The PLFA profiling method was adopted and used to determine changes in microbial community structure and abundance along natural and human-induced environmental gradients. The presented studies were based on field sampling campaigns combined with targeted laboratory experiments. According to the aims of particular studies, microbial PLFA fingerprinting was combined with the auxiliary below- and aboveground ecosystem characteristics to identify the drivers of microbial responses to environmental changes or with 13C-labelling and metagenomics to obtain more complex information about running processes and involved microorganisms.

Biofumigation is an important crop protection practice that uses a plant’s natural defence mechanisms to control agricultural crop pathogens and diseases. Glucosinolates are volatile compounds found in most Brassica species and when hydrolysed, it forms a range of natural toxins including isothiocyanates that act as biofumigants. Research suggests that biofumigation is a good alternative to chemical fumigants as it is effective in controlling plant pests but with lower health and environmental risks. Several studies have confirmed the effectiveness of the breakdown products, especially isothiocyanates, as fungicidal, bactericidal and nematicidal products against a series of plant pests. However, very little information is available on the effects of glucosinolates and its breakdown products on non-target and beneficial soil organisms. Negative effects on beneficial soil organisms can have serious negative impacts on soil quality especially when essential ecosystem functions such as nutrient cycling and soil bioturbation are affected. Three biofumigants, broccoli, mustard and oilseed radish, and two chemical fumigants, metham sodium and cadusafos, were investigated for possible effects on non-target and essential soil organisms such as earthworms and the soil microbial community. Sublethal endpoints, including growth and reproductive success of the earthworms, were monitored. The genotoxicity of the biologically active compounds found in the fumigants, towards earthworms, was evaluated by means of the comet assay. The DNA damage was quantified by tail intensity parameters. Furthermore, the changes in the soil microbial community function and structure were evaluated by means of community level physiological profiling (CLPP) and phospholipid fatty acid (PLFA) analyses respectively. All exposures were done in artificial soil prepared according to the OECD standard guidelines. In the biofumigant treated soils, results varied and different effects were observed on the non-target soil organisms. Broccoli reduced cocoon production and the number of hatchlings while mustard induced more DNA strand breaks in earthworm cells compared to the control. All the biofumigants stimulated microbial growth but broccoli and oilseed radish changed the microbial functional diversity. Mustard had no lasting effect on the functional diversity but altered the microbial community structure. The chemical fumigants had a marked negative impact on the survival, growth, reproduction and the genotoxicity of the earthworms with metham sodium causing greater harm than cadusafos. The effects on the microbial community varied. Both chemicals had an inhibitory effect on the microbial growth in terms of the viable biomass determined by PLFA and the average well colour development in the Biolog™ Ecoplates. No lasting effects were observed in the community structure. Overall, cadusafos had a more pronounced effect on the microbial community functional diversity than metham sodium. Results indicated that each bioindicator species illustrates effects at their own level of organisation / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

Biofumigation is an important crop protection practice that uses a plant’s natural defence mechanisms to control agricultural crop pathogens and diseases. Glucosinolates are volatile compounds found in most Brassica species and when hydrolysed, it forms a range of natural toxins including isothiocyanates that act as biofumigants. Research suggests that biofumigation is a good alternative to chemical fumigants as it is effective in controlling plant pests but with lower health and environmental risks. Several studies have confirmed the effectiveness of the breakdown products, especially isothiocyanates, as fungicidal, bactericidal and nematicidal products against a series of plant pests. However, very little information is available on the effects of glucosinolates and its breakdown products on non-target and beneficial soil organisms. Negative effects on beneficial soil organisms can have serious negative impacts on soil quality especially when essential ecosystem functions such as nutrient cycling and soil bioturbation are affected. Three biofumigants, broccoli, mustard and oilseed radish, and two chemical fumigants, metham sodium and cadusafos, were investigated for possible effects on non-target and essential soil organisms such as earthworms and the soil microbial community. Sublethal endpoints, including growth and reproductive success of the earthworms, were monitored. The genotoxicity of the biologically active compounds found in the fumigants, towards earthworms, was evaluated by means of the comet assay. The DNA damage was quantified by tail intensity parameters. Furthermore, the changes in the soil microbial community function and structure were evaluated by means of community level physiological profiling (CLPP) and phospholipid fatty acid (PLFA) analyses respectively. All exposures were done in artificial soil prepared according to the OECD standard guidelines. In the biofumigant treated soils, results varied and different effects were observed on the non-target soil organisms. Broccoli reduced cocoon production and the number of hatchlings while mustard induced more DNA strand breaks in earthworm cells compared to the control. All the biofumigants stimulated microbial growth but broccoli and oilseed radish changed the microbial functional diversity. Mustard had no lasting effect on the functional diversity but altered the microbial community structure. The chemical fumigants had a marked negative impact on the survival, growth, reproduction and the genotoxicity of the earthworms with metham sodium causing greater harm than cadusafos. The effects on the microbial community varied. Both chemicals had an inhibitory effect on the microbial growth in terms of the viable biomass determined by PLFA and the average well colour development in the Biolog™ Ecoplates. No lasting effects were observed in the community structure. Overall, cadusafos had a more pronounced effect on the microbial community functional diversity than metham sodium. Results indicated that each bioindicator species illustrates effects at their own level of organisation / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

