Dissertations / Theses on the topic 'Soils Soil structure'

Bibliography: leaves 147-170. Aims to determine the influence of sodicity on the nature and decomposition of organic matter; and the influence of organic matter and its components on the structural stability of sodic soils.

Copies of author's previously published articles in pocket inside back cover. Bibliography: leaves 147-160. This thesis outlines the factors affecting soil strength and structural stability and their interrelationship in salt-affected soils. The objectives of this study are to investigate the influence of clay particles on soil densification and mellowing, the mellowing of compacted soils and soil aggregates as influenced by solution composition, the disaggregation of soils subjected to different sodicities and salinities and its relationship to soil strength and dispersible clay and the effect of organic matter and clay type on aggregation of salt-affected soils.

Persistent soil compaction by heavy-axle-load vehicles is a growing concern for the long-term productivity of clay soils. For optimum soil management, however, we must be able to evaluate adequately soil structural damages. This study compares different methods of assessing soil structure as affected by compaction and subsoiling treatments in a clay soil under corn production.
The tests used were: total porosity as calculated from densimeter readings and from soil cores; structural porosity; water desorption characteristics; and soil profile examination. These tests were performed in three layers of 20 cm and evaluation was based on their practicality and their ability to differentiate between treatments and to correlate with corn yield.
The results confirm that total porosity is a poor indicator of compaction in the subsoil. In soil profile assessments, ped descriptions were preferable to examination of pores. Water content and saturation deficit at $-$4.0 and $-$100 kPa were the best indicators of treatments and plant response.

Includes bibliographical references. The beneficial effects of tillage are often negated in Australian soils by poor aggregate structural stability. If irrigation or rain falls on exposed freshly tilled soil, crusting or harsetting often develops on drying. Rainfall intensity, kinetic energy, rate of wetting, antecedent water content and soil management history have been implicated in aggregate breakdown.

Under intensive farming, soil structure degradation and soil erosion are primarily associated with losses of organic matter. Restoration of soil structure may depend on the amount and nature of the organic amendment added. The effect of the addition of humic and fibric materials, and beeswax, a naturally occurring source of long-chain aliphatics comparable to those present in humic materials, on microbial activity and the structural properties of a waterlogged silty clay low in organic carbon was investigated. The incorporation of the fibric material increased the microbial activity in proportion to the amount of material added, whereas the humic and beeswax materials had the opposite effect. All organic materials added increased the cohesion of aggregates due to non water-dispersible cements. The fibric material was predominantly composed of polysaccharides and large quantities were required to produce a positive effect. The humic material was mainly lipids and the effect was associated with the time of incubation rather than the amount of material added. Principal-component analysis showed that the humic material was more effective at stabilizing soil aggregates than the fibric material, although the fibric material had a greater effect on the resistance of aggregates to slaking forces. Further testing with beeswax showed that the clay-associated lipids increased by 3.5-4.0 times the resistance of soil aggregates to the slaking forces, whereas the effect of hydrophobic "free" lipids was transient and accessory by coating and embedding soil aggregates.

Soils of the Argentine Pampas have been developed over same parent material (loess), but evolved under different topography and land use. This led to different soil structural behaviour. In the flooding Pampa of Argentina soils (Solonetzes) are flooded each winter-spring and dried each summer, and are grazed by livestock all year round. Little is known about cattle trampling effects under these environmental conditions. In the nearby rolling Pampa, there are silty loams affected by physical deterioration and water erosion losses after long term conventional tillage (CT). After continuous zero tillage (ZT) these soils often develop shallow compaction. Little is known about abiotic and biotic mechanisms of structural recovery. The general objective of this thesis was to analyze comparatively natural and made-man factors affecting soil structural behaviour in soils with similar parent material (loess) and vegetation (grassland), but later affected by different relief and soil use factors. In the flooding Pampa results showed the occurrence of significant soil volume changes by swelling and shrinking. Soils swell during flooding because of a process of air entrapment. Livestock trampling causes the mechanical destruction of surface macropores in summer when soil dries. The regeneration of damaged pores takes place during flooding, when soils swell at maximum. Droughts -and not floods- cause negative environmental effects in this area. In the rolling Pampa similar soil macropore volumes were determined in pasture, CT and ZT situations, showing none effect from soil management. Topsoil hardening was often found after short term ZT. Results from a greenhouse experiment showed that aggregate stabilization requires a previous fragmentation by short wetting-drying cycles. Clod shrinkage curves and soil cracking studies showed that silty loams do not have the expected poor response to W/D cycles. However, their air filled porosity increases little during drying. Results showed topsoil aggregation to be mainly abiotic in the flooding Pampa, and abiotic and biotic in the rolling Pampa, showing different structural behaviour in soils evolved from same parent material but different relief and land use.

A thermo-elastic-plastic model for unsaturated soils has been presented based on the effective stress principle considering the thermo-mechanical and suction coupling effects. The thermo-elastic-plastic constitutive equations for stress-strain relations of the solid skeleton and changes in fluid content and entropy for unsaturated soils have been established. A plasticity model is derived from energy considerations. The model derived covers both associative and non-associative flow behaviours and the modified Cam-Clay is considered as a special case. All model coefficients are identified in terms of measurable parameters. To verify the proposed model, an experimental program has been developed. A series of controlled laboratory tests were carried out on a compacted silt sample using a triaxial equipment modified for testing unsaturated soils at elevated temperatures. Imageprocessing technique was used for measuring the volume change of the samples subjected to mechanical, thermal and hydric loading. It is shown that the effective critical state parameters M, ???? and ???? are independent of temperature and matric suction. Nevertheless, the shape of loading collapse (LC) curve was affected by temperature and suction. Furthermore, the temperature change affected the soil water characteristic curve and an increase in temperature caused a decrease in the air entry suction. The simulations from the proposed model are compared with the experimental results. The model calibration was performed to extract the model parameters from the experimental results. Good agreement between the results predicted using the proposed model and the experimental results was obtained in all cases.

In this thesis primarily structural induced liquefaction potential was aimed to be analyzed. Also the effect of base isolation systems both on structural performance and liquefaction potential was studied. FLAC software was chosen for the analyses so that structure and soil could be modeled together. By these means the soil structure interaction effects were also examined. Four different structures and three different sites were analyzed under two different input motions. All the structures were also analyzed as base isolated. It was mainly found that depending on the structural type and for a certain depth the liquefaction potential could be higher under the structure than the one in the free field. Also it was concluded that base isolation systems were very effective for decreasing the story drifts, shear forces in the structure and liquefaction potential in the soil. It was also found that the interaction took place between structure, soil and input motions.

The objective of this study was to determine the correlation between potentiometric surface and the depth to selected soil morphological indicators of wetness for the Glynwood (Aquic Hapludalf), Blount (Aeric Epiaqulaf), and Pewamo (Typic Argiaguoll) soils in Delaware County, Indiana. Four years of potentiometric surface measurements were averaged and compared to detailed soil descriptions performed by the Natural Resources Conservation Service. Significant correlations exist between the morphological indicators and the potentiometric surface for the Glynwood (moderately well drained) 2-m depth piezometers and 2-m depth slotted pipes, the Blount (somewhat poorly drained) top of the C horizon and 2-m depth piezometers, and the Pewamo (poorly drained) top of the B horizon piezometers. The relationships among the horizons in which potentiometric surface correlated to indicator depth may be a function of the increased persistence and shallowness of the potentiometric surface in mid-April.
Department of Natural Resources and Environmental Management

