Network-Based Biomonitoring: Exploring Freshwater Food Webs With Stable Isotope Analysis and DNA Metabarcoding

Abstract

Compson et al. Biomonitoring With DNA-Based Food Webs and food web size and complexity (assessed from heuristic food webs). Collectively, these analyses indicate that trait-based networks have properties that correspond to those of actual food webs, supporting the routine adoption of food web metrics for ecosystem biomonitoring.

Molecular Ecological Network Analyses: An Effective Conservation Tool for the Assessment of Biodiversity, Trophic Interactions, and Community Structure

“…Studies of multitrophic interactions and ecological network analysis are increasingly being used to monitor biodiversity and trophic interactions (Compson et al, 2019), but the fundamental assessment and quantification of these interactions is challenging. We assembled a real-world, high-resolution multitrophic food web (Figure 3), demonstrating that molecular ecological network analyses (MENA) from readily available fecal environmental DNA (eDNA) provides a powerful assessment of an ecosystem.…”

“…Only recently has molecular network analysis been applied to the assessment of ecological systems. Metabarcoding studies in this context have focused on varying scales: the diet of European hake (Riccioni et al, 2018); coral reef fish (Casey et al, 2019); freshwater ecosystems (Compson et al, 2019); aquatic macroinvertebrates (Bush et al, 2019); and bat (Clare et al, 2019), forest (Evans et al, 2016), and herbivore (Kartzinel et al, 2015) communities. However, to the best of our knowledge (see Sousa et al, 2019 for a review), to date a metabarcoding study has yet to use fecal eDNA to reconstruct ecological networks and unravel trophic interactions among carnivores, omnivores, and herbivores within a terrestrial mammal community to inform biodiversity assessments.…”

Key Questions for Next-Generation Biomonitoring

“…Similar kits are being developed for use by members of the public to monitor local plant and human disease prevalence and the status of pests in agricultural fields and waterways. For policy, NGB will not only achieve what classical biomonitoring currently does, such as by reporting on agreed classic indicator species or assemblages, but will also allow the inference and prediction of higher level ecosystem properties (Evans et al, 2016;Compson et al, 2019). In principle, NGB could facilitate remedial decision-making, allowing its accompanying management to be trialed before it is implemented.…”

Metabarcoding From Microbes to Mammals: Comprehensive Bioassessment on a Global Scale

“…In their simplest form, networks created from DNA metabarcoding taxonomic lists are co-occurrence networks, and like any co-occurrence network they do not measure actual connections among species; rather, they depict the possible set of interacting species in graphical form. Co-occurrence networks can be refined through filtering based on mathematical rules [e.g., probability of interaction (Morales-Castilla et al, 2015)], known phylogenetic relationships (Morales-Castilla et al, 2015), or trait matching (Compson et al, 2018(Compson et al, , 2019. By automating construction of networks and food webs, they can be linked to large biomonitoring datasets, providing new opportunities for complex, diagnostic development that will hopefully be more targeted and predictive than traditional bioindicators (Makiola et al, 2020) and, because networks provide taxa-free biodiversity estimates, will provide the potential for global indicator development [e.g., Essential Biodiversity Variables (Kissling et al, 2018)].…”