Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms.

The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3-V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach.

Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture.

Marine sediments contain a high diversity of micro- and macro-organisms which are important in the functioning of biogeochemical cycles. Traditionally, anthropogenic perturbation has been investigated by identifying macro-organism responses along gradients. Environmental DNA (eDNA) analyses have recently been advocated as a rapid and cost-effective approach to measuring ecological impacts and efforts are underway to incorporate eDNA tools into monitoring. Before these methods can replace or complement existing methods, robustness and repeatability of each analytical step has to be demonstrated. One area that requires further investigation is the selection of sediment DNA extraction method. Environmental DNA sediment samples were obtained along a disturbance gradient adjacent to a Chinook (Oncorhynchus tshawytscha) salmon farm in Otanerau Bay, New Zealand. DNA was extracted using four extraction kits (Qiagen DNeasy PowerSoil, Qiagen DNeasy PowerSoil Pro, Qiagen RNeasy PowerSoil Total RNA/DNA extraction/elution and Favorgen FavorPrep Soil DNA Isolation Midi Kit) and three sediment volumes (0.25, 2, and 5 g). Prokaryotic and eukaryotic communities were amplified using primers targeting the 16S and 18S ribosomal RNA genes, respectively, and were sequenced on an Illumina MiSeq. Diversity and community composition estimates were obtained from each extraction kit, as well as their relative performance in established metabarcoding biotic indices. Differences were observed in the quality and quantity of the extracted DNA amongst kits with the two Qiagen DNeasy PowerSoil kits performing best. Significant differences were observed in both prokaryotes and eukaryotes (p < 0.001) richness among kits. A small proportion of amplicon sequence variants (ASVs) were shared amongst the kits (~3%) although these shared ASVs accounted for the majority of sequence reads (prokaryotes: 59.9%, eukaryotes: 67.2%). Differences were observed in the richness and relative abundance of taxonomic classes revealed with each kit. Multivariate analysis showed that there was a significant interaction between "distance" from the farm and "kit" in explaining the composition of the communities, with the distance from the farm being a stronger determinant of community composition. Comparison of the kits against the bacterial and eukaryotic metabarcoding biotic index suggested that all kits showed similar patterns along the environmental gradient. Overall, we advocate for the use of Qiagen DNeasy PowerSoil kits for use when characterizing prokaryotic and eukaryotic eDNA from marine farm sediments. We base this conclusion on the higher DNA quality values and richness achieved with these kits compared to the other kits/amounts investigated in this study. The additional advantage of the PowerSoil Kits is that DNA extractions can be performed using an extractor robot, offering additional standardization and reproducibility of results.

Spatial and temporal dynamics in macrobenthos during recovery from salmon farm induced organic enrichment: when is recovery complete?

This study documents eight years of benthic recovery at a highly impacted salmon farm. Substantial recovery occurred in the first 2 years, and was assessed to be complete after ∼5 years. However, minor differences were still evident, along with some on-going benthic instability, attributable to medium-scale spatial movements and successional patterns of macrobenthos. Quantifying the endpoint of 'recovery' proved challenging due to: lack of a widely accepted definition, inherent variability in recovering sediments, differing trajectories of impact and reference sites, and statistical challenges. More complex biotic indices and metrics incorporating multiple variables were the most robust indicators. Statistical tests for 'parallelism' in the trajectories of Cage and Reference sites proved useful, but results were contingent upon how the method was applied, and should therefore be used in conjunction with data-visualisation methods. The study highlights the importance of a predetermined recovery endpoint, and using multiple indicators and a weight-of-evidence assessment approach.

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.