This thesis deals with the effect of magnetic field and organic substances, namely benzene and p-nitrophenol, on cell of PHA producing bacteria Cupriavidus necator H16 and mutant strain Cupriavidus necator PHB4, which does not produce polyhydroxyalkanoates. Static magnetic field was generated by both permanent magnet and electromagnet. The effect of magnetic field on the growth of bacterial cells was studied using growth curves. It was found that cultivation in magnetic field and mineral medium mostly inhibits bacterial growth. Also the amount of polyhydroxyalkanoates was observed using FT-IR, flow cytometry and microscopy with fluorescent dye. Growth curves and flow cytometry were also used to study the influence of organic substances on bacterial cells. It was found that while benzene does not affect either C. necator H16 or C. necator PHB4, p-nitrophenol acts as the inhibitor of bacterial growth for both cultures. Finally the impact of p-nitrophenol on the accumulation of PHA was studied using gas chromatography.

This diploma thesis focuses on the molecular characterization of selected PHA producers. Within this work, the PHA producing thermophilic isolates originating from the samples of activated sludge and compost were identified and characterized using molecular biological methods. By sequencing the 16S rRNA gene, the thermophilic isolates were identified and taxonomically classified into the Firmicutes bacterial phylum. In these bacterial isolates, the ability to produce PHA at the genotype level was determined by conventional PCR detection of the phaC gene encoding PHA synthase, which is a key enzyme in PHA biosynthesis. Class I, II and IV PHA synthases were detected in most of the isolated bacteria, wherein class I and II PHA synthases are not characteristic for these bacterial genera. The largest proportion of isolates was identified for the species of thermophilic bacterium Aneurinibacillus thermoaerophilus, in which class IV PHA synthase was detected. In the second part of the diploma thesis, the RT-qPCR method was implemented to study the expression of selected genes of the bacterium Cupriavidus necator H16 involved in PHA metabolism. As part of the implementation of this method, PCR-based detection of selected genes was optimized and quantification of genes using real-time PCR was performed. The tested method included steps of RNA isolation, cDNA synthesis and quantification of gene segments for which the critical points of the method were determined based on the obtained data.

Předložená disertační práce se zabývá studiem produkce a degradace polymerních materiálů s využitím mikroorganismů. Hlavní pozornost je upřena ke studiu produkce polyesterů bakteriálního původu - polyhydroxyalkanoátů. Tyto materiály jsou akumulovány celou řadou bakterií jako zásobní zdroj uhlíku, energie a redukční síly. Díky svým mechanickým vlastnostem, kterými silně připomínají tradiční syntetické polymery jako jsou polyetylén nebo polypropylén, a také díky své snadné odbouratelnosti v přírodním prostředí, jsou polyhydroxyalkanoáty považovány za ekologickou alternativu k tradičním plastům vyráběným z ropy. Polyhydroxyalkanoáty mají potenciál najít řadu aplikací v průmyslu, zemědělství ale také v medicíně. Významná část předložené práce je zaměřena na produkci polyhydroxyalkanoátů z odpadních substrátů pocházejících především z potravinářských výrob. Testována byla odpadní syrovátka nebo odpadní oleje z různých zdrojů. Právě využití levných odpadních substrátů je strategií, která by mohla přispět ke snížení ceny polyhydroxyalkanoátů a tím usnadnit jejich masové rozšíření. Podle výsledků dosažených v této práci jsou právě odpadní olejové substráty velice perspektivní cestou k ekonomicky rentabilní biotechnologické produkci polyhydroxyalkanoátů. Další část předložené práce se zabývá studiu spojení metabolické role polyhydroxyalkanoátů a stresové odpovědi bakterií. V této práci bylo zjištěno, že expozice bakteriální kultury řízené dávce etanolu nebo peroxidu vodíku významně navýší dosažené výtěžky a to o přibližně 30 %. Po aplikaci výše zmíněných stresových faktorů došlo k aktivaci metabolických drah vedoucí k odbourání stresového faktoru z média. Výsledkem bylo navýšení poměru NAD(P)H/NAD(P)+, což vedlo k částečné inhibici Krebsova cyklu a naopak aktivaci biosyntetické dráhy polyhydroxyalkanoátů. Mimoto došlo k významnému navýšení molekulové hmotnosti výsledných materiálů. Podle těchto výsledků se regulovaná aplikace vhodně zvolených stresových podmínek zdá být zajímavou strategií, která vede nejen k navýšení celkových výtěžků, ale také významnému zlepšení vlastností polymeru. Poslední část disertační práce se zabývala studiem procesu biodegradace polyuretanových materiálů. Polyuretanové eleastomery byly modifikovány rozličnými biopolymery za účelem navýšení jejich biodegradability. Tyto materiály byly posléze vystaveny působení směsné termofilní kultury jako modelového systému, který simuluje přirozené konsorcium bakterií. Přítomnost testovaných materiálů v kultivačním médiu vedla k neobvyklým růstovým charakteristikám bakteriální kultury. V průběhu prvních několika dní byl růst kultury silně inhibován, nicméně po překonání této neobvykle dlouhé lag-fáze došlo k intenzivnímu nárůstu kultury. Hlavní podíl na hmotnostním úbytku testovaných materiálů během experimentů měl samovolný rozpad materiálů, nicméně byl pozorován i vliv bakteriální kultury, kdy míra biotické degradace závisela na použitém modifikačním činidle. Nejvyšší míra biotické degradace byla pozorována u polyuretanového materiálu modifikovaného acetylovanou celulózou. Lag-fáze byla způsobena uvolněním nezreagovaného katalyzátoru (dibutylcínlaurát) a polyolu do kultivačního média. Bakteriální kultura se však po čase dokázala na přítomnost toxických látek v médiu adaptovat nebo je dokázala eliminovat.

