Дисертації: "MICROBIALLY"

1

Li, Kwan (Kwan Hon). "Microbially influenced corrosion in sour environments." Thesis, Massachusetts Institute of Technology, 2014. http://hdl.handle.net/1721.1/88382.

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Thesis: S.M., Massachusetts Institute of Technology, Department of Materials Science and Engineering, 2014.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 119-123).
Microbially influenced corrosion (MIC) is a costly and poorly understood source of corrosion that plagues many modern industrial processes such as oil extraction and transportation. Throughout the years, many possible mechanisms for MIC have been proposed. One specific proposed mechanism was tested in this thesis: that the metal-binding characteristic of bacterial biofilms enhanced corrosion when it appears in conjunction with an iron sulfide film. Two model biogels were used: calcium alginate, which has this metal-binding property, and agarose, which does not. In pursuit of this hypothesis, iron sulfide films were grown on mild steel coupons. Two distinct forms of iron sulfides were grown: a loose black product at low sulfide concentrations, and an adherent gold product at high sulfide concentrations. Many materials characterization techniques were attempted, and the black corrosion product was found to be a mixture of greigite and marcasite. However, this composition was observed to change irreversibly with the application of a laser that caused the material to either heat and/or dry. The resulting golden-colored corrosion product was found to consist mainly of monosulfides, implying the presence of mackinawite or pyrrhotite. By using electrochemical polarization experiments, it was found that calcium alginate enhanced the rate of corrosion; agarose reduced the rate of corrosion. This is in contrast to previously published literature. Contrary to the initial hypothesis, adding an underlying iron sulfide film did not appreciably alter the measured rate of corrosion. Additionally, it was found that biofilms generated by sulfate-reducing bacteria (SRB) enhanced corrosion in a manner similar to the calcium alginate gel, and lysing the cells within the biofilm did nothing to alter this effect. This implies that the biofilm itself, even in the absence of active bacterial metabolic activity, can enhance corrosion rates observed in MIC.
by Kwan Li.
S.M.

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2

Montross, Scott Norman. "Geochemical evidence for microbially mediated subglacial mineral weathering." Thesis, Montana State University, 2007. http://etd.lib.montana.edu/etd/2007/montross/MontrossS0507.pdf.

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Interactions between dilute meltwater and fine-grained, freshly comminuted debris at the bed of temperate glaciers liberate significant solute. The proportions of solute produced in the subglacial environment via biotic and abiotic processes remains unknown, however, this work suggests the biotic contribution is substantial. Laboratory analyses of microbiological and geochemical properties of sediment and meltwater from the Haut Glacier d\'Arolla (HGA) indicates that a metabolically active microbial community exists in water-saturated sediments at the ice-bedrock interface. Basal sediment slurries and meltwater were incubated in the laboratory for 100 days under near in situ subglacial conditions. Relative proportions of solute produced via abiotic v. biotic mineral weathering were analyzed by comparing the evolved aqueous chemistry of biologically active (live) sediment slurries with sterilized controls. Aqueous chemical analyses indicate an increase in solute produced from mineral weathering coupled with nitrate depletion in the biologically active slurries compared with the killed controls. These results infer that microbial activity at HGA is likely an important contributor to chemical weathering associated solute fluxes from the glaciated catchment. Due to the magnitude of past glaciations throughout geologic time (e.g., Neoproterozoic and Late-Pleistocene), and evidence that subglacial microbial activity impacts mineral weathering, greater consideration needs to be given to cold temperature biogeochemical weathering and its impact on global geochemical cycles.

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3

Lu, Xinxin. "Microbially Mediated Transformation of Dissolved Nitrogen in Aquatic Environments." Kent State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=kent1429540424.

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4

Porter, Hannah Elizabeth. "Stabilisation of Geomaterials using Microbially Induced Calcium Carbonate Precipitation." Thesis, Curtin University, 2018. http://hdl.handle.net/20.500.11937/75981.

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The Australian landscape has a large number of naturally cemented structures, which provide inspiration for a sustainable cementing material which does not produce carbon dioxide during the manufacturing phase. Structures such as corals, beach rocks and stromatolites are cemented through the process of Microbially Induced Calcium Carbonate Precipitation, (MICP). This thesis reports on the potential for MICP as a replacement or augmentation to chemical binders in geomaterials and evaluates the sustainability of MICP using Life Cycle Analysis.

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5

Asare, Noble Kwame. "Microbially-mediated methyl iodide cycling in a particle-rich estuary." Thesis, University of Plymouth, 2007. http://hdl.handle.net/10026.1/2611.

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The dynamics of aquatic systems (e.g. estuarine systems) are known to facilitate the formation of particle aggregates. These nutrient-rich particulate matter provide suitable substrate for bacteria colonization. Although bacteria-aggregate association is known to result in the degradation of particulate organic matter (POM) in aquatic systems, it has never been attributed to the production of methyl iodide (CH3I) (an environmentally important biogas that has the potential to impact on atmospheric chemistry). From literature, there are evidences which suggest that, certain bacteria (methylotrophs) are capable of oxidizing methyl halides including CH3I. Therefore this study investigates microbial production and removal of CH3I in estuarine water through their association with aggregates and assesses the effect of physicochemical variables on bacterial-mediated production and removal of CH3I. From the study, bacteria-aggregate processes were found to elevate the concentration of CH3I between 15-22% of the total observed CH3I concentration over the study period. Aggregate-attached bacteria which were estimated to represent about 17% of the total bacteria population were responsible for about 37% of the overall bacterial activity. To investigate bacterial-mediated removal of CH3I in estuarine systems, a reliable and reproducible method through adaptations and modifications of existing methods was developed. This method involved the use of [14C] radiolabelled CH3I to estimate bacterial utilization of CH3I. The application of the method confirmed the removal of CH3I by methylotrophs in estuarine water with the total recorded amount in bacterial cells and oxidized C02 ranging between 9.3 - 24.5% (depending on the amount of the added substrate). However, this could only represent the potential microbial CH3I removal in the natural aquatic environment. An investigation into spatial and temporal trends in bacterial-mediated removal of CH3I in the Tamar estuary revealed no significant spatial variation but rather a strong seasonality in methylotrophic bacterial CH3I removal. Spatial trends in CH3I removal was found to be mostly influenced by temperature, bacterial abundance and dissolved oxygen concentration whilst the seasonality in the estuary was influenced by temperature, bacterial abundance, suspended particulate matter (SPM) and CH3I concentration. Temperature was identified to be the single most influential physicochemical variable on both spatial and seasonal variation in bacterial CH3I removal in the Tamar estuary. CH3I concentration along the Tamar estuary was also investigated and using this data the total water to air flux of CH3I over the estuary was estimated to be 0.31 x 10³ g yˉ¹. From this study, it was apparent that bacteria activity in estuarine systems is potentially an important source of CH3I in the aquatic environment when associated with aggregates or as sink of CH3I through methylotrophic activity in estuaries.

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6

Leitholf, Andrew M. "Iron Cycling In Microbially Mediated Acid Mine Drainage Derived Sediments." University of Akron / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=akron1434976163.

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7

Cheng, Liang. "Innovative ground enhancement by improved microbially induced CaCO3 precipitation technology." Thesis, Cheng, Liang (2012) Innovative ground enhancement by improved microbially induced CaCO3 precipitation technology. PhD thesis, Murdoch University, 2012. https://researchrepository.murdoch.edu.au/id/eprint/15329/.

