Isolation and Physiology of Bacteria from Contaminated Subsurface Sediments
Open Access
- 15 November 2010
- journal article
- research article
- Published by American Society for Microbiology in Applied and Environmental Microbiology
- Vol. 76 (22), 7413-7419
- https://doi.org/10.1128/aem.00376-10
Abstract
The majority of environmental microorganisms cannot be grown by traditional techniques. Here we employed, and contrasted with conventional plating, an alternative approach based on cultivation of microorganisms inside diffusion chambers incubated within natural samples, followed by subculturing in petri dishes. Using this approach, we isolated microorganisms from subsurface sediments from the Field Research Center (FRC) in Oak Ridge, TN. The sediments were acidic and highly contaminated with uranium, heavy metals, nitrate, and organic pollutants. Phylogenetic analysis of 16S rRNA gene sequences revealed clear differences between diversity of isolates obtained by the diffusion chamber approach and those obtained by conventional plating. The latter approach led to isolation of members of the Alpha - and Gammaproteobacteria , Actinobacteria , and Verrucomicrobia . Isolates obtained via the diffusion chamber approach represented the Alpha -, Beta -, and Gammaproteobacteria , Actinobacteria , Firmicutes , and Bacteroidetes . Notably, one-third of the isolates obtained by the new method were closely related to species known from previous molecular surveys conducted in the FRC area. Since the initial growth of microorganisms inside diffusion chambers occurred in the presence of the environmental stress factors, we expected the isolates we obtained to be tolerant of these factors. We investigated the physiologies of selected isolates and discovered that the majority were indeed capable of growth under low pH and/or high concentrations of heavy metals and nitrate. This indicated that in contrast to conventional isolation, the diffusion chamber-based approach leads to isolation of species that are novel, exhibit tolerance to extant environmental conditions, and match some of the species previously discovered by molecular methods.Keywords
This publication has 42 references indexed in Scilit:
- Denitrifying Bacteria Isolated from Terrestrial Subsurface Sediments Exposed to Mixed-Waste ContaminationApplied and Environmental Microbiology, 2010
- Proteogenomic Monitoring of Geobacter Physiology during Stimulated Uranium BioremediationApplied and Environmental Microbiology, 2009
- Caulobacter crescentus as a Whole-Cell Uranium BiosensorApplied and Environmental Microbiology, 2007
- Incubation of Environmental Samples in a Diffusion Chamber Increases the Diversity of Recovered IsolatesApplied and Environmental Microbiology, 2007
- Changes in Microbial Community Composition and Geochemistry during Uranium and Technetium BioimmobilizationApplied and Environmental Microbiology, 2007
- Identification and Isolation of a Castellaniella Species Important during Biostimulation of an Acidic Nitrate- and Uranium-Contaminated AquiferApplied and Environmental Microbiology, 2007
- Application of a High-Density Oligonucleotide Microarray Approach To Study Bacterial Population Dynamics during Uranium Reduction and ReoxidationApplied and Environmental Microbiology, 2006
- Environmental Whole-Genome Amplification To Access Microbial Populations in Contaminated SedimentsApplied and Environmental Microbiology, 2006
- Horizontal Gene Transfer of P IB -Type ATPases among Bacteria Isolated from Radionuclide- and Metal-Contaminated Subsurface SoilsApplied and Environmental Microbiology, 2006
- Complete genome sequence of Caulobacter crescentusProceedings of the National Academy of Sciences of the United States of America, 2001