CTHB Academic Internship

FABI News

News Archive

10 Jun 2025

FABIans visit Kenya for a Mycobiomics expedition

Three FABIans represented FABI at a recent during a multinational- collaborative Mycobiomics field expedition in Kenya.

9 Jun 2025

Dr Neriman Yilmaz represents FABI at the 46<sup>th</sup> Mycotoxin Workshop in Italy

Dr Neriman Yilmaz represents FABI at the 46^th Mycotoxin Workshop in Italy

Dr Neriman Yilmaz recently participated in the 46^th Mycotoxin Workshop in Martina Franca, Italy.

6 Jun 2025

International vistors tour FABI

Twenty five international delegates attending the Mycobiomics Conference at FABI were given a tour of FABI by the founding Director, Prof. Mike Wingfield.

30 May 2025

Prof. Romina Gaziz visits FABI

Professor Romina Gaziz from the University of Florida’s Tropical Research and Education Centre recently visited FABI to attend and participate in the 36th Annual Meeting TPCP.

27 May 2025

Melissa's PhD research sheds light on poorly understood viroid impacting avocado

FABI celebrated the successful completion of Melissa Joubert’s PhD that has lays the foundation for understanding a viroid impacting avocado.

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FABI Events

Monday Morning Meeting

26 June 08h30

Student Seminars

FABI in a nutshell

Research Features

Archive

Review emphasizes the importance of understanding the genetics of sex determination for effective genetic pest management in insects.

Eleven new Penicillium and Talaromyces species discovered in South African culture collections.

A new study reveals the presence of Mycotoxins in Eastern Cape maize in South Africa.

Eurotiales update: FABIans Prof. Cobus Visagie and Dr Neriman Yilmaz and their collaborators have published a review of recently described Eurotiales species, including the economically important Aspergillus, Penicillium, Paecilomyces and Talaromyces.

Da Vinci's Yeast: FABIans Prof. Cobus Visagie, Dr Neriman Yilmaz, and their collaborators have recently described and named a newly discovered yeast species of the famous Italian painter, draughtsman, engineer, scientist, theorist, sculptor, and architect Leonardo da Vinci.

The potential economic impact of the PSHB invasion in South Africa has been calculated to be a massive R275 billion over the next ten years, if nothing is done to stop the spread of this invasive beetle. Researchers from FABI collaborated with Stellenbosch University ecologists and economists to model the unmitigated economic impact of this invasion.

A recently published paper in the journal Current Forestry Reports documents a collaboration between an international team of forest pathologists and invasion scientists. Led by Dr Trudy Paap, the authors present a framework for conceptualizing and managing invasive forest pathogens.

A recently published review article by Dr Andi Wilson in a special issue of the journal 'Microbiology & Molecular Biology Reviews' provides details of the genes that are essential to the sexual cycle in filamentous Ascomycete fungi and further describes their functions in a variety of model and non-model species.

Penicillium section Canescentia re-evaluated and five new species described from the fynbos biome in South Africa.

In November 2019, the DSI-NRF Centre of Excellence for Invasion Biology hosted a workshop on ‘Frameworks used in Invasion Science’. The workshop led to a NeoBiota special issue on this theme, and includes a review by FABI researchers and international colleagues, exploring frameworks in the context of forest pathology.

A doctoral study in FABI confirms for the first time the presence of Xylosandrus crassiusculus, a polyphagous ambrosia beetle and its fungal symbiont, Ambroseilla roeperi, in three provinces in South Africa. The authors warn that this beetle species could be a threat to native and plantation trees.

A review on invasive gall-forming wasps that threaten non-native Eucalyptus plantations by researchers in the TPCP appears in Agricultural and Forest Entomology. They profile several species of likely Australian origin that have established on non-native Eucalyptus plantations globally and discuss various challenges to their management.

A study in the TPCP confirms the identity of seven novel fungal species associated with Dendroctonus valens, the red turpentine beetle. The study follows on surveys on the fungal associates of the beetle in China and North America. Results from this work appear in Persoonia.

A postdoctoral study in the TPCP describes two novel Huntiella species in the African clade, bringing the number of known species in the genus to 31. Though closely related, the two species display different mating systems. Outcomes from this study appear in the journal MycoKeys.

A review of the invasion history and global management strategies of Eucalyptus snout beetles in the Gonipterus scutellatus species complex by researchers in the TPCP appears in the Journal of Pest Science.

In a collaborative venture with Dr Jos Houbraken (Westerdijk Fungal Biodiversity Institute, the Netherlands), Prof. Cobus M Visagie, Dr Neriman Yilmaz (both from FABI) and others have recently completed and published a major study updating the taxonomy of the Eurotiales.

A study in the Forest Molecular Genetics (FMG) Programme at FABI interrogates the benefits of implementing genomic selection for growth and wood quality traits in an established Eucalyptus grandis breeding programme in South Africa. Outcomes from this study appear in an article.

