Functional genes and gene array analysis as tools for monitoring hydrocarbon biodegradation

Bioremediation, which is the exploitation of the intrinsic ability of environmental microbes to degrade and remove harmful compounds from nature, is considered to be an environmentally sustainable and cost-effective means for environmental clean-up. However, a comprehensive understanding of the biodegradation potential of microbial communities and their response to decontamination measures is required for the effective management of bioremediation processes. In this thesis, the potential to use hydrocarbon-degradative genes as indicators of aerobic hydrocarbon biodegradation was investigated. Small-scale functional gene macro- and microarrays targeting aliphatic, monoaromatic and low molecular weight polyaromatic hydrocarbon biodegradation were developed in order to simultaneously monitor the biodegradation of mixtures of hydrocarbons. The validity of the array analysis in monitoring hydrocarbon biodegradation was evaluated in microcosm studies and field-scale bioremediation processes by comparing the hybridization signal intensities to hydrocarbon mineralization, real-time polymerase chain reaction (PCR), dot blot hybridization and both chemical and microbiological monitoring data. The results obtained by real-time PCR, dot blot hybridization and gene array analysis were in good agreement with hydrocarbon biodegradation in laboratory-scale microcosms. Mineralization of several hydrocarbons could be monitored simultaneously using gene array analysis. In the field-scale bioremediation processes, the detection and enumeration of hydrocarbon-degradative genes provided important additional information for process optimization and design. In creosote-contaminated groundwater, gene array analysis demonstrated that the aerobic biodegradation potential that was present at the site, but restrained under the oxygen-limited conditions, could be successfully stimulated with aeration and nutrient infiltration. During ex situ bioremediation of diesel oil- and lubrication oil-contaminated soil, the functional gene array analysis revealed inefficient hydrocarbon biodegradation, caused by poor aeration during composting. The functional gene array specifically detected upper and lower biodegradation pathways required for complete mineralization of hydrocarbons. Bacteria representing 1 % of the microbial community could be detected without prior PCR amplification. Molecular biological monitoring methods based on functional genes provide powerful tools for the development of more efficient remediation processes. The parallel detection of several functional genes using functional gene array analysis is an especially promising tool for monitoring the biodegradation of mixtures of hydrocarbons.

Two ex situ fungal technologies to treat contaminated soil

Wood-degrading fungi are able to degrade a large range of recalcitrant pollutants which resemble the lignin biopolymer. This ability is attributed to the production of lignin-modifying enzymes, which are extracellular and non-specific. Despite the potential of fungi in bioremediation, there is still an understanding gap in terms of the technology. In this thesis, the feasibility of two ex situ fungal bioremediation methods to treat contaminated soil was evaluated. Treatment of polycyclic aromatic hydrocarbons (PAHs)-contaminated marsh soil was studied in a stirred slurry-phase reactor. Due to the salt content in marsh soil, fungi were screened for their halotolerance, and the white-rot fungi Lentinus tigrinus, Irpex lacteus and Bjerkandera adusta were selected for further studies. These fungi degraded 40 - 60% of a PAH mixture (phenanthrene, fluoranthene, pyrene and chrysene) in a slurry-phase reactor (100 ml) during 30 days of incubation. Thereafter, B. adusta was selected to scale-up and optimize the process in a 5 L reactor. Maximum degradation of dibenzothiophene (93%), fluoranthene (82%), pyrene (81%) and chrysene (83%) was achieved with the free mycelium inoculum of the highest initial biomass (2.2 g/l). In autoclaved soil, MnP was the most important enzyme involved in PAH degradation. In non-sterile soil, endogenous soil microbes together with B. adusta also degraded the PAHs extensively, suggesting a synergic action between soil microbes and the fungus. A fungal solid-phase cultivation method to pretreat contaminated sawmill soil with high organic matter content was developed to enhance the effectiveness of the subsequent soil combustion. In a preliminary screening of 146 fungal strains, 28 out of 52 fungi, which extensively colonized non-sterile contaminated soil, were litter-decomposing fungi. The 18 strains further selected were characterized by their production of lignin-modifying and hydrolytic enzymes, of which MnP and endo-1,4-β-glucanase were the main enzymes during cultivation on Scots pine (Pinus sylvestris) bark. Of the six fungi selected for further tests, Gymnopilus luteofolius, Phanerochaete velutina, and Stropharia rugosoannulata were the most active soil organic matter degraders. The results showed that a six-month pretreatment of sawmill soil would result in a 3.5 - 9.5% loss of organic matter, depending on the fungus applied. The pretreatment process was scaled-up for a 0.56 m3 reactor, in which perforated plastic tubes filled with S. rugosoannulata growing on pine bark were introduced into the soil. The fungal pretreatment resulted in a soil mass loss of 30.5 kg, which represents 10% of the original soil mass (308 kg). Despite the fact that Scots pine bark contains several antimicrobial compounds, it was a suitable substrate for fungal growth and promoter of the production of oxidative enzymes, as well as an excellent and cheap natural carrier of fungal mycelium. This thesis successfully developed two novel fungal ex situ bioremediation technologies and introduce new insights for their further full-scale application. Ex situ slurry-phase fungal reactors might be applied in cases when the soil has a high water content or when the contaminant bioavailability is low; for example, in wastewater treatment plants to remove pharmaceutical residues. Fungal solid-phase bioremediation is a promising remediation technology to ex situ or in situ treat contaminated soil.

