Nitrification (DMPP) and urease (NBPT) inhibitors had no effect on pasture yield, nitrous oxide emissions nor nitrate leaching under irrigation in a hot-dry climate

Modern dairy farming in Australia relies on substantial inputs of fertiliser nitrogen (N) to underpin economic production. However, N lost from dairy systems represents an opportunity cost and can pose a number of environmental risks. Nitrogen cycle inhibitors can be co-applied with N fertilisers to slow the conversion of urea to NH4+ to reduce losses via volatilisation, and slow the conversion of NH4+ to NO3- to minimize leaching of NO3- and gaseous losses via nitrification and denitrification. In a field campaign in a high input ryegrass-kikuyu pasture system we compared the soil N pools, losses and pasture production between a) urea coated with the nitrification inhibitor (3,4-dimethyl pyrazole phosphate - DMPP) b) urea coated with the urease inhibitor (N-(n-butyl) thiophosphoric triamide - NBPT) and c) standard urea. There was no treatment effect (P>0.05) on soil mineral N, pasture yield, N2O flux nor leaching of NO3- cf. standard urea. We hypothesise that at our site, because gaseous losses were highly episodic (rainfall was erratic and displayed no seasonal rainfall nor soil wetting pattern) that there was a lack of coincidence of N application and conditions conducive to gaseous losses, thus the effectiveness of the inhibitor products was minimal and did not result in an increase in pasture yield. There remains a paucity of knowledge on N cycle inhibitors in relation to their effective use in field system to increase N use efficiency. Further research is required to define under what field conditions inhibitor products are effective in order to be able to provide accurate advice to managers of nitrogen in production systems.

Microbial communities in Pb contaminated boreal forest soil

Lead contamination in the environment is of particular concern, as it is a known toxin. Until recently, however, much less attention has been given to the local contamination caused by activities at shooting ranges compared to large-scale industrial contamination. In Finland, more than 500 tons of Pb is produced each year for shotgun ammunition. The contaminant threatens various organisms, ground water and the health of human populations. However, the forest at shooting ranges usually shows no visible sign of stress compared to nearby clean environments. The aboveground biota normally reflects the belowground ecosystem. Thus, the soil microbial communities appear to bear strong resistance to contamination, despite the influence of lead. The studies forming this thesis investigated a shooting range site at Hälvälä in Southern Finland, which is heavily contaminated by lead pellets. Previously it was experimentally shown that the growth of grasses and degradation of litter are retarded. Measurements of acute toxicity of the contaminated soil or soil extracts gave conflicting results, as enchytraeid worms used as toxicity reporters were strongly affected, while reporter bacteria showed no or very minor decreases in viability. Measurements using sensitive inducible luminescent reporter bacteria suggested that the bioavailability of lead in the soil is indeed low, and this notion was supported by the very low water extractability of the lead. Nevertheless, the frequency of lead-resistant cultivable bacteria was elevated based on the isolation of cultivable strains. The bacterial and fungal diversity in heavily lead contaminated shooting sectors were compared with those of pristine sections of the shooting range area. The bacterial 16S rRNA gene and fungal ITS rRNA gene were amplified, cloned and sequenced using total DNA extracted from the soil humus layer as the template. Altogether, 917 sequenced bacterial clones and 649 sequenced fungal clones revealed a high soil microbial diversity. No effect of lead contamination was found on bacterial richness or diversity, while fungal richness and diversity significantly differed between lead contaminated and clean control areas. However, even in the case of fungi, genera that were deemed sensitive were not totally absent from the contaminated area: only their relative frequency was significantly reduced. Some operational taxonomic units (OTUs) assigned to Basidiomycota were clearly affected, and were much rarer in the lead contaminated areas. The studies of this thesis surveyed EcM sporocarps, analyzed morphotyped EcM root tips by direct sequencing, and 454-pyrosequenced fungal communities in in-growth bags. A total of 32 EcM fungi that formed conspicuous sporocarps, 27 EcM fungal OTUs from 294 root tips, and 116 EcM fungal OTUs from a total of 8 194 ITS2 454 sequences were recorded. The ordination analyses by non-parametric multidimensional scaling (NMS) indicated that Pb enrichment induced a shift in the EcM community composition. This was visible as indicative trends in the sporocarp and root tip datasets, but explicitly clear in the communities observed in the in-growth bags. The compositional shift in the EcM community was mainly attributable to an increase in the frequencies of OTUs assigned to the genus Thelephora, and to a decrease in the OTUs assigned to Pseudotomentella, Suillus and Tylospora in Pb-contaminated areas when compared to the control. The enrichment of Thelephora in contaminated areas was also observed when examining the total fungal communities in soil using DNA cloning and sequencing technology. While the compositional shifts are clear, their functional consequences for the dominant trees or soil ecosystem remain undetermined. The results indicate that at the Hälvälä shooting range, lead influences the fungal communities but not the bacterial communities. The forest ecosystem shows apparent functional redundancy, since no significant effects were seen on forest trees. Recently, by means of 454 pyrosequencing , the amount of sequences in a single analysis run can be up to one million. It has been applied in microbial ecology studies to characterize microbial communities. The handling of sequence data with traditional programs is becoming difficult and exceedingly time consuming, and novel tools are needed to handle the vast amounts of data being generated. The field of microbial ecology has recently benefited from the availability of a number of tools for describing and comparing microbial communities using robust statistical methods. However, although these programs provide methods for rapid calculation, it has become necessary to make them more amenable to larger datasets and numbers of samples from pyrosequencing. As part of this thesis, a new program was developed, MuSSA (Multi-Sample Sequence Analyser), to handle sequence data from novel high-throughput sequencing approaches in microbial community analyses. The greatest advantage of the program is that large volumes of sequence data can be manipulated, and general OTU series with a frequency value can be calculated among a large number of samples.

