Phytophthora Root Rot

FABI News

News Archive

2 Feb 2026

FABI and the ICFR combine expertise in Ethiopia

In January, three FABIan and colleagues from the ICFR travelled to Ethiopia for a research field trip

29 Jan 2026

Anneri starts the year on a high!

FABI celebrated the first Prestige Seminar of the year

28 Jan 2026

FABI bids the CPHB Interns farewell

The 2025 cohort of interns from the CPHB Internship in Phytosanitation and Biosecurity programme celebrated the completion of their 12-month training programme

27 Jan 2026

A second fungal genome assembly workshop held in FABI

Dr Janneke Alyward and Dr Andi Wilson recently hosted a Genome Assembly Workshop in FABI.

26 Jan 2026

FABI fabulous at the 54<sup>th</sup> Biennial SASPP meeting

FABI fabulous at the 54^th Biennial SASPP meeting

A large group of FABIans participated in the 54^th Biennial congress of the Southern African Society of Plant Pathology (SASPP).

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FABI Events

09 February 08h30

Monday Morning Meeting

FABI in a nutshell

Research Features

Archive

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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Phytophthora root rot (PRR) is the most severe and damaging disease in avocado plantations in South Africa. The causal agent of PRR is the notorious oomycete, Phytophthora cinnamomi (Pc). This pathogen has an extensive host range making it an economically important plant pathogen. The pathogen is a heterothallic species that can reproduce by sexual or asexual means. Furthermore, Pc is hemibiotrophic, meaning it has an initial biotrophic stage prior to switching to the nectrophic stage at later stages of infection. It can persist in soil or infected plant material for extended periods of time, and there is no means to eradicate this oomycete from infected areas once the pathogen has successfully established in soils. Currently, phosphite injections, along with the use of good agricultural practices, are commonly used as methods of control for PRR.

Research within the ARP has provided some insight into the biology, population diversity and the molecular basis for the Pc-avocado interaction. The sequencing of the genome of a South African Pc isolate and the availability of RNA sequencing data from a Pc-avocado infection trial has allowed the group to delve further into understanding how the pathogen is able to manipulate and suppress plant immunity during infection. Current work in the ARP involves identifying and functionally characterising effector genes which are known to play roles during infection. The group is currently on three groups of effectors; the NLPs, RxLRs and Crinklers; and the aim is to determine how these effectors contribute to the pathogenicity of this pathogen and the strategies by which they are able to manipulate or suppress plant immunity to establish infection.

* Read more about Phytophthora cinnamomi on our Fact sheet here.

ARP Team Members

Katelyn Baird: Characterising the role of Phytophthora cinnamomi NLP proteins in plant cell infection.

Ncobile Kunene: Elucidating the role of Phytophthora cinnamomi RxLR effector genes during Persea americana infection.

Kayla Midgley: Characterising the role of Phytophthora cinnamomi CRN effector proteins in host plant cell death.

Susanna Anbu: Expression profiling of Nep-like protein (NLP) effector genes during infection in avocado.

Workshops & Symposia

Archive

The TPCP / FMG-EPPI Symposium 2026

New Publications

Postma A, Klynsmith L, Duong TA, Allison JD, Smidt W, Waterhouse RM, Lesny P, Oeyen JP, Petersen M, Martin S, Liu S, Zhou X, Ziesmann T, Donath A, Mayer C, Misof B, Niehuis O, Peters RS, Podsiadlowski L, Coetzee MPA, Joubert F, Slippers B. (2026) Genome and transcriptome-based identification and expression profiling of chemosensory gene families across developmental stages and tissues in Sirex noctilio (Hymenoptera: Siricidae). Insect Molecular Biology :1-14. 10.1111/imb.70029

Liu QL, Wingfield MJ, Duong TA, Wingfield BD, Crous PW. (2026) Taxonomy, distribution and dispersal of Calonectria species: Important pathogens of forestry, agricultural and horticultural crops. Current Forestry Reports 12(4) 10.1007/s40725-025-00262-8

Nethononda PD, Hurley BP, Slippers B, Makhura MN. (2026) Smallholder farmers’ knowledge, perception and management of Spodoptera frugiperda (Lepidoptera: Noctuidae) on Zea mays at irrigation schemes in Limpopo province, South Africa. Crop Protection :107457. 10.1016/j.cropro.2025.107457

Botha I, De Canha MN, Oberlander K, Botes J, Lall N, Berger DK. (2025) DNA barcoding and anti-tyrosinase activities of three species-representative populations of the genus Greyia Hook & Harv. South African Journal of Botany 189:55-67. 10.1016/j.sajb.2025.11.035