The first study on alternative weed and cultivated hosts of Spongospora subterraneaf. sp. subterranea (Sss), in southern Africa identifies two species as ideal trap crops for rotation with potatoes. The study also introduces three new families to the known hosts of Sss in the region.

A consortium of microbiologists from around the globe, FABI included, is pushing for an overhaul in how scientific names are assigned to uncultivated bacteria and archaea. Despite their ecological, agricultural and medical importance, these organisms traditionally have not been recognized by the international body governing the nomenclature of prokaryotes.

Professor Cobus Visagie is a researcher in the Applied Mycology group at FABI. One of the group’s research goals is to discover fungal diversity in South Africa, and Cobus’ research is strongly focussed on the economically important genera Aspergillus, Penicillium and Talaromyces.

Postdoctoral research by Dr Norman Muzhinji in the Potato Pathology Programme at the Forestry and Agricultural Biotechnology Institute (FABI) sheds light on the genetic structure and diversity of Spongospora subterranea f. sp. subterranea in four potato-growing regions in South Africa, providing valuable insights on its management.

An MSc study by Kira Lynn in the RGE-FABI Tree Health Programme at the University of Pretoria has described a new Fusarium species, Fusarium rekanum sp. nov., associated with Euwallacea perbrevis, an ambrosia beetle species infesting Acacia crassicarpa plantations in Riau, Indonesia.

FABI postdoctoral Fellow Dr Andi Wilson has established a CRISPR-Cas9-based genome editing protocol for use in Huntiella omanensis, a tree-inhabiting fungus belonging to the Ceratocystidaceae family.

Research undertaken as part of a PhD study by Molly Malefo at the University of Pretoria’s Department of Plant and Soil Sciences and Forestry and Agricultural Biotechnology Institute sheds more light on the role of protease inhibitors in plants under drought stress.

The South African National Biodiversity Institute (SANBI) has funded a postdoctoral research project dedicated to monitoring plant health in botanical gardens and arboreta across South Africa. Two postdoctoral Fellows at the University of Pretoria’s Forestry and Agricultural Biotechnology Institute have held these fellowships.

The first comprehensive study mapping the distribution and genetic diversity of invasive Eucalyptus insect pests in sub-Saharan Africa confirms the presence of five major foliage-feeding species in 14 countries. The results of this study have implications on the quarantine, future research and management of these pests on the continent and beyond.

Dr Joey Hulbert broke new ground when he became the first candidate at the Forestry and Agricultural Biotechnology Institute to complete a PhD study incorporating citizen science. Citizen science is an approach that involves members of the public as active participants in scientific research.

FABI technology unravels the genetics behind fungal genome evolution The RIPper is a bioinformatics tool for the for quantifying genome-wide RIP mutations in fungal genomes. The strength of this software lies in the automation of laborious techniques to study the mutation process called Repeat-Induced Point mutations (RIP). The RIPper applies these technique

With the increased availability in genome data, inferences regarding evolutionary relationships among taxa can now be performed on a genome-wide scale. But it is widely accepted that not all parts of such massive datasets support the same evolutionary hypothesis. Because of this, a group of researchers at FABI recently investigated the effect of this.

The use of genome data to characterize species and elucidate relationships, particularly between problematic taxa, has become routine practice in bacteria. Recently, researchers from FABI joined in an international effort to describe two novel genera and characterize these within the larger context of the important bacterial group Burkholderia.

A PhD student in FABI, Runlei Chang, has discovered and described 19 new fungal species from China as part of the research for his thesis. These fungi are all associated with conifer-infesting bark beetles and their mites and belong to well-known genera such as Ophiostoma and Leptographium.

Two research papers from FABI were selected as cover stories in two consecutive issues of the international journal, Plant Pathology. The journal is published by Wiley for the British Society of Plant Pathology.

Plastids play an integral role in wood formation, and yet they are routinely ignored in the study of xylogenesis in forest trees. Desre Pinard and Dr Eshchar Mizrachi have published a review highlighting the unique biology of plastids in wood, suggesting that a new type of plastid, the xylopast, exists.

Approaches for characterizing metabolic potential from genomic sequences have previously been predicted to be useful in the description of bacterial taxa. Dr Marike Palmer, has recently employed these approaches for identifying biological processes contributing to the divergence of bacteria with a variety of lifestyles.

Comparative genomics is shaping our notion of what fungal species are. Based on current data, these unique evolutionary units are separated from one another by boundaries that are porous under certain conditions. This affects our expectations regarding their population biology and evolution, and our strategies for recognizing and controlling them.

The Polyphagous Shot Hole Borer is an ambrosia beetle native to Southeast Asia. In 2017 this pest was detected in South Africa. Its presence has since been confirmed in all provinces except Limpopo. The beetle has a symbiotic relationship with the fungus Fusarium euwallaceae, which causes branch die-back and death of susceptible trees.

