FABI News
16 Jul 2025
FABI makes a strong impression at the 24th ESSA Congress in Bloemfontein
FABI had a strong presence at the 24th Congress of the Entomological Society of Southern Africa (ESSA), with 18 members in attendance.
3 Jul 2025
FABI is serie-ous too
FABIans once again got the opportunity to share which TV series they really enjoyed watching over the past year.
20 Jun 2025
Strengthening mycology in South Africa: FABI hosts NICD researchers
FABI recently hosted a meeting to establish linkages between medical mycologists and those working mainly on fungi in the environment.
19 Jun 2025
FABIans conquer the 2025 Comrades Marathon
FABI is proud of Steven Shange and Josias Letaoana who conquered the gruelling Comrades Marathon.
13 Jun 2025
Science, culture, and collaboration: Mycobiomics Meeting at FABI
International visitors attending the Mycobiomics meeting at FABI also had a chance to go on several tours on the UP campus and visit the Pilanesberg National Park.
FABI in a nutshell
Research Features
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.
Forest Biotechnology Platform
Applied Chemical Ecology
Chemical ecology is the study of the role that chemicals play mediating interactions between organisms and organisms and their environment, and the consequences of those interactions in ecological and evolutionary time. It is not an autonomous discipline but rather an approach to ecology, one of viewing ecological interactions through a chemical lens world.
DST-NRF Centre of Excellence in Plant Health Biotechnology
The CTHB promotes the health of trees indigenous to South Africa through the use of biotechnology. This is accomplished through projects that typically consider the pathogens and pests associated with native trees and woody hosts. The CTHB also explores the possible effects that factors such as climate change, society, natural forest health and plant genetics may have on the health of native woody resources and ecosystems.
Eucalyptus Pine Pathogen Interactions
The EPPI group undertakes to gain an understanding of host broad-spectrum resistance to curb disease or pest incidence in Eucalyptus and Pine. Genomic approaches are employed to investigate Eucalyptus interactions to the insect pest Leptocybe invasa, the oomycete pathogen Phytophthora cinnamomi and the fungal pathogen Chrysoporthe austroafricana. In Pine, induced resistance is being investigated as a means to improve tolerance against Fusarium circinatum.
Forest Molecular Genetics
The Forest Molecular Genetics (FMG) Programme focuses on the genetic control of wood development in fast-growing plantation trees. We utilise a number of research and technology platforms, namely: tree genomics; high-throughput DNA marker analysis; functional genetics; as well as wood pheno¬typing. We work in close collaboration with South African forestry companies to develop capacity and resources for the application of tree biotechnology in operational tree improvement programmes.
PSHB Research Network
The Polyphagous Shothole Borer (PSHB) outbreak in South Africa is the largest geographical outbreak of this beetle in the world. It is affecting trees in all sectors: the agricultural and commercial forestry sector, urban trees (public spaces, streets, gardens), as well as native trees in natural forests. Over the past year or more, researchers at FABI had been in contact with senior academics from seven universities in relation to PSHB research.
RGE-FABI Tree Health Programme
The RGE-FABI Tree Health Programme (RGE-FABI THP) was established in 2018 as a collaborative venture between the Indonesian-based Royal Golden Eagle (RGE) Group and the Forestry and Agricultural Biotechnology Institute (FABI) at the University of Pretoria. This partnership addresses challenges posed by pests and diseases to RGE’s forestry operations in Indonesia and Brazil. The initiative involves FABI researchers working in partnership with RGE’s divisions: Asia Pacific Resources International Holdings Limited (APRIL) and Brazil based Bracell Limited.
Tree Protection Co-operative Programme
The Tree Protection Cooperative Programme (TPCP) represents a cooperative venture between the major players in the South African Forestry Industry and the University of Pretoria, to deal with tree disease problems. The programme is based on a membership concept where forestry organisations are members and contribute to a collaborative effort through the payment of annual fees. The University of Pretoria in turn provides the infrastructure necessary to conduct research into tree pests and diseases, which is technologically complicated and thus expensive.
