New and rapid techniques for the characterization and identification of bacteria would have an important role in clinical microbiology and in food analysis because of an increasing prevalence of infectious diseases and In this work we carried out two approaches. In the first study the characterization and differentiation of mesophilic and thermophilic bacteria were investigated by using Fourier Transform Infrared (FTIR) Spectroscopic technique. In the second study, we investigated the characterization and identification of 3 Bacillus and Micrococcus species Our results from first approach show that there was a dramatic difference between mesophilic and thermophilic bacteria. The protein concentration was high, lipid concentration, the level of triglycerides and the unsaturated acyl chains decreased in thermophilic bacteria. We found that in thermophilic bacteria PO- 2 groups become hydrogen bounded. In addition, our results suggest that the cellular DNA content was low in thermophilic bacteria. Moreover there were characteristic peaks for both mesophilic and thermophilic bacteria and these peaks can be used for the differentiation of these two bacteria group. There were also some specific peaks that can be used for the differentiation of Escherichia coli and Lactobacillus plantarum at species level. In the second approach, our results show that there were significant spectral differences between Bacillus and Micrococcus species such as the proportion of unsaturated acyl chains in triglycerides were higher in Micrococcus species. Moreover we observed different bands that may be explained by an acetate oxidation via the tricarboxylic acid cycle and an exopolymer formation in Micrococcus species. In addition to that another band similar to glycogen, may be explained by a glycogen-like storage material in Micrococcus species. Also there are characteristic peaks that can be used for identification of Micrococcus spp.

A cadeia sucroenergética tem uma grande influência para economia nacional. Ao longo da safra 2013/2014, a cadeia movimentou cerca de US$ 100 bilhões, sendo que somente o açúcar gerou uma arrecadação de cerca de US$ 5.55 bilhões as usinas. O Produto Interno Bruto chegou a US$ 43 bilhões, representando assim aproximadamente 2,0% do PIB Nacional. Todavia, o setor está atravessando uma crise econômica que foi potencializada pela queda no valor da saca de açúcar e por uma severa seca que atingiu em especial o estado de São Paulo. A diminuição de perdas se torna essencial em momentos de dificuldades e uma maneira de atingir esse objetivo é melhorando o monitoramento do processo. Nesse cenário, o presente pesquisa monitorou a degradação de sacarose ao coletar amostras em uma usina da região de Piracicaba-SP, associando como causador não somente as elevadas temperaturas, como outros fatores e medidas utilizadas pela indústria. Conforme esperado aumentou a concentração de sacarose ao longo do processo, iniciando com média de 137,69 g/L na moenda e finalizando com 812,91 g/L no açúcar que saiu do secador. Todavia também apresentou um aumento de açúcares redutores (182,38 g/L no caldo da moenda para 245,81 g/L no xarope), indicando a degradação de sacarose. Inclusive, percebe-se uma razão de inversão maior durante da evaporação do que no tratamento (0,46 e 0,28, respectivamente). A justificativa pode estar associada a possível queda no pH, a evidente utilização de maior quantidade de calor em especial no primeiro efeito, a um tempo de residência maior do que o normal nos evaporadores ou mesmo através da entrada de vapor nos corpos, sendo o último mais raro. Os outros parâmetros levantados da degradação térmica de sacarose, 5-hidroximetilfurfural, furfural e as melanoidinas apresentaram uma alta correlação em função da concentração de açúcares redutores (0,99 para o HMF, 0,98 furfural e 0,96 melanoidinas), confirmando a tendência de perdas da molécula de interesse. Também foram levantadas as populações de bactérias mesófilas totais, cujas presenças estão associadas com as condições sanitárias