January 2019

Pre-order revised edition Laboratory Manual now
Tracing the fungal carbon metabolic roadmap in Aspergillus niger
Thesis reveals tricks of dung fungus Podospora anserina and tropical fungus Trichoderma reesei
Interesting thesis on the biology of black yeasts
Comprehensive study of Banana & Fusarium wilt in Indonesia
A study of fungal-based wood finishes
Thickest thesis of Westerdijk PhD ever: ‘Mycospaerellaceae revisited’
Volume 92 of Studies in Mycology
(March 2019) is now available. 
Volume 9(2) of IMA Fungus

Pre-order revised edition Laboratory Manual now

The second edition of the highly popular “Westerdijk Laboratory Manual Series No. 1: Fungal Biodiversity” is now available. The volume (hard copy, full colour) is extended with 150 pages. This Laboratory Manual focuses on techniques for isolation, cultivation, molecular and morphological study of filamentous fungi and yeasts. It has been developed as a general text over many years, which is based on the annual mycology course given at the Westerdijk Fungal Biodiversity Institute in Utrecht, The Netherlands.

The manual provides an introductory text to systematic mycology, starting with a concise treatise of Hyphochytridiomycota and Oomycota, which have long been subject of study by mycologists, but are now classified in the Kingdom Chromista. These are followed by sections on the groups of “true fungi”: Chytridiomycota, Blastocladiomycota, “Zygomycota”, Ascomycota and Basidiomycota. This descriptive part is illustrated by numerous full-colour figures of life-cycles and schematic line-drawings as well as photographic plates depicting most of the structures essential for the study and identification of these fungi. Special attention is given to basic principles of working with axenic cultures, good morphological analysis, and complicated issues for beginners such as conidiogenesis and the understanding of life-cycles. Exemplar taxa for each of these fungal groups, in total 69 mostly common species in various economically important genera, are described and illustrated in detail. In a chapter on general methods a number of basic techniques such as the preparation and choice of media, microscopic examination, the use of stains and preparation of permanent slides, and herbarium techniques are explained. Most importantly, this volume also sees the integration of asexual and sexual genera, following the abandonment of dual nomenclature for Fungi. Further chapters deal with commonly used molecular and phylogenetic methods and related identification tools such as BLAST and DNA Barcoding, fungal nomenclature, ecological groups of fungi such as soil-borne and root-inhabiting fungi, water moulds, and fungi on plants and of quarantine importance. Some topics of applied mycology are also treated, including fungi in the air- and indoor environment and fungi of medical importance. Common mycological terminology is explained in a glossary, with reference to illustrations in the book. A chapter providing more than 60 mycological media for fungal cultivation, and a comprehensive list of cited references are also provided. The book is concluded with an index, and dendrogram reflecting our current understanding of the evolutionary relationships within the Fungi.


Tracing the fungal carbon metabolic roadmap in Aspergillus niger

Maria Victoria Aguilar Pontes is interested in genetics, in metabolic pathways, in bioinformatics. And she also likes the idea of applied research. In her case the combination of all these interests led to research on the metabolism of Aspergillus niger and not, for example to human research. ‘I don’t like human research, I don’t like to work with human data. Besides that: I really like fungi, they look beautiful, you don’t have to feed them every day and you don’t have to feel guilty if you kill them. What I want to do in my research is to improve industrial processes by using fungal enzymes while studying A. niger primary metabolism as a whole. ’
Maria Victoria choose Aspergillus niger to work with because it is one of the best studied filamentous fungi and considered ‘an industrial workhorse’ due to its ability as producer of citric acid and plant biomass degrading enzymes.

In collaboration with Denmark Technical University (PhD student Julian Brandl), she expanded the knowledge of A. niger metabolism to three different strains (ATCC 1015, CBS 513.88 and NRRL 3) through orthology, extending the coverage of the existing model of A. niger metabolism by 940 reactions, 777 metabolites and 454 genes and thus developed the best validated genome scale model on A. niger to date.


Thesis reveals tricks of dung fungus Podospora anserina and tropical fungus Trichoderma reesei

As part of a research project initiated by prof. Ronald de Vries to understand fungal biodiversity with respect to plant biomass degradation and to design a model that enables the prediction of the ability of fungal species to utilize different carbon sources, Tiziano Benocci dissected plant biomass utilization strategies of a specialist (Podospora anserina) and a semi-specialist (Trichoderma reesei).
Fungi are highly efficient plant biomass degraders and as such, in our growing bio-based economy, of interest for industry.
Some fungi are broadly used already by the industry, like generalist Aspergillus niger and semi-specialist Trichoderma reesei, while a larger group of fungi is being mined as a source of novel enzymes.
What lacks so far however is a way to select the best fungus for a specific application; the majority of fungal biodiversity has thus remained unutilized.

 


Interesting thesis on the biology of black yeasts

Leandro Moreno successfully defended his PhD Thesis on Thursday November 15 at the University of Amsterdam, with the title  ‘The biology of black yeast genomes’. It is an interesting mix of factual and extensive explorations of the genomic diversity in black yeasts and relatives, with some more speculative chapters, like the intriguing question on understanding an infectious brain disease from the desert.

