Adoption of no-till (NT) and reduced tillage management is widespread on the Canadian prairies and together form the basic platform of soil management upon which most crop production is based. Elimination of tillage in cropping systems changes the physical and chemical characteristics of the soil profile and can affect crop growth and ultimately yield. As such, understanding how soil biota, as drivers of nutrient turnover, adapt to NT is important for maximizing crop productivity and mitigating environmental damage in agroecosystems. This work aims to achieve a greater understanding of microbial community structure and function in long-term NT versus conventionally tilled (CT) soils. Community phospholipid and DNA fingerprinting did not reveal any consistent tillage-induced shifts in microbial community structure, but demonstrated a clear influence of depth within the soil profile. While tillage did not result in broad changes in the community structure, total, bacterial and fungal biomass was consistently greater near the surface of NT soils. Further examination at one site near Swift Current, SK revealed differences in microbial biomass and community structure in NT and CT in field-formed aggregate size fractions. Measurement of mineralization and nitrification at the same site indicated that differences in the early-season turnover of N may be related to physical rather than microbial differences in NT and CT soils. Potential nitrification was higher prior to seeding than mid-season, was not affected by tillage and was correlated with ammonia oxidizer population size of archaea, but not bacteria. This work indicates that edaphic soil properties and spatial distribution of resources in the soil profile, rather than tillage management, are the primary factors driving microbial community structure in these soils.

In the Central Valley of Costa Rica in the Department of Heredia, I investigated the soil chemical properties and microbial communities under four native shade tree species in a coffee agroforestry system. In the second year of the study, Effective Microorganisms, a microbial inoculant, was applied to examine its effect on soil chemistry. The shade tree species included in this study were Anonna muricata L., Diphysa americana Mill., Persea americana Mill., and Quercus spp. L. Plots measured 20 by 30 meters and were replicated three times for each shade tree species except for Quercus spp., which only had two replications. Twelve composite soil samples were collected from each plot in 2008 and again in 2009, and twelve composite foliar samples were taken from the coffee plants in each plot in 2008. The results of this study indicated that the species of native shade tree had a significant effect on soil ammonium-N, nitrate-N, total dissolved nitrogen and magnesium. Sun or shade position had a significant effect on dissolved organic nitrogen and dissolved organic carbon. The species of native shade tree also had a significant effect on the composition of soil microbial communities. PLFA analysis revealed a significant difference in soil fungi abundance in soil samples from Annona plots relative to those from Persea plots. Effective microorganisms in combination with the tree species, as well as in combination with species and sun or shade position, had a significant interaction effect on soil ammonium-N, with the EM-treated plots showing higher concentrations of soil ammonium-N. There was a significant positive correlation between soil pH and foliar calcium, as well as soil dissolved organic nitrogen and foliar %N, at p< 0.01. This study suggests that Quercus spp. is a tree species that may help to regulate the cycling of nitrogen in the coffee agroecosystem. Annona muricata appears to inhibit the action of some fungal species and may reduce the occurrence of fungal pathogens in the soil, although the present study did not explore this issue. Although Diphysa americana is a legume, it does not appear to increase the amount of soil nitrogen in the vicinity of the coffee plants themselves. All four tree species in this study improve coffee soils by increasing soil concentrations of dissolved organic nitrogen and dissolved organic carbon. Coffee yield data and long term observations on the health of the coffee plants would clarify whether one of these species is particularly beneficial, from an agronomic perspective, for the productivity of this coffee agroecosystem.

