Doctor of Philosophy (PhD)


Plant Pathology and Crop Physiology

Document Type



Soybean plants establish associations with a great diversity of microorganisms in their surrounding environment that can be either pathogenic or beneficial for plant health and fitness, depending on the plant-microbe interaction outcomes. The goal of this research was to identify putative beneficial bacteria associated with soybean plants and to determine the biological mechanisms of the soybean-associated beneficial bacteria (SABBs) applied as a seed treatment, particularly on how they affect the microbial community associated with soybean plants and on the soybean gene expression profiles in response to a soilborne pathogen, Rhizoctonia solani.

In line with this, culture-dependent techniques to test putative beneficial bacteria and formulate SABB consortia that promote plant growth and health were undertaken through a series of isolation, screening, and testing for compatibility among isolates, and efficacy in the laboratory, greenhouse and field conditions. Initial studies revealed the efficacy of single SABB in the laboratory and greenhouse conditions but a marginal efficacy in the field settings. SABB consortia were formulated based on the compatibility among the isolates having plant growth-promoting and antifungal activities. In field tests, SABB consortia performed better than single isolates, suggesting that multiple species with various beneficial activities likely maintain associated plant functions better in the field setting.

Microbial community analysis of the soybean root endosphere and rhizosphere with SABB seed treatment revealed no to marginal differences in alpha and beta diversity. Nevertheless, the soybean microbiome with seed treatments showed an increasing trend of species richness. The persistence of the seed treatment strains, Bacillus sp., Pseudomonas sp. D4, Enterobacter hormaechei, Achromobacter xylosoxidans, and Agrobacterium radiobacter, were consistently identified based on sequence-read similarity, differential abundance, and random forest (RF). The co-occurrence network revealed a complex structure with a non-random co-occurrence pattern suggesting mutualistic interactions of seed treatment strains with the key bacterial species in the soybean microbial communities.

Finally, the SABB seed treatment induced high levels of defense-related genes in soybeans before inoculation and upregulation of stress response genes involved in multiple biosynthesis and detoxification pathways upon infection of Rhizoctonia solani. This indicates that the SABB consortium improves plant fitness through a biopriming mechanism.

Overall, the results of this dissertation contribute to our understanding of how SABBs affect the soybean microbiome and the gene expression profiles in response to Rhizoctonia solani infection. This study provides valuable insights into the practical use of beneficial organisms in sustainable soybean production.



Committee Chair

Hyun Ham, Jong



Available for download on Monday, July 09, 2029

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