Tracking microbial community dynamics in commercial barramundi larviculture: Insights from flow cytometry and 16S rRNA gene sequencing

Barramundi ( Lates calcarifer ), native to the Indo-Pacific, has rapidly become the fastest-growing aquaculture species worldwide. However, maintaining stable production during the larviculture stage remains challenging, with larval mortality often reaching 100%. As hatchery management practices play a crucial role in regulating water microbiota, understanding microbiome dynamics is essential for improving survival rates. From day post hatch (DPH) 0 to DPH 17 at a commercial barramundi larviculture facility in Vietnam, microbial dynamics and community assembly in rearing tanks were analyzed using flow cytometry (FCM) and 16S rRNA gene amplicon sequencing. The analysis revealed persistent tank-specific differences in microbial communities that fluctuated over time. Stochastic factors played a significant role in microbial assembly, leading to variability between tanks even under similar operational conditions and underscoring the complexity of microbial community dynamics in larviculture systems. Flow cytometry and 16S rRNA sequencing showed moderately correlated diversity metrics and captured comparable overall trends in community composition, reflecting their potential complementarity in monitoring microbial dynamics. This underscores the potential of FCM as a complementary, rapid, and cost-effective approach for monitoring microbial community dynamic in aquaculture. • Temporal microbial dynamics were described in a commercial barramundi hatchery in Vietnam. • Phenotypic and taxonomic bacterial diversity metrics were correlated to each other across samples. • Tank-specific divergence in microbial composition persisted under identical conditions. • Stochastic processes were identified as major drivers of community assembly. • Flow cytometry demonstrated potential in aquaculture research as a rapid, high-resolution monitoring tool.