Extensive research conducted over the last decade has demonstrated the great potential of phytostabilization for the reclamation of abandoned mine tailing piles. The right combination of plant species and soil amendments can facilitate the growth of a permanent vegetative cover on the tailings that will help minimize the mobilization of metal-bearing particles by means of wind dispersion and water erosion. Despite previous research efforts, the diversity and potential role of microbial populations inhabiting the root zone of the plants on the stabilization of the metal(loid) contaminants remains mostly unresolved. The study presented in this dissertation represents one of the first comprehensive efforts aimed to understand the ecology and dynamics of microbial communities colonizing both bulk and rhizosphere tailings during phytostabilization as an initial step towards elucidating the role of microbes in the stabilization of metal(loid) contaminants during the remediation treatment. This study was divided into two main projects: (1) the first aimed to monitor the temporal variations in functional and taxonomic diversity of prokaryotic populations in acid-generating metalliferous mine tailings during phytostabilization to determine how they respond to and/or influence changes in environmental parameters and to identify key patterns in their composition that may serve as bioindicators of soil health and the success of the remediation treatment; and (2) the second aimed to expand our understanding of the dynamics of root-associated bacterial, fungal and archaeal communities during mine tailing phytostabilization and how the dynamic behavior of the communities correspond to the growth of plants, the addition of soil amendments, and fluctuations in environmental conditions. The results presented here demonstrate that different microbial groups respond differently to changes in environmental conditions during phytostabilization, suggesting that by monitoring the behavior of specific microbial groups in the systems (as bioindicators) we may be able to assess the effectiveness of the remediation treatment. Furthermore, the results from the taxonomic and functional analysis of the microbial communities served as the basis for the development of a model that explains the ecology and distribution of dominant microbial groups in the tailings that may significantly contribute to the oxidation of iron-sulfides, the production of acid mine drainage, and to facilitate plant establishment and survival during phytostabilization.

Increased amounts of pesticide production and application of pesticides for agriculture, plant protection and animal health has resulted in soil, water and air pollution, consequently relating a serious risk to the environment and also to human health. Pesticides include several groups of compounds, herbicides, insecticides, rodenticides and fumigants consisting of several hundred individual chemicals. Herbicides are an integral pan of modem agriculture and for industries requiring total vegetation control. Most herbicides are soil applied and more and more concern is raised that herbicides not only affect target organisms but also the microbial community present in soil. The ESKOM sub-station Zeus, in Mpumalanga (South Africa) used to apply an industrial weed control program for the eradication of vegetation, which led to the contamination of soil by several herbicides. These herbicides consisted of Bromacil, Tebuthiuron and Ethidimuron which are all photosynthesis inhibitors, more specifically, they disrupt the plastoquinone protein during electron transport at photosystem I1 (PSII). In this study the effect of biostimulation and bio-augmentation of a specific bioremediation agent (B350) as prescribed by ESKOM, on residual herbicides, Bromacil, Tebuthiuron and Ethidimuron was evaluated by monitoring the soil physical and chemical properties, microbial attributes, including potential microbial activity and community structure, as well as the physiological effect experienced by plants (Cynodoh dactylon and Zea mays). Results from soil physical and chemical analyses were correlated with results obtained for the functional and structural diversity of microbial communities. All results were investigated through statistical and multivariate analysis and the most prominent soil physical and chemical parameters that influence the biological and biochemical properties of the soil were identified. Results obtained from this study indicated that there were no significant difference (p < 0.05) between the treatments, with bioremediation agent, irradiated agent and without the agent based on results obtained from soil microbial properties and plant physiology. Before the trial started the uncontaminated soil showed an active microbial function, characterised by dehydrogenase, urease and arylsulphatase activity, but community structure was not very diverse. The contaminated soil, irradiated contaminated soil and silica sand showed less enzymatic function and was characterised by phospholipid fatty acid groups, mid-branched saturated fatty acids, terminally branched saturated fatty acids, normal saturated fatty acids and monosaturated fatty acids which are indicative of microorganisms that survive better in harsh environments. Three weeks after the addition of the specific bioremediation took place, the uncontaminated soil showed an increase in P-glucosidase activity and percentage organic carbon (%C), which could be a result of the presence of available plant material. Furthermore, an increase in major PLFA groups were seen, suggesting that an increase in diversity within the soil community