Thomas C, Wilken PM, Coetzee MPA, Visagie CM. (2025) Advancing the taxonomy of Sclerotinia (Helotiales, Sclerotiniaceae): a review and recommendations for an important plant-pathogenic genus. IMA Fungus 17:e175737. 10.3897/imafungus.17.175737

Townsend G, Hill M, Hurley BP, Nel WJ, Crous C, Roets F. (2025) First report of the ambrosia beetle, Amasa parviseta (Curculiondae: Scolytinae), in South Africa. African Entomology 10.17159/2254-8854/2025/a24167

Roux J, del M Angel L, Barnes I. (2025) First report of the eucalypt stem canker pathogen Teratosphaeria gauchensis in South Africa. New Disease Reports 52(2):e70091. 10.1002/ndr2.70091

Nel WJ, Barnes I, Jali S, Impson F, Oberprieler RG, Hurley BP. (2025) First report of Melanterius inconspicuus (Coleoptera: Curculionidae: Cleogonini) from KwaZulu-Natal, South Africa, with observations of its development in black wattle. Southern Forests 10.2989/20702620.2025.2537823

Regasa K, Beze W, Anjulo A, Wondafrash M, Hurley BP, Lawson SA, Healey M, Germishuizen I. (2025) Evaluating fungicides for the management of rust (Uromycladium acaciae) on black wattle nursery seedlings in Awi zone, Amhara regional state, Ethiopia. International Journal of Forestry Research 10.1155/ijfr/5547814

Ramantswana TM, Malatji DP, Pierneef RE, Soma P, Van Der Nest MA, Muchadeyi FC. (2025) Differential gene expression analysis of Dohne Merino sheep naturally infected with Haemonchus contortus. Scientific Reports 15:41843. 10.1038/s41598-025-25782-y

Nadasen T, Buitendag C, Visser R, Welgemoed T, Hein I, Berger DK. (2025) A latent invader: transcriptomics reveals Cercospora zeina’s stealth infection strategy of maize and immune-activating effectors. Frontiers in Plant Science 16:1-23. 10.3389/fpls.2025.1703682

Wilson AM, Wingfield MJ, Duong TA, Wingfield BD. (2025) Thermotolerance and post-fire growth in Rhizina undulata is associated with the expansion of heat stress-related protein families. BMC Genomics 26:1041. 10.1186/s12864-025-11902-5

Fuchs T, Vismer HF, Visagie CM, Wingfield BD, Wingfield MJ. (2025) Low genotypic diversity and first reports of clinical Sporothrix from retrospective samples in South Africa. Medical Mycology 10.1093/mmy/myaf102

Yilmaz N, Verheecke-Vaessen C. (2025) Mycotoxins: An ongoing challenge to food safety and security. PLOS Pathogens 21(11) 10.1371/journal.ppat.1013672

Coelho MA, David-Palma M, Kachalkin AV, Kolařík M, Turchetti B, Sampaio JP, Wingfield MJ, Fisher MC, Yurkov AM, Heitman J. (2025) Genomic and phenotypic insights into the expanding phylogenetic landscape of the Cryptococcus genus. PLOS Genetics 21(11) 10.1371/journal.pgen.1011945

Ramatsitsi NM, Manyevere A, Motloba T. (2025) Myco-ecological warfare with Meloidogyne species. Archives of Agronomy and Soil Science 71(1):1-15. 10.1080/03650340.2025.2579892

Shaw PL, Slippers B, Wingfield BD, Laurent B, Penaud B, Wingfield MJ, Crous PW, Bihon W, Duong TA. (2025) Chromosome-level genome assemblies for the latent pine pathogen, Diplodia sapinea, reveal two accessory chromosomes with distinct genomic features and evolutionary dynamics. G3 Genes|Genomes|Genetics :jkaf239. 10.1093/g3journal/jkaf239

Coelho MA, David-Palma M, Marincowitz S, Aylward J, Pham NQ, Yurkov AM, Wingfield BD, Wingfield MJ, Sheng S, Heitman J. (2025) The complex evolution and genomic dynamics of mating-type loci in Cryptococcus and Kwoniella. PLoS Biology 23:e3003417. 10.1371/journal.pbio.3003417

Visagie CM, Houbraken J, Overy DP, Sklenář F, Bensch K, Frisvad JC, Mack J, Perrone G, Samson RA, van Vuuren NI, Yilmaz N, Hubka V. (2025) From chaos to tranquillity: a modern approach to the identification, nomenclature and phylogeny of Aspergillus, Penicillium and other Eurotiales, including an updated accepted species list. Studies in Mycology 112:117–260. 10.3114/sim.2025.112.04

