This study was conducted to set up a systematic approach utilizing advantages of both wet lab and bioinformatic methodologies to study biodegradation abilities and microbial bacterial-functional relationship within bioremediation communities. Firstly, 11pharmaceuticals and personal care products (PPCPs)were selected as target chemicals for establishing an effective determination process in analyzing trace-level concentrations in the environment, and understanding the removal routes during pollutants removal process in wastewater treatment process using activated sludge. Ultra performance liquid chromatography-tandem mass spectrometry was utilized to develop a rapid, sensitive and reliable method without solid phase extraction pre-concentration for trace analysis of 11 PPCPs in influent and effluent from municipal wastewater treatment plants. Shorten the detection time and significant reduction of detection cost were achieved due to the omitting usage of solid phase extraction (SPE)process and avoiding the consumption of hydrophiliclipophilic balancced (HLB)cartridge. Research on removal routes of ten selected PPCPs in activated sludge found activated sludge hardly removed carbamazepine. Biodegradation was the sole route to remove acyclovir, metronidazole, benzylparaben, ethylparaben, methylparaben and propylparaben. Both adsorption and biodegradation were involved in the removal of ranitidine and benzophenone-3, while fluoxetine could be totally removed by adsorption in activated sludge. Secondly, as the target microbial community, activated sludge community was used to set up the global bioinformatic analysis process. Both metagenomic and metatranscriptomic approaches were processed to characterize microbial structure and gene expression of activated sludge community. The taxonomic profile showed thatactivated sludge was dominated by Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Verrucomicrobiaphyla. Gene expression annotation of nitrogen removal revealed that denitrification-related genes sequences dominated in both DNA and cDNA datasets while nitrifying genes were also expressed in relative high levels. Specially, ammonia monooxygenase and hydroxylamine oxidase demonstrated the high cDNA/DNA ratios, indicating strong nitrification activity. Ammonia-oxidizing bacteria present mainly belonged to Nitrosomonas and Nitrosospira species. A fast method to construct local sub-databases has been established for the quick similarity search and annotation of huge metagenomic datasets. The conducted tests showed sub-database annotation pipeline achieved a speedup of ~150-385 times, and got exactly the same annotation results with those of the direct NCBI-nr database BLAST-MEGAN method. This approach provides a new time-efficient and convenient annotation similarity search strategy for laboratories without access to high performance computing facilities. Thirdly, bisphenol A(BPA), which has a partially known biodegradation pathway and relevant bioremediating genes, was chosen as a model to establish a pipeline for systematical understanding the pathways and gene/bacteria relationships in an enriched microbial community. 11 new metabolites were detected during BPA degradation. Thereby, a novel pathway of degrading BPA metabolite was proposed. Sphingomonas strains were dominant taxa in initial degradation of BPA, while the other taxa were competing BPA metabolites during degradation. Metagenomic binning results showed a cytochrome P450 monooxygenase system, which was previously reported BPA mediator, was sharing by two Sphingomonas strains, showing the undergoing mechanism of competition of the two strains. The observations suggested bacterial specialization may occur in that community that each taxon was selected to degrade certain metabolite in a community economical way. / published_or_final_version / Civil Engineering / Doctoral / Doctor of Philosophy

Experiments were conducted to examine the cause of lag-phase growth during phenol degradation by mixed microbial cultures that had been acclimated to one of four substrates. Four aerated Imhoff cones were inoculated with wastewater sludge and fed one of four substrates: acetate, egg albumin, vegetable oil, or phenol. Inocula from these cones were injected into batch reactors containing phenol. Time-dependent growth was measured by two methods: most probable number (MPN) and epifluorescence microscopy (EM). The MPN technique was used to distinguish two cell concentrations: total cells and a phenol-degrading community within the total; EM was also used to count total cells. The results indicated that a lag in phenol utilization for all cultures, except the phenol-acclimated cultures, was a result of growth of a phenol-degrading subpopulation, and not due to enzyme induction of the existing population. Similar experiments were conducted using 2,4-dichlorophenol (2,4-DCP), which resulted in no growth and no degradation of 2,4-DCP.

