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Lewis M, Lainé K, Dawnay L, Lamont D, Scott K, Mariani S, Hӓnfling B, Dawnay N. The forensic potential of environmental DNA (eDNA) in freshwater wildlife crime investigations: From research to application. Sci Justice 2024; 64:443-454. [PMID: 39025568 DOI: 10.1016/j.scijus.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 06/07/2024] [Accepted: 06/15/2024] [Indexed: 07/20/2024]
Abstract
Environmental DNA (eDNA) is widely used in biodiversity, conservation, and ecological studies but despite its successes, similar approaches have not yet been regularly applied to assist in wildlife crime investigations. The purpose of this paper is to review current eDNA methods and assess their potential forensic application in freshwater environments considering collection, transport and persistence, analysis, and interpretation, while identifying additional research required to present eDNA evidence in court. An extensive review of the literature suggests that commonly used collection methods can be easily adapted for forensic frameworks providing they address the appropriate investigative questions and take into consideration the uniqueness of the target species, its habitat, and the requirements of the end user. The use of eDNA methods to inform conservationists, monitor biodiversity and impacts of climate change, and detect invasive species and pathogens shows confidence within the scientific community, making the acceptance of these methods by the criminal justice system highly possible. To contextualise the potential application of eDNA on forensic investigations, two test cases are explored involving i) species detection and ii) species localisation. Recommendations for future work within the forensic eDNA discipline include development of suitable standardised collection methods, considered collection strategies, forensically validated assays and publication of procedures and empirical research studies to support implementation within the legal system.
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Affiliation(s)
- Matthew Lewis
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, UK
| | - Katie Lainé
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, UK
| | - Louise Dawnay
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, UK; International Study Centre, Liverpool John Moores University, Mount Pleasant, Liverpool, UK
| | - David Lamont
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, UK; Forensic Research Institute, Liverpool John Moores University, Byrom Street, Liverpool, UK
| | - Kirstie Scott
- School of Biological and Environmental Sciences, Liverpool John Moores University, Byrom Street, Liverpool, UK; Forensic Research Institute, Liverpool John Moores University, Byrom Street, Liverpool, UK
| | - Stefano Mariani
- School of Biological and Environmental Sciences, Liverpool John Moores University, Byrom Street, Liverpool, UK; Forensic Research Institute, Liverpool John Moores University, Byrom Street, Liverpool, UK
| | - Bernd Hӓnfling
- Institute for Biodiversity and Freshwater Conservation, University of the Highlands and Islands, Inverness, UK
| | - Nick Dawnay
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, UK; Forensic Research Institute, Liverpool John Moores University, Byrom Street, Liverpool, UK.
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2
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Urban P, Jacobsen MW, Bekkevold D, Nielsen A, Storr-Paulsen M, Nijland R, Nielsen EE. eDNA based bycatch assessment in pelagic fish catches. Sci Rep 2024; 14:2976. [PMID: 38316827 PMCID: PMC10844201 DOI: 10.1038/s41598-024-52543-0] [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: 05/25/2023] [Accepted: 01/19/2024] [Indexed: 02/07/2024] Open
Abstract
Pelagic fish like herring, sardines, and mackerel constitute an essential and nutritious human food source globally. Their sustainable harvest is promoted by the application of precise, accurate, and cost-effective methods for estimating bycatch. Here, we experimentally test the new concept of using eDNA for quantitative bycatch assessment on the illustrative example of the Baltic Sea sprat fisheries with herring bycatch. We investigate the full pipeline from sampling of production water on vessels and in processing factories to the estimation of species weight fractions. Using a series of controlled mixture experiments, we demonstrate that the eDNA signal from production water shows a strong, seasonally consistent linear relationship with herring weight fractions, however, the relationship is influenced by the molecular method used (qPCR or metabarcoding). In four large sprat landings analyzed, despite examples of remarkable consistency between eDNA and visual reporting, estimates of herring bycatch biomass varied between the methods applied, with the eDNA-based estimates having the highest precision for all landings analyzed. The eDNA-based bycatch assessment method has the potential to improve the quality and cost effectiveness of bycatch assessment in large pelagic fisheries catches and in the long run lead to more sustainable management of pelagic fish as a precious marine resource.
