Emma Steenkamp - Consortium for the Barcode of Life

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Feb 20, 2013 (4 years and 3 months ago)

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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 in

Southern Africa

South Africa: ~10%
of all plant species

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
.

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 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
.


Pathogens of exotic trees

Fungi of native trees

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

Healthy
vs

diseased
S. cordatum

inflorescence

Fungal Diversity of Native Trees

Example
:

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. brevicatenulatum

F. pseudoanthophilium

77/86/1.00

90/8100/1.00

99/100/1.00

93/98/1.00

93/100/1.00

85/87/0.96

99/100/1.00

95/96/1.00

85/84/1.00

100/100/1.00

100/100/1.00

99/96/1.00

100/100/1.00

100/100/1.00

95/99/1.00

100/100/1.00

97/97/1.00

65/76/0.95

74/88/0.99

95/95/1.00

97/930.95

97/98/1.00

73/99/1.00

85/89/1.00

78/75/0.97

96/96/1.00

100/100/1.00

99/100/1.00

100/100/1.00

88/92/1.00

100/99/1.00

98/100/1.00

100/100/1.00

100/100/1.00

100/100/1.00

91/96/1.00

maize

mango

sugar cane

coffee

Pinus

species

Begonia

species

sweet potato

rice

pineapple

fig

Sansevieria

species

maize, sorghum, mango, asparagus

maize

sorghum

pigeon pea

TEF

+
䉥瑡
-

瑵t畬楮


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. brevicatenulatum

F. pseudoanthophilium

77/86/1.00

90/8100/1.00

99/100/1.00

93/98/1.00

93/100/1.00

85/87/0.96

99/100/1.00

95/96/1.00

85/84/1.00

100/100/1.00

100/100/1.00

99/96/1.00

100/100/1.00

100/100/1.00

95/99/1.00

100/100/1.00

97/97/1.00

65/76/0.95

74/88/0.99

95/95/1.00

97/930.95

97/98/1.00

73/99/1.00

85/89/1.00

78/75/0.97

96/96/1.00

100/100/1.00

99/100/1.00

100/100/1.00

88/92/1.00

100/99/1.00

98/100/1.00

100/100/1.00

100/100/1.00

100/100/1.00

91/96/1.00

TEF

+
䉥瑡
-

瑵t畬楮

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


Armillaria


Botryosphaeriaceae


Ceratocystis


Coniothyrium


Chrysoporthe


Cryphonectria


Cylindrocladium


Ganoderma


Fusarium


Grosmannia


Leptographium


Ophiostoma


Phoma
species


Uredinales

Fungal Groups

Plants

Native fungi cause disease on introduced hosts

African Botryosphaeriaceae

Native
Syzigium

species
vs

non
-
native
Eucalyptus

species

African
Chrysoporthe

species

Native
Myrtaceae

species
vs

non
-
native
Eucalyptus


and
Tibouchina

species

African
Ceratocystis

species

Diverse 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

Collaborators

SUB
-
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 COLLECTIONS

CAMS

(~1500 fungi)

CMW, FCC, BOT

(~25000 fungi)

UP

(~300 fungi)

SAPPI

(+/
-

400 fungi)

CSIR

(~5300 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)