Projects

FABI News

News Archive

26 Apr 2024

Eighteen new mentorship students welcomed in the CPHB-FABI Mentorship Program for 2024

Eighteen undergraduate students have joined the 2024 CPHB-FABI Mentorship Programme.

23 Apr 2024

FABIans attend EPN conference in Spain

FABIans Prof. Brett Hurley and Innocent Rakubu attended a congress in Spain to celebrate a century of the discovery of Steinernema kraussei Steiner.

22 Apr 2024

Congratulations Firehiwot!

FABI congratulates Dr Firehiwot Eshetu on the successful completion of her PhD degree.

19 Apr 2024

FABIans celebrate Jackie Robinson Day

Some 60 FABIans gathered at the University of Pretoria’s LC de Villiers sports campus on the afternoon of 15 April to celebrate Jackie Robinson Day.

19 Apr 2024

Using art as a gateway to systems thinking, biomedical careers and health equity

Dr Jeb Owen presented an interesting and thought-provoking seminar “Using art to scaffold systems thinking and biomedical career pathways in young learners” at FABI’s Monday Morning Meeting.

‹ ›

FABI Events

Monday Morning Meeting

07 May 08h00

TPCP/CPHB Symposium

FABI in a nutshell

Research Features

Archive

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.

‹ ›

ONGOING PROJECTS

NATIONAL MONITORING

National Monitoring and diagnostic services, compilation of official host list & distribution
Team: FABI diagnostic clinic team (FABI, UP), Dr T. Paap, Prof. W. de Beer
Funding: FABI, DEFF

Monitoring in commercial plantations (pines, eucalypts, wattles)
Team: Prof. B. Hurley & Tree Protection Cooperative Programme (TPCP) team (FABI, UP)
Funding: TPCP, FABI

Monitoring in commercial avocado orchards
Team: Prof. Noelani van den Berg & Avocado Research Programme (ARP) team, FABI diagnostic clinic team
Funding: (FABI, UP), Hans Merensky Foundation

Monitoring in commercial macadamia orchards
Team: Dr Gerda Fourie & Macadamia Protection Programme (MPP) (FABI, UP), team, FABI diagnostic clinic team
Funding: Macadamia South Africa NPC (SAMAC)

Monitoring in commercial pecan orchards
Team: Prof. W. de Beer (FABI), H. du Toit, I. Schubach (SAPPA) & FABI diagnostic clinic team
Funding: South African Pecan Producers Association (SAPPA)

Monitoring in botanical gardens countrywide
Team: Drs Mesfin Gossa, T Paap, Prof. M. Wingfield, FABI diagnostic clinic team
Funding: SANBI, FABI, supported by IPSN framework

Development of PSHB surveillance app
Team: Prof. B. Slippers, Mr Roedolph Nieuwenhuis,
Funding: Cropwatch Africa, FABI

REGIONAL MONITORING

Monitoring Tshwane outbreak of PSHB
Team: Shawn Fell, FABI diagnostic clinic team, Prof. W de Beer, Drs T. Paap, M. Gossa
Funding: FABI

Monitoring Tshwane parks & Pretoria National Botanical Garden
Team: Shawn Fell, FABI diagnostic clinic team, Prof. W de Beer, Drs T. Paap, M. Gossa
Funding: FABI

Monitoring in native forests in the greater Durban area
Team: Profs W. de Beer (FABI), F. Roets (US), M. Hill (RU), Garyn Delport
Funding: FABI, DEFF

Monitoring Durban Botanical Gardens & Zimbali Coastal Estate in KZN
Team: Drs Indrani Hazel Govender, Mesfin Gossa, T Paap & DUT students and interns
Funding: FABI, Durban University of Technology, Zimbali Environmental Management Agency

Monitoring the Upper Highway area of eThekwini, KwaZulu-Natal
Team: Andrew Botterill, Dr Kerry Slater (UNISA), Drs Mesfin Gossa, T Paap
Funding: FABI, DEFF, supported by UNISA

Monitoring in native forests in Garden Route & Tsitsikamma
Team: Profs W. de Beer (FABI), F. Roets (US), M. Hill (RU), Garyn Delport
Funding: FABI, DEFF

Monitoring in Southwestern Cape, tree growers, grapevine and & deciduous fruit trees
Team: Prof. F. Roets (US), City of Cape Town
Funding: Vergelegen Estate, City of Cape Town, growers

Monitoring in Kruger National Park
Team: Mr Roedolf Nieuwenhuis (Cropwatch Africa), Profs B. Hurley, W. de Beer, B. Slippers & FABI diagnostic clinic team
Funding: Cropwatch Africa, FABI

