– ABOUT
AUSTRALIAN functional fungi INITIATIVE
This national program, initiated in 2022, aims to create foundational genomic, metabolomic and proteomic data resources to fast-track knowledge and innovation in Australian fungi.
The fungal kingdom is taxonomically separated from both plants and animals and as such have unique characteristics including structure, metabolites, nutritional properties and ecological functions. However, we have very little knowledge surrounding the identification and function of Australia’s native fungi. This knowledge gap creates immense opportunity for exploration and innovative translation of ‘omics data from Australian native fungi.
The generation of open access ‘omics data will enable insight into the unique functions of native fungi that may provide new avenues for emerging industries and applications, for example, diagnostic development of human fungal pathogens, bioactive compound investigations, native foods, biomaterial engineering, ecosystem management and conservation, land restoration, waste management and circular economies.
OBJECTIVES
Through this program of research, the creation of referential multi-‘omics data resources of Australian native fungi will:
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- Fast-track fundamental research in native Australian fungi, including resolving taxonomy and supporting investigations in plant associations including ecosystem function discovery, land regeneration, ecosystem resilience, biodiversity conservation.
- Accelerate foundational biological discovery including identification of unique pathways, compounds or enzymes in Australian native fungi.
- Support industry translation to leverage the potential of native fungi including food, medicinal, biomaterials and circular economy.
DATA
For further information and to view and access initiative data, please go to the Bioplatforms Australia Data Portal.
PROJECTS
| Project name | Project Summary | Species name | Data Strategy | Project Lead |
|---|---|---|---|---|
| Investigation of the phylogenomics of Australian magic mushrooms | Fungi that are edible or fermentative were domesticated through selective cultivation of their desired traits. Domestication is often associated with inbreeding or selfing, which may fix traits other than those under selection, and causes an overall decrease in heterozygosity. A hallucinogenic mushroom, Psilocybe cubensis, was domesticated from its niche in livestock dung for production of psilocybin. It has caused accidental poisonings since the 1940s in Australia, which is a population hypothesised to be introduced from an unknown center of origin. The project will investigate the phylogeny of Australian magic mushrooms through whole genome sequencing. | Magic mushrooms (Psilocybe spp.) | Reference genome (Illumina whole genome sequencing) | Dr. Alistair McTaggart (Psymbiotika Lab) |
| Identifying diagnostic targets for pathogenic Rhizopus arrhizus strains | This project focuses on mucormycosis, a deadly fungal infection caused by Rhizopus arrhizus. By generating whole-genome sequencing and transcriptomic datasets from Australian clinical and environmental strains, the study aims to uncover the factors driving the fungus's invasiveness and pathogenicity, ultimately identifying new targets for disease control. | Black bread mold (Rhizopus arrhizus) | Reference genome (ONT, Illumina whole genome sequencing, transcriptomes) | Dr. Caterina Selva (Flinders University, College of Medicine and Public Health) |
| Characterisation of secondary metabolites in commercial magic mushrooms | This project examines magic mushrooms, which produce psilocybin, a compound with potential to treat mental health disorders like addiction, depression, and PTSD. By studying genetic differences in the psilocybin pathway, the research aims to determine if these variations lead to differences in psilocybin concentration. The goal is to identify the best mushroom genotypes for clinical use. | Magic mushroom (Psilocybe cubensis, Psilocybe subaeruginosa) | Metabolomics (targetted) | Dr. Alistair McTaggart (Psymbiotika Lab) |
| Novel Australian Eurotiales | Eurotiales, dominated by four key genera, are under-explored in Australia. Microbial Screen Technologies (MST) has isolated ~2,000 Australian Eurotiales cultures with unique metabolomics. This project combines genomics and metabolite discovery to enhance fungal research and commercial applications. MST aims to unlock novel fungal metabolites, advancing drug discovery and Australian science. | Various species (Aspergillus, Paecilomyces, Penicillium, Talaromyce) | Reference genome (Illumina whole genome sequencing) | Dr. Ernest Lacey (Microbial Screening Technologies) |
