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Soil, also commonly referred to as earth, is a mixture of organic matter, minerals, gases, liquids, and organisms that together support life of plants and soil organisms. Some scientific definitions distinguish dirt from soil by restricting the former term specifically to displaced soil. Soil consists of a solid phase of minerals and organic matter (the soil matrix), as well as a porous phase that holds gases (the soil atmosphere) and water (the soil solution). Accordingly, soil is a three-state system of solids, liquids, and gases. Soil is a product of several factors: the influence of climate, relief (elevation, orientation, and slope of terrain), organisms, and the soil's parent materials (original minerals) interacting over time. It continually undergoes development by way of numerous physical, chemical and biological processes, which include weathering with associated erosion. Given its complexity and strong internal connectedness, soil ecologists regard soil as an ecosystem.

Assessment of microbial community changes and limiting factors during bioremediation of hydrocarbon-polluted soil with new miniaturized physiological methods

Karin Kaufmann

Due to human activities, organic pollutants are spilled to the environment where they threaten public health, often as contaminants of soil or groundwater. Living organisms are able to transform or mineralize many organic pollutants, and bioremediation techniques have been developed to remove pollutants from a contaminated site. However, fast and easy methods to document both the efficacy of bioremediation and the changes in soil microbial communities during bioremediation are not well developed. The major aim of this thesis was to develop miniaturized methods targeting the physiology of microbial communities during pollutant degradation in soil and to assess pollution-induced community changes. Furthermore, the methods should identify factors limiting efficient pollutant biodegradation. Petroleum hydrocarbons have been chosen as pollutants because these compounds are frequently spilled, readily water-soluble, partly toxic and carcinogenic, and therefore undesirable in soils and drinking water supplies. The influence of petroleum hydrocarbons on a microbial community in the vadose zone was assessed under field conditions. An artificial hydrocarbon mixture consisting of volatile and semi-volatile compounds similar to jet-fuel was emplaced in a previously uncontaminated vadose zone in nutrient-poor glacial melt water sand. The experiment included monitoring of microbial parameters and CO2 concentrations in soil gas over 3 months, in- and outside the hydrocarbon vapor plume that formed around the buried petroleum. Microbial and chemical analyses of vadose zone samples were performed on material from 9 cores drilled on 3 days at 3 distances from the buried petroleum mass to 3.3 m depth. Significantly elevated CO2 concentrations were observed after contamination. Total cell numbers as determined by fluorescence microscopy were strongly correlated with soil organic carbon and nitrogen content but varied little with contamination. Redundancy analysis (RDA) allowed direct analysis of effects of selected environmental variables or the artificial contamination on microbiological parameters. Variation in biomass and CO2 production was to 46 % explained by soil parameters and to 39.8 % by the duration of contamination. The microbial community structure was assessed by community-level physiological profile analysis using BiologTM EcoPlates. Only 35.9 % of variation in BiologTM data could be attributed to soil parameters and contamination, however, the samples with greatest exposure to hydrocarbons grouped together on RDA plots. It is concluded that at this nutrient-poor site, the microbial community was dominated by the natural heterogeneity and that the influence of petroleum hydrocarbon vapor was weak. BiologTM Eco-Plates combined with RDA were able to distinguish between samples with high and low hydrocarbon exposure. However, the method was not sensitive enough to produce consistent patterns in three replicates when extracts from subsurface soils with low cell numbers were inoculated. A more sensitive, MPN-based system was therefore developed and its ability to provide information about specific pollutant degraders was tested in alluvial sand. Eight dilutions of sand extracts were inoculated on medium- and substrate-containing polypropylene deep-well plates. To keep the concentrations of the volatile substrates constant over several days of incubation without intoxicating the soil community, a substrate-containing organic carrier phase was applied to each vial. The biochemically inert 2,2,4,4,6,8,8-heptamethylnonane (HMN) was appropriate for this purpose. Thus, the volatile substrates partition from HMN into the microorganism-containing soil water where they achieve relatively low concentrations. The sensitive watersoluble tetrazolium dye (WST-1) was added to each well after 7 days incubation to detect dehydrogenase activity. A dark yellow signal was developed for the substrates toluene, n-octane, n-dodecane, 1,2,4-trimethylbenzene and methylcyclohexane but not for isooctane, being strongest in n-alkane amended wells. With this method, more hydrocarbon degrading bacteria were detected in an alluvial sand exposed to kerosene for 72 hours compared to the community in the pristine sand. Both communities were mainly composed of n-alkane degraders. Although encouraging results were achieved, we noticed that the tetrazolium reduction was inhibited in some cases. Wells with high cell numbers, in which obvious growth occurred, did not produce a signal. In a next step, the two-liquid phase system with HMN was applied to modify a miniaturized respiration detection system using whole soil samples instead of soil extracts (Campbell et al., AEM 69, p. 3593). Soil was incubated in deep-well plates in presence of single volatile organic hydrocarbons. The carrier phase was added to the interstitial space in a bead layer on the bottom of the well (below the soil sample), and the hydrocarbons diffused into the soil-water. The soil activity was determined by means of an agar plate containing a pH indicator, which changes color as a function of the produced CO2. Physiological profiles specific to petroleum hydrocarbons in pristine and contaminated soils were assessed. The substrate concentrations, which induced highest microbial activity, as well as concentrations causing inhibition, were determined with effect-concentration curves. Community-level physiological profiles based on hydrocarbon degradation were obtained by applying multivariate analysis on the CO2 yields. The first measurement period of 0-6 hours after addition of relatively high hydrocarbon concentrations to the system yields values, which best separated soil types as well as pristine and contaminated soils. If low concentrations were applied, we obtained only significant separations after 24 hours incubation, probably after a growth step. The same micro-respiration system equipped with a 14CO2 detection plate was applied to study N and P limitation of aerobic mineralization of 14C-toluene in a soil previously exposed to petroleum. Significant nutrient limitation during short-term tests (24-48 hours) was identified and the optimized combination of nutrient addition was determined. Conclusively, miniaturized physiological methods have been proven to detect soil microbial community changes in petroleum hydrocarbon-contaminated soils. Adding an organic carrier phase to the miniaturized systems allowed assuring a volatile organic hydrocarbon supply in non-toxic concentrations in the soil water or the medium for several days. Thus simple, cost-effective systems to investigate the soil community during bioremediation and to address questions of nutrient shortage in soils have been provided with this thesis.

