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Additional file 2. Figure S1. MALDI-TOF MS spectra generated from a subset of bacteria isolated from G. clandestina and G. max seeds. The bacterial isolates were identified using an in-house endophyte library and Bruker database. The isolates selected for WGS are labelled next to the representative clade.

Additional file 1. Table S1. Accession ID, hosts and length of H3-D region of the sequences used for constructing ML tree. Table S2. Shannon diversity indices of seed samples grouped by plant species and seed accession. Table S3. The Kruskal Wallis pairwise test results calculating significant differences between the bacterial diversity associated with G. clandestina and G. max seed when samples are grouped based on “Plant Species” and “Seed Accession”. Table S4. PERMANOVA and PERMDISP results calculating significant differences in bacterial composition associated with G. clandestina and G. max when data was grouped based on “Plant Species” and “Seed Accession”. Table S5. The relative abundance of bacterial genera associated with both “Plant species”. Taxa occurring at > 0.1% are highlighted in bold. Table S6. The relative abundance of bacterial genera associated with different G. clandestina seed accessions. Taxa occurring at > 0.1% are highlighted in bold. Table S7. The relative abundance of bacterial genera associated with different G. max seed accessions. Taxa occurring at > 0.1% are highlighted in bold. Table S8. Closest taxonomy ID identified by Kraken2 for the isolated bacterial and fungal sequences with > 96% similarity along with the source of seed accessions. Genome sequences for fungal and bacterial isolates are described under the NCBI BioProjectID PRJNA807720 and PRJNA807698. Figure S1. Map highlighting the sites (in yellow) selected for G. clandestina seed collection in the Greater Melbourne region, Victoria. Figure S2. G. clandestina (A) and G. max (B) seedlings at the unfolded cotyledon growth stage. Figure S3. Maximum Likelihood Consensus Tree with a bootstrap node support of 70% was inferred from the histone H3-D gene sequences of six Glycine taxa used in this study and the 17 references sequences retrieved from NCBI using MEGA X with 1000 bootstrap replications. The best nucleotide substitution model, the Tamura–Nei model, was used. The ten phylogenetic clades identified within the tree are highlighted in different shades. Sequences reading down (light green, dark green, light blue, yellow, grey, orange, sky blue, violet red and dark red) belong to clades 1 through to 10, respectively. Figure S4. The relative abundance of bacterial communities across Glycine seeds at phylum level based on “Plant Species” (A), and “Seed Accession” (B, C).