Succession patterns, environmental connections, and assembly mechanisms of gut microbiota in the giant freshwater prawn (Macrobrachium rosenbergii) across lifespan

The ecological succession patterns and assembly mechanisms governing gut microbiome dynamics during aquatic host ontogeny remain underexplored, particularly regarding environmental connectivity and habitat transitions. Using the giant freshwater prawn (Macrobrachium rosenbergii) as a model, we surveyed gut microbiota dynamics from egg to adult across 16 developmental stages through brackish-to-freshwater transition over 140 days, using 16S RNA gene amplicon sequencing. Results revealed distinct alpha diversity patterns characterized by U-shaped during larviculture and unimodal during pond culture. Random forest identified 11 life-stage-associated microbial biomarkers (e.g., Chthoniobacteraceae enriched in juveniles) functionally linked to nutrient acquisition. SourceTracker analysis demonstrated limited acquisition from environmental sources (water: 0.1–18.6 %; sediment: 0.1–3.2 %) when incorporating prior-stage gut microbiota as the internal source. Gut microbial colonization exhibited pulsed-attenuation dynamics with four distinct bacterioplankton recruitment pulses (Zoea I, VI, XI, juvenile) followed by gradual attenuation, highlighting critical windows for probiotic intervention. Community assembly processes transitioned from homogenizing dispersal during the early stages (Zoea I-III) to homogeneous selection during the mid-late stages (Zoea VI-XII), with habitat transition significantly influencing successional patterns. These findings provide comprehensive insights into prawn gut microbiota assembly mechanisms by integrating host development, environmental sources, and habitat transitions.