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Unleashing the hidden potential of the anaerobic fungi

Unleashing the hidden potential of the anaerobic fungi

Sabine Podmirseg (ORCID: 0000-0003-1775-2412)
  • Grant DOI 10.55776/I3808
  • Funding program Principal Investigator Projects International
  • Status ended
  • Start March 1, 2019
  • End August 31, 2023
  • Funding amount € 399,439
  • Project website
  • E-mail

DACH: Österreich - Deutschland - Schweiz

Disciplines

Biology (80%); Environmental Biotechnology (20%)

Keywords

    Anaerobic Fungi, Molecular Tools, Bioinformatics, Lignocellulose, Continuous Cultivation, Growth Requirements

Abstract Final report

The microorganisms thriving in the ruminants digestive tract deliver the metabolic potential for degrading recalcitrant lignocellulose-rich organic matter and rendering it digestible. Amongst the microbiota thriving in the rumen, anaerobic fungi (AF) with the unpronounceable name Neocallimastigomycota host a complex array of enzymes that are especially adapted for degradation of lignocellulosic biomass like straw. In addition, their appressoria attach to the macromolecule structures and physically penetrate them, thus enhancing the enzymatic action. Cultivation of these fungi has often ended in frustration for researchers as the understanding of cultivation requirements is very poor. However, scientists see the great potential of these organisms for biotechnological use, in particular for the utilization of lignocellulosic residues (LCR) in closed loop recycling management. For this project, a consortium from Austria (leading agency; PI: Dr. Sabine Marie Podmirseg), Germany (PI: Dr. Michael Lebuhn) and Switzerland (PI: Prof. Urs Baier), all engaged in the harnessing of AF, is cooperating in close connection with research groups in the United Kingdom and in the Czech Republic. The overarching aim of the proposed project will be to remove existing methodological obstacles preventing the biotechnological utilization of anaerobic fungi. For that purpose, the consortium starts with the crucial basics, explores the cultivation requirements of Neocallimastigomycota, develops suitable culturing and detection methods and finally evaluates their biotechnological application for LCR disintegration. The working hypotheses are, amongst others: (i) the ecological niche for AF is larger than assumed to date; (ii) distinct requirements for micronutrients or supplements have to be met for long-time cultivation; (iii) cultivation without rumen fluid is possible for many strains; (iv) novel AF can be isolated from various also non-rumen habitats. The project will combine classical microbiological methods (microscopy, batch and continuous cultivation, enzymology) with molecular approaches (fluorescence in situ hybridization, quantitative PCR, direct RNA and next generation sequencing). It is expected to develop suitable protocols for the cultivation of anaerobic fungi and provide the basics for up-scaled production. The projects goal is to enable researchers and the society to make use of the AF for energetic and material use of LCR.

With more than 200 million tons generated world-wide, lignocellulosic waste (especially plant biomass) is one of the most abundant waste streams available. Turning this waste into renewable energy is crucial for achieving a sustainable, circular economy. Unfortunately, breaking down plant material, especially in oxygen-free environments like biogas reactors, is notoriously difficult. Cows and other herbivores, however, have all along been efficiently transforming plant biomass into energy. How? Well, herbivores have an ace up their guts: Neocallimastigomycota, the only fungal group known to thrive strictly under anoxic (oxygen-free) conditions, are experts in plant matter decomposition. Despite their potential our understanding of anaerobic gut fungi (AGF) is limited. Knowledge on their distribution in herbivorous host animals, on how to cultivate them continuously, and how to effectively detect and characterize them, is spotty. A teamofscientistsfrom Austria (Universität Innsbruck), Germany (LFL Freising, TU München, CeBiTec Bielefeld), and Switzerland (ZHAW) set out tochangethat. Joined by renowned researchers from the United Kingdom (IBERS) and the Czech Republic (IAPG), the "HiPoAF" team aimed to close fundamental knowledge gaps to eventually unleash the "high potential of anaerobic fungi". They investigated and optimized cultivation conditions, looked into effective preservation methods, optimized existing and developed complementary detection techniques. Main accomplishments include a standardized cultivation and preservation protocol, a novel AGF specific primer system, a reactor system optimized for continuous AGF growth, a global AGF habitat survey and first successes in the development of novel detection techniques (HCR-FISH,NIR spectrometry, mass spectrometry anddigital droplet PCR). In addition to their scientific endeavors, the HiPoAF team actively engaged in the international Anaerobic Fungi Network (www.anaerobicfungi.org), leading to a number of successful joint adventures and acknowledgement of AGF expertise on an international stage. Several national and international collaborations arose partially due to the HiPoAF team's active scientific outreach activities, e.g. the project homepage (https://www.hipoaf.com/home), a radio show, and considerable contribution in the organization of the first international AGF conference (IAFC2022). The HiPoAF team emphasized the importance of educating students, sprouting four PhD-, seven Master- and eight Bachelor theses and seven student apprenticeships. AGF are now well integrated in teaching at Universität Innsbruck and ZHAW, and even in the projected Science Center (https://www.mikrobalpina.org/en/) that shall be installed in Austria (near Innsbruck). While the unpronounceable name of this fascinating microbial group might slip the memory of the visitors there, the potential of Neocallimastigomycota for sustainable energy production certainly will not. Finally, illuminatingsome basic knowledge gaps in AGF research, the HiPoAFconsortiumwas abletotake one step ahead and acquire funding fora subsequent project (www.hipoaf.com), aiming at implementing thesesuccessful biomass degraders in biogas production from lignocellulosic wastes.

