Constraint-based modelling of mixed microbial populations: Application to polyhydroxyalkanoates production

Dissertação para obtenção do Grau de Doutor em Engenharia Química e Bioquímica

Optimization of a polyhydroxyalkanoates production process using a halotolerant mixed microbial culture

The rate at which petroleum based plastics are being produced, used and thrown away is increasing every year because of an increase in the global population. Polyhydroxyalkanoates can represent a valid alternative to petroleum based plastics. They are biodegradable polymers that can be produced by some microorganisms as intracellular reserves. The actual problem is represented by the production cost of these bioplastics, which is still not competitive if compared to the one of petroleum based plastics. Mixed microbial cultures can be fed with substrates obtained from the acidogenic fermentation of carbon rich wastes, such as cheese whey, municipal effluents and various kinds of food wastes, that have a low or sometimes even inexisting cost and in this way wastes can be valorized instead of being discharged. The process consists of three phases: acidogenic fermentation in which the substrate is obtained, culture selection in which a PHA-storing culture is selected and enriched eliminating organisms that do not show this property and accumulation, in which the culture is fed until reaching the maximum storage capacity. In this work the possibility to make the process cheaper was explored trying to couple the selection and accumulation steps and a halotolerant culture collected from seawater was used and fed with an artificially salted synthetic substrated made of an aqueous solution containing a mixture of volatile fatty acids in order to explore also if its performance can allow to use it to treat substrates derived from saline effluents, as these streams cannot be treated properly by bacterias found in activated sludge plants due to inhibition caused by high salt concentrations. Generating and selling the produced PHAs obtained from these bacterias it could be possible to lower, nullify or even overcome the costs associated to the new section of a treating plant dedicated to saline effluents.

Food waste valorization through the production of polyhydroxyalkanoates by mixed microbial cultures

Dissertação para obtenção do Grau de Mestre em Engenharia Química e Bioquímica

Impact of carbon/nitrogen feeding strategy on polyhydroxyalkanoates production using mixed microbial cultures

Polyhydroxyalkanoates (PHA) production using mixed microbial cultures (MMC) requires a multi-stage process involving the microbial selection of PHA-storing microorganisms, typically operated in sequencing batch reactors (SBR), and an accumulation reactor. Since low-cost renewable feedstocks used as process feedstock are often nitrogen-deficient, nutrient supply in the selection stage is required to allow for microbial growth. In this context, the possibility to uncouple nitrogen supply from carbon feeding within the SBR cycle has been investigated in this study. Moreover, three different COD:N ratios (100:3.79, 100:3.03 and 100:2.43) were tested in three different runs which also allowed the study of COD:N ratio on the SBR performance. For each run, a synthetic mixture of acetic and propionic acids at an overall organic load rate of 8.5 gCOD L-1 d-1 was used as carbon feedstock, whereas ammonium sulfate was the nitrogen source in a lab-scale sequence batch reactor (SBR) with 1 L of working volume. Besides, a sludge retention time (SRT) of 1 d was used as well as a 6 h cycle length. The uncoupled feeding strategy significantly enhanced the selective pressure towards PHA-storing microorganisms, resulting in a two-fold increase in the PHA production (up to about 1.3 gCOD L-1). A high storage response was observed for the two runs with the COD:N ratios (gCOD:gN) of 100:3.79 and 100:3.03, whereas the lowest investigated nitrogen load resulted in very poor performance in terms of polymer production. In fact, strong nitrogen limitation caused fungi to grow and a very poor storage ability by microorganisms that thrived in those conditions. The COD:N ratio also affected the polymer composition, indeed the produced poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) showed a variable HV content (1-20 %, w/w) among the three runs, lessening as the COD:N increased. This clearly suggests the possibility to use the COD:N ratio as a tool for tuning polymer properties regardless the composition of the feedstock.

Effects of residues on the degradation of PHA produced from mixed microbial cultures and processed in extrusion

Thermal degradation upon melting is one of the major drawbacks reported for polyhydroxyalkanoates (PHA). However, the role of residues originating from the fermentation and the extraction steps on the thermal stability of this class of biopolymers still needs to be clarified. In the particular case of PHA produced from mixed microbial cultures (MMC), this topic is even less documented in the literature. Here, two polyhydroxy(butyrate-co-valerate) (PHBV) produced from MMC enriched in PHA accumulating organisms and fed with cheese whey were studied. A micro extrusion line is used to produce filaments and assess the processability and the degradation of processed PHBV. The prototype micro extrusion line allows for studying grams of materials. The two PHBV contain 18 mol% HV. PHBV was recovered with 11 wt% residues, and further submitted to a purification procedure resulting in a second biopolyester containing less than 2 wt% impurities. The thermorheological characterization of the two PHBV is first presented, together with their semicrystalline properties. Then the processing windows of the two biopolyesters are presented. Finally, the properties of extruded filaments are reported and the thermomechanical degradation of PHBV is extensively studied. The structure was assessed by wide angle X-ray diffraction, mechanical and rheological properties are reported, thermal properties are studied with differential scanning calorimetry and thermogravimetric analysis, whereas Fourier Transform Infrared spectroscopy was used to assess the impact of the extrusion on PHBV chemical structure. All results obtained with the two PHBV are compared to assess the effects of residues on both PHBV processability and degradation.

