Fungal flora of rice field soils

Qualitative and quantitative assessment of the fungal flora of rice field soils yielded 102 species of fungi belonging to 44 genera, when dilution plate, soil plate, root-washing and baiting techniques were employed. The order of efficacy of the methods used was: root-washing > soil plate > dilution plate > baiting. Baiting method, used specifically to isolate aquatic and keratinophilic fungi from soils was studied in detail with reference to the former. Qualitatively, corn leaf bait was the most efficient one while pine pollens and hemp seeds were least efficient. A semi-quantitative method was employed to study the statistically significant differences among the different factors used. Among the keratinophilic baits,viz., human hair, fowl’s feather and wool, wool bait was least efficient. The results of this investigation are discussed.

Microbial activities in boreal soils: Biodegradation of organic contaminants at low temperature and ammonia oxidation

This thesis deals with the response of biodegradation of selected anthropogenic organic contaminants and natural autochthonous organic matter to low temperature in boreal surface soils. Furthermore, the thesis describes activity, diversity and population size of autotrophic ammonia-oxidizing bacteria (AOB) in a boreal soil used for landfarming of oil-refinery wastes, and presents a new approach, in which the particular AOB were enriched and cultivated in situ from the landfarming soil onto cation exchange membranes. This thesis demonstrates that rhizosphere fraction of natural forest humus soil and agricultural clay loam soil from Helsinki Metropolitan area were capable of degrading of low to moderate concentrations (0.2 50 µg cm-3) of PCP, phenanthrene and 2,4,5-TCP at temperatures realistic to boreal climate (-2.5 to +15 °C). At the low temperatures, the biodegradation of PCP, phenanthrene and 2,4,5-TCP was more effective (Q10-values from 1.6 to 7.6) in the rhizosphere fraction of the forest soil than in the agricultural soil. Q10-values of endogenous soil respiration (carbon dioxide evolution) and selected hydrolytic enzyme activities (acetate-esterase, butyrate-esterase and β-glucosidase) in acid coniferous forest soil were 1.6 to 2.8 at temperatures from -3 to +30 °C. The results indicated that the temperature dependence of decomposition of natural autochthonous soil organic matter in the studied coniferous forest was only moderate. The numbers of AOB in the landfarming (sandy clay loam) soil were determined with quantitative polymerase chain reaction (real-time PCR) and with Most Probable Number (MPN) methods, and potential ammonium oxidation activity was measured with the chlorate inhibition technique. The results indicated presence of large and active AOB populations in the heavily oil-contaminated and urea-fertilised landfarming soil. Assessment of the populations of AOB with denaturing gradient gel electrophoresis (DGGE) profiling and sequence analysis of PCR-amplified 16S rRNA genes showed that Nitrosospira-like AOB in clusters 2 and 3 were predominant in the oily landfarming soil. This observation was supported by fluorescence in situ hybridization (FISH) analysis of the AOB grown on the soil-incubated cation-exchange membranes. The results of this thesis expand the suggested importance of Nitrosospira-like AOB in terrestrial environments to include chronically oil-contaminated soils.

