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.

Diatoms associated with foraminifers of the genus Amphistegina were assessed using a combination of morphological and molecular techniques. These included: 1) microscopic identification of diatoms cultured from the host, 2) sequencing of portions of the small subunit of the ribosomal RNA gene (18S) and the large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase [i.e., RubisCO] gene (rbcL) from DNA extracted directly from the Amphistegina hosts and also from diatoms cultured from these hosts, and 3) denaturing gradient gel electrophoresis (DGGE) profiles of rbcL and internal transcribed spacer 1 (ITS1) PCR amplicons from DNA extracted directly from hosts and from cultures. Consistent with previous culture studies, multiple species of pennate diatoms of the genera Nitzschia, Fragilaria (including Nanofrustulum), Amphora, and Navicula, were cultured from >900 host specimens collected from >20 sites in the western Atlantic and four sites in the Pacific. Diatoms of the genus Nitzschia grew in about half of all successful cultures. The genetic identities of selected cultures were consistent with those based on morphological taxonomy. Diatom sequences from DNA extracted directly from the cytoplasm of the Amphistegina hosts were species specific and distinct from sequences obtained from cultured diatoms and from sequences in GenBank of diatom taxa previously reported as endosymbionts. Multiple phylogenetic analyses revealed that the 18S and rbcL diatom sequences from specimens of A. gibbosa collected from the Atlantic sites and of Amphistegina spp. from Hawai’i were most similar to the 18S and rbcL sequences of an unnamed Fragilariaceae diatom in GenBank (Accession # JX413542.1 for 18S and JX413559.1 for rbcL) and other closely related diatoms in that family. Of diatom taxa previously reported as endosymbionts of larger foraminifers, Nanofrustulum shiloi was the most similar, but not identical, to the sequences from hosts collected from the Atlantic and Hawai’i. The 18S and rbcL diatom sequences from the Atlantic host species, A. gibbosa, were all nearly identical, but small intra-species differences (subclades) were observed from specimens collected from the deepest (75 m) site in the Florida Keys and also from the eastern-most site, Young Island near St. Vincent. The 18S and rbcL diatom sequences from the two host species from Hawai’i, A. lobifera and A. lessonii, were more variable but still within the family Fragilariaceae. The diatom sequences from A. radiata collected from two sites in Papua New Guinea (PNG) were most similar to diatoms of the family Plagiogrammaceae and therefore distinct from sequences obtained from other Amphistegina species in this study, as well as from all diatoms previously reported as endosymbionts. A small difference was observed between the diatom sequences from host specimens collected from a Pacific site as compared to a Bismarck Sea site. The ITS1 DGGE profiles of DNA extracted directly from A. gibbosa specimens at different depths, locations, and seasons in the western Atlantic were nearly identical. Differences were seen between rbcL DGGE profiles of DNA extracted directly from the different Amphistegina host species. The rbcL DGGE profiles directly from all hosts were clearly different from those extracted from diatoms cultured from the same host specimens, as well as from Nitzschia laevis, a commonly reported diatom endosymbiont in past culture-based studies. My findings are consistent with ultrastructural studies of endosymbionts of Amphistegina published in the early 1980s and congruent with recent molecular studies of endosymbionts in other diatom-bearing foraminifers, all of which indicate specificity. Nevertheless, the consistency with which several diatom taxa have been reported in culture studies from all oceans indicates the possibility of some relationship with Amphistegina spp., either as important food items, epiphytes, or minor opportunistic symbionts that can thrive in culture media.

