The role of rhizosphere small RNAs in soil disease suppressive community

Author: Shivangiben Panchal

  • Thesis download: available for open access on 9 Jan 2026.

Panchal, Shivangiben, 2023 The role of rhizosphere small RNAs in soil disease suppressive community, Flinders University, College of Medicine and Public Health

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Plant-microbe interactions in the rhizosphere are complex and dynamic in which numerous organisms interact with each other and with the plant. Understanding these interactions is crucial for sustainable disease control. Although the use of omics techniques such as metagenomics, transcriptomics, and amplicon (16S rRNA and ITS region) sequencing has increased the knowledge of microbiome composition and microbe-plant interactions, the causes and consequences of such interactions remain obscure, especially in disease suppressive soils. To gain a deeper understanding of the molecular mechanism of the rhizosphere-plant interaction, this thesis investigated the possible role of small RNAs (sRNA) in the rhizosphere-plant interaction in soils, collected from agricultural fields in South Australia, with different suppression capacities of Rhizoctonia solani AG-8. It has been suggested that sRNAs can be central to the regulation of gene expression in plants, animals, and humans, typically by cleaving and inhibiting target mRNAs involved in modulating the immune system during host-pathogen interactions and facilitating communication between pathogenic organisms and plants, affecting plant health. Bioinformatic analysis of microbial sRNA data from the SP and NSP soils were done using customized pipelines developed in this study. Results indicated that rhizosphere sRNAs had specific compositional properties that may be important in rhizosphere microbe-plant interactions. Particularly, sRNAs below 30 nt were enriched with previously reported fungal and plant-like sRNAs, with some notable features related to soil samples reflecting the overall quality and biological meaning of the data. For example, 29 nt sRNAs were pronounced in NSP sample as compared to SP sample. Furthermore, wheat and Rhizoctonia specific sRNAs were identified from the rhizosphere sRNAs with specific characteristics features. Notably, most sRNAs were enriched in cytosine at the 5 prime nucleotide position except 24 nt wheat specific sRNAs which was biased for adenine. Such biases at the 5’ position signify how these sRNAs might be loaded into host plants to dictate gene regulations. To identify possible bacterial sRNAs, the de novo assembled metagenomes were used as references for sRNA mapping. A total of 189 and 191 sRNA loci were differentially expressed when mapped to de novo assembled SP and NSP metagenomes. Based on root transcriptomics data from the two soils, 51 transcripts were significantly upregulated in SP samples, of which 14 transcripts were flagged for a possible role in plant defence. Five transcripts of this set encoding ATP synthase, UDPGP, ribosomal S3-C, COX1 were further validated through the laboratory analysis using real-time quantitative polymerase chain reaction. In conclusion, this is the first study that shows a comprehensive overview of rhizosphere sRNAs and their corresponding plant transcripts in the context of biological disease suppression in agricultural soils, providing early evidence of microbiome-plant trans-kingdom RNAi.

Keywords: small RNA, suppressive soil, non-suppressive soil, Rhizosphere, cross-kingdom RNAi, disease suppression, R. solani AG-8.

Subject: Biotechnology thesis

Thesis type: Masters
Completed: 2023
School: College of Medicine and Public Health
Supervisor: Dr. Roshan Regmi