for five days through multiple hydrological catchments of the Swiss Alps. Using peristaltic pumps, we filtered 60 L of water at five sites per catchment for a total volume of 1800 L. Using an eDNA metabarcoding approach focusing on vertebrates and plants, we detected 86 vertebrate taxa spanning 41 families and 263 plant taxa spanning 79 families across ten catchments. For mammals, fishes, amphibians and plants, the detected taxa covered some of the most common species in the region according to long-term records while including a few more rare taxa. We found marked turnover among samples from distinct elevational classes indicating that the biological signal in alpine rivers remains relatively localised and is not aggregated downstream. Accordingly, species compositions differed between catchments and correlated with catchment-level forest and grassland cover. Biomonitoring schemes based on capturing eDNA across rivers within biologically integrated catchments may pave the way toward a spatially comprehensive estimation of biodiversity.
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Affiliation(s)
- Merin Reji Chacko
- Unit of Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland.
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Fabian Fopp
- Unit of Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Geopolis, Lausanne, Switzerland
| | - Thomas Keggin
- Unit of Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | - Arnaud Lyet
- World Wildlife Fund, Wildlife Conservation Team, Washington, DC, USA
| | - Pierre-Louis Rey
- Institute of Earth Surface Dynamics, University of Lausanne, Geopolis, Lausanne, Switzerland
| | - Eilísh Richards
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | | | - Conor Waldock
- Unit of Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | - Loïc Pellissier
- Unit of Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
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Gutiérrez-López R, Egeter B, Paupy C, Rahola N, Makanga B, Jiolle D, Bourret V, Melo M, Loiseau C. Monitoring mosquito richness in an understudied area: can environmental DNA metabarcoding be a complementary approach to adult trapping? BULLETIN OF ENTOMOLOGICAL RESEARCH 2023; 113:456-468. [PMID: 37183666 DOI: 10.1017/s0007485323000147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Mosquito surveillance programmes are essential to assess the risks of local vector-borne disease outbreaks as well as for early detection of mosquito invasion events. Surveys are usually performed with traditional sampling tools (i.e., ovitraps and dipping method for immature stages or light or decoy traps for adults). Over the past decade, numerous studies have highlighted that environmental DNA (eDNA) sampling can enhance invertebrate species detection and provide community composition metrics. However, the usefulness of eDNA for detection of mosquito species has, to date, been largely neglected. Here, we sampled water from potential larval breeding sites along a gradient of anthropogenic perturbations, from the core of an oil palm plantation to the rainforest on São Tomé Island (Gulf of Guinea, Africa). We showed that (i) species of mosquitoes could be detected via metabarcoding mostly when larvae were visible, (ii) larvae species richness was greater using eDNA than visual identification and (iii) new mosquito species were also detected by the eDNA approach. We provide a critical discussion of the pros and cons of eDNA metabarcoding for monitoring mosquito species diversity and recommendations for future research directions that could facilitate the adoption of eDNA as a tool for assessing insect vector communities.
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Affiliation(s)
- Rafael Gutiérrez-López
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio, Laboratório Associado, University of Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
- Animal Health Research Center, National Food and Agriculture Research and Technology Institute (INIA-CISA-CSIC), Valdeolmos, Spain
| | - Bastian Egeter
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio, Laboratório Associado, University of Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Christophe Paupy
- MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier 34394, France
| | - Nil Rahola
- MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier 34394, France
| | - Boris Makanga
- Institut de Recherche en Écologie Tropicale/CENAREST, BP 13354 Libreville, Gabon
| | - Davy Jiolle
- MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier 34394, France
| | - Vincent Bourret
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio, Laboratório Associado, University of Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
- INRAE - Université de Toulouse UR 0035 CEFS, 31326 Castanet Tolosan, France
| | - Martim Melo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio, Laboratório Associado, University of Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
- MHNC-UP - Natural History and Science Museum of the University of Porto, Porto, Portugal
- FitzPatrick Institute of African Ornithology, University of Cape Town, Cape Town, South Africa
| | - Claire Loiseau
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio, Laboratório Associado, University of Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
- CEFE, Université de Montpellier, CNRS, Montpellier, France
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Jo TS. Pooling of intra-site measurements inflates variability of the correlation between environmental DNA concentration and organism abundance. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:936. [PMID: 37436641 DOI: 10.1007/s10661-023-11539-5] [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: 11/15/2022] [Accepted: 06/19/2023] [Indexed: 07/13/2023]
Abstract
Environmental DNA (eDNA) analysis can promote efficient ecosystem monitoring and resource management. However, limited knowledge of the factors affecting the relationship between eDNA concentration and organism abundance causes uncertainty in relative abundance estimates based on eDNA concentration. Pooling of data points obtained from multiple locations within a site has been used to mitigate intra-site variation in eDNA and abundance estimates, but decreases the sample size used for estimating the relationship. I here assessed how the pooling of intra-site measurements of eDNA concentration and organism abundance impacted the reliability of the correlative relationship between eDNA concentration and organism abundance. Mathematical models were developed to simulate measurements of eDNA concentrations and organism abundances from multiple locations in a given survey site, and the CVs (coefficient of variability) of the correlations were compared depending on whether data points from different locations were individually treated or pooled. Although the mean and median values of the correlation coefficients were similar between the scenarios, the CVs of the simulated correlations were substantially higher under the pooled scenario than the individual scenario. Additionally, I re-analyzed two empirical studies conducted in lakes, both showing higher CVs of the correlations by pooling intra-site measurements. This study suggests that it would make eDNA-based abundance estimation more reliable and reproducible to individually analyze target eDNA concentrations and organism abundance estimates.
