1
|
Zhang S, Zhao J, Yao M. Urban landscape-level biodiversity assessments of aquatic and terrestrial vertebrates by environmental DNA metabarcoding. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 340:117971. [PMID: 37119629 DOI: 10.1016/j.jenvman.2023.117971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/28/2023] [Accepted: 04/16/2023] [Indexed: 05/12/2023]
Abstract
Globally, expansive urbanization profoundly alters natural habitats and the associated biota. Monitoring biodiversity in cities can provide essential information for conservation management, but the complexity of urban landscapes poses serious challenges to conventional observational and capture-based surveys. Here we assessed pan-vertebrate biodiversity, including both aquatic and terrestrial taxa, using environmental DNA (eDNA) sampled from 109 water sites across Beijing, China. Using eDNA metabarcoding with a single primer set (Tele02), we detected 126 vertebrate species, including 73 fish, 39 birds, 11 mammals, and 3 reptiles belonging to 91 genera, 46 families, and 22 orders. The probability of detection from eDNA varied substantially among species and was related to their lifestyle, as shown by the greater detectability of fish compared to that of terrestrial and arboreal (birds and mammals) groups, as well as the greater detectability of water birds compared to that of forest birds (Wilcoxon rank-sum test p = 0.007). Furthermore, the eDNA detection probabilities across all vertebrates (Wilcoxon rank-sum test p = 0.009), as well as for birds (p < 0.001), were higher at lentic sites in comparison with lotic sites. Also, the detected biodiversity was positively correlated with lentic waterbody size for fish (Spearman p = 0.012), but not for other groups. Our results demonstrate the capacity of eDNA metabarcoding to efficiently surveil diverse vertebrate communities across an extensive spatial scale in heterogenous urban landscapes. With further methodological development and optimization, the eDNA approach has great potential for non-invasive, efficient, economic, and timely assessments of biodiversity responses to urbanization, thus guiding city ecosystem conservation management.
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
| | - 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
| | - 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.
| |
Collapse
|
2
|
Takahashi M, Saccò M, Kestel JH, Nester G, Campbell MA, van der Heyde M, Heydenrych MJ, Juszkiewicz DJ, Nevill P, Dawkins KL, Bessey C, Fernandes K, Miller H, Power M, Mousavi-Derazmahalleh M, Newton JP, White NE, Richards ZT, Allentoft ME. Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162322. [PMID: 36801404 DOI: 10.1016/j.scitotenv.2023.162322] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species and community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this is only possible with an in-depth overview of the technological advancements and a discussion of the pros and cons of available methods. We therefore conducted a systematic literature review of 407 peer-reviewed papers on aquatic eDNA published between 2012 and 2021. We observed a gradual increase in the annual number of publications from four (2012) to 28 (2018), followed by a rapid growth to 124 publications in 2021. This was mirrored by a tremendous diversification of methods in all aspects of the eDNA workflow. For example, in 2012 only freezing was applied to preserve filter samples, whereas we recorded 12 different preservation methods in the 2021 literature. Despite an ongoing standardisation debate in the eDNA community, the field is seemingly moving fast in the opposite direction and we discuss the reasons and implications. Moreover, by compiling the largest PCR-primer database to date, we provide information on 522 and 141 published species-specific and metabarcoding primers targeting a wide range of aquatic organisms. This works as a user-friendly 'distillation' of primer information that was hitherto scattered across hundreds of papers, but the list also reflects which taxa are commonly studied with eDNA technology in aquatic environments such as fish and amphibians, and reveals that groups such as corals, plankton and algae are under-studied. Efforts to improve sampling and extraction methods, primer specificity and reference databases are crucial to capture these ecologically important taxa in future eDNA biomonitoring surveys. In a rapidly diversifying field, this review synthetises aquatic eDNA procedures and can guide eDNA users towards best practice.
