Dissertations / Theses on the topic 'Xeric'

The distribution and abundance of organisms is influenced by historical, abiotic, and biotic factors. The goal of my dissertation was to determine the distribution of anurans in the Big Bend region of the Chihuahuan Desert and to examine how abiotic and biotic factors shape the composition and structure of anuran communities at multiple spatial scales. My approach relied on extensive field surveys, laboratory and field experiments, and GIS modeling. Results from field surveys and reciprocal transplant studies of tadpoles indicate that abiotic conditions of the breeding site most likely do not play a significant role in causing the segregation of species among individual breeding pools. I used laboratory and mesocosm experiments to test for indirect and direct effects of predators on growth and survival of S. couchii tadpoles. I found that S. couchii tadpoles do not alter their behavior in the presence of predators and are very susceptible to predation. Although tadpoles reared with predators suffered high mortality rates, they metamorphosed significantly faster than tadpoles reared without predators. The reduced time to metamorphose is likely a result of the thinning of intraspecific competitors. Because the primary cause of death for S. couchii tadpoles is desiccation due to pond drying, predators may play an important role in facilitating metamorphosis by decreasing competitors and thus increasing per capita resources, therefore decreasing time to metamorphosis for the surviving tadpoles. At the landscape level anuran distributions seem to be influenced by environmental factors that influence the survival of the adult stage. At the level of the breeding site, microhabitat and abiotic components of the aquatic environment do not seem to play an important role in influencing breeding site use by different species. Rather, it seems likely that predation on tadpoles by predators is important in limiting the distribution of some species and that the fast-developing S. couchii may exclude other species from using sites via oophagy and predation on small tadpoles. My research elucidates the fact that in order to understand factors important in regulating ecological communities it is important to examine both abiotic and biotic factors at multiple spatial scales.

This study looks at the impact of elephant feeding on the Xeric Succulent Thicket component of Eastern Cape Subtropical Thicket (ECST) in Addo Elephant National Park (AENP). Observations of elephant feeding were carried out and vegetation transects were surveyed for impact of elephant feeding. The results indicated that the Nyati elephants spent the majority of their time grazing (nearly 90%), particularly the cow-young herds, and especially when the herd gathered in larger numbers. Browsing events were concentrated on Acacia karroo (81%) and there was no significant difference between the sexes in their preference for this species. Despite being subjected to most of the browsing, the majority of A. karroo trees were undamaged and the effect of elephants was generally light. It appears unlikely that, three years after re-introduction to Nyati, the elephants have had an effect on community structure of the vegetation. Surveys were conducted on stands of the alien invasive weed prickly pear Opuntia ficus-indica, and it was recorded that elephants in Nyati have had a dramatic effect on prickly pear, utilising all adult plants assessed and destroying 70% of them. This level of destruction in such a short period of time suggests that prickly pear is a highly favoured species. The results from the present study suggest that elephants can play a role in the control of prickly pear. Results are discussed in terms of elephants as both megaherbivores and keystone species, and as agents of intermediate disturbance.

Bibliography: leaves 100-114.
Human-induced land management practices are key factors which influence the dynamics of landscapes, land elements and biotic communities in Xeric Succulent Thicket, a notoriously fragile and low resilience ecosystem in the Eastern Cape, South Africa. In its natural state this vegetation type is characterized by a continuous mosaic of clumps of diverse woody shrubs in a matrix of grass, hardy dwarf shrubs and bare ground. When indigenous herbivores are replaced by domestic livestock at unsustainable stocking rates, the ratio of clump to interclump areas decreases. This has impacts on biodiversity at the landscape level, and affects the composition and species richness of plant, arthropod and reptile communities and fungal symbionts. The study has two main objectives: 1) to detennine the local-level effects of different types of land use on biodiversity in Xeric Succulent Thicket; and 2) to better understand the factors which affect biodiversity in different taxonomic groups and at different spatial scales, so that the preservation function of protected areas could be enhanced. The key questions which are addressed in the thesis are what does 'biodiversity' mean, and what are its different dimensions in Xeric Succulent Thicket; what roles do protected areas and other lands play in preserving biodiversity, how are different taxonomic groups affected by different types of land use; and how can biodiversity be monitored and measured? . The regional 'conservation landscape' is seen as the protected area plus the land immediately adjoining it, and is viewed as an integrated mosaic of anthropogenic landscapes (land management units), land elements (patches within landscapes). producer communities (assemblages of interacting plant species), consumer communities (assemblages of interacting herbivores and predators) and soil microorganisms. From a process point of view, the research relates the intensity of disturbance, mainly as a result of herbivory, to landscape complexity, the structure of land elements, and the species richness of producers and consumers within land elements. The patterns which emerge are interpreted in the context of ecosystem functioning, from the point of view of a practicing conservation biologist.

The investigation was designed to explore the structure, composition and activity of a biological soil crust on an acidic, sandy soil from a temperate climate. The crust covers several hundreds of square meters on the hilltop of a large terminal moraine. The conjugate alga Zygogonium ericetorum forms the essential matrix for the crust, a dense web of algal filaments with interspersed lichens and mosses. The crust is composed of three layers, with an uppermost layer consisting nearly entirely of a dense algal mat. In lower layers, a parasitic fungus, penetrating the algal cells, is another important component of the crust community. In this soil crust, photosynthetic and respiratory activity is stabilized at low water activities.

Thesis (M.S.)--University of Nevada, Reno, 2008.
"May, 2008." Includes bibliographical references (leaves 39-44). Library also has microfilm. Ann Arbor, Mich. : ProQuest Information and Learning Company, [2009]. 1 microfilm reel ; 35 mm. Online version available on the World Wide Web.

Includes bibliographical references.
Within the savannas of the southern Kalahari, land use practices can change habitat structure profoundly, so that rangelands either became densely wooden through bush thickening or are cleared completely using arboricides or manual tree felling and bush clearance, or are at some stage in between. Demands for the wood of camelthorn trees (Acacia reioloba), (the largest tree species growing on semi-arid and arid Kalahari sands) for firewood has also impacted habitat structure. Large trees are important in the Kalahari ecosystem because they provide shade, nesting and foraging sites for birds and mammals, as well as microhabitats that facilitate the existence of a suite of subcanopy plants. Indeed, large A. erioloba tress have been mooted as a context-depend keystones species, important to other biota and ecological prcesess. The primary aim of this study was to investigate the importance of A. erioloba to biodiversity, focusing on plants and birds.