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Affiliation(s)
- Toshiaki S Jo
- Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan.
- Ryukoku Center for Biodiversity Science, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga, 520-2194, Japan.
- Faculty of Advanced Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga, 520-2194, Japan.
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Adcock ZC, Adcock ME, Forstner MRJ. Development and validation of an environmental DNA assay to detect federally threatened groundwater salamanders in central Texas. PLoS One 2023; 18:e0288282. [PMID: 37428788 DOI: 10.1371/journal.pone.0288282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
The molecular detection of DNA fragments that are shed into the environment (eDNA) has become an increasingly applied tool used to inventory biological communities and to perform targeted species surveys. This method is particularly useful in habitats where it is difficult or not practical to visually detect or trap the target organisms. Central Texas Eurycea salamanders inhabit both surface and subterranean aquatic environments. Subterranean surveys are challenging or infeasible, and the detection of salamander eDNA in water samples is an appealing survey technique for these situations. Here, we develop and validate an eDNA assay using quantitative PCR for E. chisholmensis, E. naufragia, and E. tonkawae. These three species are federally threatened and constitute the Septentriomolge clade that occurs in the northern segment of the Edwards Aquifer. First, we validated the specificity of the assay in silico and with DNA extracted from tissue samples of both target Septentriomolge and non-target amphibians that overlap in distribution. Then, we evaluated the sensitivity of the assay in two controls, one with salamander-positive water and one at field sites known to be occupied by Septentriomolge. For the salamander-positive control, the estimated probability of eDNA occurrence (ψ) was 0.981 (SE = 0.019), and the estimated probability of detecting eDNA in a qPCR replicate (p) was 0.981 (SE = 0.011). For the field control, the estimated probability of eDNA occurring at a site (ψ) was 0.938 (95% CRI: 0.714-0.998). The estimated probability of collecting eDNA in a water sample (θ) was positively correlated with salamander relative density and ranged from 0.371 (95% CRI: 0.201-0.561) to 0.999 (95% CRI: 0.850- > 0.999) among sampled sites. Therefore, sites with low salamander density require more water samples for eDNA evaluation, and we determined that our site with the lowest estimated θ would require seven water samples for the cumulative collection probability to exceed 0.95. The estimated probability of detecting eDNA in a qPCR replicate (p) was 0.882 (95% CRI: 0.807-0.936), and our assay required two qPCR replicates for the cumulative detection probability to exceed 0.95. In complementary visual encounter surveys, the estimated probability of salamanders occurring at a known-occupied site was 0.905 (SE = 0.096), and the estimated probability of detecting salamanders in a visual encounter survey was 0.925 (SE = 0.052). We additionally discuss future research needed to refine this method and understand its limitations before practical application and incorporation into formal survey protocols for these taxa.
