Plant–animal interactions in the era of environmental DNA (eDNA)—A review

Abstract

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 the 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, nondestructive approach for biodiversity monitoring, which could help to elucidate PAI. Here, we aim to provide an overall discussion on the potential of using eDNA to study PAI. We assessed the existing literature on this subject from 2009 to 2021 using a freely accessible web search tool. The search was conducted by using keywords involving eDNA and PAI, including both speciesspecific and metabarcoding approaches, recovering 43 studies. We summarized the advantages and current limitations of such approaches, and we outline research priorities to improve future eDNA-based methods for PAI analysis. Among the 43 studies identified using eDNA to measure PAI such as pollination, herbivory, mutualistic, and parasitic relationships, they have often identified higher taxonomic diversity in several direct comparisons with DNA-based gut/bulk sampling and conventional survey methods. Research needs include the following: better understanding of the influencing factors of eDNA detection involved in PAI (e.g., eDNA degradation, origin, and types), methodological standardization (sampling methods and primer development), and more inclusive sequence reference databases. If these research priorities are addressed, it will have a significant impact to enable PAI biodiversity monitoring with eDNA. In the future, the implementation of eDNA methods to study PAI can particularly benefit the scalability of environmental biomonitoring surveys that are imperative for ecosystem health assessments.

Temporal collections to study invasion biology

“…Methods to quantify species interactions at the trait or organismal level can, however, be laborious and typically permit the study of only a small number of species (Banerjee et al, 2022) interaction networks in complex biological communities using DNA (e.g., Banerjee et al, 2022;Valentini et al, 2009). Importantly, this technology can also be applied to ancient and historical samples.…”

“…Methods to quantify species interactions at the trait or organismal level can, however, be laborious and typically permit the study of only a small number of species (Banerjee et al., 2022). As an alternative, studies have highlighted the possibility of reconstructing interaction networks in complex biological communities using DNA (e.g., Banerjee et al., 2022; Valentini et al., 2009). Importantly, this technology can also be applied to ancient and historical samples.…”

Insights into Ecological & Evolutionary Processes via community metabarcoding

“…Another major area of study examined interaction networks, and how the properties of the networks might reflect the health and functioning of both macro‐organismal (Banerjee et al., 2022) and micro‐organismal (Peixoto et al., 2022) communities. Metabarcoding provides an ideal opportunity to examine questions relating to interaction networks and can provide quantitative assessment of resilience to perturbation.…”

Opportunities and inherent limits of using environmental DNA for population genetics

“…DNA retrieved from environmental or community samples is already extensively used for a wide range of ecological applications (Deiner et al, 2017; Leray & Knowlton, 2016; Taberlet, Coissac, Hajibabaei, & Rieseberg, 2012; Taberlet, Coissac, Pompanon, et al, 2012). These new DNA templates (Lacoursière‐Roussel & Deiner, 2021) have been broadly applied in community ecology and functional ecology to answer questions regarding biodiversity patterns (e.g., Blackman et al, 2021; Lacoursière‐Roussel et al, 2018; Zenker et al, 2020; Zinger et al, 2019), species' range dynamics (e.g., Hobbs et al, 2019; Valsecchi et al, 2022), spatio‐temporal turn‐over in species composition (e.g., Bálint et al, 2018; Bista et al, 2017; Chain et al, 2016), or trophic networks (e.g., Banerjee et al, 2022; Blackman et al, 2022; Carroll et al, 2019). Additionally, eDNA has been used in conservation biology, for instance for the monitoring of rare or endangered species (e.g., Burgoa et al, 2020; Niemiller et al, 2018), or for the detection of invasive species (e.g., Couton et al, 2022; Zaiko et al, 2018), as well as for the calculation of biotic indices (e.g., Brantschen et al, 2021; Pawlowski et al, 2018).…”