(Project Code: FFIRFP1-1)
Project Lead: Dr. Caterina Selva (Flinders University, College of Medicine and Public Health)
Collaborators: Dr. Julian Schwerdt, Dr. Long Yu, Prof. Vincent Bulone (Flinders University, College of Medicine and Public Health)
Project summary: Mucormycosis is a severe fungal infection caused by species within the Mucorales order and is associated with extremely high mortality rates. This project will generate whole-genome sequencing and transcriptomic datasets from Australian clinical and environmental strains of Rhizopus arrhizus, the most common mucormycosis agent. These datasets will be used to investigate the underlying invasiveness and pathogenicity of this fungus and identify novel targets for disease control.
(Project Code: FFIRFP1-2)
Project Lead: Dr. Alistair McTaggart (Funky Fungus)
Collaborators: Christopher Appleyard (Funky Fungus), Dr. Donald Gardiner (University of Queensland), Assoc. Prof. Esteban Marcellin Saldana (Metabolomics Australia)
Project summary: Magic mushrooms are fungi that produce psilocybin, a compound with breakthrough potential for treatment of mental health disorders such as addiction, anxiety, depression, post-traumatic stress disorder, and patients who are terminally ill. Designer magic mushrooms were bred based on allelic differences in the psilocybin secondary metabolite pathway. The project aims to identify whether genetic differences in the genes that control production of psilocybin translate to phenotypic differences in concentration of psilocybin and its related tryptamines. The outcome of this research is to identify the best genotypes of magic mushroom for clinical use.
(Project Code: FFIRFP1-3)
Project Lead: Dr. Ernest Lacey (Microbial Screening Technologies)
Collaborators: Assoc. Prof Andrew Piggott (Macquarie University), Assoc. Prof. Heng Chooi (University of Western Australia), Dr Yu Pei Tan (Queensland Department of Agriculture and Fisheries), Prof. Roger Shivas (Queensland Department of Agriculture and Fisheries)
Project summary: Eurotiales are 1 of 160 taxonomic orders of fungi according to the Catalogue of Life and are dominated by 4 genera (Aspergillus, Paecilomyces, Penicillium, and Talaromyces) that represent 85 % of the Eurotiales and ~1.5 % of all known fungi. Despite their global abundance the genera are grossly under-explored, particularly in Australia. Microbial Screen Technologies (MST) has isolated ~2,000 cultures of Eurotiales from around Australia, collected during the 1990s and early 2000s. These species possess interesting and unusual metabolomics, and a sub-sample of these species has led to isolation of >1,000 commercial laboratory fine chemicals and many new metabolites. This project complements metabolite discovery with genomics to broaden the scientific knowledge of fungi, and enhance the valuable commercial applications and production of fungal metabolites by understanding and leveraging the associated gene pathways. By creating genomic resources for individual fungi alongside metabolite profiling, MST is expanding their contribution to Australian science by unlocking novel fungal secondary metabolites to accelerate the knowledge of fungal functions and drug discovery.
(Project Code: FFIRFP1-4)
Project Lead: Dr. Ernest Lacey (Microbial Screening Technologies)
Collaborators: Assoc. Prof Andrew Piggott (Macquarie University), Dr Yu Pei Tan (Queensland Department of Agriculture and Fisheries), Prof. Roger Shivas (Queensland Department of Agriculture and Fisheries)
Project Summary: In the order Hypocreales, entomopathogens (pathogens of insects) belong primarily to three families: Clavicipitaceae, Cordycipitaceae, and Ophiocordycipitaceae. Comprising approximately 700 species across 90 genera, these fungi represent a mere 1% of all fungi, with likely underestimation due to recent active collection and cultivation efforts. The Queensland Fungi Collection (BRIP) have amassed a remarkable collection of 1,094 strains of entomopathogens over two decades, making it one of the world’s largest repositories. Derived from ants, flies, and spiders in tropical Australian rainforests, these strains span 61 genera within Clavicipitaceae, Cordycipitaceae, and Ophiocordycipitaceae. Most of the isolates have not been identified to species level and this Collection undoubtedly holds many taxa that represent novel species, which await classification and understanding. This project aims to expand our knowledge of Australia entomopathogenic diversity, enhance genomic and metabolomic discovery of new fungal taxa and metabolites, and provide a resource for biodiscovery and fine chemical production.
