Effect of soil structure on temporal and spatial dynamics of bacteria

Soil is a complex heterogeneous system comprising of highly variable and dynamic micro-habitats that have significant impacts on the growth and activity of resident microbiota. A question addressed in this research is how soil structure affects the temporal dynamics and spatial distribution of bacteria. Using repacked microcosms, the effect of bulk-density, aggregate sizes and water content on growth and distribution of introduced Pseudomonas fluorescens and Bacillus subtilis bacteria was determined. Soil bulk-density and aggregate sizes were altered to manipulate the characteristics of the pore volume where bacteria reside and through which distribution of solutes and nutrients is controlled. X-ray CT was used to characterise the pore geometry of repacked soil microcosms. Soil porosity, connectivity and soil-pore interface area declined with increasing bulk-density. In samples that differ in pore geometry, its effect on growth and extent of spread of introduced bacteria was investigated. The growth rate of bacteria reduced with increasing bulk-density, consistent with a significant difference in pore geometry. To measure the ability of bacteria to spread thorough soil, placement experiments were developed. Bacteria were capable of spreading several cm’s through soil. The extent of spread of bacteria was faster and further in soil with larger and better connected pore volumes. To study the spatial distribution in detail, a methodology was developed where a combination of X-ray microtopography, to characterize the soil structure, and fluorescence microscopy, to visualize and quantify bacteria in soil sections was used. The influence of pore characteristics on distribution of bacteria was analysed at macro- and microscales. Soil porosity, connectivity and soil-pore interface influenced bacterial distribution only at the macroscale. The method developed was applied to investigate the effect of soil pore characteristics on the extent of spread of bacteria introduced locally towards a C source in soil. Soil-pore interface influenced spread of bacteria and colonization, therefore higher bacterial densities were found in soil with higher pore volumes. Therefore the results in this showed that pore geometry affects the growth and spread of bacteria in soil. The method developed showed showed how thin sectioning technique can be combined with 3D X-ray CT to visualize bacterial colonization of a 3D pore volume. This novel combination of methods is a significant step towards a full mechanistic understanding of microbial dynamics in structured soils.

THE DISTRIBUTION AND FUNCTION OF DENITRIFICATION GENES: EXPLORING AGRICULTURAL MANAGEMENT AND SOIL CHEMICAL IMPLICATIONS

Denitrification is a microbially-mediated process that converts nitrate (NO3-) to dinitrogen (N2) gas and has implications for soil fertility, climate change, and water quality. Using PCR, qPCR, and T-RFLP, the effects of environmental drivers and land management on the abundance and composition of functional genes were investigated. Environmental variables affecting gene abundance were soil type, soil depth, nitrogen concentrations, soil moisture, and pH, although each gene was unique in its spatial distribution and controlling factors. The inclusion of microbial variables, specifically genotype and gene abundance, improved denitrification models and highlights the benefit of including microbial data in modeling denitrification. Along with some evidence of niche selection, I show that nirS is a good predictor of denitrification enzyme activity (DEA) and N2O:N2 ratio, especially in alkaline and wetland soils. nirK was correlated to N2O production and became a stronger predictor of DEA in acidic soils, indicating that nirK and nirS are not ecologically redundant.

Compréhension des différences de distribution spatiale des anchois et de leurs œufs

La campagne PELGAS participe à la gestion du stock d’anchois du Golfe de Gascogne, en réalisant une évaluation directe à la mer de la biomasse d’anchois. Pour déterminer la biomasse totale, des appareils acoustiques envoyant des ultra-sons dans l’eau pour détecter les bancs de poisson sont utilisés. Ensuite des pêches sont effectuées sur les zones détectées pour déterminer la composition des bancs (espèces, poids, longueurs…). En parallèle, les oeufs d’anchois sont comptés. A partir des données récoltées de 2000 à 2015, j’ai pu réaliser des cartes de distribution spatiale des anchois et de leurs oeufs, ainsi que des analyses statistiques afin de comprendre les différences de distribution entre les deux. Il s’avère que les oeufs sont plus au large que les anchois, ce qui est dû à une question de poids moyen et de fécondité. Les anchois les plus gros seraient plus féconds et se localisent plus au large, d’où la répartition des oeufs plus éloignées des côtes que la biomasse totale d’anchois. La fécondité et le poids des anchois font parties des paramètres qui ont une influence sur la distribution des oeufs.

