A multifaceted analysis of bacterial blotch diseases of mushrooms

Similar to most agro-ecological systems, cultivation of button mushrooms relies heavily on the dynamic interactions between the host, Agaricus bisporus, and soil microorganisms. Mushroom cropping systems are diverse ecosystems, inhabited by good (growth-promoters), bad (mushroom pathogens) and ugly (human pathogens) microorganisms together. In this research, we investigate bacterial pathogens of mushrooms, and their  interactions with the host and the soil microbiome, in order to better understand the key factors determining disease outbreaks in mushroom cultivation. To address these research questions, several genomic, microbial, physico-chemical and phytopathological experiments were performed, the results of which are described and discussed in seven chapters of this thesis. In Chapter 1, we introduce bacterial blotch a group of diseases that result in discoloration and disfiguration of mushroom caps of A. bisporus. Blotch not only reduces the total marketable crop due to compromised aesthetic value, it also lessens the overall yields due to pin death and lowers the shelf-life post-harvest, leading to severe economic losses globally. Despite being studied for over a century, the identity and taxonomy of blotch-causing organisms still remains unclear. Chapter 2 provides a detailed overview of genetic and regional diversity and the virulence of blotch causing organisms in Western Europe. It describes the molecular characterization of the phylogenetic and phenotypic diversity of bacteria colonizing the caps of diseased mushrooms, using prokaryotic genomics, with large implications in the study of symptomatic disease expression, development of diagnostic tools and design of localized strategies for disease management. Chapter 3 describes the development of multiplex TaqmanTM-qPCR assays for the detection of three blotch pathogens at low densities in environmental samples. It reports the diagnostic sensitivity and specificity, reproducibility and repeatability of the assays. Moreover, it includes successful validation and application of the assays for routine testing of samples associated with mushroom cropping systems, such as water, compost, peat source and casing soil. Chapter 4 investigates the infection dynamics and population dynamics of newly discovered brown blotch pathogen, P. salomonii, with that of ginger blotch pathogen, ‘P. gingeri’. It identifies the soil inoculum thresholds for both pathogens and elucidates the role of abiotic and biotic parameters such as casing soil composition and environmental humidity for their blotch outbreaks. It also studies the endemic and inoculated pathogen populations in various casing soils. Chapter 5 reports the development of soil suppressiveness to ginger blotch in consecutive mushroom cultivation cycles, despite increasing pathogen populations. It describes changes in the soil microbial community due to pathogen invasion, pathogen establishment and blotch suppression, and identifies specific bacterial and fungal genera that are associated with blotch suppression. It also reports on the transferability of blotch suppressiveness to conducive soils with aqueous soil extracts. Chapter 6 proposes three circular alternatives for replacement of peat in mushroom casing soils. It evaluates the agronomical performance, physico-chemical characteristics, and the soil microbiome of these peat-reduced growing media. It addresses trade-offs between productivity and disease pressure in these circular cropping systems, with regard to the diversity, composition and interactions within their microbiomes. It also comments on the accessibility and sustainability of these peat-alternatives. Chapter 7 discusses the main findings presented in this thesis, integrates these results with existing knowledge on bacterial blotch and elaborates on their advantages and limitations, with particular focus on blotch management. Finally, it places this research in context for localized and ecological management of soil-borne diseases in mushroom cropping systems, and the future research required to achieve sustainable and blotch-free mushroom cultivatio