EPFL2004

Fonctionnement hydrique de différents types de placages sableux dans le sahel burkinabè

Dial Niang

The study was performed in the Sahelian part of Burkina Faso. The country is subject to difficult climatic conditions, a strong demographic growth and a continuous decrease in soil fertility. The resulting degradation affects the processes which govern ecological systems and leads, on the long run, to a modification of the ecosystems. This is particularly the case of the eolian formations, the only ecological units susceptible of being useful in the area, since they present good infiltration capacity and support the main part of the vegetation. Field measurements (rainfall, runoff, saturated hydraulic conductivity, bulk density, hydraulic conductivity function, soil water content and pressure head) have been done to asses the impacts of the environmental degradation on the hydrodynamic behavior of these formations. Within this context, an experimental device made of seven measurement sites has been installed in three contrasting zones. The results show significant differences in the hydrodynamic behavior of the soils, according to their surface properties. On one hand, the sites located on an erosion crust as well as on a drying crust in transition towards an erosion crust, are characterized by a low infiltration capacity which favors runoff. The quantity of infiltrated water is very low when compared to total precipitation. Water is stored near the soil surface (in the first 30 cm) favoring evaporation in the days following rainfall events. Thus, little water is available for plants. The resulting water stress causes a weak density, or even complete absence of plants which have difficulties to colonize such surfaces. Surface runoff is favored with runoff coefficients ranging from 50 to 80 %. On the other hand, the sites situated on drying crusts are characterized by good hydraulic conductivity and infiltration capacity. The storage of water in the root zone is more important. Water flows deeper into the soil and, occasionally, drains at the reference depth of 50 cm. The runoff coefficients were found to be lower than in the other sites (30 to 40 %). This differentiated behavior is one of the main factors affecting the formation of different landscapes in the area through the existence of a relationship between soil surface properties, the type of landscape and the ratio runoff/infiltration. The sites located on an erosion crust and those in transition towards an erosion crust behave like impluviums, while those situated on drying crusts are more favorable to infiltration. Observation of the evolution of the hydraulic properties of the soil surface shows a progressive alteration that frequently leads to strongly degraded mediums unfavorable to plants. Control and rehabilitation methods considered in the study, namely "restoration" and "mise en défens" have only partial and time-limited effects; they do not make it possible to stop durably degradation or to favor rehabilitation. Among the other measures assessed on the INERA plots, only the restitution to the soil of the beforehand mown plants causes an improvement of the soil surface properties; the restitution causes the formation of an important macroporal system favoring water infiltration and circulation in the soil. The effects of those different measures occur mainly in the first years after their introduction and concern especially vegetation regeneration, soil protection against degradation factors, improvement of hydrodynamic soil properties, reduction of runoff and erosion. They make it possible to slow down soil degradation, but not to stop it definitively. Within this context, proposals of further studies focussed on other measures to control and rehabilitate degraded areas have been suggested, taking into account the specificity of the sahelian zone, the endogenous knowledge of the agro-pastors, as well as socio-economic and ecological conditions.

