A Taxonomic and Phylogenetic Investigation of Conifer Endophytes of Eastern Canada

Abstract

Research interest in endophytic fungi has increased substantially, yet is the current research paradigm capable of addressing fundamental taxonomic questions?More than half of the ca. 30,000 endophyte sequences accessioned into GenBank are unidentified to the family rank and this disparity grows every year. The problems with identifying endophytes are a lack of taxonomically informative morphological characters in vitro and a paucity of relevant DNA reference sequences. A study involving ca. 2,600Picea endophyte cultures from the Acadian Forest Region in Eastern Canada sought to address these taxonomic issues with a combined approach involving molecular methods, classical taxonomy, and field work. It was hypothesized that foliar endophytes have complex life histories involving saprotrophic reproductive stages associated with the host foliage, alternative host substrates, or alternate hosts. Based on inferences from phylogenetic data, new field collections or herbarium specimens were sought to connect unidentifiable endophytes with identifiable material. Approximately 40 endophytes were connected with identifiable material, which resulted in the description of four novel genera and 21 novel species and substantial progress in endophyte taxonomy. Endophytes were connected with saprotrophs and exhibited reproductive stages on non-foliar tissues or different hosts. These results provide support for the foraging ascomycete hypothesis, postulating that for some fungi endophytism is a secondary life history strategy that facilitates persistence and dispersal in the absence of a primary host. This thesis provides an alternate approach to identifying endophytes by considering the whole fungus interacting within its natural habitat.iii Acknowledgements I would first like to thank my supervisor Dr. Keith A. Seifert for providing me with the freedom and support to conduct the research presented in this thesis as well as many other side projects and curiosities. Keith generously provided many opportunities to travel to domestic and international conferences, which made me more aware of the directions of global mycological research and provided the opportunity to meet many of the great mycological heroes and their contemporaries. Our discussions over the last five years have contributed to my development as a more well-rounded and openminded researcher, professional, and person; his honesty and integrity are qualities that all professionals should aspire to have. I am indebted to Keith for the knowledge, experience, and personal growth I gained over the last five years in his lab. I thank Dr. J. David Miller for providing stimulating discourse, travel and collecting opportunities, and of course the unique opportunity to work on this project, which proved to be an exciting and captivating experience. I hope that we can continue collaborating on this and other projects in the near future. Myron Smith provided support and advice throughout this process. The Carleton University Graduate Administrators Darlene Moss and Lisa Chiarel...

Analysis of fungal endophytes in Scottish Sitka spruce plantations shows extensive infections, novel host partners and gives insights into origins

“…Strains in this UNITE species hypothesis have previously been reported associated with lesions on Norway spruce (P. abies) in Norway, but are not reported to be pathogenic (Børja, Solheim, Hietala, & Fossdal, 2006). There is evidence of Diaporthe strains being beneficial in Picea (Tanney, 2016). Similar host range or taxonomic issues are evident for the isolate identified as Septoria matthiolae, which has only been isolated from Matthiola incana in New Zealand, and the isolate identified as Cryptosporiopsis actinidiae, which is a post-harvest pathogen of Kiwi fruit (Actinidia species) and is recorded from New Zealand and more recently Australia (Davison, Cunnington, & Tay, 2009).…”

Isolation and Characterization of Biologically Active Secondary Metabolites Produced by Foliar Endophytes of Red and Black Spruce from the Acadian Forest

“…Pathogens can occasionally produce visible host disease symptoms, potentially leading to plant mortality. The current definition of an endophyte is somewhat ambiguous, and represents a group of phylogenetically diverse fungi which inhabit healthy plant tissue, without producing disease symptoms (Carroll, 1988;Tanney, 2016). Endophytes have been discovered in all plants on the planet to date (Carroll, 1988;Rodriguez et al, 2009).…”

“…First healthy needles are collected, surface sterilized, and mycelium is sub-cultured once it emerges from a needle section on solid growth medium. Sporulation can occur spontaneously, or it can be induced which sometimes involves labour intensive protocols (Tanney, 2016). Sporulation facilitates morphological comparisons and provides taxonomically important information.…”

“…This step is complicated by the difficulty in differentiating morphologically similar taxa, which may be phylogenetically distinct (Tanney et al, 2015). Endophytes are frequently sterile in culture, and therefore cannot be identified based on characteristic sporulation morphologies (Tanney, 2016). If the axenic culture is sterile and sporulation cannot be induced, DNA is extracted and the ITS barcode is sequenced.…”

“…Using the ITS region alone is questionable, as it cannot differentiate between closely related taxa (Schoch et al, 2012;Sun & Guo, 2012). Identifying endophytes based on genetic sequence information is also complicated due to their enormous phylogenetic diversity, and absence of reference sequences in public databases and scientific literature (Tanney, 2016). There are currently more than 30, 000 unidentified endophyte ITS sequences published in GenBank, which can be attributed to these difficulties in identification.…”