HR: 0800h
AN: H21A-0992 INVITED     [Abstracts]
TI: Use of Microarray-based Genomic Technologies for Assessing Microbial Community Composition and Dynamics in Contaminated Groundwater
AU: * Zhou, J
EM: zhouj@ornl.gov
AF: Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831 United States
AU: Schadt, C
AF: Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831 United States
AU: Gentry, T
AF: Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831 United States
AU: He, Z
AF: Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831 United States
AU: Wu, L
AF: Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831 United States
AU: Rhee, S
AF: Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831 United States
AU: Liu, X
AF: Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831 United States
AU: Liebich, J
AF: Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831 United States
AU: Chong, S
AF: Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831 United States
AU: Yang, Z
AF: Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831 United States
AU: Gao, H
AF: Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831 United States
AB: To effectively monitor microbial populations involved in various important processes, a 50-mer-based oligonucleotide microarray was developed based on known genes and pathways involved in: biodegradation, metal resistance and reduction, denitrification, nitrification, nitrogen fixation, methane oxidation, methanogenesis, carbon polymer decomposition, and sulfate reduction. This array contains approx 2000 unique and group-specific probes with $<$85% similarity to their non-target sequences. Based on artificial probes, our results showed that at hybridization conditions of 50$^{o}$C and 50% formamide, the 50-mer microarray hybridization can differentiate sequences having $<$88% similarity. Specificity tests with representative pure cultures indicated that the designed probes on the arrays appeared to be specific to their corresponding target genes. Detection limits were about 5-10ng genomic DNA in the absence of background DNA, and 50-100ng ($\sim$1.3 ­A10$^{7}$ cells) in the presence background DNA. Strong linear relationships between signal intensity and target DNA and RNA concentration were observed (r$^{2}$ = 0.95-0.99). Real-time PCR analysis of 12 representative genes was consistent with microarray-based quantification (r$^{2}$ = 0.95). Also novel approaches were developed and used to increase microarray detection sensitivity of both DNA and mRNA. Application of these array-based technologies to analyze microbial communities in contaminated groundwaters from the US Department of Energy­_s Natural and Accelerated Bioremediation Research Program (NABIR) Field Research Center at Oak Ridge, TN, demonstrated that it is feasible to biostimulate the indigenous microbial populations for contaminant remediation but the process could be very complicated due to highly spatial heterogeneous microbial distributions. Based on these results, more comprehensive functional gene arrays containing $\sim$27,000 probes from the genes important for biogeochemical cycling of C, N, S, P, metal resistance and contaminant degradation have been designed and constructed. This is the most comprehensive array available so far for environmental studies and will also be useful for biogeochemistry studies in general.
DE: 4805 Biogeochemical cycles (1615)
DE: 4815 Ecosystems, structure and dynamics
DE: 4803 Bacteria
DE: 1894 Instruments and techniques
DE: 1615 Biogeochemical processes (4805)
SC: Hydrology [H]
MN: 2004 AGU Fall Meeting