Abstract
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. Experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036–0.025% false-positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, 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.
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Acknowledgements
This work is supported by the Genomics:GTL program through the Virtual Institute of Microbial Stress and Survival (VIMSS; http://vimss.lbl.gov) as part of contract no. DE-AC02–05CH11231 between the US Department of Energy and Lawrence Berkeley National Laboratory, the United States Department of Agriculture (Project 2007–35319–18305) through NSF-USDA Microbial Observatories Program, the Environmental Remediation Science Program, the Oklahoma Bioengery Center (OBC) of State of Oklahoma, and the Oklahoma Applied Research Support (OARS), Oklahoma Center for the Advancement of Science and Technology (OCAST), the State of Oklahoma.
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He, Z., Deng, Y., Van Nostrand, J. et al. GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. ISME J 4, 1167–1179 (2010). https://doi.org/10.1038/ismej.2010.46
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DOI: https://doi.org/10.1038/ismej.2010.46
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