Endophytic bacterial and fungal dynamics of community structures in lettuce stem and soil during invasion by the fungal pathogen Sclerotinia sclerotiorum

Lettuce stem is considered an essential and important fresh edible vegetable tissue worldwide. The regulation of beneficial endophytic microbes in host stems is vital to plant growth and yield, but information about microbial community structures in lettuce stems remains limited. In this study, endophytic bacterial and fungal community structures in stems and soil at three stem-expansion stages were analyzed through Illumina sequencing. Results showed that the Shannon index of bacteria in lettuce soil was greatly higher than the number of endophytic bacteria in the stems. A total of 212 core operational taxonomic units (OTUs) were observed in the bacterial group; and 16, in the fungal group. The distribution of endophytic bacteria and fungi varied in the stem and soil, showing changes in the stem with rotting due a fungal pathogen (Sclerotinia sclerotiorum) invasion. Bacterial groups, such as Gammaproteobacteria, had high abundances in the stems. The dominant bacterial group in soil included Gammaproteobacteria, Alphaproteobacteria, and Actinobacteria, and the number of Sclerotiniaceae extensively increased in the rotten stem. Bacterial genes in soil are mainly involved in quorum sensing and carbon, glyoxylate, and dicarboxylate metabolism. Meanwhile, bacterial genes inside stems are mainly involved in bacterial chemotaxis, biofilm formation, and amino acid biosynthesis. Fungal genes in rotten stem have similar function pathways to those in soil samples. This work clarifies the bacterial and fungal community shifts in lettuce stems and root soil, and the findings provide insights as to how to promote lettuce growth and control the occurrence of sclerotinia stem rot.