occurred. The contaminated soil, irradiated contaminated soil and silica sand once again was characterised by a low microbial function and diversity, showing no improvement. Fluorescence data clearly show a decline in PS 11 function that result in the decline of the rate of photosynthesis, which was seen from COz gas exchange rates. Furthermore, the decrease in photosynthetic activity after three weeks was too severe to supply additional information about the mechanism within photosynthesis or the photoprotective mechanisms. A detailed study was conducted in which a 3: 1 dilution of contaminated soil with silica sand, was also monitored for changes within plant physiology. Results revealed that inhibition of PS I1 function already takes place within a few days time and the decline in photosynthesis is as a result of electron transport that does not supply adenosine triphosphate (ATP) and P-nicotinamide adenine dinucleotide (NADPH) to the Calvin cycle (or Reductive Pentose Phosphate pathway). It does not appear that rubulose-1,sbisphosphate carboxylase-oxygenase (Rubisco) is affected within the Calvin cycle. As a result of PS I1 function failure, reaction centres are damaged by the production of harmful singlet oxygen and photoprotective mechanisms (xanthophyll cycle) can not be activated. Thus, except for dealing with ineffective electron transport, additional damage is caused to physiological functions. After six weeks a decrease in the estimated viable biomass for all growth mediums was found. Results of the of trans- to cis- monoenoic fatty acids and cyclopropyl fatty acids to their monoenoic precursors ratios indicated that the soil microbial community for the contaminated growth mediums, all experienced nutritional stress throughout this trail. The specific bioremediation agent (B350) used, seemed to have no effect on the microbial function and community structure within soil and as agent had no effect on the residual herbicides or the plant physiology which experienced an extreme decline in major metabolic functions. / Thesis (M. Environmental Science)--North-West University, Potchefstroom Campus, 2

Mining activities cause severe disturbance to the soil environment in terms of soil quality and productivity and are of serious concern worldwide. Under South African legislation, developers are required to ecologically rehabilitate damaged environments. The application of agronomic approaches for the rehabilitation of coal discard sites has failed dismally in the arid areas of southern Africa. It is obvious that compliance with mitigation and rehabilitation requirements cannot be enforced without a thorough understanding of the ecological principles that ensure ecological stability and subsequent sustainability of soil ecosystems. Soil micro organisms are crucial role-players in the processes that make energy and nutrients available for recycling in the soil ecosystem. Poor management practices and other negative impacts on soil ecosystems affect both the physical and chemical properties of soil, as well as the functional and structural properties of soil microbial communities. Disturbances of soil ecosystems that impact on the normal functioning of microbial communities are potentially detrimental to soil formation, energy transfers, nutrient cycling, plant reestablishment and long-term stability. In this regard, an extensive overview of soil properties and processes indicated that the use of microbiological and biochemical soil properties, such as microbial biomass, enzymatic activity and the analysis of microbial community structure by the quantification of specific 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 the physical and chemical characteristics and different biological indicators of soil quality in the topsoil covers of seven coal discard sites under rehabilitation in South Africa, as well as three reference sites was investigated. Through the assimilation of basic quantitative data and the assessment of certain physical, chemical and biological properties of the topsoil covers obtained from the various coal discard sites as well as the reference sites, the relative success or progress of rehabilitation and the possible correlation between the biological indicators of soil quality and the establishment of self sustaining vegetation covers was determined. Results from soil physical and chemical analyses and percentage vegetation cover were correlated with the results obtained for the functional and structural diversity of microbial communities at the various sites. All results were investigated through statistical and multivariate analysis and the most prominent physical and chemical parameters that influence the biological and biochemical properties of the soil and possibly the establishment of self-sustainable vegetation cover on these mine-tailing sites were identified. Results obtained from this study indicated no significant difference (p>0.05) between the various discard sites based on conventional microbiological enumeration techniques. However, significant differences (p<0.05) could be observed between the three reference sites. All enzymatic activities assayed for the rehabilitation sites, with the exception of urease and alkaline phosphatase displayed a strong, positive association with the organic carbon content (%C). Ammonium concentration had a weak association with all the enzymes studied and pH only showed a negative association with acid phosphatase activity. A positive association was observed between the viable microbial biomass, vegetation cover and the organic carbon content, ammonium, nitrate and phosphorus concentrations of the soil. The various rehabilitation