NATIONAL STRATEGY

Development of a National Strategy for PSHB
Team: Dr Stuart Christie (4SightFutures)
Funding: DEFF, DALRRD

BIOLOGICAL CONTROL

Project: Exploring potential biocontrol agents for PHSB control
Dr Wilma Nel (FABI, UP, Postdoctoral fellow)
Supervisors: Profs B. Hurley, B. Slippers, W. de Beer, M. Hill
Funding: DEFF, FABI

Project: Impact of PSHB on Native forests in South Africa & exploration in SA forests for biocontrol options & understanding the native landscape for biocontrol release
Garyn Townsend (FABI, Rhodes, PhD student)
Supervisors: Profs B. Hurley, W. de Beer, M. Hill, F. Roets
Funding: DEFF, CTHB, FABI, CBC

Project: Laboratory rearing of PSHB for biocontrol experiments
Shawn Fell (FABI, UP, Technical)
Supervisors: Profs B. Hurley, B. Slippers, W. de Beer,
Funding: DEFF, FABI

GENERAL BIOLOGY OF PSHB IN THE SOUTH AFRICAN CONTEXT

Project: Population genetics, mating type genes & whole genome sequencing of Fusarium euwallaceae in South Africa
Claire Randolph (FABI, UP, MSc student)
Supervisors: Prof. W. de Beer, Prof. I. Barnes, Dr Trudy Paap
Funding: FABI, DEFF

Project: Population study & whole genome sequencing of PHSB in South Africa
Dr Anandi Bierman (US, Postdoctoral fellow)
Supervisors: Profs J. Terblanche, F. Roets, W. de Beer (advisor)
Funding: DSI-NRF Centre of Excellence for Invasion Biology

Project: Whole genome and transcriptome sequencing of PHSB and its Fusarium fungal symbiont in South Africa
Dr Anandi Bierman (US, Postdoctoral fellow)
Supervisors: Profs J. Terblanche, F. Roets, Dr. Heiko Vogel (Max Planck)
Funding: diverse sources including DSI-NRF Centre of Excellence for Invasion Biology NRMP and Max Planck

Project: Thermal performance of the Polyphagous Shot Hole Borer
Madeleine Pienaar (US, MSc student)
Supervisors: Dr. A. Bierman, Profs J. Terblanche and F. Roets
Funding: DSI-NRF Centre of Excellence for Invasion Biology

Project: Assessing Fusarium euwallaceae virulence to hosts: the effect of host phylogeny
Group of Honours students (US, Honours students)
Supervisor: Prof F. Roets
Funding: Stellenbosch University

Project: Understanding the interaction between E. fornicatus & E. xanthopus and their fungal symbionts in South Africa
Dr W. Nel (FABI, Postdoctoral fellow)
Supervisors/collaborators: Prof. W. de Beer, F. Roets, B. Hurley, Drs Trudy Paap, Anandi Bierman
Funding: FABI, DEFF, DSI-NRF Centre of Excellence for Invasion Biology

AGRICULTURAL CROP TREES

Project: Impact of PSHB on Pecan trees in South Africa
Shawn Fell (MSc student, FABI)
Supervisors: Wilhelm de Beer, Brett Hurley
Funding: SAPPA

Project: Testing the impact of F. euwallaceae on deciduous fruit trees & grapevines and developing rapid screening technique
Team: Profs F. Roets and P. Addison (US)
Funding: US, Hortgrow, Winetech

URBAN FORESTS

Project: PSHB in Urbanised Cape Town and surrounds: monitoring, chemical control, and the effect of plant stress
Heather Nependa (US, PhD student)
Supervisors: Profs F. Roets, W. de Beer
Funding: Vergelegen Estate

Project: PSHB at Lourensford estate: chemical control and management strategies
Elise Roberts (US, MSc student)
Supervisor: Prof F. Roets
Funding: Lourensford Estate

Project: PSHB risk assessment and strategy planning for urban areas (Johannesburg & Soweto)
Project team: Profs B. Slippers, W. de Beer, B. Hurley, Dr T. Paap (FABI, UP), Prof. M. Byrne, Dr S. Newete (Wits), Dr S. Christie
Funding: Johannesburg Cityparks, FABI

Project: Remote sensing tools for PSHB risk assessment in urban areas (Johannesburg & Soweto)
Marko Mudede (Wits, PhD student)
Supervisors: Profs M. Byrne, Dr S. Newete
Funding: Wits, Johannesburg Cityparks

Project: Survey of PSHB outbreak on Fagaceae hosts in Durban Botanical Gardens
Students: Three Durban University of Technology students
Supervisors: Dr Mesfin Gossa, Dr T Paap, Indrani Hazel Govender
Funding: FABI, Durban University of Technology