>Magister Scientiae - MSc / The class Actinobacteria consists of a heterogeneous group of filamentous, Gram-positive bacteria that colonise most terrestrial and aquatic environments. The industrial and biotechnological importance of the secondary metabolites produced by members of this class has propelled it into the forefront of metagenomics studies. The Ethiopian Rift Valley lakes are characterized by several physical extremes, making it a polyextremophilic environment and a possible untapped source of novel actinobacterial species. The aims of the current study were to identify and compare the eubacterial diversity between three geographically divided soda lakes within the ERV focusing on the actinobacterial subpopulation. This was done by means of a culture-dependent (classical culturing) and culture-independent (DGGE and ARDRA) approach. The results indicate that the eubacterial 16S rRNA gene libraries were similar in composition with a predominance of α-Proteobacteria and Firmicutes in all three lakes. Conversely, the actinobacterial 16S rRNA gene libraries were significantly different and could be used to distinguish between sites. The actinobacterial OTUs detected belonged to both the Rubrobacterales and Actinomycetales orders with members of the genus Arthrobacter being found in all three lakes. Geochemical properties were significantly different between the lakes, although more than one property attributed to the variance between community compositions. The diversity detected in the culture-based study differed significantly and all isolates belonged to the genus Streptomyces. Two novel strains were characterized by means of phylogenetic (16S rRNA gene sequence), physiological, morphological and biochemical analyses. Both novel isolates were capable of growing under "extreme" conditions- pH 12, 10% NaCl and 45°C. Partial enzyme characterization revealed that both strains produced xylanase enzymes that were active at pH 6.5 and 8.5 with an increase in activity up to 45°C. The results obtained revealed a previously undetected diversity of actinobacteria in the Ethiopian Rift Valley with a potentially novel subpopulation adapted to haloalkaline conditions. The low 16S rRNA sequence similarity of a substantial proportion of the libraries suggests that culture-based isolation may play a vital role in deciphering the community fingerprint. / The National Research Foundation and the Norwegian Research Council

No description available.

No description available.

