Conselho Nacional de Desenvolvimento Científico e Tecnológico / Alguns Bastonetes Gram-negativos não fermentadores (BGNNF) costumam ser considerados clinicamente pouco significantes e a sua implicação em infecções é subestimada. Devido à similaridade fenotípica, mudanças taxonômicas, baixa reatividade bioquímica e limitações nos bancos de dados em sistemas comerciais, a identificação de BGNNF é frequentemente equivocada, culminando com a denominação de diferentes micro-organismos apenas como BGNNF, por falta de melhor diferenciação. O objetivo desse estudo foi avaliar, por métodos fenotípico convencional, proteômico e molecular, a identificação de BGNNF incomuns isolados em hemoculturas de pacientes atendidos em um hospital universitário no Rio de Janeiro. Foram selecionadas 78 amostras isoladas de hemoculturas caracterizadas no laboratório clinico como BGNNF para a identificação por sequenciamento dos genes 16S RNA e recA, por um conjunto amplo de testes fenotípicos manuais e por MALDI-TOF MS. Os micro-organismos predominantes na amostragem foram genotipados pela técnica de eletroforese em gel de campo pulsado (PFGE). Pelo sequenciamento do gene 16S rRNA, a maioria das amostras (n=31; 40%) foi incluída no gênero Burkholderia, seguido de Pseudomonas stutzeri (10%) e Delftia acidovorans (4%). Os demais isolados foram agrupados em 27 diferentes espécies. O sequencimento do gene recA identificou a maioria das espécies de Burkholderia como Burkholderia contaminans (n=19; 24%). Os testes fenotípicos incluíram as 31 amostras apenas no CBc e para as outras 47 amostras, a concordância com o sequenciamento do gene 16S rRNA em nível de espécie foi de 64% (n=30) e apenas em gênero a concordância foi de 17% (n=8). A análise comparativa geral da identificação por MALDI-TOF MS com o sequenciamento do gene16S rRNA mostrou que 42% (n=33) das 78 amostras foram concordantes em nível de espécie e 45% (n=35) apenas em gênero. Excluindo as amostras do CBc, houve um aumento da concordância em nível de espécie para 60%. As discordâncias parecem ser devido às diferenças nos perfis proteicos das amostras em relação às amostras-referência do banco de dados do equipamento e podem ser aprimorados com a atualização de perfis no sistema. A análise do polimorfismo genético de B. contaminans mostrou a ausência de um clone disseminado causando surto, além da provável origem ambiental das infecções. Os setores de nefrologia e hemodiálise contribuíram com maior número de pacientes com amostras positivas (5 pacientes e 9 amostras). Os grupos clonais BcoD e BcoE foram encontrados em pacientes assistidos no mesmo setor com diferença de quatro meses (BcoD, nefrologia) e 1,5 ano (BcoE, hemodilálise), entre as culturas, respectivamente. As discordâncias entre as técnicas ocorreram principalmente devido a dificuldade de identificação das espécies do CBc. Os BGNNF incomuns são de difícil caracterização independente da metodologia usada e nenhum método por si só foi capaz de identificar todas as amostras. / Some nonfermenting Gram-negative Bacilli (NFGNB) are considered of low clinical significance, and their implication in infections is usually underestimated. Due to their phenotypic similarities, frequent taxonomic changes and low biochemical reactivity, as well as to limitations of bacterial identification commercial system databases, these NFGNB are frequently misidentified and are collectively referred to as NFGNB group, in the lack of a better differentiation. The aim of the present study was to evaluate the performance of the conventional phenotypic method, the proteomic matrix-assisted laser desorption ionization time of flight mass spectometry method (MALDI-TOF MS) and of molecular methods (16S RNA and recA gene sequencing) in the identification of 78 unusual NFGNB isolated from blood cultures of pacients treated at an university hospital in Rio de Janeiro. Clonality of the predominant species identified within these isolates was determined by pulsed-field gel electrophoresis (PFGE). By the 16S rRNA gene sequence analysis, most strains (n = 31; 40%) were included in the Burkholderia spp. followed by Pseudomonas stutzeri (n = 8; 10%), Delftia acidovorans (n = 3; 4%) and Stenotrophomonas maltophilia (n = 3; 4%). The remaining bacterial isolates were included in 27 different species. By the recA gene sequencing technique, most bacteria from the Burkholderia cepacia complex (BCC), samples were classified as Burkholderia contaminans (n=19; 24%). Phenotypic tests provided accurate identification of all 31 isolates included in the BCC by the 16S rRNA gene sequence analysis. For the other 47 samples, agreement of the results obtained with these two techniques in species and genus level identifications occurred in 30 (63,8%) and 17 samples (36,2%), respectively. The results obtained by the MALDI-TOF MS and 16S rRNA gene sequencing methods agreed at species and genus levels in 33 (42%) and 35 isolates (45%), respectively. When bacteria from the BCC were excluded from the analysis, the agreement between the two techniques at species level increased to 60%. Misidentification by the MALDI-TOF MS method may be due to differences in protein spectra between the samples and the reference strains in the equipment database. PFGE analysis of B. contaminans isolates revealed the absence of a disseminate clone causing an outbreak, and the probable environmental source of infections. The nefrology ang dialisis sectors contributed to the greatest number of patients with positive cultures (5 pacients and 9 isolates). Clones BcoD and BcoE were found in blood cultures of pacientes treated in a same sector with differences of 4 months (BcoD, nefrology) and 1.5 year (BcoE, dialisis). The misidentifications occurred mainly due to the hard differentiation of BCC species. Unusual NFGNB are of difficult characterization whatever the methodology used and no method alone was able to identify all the isolates.

