Rapid Nanopore cloud-based monitoring and analysis of commercial aquaculture microbiomes

Aquaculture stands as a crucial component of global food security and sustainable development, yet it faces challenges in disease management and ecological balance. Here, we present a novel approach using rapid nanopore sequencing, cloud-based monitoring and analysis for aquaculture microbiomes. Our study aimed to perform untargeted, agnostic biological monitoring of a commercial aquaculture facility, emphasizing rapidity, specificity, and sensitivity. We employed Oxford Nanopore Technologies’ MinION sequencer with an optimised rapid sequencing protocol, enabling on-site operation by facility staff. Three separate sampling efforts resulting in thirteen sequencing runs were conducted, revealing a representative microbiome baseline across aquaculture system components within a 24-hour timeframe. Our results demonstrated the feasibility of rapid monitoring and analysis of nitrogen-associated organisms, essential for same-day water quality management and infection event detection. Notably, Moving Bed Biofilm Reactor (MBBR media) or BioDiscs exhibited the highest diversity and abundance of nitrogen-associated organisms, confirming a pivotal role in nitrification processes. Critically, our approach addressed challenges in metagenomic sample purity and false positives, offering insights for future refinement and application. Our findings underscore the potential of rapid sequencing technologies in enhancing aquaculture management and sustainability. This approach holds promise for mitigating disease outbreaks, optimizing productivity, and advancing ecological balance in aquaculture systems.