Bioremediation of PAHs - Limitations and soultions

Introduction 1.1 Occurrence of polycyclic aromatic hydrocarbons (PAH) in the environment Worldwide industrial and agricultural developments have released a large number of natural and synthetic hazardous compounds into the environment due to careless waste disposal, illegal waste dumping and accidental spills. As a result, there are numerous sites in the world that require cleanup of soils and groundwater. Polycyclic aromatic hydrocarbons (PAHs) are one of the major groups of these contaminants (Da Silva et al., 2003). PAHs constitute a diverse class of organic compounds consisting of two or more aromatic rings with various structural configurations (Prabhu and Phale, 2003). Being a derivative of benzene, PAHs are thermodynamically stable. In addition, these chemicals tend to adhere to particle surfaces, such as soils, because of their low water solubility and strong hydrophobicity, and this results in greater persistence under natural conditions. This persistence coupled with their potential carcinogenicity makes PAHs problematic environmental contaminants (Cerniglia, 1992; Sutherland, 1992). PAHs are widely found in high concentrations at many industrial sites, particularly those associated with petroleum, gas production and wood preserving industries (Wilson and Jones, 1993). 1.2 Remediation technologies Conventional techniques used for the remediation of soil polluted with organic contaminants include excavation of the contaminated soil and disposal to a landfill or capping - containment - of the contaminated areas of a site. These methods have some drawbacks. The first method simply moves the contamination elsewhere and may create significant risks in the excavation, handling and transport of hazardous material. Additionally, it is very difficult and increasingly expensive to find new landfill sites for the final disposal of the material. The cap and containment method is only an interim solution since the contamination remains on site, requiring monitoring and maintenance of the isolation barriers long into the future, with all the associated costs and potential liability. A better approach than these traditional methods is to completely destroy the pollutants, if possible, or transform them into harmless substances. Some technologies that have been used are high-temperature incineration and various types of chemical decomposition (for example, base-catalyzed dechlorination, UV oxidation). However, these methods have significant disadvantages, principally their technological complexity, high cost , and the lack of public acceptance. Bioremediation, on the contrast, is a promising option for the complete removal and destruction of contaminants. 1.3 Bioremediation of PAH contaminated soil & groundwater Bioremediation is the use of living organisms, primarily microorganisms, to degrade or detoxify hazardous wastes into harmless substances such as carbon dioxide, water and cell biomass Most PAHs are biodegradable unter natural conditions (Da Silva et al., 2003; Meysami and Baheri, 2003) and bioremediation for cleanup of PAH wastes has been extensively studied at both laboratory and commercial levels- It has been implemented at a number of contaminated sites, including the cleanup of the Exxon Valdez oil spill in Prince William Sound, Alaska in 1989, the Mega Borg spill off the Texas coast in 1990 and the Burgan Oil Field, Kuwait in 1994 (Purwaningsih, 2002). Different strategies for PAH bioremediation, such as in situ , ex situ or on site bioremediation were developed in recent years. In situ bioremediation is a technique that is applied to soil and groundwater at the site without removing the contaminated soil or groundwater, based on the provision of optimum conditions for microbiological contaminant breakdown.. Ex situ bioremediation of PAHs, on the other hand, is a technique applied to soil and groundwater which has been removed from the site via excavation (soil) or pumping (water). Hazardous contaminants are converted in controlled bioreactors into harmless compounds in an efficient manner. 1.4 Bioavailability of PAH in the subsurface Frequently, PAH contamination in the environment is occurs as contaminants that are sorbed onto soilparticles rather than in phase (NAPL, non aqueous phase liquids). It is known that the biodegradation rate of most PAHs sorbed onto soil is far lower than rates measured in solution cultures of microorganisms with pure solid pollutants (Alexander and Scow, 1989; Hamaker, 1972). It is generally believed that only that fraction of PAHs dissolved in the solution can be metabolized by microorganisms in soil. The amount of contaminant that can be readily taken up and degraded by microorganisms is defined as bioavailability (Bosma et al., 1997; Maier, 2000). Two phenomena have been suggested to cause the low bioavailability of PAHs in soil (Danielsson, 2000). The first one is strong adsorption of the contaminants to the soil constituents which then leads to very slow release rates of contaminants to the aqueous phase. Sorption is often well correlated with soil organic matter content (Means, 1980) and significantly reduces biodegradation (Manilal and Alexander, 1991). The second phenomenon is slow mass transfer of pollutants, such as pore diffusion in the soil aggregates or diffusion in the organic matter in the soil. The complex set of these physical, chemical and biological processes is schematically illustrated in Figure 1. As shown in Figure 1, biodegradation processes are taking place in the soil solution while diffusion processes occur in the narrow pores in and between soil aggregates (Danielsson, 2000). Seemingly contradictory studies can be found in the literature that indicate the rate and final extent of metabolism may be either lower or higher for sorbed PAHs by soil than those for pure PAHs (Van Loosdrecht et al., 1990). These contrasting results demonstrate that the bioavailability of organic contaminants sorbed onto soil is far from being well understood. Besides bioavailability, there are several other factors influencing the rate and extent of biodegradation of PAHs in soil including microbial population characteristics, physical and chemical properties of PAHs and environmental factors (temperature, moisture, pH, degree of contamination). Figure 1: Schematic diagram showing possible rate-limiting processes during bioremediation of hydrophobic organic contaminants in a contaminated soil-water system (not to scale) (Danielsson, 2000). 1.5 Increasing the bioavailability of PAH in soil Attempts to improve the biodegradation of PAHs in soil by increasing their bioavailability include the use of surfactants , solvents or solubility enhancers.. However, introduction of synthetic surfactant may result in the addition of one more pollutant. (Wang and Brusseau, 1993).A study conducted by Mulder et al. showed that the introduction of hydropropyl-ß-cyclodextrin (HPCD), a well-known PAH solubility enhancer, significantly increased the solubilization of PAHs although it did not improve the biodegradation rate of PAHs (Mulder et al., 1998), indicating that further research is required in order to develop a feasible and efficient remediation method. Enhancing the extent of PAHs mass transfer from the soil phase to the liquid might prove an efficient and environmentally low-risk alternative way of addressing the problem of slow PAH biodegradation in soil.

