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Funded PhD Studentship: Biotechnological exploitation of gut microorganisms and lignocellulosic substrates

fatty acids and microbial proteins to ‘feed’ the animal. Two members of the digestive tract consortium, the anaerobic fungi and their associated methanogenic partners, are of particular interest in

PhD position - Climate resilience and conservation of species interactions in a changing world

Your job Are you a highly motivated and enthusiastic individual with a strong background in plant ecology, biotic interactions (especially plant-mycorrhizal fungi ), and conservation? Do you want

PhD candidate on soil fungal ecology

of the fungal community to recover the loss of soil multifunctionality. This will be achieved by combination of field characterization of fungi and their functions across land use gradients and by experimental

PhD position - Biogeochemical Soil and Rhizosphere Modeling

on soil hydraulic properties and growth of arbuscular mycorrhizal fungi associated to plant roots Literature research and (meta-)analysis to gain evidence-based knowledge for model parameterization Model

Five industrial PhD students to the Research School in Future Silviculture

is to identify molecular, ecological, and practical aspects of ectomycorrhizal soil fungi that allow increasing drought resistance in pine seedlings. In your research, you will use a combination of

PhD Studentship: Epigenetic Profiling of Cereal Fungal Invaders (SAUNDERS_J24DTP1)

Primary supervisor - Professor Diane Saunders Wheat blast and rusts are fungal diseases that severely damage cereal production worldwide. During infection, these fungi secrete proteins into wheat

PhD position in Evolutionary Genomics

study hidden fungal diversity. The project focuses on the Archaeorhizomycetes which, based on environmental DNA data, is a species rich and abundantly occurring class of soil and root associated fungi

PhD position in Mathematical modelling of drug resistance evolution

lifestyle. The target organisms will be bacteria, fungi and parasitic worms. While the position is theoretical, the student is encouraged and expected to collaborate with our experimental collaborators. More

Industry and collaboration PhD student in forest microbiology

to identify molecular, ecological, and practical aspects of ectomycorrhizal soil fungi that allow increasing drought resistance in pine seedlings. You are expected to conduct research, in collaboration

PhD Studentship: Microbial Hydroponics - Novel Hydroponics Using Microbial Fuel Cells

biofilm as a prosthetic rhizosphere for plant roots (which utilize symbiotic relationships between fungi & bacteria to obtain nutrients from the environment) to optimize N utilisation (synthesis

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Fungal Biology

Experimental models.

Saccharomyces cerevisiae. Image courtesy of Dr. Paul Cullen.

Focus on fungi to understand cellular processes

Faculty explore how filamentous fungi and budding yeasts assess nutrient availability and respond appropriately by adjusting gene expression, budding patterns, cell morphology, and cell wall structure. Some of these studies involve opportunistic fungal pathogens. Our faculty also use yeast as a model organism to investigate the molecular basis of gene expression, including transcription, RNA processing and translation.

The Fungal Biology faculty includes Drs. Paul Cullen, Laura Rusche, Sarah Walker, Zhen Wang, and, Michael Yu.

Fungal Biology Research Faculty

• 3/19/18 Paul Cullen
• 3/19/18 Laura Rusche
• 3/19/18 Sarah E. Walker
• 11/30/21 Zhen Q. Wang
• 3/19/18 Michael C. Yu

Southeastern Mycology Symposium 2018

Fungal biology - an interdisciplinary group.

Fungi range from microscopic, single-celled yeasts to vast underground mycelial colonies covering hundreds of acres. They are heterotrophs that play major roles in recycling environmental carbon, cause diseases of plants and animals, and make many industrial products. Because they are more closely related to animals than to plants and because their biology and genetics are easily manipulated, fungi are great model organisms.

With ~15 labs dedicated to the study of yeasts and filamentous fungi, the University of Georgia is an international hot spot for fungal biology. Fungal researchers at UGA study ecologically diverse organisms to investigate topics ranging from plant pathology to population genetics to developmental biology. The combination of courses focused on fungi and related research methodologies provides a strong curriculum for graduate students and a productive training environment for postdocs interested in fungi.

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The Center of Excellence in Fungal Research (CEFR)

To become a leading fungal research center in Thailand, Asia and the world

• Conducting research in areas of fungal diversity, function and global change, taxonomy, phylogeny and evolution of fungi, plant pathology and endophytes, mushroom cultivation, chemical discovery from fungi, and community service
• Housing a regional culture collection and herbarium for Thailand
• Developing allied research in mushroom products and agricultural products using unique cultures
• Training new mycologists in term of taxonomy and phylogeny of fungi, mushroom science, agricultural use from fungi
• Providing valuable workshops for regional participants

Director of the Center

Emeritus Prof. Dr. Kevin David Hyde E-mail: [email protected] Expertise : Taxonomy, phylogeny and biodiversity of fungi

Outstanding Works

• The Center publishes more than 100 SCI research articles in reputed journals each year. 
• The Center introduced more than 700 new species of Thai fungi, as 65% of fungal studies in Thailand from CEFR.
• The Center has 10000 strain in MFLUCC and 20000 in fungarium that very high biodiversity for industrial use and many novel mushrooms for industrial cultivation.
• More than 25 PhD and 6 MS graduates from CEFR (between 2011-2018).
• Presently, the center has more than 65 PhD students and recruiting at least ten new PhD scholars in each year. 
• The Center is proposing to organize training workshops for regional participants in key areas such as community development, mushroom cultivation and production, pathogenic fungal identification.

Center of Excellence in Fangal Research (CEFR) Tel: +66(0) 5391 6961 E-mail: [email protected]

http://fungalcenter.mfu.ac.th

Fungal Biology and Biotechnology

Check your eligibility to publish open access with your fees covered.

Many institutions now cover OA publishing costs for affiliated researchers, as part of an OA agreement with Springer Nature. Find out more about OA agreements and whether you may be entitled to publish OA with your fees covered.

Aims and scope

Fungal Biology and Biotechnology is a peer-reviewed journal that publishes original scientific research and reviews covering all areas of fundamental and applied research which involve unicellular and multicellular fungi.

• Most accessed

Increasing the efficiency of CRISPR/Cas9-mediated genome editing in the citrus postharvest pathogen Penicillium digitatum

Authors: Carolina Ropero-Pérez, Jose F. Marcos, Paloma Manzanares and Sandra Garrigues

A review on the cultivation, bioactive compounds, health-promoting factors and clinical trials of medicinal mushrooms Taiwanofungus camphoratus , Inonotus obliquus and Tropicoporus linteus

Authors: Phoebe Yon Ern Tee, Thiiben Krishnan, Xin Tian Cheong, Snechaa A. P. Maniam, Chung Yeng Looi, Yin Yin Ooi, Caroline Lin Lin Chua, Shin-Yee Fung and Adeline Yoke Yin Chia

Genomic deletions in Aureobasidium pullulans by an AMA1 plasmid for gRNA and CRISPR/Cas9 expression

Authors: Audrey Masi, Klara Wögerbauer, Robert L. Mach and Astrid R. Mach-Aigner

An improved expression and purification protocol enables the structural characterization of Mnt1, an antifungal target from Candida albicans

Authors: Patrícia Alves Silva, Amanda Araújo Souza, Gideane Mendes de Oliveira, Marcelo Henrique Soller Ramada, Nahúm Valente Hernández, Héctor Manuel Mora-Montes, Renata Vieira Bueno, Diogo Martins-de-Sa, Sonia Maria de Freitas, Maria Sueli Soares Felipe and João Alexandre Ribeiro Gonçalves Barbosa

Genetic regulation of l -tryptophan metabolism in Psilocybe mexicana supports psilocybin biosynthesis

Authors: Paula Sophie Seibold, Sebastian Dörner, Janis Fricke, Tim Schäfer, Christine Beemelmanns and Dirk Hoffmeister

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Growing a circular economy with fungal biotechnology: a white paper

Authors: Vera Meyer, Evelina Y. Basenko, J. Philipp Benz, Gerhard H. Braus, Mark X. Caddick, Michael Csukai, Ronald P. de Vries, Drew Endy, Jens C. Frisvad, Nina Gunde-Cimerman, Thomas Haarmann, Yitzhak Hadar, Kim Hansen, Robert I. Johnson, Nancy P. Keller, Nada Kraševec…

Fungi as source for new bio-based materials: a patent review

Authors: Kustrim Cerimi, Kerem Can Akkaya, Carsten Pohl, Bertram Schmidt and Peter Neubauer

How a fungus shapes biotechnology: 100 years of Aspergillus niger research

Authors: Timothy C. Cairns, Corrado Nai and Vera Meyer

Current state and future prospects of pure mycelium materials

Authors: Simon Vandelook, Elise Elsacker, Aurélie Van Wylick, Lars De Laet and Eveline Peeters

Current challenges of research on filamentous fungi in relation to human welfare and a sustainable bio-economy: a white paper

Authors: Vera Meyer, Mikael R. Andersen, Axel A. Brakhage, Gerhard H. Braus, Mark X. Caddick, Timothy C. Cairns, Ronald P. de Vries, Thomas Haarmann, Kim Hansen, Christiane Hertz-Fowler, Sven Krappmann, Uffe H. Mortensen, Miguel A. Peñalva, Arthur F. J. Ram and Ritchie M. Head

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Mycology at Springer Nature

At Springer Nature, we are committed to raising the quality of academic research across Microbiology. We've created a new page, highlighting our mycology journals and mycology content. 

We are pleased to announce that all articles published in Fungal Biology and Biotechnology  are included in PubMed and PubMed Central.

Fungal Biology and Biotechnology is also included in Scopus.

Featured blog series

In a new blog series, Kustrim Cerimi looks at emerging fungal-based products and trends.

The Importance of Fungi in Securing and Threatening Food Supply For a Growing Human Population

Engineering Microbiomes for Green Technologies

Beyond the assembly line - showcasing the complexities of fungal natural product biosynthesis

Connecting material science and fungal biology

Fungal biotechnology's potential to sustainably produce textiles as well as materials for construction, furniture and transportation industries has the potential to significantly contribute to the United Nation’s sustainable development goals. The aim of this collection is to provide fungal and material experts a forum for discussion on the multidisciplinary approaches important in the rapidly evolving field of fungal biomaterials, to highlight recent breakthroughs and to exchange ideas and visions. 

Do you have an idea for a thematic series? Let us know!

Technical notes.

Fungal Biology and Biotechnology  is now considering Technical notes . This article type should present a new experimental or computational method, test or procedure, showing a novel or improved approach, a well tested method, and ideally proven value. Check out here for more details about submission guidelines.

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About the Editors

Vera Meyer runs the Chair of Molecular and Applied Microbiology at TU Berlin since 2011. The focus is on researching and optimising fungal cell factories, with the aim of making more effective use of fungal metabolic potentials for the production of medicines, platform chemicals, enzymes and biomaterials. Together with her team, she develops and combines methods from systems biology and synthetic biology. Her inter- and transdisciplinary research projects combine natural and engineering sciences with art, design and architecture and create bio-based scenarios for possible living environments of the future. Vera Meyer is also active as a visual artist under the pseudonym V. meer and uses the means of art to make society more aware of the potential of fungi for a sustainable future.

Yvonne Nygård has a PhD in Molecular Biotechnology from Aalto University and currently works as Research Professor at VTT Technical Research Centre of Finland and as Associate Professor at Chalmers University of Technology in Sweden. Moreover, she is the CSO of a fungal start-up, Cirkulär AB. Yvonne’s main research interest is to develop microbial cell factories for industrial applications. She combines synthetic biology with high throughput screening and works with different yeast and fungi.

