Isolation and Characterization of Novel Antibiotic-Producing Actinobacteria from the Rhizosphere of Indonesian Mangrove Forests
Article Sidebar
-
Actinobacteria, Antibiotic, Mangrove
Abstract
The rise of antimicrobial resistance is a global health crisis, demanding the urgent discovery of novel antibiotics. Indonesian mangrove forests, as a unique and underexplored ecosystem, represent a promising frontier for bioprospecting novel microorganisms. The plant rhizosphere, a zone of intense microbial activity, is particularly rich in actinobacteria, a phylum renowned for its prolific production of bioactive secondary metabolites. This research aimed to isolate and characterize novel antibiotic-producing actinobacteria from the rhizosphere of Indonesian mangrove plants. Rhizosphere soil samples were collected, and actinobacteria were isolated using selective media. All isolates were screened for antimicrobial activity against Staphylococcus aureus, Escherichia coli, and Candida albicans via the agar well diffusion method. The most potent isolate was subsequently characterized using morphological, biochemical, and 16S rRNA gene sequencing. From 72 distinct isolates, 15 displayed antimicrobial activity. One isolate, designated MGR-17, demonstrated exceptionally potent, broad-spectrum inhibition against all tested pathogens. Based on polyphasic taxonomy, MGR-17 was identified as a potentially novel species of the genus Streptomyces. In conclusion, the rhizosphere of Indonesian mangroves is a fertile source for discovering unique actinobacteria capable of producing novel antibiotics, and the discovery of Streptomyces sp. MGR-17 underscores this potential.
Full text article
References
Barreiro, C., Albillos, S. M., & Garcia-Estrada, C. (2024). Penicillium chrysogenum: Beyond the penicillin. In Advances in Applied Microbiology (Vol. 127, pp. 143–221). Elsevier. https://doi.org/10.1016/bs.aambs.2024.02.006
Behera, S., & Das, S. (2023). Environmental impacts of microplastic and role of plastisphere microbes in the biodegradation and upcycling of microplastic. Chemosphere, 334, 138928. https://doi.org/10.1016/j.chemosphere.2023.138928
Cai, F. M., Jiang, S., Daly, P., Bakhshi, M., Cartwright, K., & Druzhinina, I. S. (2025). Guidelines toward ecologically-informed bioprospecting for microbial plastic degradation. Biotechnology Advances, 82, 108590. https://doi.org/10.1016/j.biotechadv.2025.108590
Carroll, A. R., Copp, B. R., Grkovic, T., Keyzers, R. A., & Prinsep, M. R. (2024). Marine natural products. Natural Product Reports, 41(2), 162–207. https://doi.org/10.1039/D3NP00061C
Chen, H., Huang, D., Zhou, W., Deng, R., Yin, L., Xiao, R., Li, S., Li, F., & Lei, Y. (2024). Hotspots lurking underwater: Insights into the contamination characteristics, environmental fates and impacts on biogeochemical cycling of microplastics in freshwater sediments. Journal of Hazardous Materials, 476, 135132. https://doi.org/10.1016/j.jhazmat.2024.135132
Dai, Z., Yuan, R., Yang, X., Xi, H., Zhuo, M., & Wei, M. (2025). Salinity-responsive key endophytic bacteria in the propagules of Kandelia obovata enhance salt tolerance in rice. Journal of Integrative Agriculture, 24(5), 1738–1753. https://doi.org/10.1016/j.jia.2024.01.033
Das, P., Sarkar, B., & Mandal, S. (2023). Endophytic microbes: A potential source of bioactive metabolites with therapeutic values. In Endophytic Association: What, Why and How (pp. 435–457). Elsevier. https://doi.org/10.1016/B978-0-323-91245-7.00004-3