The degradation of toxic and volatile contaminants in aqueous streams is considered a challenge using conventional bioremediation strategies. At moderate concentrations, toxic contaminants induce microbial inhibition, which results in an overall decrease of reaction rates. On the other hand, volatile compounds are often stripped out of solution into the atmosphere during aeration in conventional wastewater treatments, and are not treated. The addition of a second non-aqueous phase with affinities for the contaminants can reduce aqueous concentrations to sub-inhibitory levels and also decrease contaminant volatilization, while still allowing controlled release of contaminants back to the microbial population; such systems have been denoted as Two Phase Partitioning Bioreactor (TPPB). The current work examined and compared the performance of solid-liquid TPPB to a liquid-liquid TPPB and a single phase system. The systems were compared in the simultaneous degradation of phenol and butyl acetate, two substrates known for their relatively high levels of toxicity and volatility, respectively. The solid-liquid TPPB, using 2 polymers selected heuristically, showed an improvement of 40 and 54 % in phenol degradation rates compared to the single phase and the liquid-liquid systems. Additionally, the solid-liquid system presented a 55 and 11 % enhancement in the amount of butyl acetate degraded. At higher initial substrate concentration the solid-liquid TPPB showed an improvement in the phenol degradation rate and the amount of butyl acetate degraded of 44 and 94 % respectively, compared to the single phase system. In order to rationalize polymer screening for solid-liquid TPPBs, selection criteria based on first principles were developed, and were based on consideration of polymer accessibility and polymer-solute thermodynamic affinity. Polymer accessibility was evaluated by considering glass transition temperature (Tg) and degree of crystallinity, while polymer-solute thermodynamic affinity was assessed using three different methods, Hildebrand solubility parameters, Hansen iii Solubility Parameters (HSP) and activity coefficients at infinite dilution. It was found that the HSP method gave the best trends and its predictions had better agreement with the experimental results. Consequent biodegradation experiments with a single, rationally selected polymer, and a mixture of waste polymers, demonstrated the superior performance of rational selected polymers. / Thesis (Master, Chemical Engineering) -- Queen's University, 2013-05-02 16:24:39.655

Biopiles are a common treatment for the ex-situ remediation of contaminated soil. Much research has been carried out on understanding and modelling of bioremediation techniques related to biopiles, but hitherto no study has attempted to model the effect on a biopile by its ambient surroundings. A hydraulics-based approach to simulating a biopile in the context of its ambient surroundings is presented in this study, taking into account physical, chemical and biological processes within the pile, external conditions of wind and temperature, the location of aeration pipes and venting pressure, and considering the spatial distribution of treatment as well as contaminant within the pile. The simulation approach was based upon a fluid flow model which couples Eulerian multiphase flow model and Darcy’s Law for immiscible fluid flow through porous media, a species transport model integrating advection, diffusion/dispersion and biodegradation, and a heat transfer model considering the interphase temperature equilibrium. A Computational Fluid Dynamics (CFD) system has been developed to solve this set of mathematical models by applying the commercial CFD package FLUENT, and various trial simulations have been carried out to examine the potential of the hydraulics approach for practical applications. The simulation produces reasonable results: the biodegradation process relates to the temperature within the pile, and the temperature in turn relates to wind speed and aeration details; due to the various fluid flow patterns, the contribution of each remediation mechanism (contaminant loss to atmosphere via pile surface, contaminant loss to aeration pipe and biodegradation) varies according to the aeration method; contaminant interphase transfer between different pairs of phases have greatly different impacts on contaminant removal. A number of counter-intuitive results are presented, indicating that simulations of this type will give valuable insight into the practical design of biopiling systems. The simulation system also allows the total environmental footprint of biopiling to be considered, examining not just degradation of contaminant but also its removal via volatilization and the energy used in heating air for venting. Further, the application of the approach formulated in this study is not limited to biopiles, but can also be expanded to related in situ bioremediation techniques.