Project: PSHB Assessment at Zimbali Coastal Estate in KZN
Students: Durban University of Technology students & interns
Supervisors: Dr Indrani Hazel Govender
Funding: FABI, Durban University of Technology

Project: An assessment to establish the level of infestation of the alien invasive Polyphagous Shot Hole Borer (Euwallacea fornicatus) beetle in the Upper Highway area of eThekwini, KwaZulu-Natal.
Student: Andrew Botterill
Supervisors: Dr Kerry Slater (UNISA), Drs T Paap, Mesfin Gossa, W. de Beer (FABI)
Funding: FABI, Durban University of Technology

COMPLETED PROJECTS

ECONOMIC ASSESSMENT OF IMPACT OF PSHB

Project: Invasion of the Polyphagous Shot Hole Borer Beetle in South Africa: A preliminary assessment of the economic impacts
Project leader: Prof. D. Richardson
Collaborators: MP De Wit, DJ Crookes, JN Blignaut, ZW de Beer, T Paap, F Roets, C Van der Merwe, DM Richardson.
Funding: CIB, CBC, CTHB, FABI, DEFF

NATURAL FORESTS

Project: Impact of PSHB on Southern & Eastern Cape Native forests
Garyn Townsend (FABI, UP, MSc student)
Supervisors: Profs W. de Beer, M. Hill, F. Roets
Funding: CBC, CTHB, FABI, DEFF

Project: Review of PSHB in South Africa and Impact of PSHB on Southern & Eastern Cape Native forests
Elmar Van Rooyen (US, MSc student)
Supervisors: Prof. F. Roets, W. de Beer, M. Hill
Funding: CTHB, US, FABI, DEFF

AGRICULTURAL CROP TREES

Project: Impact of PHSB on Avocado trees in South Africa
Michael du Toit (FABI, UP, MSc student)
Supervisors: Profs N. van den Berg, W. de Beer, Dr G. Fourie
Funding: Hans Merensky

Project: Survey of PSHB in commercial tree nurseries in Gauteng
Claire Randolph (FABI, UP, Honours student)
Supervisors: Prof. W. de Beer, Dr Trudy Paap
Funding: FABI

Project: Impact of PHSB on macadamia trees in South Africa
Dee Twiddy (FABI, UP, Honours student)
Supervisors: Dr G. Fourie, Profs. N. van den Berg, W. de Beer
Funding: SAMAC

OTHER RELATED PROJECTS

Project: Euwallacea spp. and their fungal mutualists infesting commercial Acacia crassicarpa in Indonesia.
Kira Lynn (FABI, UP, MSc student)
Supervisors: Profs Irene Barnes, M. Wingfield, W. de Beer
Funding: RGE-FABI Tree Health Programme (RGE-FABI THP).

Workshops & Symposia

Archive

The 35<sup>th</sup> Annual Meeting of the Tree Protection Co-operative Programme (TPCP) and DSI-NRF Centre of Excellence in Plant Health Biotechnology (CPHB)

The 35^th Annual Meeting of the Tree Protection Co-operative Programme

New Publications

Marais I, Buitendag C, Duong TA, Crampton BG, Theron J, Kidanemarium D, Berger DK. (2024) Double-stranded RNA uptake for the control of the maize pathogen Cercospora zeina. Plant Pathology Online first:1-11. 10.1111/ppa.13909

van Heerden A, Pham NQ, Wingfield BD, Wingfield MJ, Muro Abad JI, Durán A, Wilken PM. (2024) LAMP assay to detect Elsinoë necatrix; an important Eucalyptus shoot and leaf pathogen. Plant Disease 10.1094/PDIS-01-24-0086-RE

Silva GA, Oliveira MES, Rêgo GMS, Wingfield BD, Wingfield MJ, Ferreira MA. (2024) Chrysoporthe brasiliensis sp. nov. pathogenic to Melastomataceae in southeast Brazil. Fungal Biology 10.1016/j.funbio.2024.04.001

Fick A, Swart V, Bombarely A, van den Berg N. (2024) Comparative transcriptional analysis of Persea americana MYB, WRKY and AP2/ERF transcription factors following Phytophthora cinnamomi infection. Molecular Plant Pathology 25(4):e13453. 10.1111/mpp.13453

Van Lill M, Venter SN, Muema EK, Palmer M., Beukes CW, Chan WY, Steenkamp ET. (2024) SeqCode facilitates naming of South African rhizobia left in limbo. Systematics and Applied Microbiology 47(2-3):126504. 10.1016/j.syapm.2024.126504

5
10
20
30
50
100
Export to RIS