Leandro focuses on the order Chaetothyriales (Pezizomycotina, Ascomycetes). Members of this order ‘exhibit a complex ecological variation, and species are found in habitats characterised by extreme and adverse conditions, like rock surfaces in hot arid climates, in toxic niches with hydrocarbons and heavy metals and remarkably often in vertebrates as opportunistic pathogens.’
Some species cause horrific mutilating or even fatal infectious diseases in humans, often in apparently healthy individuals. Exactly this combination of properties makes the black yeasts and their relatives so interesting.



Comprehensive study of Banana & Fusarium wilt in Indonesia

‘A complex relationship, Banana & Fusarium wilt in Indonesia’ is the full title of the thesis of Nani Maryani, and complex it is. Nani comes from Indonesia, the centre of origin of banana and thus, from the co-evolutionary standpoint also the centre of origin of major pathogens threatening the crop. She is the first person to make a comprehensive study of sympatric speciation of Fusarium spp. pathogenic on bananas in Indonesia.
Fusarium wilt is one of the most devastating plant diseases in agricultural history. In the beginning of 1960’s Fusarium wilt disease (also called Panama disease because of the first place it occurred) wasted around 40.000 ha of Gros Michel bananas. The fungus is particularly devastating because it stays for years in the soil.

 


A study of fungal-based wood finishes

A fungus that does not attack wood, but preserves it. It sounds strange, but it is possible. Elke van Nieuwenhuijzen received her doctorate on Wednesday 7 November at Eindhoven University of Technology for her study of black fungi on oiled wood that behave like a 'biofinish'. This layer colors the wood and protects it from wood rot and degradation by sunlight. An additional advantage: the fungus automatically repairs damage in the protective layer.

The discovery had already been made almost 20 years ago, by chance, by researcher Michael Sailer who investigated whether vegetable oil can conserve wood. He discovered that pieces of coniferous wood impregnated with linseed oil and hemp oil turned black after being exposed to wind and weather. But the discolored wood did not become soft, like rotten wood, it remained hard. The wood was possibly protected by the black layer, which the microscope showed to be fungus.


Thickest thesis of Westerdijk PhD ever: ‘Mycospaerellaceae revisited’

Sandra I.R. Videira studied biology in Coimbra in Portugal before she came for her PHD to the Netherlands.. Since her MSc she fell in love with fungi. That fact is mentioned by Pedro Crous in his Judicium today: ‘You started with studying the ecology and management of commercially harvested macrofungi like Tricholoma flavovirens in Portugal. It is funny that this mushroom is commercially harvested in Portugal, while in Dutch Mycology books this fungus is documented as being doubtful to eat. You then studied the biodiversity of microfungi occurring on historical documents by molecular tools and evaluated whether they could be controlled by gamma radiation. With all this expertise you were the favourite candidate for a PhD project at the Westerdijk Institute.’ 
She never envisioned a thesis of 589 pages, and she never thought it would take her more than 4 to 5 years for her promotion. Yet today, about 7 years after she started, Sandra succesfully defended her 589 pages record-breaking thesis. Well, maybe in history a few equally heavy manuscripts have been reported, but not more than a handful. ‘Mycospaerellaceae revisited’ the thesis is called. 


Volume 92 of Studies in Mycology (March 2019) is now available. 

This issue includes seven research papers that deal with several important genera of fungal plant pathogens. Damm et al. revise the Colletotrichum dracaenophilum, C. magnum and C. orchidearum species complexes, introducing 12 new species. Marin-Felix et al. revise 20 genera of phytopathogenic fungi, introducing 26 new species. Vu et al. release an unprecedented large number of DNA barcodes for Fungi, namely 24 000 DNA barcode sequences of 12 000 ex-type and manually validated filamentous fungal strains of 7 300 accepted species. Furthermore, the optimal identity thresholds to discriminate filamentous fungal species were predicted as 99.6 % for ITS and 99.8 % for LSU. Maryani et al. deal with the complex issue of Panama disease of banana, and formally name 11 new species, introducing Fusarium odoratissimum for what was formally known as Fusarium oxysporum f. sp. cubense (Foc), the causal agent of Fusarium wilt or Panama disease on banana. Fehrer et al. present a phylogenetic study of the prominent ericoid mycorrhizal fungus Rhizoscyphus ericae. Giraldo & Crous treat the Plectosphaerellaceae, and resolve 22 genera in the family, including 12 new genera, 15 new species and 10 new combinations. Liu et al. treat the Sporocadaceae, finally adding DNA sequence data to many genera of appendaged coelomycetes, resolving 23 known and introducing seven new genera and 51 new species.


Volume 9(2) of IMA Fungus

After nine years, Volume 9(2) of IMA Fungus also sees the final volume of the official journal of the International Mycological Association produced by the Westerdijk Institute.  This volume contains several subsections, including the Editorial, News, Reports, Awards and Personalia, Research News, MycoLens, Correspondence, Book News, Forthcoming Meetings, and a set of 10 research papers, covering the breadth of mycology (www.IMAfungus.org). From January 2019 onwards, the journal will be hosted and published by the Springer-Nature group (see IMA-mycology.org for details).

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