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Background  Microbiome assembly in early life may have a long-term impact on host health. Larval nursery is a crucial period that determines the success in culture of  Litopenaeus vannamei , the most productive shrimp species in world aquaculture industry. However, the succession patterns and assembly mechanisms of larval shrimp bacterial community still lack characterization at a fine temporal scale. Here, using a high-frequency sampling strategy and 16S rRNA gene amplicon sequencing, we investigated dynamics of larval shrimp bacterial community and its relationship with bacterioplankton in the rearing water across the whole developmental cycle in a realistic aquaculture practice.    Results  Alpha-diversity of larval shrimp bacteria showed a U-shaped pattern across the developmental cycle with the stages  zoea  and  mysis  as the valley. Correspondingly, the compositions of dominant bacterial taxa at the stages  nauplius  and early  postlarvae  were more complex than other stages. Remarkably,  Rhodobacteraceae  maintained the overwhelming dominance after the mouth opening of larvae ( zoea  I~early  postlarvae ). The taxonomic and phylogenetic compositions of larval bacterial community both showed stage-dependent patterns with higher rate of taxonomic turnover, suggesting that taxonomic turnover was mainly driven by temporal switching among closely related taxa (such as  Rhodobacteraceae  taxa). The assembly of larval bacteria was overall governed by neutral processes (dispersal among individuals and ecological drift) at all the stages, but bacterioplankton also had certain contribution during three sub-stages of  zoea , when larval and water bacterial communities were most associated. Furthermore, the positive host selection for  Rhodobacteraceae  taxa from the rearing water during the  zoea  stage and its persistent dominance and large predicted contribution to metabolic potentials of organic matters at post-mouth opening stages suggest a crucial role of this family in larval microbiome and thus a potential source of probiotic candidates for shrimp larval nursery.    Conclusions  Our results reveal pronounced succession patterns and dynamic assembly processes of larval shrimp bacterial communities during the developmental cycle, highlighting the importance of the mouth opening stage from the perspective of microbial ecology. We also suggest the possibility and potential timing in microbial management of the rearing water for achieving the beneficial larval microbiota in the nursery practice.Video Abstract

Fine-scale succession patterns and assembly mechanisms of bacterial community of Litopenaeus vannamei larvae across the developmental cycle