A comparative observational study of prokaryotic microbial community dynamics across different Litopenaeus vannamei cultivation systems

IntroductionMicrobial communities are key indicators of ecosystem health in aquaculture, yet their temporal dynamics under different cultivation systems remain poorly characterized. This study compares prokaryotic community succession across three commercial Litopenaeus vannamei cultivation systems with contrasting pond construction, salinity, and water-exchange intensity.MethodsWe collected 85 water samples from five sub-ponds per system at 15-day intervals and characterized prokaryotic communities via 16S rRNA amplicon sequencing, combined with α/β diversity, LEfSe, and PICRUSt2-based functional analyses.ResultsCommunity composition and diversity differed markedly among systems: α-diversity was highest in the earthen brackish pond (EBXS) and lowest in the concrete seawater pond (HSDT). Proteobacteria dominated all systems, while Actinobacteria prevailed in EBXS, which also showed increasing relative abundances of potentially pathogenic genera (Aeromonas, Mycobacterium, Rickettsia) over time. HSDT exhibited the highest predicted metabolic potential (90 enriched KEGG pathways). Temporally, EBXS displayed more stable succession and higher overall similarity, whereas high-level ponds showed greater species turnover.DiscussionSalinity and cultivation system emerged as major correlates of community variation, though inherently confounded in our observational design. These patterns suggest a trade-off between community stability and pathogenic risk across production strategies. Our findings offer empirical baselines and testable hypotheses for future controlled studies to disentangle the individual effects of salinity, pond construction, and water management on microbial assembly in aquaculture systems.