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Take-all in Wheat: PCR Identification of the Pathogen and the Interactions Amongst Potential Biological Control AgentsGenowati, Indira 18 September 2001 (has links)
<i>Gaeumannomyces graminis var. triciti (Ggt)</i>, the causal agent of take-all in wheat, is difficult to detect accurately and rapidly due to its similarity to fungi in the Gaeumannomyces-Phialophora complex. My objectives are to detect the fungus in infested plants and soil, and to predict effective combinations of bacteria as biological control agents. Detection was based on avenacinase-based primers and polymerase chain reaction (PCR) conditions specified by earlier research. PCR conditions were modified to effect detection. The annealing temperature was lowered from 68 to 62°C for plant and soil extracts, and the concentration of Taq polymerase was doubled for soil extracts. The lowest detection limit for plant extraction was with plant grown on 4 g Ggt-infested millet seed per kg soil, and that for soil extraction was 16 <span style="font-family:Symbol">m</span>g of purified Ggt DNA per g soil. Chemical and cultural control methods are currently inadequate. Biological control using bacteria is an alternative. Combinations of several bacterial strains are expected to work better than a single strain, but they may be less effective if bacteria antagonize each other or compete for the same rhizosphere habitat. Antagonism of potential biological control agents were assessed using a Petri plate assay. To estimate possible habitat competition, nutritional profiles of the strains were evaluated using the BIOLOG system. I hypothesized that bacteria not antagonistic to each other and having low coefficients of nutritional similarity would make better biological control combinations. Six bacterial combinations gave better mean root weight in the greenhouse experiment but not in the field. / Master of Science
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Modélisation du développement spatio-temporel des maladies d'origine telluriqueGosme, Marie 29 January 2007 (has links) (PDF)
Les maladies d'origine tellurique sont difficilement contrôlables par la lutte chimique ou variétale et se caractérisent par des processus et des échelles spatio-temporelles différents de ceux des maladies aériennes. En particulier, les modes de dispersion des agents pathogènes du sol permettent l'apparition et le maintien d'une forte structure spatiale de ces maladies, qui se développent souvent sous forme de foyers. Cette agrégation influence à la fois la dynamique temporelle des épidémies et la relation dégâts-dommages, ce qui en fait un élément important du raisonnement des méthodes de lutte. L'objectif de cette thèse est de comprendre et de modéliser le développement spatio-temporel des épidémies d'origine tellurique afin d'en déduire des stratégies de gestion susceptibles de limiter les risques associés, en particulier en agissant sur la structure spatiale de ces maladies. Pour ce faire, deux modèles ont été développés. Le premier, spatialement explicite et assez détaillé biologiquement, a été paramétré en conditions contrôlées dans le cas du piétin-échaudage du blé. Le test de ce modèle à l'aide de données issues du champ montre une bonne précision malgré un biais positif et indique des pistes pour améliorer la valeur prédictive du modèle. Le second modèle, plus simple et plus générique, utilise la théorie de la hiérarchie pour simuler le développement d'épidémies à plusieurs échelles spatiales simultanément. Il permet de tester des hypothèses concernant le fonctionnement des épidémies et les liens entre incidences à différentes échelles, et en particulier l'effet de la structure spatiale du peuplement hôte et de l'inoculum primaire sur la dynamique et l'agrégation de la maladie. Dans le cas du piétin-échaudage, pour lequel nous avons montré l'importance de la structure spatiale de l'inoculum primaire, ces simulations conduisent à préconiser des semis différents en fonction du rang dans la succession culturale.
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Soilborne disease suppressiveness / conduciveness : analysis of microbial community dynamics / by Johannes Hendrikus HabigHabig, Johannes Hendrikus January 2003 (has links)
Take-all is the name given to the disease caused by a soilborne fungus
Gaeumannomyces graminis (Sacc.) von Arx and Olivier var. tritici Walker (Ggt), an
ascomycete of the family Magnaportheaceae (Cook, 2003). This fungus is an
aggressive soil-borne pathogen causing root rot of wheat (primary host), barley and rye
crops (secondary host). The flowering, seedling, and vegetative growth stages can be
affected by the infection of the whole plant, leaves, roots, and stems. Infections of roots
result in losses in crop yield and quality primarily due to a lowering in nutrient uptake.
Take-all is most common in regions where wheat is cultivated without adequate crop
rotation. Crop rotation allows time between the planting dates of susceptible crops,
which causes a decrease in the inoculum potential of soilborne plant pathogens to
levels below an economic threshold by resident antagonistic soil microbial communities.