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The possibility of using microbiological processes to improve the mechanical properties of soil by undisturbed in-situ application has gained attention over recent years. This study has contributed to the technology of biocement, based on microbially induced carbonate precipitation (MICP), for the purpose of soil reinforcement application. MICP involves both the hydrolysis of urea by bacterial urease enzyme and calcium carbonate precipitation in the presence of dissolved calcium ions. Other previously published approaches were based on saturated flow (submersed flow), which is accomplished by pumping solutions from an injection point to a recovery point which is limited exclusively to water saturated soil. This work describes a new variation of in-situ soil reinforcement technology by using surface percolation via – for example – spray irrigation onto dry, free draining ground, such as dunes or dykes. In order to accomplish bacterial immobilization by surface percolation, it was necessary to alternately percolate bacterial suspension and cementation solution (CaCl2 and urea) to form sequential solution layers within the sand columns. By allowing Ca2+ ions diffusion between each layer bacterial immobilization could be enhanced from 30% to 80%. For a limited number of about 3 to 4 treatments this novel application method of cementation allowed homogeneous strength over the depth of the entire 1 m sand column. Although the strength was homogenous, CaCO3 analysis showed that about 3 times less crystals were precipitated in the top layer compared to the bottom layers suggesting differences in efficiency of the calcite crystal to provide strength. This work demonstrated that this efficiency of calcite crystals was related to the pore water content of the continuously drained column with less water content enabling more efficient strength formation. The geotechnical properties of bio-cemented sand samples under different degrees of saturation confirmed that higher strength could be obtained at lower degrees of saturation. To our knowledge, this study was the first study to demonstrate that the calcite crystals formed under a lower degree of saturation had more crystals formed in the contact points, contributing to the strength of the cemented samples. These preferred crystal formation was caused by the retained cementation solution situated in the form of menisci between sand particles at low degree of saturation. Scanning electron microscopy supported the idea that lower water contents lead to selective positioning of crystals at the bridging points between sand grains. After biocementation treatment, fine sand samples exhibited significant increase in cohesion from 1.1 to 280 kPa and friction angle from 23o to 41o. Similar improvements were also obtained for coarse sand samples. Overall, fine sand sample indicated higher cohesion but lower friction angle than coarse sand samples having similar CaCO3 content. The performance of cementation in large (2 m) laboratory scale trials indicated that subsequent treatments of more 4 times in fine sand caused clogging close to the injection end, resulting in limited cementation depth less than 1 m. This clogging problem was not observed in the 2 m treated coarse sand column, which had strength varying between 850 to 2067 kPa. This showed that the surface percolation technology was more applicable for coarse sand soil. The laboratory large scale application (80 L) of fine sand cementation indicated that relatively homogenous cementation in the horizontal direction could be achieved with 80% of cemented sand having strength between 2 to 2.5 MPa. This suggested that although the liquid infiltration flow paths could not be controlled in the surface percolation method, self-adjusting flow paths were triggered by the changed internal flow resistance caused by the precipitated crystals, favoring the homogeneous cementation. A simple mathematical model demonstrated that the cementation depth is dependent on the infiltration rate of cementation solution and the immobilized urease activity. Higher infiltration rate and lower urease activity will enable in deeper cementation. The model also predicted that repeated treatments will enhance sand clogging close to the injection point. The traditional production of ureolytic bacteria used for biocementation is very expensive, because of strictly sterile processing. This study described the sustainable, non-sterile production of urease enzyme using activated sludge as inoculum. By using selective conditions (high pH and high ammonia concentration) for the target ureolytic bacteria plus the presence of urea as the enzyme substrate, highly active ureolytic bacteria, physiologically resembling Bacillus pasteurii were enriched and continuously produced from chemostat operation of the bioreactor. When using a pH of 10, and about 0.17 M urea in a yeast extract based medium ureolytic bacteria developed under aerobic chemostat operation at hydraulic retention times of about 10 h with urease levels of about 60 U/ml culture. This activity is six times higher than required for successful biocementation. The protein rich yeast extract medium could be replaced by commercial milk powder or by lysed activated sludge, which could make the industrial production less costly. A method of in-situ production of urease activity was developed. This method involved providing selective growth medium to allow ureolytic bacteria to proliferate and produce urease activity in-situ of sand column. The aerobic ureolytic bacteria inoculum could only be enriched in unsaturated coarse sand column, where sufficient oxygen was available. However, high urease activities of 20 and 10 U/mL were obtained by growing soil bacteria under aerobic and anaerobic conditions respectively. The successful enrichment of highly urease active bacteria under anaerobic conditions could allow the in-situ production of urease activity at water logged soils. The in-situ produced urease activities by the enriched soil ureolytic bacteria were sufficient to allow successful cementation of fine (>500 kPa) and coarse (>1000 kPa) sand columns. The strength and CaCO3 analysis indicated that the common obstacle of surface clogging in deeper fine sand column was avoided, explained by avoiding bacterial accumulation at the top of the column. In combination, all findings of the present study imply that the cost of MICP technology can be reduced by optimizing the conditions for effective crystals precipitation by providing low saturation conditions when the cementation is operated. The cost reduction can also be achieved by producing urease activity more economically by omitting the requirement of sterilization (non-sterile cultivation) and bioreactor (in-situ growth). These are expected to make this technology more readily acceptable for field applications.

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8

Arthur, Mickey Francis. "Soils containing 2,3,7,8-tetrachlorodibenzo-p-dioxin : aspects of their microbial activity and the potential for their microbially-mediated decontamination /." The Ohio State University, 1987. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487330761218489.

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9

Dawoud, Osama M. F. "The applicability of microbially induced calcite precipitation (MICP) for soil treatment." Thesis, University of Cambridge, 2016. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.709509.

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10

Doloman, Anna. "Optimization of Biogas Production by Use of a Microbially Enhanced Inoculum." DigitalCommons@USU, 2019. https://digitalcommons.usu.edu/etd/7531.

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A renewable energy source, biogas, comprises of methane (80%) and carbon dioxide (15%), and is a great alternative to the conventional fossil-based fuels, such as coal, gas and oil. Biogas is created during anaerobic biological digestion of waste materials, such as landfill material, animal manure, wastewater, algal biomass, industrial organic waste etc. A biogas potential from organic waste in the United States is estimated at about 9 million tons per year and technology allows capture of greenhouse gases, such as methane and carbon dioxide, into a form of a fuel. In the light of global climate change and efforts to decrease carbon footprint of fuels in daily life, usage of biogas as an alternative fuel to fossil fuels looks especially promising. The goal of this research was to develop and test an approach for optimization of biogas production by engineering microorganisms digesting organic waste. Specifically, bacteria that can digest algal biomass, collected from the wastewater lagoons or open waterbodies. The research also expands on the previous efforts to analyze microbial interactions in wastewater treatment systems. A computational model is developed to aid with prognosis of microbial consortia ability to form complex aggregates in reactors with upflow mode of feeding substrate. Combining modeling predictions and laboratory experiments in organic matter digestion will lead to more stable engineered systems and higher yields of biogas.

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11

Dieser, Markus. "Ecosystem dynamics and temporal variations in a microbially dominated, coastal antarctic lake." Thesis, Montana State University, 2009. http://etd.lib.montana.edu/etd/2009/dieser/DieserM1209.pdf.

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This study investigated the microbial ecology of Pony Lake, Antarctica. The main objectives of this research were to 1) characterize physicochemical parameters in Pony Lake during the transition from ice covered to ice free, 2) highlight seasonal and inter-seasonal alterations in lake parameters, 3) relate the physicochemical conditions in the ice and water column to microbial processes and community structure, 4) characterize the effects of phototransformation of dissolved organic matter (DOM) on its bioavailability to bacteria, and 5) demonstrate the role of carotenoid pigments in protecting cells against environmental stresses. Also included are results from three McMurdo Dry Valley lakes on the survivability of microbes encapsulated within the lake ice covers. The results of this study highlight the sensitivity of Antarctic environments and the close coupling of environmental conditions and biological processes. Inter-seasonal differences in weather conditions and snow accumulation strongly affected the physicochemistry of this lacustrine system. Biological processes were closely tied to the physicochemical lake conditions. As a consequence planktonic abundances, production rates, and community structure evolved distinctly in each year. Bacterial production was regulated by the quality of DOM. Whereas nutrient availability appeared to play a minor role in eutrophic Pony Lake water, it became more critical for microbial communities found within the ice column of Antarctic lakes. Especially in the ice cover of the McMurdo Dry Valley lakes, enhanced microbial diversity and survivability was associated with particles (nutrient enriched micro-zones) within an otherwise ultra-oligotrophic habitat. In Pony Lake ice, microbial activity and community structure differed with respect to different strata within the ice column, induced by freeze-concentration of solutes, bioavailability of DOM, and oxygen gradients. A comparison of carotenoid pigmented and non-pigmented heterotrophic bacteria indicated that pigmentation provides enhanced resistance to environmental stresses such as freeze-thaw cycles or solar radiation. Collectively, the Pony Lake data demonstrated that microorganisms that persist throughout the year were able to survive much more severe conditions while entrapped within the ice compared to those observed in the lake water during summer months. Further, this study contributes to a better understanding of the biogeochemical carbon cycle in a microbially dominated system.

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12

Sutton, Jeremy. "Microbially influenced corrosion (MIC) of steels in mono- and hyper-baric environments." Thesis, Robert Gordon University, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.241029.

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13

Nasr, Mostafa M. "Mitigation of Microbially Induced Concrete Corrosion in Wastewater Infrastructure using Surface Treatments." Youngstown State University / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=ysu1619950217448915.

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14

Eismin, Ryan J., and Ryan J. Eismin. "Surface, Aggregation, and Phase Characterization of Microbially-Produced & Chemically-Synthesized Monorhamnolipids." Diss., The University of Arizona, 2017. http://hdl.handle.net/10150/623026.

