Digital PCR assays quantify bacterial bioindicators across environmental quality gradients in salmon aquaculture sediments

Organic enrichment beneath marine finfish aquaculture installations alters benthic ecosystem structure and sediment biogeochemistry, creating pronounced environmental gradients that require effective and scalable monitoring tools. High-throughput sequencing has revealed consistent associations between benthic bacterial communities and organic enrichment beneath salmon farms, yet regulatory implementation remains constrained by the compositional nature of sequencing data. Relative read abundances do not directly demonstrate whether candidate indicator taxa undergo absolute population shifts along impact gradients, limiting their deployment as quantitative decision-support tools. Here, we test whether sequencing-derived bacterial bioindicators reflect measurable abundance changes under real-world aquaculture conditions. Bacterial amplicon sequence variants (ASVs) previously associated with contrasting levels of sediment enrichment were targeted using ASV-specific digital PCR (dPCR) assays and quantified across multiple Scottish salmon farms spanning a gradient of ecological quality defined by the Infaunal Quality Index. Enrichment-associated taxa showed significant declines in absolute copy number as organic enrichment decreased, whereas a reference-associated indicator signature increased toward less enriched environments. These abundance-quality relationships were consistent across farms and aligned with redox-structured sediment succession, indicating that sequencing-derived indicators correspond to genuine population shifts rather than purely relative community dynamics. Targeted dPCR thereby provides a practical bridge between microbial community profiling and quantitative marine aquaculture impact assessment. Beyond relative abundance patterns, targeted bacterial indicators offer a transferable, mechanistically grounded approach for strengthening benthic marine monitoring frameworks. • Digital PCR quantified bacterial indicators of salmon farm organic enrichment. • Absolute copy numbers quantitatively reflect gradients of aquaculture impact. • Indicator abundances align with regulatory Infaunal Quality Index classifications. • Responses are consistent across independent farms along enrichment gradients. • Targeted dPCR provides quantitative framework for benthic monitoring.