Mycorrhizal networks (MNs) can influence tree establishment and resource competition but little is known regarding their underlying architecture in situ. This study examined the socio-spatial architecture of MNs between Rhizopogon spp. genets and interior Douglas-fir (Pseudotsuga menziesii var. glauca (Beissn.) Franco) trees in an old-growth forest. MN features were contrasted between plots with xeric versus mesic soil moisture regimes as a proxy for changes in site water stress anticipated with climate change. My objectives were to: (1) describe the fine-scale spatial patterns and autecological traits of R. vesiculosus and R. vinicolor mycelia systems and compare these between xeric and mesic plots; (2) describe the spatial patterns and architecture of Rhizopogon spp. MNs at the forest stand scale; (3) contrast MN architectures between phytocentric and mycocentric perspectives and between xeric and mesic plots, and identify critical determinants of MN architectures. Rhizopogon vesiculosus mycelia occurred deeper, were more spatially prolific, and colonized more tree roots than R. vinicolor mycelia. Both species were associated with moist microsites within plots, and had more prolific mycelia in mesic compared to xeric plots. The occurrence of R. vesiculosus shifted in the presence of R. vinicolor towards deeper soil horizons, suggesting competition and foraging strategy are important for niche partitioning between these species. At the forest stand scale, Rhizopogon spp. genets spanned tens of metres and colonized up to 19 trees, but R. vesiculosus genets were larger and linked more trees than R. vinicolor genets. Multiple tree cohorts were linked, with saplings and mature trees sharing the same fungal genets. Across all plots, the physical size of individual trees or fungal genets was positively related to their MN connectivity. This together with size asymmetries among different genets and trees resulted in the self-organization of complex, hierarchical scale-free MN architectures. The MNs appear robust to random perturbations but susceptible to the loss of large trees or fungal genets. No MN structural differences were found between phytocentric and mycocentric models or between xeric versus mesic plots. The pervasive mycelia and extensive MNs formed by these Rhizopogon spp. could influence interior Douglas-fir stand dynamics and resistance to water stress.

The historically poorly conserved subtropical transitional thicket (STT) of the Eastern Cape is overutilised by domestic stock and game in the more xeric areas, and has shown no signs of recovery from this grazing pressure. It has been postulated that no regeneration through seeding occurs. This project was undertaken to determine: 1) how much STT has disappeared between 1950 and present, and what the current conservation status is; and 2) whether regeneration of the xeric succulent thicket is taking place through seeding, and if so, where. The study was conducted at the Andries Vosloo Kudu Reserve near Grahamstown. Approximately one-third less STT was mapped in this study, based on 1981 Landsat images, than was mapped in 1950. Approximately 10 % of all remaining STT is conserved. The order Kaffrarian thicket is poorly conserved. Newly germinated seedlings of a wide range of shrub species occurred under the canopies of a wide range of shrubs which served as nurse plants, throughout a gradient of veld condition. Seedlings of Portulacaria afra, the dominant shrub in xeric succulent thicket, were most common. Similarly all saplings recorded in a survey of saplings were associated with bushclumps. One-third of all saplings have the potential to contribute to the spread of bushclumps. Regeneration of xeric succulent thicket through seeding probably does occur, contrary to current ideas. Ptareoxylon obliquum was the most common sapling, despite mature trees now being scarce following earlier heavier utilisation . P. obliquum was also the nurse plant which supported the highest density of newly germinated seedlings. The possible role of P. obliquum in the functioning of xeric succulent thicket is discussed. The confinement of seedlings and saplings to areas under the canopies of trees and shrubs implies that the xeric succulent thicket will not recover rapidly if allowed to rest. Active management techniques will be necessary if rapid recovery is required. Bare areas between bushclumps may no longer be suitable germination habitats because of high Al concentrations. There was no evidence to support the idea that germination and establishment of shrubs in clear areas is linked to episodic climatic events. Dung middens of recently reintroduced black rhinoceros may however aid in germination of seeds and establishment of seedlings under certain climatic conditions. Recommendations for further studies, based on the findings of this project, are made. Possible management techniques aimed at the rapid recovery of this veld are suggested, and management proposals for the Sam Knott Nature Reserve/Andries Vosloo Kudu Reserve complex are made.