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The purpose of this research has been to explore the native monorhamnolipid (mRL) mixture produced by Pseudomonas aeruginosa ATCC 9027, as well as newly- synthesized monorhamnolipid diastereomers (R,R)-Rha-C10-C10, (R,S)-Rha-C10-C10, (S,S)-Rha-C10-C10 and (S,R)-Rha-C10-C10, to understand their aggregation and phase behavior in aqueous solution. This work is in response to the consideration that biosurfactants offer a "greener" alternative to conventional surfactants. Relationships between chemical structure of the diastereomers and surface activity were studied using surface tension measurements. It was found that the critical aggregation concentration (CAC) values are lower for deprotonated (R,S)-Rha-C10-C10 and higher for protonated (R,S)-Rha-C10-C10 compared to the other diastereomers or the native mRL mixture. Furthermore, the 1:1:1:1 diastereomeric mixture has the overall lowest cross-sectional area for deprotonated rhamnolipids. Dynamic light scattering (DLS) was used to study the hydrodynamic radii (Rh) of the mRL aggregates and the four diastereomers in aqueous solution. In all five surfactants studied, each observed at pH 8.0 and 4.0, three aggregate populations were observed. For all deprotonated rhamnolipids the micelle, at a hydrodynamic radius of ~2 nm, was found to be in the highest abundance where the two lower abundant other population take on a lamellar aggregate structure. Data to support this were collected using fluorescence probing techniques. For the surfactants in the protonated state, pH 4.0, it was found that all form primarily lamellar structures, also confirmed using fluorescence probing. The average aggregation numbers (Nagg) of the micelles for the deprotonated native mRL mixture and the four diastereomers were studied using steady-state and time-resolved fluorescence quenching measurements. Somewhat unexpectedly, the Nagg values were observed to be a strong function of the rhamnolipid concentration for all systems. At low concentrations, pre-micellar aggregates with aggregation numbers too small for micelles were observed. A critical concentration is identified at which a critical aggregation number is defined; this is proposed to be the smallest fully-formed micelle in solution with values of ~25-30 molecules/micelle for the native mRL mixture and all four diastereomers. Thus, the aggregation properties of the native mRL mixture and the four diastereomers are generally similar at this critical concentration. However, the increase in aggregation number above this critical point varies for all the surfactants, where the (R,R)-Rha-C10-C10 diastereomer has the greatest increase in monomers with concentration and the (S,S) and (R,S) diastereomers have the lowest. The increased observed aggregation number is consistent with the computational work showing increased growth with concentration for the deprotonated rhamnolipid micelles. Furthermore, these computations have confirmed the ability of protonated rhamnolipids to form lamellar structures in solution. Fluorescence probing work was also used to study rhamnolipid phase behavior as a function of varying solution conditions, such as ionic strength, solution pH, surfactant concentration, and temperature. Steady-state fluorescence methods are utilized to probe the surfactant microenvironment using the polarity-sensitive dyes prodan and laurdan. By dissolving the dye within the rhamnolipid aggregates and observing their solvatochromic behavior, all surfactants studied are known to form more micellar aggregates at high pH and low surfactant concentration, whereas elongation of the micelle is observed at low pH and moderate to high surfactant concentration.

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15

Cook, Joseph. "Microbially mediated carbon fluxes on the surface of glaciers and ice sheets." Thesis, University of Sheffield, 2012. http://etheses.whiterose.ac.uk/2882/.

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Measurements from Austre Brøggerbreen (Svalbard, 2009) and the Greenland Ice Sheet (GrIS, near Kangerlussuaq, 2010) are used to examine microbially mediated supraglacial carbon fluxes and feedbacks between these fluxes and the abiotic conditions at the ice surface. Linear relationships between mass and area of cryoconite deposits indicate constant sediment layer thicknesses at a range of Arctic locations. This is suggested to result from a tendency for cryoconite to form a layer of single grains, with the thickness determined by grain diameter. A thermodynamic mechanism of single grain layer (SGL) maintenance is proposed, in which holes expand laterally to accommodate increased sediment volumes. This is shown to reduce ice surface albedo and promote photosynthesis because the greatest possible surface area for irradiance of cryoconite is maintained. Since cryoconite only contributes to supraglacial carbon fluxes while it resides upon ice surfaces, two major mechanisms of sediment evacuation are examined: melt-out and hydraulic removal. Energy balance modelling indicates that melt out is unlikely unless high air temperature and low incident radiation persist for multiple days. Stream migration is proposed to be the most likely mechanism of sediment removal; however for the majority of holes, multi-year residence times can be expected. This thesis also provides new estimates of microbially mediated carbon fluxes from the GrIS. New models estimate carbon fluxes from a section of GrIS for which spatially variable parameter values were derived from point-to-point interpolation of field data. An algal ecosystem is included for the first time. The results indicate that cryoconite can fix about four times more carbon than previously predicted, and surface algal ecosystems fix about eleven times more carbon than cryoconite. Biologically mediated carbon fluxes on the GrIS are therefore shown to be much higher than previously thought. Further, the GrIS is shown to be in a relatively stable state of net autotrophy.

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16

McKinzi, Adonia. "A microbially-driven Fenton reaction for oxidative dechlorination of pentachlorophenol by shewanella putrefaciens." Diss., Georgia Institute of Technology, 1999. http://hdl.handle.net/1853/30637.

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17

Poggenburg, Christine [Verfasser]. "Microbially-mediated transformation and mobilization of Fe-organic associations in the soil / Christine Poggenburg." Hannover : Technische Informationsbibliothek (TIB), 2018. http://d-nb.info/1163206032/34.

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18

Widanagamage, Inoka Hasanthi. "STABLE STRONTIUM ISOTOPE FRACTIONATION IN ABIOTIC AND MICROBIALLY MEDIATED BARITE IN MODERN CONTINENTAL SETTINGS." Kent State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=kent1445344122.

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19

Johnston, Lori A. "Investigation and sustainable management of microbially induced biofouling in porous media using electro-motive forces." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/MQ59504.pdf.

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20

Sima, Hong. "Selective inhibition of acidophilic thiobacilli for application of controlling microbially-induced corrosion in concrete sewers." Diss., The University of Arizona, 1992. http://hdl.handle.net/10150/185991.

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Recent interest in Thiobacillus thiooxidans has arisen from its central role in rapid, costly corrosion of concrete sewers. This study focuses on biochemical and ultrastructural responses of the intact cells and isolated carboxysomes, the polyhedral inclusions and CO₂ fixation sites, of the chemolithoautotroph to chemical inhibitors. Inhibition experiments were conducted in pure, batch cultures, grown in a basal salts medium using elemental sulfur as the energy source. D-ribulose 1,5-bisphosphate carboxylase (RuBPCase), the key enzyme of CO2 assimilation in T. thiooxidans, was chosen as the target for chemical inhibition. Observations were based on multiple metabolic measurements of cell growth, acid production, O2 respiration, CO₂ assimilation, intracellular ATP, and subcellular ultrastructure. Weak organic acids proved capable of inhibiting thiobacillus metabolism. Bacterial sensitivity was strongly dependent upon culture pH relative to the respective pKₐ values. Pyruvate and oxaloacetate were strong growth inhibitors. 2-c-carboxy-Darabinitol 1,5-bisphosphate (CABP) and hydroxylamine blocked in vivo CO2 assimilation and growth of T. thiooxidans without affecting on bacterial respiration. Evidence that the primary site of the selective inhibition lies on the biosynthetic side was supported by measurements of intracellular ATP and transmission electron microscopy (TEM). Dimethyl sulfoxide (DMSO) substantially promoted CABP inhibition of CO2 fixation by increasing cell membrane permeability. Carboxysomes were observed in intact cells of T. thiooxidans and characterized in the isolated form. Cell partitioning experiments showed that RuBPCase is sequestered and concentrated in these polyhedral inclusions. TEM observations were performed in conjunction with inhibitor studies. Treatment with the specific inhibitors, such as CABP and hydroxylamine, more than doubled the numbers of carboxysomes per cell without altering the shape and structure of the inclusion bodies, while effectively blocking both in vivo and in vitro CO₂ fixation. In contrast, non-specific inhibitors (cyanide, etc.) caused general intracellular disorder in thiobacilli and structural damage among isolated carboxy somes at concentrations that inhibited metabolic activities. Results suggest that by targeting critical, unique biochemical features of the acidophilic thiobacilli, it is possible to selectively inhibit these organisms, thereby mitigating the severity of sewer corrosion, without affecting general sewer biota or endangering down-stream biological wastewater treatment operations.

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21

Schalnat, Tracey. "Metal Complexation and Interfacial Behavior of the Microbially Produced Surfactant Monorhamnolipid by Pseudomonas Aeruginosa ATCC 9027." Diss., The University of Arizona, 2012. http://hdl.handle.net/10150/268577.

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The purpose of the research reported in this dissertation is to expand the general knowledge of the chemical properties of monorhamnolipids (produced by P. aeruginosa ATCC 9027) and monorhamnolipid-metal complexes in solution and at interfaces in order to advance the application of these biosurfactants in a variety of applications.The speciation and fragmentation behavior of monorhamnolipids (mRLs) using mass spectrometry at low and high resolution in positive ion mode was investigated as a function of pH, which has yet to be fully discussed to date in the literature. This study laid the groundwork for the speciation and fragmentation behavior of mRLs with two environmentally-relevant heavy metals, Pb²⁺ and UO₂²⁺. It was determined that mRLs form 1:1 and 2:1 mRL-metal complexes with both metal cations across the pH range investigated (pH 4.0, 6.0 and 8.0). mRL-metal complexes were found to fragment differently than free mRLs suggesting coordination of the metal cation in a binding pocket comprised of the mRL carboxylic acid moiety and the rhamnose sugar hydroxyls. This coordination environment was further verified as a function of solution pH using infrared spectroscopy (IR), nuclear magnetic resonance spectrometry (NMR) and hydrogen-deuterium exchange (HDX) mass spectrometry. Adsorption isotherms for mRLs and mRL-metal complexes on two soil components, silica and goethite, were characterized as a function of solution pH using ATR-FTIR and successfully fit to the Frumkin-Fowler-Guggenhiem isotherm to extract relevant thermodynamic adsorption parameters. These studies showed that at low pH, mRLs form bilayers on these surfaces, but the adsorption affinity of the mRLs is dictated by the molecular interactions these species have with the specific oxide surface. At neutral and basic pH values, mRLs were found to adsorb to silica despite the fact that both the surface and the mRLs are negatively charged. The Lewis acid/base interactions of mRLs with goethite at neutral and basic pH values results in multilayer adsorption. Adsorption of mRL-metal complexes on silica and goethite suggests that the interactions between these complexes and soil surfaces may have a direct impact on metal ion remediation efficiencies using mRLs. The adsorption affinity of mRL-Pb²⁺ complexes to silica is greater than that of mRL-UO₂²⁺ complexes; however, mRL-UO₂²⁺ complexes precipitate at the interface. The adsorption affinity of mRL-metal complexes on goethite is not significantly lower than for free mRLs; however, the surface coverage decreases.