EPFL2006

Improving slash-and-burn agriculture in Central Menabe, Madagascar

Justine Marie Gay des Combes

Slash-and-burn agriculture is considered as an important driver of deforestation in the tropics. In Madagascar, a biodiversity hotspot, this type of agriculture particularly threatens the tropical forest cover. On the south-western coast of the island, in Central Menabe, the dry tropical forest of Kirindy suffers from an annual deforestation of 2.6%. At such alarming rate, the forest will have entirely disappeared by 2050. The attention of past research programs and conservation actions were mainly on studying the forest or the general interactions between local populations and the forest, with little focus on the slash-and-burn agricultural system itself. Hence, understanding the cultivation practices and assessing alternatives to them is crucial to improve the current forest conservation initiatives. The present thesis answers to the need of an in-depth study of the agricultural practices in Central Menabe. The project aims to (1) analyze the practices of slash-and-burn cultivation in Kirindy forest, (2) explore alternative slash-and-burn practices which may be more sustainable for the forest, (3) determine the implementation perspectives of these alternatives. In a first stage, we have characterized soil productivity along repetitive slash-and-burn cultivation cycles and the farmerâs perception of their agricultural system. Then, we experimented a selective slash-and-burn agriculture (where trees are left intentionally within the cultivated fields), coupled with compost amendment. Finally, we have assessed the implementation potential of that technique through interviews and participating workshops with local farmers. Our findings highlighted that soil depletion due to plant uptake and erosion or leaching by heavy rains, as well as weed invasion were important problems of slash-and-burn cultivation in Central Menabe. Farmers perceive weeding as a work overload. Decrease in grain yield due to slash-and-burn agriculture reaches about 40% after three years of cultivation on the same field (from 4 to 2.5 t ha-1), and decreases up to 75% after a single cyclonic rainy season (from 4 to 1 t ha-1). Further, we demonstrated that combining compost and wood ashes (from the burnings) seems a promising solution to sustain cultivation on the fields. Compost, combined with wood ashes, multiplied corn yield by 5 compared to traditional slash-and-burn agriculture. Growth rates were accelerated and phenology stages of maize plants advanced. Furthermore, this combination also increased soil security by improving the remaining stock of nutrients after a rain simulation. On the other hand, a partial remaining tree cover (selective slash-and-burn agriculture) improved corn yields only when the soil was amended with ashes, not with compost, nor the combination of both. Implementing composting in the forest dwelling communities appears to be a challenging task. Several barriers were highlighted, among them the most important was the water constraints during a consequent period of time related to compost maintenance. Alternative slash-and-burn practices have not been much studied so far because the use of fire was always considered as destructive. Thus, our result will contribute to the development of new forest management strategies which would balance conservation of habitats and rural communities agricultural needs, while minimizing the impact on primary forest.

EPFL2017