Nas paisagens de montanha da região sudeste brasileira, áreas de afloramentos rochosos denunciam ao observador a natureza geológica de uma vegetação cuja existência local e distribuição relacionam-se às características de profundidade do solo e a efeitos da topografia. A serra do Itapetinga é uma elevação localizada ao norte da cidade de São Paulo onde afloram mais de 100 corpos pertencentes ao Neoproterozóico e que abrigam formações vegetais pleistocênicas persistentes pertencentes aos “complexos rupestres de granito”. Esta vegetação se encontra refugiada em sítios cujas condições edáfica e climática propiciam elevada diversidade biológica, além de endemismos e espécies pecilohídricas. Tais nuances edáficas e microclimáticas possibilitam a formação de microhabitats dotados de peculiaridades interessantes a grupamentos específicos de plantas. Dentre estes, as ilhas de solo constituem formações vegetais isoladas por matriz de rocha e que podem ser utilizadas como modelo de ilhas ecológicas em estudos de comunidades. As formas de vida prevalentes nos campos rupestres do sudeste brasileiro são determinadas por plantas hemicriptófitas e caméfitas. A proporção de fanerófitas varia em função da existência de microhabitats que propiciem o acúmulo de sedimentos, além de aumentar abruptamente no perímetro da rocha. A importância de terófitas é reduzida em relação a todas as demais formas, remetendo normalmente a ervas de comportamento ruderal. Apesar de sua ocorrência proporcionalmente menor nos afloramentos do sudeste brasileiro, plantas geófitas, após as hemicriptófitas, constituem a forma de vida mais frequente nas ilhas de solo - os microhabitats mais representativos da flora rupestre. O desaparecimento recente de tal vegetação relaciona-se diretamente com o aumento da procura do local para atividades de contemplação da natureza, para esportes de aventura e para coleta de plantas ornamentais, sendo comum o uso do fogo nas atividades relacionadas à contemplação e para controle do crescimento da vegetação em propriedades locadas na serra do Itapetinga e em seu entorno. Este estudo objetivou determinar a composição e a estrutura da vegetação nos afloramentos rochosos do Itapetinga, procedendo a análise das fontes de distúrbios sobre os ecossistemas para identificar evidências de impactos atuantes sobre tais comunidades vegetais rupestres. Para tal, procederam-se em 10 afloramentos coletas de plantas para identificação de morfotipos, atribuição de formas de vida e microhabitats utilizados pelas plantas, além de levantamentos de atividades humanas e evidências de impacto para utilização da matriz Pressão-Estado-Impacto-Resposta. As famílias mais representativas foram Asteraceae, Poaceae, Orchidaceae e Myrtaceae. As plantas hemicriptófitas, geófitas, helófitas e litófitas, aproximaram as proporções de formas de vida observadas das proporções esperadas para as classes de Raunkier, o que corrobora para a caracterização de uma fisionomia essencialmente campestre. A análise de matriz mostrou a prevalência de impactos negativos sobre positivos e a significância de atividades turísticas, esportivas e de infraestrutura em sua geração. Os afloramentos que concentram a riqueza rara e ameaçada são os que concentram o uso pela população, de forma que estratégias para a conservação destes relictos de vegetação perpassam invariavelmente por mudanças na forma de uso das rochas e de seu entorno
In the mountain landscapes of Brazilian Southeast, outcrops report to the observer the geological details of a vegetation whose its local existency and distribution is related to characteristics such as soil depth and effects of the topography. Serra do Itapetinga is an elevation located in the north of the city of São Paulo, where over a hundred of corps belonging to the Neoproterozoic spring out and contain persistent Pleistocene vegetation groups as part of the “granite cave formations”. This vegetation finds itself sheltered in sites in whose soil and climate conditions provide great biological diversity, besides endemisms and poikilohydry species. These soil and microclimate nuances allow the formation of microhabitats equipped with interesting peculiarities and specifc groups of plants. Among them, the soil islands compose vegetal formations cut off by a rock matrix that might be used as a model of ecological islands when studying communities. The forms that lives prevailing in the rupestrian fields of Brazilian southeast are determined by hemichryptophyte and chamaephyte plants. The proportion of phanerophyte varies according to the existence of microhabitats that propitiate accumulation of sediments, besides abruptly rise in the rock perimeter. The importance of therophyte is reduced in comparison with all the other forms, normally referring to species with ruderal behavior. Besides its smaller presence in the outcrops of Brazilian southeast, geophyte plants, after the hemichryptophyte, represent the most frequent form of life in the soil islands - the most characteristic microhabitats of the rupestral flora. The recent disappearance of this vegetation form is strictly related to the increase of the search of these locations for observation of nature, adventure sports and harvest of native plants, where the fire use is common for clearing lands. This study aimed to determinate the vegetation structures and composition on the outcrops of Itapetinga, followed by the analysis of the disturbance sources on ecosystem to identify the evidences of impact on the ancestry vegetation communities. Ten different outcrops were studied within its relation with the local human interference in other to identify evidences of impact. The more representative groups were Asteraceae, Poaceae, Orchidaceae and Myrtaceae. The study showed the expected proportions for the Raunkier classes which supports characterization of an essentially rural physiognomy. The analysis showed the prevalence of negative impact and significant touristic, sportive and infrastructure activities. The outcrops that concentrate rare and threatened richness are the ones frequented by the public in what way conservation strategies intervene changes in the rock use and its surroundings

Thesis (M.S.)--West Virginia University, 2008.
Title from document title page. Document formatted into pages; contains ix, 173 p. : ill. (some col.), col. maps. Includes abstract. Includes bibliographical references.

The tyrosine recombinases XerC and XerD function in the monomerisation of circular dimer replicons in many bacteria. The recombining complex contains two synapsed recombination sites and two molecules each of XerC and XerD. Recombination proceeds through two sequential steps of DNA strand exchanges separated in time and space. A specific pair of recombinases initiates the reaction forming a Holliday junction intermediate, which undergoes a conformational change to allow resolution to recombinant products by the other pair of enzymes. In an attempt to understand the molecular basis of recombination machine assembly and coordination of catalysis, chimeras of XerC and XerD were constructed and their properties studied in partial and complete recombination reactions. XerC and XerD are two-domain proteins, whose C-terminal regions contain all of the catalytic residues. It is demonstrated here that XerC or XerD variants lacking their N-terminal domains are active in recombination when combined with their wild type partners. However, the normal pattern of catalysis is dramatically altered: strand exchange by the recombinase variant is stimulated, while that by the wild type partner is impaired. The primary determinants for the mutant phenotype are shown to reside in the region of a-helix B of XerCD. It is also demonstrated that the exchange of the extreme C-termini of XerCD has a profound effect on the direction of HJ resolution. These observations confirm the importance of the cyclic C-terminal "donor-acceptor" interactions between XerC and XerD. Finally, the recombination reaction catalysed by ResD, a tyrosine recombinase encoded by the F-plasmid of E. coli, which is believed to function in the monomerisation of F-plasmid dimers, was reconstituted in vitro. Recombination is intramolecular and shows topological selectivity. ResD lacks a region corresponding to the N-terminal domains of XerCD, and hence its characterisation might supply further insights about the roles of the N-terminal domains of tyrosine recombinases.

