Articles

Assessing the efficacy of CRISPR/Cas9 genome editing in the wheat pathogen Parastagonspora nodorum

The genome-editing tool CRISPR/Cas9 has revolutionized gene manipulation by providing an efficient method to generate targeted mutations. This technique deploys the Cas9 endonuclease and a guide RNA (sgRNA) wh...

Authors: Haseena Khan, Megan C. McDonald, Simon J. Williams and Peter S. Solomon

Promoter tools for further development of Aspergillus oryzae as a platform for fungal secondary metabolite production

The filamentous fungus Aspergillus oryzae is widely used for secondary metabolite production by heterologous expression; thus, a wide variety of promoter tools is necessary to broaden the application of this spec...

Authors: Maiko Umemura, Kaoru Kuriiwa, Linh Viet Dao, Tetsuya Okuda and Goro Terai

Enabling community-based metrology for wood-degrading fungi

Lignocellulosic biomass could support a greatly-expanded bioeconomy. Current strategies for using biomass typically rely on single-cell organisms and extensive ancillary equipment to produce precursors for dow...

Authors: Rolando Perez, Marina Luccioni, Rohinton Kamakaka, Samuel Clamons, Nathaniel Gaut, Finn Stirling, Katarzyna P. Adamala, Pamela A. Silver and Drew Endy

Towards a better understanding of the role of nectar-inhabiting yeasts in plant–animal interactions

Flowers offer a wide variety of substrates suitable for fungal growth. However, the mycological study of flowers has only recently begun to be systematically addressed from an ecological point of view. Most re...

Authors: Joon Klaps, Bart Lievens and Sergio Álvarez-Pérez

Evaluation of synthetic formaldehyde and methanol assimilation pathways in Yarrowia lipolytica

Crude glycerol coming from biodiesel production is an attractive carbon source for biological production of chemicals. The major impurity in preparations of crude glycerol is methanol, which is toxic for most ...

Authors: Eija Vartiainen, Peter Blomberg, Marja Ilmén, Martina Andberg, Mervi Toivari and Merja Penttilä

Correction to: Functional exploration of co-expression networks identifies a nexus for modulating protein and citric acid titres in Aspergillus niger submerged culture

Following publication of the original article [1], the authors provided revised images for Figs. 4, 6 and 7 which were not processed by the typesetter during proof-correction stage. The corrected figures are g...

Authors: Timothy C. Cairns, Claudia Feurstein, Xiaomei Zheng, Li Hui Zhang, Ping Zheng, Jibin Sun and Vera Meyer

A new vector system for targeted integration and overexpression of genes in the crop pathogen Fusarium solani

Besides their ability to produce several interesting bioactive secondary metabolites, members of the Fusarium solani species complex comprise important pathogens of plants and humans. One of the major obstacles i...

Authors: Mikkel Rank Nielsen, Anna Karolina Rilana Holzwarth, Emmett Brew, Natalia Chrapkova, Samba Evelyne Kabemba Kaniki, Kenneth Kastaniegaard, Trine Sørensen, Klaus Ringsborg Westphal, Reinhard Wimmer, Teis Esben Sondergaard and Jens Laurids Sørensen

Bidirectional histone-gene promoters in Aspergillus: characterization and application for multi-gene expression

Filamentous fungi are important producers of enzymes and bioactive secondary metabolites and are exploited for industrial purposes. Expression and characterization of biosynthetic pathways requires stable expr...

Authors: Jakob K. H. Rendsvig, Christopher T. Workman and Jakob B. Hoof

On mycohuman performances: fungi in current artistic research

This review reflects several artists and their artistic research in the field of hybrid art, bio art, or science art, working with Fungi as both subject matter and medium. The work of Saša Spačal, Tarsh Bates ...

Authors: Regine Rapp

Interaction between arbuscular mycorrhizal fungi and Bacillus spp. in soil enhancing growth of crop plants

Soil microorganisms play an important role in enhancing soil fertility and plant health. Arbuscular mycorrhizal fungi and plant growth promoting rhizobacteria form a key component of the soil microbial populat...

