GeoChip: A comprehensive microarray for investigating biogeochemical, ecological and environmental processes

Zhili He; Terry J. Gentry; Christopher W. Schadt; Liyou Wu; Jost Liebich; Song C. Chong; Zhijian Huang; Weimin Wu; Baohua Gu; Phil Jardine; Craig Criddle; Jizhong Zhou

doi:10.1038/ismej.2007.2

GeoChip: A comprehensive microarray for investigating biogeochemical, ecological and environmental processes

Zhili He
, Terry J. Gentry
, Christopher W. Schadt
, Liyou Wu
, Jost Liebich
, Song C. Chong
, Zhijian Huang
, Weimin Wu
, Baohua Gu
, Phil Jardine
, Craig Criddle
, Jizhong Zhou

Integrative Microbiomics

Research output: Contribution to journal › Article › peer-review

504 Scopus citations

Abstract

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.

Original language	English
Pages (from-to)	67-77
Number of pages	11
Journal	ISME Journal
Volume	1
Issue number	1
DOIs	https://doi.org/10.1038/ismej.2007.2
State	Published - May 2007

Funding

This research was supported by The United States Department of Energy under the Environmental Remediation Science Program, Genomics: GTL program through the Virtual Institute of Microbial Stress and Survival (VIMSS; http://vimss.lbl.gov), Biotechnology Investigations-Ocean Margins program and Carbon Sequestration program (as part of the consortium on research to enhance Carbon Sequestration in Terrestrial Ecosystems – CSiTE) of the Office of Biological and Environmental Research, Office of Science. Oak Ridge National Laboratory is managed by University of Tennessee UT-Battelle LLC for the Department of Energy under contract DE-AC05-00OR22725. Jost Liebich was supported by a fellowship within the postdoctoral program of the German Academic Exchange Service (DAAD).

Keywords

Bioremediation
Functional genes
Microarray
Microbial community

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10.1038/ismej.2007.2

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title = "GeoChip: A comprehensive microarray for investigating biogeochemical, ecological and environmental processes",

abstract = "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.",

keywords = "Bioremediation, Functional genes, Microarray, Microbial community",

author = "Zhili He and Gentry, \{Terry J.\} and Schadt, \{Christopher W.\} and Liyou Wu and Jost Liebich and Chong, \{Song C.\} and Zhijian Huang and Weimin Wu and Baohua Gu and Phil Jardine and Craig Criddle and Jizhong Zhou",

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AU - He, Zhili

AU - Gentry, Terry J.

AU - Schadt, Christopher W.

AU - Wu, Liyou

AU - Liebich, Jost

AU - Chong, Song C.

AU - Huang, Zhijian

AU - Wu, Weimin

AU - Gu, Baohua

AU - Jardine, Phil

AU - Criddle, Craig

AU - Zhou, Jizhong

PY - 2007/5

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N2 - 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.

AB - 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.

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KW - Functional genes

KW - Microarray

KW - Microbial community

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GeoChip: A comprehensive microarray for investigating biogeochemical, ecological and environmental processes

Abstract

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Keywords

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