Deserts are the largest terrestrial ecosystem (Laity, 2009). It is estimated that 69% of desert lands that are used for agriculture around the world are either degraded or undergoing desertification as a consequence of climatic variation or intensive human activity (UNEP, 1992; Souvignet et al., 2012). Additionally, climate change models predict that the variability of rainfall events will intensify in desert regions (Faramarzi et al., 2013). Because desert environments contain a limited range of higher plants and animals, soil microbial communities are likely the most productive component of these systems as well as the dominant drivers of biogeochemical cycling (Makhalanyane et al., 2015). As a result, understanding how microbial communities respond to varying degrees of moisture input and xeric stress is important for developing sustainable resource management and agriculture practices, as well as predicting the impacts of global climate change on terrestrial systems (Paul, 2014). This study focuses on the Namib Desert in western Namibia, the oldest and one of the driest deserts on the planet (Prestel et al., 2008). In the Namib Desert, sporadic rainfall events provide 25 mm of mean annual rainfall a year; however, near the coast, consistent fog formation provides a form of available water to an area that would otherwise be hyperarid (Eckardt et al., 2013b). We examined the effect of xeric stress on microbial community structure and function in these desert soils, taking advantage of the naturally occurring gradient of water availability. Soil samples were collected every 10 km on a 190 km transect from the fog-dominated coastal region, through an inland area of high aridity, into a region of increased rainfall. Soil physicochemical properties and microbial community structure and function were assessed across the transect. Both microbial community structures and functions differentiated based on three a priori defined zones of differing xeric stress (i.e., the Fog , Dry , and Rain zones). Water availability was indicated as significantly shaping the microbial community structure and function in the central Namib Desert. In the fog dominated regions, stochastic processes dominated community assembly, while the deterministic effects of environmental filtering shaped community structure in the rest of the transect. In addition, a significant relationship between community structure and function was found (Mantel r = 0.2; p < 0.01), indicating changes in community structure coincided with changes in function.
Dissertation (MSc)--University of Pretoria, 2016.
tm2016
Microbiology and Plant Pathology
MSc
Unrestricted

Rotating wheat with other crops is a common practice in the Willamette Valley of western Oregon. Depending upon previous crop and soil type, current N fertilizer recommendations for wheat in the Willamette Valley vary widely. Excessive fertilizer poses environmental risk, whereas lower N inputs than required by the crop represent economic losses to growers. Growers and their advisors face the challenge to minimize the environmental risk, and at the same time to maintain or increase economic returns. Questions are often raised concerning the efficient use of N fertilizer and accurately predicting the amount of N needed by wheat following different crops. The first study measured growth, N uptake and N use efficiency (NUE) of winter wheat grown after either a legume or oat for three years. In all three growing seasons, winter wheat showed higher biomass, N uptake and NUE when grown after a legume than after oat. The contribution of legume was evident before the wheat was fertilized in spring, indicating that legume N had mineralized in fall or winter. Contribution of soil N to wheat suggested that fertilizer N can be reduced by 44 kg N ha����� if a legume is grown previously. Nitrogen use efficiency estimated 50 to 70 days after N application by isotopic method (24 to 94%) was comparable with that estimated simply by difference (21 to 94%) at the same time. The second study predicted gross mineralization rates using analytical models. Comparable N mineralization was predicted by a model assuming remineralization and a model assuming no remineralization, suggesting that remineralization was negligible. In the spring, mineralization-immobilization turnover was at a lower pace than expected in both rotations. In two growing seasons, gross mineralization rates were higher where the previous crop was legume (0.37 to 0.74 kg����� ha����� day�����) as compared to where oat was grown previously (0.14 to 0.6 kg����� ha����� day). Negative net mineralization indicated that fertilizer N was immobilized in the oat-wheat rotation. The third study evaluated calibration and digestion techniques used to determine elemental concentration in grasses. Use of a dry ashed standard to calibrate the ICP spectrometer generated highly variable calibration curves and was not a viable calibration method. Good agreement was found between chemical and microwave digested standards. Dry ashing resulted in considerable S and Mn losses, whereas, perchloric acid digestion and microwave digestion showed similar results. Our study suggests that if routine analysis are to be performed for macro nutrients or involve trace level work, the best method is microwave digestion with chemical standard calibration of ICP spectrometer.
Graduation date: 1999

