51
|
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.
Collapse
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
| |
Collapse
|
52
|
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.
Collapse
|
53
|
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.
Collapse
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
| |
Collapse
|
54
|
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.
Collapse
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
| |
Collapse
|
55
|
Oginah SA, Posthuma L, Maltby L, Hauschild M, Fantke P. Linking freshwater ecotoxicity to damage on ecosystem services in life cycle assessment. ENVIRONMENT INTERNATIONAL 2023; 171:107705. [PMID: 36549223 PMCID: PMC9875201 DOI: 10.1016/j.envint.2022.107705] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/05/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Freshwater ecosystems provide major benefits to human wellbeing-so-called ecosystem services (ES)-but are currently threatened among others by ecotoxicological pressure from chemicals reaching the environment. There is an increased motivation to incorporate ES in quantification tools that support decision-making, such as life cycle assessment (LCA). However, mechanistic models and frameworks that can systematically translate ecotoxicity effect data from chemical tests into eventual damage on species diversity, functional diversity, and ES in the field are still missing. While current approaches focus on translating predicted ecotoxicity impacts to damage in terms of species loss, no approaches are available in LCA and other comparative assessment frameworks for linking ecotoxicity to damage on ecosystem functioning or ES. To overcome this challenge, we propose a way forward based on evaluating available approaches to characterize damage of chemical pollution on freshwater ES. We first outline an overall framework for linking freshwater ecotoxicity effects to damage on related ES in compliance with the boundary conditions of quantitative, comparative assessments. Second, within the proposed framework, we present possible approaches for stepwise linking ecotoxicity effects to species loss, functional diversity loss, and damage on ES. Finally, we discuss strengths, limitations, and data availability of possible approaches for each step. Although most approaches for directly deriving damage on ES from either species loss or damage to functional diversity have not been operationalized, there are some promising ways forward. The Threshold Indicator Taxa ANalysis (TITAN) seems suitable to translate predicted ecotoxicity effects to a metric of quantitative damage on species diversity. A Trait Probability Density Framework (TPD) approach that incorporates various functional diversity components and functional groups could be adapted to link species loss to functional diversity loss. An Ecological Production Function (EPF) approach seems most promising for further linking functional diversity loss to damage on ES flows for human wellbeing. However, in order to integrate the entire pathway from predicted freshwater ecotoxicity to damage on ES into LCA and other comparative frameworks, the approaches adopted for each step need to be harmonized in terms of assumptions, boundary conditions and consistent interfaces with each other.
Collapse
Affiliation(s)
- Susan A Oginah
- Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, Produktionstorvet 424, 2800 Kgs. Lyngby, Denmark
| | - Leo Posthuma
- National Institute for Public Health and the Environment, PO Box 1, 3720 Bilthoven, the Netherlands; Department of Environmental Science, Radboud University Nijmegen, Heyendaalseweg, Nijmegen, the Netherlands
| | - Lorraine Maltby
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Michael Hauschild
- Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, Produktionstorvet 424, 2800 Kgs. Lyngby, Denmark
| | - Peter Fantke
- Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, Produktionstorvet 424, 2800 Kgs. Lyngby, Denmark.
| |
Collapse
|
56
|
Kamoroff C, Goldberg CS, Grasso RL. Rapid detection of amphibian chytrid fungus Batrachochytrium dendrobatidis using in situ DNA extraction and a handheld mobile thermocycler. DISEASES OF AQUATIC ORGANISMS 2022; 152:99-108. [PMID: 36519681 DOI: 10.3354/dao03708] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The amphibian chytrid fungus (Bd) has caused declines and some extinctions of amphibian populations worldwide. Early and accurate Bd detection is essential for management of susceptible anurans. We analyzed the effectiveness of in situ DNA extraction with a handheld mobile quantitative PCR (qPCR) thermocycler to detect Bd on frog skin swabs and in water samples using environmental DNA (eDNA). We collected duplicate eDNA samples and skin swabs from 3 Bd-positive Rana sierrae populations. We processed one set of samples using a field protocol (a handheld thermocycler) and the other half using a standard lab protocol. We detected Bd DNA in all R. sierrae swabbed using both the field and lab protocols. We also detected Bd DNA in eDNA samples at all sites, although the field and lab protocols failed to detect Bd eDNA at separate singular sites; results from the field and lab eDNA protocol did not match. The probability of detecting Bd DNA in the technical replicates was lower for the field protocol than the lab protocol, suggesting the field protocol has lower sensitivity and may not detect low quantities of DNA. Our results suggest that the field extraction protocol using a handheld qPCR platform is a promising tool for rapid detection of Bd in susceptible amphibian populations, yielding accurate results in less than 60 min. However, the applied field protocol may be prone to false negatives when analyzing low-quantity DNA samples such as eDNA water samples or frog swabs with low pathogen loads.
Collapse
Affiliation(s)
- Colleen Kamoroff
- Resources Management and Science, Yosemite National Park, CA 95318, USA
| | | | | |
Collapse
|
57
|
van der Heyde M, Bunce M, Nevill P. Key factors to consider in the use of environmental DNA metabarcoding to monitor terrestrial ecological restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157617. [PMID: 35901901 DOI: 10.1016/j.scitotenv.2022.157617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Ecological restoration of terrestrial environments is a globally important process to combat the loss of biodiversity and ecosystem services. Holistic monitoring of restored biota and active management of restoration is necessary to improve restoration processes and outcomes, and provide evidence to stakeholders that targets are being achieved. Increasingly, environmental DNA (eDNA) metabarcoding is used as a restoration monitoring tool because it is able to generate biodiversity data rapidly, accurately, non-destructively, and reliably, on a wide breadth of organisms from soil microbes to mammals. The overall objective of this review is to discuss the key factors to consider in the use of environmental DNA for monitoring of restored terrestrial ecosystems, hopefully improving monitoring, and ultimately, restoration outcomes. We identified that the majority of eDNA based studies of ecosystem restoration are currently conducted in Europe, North America, and Australia, and that almost half of total studies were published in 2021-22. Soil was the most popular sample substrate, soil microbial communities the most targeted taxa, and forests the most studied ecosystem. We suggest there is no 'one size fits all' approach to restoration monitoring using eDNA, and discuss survey design. Factors to consider include substrate selection, sample collection and storage, assay selection, and data interpretation, all of which require careful planning to obtain reliable, and accurate information that can be used for restoration monitoring and decision making. We explore future directions for research and argue that eDNA metabarcoding can be a useful tool in the restoration monitoring 'toolkit', but requires informed application and greater accessibility to data by a wide spectrum of stakeholders.
Collapse
Affiliation(s)
- Mieke van der Heyde
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia 6102, Australia; Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPO Box U1987, Perth, Western Australia 6102, Australia.
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPO Box U1987, Perth, Western Australia 6102, Australia; Institute of Environmental Science and Research (ESR), Kenepuru, Porirua 5022, New Zealand
| | - Paul Nevill
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia 6102, Australia; Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPO Box U1987, Perth, Western Australia 6102, Australia
| |
Collapse
|
58
|
Prabhakaran GK, Sunkara M, Raghavan R, Umapathy G. Development of a species-specific qPCR assay for the detection of invasive African sharptooth catfish (Clarias gariepinus) using environmental DNA. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02969-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
59
|
Gold Z, Wall AR, Schweizer TM, Pentcheff ND, Curd EE, Barber PH, Meyer RS, Wayne R, Stolzenbach K, Prickett K, Luedy J, Wetzer R. A manager's guide to using eDNA metabarcoding in marine ecosystems. PeerJ 2022; 10:e14071. [PMID: 36405018 PMCID: PMC9673773 DOI: 10.7717/peerj.14071] [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: 06/24/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemble or develop comprehensive barcode reference databases; (3) apply rigorous site occupancy based decontamination pipelines; (4) conduct pilot studies to define spatial and temporal variance of eDNA; and (5) archive samples, extracts, and raw sequence data. We demonstrate the importance of each of these considerations using a case study of eDNA metabarcoding in the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches detected 94.1% (16/17) of species observed in paired trawl surveys while identifying an additional 55 native fishes, providing more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and confidence in species detections while providing archived genetic resources for future analyses. Well designed and validated eDNA metabarcoding approaches are ideally suited for biomonitoring applications that rely on the detection of species, including mapping invasive species fronts and endangered species habitats as well as tracking range shifts in response to climate change. Incorporating these considerations will enhance the utility and efficacy of eDNA metabarcoding for routine biomonitoring applications.
Collapse
Affiliation(s)
- Zachary Gold
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Adam R. Wall
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
| | - Teia M. Schweizer
- Department of Fish and Wildlife Conservation Biology, Colorado State University, Fort Collins, CO, United States of America
| | - N. Dean Pentcheff
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
| | - Emily E. Curd
- Department of Natural Sciences, Landmark College, Putney, VT, United States of America
| | - Paul H. Barber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Rachel S. Meyer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America,Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Robert Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Kevin Stolzenbach
- Wood Environment and Infrastructure, Inc., San Diego, CA, United States of America
| | - Kat Prickett
- Port of Los Angeles, Los Angeles, CA, United States of America
| | - Justin Luedy
- Port of Long Beach, Long Beach, CA, United States of America
| | - Regina Wetzer
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
| |
Collapse
|
60
|
Walker FM, Sanchez DE, Froehlich EM, Federman EL, Lyman JA, Owens M, Lear K. Endangered Nectar-Feeding Bat Detected by Environmental DNA on Flowers. Animals (Basel) 2022; 12:ani12223075. [PMID: 36428303 PMCID: PMC9686659 DOI: 10.3390/ani12223075] [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: 10/17/2022] [Revised: 10/30/2022] [Accepted: 11/03/2022] [Indexed: 11/11/2022] Open
Abstract
Leptonycteris nivalis (the Mexican long-nosed bat) is an endangered nectar-feeding bat species that follows "nectar corridors" as it migrates from Mexico to the southwestern United States. Locating these nectar corridors is key to their conservation and may be possible using environmental DNA (eDNA) from these bats. Hence, we developed and tested DNA metabarcoding and qPCR eDNA assays to determine whether L. nivalis could be detected by sampling the agave flowers on which it feeds. We sampled plants with known bat visitations in the Sierra Madre Oriental in Laguna de Sanchez (LS), Nuevo León, Mexico, and in the Chisos Mountains in Big Bend National Park, TX, USA (CB). A total of 13 samples included both swabs of agave umbels and cuttings of individual flowers. DNA metabarcoding was performed as a PCR multiplex that targeted bats (SFF-COI), arthropods (ANML-COI), and plants (ITS2 and rbcL). We targeted arthropods and plants in parallel with bats because future metabarcoding studies may wish to examine all the pollinators and plants within the nectar corridor. We developed and tested the sensitivity and specificity of two qPCR assays. We found that both DNA metabarcoding and qPCR were highly successful at detecting L. nivalis (11 of 13 for DNA metabarcoding and 12 of 13 for qPCR). Swabs and flower cuttings and both qPCR assays detected the species over four replicates. We suggest that L. nivalis leaves substantial DNA behind as it forages for nectar. We also suggest that future studies examine the time since sampling to determine its effect on detection success. The DNA metabarcoding multiplex will be useful for parallel questions regarding pollination ecology, while, with further testing, the qPCR assays will be effective for large-scale sampling for the detection of migration corridors and foraging areas. This work may be relevant to other nectar-feeding bat species, which can likely be detected with similar methodologies.
