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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.
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Hervé A, Domaizon I, Baudoin JM, Dejean T, Gibert P, Jean P, Peroux T, Raymond JC, Valentini A, Vautier M, Logez M. Spatio-temporal variability of eDNA signal and its implication for fish monitoring in lakes. PLoS One 2022; 17:e0272660. [PMID: 35960745 PMCID: PMC9374266 DOI: 10.1371/journal.pone.0272660] [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: 03/08/2022] [Accepted: 07/24/2022] [Indexed: 11/18/2022] Open
Abstract
Environmental DNA (eDNA) metabarcoding is revolutionizing the monitoring of aquatic biodiversity. The use of eDNA has the potential to enable non-invasive, cost-effective, time-efficient and high-sensitivity monitoring of fish assemblages. Although the capacity of eDNA metabarcoding to describe fish assemblages is recognised, research efforts are still needed to better assess the spatial and temporal variability of the eDNA signal and to ultimately design an optimal sampling strategy for eDNA monitoring. In this context, we sampled three different lakes (a dam reservoir, a shallow eutrophic lake and a deep oligotrophic lake) every 6 weeks for 1 year. We performed four types of sampling for each lake (integrative sampling of sub-surface water along transects on the left shore, the right shore and above the deepest zone, and point sampling in deeper layers near the lake bottom) to explore the spatial variability of the eDNA signal at the lake scale over a period of 1 year. A metabarcoding approach was applied to analyse the 92 eDNA samples in order to obtain fish species inventories which were compared with traditional fish monitoring methods (standardized gillnet samplings). Several species known to be present in these lakes were only detected by eDNA, confirming the higher sensitivity of this technique in comparison with gillnetting. The eDNA signal varied spatially, with shoreline samples being richer in species than the other samples. Furthermore, deep-water samplings appeared to be non-relevant for regularly mixed lakes, where the eDNA signal was homogeneously distributed. These results also demonstrate a clear temporal variability of the eDNA signal that seems to be related to species phenology, with most of the species detected in spring during the spawning period on shores, but also a peak of detection in winter for salmonid and coregonid species during their reproduction period. These results contribute to our understanding of the spatio-temporal distribution of eDNA in lakes and allow us to provide methodological recommendations regarding where and when to sample eDNA for fish monitoring in lakes.
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Affiliation(s)
- Alix Hervé
- SPYGEN, Le Bourget du Lac, France
- Pole R&D ECLA, Le Bourget-du-Lac, France
- INRAE, Aix Marseille Université, RECOVER, Aix-en-Provence, France
| | - Isabelle Domaizon
- Pole R&D ECLA, Le Bourget-du-Lac, France
- INRAE, UMR CARRTEL, Thonon-les-Bains, France
| | - Jean-Marc Baudoin
- Pole R&D ECLA, Le Bourget-du-Lac, France
- OFB, Direction de la Recherche et de l’Appui Scientifique, Route Cézanne, Aix-en-Provence, France
| | | | - Pierre Gibert
- Pole R&D ECLA, Le Bourget-du-Lac, France
- INRAE, Aix Marseille Université, RECOVER, Aix-en-Provence, France
| | | | - Tiphaine Peroux
- Pole R&D ECLA, Le Bourget-du-Lac, France
- INRAE, Aix Marseille Université, RECOVER, Aix-en-Provence, France
| | - Jean-Claude Raymond
- Pole R&D ECLA, Le Bourget-du-Lac, France
- OFB, DR AURA, Thonon-les-Bains, France
| | | | - Marine Vautier
- Pole R&D ECLA, Le Bourget-du-Lac, France
- INRAE, UMR CARRTEL, Thonon-les-Bains, France
| | - Maxime Logez
- Pole R&D ECLA, Le Bourget-du-Lac, France
- INRAE, Aix Marseille Université, RECOVER, Aix-en-Provence, France
- INRAE, UR RIVERLY, Villeurbanne, France
- * E-mail:
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53
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Seeber PA, Epp LS. Environmental
DNA
and metagenomics of terrestrial mammals as keystone taxa of recent and past ecosystems. Mamm Rev 2022. [DOI: 10.1111/mam.12302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Peter A. Seeber
- Limnological Institute University of Konstanz Konstanz Germany
| | - Laura S. Epp
- Limnological Institute University of Konstanz Konstanz Germany
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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] [Key Words] [Grants] [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.