and reference sites could be differentiated based on the microbial community structure as determined by phospholipid fatty acid (PLFA) analysis. It is hypothesised that the microbial community structure of the Hendrina site is not sustainable when classified along an r-K gradient and that the high percentage of vegetation cover and high levels of estimated viable microbial biomass are an artificial reflection of the current management practices being employed at this site. Results obtained during this study, suggest that an absence or low percentage of vegetation cover and associated lower organic matter content of the soil have a significant negative impact on soil biochemical properties (enzymatic activity) as well as microbial population size. Furthermore, prevailing environmental physico-chemical and management characteristics significantly influences the vegetation cover and subsequently the microbial community structure. The results indicate that the microbial ecosystems in the coal discard sites could become more stable and ecologically self-regulating, provided effective management to enhance the organic carbon content of the soil. This could enhance nutrient cycling, resulting in changes of soil structure and eventually an improved soil quality which could facilitate the establishment of self sustaining vegetation cover. Results obtained during this study suggest that a polyphasic assessment of physical and chemical properties; microbial activities by enzymatic analysis; the characterisation of microbial community structure by analysis of phospholipid fatty acids; and the multifactorial analysis of the data obtained can be used as complementary assessment criteria for the evaluation of the trend of rehabilitation of mine tailings and discard sites. Strategic management criteria are recommended based on the soil quality environmental sustainability indices to facilitate the establishment of self sustainable vegetation covers. The contribution of this research to soil ecology is significant with regards to the intensive investigation and explanation of characteristics and processes that drive ecological rehabilitation and determine the quality of the soil environment. The multidisciplinary approach that is proposed could, furthermore, assist in the successful rehabilitation and establishment of self-sustaining vegetation covers at industrially disturbed areas, as well as assist in improving degraded soil quality associated with both intensive and informal agriculture. Additionally, this approach could negate the negative social and environmental impacts frequently associated with these activities. / Thesis (M. Environmental Science)--North-West University, Potchefstroom Campus, 2004.

A standardized method to examine soil microbial health incorporating biomass, activity, and diversity measurements is currently lacking, limiting the use of this ecologically relevant endpoint in ecological risk assessments. The soil microbial health of a petroleum hydrocarbon-contaminated boreal forest soil, relative to a reference soil, was examined using a suite of tests. Microbial health impacts in the contaminated soil were observed using nitrification, organic matter decomposition, bait lamina, denaturing gradient gel electrophoresis, community level physiological profiling, and most enzyme assays. Results of heterotrophic plate count and respiration tests indicated higher culturable numbers and activity in the contaminated soil. A data integration technique was developed to incorporate the results from individual tests into an overall conclusion, indicating that soil contamination at the site moderately to severely impacted microbial health. The research presented lays the foundation for the development of a soil microbial health standardized method.

No description available.

Tall fescue (Lolium arundinaceum (Schreb.) Darbysh.) is a cool-season perennial grass used in pastures throughout the Southeastern United States. The grass can harbor a fungal endophyte (Epichloë coenophiala) thought to provide the plant with enhanced resistance to biotic and abiotic stress. However, the alkaloids produced by the common variety of the endophyte cause severe animal health issues resulting in a considerable amount of research focused on eliminating the toxic class of alkaloids while retaining the positive abiotic and biotic stress tolerance attributes of the other alkaloids. In doing so, very little attention has been paid to the direct influence the fungal-plant symbiosis has on rhizosphere processes. Therefore, my objectives were to study the influence of this relationship on plant biomass production, root exudate composition, and soil biogeochemical processes using tall fescue cultivars PDF and 97TF1 without an endophyte (E-), or infected with the common toxic endophyte (CTE+), or with two novel endophytes (AR542E+, AR584E+). I found that root exudate composition and plant biomass production were influenced by endophyte status, tall fescue cultivar, and the interaction of cultivar and endophyte. Cluster analysis showed that the interaction between endophyte and cultivar results in a unique exudate profile. These interactions had a small but perceptible impact on soil microbial community structure and function with an equally small and perceptible impact on carbon and nitrogen cycling in soils from rhizobox and field sites. These studies represent the first comprehensive analysis of root exudate chemistry from common toxic and novel endophyte infected tall fescue cultivars and can be used to help explain in part the observed changes in C and N cycling and storage in pastures throughout the Southeast U.S..

