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Isolation and Identification of a Bacillus sp. from Freshwater Sediment Displaying Potent Activity Against Bacteria and Phytopathogen Fungi

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Abstract

A bacterium strain isolated from freshwater sediment of San Pablo river of Santiago de Cuba, Cuba was identified as a Bacillus sp. by Matrix-Assisted Laser Desorption/Ionization Time Of Flight Mass Spectrometry. A 16S rRNA gene analysis showed that the isolate A3 belongs to the operational group Bacillus amyloliquefaciens, while the phylogenetic analysis of the gyrA gene sequence grouped it within B. amyloliquefaciens subsp. plantarum cluster, referred now as Bacillus velezensis. In vitro antibacterial studies demonstrated the capacity of the isolate A3 to produce bioactive metabolites against Bacillus subtilis ATCC 11,778, Bacillus cereus ATCC 6633, and Staphylococcus aureus ATCC 25,923 by cross-streak, overlay, and microdilution methods. The strain also showed a high potential against the multidrug-resistant Staphylococcus aureus ATCC 700,699, ATCC 29,213, and ATCC 6538. At pH 8 and 96 h in the medium 2 of A3 culture conditions, the produced metabolites with antibacterial potential were enhanced. Some alterations in the morphology of the phytopathogens Aspergillus niger ATCC 9642, Alternaria alternata CECT 2662, and Fusarium solani CCEBI 3094 were induced by the cell-free supernatant of B. velezensis A3. A preliminary study of the nature of the bioactive compounds produced by the strain A3 showed the presence of both lipids and peptides in the culture. Those results highlight B. velezensis A3 as a promissory bacterium capable to produce bioactive metabolites with antibacterial and antifungal properties against pathogens.

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All data generated during this study are included in this article and its supplementary information file.

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Acknowledgements

The authors would like to thanks to the BCCM/LMG Bacterial Collection regarding bacterial identification. We appreciate the help of Prof. dr. Paul Cos (Department of Pharmaceutical Sciences, University of Antwerp, Belgium), and Eliza Depoorter (Laboratory of Microbiology, Faculty of Sciences, Ghent University, Belgium) for the help with antibacterial activity by broth microdilution and overlay methods, respectively.

Funding

This work was supported by the VLIR-UOS (Flemish Interuniversity Council-University Cooperation for Development) in the context of the Institutional University Cooperation Program with Universidad de Oriente; especially, by means of the P-3 project “Natural Products and Pharmaceutical Services to improve the patient quality of life in Eastern Cuban Hospital’s,” The BCCM/LMG Bacteria Collection is supported by the Federal Public Planning Service—Science Policy, Belgium.

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Authors and Affiliations

  1. Centro de Estudios de Biotecnología Industrial (CEBI), Faculty of Natural and Exact Sciences, University of Oriente, Patricio Lumumba, 90500, Santiago de Cuba, Cuba

    Miladis I. Camacho, Gabriel Llauradó, Yaneisy Lescaylle & Leonor Peña

  2. Cayo Naranjo Dolphinarium, UEB Marina Gaviota Oriente, Naranjo Bay, Km 58 Guardalavaca Highway, Rafael Freyre, Holguin, Cuba

    Janet M. García

  3. Cuban Institute for Research On Sugar Cane Derivatives, Via Blanca 804, San Miguel del Padrón, La Habana, Cuba

    Dianelis Roget

  4. Chemistry Deparment, Faculty of Exact and Natural Sciences, Universidad de Oriente, Patricio Lumumba, 90500, Santiago de Cuba, Cuba

    Armando Ferrer

  5. BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium

    Anneleen D. Wieme & Peter Vandamme

  6. Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium

    Peter Vandamme & Javier Bonne

  7. Laboratory of Antibodies and Experimental Biomodels, Prolongation of 23th Street and Caney Highway, Vista Alegre, Santiago de Cuba, Cuba

    Suyén Rodríguez

  8. Laboratory of Hygiene, Epidemiology and Microbiology, J Street, Between 1st and 2nd, Sueño Neighborhood, Santiago de Cuba, Cuba

    Thais-Len Meriño

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  1. Miladis I. Camacho
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Contributions

MIC Conceptualization, Performing experiments, Analysis, and Interpretation of data, Writing—Original Draft; SR & GLL Conceptualization, Writing—Review & Editing; PV Resources, Critical revision of the article; AW Resources, Analysis, and interpretation of data; AF Analysis and Interpretation of data; JG, DR, JB, YL, LP, & TLM Performing experiments. All authors read and approved the final manuscript.

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Correspondence to Gabriel Llauradó.

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Camacho, M.I., García, J.M., Roget, D. et al. Isolation and Identification of a Bacillus sp. from Freshwater Sediment Displaying Potent Activity Against Bacteria and Phytopathogen Fungi. Curr Microbiol 79, 398 (2022). https://doi.org/10.1007/s00284-022-03090-2

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