Bovine hair, resulting from the unhairing of hides and skins, forms a major component of tannery solid wastes that is often disposed to landfill. However, following increasing environmental legislation restricting the disposal of commercial and industrial organic wastes to landfill, alternative treatment of tannery solid hair waste is necessary. The overall aim of this research was to develop conditions favourable for the decomposition of bovine hair waste in a composting environment. In this study, chemical pretreatments of bovine hair were carried out to enhance susceptibility to enzymatic digestion. Pretreatment using a combination of potassium thioglycolate and sodium hydroxide enhanced enzymatic digestibility of hair. Comparative solubilisation of black, brown and white hair samples with sodium sulfide showed that, the percentage soluble nitrogen, from white hair was 73% (w/w) as compared to 28% (w/w) and 24% (w/w) of black and brown hair, respectively; indicating that white hair was more vulnerable to solubilisation. Although chemical pretreatment was effective, it was considered non-compatible with the composting process. Consequently, enzymatic and microbial degradation were considered suitable alternatives. The results of the preliminary biochemical studies indicated that, the breakdown of the hair structure was enhanced when treated with a combined protease solution containing proteinase K and trypsin enzymes as compared with individual enzymes. Enzymatic and microbial degradation of hair was observed to be preferential, starting with the least resistant components, in this sequence: (1) cell membrane, (2) endocuticle, (3) medulla, and (4) cytoplasmic material and fibrillar components of the cortex. The cuticle was most resistant to degradation. Synergistic action of microbial-expressed enzymes was observed to be the fundamental mechanism for the enhanced hair degradation. Composting of bovine hair, mixed with dry leaves, soil, and wood chips/sawdust was performed in a rotary drum under controlled conditions. Optimum conditions, in order to sustain thermophilic microbial flora, were found to be (1) a moisture content of 55-+2% RH, (2) pH 7-8, (3) temperature of 49-+ C, and (4) a carbon to nitrogen ratio of 35:1. Structural changes in hair, assessed during composting using scanning electron microscopy (SEM), indicated that degradation occurred under these conditions. Microscopy results further indicated that the addition of an inoculant, containing a microbial crude enzyme, expressed by the bacteria of Bacillus species, improved the biodegradation of hair during the controlled composting process. The compost stability evaluated by monitoring the humification parameters and carbon to nitrogen ratio, indicated that the final product reached the following values: degree of humification (73 - 78%), humification ratio (26 - 32%), humification index (0.29 - 0.35), and a carbon to nitrogen ratio (25 - 29). The high level of humification of the end-product indicated reasonable stability, suggesting the product from the composted bovine hair may be suitable, suggesting the product from the composted bovine hair may be suitable for agronomical purposes. The use of composting as alternative technology for the treatment of tannery solid bovine hair waste, as a value added product, has been demonstrated.

Linseed oil is very important in industry but its use is limited due to noxious vapors produced by oxidation on exposure to air. Since some of the products are toxic, release of linseed oil vapors to the environment is normally prohibited. In order to remove the odorous compounds, a biofilter system based on bacterial metabolism was designed and the major premises of bioremediation were studied. A total of five bacterial strains capable of using linseed oil vapors as their sources of carbon and energy were isolated from soil. The individual organisms were also mixed to form a bacterial consortium. The mixed population was able to degrade linseed oil vapors with more than 99 per cent efficiency. According to this research, a successful biodegradation system was designed and, theoretically, this system could be applied to the removal of linseed oil vapors in any industrial plant air stream.

Screening of possibilities of deep subsurface microflora to decompose selected organic compounds Abstract The aim of the study is to test the deep microflora bacterial strains for their ability to grow in oily environment, aliphatic hydrocarbons and toluene were taken as examples of aromatic hydrocarbons and where the cultivation of selected strain, were produced for testing its growth and microbial activity of selected strains in conditions simulating soil conditions; assess the usability these strains in practical remediation of contamination by oil. This thesis deals with the evaluation of possible use of selected strains of deep microflora for oil decomposition. It is evident, that some groups of microorganisms living in the Tertiary claystones at depths of 30-450 m below the surface are the biodegradable fossil organic matter type of kerogen. Chemical findings indicate that, this organic matter consists of various lengths of aliphatic chains, and thus the assumption that microorganisms decomposing kerogen might be able to disassemble oil and petroleum products. The findings of our experiment indicate that benzene and toluene, as well as kerogen are highly resistant to organic compounds and evidence of microbial degradation are rare. Utilization of oil as representative aliphatic compounds is better...