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Affiliation(s)
- Zachary C Adcock
- Department of Biology, Texas State University, San Marcos, Texas, United States of America
- Cambrian Environmental, Austin, Texas, United States of America
| | - Michelle E Adcock
- Department of Biology, Texas State University, San Marcos, Texas, United States of America
| | - Michael R J Forstner
- Department of Biology, Texas State University, San Marcos, Texas, United States of America
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Dahlberg AD, Waller DL, Hammond D, Lund K, Phelps NBD. Open water dreissenid mussel control projects: lessons learned from a retrospective analysis. Sci Rep 2023; 13:10410. [PMID: 37369671 DOI: 10.1038/s41598-023-36522-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Dreissenid mussels are one of the most problematic aquatic invasive species (AIS) in North America, causing substantial ecological and economic effects. To date, dreissenid mussel control efforts in open water have included physical, biological, and chemical methods. The feasibility of successful dreissenid mussel management or eradication in lakes is relatively undocumented in the freshwater management literature. This review presents information on 33 open water dreissenid mussel control projects in 23 North America lakes. We reviewed data from past dreissenid mussel control projects and identified patterns and knowledge gaps to help inform adaptive management strategies. The three key lessons learned include (1) pre- and post-treatment survey methods that are designed to meet management objectives are beneficial, e.g., by sampling for all life stages and taking into account that no survey method is completely comprehensive; (2) defining the treatment area-particularly ensuring it is sufficiently large to capture all life stages present-is critical to meeting management objectives; and (3) control projects provide an opportunity to collect water chemistry, effects on non-target organisms, and other efficacy-related data that can inform safe and effective adaptive management.
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Affiliation(s)
- Angelique D Dahlberg
- Minnesota Aquatic Invasive Species Research Center, University of Minnesota, 135 Skok Hall, 2003 Upper Buford Circle, St. Paul, MN, 55108, USA
- Department of Fisheries, Wildlife and Conservation Biology, College of Food, Agriculture and Natural Resource Sciences, University of Minnesota, 135 Skok Hall, 2003 Upper Buford Circle, St. Paul, MN, 55108, USA
| | - Diane L Waller
- U.S. Geological Survey, Upper Midwest Environmental Sciences Center, 2630 Fanta Reed Road, La Crosse, WI, 54603, USA
| | - David Hammond
- Earth Science Laboratories, Inc, 903 N 47th Street, Suite 105, Rogers, AR, 72712, USA
| | - Keegan Lund
- Minnesota Department of Natural Resources, 500 Lafayette Road, St. Paul, MN, 55155, USA
| | - Nicholas B D Phelps
- Minnesota Aquatic Invasive Species Research Center, University of Minnesota, 135 Skok Hall, 2003 Upper Buford Circle, St. Paul, MN, 55108, USA.
- Department of Fisheries, Wildlife and Conservation Biology, College of Food, Agriculture and Natural Resource Sciences, University of Minnesota, 135 Skok Hall, 2003 Upper Buford Circle, St. Paul, MN, 55108, USA.
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Osathanunkul M, Suwannapoom C. eDNA testing reveals surprising findings on fish population dynamics in Thailand. Heliyon 2023; 9:e17102. [PMID: 37416664 PMCID: PMC10320040 DOI: 10.1016/j.heliyon.2023.e17102] [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: 04/28/2023] [Revised: 05/27/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
COVID-19, a global health concern, has an effect on all aspects of the economy. The aquaculture and fishing industries were severely harmed as a result of the closures in multiple nations. Regular systems for inventory monitoring, production, and supply were disrupted. Cancellation of programmes for research, fieldwork, sampling, and tagging influences management-required data. For effective species management, fish dispersion assessments are indispensable. However, due to the difficulty of accessing sampling sites and the associated costs, there is frequently a lack of comprehensive information regarding the distribution and abundance of organisms. The COVID-19 prohibition made fish monitoring more problematic. Due to constant pressure, populations of the stone lapping minnow (Garra cambodgiensis), one of Thailand's overfished fish, are rapidly declining. Therefore, eDNA-based monitoring was devised and implemented to reveal the likely dispersal of the species in Thailand prior to and following the lockdown. At 28 locations within the Chao Phraya River Basin, water samples were collected. qPCR was used to determine the presence or absence of G. cambodgiensis in water samples. In 78 of 252 water samples, a wide range of computed copy numbers for G. cambodgiensis eDNA was observed. It was discovered that samples collected in 2021 (after the lockdown) contain a higher concentration of G. cambodgiensis eDNA than samples collected in 2018 or 2019 (prior to the lockdown). The closure appears to be a boon and may result in a substantial restocking of the fish we have studied. Overall, eDNA-based analysis is an extremely promising new survey instrument.
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Affiliation(s)
| | - Chatmongkon Suwannapoom
- School of Agriculture and Natural Resources, University of Phayao, Muang District, Phayao, Thailand
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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: 16] [Impact Index Per Article: 16.0] [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.
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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.
