Past AMS Research Grant Recipients
2025
Ellie Fajer
University of Auckland
Investigating the potential of Fungal Endophytes to Combat Kauri Dieback
Growing up exploring the Rocky Mountains in Colorado, USA, Ellie has been a keen ecologist since childhood. She completed a Bachelor’s degree in Biology and Earth Systems at Stanford University (California, USA), where she discovered her passion for mycology. She continued to complete a Master’s degree on microbial ecology and global change at Stanford, with her research focusing on how ectomycorrhizal fungal communities influence carbon sequestration in boreal forests. Ellie was awarded a Fulbright Research Fellowship in New Zealand to investigate the potential of fungal endophytes to combat kauri dieback disease. Under the co-supervision of Drs. Bruce Burns and Maj Padamsee at the University of Auckland and Manaaki Whenua Landcare Research, Ellie plans to expand her Fulbright research into a PhD.
The towering kauri trees (Agathis australis) of New Zealand’s North Island shape their rich, biodiverse ecosystem and hold great cultural significance to the Māori people and other residents of New Zealand. However, the limited remaining kauri are facing extinction due to the pathogen Phytophthora agathidicida causing widespread kauri dieback. Certain fungal endophytes, fungi that live within plant roots and tissues, have been shown to help inhibit the growth and spread of plant pathogens. Ellie is interested in studying how fungal endophytes from kauri roots may inhibit P. agathidicida and potentially serve as a biological control agent to prevent further kauri dieback. Using the AMS Research Grant, Ellie will investigate the prevalence, diversity, and potential antagonism of kauri fungal endophytes utilizing high-throughput sequencing of field-collected root and soil fungal communities.
Adam Taranto
University of Melbourne
Pandora’s Transposons: Tracking mobile elements involved in the emergence of novel fungal pathogens
Recent pan-genome studies (sequencing many individuals of a species) have uncovered surprising genetic exchanges between distantly related fungal species, including genes, transposons, and occasionally whole chromosomes. This project will investigate the role of mobile genetic elements in the horizontal transmission of genes between distantly related fungal species that interact with shared host plants.
These horizontal transfers often include genes that provide selective advantages, enabling fungi to tolerate environmental toxins, consume novel energy sources, or expand their host range. Of particular interest are several complex composite transposons that have been transferred between multiple fungal pathogens, acting as a vehicle for virulence genes.
This project aims to identify the original fungal species that donated these composite transposons by sequencing genomes of fungi in which we have found examples of closely related transposon families. These fungi also share ecological niches with pathogenic species which present opportunities for horizontal transposon transfer to occur.
Funding from this grant will enable us to generate the first high-quality annotated genomes for this species as a community resource. This will enable systematic screening for horizontal gene transfer events between our target species and known pathogens.
Understanding the mechanisms and conditions necessary for mobilizing genes between species will help us to understand how novel fungal pathogens emerge and spread to new host plants. This knowledge has significant implications for predicting and managing emerging crop diseases, potentially leading to improved strategies for protecting crops that form the foundation of global food security.
2024
Eric Kumi Asare
Edith Cowan University
Investigating myrtle rust and other foliar fungal pathogens on Agonis flexuosa
Endemic to south-west of Western Australia (swWA), Agonis flexuosa (commonly called the WA peppermint) is an important tree species that provides habitat, food, and protection for fauna, particularly the vulnerable Western Ringtail Possum (Pseudocheirus occidentalis). However, this tree species is threatened by diseases caused by fungi including Phytophthora and Neofusicoccum australe. Commonly, these fungal pathogens cause dieback resulting in tree death. Recent detection of Austropuccinia psidii (myrtle rust) in the Kimberley adds to fungal pathogens threatening A. flexuosa in WA. It is uncertain how A. flexuosa will respond to a myrtle rust incursion in swWA, given that A. flexuosa has high rust susceptibility but is genetically diverse across native range. The strategic approach towards species conservation, which forms part of my PhD thesis, includes identification of resistant A. flexuosa individuals through artificial inoculations. Phenology studies will also be undertaken to identify species vulnerability periods. Further, my PhD investigates other fungal pathogens causing diseases on A. flexuosa, aiming to build a reference library of disease symptoms and existing pathogenic fungi. The findings of this study will facilitate disease differentiation from myrtle rust and increase our knowledge of fungal pathogens on A. flexuosa.