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CENTRE OF EXCELLENCE IN TREE HEALTH BIOTECHNOLOGY (CTHB)

FORESTRY AND AGRICULTURAL BIOTECHNOLOGY INSTITUTE

FACULTY OF NATURAL AND AGRICULTURAL SCIENCES

INTERNSHIP – ACADEMIC

(12 MONTH CONTRACT APPOINTMENT FROM 1 July 2019 TO 30 June 2020)

In pursuit of the ideals of excellence and diversity, the University of Pretoria wishes to invite applications for the following vacancy.

The University of Pretoria's commitment to quality makes us one of the top research Universities in the country and gives us a competitive advantage in international science and technology development.

RESPONSIBILITIES:

The Academic Internship will provide a graduate holding a BSc Hons or MSc degree with the opportunity to have hands-on experience in academia in order to prepare them for an academic career.

The successful candidate will actively participate in the following areas:

•Research activities at the Forestry and Agricultural Biotechnology Institute (including laboratory assistance and field work) and publications;

•Receive training in various research methods;

•Community engagement activities

MINIMUM REQUIREMENTS:

Honours/Masters degree;

•South African citizen;

•At least 65% average academic record;

•Commitment to further academic development

REQUIRED COMPETENCIES (SKILLS, KNOWLEDGE AND BEHAVIOURAL ATTRIBUTES):

•Appropriate language and communication skills;

•Good interpersonal skills;

•Teamwork and

•Good computer skills (Windows, MS Office, internet).

The all-inclusive remuneration package for this contract position will be R96 000.00 per annum.

In applying for this post, please attach a comprehensive CV, proof of qualification & copy of ID and email to Mrs Heidi Fysch (email; This email address is being protected from spambots. You need JavaScript enabled to view it.)

CLOSING DATE: 31 May 2019

No application will be considered after the closing date, or if it does not comply with at least the minimum requirements.

ENQUIRIES: Prof Martin Coetzee Tel: (012) 420-4826; e-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

Should you not hear from the University of Pretoria by 23 June 2019, please accept that your application has been unsuccessful.

The University of Pretoria is committed to equality, employment equity and diversity.

In accordance with the Employment Equity Plan of the University and its Employment Equity goals and targets, preference may be given, but is not limited to candidates from under represented designated groups.

All candidates who comply with the requirements for appointment are invited to apply.

The University of Pretoria reserves the right not to make an appointment to the posts as advertised.

Workshops & Symposia

Archive

Joint IUFRO meeting of IUFRO WP 7.03.13 and 7.03.16: Intersection of Behavioural / Chemical Ecology and Biological Control in Forest Ecosystems

Joint IUFRO meeting: Intersection of Behavioural / Chemical Ecology and Biological Control in Forest Ecosystems

New Publications

Chang R, Yan Z, Jiang J, Wang Y, Si H, Bose T, Miao C. (2025) Four novel endolichenic fungi from Usnea spp. (Lecanorales, Parmeliaceae) in Yunnan and Guizhou, China: Taxonomic description and preliminary assessment of bioactive potentials. MycoKeys 118:55–80. 10.3897/mycokeys.118.155248

Lötter A, Bruna T, Duong TA, Barry K, Lipzen A, Daum C, Yoshinaga Y, Grimwood J, Jenkins JW, Talag J, Borevitz J, Lovell JT, Schmutz J, Wegrzyn JL, Myburg AA. (2025) A haplotype-resolved reference genome for Eucalyptus grandis. G3 Genes|Genomes|Genetics 10.1093/g3journal/jkaf112

Wingfield MJ, Pham NQ, Marincowitz S, Wingfield BD. (2025) Cryphonectriaceae: Biodiverse and threatening tree pathogens in the tropics and southern hemisphere. Annual Review of Phytopathology 63 10.1146/annurev-phyto-121823-030316

Magagula P, Swart V, Fourie A, Vermeulen A, Nelson JH, van Rooyen Z, van den Berg N. (2025) Avocado rhizosphere community profiling: white root rot and its impact on microbial composition. Frontiers in Microbiology 16 10.3389/fmicb.2025.1583797

Marincowitz S, Pham NQ, Wingfield BD, Wingfield MJ. (2025) Microfungi associated with dying quiver trees (Aloidendron dichotomum) in South Africa. Fungal Systematics and Evolution 16:71–80. 10.3114/fuse.2025.16.5

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FABI News

FABIans visit Kenya for a Mycobiomics expedition

Dr Neriman Yilmaz represents FABI at the 46th Mycotoxin Workshop in Italy

International vistors tour FABI

Prof. Romina Gaziz visits FABI

Melissa's PhD research sheds light on poorly understood viroid impacting avocado

FABI Events

FABI in a nutshell

Research Features

Workshops & Symposia

Joint IUFRO meeting: Intersection of Behavioural / Chemical Ecology and Biological Control in Forest Ecosystems

New Publications

Dr Neriman Yilmaz represents FABI at the 46^th Mycotoxin Workshop in Italy