Biodegradazione aerobica cometabolica di cloroformio: studio di fattibilità in reattori a biomassa adesa

Chlorinated Aliphatic Hydrocarbons (CAHs) are widespread wastewater and groundwater contaminants and represent a real danger for human health and environment. This research is related to the biodegradation technologies to treat chlorinated hydrocarbons. In particular the study of this thesis is focused on chloroform cometabolism by a butane-grown aerobic pure culture (Rhodococcus aetherovorans BCP1) in continuous-flow biofilm reactors, which are used for in-situ and on-site treatments. The work was divided in two parts: in the first one an experimental study has been conducted in two packed-bed reactors (PBRs) for a period of 370 days; in the second one a fluid dynamics and kinetic model has been developed in order to simulate the experimental data concerning a previous study made in a 2-m continuous-flow sand-filled reactor. The goals of the first study were to obtain preliminary information on the feasibility of chloroform biodegradation by BCP1 under attached-cell conditions and to evaluate the applicability of the pulsed injection of growth substrate and oxygen to biofilm reactors. The pulsed feeding represents a tool to control the clogging and to ensure a long bioreactive zone. The operational conditions implemented in the PBRs allowed the attainment of a 4-fold increase of the ratio of chloroform degraded to substrate consumed, in comparison with the phase of continuous substrate supply. The second study was aimed at identifying guidelines for optimizing the oxygen/substrate supply schedule, developing a reliable model of chloroform cometabolism in porous media. The tested model led to a suitable interpretation of the experimental data as long as the ratio of CF degraded to butane consumed was ≤ 0.27 mgchloroform /mgbutane. A long-term simulation of the best-performing schedule of pulsed oxygen/substrate supply indicated the attainment of a steady state condition characterized by unsatisfactory bioremediation performances, evidencing the need for a further optimization of the pulsed injection technique.