Eric Kumi Asare has gained experience during his research career in plant pathology as a mycologist. He has special interest in understanding how fungal pathogens spread and develop into epidemics, and management using cultural, biological and chemical control methods. However, he grows fungi for food and money. Simply, he is a mushroom farmer!
Ramalka Heshani Kasige
Western Sydney University
Build a better plant: the role of silicon and arbuscular mycorrhizal fungi to augment crop defense against Spodoptera frugiperda (Lepidoptera, Noctuidae) in Australia
Ramalka has been captivated by the insect world since childhood. She completed her Bachelor of Science (Hons.) in Zoology with First Class honors from the University of Colombo, Sri Lanka, focusing on the ecology and behavior of the Fall Armyworm (Spodoptera frugiperda) (FAW). She served as an Assistant Lecturer in university while being a volunteer, a journalist, and a Toastmaster. As she embarked on her PhD journey, her research interests shifted towards studying insect-plant interactions and uncovering natural biocontrol for pests. She is currently pursuing her PhD in Biology at Hawkesbury Institute for the Environment, Western Sydney University, under the guidance of Prof. Scott N. Johnson and Dr. Adam Frew, aiming to develop an innovative approach with silicon (Si) and arbuscular mycorrhizal (AM) fungi to manage FAW in maize.
Australian agriculture encounters serious challenges from invasive pests, especially armyworms. In the context of grasses, employing Si accumulation alongside AM fungi offers a dual approach for enhancing physical and chemical defenses against insect herbivory. Recent investigations suggest a potential augmentation of Si accumulation in the host by AM fungi while Si availability influences fungal colonization in roots. However, the implications of different fungal taxa and Si interactions on FAW remain unclear.
Using the AMS Research Grant, Ramalka will assess how AM fungal-enhanced Si uptake varying among different AM fungi in maize, different AM fungal families differentially affect plant Si, their effects on FAW and how Si and FAW effect on root-colonizing AM fungal diversity and composition. The findings will disentangle emerging patterns of the tripartite interaction and develop a framework for how fungi can alter defences in plants based on susceptibility to plant enemies. X: @Rama_Kasige
2023
Kylie A. Agnew-Francis
The University of Queensland
Exploring the Biodiversity of Australia’s Endemic Hericium Species.
Project Summary
Wood-decay fungi (also known as saprotrophic fungi) are among nature’s most efficient decomposers and nutrient recyclers. Their role as resource gatekeepers and habitat builders makes them essential to the health and survival of forest ecosystems, and particularly in supporting the restoration of rainforest environments. Accordingly, understanding the endemic diversity and distribution of wood-decay fungi is increasingly being recognised as an important marker for developing and monitoring conservation management strategies. In Australia, it is believed that there are between 50,000 – 250,000 species of fungi. Despite their abundance, recorded knowledge concerning endemic species is underdeveloped, to the extent that most species remain undescribed. Little is known as to their biological diversity, ecological importance, toxicity, medicinal properties, or other potential uses. This project will contribute to ongoing work in bridging the significant gap in knowledge surrounding Australian endemic wood-decay fungi by supporting the genetic characterisation of endemic Hericium species. Hericium is a rare genus of white-rot mushroom used in food and traditional medicine and reported to possess a variety of interesting therapeutic properties. In Australia, Hericium (designated H. aff. coralloides) are an endemic to temperate rainforests along the eastern and southern coastal regions, and throughout Tasmania, where they grow exclusively on Nothofagus (myrtle) species. The taxonomy and genetic diversity of Australian Hericium species is currently not well-established, which limits a comprehensive assessment of their biodiversity, distribution, ecological function, and conservation status. In partnership with BioPlatforms Australia (Functional Fungi Initiative), this work will utilise whole genome sequencing to provide essential genetic resources for advancing our understanding of Australian Hericium species at the molecular level. It will underpin ongoing efforts to comprehensively resolve taxonomic relationships of endemic Hericium species and improve our understanding of their ecological function and importance. Twitter: @kylieafrancis
Nicholas Chong
The University of Melbourne
Characterisation of the AbaA-BrlA-WetA module in the emerging model fungus Paecilomyces variotii
Project Summary
