Argonne National Laboratory

Abstract:
The integration of cultivation-based and cultivation-independent analyses of microbial communities is essential for improved understanding of community function and potential. Here, I report on the combined metagenomic, isolation and genomic analysis of denitrifying bacteria from the highly contaminated subsurface of the Oak Ridge Integrated Field Research Challenge (ORIFRC) site, and the implications of this analysis on denitrifying bacteria and other functional groups of microorganisms at a much broader scale.

These analyses revealed that:

• (a) commonly-used primer sets targeting functional genes are inadequate for survey purposes of environmental denitrifiers,
• (b) cultivation-based approaches can potentially produce misleading results if not coupled with whole genome sequencing, and
• (c) comparative genomics of multiple members of a single genus are important for understanding the nature of denitrification in environmental systems.

These findings call for improvements in approaches to the analysis of functional groups of microorganisms in complex environments.