Mg-enriched nutrient management enhances phyllosphere bacterial diversity, community structure, and functional traits in pomelo orchards.

Phyllosphere, the aerial surface of plants, harbors a tremendous diversity of microbes that significantly influences plant health and ecosystem functionality. Nevertheless, a holistic understanding of the effects of nutrient management, particularly magnesium (Mg) supplementation, on phyllosphere endophytes remains elusive. Herein, we conducted a five-year field experiment to investigate the impact of different nutrient management practices, including farmer practice of high N.P.K input (FP), reduced N.P.K input (OPT), and OPT supplemented with Mg (OPT+Mg), on the phyllosphere endophytic bacterial community (Illumina 16S sequencing) associated with fruit and leaf of pomelo trees across different growth stages, i.e., June (S1), July (S2), and September (S3). The results demonstrated that Mg-enriched nutrient management (OPT+Mg), significantly enhanced microbial diversity and restructured community composition, with notable increases in the relative abundance of beneficial phyla such as Actinobacteriota, Bacteroidota, and Chloroflexi compared with FP across all growing seasons. Similarly, both OPT and OPT+Mg generally supported higher microbial diversity than FP in fruit and leaf samples. Principal Coordinate Analysis (PCoA) and PERMANOVA confirmed significant differences in bacterial community structures among treatments. Ternary plot analysis further indicated the enrichment of beneficial genera under OPT and OPT+Mg treatments, which can play key roles in promoting plant growth and enhancing resilience against various stresses. In addition, Mg application was associated with more complex co-occurrence networks, highlighting its impact on promoting robust microbial communities in leaf and fruit samples. Functional predictions (FAPROTAX) suggested that Mg application was associated with higher predicted carbon and nitrogen cycling functions and lower predicted relative abundances of potential plant pathogens and intracellular parasites. This study is the first to provide long-term field-based evidence of how Mg supplementation modulates phyllosphere microbiota in fruit orchards, offering critical insights into microbiome-informed nutrient strategies. These findings highlight the unexplored role of Mg in shaping aerial plant microbiomes and present a novel avenue for enhancing sustainable pomelo production through targeted nutrient-microbiome interventions.