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Citation Impact 2023 Source Normalized Impact per Paper (SNIP): 1.260 SCImago Journal Rank (SJR): 1.068

Speed 2023 Submission to first editorial decision (median days): 8 Submission to acceptance (median days): 68

Usage 2023 Downloads: 283,844 Altmetric mentions: 138

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Companion Journals

Fungal Biology and Biotechnology is a partner journal to:

Biotechnology for Biofuels and Bioproducts

Microbial Cell Factories

Biotechnology for the Environment

Biotechnology for Sustainable Materials

Blue Biotechnology

ISSN: 2054-3085

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School of Integrative Plant Science

MS/PhD Field of Plant Pathology & Plant-Microbe Biology

Advancing understanding of pathogens and their control.

Graduate study in Cornell's Integrative School of Plant Science is organized into five Graduate Fields providing unparalleled opportunities to connect disciplines, creatively solve problems, and integrate complex systems, preparing graduates for diverse careers and futures as leaders in science and society.

The Field of Plant Pathology and Plant-Microbe Biology (PPPMB) focuses on all aspects of plant diseases and the biology of plant-microbe interactions at the molecular to ecosystem levels of organization. This Field is also the home for studying the biology, genetics, and evolution of fungi and oomycetes. Most of the faculty advisors in the Field of PPPMB are affiliated with the Section of Plant Pathology and Plant-Microbe Biology in the School of Integrative Plant Science.

Grand Challenge Fellowships

The School of Integrative Plant Science (SIPS) is offering four two-year fellowships to graduate students for research tackling our  Grand Challenges .

• Fellowships are for August 2024 admission.
• Application deadline is December 1, 2023.  (November 15, 2023 for Plant Pathology and Plant-Microbe Biology.)
• More information.

Apply to the Graduate Field of Plant Pathology & Plant-Microbe Biology

• Apply (Cornell Graduate School Application)
• Grad Field of Plant Pathology & Plant-Microbe Biology application information

Graduate Field Concentrations

The MS/PhD Graduate Field of Plant Pathology and Plant-Microbe Biology consists of three concentrations:

• Plant Pathology
• Plant-Microbe Biology
• Fungal and Oomycete Biology

Learn more about our graduate concentrations

Students in the Plant Pathology program have diverse interests in the fundamental biology, etiology, and epidemiology of plant pathogens as well as the management of plant diseases; however, they are united in the common goal of achieving a greater understanding of pathogen biology and ecology in order to predict and mitigate disease impacts.

Students in this program will master the fundamental knowledge of plant pathogens and diseases while developing conceptual knowledge and skills necessary to design and implement programs in integrated disease management.

Core concepts in the Plant Pathology program of study:

• Knowledge of all pathogen groups
• Principles of disease management
• Identification of pathogens within major pathogen groups
• Disease etiology and epidemiology
• Disease development and pathogen evolution
• Mechanisms of plant-pathogen interactions
• Experimental design and applied statistics
• Role/opportunities of plant pathology in agriculture and natural systems
• Pathogenomics in plant pathology
• Basic skills in isolation and culture of major pathogen groups

This suite of skills, knowledge, and abilities are developed through core and elective courses, research projects, teaching, extension, and outreach opportunities. In addition to the  course requirements of all PPPMB students , PhD students in the Plant Pathology program are required to complete PLSCI 5020 and two special topics courses.  Additionally, PLPPM 4190 (our field course) is strongly recommended.  The course requirements for a PhD minor in the Plant Pathology program are determined by the Special Committee, but include PLSCI 3010, PLSCI 6010, and at least one special topics course.

In addition to the course requirements of all PPPMB students, the MS major in the Plant Pathology program is required to complete PLSCI 5020 and a minimum of either one additional special topics course or PLPPM 4190.  The MS minor in the Plant Pathology program requires PLSCI 3010.  In addition to the courses listed above, the Special Committee may suggest other courses that are appropriate for the student's interests and research project.

Students in the Plant-Microbe Biology program have educational backgrounds in Molecular Biology, Plant Biology, Genetics, Biochemistry, and Microbiology. They typically conduct research on pathogenic, symbiotic, and epiphytic processes that enable microbial associations with plants and the mechanisms in plants that lead to defense, susceptibility, or cooperation.

Students in this concentration will master a fundamental understanding of the biology of the interactions between plants and microbes, particularly with respect to pathogenesis and symbiosis. They are expected to be interdisciplinary and able to bridge basic and translational research.

Core concepts in the Plant-Microbe Biology program of study:

• Pathogenic lifestyles: necrotrophs versus biotrophs
• Primary pathogenic mechanisms of necrotrophs
• Primary pathogenic mechanism of biotrophs
• The first level of induced plant defense
• The second level of effector-triggered immunity
• Systemic acquired resistance, induced systemic resistance, priming, and related plant defenses
• Major classes of antimicrobial compounds produced by plants
• Differences and antagonisms between plant defenses
• Pathogenic mechanisms of bacteria, fungi, oomycetes, viruses, and nematodes
• Development of better ways to durably protect crops

This suite of knowledge, skills, and abilities are developed from core and elective courses, research projects, and outreach opportunities. In addition to the course requirements of all PPPMB students , PhD students majoring in the Plant-Microbe Biology program are expected to complete PLSCI 5020, two special topics courses, and at least one minor in a graduate field in the core life sciences or physical sciences. The course requirements for a minor in the Plant-Microbe Biology program are determined by the Special Committee, but include at least the equivalent of PLSCI 3010 and PLSCI 6010. For students majoring in Plant Pathology or Fungal and Oomycete Biology with a minor in Plant-Microbe Biology, the Special Committee may recommend an additional life sciences course or research experience in a Plant-Microbe Biology or life sciences laboratory.

The Fungal and Oomycete Biology program serves as the center of eukaryotic microbiology on the Cornell campus. Research and teaching activities are focused on molecular and cellular biology of host associations and development, population biology, ecology and evolution, and epidemiology and management of fungi and oomycetes in natural and agricultural ecosystems.

Core concepts in the Fungal and Oomycete Biology program of study:

• Structure and function of fungal/oomycete cells
• Fungal/oomycete lifestyles
• Ecological and evolutionary relationships
• Mating systems
• Fungal/oomycete genetics and genomics
• Cell and molecular biology
• Interaction Biology
• Population genetics
• Fungal/oomycete metabolism
• Manipulating and identifying fungi/oomycetes

These concepts and skills are developed from core and elective courses, research projects, and outreach. In addition to the course requirements of all PPPMB students , PhD students majoring in Fungal and Oomycete Biology are required to complete PLSCI 4490 (Advanced Mycology), PLSCI 6380 (Filamentous Fungal Genomics and Development), and PLSCI 6490 (a current issues course in Fungal and Oomycete Biology). PhD students minoring in Fungal and Oomycete Biology are required to complete two of the above three courses.

For the MS major in the Fungal and Oomycete Biology program, students are required to complete PLSCI 4490 and PLSCI 6380 in addition to the course requirements for all PPPMB students. The minor requirements for MS students are determined by the Special Committee. In addition to the courses listed above, the Special Committee may suggest other appropriate courses given the student's interests and research focus.

Josh Balles Graduate Field Coordinator 237 Emerson Hall Phone: 607-255-9573 Email: jeb527 [at] cornell.edu (jeb527[at]cornell[dot]edu)

Sarah Pethybridge Associate Professor and Director of Graduate Studies Graduate Field of Plant Pathology & Plant-Microbe Biology sjp277 [at] cornell.edu (sjp277[at]cornell[dot]edu) Phone: (315) 787-2417

Program metrics, demographics and outcomes

Select the graduate field of interest from the pull-down menu on the linked page

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• Career outcomes

More information about grad study in PPPMB

See these links for information specific to MS/PHD studies in the Field of Plant Pathology and Plant-Microbe Biology

• Faculty in the Field of PPPMB
• More about the SIPS Section of PPPMB
• Recent theses in the Field of PPPMB
• Meet our PPPMB graduate students
• PPPMB field requirements
• PPPMB student life

Learn more about graduate study in SIPS

Five interrelated Graduate Fields are associated with the School of Integrative Plant Science (SIPS) with many resources common to all

• Financial Support
• NSF Research Traineeship
• Schmittau-Novak Small Grants Program
• SIPS People
• Campuses and Facilities
• SIPS Graduate Student Council

recruiting a phd student in fungal genomics

The Weisberg lab (Oregon State University) and Mahaffee lab (USDA-ARS) are recruiting a PhD student for research in fungal comparative genomics and evolution. Start date is flexible, if interested please include your CV and contact us by email at [email protected] to discuss it & apply!

See the full job description in the attached pdf:

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Stories from The University of Texas Health Science Center at Houston (UTHealth Houston)

McGovern Medical School researchers discover novel therapy for fungal infections

Written by: Roman Petrowski, McGovern Medical School | Updated: October 21, 2022

Recent research from the labs of   Danielle Garsin, PhD, and   Michael Lorenz, PhD, professors in the   Department of Microbiology and Molecular Genetics with McGovern Medical School at UTHealth Houston , which identified a novel potential therapeutic against fungal infections, has been published in   Nature Communications .

Fungi are a major source of disease, ranging from well-known conditions like thrush and yeast infections to more deadly infections in immunocompromised patients, including patients with AIDS, those undergoing chemotherapy, and organ transplant patients with implanted devices like bloodstream catheters.

“Unfortunately, there are few effective antifungals, and resistance to those that are available is rising,”  Garsin said. “While we often think of an infection as a contest between a human patient and a pathogen, we have many species of microbes in our body, and the role of a healthy microbiome in preventing disease is largely unknown.”

In previous studies, the two labs discovered that a protein produced by the bacterial species,   Enterococcus faecalis , which they called EntV, was able to block   Candida albicans , a major fungal pathogen. However, the protein’s size and other factors prevent EntV from being a viable potential therapeutic.

“In this new paper, we optimized EntV as a potential therapeutic by deciphering its three-dimensional structure,” Garsin said. “Using the structure as a guide, we were able to design fragments that were tested in several complementary assays, eventually designing a short sequence of 12 amino acids — less than one-fifth the size of the original protein, that retained full antifungal activity.”

The optimized EntV or “12mer” proved affective against   C. albicians   strains that are resistant to current antifungal drugs as well as other fungal species. The lab also demonstrated that the 12mer was effective in oral, bloodstream, and catheter infection models.

Garsin, an expert in bacterial pathogens, and Lorenz , an expert in fungal pathogens, collaborated with structural biologists to identify the three-dimensional shape of EntV, allowing the team to design and test peptides rapidly in Garsin’s lab. After identifying promising fragments, they then tested EntV’s efficacy against fungal structures that contribute to disease in Lorenz’s lab.

“This rigorous iterative process took advantage of the expertise of both groups collaboratively to demonstrate the potential of these fragments for further clinical optimization,” Garsin said.

Through their research, the Garsin and Lorenz labs identified a potential therapeutic against a variety of fungal infections that showed broad-spectrum efficacy. As fungal infections continue to adapt and resist current drugs, new possible therapeutic options like the one created by these labs will become necessary.

“Antifungal drug development is particularly challenging because fungal cells and animal cells are very similar, so it is difficult to find drugs that are effective but not toxic,” Lorenz said. “Our identification of a candidate compound that meets these criteria is a significant step toward providing additional tools to treat fungal infections.”

Moving forward, the labs will look to further develop EntV peptide fragments to improve stability and efficacy through rational and random approaches and also hope to identify the mechanism of action.

“Interestingly, and unlike the currently approved therapeutics, the peptide does not kill or even inhibit the growth of the target fungi. Rather it appears to inhibit disease-causing behaviors,” Lorenz said. “This is an uncommon mode of action and further understanding how this occurs can tell us more about the mechanisms by which fungal pathogens infect humans, and that might lead to additional ideas for therapeutic development.”