Bioremediation of diesel oil contaminated soil and water

Diesel spills contaminate aquatic and terrestrial environments. To prevent the environmental and health risks, the remediation needs to be advanced. Bioremediation, i.e., degradation by microbes, is one of the suitable methods for cleaning diesel contamination. In monitored natural attenuation technique are natural processes in situ combined, including bioremediation, volatilization, sorption, dilution and dispersion. Soil bacteria are capable of adapting to degrade environmental pollutants, but in addition, some soil types may have indigenous bacteria that are naturally suitable for degradation. The objectives for this work were (1) to find a feasible and economical technique to remediate oil spilled into Baltic Sea water and (2) to bioremediate soil contaminated by diesel oil. Moreover, the aim was (3) to study the potential for natural attenuation and the indigenous bacteria in soil, and possible adaptation to degrade diesel hydrocarbons. In the aquatic environment, the study concentrated on diesel oil sorption to cotton grass fiber, a natural by-product of peat harvesting. The impact of diesel pollution was followed in bacteria, phytoplankton and mussels. In a terrestrial environment, the focus was to compare the methods of enhanced biodegradation (biostimulation and bioaugmentation), and to study natural attenuation of oil hydrocarbons in different soil types and the effect that a history of previous contamination may have on the bioremediation potential. (1) In the aquatic environment, rapid removal of diesel oil was significant for survival of tested species and thereby diversity maintained. Cotton grass not only absorbed the diesel but also benefited the bacterial growth by providing a large colonizable surface area and hence oil-microbe contact area. Therefore use of this method would enhance bioremediation of diesel spills. (2) Biostimulation enhances bioremediation, and (3) indigenous diesel-degrading bacteria are present in boreal environments, so microbial inocula are not always needed. In the terrestrial environment experiments, the combination of aeration and addition of slowly released nitrogen advanced the oil hydrocarbon degradation. Previous contamination of soil gives the bacterial community the potential for rapid adaptation and efficient degradation of the same type of contaminant. When the freshly contaminated site needs addition of diesel degraders, previously contaminated and remediated soil could be used as a bacterial inoculum. Another choice of inoculum could be conifer forest soil, which provides a plentiful population of degraders, and based on the present results, could be considered as a safe non-polluted inoculum. According to the findings in this thesis, bioremediation (microbial degradation) and monitored natural attenuation (microbial, physical and chemical degradation) are both suitable techniques for remediation of diesel-contaminated sites in Finland.

Assessment of treatment capabilities of Varthur Lake, Bangalore, India

Manmade waterbodies have traditionally been used for domestic and irrigation purposes. Unplanned urbanization and ad-hoc approaches have led to these waterbodies receiving untreated sewage. This enriches and eutrophies the waterbody. A physicochemical and biological analysis of sewage-fed Varthur Lake in Bangalore was carried out and its treatment capabilities in terms of BOD removal, nutrient assimilation and self-remediation were assessed. Anaerobic conditions (0 mg/L) prevail at the inlet which improves towards the outlets due to algal aeration. This removed > 50% BOD in the monsoon season but was inhibited by floating macrophytes in all other seasons. Alkalinity, TDS, conductivity and hardness values were higher when compared to earlier studies. This study shows the lake behaves as an anaerobic~aerobic lagoon with a residence time of 4.8 d treating the wastewater to a considerable extent. Further research is required to optimise the system performance.

Cyclodextrin functionalized magnetic iron oxide nanocrystals: a host-carrier for magnetic separation of non-polar molecules and arsenic from aqueous media

A single-step magnetic separation procedure that can remove both organic pollutants and arsenic from contaminated water is clearly a desirable goal. Here we show that water dispersible magnetite nanoparticles prepared by anchoring carboxymethyl-beta-cyclodextrin (CMCD) cavities to the surface of magnetic nanoparticles are suitable host carriers for such a process. Monodisperse, 10 nm, spherical magnetite, Fe3O4, nanocrystals were prepared by the thermal decomposition of FeOOH. Trace amounts of antiferromagnet, FeO, present in the particles provides an exchange bias field that results in a high superparamagnetic blocking temperature and appreciable magnetization values that facilitate easy separation of the nanocrystals from aqueous dispersions on application of modest magnetic fields. We show here that small molecules like naphthalene and naphthol can be removed from aqueous media by forming inclusion complexes with the anchored cavities of the CMCD-Fe3O4 nanocrystals followed by separation of the nanocrystals by application of a magnetic field. The adsorption properties of the iron oxide surface towards As ions are unaffected by the CMCD capping so it too can be simultaneously removed in the separation process. The CMCD-Fe3O4 nanocrystals provide a versatile platform for magnetic separation with potential applications in water remediation.

