BIOCONTROL OF ROOT ROT COMPLEX IN FIELD PEA AND LENTIL AND COMPLETE GENOME ANALYSIS OF BIOCONTROL BACTERIA

Aphanomyces root rot (ARR), caused by the soil-borne oomycete pathogen, Aphanomyces euteiches, is a destructive disease of legumes, most notably to field pea (Pisum sativum L.) and lentil (Lens culinaris L.). It commonly occurs as root rot complex (RRC) along with other soil-borne pathogens, including Fusarium avenaceum and F. oxysporum, which collectively result in significant crop damage leading to complete loss of productivity. Currently, in Canada, the available management strategies against RRC are inadequate. However, a recent study at the University of Saskatchewan identified soil bacteria, Lysobacter capsici K-Hf-H2, Pseudomonas simiae K-Hf-L9 and Pantoea agglomerans PSV1-7, as potential biocontrol agents against ARR in field pea under controlled growth chamber condition. Therefore, the purpose of this study was to i) investigate the potential for biological control of RRC caused by A. euteiches, F. avenaceum and F. oxysporum and ii) unravel the mechanisms by which biocontrol was achieved. To achieve these objectives, L. capsici K-Hf-H2, P. simiae K-Hf-L9 and P. agglomerans PSV1-7 were evaluated against RRC in field pea and lentil under controlled growth chamber conditions, and the strains’ whole genomes were sequenced, annotated, and comparatively analyzed using bioinformatics tools. Also, laboratory-based general functional experiments, siderophores production, proteolytic and cellulolytic capacities, and desiccation tolerance were conducted. Additionally, the current state of the science "biological control of ARR" was determined via a quantitative meta-analysis review using data extracted from published articles investigating the biocontrol of ARR in pea. My meta-analysis findings suggest potential for biological control of ARR and the need for more field trials to demonstrate the higher efficacy level observed under growth chamber conditions. Compared to P. simiae K-Hf-L9 and P. agglomerans PSV1-7, L. capsici K-Hf-H2 demonstrated the highest significant biocontrol efficacy against RRC in field pea and lentil, with higher efficacy in field pea. Moreover, my genome analyses identified several genes and gene clusters encoding various traits potentially involved in the suppression of RRC. Such genetic determinants detected in L. capsici K-Hf-H2 genome include genes encoding for Heat Stable Antifungal Factor (HSAF), endoglucanase (cellulase), chitinase, extracellular zinc proteases (metalloendopeptidase), aminopeptidases and siderophores. In P. simiae K-Hf-L9 and P. agglomerans PSV1-7 genomes, gene and gene clusters encoding iron acquisition, chitin metabolism and protein degradation were detected. I also found evidence that L. capsici K-Hf-H2, P. simiae K-Hf-L9 and P. agglomerans PSV1-7 chelate iron through siderophore production and hydrolyze protein via proteolytic activity. Furthermore, L. capsici K-Hf-H2 and P. simiae K-Hf-L9 were positive for cellulolytic activity. Therefore, my findings indicate the great potential of biological control of RRC in field pea and lentil. Also, the findings in this study represent a significant contribution to the effort of biological control of RRC in field pea and lentil in Canada.

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