Identification of the causal agent of Armillaria root rot of Pinus species in South Africa

Tree health in South Africa: Retrospect and prospect

South Africa is a country with very limited natural forest cover. Consequently, the timber and fibre needs of the country cannot be provided for from indigenous forest. It is largely for this reason that South Africa initially developed a highly productive plantation forest industry, which today makes a substantial contribution to the local economy. These plantations are based on non-native species of Eucalyptus, Pinus and Australian Acacia. In the early years of establishment, South African plantations were relatively free of pest and pathogen problems. But, over time, an increasing number of insects, fungi and bacteria have emerged as serious threats to the sustainability of the forestry industry. Numerous native pests and pathogens, especially insects, have adapted to these introduced tree species to cause damage or disease. The problem is compounded by the accidental introduction of non-native pests and pathogens, and this has been at a rapidly increasing rate over the past three decades. Some of these introduced pests and pathogens also threaten the fitness and even the survival of many indigenous South African tree species. Fortunately, South Africa has developed an impressive knowledge base and range of integrated management options to deal with these problems. This development was first driven by government programmes, and in more recent years by public–private partnerships between industry, universities and government. It is clear from the pattern of emergence of pests and pathogens in recent years that South Africa will deal with an increasing number of these problems and a continuously changing tree health environment. This requires robust investment in both quarantine and mitigation mechanisms to protect the country’s biodiversity as well as to ensure the sustainability of its wood and fibre industries.

A first checklist of macrofungi for South Africa

Macrofungi are considered as organisms that form large fruiting bodies above or below the ground that are visible without the aid of a microscope. These fungi include most basidiomycetes and a small number of ascomycetes. Macrofungi have different ecological roles and uses, where some are edible, medicinal, poisonous, decomposers, saprotrophs, predators and pathogens, and they are often used for innovative biotechnological, medicinal and ecological applications. However, comprehensive checklists, and compilations on the diversity and distribution of mushrooms are lacking for South Africa, which makes regulation, conservation and inclusion in national biodiversity initiatives difficult. In this review, we compiled a checklist of macrofungi for the first time (excluding lichens). Data were compiled based on available literature in journals, books and fungorium records from the National Collection of Fungi. Even if the list is not complete due to numerous unreported species present in South Africa, it still represents an overview of the current knowledge of the macromycetes of South Africa. The list of names enables the assessment of gaps in collections and knowledge on the fungal biodiversity of South Africa, and downstream applications such as defining residency status of species. It provides a foundation for new names to be added in future towards developing a list that will be as complete as possible, and that can be used by a wide audience including scientists, authorities and the public.

IMA Genome-F 6: Draft genome sequences of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica and Penicillium freii DAOMC 242723

The genomes of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica, and Penicillium freii DAOMC 242723 are presented in this genome announcement. These six genomes are from plant pathogens and otherwise economically important fungal species. The genome sizes range from 21 Mb in the case of Ceratocystiopsis minuta to 58 Mb for the basidiomycete Armillaria fuscipes. These genomes include the first reports of genomes for the genus Endoconidiophora. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera. In addition these genome sequences through comparative studies with closely related organisms will increase our understanding of how these pathogens cause disease.

Characterization of Armillaria isolates from tea (Camellia sinensis) in Kenya

Armillaria is a primary root rot pathogen of tea (Camellia sinensis) in Kenya. The main species presently described in this country are A. mellea and A. heimii. A survey covering fourteen districts of Kenya was carried out and forty-seven isolates of Armillaria collected. Cultural morphology, rhizomorph characteristics, somatic incompatibility and features of basidiomata were used to characterize the isolates, together with molecular analysis based on randomly amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), restriction fragment length polymorphism (RFLP) of the internal transcribed spacer (ITS) and the intergenic spacer (IGS) regions and sequence of the IGS region. It can be concluded that two Armillaria species were present and they were different from A. mellea. The first group was morphologically similar to A. heimii but this was contradicted by the molecular data, suggesting that A. heimii could be a complex of several species. The second group was different from the first and morphological and molecular data strongly suggest that it could be a new Armillaria species.

Fungal phoenix rising from the ashes?

During May 2010, sporocarps of what appeared to be an Armillaria sp. were found in large clumps in historic Kirstenbosch Botanical Gardens on the foot of Table Mountain, Cape Town, South Africa. These sporocarps could be physically linked to the roots of unidentified dead trees and Protea spp. The aim of this study was to identify the Armillaria sp. found fruiting in Kirstenbosch. To achieve this goal isolates were made from the mycelium under the bark of dead roots linked to sporocarps. The ITS and IGS-1 regions were sequenced and compared to sequences of Armillaria spp. available on GenBank. Cladograms were generated using ITS sequences to determine the phylogenetic relationship of the isolates with other Armillaria spp. Sequence comparisons and phylogenetic analyses showed that the isolates represented A. mellea. They were also identical to isolates of this species previously discovered in the Company Gardens in South Africa and introduced from Europe apparently by the early Dutch Settlers. Armillaria mellea is alien and apparently invasive in Cape Town, fruits profusely and has the potential to spread to sensitive native forests on the foothills of the City.

Molecular characterisation of Armillaria species from Zimbabwe

Armillaria species are amongst the most important pathogens of trees and have a world-wide distribution. In recent years, the taxonomy of Northern Hemisphere Armillaria spp. has been extensively treated, but those occurring in Africa are poorly known. Previously, isolates of Armillaria from Zimbabwe have been grouped based on morphology and biochemical tests. In this study, six isolates representing the three previously characterized groups of Armillaria spp. occurring in Zimbabwe were analysed using DNA-based techniques. Three distinct clusters emerged from both PCR-RFLP and analysis of sequence data for the IGS-1 rRNA operon. The three groups corresponded to those previously identified based on morphology and biochemical tests. Differences in IGS-1 sequences strongly suggest that the Zimbabwean groups represent three distinct taxa. Isolates belonging to Group I, previously assumed to be to A. heimii, were similar to those identified as A. fuscipes from South Africa and La Reunion. Group II isolates resided in a clade apart from all other isolates and appear to represent A. heimii. The remaining isolates residing in Group III clustered with isolates from Zambia and Cameroon. These are different from A. heimii and A. fuscipes and apparently represent an undescribed taxon.