GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis

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	GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis
	Tu, Qichao ; Yu, Hao ; He, Zhili ; Deng, Ye ; Wu, Liyou ; Van Nostrand, Joy D. ; Zhou, Aifen ; Voordeckers, James ; Lee, Yong-Jin ; Qin, Yujia ; Hemme, Christopher L. ; Shi, Zhou ; Xue, Kai ; Yuan, Tong ; Wang, Aijie ; Zhou, Jizhong
刊名	MOLECULAR ECOLOGY RESOURCES
	2014
卷号	14 期号:5 页码:914-928
关键词	environmental technology functional gene array GeoChip 4 microbial community analysis
ISSN号	1755-098X
中文摘要	Micro-organisms play critical roles in many important biogeochemical processes in the Earth's biosphere. However, understanding and characterizing the functional capacity of microbial communities are still difficult due to the extremely diverse and often uncultivable nature of most micro-organisms. In this study, we developed a new functional gene array, GeoChip 4, for analysing the functional diversity, composition, structure, metabolic potential/activity and dynamics of microbial communities. GeoChip 4 contained approximately 82 000 probes covering 141 995 coding sequences from 410 functional gene families related to microbial carbon (C), nitrogen (N), sulphur (S), and phosphorus (P) cycling, energy metabolism, antibiotic resistance, metal resistance/reduction, organic remediation, stress responses, bacteriophage and virulence. A total of 173 archaeal, 4138 bacterial, 404 eukaryotic and 252 viral strains were targeted, providing the ability to analyse targeted functional gene families of micro-organisms included in all four domains. Experimental assessment using different amounts of DNA suggested that as little as 500 ng environmental DNA was required for good hybridization, and the signal intensities detected were well correlated with the DNA amount used. GeoChip 4 was then applied to study the effect of long-term warming on soil microbial communities at a Central Oklahoma site, with results indicating that microbial communities respond to long-term warming by enriching carbon degradation, nutrient cycling (nitrogen and phosphorous) and stress response gene families. To the best of our knowledge, GeoChip 4 is the most comprehensive functional gene array for microbial community analysis.
WOS记录号	WOS:000340425100004
公开日期	2015-03-23
内容类型	期刊论文
源URL	[http://ir.rcees.ac.cn/handle/311016/9163]
专题	生态环境研究中心_城市与区域生态国家重点实验室
推荐引用方式 GB/T 7714	Tu, Qichao,Yu, Hao,He, Zhili,et al. GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis[J]. MOLECULAR ECOLOGY RESOURCES,2014,14(5):914-928.
APA	Tu, Qichao.,Yu, Hao.,He, Zhili.,Deng, Ye.,Wu, Liyou.,...&Zhou, Jizhong.(2014).GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis.MOLECULAR ECOLOGY RESOURCES,14(5),914-928.
MLA	Tu, Qichao,et al."GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis".MOLECULAR ECOLOGY RESOURCES 14.5(2014):914-928.