Exploring the mycorrhizal interactions and deciphering the fungal diversity associated with orchid hybrids from the genus Epidendrum

Abstract

Orchids are known for their exceptional floral morphologies, as well as their symbiotic relationships with specialized fungi known as orchid mycorrhizae. Existing literature indicates a significant gap in our understanding of the complex relationship between orchids and their mycorrhizal partners. Many common orchid mycorrhizae are recognized as pathogens of crops or are well-known saprophytes. It is not clearly understood how orchids form symbiotic relationships with these non-mycorrhizal fungi. Similarly, the diversity of fungi that form symbiotic associations with orchids is also sparse. Thus, this thesis contains four chapters that are aimed to partially reduce the aforementioned knowledge gaps. ‘Chapter One’ of this thesis focused on reviewing the existing knowledge of the biochemical and molecular interactions between plants and mycorrhizal fungi, with special reference to the significant knowledge gaps about the orchid-mycorrhizae relationship and suggestions on how these gaps can be filled. 'Chapter Two’ of the thesis aimed to isolate orchid mycorrhizal fungi associated with various Epidendrum hybrids popularly available as horticultural plants in South Africa using a culture-dependent process. In this process, various fungi were isolated from the roots of sampled Epidendrum plants as well as a previously undescribed orchid mycorrhiza. ‘Chapter Three’ aimed to understand if orchids from the same genus associate with overlapping fungi across their native and introduced regions. To answer this question, root samples of Epidendrum hybrids were procured from Brazil, Columbia, Germany, Spain and six provinces of South Africa. Then, high-throughput sequencing platform was used in conjunction with fungal-specific primers to catalogue the biodiversity of fungi associated with DNA extracted from these root samples. Following that, bioinformatics and statistical pipeline were employed to explore the data to answer the research objective of this chapter. ‘Chapter Four’ aimed to improve the progress of future genomic studies associated with Rhizoctonia-like fungi. To address this, the whole genome of an orchid mycorrhizal fungus, Ceratobasidium papillatum CBS 570.83 was sequenced, assembled, and annotated.