Increased amounts of pesticide production and application of pesticides for agriculture, plant protection and animal health has resulted in soil, water and air pollution, consequently relating a serious risk to the environment and also to human health. Pesticides include several groups of compounds, herbicides, insecticides, rodenticides and fumigants consisting of several hundred individual chemicals. Herbicides are an integral pan of modem agriculture and for industries requiring total vegetation control. Most herbicides are soil applied and more and more concern is raised that herbicides not only affect target organisms but also the microbial community present in soil. The ESKOM sub-station Zeus, in Mpumalanga (South Africa) used to apply an industrial weed control program for the eradication of vegetation, which led to the contamination of soil by several herbicides. These herbicides consisted of Bromacil, Tebuthiuron and Ethidimuron which are all photosynthesis inhibitors, more specifically, they disrupt the plastoquinone protein during electron transport at photosystem I1 (PSII). In this study the effect of biostimulation and bio-augmentation of a specific bioremediation agent (B350) as prescribed by ESKOM, on residual herbicides, Bromacil, Tebuthiuron and Ethidimuron was evaluated by monitoring the soil physical and chemical properties, microbial attributes, including potential microbial activity and community structure, as well as the physiological effect experienced by plants (Cynodoh dactylon and Zea mays). Results from soil physical and chemical analyses were correlated with results obtained for the functional and structural diversity of microbial communities. All results were investigated through statistical and multivariate analysis and the most prominent soil physical and chemical parameters that influence the biological and biochemical properties of the soil were identified. Results obtained from this study indicated that there were no significant difference (p < 0.05) between the treatments, with bioremediation agent, irradiated agent and without the agent based on results obtained from soil microbial properties and plant physiology. Before the trial started the uncontaminated soil showed an active microbial function, characterised by dehydrogenase, urease and arylsulphatase activity, but community structure was not very diverse. The contaminated soil, irradiated contaminated soil and silica sand showed less enzymatic function and was characterised by phospholipid fatty acid groups, mid-branched saturated fatty acids, terminally branched saturated fatty acids, normal saturated fatty acids and monosaturated fatty acids which are indicative of microorganisms that survive better in harsh environments. Three weeks after the addition of the specific bioremediation took place, the uncontaminated soil showed an increase in P-glucosidase activity and percentage organic carbon (%C), which could be a result of the presence of available plant material. Furthermore, an increase in major PLFA groups were seen, suggesting that an increase in diversity within the soil community occurred. The contaminated soil, irradiated contaminated soil and silica sand once again was characterised by a low microbial function and diversity, showing no improvement. Fluorescence data clearly show a decline in PS 11 function that result in the decline of the rate of photosynthesis, which was seen from COz gas exchange rates. Furthermore, the decrease in photosynthetic activity after three weeks was too severe to supply additional information about the mechanism within photosynthesis or the photoprotective mechanisms. A detailed study was conducted in which a 3: 1 dilution of contaminated soil with silica sand, was also monitored for changes within plant physiology. Results revealed that inhibition of PS I1 function already takes place within a few days time and the decline in photosynthesis is as a result of electron transport that does not supply adenosine triphosphate (ATP) and P-nicotinamide adenine dinucleotide (NADPH) to the Calvin cycle (or Reductive Pentose Phosphate pathway). It does not appear that rubulose-1,sbisphosphate carboxylase-oxygenase (Rubisco) is affected within the Calvin cycle. As a result of PS I1 function failure, reaction centres are damaged by the production of harmful singlet oxygen and photoprotective mechanisms (xanthophyll cycle) can not be activated. Thus, except for dealing with ineffective electron transport, additional damage is caused to physiological functions. After six weeks a decrease in the estimated viable biomass for all growth mediums was found. Results of the of trans- to cis- monoenoic fatty acids and cyclopropyl fatty acids to their monoenoic precursors ratios indicated that the soil microbial community for the contaminated growth mediums, all experienced nutritional stress throughout this trail. The specific bioremediation agent (B350) used, seemed to have no effect on the microbial function and community structure within soil and as agent had no effect on the residual herbicides or the plant physiology which experienced an extreme decline in major metabolic functions. / Thesis (M. Environmental Science)--North-West University, Potchefstroom Campus, 2