em que o alimento foi processado e fungos (bolores e leveduras) que também diminuem o valor do produto. O tratamento de caldo mostrou-se eficiente na diminuição dos micro-organismos. Considerando a média dos dois meses, a queda foi de 4,10 x 106 UFC/mL para 6,62x102 UFC/mL para bactérias mesófilas, já para fungos a redução foi de 1,40 x 104 UFC/mL para 1,80 x 101 UFC/mL. Todavia, as altas concentrações encontradas no início e no final (bactérias apresentaram em média 3,00 x 103 UFC/g no xarope e 2,26 x 103 UFC/g no açúcar do secador, enquanto que para os fungos foram encontrados 3,50 x 101 UFC/g no xarope e 1,49 x 103 UFCmL no açúcar do secador) são indicativos de descuidos com a assepsia, aproveitando a falta de exigência de qualidade no açúcar VHP. A alta concentração do caldo da moenda apresentou potencial de estar relacionado com a perda de sacarose. Por fim, ao avaliar a situação e considerando que investimento em equipamentos novos é algo fora da realidade financeira da usina, sugere-se trabalhar em aprimorar as operações realizadas dentro e fora da indústria para se evitar as perdas. / The sugar-energy industry chain has a great influence on the Brazilian economy. Along the 2013/2014 crop, the industry accounted for about US$ 100 billion, and sugar alone yielded about US$ 5.55 billion to sugar mills. The industry yielded US$ 43 billion, accounting for approximately 2,0% of the Brazilian GDP. Nevertheless, the industry is facing an economic crisis aggravated by the drop prices of sugar bag and a severe drought that hit particularly the state of São Paulo in Brazil. Minimizing losses becomes essential in times of difficulties and a way to achieve it is to improve process monitoring. In this scenario, the present project monitored sucrose degradation in samples collected at sugar mill in the region of Piracicaba-SP, associating the degradation to high temperatures as well as other factors and measures used by the mill. As expected, sucrose concentration increased throughout the process, starting with an average of 137,69 g/L at milling and finishing with 812,91 g/L in sugar out of the dryer. However, there was also an increase of reducing sugars (182,38 g/L in milling juice to 245,81 g/L in syrup), indicating sucrose degradation. There was a larger reversal rate during evaporation than in the treatment (0,46 and 0,28, respectively). This is possibly attributed to a pH decrease, an evident use of greater amount of heat in particular in the first effect, a longer time than normal in evaporators or even due to steam inlet into the bodies, which is rarer. The other parameters arising from sucrose thermal degradation, 5-hydroxymethylfurfural, furfural and melanoidins, showed a high correlation with the concentration of reducing sugars (0,99 for HMF, 0,98 for furfural and 0,96 for melanoidins), confirming the trend for loss of the molecule of interest. We also investigated the total populations of mesophilic bacteria, whose presence is associated with health conditions where the food was processed, as well as fungi (molds and yeasts), which also decreases the value of the final product, may produce mycotoxins. The syrup treatment was effective to reduce microorganisms. Considering the average, the population of mesophilic bacteria decrease from 4,10 x 106 cfu/mL to 6,62 x102 cfu/mL. For fungi, the reduction was 1,40 x 104 cfu/mL to 1,80 x 101 cfu/mL. However, the high concentrations found at the beginning and end (Bacteria on average 3,00 x 103 cfu/g in syrup and 2,26 x 103 cfu/g in sugar at the dryer. Fungi 3,50 x 101 cfu/g in syrup and 1,49 x 103 cfu/mL in sugar at the dryer) of the process are indicative of oversights with asepsis, using the lack of demand for quality VHP sugar. The high concentration of juice at milling showed potential to be related sucrose loss. Finally, assessing the scenario and considering that investment in new equipment is something out of the financial reality of the sugar mill, improving the operations inside and outside the mill to avoid losses is suggested.