Research institution(s)
  • Universität Innsbruck - 100%
International project participants
  • Katerina Fliegerova, Academy of Sciences of the Czech Republic - Czechia
  • Michael Lebuhn, Bayerisches Staatsministerium für Ernährung, Landwirtschaft und Forsten (StMELF) - Germany
  • Urs Baier, Zürcher Hochschule für Angewandte Wissenschaften - Switzerland
  • Gareth W. Griffith, Aberystwyth University - United Kingdom

Research Output

  • 173 Citations
  • 28 Publications
  • 2 Datasets & models
  • 1 Scientific Awards
  • 3 Fundings
Publications
  • 2024
    Title Exploring near-infrared spectroscopy and hyperspectral imaging as novel characterization methods for anaerobic gut fungi
    DOI 10.1093/femsmc/xtae025
    Type Journal Article
    Author Neurauter M
    Journal FEMS Microbes
    Link Publication
  • 2025
    Title Application of MALDI TOF and DART mass spectrometry as novel tools for classification of anaerobic gut fungi strains
    DOI 10.1007/s00216-025-05846-8
    Type Journal Article
    Author Neurauter M
    Journal Analytical and Bioanalytical Chemistry
    Pages 1-12
    Link Publication
  • 2019
    Title Employing anaerobic fungi in biogas production: challenges & opportunities
    DOI 10.1016/j.biortech.2019.122687
    Type Journal Article
    Author Vinzelj J
    Journal Bioresource Technology
    Pages 122687
  • 2022
    Title Characterization and rank assignment criteria for the anaerobic fungi (Neocallimastigomycota).
    DOI 10.1099/ijsem.0.005449
    Type Journal Article
    Author Elshahed M
    Journal International journal of systematic and evolutionary microbiology
    Link Publication
  • 2024
    Title Unveiling the Potential of Anaerobic Fungi with Syntrophic Microbes for Fibre Degradation
    Type Other
    Author Joshi A
  • 2022
    Title Patterns and determinants of the global herbivorous mycobiome
    DOI 10.1101/2022.11.21.517404
    Type Preprint
    Author Meili C
    Pages 2022.11.21.517404
    Link Publication
  • 2022
    Title Medium without CRF for Neocallimastigomycota v1
    DOI 10.17504/protocols.io.36wgq779kvk5/v1
    Type Preprint
    Author Vinzelj J
  • 2022
    Title Effect of growth media on the diversity of Neocallimastigomycetes from non-rumen habitats
    DOI 10.21256/zhaw-25803
    Type Other
    Author Joshi
    Link Publication
  • 2022
    Title Simultaneous metabarcoding and quantification of neocallimastigomycetes from environmental samples : insights into community composition and novel lineages
    DOI 10.21256/zhaw-25733
    Type Other
    Author Joshi
    Link Publication
  • 2022
    Title No time to die : comparative study on preservation protocols for anaerobic fungi
    DOI 10.21256/zhaw-25752
    Type Other
    Author Joshi
    Link Publication
  • 2022
    Title Why eDNA fractions need consideration in biomonitoring
    DOI 10.1111/1755-0998.13658
    Type Journal Article
    Author Nagler M
    Journal Molecular Ecology Resources
    Pages 2458-2470
    Link Publication
  • 2022
    Title Live and Let Die: Resting Stages of Anaerobic Fungi
    Type Other
    Author Sonderegger L
  • 2022
    Title Making Them Shine: Detection of Anaerobic Fungi
    Type Other
    Author Stocker S
  • 2022
    Title Patterns and determinants of the global herbivorous mycobiome
    DOI 10.21203/rs.3.rs-2302734/v1
    Type Preprint
    Author Meili C
    Link Publication
  • 2020
    Title The Biotechnological Potential of Anaerobic Gut Fungi
    DOI 10.1007/978-3-030-49924-2_17
    Type Book Chapter
    Author Flad V
    Publisher Springer Nature
    Pages 413-437
  • 2023
    Title Editorial for Special Issue “Unleashing the Hidden Potential of Anaerobic Fungi”