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22

Coffey, Melody Roy. "Microbially Mediated Porosity Enhancement in Carbonate Reservoirs: Experiments with samples from the Salem, Sligo, and Smackover Formations." MSSTATE, 2004. http://sun.library.msstate.edu/ETD-db/theses/available/etd-10122004-105856/.

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This study used petrographic thin sections, scanning electron microscopy, and confocal laser microscopy to document microbially mediated dissolution of carbonate reservoir rocks. The samples studied came from three carbonate units that are hydrocarbon reservoirs; the Salem, Sligo, and Smackover formations. These samples were inoculated with bacteria, and then treated with nutrient solutions followed by ethanol to promote generation of acetic acid by bacteria. Dissolution occurred in calcite-dominated rocks and in dolomitized rocks. Noticeable changes first occurred after nine weeks of ethanol treatment and significant change only occurred after twelve weeks of ethanol treatment. The size of the vuggy pores created increased from 1 µm or less to over 5 µm, and rarely over 10 µm, in length.

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23

MacLachlan, Erica. "Development of a microbially induced calcite and silica bio-grout for the sealing of fine aperture fractures." Thesis, University of Strathclyde, 2017. http://digitool.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=28758.

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Geological repositories are being considered as the best feasible solution for the storage of hazardous materials such as high level nuclear waste throughout the world, including the UK. However; when crystalline rock is the chosen storage medium, the construction of the underground tunnels and caverns can enhance discontinuities within the rock. These discontinuities can be pathways by which radio-nuclides can reach the biosphere, due to their higher permeability, connectivity and density (Blyth and Freitas, 1992). Thus, depending on aperture, density and predicted travel times, it may be necessary to grout all fractures, even small aperture ones, which over thousands of years can contribute significantly to subsurface flow. Conventional cementitious and chemical grouts are unsuitable within some regions of a geological disposal facility due to concerns regarding longevity, toxicity, reactions with other barriers and/or workability issues. The four main requirements of a grout are; to be of low viscosity as the lower the viscosity the easier it is to achieve good penetration, to have a controllable gel/setting time, to be chemically inert to prevent reactions within the subsurface or have any toxic consequences during preparation, and to be durable thus able to withstand exposure to varying physic-chemical condition. MICP (Microbially Induced Calcite Precipitation) and Colloidal Silica are novel grouts which may be suitable for the sealing of fine aperture fractures in rock. MICP research has been predominantly focussed on its application in sediments, whilst colloidal silica has shown its potential for reducing the liquefaction potential of non-cohesive soils and for sealing fractures. This research examines the influence of hydraulic controls (velocity, flow rate, aperture) on the spatial distribution of microbially induced calcite precipitation (MICP) within simulated fractures using flocculated Sporosarcina pasteurii. The experimental results show that under flowing conditions, the spatial distribution of microbially induced calcite precipitate on fracture surfaces is controlled by fluid velocity. Even for a uniform initial fracture aperture with a steady flow rate, a feedback mechanism existed between velocity and precipitation that resulted in a precipitate distribution that focussed flow into a small number of self-organizing channels which remained stable. Ultimately, this feedback mechanism controlled the final aperture profile which governed flow within the fracture. To use MICP for field scale sealing operations (e.g., in aquifers and host rock surrounding nuclear waste storage sites), it is important to develop an injection strategy that ensures microbially precipitated calcite is distributed homogenously throughout the rock body to avoid preferential flow through high porosity pathways. Sporosarcina pasteurii was found to be able to hydrolyse urea for several days before the bacteria became encased within calcite preventing access to the cementing fluid. The higher rates of urea hydrolysis occurred within the first 9 hours, though significant rates of urea hydrolysis still occurred after this period. By reducing the size of bacterial flocs it is possible to reduce the impact of sedimentation and straining, promoting a more even distribution of bacteria thus calcite precipitate throughout the plate. By increasing the length of time that the bacteria flow through the fracture, more bacteria can become entrained upon the fracture surface giving a better distribution. The introduction of a filler (colloidal silica) that can also act as a nucleation site for calcite precipitation was examined as a way of reducing the time it takes for the sealing of a fracture. Both Sporosarcina pasteurii and colloidal silica have negative surface charges thus colloidal silica could be used as a nucleation surface, this plus its nanometre size which could allow for a better distribution of and could enhance calcite precipitation. A clear difference in the mass of grout retained within the fracture was seen, with MICP alone showing the greatest weight increase. During the 8 grouting cycles with MICP + colloidal silica there appeared to be pieces of calcite travelling through the open channels. This would indicate that the calcite is unable to attach to the fracture surface. Thus, adding a small amount of colloidal silica to the cementing solution as a filler was not an efficient way to produce calcite fill. However, Sporosarcina pasteurii produces ammonium ions from the hydrolysis of the non-ionic urea, which as a cation can destabilise the silica sol resulting in gelation. Batch tests were used to determine what differences in gel point, gel rate and shear strength were created by different cations, including the chemical addition of ammonium ions and the biological production of ammonium ions by the bacterium Sporosarcina pasteurii. The sensitivity of colloidal silica to calcium chloride can result in dramatic differences in gel time with small changes in molarity having great impact on whether the colloidal silica gels or not. The direct addition of ammonium salts requires ten times the concentration, compared to CaCl2, to achieve similar shear strength values. However; this concentration produces very short gel times, potentially reducing the radius of penetration. The bacterial in-situ production of ammonium ions gives the greatest gel times yet still produces the same shear strength as that of a sodium chloride accelerator. This increasing of gel times, without adversely impacting grout properties, could be beneficial for penetrating greater distances into fractured rock reducing the number of injection points required. This would be particularly useful for subsurface engineering applications where large volumes of rock are required to be grouted.

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24

Emmert, Simon [Verfasser], and Holger [Akademischer Betreuer] Class. "Developing and calibrating a numerical model for microbially enhanced coal-bed methane production / Simon Emmert ; Betreuer: Holger Class." Stuttgart : Universitätsbibliothek der Universität Stuttgart, 2021. http://d-nb.info/1239116047/34.

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25

Sjöberg, Susanne. "Microbially mediated formation of birnessite-type manganese oxides and subsequent incorporation of rare earth elements, Ytterby mine, Sweden." Licentiate thesis, Stockholms universitet, Institutionen för geologiska vetenskaper, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-148281.

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Microbes exert extensive control on redox element cycles. They participate directly orindirectly in the concentration and fractionation of elements by influencing the partitioningbetween soluble and insoluble species. Putative microbially mediated manganese (Mn) oxidesof the birnessite-type, enriched in rare earth elements (REE) + yttrium (Y) were recentlyfound in the Ytterby mine, Sweden. A poorly crystalline birnessite-type phyllomanganate isregarded as the predominant initial phase formed during microbial Mn oxidation. Owing to ahigher specific surface area, this biomineral also enhances the known sorption property of Mnoxides with respect to heavy metals (e.g. REE) and therefore has considerable environmentalimpact.The concentration of REE + Y (2±0.5% of total mass, excluding oxygen, carbon and silicon)in the Ytterby Mn oxide deposit is among the highest ever observed in secondary precipitateswith Mn and/or iron. Sequential extraction provides evidence of a mineral structure where theREE+Y are firmly included, even at pH as low as 1.5. Concentration ratios of Mn oxideprecipitates to fracture water indicate a strong preference for the trivalent REE+Y overdivalent and monovalent metals. A culture independent molecular phylogenetic approach wasadopted as a first step to analyze the processes that microbes mediate in this environment andspecifically how the microbial communities interact with the Mn oxides. Plausible players inthe formation of the investigated birnessite-type Mn oxides are mainly found within theferromanganese genera Hyphomicrobium and Pedomicrobium and a newly identified YtterbyBacteroidetes cluster most closely related to the Terrimonas. Data also indicate that thedetected microorganisms are related to the environmental constraints of the site including lowconstant temperature (8°C), absence of light, high metal content and possibly proximity to theformer storage of petroleum products.

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26

Lloyd, Karen G. Teske Andreas. "Microbially-driven methane and sulfur cycling in a Gulf of Mexico methane seep and the White Oak River estuary." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2009. http://dc.lib.unc.edu/u?/etd,2570.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2009.
Title from electronic title page (viewed Oct. 5, 2009). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Marine Sciences." Discipline: Marine Sciences; Department/School: Marine Sciences.

