GeoChip 3.0: A High Throughput Tool for Analyzing Microbial Community, Composition, Structure, and Functional Activity

doi:10.2172/986221

GSTDTAP > 地球科学

DOI	10.2172/986221
报告编号	LBNL-3801E
来源ID	OSTI ID: 986221
	GeoChip 3.0: A High Throughput Tool for Analyzing Microbial Community, Composition, Structure, and Functional Activity
	He, Zhili; Deng, Ye; Nostrand, Joy Van; Tu, Qichao; Xu, Meiying; Hemme, Chris; Wu, Liyou; Hazen, Terry; Zhou, Jizhong; Li, Xingyuan; Gentry, Terry; Yin, Yifeng; Liebich, Jost
	2010-05-17
出版年	2010
语种	英语
国家	美国
领域	地球科学
英文摘要	Microarray-based genomic technology has been widely used for microbial community analysis, and it is expected that microarray-based genomic technologies will revolutionize the analysis of microbial community structure, function and dynamics. A new generation of functional gene arrays (GeoChip 3.0) has been developed, with 27,812 probes covering 56,990 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance, and organic contaminant degradation. Those probes were derived from 2,744, 140, and 262 species for bacteria, archaea, and fungi, respectively. GeoChip 3.0 has several other distinct features, such as a common oligo reference standard (CORS) for data normalization and comparison, a software package for data management and future updating, and the gyrB gene for phylogenetic analysis. Our computational evaluation of probe specificity indicated that all designed probes had a high specificity to their corresponding targets. Also, experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036percent-0.025percent false positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which demonstrated that the structure, composition, and potential activity of soil microbial communities significantly changed with the plant species diversity. All results indicate that GeoChip 3.0 is a high throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning. To our knowledge, GeoChip 3.0 is the most comprehensive microarrays currently available for studying microbial communities associated with geobiochemical cycling, global climate change, bioenergy, agricuture, land use, ecosystem management, environmental cleanup and restoration, bioreactor systems, and human health.
英文关键词	Microarray-based genomic technology GeoChip 3.0 geobiochemical cycling
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来源平台	US Department of Energy (DOE)
引用统计
文献类型	科技报告
条目标识符	http://119.78.100.173/C666/handle/2XK7JSWQ/4926
专题	地球科学
推荐引用方式 GB/T 7714	He, Zhili,Deng, Ye,Nostrand, Joy Van,et al. GeoChip 3.0: A High Throughput Tool for Analyzing Microbial Community, Composition, Structure, and Functional Activity,2010.