(Project Code: FFIRFP1-5)
Project Lead: Dr Belinda Ferrari (University of New South Wales)
Collaborators: Prof. Brett Summerell (Royal Botanic Gardens Domain Trust, Sydney), Dr Nicole Benaud (UNSW), Dr Priyanka Majumdar (UNSW), Dr Xabier Vazquez Campos (UNSW)
Project Summary: Antarctica’s ice-free regions, marked by extreme conditions, lack extensive studies on fungal biodiversity and functions. This project will use in several targeted analyses with the intention of gaining insight into resilience strategies of fungi surviving in the nutrient poor, cold desert environments of eastern Antarctica. This project aims to provide insights into fungal species from Antarctica, while integrating genomics with standardised physiological and morphological assessments for new species descriptions. The multi omics data approach in this project will enable pivotal research to be addressed about fungal resilience and responses to environmental change in Antarctica. In addition, Antarctic fungi produce pigments as a survival strategy to protect against the environmental stresses of high UV, freeze-thaw cycles and oxidative stress. Natural pigments may offer alternatives to synthetic dyes across diverse industries and also exhibit antimicrobial potential.
(Project Code: FFIRFP1-6)
Project Lead: Dr Camille Truong (Royal Botanic Gardens Victoria)
Collaborators: Dr Teresa Lebel (State Herbarium of South Australia), Prof Anne Pringle (University of Wisconsin-Madison, USA), Dr Gareth Holmes (Royal Botanic Gardens Victoria), Dr Ed Biffin (State Herbarium of South Australia)
Project Summary: The genus Amanita contains some of the world’s most poisonous mushrooms, including the death cap A. phalloides and the fly agaric A. muscaria. Both species were introduced to Australia together with exotic trees and are currently spreading dramatically. Amanita phalloides produce potent cyclic peptide toxins, such as α-amanitin, which places it among the deadliest organisms known to mankind. Death caps are the major cause of mushroom-related fatalities and increasing numbers of emergency department visits in the country. Little is known about the toxicity of Amanita species that are native to Australia, such as A. marmorata (phalloides clade) and A. xanthocephala (muscaria clade). However, a few historical and recent poisoning cases, with some symptomology, have been linked to these native species. The increased interest for the use of wild mushrooms for recreational purposes is therefore of rising concern in Australia. This project will obtain high coverage, annotated genomes of A. phalloides, A. muscaria, and their native relatives A. marmorata and A. xanthocephala to characterise the range of toxin genes in these species and Australian populations, and decipher the genetic mechanisms (mating type genes) behind the reproductive strategy of these native and invasive species.
(Project Code: FFIRFP1-7)
Project Lead: Isobel Colson (Western Sydney University)
Collaborators: Meagan Hinds (NSW Department of Planning and Environment), Dr Jordan Bailey (NSW Department of Primary Industries), Prof. Jeff Powell (Western Sydney University), Dr Tom May (Royal Botanic Gardens Victoria)
Project Summary: This project is focused on the taxonomy, ecology and conservation of one of Australia’s protected groups of fungi, known as ‘waxcaps’. In Australia, ‘waxcap’ fungi are found in highest diversity and abundance in rainforest and forest ecosystems where they produce small, colourful fruiting bodies (basidiocarps) among mosses, leaf litter and forbs on the forest floor. This protected group of Australian fungi not only require taxonomic revision, but little is known about their true diversity and trophic status. Recent studies of carbon and nitrogen stable isotope ratios indicates that they may have a biotrophic strategy for obtaining nutrition, that is they rely on a host plant or other organism to provide them a source of carbon, however the level of specificity to a certain host is not known. A greater insight into their interactions with other organisms will help to predict their distribution, ecological functions and identify suitable habitat or host species within their range. It is anticipated that this work will contribute to global understanding of the taxonomy and ecology of this group of fungi.