Methyl tert-butyl ether (MTBE) has been used as a gasoline additive to improve the combustion efficiency and to replace lead since 1978. It is the most commonly used oxygenate now due to its low cost, convenience of transfer, and ease of blending and production. MTBE has become a prevalent groundwater contaminant because it is widely used and it has been disposed inappropriately. MTBE has been demonstrated an animal carcinogen. The US Environmental Protection Agency (US EPA) has temporarily classified MTBE as a possible human carcinogen and has set its advisory level for drinking water at 20-40 µg/L based on taste and odor concerns. The Taiwan Environmental Protection Administration (TEPA) also classifies it as the Class IV toxic chemical substances. Currently, natural attenuation (NA) as well as natural bioremediation or enhanced bioremediation are attractive remediation options for contaminated sites due to their economic benefit and environmental friendly. In general, in situ microorganisms at the contaminated site play a very important role in site restoration. Although early studies suggested that the biodegradability of MTBE was not significant, recent laboratory and field reports reveal that MTBE can be biodegraded under aerobic and anaerobic conditions. In addition, evidences and some successful cases of MTBE attenuation have been reported that make natural attenuation a considerable remedial strategy. However, the biodegrading rate might decrease if the nutritional and physiological requirements are not met. Thus, it is important to assess the biodegradability of natural microorganisms under various site conditions to obtain optimal remedial conditions. Contributions of intrinsic biodegradation and other abiotic mechanisms to the removal and control of contaminants should also be evaluated to provide sufficient information for remedial option determination. Moreover, isolation and identification of the dominant native microorganisms will be helpful to following remediation tasks. In the first part of this study, microcosm study and microbial identification technologies (denaturing gradient gel electrophoresis, DGGE) were applied to assess the biodegradability of MTBE by indigenous microbial consortia and to identify the dominant microorganisms at a MTBE-contaminated site (Site A). In the second part of this study, thorough field investigations were performed to evaluate the occurrence of natural attenuation of MTBE at two MTBE-contaminated sites (Site A and Site B). In addition, a natural attenuation model, BIOSCREEN, was performed to assess the effectiveness of natural attenuation on MTBE containment. The main objectives of this study contained the following: (1)Evaluate MTBE biodegradability under different redox conditions by the indigenous microorganisms. (2)Determine the dominant native microorganisms in MTBE biodegradation for further application. (3)Assess the feasibility of using natural attenuation to control the MTBE plume. (4)Evaluate the contributions of intrinsic biodegradation patterns on natural attenuation processes by BIOSCREEN. Results from the microcosm study reveal that MTBE could be biodegraded by aquifer sediments without the addition of extra carbon sources under aerobic conditions. The production of tert-butyl alcohol (TBA), a degradation byproduct of MTBE, was detected. Complete removal of TBA was also observed by the end of the experiment. Results from aerobic microcosms study indicate that oxygen might be the major limiting factor of MTBE biodegradation at Site A. Thus, MTBE at this site could be removed via natural biodegradation processes with the supplement of sufficient oxygen. Microcosm study with extracted supernatant of aquifer sediments as the inocula show that the indigenous microorganisms were capable of using MTBE as the sole carbon and energy source. The calculated MTBE degradation rate was 0.597 mg/g cells/h or 0.194 nmole/mg cells/h. No MTBE removal was observed under various anaerobic conditions. Results suggest that aerobic biodegradation was the dominant degradation process and aerobic bioremediation might be a more appropriate option for the site remediation. According to the results of DGGE analysis, aerobic MTBE-biodegrading bacteria, Pseudomonas sp. and Xanthomonas sp., might exist at this site. Although results of microcosm study show that MTBE could not be degraded under anaerobic conditions, the microbial identification indicates that some novel anaerobic microbes, which could degraded MTBE, might be present at this site. In addition, anaerobic microbes caused the consumption of electron acceptors (e.g., nitrate, ferric iron) and removal of benzene, toluene, ethylbenzene, xylenes (BTEX), 1,2,4-trimethyl benzene (1,2,4-TMB), and 1,3,5-trimethyl benzene (1,3,5-TMB) (TMBs) in the anaerobic microcosms. These results also indicate that the potential of anaerobes activities was high at Site A. Based on the results from the field investigation, natural attenuation of MTBE was occurring at both sites. MTBE plume at Site B could be effectively controlled via natural attenuation processes. Nevertheless, MTBE plume at Site A has migrated to a farther downgradient area and passed the boundary of the site. Field investigation results indicate that the natural attenuation mechanisms of MTBE at both sites were occurring with the first-order attenuation rates of 0.0021 and 0.0048 1/day at Sites A and B, respectively. According to BIOSCREEN simulation, biodegradation was responsible for 78% and 59% of MTBE mass reduction at Sites A and B, respectively. The intrinsic biodegradation had significant contributions on the control of MTBE plumes. Moreover, the dilution and dispersion processes might be the major mechanisms for the attenuation of MTBE in the downgradient areas. However, results also reveal that intrinsic biological processes might still fail to contain the plume if the selected point of compliance is not appropriate. Results of this study suggest that natural attenuation might be feasible to be used as a remedial option for the remediation of MTBE-contaminated site on the premise that (1) detailed site characterization has been conducted, and (2) the occurrence and effectiveness of natural attenuation processes have been confirmed. Based on the results from the field investigation and laboratory microcosm studies, MTBE could be biodegraded by natural microbial populations at the studied sites under both aerobic and anaerobic conditions and natural attenuation would be applied as a remedial option at MTBE-contaminated sites. Results from this study would be useful in determining the favorable bioremediation conditions and designing an efficient and cost-effective bioremediation system such as monitored natural attenuation (MNA) or in situ or on-site MTBE bioremediation system for field application.

Allergic diseases, for example asthma and eczema, are nowadays considered belonging to the most common chronic diseases amongst children in the West, but the cause for this increase in allergy prevalence is unknown. Since studies have indicated a connection between children's exposure of microorganisms during infancy and risk of developing allergic disease, it is suggested that this exposure is a crucial factor in question of allergy development or not. Other studies have established differences in microflora composition between healthy children and children with allergic disease, and several studies have shown that probiotic therapy can give positive results in both prevention and treatment of allergic diseases. The aim of this master's thesis was to develop a method, using PCR and denaturing gradient gel electrophoresis, to study the diversity of Lactobacillus spp. in fecal samples retrieved from a study of the probiotic strain L. reuteri ATCC 55730. The developed method was successful in detecting lactobacilli in fecal samples, but three other bacterial genera commonly found in humans were also amplified. Comparison of average numbers of detected bacterial strains and lactobacilli strains between samples belonging to the probiotics and placebo groups, respectively, showed higher numbers for the probiotics group. Also, the only fecal samples that contained L. reuteri belonged to the probiotics group. Although the results are far from statistically significant, they support the theories that probiotics may influence the intestinal microbiota.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

