Este trabalho faz parte do projeto Biota/FAPESP, Métodos de Inventário da Biodiversidade de Espécies Arbóreas, e analisou a diferença na estrutura florística entre as áreas estudadas. Na Estação Ecológica de Assis, SP, área de Cerradão, foram amostradas 102 espécies, 72 gêneros e 43 famílias; 67% das espécies foram exclusivas desta fitofisionomia. Na Floresta Estacional Semidecidual da Estação Ecológica dos Caetetus, município de Gália-SP, foram amostradas 208 espécies, 138 gêneros e 49 famílias; sendo 65% das espécies exclusivas. Na Floresta Ombrófila Densa do Parque Estadual de Carlos Botelho, município de São Miguel Arcanjo-SP, foram encontradas 410 espécies, pertencentes a 152 gêneros e 64 famílias; 84% das espécies exclusivas desta fitofisionomia. A Floresta Estacional apresentou maior similaridade com a Floresta Ombrófila do que com o Cerradão. Apesar de apresentar maior número de espécies, a Floresta Ombrófila Densa apresenta concentração de espécies nas famílias Myrtaceae e Lauraceae. Em outra análise foram calculados os índices de distinção taxonômica nas 5 grades amostrais para os métodos de amostragem testados. O método de Bitterlich apresentou tendência nos índices de diversidade e distinção taxonômica, conforme a diversidade taxonômica do sub-bosque. Esses índices apresentaram média independente e variância decrescente com o aumento da amostra. Os índices de distinção taxonômica média e variância da distinção taxonômica média também apresentaram variância decrescente. Porém, a estabilização da média ocorreu com amostras de maior tamanho, principalmente para as parcelas de área fixa na Estação Ecológica dos Caetetus. Na Floresta Ombrófila Densa, a distinção taxonômica média foi menor e a variância da distinção taxonômica média foi maior, devido a alta concentração de espécies de Myrtales e Laurales nesta fitofisionomia. / This research is part of the project Biota / FAPESP, \"Tree Species Biodiversity Inventory Methods, and analised floristic structural differences among three areas. In Assis Ecological Station, Forest Savanna area were sampled 102 species, 72 genus and 43 families, 67% of this species were exclusive of this phytophisiognomy. Semideciduous seasonal forest in the Caetetus Ecological Station, 208 species were sampled, 138 genus and 49 families, with 65% of exclusive species. Rain Forest in the Carlos Botelho State Park, were found 410 species, belonging to 152 genus and 64 families, 84% of exclusive species. The seasonal forest showed greater similarity to the rain forest than the Savanna. In spite of the greater number of species, the Rain Forest presents concentration of species in the Myrtaceae and Lauraceae families. In another analysis were calculated the taxonomic indices in tree species data provided by sampling methods tested in five sampling grids. The Bitterlich sampling method was tendecious in estimates the taxonomic diversity and taxonomic distinctness indices because the taxonomic diversity in the understory. These indices showed average independent and variance decreasing with increasing sample. The average taxonomic distinctness and variation in taxonomic distinctness also showed decreased, but the stabilization of the average occurred with samples of greater size, mainly for fixed area plots at Caetetus Ecological Station. In the Rain Forest the average taxonomic distinctness was lower and the variation of taxonomic distinctness was higher due to high concentration of species of Myrtales and Laurales in this phytophisiognomy.

Take-all is the name given to the disease caused by a soilborne fungus Gaeumannomyces graminis (Sacc.) von Arx and Olivier var. tritici Walker (Ggt), an ascomycete of the family Magnaportheaceae (Cook, 2003). This fungus is an aggressive soil-borne pathogen causing root rot of wheat (primary host), barley and rye crops (secondary host). The flowering, seedling, and vegetative growth stages can be affected by the infection of the whole plant, leaves, roots, and stems. Infections of roots result in losses in crop yield and quality primarily due to a lowering in nutrient uptake. Take-all is most common in regions where wheat is cultivated without adequate crop rotation. Crop rotation allows time between the planting dates of susceptible crops, which causes a decrease in the inoculum potential of soilborne plant pathogens to levels below an economic threshold by resident antagonistic soil microbial communities. Soilborne disease suppressiveness is an inherent characteristic of the physical, chemical, and/or biological structure of a particular soil which might be induced by agricultural practices and activities such as the cultivation of crops, or the addition of organisms or nutritional amendments, causing a change in the microfloral environment. Disturbances of soil ecosystems that impact on the normal functioning of microbial communities are potentially detrimental to soil formation, energy transfers, nutrient cycling, and long-term stability. In this regard, an overview of soil properties and processes indicated that the use of microbiological and biochemical soil properties, such as microbial biomass, the analysis of microbial functional diversity and microbial structural diversity by the quantification of community level physiological profiles and signature lipid biomarkers are useful as indicators of soil ecological stress or restoration properties because they are more responsive to small changes than physical and chemical characteristics. In this study, the relationship between physico-chemical characteristics, and different biological indicators of soil quality of agricultural soils conducive, suppressive, and neutral with respect to take-all disease of wheat as caused by the soilborne fungus Gaeumannomyces graminis var. tritici (Ggt), were investigated using various techniques. The effect of crop rotation on the functional and structural diversity of soils conducive to take-all disease was also investigated. Through the integration of quantitative and qualitative biological data as well as the physico-chemical characteristics of the various soils, the functional and structural diversity of microbial IV communities in the