FABI News
26 May 2023
FABI sampling for Phytophthora in Cape riverine ecosystems
FABI researchers recently joined Prof. Jonàs Oliva, visiting from the University of Lleida, to sample a large number of rivers draining Cape province mountains for Phytophthora species.
25 May 2023
Future Professors visit FABI
Professors Brenda Wingfield and Mike Wingfield hosted a recent visit to FABI by members of the Future Professors Programme.
24 May 2023
UP joins the world in celebrating the International Day of Plant Health.
The University of Pretoria joined the rest of the world in celebrating the IDPH on 12 May under the theme: Plant Health Innovation for Food Security.
19 May 2023
A successful 34th Annual Meeting of the TPCP
The TPCP held its 34th Annual Meeting at the Future Africa conference centre, where staff, postdoctoral Fellows and students present their work to industry and government stakeholders as feedback on the work conducted in the past year.
19 May 2023
Professor André Drenth visits FABI
World renown plant pathologist, Prof. André Drenth recently visited FABI to attend various meetings and present a workshop on "how to be an effective scientist".
FABI in a nutshell
Research Features
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.
New Publications
Katumanyane A, Slippers B, Wondafrash M, Malan AP, Hurley BP. (2023) Mechanisms behind differential white grub host susceptibility to entomopathogenic nematodes. Nematology
10.1163/15685411-bja10253
Suzuki H, Marincowitz S, Rodas CA, Wingfield BD, Wingfield MJ. (2023) First report of two Chrysoporthe species, Chrysoporthe doradensis and Chrysoporthe colombiana sp. nov. from Henriettea seemannii pathogenic to Eucalyptus in Colombia. Mycological Progress 22(44)
10.1007/s11557-023-01891-8
Si H, Su Y, Wang Y, Bose T, Chang RL. (2023) The effects of co‑culture on the expression of selected PKS genes in the lichenized fungus Xanthoparmelia taractica. Mycological Progress 22:41.
10.1007/s11557-023-01894-5
Hough B, Steenkamp ET, Wingfield B, Read DA. (2023) Fungal viruses unveiled: A comprehensive review of Mycoviruses. Viruses 15(5):1202.
10.3390/v15051202 
Paap T, Santini A, Rodas CA, Granados GM, Pecori F, Wingfield MJ. (2023) Myrtus communis in Europe threatened by the pandemic and South African strains of the myrtle rust pathogen Austropuccinia psidii (Sphaerophragmiaceae, Pucciniales). NeoBiota 84:41-46.
10.3897/neobiota.84.95823
Liu QL, Wingfield MJ, Duong TA, Wingfield BD. (2023) Leaf blight in a Eucalyptus plantation caused by Calonectria spp. originating from both leaves and soils. Research Square
10.21203/rs.3.rs-2529138/v1
Wilson AM, Wingfield MJ, Wingfield BD. (2023) Structure and number of mating pheromone genes is closely linked to sexual reproductive strategy in Huntiella. BMC Genomics 24:261.
10.1186/s12864-023-09355-9
Pal E, Allison JD, Hurley BP, Slippers B, Fourie G. (2023) Life History Traits of the Pentatomidae (Hemiptera) for the Development of Pest Management Tools. Forests 14(5)
10.3390/ f14050861
Nel WJ, Slippers B, Wingfield MJ, Yilmaz N, Hurley BP. (2023) Efficacy of commercially available Entomopathogenic agents against the Polyphagous Shot Hole Borer in South Africa. Insects 14(4)
10.3390/insects14040361
Jankowiak R, Gumulak N, Bilański P, Solheim H, Tomalak M, Wingfield MJ. (2023) Five new Graphium species from hardwood trees in Poland. Mycologia
10.1080/00275514.2023.2186676
Paap T, Nndanduleni M, Wingfield MJ. (2023) A critically endangered Proteaceae in the Cape Floristic Region threatened by an invasive pathogen. Bothalia 53(1):a6.
10.38201/btha.abc.v53.i1.6
Si H, Wang Y, Liu Y, Li S, Bose T, Chang RL. (2023) Fungal diversity associated with 38 lichen species revealed a new Genus of Endolichenic fungi, Intumescentia gen. nov. (Teratosphaeriaceae). Journal of Fungi 9(4):423.
