Divergence patterns of bacterial communities between larviculture systems of two Penaeus vannamei strains with distinct culture traits

The culture traits of Penaeus vannamei strains and environmental management during larviculture are critical for ensuring postlarval quality and determining culture success. Establishing a beneficial larval microbiota is essential for larval health; however, the interplay between shrimp strain traits and water environment in shaping larval microbiota remains underexplored. We profiled the succession trajectories of bacterial communities in larvae and water from larviculture systems of two shrimp strains with distinct traits—stress-resistant and fast-growing—exhibiting different survival rates. Water environment, coupled with larval development, influenced larval bacterial alpha-diversity more than shrimp strain or bacterioplankton diversity. However, the combined effects of host developmental stage, water environment, and bacterioplankton composition shaped larval bacterial community composition. Both strains showed early-stage dominance of Vibrionaceae and post-mouth-opening enrichment of Roseobacteraceae, yet strain-specific divergence emerged at the mysis stage, marked by a surge in abundance-differential taxa persisting into the early postlarvae stage. This divergence was primarily driven by rare and conditionally rare taxa, suggesting a common microbiome shared between strains, with rare taxa recruited for strain-specific functions such as stress resistance. Our findings highlight the timing and characteristics of microbial and environmental divergence between larviculture systems of the shrimp strains with distinct culture traits, indicating complex interactions among host genetics, environmental factors, and microbiota that may influence larval survival. These insights imply the potential for microbiome-assisted breeding strategies in shrimp aquaculture—an avenue worthy of further exploration.