Restoration of resilient plant communities in response to environmental degradation is a critical task, and a changing climate necessitates the introduction of plant communities adapted to anticipated future conditions. Ecotypes of dominant species can affect associated organisms as well as ecosystem function. The extent of ecotypic variation in dominant tallgrass prairie species and the consequences of this variation for ecosystem functioning were studied by manipulating two potential drivers of plant community dynamics: climate and the soil microbial community. Climate was manipulated indirectly through the use of reciprocal restorations across a rainfall gradient where regional sources of dominant grasses Andropogon gerardii and Sorghastrum nutans were seeded with 8 other native species that occur in tallgrass prairie. Four dominant grass sources (originating from central Kansas [CKS], eastern Kansas [EKS], southern Illinois [SIL], or a mixture of these) were reciprocally planted within four sites that occurred across a precipitation gradient in western KS (Colby, KS), CKS (Hays, KS), EKS (Manhattan, KS) and SIL (Carbondale, IL). The three grass sources and mixture of sources were sown into plots according to a randomized complete block design at each sites (n=16, 4 plots / block at each site). Aboveground net primary productivity (ANPP) was measured at the end of the 2010 and 2011 growing season at each site. In 2010, total ANPP declined from western to eastern Kansas, but increased across the geographic gradient in 2011. The dominant grasses did not comprise the majority of community ANPP in WKS, CKS or SIL in either year but did contribute most to total ANPP at the EKS site in 2011. In 2010, volunteer forbs comprised the largest proportion of ANPP in WKS, whereas and in both years planted forbs comprised the largest proportion of ANPP in SIL. Ecotypic variation in ANPP of A. gerardii was not evident, but Sorghastrum nutans ANPP exhibited a site by source effect in 2010 that did not suggest a home site advantage. Variation in the competitive environment at each site may have masked ecotypic variation during community assembly. Further, ANPP responses suggest that grasslands in early stages of establishment may respond more stochastically to climatic variation than established grasslands. Longer term studies will clarify whether ecotypes of dominant prairie grasses affect ecosystem function or community trajectories differently during restoration. Ecotypes of dominant species may support different soil microflora, potentially resulting in plant-soil feedback. A second experiment tested for local adaptation of prairie plant assemblages to their soil microbial community. Native plant assemblages from Kansas and Illinois were tested for local adaptation to their `home' soil by reciprocally crossing soil and plant source in a greenhouse experiment. Seeds and soil were obtained from two remnant prairies, one in eastern Kansas and one in central Illinois, with similar species composition but differing climate. Seeds of four species (Andropogon gerardii, Elymus canadensis, Lespedeza capitata, Oligoneuron rigidum) common to both locations were collected, germinated, and transferred to pots to create 4-species assemblages from each region. Non-prairie (NP) soil from the edge of an Illinois agricultural field was also included as an inoculum treatment to increase relevance to restoration. Kansas and Illinois plant assemblages were subjected to a fully factorial combination of soil inocula [with associated microbial communities] (3 sources: KS, IL, NP) and soil sterilization treatment (sterilized or live). Plants were harvested after 20 weeks and soil was analyzed for microbial composition using phospholipid fatty acid (PLFA) markers. Soil sources had different nutrient concentrations and sterilization resulted in a flush of NH4+, which complicated detection of soil microbial effects. However, plant sources did exhibit variation in productivity responses to soil sources, with Kansas plants more responsive to live soil sources than Illinois plants. Despite confounding variation in soil fertility, soil inoculation was successful at manipulating soil microbial communities, and plant sources responded differently to soil sources. Consideration of feedback between soil and plants may be a missing link in steering restoration trajectories.

