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Hassan S, Sabreena, Ganiee SA, Yaseen A, Zaman M, Shah AJ, Ganai BA. Unraveling the potential of environmental DNA for deciphering recent advances in plant-animal interactions: a systematic review. PLANTA 2023; 258:117. [PMID: 37957258 DOI: 10.1007/s00425-023-04267-0] [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: 05/29/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023]
Abstract
MAIN CONCLUSION Environmental DNA-based monitoring provides critical insights for enhancing our understanding of plant-animal interactions in the context of worldwide biodiversity decrease for developing a global framework for effective plant biodiversity conservation. To understand the ecology and evolutionary patterns of plant-animal interactions (PAI) and their pivotal roles in ecosystem functioning advances in molecular ecology tools such as Environmental DNA (eDNA) provide unprecedented research avenues. These methods being non-destructive in comparison to traditional biodiversity monitoring methods, enhance the discernment of ecosystem health, integrity, and complex interactions. This review intends to offer a systematic and critical appraisal of the prospective of eDNA for investigating PAI. The review thoroughly discusses and analyzes the recent reports (2015-2022) employing preferred reporting items for systematic reviews and meta-analyses (PRISMA) to outline the recent progression in eDNA approaches for elucidating PAI. The current review envisages that eDNA has a significant potential to monitor both plants and associated cohort of prospective pollinators (avian species and flowering plants, bees and plants, arthropods and plants, bats and plants, etc.). Furthermore, a brief description of the factors that influence the utility and interpretation of PAI eDNA is also presented. The review establishes that factors such as biotic and abiotic, primer selection and taxonomic resolution, and indeterminate spatio-temporal scales impact the availability and longevity of eDNA. The study also identified the limitations that influence PAI detection and suggested possible solutions for better execution of these molecular approaches. Overcoming these research caveats will augment the assortment of PAI analysis through eDNA that could be vital for ecosystem health and integrity. This review forms a critical guide and offers prominent insights for ecologists, environmental managers and researchers to assess and evaluate plant-animal interaction through environmental DNA.
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Affiliation(s)
- Shahnawaz Hassan
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India.
| | - Sabreena
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Shahid Ahmad Ganiee
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Aarif Yaseen
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Muzafar Zaman
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Abdul Jalil Shah
- Department of Pharmaceutical Sciences, University of Kashmir, Srinagar, 190006, India
| | - Bashir Ahmad Ganai
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India.
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Nolan N, Hayward MW, Klop-Toker K, Mahony M, Lemckert F, Callen A. Complex Organisms Must Deal with Complex Threats: How Does Amphibian Conservation Deal with Biphasic Life Cycles? Animals (Basel) 2023; 13:ani13101634. [PMID: 37238064 DOI: 10.3390/ani13101634] [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: 04/14/2023] [Revised: 05/08/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
The unprecedented rate of global amphibian decline is attributed to The Anthropocene, with human actions triggering the Sixth Mass Extinction Event. Amphibians have suffered some of the most extreme declines, and their lack of response to conservation actions may reflect challenges faced by taxa that exhibit biphasic life histories. There is an urgent need to ensure that conservation measures are cost-effective and yield positive outcomes. Many conservation actions have failed to meet their intended goals of bolstering populations to ensure the persistence of species into the future. We suggest that past conservation efforts have not considered how different threats influence multiple life stages of amphibians, potentially leading to suboptimal outcomes for their conservation. Our review highlights the multitude of threats amphibians face at each life stage and the conservation actions used to mitigate these threats. We also draw attention to the paucity of studies that have employed multiple actions across more than one life stage. Conservation programs for biphasic amphibians, and the research that guides them, lack a multi-pronged approach to deal with multiple threats across the lifecycle. Conservation management programs must recognise the changing threat landscape for biphasic amphibians to reduce their notoriety as the most threatened vertebrate taxa globally.
