Fire-associated shifts in the soil microbiome in western conifer forests: implications for Armillaria root disease biocontrol and management
Date
2024
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Abstract
The research presented in this thesis integrates the current understanding of environmental disturbances, plant associated microbiomes, and microbial biological control of fungal forest pathogens to contribute to improved disease management. In Chapter 2, I examined how fire disturbances affect soil microbial communities in areas where Armillaria root disease, caused by the pathogen Armillaria solidipes, is prevalent by documenting changes to bacterial and fungal community diversity and composition following three distinct levels of burn severity (high, low, and unburned) in a conifer forest in northern Idaho, United States. Expected reductions in bacterial community alpha diversity were observed when comparing burned communities with unburned communities; however, fungal communities showed a lack of significant change in alpha diversity in response to burn severity at the sampling time of 15-months post-fire. However, in both bacterial and fungal soil communities, compositional changes corresponding to burn severity levels were observed. Further examinations characterized similarities and differences between burn severity-associated communities and Armillaria species-associated communities to determine how these microbial changes might influence Armillaria root disease. At high-severity burn sites, colonization by A. solidipes and the associated microbial community was prevalent when compared with low-severity burn and unburned sites. In contrast, the presence and abundance of the weakly pathogenic species A. altimontana and its associated microbial community, including beneficial ectomycorrhizal fungi, appeared to be negatively impacted by high-severity burns. Further research is needed to determine which microbial taxa are critical for promoting or suppressing A. solidipes activity, yet the results from this study suggest that high-severity burns may create environments hospitable to this pathogen and thus monitoring for increased disease pressure following severe burns may be warranted. Chapter 3 focuses specifically on beneficial members of the native soil microbial community that exhibit antagonistic activity against A. solidipes. Because these native species are adapted to the environmental conditions and community interactions, they are more likely than foreign microbial species to successfully establish a stable population required for effective biological control. I isolated putative native biological control agents from soil samples collected under different burn severity conditions and tested their in vitro capabilities to inhibit the growth of A. solidipes with dual culture confrontation tests. Effective in vitro pathogen inhibition was observed with 10 microbial isolates, including five bacterial isolates from the genera Bacillus and Caballeronia and five fungal isolates from the genera Trichoderma and Mortierella. Further examination of the sites these microbes and communities originated from and their compositional changes documented in Chapter 2 revealed that the presence or abundance of our effective biological control organisms did not differ based on burn severity. Importantly, this suggests that fire disturbances may not directly influence the use of these species in management methods for Armillaria root disease in similar conifer forests. However, considering the increased presence of A. solidipes observed following a high-severity burn, there may be additional biotic or abiotic influences apart from biological control agents that are influencing the activity of A. solidipes after fire. These studies enhance our understanding of how abiotic and biotic influences interact to affect the presence of virulent soilborne forest pathogens and associated soil microbes. Considering the effects of these interactions is critical for the development of sustainable long-term management strategies that will help to preserve these ecosystems facing increasing environmental and pathogen-related stressors. The overall goals of this research are to build upon the growing body of research examining how the soil microbiome contributes to disease development and to provide tangible results that can be incorporated by forest managers to help reduce damage caused by Armillaria root disease in fire-prone conifer forests.