Collapse
Affiliation(s)
- Faith M. Walker
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, AZ 86011, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
- Correspondence:
| | - Daniel E. Sanchez
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, AZ 86011, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Emma M. Froehlich
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, AZ 86011, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Emma L. Federman
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, AZ 86011, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jacque A. Lyman
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, AZ 86011, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Meagan Owens
- Bat Ecology & Genetics Lab, School of Forestry, Northern Arizona University, Flagstaff, AZ 86011, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Kristen Lear
- Integrative Conservation and Forestry & Natural Resources, University of Georgia, Athens, GA 30602, USA
- Bat Conservation International, Austin, TX 78746, USA
| |
Collapse
|
61
|
Environmental DNA in human and veterinary parasitology - Current applications and future prospects for monitoring and control. Food Waterborne Parasitol 2022; 29:e00183. [DOI: 10.1016/j.fawpar.2022.e00183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 11/04/2022] [Accepted: 11/09/2022] [Indexed: 11/15/2022] Open
|
62
|
Pratomo A, Bengen DG, Zamani NP, Lane C, Humphries AT, Borbee E, Subhan B, Madduppa H. Diversity and distribution of Symbiodiniaceae detected on coral reefs of Lombok, Indonesia using environmental DNA metabarcoding. PeerJ 2022; 10:e14006. [PMID: 36312748 PMCID: PMC9610659 DOI: 10.7717/peerj.14006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 08/14/2022] [Indexed: 01/19/2023] Open
Abstract
Background Dinoflagellates of family Symbiodiniaceae are important to coral reef ecosystems because of their contribution to coral health and growth; however, only a few studies have investigated the function and distribution of Symbiodiniaceae in Indonesia. Understanding the distribution of different kinds of Symbiodiniaceae can improve forecasting of future responses of various coral reef systems to climate change. This study aimed to determine the diversity of Symbiodiniaceae around Lombok using environmental DNA (eDNA). Methods Seawater and sediment samples were collected from 18 locations and filtered to obtain fractions of 0.4-12 and >12 µm. After extraction, molecular barcoding polymerase chain reaction was conducted to amplify the primary V9-SSU 18S rRNA gene, followed by sequencing (Illumina MiSeq). BLAST, Naïve-fit-Bayes, and maximum likelihood routines were used for classification and phylogenetic reconstruction. We compared results across sampling sites, sample types (seawater/sediment), and filter pore sizes (fraction). Results Phylogenetic analyses resolved the amplicon sequence variants into 16 subclades comprising six Symbiodiniaceae genera (or genera-equivalent clades) as follows: Symbiodinium, Breviolum, Cladocopium, Durusdinium, Foraminifera Clade G, and Halluxium. Comparative analyses showed that the three distinct lineages within Cladocopium, Durusdinium, and Foraminifera Clade G were the most common. Most of the recovered sequences appeared to be distinctive of different sampling locations, supporting the possibility that eDNA may resolve regional and local differences among Symbiodiniaceae genera and species. Conclusions eDNA surveys offer a rapid proxy for evaluating Symbiodiniaceae species on coral reefs and are a potentially useful approach to revealing diversity and relative ecological dominance of certain Symbiodiniaceae organisms. Moreover, Symbiodiniaceae eDNA analysis shows potential in monitoring the local and regional stability of coral-algal mutualisms.
Collapse
Affiliation(s)
- Arief Pratomo
- Raja Ali Haji Maritime University, Tanjungpinang, Indonesia,Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia
| | - Dietriech G. Bengen
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia
| | - Neviaty P. Zamani
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia
| | - Christopher Lane
- Department of Biological Sciences, University of Rhode Island, Rhode Island, United States of America
| | - Austin T. Humphries
- Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, Rhode Island, United States of America
| | - Erin Borbee
- Department of Biological Sciences, University of Rhode Island, Rhode Island, United States of America
| | - Beginer Subhan
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia
| | - Hawis Madduppa
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia,Oceanogen Research Center, Bogor, Indonesia
| |
Collapse
|
63
|
Holmes V, Aman J, York G, Kinnison MT. Environmental DNA detects Spawning Habitat of an ephemeral migrant fish (Anadromous Rainbow Smelt: Osmerus mordax). BMC Ecol Evol 2022; 22:121. [PMID: 36280813 PMCID: PMC9594880 DOI: 10.1186/s12862-022-02073-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Anadromous rainbow smelt (Osmerus mordax) have experienced a large range reduction in recent decades and the status of remnant spawning populations is poorly known in Maine, where these fish have significant ecological, cultural, and commercial relevance. Defining the remnant range of anadromous smelt is more difficult than for many declining fish species because adults are only ephemerally present while spawning in small coastal streams at night during spring runoff periods when traditional assessments can be unreliable or even hazardous. We hypothesized that eDNA might facilitate improved survey efforts to define smelt spawning habitat, but that detection could also face challenges from adult eDNA quickly flushing out of these small stream systems. We combined daytime eDNA sampling with nighttime fyke netting to ascertain a potential window of eDNA detection before conducting eDNA surveys in four streams of varying abundance. Hierarchical occupancy modeling was in turn employed to estimate eDNA encounter probabilities relative to numbers of sampling events (date), samples within events, and qPCR replicates within samples. RESULTS Results from the combined eDNA and fyke net study indicated eDNA was detectable over an extended period, culminating approximately 8-13 days following peak spawning, suggesting developing smelt larvae might be the primary source of eDNA. Subsequently, smelt eDNA was readily detected in eDNA surveys of four streams, particularly following remediation of PCR inhibitors. Hierarchical occupancy modeling confirmed our surveys had high empirical detection for most sites, and that future surveys employing at least three sampling events, three samples per event, and six qPCR replicates can afford greater than 90% combined detection capability in low abundance systems. CONCLUSIONS These results demonstrate that relatively modest eDNA sampling effort has high capacity to detect this ephemerally present species of concern at low to moderate abundances. As such, smelt eDNA detection could improve range mapping by providing longer survey windows, safer sampling conditions, and lower field effort in low density systems, than afforded by existing visual and netting approaches.
Collapse
Affiliation(s)
- Vaughn Holmes
- grid.21106.340000000121820794Center for Genetics in the Environment and School of Biology and Ecology, University of Maine, Orono, USA
| | - Jacob Aman
- grid.448608.60000 0000 9349 2745Wells National Estuarine Research Reserve, Wells, USA
| | - Geneva York
- grid.21106.340000000121820794University of Maine Environmental DNA CORE Laboratory, Orono, USA
| | - Michael T. Kinnison
- grid.21106.340000000121820794Center for Genetics in the Environment and School of Biology and Ecology, University of Maine, Orono, USA ,grid.21106.340000000121820794University of Maine Environmental DNA CORE Laboratory, Orono, USA
| |
Collapse
|
64
|
Yao M, Zhang S, Lu Q, Chen X, Zhang SY, Kong Y, Zhao J. Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward. Mol Ecol 2022; 31:5132-5164. [PMID: 35972241 DOI: 10.1111/mec.16659] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 12/15/2022]
Abstract
Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.
Collapse
Affiliation(s)
- Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Shan Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Qi Lu
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Xiaoyu Chen
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Si-Yu Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Yueqiao Kong
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Jindong Zhao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| |
Collapse
|
65
|
Zainal Abidin DH, Mohd Nor SA, Lavoué S, A Rahim M, Mohammed Akib NA. Assessing a megadiverse but poorly known community of fishes in a tropical mangrove estuary through environmental DNA (eDNA) metabarcoding. Sci Rep 2022; 12:16346. [PMID: 36175455 PMCID: PMC9523059 DOI: 10.1038/s41598-022-19954-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 09/07/2022] [Indexed: 11/18/2022] Open
Abstract
Biodiversity surveys are crucial for monitoring the status of threatened aquatic ecosystems, such as tropical estuaries and mangroves. Conventional monitoring methods are intrusive, time-consuming, substantially expensive, and often provide only rough estimates in complex habitats. An advanced monitoring approach, environmental DNA (eDNA) metabarcoding, is promising, although only few applications in tropical mangrove estuaries have been reported. In this study, we explore the advantages and limitations of an eDNA metabarcoding survey on the fish community of the Merbok Estuary (Peninsular Malaysia). COI and 12S eDNA metabarcoding assays collectively detected 178 species from 127 genera, 68 families, and 25 orders. Using this approach, significantly more species have been detected in the Merbok Estuary over the past decade (2010–2019) than in conventional surveys, including several species of conservation importance. However, we highlight three limitations: (1) in the absence of a comprehensive reference database the identities of several species are unresolved; (2) some of the previously documented specimen-based diversity was not captured by the current method, perhaps as a consequence of PCR primer specificity, and (3) the detection of non-resident species—stenohaline freshwater taxa (e.g., cyprinids, channids, osphronemids) and marine coral reef taxa (e.g., holocentrids, some syngnathids and sharks), not known to frequent estuaries, leading to the supposition that their DNA have drifted into the estuary through water movements. The community analysis revealed that fish diversity along the Merbok Estuary is not homogenous, with the upstream more diverse than further downstream. This could be due to the different landscapes or degree of anthropogenic influences along the estuary. In summary, we demonstrated the practicality of eDNA metabarcoding in assessing fish community and structure within a complex and rich tropical environment within a short sampling period. However, some limitations need to be considered and addressed to fully exploit the efficacy of this approach.
Collapse
Affiliation(s)
- Danial Hariz Zainal Abidin
- Centre for Global Sustainability Studies (CGSS), Level 5, Hamzah Sendut Library, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia.
| | - Sébastien Lavoué
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | | | - Noor Adelyna Mohammed Akib
- Centre for Global Sustainability Studies (CGSS), Level 5, Hamzah Sendut Library, Universiti Sains Malaysia, 11800, Penang, Malaysia. .,School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
| |
Collapse
|
66
|
Inoue N, Sato M, Furuichi N, Imaizumi T, Ushio M. The relationship between eDNA density distribution and current fields around an artificial reef in the waters of Tateyama Bay, Japan. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.87415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Monitoring of artificial reefs (ARs) has been conducted through such methods as visual censuses, surveys using fishing gear, and echo sounder. These methods have disadvantages: visual census is not possible at ARs in deeper waters, fishing gear surveys are invasive to fish individuals, and echo sounders have difficulty in species identification. A new AR monitoring method is required to compensate for these disadvantages. While eDNA has become a valid monitoring tool for marine biodiversities, it is influenced by degradation and transport of the molecules that affect information about the spatio-temporal distribution of fish. An understanding of the relationship between current fields and eDNA distribution, particularly in open waters, is critical when using eDNA as an index for fish aggregation at ARs. We investigated the relationship between eDNA distribution and current fields around an AR for four dominant species (Engraulis japonicus, Parapristipoma trilineatum, Scomber spp and Trachurus japonicus) in Tateyama Bay, Japan. The highest density of fish schools is formed directly above or at the upstream side of ARs. If we assume that the center of eDNA originates at these locations at an AR and eDNA is simply transported by currents, a higher density of eDNA would distribute downstream from the AR. However, our results indicate that eDNA distribution is in accord with actual fish distribution, namely eDNA densities are more abundant in the upstream side of ARs. We thus consider that eDNA distribution is more influenced by actual distribution patterns than by the transport processes.
