title: UOklahoma_GeoChip_2.0
status: Public on Jul 10 2010
contact.city: Montreal
contact.first: Etienne
contact.last: Yergeau
contact.email: Etienne.Yergeau@cnrc-nrc.gc.ca
contact.state: Qc
contact.address: 6100 Royalmount Ave
contact.department: Environmental Microbiology
contact.country: Canada
contact.institute: NRC-BRI
organism: Bacteria
description: Owing to their vast diversity and as-yet uncultivated status, detection, characterization and quantification of microorganisms in natural settings are very challenging, and linking microbial diversity to ecosystem processes and functions is even more difficult. Microarray-based genomic technology for detecting functional genes and processes has a great promise of overcoming such obstacles. Here, a novel comprehensive microarray, termed GeoChip, has been developed, containing 24 243 oligonucleotide (50 mer) probes and covering >10 000 genes in >150 functional groups involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, and organic contaminant degradation. The developed GeoChip was successfully used for tracking the dynamics of metal-reducing bacteria and associated communities for an in situ bioremediation study. This is the first comprehensive microarray currently available for studying biogeochemical processes and functional activities of microbial communities important to human health, agriculture, energy, global climate change, ecosystem management, and environmental cleanup and restoration. It is particularly useful for providing direct linkages of microbial genes/populations to ecosystem processes and functions.
manufacture_protocol: A new version of CommOligo (Li et al., 2005) with group-specific probe design features was used to design both gene- and group-specific oligonucleotide probes based on the following criteria: (i) gene-specific probes: 90% sequence identity, 20-base continuous stretch and -35 kcal/mol free energy (Liebich et al., 2006); (ii) group-specific probes: a group-specific probe has to meet the above requirements for nontarget groups, and it also has to have 96% of sequence identity, 35-base continuous stretch and -60 kcal/mol of free energy within the group (He et al., 2005). The information about the probes and their targets is available on our web site: http://ieg.ou.edu/GeoChip2.0/GeoChip2.0-info.xls
  All designed probes were subsequently verified by ProbeChecker, and synthesized by MWG Biotech Inc. (High Point, NC, USA). The concentration of all oligonucleotides was adjusted to 100 pmol/l. All oligonucleotide probes and controls were arrayed onto Corning UltraGAPS (Corning, NY, USA) slides using a Microgrid II Arrayer (Genomic Solutions, Ann Arbor, MI, USA) as described previously (He et al., 2005)