L’objectif du travail présenté dans cette thèse est l'analyse et modélisation numérique des mécanismes de transfert de charge axiale entre sol-pieu, dans les sols granulaires. En utilisant un modèle élastoplastique tridimensionnel d'élément finis, une attention particulière est prêtée à la modélisation du comportement de l’interface sol-structure. Ainsi, les outils numériques nécessaires ont été mis en place et les outils existants ont été améliorés afin que, l'analyse de l'interaction sol-pieu soit faisable. Deux nouveaux modèles de comportement 3D sont implémentés dans le code d'éléments finis GEFDYN: un modèle d'interface et, pour le sol, une formulation axisymétrique du modèle multimécanismes de l’ECP, déjà existant et également connus sous le nom de Hujeux. La performance des deux modèles de comportement est comparée avec des résultats expérimentaux: d'abord, en utilisant des essais directs de cisaillement sol-structure et ensuite des essais de charge statiques de pieux en modèle physiques de centrifugeuse. La formulation théorique et l'exécution numérique des modèles constitutifs se sont donc avérées adéquats pour l'analyse des mécanismes de transfert de charge de sol-pieux, pour différents états initiaux du sol, différentes rugosités de la surface sol-pieux et différentes géométries. Finalement, l'applicabilité des modèles proposés est également étudiée pour un cas d’étude réel d’essais de charge statique de pieux forés et à tarière continus, menés dans le site expérimental ISC2 à l’occasion de la 2nd International Conference on the Site Characterization. L’identification des paramètres du sol et la simulation des essais de charge in-situ a été réalisé avec succés
The purpose of the work presented in this thesis, which has a theoretical and numerical character, is the analysis and numerical modelling of soil-pile load transfer mechanisms, in granular soils, when the pile is subjected to axial vertical loads. In the three dimensional elastoplastic finite element model used, particular attention is paid to modelling soil-structure interface behavior. The necessary numerical tools were implemented and the existing ones enhanced so that, the analysis of the soil-pile interaction problem is feasible. Two newly implemented 3D constitutive laws, in the GEFDYN finite element code, are proposed: an interface model and, for soil, an axisymmetric formulation of the existing ECP multimechanism model, also known as Hujeux model. The performance of both constitutive models is compared with experimental results. First, using soil-structure direct shear tests and then, using results of static pile load tests of centrifuge physical models. The theoretical formulation and numerical implementation of the constitutive models proved to be adequate for the analysis of the soil-pile load transfer mechanisms for different soil initial states, soil-pile surface roughness conditions, and different geometries. Finally, the applicability of the proposed models, is also studied for a real case study of pile static load tests carried out in the ISC'2 experimental site, at the occasion of the 2nd International Conference on the Site Characterization. Soil’s laboratory characterization tests and in-situ pile static load tests on bored and CFA piles are simulated, and results successfully compared

A constitutive model based on rate-independent elastoplasticity concepts is developed and used to simulate the behavior of geologic materials under arbitrary three-dimensional stress paths. The model accounts for various factors such as friction, stress path and stress history that influence the behavior of geologic materials. A hierarchical approach is adopted whereby models of progressively increasing sophistication are developed from a basic isotropic-hardening associative model. Nonassociativeness is introduced as correction or perturbation to the basic model. Deviation of normality of the plastic strain increments to the yield surface F is captured through nonassociativeness. The plastic potential Q is obtained by applying a correction to F. This simplified approach restricts the number of extra parameters required to define the plastic potential Q. The material constants associated with the model are identified, and they are evaluated for three different sands (Leighton Buzzard, Munich and McCormick Ranch). The model is then verified by comparing predictions with laboratory tests from which the constants were found, and typical tests not used for finding the constants. The effect of varying initial density of a material on the stress-strain and volumetric response is investigated. An empirical relation is proposed, whereby one parameter is modified based on the initial density, such that improved predictions can be obtained without increasing the total number of parameters. Implementation of the nonassociative model in a finite element program to solve boundary value problems leads to a nonsymmetric stiffness matrix. Besides, using a nonsymmetric solver, three numerical schemes are investigated. The idea of the schemes is to modify the stiffness matrix such that a symmetric equation solver can be used. Prediction of stress-strain, volumetric response and CPU time for different schemes are compared with the predictions obtained using the nonsymmetric solver. The nonsymmetric equation solver used less CPU time and the solutions were more accurate. Based on the above findings, a soil-footing system is analyzed using the finite element techniques. The associative and nonassociative models are used to predict the behavior. For the nonassociative model, solution is obtained by using a nonsymmetric solver. Results obtained from both models are compared with a model footing test performed in the laboratory.

The physical state of the seedbed is of importance to the plant environment as it influences some important processes in the soil such as seedling emergence, water and solute transport, and ease of root penetration. This is affected to a large extent by tillage process, the tillage implement type and the geometry of the implement used.
A field experiment was carried out on a clay soil to determine the effect of the geometry of bladed tillage implements on some soil physical properties after tillage. The soil properties evaluated were bulk density, mean clod size distribution and total pore space after tillage and the extent of loosening achieved.
Implement parameters considered were blade width, rake angle and depth of operation of the implement. Two blade widths of 75 and 150 mm were evaluated in combination with three rake angles of 30, 60 and 90 degrees. Each tillage implement was drawn through the soil at four operating depths of 100, 150, 200 and 250 mm.
Larger rake angles were observed to result in larger mean aggregate sizes and greater bulk density reductions when compared to smaller rake angles. Greater reduction in bulk density was observed with the wider of the two blade widths evaluated. Mean clod size after tillage was also observed to be large for the wider of the two widths evaluated. Irrespective of width and rake angle, greater operating depths resulted in larger mean clod sizes and greater reductions in bulk density as compared to shallower operating depths. Fractal analysis showed the extent of fragmentation to be greater at shallower operating depths, hence the small mean clod sizes obtained.

The understanding of the spatial distribution of lead (Pb) in soil is important in the assessment of potential risks and development of remediation strategies for Pb contaminated land. In situ heterogeneity of Pb was measured at two heavily contaminated sites in the United Kingdom using the Portable X-ray Fluorescence Spectrometer (P-XRF) over a range of spatial scales (0.02 to 50 m). The pattern of the distribution of Pb was very variable, and when expressed as heterogeneity factor (HF), it ranged from 1.2 to 3.2 (highly heterogeneous). The effect of such Pb heterogeneity on plant uptake was investigated in greenhouse pot trials. Two earlier pot trials, which assessed the effect of Pb in a fixed concentration (1000 mg/kg) and in a range of concentration (100 to 10000 mg/kg) found a significant effect of the Pb added treatments, when compared to a control treatment (0 mg/kg Pb added). Biomass and uptake varied by 20 to 100% within and between 16 species/varieties. Results enhanced the selection of two species (Brassica napus and Brassica juncea) for further pot trials. A third pot experiment with Brassica napus and Brassica juncea in simplistic binary model of heterogeneity found 20 to 60% lower uptake in the binary treatment, than homogeneous the treatment. Biomass was higher by 10 to 50% in Brassica juncea and 20 to 40% lower for B. napus in the bianary treatment, when compared to the homogeneous and control treatments. The effect of a more realistic in situ heterogeneity on plant uptake was investigated in a further pot trial, which simulated low (LH), medium) (MH) and high (HH) heterogeneity treatments, compared to a homogeneous (HO) treatment. It detected a significant (P < 0.05) impact of heterogeneity on biomass and uptake between treatments and species. Four to five fold lower biomass were recorded in HH treatment, when compared to the HO treatment. Shoot and root uptake in (mg/kg) concentration increased with increasing heterogeneity with peak uptake (twice as high as HO treatment) in LH for B. napus and in HH and MH treatments for B. juncea respectively. Shoot and root Pb masses in (μg) were maximum in HO and MH treatments respectively with 50 to 70% lower Pb mass in the HH treatment. Results showed that response to heterogeneity is species specific. A sub-experiment explored the behaviour of plant roots in HH treatment and found 20 to 80% variation in root biomass between concentric patches with same nominal soil Pb concentrations. This provided insights into varied responses of these species to realistic Pb heterogeneity. The research demonstrated that the presence and extent of in situ heterogeneity of Pb in soil plays an important role in Pb uptake by plants. It also showed that the homogeneous and simplistic binary model of heterogeneity do not give reliable estimates of plant growth and Pb uptake in realistic field conditions. This work has implications for improving the efficiency of phytoremediation of Pb contaminated land, phytomining, reliability of risk assessment and models of human exposure to Pb.

