Citrus fruit microbiome changes under copper-based and biological alternative treatments and its biocontrol potential

Citrus, a globally significant fruit crop, harbours a distinctive microbial community crucial for maintaining citrus health and enhancing disease resistance. While the structure and shaping factors, including phytosanitary treatments, of citrus root and leaf microbiomes are well documented, the carposphere (fruit surface) microbiome and its response to phytosanitary inputs remain poorly understood. In the present study, we combined culture independent (amplicon sequencing) and culture dependent techniques to analyse the citrus carposphere microbiome across three citrus hosts and its response to field-applied phytosanitary treatments (biologicals and copper-antimicrobials). Despite host-specific variation in the relative abundance of dominant taxa such as Proteobacteria, Firmicutes, and Basidiomycota, all three citrus hosts shared a core microbiome, consistently present across fruit samples. Bacterial diversity and composition were negatively influenced by copper treatments, whereas biological products (chitosan, sweet orange essential oils and their mixtures) had minimal or no negative impacts. Fungal communities, including potential pathogens, appeared less sensitive to treatments. Network analysis confirmed that copper altered microbial interactions, increasing mutual exclusion relationships between bacterial taxa compared to untreated or biologically treated samples, which were dominated by positive interactions. A parallel survey of cultivable microbiota from the same samples identified potential biocontrol agents (BCAs) against Colletotrichum gloeosporioides and Alternaria alternata. Notably, cross-referencing cultivable BCAs with core Amplicon Sequence Variants (ASVs) showed that 81.7 % of bacterial core members represent potential biocontrol agents. This study highlights the importance of management practices for sustaining beneficial microbiomes. Furthermore, it establishes a valuable resource of core-associated BCAs, offering promising avenues for the biological control of fungal pathogens.