10.3390/jof9040423
Guignard Q, Johannes Spaethe, Bernard Slippers, Natasa Nikolic, Jeremy D. Allison. (2023) Eye morphology and colour preferences in a semi-field test of the pine pest, Sirex noctilio (Hymenoptera: Siricidae). African Entomology 31
10.17159/2254-8854/2023/a13406
Aylward J, Ngubane NP, Dreyer LL, Oberlander K, Wingfield MJ, Roets F. (2023) Convergent evolution unites the population genetics of Protea-associated ophiostomatoid fungi. Fungal Ecology 63:101242.
10.1016/j.funeco.2023.101242
Tarigan M, Pham NQ, Jami F, Oliveira LSS, Saha MA, Duran A, Wingfield MJ. (2023) Calonectria species diversity on eucalypts in Indonesia. Southern Forests: a Journal of Forest Science
10.2989/20702620.2023.2179441
Aylward J, Roets F, Dreyer LL, Wingfield MJ. (2023) Unseen fungal biodiversity and complex inter-organismal interactions in Protea flower heads. Fungal Biology Reviews 45:100317.
10.1016/j.fbr.2023.100317
Bose T, Hammerbacher A, Jones W, Roux J, Slippers B, Wingfield MJ. (2023) Hybrid vigor in Eucalyptus increases resistance against Phytophthora root rot. Mycological Progress 22:24.
10.1007/s11557-023-01877-6
Migliorini D, Auger-Rozenberg M-A, Battisti A, Brockerhoff E, Eschen R, Fan J-t, Jactel H, Orazio C, Paap T, Prospero S, Ren L, Kenis M, Roques A, Santini A. (2023) Towards a global sentinel plants research strategy to prevent new introductions of non-native pests and pathogens in forests. The experience of HOMED. Research Ideas and Outcomes 9:e96744.
10.3897/rio.9.e96744
Katumanyane A, Slippers B, Wondafrash M, Malan AP, Hurley BP. (2023) Susceptibility of white grubs from forestry and sugarcane plantations in South Africa to entomopathogenic nematodes. BioControl
10.1007/s10526-023-10185-7
Meinecke CD, de Vos L, Yilmaz N, Steenkamp ET, Wingfield MJ, Wingfield BD. (2023) A LAMP assay for rapid detection of th epitch canker pathogen Fusarium circinatum. Plant Disease
10.1094/PDIS-04-22-0972-SR
Raffa KF, Brockerhoff EG, Grégoire JC, Hamelin RC, Liebhold AM, Santini A, Venette RC, Wingfield MJ. (2023) Approaches to forecasting damage by invasive forest insects and pathogens: A cross-assessment. BioScience (biac108)
10.1093/biosci/biac108
Teshome DT, Zharare GE, Ployet R, Naidoo S. (2023) Transcriptional reprogramming during recovery from drought stress in Eucalyptus grandis. Tree Physiology
10.1093/treephys/tpad022
Luki-Marie Scheepers, Jeremy D. Allison, Bernard Slippers, Egmont R. Rohwer, Patrick M. Mc Millan, Jan E. Bello. (2023) Pine Emperor moths from KwaZulu-Natal use the same pheromone component previously isolated from Nudaurelia cytherea (Lepidoptera: Saturniidae) from the Western Cape. African Entomology 31((2023)):1-9.
10.17159/2254-8854/2023/a13231
Mesarich CH, Barnes I, Bradley EL, de la Rosa S, de Wit PJGM, Gou Y, Griffiths SA, Hamelin RC, Joosten MHAJ, Lu M, McCarthy HM, Schol CR, Stergiopoulos I, Tarallo M, Zaccaron AZ, Bradshaw RE. (2023) Beyond the genomes of Fulvia fulva (syn. Cladosporium fulvum) and Dothistroma septosporum: New insights into how these fungal pathogens interact with their host plants. Molecular Plant Pathology 24(5):474-494.