Authors for the paper titled, include   Melissa Cruz   and   Shantanu Guha, PhD, from the Garsin Lab and   Shane Cristy   and   Giuseppe Buda De Cesare, PhD, from the Lorenz Lab.

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Plant pathology and plant-microbe biology, field description.

For a more complete description of the field of plant pathology and plant-microbe biology, please visit the field's  graduate page . Plant pathology and plant-microbe biology are the study of plant diseases and the biology of plant-microbe interactions at the molecular to ecosystem levels of organization. The field of plant pathology and plant-microbe biology at Cornell offers graduate degree programs in plant pathology and the biology, genetics, and evolution of fungi and oomycetes.

In addition to plant pathology and plant-microbe biology, Cornell University offers graduate programs that cover the full spectrum of plant sciences. View more information on  graduate studies  in related fields of plant sciences.

Contact Information

Data and statistics.

• Research Master's Program Statistics
• Doctoral Program Statistics

Field Manual

Subject and degrees, plant pathology.

• Plant Pathology (M.S.) (Ithaca)
• Plant Pathology (Ph.D.) (Ithaca)

Concentrations by Subject

• fungal and oomycete biology
• plant pathology
• plant-microbe biology

Maricelis Acevedo

• Campus: Ithaca
• Concentrations: Plant Pathology: fungal and oomycete biology; plant pathology
• Research Interests: cereal rust pathology and pathogen population biology, international plant pathology aspects, host resistance

Gary Carlton Bergstrom

• Concentrations: Plant Pathology: fungal and oomycete biology; plant pathology; plant-microbe biology
• Research Interests: biology, epidemiology, and integrated management of diseases of wheat, corn, soybean, forage legumes; and biofuel feedstock crops

Adam Bogdanove

• Research Interests: bacterial pathogens of plants; especially molecular interactions of Xanthomnas oryzae with rice; TAL effector biology and application; genome editing for disease resistance; fungal effector biology

Kathryn Bushley

• Research Interests: Characterization of secondary metabolism in fungi and investigating roles of secondary metabolites in host-fungal interactions. Emphasis on root endophytes and insect pathogenic and nematode parasitic fungi.

Lance E. Cadle-Davidson

• Research Interests: genetics and genomics of disease resistance; fungal and oomycete pathogens of grapevine

Clare L Casteel

• Concentrations: Plant Pathology: plant pathology; plant-microbe biology
• Research Interests: Viral pathogens of plants; vector-borne plant pathogens; ecological and molecular basis of virus-host and virus-vector-host interactions; molecular basis of plant defense responses to viruses and vectors

Kerik D. Cox

• Research Interests: orchard fungal ecology; extension pathology; pesticide management; fruit pathology

Zhangjun Fei

• Concentrations: Plant Pathology: plant-microbe biology

Melanie Filiatrault

• Research Interests: Role of small non-coding RNAs and RNA binding proteins in the biology of bacterial plant pathogens; the development of new approaches to perform global transcriptome profiling
• Research Interests: virus diseases of fruit and vegetable crops; biology, epidemiology and management; development of virus-resistant fruit crops by genetic engineering

David M Gadoury

• Research Interests: epidemiology; ecology; pathogen biology; disease of grapevine and apples; powdery and downy mildews
• Research Interests: Grape Disease Ecology & Epidemiology, oomycete biology, epidemiology, and control; data science; digital agriculture; vegetative spectroscopy; proximal and remote sensing.

Maria J. Harrison

• Concentrations: Plant Pathology: fungal and oomycete biology; plant-microbe biology
• Research Interests: elucidation of the molecular basis of the arbuscular mycorrhizal symbiosis and phosphate transport in plants

Michelle L Heck

Kathie Hodge

• Research Interests: systematics and ecology of pathogenic and symbiotic fungi, especially those that are pathogens of insects; director of the Cornell Plant Pathology Herbarium
• Research Interests: genetics of temperature responses in plants; regulation of plant defense responses

Lori Huberman

• Research Interests: How fungi interact with the environment Nutrient sensing in filamentous fungi High-throughput functional genomics
• Research Interests: Genetics of host disease resistance; Genetic improvement of disease resistance; Pathogen population genetics; International Agriculture; Current research focus is fungal (apple scab) and bacterial (fire blight) diseases and pathogens of apples

Magdalen Lindeberg

• Research Interests: identification of virulence-associated features in plant pathogenic bacteria, including Pseudomonas Syringae pathovars and Ca. species through analysis of their genome sequences

Gregory B Martin

• Research Interests: research focus is on the molecular basis of: 1) bacterial pathogenesis and host susceptibility; 2) recognition events involved in plant immunity; and 3) host signal transduction leading to defense responses; experimental approaches, including genomics, biochemistry, cell biology, molecular biology, forward and reverse genetics, and proteomics used to investigate aspects of plant-bacterial interactions

Margaret T McGrath

• Concentrations: Plant Pathology: plant pathology
• Research Interests: diseases of vegetable crops; integrated pest management; fungicide resistance; epidemiology; powdery mildew; Phytophthora; air pollutants

Patricia Mowery

• Research Interests: bacterial motility and sensing with emphasis on Xyllella fastidiosa

Rebecca Judith Nelson

• Research Interests: genetics of quantitative disease resistance; international agriculture; current focus on two diseases of maize that are important both in the United States and in Africa: northern corn leaf blight and gray leaf spot

Teresa Pawlowska

• Research Interests: biology and evolution of arbuscular mycorrhizal (AM) fungi (phylum Glomeromycota)

Keith Lloyd Perry

• Research Interests: Cucumber mosaic virus and its vector transmission, pathogen diagnostics technologies, and potato viruses; Director of the NYS Foundation Potato Seed Program and the Uihlein Laboratory and Farm

Sarah Jane Pethybridge

Jocelyn K. C. Rose

• Research Interests: structure, function and dynamics of the plant cell wall and apoplast during development and plant-pathogen interactions; coupling biochemistry with newly developed approaches involving genomics and proteomics; tomato issued as a model system to study wall and apoplastic dynamics in ripening fruits and in vegetative tissues in response to microbial challenge

Christine Durbahn Smart

• Research Interests: biology and management of vegetable diseases; host-pathogen interactions

Paul Stodghill

• Research Interests: Computational methods for analyzing large datasets from high-throughput biological experiments

Bryan Swingle

• Research Interests: Bacterial phytopathogen biology and functional genomics

Barbara Gillian Turgeon

• Research Interests: genetics and molecular biology of fungal pathogens

Xiaohong Wang

• Research Interests: molecular basis of plant-nematode interactions; host resistance to the potato cyst nematodes

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PhD Scholarship – Defining fungal genomic regions to facilitate virulence gene isolation and co-locating their interactions within the genomic regions in the crop host

The PhD student will be involved in a recently awarded Category 1 research grant involving multiple research organizations and industry. The aim of the project is to provide barley breeders with key biological knowledge and new and innovative biological and genetic tools to improve and speed up the production of net form net blotch (NFNB) disease resistant barley varieties. Fungal diseases are among the most important factors limiting the quality and yield of barley, with net form net blotch, caused by the fungus Pyrenophora teres f. teres , being particularly damaging. The most economically and environmentally friendly means to control crop diseases, such as NFNB, is to develop barley varieties with disease resistance. The PhD student will be involved in the identification of fungal virulence genes and their co-location in the host by making use of genetic mapping, bioinformatics, gene modification approaches and investigating the host/fungus interaction.

• Stipend of AUD $35,000 p.a.
• Maximum period of tenure of an award is 3 years.

To be eligible applicants must:

• have completed a research-based Master’s degree in a discipline related to the project (e.g. plant genetics and genomics, plant pathology, gene modification);  
• be native English speakers and/or meet UniSQ’s English Language Requirements for International applicants;
• not be receiving equivalent support providing a benefit greater than 75% of the student’s stipend rate;
• be eligible to commence or continue a PhD Program as soon as possible in 2024.

To be eligible applicants must:   

• Have a strong academic record and hold a qualification equivalent to an Australian research postgraduate degree;
• Have completed study and/or research experience in plant pathology, plant genetics/genomics and/or genome editing;
• Possess a good standing or potential to publish in high-quality journals in the related areas;
• Be enthusiastic, self-driven, and highly motivated;
• Possess excellent verbal and written communication skills.

To apply, please ensure you have digital copies of the below information:

• One page cover letter addressing the selection criteria;
• Curriculum vitae; encompassing any research presentations and/or publications;
• Education qualifications (testamur and academic transcripts for all undergraduate and postgraduate awards);

Application must be made via the  UniSQ Scholarship Application Management System  by the closing date.

If you require assistance in completing your application please download the Scholarship Online Application Manual .

Further information about this scholarship can be obtained from A/Prof Anke Martin by emailing [email protected]

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• v.12(11); 2022 Nov

The future of fungi: threats and opportunities

Nicola t case.

Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada

Judith Berman

Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel

David S Blehert

U.S. Geological Survey, National Wildlife Health Center, Madison, WI 53711, USA

Robert A Cramer

Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA

Christina Cuomo

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

Cameron R Currie

Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA

Iuliana V Ene

Department of Mycology, Institut Pasteur, Université de Paris, Paris 75015, France

Matthew C Fisher

MRC Centre for Global Infectious Disease Analysis, Imperial College, London W2 1PG, UK

Lillian K Fritz-Laylin

Department of Biology, University of Massachusetts, Amherst, MA 01003, USA

Aleeza C Gerstein

Department of Microbiology and Department of Statistics, University of Manitoba, Winnipeg, MB R3T 2N2, Canada

N Louise Glass

Plant and Microbial Biology Department, University of California, Berkeley, CA 94720, USA

Neil A R Gow

Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK

Sarah J Gurr

Chris todd hittinger.

Laboratory of Genetics, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA

Tobias M Hohl

Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY 10065, USA

Iliyan D Iliev

Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA

Timothy Y James

Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA

Hailing Jin

Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California—Riverside, Riverside, CA 92507, USA

Bruce S Klein

Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53706, USA

Department of Internal Medicine, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53706, USA

Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53706, USA

James W Kronstad

Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada

Jeffrey M Lorch

Victoria mcgovern.

Burroughs Wellcome Fund, Durham, NC 13901, USA

Aaron P Mitchell

Department of Microbiology, University of Georgia, Athens, GA 30602, USA

Julia A Segre

Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA

Rebecca S Shapiro

Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada

Donald C Sheppard

McGill Interdisciplinary Initiative in Infection and Immunology, Departments of Medicine, Microbiology & Immunology, McGill University, Montreal, QC H3A 0G4, Canada

Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94117, USA

Jason E Stajich

Eva e stukenbrock.

Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany

Environmental Genomics, Christian-Albrechts University, Kiel 24118, Germany

John W Taylor

Department of Plant and Microbial Biology, University of California—Berkeley, Berkeley, CA 94720, USA

Dawn Thompson

LifeMine Therapeutics, Cambridge, MA 02140, USA

Gerard D Wright

M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada

Joseph Heitman

Department of Molecular Genetics and Microbiology, Medicine, and Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA

Leah E Cowen

Associated data.

There are no new data associated with this article.

The fungal kingdom represents an extraordinary diversity of organisms with profound impacts across animal, plant, and ecosystem health. Fungi simultaneously support life, by forming beneficial symbioses with plants and producing life-saving medicines, and bring death, by causing devastating diseases in humans, plants, and animals. With climate change, increased antimicrobial resistance, global trade, environmental degradation, and novel viruses altering the impact of fungi on health and disease, developing new approaches is now more crucial than ever to combat the threats posed by fungi and to harness their extraordinary potential for applications in human health, food supply, and environmental remediation. To address this aim, the Canadian Institute for Advanced Research (CIFAR) and the Burroughs Wellcome Fund convened a workshop to unite leading experts on fungal biology from academia and industry to strategize innovative solutions to global challenges and fungal threats. This report provides recommendations to accelerate fungal research and highlights the major research advances and ideas discussed at the meeting pertaining to 5 major topics: (1) Connections between fungi and climate change and ways to avert climate catastrophe; (2) Fungal threats to humans and ways to mitigate them; (3) Fungal threats to agriculture and food security and approaches to ensure a robust global food supply; (4) Fungal threats to animals and approaches to avoid species collapse and extinction; and (5) Opportunities presented by the fungal kingdom, including novel medicines and enzymes.