Heterogeneity of contaminants in soils can vary spatially over a range of scales, causing uncertainty in environmental measurements of contaminant concentrations. Sampling designs may aim to reduce the impact of on-site heterogeneity, by using composite sampling, increased sample mass and off-site homogenisation, yet they could overlook the small scale heterogeneity that can have significant implications for plant uptake of contaminants. Moreover, composite sampling and homogenisation may not be relevant to target receptor behaviour, e.g. plants, and studies, using simplistic models of heterogeneity have shown that it can significantly impact plant uptake of contaminants. The alternative approach, to accept and quantify heterogeneity, requires further exploration as contaminant heterogeneity is inevitable within soils and its quantification should enable improved reliability in risk assessment and understanding variability in plant contaminant uptake. This thesis reports the development of a new sampling design, to characterise and quantify contaminant heterogeneity at scales, from 0.02m to 20m, using in situ measurement techniques, and 0.005m to 0.0005m, using ex situ techniques. The design was implemented at two contaminated land sites, with contrasting heterogeneity based upon historic anthropogenic activity and showed heterogeneity varying between contaminants and at different spatial scales, for Pb, Cu and Zn. Secondly, this research demonstrates how contaminant heterogeneity measured in situ can be recreated in a pot experiment, at a scale specific to the plant under study. Results, from 4 different plant species, demonstrated that existing simplistic models of heterogeneity are an inadequate proxy for plant performance and contaminant uptake under field conditions, and significant differences were found in plant contaminant concentrations between simplistic models and those based upon actual site measurements of heterogeneity. Implications of heterogeneity on plant roots were explored in the final experiment showing significant differences in root biomass between patches of differing contaminant concentrations.

Thesis (PhD) -- Stellenbosch University, 2003.
Please refer to full text to view abstract.
ENGLISH ABSTRACT: The effects of different land use practices on soil quality in South Africa were investigated in five contrasting biomes, with a particular emphasis on the tendency of soils to crust and soil C content. Soil quality is a nebulous concept and its applicability in the South African landscape is scrutinised. A wide range of chemical and physical soil properties were examined. The tendency of soils to crust was assessed using modulus of rupture, water dispersible clay and a new method of laboratory infiltration which was verified with rainfall simulation. Crusting was greater in bare, exposed soils than soils under vegetation and varied with soil parent material. Differences in crusting are explained by factors relating to clay dispersion such as clay mineralogy, soil C, labile or readily oxidisable C, concentration of soluble salts, soil texture and exchangeable Na percentage (ESP). Results from longterm bum plots in savanna and grassland revealed that annual burning can increase the tendency of soils to crust. Greater crusting in burnt plots is ascribed to greater dispersion of clay, which in tum is attributed to a decline in soil C, a decline in EC and an increase in ESP. The loss of nutrients from burnt plots over time is ascribed to removal of ash in surface runoff. Calcium, Mg, and K were lost more readily than Na probably because plants take up these nutrients in greater concentration than Na. The net effect was an increase in ESP. Crusting on burnt plots may be self-perpetuating, because increased runoff is likely to incsease the loss of soluble salts. Removal of vegetation due to cultivation, grazing or burning reduced soil C at all sites. Mean soil C in the 0-1 cm layer of unburnt plots in the Kruger National Park was more than three times greater than in burnt plots (2.7 vs 0.8%). The difference in soil C between treatments decreased with depth and illustrated that sampling to depths greater than a few centimetres can obscure effects of land use. The top few centimetres of soil have a disproportionate effect on soil infiltrability and nutrient cycling. This layer was named the pedoderm. Tree cover on burnt plots in the southern Kruger Nationa--l- Park is highly variable, and was hypothesised to be a function of herbivory pressure. Herbivores tended to congregate on plots with the greatest clay, Zn and Mn content and the lowest tree cover. It is suggested that soil properties determine the abundance of herbivores after fire, which in tum affects tree cover. In the Eastern Cape,intensive stocking with goats transforms dense thicket to an open savanna. Soils from goat-transformed sites had a greater tendency to crust than soils from intact thicket, probably due to aggregate weakening associated with a decline in soil C. Mean soil C content of intact thicket was almost double that of goat-transformed thicket (5.6 vs. 3% to a depth of 10 cm) and is exceptionally high for a semi-arid region. The potential to sequestrate carbon in degraded thicket landscapes is thus considerable. Managing the land for greater sequestration of C will have the added benefit of increasing soil aggregate stability, reducing the tendency of soils to crust and therefore increasing the rate of water infiltration through the pedoderm. The benefits of such an approach have been recognised by specialists in soil conservation and rural land use for many decades, based largely on empirical observation. The results of this thesis provide a more quantitative basis for appreciating the effects of soil C across a broad spectrum of South African biomes.
AFRIKAANSE OPSOMMING: Die invloed van verskillende landgebruikspraktyke op grondkwaliteit in Suid-Afrika is in vyf kontrasterende biome ondersoek met spesifieke klem op die neiging van gronde om korste te vorm en die grond koolstofinhoud. Grondkwaliteit is 'n vae konsep en die toepassing daarvan in die Suid-Afrikaanse grondlandskap is noukeurig ondersoek. 'n Wye reeks van chemiese en fisiese grondeienskappe is ondersoek. Die neiging van korsvorming by gronde is beraam deur die gebruik van breukmodulus, waterdispergeerbare klei en 'n nuwe metode van laboratorium-infiltrasie wat met behulp van reënvalsimulasie gekontroleer is. Korsvorming was groter in kaal, blootgestelde gronde as in gronde met 'n plantbedekking en het gewissel volgens moedermateriaal. Verskille in korsvorming word verklaar deur faktore wat verband hou met kleidispergering soos byvoorbeeld kleimineralogie, grondkoolstof, labiele of maklik oksideerbare koolstof, konsentrasie oplosbare soute, grondtekstuur en uitruilbare natriumpersentasie (UNP). Resultate van langtermyn brandpersele in savanna en grasland het getoon dat jaarlikse brand die neiging tot korsvorming kan verhoog. Meer korsvorming in brandpersele word toegeskryf aan groter kleidispergering, wat waarskynlik verband hou met 'n afname in grondkoolstof, 'n afname in elektriese geleiding (Be) en 'n toename in UNP. Plantvoedingstowwe gaan oor tyd verlore uit brandpersele, waarskynlik deur die verwydering van as in oppervlak afloop. Kalsium, Mg en K gaan meer geredelik verlore as Na, waarskynlik omdat plante hierdie voedingstowwe in groter hoeveelhede opneem as Na. Die netto effek is 'n toename in UNP. Korsvorming op brandpersele kan self instand gehou word omdat verhoogde afloop die moontlike verlies van oplosbare soute kan verhoog. Verwydering van plantegroei deur bewerking, beweiding of brand het grondkoolstof op alle plekke verlaag. Die gemiddelde grondkoolstof in die 0-1 cm laag van ongebrande persele in die Kruger Nasionale Park was meer as drie maal groter as in --.. brandpersele (2.7 vs 0.8 %). Die verskil in grondkoolstof tussen behandelings neem af met diepte wat daarop dui dat monsterneming tot dieptes groter as 'n paar sentimeters die effek van landgebruik kan verberg. Die boonste paar sentimeters van 'n grond het 'n oneweredige invloed op infiltrasie en voedingstofsirkulasie. Hierdie laag word die pedoderm genoem. Boombedekking op brandperseie in die suidelikeKruger Nasionale Park is hoogs variërend. Die hipotese was dat dit 'n funksie van druk deur planteters is. Planteters neig om op persele met die hoogste klei, Zn- en Mn-inhoud en die laagste boom bedekking te versamel. Daar word voorgestel dat grondeienskappe die hoeveelheid planteters na 'n brand bepaal. Dit beïnvloed op sy beurt weer die boombedekking. In die Oos-Kaap het intensiewe bokboerdery digte bosruigtes verander na oop savannas. Gronde van bok-veranderde lokaliteite het 'n groter neiging tot korsvorming as gronde van onveranderde bosruigtes, vermoedelik as gevolg van verswakking van aggregate met 'n. afname in grondkoolstof. Die gemiddelde grondkoolstof van onveranderde bosruigtes was byna dubbel soveel as die koolstof van bok-veranderde bosruigtes (5.6 vs 3 % tot 'n diepte van 10 cm) en buitengewoon hoog vir 'n semi-ariede streek. Die potensiaal vir koolstof sekwestrasie in degradeerde bosruigte landskappe is dus aansienlik. Bestuur van land vir groter sekwestrasie van koolstof het die bykomende voordeel van verhoogde grond aggregaatstabilteit, verlaging van die neiging tot korsvorming en daardeur 'n verhoging in die tempo van waterinfiltrasie deur die pedoderm. Die voordele van so 'n benadering is vir baie dekades deur spesialiste in grondbewaring en landelike landgebruik herken. Dit was grootliks gebaseer op empiriese waarneming. Die resultate van hierdie tesis bied 'n meer kwantitatiewe basis tot die verstaan van die invloed van grondkoolstof oor 'n breë spektrum van Suid-Afrikaanse biorne.

