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

                                                                                            

                                  

                                   

Fungal Diversity inSouthern Africa

South Africa: ~10% of all plant species

200 000 species(excluding insect

associates)

Tree Protection Co-operative ProgrammeThe 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.

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.

Centre for Applied Mycological StudiesThe 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.

Pathogens of exotic treesPathogens of exotic trees

Fungi of native treesFungi of native trees

Fungi of industrial Fungi of industrial importanceimportance

Some of the fungal groups studied at FABI

• Ophiostoma sensu latoOphiostoma sensu lato• Ceratocystis sensu latoCeratocystis sensu lato• BotryosphaeriaceaeBotryosphaeriaceae• CryphonectriaceaeCryphonectriaceae• MycosphaerellaMycosphaerella species  species • ArmillariaArmillaria species species• Gibberella fujikuroiGibberella fujikuroi complex complex

Healthy vs diseased S. cordatum inflorescence

Fungal Diversity of Native TreesExample: Fusarium spp. on Syzygium cordatum flowers

Healthy vs diseased Mangifera indica inflorescence

F. pseudonygamai F. ramigenum F. napiforme

F. sp. NRRL 26793 Striga hermonthica F. sp. 32 F. lactis

F. pseudocircinatum F. nygamai (MP G)

F. thapsinum (MP F) F. denticulatum

F. sp. 212 F. xylarioides

F. phyllophium F. udum

F. sp. NRRL 26064 Sorghum bicolor F. sp. 44

F. acutatum F. sp. NRRL 25221 Zea mays

F. sp. NRRL 26061 S. hermonthica F. sp. 137 F. sp. NRRL 26152 S. hermonthica F. dlamii

F. sp. 180 F. sp. 107

F. sp. NRRL 26756 grass F. sp. NRRL 26757 reed F. sp. NRRL 25346 I. batatas

F. sterilihyphosum F. sp. NRRL 25195

F. sp. NRRL 25807 F. konzum (MP I)

F. bulbicola F. anthophilium

F. succisae F. bactridioides

F. sp. NRRL 29124 Bidens pilosa F. sp. NRRL 29123

F. circinatum (MP H) F. subglutinans (MP E)

F. sp. 25622 Z.mays F. begoniae F. sp. NRRL 25204 F. guttiforme

F. sp. 68 F. sp. 64 F. sp. 106 F. sp. 92 F. sp. 138

F. proliferatum (MP D) F. globosum

F. fujikuroi (MP C) F. sp. 188

F. sp. NRRL 26794 Cymbidium sp F. fractiflexum

F. mangiferae F.sp. NRRL 26427

F. sp. NRRL 25309 T. aestivum F. concentricum F. sp. NRRL 25303 Osativa Japan

F. sp. 21 F. sacchari (MP B)

F. oxysporum F. inflexum

F. sp. 140 F. sp. 136

F. sp. NRRL 25615 Oryza sativa F. verticillioides (MP A)

F. brevicatenulatumF. pseudoanthophilium

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maize

mango

sugar cane

coffee

Pinus species

Begonia species

sweet potato

rice

pineapple

fig

Sansevieria species

maize, sorghum, mango, asparagus

maize

sorghum

pigeon pea

TEFBeta- tubulin

F. pseudonygamai F. ramigenum F. napiforme

F. sp. NRRL 26793 Striga hermonthica F. sp. 32 F. lactis

F. pseudocircinatum F. nygamai (MP G)

F. thapsinum (MP F) F. denticulatum

F. sp. 212 F. xylarioides

F. phyllophium F. udum

F. sp. NRRL 26064 Sorghum bicolor F. sp. 44

F. acutatum F. sp. NRRL 25221 Zea mays

F. sp. NRRL 26061 S. hermonthica F. sp. 137 F. sp. NRRL 26152 S. hermonthica F. dlamii

F. sp. 180 F. sp. 107

F. sp. NRRL 26756 grass F. sp. NRRL 26757 reed F. sp. NRRL 25346 I. batatas

F. sterilihyphosum F. sp. NRRL 25195

F. sp. NRRL 25807 F. konzum (MP I)

F. bulbicola F. anthophilium

F. succisae F. bactridioides

F. sp. NRRL 29124 Bidens pilosa F. sp. NRRL 29123

F. circinatum (MP H) F. subglutinans (MP E)

F. sp. 25622 Z.mays F. begoniae F. sp. NRRL 25204 F. guttiforme

F. sp. 68 F. sp. 64 F. sp. 106 F. sp. 92 F. sp. 138

F. proliferatum (MP D) F. globosum

F. fujikuroi (MP C) F. sp. 188

F. sp. NRRL 26794 Cymbidium sp F. fractiflexum

F. mangiferae F.sp. NRRL 26427

F. sp. NRRL 25309 T. aestivum F. concentricum F. sp. NRRL 25303 Osativa Japan

F. sp. 21 F. sacchari (MP B)

F. oxysporum F. inflexum

F. sp. 140 F. sp. 136

F. sp. NRRL 25615 Oryza sativa F. verticillioides (MP A)

F. brevicatenulatumF. pseudoanthophilium

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73/99/1.00

85/89/1.0078/75/0.97

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TEFBeta- tubulin

Fungi of native plants studied at FABI

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

ArmillariaArmillaria BotryosphaeriaceaeBotryosphaeriaceae

CeratocystisCeratocystis ConiothyriumConiothyrium ChrysoportheChrysoporthe CryphonectriaCryphonectria

CylindrocladiumCylindrocladium GanodermaGanoderma FusariumFusarium

GrosmanniaGrosmannia LeptographiumLeptographium

OphiostomaOphiostoma Phoma Phoma speciesspecies

Uredinales Uredinales

Fungal GroupsFungal GroupsPlantsPlants

Native fungi cause disease on introduced hosts

African BotryosphaeriaceaeNative Syzigium species vs non-native Eucalyptus

species

African Chrysoporthe speciesNative Myrtaceae species vs non-native Eucalyptus

and Tibouchina species

African Ceratocystis speciesDiverse native plant species vs non-native Acacia

species

SOUTH AFRICA

Dr. Hugh Glen, SANBI, KZN Herbarium, Durban

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. 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

REST OF THE WORLD

>100 collaborators and co-workers world-wide.

Including North Africa

South America

North America

Europe

Australiasia

CollaboratorsSUB-SAHARA AFRICA

Dr. Percy Chimwamurumbe, Namibian University, Windhoek

Dr. Muimba A Kangolongo, School for Natural Resources, Copperbelt University, Kitwe, Zambia

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

CULTURE COLLECTIONSCAMS

(~1500 fungi)

CMW, FCC, BOT(~25000 fungi)

UP(~300 fungi)

SAPPI(+/- 400 fungi)

CSIR(~5300 fungi)

PREM (ARC)(~8000 fungi)PREM (ARC)(~8000 fungi)

US(~1000 fungi)

MRC(~8000 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)