FABI News
13 Apr 2021
Brett Hurley appointed as ICFR Research Associate
8 Apr 2021
Engaging small holder farmers to use digital disease diagnostic support tools
FABI has partnered with Grain SA and Social Coding to engage smallholder farmers to connect with the Institute’s diagnostic clinic via its digital platform.
6 Apr 2021
FABI bids Fahimeh farewell
A small group of FABIans attended a farewell function for Dr Fahimeh Jami who leaves the Institute after 14 years to join the Agricultural Research Council (ARC).
2 Apr 2021
Discovering biologically-active fungal metabolites from unexplored species
The March guest presenter of the FABI International Seminar Series was the world-renown Prof. Marc Stadler who present on his research activities linked to the discovery of biologically active fungal metabolites from new and hitherto unexplored species.
1 Apr 2021
Partnership to bring big data techniques to Africa’s agriculture and forestry sectors
Advance.io is partnering with Innovation Africa @UP to bring artificial intelligence and big data techniques to the continent’s agricultural and forestry sectors.
FABI in a nutshell
Research Features
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
Lynn KMT, Wingfield MJ, Durán A, Oliveira LSS, de Beer ZW, Barnes I. (2021) Novel Fusarium mutualists of two Euwallacea species infesting Acacia crassicarpa in Indonesia. Mycologia
10.1080/00275514.2021.1875708 
Gwizdala M, Lebre PH, Maggs-Kölling G, Marais E, Cowan DA, Krüger TPJ. (2021) Sub-lithic photosynthesis in hot desert habitats. Environmental Microbiology
10.1111/1462-2920.15505
Sinotte VM, Conlon BH, Seibel E, Schwitalla JW, de Beer ZW, Poulsen M, Bos N. (2021) Female-biased sex allocation and lack of inbreeding avoidance in Cubitermes termites. Ecology and Evolution
10.1002/ece3.7462
Jamison-Daniels SL, Kissling WD, Botha M, Harris MA, Gordon CE, Greve M. (2021) The role of deterministic succession during forest development within a southern African savanna. bioTropica 53(2):466-476.
10.1111/btp.12890
Nel WJ, Wingfield MJ, De Beer ZW, Duong TA. (2021) Ophiostomatalean fungi associated with wood boring beetles in South Africa including two new species. Antonie van Leeuwenhoek
10.1007/s10482-021-01548-0
van der Nest MA, Chávez R, De Vos L, Duong TA, Gil-Durán C, Ferreira MA, Lane FA, Levicán G, Santana QC, Steenkamp ET, Suzuki H, Tello M, Rakoma JR, Vaca I, Valdés N, Wilken PM, Wingfield MJ, Wingfield BD. (2021) Draft genome sequences of Penicillium roqueforti, Fusarium sororula, Chrysoporthe puriensis, and Chalaropsis populi. IMA Fungus 12:5.
10.1186/s43008-021-00055-1
Phasha MM, Wingfield MJ, Wingfield BD, Coetzee MPA, Hallen-Adams H, Fru F, Swalarsk-Parry BS, Yilmaz N, Duong TA, Steenkamp ET. (2021) Ras2 is important for growth and pathogenicity in Fusarium circinatum. 150:103541.
10.1016/j.fgb.2021.103541
De Wit MP, Crookes DJ, Blignaut JN, de Beer ZW, Paap T, Roets F, Van der Merwe C, Richardson DM. (2021) Invasion of the Polyphagous Shot Hole Borer Beetle in South Africa: A preliminary assessment of the economic impacts. Biological Invasions PREPRINT
10.21203/rs.3.rs-220132/v1
Migliorini D, Messal M, Santini A, Ramos AP, Talhinhas P, Wingfield MJ, Burgess T. (2021) Metabarcoding reveals southern hemisphere fungal endophytes within wood of cultivated Proteaceae in Portugal. European Journal of Plant Pathology
10.1007/s10658-021-02233-8
Balocchi F, Wingfield MJ, Ahumada R, Barnes I. (2021) Pewenomyces kutranfy gen nov. et sp. nov. causal agent of an important canker disease on Araucaria araucana in Chile. Plant Pathology
10.1111/ppa.13353
Mullett MS, Drenkhan R, Adamson K, Boroń P, Lenart-Boroń A, Barnes I, Tomšovský M, Jánošíková Z, Adamčíková K, Ondrušková E, Queloz V, Piškur B, Musolin DL, Davydenko K, Georgieva M, Schmitz S, Kačergius A, Ghelardini L, Kranjec Orlović J, Müller M, Oskay F, Hauptman T, Halász Á, Markovskaja S, Solheim H, Vuorinen M, Heinzelmann R, Hamelin RC, Konečný A. (2021) Worldwide genetic structure elucidates the Eurasian origin and invasion pathways of Dothistroma septosporum, causal agent of Dothistroma Needle Blight. Journal of Fungi 7:111.