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27

Dlamini, Mandla. "Performance of geopolymer concrete subjected to mineral acid corrosion and related to microbially-induced corrosion (MIC) of concrete in sewers." Master's thesis, Faculty of Engineering and the Built Environment, 2021. http://hdl.handle.net/11427/33644.

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worse than degradation at the crown of the sewer pipe. Furthermore, results from this study show that high resistance under the static acid corrosion exposure condition cannot be extended to mean high resistance under the erosion-corrosion exposure condition for some concrete mixes. In this study, the static HCl test and the dynamic HCl test were used to measure the resistance of concrete mixes under the static corrosion exposure condition and erosion-corrosion exposure condition respectively. However, concretes that exhibited high resistance to the erosion-corrosion exposure condition were consistent in exhibiting high resistance to the static corrosion exposure condition. This finding is consistent with the sequence of corrosion processes in MIC, wherein dissolution of the concrete components occurs before the precipitation of corrosion products. Therefore, it expected that high resistance in the dynamic acid test (i.e. resistance to dissolution) implies high resistance in the static test, which measures the combined resistance of dissolution and resistance emanating from corrosion products. Both static and dynamic acid corrosion tests revealed that the geopolymer concretes tested in this study outperformed PC and CAC concretes. Results from the static HCl test showed that GP-ferro-quartz concrete, the most durable concrete specimen, provided a 69-fold improvement in resistance when compared to PC-dolomite mixes (control #1) and a 4.72-fold improvement in resistance when compared to CAC-dolomite mixes (control #2). Results from the dynamic HCl test show that the GP-ferro-quartz mix provided a 180-fold increase in resistance when compared to the PC-dolomite mix and a 275-fold increase when compared to CAC-dolomite mix. The CACdolomite mix was found to have the lowest resistance to the erosive-corrosive exposure conditions of the dynamic HCl test. Thus, in terms of the concrete MIC resistance properties identified in this study, it is suggested that the CAC-dolomite mix had poor kinetic resistance to dissolution. However, under the static acid test (static corrosion exposure condition), the CAC-dolomite mix performed better than the PC-dolomite mix and GP-dolomite mix. CAC-dolomite concrete performed inferiorly only to the set of GP-siliceous-aggregate mixes in the static HCl test. The difference in the performance of CAC-dolomite concrete performance between the static and dynamic test is largely attributed to the formation of alumina gel, an acid corrosion product of CAC hardened paste, which envelopes the concrete specimen and reduces the rate of surface corrosion in the static HCl test. However, under v the dynamic HCl test, the gel layer is brushed off the surface of the concrete specimen rendering it ineffective in protecting the concrete specimen from corrosion. Previous research on the acid attack of concrete posits that the chemical make-up of concrete materials has a strong bearing on corrosion behaviour. To this end, various measures have been suggested such as the ratio of calcium to silicon (Ca/Si) in concrete. The approach utilised in this study was to calculate the “basicity value” which provides the ratio of major basic to acidic oxides found in the concrete. XRF analysis of the hardened cement pastes and the 5 aggregate types used in the experiments enabled the calculation of basicity values. The combined basicity value for concrete specimens was determined by proportionally summing (according to mass) the basicity values of the aggregate and hardened cement paste parts. A strongly correlated linear relationship between the basicity value of concrete and the corrosion rate from the dynamic HCl test was established. This empirical relationship warrants further investigation and verification, as it would, in principle provide a means to estimate the dissolution rate of concrete by calculating its basicity instead of undertaking laboratory acid tests. Basicity was also found to be useful in determining the corrosion compatibility of binder type and aggregate types. It was found that the difference between the basicity value of hardened cement paste and the basicity value of the aggregate was useful in determining the type and extent of preferential corrosion of a concrete specimen tested under the dynamic HCl test. For ease of reading, this difference was called the “basicity differential”. By visually assessing corroded concrete specimens from the dynamic HCl test, it is was possible to determine whether the hardened cement paste or aggregate component was preferentially corroded, and to gauge the extent of preferential corrosion visually. GP-ferro-quartz and GP-granite concretes had the lowest levels of preferential corrosion which corresponded to their low basicity differential values. In contrast, CAC-dolomite concrete had the highest basicity discrepancy which corresponded visually to a high preferential corrosion of the hardened cement paste. Mineralogical analysis via XRD, found that the hardened cement pastes of the three binder types consisted mainly of amorphous phases (>70%). The crystalline phase of the geopolymer hardened cement paste was mostly constituted by insoluble minerals such as mullite. This partially explains the higher corrosion resistance of geopolymer concretes. However, a more comprehensive explanation needs to include analysis of the amorphous phases, which fell outside the scope of this study. SEM analysis of HCl corroded geopolymer hardened cement paste found that fly ash spheres embedded within the geopolymer matrix were preferentially corroded. This indicates that fly ash content negatively affected the rate of corrosion of the geopolymer hardened cement paste. Furthermore, SEM analysis showed that the geopolymer matrix surrounding the fly ash spheres was relatively intact.

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28

Akimana, Rosa Mystica. "Bacterial Activity and Precipitation Heterogeneity during Biomediated Calcite Precipitation for Soil Improvement." University of Toledo / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1513381445346889.

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29

Hommel, Johannes [Verfasser], and Holger [Akademischer Betreuer] Class. "Modelling biogeochemical and mass transport processes in the subsurface : investigation of microbially induced calcite precipitation / Johannes Hommel ; Betreuer: Holger Class." Stuttgart : Universitätsbibliothek der Universität Stuttgart, 2016. http://d-nb.info/1118369602/34.

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30

Lin, Wing-shan, and 林穎珊. "Synthesis and biological studies of anti-cancer rhodium(II, II) carboxylates, anti-inflammatory silver(I) thiourea and microbially fabricated silver nanoparticles." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/206649.

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Discovery of cisplatin as an effective anticancer agent has stimulated the development of metal based medicine. The recent advances in research on platinum, ruthenium and gold complexes have received much attention in medicinal chemistry, and studies of other less explored metal complexes may reveal alternative mode of mechanism as novel therapeutic agents. A series of dirhodium(II,II) complexes with carboxylate and carboxamidate ligands and thiourea complexes of coinage metals have been prepared in this study. Their biological activities and mechanisms of action have been studied. Dirhodium(II,II) carboxylate complexes with variations of alkyl and benzoyl side chains were synthesized and displayed remarkable cytotoxicities to cancer cells with potency down to submicromolar level. The cytotoxicities of rhodium complexes were found to significantly correlate with the cellular uptake of the rhodium complexes. As revealed by oligonucleotide microarray and bioinformatic analysis, the mode of action of the rhodium carboxylate complexes are highly similar to that of a proteasome inhibitor. Further cellular and biochemical studies showed that rhodium carboxylate complexes induced an accumulation of ubiquitinated proteins, inhibited the proteolytic activities of purified 20S proteasome and proteasomal deubiquitinating enzyme. These results corroborate that the impairment of the ubiquitin-proteasome system is linked to the cytotoxic action of rhodium carboxylate complexes. Silver is known to be an anti-inflammatory agent for topical treatment. A silver complex of N, N’-disubstituted cyclic thiourea that is reasonably stable towards reduced glutathionewas found to potently inhibit the NF-B transcriptional activity. Treatment of cells with silver thiourea inhibited TNF-α-stimulated IκB kinase activity, IκBα phosphorylation and degradation, nuclear translocation of NF-κB p65 and eventually the stimulated gene expression of inflammatory cytokines. Suppression of IκB kinase activity was associated with modification of sensitive cysteine residues and disruption of IκB kinase assembly. These data demonstrated that the inhibitory properties of Ag+ ions on an anti-inflammatory and anti-cancer drug target could be effectively delivered via the thiourea ligand. Silver is also an antimicrobial metal, and this study was also extended to understand the silver-bacteria interaction using a silver resistant bacteria as a model. Many silver resistant bacteria often produce considerable amount of silver particles when exposed to high concentrations of silver salts but the mechanism of biosynthesis is not well understood. A silver resistant E. coli that displays active silver efflux was shown to synthesize zero-valent silver nanoparticles in the periplasmic space through reduction of silver ions under anaerobic conditions. As the microbial c-type cytochromes are known to mediate respiratory metal reduction, their role in the biosynthesis of silver nanoparticles was examined. A deletion mutant of the cytoplasmic membrane-anchored tetra-heme c-type cytochrome subunit of periplasmic nitrate reductase (NapC) showed marked reduction of accumulation of silver nanoparticles. This study identified a molecular mechanism of biosynthesis of silver nanoparticles that may have implication in bioenvironmental processes and synthetic biology of metal nanomaterials.
published_or_final_version
Chemistry
Doctoral
Doctor of Philosophy

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31

Okafor, O. J. "Comparison of microbially induced sedimentary structures in the Palaeoproterozoic Magaliesberg (Transvaal Supergroup) and Makgabeng (Waterberg Group) Formations, Kaapvaal craton, South Africa." Diss., University of Pretoria, 2014. http://hdl.handle.net/2263/45922.

