BARCODING CAN PROMOTE MYCOLOGY IN AFRICA

1. BARCODING CAN PROMOTE MYCOLOGY IN AFRICA Marieka Gryzenhout

2. 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)

3. 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)

4. 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)

5. Ecological threats to fungi in Africa • 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, Cantharellusand 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 (Gryzenhout et al., 2010; Ngala & Gryzenhout , 2010; Nourou, 2011)

6. Practical threats to fungi in Africa • 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 (Gryzenhout et al., 2010; Ngala & Gryzenhout , 2010; Nourou, 2011)

7. Practical threats to fungi in Africa • 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 (Gryzenhout et al., 2010; Ngala & Gryzenhout , 2010; Nourou, 2011; MycoAfrica 2010, 2011)

8. 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

9. CapacityMycology in Africa: what is needed • Collection trips

10. CapacityMycology in Africa: what is needed • Processing, preserving and identification

11. 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

12. 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

13. 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?

14. 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

15. How BARCODE OF LIFE can help Pyrosequence data of endophytes. • 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

16. Challenges • 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

17. 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

18. Acknowledgements Dr Joyce Jefwa, Kenya (Kenya) http://www.toyotaoutreach.com/