Hybridization of Environmental Microbial Community Nucleic Acids by GeoChip

Joy D Van Nostrand; Huaqin Yin; Liyou Wu; Tong Yuan; Jizhong Zhou

doi:10.1007/978-1-4939-3369-3_11

Hybridization of Environmental Microbial Community Nucleic Acids by GeoChip

Methods Mol Biol. 2016:1399:183-96. doi: 10.1007/978-1-4939-3369-3_11.

Authors

Joy D Van Nostrand¹, Huaqin Yin¹, Liyou Wu¹, Tong Yuan¹, Jizhong Zhou²

Affiliations

¹ Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
² Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA. jzhou@ou.edu.

PMID: 26791504
DOI: 10.1007/978-1-4939-3369-3_11

Abstract

Functional gene arrays, like the GeoChip, allow for the study of tens of thousands of genes in a single assay. The GeoChip array (5.0) contains probes for genes involved in geochemical cycling (N, C, S, and P), metal homeostasis, stress response, organic contaminant degradation, antibiotic resistance, secondary metabolism, and virulence factors as well as genes specific for fungi, protists, and viruses. Here, we briefly describe GeoChip design strategies (gene selection and probe design) and discuss minimum quantity and quality requirements for nucleic acids. We then provide detailed protocols for amplification, labeling, and hybridization of samples to the GeoChip.

Keywords: Fluorescent labeling; Functional gene array; GeoChip; Hybridization; Microbial communities; Microbial ecology; Whole community genome amplification.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bacteria / genetics
Drug Resistance, Microbial / genetics
Fungi / classification
Fungi / genetics
Genetic Variation*
Nucleic Acid Hybridization / methods*
Oligonucleotide Array Sequence Analysis / methods*
Soil Microbiology*
Viruses / classification
Viruses / genetics