Comparative Microbiome Study of Mummified Peach Fruits by Metagenomics and Metatranscriptomics

The dried peach fruits clinging to peach trees or lying on the ground nearby are known as mummified peach fruits. Here, we examined the microbiome communities of three different mummified peach fruits from the nectarine cultivar Hahong by DNA- and RNA-sequencing. We found the dominance ofMonilinia fructigenafollowed bySclerotinia borealis,S. sclerotiorum, andBotrytis cinereain the mummified peach fruits. Moreover, we found a high number of Proteobacteria, includingFrateuria aurantia,Neoasaia chiangmaiensis,Robbsia andropogonis, andEwingella Americana. Furthermore, we identified several viruses and viroids. Bacteriophages were identified by DNA- and RNA-sequencing, while viruses and viroids with RNA genomes were identified by only RNA-sequencing. Moreover, we identified a novel mycovirus referred to asMoniliniaumbra-like virus 1 (MULV1) fromM. fructigena. Our results revealed the co-inhabitance of fungi and bacteria in the mummified peach fruits, although dominant microorganisms were present. RNA-sequencing revealed that several fungal and bacterial genes were actively transcribed. Comparative analyses suggested that RNA-sequencing provides more detailed information on microbial communities; however, combining DNA- and RNA-sequencing results increased the diversity of microorganisms, suggesting the importance of databases and analysis tools for microbiome studies. Taken together, our study provides a comprehensive overview of microbial communities in mummified peach fruits by DNA shotgun sequencing and RNA-sequencing.