Dashti, Y., & Errington, J. (2024). Chemistry and biology of specialized metabolites produced by Actinomadura. Natural Product Reports, 41(3), 370–401. https://doi.org/10.1039/D3NP00047H
De Vasconcellos, S. P., Dos Santos Lima, L. M., Roswell, M. R., & Lacava, P. T. (2023). Tropical biomes as microbial sources for efficient biocatalysts to environmental purposes. In Microbial Inoculants (pp. 229–252). Elsevier. https://doi.org/10.1016/B978-0-323-99043-1.00003-7
Dhar, G. A., Chaudhuri, D., Mallick, B., & Ganguli, S. (2024). Insights into economically important endophytic and rhizospheric bacteria of true mangroves of Indian Sundarbans using high throughput mapping. In Biotechnology of Emerging Microbes (pp. 299–325). Elsevier. https://doi.org/10.1016/B978-0-443-15397-6.00015-2
Dutta, R., Santra, H. K., & Banerjee, D. (2024). Microbial plant growth promotors and their role in abiotic stress management. In Fungal Secondary Metabolites (pp. 317–335). Elsevier. https://doi.org/10.1016/B978-0-323-95241-5.00002-2
Farha, M. A., Tu, M. M., & Brown, E. D. (2025). Important challenges to finding new leads for new antibiotics. Current Opinion in Microbiology, 83, 102562. https://doi.org/10.1016/j.mib.2024.102562
Garg, D., Patel, N., Rawat, A., & Rosado, A. S. (2024). Cutting edge tools in the field of soil microbiology. Current Research in Microbial Sciences, 6, 100226. https://doi.org/10.1016/j.crmicr.2024.100226
Imchen, M., Moopantakath, J., Sreevalsan, A., & Kumavath, R. (2024). Metagenomic insights of microbial diversity in mangrove forest environment. In Applications of Metagenomics (pp. 253–269). Elsevier. https://doi.org/10.1016/B978-0-323-98394-5.00006-7
Izhar, S. K., Rizvi, S. F., Afaq, U., Fatima, F., & Siddiqui, S. (2024). Bioprospecting of Metabolites from Actinomycetes and theirApplications. Recent Patents on Biotechnology, 18(4), 273–287. https://doi.org/10.2174/0118722083269904231114154017
Kadaikunnan, S., Vijayaragavan, P., Rathi, M. A., Balamuralikrishnan, B., Alharbi, N. S., Gopalakrishnan, V. K., Purushothaman, S., & Sivanesan, R. (2024). Antibacterial and biofilm disruptive nonribosomal lipopeptides from Streptomyces parvulus against multidrug-resistant bacterial infections. Journal of Infection and Public Health, 17(3), 450–456. https://doi.org/10.1016/j.jiph.2024.01.001
Kandasamy, G. D., & Kathirvel, P. (2023). Insights into bacterial endophytic diversity and isolation with a focus on their potential applications –A review. Microbiological Research, 266, 127256. https://doi.org/10.1016/j.micres.2022.127256
Khurana, S., Ali, S., Srivastava, A. K., Singh, A., Agarwal, H., Chauhan, R., Joshi, N. C., Dufossé, L., & Chauhan, A. (2025). Bioremediation of microplastic pollution: A systematic review on mechanism, analytical methods, innovations, and omics approaches. Journal of Hazardous Materials Advances, 19, 100777. https://doi.org/10.1016/j.hazadv.2025.100777
Lebedeva, E., Panichev, A., Kiselev, K., Ryseva, Y., & Zaitseva, E. (2024). Taxonomic composition and physiological and biochemical properties of cultivated microorganisms isolated from kudurite rocks of the Primorsky Krai and the Republic of Altai (Russia). The Microbe, 5, 100214. https://doi.org/10.1016/j.microb.2024.100214
Mani, J., Kandasamy, D., Vendan, R. T., Sankarasubramanian, H., Mannu, J., & Nagachandrabose, S. (2024). Unlocking the potential of Streptomyces species as promising biological control agents against phytonematodes. Physiological and Molecular Plant Pathology, 134, 102465. https://doi.org/10.1016/j.pmpp.2024.102465