Country-scale carbon accounting of the vegetation and mineral soils of Finland

The increase in global temperature has been attributed to increased atmospheric concentrations of greenhouse gases (GHG), mainly that of CO2. The threat of severe and complex socio-economic and ecological implications of climate change have initiated an international process that aims to reduce emissions, to increase C sinks, and to protect existing C reservoirs. The famous Kyoto protocol is an offspring of this process. The Kyoto protocol and its accords state that signatory countries need to monitor their forest C pools, and to follow the guidelines set by the IPCC in the preparation, reporting and quality assessment of the C pool change estimates. The aims of this thesis were i) to estimate the changes in carbon stocks vegetation and soil in the forests in Finnish forests from 1922 to 2004, ii) to evaluate the applied methodology by using empirical data, iii) to assess the reliability of the estimates by means of uncertainty analysis, iv) to assess the effect of forest C sinks on the reliability of the entire national GHG inventory, and finally, v) to present an application of model-based stratification to a large-scale sampling design of soil C stock changes. The applied methodology builds on the forest inventory measured data (or modelled stand data), and uses statistical modelling to predict biomasses and litter productions, as well as a dynamic soil C model to predict the decomposition of litter. The mean vegetation C sink of Finnish forests from 1922 to 2004 was 3.3 Tg C a-1, and in soil was 0.7 Tg C a-1. Soil is slowly accumulating C as a consequence of increased growing stock and unsaturated soil C stocks in relation to current detritus input to soil that is higher than in the beginning of the period. Annual estimates of vegetation and soil C stock changes fluctuated considerably during the period, were frequently opposite (e.g. vegetation was a sink but soil was a source). The inclusion of vegetation sinks into the national GHG inventory of 2003 increased its uncertainty from between -4% and 9% to ± 19% (95% CI), and further inclusion of upland mineral soils increased it to ± 24%. The uncertainties of annual sinks can be reduced most efficiently by concentrating on the quality of the model input data. Despite the decreased precision of the national GHG inventory, the inclusion of uncertain sinks improves its accuracy due to the larger sectoral coverage of the inventory. If the national soil sink estimates were prepared by repeated soil sampling of model-stratified sample plots, the uncertainties would be accounted for in the stratum formation and sample allocation. Otherwise, the increases of sampling efficiency by stratification remain smaller. The highly variable and frequently opposite annual changes in ecosystem C pools imply the importance of full ecosystem C accounting. If forest C sink estimates will be used in practice average sink estimates seem a more reasonable basis than the annual estimates. This is due to the fact that annual forest sinks vary considerably and annual estimates are uncertain, and they have severe consequences for the reliability of the total national GHG balance. The estimation of average sinks should still be based on annual or even more frequent data due to the non-linear decomposition process that is influenced by the annual climate. The methodology used in this study to predict forest C sinks can be transferred to other countries with some modifications. The ultimate verification of sink estimates should be based on comparison to empirical data, in which case the model-based stratification presented in this study can serve to improve the efficiency of the sampling design.

Experimental study on shrinkage behaviour and prediction of shrinkage magnitudes of residual soils

The present study examines the shrinkage behaviour of residually derived black cotton (BC) soil and red soil compacted specimens that were subjected to air-drying from the swollen state. The soil specimens were compacted at varying dry density and moisture contents to simulate varied field conditions. The void ratio and moisture content of the swollen specimens were monitored during the drying process and relationship between them is analyzed. Shrinkage is represented as reduction in void ratio with decrease in water content of soil specimens. It is found to occur in three distinct stages. Total shrinkage magnitude depends on the type of clay mineral present. Variation in compaction conditions effect marginally total shrinkage magnitudes of BC soil specimens but have relatively more effect on red soil specimens. A linear relation is obtained between total shrinkage magnitude and volumetric water content of soil specimens in swollen state and can be used to predict the shrinkage magnitude of soils.

Optimum design of cantilever sheet pile walls in sandy soils using inverse reliability approach

In this paper an approach for obtaining depth and section modulus of the cantilever sheet pile wall using inverse reliability method is described. The proposed procedure employs inverse first order reliability method to obtain the design penetration depth and section modulus of the steel sheet pile wall in order that the reliability of the wall against failure modes must meet a desired level of safety. Sensitivity analysis is conducted to assess the effect of uncertainties in design parameters on the reliability of cantilever sheet pile walls. The analysis is performed by treating back fill soil properties, depth of the water table from the top of the sheet pile wall, yield strength of steel and section modulus of steel pile as random variables. Two limit states, viz., rotational and flexural failure of sheet pile wall are considered. The results using this approach are used to develop a set of reliability based design charts for different coefficients of variation of friction angle of the backfill (5%, 10% and 15%). System reliability considerations in terms of series and parallel systems are also studied.