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Affiliation(s)
- Paulina Urban
- Section for Marine Living Resources, National Institute of Aquatic Resources (DTU Aqua), Technical University of Denmark (DTU), Silkeborg, Denmark.
| | - Magnus Wulff Jacobsen
- Section for Marine Living Resources, National Institute of Aquatic Resources (DTU Aqua), Technical University of Denmark (DTU), Silkeborg, Denmark
| | - Dorte Bekkevold
- Section for Marine Living Resources, National Institute of Aquatic Resources (DTU Aqua), Technical University of Denmark (DTU), Silkeborg, Denmark
| | - Anders Nielsen
- Section for Marine Living Resources, National Institute of Aquatic Resources (DTU Aqua), Technical University of Denmark (DTU), Lyngby, Denmark
| | - Marie Storr-Paulsen
- Section for Monitoring and Data, National Institute of Aquatic Resources (DTU Aqua), Technical University of Denmark (DTU), Lyngby, Denmark
| | - Reindert Nijland
- Marine Animal Ecology Group, Wageningen University, Wageningen, The Netherlands
| | - Einar Eg Nielsen
- Section for Marine Living Resources, National Institute of Aquatic Resources (DTU Aqua), Technical University of Denmark (DTU), Silkeborg, Denmark.
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3
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Zhang H, Vandesompele J, Braeckmans K, De Smedt SC, Remaut K. Nucleic acid degradation as barrier to gene delivery: a guide to understand and overcome nuclease activity. Chem Soc Rev 2024; 53:317-360. [PMID: 38073448 DOI: 10.1039/d3cs00194f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Gene therapy is on its way to revolutionize the treatment of both inherited and acquired diseases, by transferring nucleic acids to correct a disease-causing gene in the target cells of patients. In the fight against infectious diseases, mRNA-based therapeutics have proven to be a viable strategy in the recent Covid-19 pandemic. Although a growing number of gene therapies have been approved, the success rate is limited when compared to the large number of preclinical and clinical trials that have been/are being performed. In this review, we highlight some of the hurdles which gene therapies encounter after administration into the human body, with a focus on nucleic acid degradation by nucleases that are extremely abundant in mammalian organs, biological fluids as well as in subcellular compartments. We overview the available strategies to reduce the biodegradation of gene therapeutics after administration, including chemical modifications of the nucleic acids, encapsulation into vectors and co-administration with nuclease inhibitors and discuss which strategies are applied for clinically approved nucleic acid therapeutics. In the final part, we discuss the currently available methods and techniques to qualify and quantify the integrity of nucleic acids, with their own strengths and limitations.
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Affiliation(s)
- Heyang Zhang
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Stefaan C De Smedt
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Katrien Remaut
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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Duarte S, Simões L, Costa FO. Current status and topical issues on the use of eDNA-based targeted detection of rare animal species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166675. [PMID: 37647964 DOI: 10.1016/j.scitotenv.2023.166675] [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: 06/13/2023] [Revised: 08/26/2023] [Accepted: 08/27/2023] [Indexed: 09/01/2023]
Abstract
Animal detection through DNA present in environmental samples (eDNA) is a valuable tool for detecting rare species, that are difficult to observe and monitor. eDNA-based tools are underpinned by molecular evolutionary principles, key to devising tools to efficiently single out a targeted species from an environmental sample. Here, we present a comprehensive review of the use of eDNA-based methods for the detection of targeted animal species, such as rare, endangered, or invasive species, through the analysis of 549 publications (2008-2022). Aquatic ecosystems have been the most surveyed, in particular, freshwaters (74 %), and to a less extent marine (14 %) and terrestrial systems (10 %). Vertebrates, in particular, fish (38 %), and endangered species, have been the focus of most of these studies, and Cytb and COI are the most employed markers. Among invertebrates, assays have been mainly designed for Mollusca and Crustacea species (21 %), in particular, to target invasive species, and COI the most employed marker. Targeted molecular approaches, in particular qPCR, have been the most adopted (75 %), while eDNA metabarcoding has been rarely used to target single or few species (approx. 6 %). However, less attention has been given in these studies to the effects of environmental factors on the amount of shed DNA, the differential amount of shed DNA among species, or the sensitivity of the markers developed, which may impact the design of the assays, particularly to warrant the required detection level and avoid false negatives and positives. The accuracy of the assays will also depend on the availability of genetic data and vouchered tissue or DNA samples from closely related species to assess both marker and primers' specificity. In addition, eDNA-based assays developed for a particular species may have to be refined for use in a new geographic area taking into account site-specific populations, as well as any intraspecific variation.
