Dynamics and Assembly Mechanisms of Bacterial Communities During Larval Development of Macrobrachium rosenbergii: A High-Frequency Sampling Study Based on 16S rRNA Absolute Quantification Sequencing

This study aimed to elucidate stage-specific dynamics, assembly mechanisms, and functional roles of bacterial communities during Macrobrachium rosenbergii larval development through high-resolution microbiota profiling. A high-frequency sampling strategy (126 samples across 11 zoeal stages and 1 post-larval stage within 21 days) and 16S rRNA absolute quantification sequencing were employed. Bacterial succession, persistent taxa, and ecological processes were analyzed using abundance-occupancy modeling, neutral community modeling, and PICRUSt2-based functional prediction. Absolute bacterial abundance exhibited a triphasic abundance trajectory. Initial accumulation: Linear increase (Dph 1–5, peak Δlog10 = +1.7). Mid-stage expansion: Peak abundance (log10 = 7.5 copies/g, Dph 7–8). Late-stage remodeling: Secondary peak (log10 = 7.1 copies/g, Dph 19). Eighty dominant amplicon sequence variants (ASVs) (dominant taxa: Herminiimonas, Maritalea, and Enterobacteriaceae) comprised > 95% of the total abundance and coexisted via niche partitioning. Community construction was dominated by ecological drift/dispersal limitation (neutral model R2 = 0.16, p < 0.01). Metabolic pathways (e.g., nutrient metabolism) shifted with dietary transition. “Phylogenetic replacement” underpinned microbiota resilience against environmental perturbations. Optimizing aquaculture environments offers a viable antibiotic-free strategy for microbial management, advancing our understanding of host microbe interactions and ecological niche differentiation in aquatic animals.