(Project Code: FFIRFP1-8)
Project Lead: Agnieszka Mudge (The University of Queensland)
Project Summary: The Basidiomycete Ganoderma P. Karst is a large genus of polypore white rot fungi in the family Ganodermataceae. This is a global genus, with various species naturally occurring in wide range of ecosystems from cool temperate to tropical climates. Members of the genus are saprophytic decomposers of dead woody material and thus play an important role in the recycling of nutrients in natural ecosystems. The data generated from this project will substantially increase our knowledge of the species composition and genetic diversity of Ganoderma in tropical and subtropical regions of Australia. This data will add information of Australian G. boninense to the genomes of G. boninense from Indonesia and Malaysia which are already available, allowing for a more representative pangenome, as well as contributing data to understand the greater diversity of Ganoderma species.
(Project Code: FFIRFP1-9)
Project Lead: Ema Corro (Mycommunity Applied Mycology Inc.)
Collaborators: Sapphire McMullan-Fisher (Fun Fungi Ecology), Gayle Osborne (Wombat Forestcare), Amanda Morgan (Fungi Solutions), Allison Wiseman (PlanTek), Terrence Ross (AT Mushrooms), Alexander Idnurm (The University of Melbourne)
Project Summary: The project is lead by a community driven organisation who are contributing to knowledge of fungi in Australia by collaborating with citizen scientists and small companies to both discover species and support the use of fungi for ecological solutions. This project will create reference data for a diverse set of taxa that are of interest to small and medium companies working across mycomaterials, food and supplements and ecology in Australia. For example, there are a number of species from different genera (especially Ganoderma) that are of interest for mycomaterials due to the structural properties of their mycelium. Using native species in these technologies would reduce the potential for introducing potentially invasive species to Australia and also provide industry incentive to preserve native species. It is also illegal to commercially grow many of the species that are used in mycomaterials in Australia as they are non-native and not covered by BICON. However, there is confusion about whether some of these species are actually native or introduced. Genomic data will allow the taxonomy of these species to be clarified.
(Project Code: FFIRFP1-10)
Project Lead: Dr Rita Busuttil (Monash University/ Alfred Hospital)
Collaborators: Prof Alex Boussioutas (Monash University/ Alfred Hospital), James Fuller (Fable Foods)
Project summary: The Cordyceps spp. are species-specific entomopathogenic fungi that have long been used in traditional Chinese Medicine. The most well-known and characterised of these is Cordyceps sinensis (caterpillar fungus), which is commonly found in Asian countries and is reported to have significant pharmacological and biological benefits. Australia has several naturally occurring species of Cordyceps, with Cordyceps gunnii being the most common and abundant. This species is of interest for human consumption, however, unlike its Chinese counterpart the medicinal properties of C. gunnii have not been well characterised. This project seeks to use untargeted metabolomic techniques to identify functionally active compounds of C. gunnii which confer cancer cell-killing properties and could ultimately be used in a clinical setting.
(Project Code: FFIRFP1-11)
Project Lead: Dr Cécile Gueidan (CSIRO, Australian National Herbarium)
Collaborators: Dr Lan Li (CSIRO, Australian National Herbarium), Dr Camille Truong (Royal Botanic Gardens Victoria), Dr Gareth Holmes (Royal Botanic Gardens Victoria), Dr Teresa Lebel (State Herbarium of South Australia), Dr Tom May (Royal Botanic Gardens Victoria), Dr Matt Barrett (Australian Tropical Herbarium, James Cook University)
Project Summary: This project will unearth the potential of our national and historic fungal collections by generating phylogenomic data of more that 400 fungal taxa that can be used to assess the diversity and taxonomy of Australian members of the focal fungal groups (Cladia, Peziza s.l., Cortinarius, Russula/Lactarius, Polyporaceae).
This project will also implement methodological protocols and assess the quality of genomic data obtained from dried fungarium specimen across ages, to inform whether old collections, and more specifically type specimens, can be used to generate reference genomes or phylogenomic data.
(Project Code: FFIRFP1-12)
Project Lead: Nonthakorn (Beatrice) Apirajkamol (PhD Candidate – Macquarie University)
Collaborators: Dr. Tom Kieran Walsh (CSIRO), Dr. Wee Tek Tay (Food standards Australia and New Zealand), Mark Rullo (Australian Wild Herbs & Mushrooms)
Project Summary: This project is exploring a key set of fungi that are pathogenic on insects including Beauveria bassiana, Cordyceps gunnii and Ophiocordyceps robertsii. Creating genomic and transcriptomic data, alongside metabolomic data for these Australian fungal species will help to understand their pathogenicity and potential to be used as as part of pest management strategies.
