Responses of foraminifera communities to aquaculture‐derived organic enrichment as revealed by environmental DNA metabarcoding

Abstract

Current monitoring methods to assess benthic impacts of marine finfish aquaculture are based on complex biological indices and/or geochemistry data. The former requires benthic macrofauna morpho‐taxonomic characterization that is time‐ and cost‐intensive, while the latter provides rapid assessment of the organic enrichment status of sediments but does not directly measure biotic impacts. In this study, sediment samples were collected from seven stations at six salmon farms in British Columbia, Canada, and analyzed for geochemical parameters and by eDNA metabarcoding to investigate linkages between geochemistry and foraminifera. Sediment texture across farm sites ranged from sand to silty loam, while the maximum sediment pore‐water sulphide concentration at each site ranged from 1,000 to 13,000 μM. Foraminifera alpha diversity generally increased with distance from cage edge. Adonis analyses revealed that farm site explained the most variation in foraminifera community, followed by sediment type, enrichment status, and distance from cage edge. Farm‐specific responses were observed in diversity analyses, taxonomic difference analyses, and correlation analyses. Results demonstrated that species diversity and composition of foraminifera characterized by eDNA metabarcoding generated signals consistent with benthic biodiversity being impacted by finfish farming activities. This substantiates the validity of eDNA metabarcoding for augmenting current approaches to benthic impact assessments by providing more cost‐effective and practicable biotic measures than traditional morpho‐taxonomy. To capitalize on this potential, further work is needed to design a new nomogram that combines eDNA metabarcoding data and geochemistry data to enable accurate monitoring of benthic impacts of fish farming in a time‐ and cost‐efficient way.

Forensics Meets Ecology – Environmental DNA Offers New Capabilities for Marine Ecosystem and Fisheries Research

“…New Zealand's Chinook salmon farms (Oncorhynchus tshawytscha) also showed that high waterflow sites had higher foraminiferal diversity than low waterflow sites, perhaps indicating higher water flow is better for the fish farm ecosystem (Dowle et al, 2015;Pochon et al, 2015). In British Columbia, foraminiferal alpha diversity was lower close to salmon cages compared to more distant reference sites, though beta diversity showed impacts may differ between farms (He et al, 2019). Importantly, shifts in foraminiferal communities were investigated with both eDNA and eRNA, the latter providing a more recent snapshot of the community at large (Dowle et al, 2015;Pochon et al, 2015).…”

“…One area would be to fully develop eDNA for discerning evolutionary change, including for population genetic and epigenetic markers (Zhao et al, 2018;Adams et al, 2019;Sigsgaard et al, 2020). Other avenues may include adding eDNA to suites of ecosystem monitoring tools, such as combining eDNA with water chemistry to obtain a more complete idea of how abiotic and biotic factors are connected within an ecosystem over time and space (He et al, 2019;Zhang, 2019). Already, eRNA has been used in conjunction with eDNA to snapshot biodiversity at shorter time scales, and potentially to understand the biological processes present (Pochon et al, 2017;Zaiko et al, 2018;Cristescu, 2019).…”

“…For example, planktonic and microbial communities may differ depending on differing dissolved organic matter found in an environment (Kujawinski, 2011;Osterholz et al, 2016;Laroche et al, 2018). A healthier, more diverse community correlates with increased dissolved oxygen (He et al, 2019). Flow of water may also influence dissolved oxygen content and, thus, community composition (Pochon et al, 2015).…”

“…Flow of water may also influence dissolved oxygen content and, thus, community composition (Pochon et al, 2015). Besides dissolved oxygen, patterns of biodiversity have also been examined when they correlate with trace metals, for instance, toxic sulfides (He et al, 2019). Indeed, less alpha diversity was found with higher sulfide concentration using eDNA methods (He et al, 2019).…”

“…Besides dissolved oxygen, patterns of biodiversity have also been examined when they correlate with trace metals, for instance, toxic sulfides (He et al, 2019). Indeed, less alpha diversity was found with higher sulfide concentration using eDNA methods (He et al, 2019). Under harsher conditions, more sensitive fauna may not be as supported, and, thus, ecosystem function overall may decline (Lohrer et al, 2012).…”