Rearing water microbiomes in white leg shrimp (Litopenaeus vannamei) larviculture assemble stochastically and are influenced by the microbiomes of live feed products

Abstract

The development of effective management strategies to reduce the occurrence of diseases in aquaculture is hampered by the limited knowledge on the microbial ecology of these systems. In this study, the dynamics and dominant community assembly processes in the rearing water of Litopenaeus vannamei larviculture tanks were determined. Additionally, the contribution of peripheral microbiomes, such as those of live and dry feeds, to the rearing water microbiome were quantified. The community assembly in the hatchery rearing water over time was dominated by stochasticity, which explains the observed heterogeneity between replicate cultivations. The community undergoes two shifts that match with the dynamics of the algal abundances in the rearing water. Source tracking analysis revealed that 37% of all bacteria in the hatchery rearing water were either introduced by the live or dry feeds, or during water exchanges. The contribution of the microbiome from the algae was the largest, followed by that of the Artemia, the exchange water and the dry feeds. Our findings provide fundamental knowledge on the assembly processes and dynamics of rearing water microbiomes and illustrate the crucial role of these peripheral microbiomes in maintaining health-promoting rearing water microbiomes. Originality-Significance StatementMost studies on rearing water microbiomes are characterized by sampling resolutions of multiple days and by few replicate cultivations. Through an 18-day sampling campaign in a Litopenaeus vannamei hatchery where five replicate cultivations were studied at a sampling resolution of one day, we studied the microbiome dynamics in this system. We show that the community assembly is dominated by stochasticity, which explains the heterogeneity between replicate cultivations. The dynamics of the algal community in the rearing water induced shifts in community composition at two differerent timepoints. Finally, we quantified the contribution of live and dry feed microbiomes to the rearing water community for the first time. We found that the contribution of each source was dependent on its taxonomic composition, the bacterial load caused by the addition of this source and the timing of the introduction. These new insights will aid in the further development of effective microbiome management to reduce the frequency and magnitude of bacterial diseases.