The rehabilitation of degraded soils, such as those associated with post-mining sites, requires knowledge of the soil ecosystem and its physical, chemical, and biological composition in order for rehabilitation efforts to fulfil the long-term goal of reconstructing a stable ecosystem for rehabilitated mine soil. This study addresses the need for appropriate assessment criteria to determine the progress of rehabilitation and subsequently the success of management practices. Significant contributions made by this investigation included the establishment of minimum and maximum values for microbial community measurements from two case studies of rehabilitated coal discard sites. Furthermore, it was shown that there was no relationship between changes in microbial community function and structure and the rehabilitation age of the sites. Following this, the considerable impact of management practices on microbial communities was illustrated. The first part of the study investigated the temporal changes in microbial community function and structure in a chronosequence of rehabilitated coal discard sites aged 1 to 11 years. The most important observation made during the investigation of the microbial communities in the different aged soil covers of the rehabilitated coal discard sites, was that there was no relationship between rehabilitation age and microbial activity or abundance of certain microbial groups. What was responsible for a clear differentiation between sites and a shift in microbial community attributes was the management practices applied. A comparison of two chronosequences of rehabilitated coal discard sites was achieved by an application of the 'space-for-time' hypothesis. Sites of different ages and at separate locations ('space') were identified to obtain a chronosequence of ages ('time'). The two chronosequences included sites aged 1 to 11 years (chronosequence A) and 6 to 17 years (chronosequence B), respectively. Sites in the same chronosequence were managed identically, while there was a distinct difference in management practices applied to each chronosequence. The long-term effect of the different management regimes on the soil microbial community function and structure was investigated. Again, there was no relationship between rehabilitation age and microbial community measurements. Fluctuations of selected microbial properties occurred in both chronosequences and similar temporal trends existed over the rehabilitation periods. However, the less intensively managed chronosequence (8) seemed more stable (less fluctuation occurred) over the rehabilitation period than the more intensively managed chronosequence (A). It was therefore concluded that the microbial communities in the less managed sites maintained their functional and structural integrity within bounds in the absence of management inputs or disturbance. While there was similarity in the trends over time for individual microbial community measurements, the seemingly more stable conditions in chronosequence 6 are important in terms of the goal of rehabilitation. / Thesis (Ph.D. (Environmental Science)--North-West University, Potchefstroom Campus, 2007

Thesis (Ph.D. (Environmental Science)--North-West University, Potchefstroom Campus, 2007.

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.

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.

