Analysis of microbial community diversity in ecological niches of Hevea brasiliensis based on high-throughput sequencing

【Objective】 This study aimed to analyze microbial community diversity in ecological niches of Hevea brasiliensis based on high-throughput sequencing， providing reference for development and utilization of characteristic microbial resources， and maintaining rubber plantation productivity. 【Method】 Four ecological niches of Hevea brasiliensis RRIM600， namely roots， stems， leaves， and rhizosphere soil， were taken as the research subjects. High-throughput sequencing based on the Illumina PE250 platform was performed to obtain the characteristic sequences of amplicon sequence variants （ASVs） of microorganisms in different ecological niches. The species composition of microbial communities in different ecological niches was analyzed， and the dominant phyla and dominant genera were identified. A phylogenetic tree of the species was constructed， and alpha diversity analysis was conducted. Principal coordinate （PCoA） analysis， beta diversity analysis， cluster analysis， and correlation analysis were performed on the microbial communities. LDA effect size （LEfSe） was used to screen for significantly different microbial communities， and the effects of different microorganisms on different ecological niches were analyzed. 【Result】 A total of 4193 fungal ASVs and 12525 bacterial ASVs were identified in four ecological niches of Hevea brasiliensis RRIM600. The numbers of unique fungal ASVs in roots， stems， leaves， and rhizosphere soil were 310， 411， 140， and 2762 respectively， while those of bacterial ASVs were 2312， 634， 2603， and 5898 respectively. Ascomycota was the most dominant fungal phylum in all four niches， with the highest relative abundance observed in leaves， reaching 94.00%. Apart from unclassified fungi， Basidiomycota was also the dominant phylum in roots， stems， and rhizosphere soil. The dominant fungal genera in roots， stems， leaves， and rhizosphere soil were Oliveonia， Strelitziana， Erysiphe， and Cladosporium respectively. Proteobacteria was the dominant bacterial phylum in all four niches， with relative abundances of 88.41%， 99.92%， 99.91%， and 88.33% in roots， stems， leaves， and rhizosphere soil respectively. The shared dominant genera included Aeromonas and Thiofilum. For the fungal community in rhizosphere soil of Hevea brasiliensis， the Chao1 index， observed-features index， and Shannon index were significantly higher than those in roots， stems， and leaves （P<0.05， the same below）. For the endophytic bacterial community， the order of the three indices was root > leaf > stem. PCoA analysis results showed that the first two principal coordinates explained 56.48% and 44.77% of the variation in fungal and bacterial community composition respectively， and bacterial community composition exhibited a structural differentiation between above-ground and below-ground niches. LEfSe analysis indicated that different ecological niches had biomarkers for fungi， while no significantly enriched bacterial community was detected in leaves. Correlation analysis of the top 30 most abundant fungal and bacterial genera revealed the 140 pairs of fungi showed significantly positive correlations， and 20 pairs of fungi had significantly negative correlations； 5 pairs of bacteria showed significant positive correlations， and 3 pairs of bacteria showed significant negative significant correlations. 【Conclusion】 Microbial community diversity in ecological niches of in Hevea brasiliensis RRIM600 exhibits pronounced differentiation in both diversity and composition， with its relative abundances related to microbial sources， and different ecological niches exert selective and filtering effects on microorganisms.