Vincent C, Singh A, Michalczyk GZ, Lane SL, Kaur R, Gill AR, Dziedzic N, De Silva K, Cho A, Cardoso AA, Alade DO, Tejera-Nieves M, Sharkey TD, Schmiege SC, Pelech E, Locke AM, Leisner CP, Teshome DT. (2025) Importance of measuring and reporting environmental conditions across plant science subdisciplines. Plant Physiology 199(2) 10.1093/plphys/kiaf405

Maake MM, Beukes CW, van der Nest MA, Avontuur JR, Muema EK, Stepkowski T, Venter SN, Steenkamp ET. (2025) Argyrolobium legumes from an African centre of endemism associate with novel Bradyrhizobium species harbouring unique sets of symbiosis genes. Molecular Phylogenetics and Evolution 214:108471. 10.1016/j.ympev.2025.108471

Joubert M, van den Berg N, Theron J, Swart V. (2025) Small RNAs derived from avocado sunblotch viroid and their association with bleaching symptoms: implications for pathogenesis in avocado sunblotch disease. Archives of Virology 170(10):205. 10.1007/s00705-025-06360-z

Mavima L, Steenkamp ET, Beukes CW, Palmer M, De Meyer SE, James EK, Venter SN, Coetzee MPA. (2025) Estimated timeline for the evolution of symbiotic nitrogen fixing Paraburkholderia. Molecular Phylogenetics and Evolution 213:108447. 10.1016/j.ympev.2025.108447

Prabhu AS, Naicker P, Duong TA, Govender IS, Engelbrecht J, Backer R, Stoychev SH, van den Berg N. (2025) Phosphite inhibits Phytophthora cinnamomi by downregulating oxidoreductases and disrupting energy metabolism. Frontiers in Microbiology 16:1632726. 10.3389/fmicb.2025.1632726

Pham NQ, Liu FF, Duong TA, Wingfield BD, Chen SF, Wingfield MJ. (2025) Genetic diversity of Calonectria reteaudii isolates from infected Eucalyptus leaves and associated soils indicates a phyllosphere origin of the pathogen. Forest Pathology 55:e70037. 10.1111/efp.70037

Schröder ML, Hurley BP, Wingfield MJ, Slippers B, Garnas JR. (2025) Thermal limitations to the biological control of Gonipterus sp. n. 2 (Coleoptera: Curculionidae) in South African Eucalyptus plantations. Agricultural and Forest Entomology 10.1111/afe.70002

Lynn KMT, Wingfield MJ, Tarigan M, Durán A, Santos SA, Nel WJ, Barnes I. (2025) Investigating bark, ambrosia and nitidulid beetle (Coleoptera: Scolytinae and Nitidulidae) communities and their potential role in the movement of Ceratocystis manginecans in commercial forestry plantations in Riau, Indonesia. Agricultural and Forest Entomology 10.1111/afe.12698

Solís M, Hammerbacher A, Wingfield MJ, Naidoo S. (2025) Transcriptional responses of Eucalyptus to infection by an aggressive leaf blight pathogen reveal the role of host secondary metabolites during pathogen germination. Plant Molecular Biology 115 10.1007/s11103-025-01625-2

Coertze S, Coetzee B, Basson E, de Villiers D, Makhura T, Moster D, Slippers B, Rose LJ, Visagie CM, Read D. (2025) First Report of Clavibacter nebraskensis Causing Goss’s Bacterial Leaf Blight on Maize (Zea mays) in South Africa. Plant Disease 109:1580. 10.1094/PDIS-01-25-0164-PDN

Overy DP, Frisvad JC, Witte TE, Hicks CL, Hermans A, Sproule A, Louis-Seize G, Seifert KA, Yilmaz N, Price J, van Vuuren NI, Visagie CM. (2025) Chemodiversity of Penicillium isolated from alpine and arctic environments, including ten new species. Studies in Mycology 112:75–116. 10.3114/sim.2025.112.03

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FABI News

FABI and the ICFR combine expertise in Ethiopia

Anneri starts the year on a high!

FABI bids the CPHB Interns farewell

A second fungal genome assembly workshop held in FABI

FABI fabulous at the 54th Biennial SASPP meeting

FABI Events

FABI in a nutshell

Research Features

ARP Team Members

Workshops & Symposia

The TPCP / FMG-EPPI Symposium 2026

New Publications

FABI fabulous at the 54^th Biennial SASPP meeting