10.1111/mpp.13309
Liang XY, Wang QC, Chen SF. (2023) Phylogeny, Morphology, Distribution, and Pathogenicity of Seven Calonectria Species from Leaf Blighted Eucalyptus in HaiNai Island, China. Plant Disease
https://doi.org/10.1094/PDIS-12-22-2802-RE
Liu Y, Chen SF. (2023) Diversity and Distribution of Calonectria Species in Soils from Eucalyptus urophylla × E. grandis, Pinus massoniana, and Cunninghamia lanceolata Plantations in Four Provinces in Southern China. Journal of Fungi 9(2):198.
10.3390/jof9020198
Makunde PT, Slippers B, Bush SJ, Hurley BP. (2023) Biology of the invasive shell lerp psyllid, Spondyliaspis cf. plicatuloides (Froggatt) (Hemiptera: Aphalaridae). African Entomology 31( e13747)
10.17159/2254-8854/2023/a13747
Eshetu FB, Barnes I, Nahrung FH, Fitza KNE, Meurisse N, Slippers B. (2023) Unexpected diversity in historical biological control programs: Population genetics of the nematode Deladenus siricidicola in Australia and New Zealand. Biological Control 180:105183.
10.1016/j.biocontrol.2023.105183
Morgan SW, Read DA, Burger JT, Pietersen G. (2023) Diversity of viroids infecting grapevines in the South African Vitis germplasm collection. Virus Genes
10.1007/s11262-023-01971-7
Suzuki H, Marincowitz S, Roux J, Wingfield BD, Wingfield MJ. (2023) First report of canker caused by Chrysoporthe austroafricana on the plantation-grown eucalypt Corymbia henryi in South Africa. Forestry :1-9.
10.1093/forestry/cpac054
Bose T, Dovey S, Brachmann A, Witfeld F, Begerow D, Kemler M, Roux J, Slippers B, Vivas M, Wingfield MJ. (2023) Retention of post-harvest residues enhances soil fungal biodiversity in Eucalyptus plantations. Forest Ecology and Management 532:120806.
10.1016/j.foreco.2023.120806
Visagie CM, Yilmaz N. (2023) Along the footpath of Penicillium discovery: Six new species from the Woodville Big Tree Forest Trail. Mycologia 115:87–106.
10.1080/00275514.2022.2135915
Chepsergon J, Lucy N Moleleki. (2023) Rhizosphere bacterial interactions and impact on plant health. Current Opinion in Microbiology 73:102297.
10.1016/j.mib.2023.102297
Dzomba EF, Van der Nest MA, Mthembu JNT, Soma P, Snyman MA, Chimonyo M, Muchadeyi FC. (2023) Selection signature analysis and genome-wide divergence of South African Merino breeds from their founders. Frontiers in Genetics 13:932272.
10.3389/fgene.2022.932272
Kandasamy D, Zaman R, Nakamura Y, Zhao T, Hartmann H, Andersson MN, Hammerbacher A, Gershenzon J. (2023) Conifer-killing bark beetles locate fungal symbionts by detecting volatile fungal metabolites of host tree resin monoterpenes. PLoS biology 21(2):e3001887.
Visagie CM, Boekhout T, Theelen B, Dijksterhuis J, Yilmaz N, Seifert KA. (2023) Da Vinci's yeast: Blastobotrys davincii f.a., sp. nov. Yeast 40:7–31.
10.1002/yea.3816
Tubby K, Adamčikova K, Adamson K, Akiba M, Barnes I, Borón P, Bragança H, Bulgakov T, Burgdorf N, Capretti P, Cech T, Cleary M, Davydenko K, Drenkhan R, Elvira-Recuenco M, Enderle R, Gardner J, Georgieva M, Ghelardini L, Husson C, Iturritxa E, Markovskaja S, Mesanza N, Ogris N, Oskay F, Piškur B, Queloz V, Raitelaityt K, Raposo R, Soukainen M, Strasser L, Vahalík P, Vester M, Mullett MS. (2023) The increasing threat to European forests from the invasive foliar pine pathogen, Lecanosticta acicola. Forest Ecology and Management 536:120847.
