Fungal Barcoding –
the South African
Perspective
Emma Steenkamp
Forestry and Agricultural Biotechnology Institute (FABI)
Department of Microbiology and Plant Pathology,
University of Pretoria, South Africa
South Africa: ~10%
of all plant species
Fungal Diversity in
Southern Africa
200 000 species
(excluding insect
associates)
Tree Protection Co-operative Programme
The Tree Protection Cooperative Programme (TPCP), a programme of the Forestry and Agricultural Biotechnology Institute
(FABI), represents a cooperative venture between the major players in the South African Forestry Industry and the University
of Pretoria, to deal with tree disease problems. The programme is based on a membership concept where forestry
organisations are members and contribute to a collaborative effort through the payment of annual fees. The University of
Pretoria in turn provides the infrastructure necessary to conduct research into tree pests and diseases, which is
technologically complicated and thus expensive.
Pathogens of exotic trees
DST-NRF Centre of Excellence in Tree Health
Biotechnology
The Centre of Excellence in Tree Health Biotechnology (CTHB) at FABI represents one of six designated Science Centres
supported by the Government Department of Science and Technology (DST) and the National Research Foundation (NRF).
CTHB research concentrates on the health of native trees, particularly those in forests and it has both a national and and
international perspective. A core focus is to provide the highest possible quality of post graduate education in fields such as
plant pathology, entomology, biochemistry, genetics, molecular biology, biotechnology and ecology. The CTHB functions
alongside the Tree Protection Co-operative Programme (TPCP) with the two programmes providing synergy for each other.
Fungi of native trees
Centre for Applied Mycological Studies
The Centre for Applied Mycological Studies (CAMS) was established in 2003 through the collaboration between Council for
Scientific and Industrial Research (CSIR) Biosciences and the University of Pretoria at the Forestry and Agricultural
Biotechnology Institute (FABI). Both these institutions have joined forces in the protection and utilization of South Africa's
fungal biodiversity. CAMS functions as a vehicle to utilize and develop value added products and technologies from the
indigenous mycoflora in South Africa and the rest of the continent. The joint collaboration between FABI and CSIR
Biosciences makes CAMS the ideal means to bring research and development in mycology close to the technological
applications in the industry. CAMS also strives to address the need for developing human resources and popularizing
mycology population in South Africa.
Fungi of industrial
importance
Some of the fungal groups
studied at FABI
• Ophiostoma sensu lato
• Ceratocystis sensu lato
• Botryosphaeriaceae
• Cryphonectriaceae
• Mycosphaerella species
• Armillaria species
• Gibberella fujikuroi complex
Fungal Diversity of Native Trees
Example: Fusarium spp. on Syzygium cordatum flowers
Healthy vs diseased S. cordatum inflorescence
Healthy vs diseased Mangifera indica inflorescence
TEF + Beta- tubulin
90/8100/1.00 F. sp. 140
100/100/1.00
F. sp. 136
85/84/1.00
F. sp. NRRL 25615 Oryza sativa
maize
F. verticillioides (MP A)
F. brevicatenulatum
F. pseudoanthophilium
F. pseudonygamai
99/100/1.00
F. ramigenum
F. napiforme
99/96/1.00
F. sp. NRRL 26793 Striga hermonthica
F. sp. 32
fig
F. lactis
F. pseudocircinatum
F. nygamai (MP G)
sorghum
F. thapsinum (MP F)
F. denticulatum
sweet potato
85/87/0.96
F. sp. 212
93/98/1.00
coffee
F. xylarioides
99/100/1.00
Sansevieria species
F.
phyllophium
77/86/1.00
pigeon pea
F. udum
F. sp. NRRL 26064 Sorghum bicolor
F. sp. 44
F. acutatum
F. sp. NRRL 25221 Zea mays
93/100/1.00 F. sp. NRRL 26061 S. hermonthica
F. sp. 137
100/100/1.00
F. sp. NRRL 26152 S. hermonthica
F. dlamii
F. sp. 180
97/930.95
F. sp. 107
95/95/1.00
F. sp. NRRL 26756 grass
74/88/0.99
F. sp. NRRL 26757 reed
F. sp. NRRL 25346 I. batatas
97/97/1.00
F. sterilihyphosum
F. sp. NRRL 25195
65/76/0.95
F. sp. NRRL 25807
F. konzum (MP I)
F. bulbicola
F. anthophilium
F. succisae
100/100/1.00
F. bactridioides
100/100/1.00
F. sp. NRRL 29124 Bidens pilosa
100/100/1.00
F. sp. NRRL 29123
F. circinatum (MP H) Pinus species
96/96/1.00
F. subglutinans (MP E) maize
F. sp. 25622 Z.mays
F. begoniae
Begonia species
F.
sp.