(Project Code: FFIRFP1-13)
Project Lead: Dr Kylie Agnew-Francis (The University of Queensland)
Collaborators: Nigel Fechner (Queensland Department of Environment and Science, Queensland Herbarium), Mickey Pascoe (Future Farms Australia), Prof Ben Schulz (The University of Queensland), Prof James Fraser (The University of Queensland), Wayne Boatright (Queensland Mycological Society), Prof Avril Robertson (The University of Queensland), Dr Rhys Parry (The University of Queensland)
Project Summary: Australian rainforests are home to a remarkable diversity of native macrofungi. Despite their vital ecological roles, our knowledge of Australian mushrooms is severely lacking, and many species remain unidentified. This project intends to tackle this challenge by conducting comprehensive biomolecular surveys and biodiversity assessments of our native rainforest macrofungi. Through these efforts, we can identify new fungal species, explore their genetic and biochemical diversity, and unveil novel properties. This project aims to survey the genomic, transcriptomic, proteomic, and metabolomic architecture of a selection of native mushroom species found across Tasmania, Queensland, Victoria, and New South Wales. We will focus on genera with known or suspected medicinal, toxic, or nutritional value, including Polyporus, Ramaria, Cordyceps, Lentinula, Pleurotus, as well as species lacking formal identification.
(Project Code: FFIRFP1-14)
Project Lead: Dr Kylie Agnew-Francis (The University of Queensland)
Collaborators: Nigel Fechner (Queensland Department of Environment and Science, Queensland Herbarium), Mickey Pascoe (Future Farms Australia), Prof Ben Schulz (The University of Queensland), Prof James Fraser (The University of Queensland), Wayne Boatright (Queensland Mycological Society), Prof Avril Robertson (The University of Queensland), Dr Rhys Parry (The University of Queensland)
Project Summary: This project seeks to survey the biodiversity and molecular features of native Australian mushrooms from the Hericium genus (also known a Lions Mane). Hericium are rare species of wood-rot fungi, used widely in the northern hemisphere as food and in traditional medicines due to their positive effects on cognitive function. In Australia, Hericium are an endemic species found in the cooler months in temperate rainforests along the eastern and southern coastal regions, and throughout Tasmania. Based on the morphological diversity of these species in Australia, as well as DNA barcoding in herbarium specimens in Victoria (unpublished data), it is likely that Australia is home several undescribed species of Hericium. Native specialty mushrooms like Lion’s Mane, command prices upwards of $80/kg and global demand for specialty mushrooms is predicted to grow from 15.5mill tonnes (2021) to 24.05mill tonnes by 2028 (~$AUD77bil). Lion’s mane is currently a popular gourmet mushroom sold within in Australia due to its taste, medicinal benefits, and high nutritional content. Introduction of new native species would allow for greater penetration into both the native bushfoods and alternative proteins markets. The data generated by this project aims to identify of native Hericium with superior nutritional and bioactive metabolite content that may be developed as an innovative, uniquely Australian food product.
(Project Code: FFIRFP1-15)
Project Lead: Assoc. Prof. Yit Heng Chooi (University of Western Australia)
Collaborators: Dr Nicolau Sbaraini (University of Western Australia), Prof Megan Ryan (University of Western Australia), Prof Martin Barbetti (University of Western Australia), Dr Mingpei You (University of Western Australia), Dr Kar-Chun Tan (Curtin University, Centre for Crop and Disease Management)
Project Summary: The Sordariomycetes is a significant class of Ascomycota fungi, boasting nearly 30,000 described species. These organisms exhibit remarkable variability in morphology, habitat, host, and growth form. Their vast genomic plasticity allows them to produce a variety of enzymes and secondary metabolites. Among the extensive diversity of Sordariomycetes, those with endophytic, mycoparasitic, and coprophilic lifestyles (like the species described above) remain under-explored compared to plant and animal pathogens. Many of these fungi have potential applications in agriculture, i.e. as biocontrols for crop protection and as biostimulant to improve plant immunity, as well as biotechnological applications, e.g. production of bioactive molecules as bioherbicides and nutraceuticals. Genomic sequencing and information (genes encoding biosynthetic gene clusters) from these organisms can aid in the discovery of bioactive molecules of commercial and scientific interest, as well as understanding the mechanism of action of their biocontrol and biostimulative properties, which often associate with the metabolites they produced. This project will create whole genome and metabolomics data from a broad range of Sordariomycetes that can be used to establish a fundamental platform to understand the biology, as well as the scientific and commercial applications of endophytic, mycoparasitic, and coprophilic Australian fungi.
