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

Study of Pathogenicity Test, Antifungal Activity, and Secondary Metabolites of Bacillus spp. from Lake Bogoria as Biocontrol of Rhizoctonia solani Kühn in Phaseolus vulgaris L

The common bean (Phaseolus vulgaris L.) is a yearly herbaceous plant grown for its edible dry seeds. Despite that, pests and diseases have contributed to the decline of common bean production in Kenya. Therefore, the study aimed to identify bacteria from Lake Bogoria, assess the pathogenicity of Rhizoctonia solani Kühn, screen for effective antifungal agents, and determine secondary metabolites for the biocontrol of R. solani. A total of 49 bacteria were isolated, of which 10 isolates had varied mycelial inhibition rates of R. solani in the co-culture technique. The efficacy of volatile compounds of the three selected bacterial strains had varied mycelial growth and percent reduction against R. solani. The pathogenicity assay showed varied plant parameters and biomass of R. solani on common bean plantlets. The molecular characterization based on 16 S ribosomal RNA confirmed the selected bacterial strains' identity with a diversity similar to the Bacillus genus. Gas chromatography-mass spectrometry analysis of secondary metabolites showed different antimicrobial compounds produced by Bacillus subtilis strain TW21. In conclusion, Lake Bogoria harbors useful microbes as biocontrol agents against plant pathogens. The current study discovers the potential biocontrol bacteria isolates from Lake Bogoria as alternative bioagents against R. solani. Therefore, the isolate Bacillus subtilis strain TW21 can be assessed further for toxicological and ecotoxicological studies and registered by the Pest Control Products Board (PCPB), Kenya, as a biocontrol product against common diseases affecting common beans' production.

Transcriptomics integrated with metabolomics reveal the competitive relationship between co-cultured Trichoderma asperellum HG1 and Bacillus subtilis Tpb55

Microbial co-culture has proven to be an effective way to improve the ability of microorganisms to biocontrol. However, the interactive mechanisms of co-cultural microbes, especially between fungi and bacteria, have rarely been studied. By comparative analysis of morphology, transcriptomics and metabolomics, the interactive mechanisms of a sequential co-culture system of Trichoderma asperellum HG1 and Bacillus subtilis Tpb55 was explored in this study. The results revealed that co- culture has no significant effect on the growth and cell morphology of the two strains, but lead to mycelium wrinkling of HG1. RNA-seq analysis showed that co-culture significantly upregulated the HG1 genes concerning amino acid degradation and metabolism, proteolysis, resisting environmental stress, cell homeostasis, glycolysis, the glyoxylate cycle, and the citric acid (TCA) cycle, while Tpb55 genes related to cell homeostasis, spore formation and membrane fluidization were significantly upregulated, but genes associating to TCA, glycolytic cycles and fatty acid β-oxidation were significantly downregulated. Metabolomic results revealed that some amino acids related to energy metabolism were significantly altered in HG1, whereas palmitic acid, which is related to cell membrane functions, was upregulated in Tpb55. These results indicated that HG1 could interfere with carbon metabolism and cell membrane fluidity, but accelerate spore formation of Tpb55. Biophysical assays further convinced that co-culture could decrease ATP content and inhibit ATPase activity in HG1, and could promote spore formation and reduce the cell membrane fluidity of Tpb55. In addition, co-culture also accelerated the production of intracellular anti-oomycete compound octhilinone. The above results indicate that HG1 and Tpb55 are mainly in a competitive relationship in the co culture system. These findings provide new insights for understanding the interaction mechanism between co cultured microbes.

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

Ensuring plant resilience to drought and phosphorus (P) stresses is crucial to support global food security. The phytobiome, shaped by selective pressures, harbors stress-adapted microorganisms that confer host benefits like enhanced growth and stress tolerance. Intercropping systems also offer benefits through facilitative interactions, improving plant growth in water- and P-deficient soils. Application of microbial consortia can boost the benefits of intercropping, although questions remain about the establishment, persistence, and legacy effects within resident soil microbiomes. Understanding microbe- and plant-microbe dynamics in drought-prone soils is key. This review highlights the beneficial effects of rhizobacterial consortia-based inoculants in legume-cereal intercropping systems, discusses challenges, proposes a roadmap for development of P-solubilizing drought-adapted consortia, and identifies research gaps in crop-microbe interactions.

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

The genus Enterobacter is widely recognized for its biotechnology potential in improving soil environment and crop growth promotion. To further explore these biotechnological potentials, we sequenced and analyzed the whole genome of Enterobacter cloacae Rs-2. The analysis showed that the total length of the Rs-2 genome was 6,965,070,514 bp, and GC content was 55.80%; the annotation results of GO and COG databases showed that the genome contains a variety of growth-promoting genes, such as iscU, glnA, glnB (nitrogen fixation); iucABCD (siderophore synthesis) and fepA, fcuA, fhuA, and pfeA, etc. (siderophore transport); ipdC (secreted IAA) and gcd, pqqBCDEF (dissolved phosphorus), etc. No pathogenic factors such as virulence genes were found. The application of Rs-2 as a soil inoculant in pot experiments showed great potential for growth promotion. This study proved the plant growth-promoting ability of Rs-2 at the molecular level through genetic screening and analysis, which provided guidance for the further improvement of the strain and laid a foundation for its application in agricultural production.