The rehabilitation of degraded soils, such as those associated with post-mining sites, requires knowledge of the soil ecosystem and its physical, chemical, and biological composition in order for rehabilitation efforts to fulfil the long-term goal of reconstructing a stable ecosystem for rehabilitated mine soil. This study addresses the need for appropriate assessment criteria to determine the progress of rehabilitation and subsequently the success of management practices. Significant contributions made by this investigation included the establishment of minimum and maximum values for microbial community measurements from two case studies of rehabilitated coal discard sites. Furthermore, it was shown that there was no relationship between changes in microbial community function and structure and the rehabilitation age of the sites. Following this, the considerable impact of management practices on microbial communities was illustrated. The first part of the study investigated the temporal changes in microbial community function and structure in a chronosequence of rehabilitated coal discard sites aged 1 to 11 years. The most important observation made during the investigation of the microbial communities in the different aged soil covers of the rehabilitated coal discard sites, was that there was no relationship between rehabilitation age and microbial activity or abundance of certain microbial groups. What was responsible for a clear differentiation between sites and a shift in microbial community attributes was the management practices applied. A comparison of two chronosequences of rehabilitated coal discard sites was achieved by an application of the 'space-for-time' hypothesis. Sites of different ages and at separate locations ('space') were identified to obtain a chronosequence of ages ('time'). The two chronosequences included sites aged 1 to 11 years (chronosequence A) and 6 to 17 years (chronosequence B), respectively. Sites in the same chronosequence were managed identically, while there was a distinct difference in management practices applied to each chronosequence. The long-term effect of the different management regimes on the soil microbial community function and structure was investigated. Again, there was no relationship between rehabilitation age and microbial community measurements. Fluctuations of selected microbial properties occurred in both chronosequences and similar temporal trends existed over the rehabilitation periods. However, the less intensively managed chronosequence (8) seemed more stable (less fluctuation occurred) over the rehabilitation period than the more intensively managed chronosequence (A). It was therefore concluded that the microbial communities in the less managed sites maintained their functional and structural integrity within bounds in the absence of management inputs or disturbance. While there was similarity in the trends over time for individual microbial community measurements, the seemingly more stable conditions in chronosequence 6 are important in terms of the goal of rehabilitation. / Thesis (Ph.D. (Environmental Science)--North-West University, Potchefstroom Campus, 2007

Despite emerging water shortages, most water is only used once, and often with low efficiency. However, with appropriate treatment, water can be re–used to reduce the demand on freshwater sources. The Department of Water Affairs, South Africa, promotes industries to reduce discharges into water resources in order to sustain an overall good water quality of all water systems. All of this ultimately leads to industries striving towards zero effluent discharge. Primary Column Bottoms (PCBs) is a wastewater stream derived from the Fischer–Tropsch Gas to Liquid process and consists mainly of organic acids, but no nitrogen or phosphorous, which by implication excludes possible biodegradation. In the operation of cooling towers in industrial processes, cooling water quality has a direct impact on the cooling performance of the system, where nutrient levels may affect fouling, scaling and corrosion observed in the cooling towers. Fouling, scaling and corrosion affect the operating efficiency of cooling water systems and may necessitate the addition of chemical agents to control these phenomena. This has a financial and labour time impact on the operation of these systems. In this study a mini cooling tower test rig was operated with a synthetic PCB effluent as cooling water and various cycles of concentration, pH and linear flow velocities (LFVs). A constant delta temperature of 10 °C was maintained. Cycles of concentration (COC) evaluated included 2, 4 and 6 cycles of concentration and linear flow velocities evaluated was 0.6 m/s, 0.9 m/s and 1.2 m/s. Fouling, scaling and corrosion rates were determined using corrosion coupons and heat exchanger tubes for mild steel and stainless steel. Besides the evaluation of the various operational parameters for fouling, scaling and corrosion, the possibility for chemical oxygen demand (COD) removal by operating the cooling tower as a bioreactor was also evaluated. To this end nutrient correction was applied to the reactor to allow for a CNP ratio of 100:10:1. With regard to fouling, scaling and corrosion, mild steel was more affected by fouling, scaling and corrosion compared to stainless steel where almost no fouling, scaling and corrosion was observed. Overall increased linear flow velocities resulted in higher fouling and scaling rates, whereas lower linear flow velocities resulted in decreased corrosion rates. In terms of cycles of concentration, increased COC resulted in higher fouling, scaling and corrosion rates. Despite the high nutrient removal levels, the accompanying fouling, scaling and corrosion was still below the particular industry’s guidelines. Besides physical–chemical evaluation of the towers under the various operational conditions, culture–dependent and culture–independent methods were also employed. Concerning culture–dependent approaches the study demonstrated that aerobic and anaerobic organisms are present in both the planktonic and sessile phase of the cooling tower reactors. Heterotrophic aerobes were found to be the most abundant under all the operating conditions. Sulphate reducing bacteria were more abundant in the sessile phase of the cooling towers, and the presence of high sulphate levels in the experiments could be indicative of the sulphate reducing bacteria actively participating in the microbial community. Lower than expected corrosion levels, however, suggest that a combination of the organisms in the biofilm rather than sulphate reducing bacteria alone, contributed to the corrosion rates observed. Culture–independent methods, specifically phospholipid fatty acid analysis supported the results from the culture–dependent methods. Furthermore results demonstrated that linear flow velocity had a greater effect on the community structure than cycles of concentration. Finally molecular methods, specifically denaturing gradient gel electrophoresis, found that increasing cycles of concentration resulted in increased microbial community diversity, while increasing linear flow velocity resulted in decreased microbial community diversity. Regarding COD removal, nutrient correction of the synthetic PCB effluent achieved 89.35 % COD removal at 2 COC and 1.2 m/s LFV, while 80.85 % COD removal was achieved at 4 COC at 1.2 m/s LFV. From these results it was recommended that the operation of the cooling tower should be at 4 COC and 1.2 m/s, which despite slightly lower % COD removal, were characterised by fouling, scaling and corrosion rates well within guidelines. / Thesis (M. Environmental Science)--North-West University, Potchefstroom Campus, 2012.