Soilborne disease suppressiveness is an inherent characteristic of the physical,
chemical, and/or biological structure of a particular soil which might be induced by
agricultural practices and activities such as the cultivation of crops, or the addition of
organisms or nutritional amendments, causing a change in the microfloral environment.
Disturbances of soil ecosystems that impact on the normal functioning of microbial
communities are potentially detrimental to soil formation, energy transfers, nutrient
cycling, and long-term stability. In this regard, an overview of soil properties and
processes indicated that the use of microbiological and biochemical soil properties,
such as microbial biomass, the analysis of microbial functional diversity and microbial
structural diversity by the quantification of community level physiological profiles and
signature lipid biomarkers are useful as indicators of soil ecological stress or restoration
properties because they are more responsive to small changes than physical and
chemical characteristics. In this study, the relationship between physico-chemical
characteristics, and different biological indicators of soil quality of agricultural soils
conducive, suppressive, and neutral with respect to take-all disease of wheat as caused
by the soilborne fungus Gaeumannomyces graminis var. tritici (Ggt), were investigated
using various techniques. The effect of crop rotation on the functional and structural
diversity of soils conducive to take-all disease was also investigated. Through the
integration of quantitative and qualitative biological data as well as the physico-chemical
characteristics of the various soils, the functional and structural diversity of microbial
IV
communities in the soils during different stadia of take-all disease of wheat were
characterised. All results were evaluated statistically and the predominant physical and
chemical characteristics that influenced the microbiological and biochemical properties
of the agricultural soils during different stadia of take-all disease of wheat were identified
using multivariate analyses. Although no significant difference @ > 0.05) could be
observed between the various soils using conventional microbiological enumeration
techniques, the incidence of Gliocladium spp. in suppressive soils was increased.
Significant differences @ < 0.05) were observed between agricultural soils during
different stadia of take-all disease of wheat. Although no clear distinction could be made
between soils suppressive and neutral to take-all disease of wheat, soils suppressive
and conducive to take-all disease of wheat differed substantially in their community level
physiological profiles (CLPPs). Soils suppressive / neutral to take-all disease were
characterised by enhanced utilisation of carboxylic acids, amino acids, and
carbohydrates, while conducive soils were characterised by enhanced utilisation of
carbohydrates. Shifts in the functional diversity of the associated microbial communities
were possibly caused by the presence of Ggt and associated antagonistic fungal and
bacterial populations in the various soils. It was evident that the relationships amongst
the functionality of the microbial communities within the various soils had undergone
changes through the different stages of development of take-all disease of wheat, thus
implying different substrate utilisation capabilities of present soil microbial communities.
Diversity indices were calculated as Shannon's diversity index (H') and substrate
equitability (J) and were overall within the higher diversity range of 3.6 and 0.8,
respectively, indicating the achievement of very high substrate diversity values in the
various soils. A substantial percentage of the carbon sources were utilised, which
contributed to the very high Shannon-Weaver substrate utilisation indices. Obtained
substrate evenness (equitability) (J) indices indicated an existing high functional
diversity. The functional diversity as observed during crop rotation, differed significantly
(p < 0.05) from each other, implying different substrate utilisation capabilities of present
soil microbial communities, which could possibly be ascribed to the excretion of root
exudates by sunflowers and soybeans. Using the Sorenson's index, a clear distinction
could be made between the degrees of substrate utilisation between microbial
populations in soils conducive, suppressive, and neutral to take-all disease of wheat, as
well as during crop rotation. Furthermore, the various soils could also be differentiated
on the basis of the microbial community structure as determined by phospholipid fatty
acid (PLFA) analysis. Soil suppressive to take-all disease of wheat differed significantly
(p < 0.05) from soils conducive, and neutral to take-all disease of wheat, implying a shift
in relationships amongst the structural diversity of microbial communities within the
various soils. A positive association was observed between the microbial phospholipid
fatty acid profiles, and dominant environmental variables of soils conducive,
suppressive, and neutral to take-all disease of wheat. Soils conducive and neutral to
take-all disease of wheat were characterised by high concentrations of manganese, as
well as elevated concentrations of monounsaturated fatty acids, terminally branched
saturated fatty acids, and polyunsaturated fatty acids which were indicative of Gram-negative
bacteria, Gram-positive bacteria and micro eukaryotes (primarily fungi),
respectively. These soils were also characterised by low concentrations of
phosphorous, potassium, percentage organic carbon, and percentage organic nitrogen,
as well as low soil pH. Soil suppressive to take-all disease of wheat was characterised