Workshop Participants

Alan Bernstein, PhD , CIFAR President & CEO

Kate Geddie, PhD , CIFAR Senior Director, Research

Louis Muglia, MD, PhD , Burroughs Wellcome Fund President & CEO

Victoria McGovern, PhD , Burroughs Wellcome Fund Senior Program Officer

Leah Cowen, PhD , CIFAR Fungal Kingdom Co-Director, University of Toronto

Joseph Heitman, MD, PhD , CIFAR Fungal Kingdom Co-Director, Duke University

Neil Gow, PhD , CIFAR Fungal Kingdom Advisory Committee Member, University of Exeter

John Taylor, PhD , CIFAR Fungal Kingdom Advisory Committee Member, University of California, Berkeley

David Blehert, PhD , CIFAR Fungal Kingdom Fellow, U.S. Geological Survey

Christina Cuomo, PhD , CIFAR Fungal Kingdom Fellow, Broad Institute

Cameron Currie, PhD , CIFAR Fungal Kingdom Fellow, University of Wisconsin-Madison

Matthew Fisher, PhD , CIFAR Fungal Kingdom Fellow, Imperial College London

Lillian Fritz-Laylin, PhD , CIFAR Fungal Kingdom Fellow, University of Massachusetts Amherst

Sarah Gurr, PhD , CIFAR Fungal Kingdom Fellow, University of Exeter

Timothy James, PhD , CIFAR Fungal Kingdom Fellow, University of Michigan

Hailing Jin, PhD , CIFAR Fungal Kingdom Fellow, University of California, Riverside

Bruce Klein, MD, PhD , CIFAR Fungal Kingdom Fellow, University of Wisconsin-Madison

James Kronstad, PhD , CIFAR Fungal Kingdom Fellow, University of British Columbia

Don Sheppard, MD, PhD , CIFAR Fungal Kingdom Fellow, McGill University

Jason Stajich, PhD , CIFAR Fungal Kingdom Fellow, University of California, Riverside

Eva Stukenbrock, PhD , CIFAR Fungal Kingdom Fellow, Kiel University and Max Planck Institute of Evolutionary Biology

Gerard Wright, PhD , CIFAR Fungal Kingdom Fellow, McMaster University

Iuliana Ene, PhD , CIFAR Fungal Kingdom Azrieli Global Scholar, Institut Pasteur

Aleeza Gerstein, PhD , CIFAR Fungal Kingdom Azrieli Global Scholar, University of Manitoba

Rebecca Shapiro, PhD , CIFAR Fungal Kingdom Azrieli Global Scholar, University of Guelph

Nicola Case, CIFAR Fungal Kingdom Meeting Reporter, University of Toronto

Judith Berman, PhD , Tel Aviv University

Robert Cramer, PhD , Dartmouth

N. Louise Glass, PhD , University of California, Berkeley

Chris Todd Hittinger, PhD , University of Wisconsin-Madison

Tobias Hohl, MD, PhD , Memorial Sloan Kettering Cancer Center

Iliyan Iliev, PhD , Weill Cornell Medical College

Jeffrey Lorch, PhD , U.S. Geological Survey

Aaron Mitchell, PhD , University of Georgia

Julie Segre, PhD , National Human Genome Research Institute

Anita Sil, MD, PhD , University of California San Francisco

Dawn Thompson, PhD , LifeMine Therapeutics, Vice President, Head of Microbiology and Automation

Introduction

Despite their perception as something found in the forest or served up on a dinner plate, fungi are more than just mushrooms. They span an impressive range of sizes, from microscopic cells to among the largest organisms on Earth ( Sipos et al. 2018 ), and have a major impact on human health, agriculture, biodiversity, ecology, manufacturing, and biomedical research. Fungi are key members of aquatic ( Grossart et al. 2019 ) and terrestrial ecosystems, both as the Earth's preeminent degraders of organic matter and by forming beneficial symbioses with 90% of land plants ( Willis 2018 ), producing mycorrhizal networks that have come to be known as the “Wood-Wide Web” ( Simard et al. 1997 ). Fungal secondary metabolites have revolutionized modern medicine, as exemplified by penicillin, the world's first natural product antibiotic, and immunosuppressive drugs, like cyclosporin that enables organ transplantation, as well as anticancer and cholesterol-lowering drugs ( Keller 2019 ). From bioremediation to biofuels and beer to bread, the applications for which we employ these organisms and their products seem only limited by imagination. For example, there has been an increasing number of patent applications for fungal-based biomaterials with utility in the packaging, textile, leather, housing, and automotive industries ( Cerimi et al. 2019 ). While the fungal kingdom clearly presents enormous opportunities, it also poses major threats. Fungi can cause life-threatening bloodstream infections in humans, resulting in at least as many deaths per year as tuberculosis or malaria ( Brown, Denning, Gow et al. 2012 ; Brown, Denning, and Levitz 2012 ). The landscape of these infections continues to change with climate warming, with increases in extreme weather events such as tornados exacerbating human fungal disease ( Weinhold 2013 ). In parallel, fungi are responsible for devastating losses to staple crops that feed billions, jeopardize food security, and cause species declines and extinctions in bat and amphibian species that threaten biodiversity and ecosystem function ( Fisher et al. 2016 , 2020 ).

Inspired by colloquia held by the American Academy of Microbiology (AAM) in 2007 ( Buckley 2007 ) and 2017 ( American Academy of Microbiology 2019 ) and a long-standing partnership between the Burroughs Wellcome Fund and the mycology community, the Canadian Institute for Advanced Research (CIFAR) held a workshop in November 2021 to help chart the future challenges and opportunities presented by the fungal kingdom. Attended by members of the CIFAR Fungal Kingdom: Threats & Opportunities research program ( Case et al. 2020 ), the Burroughs Wellcome Fund, and by leading experts on fungal biology from academia and industry, participants convened to strategize on and address questions pertaining to (1) Connections between fungi and climate change and ways to avert climate catastrophe; (2) Fungal threats to humans and ways to mitigate them; (3) Fungal threats to agriculture and food security and approaches to ensure a robust global food supply; (4) Fungal threats to animals and approaches to avoid species collapse and extinction; and (5) Opportunities presented by the fungal kingdom including novel medicines and enzymes. In addition, building on the previous AAM colloquia, participants revisited the recommendations outlined in 2007 ( Buckley 2007 ) and 2017 ( American Academy of Microbiology 2019 ) reports to provide updated suggestions for accelerating fungal research.

Connections between fungi and climate change and ways to avert climate catastrophe

How can we alter plant microbiomes to enhance co 2 sequestration.

The anthropogenic production of greenhouse gases, such as CO 2 , is expected to raise global temperatures by 2–5°C in the coming decades ( Pachauri and Reisinger 2007 ). Restoring carbon balance by reducing and offsetting emissions is a major environmental sustainability goal ( Arora and Mishra 2019 ) in which vegetation, soils, and oceans play an important role by sequestering carbon, thereby removing it from the atmosphere ( Sabine et al. 2004 ; Lal 2005 ). Mycorrhizal fungi, which form symbioses with plant roots, have a remarkable impact on soil carbon sequestration ( Adamczyk 2021 ), wherein forest ecosystems dominated by different types of mycorrhizal fungi have vastly different carbon storage capabilities ( Averill et al. 2014 ). Building on this knowledge, participants suggested enhanced research in precision forest mycobiome engineering as a strategy to augment carbon sequestration by forests. In addition to contributing to carbon sequestration ( Clemmensen et al. 2013 ), fungi respire CO 2 and can cause considerable soil carbon losses ( Cheng et al. 2012 ), as well as release CO 2 from dead organic matter by contributing to its decomposition. Thus, as highlighted recently ( Tiedje et al. 2022 ), the impact of mycobiome engineering on both greenhouse gas sequestration and release would need to be assessed.

Reforestation after clear-cutting for timber harvest, tree planting to offset carbon emission, and crop farming were highlighted as existing practices where engineered mycobiomes could be applied to enhance carbon sequestration. In addition, the group suggested further investigation of the mycobiomes of seaweeds ( Suryanarayanan 2012 ), whose aquatic farming is the fastest-growing component of global food production ( Duarte et al. 2017 ). Seaweeds function as important marine CO 2 sinks ( Krause-Jensen and Duarte 2016 ) and thus understanding how fungi impact the ability of seaweed to fix CO 2 , and whether seaweed-associated fungi can be manipulated to enhance this process, are important to address. Despite the potential of these strategies to enhance CO 2 sequestration, participants identified several challenges. The importance of understanding local ecology to inform decisions on the type and combination of fungi was emphasized, as each environment has its own distinct set of biotic and abiotic factors that are likely to affect the longevity and function of the applied fungal community. Furthermore, the impact of introducing designer fungal communities on native microbes, and other potential ecological consequences, would need to be carefully considered.

How can we identify new fungal pathogens of crops and existing fungal pathogens whose geographic range is expanding due to climate change?

While fungal symbionts of plants hold promise to enhance carbon capture, fungal plant pathogens are responsible for staggering reductions in absorbed CO 2 by causing disease ( Fisher et al. 2012 ). Even more concerning is evidence that fungal pathogens of crops are moving poleward as the global climate warms ( Bebber et al. 2013 ), facilitating the interactions of pathogens with naïve hosts and environments ( Chaloner et al. 2021 ). Participants discussed increased surveillance efforts to detect and monitor fungal pathogens of crops as a proactive strategy to improve responsiveness to emerging threats. Efforts would ideally take the form of a global monitoring program, wherein widespread metagenomic sequencing of fungal communities could facilitate the identification of novel pathogens, as well as the movement of known pathogens into new areas. Recognizing the scale of such a program, the group suggested that engaging farmers in citizen science initiatives to aid with sample collection or capturing the interest of industry partners would be beneficial. In all cases, promoting open science and sharing of crop pathogen surveillance and sequencing data as they become available, such as through OpenRiceBlast and OpenWheatBlast ( Kamoun et al. 2019 ), would be empowering. In concert with increased local monitoring for crop pathogens, participants emphasized the benefits of enhanced surveillance of internationally transported plants, given the ability of global trade to exacerbate the spread of fungal pathogens ( Fisher et al. 2020 ).

How do fungi respond and adapt to climate change and increasing temperatures?

In addition to expanding the habitat of fungal pathogens, climate warming has the potential to select for environmental fungi adapted for growth at temperatures approaching that of the human body ( Garcia-Solache and Casadevall 2010 ). This poses a major problem because mammalian body temperature acts as a restrictive barrier to fungal infection given that most fungi thrive within the range of 12–30°C ( Robert and Casadevall 2009 ). Thus, if environmental fungi that are currently unable to cause infections in humans evolve increased temperature tolerance, many additional species may become pathogenic ( Garcia-Solache and Casadevall 2010 ). Previous work drawing on archived culture collection data identified fungal genera with a disproportionate number of thermotolerant species, highlighting these genera as potential sources of emerging pathogenic fungi given their propensity for adaptation to higher temperature growth ( Robert and Casadevall 2009 ). Although this study offers a starting point, participants suggested that a large survey of fungal temperature tolerance could be conducted to identify species with the greatest likelihood of overcoming the mammalian thermal barrier. In tandem, the characterization of fungal species that are close relatives to known pathogens, but currently lack thermotolerance, would be beneficial ( Garcia-Solache and Casadevall 2010 ). Such surveys are of increasing importance given the recent report that human body temperatures have decreased over the past century ( Protsiv et al. 2020 ), further narrowing the thermal barrier.