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.

As culturas da soja e milho são de grande importância econômica mundial e também para o Brasil, onde a área cultivada com essas duas culturas está estimada em 45.855.900 mil hectares, distribuídas em todos estados produtores conforme suas características. A estimativa da safra mundial de soja em 2015/16 apresentou uma redução na produção global da oleaginosa para 319,0 milhões de ton, volume 1,1 milhão de ton inferior ao levantamento de dezembro de 2015. Ainda assim, trata-se de um volume recorde. Para o milho, a produção global foi de 967,9 milhões de ton, com uma redução no volume de 5,9 milhões de ton em relação ao levantamento realizado em dezembro de 2015. Nessas duas culturas são comumente utilizadas bactérias fixadoras de nitrogênio (BFN), reduzindo ou até mesmo, eliminando a aplicação de adubos nitrogenados. Estudos apontam que a simbiose entre BFN e as culturas soja e milho pode ser otimizada mediante a coinoculação com rizobatérias promotoras de crescimento de plantas (RPCP). Apesar de promissora, o estudo da utilização de BFN em associação com RPCPs é incipiente no Brasil. Assim, o presente trabalho teve como objetivo monitorar, a partir da marcação bacteriana, a interação entre a linhagem de Burkholderia ambifaria (RZ2MS16), uma rizobactéria proveniente do guaranazeiro e previamente descrita como promotora de crescimento em soja e milho e linhagens das espécies Bradyrhizobium japonicum (SEMIA5079), Bradyrhizobium diazoefficiens (SEMIA5080) e Azospirillum brasilense (Ab-v5 e Ab-v6) que são comercialmente utilizadas como bioinoculantes nessas culturas respectivamente. Os efeitos sinergisticos da interação entre RZ2MS16 e bioinoculantes comercias foram avaliados em experimento de casa de vegetação. Também foi avaliado o efeito da coinoculação de bioinculantes com outra rizobactéria proveniente do guaranazeiro, Bacillus sp. (RZ2MS9). As linhagens foram inoculadas separadamente e coinoculadas, sendo melhores resultados observados com a coinoculação das linhagens. As linhagens marcadas com genes de fluorescência selecionadas para estudo de interação foram RZ2MS16, Ab-v5 e SEMIA5080, sendo essa interação observada por microscopia de fluorescência, com também pelo reisolamento das linhagens marcadas. As linhagens RZ2MS16:pNKGFP e Ab-v5: pWM1013 e SEMIA5080:pWM1013 colonizaram todos os nichos avaliados em milho e soja, respectivamente, sendo também caracterizadas como endofíticos. Assim se observa que estudos desta natureza são de grande importância para um melhor entendimento da interação entre bactéria planta e o efeito da coinoculação no melhor desenvolvimento de plantas comercialmente utilizadas. / The soybean and corn are of great global economic importance and also to Brazil, where the area cultivated with these two crops is estimated at 45.8559 billion hectares, distributed in all producing states according to their characteristics. The estimate of the global soybean crop in 2015/16 showed a reduction in global production of oilseeds to 319.0 million tons, volume 1.1 million tons lower than the survey of December 2015. Still, it is a record volume. For corn, the total production was 967.9 million tons, with a reduction in volume of 5.9 million tons compared to the survey conducted in December 2015. In these two crops are nitrogen fixing bacteria commonly used (BFN), reducing or even eliminating the application of nitrogenous fertilizers. Studies show that the symbiosis between BFN and cultures soy and corn can be optimized by coinoculation with rhizobacteria promoting plant growth (PGPR). Although promising, the study of the use of BFN in association with RPCPs is incipient in Brazil. Thus, this study aimed to monitor, from the bacterial marking the interaction between the strain of Burkholderia ambifaria (RZ2MS16) a rhizobacteria from the guarana and previously described as a growth promoter in soybean and corn and strains of the species Bradyrhizobium japonicum (SEMIA5079), Bradyrhizobium diazoefficiens (SEMIA5080) and Azospirillum brasilense (Ab-v5 and v6-Ab) that are commercially used as inoculant these cultures respectively. The synergistic effects of the interaction between RZ2MS16 and commercial inoculant were evaluated in a greenhouse experiment. It was also evaluated the effect of coinoculation of inoculant with other rhizobacteria from the guarana, Bacillus sp. (RZ2MS9). The strains were inoculated separately and coinoculated, with best results seen with coinoculation lineages. The lines marked with fluorescence genes selected for study interactions were RZ2MS16, Ab-v5 and SEMIA5080, this interaction being observed by fluorescence microscopy with also by reisolation of the marked strains. Strains RZ2MS16: pNKGFP and Ab-v5: pWM1013 and SEMIA5080: pWM1013 colonizing all niches evaluated in corn and soybeans, respectively, also being characterized as endophytes. Thus it is observed that such studies are of great importance for a better understanding of the interaction between plant and bacteria coinoculation the effect of the improved development of plants used commercially.