Photocatalytic degradation of gaseous toluene by using immobilized titania/silica on aluminum sheets

The aim of this study was to prepare a highly active immobilized titania/silica photocatalyst and to test its performance in situ toward degradation of toluene as one of the major toxic indoor contaminants. In this work, two different titania layers immobilized on Al sheets were synthesized via low temperature sol-gel method employing presynthesized highly active titania powders (Degussa P25 and Millennium PC500, mass ratio 1:1): (a) with a silica/titania binder and a protective layer and (b) without the binder. The photocatalysts were characterized by X-ray diffraction, nitrogen sorption measurements, scanning electron microscopy (SEM), infrared spectroscopy, and UV-vis diffuse reflectance spectroscopy (DRS). The in situ photocatalytic degradation of gaseous toluene was selected as a probe reaction to test photocatalytic activity and to verify the potential application of these materials for air remediation. Results show that nontransparent highly photocatalytically active coatings based on the silica/titania binder and homogeneously dispersed TiO2 powders were obtained on the Al sheets. The crystalline structure of titania was not altered upon addition of the binder, which also prevented inhomogeneous agglomeration of particles on the photocatalyst surface. The photoactivity results indicate that the adsorption properties and photocatalytic activity of immobilized photocatalysts with the silica/titania binder and an underlying protective layer were very effective and additionally, they exhibited considerably improved adhesion and uniformity. We present a new highly photocatalytically active immobilized catalyst on a convenient metallic support, which has a potential application in an air cleaning device.

Synthesis of zero valent iron nanoparticles and application to removal of arsenic(III) and arsenic(V) from water

Recently nano scale zero valent iron particles (nZVI) have been considered as smart adsorbent for environmental and groundwater remediation. Although several synthetic methods are available for the preparation of nZVI, air stable nZVI are not available for remediation works. Further, challenges demand synthesis of nZVI without stabilizers and capping agents. A modified methodology for the synthesis of air stable nZVI has been developed without any capping agents and characterized by powder X-Ray Diffraction (XRD), Scanning Electron Microscopy Energy-dispersive X-Ray (SEM-EDS), Transmission Electron Microscopy (TEM) and X-Ray Photoelectron Spectroscopy (XPS). The results of the present study suggest that the synthetic nZVI are air-stable over a period of one year and consists of particles of 30-40 nm in diameter. Although a layer of less than 3 am thick oxide/hydroxide is observed by TEM and XPS, it appears to be due to oxidation of outer surface during analysis. Adsorption study has shown that the synthetic nZVI are more effective adsorbent than the commercial nZVI and can remove simultaneously arsenite As-III] and arsenate As-V] from water without prior reduction of As-V to As-III. The removal process is adsorptive rather than precipitative and the removal of As-III is greater than that of As-V.

Comparative Studies on the Bioremediation of Hexavalent and Trivalent Chromium using Citrobacter freundii: Part I-Effect of parameters controlling Biosorption

The potential of Citrobacter freundii, a Gram negative bacteria for the remediation of hexavalent chromium (Cr(VI)) and trivalent chromium (Cr(III))) from aqueous solutions was investigated. Bioremediation of Cr(VI) involved both biosorption and bioreduction processes, as compared to only biosorption process observed with respect to Cr(III) bioremediation. In the case of Cr(VI) bioremediation studies, about 59 % biosorption was achieved at an equilibrium time of 2 h, initial Cr(VI) concentration of 4 mg/L, pH 1 and a biomass loading of 5x10(11) cells/mL. The remainder, 41 %, was found to be in the form of Cr(111) ions owing to bioreduction of Cr(VI) by the bacteria resulting in the absence of Cr(VI) ions in the residue, there by meeting the USEPA specifications. Similar studies were carried out using Cr(III) solution for an equilibrium time of 2 h, Cr(III) concentration of 4 mg/L, pH 3 and a biomass loading of 6.3x10(11) cells/mL., wherein a maximum biosorption of about 30 % was achieved.