Spatial choice is biased by chemical cues from conspecifics in the speckeled worm eel Myrophis punctatus

A enguia mirongo-mirim Myrophis punctatus vive em agrupamentos de alta densidade populacional e comumente se enterra ou permanece sob o substrato. Esses comportamentos podem levar a marcas químicas no subtrato e podem, portanto, modular o uso do espaço nessa espécie. Neste estudo, testamos a hipótese de que a preferência espacial da enguia mirongo-mirim é influenciada pela presença de odor do animal coespecífico no subtrato. Mostramos que as enguias evitam a área que contém tal odor, indicando que as decisões de ocupação espacial podem ser influenciadas por pistas químicas de coespecíficos. As enguias claramente detectaram o odor de um animal coespecífico e essa percepção poderia ser um indicativo da presença de um coespecífico enterrado no substrato. Visto que elas evitam uma área contendo tal odor, sugerimos que isso poderia ser uma resposta para evitar invadir o território de um animal residente.

Spatial dynamics of bovine tuberculosis in the Autonomous Community of Madrid, Spain (2010-2012)

Progress in control of bovine tuberculosis (bTB) is often not uniform, usually due to the effect of one or more sometimes unknown epidemiological factors impairing the success of eradication programs. Use of spatial analysis can help to identify clusters of persistence of disease, leading to the identification of these factors thus allowing the implementation of targeted control measures, and may provide some insights of disease transmission, particularly when combined with molecular typing techniques. Here, the spatial dynamics of bTB in a high prevalence region of Spain were assessed during a three year period (2010-2012) using data from the eradication campaigns to detect clusters of positive bTB herds and of those infected with certain Mycobacterium bovis strains (characterized using spoligotyping and VNTR typing). In addition, the within-herd transmission coefficient (β) was estimated in infected herds and its spatial distribution and association with other potential outbreak and herd variables was evaluated. Significant clustering of positive herds was identified in the three years of the study in the same location ("high risk area"). Three spoligotypes (SB0339, SB0121 and SB1142) accounted for >70% of the outbreaks detected in the three years. VNTR subtyping revealed the presence of few but highly prevalent strains within the high risk area, suggesting maintained transmission in the area. The spatial autocorrelation found in the distribution of the estimated within-herd transmission coefficients in herds located within distances <14 km and the results of the spatial regression analysis, support the hypothesis of shared local factors affecting disease transmission in farms located at a close proximity.

Relative effect of food supplementation and natural resources on female red deer distribution in a Mediterranean ecosystem

Supplementary feeding is a widespread game management practice in several red deer (Cervus elaphus) populations, with important potential consequences on the biology of this species. InMediterranean ecosystems food supplementation occurs in the rutting period, when it may change mating system characteristics. We studied the role of food supplementation relative to natural resources in the spatial distribution, aggregation, and mean harem size of females in Iberian red deer (Cervus elaphus hispanicus) during the rut. We studied 30 red deer populations of southwestern Spain, 63% of which experienced supplementary feeding. Using multivariate spatial analyses we found that food supplementation affected distribution of females in 95% of the populations in which it occurred. Green meadows present during the mating season acted as an important natural resource influencing female distribution. Additionally, the level of female aggregation and mean harem size were significantly higher in those populations in which food supplementation determined female distribution than in populations in which female distribution did not depend on supplementary feeding. Because female aggregation and mean harem size are key elements in sexual selection, supplementary feeding may constitute an important anthropogenic element with potential evolutionary implications for populations of Iberian red deer.

Spatial variability of satured soil hydraulic conductivity in the region of Araguaia River - Brazil.

This study evaluates the spatial variability of saturated hydraulic conductivity in the soil in an area of 51,850 ha at the headwaters of the Araguaia River MT/GO. This area is highly vulnerable because it is a location of recharging through natural water infiltration of the Guarani Aquifer System and an area of intense increases in agriculture since its adoption by growers in the last 30 years. Soil samples were collected at 383 points, geographically located by GPS. The samples were collected from depths of 0 - 20 cm and 60 - 80 cm. Exploratory statistics and box-plot were used in the descriptive analysis and semivariogram were constructed to determine the spatial model. The exploratory analysis showed that the mean hydraulic conductivity in the superficial layer was less than at the level of 60-80 cm; however, the greatest variability evaluated with a coefficient of variation also was from this layer. Data tended towards a normal distribution. These results can be explained by the greater soil compaction in the superficial layer. The semivariogram models, adjusted for the two layers, were exponential and demonstrated moderate and strong dependence, with ranges of 5000 and 3000 utm respectively. It was concluded that soil use is influencing the spatial distribution model of the hydraulic conductivity in the region.

Comparison of ultrafine particle release from hardcopy devices in emission test chambers and office rooms

The release of ultrafine particles (UFP) from laser printers and office equipment was analyzed using a particle counter (FMPS; Fast Mobility Particle Sizer) with a high time resolution, as well as the appropriate mathematical models. Measurements were carried out in a 1 m³ chamber, a 24 m³ chamber and an office. The time-dependent emission rates were calculated for these environments using a deconvolution model, after which the total amount of emitted particles was calculated. The total amounts of released particles were found to be independent of the environmental parameters and therefore, in principle, they were appropriate for the comparison of different printers. On the basis of the time-dependent emission rates, “initial burst” emitters and constant emitters could also be distinguished. In the case of an “initial burst” emitter, the comparison to other devices is generally affected by strong variations between individual measurements. When conducting exposure assessments for UFP in an office, the spatial distribution of the particles also had to be considered. In this work, the spatial distribution was predicted on a case by case basis, using CFD simulation.