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Affiliation(s)
- Nadine Nolan
- Conservation Science Research Group, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Matthew W Hayward
- Conservation Science Research Group, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Kaya Klop-Toker
- Conservation Science Research Group, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Michael Mahony
- Conservation Science Research Group, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Frank Lemckert
- Eco Logical Australia Pty Ltd., Perth, WA 6000, Australia
| | - Alex Callen
- Conservation Science Research Group, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
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Banerjee P, Stewart KA, Dey G, Antognazza CM, Sharma RK, Maity JP, Saha S, Doi H, de Vere N, Chan MWY, Lin PY, Chao HC, Chen CY. Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review. AOB PLANTS 2022; 14:plac031. [PMID: 35990516 PMCID: PMC9389569 DOI: 10.1093/aobpla/plac031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) analysis has recently transformed and modernized biodiversity monitoring. The accurate detection, and to some extent quantification, of organisms (individuals/populations/communities) in environmental samples is galvanizing eDNA as a successful cost and time-efficient biomonitoring technique. Currently, eDNA's application to plants remains more limited in implementation and scope compared to animals and microorganisms. This review evaluates the development of eDNA-based methods for (vascular) plants, comparing its performance and power of detection with that of traditional methods, to critically evaluate and advise best-practices needed to innovate plant biomonitoring. Recent advancements, standardization and field applications of eDNA-based methods have provided enough scope to utilize it in conservation biology for numerous organisms. Despite our review demonstrating only 13% of all eDNA studies focus on plant taxa to date, eDNA has considerable environmental DNA has considerable potential for plants, where successful detection of invasive, endangered and rare species, and community-level interpretations have provided proof-of-concept. Monitoring methods using eDNA were found to be equal or more effective than traditional methods; however, species detection increased when both methods were coupled. Additionally, eDNA methods were found to be effective in studying species interactions, community dynamics and even effects of anthropogenic pressure. Currently, elimination of potential obstacles (e.g. lack of relevant DNA reference libraries for plants) and the development of user-friendly protocols would greatly contribute to comprehensive eDNA-based plant monitoring programs. This is particularly needed in the data-depauperate tropics and for some plant groups (e.g., Bryophytes and Pteridophytes). We further advocate to coupling traditional methods with eDNA approaches, as the former is often cheaper and methodologically more straightforward, while the latter offers non-destructive approaches with increased discrimination ability. Furthermore, to make a global platform for eDNA, governmental and academic-industrial collaborations are essential to make eDNA surveys a broadly adopted and implemented, rapid, cost-effective and non-invasive plant monitoring approach.
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Affiliation(s)
- Pritam Banerjee
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Kathryn A Stewart
- Institute of Environmental Science, Leiden University, 2333 CC Leiden, The Netherlands
| | - Gobinda Dey
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Caterina M Antognazza
- Department of Theoretical and Applied Science, University of Insubria, Via J.H. Dunant, 3, 21100 Varese, Italy
| | - Raju Kumar Sharma
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Jyoti Prakash Maity
- Department of Chemistry, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar, Odisha 751024, India
| | - Santanu Saha
- Post Graduate Department of Botany, Bidhannagar College, Salt Lake City, Kolkata 700064, India
| | - Hideyuki Doi
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Natasha de Vere
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K
| | - Michael W Y Chan
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Pin-Yun Lin
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Hung-Chun Chao
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
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Evaluating eDNA for Use within Marine Environmental Impact Assessments. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10030375] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In this review, the use of environmental DNA (eDNA) within Environmental Impact Assessment (EIA) is evaluated. EIA documents provide information required by regulators to evaluate the potential impact of a development project. Currently eDNA is being incorporated into biodiversity assessments as a complementary method for detecting rare, endangered or invasive species. However, questions have been raised regarding the maturity of the field and the suitability of eDNA information as evidence for EIA. Several key issues are identified for eDNA information within a generic EIA framework for marine environments. First, it is challenging to define the sampling unit and optimal sampling strategy for eDNA with respect to the project area and potential impact receptor. Second, eDNA assay validation protocols are preliminary at this time. Third, there are statistical issues around the probability of obtaining both false positives (identification of taxa that are not present) and false negatives (non-detection of taxa that are present) in results. At a minimum, an EIA must quantify the uncertainty in presence/absence estimates by combining series of Bernoulli trials with ad hoc occupancy models. Finally, the fate and transport of DNA fragments is largely unknown in environmental systems. Shedding dynamics, biogeochemical and physical processes that influence DNA fragments must be better understood to be able to link an eDNA signal with the receptor’s state. The biggest challenge is that eDNA is a proxy for the receptor and not a direct measure of presence. Nonetheless, as more actors enter the field, technological solutions are likely to emerge for these issues. Environmental DNA already shows great promise for baseline descriptions of the presence of species surrounding a project and can aid in the identification of potential receptors for EIA monitoring using other methods.
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