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Aunins AA, Mueller SJ, Fike JA, Cornman RS. Assessing arthropod diversity metrics derived from stream environmental DNA: spatiotemporal variation and paired comparisons with manual sampling. PeerJ 2023; 11:e15163. [PMID: 37020852 PMCID: PMC10069422 DOI: 10.7717/peerj.15163] [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: 10/26/2022] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
Background
Benthic invertebrate (BI) surveys have been widely used to characterize freshwater environmental quality but can be challenging to implement at desired spatial scales and frequency. Environmental DNA (eDNA) allows an alternative BI survey approach, one that can potentially be implemented more rapidly and cheaply than traditional methods.
Methods
We evaluated eDNA analogs of BI metrics in the Potomac River watershed of the eastern United States. We first compared arthropod diversity detected with primers targeting mitochondrial 16S (mt16S) and cytochrome c oxidase 1 (cox1 or COI) loci to that detected by manual surveys conducted in parallel. We then evaluated spatial and temporal variation in arthropod diversity metrics with repeated sampling in three focal parks. We also investigated technical factors such as filter type used to capture eDNA and PCR inhibition treatment.
Results
Our results indicate that genus-level assessment of eDNA compositions is achievable at both loci with modest technical noise, although database gaps remain substantial at mt16S for regional taxa. While the specific taxa identified by eDNA did not strongly overlap with paired manual surveys, some metrics derived from eDNA compositions were rank-correlated with previously derived biological indices of environmental quality. Repeated sampling revealed statistical differences between high- and low-quality sites based on taxonomic diversity, functional diversity, and tolerance scores weighted by taxon proportions in transformed counts. We conclude that eDNA compositions are efficient and informative of stream condition. Further development and validation of scoring schemes analogous to commonly used biological indices should allow increased application of the approach to management needs.
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Affiliation(s)
- Aaron A. Aunins
- Eastern Ecological Research Center, U.S. Geological Survey, Kearneysville, West Virginia, United States
| | - Sara J. Mueller
- Wildlife and Fisheries Sciences Program, The Pennsylvania State College, State College, Pennsylvania, United States
| | - Jennifer A. Fike
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, United States
| | - Robert S. Cornman
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, United States
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Chua PYS, Bourlat SJ, Ferguson C, Korlevic P, Zhao L, Ekrem T, Meier R, Lawniczak MKN. Future of DNA-based insect monitoring. Trends Genet 2023:S0168-9525(23)00038-0. [PMID: 36907721 DOI: 10.1016/j.tig.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 03/12/2023]
Abstract
Insects are crucial for ecosystem health but climate change and pesticide use are driving massive insect decline. To mitigate this loss, we need new and effective monitoring techniques. Over the past decade there has been a shift to DNA-based techniques. We describe key emerging techniques for sample collection. We suggest that the selection of tools should be broadened, and that DNA-based insect monitoring data need to be integrated more rapidly into policymaking. We argue that there are four key areas for advancement, including the generation of more complete DNA barcode databases to interpret molecular data, standardisation of molecular methods, scaling up of monitoring efforts, and integrating molecular tools with other technologies that allow continuous, passive monitoring based on images and/or laser imaging, detection, and ranging (LIDAR).
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Affiliation(s)
- Physilia Y S Chua
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Sarah J Bourlat
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Adenauerallee 127, 53113 Bonn, Germany
| | - Cameron Ferguson
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Petra Korlevic
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Leia Zhao
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Rudolf Meier
- Museum für Naturkunde, Center for Integrative Biodiversity Discovery, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Mara K N Lawniczak
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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Sakata MK, Takeshita D, Nishizawa R, Sato T, Minamoto T. An efficient environmental DNA detection method for rare species: a case study of a small salamander (Hynobius boulengeri). ANAL SCI 2023; 39:721-728. [PMID: 36859696 DOI: 10.1007/s44211-023-00289-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/03/2023] [Indexed: 03/03/2023]
Abstract
Loss of biodiversity is a serious concern, and amphibians are particularly threatened. Most small salamanders in Japan are endangered. Distributional information is fundamental to the conservation of these rare species; however, small salamanders are generally difficult to locate or catch. Environmental DNA analysis is an effective survey method for monitoring such rare species. The conventional polymerase chain reaction (PCR) method, which combines PCR amplification with subsequent electrophoresis, and the real-time PCR method, which uses fluorescent material, are commonly used for this purpose. In this study, a comparison of these two detection methods was conducted using a rare salamander species, Hynobius boulengeri, as a model case. We compared three points: (i) detection sensitivity, (ii) influence of environmental factors related to detection, and (iii) time and financial costs of the two methods. To perform this comparison, we developed a real-time PCR detection assay, conducted field surveys, and compared the time and financial costs of conventional and real-time PCR methods. The comparison showed no statistical difference in the detection sensitivity from field samples, and the effects of environmental factors tended to be similar. In addition, the financial cost was lower for the conventional PCR method while the time cost was lower for the real-time PCR method. Therefore, selecting eDNA detection methods based on objectives, time, and financial costs will promote efficient monitoring and contribute to the conservation of rare species.