O sistema de mobilização intracelular de poli-3-hidroxibutirato (P3HB) em Burkholderia sacchari foi analisado. A busca em genomas de Burkholderia spp. identificou duas oligômero hidrolases (PhaY1 e PhaY2) e pelo menos três P3HB despolimerases intracelulares (PhaZa1, PhaZa2 e PhaZd1). Mutantes de B. sacchari afetados na mobilização de P3HB e complementados com genes de Ralstonia eutropha apresentaram um aumento expressivo nas taxas de mobilização de P3HB, especialmente quando o gene phaZa1 foi superexpresso. A superexpressão dos genes phaZa2 ou phaZa3 também conduziu a aumentos nas taxas de mobilização embora em um grau menor que os valores obtidos com phaZa1. Dois mutantes afetados na mobilização de P3HB foram obtidos utilizando o transposon mini-Tn5 (NAM03 e NAM04). NAM03 apresentou interrupção em gene que codifica uma P3HB despolimerase intracelular (PhaZa1). NAM04 apresentou interrupção em gene anotado como serino peptidase LonA. Este pode representar um ativador da mobilização ou uma nova P3HB despolimerase intracelular. / The intracellular poly-3-hydroxybutyrate (P3HB) mobilization system in Burkholderia sacchari was analyzed. A search in Burkholderia spp. genomes identified two oligomer hydrolases (PhaY1 and PhaY2) and at least three intracellular P3HB depolymerase (PhaZa1, PhaZa2 e PhaZd1). B. sacchari mutants affected on P3HB mobilization and complemented by Ralstonia eutropha genes showed an expressive increase on P3HB mobilization rates, especially when phaZa1 was overexpressed. The overexpression of phaZa2 or phaZa3 also increased the mobilization rates though to a lesser extent than phaZa1. Two mutants affected on P3HB mobilization were obtained using the transposon mini-Tn5 (NAM03 and NAM04) .NAM03 was disrupted in a gene encoding an intracellular P3HB depolymerase (PhaZa1). NAM04 was disrupted in a gene annotated as a serine peptidase LonA. This could be a mobilization activator or a new intracellular P3HB depolymerase.