A areia de fundição aglomerada com a resina fenólica se transforma num resíduo perigoso após o seu uso na indústria metalúrgica. O fenol, o meta-cresol e orto-cresol foram os principais compostos encontrados na areia de fundição. O presente trabalho tem por objetivo estudar a capacidade de degradação bacteriana do fenol, do meta-cresol e do orto-cresol. Para tanto foi isolada uma cepa proveniente de um resíduo de extração de petróleo tendo sido identificada pelo MALDI-Biotyper como sendo do gênero Burkholderia . Foi realizado o processo de ativação e crescimento bacteriano em pH 6,5, 180 rpm, 28°C e meio de cultura com mínimo de nutrientes, tendo como fonte de carbono areia de fundição contaminada com a resina fenólica. Durante os ensaios foram estudados o crescimento da bactéria bem como a degradação dos compostos fenólicos citados neste texto. A quantificação do fenol, meta-cresol e orto-cresol livres foram determinadas pelo método de cromatografia líquida de alta performance (HPLC - High Performance Liquid Chromatography ). A taxa de degradação para as três substâncias foi de 100%. / The casting sand agglomerated with the phenolic resin becomes a hazardous waste after its use in the metallurgical industry. The main compounds found in sand are phenol and its derivatives ortho-cresol and meta-cresol. The present work aims to study the bacterial degradability of the phenolic compounds present in the foundry sand. A strain from na oil extraction residue was isolated and identified by MALDI-Biotyper as Burkholderia diffusa. It was carried out the process of bacterial activation and growth at pH 6.5, 180rpm of agitation, temperature of 28°C and culture médium with minimum nutrients, using phenolic sand as the only source of carbon. During the tests the growth of the bacterium as well as the degradation of the phenolic compounds were studied. Quantification of free phenol, meta-cresol and ortho-cresol was determined by the high performance liquid chromatography (HPLC) method. The degradation rate for the three substances was 100%.

In der hier vorliegenden Studie wurden drei verschiedene Modifikationen des Calcium-Phosphat-Zementes BoneSource® sowie Vergleichssubstanzen hinsichtlich der Überprüfung ihrer Biodegradation und Biokompatibilität untersucht und verglichen. Die histomorphologische Auswertung und Beurteilung der verschiedenen Modifikationen des Calcium-Phosphat-Zementes BoneSource® bezüglich Biodegradation, Resorption und Biokompatibilität sowie die Beurteilung einer eventuellen Osteoneogenese waren damit Gegenstand der vorliegenden Arbeit. Der Calcium-Phosphat-Zement (CPZ) BoneSource® ohne Zusätze (Versuchsgruppe 1) zeigte dabei eine Osteokonduktivität im Knochen sowie im Muskel- bzw. Weichgewebe eine Biotoleranz. Eine Resorption oder Degradation war im Unterschied zu anderen Studien nicht nachweisbar. Der Calcium-Phosphat-Zement BoneSource® in einem Volumenmischungsverhältnis 1:1 mit dem osteoinduktiven Knochenkollagen (KK) Colloss® (Versuchsgruppe 2) verhielt sich in den Arealen mit BoneSource®-Anteilen (CPZ) wie in Versuchsgruppe 1 osteokonduktiv und bioinert im Knochen und wurde im Muskel- und Weichgewebe biotoleriert. Die Areale mit Colloss® (KK) im Materialgemisch zeigen ein osteoinduktives Potenzial und damit ein bioaktives Verhalten. Es ist hier eine Osteoneogenese zu verzeichnen. Trabekel neuentstandenen Knochens waren dabei sowohl in den Knochen- als auch in den Muskelpräparaten nachweisbar. Eine vollständige knöcherne Substitution der gesetzten Defekte war nicht zu verzeichnen. Der Calcium-Phosphat-Zement BoneSource® mit 1:1-Volumenverhältnismischung mit Alpha-Tricalciumphosphat (BioBase®; Versuchsgruppe 3) führte im Vergleich zur Versuchsgruppe 1 zu einer geringfügigen Verbesserung der osteokonduktiven Eigenschaften mit histologisch nachweisbarer geringfügiger oberflächlicher Degradation und partieller lokaler Resorption. Im Vergleich zur Versuchsgruppe 2 waren diese Resorptionserscheinungen jedoch deutlich weniger ausgeprägt. Bei der Versuchsgruppe 4 wurde als Kontrollgruppe das derzeit meistverwendete nichtresorbierbare polymere Implantatmaterial Polymethylmethacrylat (PMMA; Palacos®) mitgeführt. In beiden Einsatzgebieten (Knochen und Muskel) waren die Implantate eingescheidet und wurden demzufolge biotoleriert. Bei den Knochenpräparaten liegt ein bioinertes Verhalten des Lagergewebes gegenüber PMMA vor. Bei der Versuchsgruppe 5 wurde als 2. Kontrollgruppe ein Leerdefekt präpariert, der mit Gelatine gefüllt wurde, welches bei bekannter Resorptionsfähigkeit innerhalb weniger Wochen postoperativ einen vollständigen Ersatz durch körpereigenen Knochen in den Knochenpräparaten bzw. einen Ersatz durch Narbengewebe in den Muskelpräparaten aufwies. Bei der Versuchsgruppe 6 (Kontrollgruppe) wurde eine nichtoperierte Kohorte Versuchstiere mitgeführt, um alters- und/oder diätbedingte Veränderungen abschätzen bzw. beurteilen zu können. Es fanden sich bei den Versuchstieren am Ende des Versuchszeitraumes lediglich physiologische altersbedingte Veränderungen. Die großen inneren Organe der Versuchstiere wurden histologisch untersucht, um eventuelle systemische Auswirkungen der o.g. Modifikationen des Calcium-Phosphat-Zementes BoneSource® beurteilen zu können. Dabei konnten keine pathologischen Veränderungen gefunden werden. Es liegen somit keine systemischen Auswirkungen der Implantatmaterialien vor. Im Laufe der Versuchszeit traten vereinzelt Tumore auf, die jedoch nicht den Implantatmaterialien geschuldet sind und einer spontanen Tumorgenese zugeordnet werden konnten. Spontane Todesfälle sind unabhängig von den Implantatmaterialien aufgetreten. Gemessen an der Zielsetzung sind die gefundenen Ergebnisse dieser Studie statistisch auswertbar, objektivierbar und für die Weiterentwicklung von Knochenersatzmaterialien relevant. Insbesondere wird auf die in dieser Studie nicht erfolgte Degradation von CPZ und Alpha-TCP und das osteoinduktive Potenzial des untersuchten Kollagens / In this study we examined and compared three different modifications of the calcium-phosphate-cement BoneSource and also further substances in the dimensions of biodegradation and biocompatibility. The histomorphologic interpretation and assessment of different modifications of the calcium-phosphate-cement BoneSource refer to biodegradation, resorption and biocompatibility and the assessment of a possible osteogenesis were the issues of this study. The results of this study are statistically evaluatible, objective and relevant to further development of bone substitute materials. Especially we point to the nondegradation of calcium-phosphate-cements and alpha-TCP and the osteoinductive potential of the examined collagen.

