Mass Spectral Molecular Networking to Profile the Metabolome of Biostimulant Bacillus Strains

Nephali, Lerato; Steenkamp, Paul; Burgess, Karl; Huyser, Johan; Brand, Margaretha; Hooft, Justin J.J. van der; Tugizimana, Fidele


Beneficial soil microbes like plant growth-promoting rhizobacteria (PGPR) significantly contribute to plant growth and development through various mechanisms activated by plant-PGPR interactions. However, a complete understanding of the biochemistry of the PGPR and microbial intraspecific interactions within the consortia is still enigmatic. Such complexities constrain the design and use of PGPR formulations for sustainable agriculture. Therefore, we report the application of mass spectrometry (MS)-based untargeted metabolomics and molecular networking (MN) to interrogate and profile the intracellular chemical space of PGPR Bacillus strains: B. laterosporus, B. amyloliquefaciens, B. licheniformis 1001, and B. licheniformis M017 and their consortium. The results revealed differential and diverse chemistries in the four Bacillus strains when grown separately, and also differing from when grown as a consortium. MolNetEnhancer networks revealed 11 differential molecular families that are comprised of lipids and lipid-like molecules, benzenoids, nucleotide-like molecules, and organic acids and derivatives. Consortium and B. amyloliquefaciens metabolite profiles were characterized by the high abundance of surfactins, whereas B. licheniformis strains were characterized by the unique presence of lichenysins. Thus, this work, applying metabolome mining tools, maps the microbial chemical space of isolates and their consortium, thus providing valuable insights into molecular information of microbial systems. Such fundamental knowledge is essential for the innovative design and use of PGPR-based biostimulants.