FABI News
26 Jan 2022
CPHB Interns graduate
FABI celebrated the graduation of nine interns in the FABI Internship in Phytosanitation and Biotechnology programme on 19 January.
25 Jan 2022
First fieldtrip for the Mad Macs in 2022
Four members of the Macadamia Protection Programme (MPP) in FABI, visited farms in the Mpumalanga province during a three day fieldtrip.
17 Jan 2022
Fabian presents a seminar on mycorrhizal diversity at the North Gauteng Orchid society meeting
Dr Tanay Bose present a talk on the "mycorrhizal diversity associated with orchids in South Africa" as part of the NGOS's monthly seminar series.
13 Jan 2022
FABIan presents at Genome Editing session at Science Forum South Africa 2021
Prof. Dave Berger presented in the genome editing session of the recent Science Forum South Africa 2021, where he gave an overview of current research in the field in South Africa.
17 Dec 2021
The National Grain Research Programme elects Board and representatives
The 30th of November marks a momentous day for the NGRP when its founding members from academia, industry and government adopted its constitution and voted in its first Chairperson and two Co-Directors.
FABI in a nutshell
Research Features
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
Muema EK, Steenkamp ET, Venter SN. (2022) Rhizosphere diazotrophs and other bacteria associated with native and encroaching legumes in the succulent Karoo Biome in South Africa. MDPI-Microorganisms 10(216):1-20.
10.3390/microorganisms10020216 
Makwela MC, Hammerbacher A, Coetzee MPA, Wingfield BD, van Ede G, Bose T. (2022) Fungal diversity associated with the mycorrhizosphere soil of Brachycorythis conica subsp. transvaalensis, a critically endangered and endemic terrestrial orchid from South Africa. South African Journal of Botany 00:1-8.
10.1016/j.sajb.2022.01.019
Fourie A, Venter SN, Slippers B, Fourie G. (2022) A detection assay to identify alternative food sources of the two-spotted stink bug, Bathycoelia distincta . Journal of Economic Entomology :1-7.
10.1093/jee/toab256
Chang R-L, Cao W, Wang Y, Li S, Li X, Bose T, Si H-L. (2022) Melanodevriesia, a new genus of endolichenic oleaginous black yeast recovered from the Inner Mongolia Region of China . Fungal Systematics and Evolution 9(1):1-9.
10.3114/fuse.2022.09.01
Mkandawire RI, Yilmaz N, Steenkamp ET, Kvas M, Wingfield MJ, Fourie G. (2022) Diversity of Fusarium species associated with healthy and malformed Syzygium cordatum inflorescences in South Africa.. European Journal of Plant Pathology
10.1007/s10658-021-02447-w
Guignard Q, Allison J, Slippers B. (2022) The evolution of insect visual opsin genes with specific consideration of the influence of ocelli and life history traits. 22(2)
10.1186/s12862-022-01960-8
David A. Read, Genevieve D. Thompson, Nathan Le Cordeur, Dirk Swanevelder, David Read. (2022) Genomic characterization of grapevine viruses N and O: novel vitiviruses from South Africa. Archives of Virology
10.1007/s00705-021-05333-2
Avontuur JR, Palmer M, Beukes CW, Wai YC, Tasiya T, van Zyl E, Coetzee MPA, Stepkowski T, Venter SN, Steenkamp ET. (2022) Bradyrhizobium altum sp. nov., Bradyrhizobium oropedii sp. nov. and Bradyrhizobium acaciae sp. nov. from South Africa show locally restricted and pantropical nodA phylogeographic patterns. Molecular Phylogenetics and Evolution 167
10.1016/j.ympev.2021.107338
Crous PW, Osieck ER;J, Shivas RG;Z, Bañares A;B, Burgess TI, Cabero J;C, Ferreira RJ;F, Ivanova DD;I, Lebeuf R;L, McTaggart AR, Mehrabi-Koushki M;M, Nel WJ, Nguyen TH;N, Reul M;R, Sato T;S, Tonegawa C;T, Visagie CM, C.M.; Vizzini A;V. (2022) Fungal Planet description sheets: 1284-1382. Persoonia - Molecular Phylogeny and Evolution of Fungi 47(6):1284-1382.
10.3767/persoonia.2021.47.06
Guignard Q, Allison JD, Slippers B. (2022) The evolution of insect visual opsin genes with specific consideration of the influence of ocelli and life history traits. 22:2.
