Endophytic Bacterial Community Characteristics and Their Correlation with Anthocyanin Biosynthesis in Blood Orange Pulp

To investigate the correlation between coloration and endophytic bacterial communities in blood orange pulp, this study employed microbiome analysis to compare the community structure and functional characteristics of endophytic bacteria between pigmented and non-pigmented blood orange pulp and it also evaluated their relationship with fruit quality. Results demonstrated that pigmented pulp exhibited significantly higher contents of total anthocyanins (38.78 versus 10.66 µg/g) and p-coumaric acid (0.59 versus 0.47 µg/g) and naringin (3.3 versus 1.53 µg/g) when compared with non-pigmented pulp. Microbiome profiling revealed richer bacterial diversity in pigmented pulp, containing 15 phyla, 25 classes, 46 orders, 89 families, 154 genera, and 87 species versus 11 phyla, 18 classes, 28 orders, 62 families, 103 genera, and 46 species in non-pigmented pulp. In pigmented pulp, Bacteroidetes was the dominant phylum, and Faecalibacterium, Bacteroides, Bifidobacterium, Prevotella, and Lactobacillus were the dominant genera. Correlation analysis showed that the differential Bacteroidetes species in pigmented pulp including Bacteroides vulgatus, B. caccae, and Parabacteroides goldsteinii had significantly positive correlations with anthocyanins, total flavonoids and naringin. PICRUSt2 functional prediction indicated endophytic bacterial gene functions were richer in pigmented pulp, with the significantly enriched functions mainly involved in post-synthetic modification (methylation), transport and storage of anthocyanins. These findings demonstrate that the quality of pigmented blood orange pulp is superior to that of non-pigmented blood orange pulp and that anthocyanin biosynthesis is closely related to endophytic bacteria such as B. vulgatus, B. caccae, and P. goldsteinii.