The main objective of this research was to determine the short-term effects of cropping on the aggregation and the carbohydrate fraction of a marine clay soil. When compared to a fallow (bare soil) control, cropping to barley and alfalfa for two seasons resulted in significant increases in the size and stability of soil aggregates. The increase in water-stable aggregates $>$2.0 mm was at the expense of aggregates $<$1.0 mm. Under corn, soil aggregation was not different than under fallow. After two seasons, soil under barley or alfalfa contained 15 to 25% more carbohydrates than the fallow or corn treatments. The partial correlation (r = 0.63, P = 0.001) which was observed between carbohydrate content and mean weight diameter of water-stable aggregates, and periodate oxidation tests strongly suggested that carbohydrates were at least partly responsible for the increase in macro-aggregate stability. The remaining cropping effects were removed by tetraborate which suggest the participation of more-humified though ill-defined organic matter. The nature of the changes in organic matter was further investigated using particle size fractionation. Compared to the fallow control, cropping to barley and alfalfa resulted in an enrichment in carbon, nitrogen, and carbohydrates in the sand fraction. The carbohydrate composition of the soil and of its size fractions, determined by liquid chromatography, suggested that cropping treatments had only little effect on the origin of the soil carbohydrates.

The Ethiopian Highlands have been studied extensively, hosting a large amount of research for development projects in agriculture and forestry over several decades. The encounters in these projects were also encounters of different ways of knowing that were negotiated by the actors meeting in the space provided by the projects. This research explores these encounters and the social worlds they are embedded in, drawing on actor-oriented approaches as well as theories of narratives and framing. Ways of knowing and citizen epistemologies are taken as a lens to understand the role of identities in knowledge production and use. The two case studies were agroforestry research projects in the Ethiopian Highlands. The research followed a range of qualitative and ethnographic research methods. Different types of farmers and scientists meet in the case studies. I recognise that they all have individual agency, nevertheless I use the terms ‘scientist' and ‘farmer' in this thesis. I use the terms to describe certain groups of actors who all draw on different ways of knowing, and different value systems, when interacting with each other and their environment. The results indicate that the importance of social worlds at different scales and the contexts of research projects tend to be underestimated. In spite of good intentions scientific methodologies, terminologies and narratives tend to dominate. Scientists in the case studies acknowledged the existence of farmers' ‘indigenous' knowledge, but they determined the value of knowledge by its scientific applicability and the replicability of experiments. Research systems force the scientists into a certain modus operandi with limited possibilities to experiment and to respond to the complexities and diversities of people's social worlds. Farmers in the case studies preferred observation from their parents, observing from others or the environment as a way of learning and gaining knowledge. Depending on their personalities and their life histories they also relied on alternative ways of knowing rooted in spirituality, emotions and memories. Powerful influences on ways of knowing resulted from the way languages and authority had been used. These often led to the exclusion of marginalised community members from access to knowledge and technologies. Unfortunately, common narratives prevailed in the case studies, and alternative ways of knowing were often marginalised. By acknowledging different ways of knowing and the importance of different social worlds and different ways of doing research, both scientists and farmers could benefit and develop more sustainable pathways for agricultural and forestry land use.

A field tillage tool carrier was constructed using a tractor trailer, hydraulic cylinder and steel construction material. Tillage tool blades of varying lengths, widths and angles of attack were fabricated from steel and were used in the study of the effect of tool rake angle, tool width and depth of operation on soil strength properties, draft, draft efficiency, volume of soil manipulated, degree of soil loosening and penetration resistance.
The results showed that the draft increased with tool rake angle and width. Operating at a depth of 150 mm and 100 mm depth did not make any significant difference on the draft requirement. Low angles of attack were observed to have a greater potential to loosen the soil, and the loosening increased to a depth of 150 mm then decreased. The draft efficiency was affected by the angle of attack as well as the depth of operation. The cross sectional area of the furrow and hence the volume of soil manipulated was seen to depend on the width of the tool and the operating depth.
Slender tools and high rake angles were found to loosen the soil better than wide ones. No distinct trend existed between depth to width aspect ratio and draft requirement. No variation was observed between draft efficiency and d/w ratio. Penetration resistance increased with depth of operation as well as distance from the furrow centre after tillage. Some areas of residual high strength were sometimes left within the sphere of influence of the tools. Some tools dealt with these omissions better than others.

Title from PDF of title page (University of Missouri--Columbia, viewed on March 2, 2010). The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file. Dr. William Likos, Thesis Supervisor. Vita. Includes bibliographical references.

The study aimed to determine the interrelationship between aggregate stability and microbial biomass in restored soils, and to investigate if the development of the two parameters in soils disturbed by opencast mining could be influenced by the application of slow release organic amendments. These objectives were tested using two microbiological methods; determination of adenosine triphosphate and dehydrogenase activity, and three structural measurements; determination of aggregate stability by wet-sieving, shear vane and bulk density. Soil carbon and nitrogen were also determined. The first part of the study involved a survey of 16 field areas located in Britain, 12 disturbed and four not disturbed by opencast coal mining. The areas were all grasslands which varied in the time since restoration, which was between 0-16 years. A log linear relationship between the soil biomass and stable aggregates > 2 mm was found for all field areas (y = 38 In x - 69, r = 0.51). The variation in both properties was also affected by the restoration practices at the individual sites. A cluster analysis of the measured soil properties separated the restored areas into "good" restorations, involving progressive restoration, topsoil replacement and early underdrainage, and "poor" restorations, restored without topsoil or with soil forming material. The second part of the study reported on the first 16 months of a field trial set up on a recently restored opencast coal site situated near Denby in Derbyshire in 1991. A 3 x 4 factorial design involved two organic amendments (straw and wood), and four vegetation covers. The treatment effects were obscured by natural fluctuations in the soil properties over the period studied. However, the presence of the organic amendments alleviated some of the physical problems of the soil, such as waterlogging and frost damage, which drastically affected the results in 1992. The soil properties generally improved in the order straw>wood>no amendment for the majority of soil parameters (structure, C and N), the notable exception being the soil microbiological parameters which varied substantially throughout the experiment. Differences between the vegetation covers (a MAFF, a ruderal and a species rich seed mixture) were small.

