The functional dynamics within bacterial communities are increasingly recognized as crucial to the sustainability and health of cultured aquatic species . I nterest in microbiome analysis has soared in response and , consequently, a number of studies have examined the bacterial composition of land- and sea-based aquaculture sites. The majority of investigat ions use NGS platforms to sequence the hypervariable V3/V4 region of the bacterial 16s rRNA gene , providing identification and relative abundance data for all genera . While the V3/V 4 region can also provide species-level differentiation in some cases , the necessary resolution for accurately defining closely related species or detecting uncommon or recently identified genera is lacking. Bacterial metabolism, growth strategies, and capacity for beneficial or antagonistic microbial interactions are broadly species dependent. The work presented here represents a compilation of data from our custom full-length (FL) 16S rRNA gene sequencing platform and database. We describe species-specific bacterial functions related to recirculating aquaculture system (RAS) environmental management and the monitoring of open-water sites, including: nitrification, the metabolism of eutrophication-relevant nutrients , and off-flavour chemical or cyanobacterial toxin production.
We find that full-length 16S rRNA identification of important bacterial groups such as Cyanobacteria is key to avoid overrepresenting production risk from benign species and for the selection of appropriate management methods of undesirable species . Furthermore, we have identified bacterial storage and subsequent release of nutrients as a hidden risk for water quality management and reporting in open water shellfish sites. Lastly, the prediction of biofilter establishment, maturation, function, and tolerance to change is poorly represented at a genus level, particularly amongst nitrite-oxidizing bacteria, such as Nitrospira . These examples and others will display the scientific value of full-length 16S rRNA sequencing in environmental surveillance of land and open water aquaculture sites and, therefore, critical management decisions for all aquaculture producers.