Metam sodium is a fumigant often used as a crop pretreatment in agriculture to control a wide array of pests that may inhibit plant yields. Previously, there have only been limited studies conducted on the effects of metam sodium on native soil microbial communities and plant pathogens, and results have been inconsistent. This present study utilized control and metam sodium-treated field plots to examine the effects of metam sodium on soil microbes in terms of numbers, activity, and diversity. Metam sodium did not cause significant changes in culturable heterotrophic numbers, as shown by heterotrophic plate counts, but may have adversely affected non-culturable microbes since metam sodium did affect microbial activity. Specifically, the LuminUltra® and dehydrogenase activity assays both showed a significant decrease in total activity in treated plots one day after soil treatment, with a return to pre-application conditions within seven days. Illumina Next-Generation Sequencing of the 16S rRNA gene showed slight changes in richness and community composition throughout the 28-day study, but initial and final communities were similar in both control and treated soils. Overall, some soil microbes were adversely affected by metam sodium, but the resilience of the soil microbial community allowed for an apparent rapid recovery in terms of numbers, activity, and diversity.

The boreal forest area around Flin Flon, MB, and Creighton, SK, has been the site of a metal mining and smelting complex since the 1930s. Smelter emissions, coupled with forest logging, forest fires, and subsequent soil erosion, have led to severe vegetation dieback and the development of soils containing a mixture of metals in varying concentrations. In affected areas, existing vegetation typically is stunted. Limestone applications to affected soils have served to increase pH and, in some instances, the vegetation has responded positively; however, in some areas limestone application has failed to restore vegetation, leading to an interest in examining the suitability of other soil amendments to affect revegetation in these areas. Typically revegetation programs focus on aboveground vegetation responses; however, healthy plant growth often is dependent on the presence of an equally healthy soil microbial community. Thus, this study attempted to link revegetation success with responses of the soil microbial community structure to various soil amendments. Two studies were conducted to determine the influence of soil amendments (biochar, municipal and manure compost, glauconite, and an arbuscular mycorrhizal/ectomycorrhizal inoculant) on plant growth and microbial community structure in two soils from the Flin Flon area, classified as containing high and low metal concentrations. The two studies evaluated the growth of boreal forest understory species American vetch (Vicia americana) and tufted hairgrass (Deschampsia caespitosa) and overstory species jack pine (Pinus banksiana) and trembling aspen (Populus tremuloides) after addition of soil amendments, and the subsequent effects on microbial community structure. Greenhouse experiments evaluated plant growth for a period of 8 weeks (understory species) or 19 weeks (overstory species), after which plants were analyzed for changes in biomass and metal accumulation in plant tissue. Soils were analyzed for available metal concentrations, as well as microbial biomass carbon and nitrogen, and phospholipid fatty acid concentration, which is a measure of microbial community structure. Significant effects were seen on plant growth and microbial community structure due to the metal concentrations in the soil, but no one amendment consistently impacted plant growth or metal uptake, or any measured microbial parameter. The results of this study indicate the variability of plant growth and microbial functioning in soils from the study site, as well as the inherent challenges associated with revegetating heavy metal affected soils, and underline the need for further research on plant growth and microbial community structure at this site.

This research assessed the seasonal effects of contrasting tillage and crop rotation systems on soil ammonia oxidizing bacteria (AOB) and archaea (AOA). Four different cropping systems under till and no-till were analyzed in a 30 year-old agricultural field trial. Samples were collected during the 2010 growing season at times corresponding with agronomic events. Nucleic acids were preserved in the field and subsequently analyzed by quantitative real-time polymerase chain reactions (qPCR). Tillage decreased AOB activity and abundance in the plow layer (0-15 cm) immediately after fall moldboard plow events, but observed AOB dynamics at other times suggest tillage had a long-term distribution effect across depth (0-30 cm). AOA abundance was significantly greater in no-till plots at all times indicating tillage had longer-term effects on these communities. Crop rotation had minimal effect on AOB and AOA, but there was a noted yield advantage for corn following wheat, regardless of tillage treatment. / OMAFRA Highly Qualified Personnel Program, NSERC

