A Temporally Dynamic Gut Microbiome in Atlantic Salmon During Freshwater Recirculating Aquaculture System (RAS) Production and Post-seawater Transfer

Atlantic salmon aquaculture is undergoing an expansion of land-based recirculating systems (RAS), especially for freshwater (FW) stages production. Juvenile undergo parr-smolt transformation, also known as smoltification and become pre-adapted to tolerate seawater (SW). One aspect requiring study the development microbial communities during this time, in RAS systems. Here we analyzed temporal changes microbiome associated with intestine smolt production a commercial facility followed same cohort fish post-seawater transfer (SWT), using 16S rRNA gene sequencing. Microbial diversity richness showed increase over time across FW production, but declined sharply significantly 1-week post-SWT before re-establishing itself completely different community structure after 4 weeks. Core taxa could be assigned three distinct categories; (1) omnipresent, (2) salinity specific, or (3) transient. By including diet water samples analyses, classified true core host, those diet, transient cores tank water. The rising trend observed may consequence organic load while dominance Vibrionaceae attributed higher temperatures maintained above average natural post-SWT. Functional analysis suggests modulation metabolic pathways post-SWT, downstream impacts on growth health setting remain elucidated. A deeper understanding interplay between composition functionality can play role optimizing performance tightly regulated