Isolation and identification of bacterial endomicrobiome of Syzygium cumini from Faridabad, India
Article Main
Abstract
Endomicrobiome is the diverse and dynamic microbial flora that resides in plant tissues, without harming and developing detrimental effects. Syzygium cumini, the black plum or jamun plant, is used as traditional medicine. This is a medicinal plant used against metabolic disorders like diabetes, hypertension, and obesity, etc. The present study aimed at isolating bacterial endomicrobiome from leaf and stem parts of S. cumini locally grown garden situated at 28°20′32″N 77°19′32″E, Faridabad, India. Bacterial endomicrobiome were isolated using nutrient agar plates and identified. The sterilized root and leaf explants were inoculated on the nutrient agar plate and incubated for 24 hours. Morphological, cultural, and staining features were noted for initial identification, and 16S rRNA sequencing to verify the strain. A total of 14 bacterial endomicrobiome isolates were recovered from stem and leaf samples of S. cumini. The leaf sample demonstrated a higher number of bacterial endomicrobiome isolates than the stem of S. cumini. All the obtained isolates were gram-positive, mostly endospore-forming. Morphologically, small rods, creamish, off-white, smooth with irregular margins in appearance while NS5 Bacillus sp. developed slow growing, with brownish colonies on agar medium. Bacillus genera were found as the dominating endomicrobiome of S. cumini. Molecular characterization confirmed that the endomicrobiome of S. cumini was dominated by the genus Bacillus, and Bacillus subtilis was found to be the dominant bacterial species in leaf samples. In contrast, Bacillus safensis was identified as the major bacterial endomicrobiome of S. cumini stems. The obtained sequences were deposited to NCBI under the accession no. Bacillus sp. JL2 PQ475951 and Bacillus sp. NS5 PQ495957. It is concluded that the bacterial endomicrobiome is attributed to the medicinal properties of S. cumini.
Article Details
Article Details
Endomicrobiome, Syzygium cumini, 16S rRNA, Bacillus sp. , JL2, Bacillus sp. NS5
Ambikapathy, V., Babu, S., Shanmugapriya, R., Prakash, A., & Shijila Rani, A. S. (2023). Identification of bacterial endophytes by 16S rRNA. In Springer Protocols Handbooks A. Sankaranarayanan, N. Amaresan, & M. K. Dwivedi (Eds.) Endophytic Microbes: Isolation, Identification, and Bioactive Potentials. New York: Humana Press. doi:10.1007/978-1-0716-2827-0_10.
Ameen, M., Mahmood, A., Sahkoor, A., Zia, M. A., & Ullah, M. S. (2024). The role of endophytes to combat abiotic stress in plants. Plant Stress, 12, Article 100435. doi:10.1016/j.stress.2024.100435.
Aneja, K. R. (2003). Experiments in microbiology, plant pathology and biotechnology (4th ed.). New Delhi: New Age International Publishers.
Bolivar-Anillo, H. J., González-Rodríguez, V. E., Cantoral, J. M., García-Sánchez, D., Collado, I. G., & Garrido, C. (2021). Endophytic Bacteria Bacillus subtilis, Isolated from Zea mays, as Potential Biocontrol Agent against Botrytis cinerea. Biology, 10(6), 492. doi:10.3390/biology10060492.
Burragoni, S. G., & Jeon, J. (2021). Applications of endophytic microbes in agriculture, biotechnology, medicine, and beyond. doi:10.1016/j.micres.2020.126691. Microbiological Research, 245, Article 126691.
Cappuccino, J. G., & Sherman, N. (2008). Microbiology Lab manual (7th ed.). United States: Benjamin Cummings Publishing Company.
Chaudhary, P., Agri, U., Chaudhary, A., Kumar, A., & Kumar, G. (2022). Endophytes and their potential in biotic stress management and crop production. Frontiers in Microbiology, 13, Article 933017. doi:10.3389/fmicb.2022.933017.
Chitranshi, S., Gupta, A., Sarkar, N., & Khare, P. (2022). Bacterial endophytes of Aloe vera and their potential applications. doi:10.37868/hsd.v4i1.68. Heritage and Sustainable Development, 4(1), 32–41.