Orientadores: Zigomar Menezes de Souza, Edson Eiji Matsura
Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Agrícola
Made available in DSpace on 2018-08-22T04:49:55Z (GMT). No. of bitstreams: 1 Araujo_FernandoSilva_D.pdf: 5020372 bytes, checksum: af978a8271ef4c982fd82d0d223e486b (MD5) Previous issue date: 2012
Resumo: É crescente a demanda global por fontes de energia renováveis, tais como o etanol, o qual no Brasil, possui como principal matriz energética a cultura da cana-de-açúcar. Neste contexto faz-se necessário a incorporação de novas tecnologias, como a mecanização da colheita, para o uso racional das áreas manejadas com cana-de-açúcar. O acúmulo superficial de resíduos vegetais da cana-de-açúcar na superfície do solo promove o enriquecimento das camadas superficiais com matéria orgânica bem como o incremento do intervalo hídrico ótimo, mitigando os efeitos da compactação do solo causados pelo tráfego de máquinas no sistema de cana colhida mecanicamente sem queima. Portanto, o objetivo deste trabalho foi estudar as alterações no comportamento físico e mecânico de um Latossolo Vermelho produzido pelo enriquecimento do conteúdo de matéria orgânica e, ainda, a capacidade dos resíduos vegetais acumulados na superfície do solo dissiparem cargas aplicadas sobre o mesmo, em áreas cultivadas com cana-de-açúcar colhidas com e sem queima. O projeto foi desenvolvido em três áreas cultivadas com cana-de-açúcar: 1- cana-de-açúcar sem queima e corte mecanizado, desde 1996 (com 16 anos de implantação do sistema de cana crua); 2- cana-de-açúcar sem queima e corte mecanizado, desde 2004 (com 8 anos de implantação do sistema de cana crua); 3- cana-de-açúcar com queima e corte manual, desde 1973 (cana queimada). Os atributos físicos avaliados foram: análise granulométrica, consistência do solo, densidade do solo, estabilidade de agregados, porosidade do solo e resistência do solo à penetração nas profundidades de 0,00-0,10 m, 0,10-0,20 m e 0,20-0,30 m. Determinou-se ainda o intervalo hídrico ótimo para desenvolvimento das plantas. Foram avaliadas as relações entre o teor de matéria orgânica e a compressibilidade do solo, as relações entre teor de matéria orgânica do solo e a umidade crítica para a compactação e as relações entre quantidade de resíduos vegetais na superfície e a densidade do solo obtida pelo teste Proctor. Os atributos de solo estudados apresentam estrutura de dependência espacial. O intervalo hídrico ótimo e ?p mostraram-se sensíveis as alterações ocorridas no solo em detrimento dos sistemas de manejo estudados. A área sob colheita manual da cultura da cana-de-açúcar apresentou menor valor de densidade crítica para o intervalo hídrico ótimo, sendo que a maior produtividade da cultura concentrou-se nas regiões de maior amplitude do intervalo hídrico ótimo e maior capacidade suporte de carga do solo
Abstract: An increasing global demand for renewable energy sources such as ethanol, which in Brazil, has as its primary energy matrix culture of sugar cane. In this context it is necessary to incorporate new technologies, mechanization of the harvest, for the rational use of managed areas with cane sugar. The accumulation of surface plant residues of sugar cane on the soil surface promotes the enrichment of the surface layers with organic matter as well as increasing the optimal water, mitigating the effects of soil compaction caused by machinery traffic on the system cane mechanically harvested without burning. Therefore, the aim of this work was to study the changes in physical and mechanical behavior of soil produced by enriching the content of organic matter, and also the ability of plant debris accumulated on the soil surface dissipate loads applied on it, in cultivated areas sugar cane harvested with and without burning. The project was developed in three areas cultivated with sugar cane: 1 - harvested with manual cutting and burning since 1973; 2 - mechanically harvested without burning since 2004 (8 years of implantation of sugarcane), 3 - mechanically harvested unburned since 1996 (16 years of implantation of sugarcane). The physical attributes were: particle size analysis, soil consistency, soil bulk density, and aggregate stability, soil porosity and soil resistance to penetration depths of 0.00 to 0.10 m, 0.10-0.20 me 0.20-0.30 m. It was determined the optimal water yet to identify the critical limits of soil density where resistance to penetration and aeration porosity are restrictive to plant development. We evaluated the relationship between the organic matter content and soil compressibility, the relationships between organic matter content and soil moisture critical for the compression and the relationship between the amount of crop residue on the surface and soil density obtained by the Proctor test. The soil attributes have studied the spatial dependence structure. The least limiting water range and ?p were sensitive to changes in the soil instead of studied treatments. The area under cultivation of manual harvesting cane sugar showed a lower value of the critical density for optimal water, and the greater crop concentrated in regions of higher altitude and lower load-bearing capacity
Doutorado
Agua e Solo
Doutor em Engenharia Agrícola

Title from PDF of title page (University of Missouri--Columbia, viewed on Feb 25, 2010). The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file. Dissertation advisor: Dr. Erik Loehr. Vita. Includes bibliographical references.

Thesis (MSc (Microbiology))--University of Stellenbosch, 2010.
ENGLISH ABSTRACT: The relationship between various land management practices, soil properties and the soil microbial communities are complex and little is known about the effect of these interactions on plant productivity in agricultural systems. Although it would be advantageous to have a single organism or property that can be used as a measure of soil health, it may not be possible. Soil organisms which include both the microorganisms as well as soil fauna are subjected to the effect of their immediate environment. This microenvironment in turn is determined by the soil properties as well as above ground flora and their interactions. Most soil indicators interact with each other, and these interactions can modify or influence the soil properties. The complexities of the interactions between critical soil indicator values often preclude its practical use by land managers and policy makers. However, soil microbial communities (e.g. diversity and structural stability) may serve as a relative indicator of soil quality. These communities are sensitive to land management practices and changes in the microenvironment. The objective of this study was to gain an understanding of the complex relationships by investigating the effect of conventional, integrated and organic apple production systems on the physical, chemical and biological (particularly soil microbial diversity) properties of the soil. Automated Ribosomal Intergenic spacer analysis (ARISA) was used to characterise fungal (F-ARISA) and bacterial (B-ARISA) communities from soil samples obtained from an experimental apple orchard in Elgin, Grabouw. The intergenic spacer (ITS) region from the fungal rRNA operon was amplified using ITS4 and fluorescently FAM (6- carboxylfluorescein) labelled ITS5 primers. Similarly, the 16S-23S intergenic spacer region from the bacterial rRNA operon was amplified using ITSR and FAM-labelled ITSF primers. The sensitivity of the technique allowed us to discriminate between the soil microbial communities of the different treatments. From our results we observed significant increase (p < 0.05) in the fungal community diversity between the February and April samples, while the bacterial community diversity was consistent (p > 0.05). Also, treatments with mulch showed a significantly higher microbial diversity than the other treatments at a 5 % significance level. Fungal communities showed significant correlation with the potassium concentration in the soil, while bacterial communities depicted a significant correlation with the soil phosphorous concentration. Based on the results we concluded that different management practices have a significant effect on the soil microbial communities and that these communities are particularly sensitive to small changes in the environment. However, there is still a need to determine what the composition of the soil microbial communities are to be able to correlate our observations with soil health.
AFRIKAANSE OPSOMMING: Die verhouding tussen verskillende landboubestuurspraktyke, grondeienskappe en die mikrobiese gemeenskappe in grond is kompleks en weinig is bekend oor die uitwerking van hierdie interaksies op die produktiwiteit van landboustelsels. Alhoewel dit voordelig sou wees om ‘n enkele organisme of eienskap te kan hê wat die gesondheid van grond kan meet, sal dit dalk nie moontlik wees nie. Grondorganismes wat die mikroörganismes sowel as die grondfauna insluit, is onderworpe aan die invloed van hulle onmiddelike omgewings. Hierdie mikro-omgewings op hulle beurt word weer beïnvloed deur die grondeienskappe sowel as die die oppervlak flora en hulle wisselwerkinge. Meeste van die grondaanwysers toon ook wisselwerkinge met mekaar, en hierdie wisselwerkinge kan die grondeienskappe beïnvloed or selfs verander. Die kompleksiteit van die wisselwerkinge tussen kritiese grond aanwysers is meestal die rede waarom dit nie deur grondbestuurders en beleidsmakers gebruik word nie. Dit is ongeag die feit dat grond mikrobiese gemeenskappe (bv. diversiteit en stukturele stabiliteit) mag dien as ‘n relatiewe aanwyser van grondkwaliteit. Hierdie gemeenskappe is sensitief vir bestuurspraktyke en veranderinge in die mikro-omgewing. Die doel van die studie was om die ingewikkelde verhoudings in die grondgemeenskappe te bestudeer en die uitwerking van konventionele, geïntegreerde en organiese appel produksie sisteme op die fisiese, chemiese en biologiese eienskappe (veral die grond mikrobiologiese diversiteit) te bepaal. Geoutomatiseerde Ribosomale Intergeniese Spasie Analise (ARISA) is gebruik om die fungus (F-ARISA) en bakteriese (B-ARISA) gemeenskappe van grondmonsters wat vanaf ‘n proef appelboord in Elgin (Grabouw) verkry is, te bepaal. Die intergeenspasie (ITS) area van die fungus rDNA operon is vermeerder deur die ITS4 en fluoresserende FAM (6-karboxylfluorescein) gemerkte ITS5 inleiers te gebruik. Soortgelyk is die 16S-23S intergeenspasie area van die bakteriese rDNA operon vermeerder deur ITSR en FAM-gemerkte ITSF inleiers te gebruik. Die sensitiwiteit van die tegniek laat ons toe om te onderskei tussen die grond mikrobiese gemeenskappe vanaf verskillende grondbehandelings. Vanuit die resultate kon ons aflei dat daar ‘n toename (p < 0.05) in die fungus gemeenskap diversiteit vanaf Februarie to April was terwyl die bakteriese gemeenskap ‘n konstante diversteit getoon het (p > 0.05). Behandelings met grondbedekking het ook ‘n beduidend hoër mikrobiese diversiteit getoon as ander behandelings. Fungus gemeenskappe het beduidende korrelasies getoon met kalium konsentrasies in die grond, terwyl bakteriese gemeenskappe ‘n beduidende korrelasie getoon het met grond fosfor konsentrasies. Gebaseer op die resultate kon ons aflei dat verskillende bestuurspraktyke ‘n uitwerking kan hê op die grond mikrobiese gemeenskappe en dat hierdie gemeenskappe sensitief is vir klein veranderinge in die omgewing. Dit sal egter nog nodig wees om die spesifieke samestelling van die grond mikrobiese gemeenskappe te bepaal voor ons hierdie waarnemings kan korreleer met grondgesondheid.

