GeoChip: A comprehensive microarray for investigatingbiogeochemical, ecological, and environmental processes

Journal Article · Mon Sep 24 00:00:00 EDT 2007 · The ISME Journal

DOI:https://doi.org/10.1038/ismej.2007.2· OSTI ID:932980

He, Z; Gentry, T J; Schadt, C W; Wu, L; Liebich, J; Chong, S C; Wu, W; Gu, B; Jardine, P; Criddle, C; Zhou, J

Due to their vast diversity and as-yet uncultivated status,detection, characterization and quantification of microorganisms innatural settings are very challenging, and linking microbial diversity toecosystem processes and functions is even more difficult.Microarray-based genomic technology for detecting functional genes andprocesses has a great promise of overcoming such obstacles. Here, a novelcomprehensive microarray, termed GeoChip, has been developed, containing24,243 oligonucleotide (50mer) probes and covering>10,000 genes in>150 functional groups involved in nitrogen, carbon, sulfur andphosphorus cycling, metal reduction and resistance, and organiccontaminant degradation. The developed GeoChip was successfully used fortracking the dynamics of metal-reducing bacteria and associatedcommunities for an in situ bioremediation study, which is the first timeto demonstrate that uranium can be bioremediated to the concentrationsbelow the USA EPA maximum contaminant level (MCL) for drinking water.This is the first comprehensive microarray available for studyingbiogeochemical processes and functional activities of microbialcommunities important to human health, agriculture, energy, globalclimate change, ecosystem management, and environmental cleanup andrestoration. It is particularly useful for providing direct linkages ofmicrobial genes/populations to ecosystem processes andfunctions.

• Research Organization: COLLABORATION - University of Oklahoma, Norman,OK
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 932980
• Report Number(s): LBNL--63453
• Journal Information: The ISME Journal, Journal Name: The ISME Journal Journal Issue: 1 Vol. 1
• Country of Publication: United States
• Language: English

Related Subjects

54 ENVIRONMENTAL SCIENCES
59 BASIC BIOLOGICAL SCIENCES
AGRICULTURE
BACTERIA
BIOREMEDIATION
CARBON
CLIMATIC CHANGE
COMMUNITIES
DETECTION
DRINKING WATER
ECOSYSTEMS
FUNCTIONALS
GENES
MICROORGANISMS
Microarrays
functional gene
microbial community
bioremediation
NITROGEN
OLIGONUCLEOTIDES
PHOSPHORUS
PROBES
SULFUR
URANIUM
US EPA