Publication Date

5-2014

Advisor(s)

Frederick M. Cohan; Michael Singer; Camilo Ramirez

Department

Biology

Language

English

Abstract

Recent findings show that bacterial groups consisting of very close relatives, even within named bacterial species, speciate into smaller groups, ecotypesβ€”a phylogenetic group of close relatives that are ecologically interchangeable. The members of an ecotype share genetic adaptations and each ecotype is ecologically distinct from one another (Wiedenbeck submitted). Environment can drive ecological adaptations of close relatives; however, despite their varying ecologies, and the adaptations that arise, many of these groups are traditionally considered to be one taxonomic species, as noted with many bacterial species. By applying ecotype theory to Bacillus subtilis we have been able to find evidence for close relatives of B. subtilis that differ in environmental adaptations, are ecologically distinct for each other, and are unique sequence clusters.

In this study, we sampled from the rhizosphere of plants, free soil and varying elevations, to determine the groups that that differ in adaptations along these dimensions within the Bacillus subtilis clade within these environments. Members of B. subtilis are known to be plant growth promoting rhizobacteria (PGPR), which aid the growth of roots and stalks, along with defense against plant pathogens such as fungi and other bacteria. We hypothesize that B. subtilis samples will vary in their association with PGPR traits according to their origins, which are rhizosphere, free soil and varying elevations.

Using the gyrA gene we created a maximum likelihood phylogeny in MEGA5 of isolates from Death Valley. Ecotypes demarcated by Ecotype Simulation were found to be biased in their habitats, with some putative ecotypes that are associated with free soil, and others with the rhizosphere, along with differences in elevations. In order to closely examine the habitat associations we conducted a series of experiments testing the PGPR traits some Bacillus strains are known to possess. These tests helped us determine whether the habitat associations predict differences in PGPR activity. In the PGPR abilities there have been differences not only among plant source, but also ecotype, showing differentiation, and adaptation to the rhizosphere, different plant root environments, and elevation, which could show adaptations to different climates

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