Probes were summarized to gene level data in Partek Genomics Suite v6.6 (Partek Inc., St Louis, MO) by using the RMA algorithm (Irizarry et al., 2003).
Total RNAs were isolated from soil samples according to Damon et al. [ 21] for the BB sample or by using the RNA PowerSoil® Total RNA Isolation Kit (Mo Bio laboratories, Carlsbad, CA) for the PL and UP samples.
In the final step of generating the simulation data, we added Gaussian noise into each projection by using the commands FS, MO and ADD in SPIDER (Frank et al., 1996).
NiMo catalysts supported by mesoporous sieves are prepared by using the newly proposed Mo-based organic inorganic hybrid nanocrystals as precursors to load Mo and subsequently using wetness impregnation to load Ni.
Briefly, one gram of soil from each microcosm was extracted by using the UltraClean Microbial DNA Kit (Mo Bio Laboratories, CA).
Total RNA from the bacterial cells was isolated by using the TRI reagent method (Sigma, MO) and treated with Turbo DNA-free DNase kits (Ambion, TX) as described [31].
Total RNA was extracted from seedlings treated with mock or specific hormones by using the Spectrum Plant Total RNA kit (Sigma, St . Louis MO).
Genomic DNA was extracted directly from fecal samples by using the PowerSoil DNA Isolation Kit (Mo Bio, Carlsbad, CA, USA) according to the manufacturer's instructions, with the exception that fecal samples were subjected to a 5-min disruption by using 0.5-mm Zirconia/Silica beads (BioSpec Products, Inc., Bartlesville, OK, USA) instead of the beads provided by the manufacturer.
For the rep-PCR method, DNA was extracted from 10 clinical isolates by using the Ultraclean Microbial DNA Isolation Kit (MO BIO Laboratories, Carlsbad, CA, USA).
Briefly, DNA was extracted from 2 μL of an overnight VNSE culture by using the Ultraclean Microbial DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, CA, USA).