Mohamed, S. S., El Awady, M. E., Abdelhamid, S. A., Hamed, A. A., Salama, A. A. A., & Selim, M. S. (2023). Study of exopolysaccharide produced by Streptomyces rochie strain OF1 and its effect as ameliorative on osteoarthritis in rats via inhibiting TNF-?/COX2 pathway. Journal of Genetic Engineering and Biotechnology, 21(1), 12. https://doi.org/10.1186/s43141-023-00471-3
Muhilan, B. M., & Chattopadhyay, I. (2023). Endophytes and their bioactive metabolite’s role against various MDR microbes causing diseases in humans. In Endophytic Association: What, Why and How (pp. 135–158). Elsevier. https://doi.org/10.1016/B978-0-323-91245-7.00008-0
Negi, S., Kapoor, N., & Gambhir, L. (2025). Antioxidant and antiinflammatory endophytic fungal compounds for chronic diseases. In Navigating Endophytic Research for Next-Generation Therapeutics (pp. 175–200). Elsevier. https://doi.org/10.1016/B978-0-443-31484-1.00009-8
Oyedoh, O. P., Yang, W., Dhanasekaran, D., Santoyo, G., Glick, B. R., & Babalola, O. O. (2023). Rare rhizo-Actinomycetes: A new source of agroactive metabolites. Biotechnology Advances, 67, 108205. https://doi.org/10.1016/j.biotechadv.2023.108205
Pramanik, A., & Bhattacharyya, M. (2024). Microbial Community Structure of the Sundarbans Mangrove Ecosystem. In Microbial Diversity in the Genomic Era (pp. 73–88). Elsevier. https://doi.org/10.1016/B978-0-443-13320-6.00008-1
Sagar, K., & Priti, K. (2025). Metagenomics of river Ganga: A potential approach in bioremediation. In Development in Waste Water Treatment Research and Processes (pp. 649–676). Elsevier. https://doi.org/10.1016/B978-0-443-13615-3.00025-X
Sa?lam, N. G., Rachid, N. A., & Güngör, N. D. (2024). Secondary metabolites and biological compounds of actinomycetes and their applications. In Bacterial Secondary Metabolites (pp. 123–145). Elsevier. https://doi.org/10.1016/B978-0-323-95251-4.00013-2
Sagpariya, T., Srivastava, N., Katiyar, S., & Roy Choudhury, A. (2025). A comprehensive review on production, characterization, and applications of marine bacterial exopolysaccharides. International Journal of Biological Macromolecules, 331, 148391. https://doi.org/10.1016/j.ijbiomac.2025.148391
Sarma, A., Phukan, P., Phukan, P., Zorrilla, J. G., Masi, M., Cimmino, A., & Tayung, K. (2025). Fungal endophytes isolated from wild tomato produced metabolites with antifungal activity against phytopathogenic fungi. South African Journal of Botany, 186, 329–339. https://doi.org/10.1016/j.sajb.2025.09.030
Sarma, H., & Joshi, S. J. B. T. (2024). Index. In Biotechnology of Emerging Microbes (pp. 367–372). Elsevier. https://doi.org/10.1016/B978-0-443-15397-6.09999-X
Satya, S., Dashora, M., Palsania, P., Dar, M. A., & Kaushik, G. (2025). Unraveling the potential of soil microbes for simultaneous nutrient solubilization and pesticide degradation toward sustainable agriculture. Pedosphere, S1002016025000141. https://doi.org/10.1016/j.pedsph.2025.02.001
Sharma, S., Gupta, N., Kaur, S., Kumawat, K. C., & Chakkal, A. S. (2025). Soil microbial resources: Unlocking sustainable strategies for crop productivity and soil health. Current Research in Microbial Sciences, 9, 100468. https://doi.org/10.1016/j.crmicr.2025.100468
Simarmata, T., Hibatullah, F. H., Khumairah, F. H., Irwandhi, Ambarita, D. D. M., Nurbaity, A., Herdiyantoro, D., & Kamaluddin, N. N. (2025). Advancing climate-resilient rhizomicrobiome engineering for enhancing productivity and sustainability of strategic crop farming in Indonesia’s problematic soils. Environmental and Sustainability Indicators, 27, 100821. https://doi.org/10.1016/j.indic.2025.100821