This diploma thesis deals with testing, optimazing and comparing methods for the identification of bacteria producing polyhydroxyalkanoates. Work included cultivation and microscopy methods, wherein the bacterial cells were stained with lipophilic dyes Nile red and Sudan black. Further, we also used flow cytometry and spectroscopic methods - Raman spectroscopy and infrared spectroscopy with Fourier transformation, and molecular biological methods, which analyzed the presence of a gene encoding PHA synthase (phaC) by polymerase chain reaction (PCR). PCR assay consist of two reactions, the firt on eis based on amplification of phaC gene along with 16S rRNDA gene, which is common for all the bacteria (multiplex PCR). The second reaction is focused on specific amplification of PHA synthase catalyzing biosynthesis of mcl-PHA. In order to overcome false positive results typical for methods analyzing genotype and also to avoid false negative results occuring in fenotype analyzing methods, the best strategy is to combine both aproaches. According to our results, analysis of presence of phaC gene by PCR can be combined with methods capable of determining presence of PHA in bacterial cells. For this purpose, Raman microspectroscopy seems to be very promising tool, since it is able to detect low content of PHA in cells and PHA can not be confused with other lipid metabolites. The results provide an overview of test methods, their advantages and disadvantages and also to compare different criteria according to which it is possible to choose the method of identification in depending on the adjustable requirements.

The aim of the master thesis was to study the effect of the accumulation of polyhydroxyalkanoates (PHA) for bacterial resistance to selected stress factors. In the theoretical part the selected stress factors, polyhydroxyalkanoates and the involvement of polyhydroxyalkanoates into stress response of bacteria were reviewed. In the experimental part we used bacteria Cupriavidus necator H16 and its mutant strain Cupriavidus necator H16/PHB-4 unable of polyhydroxybutyrate (PHB) accumulation. The resistance of above-mentioned bacterial strains against thermal and osmotic stress was tested. According to the results of the experiment, when the bacteria were exposed to three different concentrations of NaCl (50, 100 and 200 g/l) PHB accumulating strain showed a higer resistance to hyperosmotic stress than the strain unable of PHB accumulation. There was demonstrated with Raman spectroscopy that in the hyperosmotic environment induced crystallization of the intracellular PHB granules. Transmission electron microscopy indicated that strain Cupriavidus necator H16/PHB-4 is subject to plasmolysis during hyperosmotic stress. As a consequence the hyperosmomotic stress occurs to the aggregation intracellular PHB granules in strain Cupriavidus necator H16 but there is no plasmolysis or is much less intensive.

The aim of this work is study of utilization of PHA producing bacteria in bioremediation technologies. For this study were used bacteria Pseudomonas putida KT2440 and two isolates from soil contaminated by petroleum - Pseudomonas gessardii (D2) a Pseudomonas fulva (D3). The experimental part describes especially study of feather biodegradation using selected microbial strains. All the tested bacterial strains were capable of feather degradation and utilization as the sole carbon source. During biodegradation experiment, we monitored weight loss of feather, protease and keratinase activity, concentration of bacterial biomass and PHA content as well as pH. The highest biodegradation ability and keratinase activity was observed in Pseudomonas putida. None of tested bacteria accumulated detectable amount of PHA during growth on waste feather, nevertheless, bacterial biomass grown during feather degradation can be used as an inoculum for PHA production on waste frying oil and octanoic acid. Using this experimental setup, high PHA content (54% of cell dry weight) was achiaved in Pseudomonas putida. Another part of the thesis deals with biodegradation of petroleum oil. The highest capability of growth on this carbon source were determined in Pseudomonas fulva.