Authors: Anuroopa Nanjundappa, Davis Joseph Bagyaraj, Anil Kumar Saxena, Murugan Kumar and Hillol Chakdar

Identification of novel citramalate biosynthesis pathways in Aspergillus niger

The filamentous fungus Aspergillus niger is frequently used for industrial production of fermentative products such as enzymes, proteins and biochemicals. Notable examples of industrially produced A. niger fermen...

Authors: Abeer H. Hossain, Aiko Hendrikx and Peter J. Punt

Dissecting cellobiose metabolic pathway and its application in biorefinery through consolidated bioprocessing in Myceliophthora thermophila

Lignocellulosic biomass has long been recognized as a potential sustainable source for industrial applications. The costs associated with conversion of plant biomass to fermentable sugar represent a significan...

Authors: Jingen Li, Shuying Gu, Zhen Zhao, Bingchen Chen, Qian Liu, Tao Sun, Wenliang Sun and Chaoguang Tian

Correction to: Practical guidance for the implementation of the CRISPR genome editing tool in filamentous fungi

Following publication of the original article [1], the authors reported that Table 5 was missing in the published version, although it was originally submitted and reviewed along with the rest of the manuscrip...

Authors: Min Jin Kwon, Tabea Schütze, Sebastian Spohner, Stefan Haefner and Vera Meyer

Functional exploration of co-expression networks identifies a nexus for modulating protein and citric acid titres in Aspergillus niger submerged culture

Filamentous fungal cell factories are used to produce numerous proteins, enzymes, and organic acids. Protein secretion and filamentous growth are tightly coupled at the hyphal tip. Additionally, both these pro...

Authors: Timothy C. Cairns, Claudia Feurstein, Xiaomei Zheng, Li Hui Zhang, Ping Zheng, Jibin Sun and Vera Meyer

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

The circular economy closes loops in industrial manufacturing processes and minimizes waste. A bio-based economy aims to replace fossil-based resources and processes by sustainable alternatives which exploits ...

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

Deletion of the small GTPase rac1 in Trichoderma reesei provokes hyperbranching and impacts growth and cellulase production

Trichoderma reesei is widely known for its enormous protein secretion capacity and as an industrially relevant producer of cellulases and hemicellulases. Over the last decades, rational strain engineering was app...

Authors: Elisabeth Fitz, Christian Gamauf, Bernhard Seiboth and Franziska Wanka

Practical guidance for the implementation of the CRISPR genome editing tool in filamentous fungi

Within the last years, numerous reports described successful application of the CRISPR nucleases Cas9 and Cpf1 for genome editing in filamentous fungi. However, still a lot of efforts are invested to develop a...

Authors: Min Jin Kwon, Tabea Schütze, Sebastian Spohner, Stefan Haefner and Vera Meyer

Draft genome sequence of fastidious pathogen Ceratobasidium theobromae, which causes vascular-streak dieback in Theobroma cacao

Ceratobasidium theobromae, a member of the Ceratobasidiaceae family, is the causal agent of vascular-streak dieback (VSD) of cacao, a major threat to the chocolate industry in the South-East Asia. The fastidious ...

Authors: Shahin S. Ali, Asman Asman, Jonathan Shao, Amanda P. Firmansyah, Agung W. Susilo, Ade Rosmana, Peter McMahon, Muhammad Junaid, David Guest, Tee Yei Kheng, Lyndel W. Meinhardt and Bryan A. Bailey

Efficient marker free CRISPR/Cas9 genome editing for functional analysis of gene families in filamentous fungi

CRISPR/Cas9 mediated genome editing has expedited the way of constructing multiple gene alterations in filamentous fungi, whereas traditional methods are time-consuming and can be of mutagenic nature. These de...

Authors: Tim M. van Leeuwe, Mark Arentshorst, Tim Ernst, Ebru Alazi, Peter J. Punt and Arthur F. J. Ram

The role of PKAc1 in gene regulation and trichodimerol production in Trichoderma reesei

Trichoderma reesei represents a model system for investigation of plant cell wall degradation and its connection to light response. The cyclic adenosine monophosphate pathway (cAMP pathway) plays an important rol...