Effect of soil variability on the bearing capacity of clay and in slope stability problems

Site-specific geotechnical data are always random and variable in space. In the present study, a procedure for quantifying the variability in geotechnical characterization and design parameters is discussed using the site-specific cone tip resistance data (qc) obtained from static cone penetration test (SCPT). The parameters for the spatial variability modeling of geotechnical parameters i.e. (i) existing trend function in the in situ qc data; (ii) second moment statistics i.e. analysis of mean, variance, and auto-correlation structure of the soil strength and stiffness parameters; and (iii) inputs from the spatial correlation analysis, are utilized in the numerical modeling procedures using the finite difference numerical code FLAC 5.0. The influence of consideration of spatially variable soil parameters on the reliability-based geotechnical deign is studied for the two cases i.e. (a) bearing capacity analysis of a shallow foundation resting on a clayey soil, and (b) analysis of stability and deformation pattern of a cohesive-frictional soil slope. The study highlights the procedure for conducting a site-specific study using field test data such as SCPT in geotechnical analysis and demonstrates that a few additional computations involving soil variability provide a better insight into the role of variability in designs.

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.

The effects of habitat edges and trampling intensity on vegetation in urban forests

Although changes in urban forest vegetation have been documented in previous Finnish studies, the reasons for these changes have not been studied explicitly. Especially, the consequences of forest fragmentation, i.e. the fact that forest edges receive more solar radiation, wind and air-borne nutrients than interiors have been ignored. In order to limit the change in urban forest vegetation we need to know why it occurs. Therefore, the effects of edges and recreational use of urban forests on vegetation were investigated together in this thesis to reveal the relative strengths of these effects and to provide recommendations for forest management. Data were collected in the greater Helsinki area (in the cities of Helsinki, Vantaa and Espoo, and in the municipalities of Sipoo and Tuusula) and in the Lahti region (in the city of Lahti and in the municipality of Hollola) by means of systematic and randomized vegetation and soil sampling and tree measurements. Sample plots were placed from the forest edges to the interiors to investigate the effects of forest edges, and on paths of different levels of wear and off these paths to investigate the effects of trampling. The natural vegetation of mesic and sub-xeric forest site types studied was sensitive both to the effects of the edge and to trampling. The abundances of dwarf shrubs and bryophytes decreased, while light- and nitrogen-demanding herbs and grasses - and especially Sorbus aucuparia – were favoured at the edges and next to the paths. Results indicated that typical forest site types at the edges are changing toward more nitrophilic vegetation communities. Covers of the most abundant forest species decreased considerably – even tens of percentages – from interiors to the edges indicating strong edge effects. These effects penetrated at least up to 50 m from the forest edges into the interiors, especially at south to west facing open edges. The effects of trampling were pronounced on paths and even low levels of trampling decreased the abundances of certain species considerably. The effects of trampling extended up to 8 m from path edges. Results showed that the fragmentation of urban forest remnants into small and narrow patches should be avoided in order to maintain natural forest understorey vegetation in the urban setting. Thus, urban forest fragments left within urban development should be at least 3 ha in size, and as circular as possible. Where the preservation of representative original forest interior vegetation is a management aim, closed edges with conifers can act as an effective barrier against solar radiation, wind and urban load, thereby restricting the effects of the edge. Tree volume at the edge should be at least 225-250 m3 ha-1 and the proportion of conifers (especially spruce) 80% or more of the tree species composition. Closed, spruce-dominated edges may also prevent the excessive growth of S. aucuparia saplings at urban forest edges. In addition, closed edges may guide people’s movements to the maintained paths, thus preventing the spontaneous creation of dense path networks. In urban areas the effects of edges and trampling on biodiversity may be considerable, and are important to consider when the aim of management is to prevent the development of homogeneous herb-grass dominated vegetation communities, as was observed at the investigated edges.