This master thesis deals with polyhydroxyalkanoates (PHA) and their role in bacterial biofilms. In the theoretical part the polyhydroxyalkanoates, bacterial biofilm and the relationship between them were reviewed. The experimental part focused on differences in PHA production by planktonic and biofilm cells. In order to study selected topic, bacterial strains of Burkholderia cepacia and Burkholderia sacchari were cultivated using a CDC biofilm reactor. The attention was paid to quantity and especially to the form in which PHA occurs in planktonic and biofilm cells. Results of Raman spectroscopy have shown that PHA exists exclusively in native amorphous form in planktonic bacterial cells. On the other hand, in biofilm PHA occurs also in a partially crystalline form. In addition, the resistance of planktonic and biofilm cells against various stress factors and the effect of osmotic stress on PHA production was tested too. According to the results of the experiment, when the bacteria were exposed to different stress factors (high temperature, low temperature, presence of detergent and so forth) biofilm cells showed a higher stress resistance than planktonic cells. Apart from slowing cell growth and reproduction, increased osmotic pressure in the culture medium also caused decrease of PHA production. In addition, planktonic cells responded to external stimuli more sensitively than biofilm ones.

This diploma thesis is focused on study of chemical and enzymatical hydrolysis of raw wood material. The aim of this work was to find the suitable method for pretreatment of selected lignocellulose materials. The theoretical part deals with characterization of lignocellulosic material and its components. There are also subscribed various pretreatment methods and their effect on hydrolysis of sawdust. In experimental part of the work the most appropriate approach of pretreatment and hydrolysis of sawdust was studied. Criteria for the selection of suitable method was concentration of saccharides as desired product of hydrolysis and also concentration of the most important microbial inhibitors - polyphenols. Application of 96% ethanol or 5% H2O2 were identified as the most promising pretreatment methods which enhanced yields of fermentable sugars about 30 %. Further, we also performed cultivation of bacteria Burkholderia cepacia and bacteria Burkholderia sacchari using solution obtained by hydrolysis of lignocellulose material.

The aim of this work was study of the detoxification of lignocellulose material hydrolysates and to investigate sawdust suitability as a substrate for microbial production of PHA by bacteria Burkholderia cepacia and Burkholderia sacchari. In the experimental part of the work the most suitable way of detoxification of model and real hydrolysate was studied. After that, detoxification methods used were evaluated. Criteria for evaluation were concentration of polyphenols as the most important microbial inhibitors and reduction saccharides as the main carbon substrate. Furthermore, fermentability of the hydrolysates was also tested by cultivation of two bacteria capable of PHA accumulation. Burkholderia sacchari demonstrated higher ability to accumulate PHA then Burkholderia cepacia. Then in the summary – most effective way for detoxification was ‚overliming‘. Major increase of PHB in biomass was obtained when Burkholderia sacchari was cultivated on media gained by application of overliming of real lignocellulose hydrolysate. However, total gains of PHB were more likely low and then sawdust can not be considered as a substrate for PHB production at industrial scale.

No description available.

No description available.

The aim of this study was to identify and characterise type II toxin-antitoxin (TA) systems in Burkholderia pseudomallei, the causative agent of the human disease melioidosis. 8 putative TA systems were identified within the genome of B. pseudomallei K96243. 5 of these were located witihn genome islands. Of the candidate toxins, BPSL0175 (RelE1) or BPSS1060 (RelE2) caused growth to cease when expressed in Escherichia coli, whereas expression of BPSS0390 (HicA) or BPSS1584 (HipA) (in an E. coli ΔhipBA background) caused a reduction in the number of culturable bacteria. HicA also caused growth arrest in B. pseudomallei K96243 ΔhicAB. These toxin induced phenotypes were enhanced by an <3kDa extracellular factor that accumulated in the spent medium during growth. Expression of the cognate antitoxins could restore growth and culturability of cells. Expression of hicA in E. coli gave an increased number of persister cells in response to ciprofloxacin or ceftazidime. Site directed mutagenesis studies identified two key residues within the HicA toxin that were essential for both the reduced culturability and increased persistence phenotypes. Deletion of hicAB from B. pseudomallei K96243 did not affect persister cell or survival frequencies compared to the wild type following treatment with a variety of stress conditions. Deletion of the ΔhipBA locus from B. pseudomallei K96243 also had no affect on bacterial persistence or survival under the conditions tested.