Christina, A., Christapher, V., & Bhore, S. J. (2013). Endophytic bacteria as a source of novel antibiotics: an overview. Pharmacognosy Reviews, 7(13), 11–16. doi:10.4103/0973-7847.112833.
Compant, S., Clément, C., & Sessitsch, A. (2010). Plant growth‐promoting bacteria in the rhizo‐ and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization. Soil Biology and Biochemistry, 42(5), 669–678. doi:10.1016/j.soilbio.2009.11.024.
Dan, S., Helene, R., Åsa Nilsdotter, A., Lena S., Malin, B. J. (2020). Optimization of 16S rRNA gene analysis for use in the diagnostic clinical microbiology service, Journal of Microbiological Methods. doi.org/10.1016/j.mimet.2020.105854.
Digra, S., & Nonzom, S. (2023). An insight into endophytic antimicrobial compounds: an updated analysis. Plant Biotechnology Reports, 1–31. doi:10.1007/s11816-023-00824-x.
Ding, L., Münch, J., Goerls, H., Maier, A., Fiebig, H.-H., Lin, W.-H. et al. (2010). Xiamycin, a pentacyclic indolosesquiterpene with selective anti‐HIV activity from a bacterial mangrove endophyte. Bioorganic and Medicinal Chemistry Letters, 20(22), 6685–6687. doi:10.1016/j.bmcl.2010.09.010.
Ek-Ramos, M. J., Gomez-Flores, R., Orozco-Flores, A. A., Rodríguez-Padilla, C., González-Ochoa, G., & Tamez-Guerra, P. (2019). Bioactive products from plant-endophytic Gram-positive bacteria. Frontiers in Microbiology, 10, 463. doi:10.3389/fmicb.2019.00463.
Elaine Mankge, M., Penistacia Maela, M., Mark Abrahams, A., & Hope Serepa-Dlamini, M. (2024). Screening of Bacillus spp. bacterial endophytes for protease production, and application in feather degradation and bio-detergent doi:10.1016/j.heliyon.2024.e30736. Heliyon, 10(9), Article e30736.
Emitaro, W. O., Kawaka, F., Musyimi, D. M., & Adienge, A. (2024). Diversity of endophytic bacteria isolated from leguminous agroforestry trees in western Kenya. AMB Express, 14(1), 18. doi:10.1186/s13568-024-01676-6.
Fayha, A. H., Jamal, Y. A., Kholoud, M. A., & Muhanad, W. A. (2024). Bacterial endophytes and their contributions to alleviating drought and salinity stresses in wheat: A systematic review of physiological mechanisms. Agriculture. MDPI, 14(5), 1–19.
Gayathri, M., Sharanya, R., Renukadevi, P., Nakkeeran, S., Saranya, N., Varanavasiappan, S. et al. (2024). Deciphering the antiviral nature of endophytic Bacillus spp. against groundnut bud necrosis virus in cowpea and tomato. Frontiers in Microbiology. doi:10.3389/fmicb.2024.1410677.
Hnamte, L., Vanlallawmzuali, K. A., Kumar, A., Yadav, M. K., Zothanpuia, P. K., & Singh, P. K. (2024). An updated view of bacterial endophytes as antimicrobial agents against plant and human pathogens. Current Research in Microbial Sciences, 7, Article 100241. doi:10.1016/j.crmicr.2024.100241.
Indrawati, I., Rossiana, N., & Fathurrohim, M. F. (2021). Diversity of endophytic bacteria and microfungi in Syzygium cumini fruit from west Java, Indonesia. Biodiversitas Journal of Biological Diversity, 22(9). doi:10.13057/biodiv/d220941.
Jiang, Z. D., Jensen, P. R., & Fenical, W. (1999). Lobophorins a and B, new antiinflammatory macrolides produced by a tropical marine bacterium. Bioorganic and Medicinal Chemistry Letters, 9(14), 2003 2006. doi:10.1016/s0960-894x(99)00337-6.
Kandel, S. L., Joubert, P. M., & Doty, S. L. (2017). Bacterial endophyte colonization and distribution within plants. Microorganisms, 5(4), 77. doi:10.3390/microorganisms5040077.