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.

Theoretical Investigation on the Effect of Different Nitrogen Donors on Intramolecular Se center dot center dot center dot N Interactions

The effect of different donor nitrogen atoms on the strength and nature of intramolecular Se center dot center dot center dot N interactions is evaluated for organoselenium compounds having N,N-dimethylaminomethyl (dime), oxazoline (oxa) and pyridyl (py) substituents. Quantum chemical calculations on three series of compounds [2-(dime)C6H4SeX (1a-g), 2-(oxa)C6H4SeX (2a-g), 2- (py)C6H4SeX (3-ag); X=Cl, Br, OH, CN, SPh, SePh, CH3] at the B3LYP/6-31G(d) level show that the stability of different conformers depends on the strength of intramolecular nonbonded Se center dot center dot center dot N interactions. Natural bond orbital (NBO), NBO deletion and atoms in molecules (AIM) analyses suggest that the nature of the Se center dot center dot center dot N interaction is predominantly covalent and involves nN ->sigma*(Se-X) orbital interaction. In the three series of compounds, the strength of the Se center dot center dot center dot N interaction decreases in the order 3>2>1 for a particular X, and it decreases in the order Cl > Br > OH>SPh approximate to CN approximate to SePh>CH3 for all the three series 1-3. However, further analyses suggest that the differences in strength of Se center dot center dot center dot N interaction in 1-3 is predominantly determined by the distance between the Se and N atoms, which in turn is an outcome of specific structures of 1, 2 and 3, and the nature of the donor nitrogen atoms involved has very little effect on the strength of Se center dot center dot center dot N interaction. It is also observed that Se center dot center dot center dot N interaction becomes stronger in polar solvents such as CHCl3, as indicated by the shorter r(Se center dot center dot center dot N) and higher E-Se center dot center dot center dot N values in CHCl3 compared to those observed in the gas phase.

Synthesis, Structure, and Properties of Boron- and Nitrogen-Doped Graphene

Boron- and nitrogen-doped graphenes are are prepared by the arc discharge between carbon electrodes or by the transformation of nanodiamond under appropriate atmospheres. Using a combination of experiment and theories based on first principles, systematic changes in the carrier-concentration and electronic structure of the doped graphenes are demonstrated. Stiffening of the G-band mode and intensification of the defect-related D-band in the Raman spectra are also observed.

Salmonella pathogenicity island 2 mediates protection of intracellular Salmonella from reactive nitrogen intermediates.

Salmonella typhimurium causes an invasive disease in mice that has similarities to human typhoid. A type III protein secretion system encoded by Salmonella pathogenicity island 2 (SPI2) is essential for virulence in mice, as well as survival and multiplication within macrophages. Reactive nitrogen intermediates (RNI) synthesized by inducible nitric oxide synthase (iNOS) are involved in the control of intracellular pathogens, including S. typhimurium. We studied the effect of Salmonella infection on iNOS activity in macrophages. Immunofluorescence microscopy demonstrated efficient colocalization of iNOS with bacteria deficient in SPI2 but not wild-type Salmonella, and suggests that the SPI2 system interferes with the localization of iNOS and Salmonella. Furthermore, localization of nitrotyrosine residues in the proximity was observed for SPI2 mutant strains but not wild-type Salmonella, indicating that peroxynitrite, a potent antimicrobial compound, is excluded from Salmonella-containing vacuoles by action of SPI2. Altered colocalization of iNOS with intracellular Salmonella required the function of the SPI2-encoded type III secretion system, but not of an individual "Salmonella translocated effector." Inhibition of iNOS increased intracellular proliferation of SPI2 mutant bacteria and, to a lesser extent, of wild-type Salmonella. The defect in systemic infection of a SPI2 mutant strain was partially restored in iNOS(-/-) mice. In addition to various strategies to detoxify RNI or repair damage due to RNI, avoidance of colocalization with RNI is important in adaptation of a pathogen to an intracellular life style.

Adsorption of Nitrogen on Activated Carbon-Refit of Experimental Data and Derivation of Properties Required for Design of Equipment

Volumetric method based adsorption measurements of nitrogen on two specimens of activated carbon (Fluka and Sarabhai) reported by us are refitted to two popular isotherms, namely, Dubunin−Astakhov (D−A) and Toth, in light of improved fitting methods derived recently. Those isotherms have been used to derive other data of relevance in design of engineering equipment such as the concentration dependence of heat of adsorption and Henry’s law coefficients. The present fits provide a better representation of experimental measurements than before because the temperature dependence of adsorbed phase volume and structural heterogeneity of micropore distribution have been accounted for in the D−A equation. A new correlation to the Toth equation is a further contribution. The heat of adsorption in the limiting uptake condition is correlated with the Henry’s law coefficients at the near zero uptake condition.

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.

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.

Using a structural approach to identify relationships between soil and erosion in a semi-humid forested area, South India

Biogeochemical and hydrological cycles are currently studied on a small experimental forested watershed (4.5 km(2)) in the semi-humid South India. This paper presents one of the first data referring to the distribution and dynamics of a widespread red soil (Ferralsols and Chromic Luvisols) and black soil (Vertisols and Vertic intergrades) cover, and its possible relationship with the recent development of the erosion process. The soil map was established from the observation of isolated soil profiles and toposequences, and surveys of soil electromagnetic conductivity (EM31, Geonics Ltd), lithology and vegetation. The distribution of the different parts of the soil cover in relation to each other was used to establish the dynamics and chronological order of formation. Results indicate that both topography and lithology (gneiss and amphibolite) have influenced the distribution of the soils. At the downslope, the following parts of the soil covers were distinguished: i) red soil system, ii) black soil system, iii) bleached horizon at the top of the black soil and iv) bleached sandy saprolite at the base of the black soil. The red soil is currently transforming into black soil and the transformation front is moving upslope. In the bottom part of the slope, the chronology appears to be the following: black soil > bleached horizon at the top of the black soil > streambed > bleached horizon below the black soil. It appears that the development of the drainage network is a recent process, which was guided by the presence of thin black soil with a vertic horizon less than 2 in deep. Three distinctive types of erosional landforms have been identified: 1. rotational slips (Type 1); 2. a seepage erosion (Type 2) at the top of the black soil profile; 3. A combination of earthflow and sliding in the non-cohesive saprolite of the gneiss occurs at midslope (Type 3). Types 1 and 2 erosion are mainly occurring downslope and are always located at the intersection between the streambed and the red soil-black soil contact. Neutron probe monitoring, along an area vulnerable to erosion types 1 and 2, indicates that rotational slips are caused by a temporary watertable at the base of the black soil and within the sandy bleached saprolite, which behaves as a plane of weakness. The watertable is induced by the ephemeral watercourse. Erosion type 2 is caused by seepage of a perched watertable, which occurs after swelling and closing of the cracks of the vertic clay horizon and within a light textured and bleached horizon at the top of black soil. Type 3 erosion is not related to the red soil-black soil system but is caused by the seasonal seepage of saturated throughflow in the sandy saprolite of the gneiss occurring at midslope. (c) 2006 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.