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.
Jeremy Allison
Brett Hurley
Almuth Hammerbacher
Gerda Fourie
Josephine Queffelec
Luki-Marie Scheepers
Leandrie
New Publications
Esterhuizen HJ, Slippers B, Bosman AS, Roux J, Jones W, Bose T, Hammerbacher A. (2025) Early detection of Phytophthora root rot in Eucalyptus using hyperspectral reflectance and machine learning. Computers and Electronics in Agriculture 237:110761.
10.1016/j.compag.2025.110761
Pham NQ, Wingfield BD, Marincowitz S, Brawner JT, Hulcr J, Wingfield MJ. (2025) Cryphonectria canker on Eucalyptus in Florida reconsidered. Forest Pathology 55:e70031.
10.1111/efp.70031
Nzuza P, Schröder ML, Heim RJ, Daniels L, Slippers B, Hurley BP, Germishuizen I, Sivparsad B, Roux J, Maes WH. (2025) Assessing Gonipterus defoliation levels using multispectral unmanned aerial vehicle (UAV) data in Eucalyptus plantations. Ecological Informatics 90:103301.
10.1016/j.ecoinf.2025.103301
Kunene S, Mmushi TJ, Steenkamp E, Motaung T. (2025) Pinus-derived membrane vesicles disrupt pathogenic metabolism in fungi. plant biology
10.1111/plb.70069 
Theron CA, Wingfield MJ, Ahumada R, Carnegie AJ, Fraser S, Rodas C, Barnes I. (2025) Diversity and distribution of Lophodermium species on non-native Pinus species in the southern hemisphere. Mycological Progress 24(44)
10.1007/s11557-025-02056-5
Msweli D, Geerts S, Nndanduleni M, Paap T. (2025) Evaluation of phosphite to protect a South African Proteaceae from Phytophthora root rot. Journal of Plant Pathology
10.1007/s42161-025-01945-8
Dewing C, Yilmaz N, Steenkamp ET, Wingfield BD, Visagie CM. (2025) Capturing the fungal diversity hidden in Eastern Cape dairy pastures. Mycological Progress 24(1):38.
10.1007/s11557-025-02059-2
Nel WJ, Duong TA, Fell S, Herron DA, Paap T, Wingfield MJ, de Beer ZW, Hulcr J, Johnson AJ. (2025) A checklist of South African bark and ambrosia beetles (Coleoptera: Curculionidae: Scolytinae, Platypodinae). Zootaxa 5648(1):1-101.
10.11646/zootaxa.5648.1.1
Dewing C, Yilmaz N, Steenkamp ET, Wingfield BD, Visagie CM. (2025) Capturing the fungal diversity hidden in Eastern Cape dairy pastures. Mycological Progress 24:38.
10.1007/s11557-025-02059-2
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
Pham NQ, Marincowitz S, Crous PW, Wingfield MJ. (2025) Diversity of soil-borne Gliocladiopsis from Indonesia, Malaysia and Vietnam. Fungal Systematics and Evolution 16:81–92.
10.3114/fuse.2025.16.6
Tanney JB, Kemler M, Vivas M, Wingfield MJ, Slippers B. (2025) Silent invaders: The hidden threat of asymptomatic phytobiomes to forest biosecurity. New Phytologist
10.1111/nph.70209
Fick A, Swart V, Van den Berg N. (2025) In silico prediction method for plant Nucleotide-binding leucine-rich repeat- and pathogen effector interactions. The Plant Journal 122:e70169.
10.1111/tpj.70169
Bose T, Wingfield MJ, Brachmann A, Witfeld F, Begerow D, Kemler M, Dovey S, Roux J, Slippers B, Vivas M, Hammerbacher A. (2025) Removal of organic biomass in Eucalyptus plantations has a greater impact on fungal than on bacterial networks. Forest Ecology and Management 586:122734.