10.1016/j.foreco.2023.120847
van der Nest A, Wingfield MJ, Sadiković D, Mullett MS, Marçais B, Queloz V, Adamčíková K, Davydenko K, Barnes I. (2023) Population structure and diversity of the needle pathogen Dothistroma pini suggests human-mediated movement in Europe. Frontiers in Genetics 14(1103331)
10.3389/fgene.2023.1103331
David Read, Bernard Slippers, Emma Steenkamp. (2022) Genomic characterization of a novel potyvirus infecting Barleria repens in South Africa. Archives of Virology
10.1007/s00705-022-05662-w
Francina L. Bopape, Chrizelle W. Beukes, Kopotsa Katlego, Ahmed I. Hassen, Emma T. Steenkamp, Eastonce T. Gwata. (2022) Symbiotic Performance and Characterization of Pigeonpea (Cajanus cajan L. Millsp.) Rhizobia Occurring in South African Soils. Agriculture 13(1):30.
https://doi.org/10.3390/agriculture13010030
Bian C, Takashi H, Houbraken J, Visagie CM, Ban S, Yaguchi T, D'hooge E, Sklenár F, Kusuya Y, Hubka V. (2022) Reducing the number of accepted species in Aspergillus series Nigri. Studies in Mycology 102:95–132.
10.3114/sim.2022.102.03
David Read, Ronel Roberts, Goddy Prinsloo, Genevieve Thompson. (2022) Genomic and phylogenetic characterization of wheat yellows virus, a novel tenuivirus infecting wheat in South Africa. Archives of Virology
10.1007/s00705-022-05649-7
Wanjofu EI, Venter SN, Beukes CW, Steenkamp ET, Gwata ET, Muema EK. (2022) Nodulation and Growth Promotion of Chickpea by Mesorhizobium Isolates from Diverse Sources. MDPI-Microorganisms 10(12):1-16.
Osborn RK, Castro J, Duong TA, Hulcr J, Li Y, Martínez M, Cognato AI. (2022) Symbiotic Fungi Associated With Xyleborine Ambrosia Beetles (Coleoptera: Curculionidae: Scolytinae) and the Imperative of Global Collaboration. Annals of the Entomological Society of America
10.1093/aesa/saac024
Pham NQ, Marincowitz S, Chen SF, Rodas CA, Wingfield MJ. (2022) Soil-borne Calonectria (Hypocreales, Nectriaceae) associated with Eucalyptus plantations in Colombia. MycoKeys 94:17-35.
10.3897/mycokeys.94.96301
Chang J, Duong TA, Schoeman C, Ma X, Roodt D, Barker N, Li Z, Van de Peer V, Mizrachi E. (2022) The Genome of the King Protea, Protea cynaroides. The Plant Journal
10.1111/tpj.16044
Wingfield BD, Berger DK, Coetzee MPA, Duong TA, Martin A, Pham NQ, Van den Berg N, Wilken PM, Arun-Chinnappa KS, Barnes I, Buthelezi S, Dahanayaka BA, Durán A, Engelbrecht J, Feurtey A, Fourie A, Fourie G, Hartley J, Kabwe ENK, Maphosa M, Narh Mensah DL, Nsibo DL, Potgieter L, Poudel B, Stukenbrock EH, Thomas C, Vaghefi N, Welgemoed T, Wingfield MJ. (2022) IMA genome‑F17. 13:19.
10.1186/s43008-022-00104-3
Candotti J, Christie N, Ployet R, Mostert-O’Neill MM, Reynolds SM, Neves LG, Naidoo S, Mizrachi E, Duong TA, Myburg AA. (2022) Haplotype mining panel for genetic dissection and breeding in Eucalyptus. The Plant Journal
10.1111/tpj.16026
Swalarsk Parry BS, Steenkamp ET, Van Wyk S, Santana QC, van der Nest MA, Hammerbacher A, Wingfield BD, De Vos L. (2022) Identification and characterization of a QTL for growth of Fusarium circinatum on pine-based medium. Journal of Fungi 8(11):1214.
10.3390/jof8111214
Sklenář F, Glässnerová K, Jurjević Z, Houbraken J, Samson RA, Visagie CM, Yilmaz N, Gene J, Cano J, Chen AJ, Nováková A, Yaguchi T, Kolařík M, Hubka V. (2022) Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability. Studies in Mycology 102:53–93.
10.3114/sim.2022.102.02