Soil Microbiome Characterization Protocol

Culturable bacteria, fungi, and actinomycetes in the soil were counted using the dilution plate method [27 ]. The activities of urease, sucrase, neutral phosphatase, and catalase in the soil were determined using the method of Yang and Wu [28 ]. Total DNA was extracted from soil using an E.Z.N.A. soil DNA kit (Omega Bio-tek, Norcross, GA, USA), and the gene copy numbers of four Fusarium species (F. oxysporum, F. proliferatum, F. solani, and F. moniliforme) in the soil were determined using a CFX96TM Thermal Cycler (Bio-Rad, Beijing, China) [29 (link)]. The analysis of the bacterial 16S rRNA gene and the fungal ITS region was performed on the Illumina MiSeq platform (www.i-sanger.com, accessed on 25 November 2021). The sequences of the 16S rRNA primers were 338F (5′-ACTCCTACGGGAGGCAGCAG-3′) and 806R (5′-GGACTACHVGGGTWTCTAAT-3′) [30 (link)]; the sequences of the ITS primers were ITS1F (5′-CTTGGTCATTTAGAGGAAGTAA-3′) and ITS2R (5′-GCTGCGTTCTTCATCGATGC-3′) [31 (link)].