A validated bacterial index for monitoring New Zealand's salmon farms using environmental DNA

The health of marine benthic ecosystems around New Zealand's salmon farms is currently monitored using an Enrichment State (ES) index under existing Best Management Practice guidelines. This index includes microscopic assessment of macrobenthic infauna which requires taxonomic expertise, is time consuming and expensive. Supported by a range of private/government agencies and industry partners, we have developed and tested the robustness of bacterial, eukaryotic and multi-trophic Metabarcoding Biotic Indices (b-MBI, e-MBI and mt-MBI, respectively) using a molecular Eco-Group approach. The indices were calculated via automatic computer pipelines using data collected over a period of seven years from a range of high- and low-flow salmon farms from three distinct regions in New Zealand and were validated against the established ES index. All MBIs yielded strong and highly significant relationships with Overall ES. The strongest relationship (R2 > 0.8) and narrowest confidence intervals were obtained with b-MBI. This means the b-MBI offers unprecedented precision for determining subtle changes along enrichment gradients, constituting a valuable asset for triggering appropriated management responses and improving compliance. The affordability and versatility of the b-MBI tool suggests that it could be immediately integrated into current monitoring strategies as the primary benthic assessment tool in New Zealand.