Transportation disadvantage determination framework : space-time organisation measure in determining transportation disadvantage

Transportation disadvantage has been recognised to be the key source of social exclusion. Therefore an appropriate process is required to investigate and seek to resolve this problem. Currently, determination of Transportation Disadvantage is postulate based on income, poverty and mobility level. Transportation disadvantage may best regard be based on accessibility perspectives as they represent inability of the individual to access desired activities. This paper attempts to justify a process in determining transportation disadvantage by incorporating accessibility and social transporation conflict as the essence of a framework. The framework embeds space time organisation within the dimension of accessibility to identify a rigorous definition of transportation disadvantage. In developing the framework, the definition, dimension, component and measure of accessibility were scrutinised. The findings suggest the definition and dimension are the significant approach of research to evaluate travel experience of the disadvantaged. Concurrently, location accessibility measures will be incorprated to strenghten the determination of accessibility level. Literature review in social exclusion and mobility-related exclusion identified the dimension and source of transportation disadvantage. It was revealed that the appropriate approach to justify trasnportation disadvantaged is to incorporate space-time organisation within the studied components. The suggested framework is an inter-related process consisting of component of accessibility; individual, networking (transport system) and activities (destination). The integration and correlation among the components shall determine the level of transportation disadvantage. Prior findings are used to retrieve the spatial distribution of transportation disadvantaged and appropriate policies are developed to resolve the problems.

Technical report : acoustic analysis of the natural environment

This technical report is concerned with one aspect of environmental monitoring—the detection and analysis of acoustic events in sound recordings of the environment. Sound recordings offer ecologists the potential advantages of cheaper and increased sampling. An acoustic event detection algorithm is introduced that outputs a compact rectangular marquee description of each event. It can disentangle superimposed events, which are a common occurrence during morning and evening choruses. Next, three uses to which acoustic event detection can be put are illustrated. These tasks have been selected because they illustrate quite different modes of analysis: (1) the detection of diffuse events caused by wind and rain, which are a frequent contaminant of recordings of the terrestrial environment; (2) the detection of bird calls using the spatial distribution of their component events; and (3) the preparation of acoustic maps for whole ecosystem analysis. This last task utilises the temporal distribution of events over a daily, monthly or yearly cycle.

Technical report : acoustic analysis of the natural environment

This technical report is concerned with one aspect of environmental monitoring—the detection and analysis of acoustic events in sound recordings of the environment. Sound recordings offer ecologists the potential advantages of cheaper and increased sampling. An acoustic event detection algorithm is introduced that outputs a compact rectangular marquee description of each event. It can disentangle superimposed events, which are a common occurrence during morning and evening choruses. Next, three uses to which acoustic event detection can be put are illustrated. These tasks have been selected because they illustrate quite different modes of analysis: (1) the detection of diffuse events caused by wind and rain, which are a frequent contaminant of recordings of the terrestrial environment; (2) the detection of bird calls using the spatial distribution of their component events; and (3) the preparation of acoustic maps for whole ecosystem analysis. This last task utilises the temporal distribution of events over a daily, monthly or yearly cycle.

GIS-based mapping and statistical analysis of air pollution and mortality in Brisbane, Australia

In this thesis, the relationship between air pollution and human health has been investigated utilising Geographic Information System (GIS) as an analysis tool. The research focused on how vehicular air pollution affects human health. The main objective of this study was to analyse the spatial variability of pollutants, taking Brisbane City in Australia as a case study, by the identification of the areas of high concentration of air pollutants and their relationship with the numbers of death caused by air pollutants. A correlation test was performed to establish the relationship between air pollution, number of deaths from respiratory disease, and total distance travelled by road vehicles in Brisbane. GIS was utilized to investigate the spatial distribution of the air pollutants. The main finding of this research is the comparison between spatial and non-spatial analysis approaches, which indicated that correlation analysis and simple buffer analysis of GIS using the average levels of air pollutants from a single monitoring station or by group of few monitoring stations is a relatively simple method for assessing the health effects of air pollution. There was a significant positive correlation between variable under consideration, and the research shows a decreasing trend of concentration of nitrogen dioxide at the Eagle Farm and Springwood sites and an increasing trend at CBD site. Statistical analysis shows that there exists a positive relationship between the level of emission and number of deaths, though the impact is not uniform as certain sections of the population are more vulnerable to exposure. Further statistical tests found that the elderly people of over 75 years age and children between 0-15 years of age are the more vulnerable people exposed to air pollution. A non-spatial approach alone may be insufficient for an appropriate evaluation of the impact of air pollutant variables and their inter-relationships. It is important to evaluate the spatial features of air pollutants before modeling the air pollution-health relationships.