| Zombie fungi - Australian entomopathogens | The Queensland Fungi Collection (BRIP) holds 1,094 entomopathogenic fungi strains, mainly from Australian rainforests, with many likely new species. This project aims to expand knowledge of these fungi, enhance genomic and metabolomic discovery, and support biodiscovery and chemical production. | Zombie fungi (Akanthomyces, Aschersonia, Beauveria, Cordyceps, Gibellula, Hevansia, Hirsutella, Isaria, Meira, Metarhizium, Moelleriella, Ophiocordyceps, Paeciliomyces, Pochonia, Torrubiella) | Reference genome (Illumina whole genome sequencing) | Dr. Ernest Lacey (Microbial Screening Technologies) |
| Taxonomy and functional capacities of Antarctic fungi at the fringe of habitability | This project studies fungal biodiversity in Antarctica’s extreme, nutrient-poor environments. By integrating genomics with physiological and morphological assessments, it aims to understand fungal resilience and responses to environmental changes. Additionally, it explores the potential of Antarctic fungi pigments as natural alternatives to synthetic dyes and their antimicrobial properties. | predominantly to the Agaricomycetes and Dothideomycetes classes, as well as Sordariomycetes, Exobasidiomycetes, Eurotiomycetes and Cystobasidiomycetes, Leotiomycetes, Microbotryomycetes and Tremellomycetes classes | Reference genome (ONT, Illumina whole genome sequencing, transcriptomes), metabolomics (untargetted), proteomics (untargetted) | Dr Belinda Ferrari (University of New South Wales) |
| Comparative genomics of toxic Amanita species in Australia | The Amanita genus includes highly toxic mushrooms like A. phalloides and A. muscaria, now spreading in Australia. This project will sequence and study their genomes, along with native species A. marmorata and A. xanthocephala, to explore toxin genes and reproductive strategies, addressing the rising concern over wild mushroom toxicity in Australia. | deathcap, fly agaric, marbled deathcap, vermilion Amanita (Amanita phalloides, A. muscaria, A. marmorata, A. xanthocephala) | Reference genome (ONT, Illumina transcriptomes) | Dr Camille Truong (Royal Botanic Gardens Victoria) |
| Threatened Waxcaps | In Australia, ‘waxcap’ fungi are found in highest diversity and abundance in rainforest and forest ecosystems, but little is known about their true diversity and trophic status. Genomic data will inform their diversity and distribution. | Waxcaps (Hygrocybe and affiliated genera) | Reference genome (Illumina whole genome sequencing) | Isobel Colson (Western Sydney University) |
| Ganoderma species of tropical and subtropical Australia | Ganoderma P. Karst is a large genus of polypore white rot fungi in the family Ganodermataceae. 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. | Ganoderma spp. | Reference genome (Illumina whole genome sequencing) | Agnieszka Mudge (The University of Queensland) |
| Wild Fungi DNA | Led by a community-driven organization, this project advances knowledge of fungi in Australia through collaboration with citizen scientists and small companies. It aims to create reference data for diverse fungi, benefiting industries in mycomaterials, food, supplements, and ecology. | Multiple species | Reference genome (Illumina whole genome sequencing) | Ema Corro (Mycommunity Applied Mycology Inc.) |
| Identification of the bioactive compounds in Cordyceps gunnii | The Cordyceps spp. are species-specific entomopathogenic fungi that have long been used in traditional Chinese Medicine. 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. | Dark vegetable caterpillar (Cordyceps gunnii, aka Drechmeria gunnii) | Metabolomics (untargetted) | Dr Rita Busuttil (Monash University/ Alfred Hospital) |
| Fungarium genomics | This project will unearth the potential of our national and historic fungal collections by generating phylogenomic data of more that 400 fungal taxa tht can be used to assess the diversity and taxonomy of Australian members of the focal fungal groups Cladia, Peziza s.l., Cortinarius, Russula/Lactarius and Polyporaceae. | Lichenised fungi (Lecanoromycetes, Ascomycota): Australian species from the genus Cladia, including the iconic species Cladia retipora Cup fungi (Pezizomycetes, Ascomycota): Australian species of Peziza (sensu lato) with putative ectomycorrhizal and saprobic lifestyles Webcap fungi (Agaricomycetes, Basidiomycota): Australian species of Cortinarius Russula and milkcap fungi (Agaricomycetes, Basidiomycota): Australian species of Russula and Lactarius. Bracket fungi (Agaricomycetes, Basidiomycota): Australian species of Polyporaceae | Reference genome (Illumina whole genome sequencing) | Dr Cécile Gueidan (CSIRO, Australian National Herbarium) |
