Nigel B. Keeley

Accurate assessment of the impact of salmon farming on benthic sediment enrichment using foraminiferal metabarcoding

Assessing the environmental impact of salmon farms on benthic systems is traditionally undertaken using biotic indices derived from microscopic analyses of macrobenthic infaunal (MI) communities. In this study, we tested the applicability of using foraminiferal-specific high-throughput sequencing (HTS) metabarcoding for monitoring these habitats. Sediment samples and physico-chemical data were collected along an enrichment gradient radiating out from three Chinook salmon (Oncorhynchus tshawytscha) farms in New Zealand. HTS of environmental DNA and RNA (eDNA/eRNA) resulted in 1,875,300 sequences that clustered into 349 Operational Taxonomic Units. Strong correlations were observed among various biotic indices calculated from MI data and normalized fourth-root transformed HTS data. Correlations were stronger using eRNA compared to eDNA data. Quantile regression spline analyses identified 12 key foraminiferal taxa that have potential to be used as bioindicator species. This study demonstrates the huge potential for using this method for biomonitoring of fish-farming and other marine industrial activities.

Novel observations of benthic enrichment in contrasting flow regimes with implications for marine farm monitoring and management

We examine macrofaunal and physico-chemical responses to organic enrichment beneath salmon farms in contrasting flow environments, and reveal pronounced flow-related differences in the magnitude and spatial extent of effects. Total macrofaunal abundances at high flow sites were nearly an order of magnitude greater than at comparable low flow sites, representing a significant benthic biomass. These very high abundances occurred in conjunction with moderate-to-high species richness, and were evident in the absence of appreciable organic matter accumulation. Biological responses to increasing sulfide were variable; however a significant biological threshold was evident at 1500 μM. Macrofaunal responses at high flow sites differed substantially from the Pearson-Rosenberg model. The atypical ecological conditions were attributed to (i) limited accumulation of fine sediments, (ii) maintenance of aerobic conditions in near-surface sediments, and (iii) an abundant food supply. Thus, enhanced resilience to organic waste at well-flushed sites appears related to both biological and physical processes.