Analysis of endophytic microbial community diversity and functional groups associated with white peel symptom in Passiflora edulis

【Objective】Passiflora edulis, as a characteristic tropical and subtropical cash crop, is rich in vitamins, amino acids, and bioactive substances, possessing significant economic value in fresh consumption, processing and other fields. However, the white peel symptom of P. edulis adversely affects fruit quality and often results in irregular white patches on the fruit epidermis. This not only severely impairs the fruit’s appearance quality but also reduces its commercial value and market acceptance, caus-ing substantial economic losses to growers. Currently, the mechanism underlying this symptom remains unclear. Existing studies have mainly focused on the impacts of environmental factors (e.g., light, temperature, and nutrients), while the association between endophytic microorganisms—an important component of the host’s microecosystem—and the white peel symptom has not been systematically explored. This study aims to clarify the key microbial taxa associated with the formation of the white peel symptom and identify functional microorganisms with potential regulatory roles (e.g., pathogenic-related or probiotic taxa) by analyzing the differences in endophytic microbial communities between symptomatic and normal P. edulis peel. The results are expected to provide theoretical support for revealing the microecological driving mechanism of the white peel symptom in P. edulis and a scientific basis for developing microbe-based green control technologies, thereby facilitating the sustainable development of the P. edulis industry.【Methods】During the fruiting period of P. edulis in August 2024, three samples each of mature fruits with white peel symptom and healthy fruits were collected. Using 16S rRNA and ITS high-throughput sequencing technologies (Illumina NextSeq 2000 platform), comparative analyses were conducted on the phylum and genus levels, community diversity, and community structure of endophytic microorganisms in the peel of symptomatic and normal P. edulis. For data analysis, QIIME2 software was used for sequence quality control, Operational Taxonomic Units (OTUs) clustering, and species annotation. Alpha diversity indices (Shannon index, Simpson index, Chao1 index, etc.) were employed to evaluate community richness and evenness, and ANOVA was used to test for significance of differences between groups. LEfSe (Linear Discriminant Analysis Effect Size) analysis was performed to screen for biomarkers with significant differences between the two groups (LDA score＞2.5). Meanwhile, the relative abundances of dominant taxa at the phylum and genus levels were statistically analyzed, and the chi- square test was used to assess the differences in proportions between groups.【Results】Significant differences were observed in the structural characteristics of endophytic microbial communities between the peel of P. edulis with white peel symptom and normal peel. A total of 72 phyla, 169 classes, 374 orders, 637 families, 1208 genera, 1928 species, and 3487 OTUs were identified in the endophytic bacterial communities of P. edulis with symptomatic and normal peel. Among them, the numbers of endophytic bacteria in symptomatic peel at different taxonomic levels were: 34 phyla, 76 classes, 172 orders, 296 families, 568 genera, 882 species, and 1459 OTUs; while those in normal peel were: 38 phyla, 93 classes, 202 orders, 341 families, 640 genera, 1046 species, and 2028 OTUs. In addition, a total of 14 phyla, 37 classes, 57 orders, 67 families, 82 genera, 99 species, and 165 OTUs were identified in the endophytic fungal communities of P. edulis with symptomatic and normal peel. Among them, the numbers of endophytic fungi in symptomatic peel at different taxonomic levels were: 7 phyla, 18 classes, 28 orders, 31 families, 38 genera, 49 species, and 79 OTUs; while those in normal peel were: 7 phyla, 19 classes, 29 orders, 36 families, 44 genera, 50 species, and 86 OTUs. Compared with symptomatic fruits, the number of unique bacterial and fungal OTUs in normal P. edulis peel was higher, indicating that healthy peel maintains richer microbial diversity. At the phylum level, it was observed that the relative abundances of bacteria belonging to the phylum Pseudomonadota and fungi belonging to the phylum Ascomycota in the peel of P. edulis with white peel symptom were higher than those in the peel of normal P. edulis. Specifically, their relative abundances were 1.24-fold and 1.13-fold higher that those in normal peel, respectively. At the genus level, bacterial genera including Roseateles and Pseudomonas, as well as fungal genera including Nigrospora and Cladosporium, were identified as the dominant genera with high abundance in the peel of P. edulis exhibiting white peel symptom. LEfSe (Linear Discriminant Analysis Effect Size) analysis revealed that bacterial genera Stenotrophomonas, Defluviicoccus, and Rhodopseudomonas were significantly enriched in the peel of P. edulis with white peel symptom. At the fungal level, no fungi showed significant enrichment in either the peel with white peel symptom or the normal peel of P. edulis.【Conclusion】The occurrence of white peel symptom in P. edulis is closely associated with the imbalance of endophytic microbial communities, specifically manifested as a significant reduction in community diversity, attenuation of beneficial microbial taxa in healthy peel (e.g., phylum Actinobacteriota and genus Bacillus, which have growth-promoting and antagonistic functions), and enrichment of potential pathogenic or harmful taxa. It is hypothesized that the mechanism may involve the disruption of microecological homeostasis in the peel due to the disorder of endophytic microbial communities, leading to a decline in host defense capabilities. Meanwhile, the metabolic activities of harmful microbial groups may directly or indirectly affect the peel cell structure and pigment synthesis, ultimately inducing the white peel symptom. The results suggest that regulating endophytic microbial communities (e.g., supplementing probiotics or inhibiting harmful bacteria) may serve as an effective approach to control the white peel symptom in P. edulis. Future studies can further isolate and identify key functional strains to verify their specific roles in symptom formation.