It is generally accepted that a decrease in temperature causes the rates of chemical and biochemical reactions to slow down, usually resulting in poorer performance of biological wastewater treatment systems. Despite this, early researchers repeatedly showed that excess biological phosphorus removal (EBPR) was more efficient at colder temperatures. Recent studies, however, have demonstrated that the reaction rates of EBPR processes decrease with temperature in accordance with Arrhenius' Law, resulting in an apparent contradiction in the literature. The objective of this study was to investigate the EBPR temperature controversy. The experimental systems used were two, lab-scale UCT configuration plants fed with acetate as the sole volatile fatty acid (VFA) source. The results showed that EBPR systems do perform more efficiently at colder temperatures, i.e., at 5°C compared to 20°C. The reason for better system performance was determined to be related to reduced competition for substrate in the non-oxic zones that results in an increased population of phosphate accumulating organisms (PAOs) relative to non-PAOs and, therefore, greater EBPR efficiency even though the reaction rates are slower. The proliferation of PAOs relative to non-PAOs at cold temperature indicates that some of the PAOs are psychrophilic, i.e., they have alternate biochemical pathways that give them a competitive advantage over bacteria dependent upon glycogen metabolism. The activated sludge acclimated to 20°C had relatively high polyhydroxyvalerate (PHV) and glycogen contents relative to sludge acclimated to 5°C. It was initially hypothized that there is a significant competition between PAO and glycogen accumulating organisms (GAOs) at 20°C and cold temperature (5°C) nearly eliminates this competition in favor of the PAOs. A series of batch test experiments revealed that despite similar acetate utilization by the sludges grown at the two temperatures nearly 30% less PHA was produced by the sludge taken from the 20°C reactor, indicating that GAOs were a small fraction of the population at 20°C. Transmission electron microscopy pictures showed that the biomass acclimated to 20°C had a much more diverse bacterial population than the biomass acclimated to 5°C. However, no GAO population was detected in electron microscopy samples under any temperature conditions. The decreased P removal efficiency at 20°C was then attributed to the presence of fermentative or other non poly-P bacteria that are capable of utilizing substrate under anaerobic conditions. PHA production greatly increased at 5°C, whereas glycogen metabolism substantially reduced. Even though glycogen is an essential requirement for EBPR mechanism, the EBPR microorganisms have the ability to adapt their metabolic pathways to environmental conditions and greatly reduce their need for glycogen. It is apperant that cold temperature inhibits some of the key enzymes in glycogen metabolism resulting in lower glycogen accumulation that in turn increases the EBPR performance. Therefore temperature not only exerts selective pressure on the dominant population but also alters the metabolic pathways of the EBPR process. Increased glycogen accumulation, as observed in this study at 20°C, may not be related to GAO proliferation as suggested by Filipe et al. (2001) instead it may be related to EBPR bacteria to efficiently use glycogen metabolism. Current models (Brdjanovic et al. 1997; Filipe et al. 2002) consider that GAO metabolism is an integral part of EBPR metabolism and the performance of EBPR processes depends on PAO/GAO fraction in the EBPR system. No GAO proliferation was observed even the A/O process was operated without P addition for more than 3 weeks at 10°C. Therefore such important concept should be further investigated before it is included in EBPR models. EBPR stoichiometry was presumed to be insensitive to temperatures (Brdjanovic et al. 1997). However, observed stoichiometric values of PHA storage per unit glycogen utilization and PHA utilization per unit glycogen rephlenishment were quite different at different temperatures. Temperature, therefore, not only affects the kinetics of EBPR systems but also affects the EBPR stoichiometry. Most prokaryotic cells have the ability to alter their cellular membrane fatty acid composition as temperature decreases to counteract the adverse effects of temperature on membrane fluidity (Becker et al., 1996). This unique ability is known as "homeoviscous adaptation". In this study, homeoviscous adaptation by EBPR activated sludge was investigated for a series of temperatures ranging from 20°C to 5°C using one of the lab scale EBPR systems. The fatty acid analysis results showed that the unsaturated to saturated fatty acid ratio increased from 1.40 to 3.61 as temperature dropped from 20 to 5°C. The increased cis-9-hexadecanoic acid (C16:1) at 5°C strongly indicated the presence of homeoviscous adaptation in the EBPR bacterial community. Thus the cell membranes of the EBPR community were still in a fluid state, and solute transport and proton motive force mechanisms were operable even at 5°C. It was concluded that loss of EBPR performance at low temperatures, as reported by McClintock et al. (1992) was not related to the physical state of the cellular membranes, but was probably caused by unsuitable operational conditions. Even though the transport of volatile fatty acids (e.g. acetate) is an integral part of EBPR biochemistry and stoichiometry, this important concept has been ignored. Fleet (1997) concluded that acetate entry into bacterial cells in EBPR sludge was simple passive diffusion based upon the results of a single study (Baronofsky et al. 1984). However, this study showed that neither acetate nor propionate can cross the cell membrane via simple passive diffusion. The existence of apparent saturation curves when the substrate uptake rates (acetate and propionate) were plotted against the substrate concentrations suggested that transport of volatile fatty acids obey facilitated or active transport. Following from the above results, an investigation of the impacts of operational conditions such as low solids retention time (SRT), presence of electron acceptors in the non-oxic zones, low anaerobic detention time, and lack of acclimation was performed. The results showed that the "critical, i.e., wash-out" SRT increased as temperature decreased, but if the biomass was permitted to acclimate to the lower temperature, a major population shift would occur which would increase the capacity of the system for phosphorus (P) removal. When the 5 °C sludge was allowed to acclimate at a relatively high SRT (18 d), the system's P-removal capacity greatly surpassed that of the 20 °C system. The decrease in EBPR performance because of the presence of nitrates in the non-oxic zones was determined to be greater than what would be predicted based on accepted stoichiometry. / Ph. D.