NRRL 25204
78/75/0.97
F. guttiforme
pineapple
85/89/1.00
F. sp. 68
F.
sp.
64
99/100/1.00
F. sp. 106
F. sp. 92
73/99/1.00
F. sp. 138
F. proliferatum (MP D) maize, sorghum, mango, asparagus
100/100/1.00
F. globosum
97/98/1.00
F. fujikuroi (MP C) rice
F. sp. 188
98/100/1.00 F. sp. NRRL 26794 Cymbidium sp
91/96/1.00
F. fractiflexum
100/99/1.00 F. mangiferae mango
F.sp. NRRL 26427
88/92/1.00
F. sp. NRRL 25309 T. aestivum
100/100/1.00
F. concentricum
95/99/1.00
F. sp. NRRL 25303 Osativa Japan
100/100/1.00
sugar cane
F. sp. 21
F. sacchari (MP B)
100/100/1.00
F. oxysporum
F. inflexum
100/100/1.00
95/96/1.00
TEF + Beta- tubulin
90/8100/1.00 F. sp. 140
100/100/1.00
F. sp. 136
85/84/1.00
F. sp. NRRL 25615 Oryza sativa
F. verticillioides (MP A)
F. brevicatenulatum
F. pseudoanthophilium
F. pseudonygamai
99/100/1.00
F. ramigenum
F. napiforme
99/96/1.00
F. sp. NRRL 26793 Striga hermonthica
F. sp. 32
F. lactis
F. pseudocircinatum
F. nygamai (MP G)
F. thapsinum (MP F)
F. denticulatum
85/87/0.96
F. sp. 212
93/98/1.00
F. xylarioides
99/100/1.00
F. phyllophium
77/86/1.00
F. udum
F. sp. NRRL 26064 Sorghum bicolor
F. sp. 44
F. acutatum
F. sp. NRRL 25221 Zea mays
93/100/1.00 F. sp. NRRL 26061 S. hermonthica
F. sp. 137
100/100/1.00
F. sp. NRRL 26152 S. hermonthica
F. dlamii
F. sp. 180
97/930.95
F. sp. 107
95/95/1.00
F. sp. NRRL 26756 grass
74/88/0.99
F. sp. NRRL 26757 reed
F. sp. NRRL 25346 I. batatas
97/97/1.00
F. sterilihyphosum
F. sp. NRRL 25195
65/76/0.95
F. sp. NRRL 25807
F. konzum (MP I)
F. bulbicola
F. anthophilium
F. succisae
100/100/1.00
F. bactridioides
100/100/1.00
F. sp. NRRL 29124 Bidens pilosa
100/100/1.00
F. sp. NRRL 29123
F. circinatum (MP H)
96/96/1.00
F. subglutinans (MP E)
F. sp. 25622 Z.mays
F. begoniae
F.
sp.
