Plant-animal interactions in the era of environmental DNA (eDNA) – a review

Banerjee, Pritam; Stewart, Kathryn A.; Antognazza, Caterina M.; Bunholi, Ingrid Vasconcellos; Deiner, Kristy; Barnes, Matthew A.; Saha, Santanu; Verdier, Héloïse; Doi, Hideyuki; Maity, Jyoti Prakash; Chan, Michael W.Y.; Chen, Chien‐Yen

doi:10.22541/au.162626116.66217318/v1

Cited by 3 publications

(4 citation statements)

References 68 publications

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“…Tracking plant community change is vital, because these communities often represent the foundation of an ecosystem (Wilsey and Potvin, 2000). Currently, botanical eDNA analyses have been useful for detecting plant species in a variety of environments (i.e., aquatic, ancient, contemporary sediment, airborne) of different ages, while also shedding light on environmental conditions and plant-animal interactions (Banerjee et al, 2022b). While several challenges remain for the promise of botanical eDNA analysis to be fully realized, it has clearly emerged as a viable and important tool for plant ecologists.…”

Section: Discussionmentioning

confidence: 99%

“…Botanical eDNA from a variety of sources has been leveraged to understand plant–animal interactions. Banerjee et al (2022) assessed the applications of eDNA for elucidating plant–animal interactions, highlighting studies of mutualism (Rasmussen et al, 2021), pollination (Thomsen and Sigsgaard 2019; Evans and Kitson 2020), frugivory (Monge et al, 2020), parasitism (Thomsen and Sigsgaard, 2019; Miller et al, 2021), dispersal (Harrer and Levi 2018), and herbivory (de Sousa et al, 2019) for plant species through mammals, birds, and insects. Two of the most‐studied aspects include pollinators and feces.…”

Section: Organism‐derived Samples For Botanical Ednamentioning

confidence: 99%

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Environmental DNA as an emerging tool in botanical research

Johnson

Freeland

Parducci

et al. 2023

American J of Botany

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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. K E Y W O R D Sancient botanical eDNA, aquatic botanical eDNA, botanical eDNA, eDNA, organism derived botanical eDNA, review

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Section: Discussionmentioning

confidence: 99%

Section: Organism‐derived Samples For Botanical Ednamentioning

confidence: 99%

Environmental DNA as an emerging tool in botanical research

Johnson

Freeland

Parducci

et al. 2023

American J of Botany

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“…Environmental DNA (eDNA) methods focus on the detection and monitoring of sequenced nucleic acid data extracted from environmental samples and can be classed as a form of environmental genomics. They have been successfully used to survey fish biodiversity [ 22 ], invasive species [ 23 ], detect signature bacteria associated with contaminants [ 24 ], assess environmental health and status using indicator organisms [ 25 , 26 ], for species monitoring [ 23 ], exploring trophic interactions [ 27 ] through to investigating broad biogeographic patterns [ 28 ].…”

Section: Environmental Monitoringmentioning

confidence: 99%

Omics-based ecosurveillance for the assessment of ecosystem function, health, and resilience

Beale

Jones

Bose

et al. 2022

Emerging Topics in Life Sciences

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Current environmental monitoring efforts often focus on known, regulated contaminants ignoring the potential effects of unmeasured compounds and/or environmental factors. These specific, targeted approaches lack broader environmental information and understanding, hindering effective environmental management and policy. Switching to comprehensive, untargeted monitoring of contaminants, organism health, and environmental factors, such as nutrients, temperature, and pH, would provide more effective monitoring with a likely concomitant increase in environmental health. However, even this method would not capture subtle biochemical changes in organisms induced by chronic toxicant exposure. Ecosurveillance is the systematic collection, analysis, and interpretation of ecosystem health-related data that can address this knowledge gap and provide much-needed additional lines of evidence to environmental monitoring programs. Its use would therefore be of great benefit to environmental management and assessment. Unfortunately, the science of ‘ecosurveillance’, especially omics-based ecosurveillance is not well known. Here, we give an overview of this emerging area and show how it has been beneficially applied in a range of systems. We anticipate this review to be a starting point for further efforts to improve environmental monitoring via the integration of comprehensive chemical assessments and molecular biology-based approaches. Bringing multiple levels of omics technology-based assessment together into a systems-wide ecosurveillance approach will bring a greater understanding of the environment, particularly the microbial communities upon which we ultimately rely to remediate perturbed ecosystems.

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“…Additionally, eDNA metabarcoding also allows us to figure out the trophic interaction relationships using the DNA from stomach content, feces samples, and even from the surface of organisms etc. [ 39 , 104 , 105 , 106 ]. Thus, eDNA-based methods provide information about trophic level interactions which is strongly needed for understanding more complex ecology where conventional methods failed.…”

Section: Application Of Edna In Conservation Biologymentioning

confidence: 99%

Reinforcement of Environmental DNA Based Methods (Sensu Stricto) in Biodiversity Monitoring and Conservation: A Review

Banerjee

Dey

Antognazza

et al. 2021

Biology

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Recently developed non-invasive environmental DNA-based (eDNA) techniques have enlightened modern conservation biology, propelling the monitoring/management of natural populations to a more effective and efficient approach, compared to traditional surveys. However, due to rapid-expansion of eDNA, confusion in terminology and collection/analytical pipelines can potentially jeopardize research progression, methodological standardization, and practitioner adoption in several ways. Present investigation reflects the developmental progress of eDNA (sensu stricto) including highlighting the successful case studies in conservation management. The eDNA technique is successfully relevant in several areas of conservation research (invasive/conserve species detection) with a high accuracy and authentication, which gradually upgrading modern conservation approaches. The eDNA technique related bioinformatics (e.g., taxon-specific-primers MiFish, MiBird, etc.), sample-dependent methodology, and advancement of sequencing technology (e.g., oxford-nanopore-sequencing) are helping in research progress. The investigation shows that the eDNA technique is applicable largely in (i) early detection of invasive species, (ii) species detection for conservation, (iii) community level biodiversity monitoring, (iv) ecosystem health monitoring, (v) study on trophic interactions, etc. Thus, the eDNA technique with a high accuracy and authentication can be applicable alone or coupled with traditional surveys in conservation biology. However, a comprehensive eDNA-based monitoring program (ecosystem modeling and function) is essential on a global scale for future management decisions.

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Plant-animal interactions in the era of environmental DNA (eDNA) – a review

Cited by 3 publications

References 68 publications

Environmental DNA as an emerging tool in botanical research

Environmental DNA as an emerging tool in botanical research

Omics-based ecosurveillance for the assessment of ecosystem function, health, and resilience

Reinforcement of Environmental DNA Based Methods (Sensu Stricto) in Biodiversity Monitoring and Conservation: A Review

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