Faculty of Natural and Agricultural Sciences
School of Biological Sciences
Department of Microbiology and Plant Pathology
Selected Highlights from Research Findings
Pinus radiata is a magnificent native tree of California, USA, where it exists in a few limited populations. Outside its native range this tree has thrived as one of the most successful plantation forest trees in warm temperate climates of the Southern Hemisphere. Vast plantations (>10 million Ha) of this tree in Australia, Chile, New Zealand, South Africa, Spain and elsewhere sustain multi-billion dollar industries that make important contributions to these national economies. The greatest threat to this tree in its native range (in some cases threatening populations with extinction) is the pitch canker disease caused by the fungus, Fusarium circinatum. This fungus causes typical resin-soaked cankers on trunks and lateral branches, killing the branch and eventually the whole tree. In some parts of the world it causes a serious root and root collar disease that devastate pine seedling nurseries. Since its discovery in California some 20 years ago it has spread to all other parts of the world where P. radiata is grown, most likely on seed. In these countries it also affects other Pinus spp., such as P. patula in South Africa. The Tree Protection Co-operative Program (TPCP) discovered F. circinatum in South Africa in 1994 and has since become an international leader in research on this fungus. The TPCP, under the leadership of Prof Mike Wingfield (Director: Forestry and Agricultural Biotechnology Institute), is a 17 year old research cooperative venture between the major forestry companies in South Africa and the University. This program has become the largest program in the world dealing with diseases of forest trees such as F. circinatum. Some significant research contributions of the TPCP to understand and control this pathogen include the development of highly specific molecular detection tools, with which the fungus can be identified in pure culture or directly from the plant material. These tools are essential to identify potentially infected seeds and young plants before they are introduced to new countries or areas and so spread the disease. Molecular identification is also helpful to identify the fungus from potential insect vectors. A recent study for example showed that fungus gnat flies, which live on fungus and root material and were long thought to spread the fungus, are unlikely to be the major vectors. Control strategies therefore need to be directed elsewhere. Such tools rely heavily on an understanding of the phylogenetic relationship of this fungus to other related fungi, which is based on analyses of multiple DNA sequence genealogies in which the group specialises. An important factor to consider for controlling the disease is to understand how it spreads and how diverse it is in a country. The latter has to do with how many individuals have been introduced into an environment, and whether they reproduce sexually or not (the fungus can also reproduce asexually if only one mating type is present). The TPCP has done groundbreaking work to characterise the mating behaviour of the fungus in the lab and has developed molecular markers to determine its influence in the field. It is clear from this work that F. circinatum has been introduced numerous times into South Africa and is reproducing sexually in the country. Unfortunately this complicates control efforts. It is now also clear how the fungus has spread into other areas of the world, informing future quarantine and international control efforts. In nurseries, sanitation and chemical control plays a vital role to suppress the pathogen population. In the field on mature trees this is not viable and the only way to control the disease is through breeding and selection of resistant planting stock. For this reason, and using the knowledge of diversity and virulence of the fungus gained over the years, the TPCP now screens Pine families from commercial breeding operations on a routine basis. This helps to ensure that there will be resistant material in future to sustain this important industry. Most recently detailed analysis of progeny of an inter-specific cross has given the TPCP the opportunity to map the genome of F. circinatum. This molecular map of the genetic organisation of the fungus allows powerful analyses of the molecular machinery that control factors such as virulence and mating in the fungus. This work will form the foundation of a future genome sequencing effort which will give unprecedented opportunities to understand and characterise the factors that make this fungus such a devastating pathogen, and how to overcome it.
Contact person: Prof TA Coutinho.