soils during different stadia of take-all disease of wheat were characterised. All results were evaluated statistically and the predominant physical and chemical characteristics that influenced the microbiological and biochemical properties of the agricultural soils during different stadia of take-all disease of wheat were identified using multivariate analyses. Although no significant difference @ > 0.05) could be observed between the various soils using conventional microbiological enumeration techniques, the incidence of Gliocladium spp. in suppressive soils was increased. Significant differences @ < 0.05) were observed between agricultural soils during different stadia of take-all disease of wheat. Although no clear distinction could be made between soils suppressive and neutral to take-all disease of wheat, soils suppressive and conducive to take-all disease of wheat differed substantially in their community level physiological profiles (CLPPs). Soils suppressive / neutral to take-all disease were characterised by enhanced utilisation of carboxylic acids, amino acids, and carbohydrates, while conducive soils were characterised by enhanced utilisation of carbohydrates. Shifts in the functional diversity of the associated microbial communities were possibly caused by the presence of Ggt and associated antagonistic fungal and bacterial populations in the various soils. It was evident that the relationships amongst the functionality of the microbial communities within the various soils had undergone changes through the different stages of development of take-all disease of wheat, thus implying different substrate utilisation capabilities of present soil microbial communities. Diversity indices were calculated as Shannon's diversity index (H') and substrate equitability (J) and were overall within the higher diversity range of 3.6 and 0.8, respectively, indicating the achievement of very high substrate diversity values in the various soils. A substantial percentage of the carbon sources were utilised, which contributed to the very high Shannon-Weaver substrate utilisation indices. Obtained substrate evenness (equitability) (J) indices indicated an existing high functional diversity. The functional diversity as observed during crop rotation, differed significantly (p < 0.05) from each other, implying different substrate utilisation capabilities of present soil microbial communities, which could possibly be ascribed to the excretion of root exudates by sunflowers and soybeans. Using the Sorenson's index, a clear distinction could be made between the degrees of substrate utilisation between microbial populations in soils conducive, suppressive, and neutral to take-all disease of wheat, as well as during crop rotation. Furthermore, the various soils could also be differentiated on the basis of the microbial community structure as determined by phospholipid fatty acid (PLFA) analysis. Soil suppressive to take-all disease of wheat differed significantly (p < 0.05) from soils conducive, and neutral to take-all disease of wheat, implying a shift in relationships amongst the structural diversity of microbial communities within the various soils. A positive association was observed between the microbial phospholipid fatty acid profiles, and dominant environmental variables of soils conducive, suppressive, and neutral to take-all disease of wheat. Soils conducive and neutral to take-all disease of wheat were characterised by high concentrations of manganese, as well as elevated concentrations of monounsaturated fatty acids, terminally branched saturated fatty acids, and polyunsaturated fatty acids which were indicative of Gram-negative bacteria, Gram-positive bacteria and micro eukaryotes (primarily fungi), respectively. These soils were also characterised by low concentrations of phosphorous, potassium, percentage organic carbon, and percentage organic nitrogen, as well as low soil pH. Soil suppressive to take-all disease of wheat was characterised by the elevated levels of estimated of biomass and elevated concentrations of normal saturated fatty acids, which is ubiquitous to micro-organisms. The concentration of normal saturated fatty acids in suppressive soils is indicative of a low structural diversity. This soil was also characterised by high concentrations of phosphorous, potassium, percentage organic carbon, and percentage organic nitrogen, as well as elevated soil pH. The relationship between PLFAs and agricultural soils was investigated using principal component analysis (PCA), redundancy analysis (RDA) and discriminant analysis (DA). Soil suppressive to take-all disease of wheat differed significantly (p < 0.05) from soils conducive, and neutral to take-all disease of wheat, implying a shift in relationships amongst the structural diversity of microbial communities within the various soils. A positive association was observed between the microbial phospholipid fatty acid profiles, and dominant environmental variables of soils conducive, suppressive, and neutral to take-all disease of wheat. Hierarchical cluster analysis of the major phospholipid fatty acid groups indicated that the structural diversity differed significantly between soils conducive, suppressive, and neutral to take-all disease of wheat caused by Gaeumannomyces graminis var. tritici. The results indicate that the microbial community functionality as well as the microbial community structure was significantly influenced by the presence of take-all disease of wheat caused by Gaeumannomyces graminis var. tritici, and that the characterisation of microbial functional and structural diversity by analysis of community level physiological profiles and phospholipid fatty acid analysis, respectively, could be successfully used as an assessment criteria for the evaluation of agricultural soils conducive, suppressive, and neutral to take-all disease of wheat, as well as in crop rotation systems. This methodology might be of significant value in assisting in the management and evaluation of agricultural soils subject to the prevalence of other soilborne diseases. / Thesis (M.Sc. (Microbiology))--North-West University, Potchefstroom Campus, 2004.