Microbial ecology of biotechnological processes

The investigation of phylogenetic diversity and functionality of complex microbial communities in relation to changes in the environmental conditions represents a major challenge of microbial ecology research. Nowadays, particular attention is paid to microbial communities occurring at environmental sites contaminated by recalcitrant and toxic organic compounds. Extended research has evidenced that such communities evolve some metabolic abilities leading to the partial degradation or complete mineralization of the contaminants. Determination of such biodegradation potential can be the starting point for the development of cost effective biotechnological processes for the bioremediation of contaminated matrices. This work showed how metagenomics-based microbial ecology investigations supported the choice or the development of three different bioremediation strategies. First, PCR-DGGE and PCR-cloning approaches served the molecular characterization of microbial communities enriched through sequential development stages of an aerobic cometabolic process for the treatment of groundwater contaminated by chlorinated aliphatic hydrocarbons inside an immobilized-biomass packed bed bioreactor (PBR). In this case the analyses revealed homogeneous growth and structure of immobilized communities throughout the PBR and the occurrence of dominant microbial phylotypes of the genera Rhodococcus, Comamonas and Acidovorax, which probably drive the biodegradation process. The same molecular approaches were employed to characterize sludge microbial communities selected and enriched during the treatment of municipal wastewater coupled with the production of polyhydroxyalkanoates (PHA). Known PHA-accumulating microorganisms identified were affiliated with the genera Zooglea, Acidovorax and Hydrogenophaga. Finally, the molecular investigation concerned communities of polycyclic aromatic hydrocarbon (PAH) contaminated soil subjected to rhizoremediation with willow roots or fertilization-based treatments. The metabolic ability to biodegrade naphthalene, as a representative model for PAH, was assessed by means of stable isotope probing in combination with high-throughput sequencing analysis. The phylogenetic diversity of microbial populations able to derive carbon from naphthalene was evaluated as a function of the type of treatment.

Molecular cloning and characterization of an amidase from Arabidopsis thaliana capable of converting indole-3-acetamide into the plant growth hormone, indole-3-acetic acid

Acylamidohydrolases from higher plants have not been characterized or cloned so far. AtAMI1 is the first member of this enzyme family from a higher plant and was identified in the genome of Arabidopsis thaliana based on sequence homology with the catalytic-domain sequence of bacterial acylamidohydrolases, particularly those that exhibit indole-3-acetamide amidohydrolase activity. AtAMI1 polypeptide and mRNA are present in leaf tissues, as shown by immunoblotting and RT-PCR, respectively. AtAMI1 was expressed from its cDNA in enzymatically active form and exhibits substrate specificity for indole-3-acetamide, but also some activity against l-asparagine. The recombinant enzyme was characterized further. The results show that higher plants have acylamidohydrolases with properties similar to the enzymes of certain plant-associated bacteria such as Agrobacterium-, Pseudomonas- and Rhodococcus-species, in which these enzymes serve to synthesize the plant growth hormone, indole-3-acetic acid, utilized by the bacteria to colonize their host plants. As indole-3-acetamide is a native metabolite in Arabidopsis thaliana, it can no longer be ruled out that one pathway for the biosynthesis of indole-3-acetic acid involves indole-3-acetamide-hydrolysis by AtAMI1.

Identification of active sites in amidase: Evolutionary relationship between amide bond- and peptide bond-cleaving enzymes

Mainly based on various inhibitor studies previously performed, amidases came to be regarded as sulfhydryl enzymes. Not completely satisfied with this generally accepted interpretation, we performed a series of site-directed mutagenesis studies on one particular amidase of Rhodococcus rhodochrous J1 that was involved in its nitrile metabolism. For these experiments, the recombinant amidase was produced as the inclusion body in Escherichia coli to greatly facilitate its recovery and subsequent purification. With regard to the presumptive active site residue Cys203, a Cys203 → Ala mutant enzyme still retained 11.5% of the original specific activity. In sharp contrast, substitutions in certain other positions in the neighborhood of Cys203 had a far more dramatic effect on the amidase. Glutamic acid substitution of Asp191 reduced the specific activity of the mutant enzyme to 1.33% of the wild-type activity. Furthermore, Asp191 → Asn substitution as well as Ser195 → Ala substitution completely abolished the specific activity. It would thus appear that, among various conserved residues residing within the so-called signature sequence common to all amidases, the real active site residues are Asp191 and Ser195 rather than Cys203. Inasmuch as an amide bond (CO-NH2) in the amide substrate is not too far structurally removed from a peptide bond (CO-NH-), the signature sequences of various amidases were compared with the active site sequences of various types of proteases. It was found that aspartic acid and serine residues corresponding to Asp191 and Ser195 of the Rhodococcus amidase are present within the active site sequences of aspartic proteinases, thus suggesting the evolutionary relationship between the two.