Little is known about the original properties of soils in the East. Eight virgin soils and associated southern Appalachian hardwood vegetation were studied in western North Carolina. The study sites ranged in elevation from 720 to 1200 m on steep slopes. Overall these soils are quite deep and highly weathered due to high rainfall (>200 cm) and soluble feldspathic parent material. Organic matter contents of the surface·horizons were quite high (4.5 - 16 %), and they contained moderate to strong crumb structure. All but one soil contained cambic subsurface horizons and were either Typic Haplumbrepts or Umbric Dystrochrepts. The majority of soils in the watershed are formed in colluvium, but significant amounts of residual soils occur on sideslopes, and appear to be quite stable. The present day landforms appear to be the result of periglacial activity. North-facing soils were higher in whole soil clay, organic matter, and A horizon exchangeable cations than south-facing soils. Cation exchange capacity in these soils is almost totally dependent on organic matter content, and the mineral fraction is relatively inert. All soils were in the oxidic mineralogy class. Bibbsite was common throughout all soils and hydroxy-interlayered vermiculite (HIV) is the dominant clay-sized phyllosilicate in surface horizons. Kaolinite was low in all soils, but was more abundant on south-facing slopes. The silt fractions and sand fractions contained significant quantities of weathered 2:1-type minerals The vegetation varied from mixed-mesophytic cove hardwoods on north-facing slopes to mixed oak-hickory and oak-pine on south-facing slopes. Many trees in coves exceed 1.3 m in diameter and 50 m in height. Total litter production averaged 3494 kg/ha, and the litter layers were typified by thin leaf (L), and well developed fermentation (F) and humus (H) layers. Cations and P are concentrated in the litter layers and immediate surface soil, while N is mixed deep into the profile. Due to their oxidic mineralogy, low CEC, decreasing clay content with depth, and concentration of cations and P in litter and standing biomass these soils highly resemble tropical Oxisols.
Ph. D.

The objective of this research was to further understand the behavior of the soil under the action of a tillage tool, with the purpose of finding a relation between the tool geometry and the resultant soil seed bed. Thus the problem consisted of understanding the mechanics of producing soil break up and to find a logical method of analyzing it.
The problem was solved using fundamental principles of soil mechanics and force equilibrium analyzis. As a result, a mathematical model was developed which describes three failure zones within the cut soil volume. The model can be programmed into a computer to generate maps of normal and shear stresses to visualize the three failure zones.
The failure zones are the shear failure zone, the tensile fracturing zone and the no failure zone. The tensile fracturing zone is delimited by the tensile stress reaching the tensile strength of the soil at the given soil moisture content and soil density. The tensile strength of the soil was measured using an apparatus and method designed in this research.
The mathematical model gives an explanation of the mechanics of crumbling and the shape of the failed volume, but it does not give information concerning soil aggregate quality and arrangement within the soil furrow. Then, a method of analyzing the formed aggregates was developed which considers some soil physical properties of aggregates.
The study concluded that the smaller tool width and the smaller tool rake angle, among the ones used in this research, produced the most efficient geometry in producing the largest amount of soil break up, the most uniform aggregate formation and the most stable aggregate arrangement. The same tool geometry requires less energy per unit volume of soil disturbed. The best performance is produced at the lowest soil water content among those tested.

Se ha llevado a cabo:

A) Un estudio de las propiedades básicas del suelo no saturado (tipo limo) a escala microestructural, incluyendo esqueleto sólido, fase liquida y fase gaseosa.

B) Elaboración de un modelo conceptual discontinuo de comportamiento. La geometría interna esta construida por partículas, agua retenida en forma de meniscos alrededor de los contactos y aire ocupando los restantes poros. La interfase liquido gas esta gobernada por la succión y la tensión superficial. Los meniscos tienen un efecto rigidizador del esqueleto.
Se observa la posible redistribución de la humedad y del aire, quedando acoplados en definitiva los aspectos mecánicos y de flujo.

C) En base a lo anterior, implementación de un modelo numérico discontinuo de ensayo de comportamiento basado en ordenador. Se ha adaptado y modificado el D.E.M. de P.A. Cundall (diferencias finitas explicitas en el tiempo), indicado en el caso que se trata, con no-linealidades geométricas. Se han desarrollado importantes algoritmos de control geométrico.

D) Verificación parcial del modelo y aplicación a casos típicos en suelo no saturado, especialmente el colapso.

En conjunto es una herramienta útil para su estudio y permite apreciar algunos interesantes mecanismos de actuación de la succión a escala microscópica.

Se ha llevado a cabo:A) Un estudio de las propiedades básicas del suelo no saturado (tipo limo) a escala microestructural, incluyendo esqueleto sólido, fase liquida y fase gaseosa. B) Elaboración de un modelo conceptual discontinuo de comportamiento. La geometría interna esta construida por partículas, agua retenida en forma de meniscos alrededor de los contactos y aire ocupando los restantes poros. La interfase liquido gas esta gobernada por la succión y la tensión superficial. Los meniscos tienen un efecto rigidizador del esqueleto.Se observa la posible redistribución de la humedad y del aire, quedando acoplados en definitiva los aspectos mecánicos y de flujo.C) En base a lo anterior, implementación de un modelo numérico discontinuo de ensayo de comportamiento basado en ordenador. Se ha adaptado y modificado el D.E.M. de P.A. Cundall (diferencias finitas explicitas en el tiempo), indicado en el caso que se trata, con no-linealidades geométricas. Se han desarrollado importantes algoritmos de control geométrico. D) Verificación parcial del modelo y aplicación a casos típicos en suelo no saturado, especialmente el colapso.En conjunto es una herramienta útil para su estudio y permite apreciar algunos interesantes mecanismos de actuación de la succión a escala microscópica.

Thesis (M. Phil.)--University of Hong Kong, 1994.
Some illustrations are mounted photos. Some illustrations accompanied by transparent guard sheets with outline drawings. Includes bibliographical references (leaves 234-244).

Thesis (Ph.D.)--University of Missouri-Columbia, 2004.
(tm) after EM in title is for Trademark symbol. Typescript. Vita. Includes bibliographical references (leaves 120-142). Also available on the Internet.

Four fields of 117 ha area located at the University of Arizona's Maricopa Agricultural Center were selected for this study. Two soil series, the Casa Grande sandy clay loam and Trix clay loam occur. Surface samples (0-25 cm) were collected on a 98 m interval and 3 rows providing 47 sites per field. Sites were classified either as surveying (32) or testing (15) in each of the four fields. Additional samples at 25-50, 50-75, 75-100, and 100-125 cm were obtained with duplicate surface undisturbed cores at 5 sites per field. Soil parameters include bulk density, saturated hydraulic conductivity, moisture retention, particle size analysis, pH, EC, soluble cations, SAR, and ESP. A quantification of the spatial interdependence of samples was developed based on the variogram of soil parameters. A linear model was best fitted to the clay, EC, Ca²⁺, Mg²⁺, Na⁺, SAR and ESP, and a spherical model to the sand, silt, pH, and K⁺ observed variograms. A comparison of variograms obtained conventionally and with the robust estimation of Cressie and Hawkins (1980) for sand and Ca²⁺ were performed with a fixed couples number per class and with a fixed class size. Additionally, a negative log-likelihood function along with cross-validation criteria were used with the jackknifing method to validate and determine variogram parameters. Three interpolation techniques have been compared for estimating 11 soil properties at the test sites. The techniques include Arithmetic Mean, Inversely Weighted Average, and Kriging with various numbers of neighbor estimates. Using 4 point estimates resulted in nearly identical results, but the 8 point estimates gave more contrast for results among the alternative techniques. Jackknifing was used with 4, 8, 15, 25 neighbors for estimating 188 points of sand and Ca²⁺ with the three techniques. Sand showed a definite advantage of Kriging by lowering the Mean Square Error with increasing neighbor number. The simple interpolator Arithmetic Mean was comparable and sometimes even better than the other techniques. Kriging, the most complex technique, was not the absolute best interpolator over all situations as perhaps expected. The spatial dependence for the 11 soil variables was studied by preparing contour maps by punctual Kriging. Sand and Ca²⁺ were also mapped by block Kriging estimates.

