Dissertation/Thesis Abstract

Identification of Factors That Drive Taxonomic, Phylogenetic, and Functional Composition of Microbial Communities Using DNA Sequence Analyses
by Bhatnagar, Srijak, Ph.D., University of California, Davis, 2017, 136; 10623208
Abstract (Summary)

Microbial life represents the majority of the diversity of life on planet earth. Microbes are found in all ecosystems. The microbial community of an ecosystem can be an indicator of its health and the foundation of the ecosystem function. Thus, an understanding of the microbial community of an ecosystem is vital to understanding the ecosystem itself. To fully grasp the microbial community structure, it is essential to understand the factors that shape the community composition and diversity of the ecosystem. This works focusses on the primary drivers of microbial composition in three ecosystems: an estuary, the gut of Drosophila melanogaster, and walnut grove soil.

In the benthic estuarine environment of Trunk River, physical perturbations in the water column above decaying seagrass altered the composition of the microbial community causing a visible microbial bloom. To understand the microbial community progression in the bloom, we simulated perturbed sites in the river and studied four different depths in the water column for two weeks. We found the bloom was largely made up of Prosthecochloris vibrioformis, a phototrophic sulfur oxidizer. The bloom appears to be driven by pH, salinity, and sulfide gradients, forming at a depth of ≈ 25cm beneath the surface of the water.

For the third chapter, we explored the effect of host diet on its gut microbial community. We created a controlled experiment in Drosophila melanogaster, a model organism. A population of D. melanogaster preconditioned on a balanced lab diet was split into two treatment diets, a high-sugar diet and a high-yeast diet. The microbial communities in the fecal matter of the flies were sampled for 4 days to understand their compositional changes. We found that a shift in the diet of D. melanogaster changed the phylogenetic, taxonomic, and functional compositions of the microbial communities. Each dietary change led to a distinct taxonomic, phylogenetic, and functional composition by the end of the experiment. The functional diversity of both treatment groups decreased, indicating a shift away from a diverse set of metabolic capabilities when subjected to a more comprehensive nutrition to a more specific set of metabolic capabilities adapted for the main nutrient, either sucrose or yeast extract.

In the fourth chapter, Pesticide-treated orchard soils were used to understand the effects of deliberate intervention (external factors) on microbial ecosystems. We also studied the potential of pathogens to colonize soil that had been exposed to such external factors. In a controlled experiment, soil was subjected to different fumigation treatments with and without subsequent amendment. It was then inoculated and incubated with Agrobacterium tumefaciens. The results indicate a fumigant-specific shift in the phylogenetic, taxonomic, genic, and functional composition of the soil. The low diversity fumigated soil was also better colonized by the A. tumefaciens. However, post-fumigation amendment with vermicompost increased the diversity, shifting the compositions towards non-fumigated vermicompost and suppressing A. tumefaciens colonization.

With this work, we have been able to implicate some of the important factors at play in the determination of microbial composition in various ecosystems. Additionally, we showed that the influence of these factors on microbial community is measurable on different metrics of composition.

Indexing (document details)
Advisor: Eisen, Jonathan A.
Commitee: Bennett, Alan B., Dawson, Scott C.
School: University of California, Davis
Department: Microbiology
School Location: United States -- California
Source: DAI-B 79/02(E), Dissertation Abstracts International
Source Type: DISSERTATION
Subjects: Microbiology
Keywords: Functional composition, Metagenomics, Microbial community composition, Microbial ecology, Phylogenetic composition
Publication Number: 10623208
ISBN: 9780355451634
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