Paecilomyces variotii is an emerging model species that is commonly found as an environmental mold. AbaA, BrlA, and WetA make up a set of genes that is highly conserved in fungi that are commonly encountered in the environment, where the genes play fundamental roles in development, as well as other aspects of fungal biology. However, although the genes are conserved, how they function in specific species differs. This project will characterise these genes in P. variotii, including assessing gene expression, secondary metabolite production, in vitro alterations to various stresses, and electron microscopy. Further, an additional aim is to define the subcellular localisation of WetA, which has not been experimentally proven to date. The proposed strategy is to generate a transgenic strain expressing a functional WetA-Green Fluorescent Protein fusion to determine where WetA is primarily expressed and concentrated. This study will provide insights into the highly conserved AbaA-BrlA-WetA module in fungi broadly, as well as the specific functions in P. variotii, and further define its role in fungal development. Twitter: @nickchong_
2022
Aaron Brace
Edith Cowan University, Western Australia
How the soil fungal communities of Banksia woodlands respond to changing fire regimes
Project Summary
The impacts of changing fire regimes on native plant communities are more often viewed through a macroorganism focused lense, with less attention paid to microorganisms. This is despite their importance and how they interact with above ground biota. Soil fungi play instrumental roles in ecosystem function, yet in many ecosystems little is known about how soil fungi interact with plants to influence their survival and persistence. Fire-associated changes to above-ground biodiversity are well studied and often substantial with impacts likely of similar magnitude for soil fungal communities with implications for regeneration, recruitment, and ecosystem stability in fragile, high diversity ecosystems. This project aims to understand how soil fungi in Banksia woodlands around Perth, WA respond to fire in the first ~15 months following fires of varying severity and type. Insights will help to identify effects of fire severity and timing informing application of tools such as prescribed burning Twitter: @AaronBrace
Allison Mertin
University of Melbourne, Victoria
Understanding the diversity, biology and biogeography of Native Australian Seed Fungi for improving restoration and ex-situ conservation outcomes
Project Summary
This project will increase our knowledge of the unexplored diversity of fungal endophytes of native Australian plants. We will contribute to increasing our understanding of seed fungal endophyte biology and raise awareness of the unknown microbial diversity within native Australian seeds and their potential role in ecosystem function and plant survival, with applications to restoration and ex situ conservation. Specifically, through investigating biogeographical patterns we will increase our understanding of fungal endophyte dispersal methods and environmental factors that shape the seed ‘mycobiome’. Knowledge of seed mycobiomes from multiple co-occurring host species, will facilitate a better model of host ‘specificity’ for key seed fungal species. I will combine mycobiome identity (obtained from internal transcribed spacer (ITS) metabarcoding) with plant growth promotion potential (PGPP) phenotypes of isolated fungal strains to better understand the potential function of seed endophytes for Australian native plants. This project will promote the conservation of seed fungi by identifying fungal diversity in seed from field sites and comparing this diversity with that in seed from seed banks. A synthesized knowledge of seed microbiota will accelerate discovery and help future practices promoting the presence of important seed microorganisms for plant health and productivity. Twitter: @AllisonMertin
2020
Congratulations to our 2020 AMS Research Award recipients
The executive committee approved the awarding of three Research Awards for 2020:
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Elaine Davison, Research Associate, Curtin University, Project title: “Amanita umbrinella and its relatives”.
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Leanne Greenwood, PhD Candidate, Charles Sturt University. Project title: “How does fire effect arid fungal communities?”
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Rebecca Jane Webb, PhD candidate, James Cook University. Project title: “Glutathione biosynthesis in the amphibian fungus, Batrachochytrium dendrobatidis”.
2017
Amelia-Grace Boxshall
University of Melbourne, Victoria
Investigation of toxicity within southern Australian members of the mushroom genus Agaricus L. in a phylogenetic context.
Project Summary
Amelia-Grace is a student at the University of Melbourne. Her masters project unites the University of Melbourne, the Royal Botanic Gardens Victoria, and Deakin University, through supervision by Drs Joanne Birch, Teresa Lebel and Damien Callahan. Amelia-Grace’s project is the first to investigate the morphological diversity, evolutionary relationships, and chemical toxicity variation of yellow-staining Agaricus species in Australia.