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Affiliation(s)
- Masayuki K Sakata
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan. .,Graduate School of Human Development and Environment, Kobe University, 3-11, Tsurukabuto, Nada-ku, Kobe, Hyogo, 657-8501, Japan.
| | - Daiki Takeshita
- Graduate School of Human Development and Environment, Kobe University, 3-11, Tsurukabuto, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Ryohei Nishizawa
- Graduate School of Human Development and Environment, Kobe University, 3-11, Tsurukabuto, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Takuya Sato
- Center for Ecological Research, Kyoto University, 2-509-3, Hirano, Otsu, Shiga, 520-2113, Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, 3-11, Tsurukabuto, Nada-ku, Kobe, Hyogo, 657-8501, Japan
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Dominant barriers and the solutions to the social application of environmental DNA. LANDSCAPE AND ECOLOGICAL ENGINEERING 2023. [DOI: 10.1007/s11355-023-00549-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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Quebedeaux KB, Taylor CA, Curtis AN, Larson ER. A multi-method approach for assessing the distribution of a rare, burrowing North American crayfish species. PeerJ 2023; 11:e14748. [PMID: 36846445 PMCID: PMC9948742 DOI: 10.7717/peerj.14748] [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: 10/19/2022] [Accepted: 12/27/2022] [Indexed: 02/22/2023] Open
Abstract
Primary burrowing crayfishes face high extinction risk, but are challenging to study, manage, and conserve due to their difficult-to-sample habitat (i.e., terrestrial burrows) and low population densities. We apply here a variety of methods to characterize the distribution, habitat associations, and conservation status of the Boston Mountains Crayfish Cambarus causeyi (Reimer, 1966), an endemic burrowing crayfish found only in the Ozark Mountains of Arkansas, United States. We used species distribution modeling (SDM) on historic occurrence records to characterize the distribution and macro-scale habitat associations of this species. We then ground-truthed SDM predictions with conventional sampling, modeled fine-scale habitat associations with generalized linear models (GLM), and lastly developed and tested an environmental DNA (eDNA) assay for this species in comparison to conventional sampling. This represents, to our knowledge, the first successful eDNA assay for a terrestrial burrowing crayfish. Our MaxEnt-derived SDM found a strong effect of average annual precipitation on the historic distribution of C. causeyi, which occurred most frequently at locations with moderately high average annual precipitation (140-150 cm/yr) within our study region. Cambarus causeyi was difficult to detect by conventional sampling in 2019 and 2020, found at only 9 of 51 sites (17.6%) sampled by searching for and manually excavating crayfish burrows. Surprisingly, habitat suitability predicted from our MaxEnt models was not associated with contemporary C. causeyi occurrences per GLMs. Instead, C. causeyi presence was negatively associated with both sandy soils and the presence of other burrowing crayfish species. Poor SDM performance in this instance was likely caused by the omission of high resolution fine-scale habitat data (e.g., soils) and biotic interactions from MaxEnt models. Finally, our eDNA assay detected C. causeyi from six of 25 sites (24.0%) sampled in 2020, out-performing conventional surveys by burrow excavation for this species. Given the difficulty of studying primary burrowing crayfishes and their high conservation need, we propose that eDNA may become an increasingly important monitoring tool for C. causeyi and similar species.