Soil microbial communities mediate important ecological processes and play essential roles in biogeochemical cycling. Ecosystem disturbances such as surface mining significantly alter soil microbial communities, which could lead to changes or impairment of ecosystem functions. Reforestation procedures were designed to accelerate the reestablishment of plant community and the recovery of the forest ecosystem after reclamation. However, the microbial recovery during reforestation has not been well studied even though this information is essential for evaluating ecosystem restoration success. In addition, the similar starting conditions of mining sites of different ages facilitate a chronosequence approach for studying decades-long microbial community change, which could help generalize theories about ecosystem succession. In this study, the recovery of microbial communities in a chronosequence of reclaimed mine sites spanning 30 years post reforestation along with unmined reference sites was analyzed using next-generation sequencing to characterize soil-microbial abundance, richness, taxonomic composition, interaction patterns and functional genes. Generally, microbial succession followed a trajectory along the chronosequence age, with communities becoming more similar to reference sites with increasing age. However, two major branches of soil microbiota, bacteria and fungi, showed some contrasting dynamics during ecosystem recovery, which are likely related to the difference in their growth rates, tolerance to environmental change and relationships with plants. For example, bacterial communities displayed more intra-annual variability and more complex co-occurrence networks than did fungi. A transition from copiotrophs to oligotrophs during succession, suggested by taxonomic composition shifts, indicated that the nutrient availability is one important factor driving microbial succession. This theory was also supported by metagenomic analysis of the functional genes. For example, the increased abundance of genes involved in virulence, defense and stress response along ages indicated increased competition between microorganisms, which is likely related to a decrease of available nutrients. Metagenomic analysis also revealed that lower relative abundances of methanotrophs and methane monooxygenase at previously-mined sites compared with unmined sites, which supports previous observations that ecological function of methane sink provided by many forest soils has not recovered after 30 years. Because of the difficulty identifying in situ functional mechanisms that link soil microorganisms with environmental change, modeling can be a valuable tool to infer those relationships of microbial communities. However, the extremely high richness of soil microbial communities can result in extremely complicated models that are difficult to interpret. Furthermore, uncertainty about the coherence of ecological function at high microbial taxonomic levels, grouping operational taxonomic units (OTUs) based on phylogenetic linkages can mask trends and relationships of some important OTUs. To investigate other ways to simplify soil microbiome data for modeling, I used co-occurrence patterns of bacterial OTUs to construct functional groups. The resulting groups performed better at characterizing age-related microbial community dynamics and predicted community structures and environmental factors with lower error.
PHD