Although enhanced biological phosphorus removal (EBPR) and complete biological nutrient removal (BNR) systems can be operated successfully by experienced operators, the accuracy of design and strength of the scientific background need to be reinforced to enable accurate modeling and economically optimal design. One way to accomplish this would be through a better understanding of the biochemical mechanisms and microbial population dynamics that determine the reliability and efficiency of EBPR, and the utilization of this information to improve the design and operation of BNR plants. Such knowledge will also contribute to better structure of modeling tools that are used for design and educational purposes. The current body of knowledge is limited to observational studies that lack detailed biochemical explanations backed with a series of well planned experiments, and this has introduced uncertainties and inaccuracies into the biochemical and design models. Therefore, this study mainly covers a biochemical survey of the underlying metabolisms of active populations in BNR sludges. BNR biomass with biological phosphorus removal (BPR) capability was cultivated in continuous flow reactor (CFR) systems, configured as either University of Cape Town (UCT) and anoxic/oxic (A/O) systems. Following an acclimation period at 20°C, low temperature stress (5°C) was imposed on one UCT system for investigation of the response of the microbial consortium responsible from EBPR activity under cold temperature. Once a stable population with EBPR capabilities is established in each system, activities of ten enzymes that are hypothesized to be taking part in the EBPR metabolism were measured. These enzymes were selected among those that take part in major known pathways of bacterial energy and growth metabolism. Also, 13C-NMR was used as a tool to monitor the flux of labeled carbon in and out of pools of cellular storage; i.e. glycogen and polyhydroxyalkanoates (PHA). Combining the gathered information, accurate mass balances of carbons and reducing equivalents were calculated, eventually leading to determination of the biochemical pathways utilized by the EBPR consortium. Additionally, anaerobic stabilization of COD, a long debated but empirically established phenomenon, was addressed during the study. Considering the pathways proposed to be operative under different conditions imposed on the EBPR systems, a biochemical explanation for the occurrence of COD stabilization in wastewater treatment systems that incorporate anaerobic zones was proposed. Accordingly, depending on the pathways actively used by a microbial consortium, electrons stored in NADH and FADH2 can either be transferred to the terminal electron acceptor, oxygen, or they can be incorporated into storage polymers such as glycogen for future use. Such differences in metabolism reflect in the quantity of the oxygen consumed in the aerobic reactors. Thus, the correct incorporation of anaerobic stabilization of COD into process design would reduce design aeration requirements and result in economic savings during both construction and operation. / Ph. D.