Urbanisation is an ever-growing global phenomenon which creates altered environments characterised by increased human habitation, exotic species, impermeable surfaces, artificial structures, landscape fragmentation, habitat loss, and modified energy– and resource pathways. The vulnerable Rand Highveld Grassland vegetation unit in the Tlokwe Municipal area, South Africa, has been extensively degraded and transformed by urbanisation and agriculture. Only 1% of this endangered ecosystem is currently being actively conserved. Grassland fragments in urban areas are considered to be less species rich and less functional than their more “natural” counterparts, and are therefore not a priority for conservation. In this study the effects of landscape matrix quality on intra patch variables, namely plant species diversity and functional diversity, and fine-scale biogeochemical landscape function (as determined by Landscape Function Analysis or LFA) of 30 fragments of the Rand Highveld Grassland vegetation unit were explored. Four urbanisation measures (percentage urban land cover, percentage grass land cover, edge density, and density of people), acting as indicators for patterns and processes associated with urban areas, were calculated for matrix areas with a 500m radius surrounding each selected grassland fragment to quantify the position of each grassland remnant along an urban-to-rural gradient. Using the specific urbanisation measures, the grassland fragments were objectively classified into two classes of urbanisation, namely “rural/peri-urban” and “urban”, to allow for statistical comparisons between intra-patch variables for grassland remnants exposed to similar urbanisation pressures. Plant species composition and diversity were determined in the selected grassland fragments and nine functional traits were described for each species. Plant functional diversity was determined by five functional diversity indices, namely functional richness, evenness, divergence, dispersion, and specialisation. Fine-scale biogeochemical landscape function was determined by executing the LFA method. LFA assesses fine-scale landscape patchiness and 11 soil surface indicators to produce three main LFA parameters (stability, infiltration, and nutrient cycling), which indicates how well a system is functioning in terms of resource conservation and soil processes. Possible relationships between fine-scale biogeochemical landscape function and plant species- and functional diversity were also investigated. NMDS ordinations and basic statistics were used to determine trends and effects within the data. The results indicated that urban grassland remnants had lower mean plant species richness, Shannon species diversity (significantly), and Pielou species evenness than rural/peri-urban grassland fragments. Urban grassland fragments also contained significantly higher percentage of exotic species. Correlations were found between the four urbanisation measures and percentage species of the total species richness possessing certain functional attributes. This indicated that increased urbanisation may influence the species composition and the occurrence of certain plant traits in the selected grassland fragments. Urbanisation seems to have no effect on fine-scale landscape heterogeneity of the selected grassland fragments. Rural/peri-urban grassland fragments had higher infiltration capacity, nutrient cycling potential, and total SSA functionality (although not significantly), which may be ascribed to differences in management practices, such as mowing in urban areas and grazing in rural areas. Rand Highveld Grassland fragments in the urban landscape matrix of Potchefstroom city are just as conservable in terms of plant species diversity and functional diversity, as well as on a biophysical function level involving soil processes than rural/peri-urban grassland fragments. High plant species diversity and the presence of certain plant traits did not contribute to high soil surface stability, infiltration capacity, nutrient cycling potential and total soil surface functioning. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2013

Urbanisation is an ever-growing global phenomenon which creates altered environments characterised by increased human habitation, exotic species, impermeable surfaces, artificial structures, landscape fragmentation, habitat loss, and modified energy– and resource pathways. The vulnerable Rand Highveld Grassland vegetation unit in the Tlokwe Municipal area, South Africa, has been extensively degraded and transformed by urbanisation and agriculture. Only 1% of this endangered ecosystem is currently being actively conserved. Grassland fragments in urban areas are considered to be less species rich and less functional than their more “natural” counterparts, and are therefore not a priority for conservation. In this study the effects of landscape matrix quality on intra patch variables, namely plant species diversity and functional diversity, and fine-scale biogeochemical landscape function (as determined by Landscape Function Analysis or LFA) of 30 fragments of the Rand Highveld Grassland vegetation unit were explored. Four urbanisation measures (percentage urban land cover, percentage grass land cover, edge density, and density of people), acting as indicators for patterns and processes associated with urban areas, were calculated for matrix areas with a 500m radius surrounding each selected grassland fragment to quantify the position of each grassland remnant along an urban-to-rural gradient. Using the specific urbanisation measures, the grassland fragments were objectively classified into two classes of urbanisation, namely “rural/peri-urban” and “urban”, to allow for statistical comparisons between intra-patch variables for grassland remnants exposed to similar urbanisation pressures. Plant species composition and diversity were determined in the selected grassland fragments and nine functional traits were described for each species. Plant functional diversity was determined by five functional diversity indices, namely functional richness, evenness, divergence, dispersion, and specialisation. Fine-scale biogeochemical landscape function was determined by executing the LFA method. LFA assesses fine-scale landscape patchiness and 11 soil surface indicators to produce three main LFA parameters (stability, infiltration, and nutrient cycling), which indicates how well a system is functioning in terms of resource conservation and soil processes. Possible relationships between fine-scale biogeochemical landscape function and plant species- and functional diversity were also investigated. NMDS ordinations and basic statistics were used to determine trends and effects within the data. The results indicated that urban grassland remnants had lower mean plant species richness, Shannon species diversity (significantly), and Pielou species evenness than rural/peri-urban grassland fragments. Urban grassland fragments also contained significantly higher percentage of exotic species. Correlations were found between the four urbanisation measures and percentage species of the total species richness possessing certain functional attributes. This indicated that increased urbanisation may influence the species composition and the occurrence of certain plant traits in the selected grassland fragments. Urbanisation seems to have no effect on fine-scale landscape heterogeneity of the selected grassland fragments. Rural/peri-urban grassland fragments had higher infiltration capacity, nutrient cycling potential, and total SSA functionality (although not significantly), which may be ascribed to differences in management practices, such as mowing in urban areas and grazing in rural areas. Rand Highveld Grassland fragments in the urban landscape matrix of Potchefstroom city are just as conservable in terms of plant species diversity and functional diversity, as well as on a biophysical function level involving soil processes than rural/peri-urban grassland fragments. High plant species diversity and the presence of certain plant traits did not contribute to high soil surface stability, infiltration capacity, nutrient cycling potential and total soil surface functioning. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2013

Take-all is the name given to the disease caused by a soilborne fungus Gaeumannomyces graminis (Sacc.) von Arx and Olivier var. tritici Walker (Ggt), an ascomycete of the family Magnaportheaceae (Cook, 2003). This fungus is an aggressive soil-borne pathogen causing root rot of wheat (primary host), barley and rye crops (secondary host). The flowering, seedling, and vegetative growth stages can be affected by the infection of the whole plant, leaves, roots, and stems. Infections of roots result in losses in crop yield and quality primarily due to a lowering in nutrient uptake. Take-all is most common in regions where wheat is cultivated without adequate crop rotation. Crop rotation allows time between the planting dates of susceptible crops, which causes a decrease in the inoculum potential of soilborne plant pathogens to levels below an economic threshold by resident antagonistic soil microbial communities. Soilborne disease suppressiveness is an inherent characteristic of the physical, chemical, and/or biological structure of a particular soil which might be induced by agricultural practices and activities such as the cultivation of crops, or the addition of organisms or nutritional amendments, causing a change in the microfloral environment. Disturbances of soil ecosystems that impact on the normal functioning of microbial communities are potentially detrimental to soil formation, energy transfers, nutrient cycling, and long-term stability. In this regard, an overview of soil properties and processes indicated that the use of microbiological and biochemical soil properties, such as microbial biomass, the analysis of microbial functional diversity and microbial structural diversity by the quantification of community level physiological profiles and signature lipid biomarkers are useful as indicators of soil ecological stress or restoration properties because they are more responsive to small changes than physical and chemical characteristics. In this study, the relationship between physico-chemical characteristics, and different biological indicators of soil quality of agricultural soils conducive, suppressive, and neutral with respect to take-all disease of wheat as caused by the soilborne fungus Gaeumannomyces graminis var. tritici (Ggt), were investigated using various techniques. The effect of crop rotation on the functional and structural diversity of soils conducive to take-all disease was also investigated. Through the integration of quantitative and qualitative biological data as well as the physico-chemical characteristics of the various soils, the functional and structural diversity of microbial IV communities in the soils during different stadia of take-all disease of wheat were characterised. All results were evaluated statistically and the predominant physical and chemical characteristics that influenced the microbiological and biochemical properties of the agricultural soils during different stadia of take-all disease of wheat were identified using multivariate analyses. Although no significant difference @ > 0.05) could be observed between the various soils using conventional