Ecological niche imprints the structure and network of microbial communities in Lonicera japonica Thunb

Plant-associated microbiomes play pivotal roles in promoting plant health, productivity, and resistance to diseases. However, the differential adaptability of microorganisms to different ecological niches in Lonicera japonica remains unclear, which hinders their application in agriculture. Here, the structure and network of bacterial and fungal communities in six compartment niches (bulk soil, rhizosphere soil, root, stem, leaf, and flower) of L. japonica were explored using three host ecotypes. The keystone taxa of each niche were then analyzed, followed by source tracking analysis. Results demonstrated that the structure and assembly of microbiomes along the soil–plant continuum were primarily governed by compartment niches rather than host ecotypes. Bacterial diversity and network complexity gradually decreased from the soil to the root and, ultimately, to the flower; however, fungal diversity and network complexity gradually decreased from the soil to the stem but increased from the stem to the leaf and flower. The bacterial keystone taxa Proteobacteria, Pseudomonas, Pantoea, Kluyvera, and Enterobacter were dominated in endosphere samples. Meanwhile, the core fungal keystone taxa Cryptococcus, Alternaria, and Erysiphe were dominated by endosphere samples. However, Mortierella and Fusarium were dominated by rhizosphere soil. Microbiota was mainly derived from bulk soil and then filtered in each compartment niches. This work provides new insights into the microbial communities of L. japonica, highlighting the potential roles of microbiomes in plant growth, environmental adaptation, and bioactive compound synthesis.