Applications of functional gene microarrays for profiling microbial communities

被引：54

作者：

He, Zhili ^{[1
]}

Van Nostrand, Joy D. ^{[1
]}

Zhou, Jizhong ^{[1
]}

机构：

[1] Univ Oklahoma, Dept Bot & Microbiol, Inst Environm Genom, Norman, OK 73019 USA

来源：

CURRENT OPINION IN BIOTECHNOLOGY | 2012年 / 23卷 / 03期

关键词：

GEOCHIP-BASED ANALYSIS; OLIGONUCLEOTIDE MICROARRAY; MESSENGER-RNA; DIVERSITY; SOIL; DNA; BACTERIAL; HETEROGENEITY; POPULATIONS; RESPONSES;

D O I：

10.1016/j.copbio.2011.12.021

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Functional gene arrays (FGAs) have been considered as a specific, sensitive, quantitative, and high throughput metagenomic tool to detect, monitor and characterize microbial communities. Especially GeoChips, the most comprehensive FGAs have been applied to analyze the functional diversity, composition, structure, and metabolic potential or activity of a variety of microbial communities from different habitats, such as aquatic ecosystems, soils, contaminated sites, extreme environments, and bioreactors. FGAs are able to address fundamental questions related to global change, bioremediation, land use, human health, and ecological theories, and link the microbial community structure to environmental properties and ecosystem functioning. This review focuses on applications of FGA technology for profiling microbial communities, including target preparation, hybridization and data processing, and data analysis. We also discuss challenges and future directions of FGA applications.

引用

页码：460 / 466

页数：7

共 58 条

[41] Tracking Functional Guilds: "Dehalococcoides" spp. in European River Basins Contaminated with Hexachlorobenzene [J].

Tas, Neslihan ;

van Eekert, Miriam H. A. ;

Schraa, Gosse ;

Zhou, Jizhong ;

de Vos, Willem M. ;

Smidt, Hauke .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2009, 75 (14) :4696-4704

[42] Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere [J].

Trivedi, Pankaj ;

He, Zhili ;

Van Nostrand, Joy D. ;

Albrigo, Gene ;

Zhou, Jizhong ;

Wang, Nian .

ISME JOURNAL, 2012, 6 (02) :363-383

[43] Dynamics of Microbial Community Composition and Function during In Situ Bioremediation of a Uranium-Contaminated Aquifer [J].

Van Nostrand, Joy D. ;

Wu, Liyou ;

Wu, Wei-Min ;

Huang, Zhijian ;

Gentry, Terry J. ;

Deng, Ye ;

Carley, Jack ;

Carroll, Sue ;

He, Zhili ;

Gu, Baohua ;

Luo, Jian ;

Criddle, Craig S. ;

Watson, David B. ;

Jardine, Philip M. ;

Marsh, Terence L. ;

Tiedje, James M. ;

Hazen, Terry C. ;

Zhou, Jizhong .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2011, 77 (11) :3860-3869

[44] GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer [J].

Van Nostrand, Joy D. ;

Wu, Wei-Min ;

Wu, Liyou ;

Deng, Ye ;

Carley, Jack ;

Carroll, Sue ;

He, Zhili ;

Gu, Baohua ;

Luo, Jian ;

Criddle, Craig S. ;

Watson, David B. ;

Jardine, Philip M. ;

Marsh, Terence L. ;

Tiedje, James M. ;

Hazen, Terry C. ;

Zhou, Jizhong .

ENVIRONMENTAL MICROBIOLOGY, 2009, 11 (10) :2611-2626

[45]

Verdick D, 2002, KEY CONSIDERATIONS A

[46] GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent [J].

Wang, Fengping ;

Zhou, Huaiyang ;

Meng, Jun ;

Peng, Xiaotong ;

Jiang, Lijing ;

Sun, Ping ;

Zhang, Chuanlun ;

Van Nostrand, Joy D. ;

Deng, Ye ;

He, Zhili ;

Wu, Liyou ;

Zhou, Jizhong ;

Xiao, Xiang .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (12) :4840-4845

[47] Microarray image enhancement by denoising using stationary wavelet transform [J].

Wang, XH ;

Istepanian, RSH ;

Song, YH .

IEEE TRANSACTIONS ON NANOBIOSCIENCE, 2003, 2 (04) :184-189

[48] Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the gulf of Mexico [J].

Wu, Liyou ;

Kellogg, Laurie ;

Devol, Allan H. ;

Tiedje, James M. ;

Zhou, Jizhong .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2008, 74 (14) :4516-4529

[49] Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification [J].

Wu, Liyou ;

Liu, Xueduan ;

Schadt, Christopher W. ;

Zhou, Jizhong .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2006, 72 (07) :4931-4941

[50] GeoChip-Based Analysis of the Functional Gene Diversity and Metabolic Potential of Microbial Communities in Acid Mine Drainage [J].

Xie, Jianping ;

He, Zhili ;

Liu, Xinxing ;

Liu, Xueduan ;

Van Nostrand, Joy D. ;

Deng, Ye ;

Wu, Liyou ;

Zhou, Jizhong ;

Qiu, Guanzhou .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2011, 77 (03) :991-999

← 1 2 3 4 5 6 →