Collapse
|
67
|
Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity. BIOLOGY 2022; 11:biology11091297. [PMID: 36138776 PMCID: PMC9495823 DOI: 10.3390/biology11091297] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/20/2022]
Abstract
Simple Summary The innovative concept of environmental DNA has found its foot in aquatic ecosystems but remains an unexplored area of research concerning terrestrial ecosystems. When making management choices, it is important to understand the rate of eDNA degradation, the persistence of DNA in terrestrial habitats, and the variables affecting eDNA detectability for a target species. Therefore an attempt has been made to provide comprehensive information regarding the exertion of eDNA in terrestrial ecosystems from 2012 to 2022. The information provided will assist ecologists, researchers and decision-makers in developing a holistic understanding of environmental DNA and its applicability as a biodiversity monitoring contrivance. Abstract The dearth of cardinal data on species presence, dispersion, abundance, and habitat prerequisites, besides the threats impeded by escalating human pressure has enormously affected biodiversity conservation. The innovative concept of eDNA, has been introduced as a way of overcoming many of the difficulties of rigorous conventional investigations, and is hence becoming a prominent and novel method for assessing biodiversity. Recently the demand for eDNA in ecology and conservation has expanded exceedingly, despite the lack of coordinated development in appreciation of its strengths and limitations. Therefore it is pertinent and indispensable to evaluate the extent and significance of eDNA-based investigations in terrestrial habitats and to classify and recognize the critical considerations that need to be accounted before using such an approach. Presented here is a brief review to summarize the prospects and constraints of utilizing eDNA in terrestrial ecosystems, which has not been explored and exploited in greater depth and detail in such ecosystems. Given these obstacles, we focused primarily on compiling the most current research findings from journals accessible in eDNA analysis that discuss terrestrial ecosystems (2012–2022). In the current evaluation, we also review advancements and limitations related to the eDNA technique.
Collapse
|
68
|
Sakata MK, Sato M, Sato MO, Watanabe T, Mitsuishi H, Hikitsuchi T, Kobayashi J, Minamoto T. Detection and persistence of environmental DNA (eDNA) of the different developmental stages of a vector mosquito, Culex pipiens pallens. PLoS One 2022; 17:e0272653. [PMID: 35947597 PMCID: PMC9365122 DOI: 10.1371/journal.pone.0272653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 07/24/2022] [Indexed: 11/18/2022] Open
Abstract
Preventing mosquito-borne infectious diseases requires that vector mosquitoes are monitored and controlled. Targeting immature mosquitoes (eggs, larvae, and pupae), which have less mobility than adults, is an effective management approach. However, conducting these surveys is often difficult due to the limitations of morphological classification and survey costs. The application of environmental DNA (eDNA) analysis can solve these issues because it allows easy estimation of species distribution and morphology-independent species identification. Although a few previous studies have reported mosquito eDNA detection, there is a gap in knowledge regarding the dynamics related to the persistence of immature mosquito eDNA. We used Culex pipiens pallens, a vector of West Nile fever, as a model species. First, we developed a species-specific detection assay and confirmed its specificity using in silico and in vitro tests. Next, we conducted laboratory experiments using breeding tanks. Water samples were collected at each developmental stage. In addition, water samples were collected daily until the seventh day after emergence from the pupae. We quantified eDNA using real-time PCR with the developed assay to investigate the dynamics of mosquito eDNA. The specificity of the developed assay was confirmed by in silico and in vitro tests. Mosquito eDNA was detected at all developmental stages and detected up to seven days after emergence of pupae. In particular, high concentrations of eDNA were detected immediately after hatching from eggs and after emergence from pupae. Highly frequent positive eDNA signals were continuously detected between egg hatching and pupa hatching. Mosquito eDNA was detected immediately after the eggs were introduced, and eDNA-positive detections continued until pupae emergence, suggesting that eDNA analysis is useful for monitoring mosquito larvae. In the future, monitoring immature mosquitoes using eDNA analysis will contribute to prevent mosquito-borne infectious diseases.
Collapse
Affiliation(s)
- Masayuki K. Sakata
- Graduate School of Human Development and Environment, Kobe University, Kobe City, Japan
- Kobe University Innovation, Co., Ltd, Kobe City, Japan
- * E-mail:
| | - Megumi Sato
- Graduate School of Health Sciences, Niigata University, Niigata, Japan
| | - Marcello Otake Sato
- Laboratory of Tropical Medicine and Parasitology, Dokkyo Medical University, Tochigi, Japan
| | - Tomoe Watanabe
- Dainihon Jochugiku Co., Ltd Research & Development Laboratory Biological Research Section 1–11, Osaka, Japan
| | - Honami Mitsuishi
- Dainihon Jochugiku Co., Ltd Research & Development Laboratory Biological Research Section 1–11, Osaka, Japan
| | - Tomoyuki Hikitsuchi
- Dainihon Jochugiku Co., Ltd Research & Development Laboratory Biological Research Section 1–11, Osaka, Japan
| | - Jun Kobayashi
- Graduate School of Health Sciences, University of the Ryukyus, Okinawa, Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, Kobe City, Japan
| |
Collapse
|
69
|
Defining the current distribution of the imperiled Black-spotted Newt across south Texas, USA. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
70
|
Feist SM, Guan X, Malmfeldt MP, Lance RF. Two novel qPCR assays to enhance black rail (Laterallus jamaicensis) eDNA surveys in the United States. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01279-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractBlack rails (Laterallus jamaicensis) are a rare and protected bird species. They are also notoriously difficult to monitor. eDNA surveys have proven beneficial for the detection of this elusive species, but additional developments are needed to enhance eDNA survey utility (including reliability of outcomes) in light of black rail status and associated high-profile conservation actions. The use of multiple assays functions to increase eDNA detection confidence by increasing the probability of amplification in low concentration, highly degraded samples (i.e., reducing the risk of false negatives) and by providing a multiplicative test for ruling out contamination as the source of qPCR amplification (i.e., reducing the risk of false positives). The two eDNA assays developed, optimized, and validated in this study will prove valuable for the continued surveillance of the secretive black rail, offering data to measure its distribution and occurrence over time and as influenced by anticipated climate-change-induced disturbances and/or habitat restoration/creation initiatives. The assays are applicable to both Eastern black rails and California black rails, and do not exhibit qPCR amplification in non-target, co-distributed taxa (including other Rallidae species) in the United States.
Collapse
|
71
|
Franklin TW, Dysthe JC, Neville H, Young MK, McKelvey KM, Schwartz MK. Lahontan Cutthroat Trout (Oncorhynchus clarkii henshawi) and Paiute Cutthroat Trout (Oncorhynchus clarkii seleniris) Detection from Environmental DNA Samples: A Dual-Purpose Assay. WEST N AM NATURALIST 2022. [DOI: 10.3398/064.082.0212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Thomas W. Franklin
- U.S. Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, MT 59801
| | - Joseph C. Dysthe
- U.S. Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, MT 59801
| | | | - Michael K. Young
- U.S. Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, MT 59801
| | - Kevin M. McKelvey
- U.S. Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, MT 59801
| | - Michael K. Schwartz
- U.S. Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, MT 59801
| |
Collapse
|
72
|
Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary. PLoS One 2022; 17:e0266720. [PMID: 35714082 PMCID: PMC9205523 DOI: 10.1371/journal.pone.0266720] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 03/26/2022] [Indexed: 12/21/2022] Open
Abstract
Metabarcoding of environmental DNA is increasingly used for biodiversity assessments in aquatic communities. The efficiency and outcome of these efforts are dependent upon either de novo primer design or selecting an appropriate primer set from the dozens that have already been published. Unfortunately, there is a lack of studies that have directly compared the efficacy of different metabarcoding primers in marine and estuarine systems. Here we evaluate five commonly used primer sets designed to amplify rRNA barcoding genes in fishes and compare their performance using water samples collected from estuarine sites in the highly biodiverse Indian River Lagoon in Florida. Three of the five primer sets amplify a portion of the mitochondrial 12S gene (MiFish_12S, 171bp; Riaz_12S, 106 bp; Valentini_12S, 63 bp), one amplifies 219 bp of the mitochondrial 16S gene (Berry_16S), and the other amplifies 271 bp of the nuclear 18S gene (MacDonald_18S). The vast majority of the metabarcoding reads (> 99%) generated using the 18S primer set assigned to non-target (non-fish) taxa and therefore this primer set was omitted from most analyses. Using a conservative 99% similarity threshold for species level assignments, we detected a comparable number of species (55 and 49, respectively) and similarly high Shannon’s diversity values for the Riaz_12S and Berry_16S primer sets. Meanwhile, just 34 and 32 species were detected using the MiFish_12S and Valentini_12S primer sets, respectively. We were able to amplify both bony and cartilaginous fishes using the four primer sets with the vast majority of reads (>99%) assigned to the former. We detected the greatest number of elasmobranchs (six species) with the Riaz_12S primer set suggesting that it may be a suitable candidate set for the detection of sharks and rays. Of the total 76 fish species that were identified across all datasets, the combined three 12S primer sets detected 85.5% (65 species) while the combination of the Riaz_12S and Berry_16S primers detected 93.4% (71 species). These results highlight the importance of employing multiple primer sets as well as using primers that target different genomic regions. Moreover, our results suggest that the widely adopted MiFish_12S primers may not be the best choice, rather we found that the Riaz_12S primer set was the most effective for eDNA-based fish surveys in our system.
Collapse
|
73
|
Qiu X, Liu X, Lu Q, Chen J, Liang T, Wang W, Ouyang S, Zhou C, Wu X. Seasonal and spatial variability of zooplankton diversity in the Poyang Lake Basin using DNA metabarcoding. Ecol Evol 2022; 12:e8972. [PMID: 35784091 PMCID: PMC9168339 DOI: 10.1002/ece3.8972] [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: 01/20/2022] [Revised: 04/27/2022] [Accepted: 05/12/2022] [Indexed: 11/20/2022] Open
Abstract
Freshwater ecosystems face multiple threats to their stability globally. Poyang Lake is the largest lake in China, but its habitat has been seriously degraded because of human activities and natural factors (e.g. climate change), resulting in a decline in freshwater biodiversity. Zooplankton are useful indicators of environmental stressors because they are sensitive to external perturbations. DNA metabarcoding is an approach that has gained significant traction by aiding ecosystem conservation and management. Here, the seasonal and spatial variability in the zooplankton diversity were analyzed in the Poyang Lake Basin using DNA metabarcoding. The results showed that the community structure of zooplankton exhibited significant seasonal and spatial variability using DNA metabarcoding, where the community structure was correlated with turbidity, water temperature, pH, total phosphorus, and chlorophyll‐a. These results indicated habitat variations affected by human activities and seasonal change could be the main driving factors for the variations of zooplankton community. This study also provides an important reference for the management of aquatic ecosystem health and conservation of aquatic biodiversity.
