This thesis focuses on fluorescent analysis of viability and PHA content in bacterial cultures, the main methods of investigation were flow cytometry and fluorescent microscopy. In order to determine viability of C. necator H16, several viability probes were tested, nevertheless, only BacLightTM kit and propidium iodide can be used to estimate portion of viable and live bacterial cell in samples. Further, Acridine orange was used to monitor physiological state of bacterial culture and two hydrophobic probes, Nile Red and BODIPY 493/503, were used to investigate PHA content in bacterial cells. Application of BODIPY 493/503 seems to be promising since this probe does not require permeabilization of bacteria cells and it can be used along with propidium iodide. Furthermore, several fluorophores were tested in the microscopic part. In was found that concentrations used in cytometric analyses were too high for microscopic use. Emission from the SYTO9 fluorophore is seen mainly in the green channel but because of the high concentration some emission was visible in the red channel. Cells stained with BODIPY 493/503 had very high fluorescence intensities when the stain concentration was 10 . At the same time, negative amplitudes of fluorescence were measured in both strains of C. necator, but in case of C. necator H16 that amplitude was much more pronounced. In this strain surprising high concentration of BODIPY stain was observed on the surface of PHB granules. Anisotropy of the fluorophore was nearing 0 which is very surprising.

Proposed doctoral thesis deals with microbial production of biopolymers (polysaccharides and polyesters) using renewableble inexpensive resources as carbon and nitrogen source. At first, production of extracellular metabolites, mainly pullulan and poly-L-malic acid, by polymorphic microorganism Aureobasisium pullulans was studied. Further part of thesis was focused on production of bacterial biopolyesters polyhydroxyalkanoates (PHA). PHA are produced in the form of intracellular granules by various bacteria species. During the study of PHA production, sythesis of poly(3-hydroxybutyrate) and technologically significant copolymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate) was investigated as well with regard to waste substrate utilization in biorafinery concept. Spent coffee ground seemed to be applicable waste in biorefinery proces. One of the coffee wastes used for PHA production was spent coffee ground hydrolysate which was converted to PHA by Burkholderia cepacia. Moreover, copolymer of 3HB and 3HV was accumulated when SCGH was used as a sole carbon source, no precursor had to be added. Another coffee waste, which was utillized by Cupriavidus necator H16, is represented by oil extracted from spent coffee grounds. Hydrolysis proces of waste substrates had to be optimized, to reach the highest possible saccharide concentration. Due to the hydrolysis process several toxic compounds can be formed, hence, influence of hydrolysis procesings on polyphenols content in hydrolysates was monitored. Waste substrates were also tested as potentional complex nitrogen source for PHA production. Hydrolysates of cheese whey and chicken feather were used as inexpensive complex nitrogen source for PHA production by C. necator, when waste frying oil was used as a carbon substrate. The finnal part of the thesis is dealing with possibilities how the PHA can be processed into atractive aplication forms. Liposomes with partial content of PHB had been prepared, moreover, for improving of antioxidant activity and antimicrobial effect the waste coffee oil was added. Micro-fibrous PHB materials were prepared for the purposes of water filtration. Higher filtration effectivity was observed when composite PHB fibrous material containing active charcoal or metal oxides was used. Important part of thesis is represented by study of degradation processes of prepared PHA-based aplication forms. Various microorganisms were tested on PHA depolymerases production. Biodegradability of PHA materials was tested in of composting conditions by standard composting test IS/ISO 20200. Changes in mechanical properties of polyurethan, where polyol was partialy replaced by PHB, were tested depending on the exposure of composting condition.

Vascular networks are required to support the formation and function of three-dimensional tissues. Biodegradable scaffolds are being considered in order to promote vascularization where natural regeneration of lost or destroyed vascular networks fails. Particularly; composite materials are expected to fulfill the complex demands of a patient's body to support wound healing. Microbial biopolyesters are being regarded as such second and third generation biomaterials. Methylobacterium extorquens is one of several microorganisms that should be considered for the production of advanced polyhydroxyalkanoates (PHAs). M. extorquens displays a distinct advantage in that it is able to utilize methanol as an inexpensive substrate for growth and biopolyester production. The design of functionalized PHAs, which would be made of both saturated short-chain-length (scl, C [less than or equal to] 5) and unsaturated medium-chain-length (mcl, 6 [less than or equal to] C [less than or equal to] 14) monomeric units, aimed at combining desirable material properties of inert scl/mcl-PHAs with those of functionalized mcl-PHAs. By independently inserting the phaC1 or the phaC2 gene from Pseudomonas fluorescens GK13, recombinant M. extorquens strains were obtained which were capable of producing PHAs containing C-C double bonds. A fermentation process was developed to obtain gram quantities of biopolyesters employing the recombinant M. extorquens ATCC 55366 strain which harbored the phaC2 gene of P. fluorescens GK13, the better one of the two strains at incorporating unsaturated monomeric units. The PHAs produced were found in a blend of scl-PHAs and functionalized scl/mcl-PHAs (4 [less than or equal to] C [less than or equal to] 6), which were the products of the native and of the recombinant PHA synthase, respectively. Thermo-mechanical analysis confirmed that the functionalized scl/mcl-PHAs exhibited the desirable material properties expected. This project contributed to current research on polyhydroxyalkanoates at different levels. The terminal double bonds of the functionalized scl/mcl-PHAs are amenable to chemical modifications and could be transformed into reactive functional groups for covalently linking other biomacromolecules. It is anticipated that these biopolyesters will be utilized as tissue engineering materials in the future, due to their functionality and thermo-mechanical properties.