Fungal threats to humans and ways to mitigate these threats

How did candida auris emerge to cause disease globally and where is it present in the environment.

Candida auris is hypothesized to be the first human fungal pathogen to emerge due to thermal adaptation in response to climate change ( Casadevall et al. 2019 ); however, its origin is still a mystery. Initially detected in 2009 ( Satoh et al. 2009 ), C. auris emerged near-simultaneously on 3 continents ( Lockhart et al. 2017 ) and has since spread across the globe ( Chakrabarti and Sood 2021 ). C.auris poses a major new threat to human health due to its high rate of antifungal resistance, ability to persist on hospital surfaces, and rising number of cases ( Chakrabarti and Sood 2021 ). Recently, C. auris was isolated environmentally from a salt marsh and sandy beach on the Andaman Islands in India, suggesting it may be associated with the marine ecosystem ( Arora et al. 2021 ). Some participants postulated that prior to its emergence as a human fungal pathogen, C. auris may have transiently colonized human skin several times before being carried into a hospital environment and exposed to a susceptible host, leading to amplification and outbreaks. In partial alignment with this hypothesis, screening for C. auris skin colonization of patients in a nursing facility identified multiple skin sites including nares, fingers, and toe webs as frequently colonized body sites ( Proctor et al. 2021 ). The group suggested that additional environmental sampling for C. auris in conjunction with studies of the human skin mycobiome would be beneficial, especially in areas where C. auris is endemic.

Are agricultural practices driving antifungal drug resistance in species beyond Aspergillus ?

Azoles are widely deployed in agriculture as fungicides but are also used as therapeutics to treat fungal infections in humans and animals ( Fisher et al. 2018 ). The dual use of azoles in agriculture and in the clinic has led to the global emergence of azole resistance in the major human fungal pathogen Aspergillus fumigatus ( Meis et al. 2016 ; Fisher et al. 2018 ). As a result, azoles are losing utility as a frontline antifungal therapy, leading to increases in patient mortality ( Meis et al. 2016 ). Azole resistance is also exceedingly common in isolates of C. auris ( Chow et al. 2020 ), raising the question of whether the extensive use of azoles in agriculture also promoted the development of resistance in this emergent fungal pathogen. In addition, participants highlighted that consumption of azole-treated foods may impact resistance in commensal fungi, including those with the potential to be pathogenic. The identification of azole resistance in multiple fungal pathogens underscores the timeliness for application of a ‘One Health’ perspective to antifungal drug deployment, which recognizes that human, plant, and animal health are interconnected ( American Academy of Microbiology 2019 ; Fisher and Murray 2021 ). Applying a ‘One Health’ approach recognizes stewardship of existing compounds as well as new methods for treating and preventing fungal infections in plants and humans ( Fisher et al. 2018 ; American Academy of Microbiology 2019 ). Strategies for curbing resistance to antifungals could include retaining newly developed therapies for use in either agriculture or medicine. However, limiting antifungals with broad utility for clinical use alone would likely require the implementation of government regulations or incentives given the larger market for use in agriculture.

How can we accelerate fungal vaccine development and promote the development of newer antifungals and their approval?

New strategies are needed to combat human fungal pathogens given the rising resistance to currently available antifungals and ever-changing landscape of human disease, with novel viruses like SARS-CoV2 producing new patient populations that are vulnerable to fungal infections ( Gangneux et al. 2022 ; Hoenigl et al. 2022 ). Despite the substantial health burden posed by fungal pathogens and numerous efficacious vaccines against bacteria and viruses, there are no clinically approved vaccines or monoclonal antibodies to protect against fungal infections ( Oliveira et al. 2021 ). Although several fungal vaccines ( Oliveira et al. 2021 ), immunotherapies ( Da Glória Sousa et al. 2011 ), and monoclonal antibodies ( Rudkin et al. 2018 ) are in development and some have reached clinical trials, challenges pose barriers to the fungal vaccine pipeline, recently reviewed in Oliveira et al. (2021) . Gut commensal fungi can induce germinal center B-cell expansion and systemic antibodies that are protective against disseminated Candida albicans or C. auris infections, highlighting new opportunities for exploration of the natural human antibody repertoire against gut mycobiota for development purposes ( Doron et al. 2021 ). Major advances in mRNA vaccine technology, largely fueled by the ongoing coronavirus disease 2019 (COVID-19) pandemic ( Chaudhary et al. 2021 ), present an opportunity for the development of novel fungal vaccines. In all cases, it would be prudent to explore the biological and immunological implications of fungal vaccines on commensal fungi, fungi consumed as food, and fungal allergens, which are currently unknown. In the development of fungal vaccines, immunotherapies, and antifungals, the group highlighted major regulatory, licensing, and distribution barriers, as well as a lack of financial incentives, as roadblocks. Many of the same problems have been identified in the antibiotics pipeline, which led the United Kingdom to trial a model wherein antibiotics are paid for through a subscription, rather than on a per-pill basis ( Glover et al. 2019 ; Mahase 2020 ). A similar pilot program, the Pioneering Antibiotic Subscriptions to End Upsurging Resistance (PASTEUR) Act, was introduced to the United States Congress in 2021 ( Outterson 2021 ). Some participants thought the antifungal pipeline could also benefit from governments buying into a “subscription model” for antifungals, which would decouple revenue from the volume of drugs sold to help encourage new development by offsetting costs.

Fungal threats to agriculture and food security and approaches to ensure a robust global food supply

Are there ways to breed crops for resistance or new fungicides to deploy such as those based on rna.

Genetically modifying crops to enhance resistance to microbial infection offers an alternative to chemical agents ( Dong and Ronald 2019 ). However, genetically modified organisms (GMOs) are banned in a number of countries, including many in the European Union, necessitating alternative approaches for crop protection ( Turnbull et al. 2021 ). A promising avenue is the use of RNA interference, a cellular process whereby gene transcript expression is reduced in a sequence-specific manner without modifying the genome ( Hernández-Soto and Chacón-Cerdas 2021 ), thereby circumventing the regulatory processes that limit GMOs. In a method known as spray-induced gene silencing (SIGS), RNAs targeting pathways essential for growth or virulence of the pathogen are sprayed on the plant ( Hernández-Soto and Chacón-Cerdas 2021 ). These RNAs are subsequently taken up by the pathogen, where they act inside the cell to inhibit growth or virulence, thereby protecting the plant from infection ( Hernández-Soto and Chacón-Cerdas 2021 ). Although SIGS may offer a versatile, effective, safe, and eco-friendly approach for crop protection, the group highlighted the need to explore potential off-target effects of SIGS on fungal symbionts of plants, like endophytes and mycorrhizae. Research on the evolution of resistance to RNA uptake was also emphasized as an important area for future research, given that the effectiveness of SIGS for fungal disease control is dependent on the efficiency of RNA uptake by the pathogen ( Qiao et al. 2021 ). In addition, some participants highlighted mycoviruses, which are viruses that infect fungi, as potential biological control agents for crop fungal disease ( Nuss 2005 ; Xie and Jiang 2014 ). Although mycoviruses have been identified to cause reduced virulence in some fungal crop pathogens ( Cho et al. 2013 ; Pearson and Bailey 2013 ), relatively little is known about mycoviruses, underscoring that additional sampling and sequencing to detect mycoviruses, as well as assays to determine their phenotypic effects on different fungal species would be valuable.

Can we modify the plant mycobiome to enhance resistance to pathogens?

Fungal endophytes, which live within plant tissues, have been widely reported to protect their host plants against herbivore pests ( Bamisile et al. 2018 ). Less well studied is the ability of fungal endophytes to protect plants against fungal plant pathogens, although some cases have been reported ( Bamisile et al. 2018 ). Despite the promise of fungal endophytes to act as biological control agents against plant fungal pathogens, the group identified 3 major challenges to overcome. First, more insight into the mechanisms by which fungal endophytes confer protection, whether it be directly, through microbial competition or secretion of compounds with antifungal activity, or indirectly, through priming the host immune system, would be beneficial. Second, the best method and location (roots, stem, leaves, or soil) for applying beneficial symbionts would need further investigation. Last, a plant-, pathogen-, and environment-specific approach would be valuable to identify endophyte combinations that lead to stable colonization and effective, long-term protection. Thus, a “look locally first” strategy could be applied, where beneficial endophytes are identified within the local environment, then reapplied in combinations to the host plant. Such a strategy would limit the transport of fungi into non-native ecosystems and ensure endophyte cocktails are adapted to the environment in which they are applied, promoting longevity.

How do we protect crops from postharvest fungal damage?

While microbial pathogens cause approximately 15% losses in yield by damage to crops in the field ( Oerke 2006 ), the destruction caused by postharvest disease amounts to an additional 20–25% reduction, depending on the country ( Sharma et al. 2009 ). Current postharvest disease mitigation strategies rely heavily on chemicals, which pose a threat to human health and the environment. Similar to its utility in protecting preharvest crops, SIGS has been identified as a method for safe and powerful plant protection of postharvest products ( Wang et al. 2017 ). In addition, plant ( Utama et al. 2002 ) and bacterial ( Gao et al. 2018 ; Carter-House et al. 2020 ) volatiles are being investigated for their ability to suppress the growth of fungal pathogens that commonly cause postharvest decay. Some members of the group proposed that microbes that produce fungal growth-inhibiting volatiles could be applied to the packaging of postharvest products to provide a continuous source of volatiles to suppress fungal growth. Padding is already routinely included in the packaging of many fruits to absorb moisture and provide cushioning to prevent damage, thus microbes could readily be applied to these pads to provide a natural solution to postharvest decay caused by fungi. However, care would be needed to ensure the applied microbes cannot cause decay themselves or readily adapt to do so and do not pose a threat to human health.

Fungal threats to animals and approaches to avoid species collapse and extinction

Are there ways to protect frogs and salamanders from chytrid pathogens.

The amphibian fungal disease chytridiomycosis, caused by Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans , has driven global declines and extinctions in over 500 species of amphibians, amounting to the greatest recorded loss of biodiversity attributable to a pathogen ( Scheele et al. 2019 ). International trade in amphibians has been linked to the spread of chytrid pathogens and their introduction into naïve hosts, resulting in disease outbreaks ( O’Hanlon et al. 2018 ). Strengthening of transcontinental biosecurity, such as restrictions on salamander import, have helped mitigate disease transmission ( Klocke et al. 2017 ), but continued precautions and strategies for supporting the recovery of endangered populations are needed. Participants emphasized that domestic amphibian breeding programs could be implemented to provide a supply of disease-free animals to the pet trade. Domestic breeding programs would prevent large-scale mining of amphibians from the wild, thereby enabling more stringent import regulations to limit the continued global spread of chytrid pathogens.

Strategies for mitigating the impact of chytridiomycosis on wild amphibian populations would also be valuable. Diverse avenues have been explored, such as antifungal treatment of tadpoles coupled with environmental disinfection ( Bosch et al. 2015 ), and probiotic therapy through bioaugmentation of microbes that confer defense against chytrids ( Bletz et al. 2013 ; Kearns et al. 2017 ; Woodhams et al. 2020 ); but the broad applicability and scalability of these methods have yet to be determined. Additional strategies discussed by the group included biological control using mycoviruses, which has been applied against the fungal agent responsible for chestnut blight ( Rigling and Prospero 2018 ), and the introduction of nonpathogenic chytrid lineages to outcompete virulent lineages. However, more research into the potential impacts of introducing novel mycoviruses or less pathogenic chytrid strains warrant careful study before implementation.