10.1016/j.foreco.2025.122734
Woodward S, Amin H, Mártin-Gárcia J, Solla A, Diaz-Vazquez R, Romeralo C, Alves A, Pinto G, Herron D, Fraser S, Zas R, Doğmuş-Lehtijärvi HT, Bonello P, Wingfield MJ, Witzell J, Diez JJ. (2025) Host-pathogen interactions in the Pine-Fusarium circinatum pathosystem and the potential for resistance deployment in the field. Forest Pathology 55(2):e70020.
10.1111/efp.70020
Maduke N, Slippers B, Van der Linde E, Wingfield M, Fourie G. (2025) Botryosphaeriaceae associated with racemes, fruits and leaves of macadamia in South Africa. Plant Pathology 0:1–15:1–15.
10.1111/ppa.14107
Hulcr J, Barnes I, Barnes M, Gazis R, Hammerbacher A, Johnson AJ, Lynch S, Lynn K, Marais GC, Mayers CG, Nel W, Villari C, Wingfield BD, Wingfield MJ. (2025) From forest to fungus: A roadmap to bark beetle mycobiome research. Phytoparasitica 53(45)
10.1007/s12600-025-01246-x
Knoppersen RS, Bose T, Coutinho TA, Hammerbacher A. (2025) Inside the Belly of the Beast: Exploring the Gut Bacterial Diversity of Gonipterus sp. n. 2. Microbial Ecology 88:27.
10.1007/s00248-025-02524-1
Bose T, Roux J, Titshall L, Dovey SB, Hammerbacher A. (2025) Mulching of post-harvest residues and delayed planting improves fungal biodiversity in South African Eucalyptus plantations and enhances plantation productivity. Applied Soil Ecology 210:106091.
10.1016/j.apsoil.2025.106091
Wychkuys KA, Giron E, Hyman G, Barona E, Castro-Llanos FA, Sheil D, Yu L, Du Z, Hurley BP, Slippers B, Germishuizen I, Bojacá CR, Rubiano M, Sathyapala S, Verchot L, Zhang W. (2025) Biological control protects carbon sequestration capacity of plantation forests. Entomologia Generalis
10.1127/entomologia/2025/3015
Balocchi F. (2025) Risk Analysis for Alien Taxa (RAAT) for Phytophthora cinnamomi in South Africa.
10.5281/zenodo.14858265
Paap T, Balocchi F, Wingfield MJ. (2025) The root rot pathogen Phytophthora cinnamomi: a long-overlooked threat to the Cape Floristic Region of South Africa. Biological Invasions 27(4)
10.1007/s10530-025-03570-z
Harikrishnan K, Rajeshkumar KC, Patil PM, Jeewon R, Visagie CM. (2025) Aspergillus dhakephalkarii and A. patriciawiltshireae spp. nov., two new species in Aspergillus sect. Nigri ser. Japonici (Eurotiales, Aspergillaceae) from India. Phytotaxa 695:57–79.
10.11646/phytotaxa.695.1.2
Wilson A, van Dijk A, Marx B, du Plessis D, Terblanche G, Bornman S, Wilken PM, Duong TA, De Fine Licht HH, Wingfield BD. (2025) Extracting Protoplasts from Filamentous Fungi Using Extralyse, An Enzyme Used in the Wine Industry. Current Protocols 5(e70122):1-29.
10.1002/cpz1.70122
Dewing C, Visagie CM, Steenkamp ET, Wingfield BD, Yilmaz N. (2025) Three new species of Fusarium (Nectriaceae, Hypocreales) isolated from Eastern Cape dairy pastures in South Africa. MycoKeys 115:241–271.
10.3897/mycokeys.115.148914
Coertze S, Visagie CM, Rose L, Slippers B, Mostert D, Makhura T, de Villiers D, Basson E, Coetzee B, Read D. (2025) First report of Clavibacter nebraskensis, causing Goss’s bacterial leaf blight on maize (Zea mays L.) in South Africa. Plant Disease
10.1094/PDIS-01-25-0164-PDN