Plant-beneficial functions and interactions of Bacillus subtilis SL-44 and Enterobacter cloacae Rs-2 in co-culture by transcriptomics analysis

Abstract

The development of mixed microbial agents can reduce the use of pesticides and fertilizers in agriculture. However, most previous studies focused only on the overall effects of mixed microbial agents and ignored the interactions between bacteria in mixed systems. In this study, Bacillus subtilis SL-44 and Enterobacter cloacae Rs-2 were used to explore the interactions between two different functional plant growth-promoting rhizobacteria (PGPR). The plant growth-promotion properties and inhibition rate of Rhizoctonia solani were determined, and the mechanism of the interactions under single and co-culture conditions was elucidated via transcriptomics analysis under single and co-culture conditions. Results showed that the coculture was not conducive to B. subtilis SL-44 growth. Furthermore, the differentially expressed genes related to B. subtilis SL-44 developmental process and cell differentiation were downregulated by 82.7% and 84.8% respectively. Moreover, among the properties, only siderophore production by the mixed culture was higher than that of single cultures because of the upregulation of the siderophore-related genes of B. subtilis SL-44. In addition, results revealed the altruistic relationship between the two strains, and the chemical and non-chemical signals of their interaction. This study provides unique insights into PGPR interactions and offers guidance for the development and application of mixed microbial agents.

Bioinoculants as a means of increasing crop tolerance to drought and phosphorus deficiency in legume-cereal intercropping systems

“…Yet, the interaction between microorganisms among themselves, especially the one taking place in the proximity of the soil-root interface remains poorly understood. Meanwhile, the extent to which the interspecies interaction shapes the rhizosphere microbial assemblages and functional dynamics are still a matter of discussion 77 . Additionally, the molecular mechanisms underlying behind the ecological inter-microbial interaction, notably, cooperation, resource competition, persistence, and co-existence in microbial mixtures in both, natural environments, or laboratory-controlled conditions, are still not fully explored or still in its infancy 65 , 67 , 78 , 79 .…”

“…For example, in the presence of Enterobacter cloacae Rs-2, the growth of B. subtilis SL-44 was restricted as indicated by the downregulation of genes associated with development and cell differentiation. However, this inhibitory effect has led to the upregulation of genes related to siderophores biosynthesis, thus providing more siderophores to the community 77 .…”

Biochar-based Bacillus subtilis inoculant for enhancing plants disease prevention: microbiota response and root exudates regulation

“…Bacillus, a plant growth-promoting rhizobacteria (PGPR), has been used as a biotic exogenous addition. It could be recruited by organic acids, amino acids, and flavonoid compounds from root exudates (Sharma et al 2020;Wen et al 2023;Zhou et al 2023a) and produce antifungal compounds, such as surfaceacins, iturin, and fengycin, to further enhance plant disease resistance (Huang et al 2017;Li et al 2021). Some researchers have shown that exogenous beneficial microbes could help plants enhance the defense system (Shalev et al 2022;Wu et al 2022).…”

Whole genome analysis of Enterobacter cloacae Rs-2 and screening of genes related to plant-growth promotion

“…Enterobacter cloacae Rs-2 was isolated from pepper rhizosphere soil of saline-alkali land. The previous experiments have shown that Rs-2 has good biological control and plant growth promotion properties (Li et al, 2021). However, the metabolic pathways and mechanisms of action for these functions are still unclear.…”