O presente estudo teve como objetivo realizar a triagem de PHA sintases numa biblioteca metagenômica de solo de Mata Atlântica, empregando duas técnicas de busca: o método de detecção fenotípica e a técnica de PCR. Resultados positivos foram obtidos com este último, empregando iniciadores descritos na literatura e iniciadores descritos neste trabalho. Em 10.67% dos clones da biblioteca foram obtidos amplicons, dos quais 7 foram seqüenciados, apresentando similaridade para os genes phaC dos tipos II e IV. Adicionalmente, 67 clones positivos para a classe III foram obtidos e 4 destes foram seqüenciados. Duas das seqüências obtidas mostraram alta similaridade com o gene codificador da enzima glutamina sintetase tipo I, outro deles para a proteína hipotética conservada pertencente à família de enzimas oxidoredutases e a outra para o componente D do gene hidrogenase-4. A partir da análise dos resultados, iniciadores mais específicos são propostos. Assim, a técnica de PCR foi mais eficiente na detecção de genes da biossíntese de PHA na biblioteca metagenômica estudada. / To perform a PHA synthase screening in a metagenomic library from Atlantic forest soil two search methods were applied: phenotypic detection and PCR. Positive results with PCR were obtained by using primers described in the literature and proposed in this study. Amplicons were obtained in 10.67% of the library, 7 of them were sequenced showing similarity with class II and IV phaC genes. In addition, 67 positive clones for class III were obtained and 4 of them were sequenced. Two of these sequences showed high similarity to the glutamine synthase gene type I, the third one showed similarity to the conserved hypothetical protein of the reductase family, and the forth presented similarity to the component D of the hidrogenase-4. According to the results, more specific primers are suggested. Therefore, PCR was more efficient in the detection of PHA biosynthesis genes in the studied metagenomic library.

A xilose é um dos principais componentes dos materiais lignocelulósicos, os quais são de grande interesse para produção de bioprodutos como etanol e polihidroxialcanoatos (PHA). Visando melhorar o consumo de xilose em Burkholderia sacchari, uma grande produtora de PHA, os seguintes genes codificadores de xilose isomerase foram nela inseridos e avaliados: xylABs, xylABc, xylAPl, xylABp e xylABx, respectivamente de B. sacchari, B. cenocepacia, Photorhabdus luminescens, B. phymatum e B. xenovorans. Foi ainda sintetizado o gene de B. sacchari (xylA*) no qual foram inseridas modificações descritas na literatura como capazes de aumentar o consumo de xilose em outros organismos. As linhagens recombinantes de B. sacchari abrigando os genes xylABs e xylA* tiveram um aumento de aproximadamente 30%, e aquelas abrigando os genes xylABp e xylABx de 23%, no consumo de xilose quando comparadas com a linhagem controle. Essas quatro linhagens recombinantes foram aquelas que conseguiram produzir maior quantidade de P3HB, aproximadamente 70% a mais do que linhagem controle. / Xylose is a major component of lignocellulosic materials, which are of great interest for the production of bio-products, such as ethanol and polyhydroxyalkanoates (PHA). To improve the consumption of xylose in Burkholderia sacchari, a major PHA producer, the following genes, encoding xylose isomerase, were introduced in these bacteria: xylABs, xylABc, xylAPl, xylABp and xylABx, respectively from B. sacchari, B. cenocepacia, Photorhabdus luminescens, B. phymatum e B. xenovorans. The gene of B. sacchari (xylA*) was also synthesized with several modifications described in the literature as able to increase the consumption of xylose in other organisms. Recombinant strains harboring B. sacchari xylABs and xylA* gene had an increase of approximately 30% in the xylose consumption compared to the control strain, and those harboring xylABx and xylABp gene an increase of 23%. These four recombinant strains were those that were able to produce more P3HB, approximately 70% more than the control strain.