Authors: Wolfgang Hinterdobler, André Schuster, Doris Tisch, Ezgi Özkan, Hoda Bazafkan, Johann Schinnerl, Lothar Brecker, Stefan Böhmdorfer and Monika Schmoll

A closer look at Aspergillus: online monitoring via scattered light enables reproducible phenotyping

Filamentously growing microorganisms offer unique advantages for biotechnological processes, such as extraordinary secretion capacities, going along with multiple obstacles due to their complex morphology. How...

Authors: Roman P. Jansen, Carina Beuck, Matthias Moch, Bianca Klein, Kira Küsters, Holger Morschett, Wolfgang Wiechert and Marco Oldiges

Publisher Correction to: Fungal Biology and Biotechnology, volume 6

An error occurred during the publication of a number of articles in Fungal Biology and Biotechnology. Several articles were published in volume 6 with a duplicate citation number.

Authors:

The fungal gene cluster for biosynthesis of the antibacterial agent viriditoxin

Viriditoxin is one of the ‘classical’ secondary metabolites produced by fungi and that has antibacterial and other activities; however, the mechanism of its biosynthesis has remained unknown.

Authors: Andrew S. Urquhart, Jinyu Hu, Yit-Heng Chooi and Alexander Idnurm

Increasing access to microfluidics for studying fungi and other branched biological structures

Microfluidic systems are well-suited for studying mixed biological communities for improving industrial processes of fermentation, biofuel production, and pharmaceutical production. The results of which have t...

Authors: Larry J. Millet, Jayde Aufrecht, Jessy Labbé, Jessie Uehling, Rytas Vilgalys, Myka L. Estes, Cora Miquel Guennoc, Aurélie Deveau, Stefan Olsson, Gregory Bonito, Mitchel J. Doktycz and Scott T. Retterer

A protoplast generation and transformation method for soybean sudden death syndrome causal agents Fusarium virguliforme and F. brasiliense

Soybean production around the globe faces significant annual yield losses due to pests and diseases. One of the most significant causes of soybean yield loss annually in the U.S. is sudden death syndrome (SDS)...

Authors: Mitchell G. Roth and Martin I. Chilvers

Cpf1 enables fast and efficient genome editing in Aspergilli

CRISPR technology has revolutionized fungal genetic engineering by increasing the speed and complexity of the experiments that can be performed. Moreover, the efficiency of the system often allows genetic engi...

Authors: Katherina Garcia Vanegas, Zofia Dorota Jarczynska, Tomas Strucko and Uffe Hasbro Mortensen

Merging science and art through fungi

Science and art have long been studied interchangeably, with notable polymaths emerging in the Renaissance such as Leonardo da Vinci (artist, inventor, engineer and anatomist) and Alexander von Humboldt (explo...

Authors: Vera Meyer

Pycnoporus cinnabarinus glyoxal oxidases display differential catalytic efficiencies on 5-hydroxymethylfurfural and its oxidized derivatives

5-Hydroxymethylfurfural (HMF), a major residual component of a lignocellulosic bio-refinery process, can be transformed into fundamental building blocks for green chemistry via oxidation. While chemical method...

Authors: Marianne Daou, Bassem Yassine, Saowanee Wikee, Eric Record, Françoise Duprat, Emmanuel Bertrand and Craig B. Faulds

Development of microtiter plate scale CRISPR/Cas9 transformation method for Aspergillus niger based on in vitro assembled ribonucleoprotein complexes

The CRISPR/Cas9 is currently the predominant technology to enhance the genome editing efficiency in eukaryotes. Established tools for many fungal species exist while most of them are based on in vivo expressed...

Authors: Joosu Kuivanen, Veera Korja, Sami Holmström and Peter Richard

Modulating CRISPR gene drive activity through nucleocytoplasmic localization of Cas9 in S. cerevisiae

The bacterial CRISPR/Cas genome editing system has provided a major breakthrough in molecular biology. One use of this technology is within a nuclease-based gene drive. This type of system can install a geneti...

Authors: Megan E. Goeckel, Erianna M. Basgall, Isabel C. Lewis, Samantha C. Goetting, Yao Yan, Megan Halloran and Gregory C. Finnigan

Itaconic acid degradation in Aspergillus niger: the role of unexpected bioconversion pathways

Itaconic acid (IA), a C5-dicarboxylic acid, has previously been identified as one of the top twelve biochemicals that can be produced by biotechnological means. IA is naturally produced by Aspergillus terreus, ho...