Tese de mestrado, Microbiologia Aplicada, Universidade de Lisboa, Faculdade de Ciências, 2019
The effects of increased nitrogen (N) input in the ecosystems have brought concern for some time, however, the long-term consequences of this input to Mediterranean ecosystems are poorly studied. The Mediterranean ecosystem is considered a hotspot of biodiversity; the Mediterranean basin was considered one of the places in the world with most biodiversity. Taking in consideration that these ecosystems are regarded as environments under N limitation, changes in N availability will alter the relationships between the organisms. The research presented here was carried out on the Mediterranean basin and it is part of an ongoing study over the last 10 years, in which fields were fertilized with different quantities and forms of N. To understand the consequences of this fertilization, diazotrophic bacteria were isolated from rhizospheric soil of Ulex densus subjected to different N addition and characterized in terms of the structural and functional diversity of the communities, using this community as an ecological marker for comparing the different treatments. The methodology applied to understand the ecological consequences was the isolation of the rhizospheric bacteria in N free media and characterization of this collection of isolates, in terms of diversity (phenotypic and genotypic), morphophysiology (distribution of the isolates by different morphotypes), structure (identification of the genera associated with the treatments), functionality (ability to perform ammonification, nitrification and/or denitrification) and metabolic plasticity (ability to use different carbon sources). The N fixation of these isolates was confirmed by their growth in solid and liquid N free media and by isotopic characterization of the ratio of 15N over 14N; a search for the nifH gene was also performed. For this community there were no differences in diversity nor at the morphophysiological level between the different treatments. However, a higher number of isolates was detected in the treatments with higher NH4+ inputs (40A, and 80AN). The ability to perform N fixation was confirmed through multiple passages in solid and liquid N-free media and nifH gene was detected through PCR and dot-blot hybridization, though this was not possible for every representative isolate. Differences with genera associated with the form and quantity of N added to the soil were observed, with some genera only appearing in certain treatments. Every isolate presented more than one function in the N cycle and a decrease in nitrification together with an increase of denitrification was observed along with the increase of bioavailable N. Isolates belonging to genera detected exclusively in treatment 80AN presented higher N content and higher denitrification rates. The variation of the metabolic plasticity between the treatments increased with N fertilization, since the control treatment had the more consistent response for metabolic plasticity. The increase on the isolates number followed the same pattern as the proliferation of U. densus, showing that the potential for N fixation was not inhibited by NH4+ addition. The differences in genera associated with the treatments evidenced a change in the structure of the community. The results of multifunctionality showed a shift in the diazotrophic community, since nitrification and denitrification presented specificity towards different forms of fertilization. The higher variation of the metabolic plasticity associated with N fertilization can be related to changes in carbon source availability in the soil. From the work presented here and future work can arise a platform to direct alterations on the agriculture and ecological guidelines. These alterations are essential to protect this kind of ecosystem, which is extremely important due to the unique biodiversity associated with it.
Há algum tempo que os efeitos do aumento de nitrogénio (N) introduzido nos ecossistemas leva a preocupação, no entanto, as consequências a longo prazo desta introdução nos ecossistemas mediterrânicos estão pouco estudadas. O ecossistema mediterrânico é considerado um hotspot de biodiversidade; a bacia mediterrânica é um dos locais com mais biodiversidade no mundo. Tendo em consideração que estes ecossistemas são considerados ambientes com limitações ao nível do N, as mudanças na disponibilidade de N vão alterar as relações entre os organismos. O estudo aqui apresentado foi levado a cabo na bacia mediterrânica e faz parte de um estudo que já começou há 10 anos e continua a ser efetuado, em que os talhões foram fertilizados com diferentes formas e quantidades de N. De forma a entender as consequências desta fertilização, foi isolada a comunidade de bactérias diazotróficas a partir de solo rizosférico de Ulex densus sujeito a diferentes adições de N e foi caracterizada a diversidade estrutural e funcional da comunidade. A comunidade diazotrófica foi utilizada como um marcador ecológico para a comparação entre os diferentes tratamentos. Os microrganismos que conseguem realizar a fixação de N, ou seja, a conversão de N2 em NH3, são chamados de diazotróficos. Esta conversão ocorre através da ação da enzima nitrogenase, e existem três tipos desta enzima que variam no cofator associado: Mo, Va ou Fe. A estrutura da comunidade diazotrófica não apresentou diferenças entre os tratamentos em termos de diversidade, no entanto o índice de diversidade genotípico apresentou um poder de discriminação maior que o índice de diversidade fenotípico entre os isolados e, portanto, é essencial complementar os resultados fenotípicos com o perfil genotípico obtido por PCR fingerprinting. Foi detetado um número mais elevado de isolados diazotróficos heterotróficos nos tratamentos com maior adição de NH4+ (40A e 80AN), estes são os mesmos tratamentos em que existe proliferação de Ulex densus, mostrando assim que o potencial para a fixação de N não foi inibido pela adição desta forma de N. Foram observadas diferenças entre os géneros identificados dependendo da forma e quantidade de N adicionado ao solo, mostrando mudanças na estrutura da comunidade. Para esta identificação foram escolhidos 40 representantes, sendo 10 de cada tratamento, e foram considerados uma boa representação da coleção de isolados por não apresentarem valores de semelhança superiores a 55%. A maioria dos géneros que foram identificados estão associados com a fixação de N ou pelo menos apresentam um espécie pertencente ao género que apresenta a capacidade de realizar fixação de N. A capacidade de realizar fixação de N foi confirmada através de múltiplas passagens por meio sem N quer na forma líquida quer na forma sólida e o gene nifH foi detetado através da técnica de PCR e por hibridação dot-blot. Apesar de os isolados representantes terem sido identificados como sendo pertencentes a géneros associados com a capacidade de realizar a fixação de N e os pares de primers escolhidos serem capazes de amplificar o gene nifH dos clusters onde estes géneros estão incluídos, não foi possível amplificar e/ou detetar o gene nifH da maioria dos isolados. Isto pode significar que o gene nifH destes isolados é diferente das sequências utilizadas para desenhar os primers. Até há pouco tempo, era comum associar determinados grupos de microrganismos a uma biotransformação especifica do ciclo do N. Contudo ultimamente tem sido exposto que a maioria dos isolados tem potencial para realizar diversas biotransformações de N, nomeadamente combinações de fixação de N, amonificação, nitrificação e desnitrificação. Isto representa um fator extremamente importante, uma vez que a multifuncionalidade é essencial para a adaptação dos microrganismos ao meio ambiente. Os isolados representantes de cada um dos tratamentos foram testados para diferentes processos do ciclo do N: amonificação, nitrificação e desnitrificação. Todos os isolados apresentaram mais do que uma função no ciclo do N. Pode ser observada uma mudança na multifuncionalidade da comunidade diazotrófica devido ao aumento da biodisponibilidade de N. De facto, a capacidade de realizar nitrificação foi encontrada mais frequentemente entre os isolados representantes da comunidade de tratamentos que recebem mais baixas quantidade de NH4+ (tratamento controlo e 40AN), o que está de concordo com o que foi reportado em estudos anteriores, em que o aumento da disponibilidade de NH4+ leva a uma inibição na nitrificação. Foi encontrada capacidade desnitrificante em todos os tratamentos, no entanto os isolados do tratamento 80AN (recebe mais nitrato) apresentaram taxas de desnitrificação mais elevadas. Taxas de desnitrificação mais elevadas podem ser relevantes como mecanismo de desintoxicação de nitrato, uma vez que elevadas concentrações de nitrato podem inibir a fixação de N. A alteração da multifuncionalidade microbiana associada com biotransformações de N está associada a mudanças na composição da comunidade diazotrófica, sendo corroborado pelas diferenças nos géneros identificados nos diferentes tratamentos. Com base nos resultados apresentados, é sugerido que o isolado identificado como pertencente ao género Pedobacter apresente uma sensibilidade para concentrações elevadas de N, e por isso pode ser possível que a ausência deste género possa estar associada a um aumento da disponibilidade de N. Por esta razão, este género pode ser um candidato a indicador biológico das alterações no ecossistema. Não foi possível associar a multifuncionalidade dos isolados com a plasticidade metabólica. No entanto, quando foram analisados dois géneros comuns a diferentes tratamentos - Pseudomonas e Stenotrophomonas - foi possível observar diferenças na resposta à adição de N. Os isolados identificados como Pseudomonas apresentaram uma resposta uniforme ao longo dos diferentes tratamentos, correspondendo a uma elevada plasticidade metabólica. Contudo, no caso dos isolados identificados como Stenotrophomonas o mesmo já não foi observado, pois a plasticidade metabólica aumenta com o aumento da disponibilidade de N. Isto pode dever-se à adaptação destes microrganismos ao aumento da disponibilidade de N ou os isolados podem pertencer a espécies distintas com diferente plasticidade metabólica. Apesar de ser possível identificar algumas diferenças entre os tratamentos em termos das propriedades funcionais da comunidade, estas diferenças não são tão evidentes como seria de esperar, de acordo com a literatura, e não corroboram completamente a teoria de que a comunidade diazotrófica devia ser afetada pela adição de N. Estas discrepâncias podem dever-se ao ecossistema que está a ser estudado, o ecossistema mediterrânico, que apresenta características distintas dos outros ecossistemas estudados em trabalhos semelhantes, e por isso os efeitos da adição de N podem não ser os mesmos. Por último, a comunidade escolhida neste trabalho como indicador das respostas do ecossistema, a comunidade diazotrófica, pode não ter sido a escolha certa, uma vez que não se verificam grandes alterações estruturais com o aumento da biodisponibilidade de N. A comunidade estudada foi isolada a partir do solo rizosférico de Ulex densus que é uma espécie que prolifera nos tratamentos com maior disponibilidade de N. Desta forma a planta pode estar a contrabalançar os efeitos da adição de N levando a que não haja diferenças na comunidade diazotrófica entre os tratamentos. Pode ainda ser o facto de a comunidade rizosférica conseguir aguentar as pressões ecológicas e manter este grupo de microrganismos, uma vez que estes apresentam uma função importante que pode ser benéfica para a comunidade rizosférica quando em condições de N limitante. O trabalho apresentado neste estudo, e trabalho futuro que possa advir dele, pode criar uma plataforma para alterações nas políticas agrícolas e ambientais, que são necessárias para a preservação deste tipo de ecossistemas que apresentam uma biodiversidade única.