Effects of fermentation residues on the melt processability and thermomechanical degradation of PHBV produced from cheese whey using mixed microbial cultures

"Available online 28 March 2016"

Assessing the impact of ammonia content in VFA-rich streams on the PHA-storing MMC acclimatization and the PHA production stage

The use of environmentally friendly products increased the interest in renewable resources as alternatives to petrochemical products. Polyhydroxyalkanoates (PHAs) are examples of such promising products, as they are biodegradable polymers with numerous potential applications. PHA production approach consists of using an open mixed microbial culture (MMC) and inexpensive feedstocks (waste or industry byproducts feedstock). The PHA process generally comprises three stages: (1) acidogenic fermentation (AF) stage (conversion of organic carbon into fermentation products); (2) culture selection stage (enrichment in PHA-storing organisms by applying Feast and Famine regime); and (3) PHA production stage (PHA accumulation up to the culture’s maximum capacity). AF of protein-rich residues results in ammonia-rich fermented streams, which can be presented as a challenge for the PHA production stage. The presence of ammonia during this stage may induce organisms to grow instead of producing PHAs. For this reason, the assessment of the effect of a high content of ammonia on PHA production it is the utmost importance. The main goal of the current project is to select a MMC enriched in PHA-accumulating organisms in conditions of high ammonia content and to evaluate the effects of ammonia presence during PHA accumulation. The culture was selected applying the Feast & Famine strategy, and fed, firstly, using a synthetic mixture of VFAs and later using a fermented stream obtained from the fermentation of protein-rich raw materials. The selected culture could accumulate up to 24% PHA per VSS with the synthetic mixture of VFAs and up to 29% for the real fermented stream. The PHA accumulation resulted in different production in the presence and absence of ammonia. Regarding to the synthetic feed, 59%wt. PHA (VSS basis) in the absence of ammonia, and 55%wt. (VSS basis) in the presence, were obtained. For the real feed, the PHA content was about 40%wt. (VSS basis) in both reactors.

Polyhydroxyalkanoates production from salted food waste using mixed microbial cultures.

Plastic is an essential asset for the modern lifestyle, given its superiority as a material from the points of view of cost, processability and functional properties. However, plastic-related environmental pollution has become nowadays a very significant problem that can no longer be overlooked. For this reason, in recent decades, the research for new materials that could replace fossil fuel-based plastics has been focused on biopolymers with similar physicochemical properties to fossil fuel-based plastics, such as Polyhydroxyalkanoates (PHA). PHAs are a family of biodegradable polyesters synthesized by many microorganisms as carbon and energy reserves. PHA appears as a good candidate to substitute conventional petroleum-based plastics since it has similar properties, but with the advantage of being biobased and biodegradable, and has a wide range of applications (e.g., packaging). However, the PHA production cost is almost four times higher (€5/kg) than conventional plastic manufacturing. The PHA production by mixed microbial cultures (MMC) allows to reduce production costs as it does not require aseptic conditions and it enables the use of inexpensive by-products or waste streams as these cultures are more amenable to deal with complex feedstocks. Saline wastewaters (WWs), generated by several industries such as seafood, leather and dairy, are often rich in organic compounds and, due to a strong salt inhibition, the biological treatments are inefficient, and their disposal is expensive. These saline WWs are a potential feedstock for PHA production, as they are an inexpensive raw material. Moreover, saline WWs could allow the utilization of seawater in the process as dilution and cleaning agent, further decreasing the operational costs and the environmental burden of the process. The main goal of the current project is to assess and optimize the PHA production from a mixture of food waste and brine wastewater from the fishery industry by MMC.