Singh, J., & Sharma, V. B. T. R. (2025). Index. In Rhizomicrobiome in Sustainable Agriculture and Environment (pp. 541–563). Elsevier. https://doi.org/10.1016/B978-0-443-23691-4.20001-8
Singh, P., Dhanorkar, M., Patil, Y., & Rale, V. (2024). Agriculturally important functioning of beneficial microorganisms for healthy ecosystem maintenance. In The Potential of Microbes for a Circular Economy (pp. 149–183). Elsevier. https://doi.org/10.1016/B978-0-443-15924-4.00007-2
Siro, G., & Pipite, A. (2024). Mini-review on the antimicrobial potential of actinobacteria associated with seagrasses. Exploration of Drug Science, 117–125. https://doi.org/10.37349/eds.2024.00038
Tedsree, N., Yimyong, S., Tedsree, K., & Tanasupawat, S. (2025). Genomic insight of new Streptomyces strain DZ1-3 from rhizosphere soil with potent antifungal compounds. Rhizosphere, 35, 101157. https://doi.org/10.1016/j.rhisph.2025.101157
Teotia, N., & Chaudhary, D. R. (2024). Application of halophyte microbiome for development of salt tolerance in crops. In Improving Stress Resilience in Plants (pp. 143–164). Elsevier. https://doi.org/10.1016/B978-0-443-18927-2.00001-7
Trenozhnikova, L. P., Baimakhanova, G. B., Baimakhanova, B. B., Balgimbayeva, A. S., Daugaliyeva, S. T., Faizulina, E. R., Tatarkina, L. G., Spankulova, G. A., Berillo, D. A., & Beutler, J. A. (2024). Beyond traditional screening: Unveiling antibiotic potentials of actinomycetes in extreme environments. Heliyon, 10(22), e40371. https://doi.org/10.1016/j.heliyon.2024.e40371
Tripathi, A., Jaiswal, A., Kumar, D., Chavda, P., Pandit, R., Joshi, M., Blake, D. P., Tomley, F. M., Joshi, C. G., & Dubey, S. K. (2024). Antimicrobial resistance in plant endophytes associated with poultry-manure application revealed by selective culture and whole genome sequencing. Journal of Hazardous Materials, 480, 136166. https://doi.org/10.1016/j.jhazmat.2024.136166
Ullah, Z., Iqbal, J., Abbasi, B. A., Ijaz, S., Yaseen, T., Majeed, M., Iqbal, R., Murtaza, G., Ali, H., Kanwal, S., & Mahmood, T. (2025). Role of crop microbiomes in crop production under changing climate: Past, present, and future. In Phytomicrobiome and Stress Regulation (pp. 189–234). Elsevier. https://doi.org/10.1016/B978-0-443-33594-5.00016-0
Xu, C., Feng, Y., Li, H., Li, Y., Yao, Y., & Wang, J. (2024). Constructed wetlands for mariculture wastewater treatment: From systematic review to improvement measures and insights. Desalination, 579, 117505. https://doi.org/10.1016/j.desal.2024.117505
Xu, M., Selvaraj, G.-K., & Lu, H. (2023). Environmental sporobiota: Occurrence, dissemination, and risks. Science of The Total Environment, 869, 161809. https://doi.org/10.1016/j.scitotenv.2023.161809
Yang, G., Zhen, Z., Wu, W., Yang, C., Li, Q., Li, X., Yin, J., Zhong, X., Lin, Z., & Zhang, D. (2025). Mechanisms of Sulfamethoxazole biodegradation in mangrove rhizosphere by metagenomic and metabolic pathways. Environmental Technology & Innovation, 37, 103970. https://doi.org/10.1016/j.eti.2024.103970
Yang, S., Williams, S. J., Courtney, M., & Burchill, L. (2025). Warfare under the waves: A review of bacteria-derived algaecidal natural products. Natural Product Reports, 42(4), 681–719. https://doi.org/10.1039/D4NP00038B
Ye, J., Cen, J., Wu, J., Wen, Z., Chen, H., & Xu, J. (2024). A new tyrosine derivative isolated from an actinomycin D producing mangrove rhizosphere soil-derived Streptomyces parvulus A-30. Natural Product Research, 1–5. https://doi.org/10.1080/14786419.2024.2429114
Authors
Copyright (c) 2025 Nike Triwahyuningsih, Chen Mei, Anna Schneider
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