Fire suppression in the southern and central Appalachian Mountains has resulted in an alteration to vegetation structure and composition. For this research the dominant species, abundance, density and age structure of the ericaceous shrub layer is characterized on four sites across the southern and central Appalachian Mountains. Fire histories for each of the sites varied, and were determined in previous research using dendroecological techniques. Over 800 ericaceous shrubs were collected, species included Pieris floribunda (Pursh) Bentham & Hooker f., Rhododendron maximum L. and Kalmia latifolia L.. Basal area of ericaceous shrubs was significantly different between sites. Age structures show that when fire suppression started Ericaceae began to establish. A few Ericaceae cross-sections displayed scars, that are likely associated with fire events, suggesting they probably survived mild fire events. Ericaceous shrub age structures were also compared to SPB outbreaks and PDSI. There were no significant correlations, but field observations suggest that SPB may be providing conditions suitable for Ericaceae establishment. Topographic patterns reveal that Kalmia latifolia is most abundant at mid-slope positions and decreases at higher and lower slope positions. There were significant differences in the density between slope positions averaged across all sites. Sites with the most recent and frequent fires did not have any of the three ericaceous shrubs collected at the slope bottom or ridge-top. At the most fire-suppressed site Ericaceae are present at every slope position. Age structures reveal that the oldest Ericaceae are found at the mid-slope positions while the age of thickets appears to decrease away from the mid-slope position. This pattern suggests that Ericaceae are moving into slope positions where they were previously less abundant. Sites with the most recent frequent fire regime seem to have prevented Ericaceae from heavily inhabiting high and low topographic positions while also reducing the overall basal area and density of Ericaceae.

The taxonomic composition, structure, and diversity of current local species assemblages results from an interacting complex of historical, regional ecological and local ecological factors. Structural differences between such current species assemblages are primarily determined by changing ecological conditions across spatial gradients. These conditions may change abruptly or they may represent a gradual divergence. Across the Botswana Kalahari basin there is a gradual northeast-southwest aridity and dung type gradient, which was demonstrated to strongly influence dung beetle assemblage structure at six study sites from Chobe National Park to the Central Kalahari Reserve to the Kgalagadi Transfrontier Park using carrion and four dung types as bait (pig, elephant, cattle, sheep). Regional patterns were primarily influenced by climate (rainfall) while dung type mainly showed a local influence on patterns of variation. Four distinct biogeographical groups were defined for the study region comprising widespread, northeast/widespread, northeast, and arid southwest Kalahari-centred species. Biogeographical diversity was higher in the more mesic NE than the arid SW but varied somewhat between bait types. In the SW, Kalahari endemics dominated all bait types. In general, abundance and species richness declined along the aridity gradient although the pattern was uneven due to low numbers in the north of the Central Kalahari Game Reserve. Species showed high turnover (beta – diversity), particularly between the moister NE and the Kalahari/Savanna ecotone. Hierarchical Analysis of Oblique Factors showed statistically distinct separation between assemblage structure at the six study sites and that the proportion of mesic NE shared influence on assemblage composition declined towards the SW where there was an increase in Kalahari endemics. Similarly the proportion of arid SW shared influence declined towards the NE. Plotting these results onto a map showed that the point of intersection between shared NE or SW influence lay very close to the ecotone between SW (Kalahari Xeric Savanna) and NE-centred ecoregions (Acacia-Baikiaea Savanna) defined for the area by Olson et al. (2001). In terms of dung type diversity, increasing aridity across the Kalahari represents a gradient of diminishing resources with the loss of large dung types to the SW and increasing dominance of dung pellets. Several different patterns of response were shown using different methods. Four principal patterns of bait type association were indicated by one method. Another method showed that, rather than diminishing numbers of competing species leading to widening niche widths to the SW, niche widths were narrowest at the Kalahari / mesic Savanna ecotone. Using several other multivariate techniques, three different patterns of dung type resource partitioning were demonstrated that paralleled the aridity gradient, one common to the NE and two to the SW. The historical, regional and local ecological factors influencing these patterns of dung beetle assemblage structure are discussed as well as implications and recommendations for conservation.
Thesis (PhD)--University of Pretoria, 2011.
Zoology and Entomology
unrestricted