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Affiliation(s)
- Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Luara Simões
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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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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Lowder SR, Neill TM, Peetz AB, Miles TD, Moyer MM, Oliver C, Stergiopoulos I, Ding S, Mahaffee WF. A Rapid Glove-Based Inoculum Sampling Technique to Monitor Erysiphe necator in Commercial Vineyards. PLANT DISEASE 2023; 107:3096-3105. [PMID: 37079020 DOI: 10.1094/pdis-02-23-0216-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Information on the presence and severity of grape powdery mildew (GPM), caused by Erysiphe necator, has long been used to guide management decisions. While recent advances in the available molecular diagnostic assays and particle samplers have made monitoring easier, there is still a need for more efficient field collection of E. necator. The use of vineyard worker gloves worn during canopy manipulation as a sampler (glove swab) of E. necator was compared with samples identified by visual assessment with subsequent molecular confirmation (leaf swabs) and airborne spore samples collected by rotating-arm impaction traps (impaction traps). Samples from United States commercial vineyards in Oregon, Washington, and California were analyzed using two TaqMan qPCR assays targeting the internal transcribed spacer regions or cytochrome b gene of E. necator. Based on qPCR assays, visual disease assessments misidentified GPM up to 59% of the time with a higher frequency of misidentification occurring earlier in the growing season. Comparison of the aggregated leaf swab results for a row (n = 915) to the row's corresponding glove swab had 60% agreement. The latent class analysis (LCA) indicated that glove swabs were more sensitive than leaf swabs in detecting E. necator presence. The impaction trap results had 77% agreement to glove swabs (n = 206) taken from the same blocks. The LCAs estimated that the glove swabs and impaction trap samplers varied each year in which was more sensitive for detection. This likely indicates that these methods have similar levels of uncertainty and provide equivalent information. Additionally, all samplers, once E. necator was detected, were similarly sensitive and specific for detection of the A-143 resistance allele. Together, these results suggest that glove swabs are an effective sampling method for monitoring the presence of E. necator and, subsequently, the G143A amino acid substitution associated with resistance to quinone outside inhibitor fungicides in vineyards. Glove swabs could reduce sampling costs due to the lack of need for specialized equipment and time required for swab collection and processing.
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Affiliation(s)
- Sarah R Lowder
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Tara M Neill
- USDA-ARS Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97330
| | - Amy B Peetz
- Revolution Crop Consultants, LLC, Albany, OR 97321
| | - Timothy D Miles
- Department of Plant, Soil, and Microbial Science, Michigan State University, East Lansing, MI 48824
| | - Michelle M Moyer
- Department of Viticulture and Enology, Washington State University, Prosser, WA 99350
| | | | | | - Shunping Ding
- Department of Wine and Viticulture, California Polytechnic State University, San Luis Obispo, CA 93407
| | - Walter F Mahaffee
- USDA-ARS Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97330
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7
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Kestel JH, Bateman PW, Field DL, White NE, Lines R, Nevill P. eDNA metabarcoding of avocado flowers: 'Hass' it got potential to survey arthropods in food production systems? Mol Ecol Resour 2023; 23:1540-1555. [PMID: 37237427 DOI: 10.1111/1755-0998.13814] [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: 12/14/2022] [Revised: 04/26/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023]
Abstract
In the face of global biodiversity declines, surveys of beneficial and antagonistic arthropod diversity as well as the ecological services that they provide are increasingly important in both natural and agro-ecosystems. Conventional survey methods used to monitor these communities often require extensive taxonomic expertise and are time-intensive, potentially limiting their application in industries such as agriculture, where arthropods often play a critical role in productivity (e.g. pollinators, pests and predators). Environmental DNA (eDNA) metabarcoding of a novel substrate, crop flowers, may offer an accurate and high throughput alternative to aid in the detection of these managed and unmanaged taxa. Here, we compared the arthropod communities detected with eDNA metabarcoding of flowers, from an agricultural species (Persea americana-'Hass' avocado), with two conventional survey techniques: digital video recording (DVR) devices and pan traps. In total, 80 eDNA flower samples, 96 h of DVRs and 48 pan trap samples were collected. Across the three methods, 49 arthropod families were identified, of which 12 were unique to the eDNA dataset. Environmental DNA metabarcoding from flowers revealed potential arthropod pollinators, as well as plant pests and parasites. Alpha diversity levels did not differ across the three survey methods although taxonomic composition varied significantly, with only 12% of arthropod families found to be common across all three methods. eDNA metabarcoding of flowers has the potential to revolutionize the way arthropod communities are monitored in natural and agro-ecosystems, potentially detecting the response of pollinators and pests to climate change, diseases, habitat loss and other disturbances.
