Development of a Four-Strain Rhizobacterial Consortium: Detection in the Field by Strain-Specific qPCR and Impact on the Wheat Rhizosphere Microbiome

Multi-strain consortia are expected to protect plants more reliably than single strains, yet this is rarely tested directly, and the behavior of introduced strains in the field is difficult to follow. We assembled a consortium of Stenotrophomonas rhizophila MGMM118, Bacillus halotolerans MGMM119, Pseudomonas grimontii MGMM120 and Pseudomonas viciae MGMM121 strains isolated from the winter wheat rhizosphere and characterized their hydrolytic activities, auxin production, and analyzed their genomes. The consortium increased shoot and root length of wheat. In biocontrol experiments on barley, the consortium reduced the root rot disease index caused by Fusarium culmorum by approximately ten-fold (5.6% vs. 59.7%), outperforming each individual strain (11.9–17.9%). The consortium also reduced Fusarium root rot in tomato by two-fold. In a field experiment on wheat, strain-specific qPCR detected all introduced microorganisms in the wheat rhizosphere at up to 106 CFU per gram of soil, demonstrating different dynamics for each individual strain. Metabarcoding showed that community structure depended on plant developmental stage rather than on the consortium application. Since metabarcoding could not reliably identify the introduced strains, we suppose that strain-specific qPCR is a more appropriate tool for monitoring of inoculants, particularly in complex soil microbial communities.