Development of Microarrays-based Metagenomics Technology for Monitoring Sulfate-Reducing Bacteria in Subsurface Environments

Due to their vast diversity and as-yet uncultivated status, detecting, characterizing and quantifying microorganisms in natural settings are of grand challenge, and understanding the mechanistic linkages between microbial diversity and ecosystem functioning and their feedback responses to human activities and climate change is even more difficult. There is an urgent need to develop rapid high throughput metagenomics technologies for characterizing microbial community structure, functions and activities. Large-scale genome sequencing and associated metagenomic technologies such as GeoChip have revolutionized the study of microbial communities. The GeoChip is a revolutionary high throughput genomics technology for linking microbial community structure to functions, allowing researchers to address scientific questions which could not be approached previously. GeoChip-based technologies, OU GeoChip, won one of R & amp;D 100 Awards of 2009, which recognize 100 most technological innovations with the greatest commercial potentials. In this Phase I project, we will further develop the GeoChip-based metagenomic technology and associated computational tools in coupling with high throughput sequencing for simultaneously detecting many sulfate reducing bacteria (SRB) in subsurface environments important to environmental cleanup and management. We will first develop novel computational approaches to design specific gene probes for microarray fabrication. We will then use high throughput sequencing approaches to examine the diversity of SRB in the ERSP Field Research Center at Oak Ridge, followed by developing more representative GeoChip for detecting SRB for bioremediation of uranium and other heavy metals. Commercial Applications and Other Benefits: New software tools for designing specific probes and a prototype dsrAB microarray for detecting SRB populations will be developed through the Phase I support. On one hand, this will directly help address the outlined objectives of the proposed Phase II study for developing more comprehensive GeoChip of commercial values for studying subsurface biogeochemical processes important to environmental cleanup and management. On the other hand, the richer information on SRB will strengthen the commercial potential and sales of the current version of GeoChip for studying subsurface microbial communities, which has been utilized by many scientists from different countries. In addition, the developed GeoChip and computational tools will be not only important for assessing subsurface microbial communities, but also useful for studying microbial communities in general from other environments such as soils, marine sediments, waste waters, and biocorrosion.