| Entomopathogenic fungi for biological control | 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. | Beauveria sp. sometime are known as white muscardine caterpillar (O. robertsii also known as vegetable caterpillar or āwhato and āwheto in Māori), Five isolates of Beauveria bassiana, one isolate of Cordyceps gunnii, and one isolate of Ophiocordyceps robertsii | Reference genome (ONT, Illumina transcriptomes), metabolomics (untargetted), proteomics (untargetted) | Nonthakorn (Beatrice) Apirajkamol (Macquarie University) |
| Functional food or deadly toxin? Bioprospecting in Australian rainforest macrofungi | 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. | Oyster, Shiitake, Ghost fungi, Coral, Beefsteak, incl. strawberry bracket, curry punk, etc, Puffballs (Pleurotus sp., Lentinus sp., Omphalotus nidiformis, Ramaria sp., Sanguinoderma sp., Dentipellus sp., Russula sp., Clavulinopsis sp., Cordyceps sp., Fistulina sp., Polyporus sp., Phaeolus sp., Postia sp., Lycoperdon sp.) | Reference genome (Illumina whole genome sequencing, transcriptomes), metabolomics (untargetted), proteomics (untargetted) | Dr Kylie Agnew-Francis (The University of Queensland) |
| Exploring the molecular diversity of native Australian Hericium mushrooms | This project seeks to survey the biodiversity and molecular features of native Australian mushrooms from the Hericium genus (also known a Lions Mane). The data generated by this project aims to identify native Hericium with superior nutritional and bioactive metabolite content. | Coral tooth or lion’s mane (Hericium sp.) | Metabolomics (targetted) | Dr Kylie Agnew-Francis (The University of Queensland) |
| Western Australian endophytic, mycoparasitic and croprophilic fungi for agricultural and biotechnological applications | The Sordariomycetes is a significant class of Ascomycota fungi, boasting nearly 30,000 described species that produce a variety of enzymes and secondary metabolites. This project crombines whole genome and metabolomics data from a broad range of Sordariomycetes that can be used to understand the biology, as well as the scientific and commercial applications of endophytic, mycoparasitic, and coprophilic Australian fungi. | Primarily Sordariomycetes, including fungi from the genera Cladobotryum, Escovopsis, Hypomyces, Trichoderma, Acremonium, Podospora, Clonostachys, Epichloë, Lecanicillium, Simplicillium, Melanospora, Nigrosabulum, Sordaria, Selinia, Chaetomium, Thielavia, Poronia, Gilmaniella, Annulohypoxylon, Hypoxylon, and Xylaria. | Reference genome (Illumina whole genome sequencing) | Yit Heng Chooi (University of Western Australia) |
| Sequencing under represented fungal diversity in the department of agriculture BRIP collection | 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. | non-pathogenic fungi from lineages commonly identified as being members of the core microbiome of plants, animals (mostly insects), and soils | Reference genome (Illumina whole genome sequencing) | Dr Paul Dennis (University of Queensland) |
| Characterisation of secondary metabolites and gene expression in commercial magic mushrooms treated with ‘Rainstick’ electrostatic wave forms | Rainstick is an Australian Indigenous lead Start-up company developing 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 Psymbiotica Lab will explore how and why electrostatic waveforms impact the genetics and metabolic expression of magic mushrooms. | Magic mushroom (Psilocybe cubensis, Psilocybe subaeruginosa) | Reference genome (Illumina transcriptomes), metabolomics (targetted), proteomics (targetted) | Chris McLoghlin (Rainstick) |
| Characterisation of secondary metabolites and gene expression in commercial edible mushrooms treated with ‘Rainstick’ electrostatic wave forms | Rainstick is an Australian Indigenous lead Start-up company developing technology to benefit industries that grow fungi and plants, whether through activating desired phenotypes, increasing growth and metabolite production, or decreasing contamination. This project will explore how and why electrostatic waveforms impact the genetics and metabolic expression of edible mushrooms. | tbc | Reference genome (Illumina transcriptomes), metabolomics (untargetted), proteomics (untargetted) | Chris McLoghlin (Rainstick) |
