Deciphering the rhizosphere bacteriome associated with biological control of tobacco black shank disease

Yi-Nan Ma; Yi-Lin Gu; Jing Liu; Yuqin Zhang; Xinwei Wang; Zhenyuan Xia; Hai-Lei Wei

doi:10.3389/fpls.2023.1152639

Deciphering the rhizosphere bacteriome associated with biological control of tobacco black shank disease

Front Plant Sci. 2023 Apr 3:14:1152639. doi: 10.3389/fpls.2023.1152639. eCollection 2023.

Authors

Yi-Nan Ma¹, Yi-Lin Gu¹, Jing Liu², Yuqin Zhang³, Xinwei Wang⁴, Zhenyuan Xia⁵, Hai-Lei Wei¹

Affiliations

¹ Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.
² Zunyi Tobacco Company of Guizhou Provincial Tobacco Corporation, Zunyi, China.
³ China National Tobacco Corporation Shandong Branch, Jinan, China.
⁴ Key Laboratory of Tobacco Pest Monitoring & Integrated Management in Tobacco, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China.
⁵ Yunnan Academy of Tobacco Agricultural Science, Kunming, China.

Abstract

Introduction: The black shank disease seriously affects the health of tobacco plants. Conventional control methods have limitations in terms of effectiveness or economic aspects and cause public health concerns. Thus, biological control methods have come into the field, and microorganisms play a key role in suppressing tobacco black shank disease.

Methods: In this study, we examined the impact of soil microbial community on black shank disease basing on the structural difference of bacterial communities in rhizosphere soils. We used Illumina sequencing to compare the bacterial community diversity and structure in different rhizosphere soil samples in terms of healthy tobacco, tobacco showing typical black shank symptoms, and tobacco treated with the biocontrol agent, Bacillus velezensis S719.

Results: We found that Alphaproteobacteria in the biocontrol group, accounted for 27.2% of the ASVs, was the most abundant bacterial class among three groups. Heatmap and LEfSe analyses were done to determine the distinct bacterial genera in the three sample groups. For the healthy group, Pseudomonas was the most significant genus; for the diseased group, Stenotrophomonas exhibited the strongest enrichment trend, and Sphingomonas showed the highest linear discriminant analysis score, and was even more abundant than Bacillus; for the biocontrol group, Bacillus, and Gemmatimonas were the largely distributed genus. In addition, co-occurrence network analysis confirmed the abundance of taxa, and detected a recovery trend in the network topological parameters of the biocontrol group. Further functional prediction also provided a possible explanation for the bacterial community changes with related KEGG annotation terms.

Discussion: These findings will improve our knowledge of plant-microbe interactions and the application of biocontrol agents to improve plant fitness, and may contribute to the selection of biocontrol strains.

Keywords: amplicon sequencing; biocontrol agent; co-occurrence network; microbiome; tobacco black shank.

Grants and funding

This work was financially supported by the Science and Technology Programs of the Zunyi Tobacco (2021XM03) and Shandong Tobacco (KN273) and the Major Science and Technology Project of China National Tobacco Corporation [110202201005 (JY-05)]. The authors declare that this study received funding from Zunyi Tobacco and Shandong Tobacco. The funders were not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication.