Plasmids and aromatic degradation in Sphingomonas for bioremediation : Aromatic ring cleavage genes in soil and rhizosphere

Microbial degradation pathways play a key role in the detoxification and the mineralization of polyaromatic hydrocarbons (PAHs), which are widespread pollutants in soil and constituents of petroleum hydrocarbons. In microbiology the aromatic degradation pathways are traditionally studied from single bacterial strains with capacity to degrade certain pollutant. In soil the degradation of aromatics is performed by a diverse community of micro-organisms. The aim of this thesis was to study biodegradation on different levels starting from a versatile aromatic degrader Sphingobium sp. HV3 and its megaplasmid, extending to revelation of diversity of key catabolic enzymes in the environment and finally studying birch rhizoremediation in PAH-polluted soil. To understand biodegradation of aromatics on bacterial species level, the aromatic degradation capacity of Sphingobium sp. HV3 and the role of the plasmid pSKY4, was studied. Toluene, m-xylene, biphenyl, fluorene, phenanthrene were detected as carbon and energy sources of the HV3 strain. Tn5 transposon mutagenesis linked the degradation capacity of toluene, m-xylene, biphenyl and naphthalene to the pSKY4 plasmid and qPCR expression analysis showed that plasmid extradiol dioxygenases genes (bphC and xylE) are inducted by phenanthrene, m-xylene and biphenyl whereas the 2,4-dichlorophenoxyacetic acid herbicide induced the chlorocatechol 1,2-dioxygenase gene (tfdC) from the ortho-pathway. A method to study upper meta-pathway extradiol dioxygenase gene diversity in soil was developed. The extradiol dioxygenases catalyse cleavage of the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage). A high diversity of extradiol dioxygenases were detected from polluted soils. The detected extradiol dioxygenases showed sequence similarity to known catabolic genes of Alpha-, Beta-, and Gammaproteobacteria. Five groups of extradiol dioxygenases contained sequences with no close homologues in the database, representing novel genes. In rhizoremediation experiment with birch (Betula pendula) treatment specific changes of extradiol dioxygenase communities were shown. PAH pollution changed the bulk soil extradiol dioxygenase community structure and birch rhizosphere contained a more diverse extradiol dioxygenase community than the bulk soil showing a rhizosphere effect. The degradation of pyrene in soil was enhanced with birch seedlings compared to soil without birch. The complete 280,923 kb nucleotide sequence of pSKY4 plasmid was determined. The open reading frames of pSKY4 were divided into putative conjugative transfer, aromatic degradation, replication/maintaining and transposition/integration function-encoding proteins. Aromatic degradation orfs shared high similarity to corresponding genes in pNL1, a plasmid from the deep subsurface strain Novosphingobium aromaticivorans F199. The plasmid backbones were considerably more divergent with lower similarity, which suggests that the aromatic pathway has functioned as a plasmid independent mobile genetic element. The functional diversity of microbial communities in soil is still largely unknown. Several novel clusters of extradiol dioxygenases representing catabolic bacteria, whose function, biodegradation pathways and phylogenetic position is not known were amplified with single primer pair from polluted soils. These extradiol dioxygenase communities were shown to change upon PAH pollution, which indicates that their hosts function in PAH biodegradation in soil. Although the degradation pathways of specific bacterial species are substantially better depicted than pathways in situ, the evolution of degradation pathways for the xenobiotic compounds is largely unknown. The pSKY4 plasmid contains aromatic degradation genes in putative mobile genetic element causing flexibility/instability to the pathway. The localisation of the aromatic biodegradation pathway in mobile genetic elements suggests that gene transfer and rearrangements are a competetive advantage for Sphingomonas bacteria in the environment.

Seismic behaviour of rigid-faced reinforced soil retaining wall models:reinforcement effect

This paper presents the results of shaking table tests on models of rigid-faced reinforced soil retaining walls in which reinforcement materials of different tensile strength were used. The construction of the model retaining walls in a laminar box mounted on a shaking table, the instrumentation and the results from the shaking table tests are described in detail and the effects of the reinforcement parameters on the acceleration response at different elevations of the retaining wall, horizontal soil pressures and face deformations are presented. It was observed from these tests that the horizontal face displacement response of the rigid-faced retaining walls was significantly affected by the inclusion of reinforcement and even low-strength polymer reinforcement was found to be efficient in significantly reducing the deformation of the face. The acceleration amplifications were, however, observed to be less influenced by the reinforcement parameters. The results obtained from this study are helpful in understanding the relative performance of reinforced soil retaining walls under the different test conditions used in the experiments.