Thesis (MScAgric)--Stellenbosch University, 2013.
ENGLISH ABSTRACT: Soil is a fundamental, non-renewable resource in any ecosystem. To uphold food production for increasing global human populations, it is imperative to develop ways in which to sustain healthy biological productivity and sustainability of agricultural soils. Nematodes are one of the most abundant groups of Metazoa occurring in all soils, and form an integral part of the soil food web at several trophic levels. They respond rapidly to changes within their environments, and can easily be extracted from soil, identified and characterised into functional guilds. Nematodes thus have the potential to impart insight into the condition of the soil food web. This study aims to establish whether nematodes will be suitable bio-indicators of soil health for the deciduous fruit industry in the Western Cape. Three different objectives have been set to determine the practical use of nematode community structures as a tool for the measurement of soil health. The objectives include describing the nematode community structure, biodiversity and functionality within Fynbos soils; the characterization of organic and conventional orchards; and the differences in nematode soil communities in differently managed soils in an apple orchard. The number of nematodes in each soil sample was quantified and identified to family level. The nematode biodiversity and functionality for each site was determined by evaluating the nematode food webs for trophic group distribution, as enumerated by the Maturity Index (MI), the Enrichment Index (EI), the Structure Index (SI), the Basal Index (BI) and the Channel Index (CI), based on the weighted abundance of coloniser-persister guilds. The functional guild analysis of Fynbos samples indicated that the enrichment and the structure of any given sample were not bound to a certain area, but it was representative of each of the four quadrats within the faunal analysis. Different geographic areas were found to differ in nematode diversity and functionality, which was mainly associated with dominant plant families and species (such as strong associations between Fynbos families Fabaceae, Solanaceae and Celestraceae with the nematode family Pratylenchidae). The most abundant nematode families present in the Fynbos were Tylenchidae, which are plant-feeding nematodes, and Cephalobidae which are bacterial-feeding nematodes. Despite Tylenchidae and Cephalobidae both having coloniser-persister values (cp-values) of two, they are split up into different feeding types. Cp-2 nematodes are tolerant to disturbances, and occur in all environments. Only one omnivorous family, the Dorylaimida, was identified in Fynbos samples. The average MI value for Fynbos was found to be very low, with a mean value of 1.26. The value obtained indicated the presence of taxa with tolerance to disturbance, which, in turn, indicated the presence of a disturbed soil, in general. The number of plant-parasitic nematodes within the Fynbos soils was low, which was supported by the low plant-parasitic index (PPI) of 0.85. The diversity, richness and evenness values were low, indicating low nematode diversity, but a distribution of abundances amongst the families. The average Hill’s N0 index value was 8.0, indicating that, in general, eight nematode families would have been present in a Fynbos soil sample. A study was done to determine the biodiversity and the functionality of the nematodes associated with deciduous fruit orchards that were conventionally, or organically, managed. Herbivores were dominant in all the orchards. The organic apple orchard had the lowest numbers of herbivores and fungivores, with the highest number of carnivores. When comparing organic and conventional apricot orchards, higher numbers of plant-parasitic nematodes were found in the organic orchard. Criconematidae occurred in higher numbers in conventional apricot orchard soil. When comparing organic apricots and apples, higher numbers of Criconematidae occurred within the organic apple soil. Overall, higher levels of plant-parasitic nematodes occurred in the organic apricot orchard. The MI indicated that all orchard soils had values below 1.5, indicating disturbance. Conventionally managed apricot orchard soil had the highest MI value of 1.48. The PPI value was highest in organically managed apricot orchards. All orchard soils were located within Quadrat B of the faunal analysis, indicating enrichment and structure. Regarding the diversity, richness and evenness of the distribution, conventional apricot soil had the highest species richness, while organic apple soil had the most even family distribution. Different management practices did not show marked differences in community composition and structure. The species richness of Fynbos soils was comparable to those of deciduous fruit orchards. Soil samples from eight different soil surface treatments were collected from an apple orchard in the Grabouw area. Treatments were combined according to the soil surface treatments received (chemical control of cover crops and weeds, mulch and mulch + effective micro-organism spray). Bacterivores were dominant in all soil treatments, with the least number being present in the chemical control (of cover crops and weeds) treatment. Sites which received chemical control of cover crops and weeds had higher levels of fungivores, compared to the levels at the other sites. High numbers of Rhabditidae occurred within mulch and mulch + effective micro-organism (EM) treatment sites, while high numbers of Aphelenchidae occurred in chemical control sites. The carnivorous family Ironidae only occurred in mulch + EM sites. Strong associations were found between soil surface applications and nematode families present within the soil. Chemical control (of cover crops and weeds) applications had the highest MI value, while values were equal for the other soil applications. The faunal analysis indicated that the mulch and the chemical control fell within Quadrat A, indicating enriched, but unstructured, soil, while the mulch + EM treatment fell within Quadrat B, indicating enrichment and structure, as well as good overall soil conditions. All the systems were dominated by bacterial decomposition pathways. Controversially, sites that received chemical control of the cover crops and weeds had the highest species richness of all three applications, as well as the highest level of diversity, according to the Simpson Index. As only the cover crops and the weeds were chemically controlled, the soil can be regarded as undisturbed, which explains the results obtained in this study. Clear differences in nematode community structure and composition were observed between the different soil applications in the apple orchard.
AFRIKAANSE OPSOMMING: Grond is 'n fundamentele, nie-hernubare hulpbron binne enige ekosisteem. Ten einde voedselproduksie vir die toenemende globale menslike bevolking te handhaaf, is dit noodsaaklik om maniere te ontwikkel om gesonde biologiese produktiwiteit en volhoubaarheid van landbougrond in stand te hou. Nematodes is een van die volopste Metazoa in alle gronde en vorm 'n integrale deel van die grond voedsel-web op verskeie trofiese vlakke. Hulle reageer vinnig op veranderinge binne hul omgewings, kan maklik ekstraheer en identifiseer word; en ook maklik in funksionele gildes ingedeel word. Nematodes het ook die potensiaal om insig oor te dra ten opsigte van die toestand van die grond voedsel-web. Hierdie studie het ten doel om vas te stel of nematodes geskikte bio-indikatore van grond gesondheid kan wees spesifiek vir die sagtevrugte bedryf in die Wes-Kaap. Drie verskillende doelwitte is gestel om die praktiese gebruik van nematode populasie samestelling as 'n instrument vir die meting van grond gesondheid te gebruik. Die doelwitte sluit in die nematode populasie samestelling, biodiversiteit en funksionaliteit binne natuurlike Fynbos; organies verboude versus konvensionele boorde; en die verskil in nematode populasie samestelling tussen verskillend behandelde en bestuurde grondpersele binne ʼn appel boord. Die nematode biodiversiteit en funksionaliteit vir elke perseel was bepaal deur die evaluering van die nematode voedselweb vir trofiese groep verspreiding en enumerering deur die Maturity Index (MI) en die Enrichment Index (EI), Strukturele Indeks (SI), Basale Indeks (BI) en Channel Index (CI) wat gebaseer is op die geweegde oorvloed van koloniseerder-persister gildes. Die funksionele gilde vir Fynbos monsters het aangedui dat die verryking en struktuur van enige gegewe perseel nie gebonde is aan ʼn bepaalde gebied nie, aangesien dit verteenwoordig was in elk van die vier kwadrante van die Fauna Analiseerder. Daar is gevind dat verskillende areas verskil in nematode diversiteit en funksionaliteit, wat hoofsaaklik geassosieer was met die dominante plant families en spesies in die omgewing. Die volopste nematode familie wat teenwoordig was in die Fynbos was Tylenchidae, wat plant-voedende nematodes is, en Cephalobidae, wat bakterie-voedend is. Tylenchidae en Cephalobidae het beide ʼn cp-waarde van twee, maar is verdeel in verskillende VIII tipes voedingsgroepe. Die cp-2 nematodes is verdraagsaam vir versteurings en kom in alle omgewings voor. Slegs een omnivoor familie is geïdentifiseer in Fynbos monsters, nl. die Dorylaimidae. Die gemiddelde MI waarde vir Fynbos was laag, met 'n gemiddelde waarde van 1.26. Hierdie waarde is ʼn aanduiding van die teenwoordigheid van taxa met verdraagsaamheid tot versteuring, wat op sy beurt 'n versteurde grond in die algemeen aangedui het. Die aantal plant-parasitiese nematodes binne die Fynbos-gronde was laag, wat ondersteun word deur die lae PPI-waarde van 0.85. Die waardes vir die diversiteit, spesie-rykheid en egaligheid was laag, wat dui op 'n lae nematode diversiteit, maar 'n egalige verspreidings onder families. Die Hill’s N0 indeks waarde was gelyk aan 'n gemiddelde van 8.0 en dui daarop dat in die algemeen agt nematode families teenwoordig sal wees in 'n Fynbos grondmonster. 'n Studie is gedoen om die biodiversiteit en funksionaliteit van nematodes wat verband hou met vrugteboorde wat organies en konvensioneel bestuur is te bepaal. Herbivore was dominant in alle boorde. Organiese appels het die laagste aantal herbivore en fungivore gehad en die hoogste aantal karnivore. Wanneer organiese en konvensionele appelkoosboorde met mekaar vergelyk is, was hoër getalle van plant-parasitiese nematodes gevind in die organiese boord. Criconematidae was teen ʼn groter aantal in die grond van die konvensionele appelkoosboord gevind. Met die vergelyking van organiese appelkose en appels word, is ʼn hoër aantal Criconematidae binne die organiese appelgrond aangetref. In die algemeen was hoër vlakke van plant-parasitiese nematodes gevind in die organiese appelkoosboord. Die MI het getoon dat alle boord waardes laer as 1.5 gehad het, wat daarop dui dat die gronde versteurd is. Die konvensioneel bestuurde appelkoosboord het die hoogste MI waarde gehad met ʼn vlak van 1.48. Die waarde vir die PPI was die hoogste in organies bestuurde appelkoosboorde. Alle boord gronde is geleë binne kwadrant B van die Fauna Analiseerder, wat dui op verryking met struktuur. Met betrekking tot die diversiteit, spesie-rykheid en egaligheid van die verspreiding van families, het konvensionele appelkoos grond die hoogste spesierykheid, terwyl die gronde van die organiese appelboord die mees egalige familie verspreiding vertoon het. Verskillende bestuurspraktyke nie toon nie merkbare verskille in die gemeenskap samestelling en struktuur nie. Die spesie-rykheid van Fynbos gronde is vergelykbaar met dié van sagtevrugte-boorde. Monsters is geneem van agt verskillende grondeoppervlak-behandelings in ‘n appelboord in die Grabouw area. Die behandelings is gekombineer volgens die grond toediening wat dit ontvang het (chemiese beheer van dekgewasse en onkruid, deklaag en ‘n deklaag + effektiewe mikro- IX organismes). Bakterievoedende nematodes was dominant in elke grondoppervlak-behandeling, met die minste teenwoordig in die behandelings wat chemiese beheer van die dekgewasse en onkruid ontvang het. Behandelings wat chemiese beheer van die dekgewasse en onkruid ontvang het, het ook hoër vlakke van fungivore in vergelyking met die ander behandelings. ʼn Hoë aantal Rhabditidae het voorgekom in grondmonsters van die deklaag en die deklaag + EM (effektiewe mikro-organismes) behandeling persele, terwyl ʼn groot aantal Aphelenchidae voorgekom het in chemiese beheer persele. Die predatoriese familie, Ironidae, het slegs voorgekom in persele wat die deklaag + EM behandeling ontvang het. Sterk assosiasies bestaan tussen grond behandeling en nematode families wat in die grond teenwoordig was. Die chemiese beheer behandeling het die hoogste MI waarde getoon, terwyl waardes vir die ander behandelings laer en gelyk was. Die fauna analise het daarop gedui dat die deklaag en chemiese beheer binne kwadrant A is en dus verryk, maar ook ongestruktureerd is. Die deklaag + EM behandeling het binne kwadrant B geval wat aandui op toestande van verryking en struktuur wat 'n goeie algehele grondtoestand tot gevolg gehad het. Al die stelsels is oorbruggingsweë wat oorheers was deur bakteriële ontbinding. Kontroversieel, het persele wat chemiese beheer van die dekgewasse en onkruid ontvang het, die hoogste spesierykheid van al drie behandelings getoon asook die hoogste vlak van diversiteit volgens die Simpson-indeks. Slegs die dekgewasse en onkruid is chemies behandel, nie die grond nie, en dus kan die grond as onversteurd beskou word en die resultate wat verkry is in die studie verklaar. Duidelike verskille in die nematode gemeenskap struktuur en samestelling is waargeneem tussen die verskillende grond behandelings in appel boorde.

A field test is developed to assess the collapse susceptibility of soils rapidly and inexpensively. The in situ collapse test device measures the vertical deformations which occur in soils when they are subjected to stress and given access to water while under continuous load. Principles of statistics were employed to show that laboratory testing of soil specimens overestimate the magnitude of collapse as measured in the field and that the magnitude of collapse is, in part, a function of the soil moisture content at the time of loading and at the time of collapse. Good correlation was found between the spatial variability of collapsible soils with the location of alluvium terrace deposits and structurally damaged buildings.