Climate change is likely to alter plant species composition and interactions between plants and soil microbes that together dictate the quantity and quality of forage produced in pastures, the base of animal production in central Kentucky. This study assessed the seasonal dynamics of soil microbes and their response to increased temperature (+3oC) and growing season precipitation (+30% of the mean annual). Total soil microbial biomass, community composition, enzyme activities, potential carbon mineralization, and catabolic responses to selected substrates were measured seasonally in the different climate treatments. In this system, seasonal variability was a dominant driving factor for all the soil microbial characteristics that I investigated. Summer maxima and winter minima were identified in the active microbial biomass, while soil microbial community structure differed between each season. Extracellular enzyme activities were generally highest in either the spring or summer, while seasonal patterns for each substrate were unique across catabolic response profiles. Climate treatments produced few significant main or interactive effects on the soil microbial biomass and function. This resiliency, coupled with evidence of functional redundancy, suggests that central Kentucky pasture ecosystems may be well-equipped to handle future environmental stress associated with climate change and to maintain critical ecosystem services.

The loss of biodiversity is affecting all ecosystems on Earth, one of the greatest threats to biodiversity being climate change. Forests have been highlighted for the potential to mitigate climate change by storing carbon above- and belowground in soils. In this thesis, I studied the effects of tree diversity on carbon cycling in subtropical Chinese forests. I aimed to explore the mechanisms behind tree diversity effects on carbon cycling by focusing on microbial-based processes and the consequences of tree diversity-induced spatial heterogeneity. First, my colleagues and I tested the effects of tree diversity on litterfall spatial patterns and the consequences for litter decomposition and quantified the importance of microbial community in decomposition processes. Second, we explored the effects of tree diversity on relationships between soil microbial facets and soil microbial functions. Third, we tested the effects of tree diversity on soil microbial biomass and carbon concentrations, and their mediation by biotic and abiotic conditions. Finally, we explored the consequences of diversifying forests for re-/afforestation initiatives and plantations to reduce atmospheric carbon levels, and the benefits of diversity for mitigating the effects of climate change on ecosystems and human well-being. We highlighted the positive effects of tree diversity on tree productivity. By increasing the amount and diversity of litterfall, tree diversity increased litter decomposition and subsequently the assimilation of tree products into the forest soils. Our investigation has shown the key role of microbial communities for forests carbon dynamics by carrying out litter decomposition, soil heterotrophic respiration, and soil carbon stabilization. Most notably, tree diversity effects on soil microbial respiration were mainly mediated by soil microbial biomass rather than soil microbial community taxonomic or functional diversity. The effects of tree diversity on microbial biomass were mediated by biotic and abiotic conditions. Taken together, we revealed the importance of considering space to understand biodiversity-ecosystem functioning relationships. Finally, we argued that tree diversity is a promising avenue to maximize the potential of re-/afforestation projects to mitigate increasing atmospheric carbon. Moreover, we highlighted that diversifying forests in re-/afforestation initiatives can help to reduce climate change effects on ecosystems: first, by increasing resistance and resilience to extreme climatic events, and second, by buffering microclimatic conditions in natural and urban areas. My investigation highlighted that tree diversity effects on ecosystem functioning could be explained by both mass and diversity effects on higher trophic levels and their functions. In addition, I showed the key role of tree diversity-induced spatial heterogeneity and the need to consider space and time in further research. Moreover, these results need to be combined with practitioner constraints to enable feasible restoration projects.:Summary table Bibliographic information .................................................................................... I ~ XV Main body ......................................................................................................... 1 ~ 212 Supplementary materials ..................................................................................... i ~ xv Scientific supplementary materials ............................................................. -1- ~ - 154- Table of Contents Table of figures .......................................................................................................... XI Table of scientific supplementary materials ............................................................. XIII Glossary ................................................................................................................... XV Introduction ................................................................................................................. 3 Chapter I - Tree diversity effects on litter decomposition are mediated by litterfall and microbial processes .................................................................................................. 35 Transition I - II ........................................................................................................... 67 Chapter II - Tree diversity and soil chemical properties drive the linkages between soil microbial community and ecosystem functioning................................................ 71 Transition II - III ....................................................................................................... 107 Chapter III - Abiotic and biotic drivers of scale-dependent tree trait effects on soil microbial biomass and soil carbon concentration ................................................... 111 Transition III - IV ..................................................................................................... 155 Chapter IV – Diverse forests are cool: promoting diverse forests to mitigate carbon emissions and climate change ............................................................................... 159 General discussion ................................................................................................. 173 Abstract .................................................................................................................. 195 General acknowledgments ..................................................................................... 209 Supplementary materials ..............................................................................................i