Production and characterization of bioflocculants for mineral processing applications

A comparative study of two bacterial strains namely, Bacillus licheniformis and Bacillus firmus in the production of bioflocculants was made. The highest bioflocculant yield of 16.55 g/L was obtained from B. licheniformis (L) and 10 g/L from B. firmus (F). The bioflocculants obtained from the bacterial species were water soluble and insoluble in organic solvents. FTIR spectral analysis revealed the presence of hydroxyl, carboxyl and sugar derivatives in the bioflocculants. Thermal characterization by differential scanning calorimetry (DSC) showed the crystalline transition and the melting point (T-m) at 90-100 degrees C. Effects of bioflocculant dosage and pH on the flocculation of clay fines were evaluated. Highest bioflocculation efficiency on kaolin clay suspensions was observed at an optimum bioflocculant dosage of 5 g/L. The optimum pH range for the maximum bioflocculation was at pH 7-9. Bioflocculants exhibited high efficiency in dye decolorization. The maximum Cr (VI) removal was found to be 85 % for L (bioflocculant dosage at 2 g/L). This study demonstrates that microbial bioflocculants find potential applications in mineral processing such as selective flocculation of mineral fines, decolorization of dye solutions and in the remediation of toxic metal solutions. (C) 2015 Elsevier B.V. All rights reserved.

Tungsten-based nanomaterials (WO3 & Bi2WO6): Modifications related to charge carrier transfer mechanisms and photocatalytic applications

Heterogeneous photocatalysis is an ideal green energy technology for the purification of wastewater. Although titania dominates as the reference photocatalyst, its wide band gap is a bottleneck for extended utility. Thus, search for non-TiO2 based nanomaterials has become an active area of research in recent years. In this regard, visible light absorbing polycrystalline WO3 (2.4-2.8 eV) and Bi2WO6 (2.8 eV) with versatile structure-electronic properties has gained considerable interest to promote the photocatalytic reactions. These materials are also explored in selective functional group transformation in organic reactions, because of low reduction and oxidation potential of WO3 CB and Bi2WO6 VB, respectively. In this focused review, various strategies such as foreign ion doping, noble metal deposition and heterostructuring with other semiconductors designed for efficient photocatalysis is discussed. These modifications not only extend the optical response to longer wavelengths, but also prolong the life-time of the charge carriers and strengthen the photocatalyst stability. The changes in the surface-bulk properties and the charge carrier transfer dynamics associated with each modification correlating to the high activity are emphasized. The presence of oxidizing agents, surface modification with Cu2+ ions and synthesis of exposed facets to promote the degradation rate is highlighted. In depth study on these nanomaterials is likely to sustain interest in wastewater remediation and envisaged to signify in various green energy applications. (C) 2015 Elsevier B.V. All rights reserved.

Isolation and characterization of a bioflocculant from Bacillus megaterium for turbidity and arsenic removal

A biodegradable flocculant was produced during growth of Bacillus megaterium. The major component of the bioflocculant was found to be a polysaccharide composed of some proteins. Fourier transform infrared (FTIR) spectra analysis revealed the presence of carboxyl and hydroxyl groups in the bioflocculant, and thermal characterization by differential scanning calorimetly (DSC) showed the transition and crystalline melting point at 90-105 degrees C. The effects of bioflocculant dosage and pH on the flocculation of mineral suspensions were evaluated. The bioflocculant exhibited good flocculating capability on mineral suspensions and achieved flocculating efficiencies of 90 percent for k-aolinite and 85 percent for hematite suspensions at a dosage of only 5 mL/L. The maximum arsenite removal was found to be 90 percent at a bioflocculant dosage of 2 g/L, which is better than traditional chemicalflocculants. This study demonstrates that microbial bioflocculants have potential for application in environmental cleanup, such as in the flocculation of mineral fines and in the remediation of solutions that contain toxic heavy metals.

Macroporous three-dimensional graphene oxide foams for dye adsorption and antibacterial applications

Several reports illustrate the wide range applicability of graphene oxide (GO) in water remediation. However, a few layers of graphene oxide tend to aggregate under saline conditions thereby reducing its activity. The effects of aggregation can be minimized by having a random arrangement of GO layers in a three dimensional architecture. The current study emphasizes the potential benefits of highly porous, ultralight graphene oxide foams in environmental applications. These foams were prepared by a facile and cost effective lyophilization technique. The 3D architecture allowed the direct use of these foams in the removal of aqueous pollutants without any pretreatment such as ultrasonication. Due to its macroporous nature, the foams exhibited excellent adsorption abilities towards carcinogenic dyes such as rhodamine B (RB), malachite green (MG) and acriflavine (AF) with respective sorption capacities of 446, 321 and 228 mg g(-1) of foam. These foams were also further investigated for antibacterial activities against E. coli bacteria in aqueous and nutrient growth media. The random arrangement of GO layers in the porous foam architecture allowed it to exhibit excellent antibacterial activity even under physiological conditions by following the classical wrapping-perturbation mechanism. These results demonstrate the vast scope of GO foam in water remediation for both dye removal and antibacterial activity.