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Affiliation(s)
- Joshua H Kestel
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup, Australia
| | - Philip W Bateman
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
- Behavioural Ecology Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - David L Field
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Rose Lines
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
- Department of Primary Industries and Regional Development, Perth, Western Australia, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
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Minamoto T. Environmental DNA analysis for macro-organisms: species distribution and more. DNA Res 2022; 29:6598799. [PMID: 35652724 PMCID: PMC9187915 DOI: 10.1093/dnares/dsac018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/31/2022] [Indexed: 11/14/2022] Open
Abstract
In an era of severe biodiversity loss, biological monitoring is becoming increasingly essential. The analysis of environmental DNA (eDNA) has emerged as a new approach that could revolutionize the biological monitoring of aquatic ecosystems. Over the past decade, macro-organismal eDNA analysis has undergone significant developments and is rapidly becoming established as the golden standard for non-destructive and non-invasive biological monitoring. In this review, I summarize the development of macro-organismal eDNA analysis to date and the techniques used in this field. I also discuss the future perspective of these analytical methods in combination with sophisticated analytical techniques for DNA research developed in the fields of molecular biology and molecular genetics, including genomics, epigenomics, and single-cell technologies. eDNA analysis, which to date has been used primarily for determining the distribution of organisms, is expected to develop into a tool for elucidating the physiological state and behaviour of organisms. The fusion of microbiology and macrobiology through an amalgamation of these technologies is anticipated to lead to the future development of an integrated biology.
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Affiliation(s)
- Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University , Kobe, Hyogo 657-8501, Japan
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Mauvisseau Q, Harper LR, Sander M, Hanner RH, Kleyer H, Deiner K. The Multiple States of Environmental DNA and What Is Known about Their Persistence in Aquatic Environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:5322-5333. [PMID: 35435663 PMCID: PMC9069692 DOI: 10.1021/acs.est.1c07638] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Increased use of environmental DNA (eDNA) analysis for indirect species detection has spurred the need to understand eDNA persistence in the environment. Understanding the persistence of eDNA is complex because it exists in a mixture of different states (e.g., dissolved, particle adsorbed, intracellular, and intraorganellar), and each state is expected to have a specific decay rate that depends on environmental parameters. Thus, improving knowledge about eDNA conversion rates between states and the reactions that degrade eDNA in different states is needed. Here, we focus on eukaryotic extraorganismal eDNA, outline how water chemistry and suspended mineral particles likely affect conversion among each eDNA state, and indicate how environmental parameters affect persistence of states in the water column. On the basis of deducing these controlling parameters, we synthesized the eDNA literature to assess whether we could already derive a general understanding of eDNA states persisting in the environment. However, we found that these parameters are often not being measured or reported when measured, and in many cases very few experimental data exist from which to draw conclusions. Therefore, further study of how environmental parameters affect eDNA state conversion and eDNA decay in aquatic environments is needed. We recommend analytic controls that can be used during the processing of water to assess potential losses of different eDNA states if all were present in a water sample, and we outline future experimental work that would help determine the dominant eDNA states in water.
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Affiliation(s)
- Quentin Mauvisseau
- Natural
History Museum, University of Oslo, Sars’ gate 1, 0562 Oslo, Norway
| | - Lynsey R. Harper
- Nature
Metrics Ltd, CABI Site, Bakeham Lane, Egham, Surrey TW20 9TY, United Kingdom
| | - Michael Sander
- Department
of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, CH-8092 Zurich, Switzerland
| | - Robert H. Hanner
- Department
of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Hannah Kleyer
- Department
of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, CH-8092 Zurich, Switzerland
| | - Kristy Deiner
- Department
of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, CH-8092 Zurich, Switzerland
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Danziger AM, Olson ZH, Frederich M. Limitations of eDNA analysis for Carcinus maenas abundance estimations. BMC Ecol Evol 2022; 22:14. [PMID: 35130838 PMCID: PMC8822865 DOI: 10.1186/s12862-022-01969-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 01/24/2022] [Indexed: 12/15/2022] Open
Abstract
Background Environmental DNA (eDNA) is an effective tool for the detection and monitoring of presence or absence of rare and invasive species. These techniques have been extended to quantify biomass in vertebrates, particularly in fish species. However, the efficacy of eDNA techniques to quantify biomass in invertebrate species has rarely been examined. This study tested whether eDNA could be used to determine the biomass of the world-wide invasive green crab, Carcinus maenas. In a controlled laboratory study, the relationship between biomass and C. maenas eDNA concentration was examined in the context of different biotic (activity) and abiotic (temperature) parameters. Results When incubating different numbers of crabs in sterile saltwater for up to 7 days, a relationship between eDNA concentration and biomass was observed at temperatures of 6.7 ℃ and 18.7 ℃, but not at 12.8 ℃. Additionally, motor activity, aggression level, time of sampling, and features of organismal decay had significant impact on the concentration of C. maenas eDNA collected. Conclusions We show that eDNA concentration did not correlate with biomass, and that biomass, temperature, organismal characteristics, and potentially many more parameters affect shedding and degradation rates for eDNA in this species, thus, impacting the recoverable eDNA concentration. Therefore, eDNA techniques are not likely to provide a reliable signal of biomass in the invasive invertebrate species C. maenas. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01969-z.
