We are a team of scientists from Austria, Germany and Switzerland working closely together combining microbiology, biotechnology and bioinformatics to investigate potential benefits deriving from the biotechnological usage of anaerobic fungi.

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Impressum

The Team

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Creating major synergies, the consortium brings together the most prominent researchers in the field of anaerobic fungi in Europe, either as consortium members or with an ancillary role. Members of this consortium are well integrated into the international Anaerobic Fungi Network and the specific strengths of each group complement each other perfectly. A few to mention are mycology, molecular detection methods and phylogenetics, molecular analytics and bioinformatics, microscopy, anaerobic digestion and microbial culturing , continuous anaerobic culturing and anaerobif fungi enzyme activity measurements. The synergism among working groups will minimise the duplication of efforts and is key to the efficient and successful completion of the project.

 

You can learn about individual competences and responsibilities by clicking on their profiles.

LfL (D)
UIBK (A)
ZHAW (CH)
UIBK (A)
IAPG (CZ)
ZHAW (CH)
UIBK (A)
LfL (D)
CeBiTec (D)
UIBK (A)
IBERS (UK)
UIBK (A)
UIBK (A)
ZHAW (CH)
UIBK (A)
TUM (D)
LfL (D)
UIBK (A)
ZHAW (CH)

Austria

 

The Institute of Microbiology at the University of Innsbruck was founded in 1972 and has a long tradition in environmental microbiology and fungal taxonomy. Upgrading and recycling of biomass-based wastes has become a research focus, and in the field of mycology, UIBK is among the leading ones in the D.A.CH region. The Institute is involved in numerous (inter)national co-operations, and around 60 scientific papers are published every year. UIBK is the only University partner in the consortium and thus will have the major role in PhD supervision. The working group microbial resource management, headed by Prof. Insam, is dedicated to environmental microbiology including intensive research on anaerobic fungi and lignocellulose degradation during anaerobic digestion.

 

In 2012, Dr. Podmirseg conducted a FFG feasibility study initializing the anaerobic fungi research focus at the Institute of Microbiology. Since then several master theses and ongoing doctoral theses have been dedicated to this research area. The working group studies effects of fungal implementation into bioreactors and investigates the feasibility of various detection- and activity assessment methods on molecular (RNA-qPCR, extracellular vs. intracellular DNA) and microscopy (FISH, FDA/PI) basis, and metatranscriptomics experiments on anaerobic fungi and their microbial consortia have been performed. Isolation and continuous batch cultivation of anaerobic fungi is routinely done, a cryoculture collection of several anaerobic fungi strains is featured. The infrastructure offers all necessary facilities and instrumentation for measuring nutrient- and trace metal contents (photometry, ICP and AAS), a CNS analyser and also microscopy facilities (CLSM, fluorescent microscopy, SEM). Further, all standard and up-to date methods and know-how for microbiome analysis (PCR, qPCR, RFLP, capillary electrophoresis, access to sequencing facilities, SIP, etc.) are available.

Germany

Micro- and Molecular Biology research group,

Bavarian state research Center for Agriculture (LfL), Freising

The Micro- and Molecular Biology research group at the Bavarian State Research Center for Agriculture (LfL), Freising, Germany, is led by Dr. Lebuhn. The scientific focus of LfL is the development and improvement of analytical methods in relation to agriculture, including hygiene issues of biogas processes, analysis and optimization of the biogas producing microbial community, and the involvement of specialists such as anaerobic fungi.

 

A combination of molecular and bioinformatics tools along with cultivation routines is used to address these questions. Our expertise is based on years of experience with the optimization of molecular detection techniques, including nucleic acid extraction methods, quality control of nucleic acids, design of specific primers and probes, (q)PCR and RT(q)PCR based approaches to assess the quantity and the activity of microorganisms, analysis of microbiota and bioinformatics based evaluation of sequence data. LfL is well equipped for the cultivation and microscopic observation of (an)aerobes.