NRRL 25204
78/75/0.97
F. guttiforme
85/89/1.00
F. sp. 68
99/100/1.00 F. sp. 64
F. sp. 106
F. sp. 92
73/99/1.00
F. sp. 138
F. proliferatum (MP D)
100/100/1.00
F. globosum
97/98/1.00
F. fujikuroi (MP C)
F. sp. 188
98/100/1.00 F. sp. NRRL 26794 Cymbidium sp
91/96/1.00
F. fractiflexum
100/99/1.00 F. mangiferae
F.sp. NRRL 26427
88/92/1.00
F. sp. NRRL 25309 T. aestivum
100/100/1.00
F. concentricum
95/99/1.00
F. sp. NRRL 25303 Osativa Japan
100/100/1.00
F. sp. 21
F. sacchari (MP B)
100/100/1.00
F. oxysporum
F. inflexum
100/100/1.00
95/96/1.00
Fungi of native plants
studied at FABI
Plants
Fungal Groups
Acacia karoo
Acacia mellifera
Proteaceae
Adansonia digitata (Baobab)
Pterocarpus angolensis (Kiaat)
Sclerocarya birrea (Marula)
Syzygium species
Terminalia species
Widdringtonia species
Podocarpus species
Aloe species
Cichorium species
Armillaria
Botryosphaeriaceae
Ceratocystis
Coniothyrium
Chrysoporthe
Cryphonectria
Cylindrocladium
Ganoderma
Fusarium
Grosmannia
Leptographium
Ophiostoma
Phoma species
Uredinales
Native fungi cause disease on introduced hosts
African Chrysoporthe species
Native Myrtaceae species vs non-native Eucalyptus
and Tibouchina species
African Botryosphaeriaceae
Native Syzigium species vs non-native Eucalyptus
species
African Ceratocystis species
Diverse native plant species vs non-native Acacia
species
Collaborators
SOUTH AFRICA
SUB-SAHARA AFRICA
Dr. Hugh Glen, SANBI, KZN Herbarium, Durban
Dr. Percy Chimwamurumbe, Namibian University, Windhoek
Dr. Andre Cilliers, 14 Field Road, Lilianton, Boksburg,
Gauteng
Dr. Marieka Schoeman, Institute for Tropical and
Subtropical Crops, Nelspruit
Prof. Steven Chown, University of Stellenbosh
Prof. Coert Geldenhuys, University of Stellenbosch
Dr. Karin Jacobs, University of Stellenbosch
Ms. Thembi Khoza, Science Liaison Officer, Kruger
National Park
Prof. Braam van Wyk, University of Pretoria
Prof. Paulette Bloomer, University of Pretoria
Counsellor Lee, Chinese Consulate in South Africa
Dr. Oliver Preisig, Inqaba biotech, Pretoria
Mr. Leon Visser, Trees Unlimited, Stellenbosch
Prof. Egmont Rohwer, University of Pretoria
Dr. Muimba A Kangolongo, School for Natural Resources,
Copperbelt University, Kitwe, Zambia
Dr. Ben Eisenberg, Dept Statistics, University of Pretoria
Dr. Hester Vismer, PROMEC, Medical Research Council,
Tygerberg
Dr Leanne Dreyer, University of Stellenbosch
Ms Riana Jacobs, Mycology Unit, Biosystematics Division,
PPRI-ARC, Pretoria
Mr. Gerald Meke, Zomba, Malawi
Mr. Fabian Mlambo, Copperbelt University, Kitwe, Zambia,
Dr. Eddie Mwenje, Dept. Applied Biology and Biochemistry,
NUST, Bulawayo Zimbabwe
Mr. H Nemato, Dept. Applied Biology and Biochemistry, NUST,
Bulawayo, Zimbabwe
Dr. Grace Nakabonge, Makerere University, Uganda
Ms Jane Njuguna, Kenai Forestry Research, Nairobi, Kenai
SA Forestry Industries located in SADC countries
REST OF THE WORLD
>100 collaborators and co-workers world-wide.
Including North Africa
South America
North America
Europe
Australiasia
CULTURE COLLECTIONS
CAMS
(~1500 fungi)
CMW, FCC, BOT
(~25000 fungi)
UP
(~300 fungi)
MRC
(~8000 fungi)
CSIR
(~5300 fungi)
SAPPI
(+/- 400 fungi)
PREM (ARC)
(~8000 fungi)
US
(~1000 fungi)
“Given the current importance placed on ecotourism
and the preservation of unique southern African flora
and fauna, it is clearly timely that some thought,
financial resources and research be focused on
preserving the basal links of the ecosystem, which
are the fungi. Clearly, South Africa’s undescribed
fungi represent a vast biological resource which has
yet to be collected, cultured and studied.
Undoubtedly the fungi of southern Africa contain
numerous beneficial biological properties and other
attributes that could be used to greatly improve the
quality of life for all future generations of humanity.”
(Crous et al. 2006)