10.3390/jof7020111
van Wyk S, Wingfield B, De Vos L, van der Merwe A, Steenkamp E. (2021) Genome-Wide Analyses of Repeat-Induced Point Mutations in the Ascomycota. Frontiers in Microbiology 11(Article 622368):1-17.
10.3389/fmicb.2020.622368
Nsibo DL, Barnes I, Omondi DO, Dida MM, Berger DK. (2021) Population genetic structure and migration patterns of the maize pathogenic fungus, Cercospora zeina in East and Southern Africa. Fungal Genetics and Biology (103527)
10.1016/j.fgb.2021.103527
Van der Nest M, Hlongwane N, Hadebe K, Chan W, Van der Merwe N, De Vos L, Greyling B, Kooverjee B, Soma P, Dzomba E, Bradfield M, Muchadeyi F. (2021) Breed ancestry, divergence, admixture, and selection patterns of the Simbra crossbreed. Frontiers in Genetics 11:1796.
10.3389/fgene.2020.608650
Pham NQ, Marincowitz S, Solís M, Duong TA, Wingfield BD, Barnes I, Slippers B, Muro Abad JI, Durán A, Wingfield MJ. (2021) Eucalyptus scab and shoot malformation: A new and serious foliar disease of Eucalyptus caused by Elsinoe necatrix sp. nov.. Plant Pathology
10.1111/ppa.13348
Sukhorukov AP, Kushunina M, Reinhardt CF, Bezuidenhout H, Vorster BJ. (2021) First records of Amaranthus palmeri, a new emerging weed in southern Africa with further notes on other poorly known alien amaranths in the continent . BioInvasion Records 10(1):1-9.
10.3391/bir.2021.10.1.01
Fraser S, McTaggart AR, Roux J, Nel J, Potgieter J, Shuey L, Somchat C, Wingfield MJ. (2021) The life cycle and field epidemiology of Uromycladium acaciae (Pucciniales) on Acacia mearnsii in South Africa. Annals of Applied Biology
10.1111/aab.12677
Wu WX, Chen SF. (2021) Species diversity, mating strategy, and pathogenicity of Calonectria species from diseased leaves and soils in the Eucalyptus plantation in southern China. Journal of Fungi 7
10.3390/jof7020073
Soares AM, Toome-Heller M, Smith ME, Sandoval-Denis M, Hyde KD, Larsson K-H, Hansen K, Runnel K, Pärtel K, Wijayawardene NN, Menolli N, Corrales A, Tokarev Y, Davis W, Læssøe T, Gibertoni TB, Maharachchikumbura SSN, Drenkhan R, Reynolds NK, Põldmaa K, Pawlowska J, Liu J-K, Lindahl BD, Clemmensen KE, Kauserud H, Nguyen N, Kjøller R, Bates ST, Baldrian P, Adojaan K, Frøslev TG, Nordén J, Madrid H, Järv H, Baral H-O, Pfister D, Suija A, Vizzini A, Põlme S, Abarenkov K, Henrik Nilsson R. (2021) FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Diversity
10.1007/s13225-020-00466-2
Vacant positions
Postdoctoral position: Utilisation of the Phytophthora cinnamomi-tobacco pathosystem for functional characterisation of avocado defense genes
A position is available for a talented Postdoctoral Fellow to work with Prof. Noëlani van den Berg, who holds the Hans Merensky Chair in Avocado Research. The Fellow will be hosted by the Avocado Research Programme, Forestry and Agricultural Biotechnology Institute (FABI) at the University of Pretoria, South Africa. The Fellow will be expected to construct vectors and perform transient and stable transformation in Nicotiana benthamiana for functional studies of avocado defense genes. Opportunities for academic development, student co-supervision, international conference attendance and engagement with industry stakeholders will be available.
Click here for more information and how to apply.
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