FABI News
19 Sep 2023
Amy returns from RAIZ
Amy Collop returned from a recent trip to RAIZ where she gained first-hand experience rearing a potential biological control agent of the Eucalyptus snout beetle.
18 Sep 2023
FABIan presents at the NSSA symposium
Innocent Rakubu, a Ph.D. candidate in FABI attended the NSSA Symposium where he also won an award for his presentation.
15 Sep 2023
FABIans welcome Spring!
ABI welcomed Spring at the Institute's its annual Spring Day tea on 15 September.
15 Sep 2023
Maize disease outreach extends to Kenya
Building on maize disease outreach activities with smallholder farmers in South Africa, two FABIans represented the University of Pretoria in farmer outreach activities in Kenya.
14 Sep 2023
Lydia celebrates 20 years at FABI
FABI celebrated Lydia Twala’s 20 year service anniversary at a gathering of friends and colleagues on 8 September.
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
Robert Mangani, Kpoti M. Gunn, Nicky Creux. (2023) Projecting the effect of climate change on planting date and cultivar choice for South African dryland maize production. Agricultural and Forest Meteorology 341(15):109695.
10.1016/j.agrformet.2023.109695
Tarigan M, Wingfield MJ, Marpaung YMAN, Duran A, Pham NQ. (2023) Quambalaria eucalypti found on Eucalyptus in Indonesia. Forest Pathology :e12829.
10.1111/efp.12829 
Narh Mensah DL , Wingfield BD, Coetzee MPA. (2023) A practical approach to genome assembly and annotation of Basidiomycota using the example of Armillaria. BioTechniques
10.2144/btn-2023-0023
Avontuur JR, Wilken PM, Palmer M, Coetzee MPA, Stępkowski T, Venter SN, Steenkamp ET. (2023) Complex evolutionary history of photosynthesis in Bradyrhizobium. Microbial Genomics 9(9)
10.1099/mgen.0.001105
Anneri Lötter, Tuan A Duong, Julia Candotti, Eshschar Mizrachi, Jill L Wegrzyn, Alexander A Myburg. (2023) Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids. GigaScience 12
10.1093/gigascience/giad064
Balocchi F, Barnes I, Wingfield MJ, Ahumada R, Visagie CM. (2023) New Resinogalea species from Araucaria araucana resin in Chile and reclassification of the genus in the Cryptocaliciomycetidae. IMA Fungus 14
10.1186/s43008-023-00122-9
Claassens R, Venter SN, Beukes CW, Stępkowski T, Chan WY, Steenkamp ET. (2023) Bradyrhizobium xenonodulans sp. nov. isolated from nodules of Australian Acacia species invasive to South Africa. Systematic and Applied Microbiology
10.1016/j.syapm.2023.126452
Johannes Joubert, Benice Sivparsad, Michelle Schroder, Ilaria Germishuizen, Jingyuan Chen, Brett Hurley, Jeremy Allison, Almuth Hammerbacher. (2023) Susceptibility of Eucalyptus trees to defoliation by the Eucalyptus snout beetle, Gonipterus sp. n. 2, is enhanced by high foliar contents of 1,8-cineole, oxalic acid and sucrose and low contents of palmitic and shikimic acid. Plant, Cell & Environment
10.1111/pce.14696
Pham NQ, Wingfield MJ, Marincowitz S, Tanga AA, Tiki KR, Kassie WB, Hurley BP, Germishuizen I, Lawson SA, Healey MA, Wondafrash M. (2023) First report of the wattle rust pathogen, Uromycladium acaciae (Raveneliaceae, Pucciniales) in Ethiopia. Forestry: An International Journal of Forest Research :1–8.
10.1093/forestry/cpad040
Swanepoel S, Visser EA, Shuey SS, Naidoo S. (2023) The In Planta Gene Expression of Austropuccinia psidii in Resistant and Susceptible Eucalyptus grandis. Phytopathology 113(6):1066-1076.
10.1094/PHYTO-07-22-0257-R
Paap T, Marincowitz S, Pham NQ, Roets F, Basson RJ, Wingfield BD, Oberlander K, Wingfield MJ. (2023) A novel species of Microsphaeropsis causing cankers on Rafnia amplexicaulis in South Africa . Fungal Systematics and Evolution 12:73-80.
10.3114/fuse.2023.12.05
Marincowitz S, Pham NQ, Wingfield BD, Roets F, Wingfield MJ. (2023) Microfungi associated with dying Euphorbia mauritanica in South Africa and their relative pathogenicity. Fungal Systematics and Evolution 12:59-71.
10.3114/fuse.2023.12.04
Kooverjee BB, Soma P, van der Nest MA, Scholtz MM, Neser FWC. (2023) Copy Number Variation Discovery in South African Nguni-Sired and Bonsmara-Sired Crossbred Cattle. Animals 13(15):2513.
10.3390/ani13152513
Makunde PT, Joubert JC, Slippers B, Hurley BP, Hammerbacher A. (2023) Leaf surface traits may influence host specificity in psyllids of Eucalyptus, Spondyliaspis cf. plicatuloides (Froggatt) and Glycaspis brimblecombei Moore (Hemiptera: Aphalaridae). Chemoecology 33:83-98.