Collapse
Affiliation(s)
- Xuemei Qiu
- School of Life Sciences Nanchang University Nanchang China
- School of Life Sciences Jiangxi Science and Technology Normal University Nanchang China
| | - Xiongjun Liu
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas School of Life Science Jiaying University Meizhou China
| | - Quanfeng Lu
- School of Life Sciences Nanchang University Nanchang China
| | - Jinping Chen
- School of Life Sciences Nanchang University Nanchang China
| | - Tao Liang
- School of Life Sciences Nanchang University Nanchang China
| | - Weikai Wang
- School of Life Sciences Nanchang University Nanchang China
| | - Shan Ouyang
- School of Life Sciences Nanchang University Nanchang China
| | - Chunhua Zhou
- School of Life Sciences Nanchang University Nanchang China
| | - Xiaoping Wu
- School of Life Sciences Nanchang University Nanchang China
| |
Collapse
|
74
|
Nordstrom B, Mitchell N, Byrne M, Jarman S. A review of applications of environmental DNA for reptile conservation and management. Ecol Evol 2022; 12:e8995. [PMID: 35784065 PMCID: PMC9168342 DOI: 10.1002/ece3.8995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/15/2022] [Accepted: 05/19/2022] [Indexed: 11/28/2022] Open
Abstract
Reptile populations are in decline globally, with total reptile abundance halving in the past half century, and approximately a fifth of species currently threatened with extinction. Research on reptile distributions, population trends, and trophic interactions can greatly improve the accuracy of conservation listings and planning for species recovery, but data deficiency is an impediment for many species. Environmental DNA (eDNA) can detect species and measure community diversity at diverse spatio‐temporal scales, and is especially useful for detection of elusive, cryptic, or rare species, making it potentially very valuable in herpetology. We aim to summarize the utility of eDNA as a tool for informing reptile conservation and management and discuss the benefits and limitations of this approach. A literature review was conducted to collect all studies that used eDNA and focus on reptile ecology, conservation, or management. Results of the literature search are summarized into key discussion points, and the review also draws on eDNA studies from other taxa to highlight methodological challenges and to identify future research directions. eDNA has had limited application to reptiles, relative to other vertebrate groups, and little use in regions with high species richness. eDNA techniques have been more successfully applied to aquatic reptiles than to terrestrial reptiles, and most (64%) of studies focused on aquatic habitats. Two of the four reptilian orders dominate the existing eDNA studies (56% Testudines, 49% Squamata, 5% Crocodilia, 0% Rhynchocephalia). Our review provides direction for the application of eDNA as an emerging tool in reptile ecology and conservation, especially when it can be paired with traditional monitoring approaches. Technologies associated with eDNA are rapidly advancing, and as techniques become more sensitive and accessible, we expect eDNA will be increasingly valuable for addressing key knowledge gaps for reptiles.
Collapse
Affiliation(s)
- Bethany Nordstrom
- School of Biological Sciences The University of Western Australia Crawley Western Australia Australia
| | - Nicola Mitchell
- School of Biological Sciences The University of Western Australia Crawley Western Australia Australia
| | - Margaret Byrne
- School of Biological Sciences The University of Western Australia Crawley Western Australia Australia
- Department of Biodiversity, Conservation and Attractions Biodiversity and Conservation Science Perth Western Australia Australia
| | - Simon Jarman
- School of Biological Sciences The University of Western Australia Crawley Western Australia Australia
- UWA Oceans Institute The University of Western Australia Crawley Western Australia Australia
| |
Collapse
|
75
|
Keller AG, Grason EW, McDonald PS, Ramón-Laca A, Kelly RP. Tracking an invasion front with environmental DNA. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2561. [PMID: 35128750 DOI: 10.1002/eap.2561] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/21/2021] [Accepted: 12/14/2021] [Indexed: 05/03/2023]
Abstract
Data from environmental DNA (eDNA) may revolutionize environmental monitoring and management, providing increased detection sensitivity at reduced cost and survey effort. However, eDNA data are rarely used in decision-making contexts, mainly due to uncertainty around (1) data interpretation and (2) whether and how molecular tools dovetail with existing management efforts. We address these challenges by jointly modeling eDNA detection via qPCR and traditional trap data to estimate the density of invasive European green crab (Carcinus maenas), a species for which, historically, baited traps have been used for both detection and control. Our analytical framework simultaneously quantifies uncertainty in both detection methods and provides a robust way of integrating different data streams into management processes. Moreover, the joint model makes clear the marginal information benefit of adding eDNA (or any other) additional data type to an existing monitoring program, offering a path to optimizing sampling efforts for species of management interest. Here, we document green crab eDNA beyond the previously known invasion front and find that the value of eDNA data dramatically increases with low population densities and low traditional sampling effort, as is often the case at leading-edge locations. We also highlight the detection limits of the molecular assay used in this study, as well as scenarios under which eDNA sampling is unlikely to improve existing management efforts.
Collapse
Affiliation(s)
- Abigail G Keller
- School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA
| | - Emily W Grason
- Washington Sea Grant, University of Washington, Seattle, Washington, USA
| | - P Sean McDonald
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Ana Ramón-Laca
- CICOES, University of Washington at Northwest Fisheries Science Center, Seattle, Washington, USA
| | - Ryan P Kelly
- School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, USA
| |
Collapse
|
76
|
Osathanunkul M, Madesis P. Environmental DNA detection of giant snakehead in Thailand's major rivers for wild stock assessment. PLoS One 2022; 17:e0267667. [PMID: 35536840 PMCID: PMC9089910 DOI: 10.1371/journal.pone.0267667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 04/12/2022] [Indexed: 11/30/2022] Open
Abstract
Capture-based aquaculture is now gaining much attention in Southeast Asia. This system was used to produce several fish species with social and economic implications, including the giant snakehead (Channa micropeltes). As wild harvesting of organisms for seed stock is one of main practices in capture-based aquaculture, abundance and distribution of the wild stock are essential for both environmental impact evaluation and stock management. Mark and recapture, visual observation and physical capture of target species are costly, ineffective, and labour intensive for fish surveys in several cases. Detection of target organisms using eDNA (environmental DNA) could be a good alternative as it has proved to be a non-invasive, rapid, and sensitive method for aquatic species monitoring and surveying. Here, we developed a TaqMan assay that targets the 16S region of giant snakehead DNA to amplify eDNA captured in water samples. 300 µl of water samples were collected from 15 sites located in the Chao Phraya River Basin (Ping, Wang, Yom, Nan, and Chao Phraya River) and filtered with 0.7 µm glass fibre membrane filter. Giant snakehead eDNA was detected in most tributaries (60%) with concentrations ranging from 74.0 copies/ml in Wang River sites to 7.4 copies/ml in Nan River sites. As intensification of capture-based aquaculture could lead to depleting of wild fish stocks, urgent management is needed. However, the existing conventional approaches for assessment of fish overexploitation, survey and monitoring have several limitations.
Collapse
Affiliation(s)
- Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Panagiotis Madesis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
- Laboratory of Molecular Biology of Plants, Department of Agriculture, Crop Production and Rural Environment, University of Thessaly, Volos, Magnesia, Greece
| |
Collapse
|
77
|
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: 20] [Impact Index Per Article: 10.0] [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.
Collapse
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
| |
Collapse
|
78
|
Villacorta-Rath C, Espinoza T, Cockayne B, Schaffer J, Burrows D. Environmental DNA analysis confirms extant populations of the cryptic Irwin’s turtle within its historical range. BMC Ecol Evol 2022; 22:57. [PMID: 35501685 PMCID: PMC9059348 DOI: 10.1186/s12862-022-02009-6] [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: 03/03/2022] [Accepted: 04/13/2022] [Indexed: 11/24/2022] Open
Abstract
Background Approximately 50% of freshwater turtles worldwide are currently threatened by habitat loss, rural development and altered stream flows. Paradoxically, reptiles are understudied organisms, with many species lacking basic geographic distribution and abundance data. The iconic Irwin’s turtle, Elseya irwini, belongs to a unique group of Australian endemic freshwater turtles capable of cloacal respiration. Water resource development, increased presence of saltwater crocodiles and its cryptic behaviour, have made sampling for Irwin’s turtle in parts of its range problematic, resulting in no confirmed detections across much of its known range for > 25 years. Here, we used environmental DNA (eDNA) analysis for E. irwini detection along its historical and contemporary distribution in the Burdekin, Bowen and Broken River catchments and tributaries. Five replicate water samples were collected at 37 sites across those three river catchments. Environmental DNA was extracted using a glycogen-aided precipitation method and screened for the presence of E. irwini through an eDNA assay targeting a 127 base pair-long fragment of the NADH dehydrogenase 4 (ND4) mitochondrial gene. Results Elseya irwini eDNA was detected at sites within its historic distribution in the lower Burdekin River, where the species had not been formally recorded for > 25 years, indicating the species still inhabits the lower Burdekin area. We also found higher levels of E. iriwni eDNA within its contemporary distribution in the Bowen and Broken Rivers, matching the prevailing scientific view that these areas host larger populations of E. irwini. Conclusions This study constitutes the first scientific evidence of E. irwini presence in the lower Burdekin since the original type specimens were collected as part of its formal description, shortly after the construction of the Burdekin Falls Dam. From the higher percentage of positive detections in the upper reaches of the Broken River (Urannah Creek), we conclude that this area constitutes the core habitat area for the species. Our field protocol comprises a user-friendly, time-effective sampling method. Finally, due to safety risks associated with traditional turtle sampling methods in the Burdekin River (e.g., estuarine crocodiles) we propose eDNA sampling as the most pragmatic detection method available for E. irwini. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02009-6.
Collapse
|
79
|
van Rees CB, Hand BK, Carter SC, Bargeron C, Cline TJ, Daniel W, Ferrante JA, Gaddis K, Hunter ME, Jarnevich CS, McGeoch MA, Morisette JT, Neilson ME, Roy HE, Rozance MA, Sepulveda A, Wallace RD, Whited D, Wilcox T, Kimball JS, Luikart G. A framework to integrate innovations in invasion science for proactive management. Biol Rev Camb Philos Soc 2022; 97:1712-1735. [PMID: 35451197 DOI: 10.1111/brv.12859] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 11/26/2022]
Abstract
Invasive alien species (IAS) are a rising threat to biodiversity, national security, and regional economies, with impacts in the hundreds of billions of U.S. dollars annually. Proactive or predictive approaches guided by scientific knowledge are essential to keeping pace with growing impacts of invasions under climate change. Although the rapid development of diverse technologies and approaches has produced tools with the potential to greatly accelerate invasion research and management, innovation has far outpaced implementation and coordination. Technological and methodological syntheses are urgently needed to close the growing implementation gap and facilitate interdisciplinary collaboration and synergy among evolving disciplines. A broad review is necessary to demonstrate the utility and relevance of work in diverse fields to generate actionable science for the ongoing invasion crisis. Here, we review such advances in relevant fields including remote sensing, epidemiology, big data analytics, environmental DNA (eDNA) sampling, genomics, and others, and present a generalized framework for distilling existing and emerging data into products for proactive IAS research and management. This integrated workflow provides a pathway for scientists and practitioners in diverse disciplines to contribute to applied invasion biology in a coordinated, synergistic, and scalable manner.
