BARCODING CAN PROMOTE MYCOLOGY IN AFRICA

Marieka Gryzenhout

Mycology in Africa• Unique biomes and wildlife

– Countless UNESCO world heritage sites

• Incredibly diverse– 8 biodiversity hotspots

• Mostly third world with large and growing human populations that threatens and puts great strain on the environment

• Crops are threatened by plant pathogens, and humans and live stocks by several microbes

St Lucia World Heritage Site, South Africa

(Gryzenhout, Roets & De Villiers, 2010)

Mycology in Africa• Millions of species of fungi estimated to exist

– Metagenetics reveal even more

• How many occur in Africa?– Proper inventories and checklists are not existing, although some

countries have some information– In South Africa alone, a survey based on the number of plants, with a

certain number of fungi assigned to each species, estimated c. 200 000 species in South Africa alone (Crous et al. 2006)

• Only 4% has names (Crous et al. 2006)

• Who is working with them?– Very few mycologists

• In South Africa c. 20 mycologists who like systematics but mostly have other responsibilities

• FUNGAL DIVERSITY IN AFRICA VASTLY UNDERSTUDIED AND LIMITED CAPACITY EXISTS

(Abdel-Azeem, 2010; Gryzenhout et al., 2010; Ngala & Gryzenhout, 2010)

Why is it important to look at the fungi?

• Incredibly numerous

• Foundation of any ecosystem

• Contributes to health of plants and animals

• Symbionts and other close assocations

• Impact hugely on the lives of humans (plant pathogens, human pathogens, animal pathogens, mycotoxins, food spoilage, industrial aplications, industrial and commercial problems, useful by-products…)

• Could be useful ecological indicators

• They are endangered too and deserve protection, yet underrepresented in the larger biological community and government circles

Minter (2010)

Ecological threats to fungi in Africa

(Gryzenhout et al., 2010; Ngala & Gryzenhout , 2010; Nourou, 2011)

• Diversity and functionality understudied, impact of human activities unknown and need of conservation ignored

• Encroachment, fragmentation, poor land management, alteration, degradation and transformation – fungi not included

• Invasive microbes

• Indiscriminate spraying of especially non-selective fungicides by farmers, especially subsistence farmers

• Illegal trading and overharvesting of edible mushrooms (Terfezia, Cantharellus and Boletus)

• Loss of habitat due to deforestation:– Especially slash and burn for agricultural land, – Use of trees for firewood and charcoal, timber, tourist

ornaments– Overgrazing – Medicinal plant collection practices (role of pathogens) – Reforestation with exotic tree species

• Climate change

• Threat to indigenous knowledge

• Perceptions and mycophobia

• Poverty

• Land use issues

• More scientific input by mycologists in political issues

• Lack of interest and ignorance in government, conservation and public circles

• Lack of collaborations and little communication of work to others

• Political changes and inner politics of the scientific community

Practical threats to fungi in Africa

(Gryzenhout et al., 2010; Ngala & Gryzenhout , 2010; Nourou, 2011)

• Legislation and permitting, often coupled with corruption

• Still compiling basic checklists of fungi and have huge numbers of undescribed species – lack of capacity

• Funding for collections and herbaria

• Funding from government for private collections lacking

• Funding for basic mycology scarce

• Infrastructure, centres of excellence and training lacking

• Brain drain

Practical threats to fungi in Africa

(Gryzenhout et al., 2010; Ngala & Gryzenhout , 2010; Nourou, 2011; MycoAfrica 2010, 2011)

Needs and resources• Financial

• Infrastructure

• Guidance and support

• Training

• Assistance with identification

• Better sampling, encompassing checklists

• Opportunity

• Filling the fungal gaps

• Engagement and meeting others

CapacityMycology in Africa: what is needed• Collection trips

• Processing, preserving and identification

CapacityMycology in Africa: what is needed

But what is unique, what is exciting• Clean slate

• Untapped and unique biodiversity to be explored

• Untapped and unique applications, various technologies

• Unique indigenous knowledge

• Incredibly talented, diverse and passionate people doing much with little, often at an international level

• Global connections and assistance

• Emerging good will in country constitutions towards biological research

• Fungal conservation• No fungi are on red lists of any country

Creating awareness • Ethnomycology

• SaFungi (www.SaFungi.org) – amateur mycology

• African Mycological Association (www.africanmycology.org) – professional and amateur

• African Workgroup for Fungal Conservation, affiliated to International Society for

Fungal Conservation

• And other initiatives

The possible way forward

• How can we deal with so many fungi, so few mycologists, so many pressures and so few resources?

• How can we get message across to government, conservationists, biodiversity officials and the public that we need to work with these fungi?

• How to promote sustainable projects and stimulate mycological research?

A common goal to enthuse and unite• Explore and document biodiversity in a systematic,

targeted way

• High quality data

• Boost collections and checklists

• Explore potential uses of fungi

• Applications in fields impacting on humans, i.e. plant pathology, mycotoxins, industrial mycology

• New technologies to do large scale ecological studies using metagenetics

Establishing networks or consortia and producing focused research

Xylariales1%

Dothideales1%

Pleosporales3%

Hypocreales6%

Capnodiales 27%

Unknown59%

Other3%

OtherSaccharomycetales 0.01% Phyllachoraceae 0.02% Calosphaeriales 0.04% Diaporthales 0.07% Lecanorales 0.1 %Mitosporic ascomycota 0.4%Eurotiales 0.5%Botryosphaeriales 0.62%Agriales 0.8 &

How BARCODE OF LIFE can help

• Pipelines

• Data management

• Identification of gaps

• Assistance, training and expertise, including understanding of legislature

• Infrastructure and capacity

• Networks, aids collaboration, assist meetings, recruits people, especially on an international level

• Outreach, raising awareness and dissemination

• New technologies

• Quality control

• Leverage and assistance with fund raising

Pyrosequence data of endophytes.

• For a group of fungi that are poorly described in a continent with a large proportion of undiscovered fungi, barcoding has some challenges– First level:

• Most are new species• Assistance is needed even with known species• Difficulty when blasting

– Second level:• Deciding on species limits, % similarity cut-offs and meaning of snp’s• Multiple genes and phylogenetic analyses necessary for proper

identification of known groups• Taxonomic descriptions

• Standardized pipeline and coordination necessary• Solid, high quality foundation necessary is thus needed

Challenges

• Series of carefully planned surveys needed to build library systematically

• Building of a database or library enriched with taxonomic studies will be very useful to aid in identification based on barcoding– Enables local sequence searches– Future collections may expand species with few isolates or

singleton or doubleton species, and more species will improve resolution

– Vouchers exists and quality control

• Use of environmental barcoding to make meaningful impact to study large numbers and diversity of fungi in Africa

Challenges

Acknowledgements

Dr Joyce Jefwa, Kenya (Kenya)

http://www.toyotaoutreach.com/