Abstract
Genomic and metabolomic studies of endolithic bacteria are essential for understanding their adaptations to extreme conditions of the rock environment and their contributions to mineralization and weathering processes. The endoliths of arid serpentine rocks are exposed to different environmental stresses, including desiccation and re-hydration, temperature fluctuations, oligotrophy, and high concentrations of heavy metals. Bacteria of the genus Rhodococcus commonly inhabit endolithic environments. Here, we describe genomic and metabolomic analyses of the non-pathogenic wild-type Rhodococcus fascians strain S11, isolated from weathered serpentine rock at the arid Khalilovsky massif, Russia. We found that strain S11 lacks the virulence plasmid that functions in the phytopathogenecity of some R. fascians strains. Phenotypic profiling revealed a high pH tolerance, phytase activity and siderophore production. A widely untargeted metabolome analysis performed using an Orbitrap LC–MS/MS method demonstrated the presence of chrysobactin-type siderophores in the culture medium of strain S11. The natural variation of secondary metabolites produced by strain S11 might provide a practical basis for revealing antibacterial, fungicide or insecticidal activities. Finally, plant infection and plant growth stimulation studies showed no observable effect of exposure strain S11 bacteria on the aerial and root parts of Arabidopsis thaliana plants. Based on our findings, R. fascians strain S11 might be promising tool for investigations of organo-mineral interactions, heavy metal bioremediation, and mechanisms of bacterial mediated weathering of plant-free serpentine rock to soil.
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Acknowledgements
This work was supported in part by the Kazan Federal University Strategic Academic Leadership Program (PRIORITY-2030) and by the subsidy allocated to Kazan Federal University for the state assignment in the sphere of scientific activities (project #0671-2020-0058). Dr. Irina Khilyas was also supported by the scholarship of the President of the Russian Federation for young scientists and graduate students and by the joint Russian-Germane program DAAD Mikhail Lomonosov. The authors are grateful to the Interdisciplinary Center for Collective Use (ID RFMEFI59414X0003) sponsored by the Ministry of Education and Science of the Russian Federation. Microscopy studies were carried out at the Interdisciplinary Center of Analytical Microscopy of Kazan Federal University.
Funding
This work was partially funded by the Kazan Federal University Strategic Academic Leadership Program (PRIORITY-2030) and by the subsidy allocated to Kazan Federal University for the state assignment in the sphere of scientific activities (Project Number 0671-2020-0058). Dr. Irina Khilyas was supported by the scholarship of the President of the Russian Federation for young scientists and graduate students and by the joint Russian-Germane program DAAD Mikhail Lomonosov. The authors are grateful to the Interdisciplinary Center for Collective Use (ID RFMEFI59414X0003) sponsored by the Ministry of Education and Science of the Russian Federation. Microscopy studies were carried out at the Interdisciplinary Centre of Analytical Microscopy of Kazan Federal University.
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Conceptualization: IVK, MFC, and MRS. Investigation and Formal Analysis: IVK, MIM, LRV, ASG, AVS, LTS, RIT, EIS, ESB and GL. Data Curation: IVK, MFC, MRS and GL. Resources: IVK and MRS. Writing—Original Draft Preparation: IVK, MFC.
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Khilyas, I.V., Markelova, M.I., Valeeva, L.R. et al. Genomic and metabolomic profiling of endolithic Rhodococcus fascians strain S11 isolated from an arid serpentine environment. Arch Microbiol 204, 336 (2022). https://doi.org/10.1007/s00203-022-02955-1
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DOI: https://doi.org/10.1007/s00203-022-02955-1