A soil-based microbial biofilm exposed to 2,4-D: bacterial community development and establishment of conjugative plasmid pJP4

A soil suspension was used as a source to initiate the development of microbial communities in flow cells irrigated with 2,4-dichlorophenoxyacetic acid (2,4-D) (25 mu g ml(-1)). Culturable bacterial members of the community were identified by 16S rRNA gene sequencing and found to be members of the genera Pseudomonas, Burkholderia, Collimonas and Rhodococcus. A 2,4-D degrading donor strain, Pseudomonas putida SM 1443 (pJP4::gfp), was inoculated into flow cell chambers containing 2-day old biofilm communities. Transfer of pJP4::gfp from the donor to the bacterial community was detectable as GFP fluorescing cells and images were captured using confocal scanning laser microscopy (GFP fluorescence was repressed in the donor due to the presence of a chromosomally located lacl(q) repressor gene). Approximately 5-10 transconjugant microcolonies, 20-40 mu m in diameter, could be seen to develop in each chamber. A 2,4-D degrading transconjugant strain was isolated from the flow cell system belonging to the genus Burkholderia.

Screening, characterization and flocculating property of carbohydrate polymer from newly isolated Enterobacter cloacae WD7

A total of 188 carbohydrate polymer-producing bacterial strains were isolated from recycled sludge of five seafood processing plants. Among three selected isolates, identified as Enterobacter cloacae WD7, Enterobacter agglomerans WD50 and Pseudomonas alcaligenes WD22. E. cloacae WD7 generated a viscous culture broth exhibiting the highest flocculating activity and a crude polymer yield of 2.27 g/L after 3 days cultivation. Partial purification of this polymer was performed by precipitation with 95% ethanol, dialysis and freeze-drying. It was characterized as an acidic heteropolysaccharide, composed of neutral sugars (29.4%), uronic acids (14.2%) and amino sugars (0.93%). The functional group analysis by FT-IR spectroscopy showed the presence of hydroxyl, carboxyl, carbonyl and methoxyl groups. Thermal analysis by DSC showed the crystalline transition and the crystalline melting point (T-m) at 300 degrees C. This polysaccharide was soluble in water and insoluble in any organic solvents tested; gelation occurred under alkaline conditions in the presence of divalent cations in which copper as CuSO4 gave the best result. Studies on the flocculation property revealed that this polysaccharide was stable at 4-60 degrees C and pH 5-7. The optimal concentrations for the flocculating activity were 2 mg/L polysaccharide and 40 mM CaCl2 which played the synergistic effect on kaolin flocculation. Moreover, this polysaccharide could flocculate the kaolin suspension over a wide range of pH (pH 2-8) and temperature (4-50 degrees C) tested in the presence of CaCl2. (c) 2006 Elsevier Ltd. All rights reserved.