Support vector machine applied to settlement of shallow foundations on cohesionless soils

The determination of settlement of shallow foundations on cohesionless soil is an important task in geotechnical engineering. Available methods for the determination of settlement are not reliable. In this study, the support vector machine (SVM), a novel type of learning algorithm based on statistical theory, has been used to predict the settlement of shallow foundations on cohesionless soil. SVM uses a regression technique by introducing an ε – insensitive loss function. A thorough sensitive analysis has been made to ascertain which parameters are having maximum influence on settlement. The study shows that SVM has the potential to be a useful and practical tool for prediction of settlement of shallow foundation on cohesionless soil.

Seismic passive earth pressures in soils

Seismic passive earth pressure coefficients were computed by the method of limit equilibrium using a pseudostatic approach for seismic forces. Composite curved rupture surfaces were considered in the analysis. While earlier studies using this type of analysis were mainly for sands, seismic passive earth pressure coefficients were obtained in the present study considering the effects of cohesion, surcharge, and own weight. The minimum seismic passive force was obtained by adding the individual minimum values of these components and the validity of the principle of superposition was examined. Other parameters considered in the analysis were wall batter angle, ground surface slope, soil friction angle, wall friction angle, wall adhesion to soil cohesion ratio, and horizontal and vertical seismic accelerations. The seismic earth pressure coefficients were found to be highly sensitive to the seismic acceleration coefficients both in the horizontal and vertical directions. Results of the study are presented in the form of figures and tables. Comparisons of the proposed method with available theories in the seismic case are also presented.

A method for the preferential isolation of actinomycetes from soils

A successful plate-method for the preferential isolation of actinomycetes from soils is described. The principles underlying it are: (1) the inhibition of growth of non-sporulating bacteria by pre-incubation at a high temperature (110 C) for 10 min, and (2) limiting the spreading growth of sporeforming bacteria and fungi by the use of dried plates. The majority of the 191 species isolated by this method from 82 soil samples were shown to be pectinolytic.

Liquid Limit Of Kaolinitic Soils

This paper elucidates the relative importance of soil structure and various compositional factors in influencing the liquid limit of natural kaolinitic soils. Earlier studies dealt with purified systems and anticipated that the liquid limit of the soils would increase with percentage clay size fraction and surface area, and that soils with a greater degree of paricle flocculation would possess a higher liquid limit than soils with a more parallel particle arrangement. The results revealed that the inter-particle attraction and repulsion forces have a prominent role in determining the liquid limit of kaolinitic soils. These forces determine the particle arrangement (clay fabric) which in turn regulates the liquid limit values. The influence of clay fabric was ascertained from the relationships of liquid limit with shrinkage limit and sediment volume (in water) values. It was anticipated that kaolinitic soils with a greater degree of particle flocculatin and a higher liquid limit would shrink less and occupy a higher sedimentation volume. As expected an increase in liquid limit was accompanied by an increase in shrinkage limit and sediment volume in water.

Microbiological characterisation of soils : Evaluation of some critical steps in data collection and experimental design

The study of soil microbiota and their activities is central to the understanding of many ecosystem processes such as decomposition and nutrient cycling. The collection of microbiological data from soils generally involves several sequential steps of sampling, pretreatment and laboratory measurements. The reliability of results is dependent on reliable methods in every step. The aim of this thesis was to critically evaluate some central methods and procedures used in soil microbiological studies in order to increase our understanding of the factors that affect the measurement results and to provide guidance and new approaches for the design of experiments. The thesis focuses on four major themes: 1) soil microbiological heterogeneity and sampling, 2) storage of soil samples, 3) DNA extraction from soil, and 4) quantification of specific microbial groups by the most-probable-number (MPN) procedure. Soil heterogeneity and sampling are discussed as a single theme because knowledge on spatial (horizontal and vertical) and temporal variation is crucial when designing sampling procedures. Comparison of adjacent forest, meadow and cropped field plots showed that land use has a strong impact on the degree of horizontal variation of soil enzyme activities and bacterial community structure. However, regardless of the land use, the variation of microbiological characteristics appeared not to have predictable spatial structure at 0.5-10 m. Temporal and soil depth-related patterns were studied in relation to plant growth in cropped soil. The results showed that most enzyme activities and microbial biomass have a clear decreasing trend in the top 40 cm soil profile and a temporal pattern during the growing season. A new procedure for sampling of soil microbiological characteristics based on stratified sampling and pre-characterisation of samples was developed. A practical example demonstrated the potential of the new procedure to reduce the analysis efforts involved in laborious microbiological measurements without loss of precision. The investigation of storage of soil samples revealed that freezing (-20 °C) of small sample aliquots retains the activity of hydrolytic enzymes and the structure of the bacterial community in different soil matrices relatively well whereas air-drying cannot be recommended as a storage method for soil microbiological properties due to large reductions in activity. Freezing below -70 °C was the preferred method of storage for samples with high organic matter content. Comparison of different direct DNA extraction methods showed that the cell lysis treatment has a strong impact on the molecular size of DNA obtained and on the bacterial community structure detected. An improved MPN method for the enumeration of soil naphthalene degraders was introduced as an alternative to more complex MPN protocols or the DNA-based quantification approach. The main advantage of the new method is the simple protocol and the possibility to analyse a large number of samples and replicates simultaneously.