microbiological enumeration techniques, the incidence of Gliocladium spp. in suppressive soils was increased. Significant differences @ < 0.05) were observed between agricultural soils during different stadia of take-all disease of wheat. Although no clear distinction could be made between soils suppressive and neutral to take-all disease of wheat, soils suppressive and conducive to take-all disease of wheat differed substantially in their community level physiological profiles (CLPPs). Soils suppressive / neutral to take-all disease were characterised by enhanced utilisation of carboxylic acids, amino acids, and carbohydrates, while conducive soils were characterised by enhanced utilisation of carbohydrates. Shifts in the functional diversity of the associated microbial communities were possibly caused by the presence of Ggt and associated antagonistic fungal and bacterial populations in the various soils. It was evident that the relationships amongst the functionality of the microbial communities within the various soils had undergone changes through the different stages of development of take-all disease of wheat, thus implying different substrate utilisation capabilities of present soil microbial communities. Diversity indices were calculated as Shannon's diversity index (H') and substrate equitability (J) and were overall within the higher diversity range of 3.6 and 0.8, respectively, indicating the achievement of very high substrate diversity values in the various soils. A substantial percentage of the carbon sources were utilised, which contributed to the very high Shannon-Weaver substrate utilisation indices. Obtained substrate evenness (equitability) (J) indices indicated an existing high functional diversity. The functional diversity as observed during crop rotation, differed significantly (p < 0.05) from each other, implying different substrate utilisation capabilities of present soil microbial communities, which could possibly be ascribed to the excretion of root exudates by sunflowers and soybeans. Using the Sorenson's index, a clear distinction could be made between the degrees of substrate utilisation between microbial populations in soils conducive, suppressive, and neutral to take-all disease of wheat, as well as during crop rotation. Furthermore, the various soils could also be differentiated on the basis of the microbial community structure as determined by phospholipid fatty acid (PLFA) analysis. Soil suppressive to take-all disease of wheat differed significantly (p < 0.05) from soils conducive, and neutral to take-all disease of wheat, implying a shift in relationships amongst the structural diversity of microbial communities within the various soils. A positive association was observed between the microbial phospholipid fatty acid profiles, and dominant environmental variables of soils conducive, suppressive, and neutral to take-all disease of wheat. Soils conducive and neutral to take-all disease of wheat were characterised by high concentrations of manganese, as well as elevated concentrations of monounsaturated fatty acids, terminally branched saturated fatty acids, and polyunsaturated fatty acids which were indicative of Gram-negative bacteria, Gram-positive bacteria and micro eukaryotes (primarily fungi), respectively. These soils were also characterised by low concentrations of phosphorous, potassium, percentage organic carbon, and percentage organic nitrogen, as well as low soil pH. Soil suppressive to take-all disease of wheat was characterised by the elevated levels of estimated of biomass and elevated concentrations of normal saturated fatty acids, which is ubiquitous to micro-organisms. The concentration of normal saturated fatty acids in suppressive soils is indicative of a low structural diversity. This soil was also characterised by high concentrations of phosphorous, potassium, percentage organic carbon, and percentage organic nitrogen, as well as elevated soil pH. The relationship between PLFAs and agricultural soils was investigated using principal component analysis (PCA), redundancy analysis (RDA) and discriminant analysis (DA). Soil suppressive to take-all disease of wheat differed significantly (p < 0.05) from soils conducive, and neutral to take-all disease of wheat, implying a shift in relationships amongst the structural diversity of microbial communities within the various soils. A positive association was observed between the microbial phospholipid fatty acid profiles, and dominant environmental variables of soils conducive, suppressive, and neutral to take-all disease of wheat. Hierarchical cluster analysis of the major phospholipid fatty acid groups indicated that the structural diversity differed significantly between soils conducive, suppressive, and neutral to take-all disease of wheat caused by Gaeumannomyces graminis var. tritici. The results indicate that the microbial community functionality as well as the microbial community structure was significantly influenced by the presence of take-all disease of wheat caused by Gaeumannomyces graminis var. tritici, and that the characterisation of microbial functional and structural diversity by analysis of community level physiological profiles and phospholipid fatty acid analysis, respectively, could be successfully used as an assessment criteria for the evaluation of agricultural soils conducive, suppressive, and neutral to take-all disease of wheat, as well as in crop rotation systems. This methodology might be of significant value in assisting in the management and evaluation of agricultural soils subject to the prevalence of other soilborne diseases. / Thesis (M.Sc. (Microbiology))--North-West University, Potchefstroom Campus, 2004.

