Compartment‐Specific Functional and Taxonomic Responses of Plant Growth‐Promoting Microbiomes Following Oxytetracycline Trunk Injection in Citrus

ABSTRACT Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus, is the most destructive disease affecting citrus production worldwide. Trunk injection of oxytetracycline (OTC) is increasingly used to suppress the pathogen and improve tree performance, yet its ecological consequences for plant‐associated microbiomes remain poorly understood. Here, we evaluated the compartment‐specific responses of plant growth–promoting microbiomes to systemic OTC treatment in HLB‐affected citrus trees under commercial orchard conditions. Using shotgun metagenomics combined with targeted detection of plant growth–promoting genes, we analyzed functional and taxonomic dynamics across leaves, bark, roots, and rhizosphere at three time points (3 days, 3 weeks, and 3 months) following treatment. OTC injection reduced pathogen abundance in leaves and improved yield, fruit weight, and juice quality. Aggregated plant growth–promoting functional profiles remained largely stable across compartments. However, taxonomic shifts were nonetheless detected within microbial lineages carrying these functions, suggesting that comparable functional potential may be maintained despite changes in the microbial lineages encoding it. Bark communities showed transient enrichment of nutrient acquisition and interaction‐related functions, while the rhizosphere exhibited taxonomic turnover without consistent functional shifts. In contrast, root microbiomes displayed temporally structured reorganization of interaction‐associated functions and were the only compartment where functional composition correlated with plant performance. Genome‐resolved analyses further suggested early enrichment of stress‐tolerant and metabolically versatile taxa following treatment. We conclude that systemic OTC trunk injection in citrus was associated with taxonomic redistribution rather than broad functional loss of plant‐associated microbiomes, with functionally relevant consequences emerging selectively in the root microbiome. These findings highlight the importance of spatially resolved microbiome analyses for understanding the ecological impacts of antibiotic use in perennial crop systems and for evaluating the sustainability of disease‐management strategies.