| Australian Morels | Morel mushrooms (Morchella spp.) are a highly sought after culinary wild mushroom, with approximately 80 species worldwide. 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. 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. | Morel (Morchella sp.) | Peter Wenzel (Fungi Co) | |
| Identifying genes involved in mycorrhizal fungal recognition and nutrient exchange in orchid- and barley-fungal interactions | Ulasnella, Serendipita, and Ceratobasidium are key mycorrhizal fungi for orchids, essential for seed germination and adult nutrition. This project will conduct a transcriptomic study comparing in vitro fungi with symbiotically germinated seeds and natural roots to identify genes involved in fungal recognition and nutrient exchange, advancing our understanding of plant-microbe interactions. | Orchid mycorrhizal fungi (multiple) (Tulasnella prima, Tulasnella multinucleata, Serendipita secunda, Serendipita warcupii, Serendipita communis, Serendipita occidentalis) | Prof. Celeste Linde (Australian National University) | |
| Genomics and transcriptomics of fungal hyperparasites of rust fungi | This project will investigate hyperparasitic fungi of rusts, which cause major agricultural and ecological diseases in Australia, such as cereal rusts and myrtle rust. With limited control options available, we are exploring fungal hyperparasites isolated from rust-infected plants. Sequencing and transcriptomic analysis will identify genes linked to hyperparasitism, aiming to develop new rust control strategies. | fungal hyperparasites of rust fungi (multiple) | Prof. John Rathjen (Australian National University) | |
| Indigenous Mycology | Kakadu, Australia's largest national park, protects diverse ecosystems and has been home to the Bininj/Mungguy Peoples for over 50,000 years. This project aims to expand on traditional knowledge of macrofungi with Traditional Owners using genomic, metabolomic, and proteomic techniques. 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. | Bracket/Shelf Fungi (Polyporus) Bracket/Shelf Fungi (Ganoderma) Hoof, Tinder Fungus (Hexagonia) Cramp Balls, King Alfred Cakes (Daldinia) | Reference genome (ONT, Illumina whole genome sequencing), metabolomics (untargetted), proteomics (untargetted) | Sherie Bruce (University of Queensland) |
| Wild yeasts | Globally, fermented food and beverage production is dominated by yeasts discovered and then domesticated in the Northern Hemisphere. In the case of beer, sales are dominated by lager – and yet the yeasts responsible have a Southern Hemisphere connection. Lager yeast is a hybrid of Saccharomyces cerevisiae and another Patagonian species, with closely related species found ro have a Gondwanan distribution. Australian Saccharomyces sp. may have novel fermentation characteristics that would make them valuable within the food and beverage industry, with potential broader application in agriculture, biofuel production and medical science. Investigation of wil Australian Saccharomyces may also help us understand evolution beyond this genus. As industry partner for this project, Itsy-Bitsy Beer has a particular interest in novel genes of value in fermentation, specifically: Maltose metabolism, Extra-cellular amylases, Biotransformation enzymes (i.e. β-glucosidase and β-lyase), Glycerol production, Cryotolerance, Heat tolerance. | Wild yeasts (Saccharomyces) | Reference genome (ONT) | Jonathan Arundel (Itsy-Bitsy beer) |
PARTNERS
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advisory committee members
Benjamin Schwessinger – Australian National University
Alistair McTaggart – Psymbiotika Lab
Brett Summerell – Royal Botanic Gardens, Sydney
Teresa Lebel – DEW, South Australian Government
Heng Chooi – University of Western Australia
Markus Herderich – Australian Wine Research Institute
Cecile Gueidan – CSIRO
Jim Fuller – Fable Food
Teresa Lebel – DEW, South Australian Government
Heng Chooi – University of Western Australia
Markus Herderich – Australian Wine Research Institute
Cecile Gueidan – CSIRO
Jim Fuller – Fable Food
Kelly Scarlett – Bioplatforms Australia
CONTACT US
Project Manager
Sophie Mazard – Bioplatforms Australia
smazard@bioplatforms.com
Partnerships and Engagement Lead
Kelly Scarlett – Bioplatforms Australia
kscarlett@bioplatforms.com