Bioinformatics
All the sequenced samples, including bulk soil, rhizosphere, endosphere and nodule tissue, were combined for bioinformatics using the Quantitative Insights Into Microbial Ecology 2 (QIIME2) platform (Bolyen et al., 2019). Firstly, raw sequences were demultiplexed by the “q2-demux” plugin, and then trimmed and quality controlled using “q2-cutadapt” plugin, followed by denoising with DADA2 (“q2-dada2” plugin, Callahan et al., 2016) to generate an amplicon sequence variants (ASVs) table. The taxonomic annotation of ASVs was conducted by “q2-feature-classifier” plugin based on the SILVA reference database (vs. 132, Quast et al., 2012). Low abundance ASVs (ASVs with less than 5% chance appeared in all the samples) and organellar ASVs (ASVs assigned to chloroplast or mitochondria) were removed. The raw sequenced data from the Illumina MiSeq platform are available at National Center for Biotechnology Information (NCBI), Sequence Read Archive (https://www.ncbi.nlm.nih.gov/sra) with the accession number PRJNA595445.