Differences in Bacterial Community Structure and Composition in the Rhizosphere Soil of Tobacco and the Weed Cyperus rotundus

Background and Objectives:The bacterial wilt pathogen, Ralstonia solanacearum, can overwinter within the roots and rhizosphere soil of C. rotundus, establishing a reservoir for primary and secondary infections in the following growing season. This project aims to investigate the differences in bacterial community composition within the rhizosphere soils of tobacco and the adjacent weed C. rotundus across various stages of tobacco bacterial wilt progression. By conducting amplicon sequencing on soil samples collected at different disease phases, we seek to elucidate how the rhizosphere microbiome of both plants shifts in relation to disease development and to understand the potential role of the weed rhizosphere in pathogen persistence.Experimental Design and Methods:Rhizosphere soil samples from tobacco (Nicotiana tabacum) and the surrounding weed C.rotundus were collected from Yangwu Town, Anshun City, Guizhou Province, China.Sampling was conducted at four distinct stages corresponding to the progression of tobacco bacterial wilt in the field:1. Stage 1 (Pre-disease): Before any visible symptoms of bacterial wilt appeared on tobacco plants.2. Stage 2 (Initial onset): At the first appearance of disease symptoms on tobacco plants.3. Stage 3 (Severe infection): When disease symptoms were widespread and severe.4. Stage 4 (Late stage): During the advanced phase of the disease epidemic.Sequencing Technology: High-throughput amplicon sequencing was performed using the Illumina MiSeq platform. The V3-V4 hypervariable regions of the bacterial 16S rRNA gene were targeted for amplification and sequencing to profile the bacterial community.Findings and Significance:Analysis of bacterial community alpha diversity (Chao1 index) indicated no statistically significant differences between tobacco and C. rotundus rhizosphere soils across the different disease stages. However, a general declining trend in species richness was observed as the disease progressed.Principal Coordinates Analysis (PCoA) based on Bray-Curtis distances revealed significant differences in bacterial community structure among the rhizosphere soils of tobacco and C. rotundus collected at different disease stages.Data Application and Impact:This dataset provides a crucial framework for understanding the field epidemiology of tobacco bacterial wilt. It moves beyond the traditional focus solely on the pathogen itself by integrating the dynamics of the broader rhizosphere microbiome of both the crop and a key weed reservoir. The findings highlight the compositional shifts in bacterial communities associated with disease stages and host plants, offering insights into potential microbial indicators of disease progression and the ecological role of weeds in pathogen survival. This resource is valuable for researchers studying plant-microbe interactions, soil-borne disease ecology, and developing integrated pest management strategies that consider the microbiome.