Mining activities cause severe disturbance to the soil environment in terms of soil quality and productivity and are of serious concern worldwide. Under South African legislation, developers are required to ecologically rehabilitate damaged environments. The application of agronomic approaches for the rehabilitation of coal discard sites has failed dismally in the arid areas of southern Africa. It is obvious that compliance with mitigation and rehabilitation requirements cannot be enforced without a thorough understanding of the ecological principles that ensure ecological stability and subsequent sustainability of soil ecosystems. Soil micro organisms are crucial role-players in the processes that make energy and nutrients available for recycling in the soil ecosystem. Poor management practices and other negative impacts on soil ecosystems affect both the physical and chemical properties of soil, as well as the functional and structural properties of soil microbial communities. Disturbances of soil ecosystems that impact on the normal functioning of microbial communities are potentially detrimental to soil formation, energy transfers, nutrient cycling, plant reestablishment and long-term stability. In this regard, an extensive overview of soil properties and processes indicated that the use of microbiological and biochemical soil properties, such as microbial biomass, enzymatic activity and the analysis of microbial community structure by the quantification of specific 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 the physical and chemical characteristics and different biological indicators of soil quality in the topsoil covers of seven coal discard sites under rehabilitation in South Africa, as well as three reference sites was investigated. Through the assimilation of basic quantitative data and the assessment of certain physical, chemical and biological properties of the topsoil covers obtained from the various coal discard sites as well as the reference sites, the relative success or progress of rehabilitation and the possible correlation between the biological indicators of soil quality and the establishment of self sustaining vegetation covers was determined. Results from soil physical and chemical analyses and percentage vegetation cover were correlated with the results obtained for the functional and structural diversity of microbial communities at the various sites. All results were investigated through statistical and multivariate analysis and the most prominent physical and chemical parameters that influence the biological and biochemical properties of the soil and possibly the establishment of self-sustainable vegetation cover on these mine-tailing sites were identified. Results obtained from this study indicated no significant difference (p>0.05) between the various discard sites based on conventional microbiological enumeration techniques. However, significant differences (p<0.05) could be observed between the three reference sites. All enzymatic activities assayed for the rehabilitation sites, with the exception of urease and alkaline phosphatase displayed a strong, positive association with the organic carbon content (%C). Ammonium concentration had a weak association with all the enzymes studied and pH only showed a negative association with acid phosphatase activity. A positive association was observed between the viable microbial biomass, vegetation cover and the organic carbon content, ammonium, nitrate and phosphorus concentrations of the soil. The various rehabilitation and reference sites could be differentiated based on the microbial community structure as determined by phospholipid fatty acid (PLFA) analysis. It is hypothesised that the microbial community structure of the Hendrina site is not sustainable when classified along an r-K gradient and that the high percentage of vegetation cover and high levels of estimated viable microbial biomass are an artificial reflection of the current management practices being employed at this site. Results obtained during this study, suggest that an absence or low percentage of vegetation cover and associated lower organic matter content of the soil have a significant negative impact on soil biochemical properties (enzymatic activity) as well as microbial population size. Furthermore, prevailing environmental physico-chemical and management characteristics significantly influences the vegetation cover and subsequently the microbial community structure. The results indicate that the microbial ecosystems in the coal discard sites could become more stable and ecologically self-regulating, provided effective management to enhance the organic carbon content of the soil. This could enhance nutrient cycling, resulting in changes of soil structure and eventually an improved soil quality which could facilitate the establishment of self sustaining vegetation cover. Results obtained during this study suggest that a polyphasic assessment of physical and chemical properties; microbial activities by enzymatic analysis; the characterisation of microbial community structure by analysis of phospholipid fatty acids; and the multifactorial analysis of the data obtained can be used as complementary assessment criteria for the evaluation of the trend of rehabilitation of mine tailings and discard sites. Strategic management criteria are recommended based on the soil quality environmental sustainability indices to facilitate the establishment of self sustainable vegetation covers. The contribution of this research to soil ecology is significant with regards to the intensive investigation and explanation of characteristics and processes that drive ecological rehabilitation and determine the quality of the soil environment. The multidisciplinary approach that is proposed could, furthermore, assist in the successful rehabilitation and establishment of self-sustaining vegetation covers at industrially disturbed areas, as well as assist in improving degraded soil quality associated with both intensive and informal agriculture. Additionally, this approach could negate the negative social and environmental impacts frequently associated with these activities. / Thesis (M. Environmental Science)--North-West University, Potchefstroom Campus, 2004.