GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes - PubMed (original) (raw)
doi: 10.1038/ismej.2007.2.
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
Affiliations
- PMID: 18043615
- DOI: 10.1038/ismej.2007.2
Free article
GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes
Zhili He et al. ISME J. 2007 May.
Free article
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.
Similar articles
- GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis.
Tu Q, Yu H, He Z, Deng Y, Wu L, Van Nostrand JD, Zhou A, Voordeckers J, Lee YJ, Qin Y, Hemme CL, Shi Z, Xue K, Yuan T, Wang A, Zhou J. Tu Q, et al. Mol Ecol Resour. 2014 Sep;14(5):914-28. doi: 10.1111/1755-0998.12239. Epub 2014 Mar 14. Mol Ecol Resour. 2014. PMID: 24520909 - GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity.
He Z, Deng Y, Van Nostrand JD, Tu Q, Xu M, Hemme CL, Li X, Wu L, Gentry TJ, Yin Y, Liebich J, Hazen TC, Zhou J. He Z, et al. ISME J. 2010 Sep;4(9):1167-79. doi: 10.1038/ismej.2010.46. Epub 2010 Apr 29. ISME J. 2010. PMID: 20428223 - Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest.
Cong J, Liu X, Lu H, Xu H, Li Y, Deng Y, Li D, Zhang Y. Cong J, et al. BMC Microbiol. 2015 Aug 20;15:167. doi: 10.1186/s12866-015-0491-8. BMC Microbiol. 2015. PMID: 26289044 Free PMC article. - Development of functional gene microarrays for microbial community analysis.
He Z, Deng Y, Zhou J. He Z, et al. Curr Opin Biotechnol. 2012 Feb;23(1):49-55. doi: 10.1016/j.copbio.2011.11.001. Epub 2011 Nov 16. Curr Opin Biotechnol. 2012. PMID: 22100036 Review. - Microbial solubilization and immobilization of toxic metals: key biogeochemical processes for treatment of contamination.
White C, Sayer JA, Gadd GM. White C, et al. FEMS Microbiol Rev. 1997 Jul;20(3-4):503-16. doi: 10.1111/j.1574-6976.1997.tb00333.x. FEMS Microbiol Rev. 1997. PMID: 9299717 Review.
Cited by
- Profile of Bacterial Communities in Copper Mine Tailings Revealed through High-Throughput Sequencing.
Jiménez-Venegas J, Zamora-Leiva L, Univaso L, Soto J, Tapia Y, Paneque M. Jiménez-Venegas J, et al. Microorganisms. 2024 Sep 3;12(9):1820. doi: 10.3390/microorganisms12091820. Microorganisms. 2024. PMID: 39338494 Free PMC article. - Four years of climate warming reduced dark carbon fixation in coastal wetlands.
Liu B, Qi L, Zheng Y, Zhang C, Zhou J, An Z, Wang B, Lin Z, Yao C, Wang Y, Yin G, Dong H, Li X, Liang X, Han P, Liu M, Zhang G, Cui Y, Hou L. Liu B, et al. ISME J. 2024 Jan 8;18(1):wrae138. doi: 10.1093/ismejo/wrae138. ISME J. 2024. PMID: 39052319 Free PMC article. - CyanoStrainChip: A Novel DNA Microarray Tool for High-Throughput Detection of Environmental Cyanobacteria at the Strain Level.
Shu HY, Zhao L, Jia Y, Liu FF, Chen J, Chang CM, Jin T, Yang J, Shu WS. Shu HY, et al. Environ Sci Technol. 2024 Mar 19;58(11):5024-5034. doi: 10.1021/acs.est.3c11096. Epub 2024 Mar 7. Environ Sci Technol. 2024. PMID: 38454313 Free PMC article. - Water Level Fluctuations Modulate the Microbiomes Involved in Biogeochemical Cycling in Floodplains.
Hao Z, Wang Q, Wang J, Deng Y, Yan Z, Tian L, Jiang H. Hao Z, et al. Microb Ecol. 2023 Dec 30;87(1):24. doi: 10.1007/s00248-023-02331-6. Microb Ecol. 2023. PMID: 38159125 - Consider the Anoxic Microsite: Acknowledging and Appreciating Spatiotemporal Redox Heterogeneity in Soils and Sediments.
Lacroix EM, Aeppli M, Boye K, Brodie E, Fendorf S, Keiluweit M, Naughton HR, Noël V, Sihi D. Lacroix EM, et al. ACS Earth Space Chem. 2023 Aug 23;7(9):1592-1609. doi: 10.1021/acsearthspacechem.3c00032. eCollection 2023 Sep 21. ACS Earth Space Chem. 2023. PMID: 37753209 Free PMC article. Review.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Miscellaneous