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The MRS/MISS of the Makgabeng Formation encompasses sand cracks, wrinkle marks, mat fragments, mat chips and roll-ups and those of the Magaliesberg formation are wrinkle marks, petees/petee ridges, sand cracks, and multi-directional ripples. The sedimentary process that moderated the formational mechanism of the MISS of the Makgabeng Formation is (descriptively allochthonous) of high energy (inter-dune depositional setting) that eroded, transported and re-deposited mat bound sediments. The genetic mechanism of the MISS of the Magaliesberg Formation is descriptively authochthonous because of enhanced resistance of biostabilized sediments to being reworked. XRF (major and trace) and XRD analysis (qualitative and quantitative) was done on MISS bearing sedimentary rock layers (A) and underlying sedimentary sections (B) of Magaliesberg and Makgabeng samples. Result show high quartz content of all the analyzed samples compared to average sandstones. This premise suggests a relation of microbes (e.g. cyanobacteria) to phototrophy and/photoautotrophy because of the conduction properties of translucent quartz. Also plausible inference is that the intense chemical weathering that produced the quartz arenite was positively influenced by microbes, as noted in some Proterozoic basins. There is higher concentration of Ba in all A samples compared to B (Makgabeng and Magaliesberg) which might be emblematic of biogenicity. The Magaliesberg analyzed samples (MAG 101, 102, 103) exhibit homogeneity by the higher concentration of Al2O3, TiO2, K2O, and P2O5, and lower concentration of SiO2 in the A compared to the B subsamples of a particular sample. Also, Magaliesberg analyzed samples (MAG 101, 102, 103) exhibit homogeneity by the lower concentration of quartz and higher concentration of muscovite in the A compared to the B subsamples. This exact established negative correlation between the duo of SiO2 and quartz, and the quartet of Al2O3, TiO2, K2O, and P2O5, and muscovite as in Magaliesberg samples pertains also to a Makgabeng sample (MKG 102; roll-up). MKG 101 (mat fragment) deviates from this mineralogical and geochemical trend. Each of the A samples of MAG 101, 102, 103, are uniformly of higher concentration in Ce, Cr, Nb, Th, V, Y, Zn, Zr compared to the B version of that sample. MKG 101 and 102 are uniformly of lower concentration of Ce, Cr, Nb, Th, V, Y, Zn, Zr in A compared to the B version of that sample. The A of each of the samples MAG 101, 102, and 103 has higher concentration of Hf and Rb compared to its B; a character that is also exhibit in MKG 102, and MKG 101 is vice versa. Microscopy shows that A of all the samples is of smaller grain size compared to B, espousing affinity of microbes to fine-medium grained sandstones. Microscopy of the Magaliesberg Formation samples show Pseudo petee ridges and pseudo cross lamination which reflect biostabilization, and microscopy of the Makgabeng Formation show roll-ups, mat chips and composite mat chips. The MISS genetic difference of the two formations is related to energy, water residence time (emergence and inundation), Ph, and similarity is related to mutuality in shallow water environment. Mat types are inferred to be biologically, physically and chemically moderated adaptations of microbial communities to specific cum peculiar locally prevailing environmental conditions; factors that are premised on taphonomy and ecology.
Dissertation (MSc)--University of Pretoria, 2014.
tm2015
Geology
MSc
Unrestricted

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32

Chutko, Krystopher John. "Sedimentary structural indicators of Arctic terrestrial and aquatic processes." Thesis, Kingston, Ont. : [s.n.], 2008. http://hdl.handle.net/1974/1220.

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33

Khanthongthip, Passkorn. "The Biological Sludge Reduction by anaerobic/aerobic cycling." Diss., Virginia Tech, 2010. http://hdl.handle.net/10919/37592.

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An activated sludge system that incorporates a sidestream anaerobic bioreactor, called the Cannibal process, was the focus of this study. A prior study of this process (Novak et al., 2007) found that this system generated about 60% less solids than conventional activated sludge without any negative effects on the effluent quality. Although that study showed substantial solids reduction, questions remain concerning the specific mechanism(s) that account for the solids loss. In this study, the mechanisms that account for the loss of biological solids was the focus of the investigation. The first part of this study was conducted to evaluate those effects in terms of the role of iron in the influent wastewater and feeding patterns on the performance of the Cannibal system. It was found that the Cannibal system with high iron in the influent produced less biological solids than the system receiving low iron. The data also showed that the Cannibal system operated under fast feed (high substrate pressure) produced much less solids than the system with slow feed (low substrate pressure). The high substrate pressure was achieved by feeding the influent wastewater to the Cannibal system over a short time period so that the substrate concentration would initially peak and then decline as degradation occurred. This is called â fast feed.â For low substrate pressure, the influent was added slowly so the substrate concentration remained low at all times. This is called â slow feed.â Later, an attempt to increase substrate pressure in the slow feed Cannibal system was conducted by either manipulating the aeration patterns or adding a small reactor in front of the main reactor (selector). It was found that either interrupting aeration in the aerobic reactor or providing a small aerobic reactor in front of the main reactor resulted in an increase in solids reduction. The second part of this study was to investigate the mechanisms of floc destruction in the fast and the slow feed Cannnibal systems. It was found that higher accumulation of biopolymers (proteins and polysaccharides) occurred in the fast feed system and this was associated with a greater solids reduction in the fast than the slow feed system. In addition, more protein hydrolysis and more Fe(III)-reducing microorganism activity in the fast feed environment were found to be factors in higher solids reduction. The last part of this study was to investigate the structure of the Cannibal sludge flocs generated under the fast and the slow feed conditions. It was found that the readily biodegradable (1 kDa.) protein is larger in the flocs from the fast feed than the slow feed Cannibal system. This resulted in higher floc destruction in the fast feed condition.
Ph. D.

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34

Beese-Vasbender, Pascal Fabien [Verfasser], Martin [Gutachter] Stratmann, and Karl J. J. [Gutachter] Mayrhofer. "From microbially induced corrosion to bioelectrical energy conversion : electrochemical characterization of sulfate-reducing bacteria and methanogenic Archaea / Pascal Fabien Beese-Vasbender ; Gutachter: Martin Stratmann, Karl J. J. Mayrhofer ; Fakultät für Chemie und Biochemie." Bochum : Ruhr-Universität Bochum, 2015. http://d-nb.info/119960982X/34.

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35

Oakley, Lisa Marie. "Enhanced Resolution of the Paleoenvironmental and Diagenetic Features of the Silurian Brassfield Formation." Wright State University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=wright1369340395.

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36

Smith, D. C. "Microbial halogenation." Thesis, University of Kent, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.383890.

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37

Ghadge, G. D. "Microbial enzymes." Thesis(Ph.D.), CSIR-National Chemical Laboratory, Pune, 1986. http://dspace.ncl.res.in:8080/xmlui/handle/20.500.12252/3251.

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38

Xue, Peipei. "Soil Microbial Diversity: Relating Microbial Distributions to Soil Functions." Thesis, The University of Sydney, 2022. https://hdl.handle.net/2123/28830.

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Soil microbial biodiversity is an essential component of the natural ecosystem. Soil microbes work as decomposers contributing to soil nutrient cycling, primary production, and climate regulation. The heterogeneous edaphic properties lead to the diversity of microbial community structuring and functioning. This thesis investigates microbial community distributions and functions through vertical soil profiles, at the landscape level, and along regional transects. Vertically, soil microbial communities were depicted in soil profiles to a depth of 1 m using the concept of genosoils (soil formed and still under natural vegetation) and phenosoils (the same type of soil that has undergone cultivation). Bacteria community distribution in soil profiles differed by soil types but altered by soil forms. At the local scale, factors of land use and soil types on the microbial communities were evaluated in three soil depth layers through a survey across the Hunter Valley area in NSW, Australia. Topsoil microbial communities were generally regulated by land use, while the subsoil microbial communities were shaped by soil type. Additionally, microbial interactions reveal that soil protists regulate the bacterial and fungal diversity. At the regional scale, microbial functions were investigated across two ~1000 km transects which traversed significant temperature and/or rainfall gradients in NSW. Temperature and rainfall were important drivers of soil microbial functional groups. Paired (genosoils and phenosoils) samples showed that agriculture practices led to a significant shift in microbial functional groups related to particulate organic carbon (POC) degradation. Collectively, this thesis studied the factors of depth, soil type, land use, and environment for the underground microbial community, and demonstrated the significant role of soil biodiversity in the soil ecosystem, especially for soil carbon cycling.

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39

Gilliam, Lucy. "Impact of anti-microbial GM plants on soil microbial populations." Thesis, University of Reading, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.485401.