One species of yellow-staining mushroom, Agaricus xanthodermus- which contains the poisonous chemical phenol- is responsible for 89% of the poisonings by deliberate ingestion reported to the Victorian Poisons Information Centre. However, anecdotal evidence dating back to the original description of the species by Genevier indicates variation in the toxicity of this species: sometimes consumption of this species results in gastrointestinal irritation and sometimes it doesn’t. The precise cause for the variation in toxicity is unknown but may be related to factors such as developmental stage, part of the mushroom consumed, habitat, or genetic variation in the form of cryptic species. To add to the mushrooming mystery, it has never been determined whether the Australian species currently known as A. xanthodermus is the same as the original, Northern Hemisphere species. In fact, the extensive morphological and habitat diversity of Australian individuals indicate the species name Agaricus xanthodermus may be misapplied to a number of distinct, yellow-staining species.
Amelia-Grace is using a combination of gas chromatography-mass spectrometry and high throughput amplicon sequencing. She is developing a phylogeny of Agaricus in southern Australia and is identifying factors to predict which yellow-staining Agaricus are likely to contain a high concentration of poisonous phenol and are therefore more likely to result in poisoning symptoms if consumed.
Using her AMS Research Grant, Amelia-Grace has made collections for both chemical and genetic analysis from under-collected locations across Victoria, including samples from areas of native vegetation. She’s also been able to expand sampling of herbarium specimens and increase the number of regions to be used for phylogenetic reconstruction. This has allowed Amelia-Grace to increase the taxonomic coverage of her project and capture as much of the toxicity variation present across Victoria as possible.
2016
Cecilia Li, Fungal Pathogenesis Group, Centre for Infectious Diseases and Microbiology at Westmead Institute for Medical Research
Investigating the role of the inositol polyphosphate kinase signalling pathway in fungal metabolism
Project Summary
Cecilia Li is a student at the University of Sydney, based at the Westmead Institute for Medical Research. She is currently in the final year of her PhD. She is supervised by Julie Djordjevic, Sophie Lev, and Tania Sorrell. Her project aims to investigate molecular mechanisms of Cryptococcus neoformans pathogenesis. C. neoformans initially infects the lungs and disseminates to the central nervous system (CNS), causing fatal meningoencephalitis. Up to one million cases of cryptococcal meningitis and around 600,000 deaths have been reported annually in AIDS patients alone. For C. neoformans to survive and replicate in the lungs, and disseminate to the CNS, it must adapt its metabolism to suit nutrient availability in the lung, an environment depleted of glucose.
Cecilia’s PhD studies have led to the identification and characterisation of a novel signalling pathway in C. neoformans. This pathway consists of a series of sequentially acting inositol polyphosphate kinases (IPKs: Arg1, Ipk1 and Kcs1) that convert IP3 to PP-IP5 (IP7). Cecilia’s work has established that mice infected with the IPK gene deletion mutants (which all lack PP-IP5) have lower infection burdens in the lung compared to wild type. This is due to their inability to metabolise non-glucose carbon sources. Thus, these IPK mutants fail to disseminate to the CNS. Other preliminary data suggest that mitochondrial function is compromised in the IPK mutant set, and that glycolysis is up-regulated.
Using her AMS research grant award, Cecilia has explored the role of the IPK pathway in cellular metabolism and energy production in real-time by using the Seahorse XFe24 Extracellular Flux Analyzer. Given that the instrument has never been used with non-adherent yeast cells before, Cecilia has had to optimise the attachment of cryptococcal cells, and also optimise the concentration of inhibitors needed to test metabolic flux. She is still working on optimising the concentration of one inhibitor by using an alternative substance.
Cecilia will then be in a position to identify differences in the metabolic function of IPK strains compared with the virulent wild-type strain, which could in turn provide answers to why the mutants are less virulent. This information could offer insight into how the inositol polyphosphate kinase signalling pathway regulates cellular metabolism and fungal virulence.