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12
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Amarasiri M, Furukawa T, Nakajima F, Sei K. Pathogens and disease vectors/hosts monitoring in aquatic environments: Potential of using eDNA/eRNA based approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 796:148810. [PMID: 34265610 DOI: 10.1016/j.scitotenv.2021.148810] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/20/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
Infectious diseases are spreading in to previously unreported geographical regions, and are reappeared in regions 75 or 100 years after their last reported case, as a result of environmental changes caused by anthropogenic activities. A pathogen, vector/host monitoring methodology is therefore indispensable in identifying potential transmission sites, providing early warnings and evaluating the human health risks of these infectious diseases in a given area. Recently, environmental DNA (eDNA) and environmental RNA approach (eRNA) have become widespread in monitoring organisms in the environment due to advantages like lower cost, time, and labour requirements. However, eDNA/eRNA based monitoring of pathogens and vectors/hosts using aquatic samples is limited to very few studies. In this review, we summarized the currently available eDNA/eRNA based human and non-human pathogens and vectors/hosts detection studies in aquatic samples. Species-specific shedding, transport, and decay of eDNA/eRNA in aquatic environments which is essential in estimating the abundance of pathogen, vectors/host in focus is also summarized. We also suggest the usage of eDNA/eRNA approach in urban aquatic samples like runoff in identifying the disease vectors/hosts inhabiting in locations which are not accessible easily.
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Affiliation(s)
- Mohan Amarasiri
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Kitasato University, 1-15-1, Kitasato, Sagamihara-Minami 252-0373, Japan.
| | - Takashi Furukawa
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Kitasato University, 1-15-1, Kitasato, Sagamihara-Minami 252-0373, Japan
| | - Fumiyuki Nakajima
- Environmental Science Center, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazunari Sei
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Kitasato University, 1-15-1, Kitasato, Sagamihara-Minami 252-0373, Japan
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Carvalho CS, de Oliveira ME, Rodriguez-Castro KG, Saranholi BH, Galetti PM. Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance. Mol Ecol Resour 2021; 22:1262-1273. [PMID: 34724330 DOI: 10.1111/1755-0998.13543] [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: 03/10/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 10/20/2022]
Abstract
Environmental DNA (eDNA) and invertebrate-derived DNA (iDNA) have been increasingly recognized as powerful tools for biodiversity assessment and conservation management. However, eDNA/iDNA efficiency for vertebrate diversity assessment remains uncertain, and comparisons to conventional methods are still rare. Through a meta-analysis of previously published vertebrate diversity surveys, we compared the efficiency of eDNA/iDNA against conventional methods across several types of samplers, vertebrate groups, and locations (tropical vs. temperate zones). We also assess eDNA/iDNA efficiency to estimate relative abundance or biomass over different molecular methods (qPCR and metabarcoding) and type of experiment (in the laboratory or in the field). We showed that for water sampler, fish as a target species, and studies achieved in temperate zones, eDNA presents lower risk of not detecting a species or a site with a target species than conventional methods. These results show that eDNA is an efficient tool to assess fish diversity. Moreover, eDNA data presents positive correlation with fish abundance or biomass. However, such correlation was higher in laboratory experiments than in the field. For the other samplers, vertebrate groups, and in tropical zones we were not able to draw general conclusion, highlighting the urgency of conducting more comparative studies.
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Affiliation(s)
- Carolina S Carvalho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.,Instituto Tecnológico Vale, Belém, PA, Brazil
| | | | - Karen Giselle Rodriguez-Castro
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.,Facultad de Ciencias Básicas e Ingeniería, Universidad de los Llanos, Villavicencio, Colombia
| | - Bruno H Saranholi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.,Department of Life Sciences, Imperial College London, London, UK
| | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
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