Community structure of soil microorganisms and endophytes of honeysuckle at different ecological niche specificities

Background The plant microbiome is one of the key determinants of healthy plant growth, and it has many functions, such as nitrogen fixation, iron production, phosphorus dissolution, and auxin production. However, the structural composition of the bacterial and fungal microbiomes in the plant microenvironment in different regions, especially the relationship between subsurface and aboveground communities, is complex and not fully understood. The present study investigated the niche differentiation of plant microbiomes in different regions and the diversity of microbial community structure within different niches. Methods High-throughput sequencing was used to sequence the soil and endophytes of honeysuckle. Alpha diversity analysis and principal component analysis (PCoA) were used to study the community composition structure of the soil and endophyte, and the function of endophyte bacteria and fungi was predicted based on the PICRUST2 process and FUNGuild. Results In total, there were 382 common bacterial genera and 139 common fungal genera in the soil of different producing areas of honeysuckle. There were 398 common bacterial genera and 157 common fungal genera in rhizosphere soil. More beneficial bacteria were enriched in rhizosphere soil. Endophytic bacteria were classified into 34 phyla and 770 genera. Endophytic fungi were classified into 11 phyla and 581 genera, among which there were significant differences in the dominant genera of roots, stems, leaves, and flowers, as well as in community diversity and richness. PCoA indicated that the community structure of endophytic bacteria and fungi among roots, stems, leaves, and flowers was also significantly different. Bacterial community function prediction demonstrated that the relative abundance of functional genes involved in the metabolism of endophytic bacteria was the highest, and the functions of endophytic fungi were mainly related to saprophytic bacteria. In different tissues of honeysuckle, functional genes that could fight microorganisms were also found in KEGG secondary functional genes. Conclusion There are many common bacterial genera and fungi genera in the soil and rhizosphere soil of honeysuckle. The endogenous dominant core bacteria in each part of honeysuckle plant have a high degree of overlap with the dominant bacteria in soil. Functional prediction suggested that some dominant core bacteria have antibacterial effects, providing scientific basis for further exploring the microorganisms with antibacterial function of honeysuckle to understand the medicinal value of honeysuckle.