(Project Code: FFIRFP1-17)
Project Lead: Dr Paul Dennis (University of Queensland)
Collaborators: Dr Roger Shivas (Queensland Department of Agriculture and Fisheries)
Project Summary: The core microbiomes of plants, animals, and soils comprise fungal lineages that contain both non-pathogenic and pathogenic populations. While the pathogens within these core lineages have been studied quite extensively, their non-pathogenic relative, which dominant healthy plants have been relatively ignored. Hence, their functions within healthy microbiomes are relatively poorly understood. This project will create whole genome data for a vast range of non-pathogenic fungi from lineages commonly identified as being members of the core microbiome of plants, animals (mostly insects). The information will help to understand their potential roles within their respective communities and further aid our understanding of host-fungal relationships.
(Project Code: FFIRFP1-19)
Project Lead: Chris McLoghlin (Rainstick)
Collaborators: Dr Alistair McTaggart (Funky Fungus), Assoc. Prof Esteban Marcellin Saldana (Metabolomics Australia), Christopher Appleyard (Funky Fungus), Dr Mic Black (Rainstick)
Project Summary: Rainstick is an Australian Indigenous lead Start-up company that simulates the properties of lightning to control phenotypes of plants and fungi. Preliminary work by Rainstick has prevented development of contaminant mould spores, whilst increasing overall mushroom yield by over 15%, and increasing harvest speed over 15%. Rainstick are developing a technology to benefit industries that grow fungi and plants, whether through activating desired phenotypes, increasing growth and metabolite production, or decreasing contamination. A synergy between Rainstick and Funky Fungus will explore how and why electrostatic waveforms impact the genetics and metabolic expression of magic mushrooms at different stages of their life cycle (culture, primordia, and fruiting mushrooms). This has potential implications for production dynamics including costs, sanitation, speed and composition and then subsequently treatment dynamics from efficacy to availability of psilocybin.
(Project Code: FFIRFP1-20)
Project Lead: Chris McLoghlin (Rainstick)
Collaborators: Assoc. Prof Esteban Marcellin Saldana (Metabolomics Australia), Dr Mic Black (Rainstick)
Project summary: TBD
(Project Code: FFIRFP1-21)
Project Lead: Peter Wenzel (Fungi Co)
Collaborators: Dr Andrzej Killian (Diversity Array Technologies – DArT)
Project Summary: Morel mushrooms (Morchella spp.) are a highly sought after culinary wild mushroom, with approximately 80 species worldwide. Considered elusive, they appear in the wild for limited periods, generally Springtime. Their life cycle remains poorly understood and includes species that appear to grow saprophytically and/or associated with other organisms (plant roots or bacteria), as well as other phenomena such as fire. Successful cultivation of some species has been demonstrated, however much remains to be learned about the biology and ecology of this genus worldwide. Australia has several recorded species; however these occur seasonally and for a short period. Fetching a considerable price, morels are more likely to end up in a high-end restaurant than a research laboratory. However, this project has the unique capability of obtaining a large number of native species through established collaborating networks. Genomics sequencing will contribute to the knowledge of Australia’s Morchella genus, as well as providing further insights into cultivation by using genomic data to monitor and compare growth conditions found in the native environment.