Despite emerging water shortages, most water is only used once, and often with low efficiency. However, with appropriate treatment, water can be re–used to reduce the demand on freshwater sources. The Department of Water Affairs, South Africa, promotes industries to reduce discharges into water resources in order to sustain an overall good water quality of all water systems. All of this ultimately leads to industries striving towards zero effluent discharge. Primary Column Bottoms (PCBs) is a wastewater stream derived from the Fischer–Tropsch Gas to Liquid process and consists mainly of organic acids, but no nitrogen or phosphorous, which by implication excludes possible biodegradation. In the operation of cooling towers in industrial processes, cooling water quality has a direct impact on the cooling performance of the system, where nutrient levels may affect fouling, scaling and corrosion observed in the cooling towers. Fouling, scaling and corrosion affect the operating efficiency of cooling water systems and may necessitate the addition of chemical agents to control these phenomena. This has a financial and labour time impact on the operation of these systems. In this study a mini cooling tower test rig was operated with a synthetic PCB effluent as cooling water and various cycles of concentration, pH and linear flow velocities (LFVs). A constant delta temperature of 10 °C was maintained. Cycles of concentration (COC) evaluated included 2, 4 and 6 cycles of concentration and linear flow velocities evaluated was 0.6 m/s, 0.9 m/s and 1.2 m/s. Fouling, scaling and corrosion rates were determined using corrosion coupons and heat exchanger tubes for mild steel and stainless steel. Besides the evaluation of the various operational parameters for fouling, scaling and corrosion, the possibility for chemical oxygen demand (COD) removal by operating the cooling tower as a bioreactor was also evaluated. To this end nutrient correction was applied to the reactor to allow for a CNP ratio of 100:10:1. With regard to fouling, scaling and corrosion, mild steel was more affected by fouling, scaling and corrosion compared to stainless steel where almost no fouling, scaling and corrosion was observed. Overall increased linear flow velocities resulted in higher fouling and scaling rates, whereas lower linear flow velocities resulted in decreased corrosion rates. In terms of cycles of concentration, increased COC resulted in higher fouling, scaling and corrosion rates. Despite the high nutrient removal levels, the accompanying fouling, scaling and corrosion was still below the particular industry’s guidelines. Besides physical–chemical evaluation of the towers under the various operational conditions, culture–dependent and culture–independent methods were also employed. Concerning culture–dependent approaches the study demonstrated that aerobic and anaerobic organisms are present in both the planktonic and sessile phase of the cooling tower reactors. Heterotrophic aerobes were found to be the most abundant under all the operating conditions. Sulphate reducing bacteria were more abundant in the sessile phase of the cooling towers, and the presence of high sulphate levels in the experiments could be indicative of the sulphate reducing bacteria actively participating in the microbial community. Lower than expected corrosion levels, however, suggest that a combination of the organisms in the biofilm rather than sulphate reducing bacteria alone, contributed to the corrosion rates observed. Culture–independent methods, specifically phospholipid fatty acid analysis supported the results from the culture–dependent methods. Furthermore results demonstrated that linear flow velocity had a greater effect on the community structure than cycles of concentration. Finally molecular methods, specifically denaturing gradient gel electrophoresis, found that increasing cycles of concentration resulted in increased microbial community diversity, while increasing linear flow velocity resulted in decreased microbial community diversity. Regarding COD removal, nutrient correction of the synthetic PCB effluent achieved 89.35 % COD removal at 2 COC and 1.2 m/s LFV, while 80.85 % COD removal was achieved at 4 COC at 1.2 m/s LFV. From these results it was recommended that the operation of the cooling tower should be at 4 COC and 1.2 m/s, which despite slightly lower % COD removal, were characterised by fouling, scaling and corrosion rates well within guidelines. / Thesis (M. Environmental Science)--North-West University, Potchefstroom Campus, 2012.