碩士
國立臺灣大學
語言學研究所
96
This thesis investigates the phonological change of entering tone in Sino-Xenic languages based on Optimality Theory. The research issues include (1) How is Optimality Theory applied to historical linguistics on the basis of Sino-Xenic languages? (2) How is Opacity in historical linguistics represented in Optimality Theory by means of Sino-Xenic languages? (3) How does internal syllable structure affect phonological change in Sino-Xenic languages? In this study, the data of entering tone are collected according to Fāngyán Diàochá Zìbiăo (A wordlist for dialectal research). Specifically, the layers, which are pertinent to each other, from three Sino-Xenic languages, Literal Reading (Wéndú) in Southern Min and Kan-on in Sino-Japanese and Modern Sino-Korean, are compared. In addition, instead of the traditional method, Shè, this study concentrates on vowel changes by dividing vowels into [a]-vowel group, non-[a]-vowel group and Hékŏu. First, to investigate the compatibility of historical phonology and modern phonological theories, this study adopts Faithfulness, Markedness, Dispersion-Optimality Theory (FMD-OT) (Sanders 2003), paying specific attention to vowel changes. The results show that Optimality Theory can account for the historical change of entering tone in Sino-Xenic languages and FMD-OT succinctly explains vowel changes in terms of dispersion constraints. Furthermore, this study amends Sanders’ FMD-OT by proposing a new set of constraints for central vowel. Second, this study also discusses opacity in historical phonology. To solve this problem, this study modifies and extends Candidate Chains (McCarthy 2007). It is proposed historical sound change is continual, each stage is evaluated parallelly, and new constraints are activated and reranked with previous constraints. This proposal is supported by Gĕngshè (梗攝) in Southern Min, Division III of Shēngshè (深攝) and Xiánshè (咸攝) in Sino-Japanese and Gĕngshè (梗攝) in Sino-Korean. This study finally explores the influence of syllable structure on sound changes in Sino-Xenic languages. Two factors are suggested, Phonotactic Constraints and Licensing Constraints. When the moras belong to the same branch in syllable node, there is no interaction of the segments, such as Southern Min. On the contrary, when the moras locate in different branches, the segments interact, such as Sino-Japanese and Sino-Korean. What distinguishes Sino-Japanese from Sino-Korean is whether mora is prominent or not. On one hand, if the mora is prominent, the mora is maintained, for example, Sino-Japanese. On the other hand, if the mora is not prominent, the mora is likely to be deleted, i.e. Sino-Korean, when the interaction takes place.

XerC et XerD, deux recombinases impliquées dans la recombinaison site spécifique, résolvent les multimères d’ADN en monomères. Cette réaction se produit au niveau du site dif du chromosome, et nécessite le domaine C-terminale de la protéine de division cellulaire FtsK. Caulobacter crescentus est une bactérie aquatique de type Gram-négative qui se retrouve dans plusieurs environnements. Elle présente un cycle cellulaire asymétrique avec deux types de cellules distinctes. Cette propriété peut être utilisée pour synchroniser la croissance d’une population bactérienne pour permettre l’étude de l’expression de gènes à travers le temps et les liens entre le cycle cellulaire et le développement de la bactérie. La liaison à l’ADN et la capacité de former des complexes covalents (phosphotyrosyl) avec le site dif de C. crescentus (ccdif) ont été testé pour les recombinases de C. crescentus (ccXerC et ccXerD). Les deux recombinases ont eu une meilleure liaison au demi-site gauche de ccdif et sont incapable d’effectuer une liaison coopérative, contrairement à ce qui se produit au niveau du site dif de E. coli. La formation de complexes covalents a été testé en utilisant des «substrats suicides avec bris» marqués à la fluorescence ainsi que des protéines de fusion (marquées ou non à la fluorescence). Des complexes ADN-protéines résistants à la chaleur et au SDS ont été observé lors de la réaction de ccXerC et ccXerD de type sauvage avec ccdif, mais pas lors de la réaction de mutants avec le même ADN. Des complexes covalents phosphotyrosine sont formés de façon plus efficace sur les substrats suicides avec un bris au niveau du brin supérieur que ceux ayant un bris au niveau du brin inférieur. Dans les deux cas, c’est ccXerC qui est resté lié de façon covalente à l’ADN de ccdif.
In most bacteria, the chromosomal dimer resolution process is mediated by two tyrosine recombinases, XerC and XerD, which bind cooperatively and perform the recombination reaction at the dif site near the terminus of replication. This reaction also requires the C-terminal domain of the cell division protein FtsK. Caulobacter crescentus is an aquatic Gram-negative bacterium found in various environments. This bacterium has an asymmetric cell cycle which can be used to synchronize cell growth in order to study the temporal expression of a gene and the interconnection between the cell cycle and development. The binding activity and the formation of phosphotyrosyl complex of the C. crescentus recombinases, ccXerC and ccXerD, were tested on the C. crescentus dif (ccdif) site. Both ccXerC and ccXerD bound preferentially to the left half-site of ccdif and showed reduced cooperative binding, unlike what was found with the E. coli dif site. Covalent complex formation activity was tested by using fluorescently labelled linear “nicked suicide substrates” and labelled proteins. Heat and SDS-resistant protein-DNA complexes were formed when both wild-type ccXerC and ccXerD reacted with ccdif but not in the presence of active-site tyrosine mutant proteins. Phosphotyrosine complexes formed on the top-nicked suicide substrate were found to be more efficient than on the bottom-nicked suicide substrates and surprisingly ccXerC remained bound to both top and bottom-nicked ccdif suicide substrates.

Research Doctorate - Doctor of Philosophy (PhD)
Although bacteria appear to be simple organisms when compared to eukaryotes, the systems by which they undergo chromosome replication and cell division are exceedingly complex. Due to the circular nature of many bacterial chromosomes, an odd number of crossing-over events that can result from homologous recombination lead to the formation of covalently linked chromosomes, known as “chromosome dimers”. These dimers need to be resolved before cell division can occur. Bacteria undergo this resolution of chromosome dimers via site-specific recombination. In Escherichia coli, Pseudomonas aeruginosa, Vibrio cholerae and other bacteria, the action of FtsK, XerC and XerD produces two pairs of strand-exchange reactions which resolve chromosome dimers, thus allowing cell division to proceed. Some bacteria (e.g. Lactococcus lactis) and most archaea encode only a single Xer recombinase that does both strand exchanges. FtsK interacts with specific sequences that orient the protein toward “dif” sites, positioning the chromosome so XerC/ XerD can undertake the recombination reaction. FtsK also has a role during cell division in which it pumps DNA, at an extraordinary rate, to hasten cytokinesis and chromosome segregation. The N-terminus of FtsK is primarily responsible for localisation of the protein during cell division and assembly of cell-division machinery, whilst the C-terminus forms the motor domain, responsible for translocase activity and interactions with XerD. The work conducted herein, sought to confirm structural and functional information about FtsK from E. coli and P. aeruginosa. Functionally, it was important to identify the conserved nature of the protein by performing in vitro recombination experiments across both species. These recombination assays were used in downstream FtsK inhibition experiments where a suite of inhibitory compounds was designed to target its ATPase activity in vitro and in vivo. As part of structural studies, mutagenesis of the amino acids in the E. coli FtsKγ – XerD interaction was completed, elucidating important interactions between these two protein subunits. The final stage of experimentation was dedicated to crystallography studies, aimed at identifying a high-resolution structure of FtsK in its active state. The results of the mutagenesis studies were published in October 2016 in a paper titled “Activation of Xer-recombination at dif: structural basis of the FtsKγ-XerD interaction.” This paper featured structural information of FtsKγ and XerD and how mutations in this interaction can affect its recombination effect in vitro and in vivo.

