Metagenome-Assembled Genomes from maize rhizobiome contribute to unraveling of potential plant growth promoting bacteria

The rhizosphere microbiome (rhizobiome) comprises a reservoir of ecological traits that contributes to plant nutrition, health and defense, responding in different ways to plant growth-promoting bacteria (PGPB) inoculation. PGPB are capable of nutrient cycling, modulation of phytohormones, production of secondary metabolites, suppression of disease-causing agents, pests and weeds. Metagenome-assembled genomes (MAGs) are important tools to dissect the potential of particular microbes present in the rhizobiome. Our objective was to obtain high-quality MAGs (HQM) with PGPB potential from maize rhizobiome influenced by the inoculant Azospirillum brasilense strain Ab-V5 under different levels of soil native microbiome diversity. We hypothesized that these MAGs could harbor important traits for plant nutrition, health and defense. We used a dilution-to-extinction approach on soil native microbiome to understand the effect of soil diversity in maize seed inoculation with the PGPB Azospirillum brasilense strain Ab-V5, a commercial inoculant used for crops in Brazil. Metagenomics supported by plant phenomics was used to investigate particular interactions between Ab-V5 and rhizobiome that influenced maize growth promotion. High-quality MAGs were obtained through contig binning and further analyzed through Prokka, DRAM and antiSMASH for biosynthetic gene clusters (BCGs). We identified 1 archeal and 11 bacterial HQM. Except for one HQM assigned to Ralstonia sp., all other bacterial HQM were assigned to genera with known plant growth promoter candidates. These HQM harbors BGCs of 16 distinct classes related to ROS stress alleviating, biofilm formation, plant growth promotion and defense against pathogens. Both archeal and bacterial HQM contain nitrogen, phosphorus and potassium (NPK) cycling pathways-related genes, indicating their potential as PGPB candidates. This study provides new insights into MAGs of potential PGPB previously overlooked or unknown from the maize rhizobiome