Vacuum ultraviolet/atomic oxygen erosion resistance of amorphous Si0.26C0.43N0.31 coating

An amorphous silicon carbonitride (Si1-x-yCxN y, x = 0:43, y = 0:31) coating was deposited on polyimide substrate using the magnetron-sputtering method. Exposure tests of the coated polyimide in atomic oxygen beam and vacuum ultraviolet radiation were performed in a ground-based simulator. Erosion kinetics measurements indicated that the erosion yield of the Si0.26C0.43N0.31 coating was about 1.5x and 1.8 × 10-26 cm3 /atom during exposure in single atomic oxygen beam, simultaneous atomic oxygen beam, and vacuum ultraviolet radiation, respectively. These values were 2 orders of magnitude lower than that of bare polyimide substrate. Scanning electron and atomic force microscopy, X-ray photoelectron spectrometer, and Fourier transformed infrared spectroscopy investigation indicated that during exposures, an oxide-rich layer composed of SiO2 and minor Si-C-O formed on the surface of the Si 0.26C0.43N0.31 coating, which was the main reason for the excellent resistance to the attacks of atomic oxygen. Moreover, vacuum ultraviolet radiation could promote the breakage of chemical bonds with low binding energy, such as C-N, C = N, and C-C, and enhance atomic oxygen erosion rate slightly.

Mapping the risk of soil-transmitted helminthic infections in the Philippines

Background In order to increase the efficient allocation of soil-transmitted helminth (STH) disease control resources in the Philippines, we aimed to describe for the first time the spatial variation in the prevalence of A. lumbricoides, T. trichiura and hookworm across the country, quantify the association between the physical environment and spatial variation of STH infection and develop predictive risk maps for each infection. Methodology/Principal Findings Data on STH infection from 35,573 individuals across the country were geolocated at the barangay level and included in the analysis. The analysis was stratified geographically in two major regions: 1) Luzon and the Visayas and 2) Mindanao. Bayesian geostatistical models of STH prevalence were developed, including age and sex of individuals and environmental variables (rainfall, land surface temperature and distance to inland water bodies) as predictors, and diagnostic uncertainty was incorporated. The role of environmental variables was different between regions of the Philippines. This analysis revealed that while A. lumbricoides and T. trichiura infections were widespread and highly endemic, hookworm infections were more circumscribed to smaller foci in the Visayas and Mindanao. Conclusions/Significance This analysis revealed significant spatial variation in STH infection prevalence within provinces of the Philippines. This suggests that a spatially targeted approach to STH interventions, including mass drug administration, is warranted. When financially possible, additional STH surveys should be prioritized to high-risk areas identified by our study in Luzon.

Effect of increased manganese addition and mould type on the slurry erosion characteristics of Cr-Mn iron systems

The wear resistance of high chromium iron is well recorded. However, the same is not the case as regards the use of manganese at higher percentages in high chromium irons and its influence on wear behaviour. Hence, this work highlights the slurry wear characteristics of chromium 16–19%) iron following the introduction of manganese at two levels i.e. 5 and 10%. It is known that the wear properties are dictated by the microstructural features. To alter the structure, the cooling rate of casting has been varied by adopting two different types of moulds (i.e. sand and metal) and subsequently subjecting to thermal treatment. The as-cast and heat treated samples are examined for microstructure and then evaluated for hardness and slurry erosion properties. As the manganese content is increased from 5 to 10%, the hardness showed a decrease in value both in the as-cast and heat treated conditions. The slurry erosion loss, expectedly, showed an increase irrespective of the sample condition (i.e. mould type/heat treatment adopted). The findings are corroborated with the microstructural features obtained through optical and scanning electron microscopy.

Induced swelling of kaolinitic soil in alkali solution

Unexpected swelling induced in foundation soils can cause distress to structures founded on them. In this paper, the swelling of kaolinitic soils due to interaction with alkali solution has been reported. The induced swelling is attributed to the formation of new minerals, which has been confirmed by X-ray diffraction patters and SEM studies. To understand the effect of alkali concentration and duration of interaction, two series of consolidation experiments have been carried out. In series 1, the specimen were remoulded with water and inundated with alkali solutions and in series 2, the specimen were remoulded and inundated with same alkali solutions. A steep compression during loading cycle and no abnormal swelling during unloading cycle has been noticed for the specimen remoulded with water and inundated with 1 N NaOH solutions. The steep compression is due to the segregation or break down of clay minerals due to alkali interactions. In case of specimen inundated with 4 N NaOH solutions, abnormal swelling has been observed during unloading cycle of the consolidation test. New minerals are formed on interaction of soil with 4 N solution as confirmed by X-ray diffraction patterns. These minerals are known to have very fine pores and possess high water holding capacity. The differences in the amount of swelling of samples remoulded with water and remoulded with alkali solution are due to variations in the concentration of alkali and duration of interaction.