Collapse
Affiliation(s)
- Charles B van Rees
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
| | - Brian K Hand
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
| | - Sean C Carter
- Numerical Terradynamic Simulation Group, University of Montana, ISB 415, Missoula, MT, 59812, U.S.A
| | - Chuck Bargeron
- Center for Invasive Species and Ecosystem Health, University of Georgia, 4601 Research Way, Tifton, GA, 31793, U.S.A
| | - Timothy J Cline
- U.S. Geological Survey, Northern Rocky Mountain Science Center, 2327 University Way STE 2, Bozeman MT 59717 & 320 Grinnel Drive, West Glacier, MT, 59936, U.S.A
| | - Wesley Daniel
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Jason A Ferrante
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Keith Gaddis
- NASA Biological Diversity and Ecological Forecasting Programs, 300 E St. SW, Washington, DC, 20546, U.S.A
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Catherine S Jarnevich
- U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Avenue Bldg C, Fort Collins, CO, 80526, U.S.A
| | - Melodie A McGeoch
- Department of Environment and Genetics, La Trobe University, Plenty Road & Kingsbury Drive, Bundoora, Victoria, 3086, Australia
| | - Jeffrey T Morisette
- U.S. Forest Service Rocky Mountain Research Station, 26 Fort Missoula Road, Missoula, 59804, MT, U.S.A
| | - Matthew E Neilson
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, U.S.A
| | - Helen E Roy
- UK Centre for Ecology & Hydrology, MacLean Building, Benson Lane, Crowmarsh Gifford, OX10 8BB, U.K
| | - Mary Ann Rozance
- Northwest Climate Adaptation Science Center, University of Washington, Box 355674, Seattle, WA, 98195, U.S.A
| | - Adam Sepulveda
- U.S. Forest Service Rocky Mountain Research Station, 26 Fort Missoula Road, Missoula, 59804, MT, U.S.A
| | - Rebekah D Wallace
- Center for Invasive Species and Ecosystem Health, University of Georgia, 4601 Research Way, Tifton, GA, 31793, U.S.A
| | - Diane Whited
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
| | - Taylor Wilcox
- U.S. Forest Service Rocky Mountain Research Station, 26 Fort Missoula Road, Missoula, 59804, MT, U.S.A
| | - John S Kimball
- Numerical Terradynamic Simulation Group, University of Montana, ISB 415, Missoula, MT, 59812, U.S.A
| | - Gordon Luikart
- Flathead Lake Biological Station, University of Montana, 32125 Bio Station Lane, Polson, MT, 59860, U.S.A
| |
Collapse
|
80
|
Ellis MR, Clark ZSR, Treml EA, Brown MS, Matthews TG, Pocklington JB, Stafford-Bell RE, Bott NJ, Nai YH, Miller AD, Sherman CDH. Detecting marine pests using environmental DNA and biophysical models. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151666. [PMID: 34793806 DOI: 10.1016/j.scitotenv.2021.151666] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
The spread of marine pests is occurring at record rates due to globalisation and increasing trade. Environmental DNA (eDNA) is an emerging tool for pest surveillance, allowing for the detection of genetic material shed by organisms into the environment. However, factors influencing the spatial and temporal detection limits of eDNA in marine environments are poorly understood. In this study we use eDNA assays to assess the invasive ranges of two marine pests in south-eastern Australia, the kelp Undaria pinnatifida and the seastar Asterias amurensis. We explored the temporal and spatial detection limits of eDNA under different oceanographic conditions by combining estimates of eDNA decay with biophysical modelling. Positive eDNA detections at several new locations indicate the invasive range of both pest species is likely to be wider than currently assumed. Environmental DNA decay rates were similar for both species, with a decay rate constant of 0.035 h-1 for U. pinnatifida, and a decay rate constant of 0.041 h-1 for A. amurensis, resulting in a 57-73% decrease in eDNA concentrations in the first 24 h and decaying beyond the limits of detection after 3-4 days. Biophysical models informed by eDNA decay profiles indicate passive transport of eDNA up to a maximum of 10 to 20 km from its source, with a ~90-95% reduction in eDNA concentration within 1-3 km from the source, depending on local oceanography. These models suggest eDNA signals are likely to be highly localised, even in complex marine environments. This was confirmed with spatially replicated eDNA sampling around an established U. pinnatifida population indicating detection limits of ~750 m from the source. This study highlights the value of eDNA methods for marine pest surveillance and provides a much-needed description of the spatio-temporal detection limits of eDNA under different oceanographic conditions.
Collapse
Affiliation(s)
- Morgan R Ellis
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Zach S R Clark
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Eric A Treml
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Morgan S Brown
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Ty G Matthews
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Jacqueline B Pocklington
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Environment and Science Division, Parks Victoria, Melbourne, Victoria 3000, Australia
| | - Richard E Stafford-Bell
- Department of Jobs, Precincts and Regions, 475 Mickleham Road, Attwood, Vic. 3049, Australia
| | - Nathan J Bott
- School of Science, RMIT University, PO Box 71, Bundoora, VIC 3083, Australia
| | - Yi Heng Nai
- Centre for Regional and Rural Futures, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong, Victoria, 3220, Australia
| | - Adam D Miller
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Craig D H Sherman
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia.
| |
Collapse
|
81
|
Farrell JA, Whitmore L, Mashkour N, Rollinson Ramia DR, Thomas RS, Eastman CB, Burkhalter B, Yetsko K, Mott C, Wood L, Zirkelbach B, Meers L, Kleinsasser P, Stock S, Libert E, Herren R, Eastman S, Crowder W, Bovery C, Anderson D, Godfrey D, Condron N, Duffy DJ. Detection and population genomics of sea turtle species via non-invasive environmental DNA analysis of nesting beach sand tracks and oceanic water. Mol Ecol Resour 2022; 22:2471-2493. [PMID: 35377560 DOI: 10.1111/1755-0998.13617] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/12/2022] [Accepted: 03/23/2022] [Indexed: 11/27/2022]
Abstract
Elusive aquatic wildlife, such as endangered sea turtles, are difficult to monitor and conserve. As novel molecular and genetic technologies develop, it is possible to adapt and optimize them for wildlife conservation. One such technology is environmental (e)DNA - the detection of DNA shed from organisms into their surrounding environments. We developed species-specific green (Chelonia mydas) and loggerhead (Caretta caretta) sea turtle probe-based qPCR assays, which can detect and quantify sea turtle eDNA in controlled (captive tank water and sand samples) and free ranging (oceanic water samples and nesting beach sand) settings. eDNA detection complemented traditional in-water sea turtle monitoring by enabling detection even when turtles were not visually observed. Furthermore, we report that high throughput shotgun sequencing of eDNA sand samples enabled sea turtle population genetic studies and pathogen monitoring, demonstrating that non-invasive eDNA techniques are viable and efficient alternatives to biological sampling (e.g. biopsies and blood draws). Genetic information was obtained from sand many hours after nesting events, without having to observe or interact with the target individual. This greatly reduces the sampling stress experienced by nesting mothers and emerging hatchlings, and avoids sacrificing viable eggs for genetic analysis. The detection of pathogens from sand indicates significant potential for increased wildlife disease monitoring capacity and viral variant surveillance. Together, these results demonstrate the potential of eDNA approaches to ultimately help understand and conserve threatened species such as sea turtles.
Collapse
Affiliation(s)
- Jessica A Farrell
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Liam Whitmore
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biological Sciences, University of Limerick, Limerick, Ireland
| | - Narges Mashkour
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Devon R Rollinson Ramia
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Rachel S Thomas
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Catherine B Eastman
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Brooke Burkhalter
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,The Turtle Hospital, 2396 Overseas Highway, Marathon, FL, 33050, USA
| | - Kelsey Yetsko
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biological Sciences, Florida International University, Miami, FL, 33181, USA
| | - Cody Mott
- Inwater Research Group Inc, Jensen Beach, FL, 34957, USA
| | - Larry Wood
- Florida Hawksbill Project, National Save The Sea Turtle Foundation, Ft. Lauderdale, FL, 33308, USA
| | - Bette Zirkelbach
- The Turtle Hospital, 2396 Overseas Highway, Marathon, FL, 33050, USA
| | - Lucas Meers
- Mickler's Landing Turtle Patrol, Ponte Vedra Beach, FL, 32082, USA
| | - Pat Kleinsasser
- Crescent Beach Turtle Patrol, Crescent Beach, FL, 32080, USA
| | - Sharon Stock
- Flagler Turtle Patrol, Marineland Beach, FL, 32080, USA
| | | | | | - Scott Eastman
- Florida Department of Environmental Protection, St Augustine, FL, 32080, USA
| | | | | | | | - David Godfrey
- The Sea Turtle Conservancy, Gainesville, FL, 32609, USA
| | - Nancy Condron
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Mickler's Landing Turtle Patrol, Ponte Vedra Beach, FL, 32082, USA
| | - David J Duffy
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| |
Collapse
|
82
|
Saeed M, Rais M, Akram A, Williams MR, Kellner KF, Hashsham SA, Davis DR. Development and validation of an eDNA protocol for monitoring endemic Asian spiny frogs in the Himalayan region of Pakistan. Sci Rep 2022; 12:5624. [PMID: 35379841 PMCID: PMC8979970 DOI: 10.1038/s41598-022-09084-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 03/17/2022] [Indexed: 11/09/2022] Open
Abstract
Wildlife monitoring programs are instrumental for the assessment of species, habitat status, and for the management of factors affecting them. This is particularly important for species found in freshwater ecosystems, such as amphibians, as they have higher estimated extinction rates than terrestrial species. We developed and validated two species-specific environmental DNA (eDNA) protocols and applied them in the field to detect the Hazara Torrent Frog (Allopaa hazarensis) and Murree Hills Frog (Nanorana vicina). Additionally, we compared eDNA surveys with visual encounter surveys and estimated site occupancy. eDNA surveys resulted in higher occurrence probabilities for both A. hazarensis and N. vicina than for visual encounter surveys. Detection probability using eDNA was greater for both species, particularly for A. hazarensis. The top-ranked detection model for visual encounter surveys included effects of both year and temperature on both species, and the top-ranked occupancy model included effects of elevation and year. The top-ranked detection model for eDNA data was the null model, and the top-ranked occupancy model included effects of elevation, year, and wetland type. To our knowledge, this is the first time an eDNA survey has been used to monitor amphibian species in the Himalayan region.
