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 costeffective approach for monitoring microbial community dynamic in aquaculture.
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