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Bell KL, Campos M, Hoffmann BD, Encinas-Viso F, Hunter GC, Webber BL. Environmental DNA methods for biosecurity and invasion biology in terrestrial ecosystems: Progress, pitfalls, and prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171810. [PMID: 38513869 DOI: 10.1016/j.scitotenv.2024.171810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/13/2024] [Accepted: 03/16/2024] [Indexed: 03/23/2024]
Abstract
Analysis of environmental DNA (eDNA) enables indirect detection of species without the need to directly observe and sample them. For biosecurity and invasion biology, eDNA-based methods are useful to address biological invasions at all phases, from detecting arrivals to confirming eradication of past invasions. We conducted a systematic review of the literature and found that in biosecurity and invasion biology, eDNA has primarily been used to detect new incursions and monitor spread in marine and freshwater ecosystems, with much slower uptake in terrestrial ecosystems, reflecting a broader trend common to the usage of eDNA tools. In terrestrial ecosystems, eDNA research has mostly focussed on the use of eDNA metabarcoding to characterise biodiversity, rather than targeting biosecurity threats or non-native populations. We discuss how eDNA-based methods are being applied to terrestrial ecosystems for biosecurity and managing non-native populations at each phase of the invasion continuum: transport, introduction, establishment, and spread; across different management options: containment, control, and eradication; and for detecting the impact of non-native organisms. Finally, we address some of the current technical issues and caveats of eDNA-based methods, particularly for terrestrial ecosystems, and how these might be solved. As eDNA-based methods improve, they will play an increasingly important role in the early detection and adaptive management of biological invasions, and the implementation of effective biosecurity controls.
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Affiliation(s)
- Karen L Bell
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; School of Biological Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.
| | - Mariana Campos
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; Harry Butler Institute, Murdoch University, Murdoch, Western Australia 6150, Australia
| | | | - Francisco Encinas-Viso
- CSIRO Centre of Australian National Biodiversity Research, Black Mountain, Australian Capital Territory 2601, Australia
| | - Gavin C Hunter
- CSIRO Health & Biosecurity, Black Mountain, Australian Capital Territory 2601, Australia
| | - Bruce L Webber
- CSIRO Health & Biosecurity, Floreat, Western Australia 6014, Australia; School of Biological Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
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Lin CP, Huang CH, Padgett T, Bucay MAC, Chen CW, Shen ZY, Chiu L, Tseng YC, Yu JK, Wang J, Wang MC, Hoh DZ. Environmental DNA-based biodiversity profiling along the Houdong River in north-eastern Taiwan. Biodivers Data J 2024; 12:e116921. [PMID: 38694844 PMCID: PMC11061556 DOI: 10.3897/bdj.12.e116921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/03/2024] [Indexed: 05/04/2024] Open
Abstract
Background This paper describes two datasets: species occurrences, which were determined by environmental DNA (eDNA) metabarcoding and their associated DNA sequences, originating from a research project which was carried out along the Houdong River (), Jiaoxi Township, Yilan, Taiwan. The Houdong River begins at an elevation of 860 m and flows for approximately 9 km before it empties into the Pacific Ocean. Meandering through mountains, hills, plains and alluvial valleys, this short river system is representative of the fluvial systems in Taiwan. The primary objective of this study was to determine eukaryotic species occurrences in the riverine ecosystem through the use of the eDNA analysis. The second goal was, based on the current dataset, to establish a metabarcoding eDNA data template that will be useful and replicable for all users, particularly the Taiwan community. The species occurrence data are accessible at the Global Biodiversity Information Facility (GBIF) portal and its associated DNA sequences have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI, respectively. A total of 12 water samples from the study yielded an average of 1.5 million reads. The subsequent species identification from the collected samples resulted in the classification of 432 Operational Taxonomic Units (OTUs) out of a total of 2,734. Furthermore, a total of 1,356 occurrences with taxon matches in GBIF were documented (excluding 4,941 incertae sedis, accessed 05-12-2023). These data will be of substantial importance for future species and habitat monitoring within the short river, such as assessment of biodiversity patterns across different elevations, zonations and time periods and its correlation to water quality, land uses and anthropogenic activities. Further, these datasets will be of importance for regional ecological studies, in particular the freshwater ecosystem and its status in the current global change scenarios. New information The datasets are the first species diversity description of the Houdong River system using either eDNA or traditional monitoring processes.