Collapse
Affiliation(s)
- Muhammad Saeed
- Herpetology Lab, Department of Wildlife Management, Faculty of Forestry, Range Management and Wildlife, Pir Mehr Ali Shah, Arid Agriculture University Rawalpindi, Rawalpindi, 46000, Pakistan. .,Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA.
| | - Muhammad Rais
- Herpetology Lab, Department of Wildlife Management, Faculty of Forestry, Range Management and Wildlife, Pir Mehr Ali Shah, Arid Agriculture University Rawalpindi, Rawalpindi, 46000, Pakistan.
| | - Ayesha Akram
- Herpetology Lab, Department of Wildlife Management, Faculty of Forestry, Range Management and Wildlife, Pir Mehr Ali Shah, Arid Agriculture University Rawalpindi, Rawalpindi, 46000, Pakistan
| | - Maggie R Williams
- School of Engineering and Technology, Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI, USA
| | - Kenneth F Kellner
- Global Wildlife Conservation Center, State University of New York College of Environmental Science and Forestry, Syracuse, NY, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA.,Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.,Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Drew R Davis
- School of Earth, Environmental, and Marine Science, The University of Texas Rio Grande Valley, Brownsville, TX, USA.,Biodiversity Collections, Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
83
|
Effects of Temperature on the Timeliness of eDNA/eRNA: A Case Study of Fenneropenaeus chinensis. WATER 2022. [DOI: 10.3390/w14071155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Environmental DNA (eDNA) technology has been successfully applied to detect organisms in various aquatic ecosystems. However, eDNA has been proven to exist for a long time in environmental samples. The timeliness of eDNA detection results largely depends on the rate of molecular degradation. Environmental RNA (eRNA) is considered an excellent complementary tool because most researchers believe that RNA degrades faster than DNA in vitro, while, to the best of our knowledge, the number of published articles related to eRNA is very limited. To address an important knowledge gap, this study focused on the response mechanism of eRNA degradation to water temperature change as compared with eDNA. Changes in the concentration of eDNA and eRNA of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene from Fenneropenaeuschinensis were detected at four temperatures (10, 15, 20 and 25 °C). The results showed that the degradation rate of eDNA increased with an increase in temperature. The degradation rate constants ranged from 0.011 to 0.486 h−1 and the degradation time ranged from 8 to 383 h for eDNA. The degradation rate of eRNA changed slightly with an increase in temperature. The degradation rate constants ranged from 0.190 to 0.379 h−1 and the degradation time ranged from 11 to 22 h for eRNA. eRNA showed better stability under temperature change and maintained a faster degradation rate at low temperatures. These results provide answers to the questions of whether eRNA and eDNA degradation rates are fast or slow. Furthermore, this study may suggest the potential superiority of eRNA over eDNA and promote further study of eRNA in future research.
Collapse
|
84
|
Couton M, Lévêque L, Daguin-Thiébaut C, Comtet T, Viard F. Water eDNA metabarcoding is effective in detecting non-native species in marinas, but detection errors still hinder its use for passive monitoring. BIOFOULING 2022; 38:367-383. [PMID: 35575060 DOI: 10.1080/08927014.2022.2075739] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/21/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Marinas are high-priority targets for marine non-indigenous species (NIS), where they compose a large portion of the biofouling communities. The practicality of water samples collection makes environmental DNA (eDNA) metabarcoding an interesting tool for routine NIS surveys. Here the effectiveness of water-eDNA-metabarcoding to identify biofouling NIS, in 10 marinas from western France, was examined. Morphological identification of specimens collected in quadrats brought out 18 sessile benthic NIS beneath floating pontoons. Water-eDNA-metabarcoding detected two thirds of them, failing to detect important NIS. However, sampling and bioinformatics filtering steps can be optimized to identify more species. In addition, this method allowed the detection of additional NIS from neighboring micro-habitats. Caution should, however, be taken when reporting putative novel NIS, because of errors in species assignment. This work highlights that water-eDNA-metabarcoding is effective for active (targeted) NIS surveys and could be significantly improved for its further use in marine NIS passive surveys.
Collapse
Affiliation(s)
- Marjorie Couton
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Laurent Lévêque
- Sorbonne Université, CNRS, FR 2424, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Claire Daguin-Thiébaut
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Thierry Comtet
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Frédérique Viard
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| |
Collapse
|
85
|
Svenningsen AKN, Pertoldi C, Bruhn D. eDNA Metabarcoding Benchmarked towards Conventional Survey Methods in Amphibian Monitoring. Animals (Basel) 2022; 12:ani12060763. [PMID: 35327161 PMCID: PMC8944553 DOI: 10.3390/ani12060763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 03/07/2022] [Accepted: 03/16/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Amphibian species are declining worldwide, and precise monitoring is key to ensuring timely protection and thereby ceasing deteriorating populations. Conventional monitoring methods are invasive, time-consuming, and dependent on expert knowledge. eDNA methods have been suggested as a replacement for or supplement to conventional survey methods. The present study assessed amphibian detection of conventional survey methods and eDNA metabarcoding in Danish lakes and ponds to address how the application of eDNA surveys can supplement the currently applied methodology. The study found eDNA metabarcoding to detect five out of six species detected through conventional methods. Furthermore, it is expected that the results in the present study reflect the time of sampling for the applied methods. The findings in the present study indicate that eDNA metabarcoding detects multiple Danish amphibian species and can produce knowledge on the occurrence and distribution for amphibian species. Implementing it as a supplement for conventional survey methods in nature monitoring will enable a higher frequency of monitoring and yield knowledge of species composition. Abstract A keystone in protection work is accurate and thorough the monitoring of amphibian species, and the currently applied conventional survey methods are invasive, time-consuming, and dependent on expert knowledge. Research suggests that eDNA metabarcoding is a precise and cost-efficient method that could supplement the currently applied methods. The present study assessed the efficiency of conventional survey methods and eDNA metabarcoding in terms of species richness, the average number of detected species per site, the relative frequency of species occurrence, and the similarity of applied methods. The study found eDNA metabarcoding surveys to detect Lissotriton vulgaris (smooth newt), Triturus cristatus (great crested newt), Rana arvalis (moor frog), Rana temporaria (common frog), and Bufo bufo (common toad), as well as an average of 0.9 species per site, reflecting the species composition at the time of sampling in mid-July 2020. In addition to the species mentioned above, the conventional survey detected Epidalea calamita (natterjack toad) and an average of 1.7 species per site, reflecting the species composition at the time of sampling in early June 2020. The similarity between the methods applied in the present study was 27%, thus indicating a large number of unique observations of both eDNA metabarcoding and conventional surveys. The differences in detection can most likely be explained by the time of sampling, which was conducted a month apart. eDNA metabarcoding was efficient in detecting multiple amphibian species and produced unique observations that were not detected using conventional survey methods. Applying eDNA techniques as a supplement will most likely produce important knowledge on species distribution and presence, as well as enable more frequent monitoring due to cost efficiency and disturbance.
Collapse
Affiliation(s)
- Anne Katrine Nørgaard Svenningsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220 Aalborg, Denmark; (C.P.); (D.B.)
- Correspondence:
| | - Cino Pertoldi
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220 Aalborg, Denmark; (C.P.); (D.B.)
- Aalborg Zoo, Mølleparkvej 63, DK-9000 Aalborg, Denmark
| | - Dan Bruhn
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220 Aalborg, Denmark; (C.P.); (D.B.)
| |
Collapse
|
86
|
Bernos TA, Jeffries KM, Mandrak NE. Aquatic invasive species specialists’ perceptions on the importance of genetic tools and concepts to inform management. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02758-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
87
|
Sakata MK, Kawata MU, Kurabayashi A, Kurita T, Nakamura M, Shirako T, Kakehashi R, Nishikawa K, Hossman MY, Nishijima T, Kabamoto J, Miya M, Minamoto T. Development and evaluation of PCR primers for environmental DNA (eDNA) metabarcoding of Amphibia. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.76534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Biodiversity monitoring is important for the conservation of natural ecosystems in general, but particularly for amphibians, whose populations are pronouncedly declining. However, amphibians’ ecological traits (e.g. nocturnal or aquatic) often prevent their precise monitoring. Environmental DNA (eDNA) metabarcoding – analysis of extra-organismal DNA released into the environment – allows the easy and effective monitoring of the biodiversity of aquatic organisms. Here, we developed and tested the utility of original PCR primer sets. First, we conducted in vitro PCR amplification tests with universal primer candidates using total DNA extracted from amphibian tissues. Five primer sets successfully amplified the target DNA fragments (partial 16S rRNA gene fragments of 160–311 bp) from all 16 taxa tested (from the three living amphibian orders Anura, Caudata and Gymnophiona). Next, we investigated the taxonomic resolution retrieved using each primer set. The results revealed that the universal primer set “Amph16S” had the highest resolution amongst the tested sets. Finally, we applied Amph16S to the water samples collected in the field and evaluated its detection capability by comparing the species detected using eDNA and physical survey (capture-based sampling and visual survey) in multiple agricultural ecosystems across Japan (160 sites in 10 areas). The eDNA metabarcoding with Amph16S detected twice as many species as the physical surveys (16 vs. 8 species, respectively), indicating the effectiveness of Amph16S in biodiversity monitoring and ecological research for amphibian communities.
Collapse
|
88
|
Larson CE, Barge JT, Hatzenbuhler CL, Hoffman JC, Peterson GS, Pilgrim EM, Wiechman B, Rees CB, Trebitz AS. Invasive Dreissena Mussel Coastal Transport From an Already Invaded Estuary to a Nearby Archipelago Detected in DNA and Zooplankton Surveys. FRONTIERS IN MARINE SCIENCE 2022; 9:1-818738. [PMID: 35450130 PMCID: PMC9016628 DOI: 10.3389/fmars.2022.818738] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Coastal waters of Lake Superior are generally inhospitable to the establishment of invasive Dreissena spp. mussels (both Dreissena polymorpha and Dreissena bugensis). Dreissena have inhabited the Saint Louis River estuary (SLRE; largest commercial port in the Laurentian Great Lakes) for over three decades, but only in the last few years have small colonies been found in the Apostle Islands National Lakeshore (APIS, an archipelago situated 85 km to the east of SLRE) A 2017 survey determined a low abundance Dreissena spatial distribution in APIS, with the largest colonies on the north and west islands which suggested potential veliger transport from the SLRE via longshore currents. Our objective in this study was to determine if Dreissena veligers are transported by currents at low densities along the south shore of Lake Superior from the SLRE to APIS. To do so, we used both eDNA (water and passive substrate samples) and zooplankton collection methods at eight sites evenly spaced between the SLRE and APIS with three sampling times over five weeks. Dreissena veligers were consistently detected along the south shore, although at low abundances (veligers per m3 range = 0-690, median = 8), and for every 1 km increase in distance from the SLRE, both veliger counts and water eDNA copy numbers decreased on average by 5 and 7%, respectively. D. polymorpha (suited to estuary habitats) was detected two times more than D. bugensis (better suited to deep-lake habitats). There was not a trend in the veliger size distribution along the south shore, and temperature and calcium concentrations fluctuated around the threshold for Dreissena veliger and adult development, averaging 11.0°C and 14.8 ppm, respectively. Three zooplankton taxa representative of the estuary community-Daphnia retrocurva, Diaphanosoma birgei, and Mesocyclops copepodites-decreased as the distance from the SLRE increased mirroring Dreissena veliger abundance patterns. Findings represent multiple sources of evidence of a propagule "conveyor belt" for Dreissena along the south shore of Lake Superior. We conclude that veligers are functioning as a propagule, using coastal currents to spread from the point of invasion, thereby traversing coastal habitat previously reported as inhospitable to distant habitats suitable for colonization.