Reindeer appear to have strong positive effects on plant productivity and nutrient cycling in strongly nutrient-limited ecosystems. While the direct effects of grazing on vegetation composition have been intensively studied, much less is known about the indirect effect of grazing on plant-soil interactions. This thesis investigated the indirect effects of ungulate grazing on arctic plant communities via soil nutrient availability and plant nutrient uptake. At high density, the deposition of dung alone increased plant productivity both in nutrient rich and nutrient poor tundra habitats without causing major changes in soil possesses. Plant community responses to dung addition was slow, with a delay of at least some years. By contrast, a 15N-urea tracer study revealed that nutrients from reindeer urine could be rapidly incorporated into arctic plant tissues. Soil and microbial N pools only sequestered small proportions of the tracer. This thesis therefore suggests a strong effect of dung and urine on plant productivity by directly providing nutrient-rich resources, rather than by stimulating soil microbial activities, N mineralization and ultimately increasing soil nutrient availability. Further, defoliation alone did not induce compensatory growth, but resulted in plants with higher nutrient contents. This grazing-induced increase in plant quality could drive the high N cycling in arctic secondary grasslands by providing litter of a better quality to the belowground system and thus increase organic matter decomposition and enhance soil nutrient availability. Finally, a 15N natural abundance study revealed that intense reindeer grazing influences how plants are taking up their nutrients and thus decreased plant N partitioning among coexisting plant species. Taken together these results demonstrate the central role of dung and urine and grazing-induced changes in plant quality for plant productivity. Soil nutrient concentrations alone do not reveal nutrient availability for plants since reindeer have a strong influence on how plants are taking up their nutrients. This thesis highlights that both direct and indirect effects of reindeer grazing are strong determinants of tundra ecosystem functioning. Therefore, their complex influence on the aboveground and belowground linkages should be integrated in future work on tundra ecosystem N dynamic.

The meals from many oilseed crops contain biocidal chemicals that are known to inhibit the growth and activity of several soil pathogens, though little is known concerning impacts on whole soil microbial communities. We investigated the effect of oilseed meals (SMs) from both brassicaceous plants, including mustard and camelina, as well as non-brassicaceous plants, including jatropha and flax, on P. omnivora (the casual agent of cotton root rot) in Branyon clay soil (at 1 and 5% application rates). We also investigated the effect of SMs from camelina, jatropha, flax, and wheat straw on microbial communities in Weswood loam soil. We also used four types of isothiocyanates (ITCs) including allyl, butyl, phenyl, and benzyl ITC to test their effects on P. omnivora growth on potato dextrose agar (PDA), as well as on soil microbial communities in a microcosm study. Community qPCR assays were used to evaluate relative abundances of soil microbial populations. Soil microbial community composition was determined through tag-pyrosequencing using 454 GS FLX titanium technology, targeting ITS and 16S rRNA gene regions for fungal and bacterial communities, respectively. The results showed that all tested brassicaceous and jatropha SMs were able to inhibit P. omnivora sclerotial germination and hyphal growth, with mustard SM being the most effective. Flax didn't show any inhibitory effects on sclerotial germination. All tested ITCs inhibited P. omnivora OKAlf8 hyphal growth, and the level of inhibition varied with concentration and ITC type. Total soil fungal populations were reduced by ITC addition, and microbial community compositions were changed following SM and ITC application. These changes varied according to the type of SM or ITC added. Our results indicated that SMs of several brassicaceous species as well as jatropha may have potential for reducing cotton root rot as well as some other pathogens. Different SMs releasing varied ITCs may result in differential impacts on soil microorganisms including some pathogens.

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.

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.