Zooplankton-associated Bacterial Communities are Dominated by Host-Specific Rather than Environmentally Random Taxa.

Zooplankton-associated bacteria (ZA) are critical to freshwater ecosystems and host health, but their assembly mechanisms and core microbiota remain poorly understood. We surveyed lakes across different altitudes in China and collected Calanoida, applying gut-emptying treatments to obtain ZA and fecal bacteria (FB). In parallel, free-living (FL) and particle-attached bacteria (PA) were sampled from waters. All bacterial communities were analyzed using 16S rRNA amplicon sequencing to compare community structures and infer potential sources of ZA. Our results showed that ZA showed lower diversity and a distinct structure compared with FB, FL, and PA, while the latter three were relatively similar. Moreover, deterministic processes dominated ZA assembly, with their influence strengthening at higher altitudes, as reflected by decreasing MST values. Core microbiota analysis revealed 31 genera consistently present in ZA. Six of these (Pseudoalteromonas, Aeromonas, Streptococcus, Vibrio, Lactococcus, and Shewanella) were predominantly enriched, suggesting a stable and host-associated core microbiota, with Pseudoalteromonas and Vibrio showing marked enrichment in high-altitude lakes. Source tracking further revealed that an average of over 70% of ZA could not be assigned to FL or PA, suggesting that most ZA members did not originate directly from environmental bacterial pools. These findings indicate that ZA are not randomly assembled from environmental bacteria but include a consistent core shared by most hosts. Our study demonstrates that zooplankton maintain specific and stable bacterial communities and, by comparing ZA, FB, FL, and PA across an altitudinal gradient, provides new insights into their assembly mechanisms and ecological roles in freshwater ecosystems.