Manipulation of rhizosphere microbiome by Microbacterium sp. GB16_1_BI to promote plant growth.
AIM: The bioinoculant properties of a newly identified ammonium-releasing novel strain of Actinomycetota-Microbacterium bengalense sp. nov. GB16_1_BI (Accession number: SRX9280401) on the microbiome structure of rice rhizosphere were assessed. METHODS AND RESULT: GB16_1_BI may inhibit most bacteria present in the rice rhizosphere as well as encouraged the growth of rare bacteria specific to the waterlogged rice rhizosphere. The genome sequence as well as untargeted metabolome analyses of GB16_1_BI showed abundance of secondary metabolites with probable antimicrobial activity. Amplicon sequencing of the 16S rRNA V3-V4 region from the rhizosphere of the black rice showed inhibition of most bacteria by GB16_1_BI. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) analysis showed increased abundance in the marker genes for nitrogen cycling (nifH, nrfA, and nrt) but not for nifD or nifK, which was also reflected in the ANOSIM analysis in the OTUs of the N-fixing bacteria. Higher abundance of the nitrogen-fixing methanotrophs, Methylosinus and Methylocystis in inoculated plants also led to study of the marker genes for methane metabolism. CONCLUSION: Microbes present in the rhizosphere contribute to the biogeochemical cycle by transforming unavailable minerals and by retaining nutrients for their growth, which get released after death for plant adsorption. However, not all microbes contribute positively to plant growth. Microbes compete with plants for nutrients, cause disease, or produce harmful greenhouse gases. Hence, GB16_1_BI could influence plant growth predominantly by suppressing microbes and encouraged niche-specific microbes specifically involved in nitrogen cycling.