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Affiliation(s)
- Bethany Nordstrom
- School of Biological SciencesThe University of Western AustraliaCrawleyWestern AustraliaAustralia
| | - Nicola Mitchell
- School of Biological SciencesThe University of Western AustraliaCrawleyWestern AustraliaAustralia
| | - Margaret Byrne
- School of Biological SciencesThe University of Western AustraliaCrawleyWestern AustraliaAustralia
- Department of Biodiversity, Conservation and AttractionsBiodiversity and Conservation SciencePerthWestern AustraliaAustralia
| | - Simon Jarman
- School of Biological SciencesThe University of Western AustraliaCrawleyWestern AustraliaAustralia
- UWA Oceans InstituteThe University of Western AustraliaCrawleyWestern AustraliaAustralia
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55
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Robinson JM, Harrison PA, Mavoa S, Breed MF. Existing and emerging uses of drones in restoration ecology. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13912] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jake M. Robinson
- Department of Landscape Architecture The University of Sheffield Sheffield UK
- College of Science and Engineering Flinders University Bedford Park SA Australia
| | - Peter A. Harrison
- ARC Training Centre for Forest Value and School of Natural Sciences University of Tasmania Hobart Australia
| | - Suzanne Mavoa
- Melbourne School of Population and Global Health University of Melbourne Melbourne Vic. Australia
| | - Martin F. Breed
- College of Science and Engineering Flinders University Bedford Park SA Australia
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56
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Gusareva ES, Gaultier NE, Uchida A, Premkrishnan BNV, Heinle CE, Phung WJ, Wong A, Lau KJX, Yap ZH, Koh Y, Ang PN, Putra A, Panicker D, Lee JGH, Neves LC, Drautz-Moses DI, Schuster SC. Short-range contributions of local sources to ambient air. PNAS NEXUS 2022; 1:pgac043. [PMID: 36713329 PMCID: PMC9802476 DOI: 10.1093/pnasnexus/pgac043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 04/07/2022] [Indexed: 06/18/2023]
Abstract
Recent developments in aerobiology have enabled the investigation of airborne biomass with high temporal and taxonomic resolution. In this study, we assess the contributions of local sources to ambient air within a 160,000 m2 tropical avian park (AP). We sequenced and analyzed 120 air samples from seven locations situated 160 to 400 m apart, representing distinct microhabitats. Each microhabitat contained a characteristic air microbiome, defined by the abundance and richness of its airborne microbial community members, supported by both, PCoA and Random Forest analysis. Each outdoor microhabitat contained 1% to 18.6% location-specific taxa, while a core microbiome of 27.1% of the total taxa was shared. To identify and assess local sources, we compared the AP dataset with a DVE reference dataset from a location 2 km away, collected during a year-round sampling campaign. Intersection of data from the two sites demonstrated 61.6% of airborne species originated from local sources of the AP, 34.5% from ambient air background, and only 3.9% of species were specific to the DVE reference site. In-depth taxonomic analysis demonstrated association of bacteria-dominated air microbiomes with indoor spaces, while fungi-dominated airborne microbial biomass was predominant in outdoor settings with ample vegetation. The approach presented here demonstrates an ability to identify local source contributions against an ambient air background, despite the prevailing mixing of air masses caused by atmospheric turbulences.
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Affiliation(s)
| | | | - Akira Uchida
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Balakrishnan N V Premkrishnan
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Cassie E Heinle
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Wen J Phung
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Anthony Wong
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Kenny J X Lau
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Zhei H Yap
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Yanqing Koh
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Poh N Ang
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Alexander Putra
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Deepa Panicker
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jessica G H Lee
- Mandai Nature, 80 Mandai Lake Rd, Singapore 729826, Singapore
| | - Luis C Neves
- Animal Care Department, Mandai Wildlife Group, 80 Mandai Lake Rd, Singapore 729826, Singapore
| | - Daniela I Drautz-Moses
- Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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57
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Lynggaard C, Littlefair JE, Bohmann K, Clare EL. Shunning the scoop: Sidestepping the race to publish. iScience 2022; 25:104080. [PMID: 35496997 PMCID: PMC9042885 DOI: 10.1016/j.isci.2022.104080] [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] [Indexed: 11/21/2022] Open
Abstract
What happens when a researcher finds out that research very similar to their own is already being conducted? What if they find out that the said research is also very close to being published? First, there is probably anxiety and panic. Maybe, there are frantic calls to collaborators. Perhaps Twitter rants about the phenomenon of scooping that plagues all researchers, especially those early-career researchers who often feel they are in a race to get their best work out to the world.
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Affiliation(s)
- Christina Lynggaard
- Section for Evolutionary Genomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Joanne E Littlefair
- School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS London, UK
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Elizabeth L Clare
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3 Canada.,School of Biological and Behavioural Sciences, Queen Mary University of London, E1 4NS London, UK
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58
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Clare EL, Economou CK, Bennett FJ, Dyer CE, Adams K, McRobie B, Drinkwater R, Littlefair JE. Measuring biodiversity from DNA in the air. Curr Biol 2021; 32:693-700.e5. [PMID: 34995488 DOI: 10.1016/j.cub.2021.11.064] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/05/2021] [Accepted: 11/26/2021] [Indexed: 12/22/2022]
Abstract
The crisis of declining biodiversity1 exceeds our current ability to monitor changes in ecosystems. Rapid terrestrial biomonitoring approaches are essential to quantify the causes and consequences of global change. Environmental DNA2 has revolutionized aquatic ecology,3 permitting population monitoring4 and remote diversity assessments matching or outperforming conventional methods of community sampling.3-5 Despite this model, similar methods have not been widely adopted in terrestrial ecosystems. Here, we demonstrate that DNA from terrestrial animals can be filtered, amplified, and then sequenced from air samples collected in natural settings representing a powerful tool for terrestrial ecology. We collected air samples at a zoological park, where spatially confined non-native species allowed us to track DNA sources. We show that DNA can be collected from air and used to identify species and their ecological interactions. Air samples contained DNA from 25 species of mammals and birds, including 17 known terrestrial resident zoo species. We also identified food items from air sampled in enclosures and detected taxa native to the local area, including the Eurasian hedgehog, endangered in the United Kingdom. Our data demonstrate that airborne eDNA concentrates around recently inhabited areas but disperses away from sources, suggesting an ecology to airborne eDNA and the potential for sampling at a distance. Our findings demonstrate the profound potential of air as a source of DNA for global terrestrial biomonitoring.
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Affiliation(s)
- Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK; Department of Biology, York University, Toronto, ON M3J 1P3, Canada.
| | - Chloe K Economou
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Frances J Bennett
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Caitlin E Dyer
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | | | | | - Rosie Drinkwater
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Joanne E Littlefair
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
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