Bacterial diversity and competition from the population to the community level


Bent, Stephen James.. (2007). Bacterial diversity and competition from the population to the community level. Theses and Dissertations Collection, University of Idaho Library Digital Collections.

Bacterial diversity and competition from the population to the community level
Bent, Stephen James.
Bacteria--Geographical distribution Rhodopseudomonas--Geographical distribution Biogeography
Bioinformatics & Computational Biology
Microbial communities in soil and sediment environments are diverse in species composition and function. While the ecological forces maintaining this extraordinary diversity are not well understood, physical and chemical heterogeneity are probably key factors. This thesis contains three chapters in which ideas are developed that advance understanding of the role of spatial heterogeneity in the maintenance of diversity. One chapter (section 2.2) presents the results of studies done to assess the biogeography of Rhodopseudomonas palustris in a 1m 2 plot, in which multiple closely related strains coexisted in small samples of wetland sediment, but no correlation was observed between genetic differences and physical distance. In section 2.3, I provide empirical laboratory microcosm data showing that spatial heterogeneity allowed for extended coexistence among bacterial strains that exhibited competitive exclusion in spatially homogeneous environments. This observation led to the development of a spatially structured metapopulation model (described in section 2.4), which simulated the dynamics of flow, nutrient depletion, and microbial growth in particulate environments. The model simulations produced competitive outcomes and nutrient levels qualitatively similar to the empirical results described in section 2.3, and suggested some mechanisms by which the spatial heterogeneity present in these systems could lead to maintenance of diversity. By combining observations of natural systems, manipulation of laboratory microcosms, and development of mathematical models, we can work towards a theoretical underpinning for microbial ecology. Since we cannot directly observe and identify prokaryotic organisms from environmental samples, investigators must rely on molecular methods to characterize DNA sequences from these communities. In sections 3.2 and 3.3, I assess and discuss differences between methods of community 'fingerprints' based on the analysis of 16S rRNA genes and phylogenetic analysis of cloned 16S rRNA genes. The former is an inexpensive way to screen differences between large numbers of samples, while the latter is a labor-intensive method for sampling individual DNA sequences from a community. The results of simulations presented here call into question the ability of community fingerprinting methods to accurately reconstruct diversity indices. Understanding the strengths and weaknesses of different methods is important for meaningful evaluation of patterns of microbial diversity in nature.
Thesis (Ph. D., Bioinformatics and Computational Biology)--University of Idaho, September 2007.
Major Professor:
Larry J. Forney.
Defense Date:
September 2007.
Format Original:
viii, 180 leaves :col. ill. ;29 cm.

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