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Affiliation(s)
- Kathleen B. Quebedeaux
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America,Department of Natural Resources and Environmental Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Christopher A. Taylor
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
| | - Amanda N. Curtis
- Program in Ecology, Evolution & Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Eric R. Larson
- Department of Natural Resources and Environmental Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
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Valsecchi E, Tavecchia G, Boldrocchi G, Coppola E, Ramella D, Conte L, Blasi M, Bruno A, Galli P. Playing "hide and seek" with the Mediterranean monk seal: a citizen science dataset reveals its distribution from molecular traces (eDNA). Sci Rep 2023; 13:2610. [PMID: 36788241 PMCID: PMC9929094 DOI: 10.1038/s41598-023-27835-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 01/09/2023] [Indexed: 02/16/2023] Open
Abstract
Animal conservation relies on assessing the distribution and habitat use of species, but for endangered/elusive animals this can prove difficult. The Monk Seal, Monachus monachus, is one of the world's most endangered species of pinniped, and the only one endemic to the Mediterranean Sea. During recent decades, direct observations have been few and scattered, making it difficult to determine its distribution away from the Aegean Sea (core distribution area of the post-decline relict population). This study relies on environmental DNA (eDNA) analysis to detect the presence of the Monk Seal in 135 samples collected in 120 locations of the central/western Mediterranean Sea, spanning about 1500 km longitudinally and 1000 km latitudinally. A recently described species-specific qPCR assay was used on marine-water samples, mostly collected during 2021 by a Citizen Science (CS) project. Positive detections occurred throughout the longitudinal range, including the westernmost surveyed area (Balearic archipelago). The distribution of the positive detections indicated six "hotspots", mostly overlapping with historical Monk Seal sites, suggesting that habitat-specific characteristics play a fundamental role. We applied single-season occupancy models to correct for detection probability and to assess the importance of site-specific characteristics. The distance from small islets and protected (or access-restricted) areas was correlated negatively with the detection probability. This novel molecular approach, applied here for the first time in an extensive CS study, proved its potential as a tool for monitoring the distribution of this endangered/elusive species.
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Affiliation(s)
- Elena Valsecchi
- Department of Environmental and Earth Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy.
- MaRHE Center, Magoodhoo Island, Faafu Atoll, Republic of Maldives.
| | - Giacomo Tavecchia
- Mediterranean Institute for Advanced Studies (IMEDEA-CSIC/UIB), IMEDEA-C/Miquel Marquès, 21, 07190, Esporles, Balearics Islands, Spain
| | - Ginevra Boldrocchi
- Department of Human Sciences, Innovation and Territory, University of Insubria, Via Valleggio 11, Como, Italy
- One Ocean Foundation, Via Gesù 10, Milan, Italy
| | | | - Denise Ramella
- Department of Environmental and Earth Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Livia Conte
- Department of Environmental and Earth Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Monica Blasi
- Filicudi Wildlife Conservation, Stimpagnato, 98055, Filicudi, Lipari (ME), Italy
| | - Antonia Bruno
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Paolo Galli
- Department of Environmental and Earth Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
- MaRHE Center, Magoodhoo Island, Faafu Atoll, Republic of Maldives
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45
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Detection of the Endangered Siamese Bat Catfish ( Oreoglanis siamensis Smith, 1933) in Doi Inthanon National Park Using Environmental DNA. Animals (Basel) 2023; 13:ani13030538. [PMID: 36766427 PMCID: PMC9913137 DOI: 10.3390/ani13030538] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/04/2023] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Siamese bat catfish (Oreoglanis siamensis Smith, 1993) has been listed as an endangered species, and its abundance has been severely declining due to habitat degradation and overfishing. To establish an appropriate management strategy, it is crucial to gain information about the distribution of this endangered species. As O. siamensis live under rocks in streams, detecting their presence is difficult. Recently, environmental DNA (eDNA)-based detection has been demonstrated to be a valid tool for monitoring rare species, such as O. siamensis. Therefore, this study developed an eDNA assay targeting a 160 bp fragment of the COI region to detect the presence of this species in its natural habitat. An amount of 300 mL of water samples (0.7 μm filtered) were collected from 15 sites in the Mae Klang sub-basin, where this fish species was visually detected at two locations. O. siamensis eDNA was detected at 12 of the 15 sites sampled with varying concentrations (0.71-20.27 copies/mL), including at the sites where this species was visually detected previously. The developed O. siamensis eDNA assay was shown to be effective for detecting the presence of this endangered species in the Klang Phat and Klang Rivers within the Doi Inthanon National Park.