Many of the most devastating human diseases have originated from mammals that we have been in close and prolonged contact with. Similarly, serious tree diseases often emerge when a pathogen jumps from its natural host to a previously uninfected host. In these cases the new host might lack resistance mechanisms to the new pathogen it is confronted with. Such host jumps might happen when trees are planted for commercial purposes in new areas, or when fungi are accidentally introduced into new areas. Two programmes at the University of Pretoria study the organisms that cause tree diseases, especially as these systems are affected by humans. The Tree Protection Co-operative Programme (TPCP) is a 17 year old cooperative program between the South African forestry companies and the University. This program, under the leadership of Prof. Mike Wingfield (Director: Forestry and Agricultural Biotechnology Institute), is the largest of its kind in the world and focuses on pests and diseases of plantation grown trees. A related program, the DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB), is one of six DST-NRF Centres of Excellence in South Africa and focuses on pests and diseases of native African trees. This program is lead by Prof. Mike Wingfield and Prof. Brenda Wingfield (Department of Genetics). A number of key discoveries in recent years by the TPCP and CTHB groups have revealed that a number of well-known pathogens of exotic commercial trees, that were previously thought to be introduced, are in fact native to South Africa. These fungi have jumped from their native hosts onto the introduced hosts. For example, Chrysoporthe austroafricana causing cankers of Eucalyptus is now known to have probably originated from native Myrtaceae in South Africa. This fungus is a cryptic relative of the South American and Asian fungus C. cubensis, with which it was confused before. Native Myrtaceae, such as Syzygium cordatum (waterberry), are important and widespread in trees in South Africa. A recent study revealed that this tree species harbours eight species of the Botryosphaeriaceae fungal family; one is a new species only found on this host, while the rest also infect exotic commercial forestry and agricultural trees. More than 10 native tree species, including native Acacia spp., have also been found to be the native hosts of Ceratocystis albifundis, a serious pathogen of plantation grown Australian Acacia mearnsii. This pattern of native fungal tree pathogens jumping to exotic hosts is clearly not uncommon. A serious concern is that these pathogens can now be introduced into the native ranges of the specific commercial trees and threaten endemic populations in countries such as Australia. The focus of the CTHB on fungi affecting native tree health is revealing a staggering diversity of fungi. For example, a recent study on the Botryosphaeriaceae on Acacia has increased the number of known species in Africa by 50 % and added a previously unknown genus to this family. Ongoing studies on the Botryosphaeriaceae from other native hosts are revealing similar numbers of undescribed species. Similarly, the numbers of Ceratocystis, Fusarium, Chrysoporthe and other fungi from Acacia, Baobab, Kiaat, Maroela, Terminalia, Waterberry and other trees are revealing both the diverse nature of the unexplored mycota of the region, as well as the extent of potential threats to native and introduced trees alike.
Contact person: Dr ET Steenkamp.
Many of the most devastating human diseases have originated from mammals that we have been in close and prolonged contact with. Similarly, serious tree diseases often emerge when a pathogen jumps from its natural host to a previously uninfected host. In these cases the new host might lack resistance mechanisms to the new pathogen it is confronted with. Such host jumps might happen when trees are planted for commercial purposes in new areas, or when fungi are accidentally introduced into new areas. Two programmes at the University of Pretoria study the organisms that cause tree diseases, especially as these systems are affected by humans. The Tree Protection Co-operative Programme (TPCP) is a 17 year old cooperative program between the South African forestry companies and the University. This program, under the leadership of Prof. Mike Wingfield (Director: Forestry and Agricultural Biotechnology Institute), is the largest of its kind in the world and focuses on pests and diseases of plantation grown trees. A related program, the DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB), is one of six DST-NRF Centres of Excellence in South Africa and focuses on pests and diseases of native African trees. This program is lead by Prof. Mike Wingfield and Prof. Brenda Wingfield (Department of Genetics). A number of key discoveries in recent years by the TPCP and CTHB groups have revealed that a number of well-known pathogens of exotic commercial trees, that were previously thought to be introduced, are in fact native to South Africa. These fungi have jumped from their native hosts onto the introduced hosts. For example, Chrysoporthe austroafricana causing cankers of Eucalyptus is now known to have probably originated from native Myrtaceae in South Africa. This fungus is a cryptic relative of the South American and Asian fungus C. cubensis, with which it was confused before. Native Myrtaceae, such as Syzygium cordatum (waterberry), are important and widespread in trees in South Africa. A recent study revealed that this tree species harbours eight species of the Botryosphaeriaceae fungal family; one is a new species only found on this host, while the rest also infect exotic commercial forestry and agricultural trees. More than 10 native tree species, including native Acacia spp., have also been found to be the native hosts of Ceratocystis albifundis, a serious pathogen of plantation grown Australian Acacia mearnsii. This pattern of native fungal tree pathogens jumping to exotic hosts is clearly not uncommon. A serious concern is that these pathogens can now be introduced into the native ranges of the specific commercial trees and threaten endemic populations in countries such as Australia. The focus of the CTHB on fungi affecting native tree health is revealing a staggering diversity of fungi. For example, a recent study on the Botryosphaeriaceae on Acacia has increased the number of known species in Africa by 50 % and added a previously unknown genus to this family. Ongoing studies on the Botryosphaeriaceae from other native hosts are revealing similar numbers of undescribed species. Similarly, the numbers of Ceratocystis, Fusarium, Chrysoporthe and other fungi from Acacia, Baobab, Kiaat, Maroela, Terminalia, Waterberry and other trees are revealing both the diverse nature of the unexplored mycota of the region, as well as the extent of potential threats to native and introduced trees alike.