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The environmental risk assessment of GM plants is a fast moving area of science. Much research has focused on developing methods to evaluate potential effects on a range of organisms. Microorganisms play an essential role in many soil processes, with the rhizosphere as the prominent site of microbial activity. There is a general need for protocols to assess the effect of anthropogenic influences, the use of different crops and crop rotation an.d as well as GM plants, on the microbial community within the soil. The rhizosp~eres of three crop plants Brassica napus (Oilseed rape), Triticum aestivum (Wheat) and Solanum tuberosum (Potato) were compared using both genetic and functional diversity methods. The rhizospheres of four cultivars of potato were compared; GM potato (variety Kardal) modified with an anti-fungal transgene, GM potato (variety Kardal) with no transgene inserted (empty vector), parental .- line of potato (variety Kardal) and a different cultivar (variety Russet-Burbank). Genetic diversity of bacterial populations isolated from the rhizosphere were compared using PCR amplified DNA of 168 rRNA with denaturing gradient gel electrophoresis (DGGE) to obtain community fingerprints. Activity of the microbial populations was assessed using Biolog G.N MicroPlateÃ‚Â™ community substrate utilisation and enzyme activity using a microplate method based on substrates linked to the fluorescent compounds methylumbelliferone (MUB) and 7-amino-4-methyl coumarin (AMC). By comparing the ~M plants to non-GM plants and other crops, observed differences are placed in context. This work shows that the GM line examined.appears to have little effect on soil microbial populations. Detected effects of1he GM potato line were minor compared with other sources of variation observed between plants cultivar or crop species, management practices and sampling time. To date, there has been little evidence that cultivation of GM plants leads to significant changes in microbial popUlations.

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40

Chew, Yi Vee. "Host and microbial factors influencing the gut microbial community structure." Thesis, The University of Sydney, 2013. http://hdl.handle.net/2123/10031.

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Gut microbial colonization begins at birth and dynamic ecological succession occurs before establishment of a stable, resilient adult community structure. Colonization outcomes in early life have long-term effects on host health. Understanding factors governing neonatal gut community structure development and adult structure modulation will allow therapeutic manipulation of the gut community for disease prevention/treatment. Submetagenomic analysis was done to identify microbial factors potentially triggering community stability in neonate piglets. Piglet faecal microbiota was fractionated before and after key points in community development using suppression subtractive hybridization. Analysis of immunoglobulin A bound to gut microbes showed that distinct groups are bound, potentially influencing colonization outcomes. Comparisons using pyrosequencing showed that colon and cecum microbiota of mice on a standard diet were similar at higher taxonomic levels, with minor differences at finer scale reflecting spatial location. Changes in host nutrient intake were found to generically drive community shift in 2 independent mouse genotypes - low energy density (LED) diet samples showed significantly higher relative abundances of mucin-degrading Verrucomicrobiae and Bacteroidia. Ability to use host secretions as an alternative energy source is predicted to confer selective advantage under reduced host nutrient intake. To track host secretion uptake, mice were intravenously injected with 13C and 15N-labeled threonine. Isotope incorporation by bacteria was tracked with nanoscale secondary ion mass spectrometry. Greater uptake was seen in LED diet mice, indicating increased importance of host secretions to bacterial nutrition relative to host-ingested nutrients. Different populations showed differential uptake, suggesting varied ability to utilise host secretions. This is expected to influence population fitness and drive community shift under host nutrient intake limitation.

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41

Thomas, D. J. "Microbial cellulase systems." Thesis, Swansea University, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.639202.

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The work presented studies the cellulolytic system of Trichoderma koningii with particular reference to its ability to produce "short fibres" in the early stages of cellulose degradation. The culture filtrate of this organism was shown to produce short fibres from both filter paper (Whatman No.1) and cotton (Texas, non-dewaxed). The optimum conditions for production were identified and an assay system developed to measure this activity. Assay using filter paper was rapid and sensitive in determining short fibre producing activity, all results were subsequently confirmed on the more resistant substrate (cotton). The cellulase system was separated using an ion exchanger with a non-carbohydrate matrix and affinity chromatography on cellulose. Initial separation on ion exchange yielded the main cellobiohydrolase (CBH 1). Another fraction from this column separated on cellulose columns gave purified fractions of β-glucosidase, CM-cellulase and the short fibres forming activity (D2Cc). Only this latter fraction produced short fibres and synergised with CM-cellulase and β-glucosidase to increase short fibre production. Short fibres produced by D2Cc were more susceptible to subsequent hydrolysis by culture filtrate or CBH 1, degraded (bacterial) cellulose showed no physical changes on action of D2Cc but subsequent hydrolysis by CBH 1 or culture filtrate was increased. The main product of D2Cc was cellobiose but some cellotriose was detected from filter paper. D2Cc was inactive against cellobiose and cellotriose, both were potent inhibitors of D2Cc activity. Cellobiose was also an inhibitor of CBH 1 but cellotriose was not. D2Cc was shown to reduce the DP of bacterial cellulose. D2Cc and CBH 1 synergised in hydrolysing degraded cellulose, filter paper and cotton. The suggested role for this enzyme component is that it produces short fibres in concert with CM-cellulase which are then attacked by CBH 1 to produce cellobiose which is utilized by the organism.

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42

Brain, Stephen. "Monitoring microbial biofilms." Thesis, London South Bank University, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.337401.

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43

Lafis, S. "Rapid microbial detection." Thesis, Cranfield University, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.357505.

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44

Pawar, H. S. "Microbial glucose isomerase." Thesis(Ph.D.), CSIR-National Chemical Laboratory, Pune, 1988. http://dspace.ncl.res.in:8080/xmlui/handle/20.500.12252/3305.

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45

Hart, Murray. "Effects of pesticides on the soil microbial biomass and microbial activity." Thesis, University of Nottingham, 1995. http://eprints.nottingham.ac.uk/11542/.

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This thesis describes research investigating the side-effects of pesticides on soil microbial biomass and microbial activity, with particular reference to two recently developed pesticides, a fungicide, epoxiconazole, and a herbicide, quinmerac. In a dose-responsee xperiment,a pplication of thesep esticidest o a sandy loam soil, at up to 10 and 20 times field rate, had no significant effect on soil microbial biomass C or ninhydrin-reactive N, over 84 days incubation. There was also no effect on soil respiration, except for the higher rate quinmerac-treated soil, which evolved 13% lessC02-Cthan the control. The rate of mineralisation of epoxiconazole and quinmerac, and their long-term effect on soil respiration, were measured in three contrasting soils: a sandy loam, a silty clay loam, and a clay soil, using 14C -labelled active ingredients. The kinetics of the pesticides' mineralisation were quite different, epoxiconazole being hyperbolic, while quinmerac was sigmoidal. The maximum amount of mineralisation of both pesticides occurred in the silty clay loam soil, which had the lowest microbial biomass content. The mineralisation of the pesticides was increased by the addition of ryegrass, with the greatest effect in the silty clay loam soil, probably because of the large ryegrass C: biomass C ratio. The mineralisation of epoxiconazole was affected by the ryegrass amendment much more than quinmerac. Further additions of the pesticides had no significant effect on soil respiration or pesticide mineralisation. The mineralisation of epoxiconazole and quimnerac was further investigated in the silty clay loam soil, using samples with different crop management histories, and the effects of ryegrass and glucose amendment. Pesticide mineralisation was shown to be related to the amount of soil microbial biomass, indicating that the difference in mineralisation rate between the three soil types above was not due to differences in their crop management, but innate differences in soil chemistry and microbiology. Ryegrass addition stimulated the mineralisation of epoxiconazole more than quinmerac, while the reverse was true for glucose, indicating that the pesticides were being degraded by two distinct fractions of the microbial biomass. The effects of long-term cumulative field application of the pesticides benomyl, chlorfenvinphos, aldicarb, triadimefon and glyphosate, on soil microbial biomass and mineralisation of soil organic matter were investigated. The addition of aldicarb consistently increased the microbial biomass, due to its beneficial effect on crop growth, but this effect was not reflected in the rate of organic matter mineralisation. However, in general, the continued application of these pesticides for up to 19 years, at slightly higher than the recommended rates, had very little effect on the soil microbial population. The effects of epoxiconazole and triadimefon on soil ergosterol content and microbial biomass C were compared in a sandy loam soil. Both pesticides temporarily reduced soil ergosterol by about 30%, while biomass C remained largely unaffected. However, when straw was added to the soils, the inhibition of ergosterol was still evident, as was an inhibitory effect on biomass C. The measurement of soil ergosterol was more sensitive to the pesticide effects than biomass C, and could be a useful test in determining changes in fungal populations.

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46

Korin, Tetyana Olegivna. "Microbial ecology of anaerobic biodegradation of benzoate : microbial communities and processes." Thesis, University of Newcastle upon Tyne, 2018. http://hdl.handle.net/10443/4138.