Este trabalho faz parte do projeto Biota/FAPESP, Métodos de Inventário da Biodiversidade de Espécies Arbóreas, e analisou a diferença na estrutura florística entre as áreas estudadas. Na Estação Ecológica de Assis, SP, área de Cerradão, foram amostradas 102 espécies, 72 gêneros e 43 famílias; 67% das espécies foram exclusivas desta fitofisionomia. Na Floresta Estacional Semidecidual da Estação Ecológica dos Caetetus, município de Gália-SP, foram amostradas 208 espécies, 138 gêneros e 49 famílias; sendo 65% das espécies exclusivas. Na Floresta Ombrófila Densa do Parque Estadual de Carlos Botelho, município de São Miguel Arcanjo-SP, foram encontradas 410 espécies, pertencentes a 152 gêneros e 64 famílias; 84% das espécies exclusivas desta fitofisionomia. A Floresta Estacional apresentou maior similaridade com a Floresta Ombrófila do que com o Cerradão. Apesar de apresentar maior número de espécies, a Floresta Ombrófila Densa apresenta concentração de espécies nas famílias Myrtaceae e Lauraceae. Em outra análise foram calculados os índices de distinção taxonômica nas 5 grades amostrais para os métodos de amostragem testados. O método de Bitterlich apresentou tendência nos índices de diversidade e distinção taxonômica, conforme a diversidade taxonômica do sub-bosque. Esses índices apresentaram média independente e variância decrescente com o aumento da amostra. Os índices de distinção taxonômica média e variância da distinção taxonômica média também apresentaram variância decrescente. Porém, a estabilização da média ocorreu com amostras de maior tamanho, principalmente para as parcelas de área fixa na Estação Ecológica dos Caetetus. Na Floresta Ombrófila Densa, a distinção taxonômica média foi menor e a variância da distinção taxonômica média foi maior, devido a alta concentração de espécies de Myrtales e Laurales nesta fitofisionomia. / This research is part of the project Biota / FAPESP, \"Tree Species Biodiversity Inventory Methods, and analised floristic structural differences among three areas. In Assis Ecological Station, Forest Savanna area were sampled 102 species, 72 genus and 43 families, 67% of this species were exclusive of this phytophisiognomy. Semideciduous seasonal forest in the Caetetus Ecological Station, 208 species were sampled, 138 genus and 49 families, with 65% of exclusive species. Rain Forest in the Carlos Botelho State Park, were found 410 species, belonging to 152 genus and 64 families, 84% of exclusive species. The seasonal forest showed greater similarity to the rain forest than the Savanna. In spite of the greater number of species, the Rain Forest presents concentration of species in the Myrtaceae and Lauraceae families. In another analysis were calculated the taxonomic indices in tree species data provided by sampling methods tested in five sampling grids. The Bitterlich sampling method was tendecious in estimates the taxonomic diversity and taxonomic distinctness indices because the taxonomic diversity in the understory. These indices showed average independent and variance decreasing with increasing sample. The average taxonomic distinctness and variation in taxonomic distinctness also showed decreased, but the stabilization of the average occurred with samples of greater size, mainly for fixed area plots at Caetetus Ecological Station. In the Rain Forest the average taxonomic distinctness was lower and the variation of taxonomic distinctness was higher due to high concentration of species of Myrtales and Laurales in this phytophisiognomy.

Made available in DSpace on 2016-08-17T14:53:20Z (GMT). No. of bitstreams: 1 dissertacao Leonardo.pdf: 864322 bytes, checksum: 557c6817aff39c2f398ebe22a59ad5c6 (MD5) Previous issue date: 2012-04-20 / FUNDAÇÃO DE AMPARO À PESQUISA E AO DESENVOLVIMENTO CIENTIFICO E TECNOLÓGICO DO MARANHÃO / Lung cancer is still the leading cause of cancer mortality worldwide, with one of the lowest survival rates after diagnosis. Therefore, early detection is important to increase the chances of curing the patient. The diagnosis is more accurate if the specialist has more information. In view of the above, this work presents a methodology for characterization about the malignancy or benignity of pulmonary nodules, acting as a second opinion for the expert. The methodology was applied in two different databases, one with 73 nodes, 26 malignant and 47 benign, and other with 1034 nodes and 517 malignant and 517 benign. The Diversity Indices of Shannon and Simpson were used as texture descriptors. The features generated were then subjected to the step of feature selection using the stepwise Discriminant Analysis. After this stage, they were classified by the Support Vector Machine (SVM) where we obtained sensitivity of 85.64%, specificity of 97.89% and accuracy of 92.78%. / O câncer de pulmão é ainda a maior causa de mortalidade por câncer em todo mundo, com uma das menores taxas de sobrevida a partir do diagnóstico. Por isso, sua detecção precoce é importante para aumentar a chances de cura do paciente, e de quanto mais informações o médico dispuser, mais preciso será o diagnóstico. Diante do exposto, o presente trabalho apresenta uma metodologia de caracterização de nódulos pulmonares, objetivando se tornar uma ferramenta computacional utilizada para sugerir sobre a malignidade ou benignidade dos mesmos, atuando como uma segunda opinião junto ao especialista. A metodologia foi aplicada em duas bases de dados diferentes, uma com 73 nódulos, sendo 26 malignos e 47 benignos, e outra com 1034 nódulos sendo 517 malignos e 517 benignos. Os Índices de Diversidade de Shannon e de Simpson foram utilizados como descritores de textura. As características geradas foram submetidas à etapa de seleção de características com a utilização da Análise Discriminante stepwise. Após essa etapa foi realizada a classificação pela Máquina de Vetores de Suporte (MVS) onde foram obtidas taxas de sensibilidade de 85,64%, especificidade de 97,89% e acurácia de 92,78%.