by the elevated levels of estimated of biomass and elevated concentrations of normal
saturated fatty acids, which is ubiquitous to micro-organisms. The concentration of
normal saturated fatty acids in suppressive soils is indicative of a low structural
diversity. This soil was also characterised by high concentrations of phosphorous,
potassium, percentage organic carbon, and percentage organic nitrogen, as well as
elevated soil pH. The relationship between PLFAs and agricultural soils was
investigated using principal component analysis (PCA), redundancy analysis (RDA) and
discriminant analysis (DA). Soil suppressive to take-all disease of wheat differed
significantly (p < 0.05) from soils conducive, and neutral to take-all disease of wheat,
implying a shift in relationships amongst the structural diversity of microbial communities
within the various soils. A positive association was observed between the microbial
phospholipid fatty acid profiles, and dominant environmental variables of soils
conducive, suppressive, and neutral to take-all disease of wheat. Hierarchical cluster
analysis of the major phospholipid fatty acid groups indicated that the structural diversity
differed significantly between soils conducive, suppressive, and neutral to take-all
disease of wheat caused by Gaeumannomyces graminis var. tritici. The results indicate
that the microbial community functionality as well as the microbial community structure
was significantly influenced by the presence of take-all disease of wheat caused by
Gaeumannomyces graminis var. tritici, and that the characterisation of microbial
functional and structural diversity by analysis of community level physiological profiles
and phospholipid fatty acid analysis, respectively, could be successfully used as an
assessment criteria for the evaluation of agricultural soils conducive, suppressive, and
neutral to take-all disease of wheat, as well as in crop rotation systems. This
methodology might be of significant value in assisting in the management and
evaluation of agricultural soils subject to the prevalence of other soilborne diseases. / Thesis (M.Sc. (Microbiology))--North-West University, Potchefstroom Campus, 2004.
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Soilborne disease suppressiveness / conduciveness : analysis of microbial community dynamics / by Johannes Hendrikus HabigHabig, Johannes Hendrikus January 2003 (has links)
Take-all is the name given to the disease caused by a soilborne fungus
Gaeumannomyces graminis (Sacc.) von Arx and Olivier var. tritici Walker (Ggt), an
ascomycete of the family Magnaportheaceae (Cook, 2003). This fungus is an
aggressive soil-borne pathogen causing root rot of wheat (primary host), barley and rye
crops (secondary host). The flowering, seedling, and vegetative growth stages can be
affected by the infection of the whole plant, leaves, roots, and stems. Infections of roots
result in losses in crop yield and quality primarily due to a lowering in nutrient uptake.
Take-all is most common in regions where wheat is cultivated without adequate crop
rotation. Crop rotation allows time between the planting dates of susceptible crops,
which causes a decrease in the inoculum potential of soilborne plant pathogens to
levels below an economic threshold by resident antagonistic soil microbial communities.
Soilborne disease suppressiveness is an inherent characteristic of the physical,
chemical, and/or biological structure of a particular soil which might be induced by
agricultural practices and activities such as the cultivation of crops, or the addition of
organisms or nutritional amendments, causing a change in the microfloral environment.
Disturbances of soil ecosystems that impact on the normal functioning of microbial
communities are potentially detrimental to soil formation, energy transfers, nutrient
cycling, and long-term stability. In this regard, an overview of soil properties and
processes indicated that the use of microbiological and biochemical soil properties,
such as microbial biomass, the analysis of microbial functional diversity and microbial
structural diversity by the quantification of community level physiological profiles and
signature lipid biomarkers are useful as indicators of soil ecological stress or restoration
properties because they are more responsive to small changes than physical and
chemical characteristics. In this study, the relationship between physico-chemical
characteristics, and different biological indicators of soil quality of agricultural soils
conducive, suppressive, and neutral with respect to take-all disease of wheat as caused
by the soilborne fungus Gaeumannomyces graminis var. tritici (Ggt), were investigated
using various techniques. The effect of crop rotation on the functional and structural
diversity of soils conducive to take-all disease was also investigated. Through the
integration of quantitative and qualitative biological data as well as the physico-chemical
characteristics of the various soils, the functional and structural diversity of microbial
IV
communities in the soils during different stadia of take-all disease of wheat were
characterised. All results were evaluated statistically and the predominant physical and
chemical characteristics that influenced the microbiological and biochemical properties
of the agricultural soils during different stadia of take-all disease of wheat were identified
using multivariate analyses. Although no significant difference @ > 0.05) could be
observed between the various soils using conventional microbiological enumeration
techniques, the incidence of Gliocladium spp. in suppressive soils was increased.
