Arabidopsis thaliana - bacterial wilt pathosystem

FABI News

News Archive

8 Sep 2026

Thirteen FABIans conferred postgraduate degrees at the UP Spring Graduation

FABI congratulates the 13 graduates from the Institute capped at UP's Spring Graduation ceremony.

7 Sep 2026

FABI hosts first CryptoADAPT workshop on <I>Cryptococcus</I> biodiversity

FABI hosts first CryptoADAPT workshop on Cryptococcus biodiversity

FABI hosted the first CryptoADAPT workshop from, bringing together researchers from five countries and seven academic institutions

4 Sep 2026

Congratulations to Lazarus on completing his PhD!

Well done Lazarus on successfully completing your PhD!

1 Sep 2026

Aaron Harvey secures second runner-up at the 2026 UP Visualise Your Thesis competition

Aaron Harvey has been awarded Second Runner-Up in the 2026 Institutional Visualise Your Thesis competition, hosted by UP’s Department of Research and Innovation.

27 Aug 2026

Bayer presentation at FABI

FABI hosted a guest presentation by Bayer’s Head of Corn Breeding, Africa

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FABI Events

10 September 08h30

Student Seminars

14 September 08h30

Monday Morning Meeting

17 September 08h30

Student Seminars

21 September 08h30

Monday Morning Meeting

FABI in a nutshell

Research Features

Archive

Tracing the past, building the future: FABI research unlocks the genetics and genomics of the Sirex woodwasp complex

FABI researcher co-authors global perspective on mycotoxins and food safety.

FABI researchers Prof. Cobus Visagie, Dr Neriman Yilmaz, and Nicole van Vuuren, together with international collaborators, have published a comprehensive taxonomic revision of the fungal order Eurotiales, which includes the economically important genera Aspergillus, Penicillium, and Talaromyces.

New publication explores the chemodiversity of Penicillium isolated from alpine and arctic environments, including ten new species.

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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Principal investigator: Prof Dave Berger

Collaborator at UP: Dr Sanushka Naidoo

Team members: Liesl van der Linden, Jane Bredenkamp, Degracious Kgoale.

The aim of the project is to understand the molecular mechanisms of plant responses to the bacterial wilt pathogen, Ralstonia solanacearum. This project is based on the model plant, Arabidopsis thaliana (mustard cress), which is known to have a range of "ecotypes" from different parts of the world. These natural variants show phenotypic differences that have a genetic basis. This was exploited in this project, wherein ecotypes were screened for resistance and susceptibility to African isolates of the bacterial pathogen, Ralstonia. Resistant and susceptible ecotypes were identified (Joanne Weich, MSc dissertation, 2004).

Arabidopsis plants inoculated with Ralstonia solanacearum and controls. L to R: ecotype A (mock-inoculated), ecotype A (no symptoms after inoculation with R. solanacearum), ecotype B (mock-inoculated), ecotype B (highly susceptible (wilted) after inoculation with R. solanacearum).

Detailed genetic, molecular and phenotypic analysis of the pathosystem has revealed an interesting case of gene-for-gene tolerance conferred by an allele of the RRS1 gene in ecotype A, which does not exhibit symptoms but harbours high numbers of the bacterial pathogen (Van der Linden et al, 2013).

Whole genome and custom Arabidopsis microarrays from SSH libraries, constructed at the ACGT Microarray Facility have been used for expression profiling of Arabidopsis plants after infection by the bacterium in a susceptible interaction (Naidoo, et al 2011). Whole genome expression profiling is also underway to explore the tolerant response. This is greatly facilitated by the availability of the Arabidopsis genome sequence and associated bioinformatics resources.

Collaboration:

This research was initiated in collaboration with Dr. Yves Marco (CNRS-INRA, Toulouse, France), and additional collaborators Dr Stephane Genin (CNRS-INRA) and Dr Katherine Denby (University of Warwick, UK) are also involved.

Publications:

Van der Linden L, J Bredenkamp, S Naidoo, J Fouché-Weich, KJ Denby, S Genin, Y Marco, DK Berger (2013) Gene-for-gene tolerance to bacterial wilt in Arabidopsis, Molecular Plant-Microbe Interactions, 26, 398-406
Naidoo S, Fouché-Weich J, Law P, Denby K, Marco Y & Berger DK (2011) A Eucalyptus bacterial wilt isolate from South Africa is pathogenic on Arabidopsis and manipulates host defenses, Forest Pathology 41(2):101-113
Law PJ, Claudel-Renard C, Joubert F, Louw AI, Berger DK (2008) MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters, BMC Genomics 9:105
Naidoo S, Murray SL, Denby KJ & Berger DK (2007). Microarray Analysis of the Arabidopsis thaliana cir1 (constitutively induced resistance 1) mutant reveals candidate defence response genes against Pseudomonas syringae pv tomato DC3000, South African Journal of Botany 73:412-421.
Fouche-Weich J, Poussier S, Trigalet-Demery D, Berger D & Countinho T (2006). Molecular identification of some African strains of Ralstonia solanacearum from Eucalyptus and potato, Journal of General Plant Pathology 72:369-373.
Naidoo S, Denby KJ, Berger DK (2005) Microarray experiments: considerations for experimental design, South African Journal of Science, 101:347-354
Murray SL, Denby KJ, Berger DK and Loake GJ. (2002). Disease Resistance Signalling in Arabidopsis: Applications for the Study of Plant Pathology in South Africa, South African Journal of Science 98:161-165

Workshops & Symposia

Archive

The TPCP / FMG-EPPI Symposium 2026

New Publications

Nadasen TR, Hein I, Berger DK. (2026) Structural phylogenetics identifies conserved effector families and cell death-inducing proteins from Cercospora zeina. Molecular Plant-Microbe Interactions First Look 10.1094/MPMI-05-26-0048-R

Mbamali SKS, Mohlomi N, Van Der Nest MA, Mchunu NP, Permaul K. (2026) Reciprocal Genome Projection Reveals Reference-Conditioned Functional Variation in Clinical Aspergillus Section Nigri Isolates. Pathogens 10.3390/pathogens15090941

Schertler A, Lenzner B, Dullinger S, Moser D, García-Rodríguez A, Krisai-Greilhuber I, Voglmayr H, Bufford JL, Santini A, Ghelardini L, Capinha C, Reino L, Wingfield MJ, Thines M, Talhinhas P, Dawson W, van Kleunen M, Kreft H, Pergl J, Pyšek P, Weigelt P, Winter M, Essl F. (2026) Are novel and co-xenic associations common in alien fungal and fungus-like plants pathogens?. New Phytologist 10.1111/nph.71455

Thango S, Nsibo DL, Berger DK, Visagie CM, Slippers B. (2026) Phenotypic variation in the in vitro and in planta aggressiveness traits among Exserohilum turcicum strains from South Africa. Plant Pathology 75(4):e70257. 10.1111/ppa.70257

Bradshaw MJ, Paul A, Villani S, Bensch K, Mitchell KJ, Pfister DH, Visagie CM, Garfinkel AR, Quesada-Ocampo L, Aime MC, Braun U. (2026) Modern taxonomy as the foundation for identifying and managing fungal and fungus like plant pathogens. Plant Disease 10.1094/PDIS-12-25-2537-FE

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