Authors: Abeer H. Hossain, Alexander Ter Beek and Peter J. Punt

The CRISPR revolution in fungal biology and biotechnology, and beyond

Authors: Alexander Idnurm and Vera Meyer

Identification of the decumbenone biosynthetic gene cluster in Penicillium decumbens and the importance for production of calbistrin

Filamentous fungi are important producers of secondary metabolites, low molecular weight molecules that often have bioactive properties. Calbistrin A is a secondary metabolite with an interesting structure tha...

Authors: Sietske Grijseels, Carsten Pohl, Jens Christian Nielsen, Zahida Wasil, Yvonne Nygård, Jens Nielsen, Jens C. Frisvad, Kristian Fog Nielsen, Mhairi Workman, Thomas Ostenfeld Larsen, Arnold J. M. Driessen and Rasmus John Normand Frandsen

Translocated duplication of a targeted chromosomal segment enhances gene expression at the duplicated site and results in phenotypic changes in Aspergillus oryzae

Translocated chromosomal duplications occur spontaneously in many organisms; segmental duplications of large chromosomal regions are expected to result in phenotypic changes because of gene dosage effects. The...

Authors: Tadashi Takahashi, Masahiro Ogawa, Atsushi Sato and Yasuji Koyama

A community-driven reconstruction of the Aspergillus niger metabolic network

Aspergillus niger is an important fungus used in industrial applications for enzyme and acid production. To enable rational metabolic engineering of the species, available information can be collected and integra...

Authors: Julian Brandl, Maria Victoria Aguilar-Pontes, Paul Schäpe, Anders Noerregaard, Mikko Arvas, Arthur F. J. Ram, Vera Meyer, Adrian Tsang, Ronald P. de Vries and Mikael R. Andersen

Truncation of the transcriptional repressor protein Cre1 in Trichoderma reesei Rut-C30 turns it into an activator

The filamentous fungus Trichoderma reesei (T. reesei) is a natural producer of cellulolytic and xylanolytic enzymes and is therefore industrially used. Many industries require high amounts of enzymes, in particul...

Authors: Alice Rassinger, Agnieszka Gacek-Matthews, Joseph Strauss, Robert L. Mach and Astrid R. Mach-Aigner

Evolutionary freedom in the regulation of the conserved itaconate cluster by Ria1 in related Ustilaginaceae

Itaconate is getting growing biotechnological significance, due to its use as a platform compound for the production of bio-based polymers, chemicals, and novel fuels. Currently, Aspergillus terreus is used for i...

Authors: Elena Geiser, Hamed Hosseinpour Tehrani, Svenja Meyer, Lars M. Blank and Nick Wierckx

Whole-genome sequencing reveals highly specific gene targeting by in vitro assembled Cas9-ribonucleoprotein complexes in Aspergillus fumigatus

CRISPR/Cas9-based genome editing is quickly becoming a powerful tool within the field of fungal genetics. Adaptation of CRISPR/Cas9 systems are allowing for rapid and highly efficient gene targeting within fun...

Authors: Qusai Al Abdallah, Ana Camila Oliveira Souza, Adela Martin-Vicente, Wenbo Ge and Jarrod R. Fortwendel

Genome-wide analysis of cytochrome P450s of Trichoderma spp.: annotation and evolutionary relationships

Cytochrome P450s form an important group of enzymes involved in xenobiotics degradation and metabolism, both primary and secondary. These enzymes are also useful in industry as biotechnological tools for bioco...

Authors: Sonia Chadha, Sayaji T. Mehetre, Ravindra Bansal, Alan Kuo, Andrea Aerts, Igor V. Grigoriev, Irina S. Druzhinina and Prasun K. Mukherjee

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

In 1917, a food chemist named James Currie made a promising discovery: any strain of the filamentous mould Aspergillus niger would produce high concentrations of citric acid when grown in sugar medium. This trica...

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

Gene regulation associated with sexual development and female fertility in different isolates of Trichoderma reesei

Trichoderma reesei is one of the most frequently used filamentous fungi in industry for production of homologous and heterologous proteins. The ability to use sexual crossing in this fungus was discovered several...

