| DOI: | 10.2172/986221
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| 报告号: | LBNL-3801E
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| 报告题名: | GeoChip 3.0: A High Throughput Tool for Analyzing Microbial Community, Composition, Structure, and Functional Activity |
| 作者: | 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
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| 出版年: | 2010
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| 发表日期: | 2010-05-17
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| 国家: | 美国
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| 语种: | 英语
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| 英文关键词: | Microarray-based genomic technology
; GeoChip 3.0
; geobiochemical cycling
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| 中文主题词: | 磷
; 硫磺
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| 主题词: | PHOSPHORUS
; SULFUR
|
| 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. |
| URL: | http://www.osti.gov/scitech/servlets/purl/986221
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| Citation statistics: |
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| 资源类型: | 研究报告
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| 标识符: | http://119.78.100.158/handle/2HF3EXSE/39810
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| Appears in Collections: | 过去全球变化的重建
影响、适应和脆弱性
科学计划与规划
气候变化与战略
全球变化的国际研究计划
气候减缓与适应
气候变化事实与影响
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| 986221.pdf（1857KB） | 研究报告 | -- | 开放获取 | | View
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| Recommended Citation: | |
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. 2010-01-01.
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