10.1186/s12862-022-01960-8
Cano-Lira JF, Badali F, Asselman P, Arenas F, Antonín V, Angelini C, Amaral AGG, Altés A, Alexandrova AV, Akhmetova G, Baghela A, Bañares A, Câmara MPS, Cabero J, Burgress TI, Bukharova NV, Biketova A, Berraf-Tebbal A, Bellanger JM, Baseia IG, Barreto RW, Ageev DV, Abrinbana M, Johnston PR, Bulgakov TS, Balashov S, Dima B, Starink-Willemse M, van Iperen AL, Boers J, Jurjević Z, Osieck ER, Morozova OV, Pinruan U, Abdollahzadeh J, Zhao L, Shivas RG, Moreno G, McMullan-Fisher S, Lebel T, Decock CA, Alvarado P, Sommai S, Crous PW. (2021) Fungal Planet description sheets: 1284-1382. Persoonia 47(29):1284-1382.
10.3767/persoonia.2021.47.06
Dittrich-Schröder G, Garnas JR, Arriagades-Cares D, Ahumada R, Hurley BP, Lawson SA, Slippers B. (2021) Diversity and Introduction History of Glycaspis brimblecombei Reflects a History of Bridgeheads and Distinct Invasions. Frontiers in Forests and Global Change 4:1-11.
10.3389/ffgc.2021.783603
McTaggart AR, James TY, Shivas RG, Drenth A, Wingfield BD, Summerell BA, Duong TA. (2021) Population genomics reveals historical and ongoing recombination in the Fusarium oxysporum species complex. Studies in Mycology 99:100132.
10.1016/j.simyco.2021.100132
Wondafrash M, Slippers B, Asfaw BA, Makowe IA, Jenya H, Bush S, Kayumba I, Nambazimana A, van der Lingen S, Hurley BP. (2021) Tracing the distribution of natural enemies of non-native invasive eucalypt insect pests in sub- Saharan Africa. Southern Forests: a Journal of Forest Science 83(3):1-10.
10.2989/20702620.2021.1960218
Solís M, Wingfield MJ, Hammerbacher A, Naidoo S. (2021) Comparison of the infection biology of Teratosphaeria destructans and Teratosphaeria epicoccoides on Eucalyptus. Plant Disease
10.1094/PDIS-09-21-1877-RE
Abdullahi Yusuf, Ayaovi Agbessenou. (2021) Temperature-dependent modelling and spatial prediction reveal suitable geographical areas for deployment of two Metarhizium anisopliae isolates for Tuta absoluta management. Scientific Reports 11
10.1038/s41598-021-02718-w
Houbraken J, Visagie CM, Frisvad J. (2021) Recommendations To Prevent Taxonomic Misidentification of Genome-Sequenced Fungal Strains. Microbiology Resource Announcements 10:e0107420.
10.1128/MRA.01074-20
Gevers CR, Slippers B, Germishuizen I, Dittrich-Schröder G, Hurley BP. (2021) The distribution and diversity of Leptocybe invasa (Hymenoptera: Eulophidae) and its gall associates in South Africa. Southern Forests
10.2989/20702620.2021.1944395
Tremblay J, Goulet M-C, Vorster J, Goulet C, Michaud M. (2021) Harnessing the functional diversity of plant cystatins to design inhibitor variants highly active against herbivorous arthropod digestive proteases. The FEBS Journal
10.1111/febs.16288
Aylward J, Wingfield MJ, Roets F, Wingfield BD. (2021) A high-quality fungal genome assembly resolved from a sample accidentally contaminated by multiple taxa. BioTechniques 72
10.2144/btn-2021-0097
Vacant positions
One-year internships in Phytosanitation and Biosecurity
The FABI Internship Programme in Phytosanitation and Biosecurity, is designed to expand the depth and breadth of the interns’ previous academic learning in the plant health domain. The Programme draws from the expertise of multiple stakeholders and the training is coordinated with the needs of relevant industries, organizations and government. Our vision is that this Programme prepares interns for careers in the forestry and agricultural sectors. Interns will be trained to provide technical support to improve the updating of outdated import requirements; assist with a higher turnover of completed pest risk information packages and pest risk assessments, as well as to contribute to pest and disease diagnostic and extension, surveillance and biological control programs.
Applications are now open for the appointment of interns, starting 1 February 2022. The closing date for applications is 22 November 2021.
Click here fore more information and how to apply.
Covid-19 portal