In human microbiome analysis, sequencing of bacterial 16S rRNA genes has revealed a role for the gut microbiota in maintaining health and contributing to various pathologies. Novel community analysis techniques must be evaluated in terms of bias, sensitivity, and reproducibility and compared to existing techniques to be effectively implemented. Next- generation sequencing technologies offer many advantages over traditional fingerprinting methods, but this extensive evaluation required for the most efficacious use of data has not been performed previously. Illumina libraries were generated from the V3 region of the 16S rRNA gene of samples taken from 12 unique sites within the gastrointestinal tract for each of 4 individuals. Fingerprint data were generated from these samples and prominent bands were sequenced. Sequenced bands were matched with OTUs within their respective libraries. The results demonstrate that denaturing gradient gel electrophoresis (DGGE) represents relatively abundant bacterial taxa (>0.1%) beta-diversity of all samples was compared using Principal Coordinates Analysis (PCoA) of UniFrac distances and Multi-Response Permutation Procedure (MRPP) was applied to measure sample cluster strength and significance; indicator species analysis of fingerprint bands and Illumina OTUs were also compared. The results demonstrate overall similarities between community profiling methods but also indicate that sequence data were not subject to the same limitations observed with the DGGE method (i.e., only abundant taxa bands are resolved, unable to distinguish disparate samples). In addition, the effect of stochastic fluctuations in ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? differ for DGGE and next-generation sequencing. I compared pooled and individual reactions for samples of high and low template concentration for both Illumina and DGGE using the combined V3-V4 region of the 16S rRNA gene, and demonstrated that template concentration has a greater impact on reproducibility than pooling. This research shows congruity between two disparate molecular methods, identifies sources of bias, and establishes new guidelines for minimizing bias in microbial community analyses.

[Truncated abstract] In Australia, there is pressure to reduce the amount of methane produced by ruminant livestock because they are the single largest source of methane emitted from anthropogenic sources, accounting for 70.7% of agricultural methane emissions. In addition, methane production represents a loss of gross energy intake to the animal. The organisms that are responsible for methane production in the animal gut are a distinct group of Archaea called methanogens. Methanogens occupy three different niches within the rumen. Some live freely in the rumen digesta (planktonic), others are attached to the outer surface of the rumen ciliates (ectosymbiotic), and some reside within the ciliates (endosymbiotic). The types and number of methanogens, as well as rumen ciliates and their symbiotic interactions, influence the amount of methane produced from the rumen. These factors in turn are affected by many factors, including diet and ruminal retention time. In this thesis, I tested the general hypothesis that increasing the amount of grain in the diet and reducing the retention time would affect the abundance and diversity of methanogens in their different niches, including their association with ruminal ciliates. Twenty-four fistulated sheep were used in a complete factorial design with the sheep randomly divided into four groups. ... The change in DGGE banding patterns and Shannon indices when sheep were fed grain indicated that the types of methanogens changed when sheep were fed low and high grain diets, but their diversity did not. In contrast, the diversity of rumen ciliates decreased when sheep were fed a high grain diet. A total of 18 bands from the DGGE analysis of the ciliates were sequenced. All except one, which was 98% similar to Cycloposthium sp. not found previously in the rumen, matched the sequences for previously identified rumen ciliates. Some of the rumen ciliates identified were not present in sheep fed the high grain diet. On a high grain diet, methanogens associate endosymbiotically with rumen ciliates to get better access to hydrogen. It appears that the association between methanogens and rumen ciliates is dictated by the availability of hydrogen in the rumen and not the generic composition of the ciliate population. Furthermore, endosymbiotic methanogens appear to produce less methane than methanogens in other niches. The pot scrubbers did not change ruminal retention time but they did reduce the acetate/propionate measurements observed in sheep on the high grain treatment. The reason why pot scrubbers had this effect remains unknown, but it is interesting to consider that some physical interaction has occurred between the pot scrubbers, the grain and the sheep that has improved the fermentation parameters in sheep fed a high grain diet. The results from this study have advanced our understanding of the interaction between methanogens and ruminal ciliates, and methanogenesis in the rumen in response to dietary changes and mechanical challenges. Extending this work to look more specifically at the species of methanogens that are most closely linked to high methane production and how they interact with the ruminal ciliates will be critical for manipulating enteric greenhouse gas emissions.