The main objective of this thesis was to assess the influence of methods and intensity of use on phytosociological evolution and biodiversity of grasslands. This work includes grasslands in terms of their distribution, different ways of management and use. An important goal of this work was to evaluate the incidence of plant species in grassland lying in selected localities of the Czech Budejovice, Slavošovice and Radostice. The next section was set calculation and maintenance of the water and nutrient regime on the site fallow and statistical processing of data at the sites.Based on the findings were prepared tables and graphs that confirm and in some cases disconfirm occurrence of plant species with different modes of grassland management (mowing, grazing, fallow).

Le nombre croissant de travaux réalisés ces dernières années a montré que la bioacoustique est particulièrement intéressante pour le suivi d’espèces discrètes. L’émergence de dispositifs d’enregistrement autonomes, associée à de nouvelles méthodes d’analyse, ont récemment participé à l’accroissement des études dans ce domaine. Au cours des 30 dernières années, le Loup gris (Canis lupus), mammifère carnivore aux mœurs discrètes connu pour ses hurlements de longue portée, a fait l’objet de nombreuses études acoustiques. Ces dernières visaient notamment à améliorer son suivi, qui s’avère complexe du fait des grandes capacités de déplacement des loups, de l’étendue de leurs territoires et de la diversité des milieux dans lesquels ils vivent. Cependant, la bioacoustique passive a jusqu’alors très peu été exploitée pour le suivi du Loup. C’est dans ce contexte que la présente thèse s’est organisée autour de trois axes de recherche. Les deux premiers axes portent sur l’apport de la bioacoustique passive pour le suivi du Loup gris en milieu naturel. En combinant des analyses acoustiques, statistiques et cartographiques, le premier objectif a été d’élaborer une méthode pour l’échantillonnage spatial de vastes zones d’étude, afin d’y détecter des hurlements de loups à l’aide de réseaux d’enregistreurs autonomes. Ce même dispositif a ensuite permis, dans un second temps, de tester la possibilité de localiser les loups grâce à leurs hurlements. Les expérimentations conduites en milieu de moyenne montagne (Massif des Vosges) et de plaine (Côtes de Meuse), sur deux zones d’étude de 30 km² et avec un réseau de 20 enregistreurs autonomes, ont permis de démontrer l’intérêt de la bioacoustique passive pour le suivi du Loup gris. En effet, près de 70% des émissions sonores (son synthétique aux propriétés similaires à celles de hurlements de loups) ont été détectés par au moins un enregistreur autonome en milieu de moyenne montagne et plus de 80% en milieu de plaine, pour des distances enregistreurs– source sonore atteignant respectivement plus de 2.7 km et plus de 3.5 km. Grâce à un modèle statistique et à un Système d’Information Géographique, la probabilité de détection des hurlements a pu être cartographiée sur les deux zones. En moyenne montagne, elle était forte à très forte (>0.5) sur 5.72 km² de la zone d’étude, contre 21.43 km² en milieu de plaine. Les sites d’émission ont été localisés avec une précision moyenne de 315 ± 617 (SD) m, réduite à 167 ± 308 (SD) m après l’application d’un seuil d’erreur temporelle défini d’après la distribution des données. Le troisième axe de travail porte quant à lui sur l’application d’indices de diversité acoustique pour estimer le nombre d’individus participant à un chorus et ainsi contribuer au suivi de l’effectif des meutes. Les valeurs obtenues pour les six indices (H, Ht, Hf, AR, M et ACI) étaient corrélées avec le nombre de loups hurlant dans les chorus artificiels testés. De bonnes prédictions de l’effectif ont été obtenues sur des chorus réels avec l’un de ces indices (ACI). L’influence de plusieurs biais sur la précision des prédictions de chacun des six indices a ensuite pu être étudiée, montrant que trois d’entre eux y étaient relativement peu sensibles (Hf, AR et ACI). Finalement, les résultats obtenus avec les enregistreurs autonomes montrent le potentiel des méthodes acoustiques passives pour la détection de la présence de loups mais aussi pour les localiser avec une bonne précision, dans des milieux contrastés et à de larges échelles spatiale et temporelle. L’utilisation des indices de diversité acoustique ouvre également de nouvelles perspectives pour l’estimation de l’effectif des meutes. Prometteuses, l’ensemble des méthodes émergeant de ce travail nécessite à présent quelques investigations complémentaires avant d’envisager une application concrète pour le suivi du Loup gris dans son milieu naturel / The growing number of studies carried out in recent years has shown that bioacoustics is particularly interesting for the monitoring of secretive species. The emergence of autonomous recording devices, combined with new methods of analysis, have recently contributed to the increase of studies in this field. Over the last 30 years, many bioacoustic studies have been developed for the Grey wolf (Canis lupus), a secretive large carnivore known for its howls spreading over distances up to several kilometers. These researches notably aimed to improve its monitoring, which is complex because of the strong wolf dispersal capacities over long distances, the large extent of their territories and the various natural contexts in which they live. In this context, this PhD thesis was organized around three research axes. The first two axes focused on the contribution of passive bioacoustics for the Grey wolf monitoring in the field. By combining acoustic, statistical and cartographic analysis, the first objective was to develop a spatial sampling method adapted to large study areas for