Collapse
Affiliation(s)
- Miwa Takahashi
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, Western Australia, Australia.
| | - Mattia Saccò
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia.
| | - Joshua H Kestel
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Georgia Nester
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Matthew A Campbell
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Mieke van der Heyde
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Matthew J Heydenrych
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Jarman Laboratory, Indian Ocean Marine Research Centre, School of Biological Sciences, University of Western Australia, Australia
| | - David J Juszkiewicz
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Kathryn L Dawkins
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Cindy Bessey
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Oceans and Atmosphere, Crawley, Western Australia, Australia
| | - Kristen Fernandes
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Haylea Miller
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, Western Australia, Australia
| | - Matthew Power
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Mahsa Mousavi-Derazmahalleh
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Joshua P Newton
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Zoe T Richards
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
3
|
Allen MC, Kwait R, Vastano A, Kisurin A, Zoccolo I, Jaffe BD, Angle JC, Maslo B, Lockwood JL. Sampling environmental DNA from trees and soil to detect cryptic arboreal mammals. Sci Rep 2023; 13:180. [PMID: 36604526 PMCID: PMC9814459 DOI: 10.1038/s41598-023-27512-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Environmental DNA (eDNA) approaches to monitoring biodiversity in terrestrial environments have largely focused on sampling water bodies, potentially limiting the geographic and taxonomic scope of eDNA investigations. We assessed the performance of two strictly terrestrial eDNA sampling approaches to detect arboreal mammals, a guild with many threatened and poorly studied taxa worldwide, within two central New Jersey (USA) woodlands. We evaluated species detected with metabarcoding using two eDNA collection methods (tree bark vs. soil sampling), and compared the performance of two detection methods (qPCR vs. metabarcoding) within a single species. Our survey, which included 94 sampling events at 21 trees, detected 16 species of mammals, representing over 60% of the diversity expected in the area. More DNA was found for the 8 arboreal versus 8 non-arboreal species detected (mean: 2466 vs. 289 reads/sample). Soil samples revealed a generally similar composition, but a lower diversity, of mammal species. Detection rates for big brown bat were 3.4 × higher for qPCR over metabarcoding, illustrating the enhanced sensitivity of single-species approaches. Our results suggest that sampling eDNA from on and around trees could serve as a useful new monitoring tool for cryptic arboreal mammal communities globally.
Collapse
Affiliation(s)
- Michael C. Allen
- grid.430387.b0000 0004 1936 8796Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901 USA
| | - Robert Kwait
- grid.430387.b0000 0004 1936 8796Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901 USA
| | - Anthony Vastano
- grid.430387.b0000 0004 1936 8796Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901 USA
| | - Alex Kisurin
- grid.430387.b0000 0004 1936 8796Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901 USA
| | - Isabelle Zoccolo
- grid.430387.b0000 0004 1936 8796Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901 USA
| | | | - Jordan C. Angle
- grid.421234.20000 0004 1112 1641ExxonMobil Upstream Research Company, Spring, TX USA
| | - Brooke Maslo
- grid.430387.b0000 0004 1936 8796Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901 USA
| | - Julie L. Lockwood
- grid.430387.b0000 0004 1936 8796Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901 USA
| |
Collapse
|
5
|
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
|
6
|
Arboreal camera trap reveals the frequent occurrence of a frugivore-carnivore in neotropical nutmeg trees. Sci Rep 2022; 12:7513. [PMID: 35525878 PMCID: PMC9079064 DOI: 10.1038/s41598-022-11568-z] [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: 01/14/2022] [Accepted: 04/25/2022] [Indexed: 11/09/2022] Open
Abstract
Arboreal and flying frugivorous animals represent primary dispersers in the Neotropics. Studies suggest a possible compensation for the loss of large species by smaller ones with expanding rampant anthropogenic pressures and declining populations of larger frugivores. However, studies on seed dispersal by frugivores vertebrates generally focus on the diurnal, terrestrial, canopy, and flying species, with the nocturnal canopy ones being less studied. Setting camera traps high in the canopy of fruiting nutmeg trees revealed for the first time the high frequency of the kinkajou (Potos flavus, Schreber, 1774, Procyonidae), an overlooked nocturnal frugivore species (Order Carnivora) in the Guianas. The diversity of the fruit species consumed by the kinkajou calls for considering it as an important seed disperser. The overlap of the size of seeds dispersed by frugivores observed in nutmeg trees suggests that the small (2-5 kg) kinkajou may compensate for the loss of large (5-10 kg) frugivorous vertebrates in the canopy. Camera traps visualise how the kinkajou is adapted to forage in the nutmeg tree crown and grab the fruit. Such information is vital for conservation because compensation of seed dispersal by small frugivores is crucial in increasing anthropogenic stressors.
Collapse
|