Collapse
Affiliation(s)
- Courtney E. Larson
- U.S. Environmental Protection Agency, Office of Research and Development, Duluth, MN, United States
- Department of Biology, University of Minnesota Duluth, Duluth, MN, United States
| | - Jonathan T. Barge
- U.S. Environmental Protection Agency, Office of Research and Development, Duluth, MN, United States
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States
| | - Chelsea L. Hatzenbuhler
- U.S. Environmental Protection Agency, Office of Research and Development, Duluth, MN, United States
- SpecPro Professional Services, Duluth, MN, United States
| | - Joel C. Hoffman
- U.S. Environmental Protection Agency, Office of Research and Development, Duluth, MN, United States
| | - Greg S. Peterson
- U.S. Environmental Protection Agency, Office of Research and Development, Duluth, MN, United States
| | - Erik M. Pilgrim
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Barry Wiechman
- Aptim Federal Services, LLC, Baton Rouge, LA, United States
| | - Christopher B. Rees
- U.S. Fish and Wildlife Service, Northeast Fishery Center, Lamar, PA, United States
| | - Anett S. Trebitz
- U.S. Environmental Protection Agency, Office of Research and Development, Duluth, MN, United States
| |
Collapse
|
89
|
Facilitative interaction promotes occupancy of a desert amphibian across a climate gradient. Oecologia 2022; 198:815-823. [DOI: 10.1007/s00442-022-05127-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/25/2022] [Indexed: 10/19/2022]
|
90
|
Moss WE, Harper LR, Davis MA, Goldberg CS, Smith MM, Johnson PTJ. Navigating the trade‐offs between environmental
DNA
and conventional field surveys for improved amphibian monitoring. Ecosphere 2022. [DOI: 10.1002/ecs2.3941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Wynne E. Moss
- Department of Ecology & Evolutionary Biology University of Colorado Boulder Colorado USA
| | - Lynsey R. Harper
- Illinois Natural History Survey Prairie Research Institute, University of Illinois at Urbana‐Champaign Champaign Illinois USA
- NatureMetrics Ltd, CABI Site Egham UK
| | - Mark A. Davis
- Illinois Natural History Survey Prairie Research Institute, University of Illinois at Urbana‐Champaign Champaign Illinois USA
| | - Caren S. Goldberg
- School of the Environment Washington State University Pullman Washington USA
| | - Matthew M. Smith
- School of the Environment Washington State University Pullman Washington USA
| | - Pieter T. J. Johnson
- Department of Ecology & Evolutionary Biology University of Colorado Boulder Colorado USA
| |
Collapse
|
91
|
Zhang S, Zheng Y, Zhan A, Dong C, Zhao J, Yao M. Environmental DNA captures native and non-native fish community variations across the lentic and lotic systems of a megacity. SCIENCE ADVANCES 2022; 8:eabk0097. [PMID: 35148174 PMCID: PMC8836804 DOI: 10.1126/sciadv.abk0097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Globally, urbanization poses a major threat to terrestrial biodiversity, yet its impact on fish diversity is poorly understood, mainly because of surveying difficulties. In this study, environmental DNA metabarcoding was used to survey fish communities at 109 lentic and lotic sites across Beijing, and how environmental variables affect fish biodiversity at fine urban spatial scales was investigated. We identified 52 native and 23 non-native taxa, with lentic and lotic waters harboring both common and habitat-specific species. Water quality strongly affected native fish diversity, especially in lentic systems, but had little influence on non-native diversity. Fish diversity showed little response to urban land cover variation, but the relative sequence abundance of non-natives in lotic waters increased linearly with distance from the city center. Our findings illustrate the complex effects of urbanization on native versus non-native fishes in different aquatic habitats and highlight the distinctive considerations needed to conserve urban aquatic biodiversity.
Collapse
Affiliation(s)
- Shan Zhang
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yitao Zheng
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Chunxia Dong
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Jindong Zhao
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Meng Yao
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
- Corresponding author. ,
| |
Collapse
|
92
|
Wood LE, Guilder J, Brennan ML, Birland NJ, Taleti V, Stinton N, Taylor NGH, Thrush MA. Biosecurity and the ornamental fish trade: A stakeholder perspective in England. JOURNAL OF FISH BIOLOGY 2022; 100:352-365. [PMID: 34699063 DOI: 10.1111/jfb.14928] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
The freshwater and marine ornamental fish industry is a primary route of hazard introduction and emergence, including aquatic animal diseases and non-native species. Prevention measures are key to reducing the risk of hazard incursion and establishment, but there is currently little understanding of the biosecurity practices and hazard responses implemented at post-border stages of the ornamental fish supply chain. This study addresses this knowledge gap, using questionnaires to collate information on actual biosecurity behaviours and hazard responses practised by ornamental fish retailers and hobbyist communities in England. Actual behaviours varied considerably within retailers and hobbyists, suggesting that reliance on preventative practices by individuals in the post-border stages of the ornamental fish supply chain is likely to be ineffective in minimizing the risk of hazard incursion and establishment. Resources should be allocated towards improving and enforcing robust pre- and at-border control measures, such as risk-based surveillance of ornamental fish imports at border controls. In addition, these findings should be used to implement targeted awareness-raising campaigns and help create directed training on biosecurity practices for individuals involved in the post-border stages of the ornamental supply chain.
Collapse
Affiliation(s)
- Louisa E Wood
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
- Centre for Blue Governance, Faculty of Economics and Law, University of Portsmouth, Portsmouth, UK
| | - James Guilder
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| | - Marnie L Brennan
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Nicola J Birland
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Virginia Taleti
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| | - Nicholas Stinton
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| | - Nick G H Taylor
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| | - Mark A Thrush
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| |
Collapse
|
93
|
Miya M. Environmental DNA Metabarcoding: A Novel Method for Biodiversity Monitoring of Marine Fish Communities. ANNUAL REVIEW OF MARINE SCIENCE 2022; 14:161-185. [PMID: 34351788 DOI: 10.1146/annurev-marine-041421-082251] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Environmental DNA (eDNA) is genetic material that has been shed from macroorganisms. It has received increased attention as an indirect marker for biodiversity monitoring. This article reviews the current status of eDNA metabarcoding (simultaneous detection of multiple species) as a noninvasive and cost-effective approach for monitoring marine fish communities and discusses the prospects for this growing field. eDNA metabarcoding coamplifies short fragments of fish eDNA across a wide variety of taxa and, coupled with high-throughput sequencing technologies, allows massively parallel sequencing to be performed simultaneously for dozens to hundreds of samples. It can predict species richness in a given area, detect habitat segregation and biogeographic patterns from small to large spatial scales, and monitor the spatiotemporal dynamics of fish communities. In addition, it can detect an anthropogenic impact on fish communities through evaluation of their functional diversity. Recognizing the strengths and limitations of eDNA metabarcoding will help ensure that continuous biodiversity monitoring at multiple sites will be useful for ecosystem conservation and sustainable use of fishery resources, possibly contributing to achieving the targets of the United Nations' Sustainable Development Goal 14 for 2030.
Collapse
Affiliation(s)
- Masaki Miya
- Natural History Museum and Institute, Chiba, Chiba 260-8682, Japan;
| |
Collapse
|
94
|
Cowart DA, Murphy KR, Cheng CHC. Environmental DNA from Marine Waters and Substrates: Protocols for Sampling and eDNA Extraction. Methods Mol Biol 2022; 2498:225-251. [PMID: 35727547 DOI: 10.1007/978-1-0716-2313-8_11] [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] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) analysis has emerged in recent years as a powerful tool for the detection, monitoring, and characterization of aquatic metazoan communities, including vulnerable species. The rapid rate of adopting the eDNA approach across diverse habitats and taxonomic groups attests to its value for a wide array of investigative goals, from understanding natural or changing biodiversity to informing on conservation efforts at local and global scales. Regardless of research objectives, eDNA workflows commonly include the following essential steps: environmental sample acquisition, processing and preservation of samples, and eDNA extraction, followed by eDNA sequencing library preparation, high-capacity sequencing and sequence data analysis, or other methods of genetic detection. In this chapter, we supply instructional details for the early steps in the workflow to facilitate researchers considering adopting eDNA analysis to address questions in marine environments. Specifically, we detail sampling, preservation, extraction, and quantification protocols for eDNA originating from marine water, shallow substrates, and deeper sediments. eDNA is prone to degradation and loss, and to contamination through improper handling; these factors crucially influence the outcome and validity of an eDNA study. Thus, we also provide guidance on avoiding these pitfalls. Following extraction, purified eDNA is often sequenced on massively parallel sequencing platforms for comprehensive faunal diversity assessment using a metabarcoding or metagenomic approach, or for the detection and quantification of specific taxa by qPCR methods. These components of the workflow are project-specific and thus not included in this chapter. Instead, we briefly touch on the preparation of eDNA libraries and discuss comparisons between sequencing approaches to aid considerations in project design.
Collapse
Affiliation(s)
- Dominique A Cowart
- Company for Open Ocean Observations and Logging (COOOL), Saint Leu, La Réunion, France
| | - Katherine R Murphy
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - C-H Christina Cheng
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana - Champaign, Urbana, IL, USA.
| |
Collapse
|
95
|
Schultz AJ, Strickland K, Cristescu RH, Hanger J, de Villiers D, Frère CH. Testing the effectiveness of genetic monitoring using genetic non-invasive sampling. Ecol Evol 2022; 12:e8459. [PMID: 35127011 PMCID: PMC8794716 DOI: 10.1002/ece3.8459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/26/2021] [Accepted: 11/26/2021] [Indexed: 01/07/2023] Open
Abstract
Effective conservation requires accurate data on population genetic diversity, inbreeding, and genetic structure. Increasingly, scientists are adopting genetic non-invasive sampling (gNIS) as a cost-effective population-wide genetic monitoring approach. gNIS has, however, known limitations which may impact the accuracy of downstream genetic analyses. Here, using high-quality single nucleotide polymorphism (SNP) data from blood/tissue sampling of a free-ranging koala population (n = 430), we investigated how the reduced SNP panel size and call rate typical of genetic non-invasive samples (derived from experimental and field trials) impacts the accuracy of genetic measures, and also the effect of sampling intensity on these measures. We found that gNIS at small sample sizes (14% of population) can provide accurate population diversity measures, but slightly underestimated population inbreeding coefficients. Accurate measures of internal relatedness required at least 33% of the population to be sampled. Accurate geographic and genetic spatial autocorrelation analysis requires between 28% and 51% of the population to be sampled. We show that gNIS at low sample sizes can provide a powerful tool to aid conservation decision-making and provide recommendations for researchers looking to apply these techniques to free-ranging systems.