Analysis of Compressibility of Sensitive Soils

Sensitive soils, in general, are prone to mechanical disturbances while sampling, handling, and testing. This necessitates the prediction of true field behavior. The compressibility response of such soils is typical of having three zones, mechanistically explained as nonparticulate, transitional, and particulate. Such zoning has enabled the development of a simple method to predict the field compressibility response of the sample. The field compression curve with sigmact act as the most probable yield stress is considered to reflect 0% disturbance. By a comparison of experimentally determined sigmac and sigmact, it is possible to estimate the degree of sample disturbance. When the value of sigmac is closer to sigmact, the sampling disturbance approaches zero. As the value of sigmac reduces, the degree of sampling disturbance increases. The possibility of using this degree of sample disturbance from compressibility data to obtain other true properties from laboratory results of the sampled specimens has been examined.

The potential of microbial ecological indicators to guide ecosophisticated management of hydrocarbon-contaminated soils

Soil is an unrenewable natural resource under increasing anthropogenic pressure. One of the main threats to soils, compromising their ability to provide us with the goods and ecosystem services we expect, is pollution. Oil hydrocarbons are the most common soil contaminants, and they disturb not just the biota but also the physicochemical properties of soils. Indigenous soil micro-organisms respond rapidly to changes in the soil ecosystem, and are chronically in direct contact with the hydrophobic pollutants on the soil surfaces. Soil microbial variables could thus serve as an intrinsically relevant indicator of soil quality, to be used in the ecological risk assessment of contaminated and remediated soils. Two contrasting studies were designed to investigate soil microbial ecological responses to hydrocarbons, together with parallel changes in soil physicochemical and ecotoxicological properties. The aim was to identify quantitative or qualitative microbiological variables that would be practicable and broadly applicable for the assessment of the quality and restoration of oil-polluted soil. Soil bacteria commonly react on hydrocarbons as a beneficial substrate, which lead to a positive response in the classical microbiological soil quality indicators; negative impacts were accurately reflected only after severe contamination. Hydrocarbon contaminants become less bioavailable due to weathering processes, and their potentially toxic effects decrease faster than the total concentration. Indigenous hydrocarbon degrader bacteria, naturally present in any terrestrial environment, use specific mechanisms to improve access to the hydrocarbon molecules adsorbed on soil surfaces. Thus when contaminants are unavailable even to the specialised degraders, they should pose no hazard to other biota either. Change in the ratio of hydrocarbon degrader numbers to total microbes was detected to predictably indicate pollutant effects and bioavailability. Also bacterial diversity, a qualitative community characteristic, decreased as a response to hydrocarbons. Stabilisation of community evenness, and community structure that reflected clean reference soil, indicated community recovery. If long-term temporal monitoring is difficult and appropriate clean reference soil unavailable, such comparison could possibly be based on DNA-based community analysis, reflecting past+present, and RNA-based community analysis, showing exclusively present conditions. Microbial ecological indicators cannot replace chemical oil analyses, but they are theoretically relevant and operationally practicable additional tools for ecological risk assessment. As such, they can guide ecologically informed and sustainable ecosophisticated management of oil-contaminated lands.