Microbial DNA was extracted for each sample by freeze-grinding and SDS-based cell lysis (Zhou, Bruns, and Tiedje 1996), and purified with the PowerSoil DNA Isolation Kit (MoBio Laboratories, Carlsbad, CA, USA). The quality of extracted DNA was assessed by the absorbance ratios of O.D. 260/230 nm and O.D. 260/280 nm with an ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA). The DNA concentration was quantified using a FLUOstar Optima fluorescence plant reader (BMG Labtech, Jena, Germany).
Label
Cy3
Label protocol
As previously described (He et al. 2010; Shi et al. 2019; Guo et al., Nature Communication, 2020), purified DNA from each sample was labeled with fluorescent dye Cy-3 dUTP.
Hybridization protocol
As previously described (Guo et al. Nature Communication, 2020), Labeled DNA was resuspended into DNase-free water, and then mixed completely with hybridization solution. After denaturation and incubation, the DNA solution was centrifuged to collect liquid at the bottom of the tube. The solution was hybridized at 67 °C for 24 h at 20 rpm in a hybridization oven.
Scan protocol
The resulting GeoChip arrays were scanned as Multi-TIFF images with a NimbleGen MS200 Microarray Scanner (Roche NimbleGen, Inc., Madison, WI, USA).
Description
16soil6N
Data processing
Raw signals extracted from scanned images were submitted to the Microarray Data Manager on our website (http://ieg.ou.edu/microarray/) for cleaning and normalizing. To remove unrepresentative data, we assigned probes detected in less than three out of twelve samples for warmed litterbag, control litterbag, warmed bulk soil, and control bulk soil samples to undetectable. We then logarithmically transformed the remaining data and scaled the sum of signal intensity for each sample with the maximum sum value.