How can we reduce the impact of bat white-nose syndrome on bat populations and ecosystems?

Bats play a crucial role in maintaining ecosystem health as seed dispersers, pollinators, and controllers of insect pests ( Ramírez-Fráncel et al. 2022 ). White-nose syndrome (WNS) is a devastating disease affecting North American hibernating bat populations that is caused by the fungus Pseudogymnoascus destructans ( Lorch et al. 2011 ). Introduced to North America by humans in 2006 ( Blehert et al. 2009 ), P. destructans is spreading across the continent, resulting in declines of more than 90% in some bat populations ( Turner et al. 2011 ). One strategy for controlling WNS involves vaccinating bats with P. destructans antigens to elicit a protective immune response ( Rocke et al. 2019 ). Vaccine administration was successful at reducing P. destructans infection of bats in a laboratory trial ( Rocke et al. 2019 ) and is currently being explored in field trials; however, additional funding would be needed to enable vaccination of afflicted populations. The group suggested raising public awareness of WNS through events such as Bat Week, and attracting companies interested in aging research, given the exceptional longevity of bats ( Brunet-Rossinni and Austad 2004 ), as strategies for garnering financial support. Raising public awareness would also be important to mitigate the spread of WNS by people exploring caves where bats live. The additional methods for managing WNS were discussed, including the use of immune receptor agonists to boost the bat antifungal response to P. destructans and sterilization or modification of bat hibernacula sediments, which are a known reservoir of P. destructans ( Verant et al. 2018 ), to remove the pathogen or suppress its growth with antagonistic microbes.

How can we increase awareness of other fungal pathogens of animals and the dangers they pose?

In addition to causing devastating disease in amphibians and bats, emerging fungal diseases have been identified in wild snakes ( Lorch et al. 2015 ), sea turtles ( Sarmiento-Ramírez et al. 2014 ), lizards ( Peterson et al. 2020 ), dolphins and porpoises ( Teman et al. 2021 ), and birds ( Arné et al. 2021 ). Despite this, fungi are often overlooked as sources of emerging infectious disease, compounding their threat to wildlife and ecosystem health ( Fisher et al. 2020 ). Given the impact of human movement on spreading infectious diseases of wildlife, participants suggested that developing communication strategies to increase public awareness of the threats fungi pose to wildlife, for use in venues such as schools and national parks, would be beneficial. Public involvement through citizen science and other nationally coordinated programs to report dead wildlife was also proposed as a strategy, which could aid in identifying trends that may indicate the emergence of infectious disease in wildlife populations. As wildlife diseases are inherently difficult to treat, the group highlighted the possible need for a paradigm shift in wildlife disease management from reactive to proactive strategies. A proactive strategy could center on managing wildlife populations for health, which would entail identifying underlying drivers of wildlife infectious diseases and mitigating these factors to prevent disease emergence. It would also involve supporting ecosystem health to help wildlife populations build resilience in the face of disease and enable recovery. Such a strategy may prove effective given the potential for wildlife populations to evolve resistance and recover from disease without human intervention, as has been predicted in bat populations affected by WNS ( Auteri and Knowles 2020 ) and documented in amphibian populations afflicted with chytridiomycosis ( Scheele et al. 2014 ).

Opportunities presented by the fungal kingdom including novel medicines and enzymes

How can we accelerate discovery of the biological activities of fungal natural products.

Fungi produce an astounding array of natural products, some of which have been developed into drugs that have revolutionized patient care ( Keller 2019 ). The fungal kingdom is exceptionally diverse, home to an estimated 2.2–3.8 million species, the majority of which have yet to be identified ( Hawksworth and Lücking 2017 ). However, progress has been slow in identifying new fungal metabolites that can be advanced into the clinic, partly owing to rediscovery of known molecules. The group discussed using CRISPR genome engineering to minimize rediscovery by inactivating biosynthetic gene clusters (BGCs) needed to make commonly identified antimicrobials in strains of interest ( Culp et al. 2019 ) and posited that this approach could be applied on a large scale to existing strain collections or environmental samples to augment the discovery of new natural products. Investigating the molecules produced by animal-associated microbes was also proposed as a strategy to accelerate the pace of drug discovery, given that these microbes appear to be enriched in compounds with low toxicity to animals ( Chevrette et al. 2019 ). In addition, genomics was highlighted as an invaluable tool for fungal natural product discovery as genes involved in the biosynthesis of fungal secondary metabolites are often arranged in BGCs, which can be predicted by algorithms ( Keller 2019 ). Thus, the sequencing of fungal genomes can provide insight into the molecules that fungi have the potential to produce, and when coupled with synthetic biology can enable BGCs from unculturable fungi to be expressed in heterologous microbial hosts ( Clevenger et al. 2017 ). Lastly, participants underscored the benefit of supporting and sustaining fungal culture collections and databases given their value in enabling natural product discovery and fungal research more broadly.

Can we harness fungi to develop clean fuels that help avert climate catastrophe?

Fungi have phenomenal potential for applications in bioremediation ( Harms et al. 2011 ; Kumar and Chandra 2020 ) and in the production of sustainable energy sources, such as in the biofuel industry and advanced biorefineries ( Hong and Nielsen 2012 ; Srivastava et al. 2018 ; Keasling et al. 2021 ). Fungi and fungal enzymes are being explored for their ability to convert renewable lignocellulosic materials (plant dry matter) into biofuels, providing environmentally friendly and sustainable alternatives to fossil-derived fuels and chemicals ( Srivastava et al. 2018 ; Lillington et al. 2021 ). Moreover, fungi possess the biochemical and ecological capacity to degrade environmental pollutants, such as toxic chemicals generated during textile and pulp production, pesticides, pharmaceuticals, plastics, and crude oil ( Harms et al. 2011 ; Zeghal et al. 2021 ). Thus, fungi harbor key enzymes and are key bioconversion chassis both for use in fuel production and its cleanup. The group emphasized the importance of industry-academia partnerships to enable the exploitation of fungi for biofuel production and bioremediation, as well as in general to make broad utilization of fungal enzymes in biotechnology and fungal natural products in drug discovery. Consulting and participation in scientific advisory boards were highlighted as avenues for building industry-academia collaborations, which can promote sharing of expertise and resources to accelerate innovation and application of fungal-derived products. Moreover, participants discussed the value of an increase in initiatives to promote these partnerships, such as programs offering funding to graduate students and postdoctoral fellows, to enable joint industrial-academic research projects.

Recommendations

The 2007 ( Buckley 2007 ) and 2017 ( American Academy of Microbiology 2019 ) AAM colloquia reports on the fungal kingdom provided recommendations to promote advances in fungal research. These recommendations were revisited during the meeting hosted by CIFAR and the Burroughs Wellcome Fund and updated to reflect the current state of the world’s fungi and to provide suggestions for accelerating the development of novel strategies to combat the threats posed by fungi and harness their extraordinary potential ( Fig. 1 ). These recommendations have been proposed within the context of relevant background information in the main text and are further distilled in a succinct format below.

Recommendations to promote advances in fungal research. Created with BioRender.com.

• Develop Facilities to Bring Diverse Mycologists Together . An interdisciplinary approach is crucial to mitigating fungal threats and identifying fungal-based solutions to global challenges. Mycology Centers of Excellence would be valuable to coordinate multidisciplinary work between mycologists that focus on fungi that infect humans, plants, and wildlife. Mycology Centers could be modeled after National Institutes of Health (NIH) Cancer Centers and would enable efficient growth and translation of scientific knowledge for application in medicine, agriculture, and ecosystem conservation.
• Enhance and Sustain Training in Fungal Biology. There is a clear benefit to training more individuals to address the diverse facets of fungal biology and the impact of fungi on human, plant, and animal health. In particular, enhanced training in medical mycology, especially in areas where mycoses are endemic, would improve accurate diagnosis and informed treatment of patients. Moreover, the development of programs to train domestic animal and wildlife veterinarians, and to include them in discussions on managing fungal diseases of livestock and wild animals, would serve to further mitigate the impacts of fungi on animal health.
• Develop and Sustain Public Education and Outreach Programs to Increase Awareness of Fungal Diseases. Fungi are not widely regarded as major agents of infectious disease, despite the substantial burden they pose to human, plant, and animal health. Programs could be developed for implementation in schools and national parks to increase public awareness of the threats posed by fungal pathogens and the actions by which humans contribute to their spread.
• Develop Programs to Promote Partnerships Between Industry and Academia. Programs offering financial support, such as funding of graduate students and postdoctoral fellows, would promote collaboration between industry and academia. In addition, these partnerships would enable sharing of resources and expertise, as well as recruit talent to work in industry, ultimately accelerating the pace of innovation.
• Support and Sustain Fungal Genome Databases. Fungal genomics, transcriptomics, proteomics, and other “omics” methods, as well as an increasing number of fungal genome sequences, have generated abundant and rich datasets. Compiling, storing, and annotating these data in an integrated format that is accessible to the community is critical to informing research and promoting advances. Developing and implementing unified taxonomy and standardized pipelines for next-generation sequencing methods would be beneficial.
• Support and Sustain Fungal Specimen and Culture Collections. Fungal specimen and culture collections are critical resources for understanding fungal biology, genetic variation, and evolution. These collections are likely to become increasingly important for examining the impact of climate change on fungi, tracking invasive species, and preserving fungal diversity. Moreover, fungal culture collections represent a rich source of chemical diversity for the identification of natural products that can be developed for clinical use. The long-term availability of these existing and new collections would be valuable in enabling fungal research.
• Report and Track Fungi That Cause Disease in Humans, Plants, and Animals. Documenting the global burden of fungal disease would enable increased understanding of disease emergence, range expansion, and the impact of drug resistance. To achieve this objective, public, domestic animal, and wildlife health agencies could implement programs to transparently report cases of fungal disease, and crop monitoring services could report fungal disease surveillance data to publicly accessible databases.
• Limit the Global Transport of Living Plants and Animals. Global trade can promote the spread of plant and animal fungal pathogens ( Fisher et al. 2020 ). Enhanced pathogen surveillance of internationally transported plants and animals coupled with stringent import regulations could limit the introduction of potential pathogens to naïve populations. Locally maintained, disease-free nursery and animal stocks would reduce the need for global import and help prevent the spread of fungal pathogens.
• Explore Strategies to Manage Wildlife Populations for Health. Management of wildlife infectious diseases has historically been reactive despite these diseases being difficult to treat. A paradigm shift toward proactive strategies that act to or are predicted to support ecosystem health and enable wildlife populations to build resilience and recover in the face of disease would be beneficial.
• Identify Fungal Threats and Opportunities That Have Emerged as a Result of the COVID-19 Global Pandemic. The COVID-19 pandemic has produced new patient populations that are vulnerable to fungal infection ( Baddley et al. 2021 ). Further research would be important to understand COVID-19-associated fungal diseases, such as mucormycosis ( Baddley et al. 2021 ). Concurrently, a Global Virome Project has been launched to discover zoonotic viral threats and stop future pandemics, which will entail sampling of bats and other animals to identify viruses ( Carroll et al. 2018 ). This initiative presents both an opportunity, to sample wildlife for fungi in tandem with viruses, and a threat, as human movement during sampling has the potential to spread disease between wildlife populations.