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Microbial conversion of hydrocarbons and other aromatic compounds has been studied extensively under various electron accepting conditions, by investigating cultured microorganisms and by using samples collected directly from diverse environments. However, the functions of the principal microbial organisms taking part in the biodegradation process are not fully understood, especially when the organisms comprise complex microbial communities. The focus of the research reported here is the identification of a microbial community enriched during methanogenic benzoate degradation using inocula from two contrasting environments, river sediment and oil sands. Benzoate is a monoaromatic compound used extensively as a model compound in studies of hydrocarbons and other aromatics. The microorganisms which were most abundant and which had been shown by earlier work to take part in syntrophic benzoate degradation were investigated. Their functional potential was also investigated using metagenomic approaches. It was found that enrichments from different environments contained different microbial communities, different members of which were thought to take part in the syntrophic degradation of benzoate. In benzoate enrichments with Tyne sediment, two types of methanogen were enriched: hydrogenotrophic Methanofollis and acetoclastic Methanosaeta. In contrast, in oil sands enrichments with benzoate, the most abundant methanogens were metabolically versatile Methanosarcina spp. The primary benzoate degrader in enrichments with Tyne sediment was Syntrophus, most likely Syntrophus aciditrophicus as was suggested by 99% sequence identity. In oil sands enrichments the supposed primary benzoate degrader was an unknown species of Desulfotomaculum. Syntrophic acetate oxidisers (e.g. Syntrophomonas) were not found in abundance in Tyne sediment cocultures with benzoate. Instead, the conversion of acetate into hydrogen and carbon dioxide appeared to be mediated by acetoclastic methanogenesis, which utilised acetate directly as has been evidenced by the enrichment of acetoclastic methanogens Methanosaeta and Methanosarcina. In the oil sands, syntrophic acetate oxidation was likely to have been carried out by the known acetoclastic methanogen Methanosarcina. However, it was conjectured that unclassified Sphingobacteriales clone WCHB1.69 could have taken part in the acetate utilisation. Regardless of the observed differences between the microbial communities, investigation of the metabolic potential showed the presence of the same pathways, key genes and enzymes that are known to take part in the degradation of benzoate iv and the production of methane. The same four pathways were found in both sets of methanogenic enrichments, namely the benzoate degradation pathway and hydrogenotrophic, acetoclastic and methylotrophic methanogenesis pathways. The same key genes that take part in benzoate degradation, namely dienoyl-CoA hydratase (dch), β-hydroxyacyl-CoA dehydrogenase (had) and β-oxoacyl-CoA hydrolase (oah) were found in high abundance in both enrichment cultures. The same key genes coding for essential proteins involved in methanogenesis were also found in high abundance in all the methanogenic archaea tested in both Tyne sediment and oil sands methanogenic enrichment cultures with benzoate, namely tetrahydromethanopterin S-methyltransferase (mtrA), methyl-coenzyme M reductase A (mcrA) and heterodisulfide reductase subunit A (hdrA). Other genes found in high abundance were methanogenic pathway specific genes, namely formylmethanofuran dehydrogenase, subunit A (fmdA) involved in hydrogenotrophic methanogenesis, phosphate acetyltransferase (pta), acetate kinase (ackA) and acetyl-CoA synthetase (ACSS) involved in acetoclastic methanogenesis and coenzyme M methyltransferase (mtaA) involved in methylotrophic methanogenesis. These results suggest that the functional capabilities of the microorganisms in different environments remain constant but the communities might vary from one environment to another. In addition, a comparison was made between two sequencing platforms, Illumina MiSeq and Ion Torrent PGM. The result suggested that, overall, the two sequencers concurred. The sequencers found the same most abundant taxa, but there were instances where both sequencers detected some microorganisms which were not detected by the other sequencer. Syntrophic degradation of many different types of compound such as alcohols, saturated and unsaturated fatty acids, hydrocarbons and aromatic compounds has been identified in methanogenic environments, suggesting the global importance of this process and of the microorganisms involved. Further work on the syntrophic processes, including methanogenesis, would clarify which microorganisms take part in syntrophy, in which environments syntrophy occurs, what substrates can be utilised, which members of the microbial community participate and how. Such knowledge would be useful in understanding the processes that attenuate the contamination of industrial land and the development of strategies for bioremediation. A quantitative model of syntrophic biodegradation could also assist in understanding the processes that release greenhouse gases. There is also a likelihood that microbial degradation could find a use in the development of sustainable and environmentally innocuous sources of energy.

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47

Carder, Phyllis. "Microbial Communities of Spinach at Various Stages of Plant Growth From Seed to Maturity." Thesis, Virginia Tech, 2010. http://hdl.handle.net/10919/34104.

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Little is known about how the leaf bacterial community is affected by the seed microbiota at different stages of plant development. The bacterial populations of spinach seed and leaves after germination were compared using DGGE, to assess bacterial community richness, and real-time PCR to compare the abundance of select phyla (total bacteria, Actinobacteria, Bacteroidetes, Firmicutes, Î±-Proteobacteria and Î²- Proteobacteria). To determine the effect of environment, the plants were grown in the field and growth chambers. Vertical transmission of bacterial community members was evident; the developmental stage of the plant affected the richness and abundance of select bacterial phyla. The bacterial richness of plants grown in the two environments was not affected. However, overall numbers of bacteria increased in field grown samples in comparison to those produced in growth chambers during development. A statistically significant interaction was seen between growth stage and environment with each of the selected phyla. Populations on cotyledons were smaller than mature leaves, but were not significantly different than the 3-4 leaf stage plants. The culturable populations of bacteria on seeds (~5 log CFU/g) were significantly smaller than determined using real time PCR (~7 log copies). Of these bacteria cultured from spinach seeds, isolates belonging to the genera Pantoea were found to inhibit growth of E. coli O157:H7 in vitro. This study highlights the importance of vertical transmission on the bacterial community of plants and suggests the importance of developing strategies to influence these communities on seed to control human and plant pathogens on the leaf surface.

Master of Science in Life Sciences

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48

Barberán, Torrents Albert. "Microbial Macroecology understanding microbial community pattems using phylogenetic and multivariate statistical tools." Doctoral thesis, Universitat de Barcelona, 2012. http://hdl.handle.net/10803/101511.

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El estudio de los microorganismos en cultivo puro ha propiciado el desarrollo de la genética, la bioquímica y la biotecnología. Sin embargo, la ecología ha permanecido reticente a incorporar a los microorganismos en su acervo teórico y experimental, principalmente debido a las dificultades metodológicas para observar a los microbios en la naturaleza, y como resultado de los caminos divergentes que han trazado las disciplinas de la microbiología y la ecología general. Esta tesis trata de demostrar que los patrones ecológicos de comunidades microbianas son susceptibles de ser analizados mediante la combinación de técnicas filogenéticas y herramientas de estadística multivariante. El uso de técnicas filogenéticas permite solventar, o al menos paliar, el hecho de la no independencia de los organismos vivos debido a la ascendencia común. Con la información ambiental adicional (como reflejo del determinismo abiótico) y la información espacial (como amalgama de eventos históricos y de dispersión), es posible explorar los posibles mecanismos que subyacen a la estructura y a la diversidad de las comunidades microbianas.
The study of microorganisms in pure laboratory culture has delivered fruitful insights into genetics, biochemistry and biotechnology. However, ecology has remained reluctant to incorporate microorganisms in its experimental and theoretical underpinnings mainly due to methodological difficulties in observing microorganisms in nature, and as a result of the different paths followed by the disciplines of microbiology and general ecology. In this dissertation, I argue that novel insights into microbial community patterns arise when phylogenetic relatedness are used in conjunction with multivariate statistical techniques in the context of broad scales of description.

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49

Shi, Yanmei Ph D. Massachusetts Institute of Technology. "Microbial metatranscriptomics : towards understanding microbial gene expression and regulation in natural habitats." Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/64570.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2011.
Cataloged from PDF version of thesis.
Includes bibliographical references (p. 195-212).
Metagenomic research has paved the way for a comprehensive understanding of the microbial gene parts list in nature, but a full understanding of microbial gene expression, regulation, and ecology remains a challenge. In this thesis, I present the methodological foundations and applications of deep sequencing-based metatranscriptomics, for profiling community transcriptomes on spatial and temporal scales. Several findings and relevant hypotheses have emerged from this work. I show that transcripts of house-keeping genes necessary for the maintenance of basic cellular machinery are abundant and readily detectable. Habitat-specific transcripts are also discernible when comparing community transcriptomes along distinct geochemical conditions. Normalization of detected transcripts to their corresponding gene abundance suggests that numerically less abundant microorganisms may nevertheless contribute actively to ecologically relevant processes. Along the same lines, it is a recurrent observation that many transcripts are of unknown function or phylogenetic origin, and have not been detected in genomic/metagenomic data sets. These novel sequences may be derived from less abundant species or variable genomic regions that are not represented in sequenced genomes. Furthermore, I applied metatranscriptomics in a microcosm experiment, where a deep water mixing event was simulated and community transcriptomes were monitored over the course of 27 hours. Relative to the control, the treatment sample showed signals of stimulated photosynthesis and carbon fixation by phytoplankton cells, enhanced chemotactic, motility, and growth responses of heterotrophic bacteria, as well as possibly altered phage-host interactions. Such experimental metatranscriptomic studies are well suited to reveal how microorganisms respond during the early stages of environmental perturbations. Finally, I show that metatranscriptomic data sets contain a wealth of highly expressed small RNAs (sRNAs), transcripts that are not translated to proteins but instead function as regulators. I propose a bioinformatics pipeline for identifying these sRNA elements, characterizing their structures and genomic contexts, and predicting possible regulatory targets. The extraordinary abundance of some of the identified sRNAs raises questions about their ecological function, which warrants further biochemical and genetic studies. Overall, this work has extended our knowledge of functional potentials and in situ gene expression of natural microbial communities.
by Yanmei Shi.
Ph.D.

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50

Gregory, Jarod. "Microbial Detection in Surface Waters: Creating a Remote-Controlled Mobile Microbial Biosensor." University of Cincinnati / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1439301079.

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