Antibiotic resistance genes and microbial diversity in major aquaculture areas of Hainan Island

This investigation aims to delineate the spatial distribution, prevalence, and diversity of antibiotic resistance genes (ARGs) within aquatic ecosystems across four coastal aquaculture zones in Hainan Province—Danzhou, Wanning, Wenchang, and Sanya. It further assesses the impact of environmental parameters on ARGs dissemination and microbial community structure. High-throughput sequencing was utilized to analyze water samples from 42 sampling sites, complemented by absolute quantitative PCR to quantify 144 ARGs variants. This approach elucidated correlations between ARGs and microbial assemblages, as well as the influence of environmental factors on these interactions. Results indicated that the number of ARGs detected per site ranged from 61 to 123, with Danzhou exhibiting 90 to 123, Wanning 74 to 123, Wenchang 68 to 122, and Sanya 61 to 109 ARGs. Notably, 16 sampling points harbored over 110 ARGs. Quantitative analysis revealed ARG concentrations ranging from 16,167 to 1,784,618 copies/ng. Co-occurrence network analysis demonstrated that most ARGs were associated with MGEs, 16S rRNA genes, transposons, and integrons, indicating these elements' critical role in horizontal gene transfer. Microbial community profiling identified 27,050 operational taxonomic units (OTUs) across 72 phyla, 153 classes, 371 orders, 459 families, and 924 genera, with Proteobacteria, Bacteroidota, Actinobacteriota, Cyanobacteria, and Planctomycetota as dominant taxa. Genus-level analysis revealed significant variations in the abundance of taxa such as Cyanobium_PCC-6307, Candidatus_Actinomarina, and HIMB11 across sampling sites. Environmental parameters, including pH, dissolved oxygen (DO), specific conductance (SPC), salinity (SAL), temperature (T), and pressure (kPa), showed strong correlations with ARG distribution and microbial community composition. Region-specific co-linearity networks indicated distinct relationships between microbial taxa and ARGs; notably, Danzhou and Wanning exhibited strong correlations with over 20 ARGs per genus, whereas Wenchang displayed a more complex association pattern, suggesting a multifaceted role in ARG transmission pathways. Overall, the findings suggest that environmental factors and microbial hosts significantly influence ARG prevalence in Hainan's coastal waters, with regional variations in microbial-ARG interactions, particularly in Wenchang, indicating heightened transmission risks. This study offers vital insights for sustainable aquaculture practices and informs regional regulatory strategies for aquaculture management.