(Project Code: FFIRFP1-22)
Project Lead: Prof. Celeste Linde (Australian National University)
Collaborators: Dr Benjamin Schwessinger (ANU), Dr Rod Peakall (ANU), Dr Darren Wong (ANU)
Project Summary: Tulasnella, Serendipita and Ceratobasidium species are the main fungal genera that are mycorrhizal to orchids. These fungi are not dependent on orchids, and survive as saprophytes in the absence of orchids. The fungi belong to the Division Basidiomycota, Class Agaricomycetes. Because orchid seed lack an endosperm, they are completely dependent on orchid mycorrhizal fungi for germination and subsequent seedling establishment. Terrestrial orchids continue to rely on mycorrhizal fungi for nutrition into adulthood. Thus, orchids cannot survive without interacting with a suitable, compatible mycorrhizal fungal partner. A major function of the OMF partners is to supply plants with essential macro- and micronutrients. The mutualistic interaction between orchids and fungi are unique in that nutrients and carbon need to be supplied during germination, whereas host plants export photosynthetically fixed carbon to the fungal partners for exchanging mineral nutrients. Although knowledge of nutrients involved in germination is crucial for ex situ conservation programs the genes involved in this exchange has been poorly studied, and often the nutrients required for germination is unknown. Unfortunately, we know very little about the genomes and genetics of orchid mycorrhizal fungi in general with only a handful of partial genomes available in the public domain. None of these resources are from Australian orchid mycorrhizal fungi. This project will perform a detailed transcriptomic study of the interaction fungi in their symbiotic host by comparing in vitro grown fungi with symbiotically germinated seeds and naturally colonised roots of adult plants. This will enable us to identify genes involved in fungal recognition and nutrient exchange, and advance our understanding of plant-microbe interactions.
(Project Code: FFIRFP1-23)
Project Lead: Prof. John Rathjen (Australian National University)
Collaborators: Jack Wess (Australian National University)
Project Summary: This novel project will explore hyperparasitic fungi of fungal rusts. Fungal rusts cause devastating diseases in agriculture and nature; important diseases in the Australian context are stem, stripe and leaf rusts of cereals, and myrtle rust of myrtaceous native species. Control options for these diseases are limited and unsatisfactory so new approaches are needed. One potential control option is fungal hyperparasites which can be isolated relatively easily from the environment on rust-infected plant material. We have a program in place which has identified about 40 such isolates. These are ascomycete fungi which are easily cultured and have small haploid genomes. We have sequenced two of these and obtained transcriptomes for axenic and hyperparasitic growth. The data will be used to identify genes associated with hyperparasitism eg by comparative transcriptomics and CRISPR knockouts. This program aims to provide foundation studies about mechanisms underlying hyperparasitism, and provide new strategies for rust control eg by deployment of hyperparasites or bioactive molecules obtained from them.
(Project Code: FFIRFP1-24)
Project Lead: Sherie Bruce (PhD Candidate – University of Queensland)
Collaborators: Prof. Yasmina Sultanbawa (UQ), Dr Alistair McTaggart (UQ), Ben Lee (Djurrubu Rangers), Kym Brennan (NT Botanist), Anna Boustead (Indigenous Carbon Industry Network), Gundjeihmi Aboriginal Corporation, Parks Australia – Kakadu
Project Summary: Kakadu is the largest National Park in Australia and one of the largest in the tropics, protecting the greatest variety of ecosystems on the Australian continent, including savannah woodlands, open forest, floodplains, mangroves, tidal mudflats, coastal areas, and monsoon forests. The park contains a diverse flora and is one of the least impacted in northern Australia. The Bininj/Mungguy Peoples have lived in Kakadu for over 50,000 years, with Kakadu’s rock art demonstrating pre-ice age Indigenous civilisation from the Pleistocene Epoch to present time. Despite the difference in geography and time, these places show continual Cultural growth. Extensive scientific research has been conducted on Bininj/Mungguy Peoples, and the flora and fauna of Kakadu National Park, with little research conducted on fungi or Aboriginal knowledge and use of fungi. This project will be utilising the existing fungal data collected by the Australian Microbiome project and then expand on the data by conducting genomic, metabolomic and proteomic analysis of macrofungi collected with Traditional Owners across Kakadu National Park. This project will provide opportunities for Aboriginal co-designed fungi research, two-way knowledge sharing and will enable Aboriginal people to enact self-determination and facilitate the creation of new food and fungal biotechnology enterprises on Country. Aboriginal communities will benefit from this data by connecting traditional knowledge to western science. This will generate evidence for the creation of Indigenous enterprises on Country and create positive, economic, social, environmental and Cultural benefits to Aboriginal communities.