Conclusions and outlook

The fungal kingdom presents enormous opportunities for applications in medicine, biotechnology, and environmental sustainability, while also posing devastating threats to human, plant, and animal health. Moreover, the breadth of fungal diversity remains relatively underexplored and the impact of climate change and emergent infectious diseases like COVID-19 on fungi have yet to be appreciated. Novel approaches would be beneficial to harness fungi to avert climate catastrophe, support plant health, mitigate wildlife disease, and identify new medicines. The goal of this report is to raise awareness on the diverse ways fungi impact health and disease, to spark innovative solutions to global challenges and fungal threats, and to provide suggestions for advancing the field of fungal biology. As highlighted in the recommendations herein, developing and sustaining infrastructure to support fungal research would catalyze the development of new strategies to mitigate the threats posed by fungi and harness their extraordinary potential.

Acknowledgments

We thank CIFAR and the Burroughs Wellcome Fund for their support and for hosting the “Future of Fungi” workshop. LEC and JH are Co-Directors and Fellows of the CIFAR program Fungal Kingdom: Threats & Opportunities . NARG and JWT are Advisory Committee Members of the CIFAR program Fungal Kingdom: Threats & Opportunities . DSB, CAC, CRC, MCF, LKF-L, SJG, TYJ, HJ, BSK, JWK, DCS, JES, EES, and GDW are Fellows of the CIFAR program Fungal Kingdom: Threats & Opportunities . IVE, ACG, and RSS are CIFAR Azrieli Global Scholars of the CIFAR program Fungal Kingdom: Threats & Opportunities . Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

NTC is supported by a CIHR Canadian Graduate Scholarships—Doctoral award. JH is supported by NIH R01 grants AI39115-24, AI50113-17, and AI133654-05. LEC is supported by CIHR Foundation grant FDN-154288, NIH R01 grants AI127375 and AI120958, and a Canada Research Chair (Tier 1) in Microbial Genomics & Infectious Disease. LKF-L is supported by NIH R35 grant GM143039, NSF CAREER award 2143464, Gordon and Betty Moore Foundation grant #9337, an Excellence in Biomedical Science award from the Smith Family Foundation, and a Pew Scholar award from the Pew Charitable Trust. AS is supported by NIH grants R01AI136735, R37AI066224, R01AI146584, and U19AI166798. CTH is supported by NSF grants DEB-1442148 and DEB-2110403, in part by the DOE Great Lakes Bioenergy Research Center (DOE Office of Science BER DE-FC02-07ER64494), the USDA National Institute of Food and Agriculture (Hatch project 1003258), and an H. I. Romnes Faculty Fellowship from the Office of the Vice Chancellor for Research and Graduate Education with funding from the Wisconsin Alumni Research Foundation. MCF is supported by the Wellcome Trust 219551/Z/19/Z, NERC grant NE/S000844/, and MRC grant MR/R015600/1. RSS is supported by an NSERC Discovery Grant (RGPIN-2018-4914) and a CIHR Project Grant (PJT 162195). TMH is supported by NIH grants R37AI093808, R01AI139632, R21AI156157, and by P30CA008748 (to Memorial Sloan Kettering Cancer Center).

Conflicts of interest

LEC is a cofounder of and shareholder in Bright Angel Therapeutics, a platform company for the development of novel antifungal therapeutics, and a Science Advisor for Kapoose Creek, a company that harnesses the therapeutic potential of fungi. NLG is a member of the Scientific Advisory Board for MycoWorks, a biotechnology company that produces materials from fungal mycelium. JES is a paid consultant for Sincarne, Inc.

Contributor Information

Nicola T Case, Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada.

Judith Berman, Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.

David S Blehert, U.S. Geological Survey, National Wildlife Health Center, Madison, WI 53711, USA.

Robert A Cramer, Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.

Christina Cuomo, Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

Cameron R Currie, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.

Iuliana V Ene, Department of Mycology, Institut Pasteur, Université de Paris, Paris 75015, France.

Matthew C Fisher, MRC Centre for Global Infectious Disease Analysis, Imperial College, London W2 1PG, UK.

Lillian K Fritz-Laylin, Department of Biology, University of Massachusetts, Amherst, MA 01003, USA.

Aleeza C Gerstein, Department of Microbiology and Department of Statistics, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.

N Louise Glass, Plant and Microbial Biology Department, University of California, Berkeley, CA 94720, USA.

Neil A R Gow, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK.

Sarah J Gurr, Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK.

Chris Todd Hittinger, Laboratory of Genetics, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.

Tobias M Hohl, Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY 10065, USA.

Iliyan D Iliev, Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA.

Timothy Y James, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.

Hailing Jin, Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California—Riverside, Riverside, CA 92507, USA.

Bruce S Klein, Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53706, USA. Department of Internal Medicine, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53706, USA. Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53706, USA.

James W Kronstad, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.

Jeffrey M Lorch, U.S. Geological Survey, National Wildlife Health Center, Madison, WI 53711, USA.

Victoria McGovern, Burroughs Wellcome Fund, Durham, NC 13901, USA.

Aaron P Mitchell, Department of Microbiology, University of Georgia, Athens, GA 30602, USA.

Julia A Segre, Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.

Rebecca S Shapiro, Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.

Donald C Sheppard, McGill Interdisciplinary Initiative in Infection and Immunology, Departments of Medicine, Microbiology & Immunology, McGill University, Montreal, QC H3A 0G4, Canada.

Anita Sil, Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94117, USA.

Jason E Stajich, Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California—Riverside, Riverside, CA 92507, USA.

Eva E Stukenbrock, Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany. Environmental Genomics, Christian-Albrechts University, Kiel 24118, Germany.

John W Taylor, Department of Plant and Microbial Biology, University of California—Berkeley, Berkeley, CA 94720, USA.

Dawn Thompson, LifeMine Therapeutics, Cambridge, MA 02140, USA.

Gerard D Wright, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada.

Joseph Heitman, Department of Molecular Genetics and Microbiology, Medicine, and Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.

Leah E Cowen, Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada.

Data Availability

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• Published: 26 April 2021

Fungal taxonomy and sequence-based nomenclature

• Robert Lücking 1 , 2 ,
• M. Catherine Aime   ORCID: orcid.org/0000-0001-8742-6685 2 , 3 ,
• Barbara Robbertse 4 ,
• Andrew N. Miller   ORCID: orcid.org/0000-0001-7300-0069 2 , 5 ,
• Takayuki Aoki 2 , 6 ,
• Hiran A. Ariyawansa 2 , 7 ,
• Gianluigi Cardinali 8 ,
• Pedro W. Crous 2 , 9 , 10 ,
• Irina S. Druzhinina   ORCID: orcid.org/0000-0003-2821-5268 2 , 11 , 12 ,
• David M. Geiser 2 , 13 ,
• David L. Hawksworth   ORCID: orcid.org/0000-0002-9909-0776 2 , 14 , 15 , 16 , 17 ,
• Kevin D. Hyde 2 , 18 , 19 , 20 , 21 ,
• Laszlo Irinyi   ORCID: orcid.org/0000-0002-4453-5539 22 , 23 , 24 , 25 ,
• Rajesh Jeewon 26 ,
• Peter R. Johnston   ORCID: orcid.org/0000-0003-0761-9116 2 , 27 ,
• Paul M. Kirk 28 ,
• Elaine Malosso 2 , 29 ,
• Tom W. May   ORCID: orcid.org/0000-0003-2214-4972 2 , 30 ,
• Wieland Meyer 22 , 23 , 24 , 25 ,
• Henrik R. Nilsson   ORCID: orcid.org/0000-0002-8052-0107 31 ,
• Maarja Öpik 2 , 32 ,
• Vincent Robert 8 , 9 ,
• Marc Stadler   ORCID: orcid.org/0000-0002-7284-8671 2 , 33 , 34 ,
• Marco Thines   ORCID: orcid.org/0000-0001-7740-6875 2 , 35 , 36 ,
• Duong Vu 9 ,
• Andrey M. Yurkov   ORCID: orcid.org/0000-0002-1072-5166 2 , 37 ,
• Ning Zhang 2 , 38 &
• Conrad L. Schoch   ORCID: orcid.org/0000-0003-1839-5322 2 , 4  

Nature Microbiology volume  6 ,  pages 540–548 ( 2021 ) Cite this article

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An Author Correction to this article was published on 27 May 2021

This article has been updated

The identification and proper naming of microfungi, in particular plant, animal and human pathogens, remains challenging. Molecular identification is becoming the default approach for many fungal groups, and environmental metabarcoding is contributing an increasing amount of sequence data documenting fungal diversity on a global scale. This includes lineages represented only by sequence data. At present, these taxa cannot be formally described under the current nomenclature rules. By considering approaches used in bacterial taxonomy, we propose solutions for the nomenclature of taxa known only from sequences to facilitate consistent reporting and communication in the literature and public sequence repositories.

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A Correction to this paper has been published: https://doi.org/10.1038/s41564-021-00921-z

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Acknowledgements

Work by C.L.S. and B.R. was supported by the Intramural Research Program of the National Library of Medicine at the National Institutes of Health in Bethesda, Maryland, USA. D.M.G. received support through the National Science Foundation (NSF) grant DEB-1655980 and Project 4655 of the Pennsylvania State Agricultural Experiment Station. E.M. acknowledges CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Brazil) and FACEPE (Fundação de Amparo à Ciência e Tecnologia de Pernambuco, Brazil). K.D.H. thanks the Thailand Research Fund, grant RDG6130001, entitled “Impact of Climate Change on Fungal Diversity and Biogeography in the Greater Mekong Subregion”. The USDA Hatch project 1010662 is acknowledged for support to M.C.A. M.Ö. was supported by the European Regional Development Fund (Centre of Excellence EcolChange). M.T. acknowledges LOEWE for funding in the framework of the Centre for Translational Biodiversity Genomics (TBG) and the German Science Foundation. N.Z. acknowledges the NSF of the United States (DEB-1452971). P.R.J. was supported through the Manaaki Whenua Biota Portfolio with funding from the Science and Innovation Group of the New Zealand Ministry of Business, Innovation and Employment. R.J. thanks the University of Mauritius for research support. We thank S. Redhead for nomenclatural advice. R. Sanders provided the update for the fungal ITS data in the SRA.

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Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Berlin, Germany

Robert Lücking

International Commission on the Taxonomy of Fungi (ICTF) https://www.fungaltaxonomy.org/

Robert Lücking, M. Catherine Aime, Andrew N. Miller, Takayuki Aoki, Hiran A. Ariyawansa, Pedro W. Crous, Irina S. Druzhinina, David M. Geiser, David L. Hawksworth, Kevin D. Hyde, Peter R. Johnston, Elaine Malosso, Tom W. May, Maarja Öpik, Marc Stadler, Marco Thines, Andrey M. Yurkov, Ning Zhang & Conrad L. Schoch

Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA

M. Catherine Aime

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

Barbara Robbertse & Conrad L. Schoch

Illinois Natural History Survey, University of Illinois, Champaign, IL, USA

Andrew N. Miller

National Agriculture and Food Research Organization, Genetic Resources Center, Ibaraki, Japan

Takayuki Aoki

Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan

Hiran A. Ariyawansa

Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy

Gianluigi Cardinali & Vincent Robert

Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands

Pedro W. Crous, Vincent Robert & Duong Vu

Laboratory of Phytopathology, Wageningen University and Research Centre (WUR), Wageningen, The Netherlands

Pedro W. Crous

Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China

Irina S. Druzhinina

Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria

Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA

David M. Geiser

Department of Life Sciences, The Natural History Museum, London, UK

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Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, UK

Geography and Environment, University of Southampton, Southampton, UK

Jilin Agricultural University, Changchun, China

CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China

Kevin D. Hyde

Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand

World Agroforestry Centre, East and Central Asia, Kunming, China

Mushroom Research Foundation, Chiang Rai, Thailand

Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia

Laszlo Irinyi & Wieland Meyer

Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, New South Wales, Australia

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Manaaki Whenua—Landcare Research, Auckland, New Zealand

Peter R. Johnston

Royal Botanic Gardens, Kew, Richmond, UK

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Departamento de Micologia, Laboratório de Hifomicetos de Folhedo, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil

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Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia

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Department Microbial Drugs, Helmholtz Center for Infection Research, Braunschweig, Germany

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Marco Thines

Senckenberg Biodiversity and Climate Research Centre, Frankfurt (Main), Germany

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Contributions

The present manuscript was first discussed among members of the ICTF. Based on contributions from this initial discussion, a first version of the manuscript was drafted by R.L., C.L.S., M.C.A., B.R. and A.N.M. This version was distributed among the ICTF and to selected colleagues outside the ICTF, and all comments were recorded and incorporated. Based on these initial comments, lead and co-authorship was determined, additional co-authors then including T.A., H.A.A., G.C., P.W.C., I.S.D., D.M.G., D.L.H., K.D.H., L.I., R.J., P.R.J., P.M.K., E.M., T.W.M., W.M., M.Ö., V.R., M.S., M.T., D.V., A.M.Y. and N.Z. The revised draft was circulated two more times among all authors for additional comments before submission. After the first review, H.R.N. was invited as an additional co-author to provide specific input regarding dark taxa and the role of the UNITE database in the proposed alternatives for dark taxa nomenclature. Apart from contributing generally to the manuscript, D.L.H. and T.W.M. revised the nomenclatural details included in Box 1 and Fig. 1. B.R. and D.V. also assisted in technical aspects regarding the SRA and Fig. 3. P.W.C., R.L., W.M., M.T. and A.M.Y. organized the photographs used in Fig. 2 from their working groups. The final draft was approved by all authors.

