Differences in rice rhizosphere bacterial community structure by application of lignocellulolytic plant-probiotic bacteria with rapid composting traits

Abstract Plant-probiotic rhizobacteria with abilities of plant growth stimulation and lignocellulosic degradation were isolated from rice rhizosphere, and were used for degradation of rice straw residues to compost. Probiotic bacterial composts formulated with Bacillus cereus RSDa2, Stenotrophomonas maltophilia RSI6 or Klebsiella pneumoniae RSI9 were characterized and applied in rice rhizosphere that significantly (P ≤ 0.05) enhanced the growth of plants. Variation in rhizosphere bacterial community of rice plants treated with probiotic bacterial compost were studied utilizing the metagenomic analysis of 16S (V3–V4) rRNA gene sequences. Proteobacteria remained the most prominent phyla in control and compost treatments, though relative abundance was lower than control. Also, the relative abundance of Firmicutes and Acidobacteria increased several fold. An unclassified genus from Xanthomonadaceae family (26.3%) dominated the rice rhizosphere population in control, while its relative dominance was highly reduced in compost treatments. Several genera including Geobacter , Geothrix , Cellulomonas , Methylomonas , Azospira were detected in all three compost treatments, which were completely absent in control. The Shannon alpha diversity index was low for control as compared to probiotic bacteria composts treatments. PCoA based on unweighted UniFrac distances placed RS16 and RS19 treatments close to each other, while, unweighted UniFrac distances placed all the treatments at different coordinates.16S (V3–V4) rRNA gene sequence datasets had been submitted to the Sequence Read Archive (SRA) under accession number SRP9811 under Bioproject no. PRJNA411879.