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Affiliation(s)
- Chieh-Ping Lin
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, TaiwanGenome and Systems Biology Degree Program, Academia Sinica and National Taiwan UniversityTaipeiTaiwan
- Biodiversity Research Center, Academia Sinica, Taipei, TaiwanBiodiversity Research Center, Academia SinicaTaipeiTaiwan
| | - Chung-Hsin Huang
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- International Graduate Degree Program for Biodiversity, Tunghai University, Taichung, TaiwanInternational Graduate Degree Program for Biodiversity, Tunghai UniversityTaichungTaiwan
| | - Trevor Padgett
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- International Graduate Degree Program for Biodiversity, Tunghai University, Taichung, TaiwanInternational Graduate Degree Program for Biodiversity, Tunghai UniversityTaichungTaiwan
| | - Mark Angelo C. Bucay
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- Department of Life Science, National Taiwan Normal University, Taipei, TaiwanDepartment of Life Science, National Taiwan Normal UniversityTaipeiTaiwan
| | - Cheng-Wei Chen
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- Department of Life Science, National Taiwan Normal University, Taipei, TaiwanDepartment of Life Science, National Taiwan Normal UniversityTaipeiTaiwan
| | - Zong-Yu Shen
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
- Department of Life Science, National Taiwan Normal University, Taipei, TaiwanDepartment of Life Science, National Taiwan Normal UniversityTaipeiTaiwan
| | - Ling Chiu
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, TaiwanMarine Research Station, Institute of Cellular and Organismic Biology, Academia SinicaYilanTaiwan
- Institute of Oceanography, National Taiwan University, Taipei, TaiwanInstitute of Oceanography, National Taiwan UniversityTaipeiTaiwan
| | - Yung-Che Tseng
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, TaiwanMarine Research Station, Institute of Cellular and Organismic Biology, Academia SinicaYilanTaiwan
| | - Jr-Kai Yu
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, TaiwanMarine Research Station, Institute of Cellular and Organismic Biology, Academia SinicaYilanTaiwan
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, TaiwanInstitute of Cellular and Organismic Biology, Academia SinicaTaipeiTaiwan
| | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei, TaiwanBiodiversity Research Center, Academia SinicaTaipeiTaiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, TaiwanBiodiversity Program, Taiwan International Graduate Program, Academia SinicaTaipeiTaiwan
| | - Min-Chen Wang
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, TaiwanMarine Research Station, Institute of Cellular and Organismic Biology, Academia SinicaYilanTaiwan
- Zoological Institute, Christian-Albrechts University of Kiel, Kiel, GermanyZoological Institute, Christian-Albrechts University of KielKielGermany
| | - Daphne Z. Hoh
- Taiwan Biodiversity Information Facility, Biodiversity Research Centre, Academia Sinica, Taipei, TaiwanTaiwan Biodiversity Information Facility, Biodiversity Research Centre, Academia SinicaTaipeiTaiwan
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Newton JP, Nevill P, Bateman PW, Campbell MA, Allentoft ME. Spider webs capture environmental DNA from terrestrial vertebrates. iScience 2024; 27:108904. [PMID: 38533454 PMCID: PMC10964257 DOI: 10.1016/j.isci.2024.108904] [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: 09/20/2023] [Revised: 11/22/2023] [Accepted: 01/10/2024] [Indexed: 03/28/2024] Open
Abstract
Environmental DNA holds significant promise as a non-invasive tool for tracking terrestrial biodiversity. However, in non-homogenous terrestrial environments, the continual exploration of new substrates is crucial. Here we test the hypothesis that spider webs can act as passive biofilters, capturing eDNA from vertebrates present in the local environment. Using a metabarcoding approach, we detected vertebrate eDNA from all analyzed spider webs (N = 49). Spider webs obtained from an Australian woodland locality yielded vertebrate eDNA from 32 different species, including native mammals and birds. In contrast, webs from Perth Zoo, less than 50 km away, yielded eDNA from 61 different vertebrates and produced a highly distinct species composition, largely reflecting exotic species hosted in the zoo. We show that higher animal biomass and proximity to animal enclosures increased eDNA detection probability in the zoo. Our results indicate a tremendous potential for using spider webs as a cost-effective means to monitor terrestrial vertebrates.