A cadeia sucroenergética tem uma grande influência para economia nacional. Ao longo da safra 2013/2014, a cadeia movimentou cerca de US$ 100 bilhões, sendo que somente o açúcar gerou uma arrecadação de cerca de US$ 5.55 bilhões as usinas. O Produto Interno Bruto chegou a US$ 43 bilhões, representando assim aproximadamente 2,0% do PIB Nacional. Todavia, o setor está atravessando uma crise econômica que foi potencializada pela queda no valor da saca de açúcar e por uma severa seca que atingiu em especial o estado de São Paulo. A diminuição de perdas se torna essencial em momentos de dificuldades e uma maneira de atingir esse objetivo é melhorando o monitoramento do processo. Nesse cenário, o presente pesquisa monitorou a degradação de sacarose ao coletar amostras em uma usina da região de Piracicaba-SP, associando como causador não somente as elevadas temperaturas, como outros fatores e medidas utilizadas pela indústria. Conforme esperado aumentou a concentração de sacarose ao longo do processo, iniciando com média de 137,69 g/L na moenda e finalizando com 812,91 g/L no açúcar que saiu do secador. Todavia também apresentou um aumento de açúcares redutores (182,38 g/L no caldo da moenda para 245,81 g/L no xarope), indicando a degradação de sacarose. Inclusive, percebe-se uma razão de inversão maior durante da evaporação do que no tratamento (0,46 e 0,28, respectivamente). A justificativa pode estar associada a possível queda no pH, a evidente utilização de maior quantidade de calor em especial no primeiro efeito, a um tempo de residência maior do que o normal nos evaporadores ou mesmo através da entrada de vapor nos corpos, sendo o último mais raro. Os outros parâmetros levantados da degradação térmica de sacarose, 5-hidroximetilfurfural, furfural e as melanoidinas apresentaram uma alta correlação em função da concentração de açúcares redutores (0,99 para o HMF, 0,98 furfural e 0,96 melanoidinas), confirmando a tendência de perdas da molécula de interesse. Também foram levantadas as populações de bactérias mesófilas totais, cujas presenças estão associadas com as condições sanitárias em que o alimento foi processado e fungos (bolores e leveduras) que também diminuem o valor do produto. O tratamento de caldo mostrou-se eficiente na diminuição dos micro-organismos. Considerando a média dos dois meses, a queda foi de 4,10 x 106 UFC/mL para 6,62x102 UFC/mL para bactérias mesófilas, já para fungos a redução foi de 1,40 x 104 UFC/mL para 1,80 x 101 UFC/mL. Todavia, as altas concentrações encontradas no início e no final (bactérias apresentaram em média 3,00 x 103 UFC/g no xarope e 2,26 x 103 UFC/g no açúcar do secador, enquanto que para os fungos foram encontrados 3,50 x 101 UFC/g no xarope e 1,49 x 103 UFCmL no açúcar do secador) são indicativos de descuidos com a assepsia, aproveitando a falta de exigência de qualidade no açúcar VHP. A alta concentração do caldo da moenda apresentou potencial de estar relacionado com a perda de sacarose. Por fim, ao avaliar a situação e considerando que investimento em equipamentos novos é algo fora da realidade financeira da usina, sugere-se trabalhar em aprimorar as operações realizadas dentro e fora da indústria para se evitar as perdas. / The sugar-energy industry chain has a great influence on the Brazilian economy. Along the 2013/2014 crop, the industry accounted for about US$ 100 billion, and sugar alone yielded about US$ 5.55 billion to sugar mills. The industry yielded US$ 43 billion, accounting for approximately 2,0% of the Brazilian GDP. Nevertheless, the industry is facing an economic crisis aggravated by the drop prices of sugar bag and a severe drought that hit particularly the state of São Paulo in Brazil. Minimizing losses becomes essential in times of difficulties and a way to achieve it is to improve process monitoring. In this scenario, the present project monitored sucrose degradation in samples collected at sugar mill in the region of Piracicaba-SP, associating the degradation to high temperatures as well as other factors and measures used by the mill. As expected, sucrose concentration increased throughout the process, starting with an average of 137,69 g/L at milling and finishing with 812,91 g/L in sugar out of the dryer. However, there was also an increase of reducing sugars (182,38 g/L in milling juice to 245,81 g/L in syrup), indicating sucrose degradation. There was a larger reversal rate during evaporation than in the treatment (0,46 and 0,28, respectively). This is possibly attributed to a pH decrease, an evident use of greater amount of heat in particular in the first effect, a longer time than normal in evaporators or even due to steam inlet into the bodies, which is