Pritam Banerjee1, 2, Kathryn A. Stewart3, Caterina M. Antognazza4, Ingrid V. Bunholi5, Kristy Deiner6, Matthew A. Barnes7, Santanu Saha8, Héloïse Verdier9, Hideyuki Doi10, Jyoti Prakash Maity2, Michael W.Y. Chan1, Chien Yen Chen2*1Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Ming-Shung, Chiayi County 62102, Taiwan2Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Ming-Shung, Chiayi County 62102, Taiwan.3 Institute of Environmental Science, Leiden University, 2333 CC Leiden, The Netherlands4 Department of Theoretical and Applied Science, University of Insubria, Via J.H. Dunant, 3, 21100, Varese, Italy5 Department of Biology, Indiana State University, Terre Haute, IN 47809, USA6 Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, CH-8092 Zurich, Switzerland7 Department of Natural Resources Management, Texas Tech University, Lubbock, TX USA8Post Graduate Department of Botany, Bidhannagar College, Salt Lake City, Kolkata 700064, India9Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France10Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, JapanAbstract Plant-animal interactions (PAI) represent major channels of energy transfer through ecosystems, where both positive and antagonistic interactions simultaneously contribute to ecosystem functioning. Monitoring PAI therefore increases understanding of environmental health, integrity and functioning, and studying complex interactions through accurate, cost-effective sampling can aid in the management of detrimental anthropogenic impacts. Environmental DNA (eDNA)-based monitoring represents an increasingly common, non-destructive approach for biomonitoring, which could help to elucidate PAI. Here, we focused our foundation to discuss the potential of eDNA in studying PAI on the literature existing from 2009 to 2021 using a freely accessible web search tool. The search was conducted by using key words involving eDNA and PAI, including both species-specific and metabarcoding approaches, recovering 43 studies. We summarise advantages and current limitations of such approaches, and we offer research priorities that will potentially improve future eDNA-based methods for PAI analysis. Our review has demonstrated that numerous studies exist using eDNA to identify PAI (e.g., pollination, herbivory, mutualistic, parasitic relationships), and although eDNA-based PAI studies remain in their infancy, to date they have identified higher taxonomic diversity in several direct comparisons to DNA-based gut/bulk sampling and conventional survey methods. Research into the influencing factors of eDNA detection involved in PAI (e.g., origin and types, methodological standardization, database limitations, validation with conventional surveys, and existing ecological models) will benefit the growth of this application. Thus, implementation of eDNA methods to study PAI can particularly benefit environmental biomonitoring surveys that are imperative for biodiversity health assessments.

Corresponding author*: [email protected] and [email protected]

In a recent paper, “Environmental DNA: What’s behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring”, Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra-organismal DNA from macro-organisms. We agree with this view. However, we are concerned that their proposed two-level terminology specifying sampling environment and targeted taxa is overly simplistic and might hinder rather than improve clear communication about environmental DNA and its use in biomonitoring. Not only is this terminology based on categories that are often difficult to assign and uninformative, but it ignores what is in our opinion the most important distinction within eDNA: the type of DNA (organismal or extra-organismal) from which ecological interpretations are derived.

The biodiverse Neotropical ecoregion remains insufficiently assessed, poorly managed, and threatened by unregulated human activities. Novel, rapid and cost-effective DNA-based approaches are valuable to improve understanding of the biological communities and for biomonitoring in remote areas. Here, we evaluate the potential of environmental DNA (eDNA) metabarcoding for assessing the structure and distribution of fish communities by analysing sediments and water from 11 locations along the Jequitinhonha River catchment (Brazil). Each site was sampled twice, before and after a major rain event in a five-week period and fish diversity was estimated using high-through-put sequencing of 12S rRNA amplicons. In total, 252 Molecular Operational Taxonomic Units (MOTUs) and 34 fish species were recovered, including endemic, introduced, and previously unrecorded species for this basin. Spatio-temporal variation of fish assemblages was detected, richness during the first campaign was nearly twice as high as in the second sampling round; though peaks of diversity were primarily associated with only four locations. No correlation between β-diversity and longitudinal distance or presence of dams was detected, but low species richness observed at sites located near dams indicates that these anthropogenic barriers might have an impact on local fish diversity. Unexpectedly high α-diversity levels recorded at the river mouth suggest that these sections should be further evaluated as putative “eDNA reservoirs” for rapid monitoring. By uncovering spatio-temporal changes, unrecorded biodiversity components, and putative anthropogenic impacts on fish assemblages, we further strengthen the potential of eDNA metabarcoding as a biomonitoring tool, especially in regions often neglected or difficult to access.