GeoChip 3.0 Improves Analysis of Microbial Community Function

The Science

Microbial communities perform a central role in mediating ecosystem biogeochemical cycles and transforming environmental contaminants. However, examining the functional properties of these communities and how they respond to changing conditions is a challenge. The GeoChip, a chip containing an array of molecular probes, enables scientists to efficiently analyze many DNA samples from environments of interest for genes involved in key functional processes including biomass breakdown, nitrogen use, organic contaminant degradation, and metal resistance. A new version of the chip, GeoChip 3.0, is now available that features twice the number of functional gene families, improved analytical tools and software, and a greatly increased capability to trace functional properties to specific community members. This new tool provides enhanced capabilities for understanding the functional processes of environmental microbes and monitoring their response to changing variables. The GeoChip was developed by a collaborative team of investigators at the University of Oklahoma and Lawrence Berkeley National Laboratory. The original version won an R&D 100 award.


A new generation of functional gene arrays (FGAs; GeoChip 3.0) has been developed, with 28 000 probes covering approximately 57 000 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. GeoChip 3.0 also 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. Computational evaluation of probe specificity indicated that all designed probes would have a high specificity to their corresponding targets.

GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which showed that the structure, composition and potential activity of soil microbial communities significantly changed with the plant species diversity. As expected, GeoChip 3.0 is a high-throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning.

BER Program Manager

Dawn Adin

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


He, Z. Y. Deng, J. D. Van Nostrand, Q. Tu, M. Xu, C. L. Hemme, X. Li, T. J. Gentry, Y. Yin, J. Liebich, T. C. Hazen, and J. Zhou. 2010. “GeoChip 3.0 as a High-Throughput Tool for Analyzing Microbial Community Composition, Structure, and Functional Activity,” ISME Journal 4, 1167–79. DOI:10.1038/ismej.2010.46.