Significant differences @ < 0.05) were observed between agricultural soils during
different stadia of take-all disease of wheat. Although no clear distinction could be made
between soils suppressive and neutral to take-all disease of wheat, soils suppressive
and conducive to take-all disease of wheat differed substantially in their community level
physiological profiles (CLPPs). Soils suppressive / neutral to take-all disease were
characterised by enhanced utilisation of carboxylic acids, amino acids, and
carbohydrates, while conducive soils were characterised by enhanced utilisation of
carbohydrates. Shifts in the functional diversity of the associated microbial communities
were possibly caused by the presence of Ggt and associated antagonistic fungal and
bacterial populations in the various soils. It was evident that the relationships amongst
the functionality of the microbial communities within the various soils had undergone
changes through the different stages of development of take-all disease of wheat, thus
implying different substrate utilisation capabilities of present soil microbial communities.
Diversity indices were calculated as Shannon's diversity index (H') and substrate
equitability (J) and were overall within the higher diversity range of 3.6 and 0.8,
respectively, indicating the achievement of very high substrate diversity values in the
various soils. A substantial percentage of the carbon sources were utilised, which
contributed to the very high Shannon-Weaver substrate utilisation indices. Obtained
substrate evenness (equitability) (J) indices indicated an existing high functional
diversity. The functional diversity as observed during crop rotation, differed significantly
(p < 0.05) from each other, implying different substrate utilisation capabilities of present
soil microbial communities, which could possibly be ascribed to the excretion of root
exudates by sunflowers and soybeans. Using the Sorenson's index, a clear distinction
could be made between the degrees of substrate utilisation between microbial
populations in soils conducive, suppressive, and neutral to take-all disease of wheat, as
well as during crop rotation. Furthermore, the various soils could also be differentiated
on the basis of the microbial community structure as determined by phospholipid fatty
acid (PLFA) analysis. Soil suppressive to take-all disease of wheat differed significantly
(p < 0.05) from soils conducive, and neutral to take-all disease of wheat, implying a shift
in relationships amongst the structural diversity of microbial communities within the
various soils. A positive association was observed between the microbial phospholipid
fatty acid profiles, and dominant environmental variables of soils conducive,
suppressive, and neutral to take-all disease of wheat. Soils conducive and neutral to
take-all disease of wheat were characterised by high concentrations of manganese, as
well as elevated concentrations of monounsaturated fatty acids, terminally branched
saturated fatty acids, and polyunsaturated fatty acids which were indicative of Gram-negative
bacteria, Gram-positive bacteria and micro eukaryotes (primarily fungi),
respectively. These soils were also characterised by low concentrations of
phosphorous, potassium, percentage organic carbon, and percentage organic nitrogen,
as well as low soil pH. Soil suppressive to take-all disease of wheat was characterised
by the elevated levels of estimated of biomass and elevated concentrations of normal
saturated fatty acids, which is ubiquitous to micro-organisms. The concentration of
normal saturated fatty acids in suppressive soils is indicative of a low structural
diversity. This soil was also characterised by high concentrations of phosphorous,
potassium, percentage organic carbon, and percentage organic nitrogen, as well as
elevated soil pH. The relationship between PLFAs and agricultural soils was
investigated using principal component analysis (PCA), redundancy analysis (RDA) and
discriminant analysis (DA). Soil suppressive to take-all disease of wheat differed
significantly (p < 0.05) from soils conducive, and neutral to take-all disease of wheat,
implying a shift in relationships amongst the structural diversity of microbial communities
within the various soils. A positive association was observed between the microbial
phospholipid fatty acid profiles, and dominant environmental variables of soils
conducive, suppressive, and neutral to take-all disease of wheat. Hierarchical cluster
analysis of the major phospholipid fatty acid groups indicated that the structural diversity
differed significantly between soils conducive, suppressive, and neutral to take-all
disease of wheat caused by Gaeumannomyces graminis var. tritici. The results indicate
that the microbial community functionality as well as the microbial community structure
was significantly influenced by the presence of take-all disease of wheat caused by
Gaeumannomyces graminis var. tritici, and that the characterisation of microbial
functional and structural diversity by analysis of community level physiological profiles
and phospholipid fatty acid analysis, respectively, could be successfully used as an
assessment criteria for the evaluation of agricultural soils conducive, suppressive, and
neutral to take-all disease of wheat, as well as in crop rotation systems. This
methodology might be of significant value in assisting in the management and
evaluation of agricultural soils subject to the prevalence of other soilborne diseases. / Thesis (M.Sc. (Microbiology))--North-West University, Potchefstroom Campus, 2004.