The influence of habitat heterogeneity on patterns of connectivity among rabbit populations in southern Queensland

Patterns of connectivity among local populations influence the dynamics of regional systems, but most ecological models have concentrated on explaining the effect of connectivity on local population structure using dynamic processes covering short spatial and temporal scales. In this study, a model was developed in an extended spatial system to examine the hypothesis that long term connectivity levels among local populations are influenced by the spatial distribution of resources and other habitat factors. The habitat heterogeneity model was applied to local wild rabbit populations in the semi-arid Mitchell region of southern central Queensland (the Eastern system). Species' specific population parameters which were appropriate for the rabbit in this region were used. The model predicted a wide range of long term connectivity levels among sites, ranging from the extreme isolation of some sites to relatively high interaction probabilities for others. The validity of model assumptions was assessed by regressing model output against independent population genetic data, and explained over 80% of the variation in the highly structured genetic data set. Furthermore, the model was robust, explaining a significant proportion of the variation in the genetic data over a wide range of parameters. The performance of the habitat heterogeneity model was further assessed by simulating the widely reported recent range expansion of the wild rabbit into the Mitchell region from the adjacent, panmictic Western rabbit population system. The model explained well the independently determined genetic characteristics of the Eastern system at different hierarchic levels, from site specific differences (for example, fixation of a single allele in the population at one site), to differences between population systems (absence of an allele in the Eastern system which is present in all Western system sites). The model therefore explained the past and long term processes which have led to the formation and maintenance of the highly structured Eastern rabbit population system. Most animals exhibit sex biased dispersal which may influence long term connectivity levels among local populations, and thus the dynamics of regional systems. When appropriate sex specific dispersal characteristics were used, the habitat heterogeneity model predicted substantially different interaction patterns between female-only and combined male and female dispersal scenarios. In the latter case, model output was validated using data from a bi-parentally inherited genetic marker. Again, the model explained over 80% of the variation in the genetic data. The fact that such a large proportion of variability is explained in two genetic data sets provides very good evidence that habitat heterogeneity influences long term connectivity levels among local rabbit populations in the Mitchell region for both males and females. The habitat heterogeneity model thus provides a powerful approach for understanding the large scale processes that shape regional population systems in general. Therefore the model has the potential to be useful as a tool to aid in the management of those systems, whether it be for pest management or conservation purposes.

Application of micro CT and computation modeling in bone tissue engineering

Computer aided technologies, medical imaging, and rapid prototyping has created new possibilities in biomedical engineering. The systematic variation of scaffold architecture as well as the mineralization inside a scaffold/bone construct can be studied using computer imaging technology and CAD/CAM and micro computed tomography (CT). In this paper, the potential of combining these technologies has been exploited in the study of scaffolds and osteochondral repair. Porosity, surface area per unit volume and the degree of interconnectivity were evaluated through imaging and computer aided manipulation of the scaffold scan data. For the osteochondral model, the spatial distribution and the degree of bone regeneration were evaluated. In this study the versatility of two softwares Mimics (Materialize), CTan and 3D realistic visualization (Skyscan) were assessed, too.

Bearing damage analysis by calculation of capacitive coupling between inner and outer races of a ball bearing

Bearing damage in modern inverter-fed AC drive systems is more common than in motors working with 50 or 60 Hz power supply. Fast switching transients and common mode voltage generated by a PWM inverter cause unwanted shaft voltage and resultant bearing currents. Parasitic capacitive coupling creates a path to discharge current in rotors and bearings. In order to analyze bearing current discharges and their effect on bearing damage under different conditions, calculation of the capacitive coupling between the outer and inner races is needed. During motor operation, the distances between the balls and races may change the capacitance values. Due to changing of the thickness and spatial distribution of the lubricating grease, this capacitance does not have a constant value and is known to change with speed and load. Thus, the resultant electric field between the races and balls varies with motor speed. The lubricating grease in the ball bearing cannot withstand high voltages and a short circuit through the lubricated grease can occur. At low speeds, because of gravity, balls and shaft voltage may shift down and the system (ball positions and shaft) will be asymmetric. In this study, two different asymmetric cases (asymmetric ball position, asymmetric shaft position) are analyzed and the results are compared with the symmetric case. The objective of this paper is to calculate the capacitive coupling and electric fields between the outer and inner races and the balls at different motor speeds in symmetrical and asymmetrical shaft and balls positions. The analysis is carried out using finite element simulations to determine the conditions which will increase the probability of high rates of bearing failure due to current discharges through the balls and races.