Microbial contribution to biofuels production

Dissertação para obtenção do Grau de Doutor em Engenharia Química e Bioquímica

Enrichment of a PHA producing microbial community in a continuous bioreactor setup

Polyhydroxyalkanoates (PHAs) are biosynthetic polyesters, biodegradable and biocompatible making them of great interest for industrial purposes. The use of low value substrates with mixed microbial communities (MMC) is a strategy currently used to decrease the elevated PHA production costs. PHA production process requires an important step for selection and enrichment of PHA-storing microorganisms which is usually carried out in a Sequencing Batch Reactor (SBR). The aim of this study was to optimize the PHA accumulating culture selection stage using a 2-stage Continuous Stirrer Tank Reactor (CSTR) system. The system was composed by two separate feast and famine bioreactors operated continuously, mimicking the feast and famine phases in a SBR system. Acetate was used as carbon source and biomass seed was highly enriched in Plasticicumulans acidivorans obtained from activated sludge. The system was operated under two different sets of conditions (setup 1 and 2), maintaining a system total retention time of 12 hours and an OLR of 2.25 Cmmol/L.h-1. An average PHB-content of 3.3 % wt was obtained in setup 1 and 4.8% wt in setup 2. Several other experiments were performed in order to better understand the continuous system behaviour, using biomass from the continuous system. With the fed-batch experiment a maximum of 8.1% PHB was stored and the maximum substrate uptake and specific growth rates obtained in the growth experiment (1.15 Cmol Cmol-1.h-1 and 0.53 Cmol Cmol-1.h-1) were close to the ones from continuous system (1.12 Cmol Cmol-1.h-1 and 0.59 Cmol Cmol-1.h-1). The microbial community was characterized trough microscopic visualization, Denaturing Gradient Gel Electrophoresis (DGGE) analysis and Fluorescent in situ hybridization (FISH). The last studied performed mimicked the continuous system by building up a SBR system with all the same operational conditions while adding an extra acetate dosage during the 12 h cycle, simulating the substrate passing from the feast to the famine reactors under continuous operation. It was shown that possibly the continuous system was not able to efficiently select for PHB storing organisms under the operational conditions imposed, although the selected culture was capable of consuming the substrate and grow fast. This main conclusion might have resulted from two major factors affecting the system performance: the ammonium concentration in the Feast reactor and the amount of substrate leaching from the Feast to the Famine reactor.

Detection of mixed microbial biofilms on central venous catheters removed from Intensive care Unit Patients

Cateteres venosos centrais inseridos em pacientes internados em unidade de terapia intensiva foram avaliados por métodos microbiológicos (cultura semi-quantitativa) e microscopia eletrônica de varredura a fim de detectar adesão microbiana e correlacionar com a cultura de sangue. Durante o período de estudo, foram avaliados 59 pacientes com cateter venoso central. A idade dos pacientes, sexo, sítio de inserção e tempo de permanência do cateter foram anotados. O cateter era de poliuretano não tunelizado e de único lúmen. O sangue para cultura foi coletado no momento da remoção do cateter. de 63 pontas de cateteres, 30 (47,6%) foram colonizadas e a infecção encontrada em 5 (23,8%) cateteres. A infecção foi mais prevalente em 26 pacientes (41,3%) com cateteres inseridos em veia subclávia do que nos 3 (3,2%) inseridos em veia jugular. A infecção foi observada com mais freqüência em cateteres com tempo de permanência maior do que sete dias. Os microrganismos isolados incluíram 32 estafilococos coagulase-negativa (29,7%), 61 bactérias Gram-negativas (52,9%), 9 estafilcocos coagulase-positiva (8,3%) e 3 leveduras (2,7%). Como agentes causais de infecções em unidade de terapia intensiva foram isolados E. aerogenes, P. aeruginosa, A. baumannii. Os antimicrobianos com maior atividade in vitro contra as bactérias Gram-negativas foram o imipenem e contra as Gram-positivas vancomicina, cefepime, penicilina, rifampicina e tetraciclina. As análises por microscopia eletrônica de varredura revelaram biofilmes sobre a superfície de todos os cateteres examinados.

Leaf-cutter ant fungus gardens are biphasic mixed microbial bioreactors that convert plant biomass to polyols with biotechnological applications

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Bioelectrochemically-assisted reductive dechlorination of 1,2-dichloroethane by a Dehalococcoides-enriched microbial culture

The aim of this study was to verify the possibility to use a polarized graphite electrode as an electron donor for the reductive dechlorination of 1,2-dichloroethane, an ubiquitous groundwater contaminant. The rate of 1,2-DCA dechlorination almost linearly increased by decreasing the set cathode potential over a broad range of set cathode potentials (i.e., from −300 mV to −900 mV vs. the standard hydrogen electrode). This process was primarily dependent on electrolytic H2 generation. On the other hand, reductive dechlorination proceeded (although quite slowly) with a very high Coulombic efficiency (near 70%) at a set cathode potential of −300 mV, where no H2 production occurred. Under this condition, reductive dechlorination was likely driven by direct electron uptake from the surface of the polarized electrode. Taken as a whole, this study further extends the range of chlorinated contaminants which can be treated with bioelectrochemical systems.

Advances on the production of polyhydroxyalkanoates (PHA) by mixed microbial cultures from sugar cane molasses

Dissertação para obtenção do Grau de Mestre em Biotecnologia

Segregated modeling and selection of populations for polyhydroxyalkanoate production by mixed microbial cultures

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia Química e Bioquímica