Neste trabalho, foram desenvolvidas estratégias para modular a composição de elastômeros biodegradáveis da família dos polihidroxialcanoatos (PHA), produzidos por Pseudomonas, a partir de ácidos graxos ou óleos vegetais, para diversificar suas aplicações, sobretudo pela inserção de monômeros insaturados. A composição do PHA produzido variou com o tipo de ácido graxo fornecido e com sua proporção em misturas. Em genomas seqüenciados, detectaram-se dois genes fadH (codificador de 2,4-dienoilCoA hidratase) em P. aeruginosa e apenas um em outras Pseudomonas. Observou-se uma correlação entre o número de cópias de fadH no genoma e maior eficiência na oxidação de ácidos graxos insaturados. Mutantes afetados no metabolismo de ácidos graxos insaturados foram obtidos utilizando-se transposon, alguns destes mutantes apresentaram maior eficiência na incorporação de monômeros insaturados ao PHA. A clonagem e seqüenciamento de fragmentos de DNA interrompidos pelo transposon permitiram a identificação dos genes afetados nesses mutantes. / Different strategies were applied to modulate the composition of biodegradable elastomeric polyhydroxyalkanoates (PHA) accumulated by Pseudomonas from fatty acids and plant oils, in order to improve the applications of this material, mainly by unsaturated monomer insertion. PHA composition varied both with fatty acid type and fatty acids ratio in mixtures supplied. Analysis of genome sequences revealed two fadH (encoding 2,4-dienoyl-CoA hydratase) copies in Pseudomonas aeruginosa and only one in other Pseudomonas species. The number of fadH copies in the genome was related to the higher oxidation of unsaturated fatty acids. Transposon-induced mutants affected on unsaturated fatty acids metabolism were obtained, some of them showing higher efficiency to incorporate unsaturated monomers do the PHA. Cloning and sequencing of transposon-disrupted DNA regions allowed to identify the genes affected in those mutants.

O trabalho é proposto visando melhorar o consumo de xilose na bactéria Burkholderia sacchari utilizando o acúmulo de PHB como modelo de produção Foi desenvolvido um processo de evolução por meio da aplicação de feast and famine e Cultivos sequenciais em fase exponencial. Foi obtida uma linhagem mutante com uma velocidade especifica de crescimento de 0,24 h -1. Foi feita uma análise de fluxos metabólicos da qual foi possível concluir que o metabolismo da xilose acontecia em sua maioria pela VP junto com a ED. Foi feito um ensaio de acumulo com carbono marcado utilizando uma solução de xilose, de 20:80 de xilose marcada 13C em todos os carbonos e xilose não marcado, para determinar quais seriam as possíveis vias metabólicas no uso da xilose por parte de B. sacharia LFM 101 e da linhagem evoluída BSEV11. Foi determinado que houve embaralhamento de carbonos, fato que só acontece quando o metabolismo da xilose e feito pela VP junto com a via ED, assim foi possível conferir a via ED como principal via para o metabolismo da xilose em B. sacchari LFM 101. / To evaluate the possibilities of improving the productivity of PHA production from xylose, evolutionary engineering techniques were applied to B. sacchari to select cells with maximum specific growth rates (max) higher than the wild type. Metabolic flux analysis was also performed to evaluate the fluxes through central pathways and the possibility of further improvements by modifying fluxes rates. The evolved strain reached a max of 0.24 ± 0.01 h-1 at the end of the evolutionary process. Strains were submitted to bioreactor experiments. A metabolic network of the strain was usedn to determine the possible distribution of metabolic fluxes. A total of 19 elementary modes were obtained. It was concluded that the metabolism of xylose occurred mostly by VP along with the ED. The ED pathway has the major activity going on in a cyclic way. It was also performed a 13C labeled xylose assay, in which it was possibly to confirm the obtained results from the metabolic flux analyses.

Os copolímeros de 3-hidroxibutirato e 3-hidroxihexanoato (P3HB-co-3HHx) são da família dos polihidroxialcanoatos (PHA), materiais termoplásticos e biodegradáveis acumulados por bactérias a partir de fontes de carbono renováveis. O P3HB-co-3HHx desperta interesse industrial para frações de 3HHx menores que 20 mol%, assemelhando-se ao polietileno de baixa densidade. Neste projeto, criou-se um sistema genético para controlar a composição do copolímero P3HB-co-3HHx pela indução de genes da biossíntese de precursores 3HB. Baseado no promotor lac foram construídas cinco versões do plasmídeo de controle de copolímero (pCC) utilizando o promotor Lac. Porém, mesmo com a versão mais aprimorada, não foi possível o controle de composição de P3HB-co-3HHx em Pseudomonas sp. LFM461. Através de experimentos de atividade enzimática e RT-qPCR do cDNA do gene phaA e phaB, foi possível indicar que o problema está na impossibilidade do promotor Lac de promover expressão dos genes de biossíntese de 3HB presentes nos pCC. / Polyhydroxyalkanoates (PHA) are polyesters material accumulated by bacteria which has thermoplastic and biodegradable proprieties and can be produced from renewable feedstocks. Copolymers of 3-hydroxybutirate and 3-hydroxyhexanoate (P3HB-co¬-3HHx) which contain less than 20mol% of 3HHx have being researched for its industrial proprieties. Recently, our laboratory has been researching a Pseudomonas sp. strain, LFM461, which can produce high 3HHx content when hosting PHA biosynthesis genes from Aeromonas. In this project, it was design a genetic system for control of P3HB-co-3HHX composition through induction of 3HB monomers biosynthesis. Thus, five versions of a copolymer control plasmid (pCC) was built based on Lac promoter. However, even through improvements on stability and expression profile of pCC it was not possible to stablish an assay of successful PHA composition control in Pseudomonas sp. LFM461. By enzymatic activity and RT-qPCR of cDNA experiments we have indications of problems of Lac promoter on driving the expression of 3HB genes in pCC.