Authors: Christoph Dattenböck, Doris Tisch, Andre Schuster, Alberto Alonso Monroy, Wolfgang Hinterdobler and Monika Schmoll

Improved microscale cultivation of Pichia pastoris for clonal screening

Expanding the application of technical enzymes, e.g., in industry and agriculture, commands the acceleration and cost-reduction of bioprocess development. Microplates and shake flasks are massively employed du...

Authors: Alexander Eck, Matthias Schmidt, Stefanie Hamer, Anna Joelle Ruff, Jan Förster, Ulrich Schwaneberg, Lars M. Blank, Wolfgang Wiechert and Marco Oldiges

Regulation of plant cell wall degradation by light in Trichoderma

Trichoderma reesei (syn. Hypocrea jecorina) is the model organism for industrial production of plant cell wall degradating enzymes. The integration of light and nutrient signals for adaptation of enzyme productio...

Authors: Monika Schmoll

Vegan-mycoprotein concentrate from pea-processing industry byproduct using edible filamentous fungi

Currently around one billion people in the world do not have access to a diet which provides enough protein and energy. However, the production of one of the main sources of protein, animal meat, causes severe...

Authors: Pedro F. Souza Filho, Ramkumar B. Nair, Dan Andersson, Patrik R. Lennartsson and Mohammad J. Taherzadeh

Correction to: Aspergillus niger is a superior expression host for the production of bioactive fungal cyclodepsipeptides

Following publication of the original article [1], the authors reported that there is a mistake in the legend of Figure 4; the explanation of the symbols has been mixed up. The corrected version of Figure 4 is...

Authors: Simon Boecker, Stefan Grätz, Dennis Kerwat, Lutz Adam, David Schirmer, Lennart Richter, Tabea Schütze, Daniel Petras, Roderich D. Süssmuth and Vera Meyer

CoIN: co-inducible nitrate expression system for secondary metabolites in Aspergillus nidulans

Sequencing of fungal species has demonstrated the existence of thousands of putative secondary metabolite gene clusters, the majority of them harboring a unique set of genes thought to participate in productio...

Authors: Philipp Wiemann, Alexandra A. Soukup, Jacob S. Folz, Pin-Mei Wang, Andreas Noack and Nancy P. Keller

Aspergillus niger is a superior expression host for the production of bioactive fungal cyclodepsipeptides

Fungal cyclodepsipeptides (CDPs) are non-ribosomally synthesized peptides produced by a variety of filamentous fungi and are of interest to the pharmaceutical industry due to their anticancer, antimicrobial an...

Authors: Simon Boecker, Stefan Grätz, Dennis Kerwat, Lutz Adam, David Schirmer, Lennart Richter, Tabea Schütze, Daniel Petras, Roderich D. Süssmuth and Vera Meyer

Cinnamomum zeylanicum bark essential oil induces cell wall remodelling and spindle defects in Candida albicans

Cinnamon (Cinnamomum zeylanicum) bark extract exhibits potent inhibitory activity against Candida albicans but the antifungal mechanisms of this essential oil remain largely unexplored.

Authors: Zinnat Shahina, Amira M. El-Ganiny, Jessica Minion, Malcolm Whiteway, Taranum Sultana and Tanya E. S. Dahms

Heterologous and endogenous U6 snRNA promoters enable CRISPR/Cas9 mediated genome editing in Aspergillus niger

U6 promoters have been used for single guide RNA (sgRNA) transcription in the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas9) genome editing system. However, no ....

Authors: Xiaomei Zheng, Ping Zheng, Jibin Sun, Zhang Kun and Yanhe Ma

Production of Aspergillus niger biomass on sugarcane distillery wastewater: physiological aspects and potential for biodiesel production

Sugarcane distillery waste water (SDW) or vinasse is the residual liquid waste generated during sugarcane molasses fermentation and alcohol distillation. Worldwide, this effluent is responsible for serious env...

Authors: Graziella Chuppa-Tostain, Julien Hoarau, Marie Watson, Laetitia Adelard, Alain Shum Cheong Sing, Yanis Caro, Isabelle Grondin, Isabelle Bourven, Jean-Marie Francois, Elisabeth Girbal-Neuhauser and Thomas Petit