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

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Bacteria belonging to the phylum Acidobacteria are ubiquitous and abundant insoil. Despite this, we know very little about soil Acidobacteria; only a smallportion of the genetic diversity within the phylum has been surveyed and thephylogenetic relationships of acidobacterial taxa have not been adequately resolved. Inaddition, the physiological characteristics of Acidobacteria and their ecological roles insoil remain largely unknown. One major reason for this is that Acidobacteria are poorlyrepresented in soil culture collections as they are difficult to culture using traditionalculturing strategies. This project has two objectives: 1) to survey and describe thegenetic diversity of soil Acidobacteria, and 2) to improve methods for the cultivation ofsoil Acidobacteria in vitro so their physiological characteristics can be assessed. Tomeet these objectives, we will collect six distinct soils from across the United States andbuild acidobacterial-specific clone libraries from extracted DNA to describe thephylogenetic diversity of soil Acidobacteria. We will then use a PCR-based screeningapproach to identify the specific conditions, or set of conditions, under whichAcidobacteria are most efficiently cultivated from soil. Our goal is to isolate and culturethose Acidobacteria which, from the results of the soil clone libraries, are found to benumerically abundant in the collected soil samples. Since our previous work suggeststhat soil Acidobacteria are strongly oligotrophic, we expect that Acidobacteria can bemost effectively cultured with nutrient-poor media and prolonged incubation times. Oncesoil Acidobacteria can be successfully isolated and cultured in vitro, their physiologicalcharacteristics can be assessed in-depth. With this project, we will significantly expandwhat we currently know about soil Acidobacteria; we will describe the genetic diversity ofthis under-surveyed taxa and, by obtaining pure culture isolates, we can begin toinvestigate the ecological roles of soil Acidobacteria. This project will provide a graduatestudent with training in both conventional microbiology (strain isolation and cultivation)and molecular microbiology (rDNA sequence analysis).