the detection of wolf howls by using autonomous recorders. Then, the same protocol was used to investigate the possibility to localize wolves thanks to their howls. Field experimentations, conducted in mid-mountain (Massif des Vosges) and lowland (Côtes de Meuse) environments, in two study areas of 30 km² and with an array of 20 autonomous recorders, demonstrated the high potential of passive bioacoustics for the Grey wolf monitoring. Indeed, nearly 70% of broadcasts (synthetic sound with similar acoustic properties to howls) were detected by at least one autonomous recorder in mid-mountain environment and more than 80% in lowland environment, for sound source-recorders distances of up to 2.7 km and 3.5 km respectively. By using statistical model and Geographic Information System, the detection probability of wolf howls was modeled in both study areas. In the mid-mountain environment, this detection probability was high or very high (greater than 0.5) in 5.72 km² of the study area, compared with 21.43 km² in lowland environment. The broadcast sites were localized with an overall mean accuracy of 315 ± 617 (SD) m, reducing until 167 ± 308 (SD) m after setting a temporal error threshold defined from the data distribution. The third axe focused on the application of acoustic diversity indices to estimate the number of howling wolves in choruses and thus to contribute to pack size monitoring. Index values of the six indices (H, Ht, Hf, AR, M, and ACI) were positively correlated with the number of howling wolves in the artificial tested choruses. Interesting size predictions based on real choruses were obtained with one of the indices (ACI). The effects of several biases on the reference values for the acoustic indices were then explored, showing that three of them were relatively insensitive (Hf, AR and, ACI). Finally, results obtained with autonomous recorders confirm the real potential of passive acoustic methods for detecting the presence of wolves but also for localizing individuals with high precision, in contrasting natural environments, at large spatial and temporal scales. The use of acoustic diversity indices also opens new perspectives for estimating pack sizes. All of the promising methods emerging from this thesis require now further investigations before considering a concrete application for monitoring the Grey wolf in its natural environment

La zone économique exclusive Mauritanienne est le siège d’upwelling et constitue une zone de transition où cohabitent des espèces d’affinités tempérée et tropicale. Pour comprendre le comportement spatio-temporel des assemblages démersaux du point de vue de leur composition, structuration, distribution de probabilité et diversité face aux préoccupations écologiques. Les facteurs abiotiques contribuent à la structuration des assemblages démersaux persistants au cours du temps. Les effets de la pêche étaient relativement faibles. Les trajectoires temporelles entre les assemblages et les conditions environnementales ont été mises en évidence pour certaines années et des zones. Dans les types d’habitats, un groupe minoritaire d’espèces très agrégatives obéissant au modèle de distribution en log-séries de Fisher et un autre majoritaire peu ou pas du tout agrégatives obéissant au modèle de distribution binomiale négative tronquée ont été identifiés. La diversité spécifique peut être divisé en deux groupes distincts et complémentaires : la richesse spécifique et l'autre associé à l’équitabilité. Un seul composant de la diversité ne peut donc pas représenter la diversité des poissons démersaux de la zone étudiée. Les GLM des indices complémentaires ont montré essentiellement un effet temporel et l’interaction Année-Strates bathymétriques. Aucun effet de l’effort de pêche n’a été observé sur la richesse spécifique, ni de la concentration en chlorophylle sur l’équitabilité. Ce travail pourrait fournir aux gestionnaires et aux scientifiques des connaissances complémentaires sur la dynamique spatio-temporelle des assemblages démersaux exploités dans des écosystèmes d’upwelling. / The Mauritanian exclusive economic zone is the seat of an upwelling phenomenon and constitutes a transition zone where species of temperate and tropical affinities coexist. To understand the spatio-temporal behavior of demersal assemblages from the point of view of their composition, structure, distribution of probability and diversity faced to ecological concerns. Abiotic factors contribute in the structuring of persistent groundfish assemblages over time. The fishing effects were relatively low, although significant in some years and in some specific geographic areas. Temporal trajectories between groundfish assemblages and environmental conditions have been highlighted for some years and in some specific areas. In each type habitats, two species groups were identified: a minority group of species very aggregative well fitted by Fisher’s log-series distribution and another majority of species little or not aggregative well fitted by the truncated negative binomial distribution. Diversity indices analyzed reveal that this set can be split into two distinct and complementary groups: a group associated with the species richness and another group associated with evenness. One component of diversity may not represent the diversity of the groundfish in the study area. GLMs of complementary indices showed essentially a temporal effect and Bathymetric strata-Year interaction. No effect of fishing effort was observed on the species richness and neither was the concentration of chlorophyll a on the evenness. This work could provide managers and scientists to further knowledge on the spatio-temporal dynamics of groundfish species assemblages exploited in upwelling ecosystems.