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Microbial factors associated with the natural suppression of take-all wheat in New ZealandChng, Soon Fang January 2009 (has links)
Take-all, caused by the soilborne fungus, Gaeumannomyces graminis var. tritici (Ggt), is an important root disease of wheat that can be reduced by take-all decline (TAD) in successive wheat crops, due to general and/or specific suppression. A study of 112 New Zealand wheat soils in 2003 had shown that Ggt DNA concentrations (analysed using real-time PCR) increased with successive years of wheat crops (1-3 y) and generally reflected take-all severity in subsequent crops. However, some wheat soils with high Ggt DNA concentrations had low take-all, suggesting presence of TAD. This study investigated 26 such soils for presence of TAD and possible suppressive mechanisms, and characterised the microorganisms from wheat roots and rhizosphere using polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE). A preliminary pot trial of 29 soils (including three from ryegrass fields) amended with 12.5% w/w Ggt inoculum, screened their suppressiveness against take-all in a growth chamber. Results indicated that the inoculum level was too high to detect the differences between soils and that the environmental conditions used were unsuitable. Comparison between the Ggt DNA concentrations of the same soils collected in 2003 and in 2004 (collected for the pot trial), showed that most soils cropped with 2, 3 and 4 y of successive wheat had reduced Ggt DNA concentrations (by 195-2911 pg g-1 soil), and their disease incidences revealed 11 of the 29 test soils with potential take-all suppressiveness. Further pot trials improved the protocols, such that they were able to differentiate the magnitudes of suppressiveness among the soils. The first of the subsequent trials, using 4% w/w Ggt inoculum level, controlled conditions at 16°C, 80% RH with alternate 12 h light/dark conditions, and watering the plants twice weekly to field capacity (FC), screened 13 soils for their suppressiveness against take-all. The 13 soils consisted of 11 from the preliminary trial, one wheat soil that had been cropped with 9 y of wheat (considered likely to be suppressive), and a conducive ryegrass soil. The results revealed that 10 of these soils were suppressive to take-all. However, in only four of them were the effects related to high levels of microbial/biological involvement in the suppression, which were assessed in an experiment that first sterilised the soils. In a repeat trial using five of the soils H1, H3, M2, P7 (previously cropped with 3, 3, 4 and 9 y successive wheat, respectively) and H15 (previously cropped with 5 y of ryegrass), three of them (H1, H3 and M2) had reduced Ggt DNA concentrations (>1000 pg g-1 soil reductions), and were confirmed to be suppressive to take-all. A pot trial, in which 1% of each soil was transferred into a γ-irradiated base soil amended with 0.1% Ggt inoculum, indicated that soils H1 and H3 (3 y wheat) were specific in their suppressiveness, and M2 (4 y wheat) was general in its suppressiveness. The microbial communities within the rhizosphere and roots of plants grown in the soils, which demonstrated conduciveness, specific or general suppressiveness to take-all, were characterised using PCR-DGGE, and identities of the distinguishing microorganisms (which differentiated the soils) identified by sequence analysis. Results showed similar clusters of microorganisms associated with conducive and suppressive soils, both for specific and general suppression. Further excision, re-amplification, cloning and sequencing of the distinguishing bands showed that some actinomycetes (Streptomyces bingchengensis, Terrabacter sp. and Nocardioides sp.), ascomycetes (Fusarium lateritium and Microdochium bolleyi) and an unidentified fungus, were associated with the suppressive soils (specific and general). Others, such as the proteobacteria (Pseudomonas putida and P. fluorescens), an actinomycete (Nocardioides oleivorans), ascomycete (Gibberella zeae), and basidiomycete (Penicillium allii), were unique in the specific suppressiveness. This indicated commonality of some microorganisms in the take-all suppressive soils, with a selected distinguishing group responsible for specific suppressiveness. General suppressiveness was considered to be due to no specific microorganisms, as seen in soil M2. An attempt to induce TAD by growing successive wheat crops in pots of Ggt-infested soils was unsuccessful with no TAD effects shown, possibly due to variable Ggt DNA concentrations in the soils and addition of nutrients during the experiment. Increasing numbers of Pseudomonas fluorescens CFU in the rhizosphere of plants, during successive wheat crops was independent of the Ggt DNA concentrations and disease incidence, suggesting that increases in P. fluorescens numbers were associated with wheat monoculture. This study has demonstrated that TAD in New Zealand was due to both specific and general suppressiveness, and has identified the distinguishing microorganisms associated with the suppression. Since most of these distinguishing microorganisms are known to show antagonistic activities against Ggt or other soilborne pathogens, they are likely to act as antagonists of Ggt in the field. Future work should focus on validating their effects either individually, or interactively, on Ggt in plate and pot assays and under field conditions.
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