Collapse
Affiliation(s)
- Anthony James Schultz
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
- Icelandic Museum of Natural History (Náttúruminjasafn Íslands)ReykjavikIceland
| | - Kasha Strickland
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
- Department of Aquaculture and Fish BiologyHólar UniversityHólarIceland
| | - Romane H. Cristescu
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
| | | | | | - Céline H. Frère
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
- School of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
| |
Collapse
|
96
|
Peterson GS, Hoffman JC, Trebitz AS, Hatzenbuhler CI, Myers JT, Ross JE, Okum SL, Pilgrim EM. Early detection monitoring for non-indigenous fishes; comparison of survey approaches during two species introductions in a Great Lakes port. Biol Invasions 2021; 24:463-478. [PMID: 35356708 PMCID: PMC8958937 DOI: 10.1007/s10530-021-02655-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Assessing relative performance of different sampling methods used for early detection monitoring (EDM) is a critical step in understanding the likelihood of detecting new non-indigenous species (NIS) in an environment of interest. EDM performance metrics are typically based on the probability of detecting established NIS or rare indigenous species; however, detection probability estimates for these proxies may not accurately reflect survey effectiveness for newly introduced NIS. We used data from three different EDM survey approaches that varied by targeted life-stage (adult-juvenile versus ichthyoplankton), media (physical fish versus environmental DNA), and taxonomic method (morphology-based versus DNA-based taxonomy) to explore relative detection sensitivity for recently introduced white bass (Morone chrysops) and gizzard shad (Dorosoma cepedianum) in the Port of Duluth-Superior, a NIS introduction hot spot within the Laurentian Great Lakes. Detection efficiency, measured by the effort (number of samples) required to achieve 95% probability of detection, differed by EDM approach and species. Also, the relative sensitivity (detection rate) of each survey approach differed by species. For both species, detection in surveys using DNA-based taxonomy was generally as good or better than the adult-juvenile survey using morphology-based taxonomy. While both species appear to have been detected at early stages of invasion, white bass were likely present up to 5 years prior to initial detection, whereas gizzard shad may have been detected in the first year of introduction. We conclude that using complimentary sampling methods can help to balance the strengths and weaknesses of each approach and provide more reliable early detection of new invaders.
Collapse
Affiliation(s)
- Greg S. Peterson
- Center for Computational Toxicology and Ecology, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, 6201 Congdon Blvd, Duluth, MN 55804, USA
| | - Joel C. Hoffman
- Center for Computational Toxicology and Ecology, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, 6201 Congdon Blvd, Duluth, MN 55804, USA
| | - Anett S. Trebitz
- Center for Computational Toxicology and Ecology, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, 6201 Congdon Blvd, Duluth, MN 55804, USA
| | - Chelsea I. Hatzenbuhler
- SpecPro Professional Services, Contractor To US Environmental Protection Agency, 6201 Congdon Blvd, Duluth, MN 55804, USA
| | - Jared T. Myers
- US Fish and Wildlife Service, Ashland Fish and Wildlife Conservation Office, 2800 Lakeshore Drive E, Ashland, WI 54806, USA
| | - Jason E. Ross
- US Fish and Wildlife Service, Ashland Fish and Wildlife Conservation Office, 2800 Lakeshore Drive E, Ashland, WI 54806, USA
| | - Sara L. Okum
- Pegasus Professional Services, Contractor To US Environmental Protection Agency, 26 Martin Luther King Dr, Cincinnati, OH 45268, USA
| | - Erik M. Pilgrim
- Center for Environmental Measurement and Modeling, Watershed and Ecosystem Characterization Division, US Environmental Protection Agency, 26 Martin Luther King Dr, Cincinnati, OH 45268, USA
| |
Collapse
|
97
|
Feist SM, Lance RF. Genetic detection of freshwater harmful algal blooms: A review focused on the use of environmental DNA (eDNA) in Microcystis aeruginosa and Prymnesium parvum. HARMFUL ALGAE 2021; 110:102124. [PMID: 34887004 DOI: 10.1016/j.hal.2021.102124] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Recurrence and severity of harmful algal blooms (HABs) are increasing due to a number of factors, including human practices and climate change. Sensitive and robust methods that allow for early and expedited HAB detection across large landscape scales are needed. Among the suite of HAB detection tools available, a powerful option exists in genetics-based approaches utilizing environmental sampling, also termed environmental DNA (eDNA). Here we provide a detailed methodological review of three HAB eDNA approaches (quantitative PCR, high throughput sequencing, and isothermal amplification). We then summarize and synthesize recently published eDNA applications covering a variety of HAB surveillance and research objectives, all with a specific emphasis in the detection of two widely problematic freshwater species, Microcystis aeruginosa and Prymnesium parvum. In our summary and conclusion we build on this literature by discussing ways in which eDNA methods could be advanced to improve HAB detection. We also discuss ways in which eDNA data could be used to potentially provide novel insight into the ecology, mitigation, and prediction of HABs.
Collapse
Affiliation(s)
- Sheena M Feist
- Environmental Lab, United States Army Corps of Engineers Research and Development Center, Vicksburg, MS, 39180, United States.
| | - Richard F Lance
- Environmental Lab, United States Army Corps of Engineers Research and Development Center, Vicksburg, MS, 39180, United States
| |
Collapse
|
98
|
Caballero S, Ortiz-Giral MC, Bohorquez L, Lozano Mojica JD, Caicedo-Herrera D, Arévalo-González K, Mignucci-Giannoni AA. Mitochondrial Genetic Diversity, Population Structure and Detection of Antillean and Amazonian Manatees in Colombia: New Areas and New Techniques. Front Genet 2021; 12:726916. [PMID: 34899829 PMCID: PMC8662808 DOI: 10.3389/fgene.2021.726916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/08/2021] [Indexed: 11/26/2022] Open
Abstract
The Antillean manatee (Trichechus manatus) and the Amazonian manatee (Trichechus inunguis) are distributed in rivers in the Caribbean and Amazonian region of Colombia respectively. For 30 years, genetic information has been obtained from these populations in order to inform conservation programs for these endangered species and decide on the location to release them back to the wild. However, in previous studies, samples from rivers in some areas of the country were not included, given the difficulties to access these regions due to either logistic or safety issues. In this study, we analyzed mitochondrial DNA (mtDNA) control region (CR) sequences of from samples of T. manatus (n = 37) and T. inunguis (n = 4) (410 and 361 bp, respectively), obtained in new and previously unexplored rivers and bays in the country, including Santa Marta, Urabá Gulf, Ayapel Marsh (San Jorge River Basin), Meta River and Magdalena Medio and the low Magdalena River (Cesar Province and Canal del Dique) as well as additional samples from Puerto Nariño in the Colombian Amazon. Our results included the discovery of two newly described mtDNA CR haplotypes for T. manatus. In addition, we confirmed significant population differentiation at the mitochondrial level between the Magdalena and Sinú rivers and differentiation among areas of the same river, including the middle and low Magdalena River. This differentiation may be related to anthropic changes in the river since construction of the Canal del Dique in the XVI century. We also tested environmental DNA sampling and analyses techniques to evaluate its potential use for manatee detection and monitoring in bodies of water in Colombia, in order to evaluate new areas for future manatee conservation initiatives. We emphasize the need to continue using genetic information to provide evidence on the potential best locations to undertake animal release to prevent outbreeding depression.
Collapse
Affiliation(s)
- Susana Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos (LEMVA), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Maria Camila Ortiz-Giral
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos (LEMVA), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Laura Bohorquez
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos (LEMVA), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Juan Diego Lozano Mojica
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos (LEMVA), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | | | - Katherine Arévalo-González
- Cabildo Verde, Sabana de Torres, Colombia
- Fundación Internacional para La Defensa de La Naturaleza y La Sustentabilidad-FINS, Chetumal, Mexico
| | - Antonio A. Mignucci-Giannoni
- Centro de Conservación de Manatíes del Caribe, Universidad Interamericana de Puerto Rico, Bayamón, Puerto Rico
- Center for Conservation Medicine and Ecosystem Health, Ross University School of Veterinary Medicine, Basseterre, St. Kitts
| |
Collapse
|
99
|
Perelman ZE, Takahashi MK, Hundermark EL, Parenzan C. An eDNA-Based Assessment of the Impact of a 207,000-Liter Gasoline Spill on Local Populations of Eastern Hellbenders (Cryptobranchus alleganiensis alleganiensis), an Imperiled Giant Salamander. Northeast Nat (Steuben) 2021. [DOI: 10.1656/045.028.0406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
| | | | | | - Carol Parenzan
- (Former) Middle Susquehanna Riverkeeper, Sunbury, PA 17801
| |
Collapse
|
100
|
Hutchins PR, Simantel LN, Sepulveda AJ. Time to get real with qPCR controls: The frequency of sample contamination and the informative power of negative controls in environmental DNA studies. Mol Ecol Resour 2021; 22:1319-1329. [PMID: 34752687 DOI: 10.1111/1755-0998.13549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/20/2021] [Accepted: 09/29/2021] [Indexed: 12/01/2022]
Abstract
Environmental (e)DNA methods have enabled rapid, sensitive and specific inferences of taxa presence throughout diverse fields of ecological study. However, use of eDNA results for decision-making has been impeded by uncertainties associated with false positive tests putatively caused by sporadic or systemic contamination. Sporadic contamination is a process that is inconsistent across samples and systemic contamination occurs consistently over a group of samples. Here, we used empirical data and laboratory experiments to (i) estimate the sporadic contamination rate for each stage of a common, targeted eDNA workflow employing best practice quality control measures under simulated conditions of rare and common target DNA presence, (ii) determine the rate at which negative controls (i.e., "blanks") detect varying concentrations of systemic contamination, and (iii) estimate the effort that would be required to consistently detect sporadic and systemic contamination. Sporadic contamination rates were very low across all eDNA workflow steps, and, therefore, an intractably high number of negative controls (>100) would be required to determine occurrence of sporadic contamination with any certainty. Contrarily, detection of intentionally introduced systemic contamination was more consistent; therefore, very few negative controls (<5) would be needed to consistently alert to systemic contamination. These results have considerable implications to eDNA study design when resources for sample analyses are constrained.
Collapse
Affiliation(s)
- Patrick R Hutchins
- U.S. Geological Survey Northern Rocky Mountain Science Center, Bozeman, Montana, USA
| | - Leah N Simantel
- U.S. Geological Survey Northern Rocky Mountain Science Center, Bozeman, Montana, USA
| | - Adam J Sepulveda
- U.S. Geological Survey Northern Rocky Mountain Science Center, Bozeman, Montana, USA
| |
Collapse
|