rarer. The other parameters arising from sucrose thermal degradation, 5-hydroxymethylfurfural, furfural and melanoidins, showed a high correlation with the concentration of reducing sugars (0,99 for HMF, 0,98 for furfural and 0,96 for melanoidins), confirming the trend for loss of the molecule of interest. We also investigated the total populations of mesophilic bacteria, whose presence is associated with health conditions where the food was processed, as well as fungi (molds and yeasts), which also decreases the value of the final product, may produce mycotoxins. The syrup treatment was effective to reduce microorganisms. Considering the average, the population of mesophilic bacteria decrease from 4,10 x 106 cfu/mL to 6,62 x102 cfu/mL. For fungi, the reduction was 1,40 x 104 cfu/mL to 1,80 x 101 cfu/mL. However, the high concentrations found at the beginning and end (Bacteria on average 3,00 x 103 cfu/g in syrup and 2,26 x 103 cfu/g in sugar at the dryer. Fungi 3,50 x 101 cfu/g in syrup and 1,49 x 103 cfu/mL in sugar at the dryer) of the process are indicative of oversights with asepsis, using the lack of demand for quality VHP sugar. The high concentration of juice at milling showed potential to be related sucrose loss. Finally, assessing the scenario and considering that investment in new equipment is something out of the financial reality of the sugar mill, improving the operations inside and outside the mill to avoid losses is suggested.

Anaerobic digestion, which is the process by which bacteria breakdown organic matter to produce biogas (renewable energy source) and digestate (biofertiliser) in the absence of oxygen, proves to be the ideal concept not only for sustainable energy provision but also for effective organic waste management. However, the production amount of biogas to keep up with the global demand is limited by the underperformance in the system implementing the AD process. This underperformance is due to the difficulty in obtaining and maintaining the optimal operating parameters/states for anaerobic bacteria to thrive with regards to attaining a specific critical population number, which results in maximising the biogas production. This problem continues to exist as a result of insufficient knowledge of the interactions between the operating parameters and bacterial community. In addition, the lack of sufficient knowledge of the composition of bacterial groups that varies with changes in the operating parameters such as temperature, substrate and retention time. Without sufficient knowledge of the overall impact of the physico-environmental operating parameters on anaerobic bacterial growth and composition, significant improvement of biogas production may be difficult to attain. In order to mitigate this problem, this study has presented a nonlinear multi-parameter system modelling of mesophilic AD. It utilised raw data sets generated from laboratory experimentation of the influence of four operating parameters, temperature, pH, mixing speed and pressure on biogas and methane production, signifying that this is a multiple input single output (MISO) system. Due to the nonlinear characteristics of the data, the nonlinear black-box modelling technique is applied. The modelling is performed in MATLAB through System Identification approach. Two nonlinear model structures, autoregressive with exogenous input (NARX) and Hammerstein-Wiener (NLHW) with different nonlinearity estimators and model orders are chosen by trial and error and utilised to estimate the models. The performance of the models is determined by comparing the simulated outputs of the estimated models and the output in the validation data. The approach is used to validate the estimated models by checking how well the simulated output of the models fits the measured output. The best models for biogas and methane production are chosen by comparing the outputs of the best NARX and NLHW models (each for biogas and methane production), and the validation data, as well as utilising the Akaike information criterion to measure the quality of each model relative to each of the other models. The NLHW models mhw2 and mhws2 are chosen for biogas and methane production, respectively. The identified NLHW models mhw2 and mhws2 represent the behaviour of the production of biogas and methane, respectively, from mesophilic AD. Among all the candidate models studied, the nonlinear models provide a superior reproduction of the experimental data over the whole analysed period. Furthermore, the models constructed in this study cannot be used for scale-up purpose because they are not able to satisfy the rules and criteria for applying dimensional analysis to scale-up.