辣椒不同生态位内生微生物群落差异及关联

Differences and associations of endophytic microbial communities in different ecological niches of chili pepper

摘要:

【目的】探究辣椒不同生态位间内生微生物群落的差异及其潜在关联，以期为辣椒内生微生物资源的挖掘和应用提供理论依据。【方法】采用16S rRNA基因和内转录间隔区(internal transcribed spacer,ITS)基因测序技术，比较分析91份辣椒材料不同生态位(根、茎、叶和果)内生细菌和真菌的群落结构特征，并进行功能注释；此外，针对内生细菌群落进行共现网络分析和溯源分析。【结果】四个生态位点内生微生物群落的操作分类单元(operational taxonomic unit,OTU)高度共享，其中，细菌的共享OTUs占比46.36%，真菌的共享OTUs占比29.66%。不同生态位间，辣椒内生细菌和真菌群落的多样性差异显著，根部的内生细菌和真菌群落与其他3个生态位显著分离(P<0.05)；内生细菌群落的Shannon指数在不同生态位间差异显著，而内生真菌则相对稳定。辣椒中的优势内生细菌为变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)和拟杆菌门(Bacteroidota)，其中，变形菌门在根部富集，而厚壁菌门和拟杆菌门则在果中占据优势。子囊菌门(Ascomycota)和担子菌门(Basidiomycota)作为主要的内生真菌优势菌群，在4个生态位中的相对丰度差异较小。功能注释结果显示，辣椒含有多种具有次生代谢物生物合成和抗生素生物合成功能的内生细菌；而在真菌群落中，病原真菌的相对丰度最高。此外，辣椒中超过80%的内生细菌来源于与其直接相连的形态学下方生态位，具有复杂的相互作用网络、较强的群落稳定性和模块结构。【结论】相较于内生真菌，辣椒内生细菌的群落组成对生态位的变化更为敏感，而真菌的生态位特异性较弱。辣椒各生态位的内生细菌主要源自其形态学下方生态位，表现出显著的生态位富集作用，且根部在内生细菌群落塑造中起着至关重要的作用。

Abstract:

[Objective] To explore the differences and potential associations of endophytic microbial communities in different niches of chili pepper and provide a theoretical basis for the exploration and application of endophytic microbial resources in chili pepper. [Methods] The 16S rRNA and internal transcribed spacer (ITS) genes sequencing were employed to study the community structure characteristics of endophytic bacteria and fungi in different ecological niches (roots, stems, leaves, and fruits) of 91 pepper germplasm accessions, along with functional annotations. Additionally, co-occurrence network analysis and traceability analysis were performed on the endophytic bacterial communities. [Results] The operational taxonomic unit (OTU) of endophytic microbial communities were highly common among the four ecological niches, including 46.36% common bacterial OTUs and 29.66% common fungal OTUs. The diversity of endophytic bacterial and fungal communities in chili pepper exhibited variations across different ecological niches, with the endophytic communities in roots being distinctly separated from those in the other three niches (P<0.05). The Shannon index of endophytic bacteria varied significantly among niches, whereas that of endophytic fungi remained relatively stable. The dominant endophytic bacteria in chili pepper were Proteobacteria, Firmicutes, and Bacteroidota, with Proteobacteria being enriched in the roots and Firmicutes and Bacteroidetes being predominant in the fruits. Ascomycota and Basidiomycota, the dominant endophytic fungal phyla, exhibited minimal differences in relative abundance across the four ecological niches. Functional annotation results indicated that chili pepper harbored various endophytic bacteria capable of synthesizing secondary metabolites and antibiotics. Within the fungal community, pathogenic fungi were found to have the highest relative abundance. Additionally, more than 80.0% of the endophytic bacteria in chili pepper originated from their directly associated morphologically lower niches, exhibiting complex interaction networks, strong community stability, and a modular structure. [Conclusion] Compared with the endophytic fungal community, the endophytic bacterial community in chili pepper is sensitive to changes in ecological niches, while the niche specificity of the fungi is comparatively weak. The endophytic bacteria associated with each niche of chili pepper primarily originate from the niche located beneath, exhibiting significant niche enrichment, where the roots serving as a crucial source in shaping the endophytic bacterial community.