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Correspondence to Conrad L. Schoch .

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Lücking, R., Aime, M.C., Robbertse, B. et al. Fungal taxonomy and sequence-based nomenclature. Nat Microbiol 6 , 540–548 (2021). https://doi.org/10.1038/s41564-021-00888-x

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Studying the Brain During Fungal Infections just got a Whole Lot Clearer

Researchers adapted microscopy techniques to identify rare instances of cryptococcus neoformans in mice brains and lungs..

Shelby is an assistant editor for The Scientist. She earned her PhD from West Virginia University in immunology and microbiology and completed an AAAS Mass Media fellowship.

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ABOVE: Clearing sample tissue allowed the team to conduct high-content imaging of the top of the nasal cavity and brain to observe the blood vessels, microglia, and nuclei in C. neoformans -infected mice. Vanessa Francis and Carolina Coelho

P rior to the video game The Last of Us , people rarely thought of fungi in the context of deadly infectious diseases. However, Cryptococcus neoformans  is a fungal pathogen that causes more than 100,000 deaths per year. While researchers knew that C. neoformans  accesses the brain within hours after infection in mice, the mechanisms behind this invasion have been  poorly understood. 1

To study this process, researchers need to identify rare instances of fungal invasion into the brain, but finding these examples requires the ability to study large sections of the organ. Carolina Coelho , a fungal immunologist at the Medical Research Council Centre for Medical Mycology at the University of Exeter, and her team tackled this problem by adapting high-content microscopy to study the brain infection in greater depth. 2 Their findings, published in mBio , offer new tools for researchers to study C. neoformans pathogenesis.

In standard fluorescence microscopy, scientists image thin sections of their sample tissues, but because of the opacity of the tissues, they glean limited information from them. Coelho searched for an approach that would allow her to overcome this limitation. “One important thing is to preserve the tissue architecture, because you need to see the spatial structure,” said Coelho. “The other thing is we needed something that was really high content.”

During her search, Coelho learned about clarification and decolorization protocols used in light-sheet microscopy to image entire organs. Although she didn’t need to visualize the whole organ, she incorporated the tissue clearing steps of the protocol to samples of lungs and brains from mice infected with C. neoformans . This allowed Coelho’s team to visualize up to 200 micrometer sections of their sample tissues. “This tool will boost any microscope you have, just because it makes [the tissue] transparent,” Coelho explained.

“It’s a big step towards understanding host pathogen interactions,” said Kiem Vu , a biochemist studying C. neoformans   invasion at the University of California, Davis who was not involved in the study.

The increased imaging capacity allowed Coelho’s team to visualize enlarged fungal cells, called titan cells, in the lung and the nasal cavity. They observed that these titan cells and normal yeast cells adhered to and invaded the nasal mucosal layer as early as 24 hours after intranasal infection. Previous work showed that titan cells promote fungal pathogenicity , but these were predominantly found in the lung. 3

“Their very early on infection in the upper airway put them in very close proximity to the brain, so maybe that’s how they get into the brain,” said Felipe Santiago-Tirado , a cell biologist at the University of Notre Dame who studies C. neoformans  pathogenesis and was not involved in the work. Vu shared this idea, citing it as a potential area for future investigation. “Was what they found [in] this paper a rare event? Or is it something that occurs more commonly as the infection progresses?”

Although scientists know that C. neoformans  infects the brain, they did not know whether it accesses this tissue as free yeast traveling in the blood or by infiltrating an immune cell and ferrying across the blood-brain barrier. Coelho and her team studied the lungs of intranasally-infected mice with their clarification and imaging method to help answer this question.

The researchers observed fungal cells independent from host cells within blood vessels in the lung of one animal seven days after infection. Sampling the blood and conducting standard plate counting culture also confirmed that the blood contained fungal cells as early as three days after intranasal infection.

 “The cool thing about it is that they're basically showing these things that were inferred by indirect evidence or by in vitro assays, now they're showing them to happen in vivo,” Santiago-Tirado said.

Because C. neoformans  enters the blood, the team intravenously infected mice with fungal cells to investigate infection in the brain. They observed that C. neoformans accessed the brain within 24 hours after infection and predominantly existed in clusters of fungal cells. The team labeled blood vessels and microglia in the brain to confirm that the yeast exited the blood brain barrier and determine if they associated with the resident immune cells.

Most fungal cells in the brain resided within microglia, indicating that they left the blood vessels. The researchers also observed that microglia with internalized C. neoformans displayed altered morphology, including multinucleated cells with reduced projections from the cell body. “It really poses the question, how are these microglia responding?” Coelho said. Next, Coelho is interested in exploring potential secreted molecules by the fungi and host cells that influence the host-pathogen interaction.

• Coelho C, et al. Intranasal inoculation of Cryptococcus neoformans in mice produces nasal infection with rapid brain dissemination . mSphere . 2019;4(4):10-1128
• Francis VI, et al. Cryptococcus neoformans rapidly invades the murine brain by sequential breaching of airway and endothelial tissues barriers, followed by engulfment by microglia . mBio . 2024;15(4):e03078-23
• Okagaki LH, et al. Cryptococcal cell morphology affects host cell interactions and pathogenicity . PLOS Pathog.  2010;6(6):10.1371

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Phd candidate on soil fungal ecology, about the employer.

Leiden University was founded in 1575 and is one of Europe’s leading international research universities.

Vacancy number 15004

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Closing date 25 August 2024 39 more days to apply

The Institute of Environmental Sciences (Faculty of Science at Leiden University) is looking for:

1 PhD candidate on soil fungal ecology

Project: Are you a enthusiastic early career researcher who is excited to work in a project on soil fungal traits and soil multifunctionality? Do you have a expertise and interest in microbial ecology, soil ecology, or a related field? And are you a team-player who likes variation in your activities with field, laboratory, computational, and analytical work? Then this could be the ideal PhD position for you!

We are hiring a PhD candidate (4 years) in a project on soil fungal traits and their relation to soil functions. The PhD will be situated at the Institute of Environmental Sciences (CML) within the VIDI project awarded to the PI.

The major overarching goals of the project are to 1) unravel the assembly and functional diversity of soil fungal communities, (2) reveal how fungal traits determine biodiversity and soil functioning, and (3) steer traits of the fungal community to recover the loss of soil multifunctionality. This will be achieved by combination of field characterization of fungi and their functions across land use gradients and by experimental manipulations of fungal communities and their functions. Communities and traits will be measure together with a postdoc using both culture-based and molecular methods and soil functions will be explored using for example stable isotope measurements and other cutting-edge measures. Further (mesocosm and field) experiments on steering soil fungal communities to improve their functionality will be performed. Hence, for this project knowledge on and interest in soil fungi and soil functions are required.

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CML is positioned in the Faculty of Science which is a world-class faculty where staff and students work together in a dynamic international environment. It is a faculty where personal and academic development are top priorities. Our people are committed to expand fundamental knowledge by curiosity and to look beyond the borders of their own discipline; their aim is to benefit science, and to make a contribution to addressing the major societal challenges of the future. The research carried out at the Faculty of Science is very diverse, ranging from mathematics, information science, astronomy, physics, chemistry and bio-pharmaceutical sciences to biology and environmental sciences. The research activities are organised in eight institutes. These institutes offer eight bachelor’s and twelve master’s programmes. The faculty has grown strongly in recent years and now has almost 2,800 staff and over 6,000 students. We are located at the heart of Leiden’s Bio Science Park, one of Europe’s biggest science parks, where university and business life come together.

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The core focus of the Institute of Environmental Sciences (CML) is to perform research and education in the interdisciplinary field of Environmental Sciences. Our people are driven by curiosity to expand fundamental knowledge and to look beyond the borders of their own discipline; their aim is to benefit science, and to contribute to addressing the major societal challenges of the future. CML focuses on the sustainable use of natural resources and preservation of natural capital and biodiversity. CML has a culture of mutual support and collaboration between researchers both within and between institutes. Presently, about 150 FTE (including postdocs and PhDs) are employed at CML. The CML has facilities to work with soil, water, microbes, and plants including growth chambers, large field experiments and molecular labs. For more information about CML see www.universiteitleiden.nl/en/science/environmental-sciences .

Terms of employment We offer a 1-year position with the possibility of extension to 4 years based on performance. Salary ranges from € 2.770 gross per month in the first year to € 3.539 gross per month in the fourth year based on a full-time position (pay scale P in accordance with the Collective Labour Agreement for Dutch Universities). Leiden University offers an attractive benefits package with additional holiday (8%) and end-of-year bonuses (8.3 %), training and career development and sabbatical leave. Our individual choices model gives you some freedom to assemble your own set of terms and conditions. For international spouses we have set up a dual career programme. Candidates from outside the Netherlands may be eligible for a substantial tax break.

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Filamentous fungi as excellent industrial strains: development and applications.

2. Industrial Application of Filamentous Fungi for the Bioproduction of High-Value Compounds

3. strategies for the development of fungal biofactories, 4. the role of -omics technologies in the development of fungal biofactories for industrial applications, 5. conclusions, conflicts of interest.

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• Yang, H.; Song, C.; Liu, C.; Wang, P. Synthetic Biology Tools for Engineering Aspergillus oryzae . J. Fungi 2024 , 10 , 34. [ Google Scholar ] [ CrossRef ] [ PubMed ]
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• Salazar-Cerezo, S.; de Vries, R.P.; Garrigues, S. Strategies for the Development of Industrial Fungal Producing Strains. J. Fungi 2023 , 9 , 834. [ Google Scholar ] [ CrossRef ] [ PubMed ]
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Share and Cite

Gandía, M.; Garrigues, S. Filamentous Fungi as Excellent Industrial Strains: Development and Applications. J. Fungi 2024 , 10 , 541. https://doi.org/10.3390/jof10080541

Gandía M, Garrigues S. Filamentous Fungi as Excellent Industrial Strains: Development and Applications. Journal of Fungi . 2024; 10(8):541. https://doi.org/10.3390/jof10080541

Gandía, Mónica, and Sandra Garrigues. 2024. "Filamentous Fungi as Excellent Industrial Strains: Development and Applications" Journal of Fungi 10, no. 8: 541. https://doi.org/10.3390/jof10080541

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