    DOI 10.3390/microorganisms11030652
    Type Journal Article
    Author Lebuhn M
    Journal Microorganisms
    Pages 652
    Link Publication
  • 2022
    Title Simultaneous Metabarcoding and Quantification of Neocallimastigomycetes from Environmental Samples: Insights into Community Composition and Novel Lineages
    DOI 10.3390/microorganisms10091749
    Type Journal Article
    Author Young D
    Journal Microorganisms
    Pages 1749
    Link Publication
  • 2022
    Title No time to die: Comparative study on preservation protocols for anaerobic fungi
    DOI 10.3389/fmicb.2022.978028
    Type Journal Article
    Author Vinzelj J
    Journal Frontiers in Microbiology
    Pages 978028
    Link Publication
  • 2022
    Title Effect of Growth Media on the Diversity of Neocallimastigomycetes from Non-Rumen Habitats
    DOI 10.3390/microorganisms10101972
    Type Journal Article
    Author Joshi A
    Journal Microorganisms
    Pages 1972
    Link Publication
  • 2023
    Title Meet & Breed: Detection and Maintenance of Neocallimastigomycota
    Type Other
    Author Vinzelj J
  • 2023
    Title Spectra: a novel method for AF identification
    Type Other
    Author Neurauter M
  • 2023
    Title MALDI TOF and DART mass spectrometry as novel tools for classification of anaerobic gut fungi strains
    Type Other
    Author Neurauter M
  • 2023
    Title Spotlight on anaerobic fungi: HCR-FISH as detection method for Neocallimastigomycota
    Type Other
    Author Karrer M
  • 2023
    Title Editorial for special issue "Unleashing the Hidden Potential of Anaerobic Fungi"
    DOI 10.21256/zhaw-29485
    Type Other
    Author Lebuhn
    Link Publication
  • 2023
    Title Patterns and determinants of the global herbivorous mycobiome
    DOI 10.60692/krtx7-7b245
    Type Other
    Author Adrienne L. Jones
    Link Publication
  • 2023
    Title Patterns and determinants of the global herbivorous mycobiome
    DOI 10.1038/s41467-023-39508-z
    Type Journal Article
    Author Meili C
    Journal Nature Communications
    Pages 3798
    Link Publication
  • 2023
    Title Patterns and determinants of the global herbivorous mycobiome
    DOI 10.60692/4zrny-n0t14
    Type Other
    Author Adrienne L. Jones
    Link Publication
  • 2021
    Title The Effect of a High-Grain Diet on the Rumen Microbiome of Goats with a Special Focus on Anaerobic Fungi.
    DOI 10.3390/microorganisms9010157
    Type Journal Article
    Author Fliegerova Ko
    Journal Microorganisms
Datasets & models
  • 2023 Link
    Title Patterns and determinants of the global herbivorous mycobiome
    DOI 10.6084/m9.figshare.22659349
    Type Database/Collection of data
    Public Access
    Link Link
  • 2023 Link
    Title Patterns and determinants of the global herbivorous mycobiome
    DOI 10.6084/m9.figshare.22659349.v1
    Type Database/Collection of data
    Public Access
    Link Link
Scientific Awards
  • 2023
    Title Best Poster Awards ISAM2023
    Type Poster/abstract prize
    Level of Recognition Continental/International
Fundings
  • 2019
    Title Unleashing the hidden potential of the anaerobic fungi
    Type Research grant (including intramural programme)
    Start of Funding 2019
    Funder Austrian Science Fund (FWF)
  • 2021
    Title 1669 Reise- und Forschungsstipendien
    Type Travel/small personal
    Start of Funding 2021
    Funder University of Innsbruck
  • 2023
    Title Interreg ABH016 - FUNGAS
    Type Research grant (including intramural programme)
    Start of Funding 2023
    Funder Europäischer Fonds für regionale Entwicklung (EFRE) Interreg VI-A Programm

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