Extracted DNA was used for GeoChip analysis as reported previously (Zhang et al., 2015a (link)). Briefly, DNA (15 ng) was amplified and fluorescently labeled by whole community genome amplification with a modified (Wu et al., 2006 (link)) TempliPhi Kit (GE Healthcare, Piscataway, NJ, United States). Amplified and labeled DNA (2 μg) was then hybridized with GeoChip 5.0.
The GeoChip 5.0 used in this study contains a total of 161,961 probes targeting 1,447 functional gene families, covering 366,891 coding sequences. Specifically, 25,234 probes (15.6%) targeted 135 genes involved in C cycling processes. At the taxonomic level, the probes may target 6465 bacterial strains, 282 archaeal strains, 1073 eukaryotic strains, 1364 bacteriophages, and uncultured/unidentified/environmental organisms (Zhang et al., 2015c (link)). Signal intensities were background-subtracted, and only spots with signal-to-noise ratio >2 were considered as positive and used for further analysis.
The GeoChip 5.0 used in this study contains a total of 161,961 probes targeting 1,447 functional gene families, covering 366,891 coding sequences. Specifically, 25,234 probes (15.6%) targeted 135 genes involved in C cycling processes. At the taxonomic level, the probes may target 6465 bacterial strains, 282 archaeal strains, 1073 eukaryotic strains, 1364 bacteriophages, and uncultured/unidentified/environmental organisms (Zhang et al., 2015c (link)). Signal intensities were background-subtracted, and only spots with signal-to-noise ratio >2 were considered as positive and used for further analysis.
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