Doctor of Philosophy (PhD)


Biological Sciences

Document Type



The limiting factor involved in past assessments of soil bacterial diversity when using culture-independent techniques has often been the lack of sampling and replication. As a result, analyses of community structural shifts across soil environments have lacked statistical power. In this study, 23 16S rRNA gene clone libraries consisting of over 11,000 clones were constructed from soils at the Central Arizona Phoenix Long Term Ecological Research (CAP LTER) site. Subsequent ARDRA fingerprinting and partial 16S rRNA gene sequencing allowed for a more robust investigation of various components that may explain any observed variations in bacterial species composition. The designated land use type of the soils best explained the overall diversity gradient. Based on Simpson’s reciprocal index, diversity was found to significantly increase when comparing urbanized and agricultural soils to open desert samples located outside the metropolitan region. Land use type appears to be a powerful indicator of overall diversity due to irrigation methods that differ greatly across land use types. Experiment-wise comparisons of complete CAP LTER clone libraries via the LIBSHUFF method yielded no statistical similarity in sequence libraries, except for two replicate libraries constructed from one urban soil. However, inter-phylum LIBSHUFF analysis of the clones also shows degrees of phylogenetic partitioning between land use categories and that open desert remnant patches located within the city limits more closely resemble those urban soils than the open deserts outside of Phoenix. Examination of constructed 16S rRNA phylogenetic trees that include CAP LTER phylotypes indicate some distinct clustering of sequences appears to be driven by land use type rather than geography, and that most of these groups may be endemic to the region. However, some ubiquitous phylotype groups were discovered and were used as templates for specific PCR primer design, allowing for the detection of ten of these groups in all soil samples analyzed. Overall, this study suggests that anthropogenic factors have altered soil bacterial communities, the biogeography of many species is controlled in some manner by land use type, and that a small subset of taxa is ecologically tolerant despite the heterogeneity of habitats within the site.



Document Availability at the Time of Submission

Release the entire work immediately for access worldwide.

Committee Chair

Fred Rainey