FABI News
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.
26 May 2025
CPHB Interns attend NAMPO Harvest Day 2025
The group of CPHB Interns were given the opportunity to visit the NAMPO Harvest Day 2025 through the generous sponsorship of Grain SA.
21 May 2025
Large cohort of FABIans capped at the UP Autumn Graduation ceremony
Congratulations to all the FABIans that were capped at the University of Pretoria’s Autumn Graduation!
25 Apr 2025
Suez University delegation visits FABI
FABI was honoured to host a visit by a delegation from Egypt’s Suez University.
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.
Videos
The impact of a tiny beetle and its deadly fungus on South Africa’s forests (Youtube 36 min) by Prof. Wilhelm de Beer, presented at the National Science and Technology Forum (NSTF) for Plant Health in South Africa on 10 June 2021.
Ecological and economic impact of the polyphagous shot hole borer (YouTube, 5 min; 2022) by Stellenbosch University. Click here to view.
International Year of Plant Health: The Polyphagous Shothole Borer’s effect on South Africa's trees (YouTube video 2.18min; 2020) by the University of Pretoria. Click here to view.
FABI Research Features
The potential economic impact of the polyphagous shot hole borer invasion in South Africa
Non-FABI Publications
Bierman A., F. Roets, J.S. Terblanche (2022) Population structure of the invasive ambrosia beetle, Euwallacea fornicatus, indicates multiple introductions into South Africa. Biological Invasions. 10.1007/s10530-022-02801-x.
de Jager M., F. Roets (2022) Pathogenicity of Fusarium euwallaceae towards apple (Malus domestica) and grapevine (Vitis vinifera). Australasian Plant Disease Notes 17. 10.1007/s13314-022-00456-0.
de Jager M., F. Roets (2022) Rapid and cost-effective detection of Fusarium euwallaceae from woody tissues. Plant Pathology. 10.1111/ppa.13600.
FABI News
Collection of Ambrosia beetle infested material in Durban
14th Online meeting of the Bark Beetle Mycobiome Network
University of Pretoria protects trees against PSHB infestation
Scouting for native natural enemies of PSHB
SANBI Sentinel Plant Project hosts a training workshop for DUT horticulture students
The PSHB takes FABI researchers to Somerset West
Polyphagous Shot Hole Borer online resource
Inspection of invasive disease and pest problems in SANBI's Cape gardens
Prof. Wilhelm de Beer receives the SAIF Distinguished Forestry Award
A webinar on Plant Health in Botanical Gardens amid the COVID-19 pandemic
Getting a PSHB research project done before the lockdown
PSHB is spreading in the Western Cape
Monitoring plant health in botanic gardens and arboreta across South Africa
PSHB survey in Northern Cape Pecan orchards
Shothole Borer meetings in the Cape Peninsula
PSHB fungus tested for pathogenicity on commercial forest trees
Shot Hole borer projects launched in forests of the Southern Cape
Shot Hole Borer invasion places FABI in the spotlight
FABI research work features on Carte Blanche
Tree health experts inspect PSHB infestation in Johannesburg suburbs
FABI Team surveys Johannesburg gardens for PSHB infestations
The impact of the Polyphagous Shothole Borer in South Africa explained in a public seminar at FABI
The PSHB is a 2mm long ambrosia beetle native to Southeast Asia that has a symbiotic relationship with three species of fungi. These include the tree pathogen, Fusarium euwallaceae. This fungus provides a food source for the beetle and its larvae, but in susceptible trees, it kills the vascular tissue, causing branch dieback and tree death.
In its native environment in Southeast Asia, it seems as if the beetle and fungus do not cause serious damage because tree species have evolved with the beetle-fungus complex and have resistance towards them, and because there are most likely a suite of natural enemies of the beetle. However, the beetle and fungus were somehow introduced into Israel and California in the early 2000s where they caused serious damage on several ornamental trees as well as avocado trees. In South Africa the impact of the beetle to date is most visible on ornamental trees.
Identification and species name of the beetle
Until December 2018 the PSHB was known as Euwallacea nr. fornicatus. However, Gomez et al. (2018) showed with DNA sequences that 'Euwallacea fornicatus' is actually a species complex including four closely related, but distinct species. These four species of Shot Hole Borer are very similar in shape, and can only be distinguished by specialists under a microscope or with DNA sequences. The four species carry different fungal species, have different host ranges, and different geographical distributions (Gomez et al. 2018). Although they suggested the name Euwallacea whitfordiodendrus should be used for the PSHB, this was an error that was corrected in a subsequent paper by Smith et al. (2019). The correct names of four Shot Hole Borer species in the E. fornicatus complex are:
1. Tea Shot Hole Borer A [TSHB-a = Euwallacea perbrevis (Schedl 1951)]
Distribution: Asia (American Samoa, China, Indonesia, Papua New Guinea, Samoa, Sri Lanka, Taiwan, Thailand), Australia, and introduced in the USA (Florida and Hawaii)
2. Tea Shot Hole Borer B [TSHB-b = Euwallacea fornicatior (Eggers 1923)]
Distribution: Asia (Malaysia, Papua New Guinea, Singapore, Sri Lanka)
3. Polyphagous Shot Hole Borer [PSHB = Euwallacea fornicatus (Eichhoff 1868), previously referred to as Euwallacea nr. fornicatus and Euwallacea whitfordiodendrus (Schedl 1942)]
Distribution: Asia (China, Hong Kong, Japan, Taiwan, Thailand, and Vietnam) and introduced in USA (California), Israel, South Africa, and Western Australia
4. Kuroshio Shot Hole Borer [KSHB = Euwallacea kuroshio Gomez and Hulcr 2018]
Distribution: Asia (Indonesia, Japan, and Taiwan) and introduced in Mexico and USA (California)
To date, only the PSHB has been found in South Africa. However, both the PSHB and KSHB have invaded California, while TSHB-a has invaded Florida. These species carry similar fungi, have similar life styles and similar effects on trees. With our borders being open for trade to Southeast Asia, the risk that one of the other species can be introduced is very high. Co-occurring species increase the chances for interbreeding which will enhance the adaptability of the beetles to new hosts and new environments, posing a greater threat. From a management perspective, they are dealt with in the same ways. In California they have thus started referring to the PSHB and KSHB jointly with the single term Invasive Shot Hole Borers (ISHB). It is recommended that for management and legislative purposes we also adopt the term ISHB in South Africa.
The Polyphagous Shot Hole Borer is an ambrosia beetle native to Southeast Asia. The beetle has a symbiotic relationship with the fungus Fusarium euwallaceae, which causes branch die-back and can kill susceptible trees. In 2017 the presence of this pest was confirmed in South Africa by the FABI team, and it has since been found in all provinces except Limpopo. This makes the PSHB invasion in South Africa 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.
At present researchers at FABI, in collaboration with colleagues from several other Universities, are coordinating monitoring efforts and leading research on the PSHB and its fungus in South Africa. The purpose of this webpage is to provide:
1. Background information on the PSHB and its management to the general public and all stake holders,
2. Updated information on its distribution and its host trees in South Africa,
3. Feedback on ongoing research and monitoring efforts by the PSHB Research Network, and
4. A platform for the public to make us aware of possible new host trees of PSHB and localities where it occurs.
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
Anneri Lötter, Jill L Wegrzyn, Jeremy Schmutz, John T Lovell, Justin Borevitz, Jayson Talag, Jerry W Jenkins, Jane Grimwood, Yuko Yoshinaga, Chris Daum, Anna Lipzen, Kerrie Barry, Tuan A Duong, Tomas Bruna, Alexander A Myburg. (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