Contact person: Dr M Gryzenhout.
Eucalyptus species, hybrids and clones are used extensively in exotic plantations in many parts of the world. The bacterium Pantoea ananatis causes blight and die-back of young trees in South Africa. This pathogen is also associated with diseases of pineapple, tomato, honeydew melons, cantaloupe fruit, onions, rice, sudan grass and maize. The phytobacteriology group which forms part of the Tree Protection Corporate Programme, (FABI) lead by Prof Teresa Coutinho and Prof Fanus Venter are trying to develop a better understanding of this pathogen. One of the most important questions is – what pathogenicity factors does Pantoea possess which allows it to infect its host. This was the primary reason why the genome of Pantoea ananatis was sequenced. Utilizing 454 pyrosequencing locally available at Inqaba Biotech the genome was sequenced. The sequencing data obtained represented 21.5–fold coverage of the genome which is estimated to be 4 650 000 bp long. On the basis of genome comparisons with other Enterobacteriacea the sequence data could preliminarily be grouped into 9 large contigs which are currently being verified by gap close procedures. Initial automated annotation using BAsys has identified more than 5000 genes. Comparisons with the genomes of closely related plant pathogens such as Pectobacterium atrosepticum, Dikeya dadantii and Pantoea stewartii have identified a number of potential pathogenicity factors. Transposon induced mutations are currently screened using a grid approach to identify mutants of the presumptive pathogenicity genes. The impact of these mutants on the virulence of the bacterium will be evaluated using pathogenicity tests. This work is being performed in collaboration with the Scottish Crop Research Institute (Dundee, United Kingdom). The genome sequence will also be used to develop a microarray to assist in identifying the genes involved in the host specificity of certain strains. Comparative genomics with the full genomes of other Enterobacteriacea is also foreseen in an effort to better understand the ecology and epidemiology of this pathogen. The information obtained will form the basis of any strategy used to manage this plant disease.
Contact person: Prof TA Coutinho.
Eucalyptus species, hybrids and clones are used extensively in exotic plantations in many parts of the world. The bacterium Pantoea ananatis causes blight and die-back of young trees in South Africa. This pathogen is also associated with diseases of pineapple, tomato, honeydew melons, cantaloupe fruit, onions, rice, sudan grass and maize. The phytobacteriology group which forms part of the Tree Protection Corporate Programme, (FABI) lead by Prof Teresa Coutinho and Prof Fanus Venter are trying to develop a better understanding of this pathogen. One of the most important questions is – what pathogenicity factors does Pantoea possess which allows it to infect its host. This was the primary reason why the genome of Pantoea ananatis was sequenced. Utilizing 454 pyrosequencing locally available at Inqaba Biotech the genome was sequenced. The sequencing data obtained represented 21.5–fold coverage of the genome which is estimated to be 4 650 000 bp long. On the basis of genome comparisons with other Enterobacteriacea the sequence data could preliminarily be grouped into 9 large contigs which are currently being verified by gap close procedures. Initial automated annotation using BAsys has identified more than 5000 genes. Comparisons with the genomes of closely related plant pathogens such as Pectobacterium atrosepticum, Dikeya dadantii and Pantoea stewartii have identified a number of potential pathogenicity factors. Transposon induced mutations are currently screened using a grid approach to identify mutants of the presumptive pathogenicity genes. The impact of these mutants on the virulence of the bacterium will be evaluated using pathogenicity tests. This work is being performed in collaboration with the Scottish Crop Research Institute (Dundee, United Kingdom). The genome sequence will also be used to develop a microarray to assist in identifying the genes involved in the host specificity of certain strains. Comparative genomics with the full genomes of other Enterobacteriacea is also foreseen in an effort to better understand the ecology and epidemiology of this pathogen. The information obtained will form the basis of any strategy used to manage this plant disease.
Contact person: Prof SN Venter.