2015
Sarah Sapsford, Murdoch University, Perth, Western Australia
The biotic and abiotic factors predisposing marri (Corymbia calophylla) to canker disease (Quambalaria coyrecup) in the southwest of Western Australia
Project Summary
Sarah is currently completing her PhD in forest pathology at Murdoch University. Her project focuses on the factors that are causing the decline of marri (Corymbia calophylla) trees in Western Australia (WA). The decline of this species has devastating effects on wildlife habitats as well as the economy: marri are an important food source and nesting location for the endangered Carnaby’s black cockatoo (Calyptorhynchus latirostris) and are also one of the major honey plants in southwest WA which beekeepers are heavily dependent on. A canker caused by the fungus Quambalaria coyrecup, believed to be endemic to WA, has devastated many marri stands in the southwest of WA. It has been observed that incidences of Q. coyrecup are much greater in areas affected by anthropogenic activities such as parks, small remnants, peri-urban areas, cleared land used for farming and/or grazing and roadsides. It is possible that a combination of factors are predisposing marri to canker disease. For example, remnant stands of marri trees on road edges that border cleared land (usually a farm) have extremely high incidences of canker. However, across the road (on the opposite road edge) where there is a forest block, the incidence of canker dramatically decreases and reaches 0% incidence on trees that are at least 20 m away from the road edge. Predisposing factors leading to the decline of marri may include the use of pesticides and herbicides on these road edges (either by local council spraying road edges or run-off from adjacent farmland), soil pathogens such as Phytophthora spp., and changes in climate. These factors can have detrimental effects on concentrations of nutrients in the soil, soil composition, soil pH and, most importantly, microbial communities in the soil.
2014
Susan Nuske, James Cook University, Cairns, Queensland.
Mammal dispersal of ectomycorrhizal fungal spores
Project Summary
Susan Nuske is currently completing her PhD in Ecology at James Cook University, Cairns. Her project investigates the dispersal of ectomycorrhizal fungi by Australian mammals. Ectomycorrhizal fungi are an important group of soil fungi that associate with plant roots. In this association the fungi mine hard-to-access nutrients from the soil and transport them to the plant. In exchange the plants give sugars to the fungi. This association benefits both plants and fungi and the ecology of these two organisms are tightly linked.
Susan’s main interest lies in the third players in this interaction; the Australian mammals that consume and disperse the spores of ectomycorrhizal fungi. While wind-dispersed mushrooms are the best known ectomycorrhizal fungi, Australia is also home to a large diversity of below-ground fruiting fungi (truffle-like species), most of which are ectomycorrhizal. These truffle-like species rely on animals to dig-up, consume and disperse their spores. A literature review Susan has performed found that at least 53 Australian mammal species consume fungi. Although we can infer that mammals are important for maintaining ectomycorrhizal diversity, we only have a limited understanding of the extent of this interaction because knowledge of ectomycorrhizal fungal communities within Australia is very limited. By examining the whole ectomycorrhizal community and comparing this to the fungal species consumed by mammals, Susan is investigating whether mammals disperse a significant proportion of the ectomycorrhizal fungal community.
The most notable of these fungal-dispersers are bettongs and potoroos that specialise in consuming truffle-like fungi. Unfortunately, the distribution of these species has reduced significantly since European arrival, including the endangered Northern Bettong. The loss of Australia’s mammal abundance and diversity may have consequences for their functional roles as spore dispersers and overall ecosystem functioning. However, the ubiquity of mammal mycophagy across remaining mammal populations is not well known. Additionally, we do not have a clear understanding of the importance of specialist fungal-dispersers (bettongs and potoroos) over the dispersal roles of the many generalist fungal consumers (mammals like bush rats and swamp wallabies that consume fungi but do not rely on it in their diet). Susan will address these knowledge gaps by examining the fungal diet of the Northern Bettong and comparing this to other mammals within the same range. This will allow us to better understand whether modern mammal populations are important for maintaining functioning ectomycorrhizal forests.
Biography
Before delving into the mycology world, Susan’s biological interest was sparked by working with animals on a high school hobby farm. She started out majoring in Zoology for her Bachelor of Science (University of Queensland), but quickly became fascinated with the role animals play in interacting with and shaping their environment. Hence, Ecology became her main focus. Susan also could see the potential using genetic techniques for answering ecological questions and gained genetic skills in a 3rd year intensive course and research project working on parentage of Antechinus. In 2010 she completed an Honours year at UQ working on a non-invasive genetic technique for estimating population size for the endangered Bridled Nailtail Wallaby. After working as a research assistant, travelling and volunteering, Susan decided to start a PhD.