The effects of manganese content and mould size on abrasion and slurry erosion behaviour of chromium-manganese iron systems investigated by positron lifetime spectroscopy

Abrasion and slurry erosion behaviour of chromium-manganese iron samples with chromium (Cr) in the range similar to 16-19% and manganese (Mn) at 5 and 10% levels have been characterized for hardness followed by microstructural examination using optical and scanning electron microscopy. Positron lifetime studies have been conducted to understand the defects/microporosity influence on the microstructure. The samples were heat treated and characterized to understand the structural transformations in the matrix. The data reveals that hardness decreased with increase in Mn content from 5 to 10% in the first instance and then increase in the section size in the other case, irrespective of the sample conditions. The abrasion and slurry erosion losses show increase with increase in the section size as well as with increase in Mn content. The positron results show that as hardness increases from as-cast to heat treated sample, the positron trapping rate and hence defect concentration showed opposite trend as expected. So a good correlation between defects concentration and the hardness has been observed. These findings also corroborate well with the microstructural features obtained from optical and scanning electron microscopy. (C) 2009 Elsevier B. V. All rights reserved.

Seismic response of reinforced soil retaining wall models: Influence of backfill relative density

This paper presents the results of shaking table tests on model reinforced soil retaining walls in the laboratory. The influence of backfill relative density on the seismic response was studied through a series of laboratory model tests on retaining walls. Construction of model retaining walls in the laminar box mounted on shaking table, instrumentation and results from the shaking table tests are described in detail. Three types of walls: wrap- and rigid-faced reinforced soil walls and unreinforced rigid-faced walls constructed to different densities were tested for a relatively small excitation. Wrap-faced walls are further tested for higher base excitation at different frequencies and relative densities. It is observed from these tests that the effect of backfill density on the seismic performance of reinforced retaining walls is pronounced only at very low relative density and at the higher base excitation. The walls constructed with higher backfill relative density showed lesser face deformations and more acceleration amplifications compared to the walls constructed with lower densities when tested at higher base excitation. The response of wrap- and rigid-faced retaining walls is not much affected by the backfill relative density when tested at smaller base excitation. The effects of facing rigidity were evaluated to a limited extent. Displacements in wrap-faced walls are many times higher compared to rigid-faced walls. The results obtained from this study are helpful in understanding the relative performance of reinforced soil retaining walls constructed to when subjected to smaller and higher base excitation for the range of relative density employed in the testing program. (C) 2007 Elsevier Ltd. All rights reserved.

Sticking and erosion at carbon-containing plasma-facing materials in fusion reactors

Controlled nuclear fusion is one of the most promising sources of energy for the future. Before this goal can be achieved, one must be able to control the enormous energy densities which are present in the core plasma in a fusion reactor. In order to be able to predict the evolution and thereby the lifetime of different plasma facing materials under reactor-relevant conditions, the interaction of atoms and molecules with plasma first wall surfaces have to be studied in detail. In this thesis, the fundamental sticking and erosion processes of carbon-based materials, the nature of hydrocarbon species released from plasma-facing surfaces, and the evolution of the components under cumulative bombardment by atoms and molecules have been investigated by means of molecular dynamics simulations using both analytic potentials and a semi-empirical tight-binding method. The sticking cross-section of CH3 radicals at unsaturated carbon sites at diamond (111) surfaces is observed to decrease with increasing angle of incidence, a dependence which can be described by a simple geometrical model. The simulations furthermore show the sticking cross-section of CH3 radicals to be strongly dependent on the local neighborhood of the unsaturated carbon site. The erosion of amorphous hydrogenated carbon surfaces by helium, neon, and argon ions in combination with hydrogen at energies ranging from 2 to 10 eV is studied using both non-cumulative and cumulative bombardment simulations. The results show no significant differences between sputtering yields obtained from bombardment simulations with different noble gas ions. The final simulation cells from the 5 and 10 eV ion bombardment simulations, however, show marked differences in surface morphology. In further simulations the behavior of amorphous hydrogenated carbon surfaces under bombardment with D^+, D^+2, and D^+3 ions in the energy range from 2 to 30 eV has been investigated. The total chemical sputtering yields indicate that molecular projectiles lead to larger sputtering yields than atomic projectiles. Finally, the effect of hydrogen ion bombardment of both crystalline and amorphous tungsten carbide surfaces is studied. Prolonged bombardment is found to lead to the formation of an amorphous tungsten carbide layer, regardless of the initial structure of the sample. In agreement with experiment, preferential sputtering of carbon is observed in both the cumulative and non-cumulative simulations

Reliability assessment of internal stability of reinforced soil structures: A pseudo-dynamic approach

