Optimizing Microbial Management in Live Food: Bio-Encapsulation of Functional Microorganisms in Rotifers and Artemia

Live food organisms like rotifers and Artemia are essential in early larval rearing but often act as vectors for opportunistic and pathogenic bacteria. This study evaluated multiple strategies to bio-encapsulate functional microorganisms (Sanolife MIC-F) and control bacterial flora during live food production. Rotifers were treated with probiotic Bacillus strains combined with a natural Vibrio controller (Sanocare SURE) at concentrations ranging from 2 × 10⁷ to 2 × 10⁸ CFU ml⁻¹, with or without daily tank dosing and germination. Artemia hatched from D-FENSE cysts were enriched with germinated Bacillus (1 g l⁻¹) either in enrichment water or post-harvest at densities up to 8 million nauplii l⁻¹. Microbial communities were assessed using plate counts on TSA and TCBS, alongside Illumina-based 16S rRNA gene amplicon sequencing. Across all treatments, combining bacteriostatic products with probiotic application significantly decreased opportunistic Proteobacteria, including Vibrio species, while increasing the relative abundance of beneficial Firmicutes (Bacillus spp.). Both enrichment-water and post-harvest applications proved effective, demonstrating operational flexibility and enhanced biosecurity for marine fish larviculture.