A capacidade de B. sacchari acumular poli-3-hidroxibutirato-co-3-hidroxihexanoato (P3HB-co-3HHx) foi confirmada, com até 2 mol% de 3HHx no PHA total (<10% do 3HHx máximo teórico a partir do ácido), indicando flexibilidade da PHA sintase por substratos, porém alta eficiência nas vias catabólicas do hexanoato. Análise da estabilidade térmica do PHA indicou uma temperatura de degradação reduzida, compatível com a presença de unidades 3HHx. Mutantes incapazes de crescer em ácido hexanóico foram obtidos com UV e transposon mini-Tn5, que ainda acumulavam 3HHx a partir de hexanoato mas com redução na capacidade do acúmulo de 3HB e 3HHx. Foram construídos recombinantes abrigando o gene phaB (codificador de 3-cetoacil-CoA redutase) de Ralstonia eutropha ou phaJ1 e phaJ2 (codificadores de enoil-CoA hidratases R-específicas) de Pseudomonas aeruginosa. A expressão de phaB ou phaJ1 aumentou a canalização de 3HB para a PHA sintase, apesar de não aumentar as frações de 3HHx. Monômeros de 3HHx e 3HO foram detectados a partir de ácidos butírico e octanóico, respectivamente. / The ability of B. sacchari to accumulate poly-3-hydroxybutyrate-co-3-hydroxyhexanoate (P3HB-co-3HHx) from glucose and hexanoic acid was confirmed. 3HHx content was up to 2 mol% of PHA (<10% of the maximum theoretical 3HHx from the acid), indicating a substrate flexibility of B. sacchari PHA synthase, but high efficiency of hexanoate catabolic pathways. Thermal stability analysis of the copolymer indicated a reduced degradation temperature compatible with 3HHx units. Mutants unable to grow on hexanoic acid were obtained with UV and mini-Tn5 transposon. They still accumulated 3HHx from hexanoate, but the ability to accumulate 3HB and 3HHx was reduced. Recombinants harboring the Ralstonia eutropha phaB (encoding 3-ketoacyl-CoA reductase) and Pseudomonas aeruginosa phaJ1 and phaJ4 genes (encoding R-specific enoyl-CoA hydratases) were constructed. Expression of both phaB and phaJ1 increased the channeling of 3HB to the PHA synthase, despite no increase on 3HHx fraction was observed. 3HHx and 3HO monomers were detected from butyric and octanoic acids, respectively.

Polyhydroxyalkanoates (PHA) are a family of biodegradable polyesters naturally synthesised by some bacteria and archaea. PHA have high industrial value as bioplastics for packaging and biomedical applications. However, their broader use is hindered by high production costs and uncontrolled variation of polymer properties. The extreme halophile Haloferax mediterranei shows bioprocess advantages that can be exploited for the low cost production of the PHA copolymer Poly(3-hydroxbutyrate-co-3-hydroxyvalterate) (PHBV). The focus of this thesis is to identify process variables responsible for the uncontrolled variation of PHA properties in order to progress towards the robust production of PHBV using H. mediterranei. The outcome of the investigation is a novel cultivation strategy for the reliable synthesis of PHBV copolymers with controlled composition and microstructure showing minor differences in material characteristics. Initially, growth kinetics and PHBV synthesis were characterised under nitrogen-excess and nitrogen-limiting conditions in ammonium and for the first time, nitrate. The nitrogen source and concentration influenced PHBV accumulation and variations in polymer composition were observed with ammonium, highlighting the importance of the control of cultivation conditions. Volatile fatty acids (VFA) were found to be a more direct approach to determine PHBV composition and for the first time were used as substrates in H. mediterranei cultures. When the cells were grown in C4:0/C5:0 mixtures, the 3HV fraction in the PHBV was proportional to the percentage of C5:0 in the feed mixture, allowing the synthesis of copolymers with a predefined composition ranging from pure PHB to pure PHV. The cultivation strategy proved effective for the synthesis of HV rich PHBV, which is not easily obtained due to the 3HV precursor toxicity. The polymer microstructure was controlled using different feeding strategies: co-feeding generated random copolymers, while sequential feeding created block and blend copolymers. The synthesis of block copolymers is of interest because the materials show enhanced yield strength and mechanical strength, making such materials more suitable for commodity uses. Bespoke random, block, and blend copolymers with 0−100 mol% 3HV were synthesized and their thermal and mechanical properties studied. Lastly, high temperature cultivation and several surfactants were tested to enhance the production of bespoke PHBV from VFA. PHBV productivity and accumulation was greatly improved in a fed-batch bioreactor fermentation at 37°C with Tween-80 and the maximum PHBV content 58.9% was obtained. The polymers from shake-flasks and from bioreactors showed minor variations in their material properties, demonstrating the scalability and the robustness of the process developed. Further understanding of the different process variables affecting polymer synthesis and composition was gained in this thesis. It is now possible to produce PHBV with controllable composition, microstructure and minor differences in material characteristics. The novel and robust production strategy developed address the bioprocess challenge of minimising the uncontrolled variation of polymer characteristics that is currently hindering the wider use of PHA hence allowing the production of high quality polymers for commodity goods, packaging and biomedical applications.