Thesis (Ph.D) -- University of the Western Cape, 2008. / Includes bibliographic references (leaves 187-206).

Thesis (M.D.S.)--University of Hong Kong, 2005.

Magister Scientiae - MSc / Antarctica provides some of the most extreme environments on earth. Low temperatures, low water availability and nutrient deficiency are contributing factors to the limited colonisation of Antarctic biotopes, particularly in the continental Dry Valleys. The survival of microorganisms in this harsh continent provides the basis for the significance of this study. This study aimed to explore microbial phylotypic diversity across a 500 m altitudinal transect in the Miers Dry Valley, Ross Desert, East Antarctica. The study also attempted to infer from phylogenetic data, the possible presence of indicative phenotypes which might contribute to a functional microbial community. / South Africa

<p> Understanding the mechanisms of microbiome assembly during host development is crucial for successful modulation of the gut microbiome to improve host health and growth. Detailed characterization of the swine gut microbiome through meta-analysis allows us to understand the dynamics of microbial community succession, as well as the transient and natural variations between timepoints and animals. A total of 3,313 fecal samples from over 349 pigs covering 60 time points (from birth to market age) from 14 publications were included in the meta-analysis in Chapter 2. Alpha diversity continuously increased during early stages of animal growth and increased at a slower rate in the following stages. Random forest regression identified 30 OTUs as potential microbiota biomarkers for modeling swine gut microbiome development and the external validation suggested the generalization and benchmarking role of our models in application to future microbiome studies conducted in suckling and weaning pigs. In Chapter 3, a total of 924 fecal samples from 44 newborn piglets over 21 time points (day one of age until 41 days of age) were collected every two days and community composition, assembly, and succession was determined using the V4 region of the 16S rRNA gene. Alpha diversity continuously increased during the suckling stage, yet there was no significant increase in alpha diversity during days post-weaning. Post-weaning in-feed antibiotics consistently decreased the microbial diversity and changed the community structure in both low birth weight (LBW) and normal birth weight (NBW) piglets. Delayed gut microbial community maturation was observed in LBW piglets on post-weaning days compared with NBW. Heterogeneity of the gut microbial community between piglets linearly decreased over time, as revealed by the within-time Bray-Curtis dissimilarities. Intra-individual variance both in community structure and genus abundance indicates the importance of repeated measurements for reliable observations. Dirichlet multinomial mixtures analysis supported an age-dependent microbiome developmental pattern and identified microbial taxa that are age-discriminatory. Our study addresses ecological processes shaping the swine gut microbiome between piglets with contrasting birth weights and receiving post-weaning antibiotics. Persistent gut microbiota immaturity in LBW piglets suggests that efforts to accelerate microbial community succession might improve LBW piglet growth performance and disease resistance. </p>

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BACKGROUND:Humans can spend the majority of their time indoors, but little is known about the interactions between the human and built-environment microbiomes or the forces that drive microbial community assembly in the built environment. We sampled 16S rRNA genes from four different surface types throughout a university classroom to determine whether bacterial assemblages on each surface were best predicted by routine human interactions or by proximity to other surfaces within the classroom. We then analyzed our data with publicly-available datasets representing potential source environments.RESULTS:Bacterial assemblages from the four surface types, as well as individual taxa, were indicative of different source pools related to the type of human contact each surface routinely encounters. Spatial proximity to other surfaces in the classroom did not predict community composition.CONCLUSIONS:Our results indicate that human-associated microbial communities can be transferred to indoor surfaces following contact, and that such transmission is possible even when contact is indirect, but that proximity to other surfaces in the classroom does not influence community composition.

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<p>Soil communities are regarded as among the most complex and diverse assemblages of microorganisms with estimated bacterial numbers in the order of 10â?¹ cells.gâ?»&sup1 / . Studies on extreme soils however, have reported lower cell densities, supporting the perception that the so-called extreme environments exhibit low species diversity. To assess the extent of microbial diversity within an extreme environment, the mineral soils of the Dry Valleys, Ross Dependency, Eastern Antarctica were investigated using 16S rDNA analysis.</p>

Peatlands make up 3% of the earth's land surface and contain about one third of the C contained in soils globally. The role of peatlands in the C cycle is as a net sink. Organic matter accumulates in these areas because the rate of net primary productivity (NPP) exceeds the rate of decay. Peatlands are often harsh environments, characterized by cold, wet and anoxic conditions, therefore it is not accelerated NPP which exerts the main control over the accumulation of peat, but the slow rate of decomposition. During the decomposition process, nearly all organic matter passes through the soil microbial pool, and so the soil microbial community is an important factor in the decomposition process. Despite the obvious importance of the soil microbial community in decomposition in peatlands, our knowledge of their role in peatland C cycling is still largely limited. This thesis addresses some aspects of the soil microbial community and investigates their role in decomposition in a raised mire. The soils in a raised mire system may be categorized according to their nutrient input into nutrient rich, mineral soils and soils of the lagg fen, and nutrient poor, soils of the mire expanse. The soil microbial community in the three soils was characterized in terms of size, activity and composition. The size of the soil microbial community in the soils of the mire expanse was small in comparison with that of the mineral soils and soils of the lagg fen, however it was very active. The hypothesis that nutrients restrict the size of the soil microbial community in the soils of the mire expanse was tested. The data showed that nutrients did not significantly effect the size of the soil microbial community. Litterbags were used to investigate the decomposition of a range of plant species found on the different soils and mass loss and C02 production were used as indicators of decomposition. C02 production was a more sensitive and reliable measure of decomposition than mass loss. The size of the soil microbial community was an important factor in decomposition rate. Litter quality of the above ground biomass was not related to decomposition rate. The relationship between the size of the microbial community in contact with decaying plant material and decomposition was investigated. In this study, microbial colonization of decaying litter was not correlated with the measure of litter quality used. This work has provided baseline information the environmental factors that influence decomposition and future work should focus on investigating the changes in the soil microbial community during the decomposition process.