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Affiliation(s)
- Joshua P. Newton
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
- Minesite Biodiversity Monitoring with eDNA (MBioMe) research group, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Paul Nevill
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
- Minesite Biodiversity Monitoring with eDNA (MBioMe) research group, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Philip W. Bateman
- Minesite Biodiversity Monitoring with eDNA (MBioMe) research group, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
- Behavioural Ecology Lab, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Matthew A. Campbell
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Morten E. Allentoft
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
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Chua PYS, Bourlat SJ, Ferguson C, Korlevic P, Zhao L, Ekrem T, Meier R, Lawniczak MKN. Future of DNA-based insect monitoring. Trends Genet 2023:S0168-9525(23)00038-0. [PMID: 36907721 DOI: 10.1016/j.tig.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 03/12/2023]
Abstract
Insects are crucial for ecosystem health but climate change and pesticide use are driving massive insect decline. To mitigate this loss, we need new and effective monitoring techniques. Over the past decade there has been a shift to DNA-based techniques. We describe key emerging techniques for sample collection. We suggest that the selection of tools should be broadened, and that DNA-based insect monitoring data need to be integrated more rapidly into policymaking. We argue that there are four key areas for advancement, including the generation of more complete DNA barcode databases to interpret molecular data, standardisation of molecular methods, scaling up of monitoring efforts, and integrating molecular tools with other technologies that allow continuous, passive monitoring based on images and/or laser imaging, detection, and ranging (LIDAR).
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Affiliation(s)
- Physilia Y S Chua
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Sarah J Bourlat
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Adenauerallee 127, 53113 Bonn, Germany
| | - Cameron Ferguson
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Petra Korlevic
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Leia Zhao
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Rudolf Meier
- Museum für Naturkunde, Center for Integrative Biodiversity Discovery, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Mara K N Lawniczak
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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Garrett NR, Watkins J, Francis CM, Simmons NB, Ivanova N, Naaum A, Briscoe A, Drinkwater R, Clare EL. Out of thin air: surveying tropical bat roosts through air sampling of eDNA. PeerJ 2023; 11:e14772. [PMID: 37128209 PMCID: PMC10148639 DOI: 10.7717/peerj.14772] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/03/2023] [Indexed: 05/03/2023] Open
Abstract
Understanding roosting behaviour is essential to bat conservation and biomonitoring, often providing the most accurate methods of assessing bat population size and health. However, roosts can be challenging to survey, e.g., physically impossible to access or presenting risks for researchers. Disturbance during monitoring can also disrupt natural bat behaviour and present material risks to the population such as disrupting hibernation cycles. One solution to this is the use of non-invasive monitoring approaches. Environmental (e)DNA has proven especially effective at detecting rare and elusive species particularly in hard-to-reach locations. It has recently been demonstrated that eDNA from vertebrates is carried in air. When collected in semi-confined spaces, this airborne eDNA can provide remarkably accurate profiles of biodiversity, even in complex tropical communities. In this study, we deploy novel airborne eDNA collection for the first time in a natural setting and use this approach to survey difficult to access potential roosts in the neotropics. Using airborne eDNA, we confirmed the presence of bats in nine out of 12 roosts. The identified species matched previous records of roost use obtained from photographic and live capture methods, thus demonstrating the utility of this approach. We also detected the presence of the white-winged vampire bat (Diaemus youngi) which had never been confirmed in the area but was long suspected based on range maps. In addition to the bats, we detected several non-bat vertebrates, including the big-eared climbing rat (Ototylomys phyllotis), which has previously been observed in and around bat roosts in our study area. We also detected eDNA from other local species known to be in the vicinity. Using airborne eDNA to detect new roosts and monitor known populations, particularly when species turnover is rapid, could maximize efficiency for surveyors while minimizing disturbance to the animals. This study presents the first applied use of airborne eDNA collection for ecological analysis moving beyond proof of concept to demonstrate a clear utility for this technology in the wild.
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Affiliation(s)
- Nina R. Garrett
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Jonathan Watkins
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Charles M. Francis
- Canadian Wildlife Service, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | | | - Amanda Naaum
- Nature Metrics North America Ltd., Guelph, Ontario, Canada
| | - Andrew Briscoe
- Nature Metrics Ltd., Surrey Research Park, Guildford, United Kingdom
| | - Rosie Drinkwater
- Palaeogenomics group, Department of Veterinary Sciences, Ludwig-Maximillian University Munich, Munich, Germany
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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.
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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
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