Internationally, biological control of plant diseases is a rapidly developing field within agricultural science. Although biocontrol products still comprise a relatively small percentage of all crop protection products, there is a global trend towards the use of non-chemical, environmentally friendly crop protection products in agriculture. The Biological Control Research Program within the Department of Microbiology and Plant Pathology has had some spectacular successes in developing effective biological control agents. One example of successful biological control has been the application of Growth-Promoting Rhizobacteria (GPRB) for control of soil-borne diseases of plants. GPRB are bacteria which occur in the root-zone ( rhizosphere) of plants and can effectively stimulate the growth of plants. Apart from their growth-promoting activity these bacteria are also effective control agents of plant pathogens. In this study root diseases of sorghum and wheat was used as model systems to test GPRB for their efficacy as biocontrol agents. The fungal pathogens Fusarium oxysporum and Pythium ultimum which cause root and crown rot in several crops including sorghum and wheat were used as target pathogens. A large collection of GPRB isolates were obtained from grass species in South Africa as well as sorghum fields in Ethiopia and subsequently tested both in-vitro and in the greenhouse for biological control activity as well as plant-growth promotion. At least 23 isolates displayed significant inhibition of in-vitro mycelial growth of F. oxysporum and also showed significant root colonization ability on sorghum seedlings. These isolates were further tested for their biocontrol ability against F. oxysporum in the greenhouse. A number of isolates showed significant activity and in some instances 100% disease suppression was recorded. The most effective isolates were identified as members of the Genus Bacillus including B. cereus, B. subtilis, B. circulans, B. licheniformis and Chromobacterium violaceum. Subsequently effective biocontrol has also been demonstrated under field conditions. Apart from the disease suppressive action bacterial isolates were also tested for their growth-promoting activity. Some isolates showed dramatic growth-promoting ability, in one instance increasing shoot and root biomass of sorghum by more than 90%. Effective isolates were studied to determine their modes of action. Effective isolates were demonstrated to produce the phytohormone indoleacetic acid and siderophores, and to solubilize tricalcium phosphate. Of the effective isolates identified by means of the API and / or sequencing of the bacterial 16S rDNA genes, 44 % were Bacillus cereus, 19% Chrysoemonas luteola, 13% Serratia marcescens, 13% Sphingomonas paucimobilis and 6% each of Stenotrophomonas maltophila and Brevibacterium laterosporus. The study clearly demonstrated the efficacy of GPRB as biocontrol and plant growth-promoting agents. A number of these bacterial strains are currently being commercialized.
Contact person: Prof N Labuschagne.
Internationally, biological control of plant diseases is a rapidly developing field within agricultural science. Although biocontrol products still comprise a relatively small percentage of all crop protection products, there is a global trend towards the use of non-chemical, environmentally friendly crop protection products in agriculture. The Biological Control Research Program within the Department of Microbiology and Plant Pathology has had some spectacular successes in developing effective biological control agents. One example of successful biological control has been the application of Growth-Promoting Rhizobacteria (GPRB) for control of soil-borne diseases of plants. GPRB are bacteria which occur in the root-zone ( rhizosphere) of plants and can effectively stimulate the growth of plants. Apart from their growth-promoting activity these bacteria are also effective control agents of plant pathogens. In this study root diseases of sorghum and wheat was used as model systems to test GPRB for their efficacy as biocontrol agents. The fungal pathogens Fusarium oxysporum and Pythium ultimum which cause root and crown rot in several crops including sorghum and wheat were used as target pathogens. A large collection of GPRB isolates were obtained from grass species in South Africa as well as sorghum fields in Ethiopia and subsequently tested both in-vitro and in the greenhouse for biological control activity as well as plant-growth promotion. At least 23 isolates displayed significant inhibition of in-vitro mycelial growth of F. oxysporum and also showed significant root colonization ability on sorghum seedlings. These isolates were further tested for their biocontrol ability against F. oxysporum in the greenhouse. A number of isolates showed significant activity and in some instances 100% disease suppression was recorded. The most effective isolates were identified as members of the Genus Bacillus including B. cereus, B. subtilis, B. circulans, B. licheniformis and Chromobacterium violaceum. Subsequently effective biocontrol has also been demonstrated under field conditions. Apart from the disease suppressive action bacterial isolates were also tested for their growth-promoting activity. Some isolates showed dramatic growth-promoting ability, in one instance increasing shoot and root biomass of sorghum by more than 90%. Effective isolates were studied to determine their modes of action. Effective isolates were demonstrated to produce the phytohormone indoleacetic acid and siderophores, and to solubilize tricalcium phosphate. Of the effective isolates identified by means of the API and / or sequencing of the bacterial 16S rDNA genes, 44 % were Bacillus cereus, 19% Chrysoemonas luteola, 13% Serratia marcescens, 13% Sphingomonas paucimobilis and 6% each of Stenotrophomonas maltophila and Brevibacterium laterosporus. The study clearly demonstrated the efficacy of GPRB as biocontrol and plant growth-promoting agents. A number of these bacterial strains are currently being commercialized.
Contact person: Prof L Korsten.
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