Os microrganismos constituem dois terços da diversidade biológica na Terra, no entanto, muitos deles não podem ser cultivados por técnicas tradicionais. Portanto, o acesso a esta diversidade tem sido feita através da utilização de técnicas independentes de cultivo. Diante deste panorama, a metagenômica apresenta-se como uma alternativa, pois dispensa a necessidade de cultivo. Tal técnica possibilita inclusive a identificação e utilização do potencial metabólico destes organismos para o desenvolvimento de novos processos e produtos. Os polihidroxialcanoatos (PHAs) são poliésteres bacterianos, acumulados intracelularmente em forma de grânulos, cujas propriedades são similares a de alguns plásticos de origem petroquímica. O objetivo deste trabalho foi identificar e avaliar a diversidade de genes relacionados à produção de PHAs em bibliotecas metagenômicas de solo. A prospecção realizada resultou na identificação de clones contendo o gene phaC. De uma forma geral, pôde-se concluir que ainda há uma grande diversidade deste gene a ser descoberta no ambiente estudado. / Microorganisms constitute two third of the Earth\'s biological diversity, however, many of them cannot be cultured by standard techniques. Therefore, access to this diversity has been achieved through the use of culture-independent techniques. Facing this scenario, the metagenomic presents itself as an alternative, since it eliminates the need for cultivation. This technique also allows the identification and use of the metabolic pathways of these organisms to develop new processes and products. The polyhydroxyalkanoates (PHAs) are bacterial polyesters accumulated as granules, whose properties are similar to some plastics of petrochemical origin. The aim of this work was to identify and access the diversity of genes related to PHAs production in soil metagenomic libraries. The screening resulted in the identification of clones containing the phaC gene. In a general way, it was concluded that there is still a considerable diversity of this gene to be discovered in the study environment.

O potencial de bactérias em produzir polihidroxialcanoatos (PHA) a partir de óleo de soja foi avaliado com ênfase em Aeromonas spp. Dez isolados apresentando características de Aeromonas spp. (colônias amarelas em GSP agar e produção de P3HB-co-3HHx) e perfis ARDRA similares foram obtidos. Dois isolados produzindo PHAMCL foram também obtidos e experimentos de identificação adicionais serão necessários para confirmar se pertencem ao gênero Aeromonas. P3HB-co-3HHx contendo diferentes frações molares de 3HHx foram produzidos. Isolados produzindo P3HB-co-3HHx a partir de óleo de soja ou ácido láurico foram incapazes de produzir P3HB a partir de glicose sugerindo sua incapacidade de gerar monômeros 3HB a partir de acetil-CoA. Introdução de plasmídeo abrigando genes de biossíntese de P3HB de Ralstonia eutropha em isolados capazes de utilizar eficientemente óleo de soja como fonte de carbono permitiu a produção de P3HB, mas não PHA contendo monômeros de cadeia média, sugerindo uma transferência ineficiente de intermediários a partir da <font face=\"Symbol\">&#946-oxidação para PHA sintase. / The potential of polyhydroxyalknoates (PHA) production from plant oils was evaluated especially in Aeromonas spp. Ten isolates presenting features of Aeromonas spp. (yellow colonies in GSP agar and production of P3HB-co-3HHx) and similar ARDRA profiles were obtained. Two isolates producing PHAMCL were also obtained and further identification experiments will be needed to confirm their position in Aeromonas genus. P3HB-co-3HHx containing different molar fractions of 3HHx were produced. Isolates producing P3HB-co-3HHx from soybean oil or lauric acid were unable to produce P3HB from glucose suggesting their incapability to generate 3HB monomers from acetyl-CoA. Introduction of a plasmid harboring P3HB biosynthesis genes from Ralstonia eutropha into isolates able to use efficiently soybean oil as carbon source allowed the production of P3HB but not PHA containing HAMCL suggesting an inefficient transfer of intermediates from &#946-oxidation to PHA synthase.