 

In 2012, the utilization of anaerobic fungi became one of the major scientific fields. A previous project was devoted to the issue if the efficiency of biogas production from fiber-rich substrates can be enhanced by anaerobic fungi. Microbial resources resting in animals, feeding on a high fiber diet, e.g. the alpine goat, were accessed. Anaerobic fungi, also novel strains, have been isolated and are being characterized for further application.

 
 

Switzerland

Environmental Biotechnology lab,

Institute of Chemistry and Biotechnology,

Zurich University of Applied Scienes (ZHAW), Wädenswil

The ICBT covers a range of scientific expertise from biological, biochemical to chemical-analytical methods. It is well equipped with up to date technology; it holds (among others) the Competence Centre for Biocatalysis, a Biofilm Lab and is affiliated to the Culture Collection of Switzerland CCOS.

 

Within the ICBT, the Environmental Biotechnology lab focuses on anaerobic digestion technology and anaerobic microbiology. Another area of expertise comprises biomass availability studies and mass- and energy flow analysis of biomass systems. Recently, the group hosted several projects for anaerobic digestion process development and for acceleration of hydrolysis of lignocellulosic biomass such as agricultural residues and dairy cow manure fractions. Expertise has been built up in thermochemical, enzymatic and microbial pretreatment methods. Within this context, the expertise of the group covers general batch and continuous cultivation of strict anaerobic microorganisms, cultivation of filamentous fungi and bioprocess parameter evaluation and optimization. A strong focus was built up in anaerobic microbiology and microbial ecology. In 2015, anaerobic fungi from rumen were successfully isolated and investigated.

Collaboratorating Institutions

The Computational Metagenomics group at the Center for Biotechnology (CeBiTec), Bielefeld University, Germany, is headed by Dr. Alexander Sczyrba. The group has strong experience in bioinformatics analyses, including large-scale metagenomics studies of the cow rumen and biogas fermenters, including large-scale assemblies of metagenomic data sets, taxonomic classification and binning of contigs into draft genomes. Other research interests include single cell genomics and cloud-based pipelines for large-scale bioinformatics applications.

At IBERS, Dr. Gareth W. Griffith has worked on AF for over 30 years and has been involved in the discovery of four of the nine acknowledged genera as well as in updating the taxonomy by molecular phylogenetics. With collaborators  at IBERS  he is exploring the ecology of all fungi including AF, with the attribution of correct names for the natural groupings, a prerequisite for the understanding of their niche specialisation. Recent innovations at IBERS include the development of DNA meta-barcoding approaches for AF population dynamics and the use of alternative loci to ITS for their classification. IBERS also possess the infrastructure for the isolation, cultivation and preservation of AF and wider research expertise on rumen microbiology permits the study of the interaction of AF with other rumen biota.

Present scientific topics of the Lab of Anaerobic Microbiology at the IAPG, Czech Academy of Sciences, range from biodiversity to biomedicine oriented research using anaerobic cultivation combined with molecular methods. The role of the microbiome of the digestive tract in veterinary medicine is studied and special attention is devoted to AF from rumen and hindgut of large herbivores. Hydrolytic activities and enzyme production of AF are studied in respect to potential industrial application in biogas production. The laboratory is characterized by extensive international collaboration and participation in multi-institutional collaborative initiatives as AF Network, Fungal Barcoding Consortium, Fungal Diversity Consortium, Global Rumen Census and RMG Network. Special emphasis is laid on AF isolation, long-term cultivation, taxonomic differentiation,
microscopic- and enzymatic characterisation and diversity studies in different hosts as well as on the industrial application of different AF genera.

The TUM will add to the project with extensive experience in isolation and characterization of microbes from various environments and microscopy of anaerobic organisms. The TUM is well equipped for the cultivation of anaerobic microorganisms (e.g. anaerobic cabinet) and their microscopic analysis (CLSM Zeiss 510 Meta). The research is application oriented and will extend the knowledge and application fields of AF. The laboratory is perfectly suited to cultivate a huge variety of microorganisms and has its own culture collection.