Starter Grant: Uncovering the Phylogenetic And Physiological Diversity of Soil Acidobacteria

University Of Colorado At Boulder, Boulder CO

Investigators

Abstract

Bacteria belonging to the phylum Acidobacteria are ubiquitous and abundant in soil. Despite this, we know very little about soil Acidobacteria; only a small portion of the genetic diversity within the phylum has been surveyed and the phylogenetic relationships of acidobacterial taxa have not been adequately resolved. In addition, the physiological characteristics of Acidobacteria and their ecological roles in soil remain largely unknown. One major reason for this is that Acidobacteria are poorly represented in soil culture collections as they are difficult to culture using traditional culturing strategies. This project has two objectives: 1) to survey and describe the genetic diversity of soil Acidobacteria, and 2) to improve methods for the cultivation of soil Acidobacteria in vitro so their physiological characteristics can be assessed. To meet these objectives, we will collect six distinct soils from across the United States and build acidobacterial-specific clone libraries from extracted DNA to describe the phylogenetic diversity of soil Acidobacteria. We will then use a PCR-based screening approach to identify the specific conditions, or set of conditions, under which Acidobacteria are most efficiently cultivated from soil. Our goal is to isolate and culture those Acidobacteria which, from the results of the soil clone libraries, are found to be numerically abundant in the collected soil samples. Since our previous work suggests that soil Acidobacteria are strongly oligotrophic, we expect that Acidobacteria can be most effectively cultured with nutrient-poor media and prolonged incubation times. Once soil Acidobacteria can be successfully isolated and cultured in vitro, their physiological characteristics can be assessed in-depth. With this project, we will significantly expand what we currently know about soil Acidobacteria; we will describe the genetic diversity of this under-surveyed taxa and, by obtaining pure culture isolates, we can begin to investigate the ecological roles of soil Acidobacteria. This project will provide a graduate student with training in both conventional microbiology (strain isolation and cultivation) and molecular microbiology (rDNA sequence analysis).