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Shollenberger KR, Janosik AM, Johnston C. Detection of the threatened snail darter Percina tanasi in the Tennessee River system using environmental DNA. JOURNAL OF FISH BIOLOGY 2023; 102:373-379. [PMID: 36371654 DOI: 10.1111/jfb.15269] [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: 01/03/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
The distribution of many fishes that occupy large rivers is poorly known, in part due to the difficulties of sampling for them. This is especially true for small-bodied or rare species, such as the snail darter Percina tanasi, 44, 469-488; 1976). This federally listed (threatened) species has a limited distribution in the Tennessee River system in Alabama and Tennessee, where it is known from a few large tributaries or small rivers. In Alabama, P. tanasi was previously known from only one locality, but has recently been found in two additional, widely separated systems. These new records raise questions regarding the accuracy of our current understanding of the range for this species. Particularly, is P. tanasi present throughout the main stem Tennessee River, and is this species dispersing into new areas from source populations in the river? To clarify the distribution of P. tanasi in Alabama, 83 unique sites were surveyed using environmental DNA analysis. This cost-effective detection tool reduces the difficulty associated with empirically sampling large rivers for small fishes. Approximately 42% of sites sampled were positive for P. tanasi DNA. This study confirmed the known localities of P. tanasi in the Bear Creek, Elk River and Paint Rock River. Several new localities were also discovered throughout the main stem Tennessee River and in Shoal Creek, near Florence, Alabama. These findings can inform biologists about where to prioritize conservation efforts and further could lead to studies assessing movement and relatedness between populations in this system.
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Affiliation(s)
- Kurtis R Shollenberger
- School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, Auburn, Alabama, USA
- Marsh & Associates LLC, Tempe, Arizona, USA
| | - Alexis M Janosik
- Department of Biology, University of West Florida, Pensacola, Florida, USA
| | - Carol Johnston
- School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, Auburn, Alabama, USA
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Johnson MD, Freeland JR, Parducci L, Evans DM, Meyer RS, Molano-Flores B, Davis MA. Environmental DNA as an emerging tool in botanical research. AMERICAN JOURNAL OF BOTANY 2023; 110:e16120. [PMID: 36632660 DOI: 10.1002/ajb2.16120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species and communities), as a means of elucidating biological interaction networks, and as a window into understanding past patterns of biodiversity. However, only recently has the potential of eDNA been realized in the botanical world. Here we synthesize the state of eDNA applications in botanical systems with emphases on aquatic, ancient, contemporary sediment, and airborne systems, and focusing on both single-species approaches and multispecies community metabarcoding. Further, we describe how abiotic and biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, and relative abundance influence the utilization and interpretation of airborne eDNA results. Lastly, we explore several areas and opportunities for further development of eDNA tools for plants, advancing our knowledge and understanding of the efficacy, utility, and cost-effectiveness, and ultimately facilitating increased adoption of eDNA analyses in botanical systems.
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Affiliation(s)
- Mark D Johnson
- Engineering Research and Development Center, Construction Engineering Research Laboratory (CERL), Champaign, IL, USA
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Joanna R Freeland
- Department of Biology, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada
| | - Laura Parducci
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE-75236, Uppsala, Sweden
| | - Darren M Evans
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Brenda Molano-Flores
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Mark A Davis
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
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48
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Chen Y, Tournayre O, Tian H, Lougheed SC. Assessing the breeding phenology of a threatened frog species using eDNA and automatic acoustic monitoring. PeerJ 2023; 11:e14679. [PMID: 36710869 PMCID: PMC9879156 DOI: 10.7717/peerj.14679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/13/2022] [Indexed: 01/25/2023] Open
Abstract
Background Climate change has driven shifts in breeding phenology of many amphibians, causing phenological mismatches (e.g., predator-prey interactions), and potentially population declines. Collecting data with high spatiotemporal sensitivity on hibernation emergence and breeding times can inform conservation best practices. However, monitoring the phenology of amphibians can be challenging because of their cryptic nature over much of their life cycle. Moreover, most salamanders and caecilians do not produce conspicuous breeding calls like frogs and toads do, presenting additional monitoring challenges. Methods In this study, we designed and evaluated the performance of an environmental DNA (eDNA) droplet digital PCR (ddPCR) assay as a non-invasive tool to assess the breeding phenology of a Western Chorus Frog population (Pseudacris maculata mitotype) in Eastern Ontario and compared eDNA detection patterns to hourly automatic acoustic monitoring. For two eDNA samples with strong PCR inhibition, we tested three methods to diminish the effect of inhibitors: diluting eDNA samples, adding bovine serum albumin to PCR reactions, and purifying eDNA using a commercial clean-up kit. Results We recorded the first male calling when the focal marsh was still largely frozen. Chorus frog eDNA was detected on April 6th, 6 days after acoustic monitoring revealed this first calling male, but only 2 days after males attained higher chorus activity. eDNA signals were detected at more sampling locales within the marsh and eDNA concentrations increased as more males participated in the chorus, suggesting that eDNA may be a reasonable proxy for calling assemblage size. Internal positive control revealed strong inhibition in some samples, limiting detection probability and quantification accuracy in ddPCR. We found diluting samples was the most effective in reducing inhibition and improving eDNA quantification. Conclusions Altogether, our results showed that eDNA ddPCR signals lagged behind male chorusing by a few days; thus, acoustic monitoring is preferable if the desire is to document the onset of male chorusing. However, eDNA may be an effective, non-invasive monitoring tool for amphibians that do not call and may provide a useful complement to automated acoustic recording. We found inhibition patterns were heterogeneous across time and space and we demonstrate that an internal positive control should always be included to assess inhibition for eDNA ddPCR signal interpretations.