10.1007/s00049-023-00387-x
Harris MA, Slippers B, Kemler M, Greve M. (2023) Opportunities for diversified usage of metabarcoding data for fungal biogeography through increased metadata quality. Fungal Biology Reviews 46:100329.
10.1016/j.fbr.2023.100329
Franić I, Allan E, Prospero S, ..., Paap T, et al.. (2023) Climate, host and geography shape insect and fungal communities of trees. Scientific Reports 13:1-13.
10.1038/s41598-023-36795-w
Katumanyane A, Slippers B, Wondafrash M, Malan AP, Hurley BP. (2023) Natural infection of white grubs (Coleoptera: Scarabaeidae) with entomopathogenic nematodes in the KwaZulu-Natal province of South Africa. Journal of Helminthology 97
10.1017/S0022149X23000378
Crous P, Pancorbo F, Luangsa-ard J, Larsson E, Esteve-Raventós F, Bishop-Hurley S, Tan Y, Shivas R, Osieck E, Balashov S. (2023) Fungal Planet description sheets: 1478–1549. Persoonia 50:158-310.
10.3767/persoonia.2023.50.05
Crous P, Cowan D, Cruz R, Czachura P, De la Peña-Lastra S, Dovana F, Drury B, Fell J, Flakus A, Fotedar R, Jurjević , Chandranayaka S, Boekhout T, Osieck E, Shivas R, Tan Y, Bishop-Hurley S, Esteve-Raventós F, Larsson E, Luangsa-ard J, Pancorbo F, Balashov S, Baseia I, Kolecka A. (2023) Fungal Planet description sheets: 1478–1549 . Persoonia 50:58 – 310.
10.3767/persoonia.2023.50.05
Nkomo T, Hammerbacher A, Wingfield BD, Bose T. (2023) Fungal Planet description sheets: 1478–1549 (Description of Tulasnella epidendrea). Persoonia - Molecular Phylogeny and Evolution of Fungi 50:290-291.
10.3767/persoonia.2023.50.05
Read DA, Thompson GD, Swanevelder DZH, Pietersen G. (2023) Metaviromic Characterization of Betaflexivirus Populations Associated with a Vitis cultivar Collection in South Africa. Viruses 15(7):1474.
10.3390/v15071474
Li WW, Chen SF, Wingfield MJ, Duong TA. (2023) Calonectria species associated with diseased leaves and soils in southern China Eucalyptus plantations. Phytopathology Research 5(29)
10.1186/s42483-023-00183-z
Roux J, Wingfield MJ, Marincowitz S, Solís M, Phungula S, Pham NQ. (2023) Eucalyptus scab and shoot malformation: a new disease in South Africa caused by a novel species, Elsinoe masingae. Forestry: An International Journal of Forest Research
10.1093/forestry/cpad031
Chepsergon J, Moleleki LN. (2023) “Order from disordered”: Potential role of intrinsically disordered regions in phytopathogenic oomycete intracellular effector proteins. Current Opinion in Plant Biology 75:102402.
10.1016/j.pbi.2023.102402
van der Walt D, Steenkamp ET, Wingfield BD, Wilken PM. (2023) Evidence of Biparental Mitochondrial Inheritance from Self-Fertile Crosses between Closely Related Species of Ceratocystis. Journal of Fungi 9(6):686.
10.3390/jof9060686
Barnes I, Abdul Rauf MR, Fourie A, Japarudin Y, Wingfield MJ. (2023) Ceratocystis manginecans and not C. fimbriata a threat to propagated Acacia spp. in Sabah, Malaysia. Journal of Tropical Forest Science 35:16-26.
10.26525/jtfs2023.35S.SI.16
Lapammu M, Warburton PM, Japarudin Y, Boden D, Wingfield MJ, Brawner JT. (2023) Verification of tolerance to infection by Ceratocystis manginecans in clones of Acacia mangium. Journal of Tropical Forest Science 35:42-50.
10.26525/jtfs2023.35S.SI.42
Wingfield MJ, Wingfield BD, Warburton P, Japarudin Y, Lapammu M, Abdul Rauf MR, Boden D, Barnes I. (2023) Ceratocystis wilt of Acacia mangium in Sabah: Understanding the disease and reducing its impact. Journal of Tropical Forest Science 35:51-66.
10.26525/jtfs2023.35S.SI.51
Chang RL, Wang Y, Liu Y, Wang Y, Li S, Zhao G, Zhang S, Dai M, Zheng X, Bose T, Si H. (2023) Nine new species of black lichenicolous fungi from the genus Cladophialophora (Chaetothyriales) from two different climatic zones of China. Frontiers in Microbiology 14:1191818.
10.3389/fmicb.2023.1191818
Mesanza N, Barnes I, van der Nest A, Raposo R, Berbegal M, Iturritxa E. (2023) Genetic diversity of Lecanosticta acicola in Pinus ecosystems in Northern Spain. Journal of Fungi 9(651)
10.3390/jof9060651