A methodology for reliability based optimum design of reinforced soil structures subjected to horizontal and vertical sinusoidal excitation based on pseudo-dynamic approach is presented. The tensile strength of reinforcement required to maintain the stability is computed using logarithmic spiral failure mechanism. The backfill soil properties, geometric and strength properties of reinforcement are treated as random variables. Effects of parameters like soil friction angle, horizontal and vertical seismic accelerations, shear and primary wave velocities, amplification factors for seismic acceleration on the component and system probability of failures in relation to tension and pullout capacities of reinforcement have been discussed. In order to evaluate the validity of the present formulation, static and seismic reinforcement force coefficients computed by the present method are compared with those given by other authors. The importance of the shear wave velocity in the estimation of the reliability of the structure is highlighted. The Ditlevsen's bounds of system probability of failure are also computed by taking into account the correlations between three failure modes, which is evaluated using the direction cosines of the tangent planes at the most probable points of failure. (c) 2009 Elsevier Ltd. All rights reserved.

Hydrogen soil deposition and atmospheric variations in the boreal zone

This research has been prompted by an interest in the atmospheric processes of hydrogen. The sources and sinks of hydrogen are important to know, particularly if hydrogen becomes more common as a replacement for fossil fuel in combustion. Hydrogen deposition velocities (vd) were estimated by applying chamber measurements, a radon tracer method and a two-dimensional model. These three approaches were compared with each other to discover the factors affecting the soil uptake rate. A static-closed chamber technique was introduced to determine the hydrogen deposition velocity values in an urban park in Helsinki, and at a rural site at Loppi. A three-day chamber campaign to carry out soil uptake estimation was held at a remote site at Pallas in 2007 and 2008. The atmospheric mixing ratio of molecular hydrogen has also been measured by a continuous method in Helsinki in 2007 - 2008 and at Pallas from 2006 onwards. The mean vd values measured in the chamber experiments in Helsinki and Loppi were between 0.0 and 0.7 mm s-1. The ranges of the results with the radon tracer method and the two-dimensional model were 0.13 - 0.93 mm s-1 and 0.12 - 0.61 mm s-1, respectively, in Helsinki. The vd values in the three-day campaign at Pallas were 0.06 - 0.52 mm s-1 (chamber) and 0.18 - 0.52 mm s-1 (radon tracer method and two-dimensional model). At Kumpula, the radon tracer method and the chamber measurements produced higher vd values than the two-dimensional model. The results of all three methods were close to each other between November and April, except for the chamber results from January to March, while the soil was frozen. The hydrogen deposition velocity values of all three methods were compared with one-week cumulative rain sums. Precipitation increases the soil moisture, which decreases the soil uptake rate. The measurements made in snow seasons showed that a thick snow layer also hindered gas diffusion, lowering the vd values. The H2 vd values were compared to the snow depth. A decaying exponential fit was obtained as a result. During a prolonged drought in summer 2006, soil moisture values were lower than in other summer months between 2005 and 2008. Such conditions were prevailing in summer 2006 when high chamber vd values were measured. The mixing ratio of molecular hydrogen has a seasonal variation. The lowest atmospheric mixing ratios were found in the late autumn when high deposition velocity values were still being measured. The carbon monoxide (CO) mixing ratio was also measured. Hydrogen and carbon monoxide are highly correlated in an urban environment, due to the emissions originating from traffic. After correction for the soil deposition of H2, the slope was 0.49±0.07 ppb (H2) / ppb (CO). Using the corrected hydrogen-to-carbon-monoxide ratio, the total hydrogen load emitted by Helsinki traffic in 2007 was 261 t (H2) a-1. Hydrogen, methane and carbon monoxide are connected with each other through the atmospheric methane oxidation process, in which formaldehyde is produced as an important intermediate. The photochemical degradation of formaldehyde produces hydrogen and carbon monoxide as end products. Examination of back-trajectories revealed long-range transportation of carbon monoxide and methane. The trajectories can be grouped by applying cluster and source analysis methods. Thus natural and anthropogenic emission sources can be separated by analyzing trajectory clusters.

Seismic response of wrap-faced reinforced soil-retaining wall models using shaking table tests

This paper presents the results of shaking table tests on geotextile-reinforced wrap-faced soil-retaining walls. Construction of model retaining walls in a laminar box mounted on a shaking table, instrumentation, and results from the shaking table tests are discussed in detail. The base motion parameters, surcharge pressure and number of reinforcing layers are varied in different model tests. It is observed from these tests that the response of the wrap-faced soil-retaining walls is significantly affected by the base acceleration levels, frequency of shaking, quantity of reinforcement and magnitude of surcharge pressure on the crest. The effects of these different parameters on acceleration response at different elevations of the retaining wall, horizontal soil pressures and face deformations are also presented. The results obtained from this study are helpful in understanding the relative performance of reinforced soil-retaining walls under different test conditions used in the experiments.

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.