Producción y caracterización de la superóxido dismutasa a (SodA) de nocardia brasiliensis en pichia pastoris

Introducción: A mediados de los años 70’s del siglo pasado el descubrimiento de la tecnología del ADN recombinante marca el inicio de la era de la biotecnología moderna. La implementación de estas tecnologías permitió la utilización de organismos como sistemas de expresión que a lo largo de los años ha generado la producción de una gran variedad de productos biológicos. Dentro de estos sistemas Pichia pastoris es un sistema de expresión ampliamente utilizado debido a sus características tales como la producción de proteínas en grandes cantidades, la liberación de los productos al medio de cultivo, la obtención de productos complejos que requieren modificaciones postraduccionales típicas de los eucariotas o que contienen puentes disulfuro, entre otras. Nocardia brasiliensis es una bacteria parcialmente ácido-alcohol resistente la cual forma colonias granulares, con hifas aéreas escasas, sus colonias exhiben un color anaranjado pardo con bordes en blanco. N. brasiliensis es patógena para el ser humano y es el agente causal del actinomicetoma. El actinomicetoma es una enfermedad crónica generalmente localizada en las extremidades. Se caracteriza por ser un proceso lento de tumefacción con nódulos, abscesos y fístulas.La Superóxido Dismutasa (SOD) es una enzima reductora polimérica que cataliza la conversión del ión superóxido a peróxido de hidrógeno y oxígeno molecular. La SOD ha sido propuesta como un factor de virulencia de microorganismos patógenos, cuya acción consiste en bloquear los efectores oxidativos del estallido respiratorio iniciado por los fagocítos en el fagolisosoma. Este mecanismo ha sido descrito para bacterias de los géneros Mycobacterium, Rhodococcus y Nocardia. Objetivo: producir y caracterizar la Superóxido Dismutasa A (SODA) de Nocardia brasiliensis en Pichia pastoris. Metodología: se realizó el diseño de primers adicionando secuencias de sitios de corte para las enzimas XhoI y AvrII, así como una cola de histidinas en el extremo 5’ para la amplificación del gen sodA de N. brasiliensis a partir del ADN genómico de Nocardia brasiliensis. El amplicón se clonó en el vector de expresión pPIC9. Se llevó a cabo la transformación por electroporación de levaduras Pichia pastoris GS115. La producción de SOD se llevó a cabo en inducciones de 96 h con metanol como agente inductor. Los sobrenadantes se dializaron con membranas de celulosa. Los dializados se observaron por SDS-PAGE y western blot. Se analizó la actividad funcional de la enzima con el SOD Assay kit de Sigma Aldrich. Resultados: Por reacción en cadena de la polimerasa se obtuvo una secuencia de 625 pb correspondiente al gen sodA. El fragmento se ligó al vector de expresión pPIC9 y fue caracterizado con las enzimas de restricción XhoI y AvrII. Las cepas trasformadas de P. pastoris GS115 se caracterizaron con el gen aox1 obteniendo cepas Mut+ y Muts. Los análisis por SDSPAGE mostraron bandas no observadas en el control negativo de expresión mientras en los western blot solo una de las clonas mostró señal. Los análisis de actividad funcional sugieren inhibición de la reacción enzimática infiriendo presencia de la proteína SOD en el medio dializado. Conclusiones: Se logró la construcción del sistema de expresión Pichia pastoris con el casete de expresión de la SOD de N. brasiliensis. Así como la generación de cepas Mut+y Muts. En los ensayos de actividad funcional se observó inhibición de la reacción enzimática.

Avaliação da biodessulfurização de 4-metildibenzotiofeno por Rhodococus rhodochrous (NRRL B-2149)

Crude oil has between 0.04 up to 5% of sulphur, the higher the oil the higher the sulphur levels. Sulphur usually gives problems such as corrosion in refinery, and once burnt produces SO2 that goes to atmosphere. This work aim to investigate the capacity of Rhodococcus rhodochrous (NRRL B-2149) to metabolize the model compound 4-methyldibenzotiophene (4-MDBT), to remove the sulphur and transform it in 2-hydroxybiphenyl (2-HBF) and sulphite using the 4S pathway. Kynetic runs were carried out in shaker at 120 rpm and 32°C. Samples were taken every 12h to assay substrate consume as well as cells production using HPLC. Results showed that R. rhodochrous NRRL B-2149 can use the 4S pathway in order to remove sulphur without change the carbon chain of the molecule as well as that cells and 4-MDBT affects the product formation. The production of 2-hydroxybiphenyl has interest for industry once it is a potent biocide. However, evaluation is necessary in order to obtain better results compatible with industry needs