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

[1] Direct detection of soil mRNAs using targeted microarrays for genes associated with lignin degradation [J].

Bailey, Vanessa L. ;

Fansler, Sarah J. ;

Bandyopadhyay, Somnath ;

Smith, Jeffrey L. ;

Waters, Katrina M. ;

Bolton, Harvey .

SOIL BIOLOGY & BIOCHEMISTRY, 2010, 42 (10) :1793-1799

[2] Afforestation Alters the Composition of Functional Genes in Soil and Biogeochemical Processes in South American Grasslands [J].

Berthrong, Sean T. ;

Schadt, Christopher W. ;

Pineiro, Gervasio ;

Jackson, Robert B. .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2009, 75 (19) :6240-6248

[3] mRNA-based parallel detection of active methanotroph populations by use of a diagnostic microarray [J].

Bodrossy, L ;

Stralis-Pavese, N ;

Konrad-Köszler, M ;

Weilharter, A ;

Reichenauer, TG ;

Schöfer, D ;

Sessitsch, A .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2006, 72 (02) :1672-1676

[4] Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation [J].

Brodie, Eoin L. ;

DeSantis, Todd Z. ;

Joyner, Dominique C. ;

Baek, Seung M. ;

Larsen, Joern T. ;

Andersen, Gary L. ;

Hazen, Terry C. ;

Richardson, Paul M. ;

Herman, Donald J. ;

Tokunaga, Tetsu K. ;

Wan, Jiamin M. ;

Firestone, Mary K. .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2006, 72 (09) :6288-6298

[5] Microbial community gene expression in ocean surface waters [J].

Frias-Lopez, Jorge. ;

Shi, Yanmei ;

Tyson, Gene W. ;

Coleman, Maureen L. ;

Schuster, Stephan C. ;

Chisholm, Sallie W. ;

DeLong, Edward F. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (10) :3805-3810

[6] Microarray-based analysis of microbial community RNAs by whole-community RNA amplification [J].

Gao, Haichun ;

Yang, Zamin K. ;

Gentry, Terry J. ;

Wu, Liyou ;

Schadt, Christopher W. ;

Zhou, Jizhong .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2007, 73 (02) :563-571

[7] Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria [J].

Hazen, Terry C. ;

Dubinsky, Eric A. ;

DeSantis, Todd Z. ;

Andersen, Gary L. ;

Piceno, Yvette M. ;

Singh, Navjeet ;

Jansson, Janet K. ;

Probst, Alexander ;

Borglin, Sharon E. ;

Fortney, Julian L. ;

Stringfellow, William T. ;

Bill, Markus ;

Conrad, Mark E. ;

Tom, Lauren M. ;

Chavarria, Krystle L. ;

Alusi, Thana R. ;

Lamendella, Regina ;

Joyner, Dominique C. ;

Spier, Chelsea ;

Baelum, Jacob ;

Auer, Manfred ;

Zemla, Marcin L. ;

Chakraborty, Romy ;

Sonnenthal, Eric L. ;

D'haeseleer, Patrik ;

Holman, Hoi-Ying N. ;

Osman, Shariff ;

Lu, Zhenmei ;

Van Nostrand, Joy D. ;

Deng, Ye ;

Zhou, Jizhong ;

Mason, Olivia U. .

SCIENCE, 2010, 330 (6001) :204-208

[8] Development and application of functional gene arrays for microbial community analysis [J].

He, Z. L. ;

Van Nostrand, J. D. ;

Wu, L. Y. ;

Zhou, J. Z. .

TRANSACTIONS OF NONFERROUS METALS SOCIETY OF CHINA, 2008, 18 (06) :1319-1327

[9] Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis [J].

He, Zhili ;

Zhou, Jizhong .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2008, 74 (10) :2957-2966

[10] GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes [J].

He, Zhili ;

Gentry, Terry J. ;

Schadt, Christopher W. ;

Wu, Liyou ;

Liebich, Jost ;

Chong, Song C. ;

Huang, Zhijian ;

Wu, Weimin ;

Gu, Baohua ;

Jardine, Phil ;

Criddle, Craig ;

Zhou, Jizhong .

ISME JOURNAL, 2007, 1 (01) :67-77

← 1 2 3 4 5 6 →