Development of bioformulations for sugar beet growth promotion and resilience using tailored microbial consortia

Abstract

Sugar beet production in Serbia is increasingly threatened by the combined effects of ‘Candidatus Phytoplasma solani’ and Macrophomina phaseolina, a pathogen pair known to interact synergistically and cause severe root rot. To evaluate whether tailored microbial consortia can improve plant performance and stabilize the microbiome under these pressures, we tested three multi-strain inoculants (Mix1, Mix2, and Mix3) in pot and semi-field conditions. In pot experiments, Mix2 enhanced above-ground biomass, while Mix3 maintained or increased microbial diversity over time. Colonization assays and metabarcoding revealed clear differences in strain persistence, with P. polymyxa C3–36, C. pusillum ED2–6 and several Bacillus spp. establishing most consistently. Phytoplasma infection markedly reduced the native root microbiota of sugar beet, indicating a strong disruption of the natural root-associated microbial community. In response, Skermanella and Blastococcus were enriched in root tissues, while Mix3 treatment notably altered the root microbial profile by enriching oligotrophic and soil-stable taxa such as ‘Candidatus Udaeobacter’, ‘Candidatus Solibacter’, Gemmatimonas, and Acidobacteria-associated lineages (e.g., RB41, Vicinamibacterales). In the rhizosphere, sugar beet actively recruited Arthrobacter and Blastococcus, whereas bacterial inoculation with Mix3 led to the enrichment of Pseudarthrobacter, Kozakia, and Streptomyces in response to phytoplasma infection. Collectively, these results highlight a stress-responsive and compartment-specific modulation of microbiome assembly driven by both phytoplasma infection and bacterial treatment, although further optimization is required to counteract phytoplasma–M. phaseolina–driven decline.