Tesis (Grado Doctor en Ciencias Biológicas)--Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Lugar de Trabajo: Goebotánica y Fitogeografía. Instituto Argentino de Investigaciones de Zonas Aridas-IADIZA-Universidad Nacional de Cuyo. CONICET-CCC Mendoza. Universidad Nacional de Córdoba. 2015 -- 131 h. con Apéndices + CD. ils.; tabls.; figuras.Contiene Referencia Bibliográfica y Publicaciones Derivadas de la Tesis. Abstract en español e inglés.
En el ambiente xérico, extra andino, del norte de Patagonia, Araucaria araucana crece en afloramientos rocosos (morros) de superficies variables, formando pequeños bosques puros, probablemente restos de una vegetación boscosa más extensa. Este tipo de bosque abarca aproximadamente un tercio del área de distribución de la especie en Argentina. Se ha postula do que en estos ambientes la regeneración de A. araucana por semilla es escasa o nula. El objetivo general de este trabajo fue estudiar las vías de reproducción y establecimiento de bosques xéricos de A. araucana. Se evaluó la abundancia de renovales de origen agámico y de semilla, la capacidad de regeneración por semillas y la supervivencia de plantines. Además, se caracterizó la condición de micrositios favorables-desfavorables para la regeneración, a través de parámetros ambientales. Se concluye, que la variación interanual en la producción de semillas, la predación y la disponibilidad de micrositios adecuados para la germinación y posterior supervivencia de plantines de A. araucana, serían limitantes para la regeneración sexual en este bosque. La vía de regeneración dominante de A. araucana en ambientes xéricos es la asexual, principalmente asociada a microambientes rocosos.

L'état circulaire du chromosome bactérien pose un problème particulier lors de la réplication. Un nombre impair d'événements de recombinaison homologue donne des chromosomes dimères concaténés qui ne peuvent pas être divisés en cellules filles. Pour résoudre ce problème, les bactéries ont mis au point un mécanisme de résolution des dimères basé sur un système de recombinaison spécifique au site. Ceci est effectué par le système Xer/dif. Dans ce système, les protéines Xer effectuent une réaction de recombinaison dans le site dif au niveau du septum cellulaire immédiatement avant la division cellulaire. Dans la plupart des bactéries, cette réaction est effectuée par deux recombinases, XerC et XerD. Cependant, Streptococcus suis, un agent pathogène zoonotique important utilise un système de recombinaison différent, constitué d'une seule enzyme recombinase appelée XerS, qui catalyse la réaction de recombinaison dans un site dif non conventionnel. Pour caractériser le mode de clivage de XerS, des expériences EMSA ont été réalisées en utilisant des fragments de PCR marqués par HEX et des "suicide substrates". Nos données suggèrent que 1.) XerS est capable de lier la séquence entière de difSL; 2.) XerS lie plus efficacement le côté gauche des mutants difSL incomplets que le côté droit; 3.) XerS coupe les brins supérieur et inférieur du site difSL, avec une réaction plus efficace au bas. 4.) Modifications des nucléotides de la région la plus externe ou de la région centrale changent les préférences de clivage. 5.) XerS n'a montré aucune activité spécifique sur un autre site dif non conventionnel des Firmicutes, 6.) XerS interagit avec la sous-unité FtsK-y. L'ensemble des résultats présentés permet de mieux comprendre le fonctionnement de la recombinaison XerS dans le système de recombinase unique de Streptococcus et comment cette recombinaison est régulée par des facteurs de l'hôte.
The circular state of the bacterial chromosome presents a specific problem during replication. An odd number of homologous recombination events results in concatenated dimer chromosomes that cannot be partitioned into daughter cells. To solve this problem, bacteria have developed a mechanism of dimer resolution based on site-specific recombination system. This is performed by the Xer/dif system. In this system, the Xer proteins perform a recombination reaction in the dif site at the cell septum immediately prior to cell division. In most bacteria this reaction is performed by two recombinases, XerC and XerD. However, an important zoonotic pathogen; Streptococcus suis harbors a different recombination system, composed by a single recombinase enzyme called XerS, that catalyzes the recombination reaction in an unconventional dif site; difSL. A region characterized by two imperfect inverted repeat regions that flank a central region of 11 bp.To characterize the mode of cleavage of XerS, EMSA experiments were performed by using HEX-labelled PCR fragments and “nicked suicide substrates”. Our data suggests that; 1.) XerS is able to bind the entire difSL sequence; 2.) XerS binds more efficiently the left half side on incomplete difSL mutants than the right half side; 3.) XerS cleaves both the top and bottom strands of the difSL site, with a more efficient reaction at the bottom strand; 4.) Nucleotides at the outermost region of a T rich region seem to be determinant for binding selectivity and modifications of the extra spacing between the inverted repeat arms as well as length modifications of the central region change cleavage preference. 5.) XerS did not show any specific activity on another unconventional dif site in Firmicutes, as tested on difH. 6.) XerS interacts with FtsK-y subunit. This research aims to understand how XerS recombination works in the single recombinase system of Streptococcus and how this recombination is regulated by host factors. Exploration of these recombinases will provide a better understanding of the mechanisms of DNA exchange and genome stability in bacteria. It can also increase our knowledge of the evolution and speciation of recombinogenic bacteria.