2.1. Soil sampling and property measuring
Paddy soil samples (n =  57) with different chemical characteristics were collected from 19 sites (3 samples/site) in June 2020 across eastern China (Fig. 1a), which are the main rice-producing areas in China. While sampling, the paddy soils were flooded for over a month, with rice plants at the tillering stage. Three composite samples were collected from each site, indicating three replicates. These composites were created by combining five surface (<10 cm) paddy soil cores. The samples were kept under ice and transported to the lab. Each soil sample was divided into the following two aliquots: one was freeze-dried for DNA extraction, and the other was stored at 4 °C for further soil chemical analysis.
Soil chemical parameters were evaluated, as reported previously (Yuan et al. 2016). Soil pH was detected with air-dried soil at a water ratio of 1:2.5 using a pH meter. Total carbon (TC) and total nitrogen (TN) were analyzed using an Elemental Analyzer (Vario EL, Elementar, Germany), and the resulting data was used for the calculation of the C/N ratio. Soil organic matter (SOM) was measured using a Muffle furnace (VULCAN 3–1750A, NEYTECH, America). Nitrate (NO3) and ammonium (NH4+) were analyzed using a Continuous Flow Analytical System (AA3, SEAL, Germany). Total iron (Fe) and manganese (Mn) analyses were performed using an Inductively Coupled Plasma Optical Emission Spectrometer (ICP-OES). The physicochemical properties of the soils are shown in Table S1. The soil properties differed significantly among different sites; for instance, the soil pH ranged from 4.8 to 8.1 (Fig. 1b), the C/N ratio ranged from 8.6 to 19.8, and the SOM content ranged from 2.81% to 39.37% (Table S1). Climatic indexes of different sites were obtained from the WorldClim database (www.worldclim.org), and the mean annual temperature (MAT) differed from 6.2 °C to 21.4 °C.