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49
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Patin NV, Goodwin KD. Capturing marine microbiomes and environmental DNA: A field sampling guide. Front Microbiol 2023; 13:1026596. [PMID: 36713215 PMCID: PMC9877356 DOI: 10.3389/fmicb.2022.1026596] [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: 08/24/2022] [Accepted: 11/22/2022] [Indexed: 01/15/2023] Open
Abstract
The expanding interest in marine microbiome and eDNA sequence data has led to a demand for sample collection and preservation standard practices to enable comparative assessments of results across studies and facilitate meta-analyses. We support this effort by providing guidelines based on a review of published methods and field sampling experiences. The major components considered here are environmental and resource considerations, sample processing strategies, sample storage options, and eDNA extraction protocols. It is impossible to provide universal recommendations considering the wide range of eDNA applications; rather, we provide information to design fit-for-purpose protocols. To manage scope, the focus here is on sampling collection and preservation of prokaryotic and microeukaryotic eDNA. Even with a focused view, the practical utility of any approach depends on multiple factors, including habitat type, available resources, and experimental goals. We broadly recommend enacting rigorous decontamination protocols, pilot studies to guide the filtration volume needed to characterize the target(s) of interest and minimize PCR inhibitor collection, and prioritizing sample freezing over (only) the addition of preservation buffer. An annotated list of studies that test these parameters is included for more detailed investigation on specific steps. To illustrate an approach that demonstrates fit-for-purpose methodologies, we provide a protocol for eDNA sampling aboard an oceanographic vessel. These guidelines can aid the decision-making process for scientists interested in sampling and sequencing marine microbiomes and/or eDNA.
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Affiliation(s)
- Nastassia Virginia Patin
- Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, Miami, FL, United States,Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States,Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United States,*Correspondence: Nastassia Virginia Patin,
| | - Kelly D. Goodwin
- Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, Miami, FL, United States,Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United States
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50
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Shea MM, Kuppermann J, Rogers MP, Smith DS, Edwards P, Boehm AB. Systematic review of marine environmental DNA metabarcoding studies: toward best practices for data usability and accessibility. PeerJ 2023; 11:e14993. [PMID: 36992947 PMCID: PMC10042160 DOI: 10.7717/peerj.14993] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/12/2023] [Indexed: 03/31/2023] Open
Abstract
The emerging field of environmental DNA (eDNA) research lacks universal guidelines for ensuring data produced are FAIR-findable, accessible, interoperable, and reusable-despite growing awareness of the importance of such practices. In order to better understand these data usability challenges, we systematically reviewed 60 peer reviewed articles conducting a specific subset of eDNA research: metabarcoding studies in marine environments. For each article, we characterized approximately 90 features across several categories: general article attributes and topics, methodological choices, types of metadata included, and availability and storage of sequence data. Analyzing these characteristics, we identified several barriers to data accessibility, including a lack of common context and vocabulary across the articles, missing metadata, supplementary information limitations, and a concentration of both sample collection and analysis in the United States. While some of these barriers require significant effort to address, we also found many instances where small choices made by authors and journals could have an outsized influence on the discoverability and reusability of data. Promisingly, articles also showed consistency and creativity in data storage choices as well as a strong trend toward open access publishing. Our analysis underscores the need to think critically about data accessibility and usability as marine eDNA metabarcoding studies, and eDNA projects more broadly, continue to proliferate.
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Affiliation(s)
- Meghan M. Shea
- Emmett Interdisciplinary Program in Environment & Resources (E-IPER), Stanford University, Stanford, CA, United States of America
| | - Jacob Kuppermann
- Earth Systems Program, Stanford University, Stanford, CA, United States of America
| | - Megan P. Rogers
- Program in Human Biology, Stanford University, Stanford, CA, United States of America
| | - Dustin Summer Smith
- Earth Systems Program, Stanford University, Stanford, CA, United States of America
| | - Paul Edwards
- Program in Science, Technology and Society, Stanford University, Stanford, CA, United States of America
| | - Alexandria B. Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America
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