A pesquisa avalia comparativamente algumas propriedades físicas e químicas da poliamida 6.6 convencional e biodegradável. Avalia também o tempo de biodegradabilidade da amostra de fio biodegradável e convencional. As propriedades físicas analisadas foram de resistência, alongamento e tenacidade. Já as propriedades químicas foram relativas ao comportamento das amostras quanto ao tingimento e avaliações de solidez posteriores ao tingimento. As amostras avaliadas foram retiradas de malhas produzidas com fio de poliamida 80 dtex f68 x 2, normal e biodegradável, sendo purgadas, alvejadas e tintas. Os resultados das análises físicas, apesar de estatisticamente diferente, possuem os valores das médias muito próximos, o que na prática representam valores aceitáveis dentro do controle estatístico de processo. Ambas as amostras normal e biodegradável apresentaram mesmo comportamento químico, não havendo nenhuma diferença. Com relação ao tempo de biodegradabilidade, sob condições laboratoriais, o dióxido de carbono produzido pelas amostras foi monitorado e medido para determinar a porcentagem de biodegradação de acordo com a norma ASTM D 5511. O fio biodegradável apresenta um tempo de biodegradação 16 vezes mais rápido do que o fio de poliamida normal, tendo 81,7% de biodegradação após 735 dias de teste. Isto representa um ganho muito grande em termos ecológicos, tratando-se de uma fibra sintética / The study evaluates comparatively some physical and chemical properties of conventional and biodegradable polyamide 6.6. It also evaluates the period of biodegradation of the biodegradable and conventional yarn. The physical properties analyzed were strength, elongation and toughness. The chemical properties were related on the behavior of the samples in dyeing and evaluation of subsequent strength dyeing. The evaluated samples were taken from knitwear produced with polyamide yarn 80 dtex f68 x 2, normal and biodegradable, being purged, bleached and dyed. The results of the physical tests, although statistically different, have values very near the average, which in practice represent acceptable values within the statistical control process. Both normal and biodegradable samples had the same chemical behavior, and there is no difference. With respect to biodegradation time under laboratory conditions, the carbon dioxide produced by the samples was monitored and measured to determine the percentage of biodegradation according to ASTM D 5511. The biodegradable yarn has a biodegradation time 16 times faster the yarn normal polyamide, having 81.7% biodegradation after 735 days of testing. This is an expressive gain in ecological terms for a synthetic fiber