Bacillus altitudinis LZP02 improves rice growth by reshaping the rhizosphere microbiome

Background and Aims Rhizosphere microorganisms play an important role in promoting plant growth and maintaining soil health. Bacillus altitudinis LZP02 (LZP02) is an efficient plant growth-promoting rhizobacterium that interacts closely with rice radicals. However, the mechanisms mediating the rhizosphere interactions of beneficial strains of microorganisms in native soil are mostly unclear. Methods This study analysed the rhizosphere-enriched taxonomic and functional properties of the rhizosphere-associated microbiome and determined how they were affected by LZP02 using metagenome sequencing and ITS sequencing after the inoculation of LZP02 in soil. And microorganisms from the rice rhizosphere were identified and cultivated using high-throughput sequencing. Results LZP02 stimulated some beneficial bacteria, such as Novosphingobium , Acidovorax , Sphingomonas , and Devosia , to the rhizosphere. The enrichment of functional attributes, nitrogen metabolism and bacterial chemotaxis demonstrated an increase in active microbe-microbe interactions in the rhizosphere. This study showed that LZP02 stimulated plant growth in three ways: (1) by increasing the relative abundance of most rhizosphere-enriched genus; (2) by increasing the relative abundance of the functional attributes involved in microbe-microbe interactions; and (3) by enriching functional components that are essential for plant fitness, such as nitrogen fixation and bacterial chemotaxis in the rhizosphere microbiome. Finally, inoculation of enriched single strains or synthetic consortia isolated from the radical-associated microbiome using high-throughput cultivation could improve plant growth. Conclusion This study proposes a new mechanism by which LZP02 influences the nitrogen metabolism of rhizosphere microorganisms and bacterial chemotaxis for rice growth by reshaping the rhizosphere microbiome.