Comparative Microbiome Study of Mummified Peach Fruits by Metagenomics and Metatranscriptomics
Yeonhwa Jo1, Chang-Gi Back2, Hoseong Choi1,3
1Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
Abstract:
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 of Monilinia fructigena followed by Sclerotinia borealis, S. sclerotiorum, and Botrytis cinerea in the mummified peach fruits. Moreover, we found a high number of Proteobacteria, including Frateuria aurantia, Neoasaia chiangmaiensis, Robbsia andropogonis, and Ewingella 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 as Monilinia umbra-like virus 1 (MULV1) from M. 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.
Insights
This study reveals the complex microbial communities within mummified peach fruits, dominated by fungi like Monilinia fructigena and bacteria such as Proteobacteria. DNA and RNA sequencing provided a comprehensive view of these co-inhabiting organisms and their active genes.
Area of Science:
- * Agricultural Microbiology
- * Plant Pathology
- * Molecular Biology
Background:
- * Mummified peach fruits harbor diverse microbial communities.
- * Understanding these microbiomes is crucial for fruit health and disease management.
- * Previous studies have not fully characterized the complex interactions within these environments.
Purpose of the Study:
- * To comprehensively analyze the fungal and bacterial microbiome of mummified peach fruits.
- * To identify viruses and viroids present in these fruits.
- * To compare the effectiveness of DNA and RNA sequencing for microbiome analysis.
Main Methods:
- * DNA and RNA shotgun sequencing of mummified peach fruits from the nectarine cultivar 'Hahong'.
- * Bioinformatic analysis to identify fungal, bacterial, viral, and viroid species.
- * Comparative analysis of DNA-only versus combined DNA/RNA sequencing data.
Main Results:
- * Dominance of *Monilinia fructigena* and *Proteobacteria* identified in the microbiome.
- * Detection of multiple fungal pathogens, bacteria, viruses, and viroids.
- * Identification of a novel mycovirus, *Monilinia* umbra-like virus 1 (MULV1).
- * RNA sequencing revealed active gene transcription in fungi and bacteria.
- * Combined sequencing increased detected microbial diversity.
Conclusions:
- * Mummified peach fruits host a complex, co-inhabiting microbiome of fungi and bacteria.
- * Integrated DNA and RNA sequencing offers a more complete understanding of microbial communities.
- * Advanced databases and analysis tools are essential for accurate microbiome profiling.