Kaur, M., & Karnwal, A. (2023). Screening of endophytic Bacteria from stress-tolerating plants for abiotic stress tolerance and plant growth-promoting properties: identification of potential strains for bioremediation and crop enhancement. Journal of Agriculture and Food Research, 14, Article 100723. doi:10.1016/j.jafr.2023.100723.
Kumar, S., & Singh, B. (2021). Syzygium cumini (Jamun) its medicinal uses. International Journal of Pharmacognosy, 8(9), 361–372. doi:10.13040/IJPSR.0975-8232.IJP.8(9).361-72.
Liu, Y., Morelli, M., Koskimäki, J. J., Qin, S., Zhu, Y.-H., & Zhang, X.-X. (2022). Editorial: Role of endophytic bacteria in improving plant stress resistance. Frontiers in Plant Science, 13. doi 10.3389/fpls.2022.1106701, Article 1106701. doi:10.3389/fpls.2022.1106701.
Luo, M., Tang, L., Dong, Y., Huang, H., Deng, Z., & Sun, Y. (2021). Antibacterial natural products lobophorin L and M from the marine‐derived Streptomyces sp. 4506. Natural Product Research, 35(24), 5581–5587. doi:10.1080/14786419.2020.1797730.
Marchut-Mikołajczyk, O., Chlebicz, M., Kawecka, M., Michalak, A., Prucnal, F., Nielipinski, M. et al. (2023). Endophytic bacteria isolated from Urtica dioica L. preliminary screening for enzyme and polyphenols production. Microbial Cell Factories, 22(1), 169. doi:10.1186/s12934-023-02167-2.
Miljaković, D., Marinković, J., & Balešević-Tubić, S. (2020). The Significance of Bacillus spp. Microorganisms, 8(7), 1037. doi:10.3390/microorganisms8071037.
Nei, M., & Kumar, S. (2000). Molecular evolution and phylogenetics. New York: Oxford University Press. doi:10.1093/oso/9780195135848.001.0001.
Nurhaida, Yenn, T. W., & Ibrahim, D. (2019). Endophytic fungi from Syzygium cumini (L.) Skeels leaves and its potential as antimicrobial agents. IOP Conference Series: Earth and Environmental Science, 364(1), Article 012023. doi:10.1088/1755-1315/364/1/012023.
Priti, D., Poonam B., & Sulekha R. (2020). Isolation, identification and characterization of endophytic bacteria from medicinal plant Tinospora cordifolia. South African Journal of Botany, 134, 43-49.
Qamar, M., Akhtar, S., Ismail, T., Wahid, M., Abbas, M. W., Mubarak, M. S. et al. (2022). Phytochemical profile, biological properties, and food applications of the medicinal plant Syzygium cumini. Foods, 11(3), 378. doi:10.3390/foods11030378.
Raimi, A., & Adeleke, R. (2023). 16S rRNA gene-based identification and plant growth-promoting potential of cultivable endophytic bacteria. Agronomy, 115(3), 1447–1462. doi:10.1002/agj2.21241.
Rather, G. J., Hamidudin Naquibuddin, M., Mohd, I., & Zaman, R. (2019). Antidiabetic potential and related activity of Jamun (Syzygium cumini Linn.) and its utilization in Unani medicine: an overview. International Journal of Herbal Medicine, 7, 7–11.
Rekha, M. G., Prathamesh, S. K., Madhuri, L. R., & Nikhil, N. J. (2015). Isolation, characterization and identification of endophytic bacteria by 16S rRNA partial sequencing technique from roots and leaves of Prosopis cineraria plant. Asian Journal of Plant Science and Research, 5(6), 36–43.
Rizvi, M. K., Rabail, R., Munir, S., Inam-Ur-Raheem, M., Qayyum, M. M. N., Kieliszek, M. et al. (2022). Astounding health benefits of jamun (Syzygium cumini) toward metabolic syndrome. Molecules, 27(21), Article 7184. doi:10.3390/molecules27217184.
Saitou, N., & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees, molecular biology. Evolution, 4(4), 406–425. doi:10.1093/oxfordjournals.molbev.a040454.
Samapti, M. M. S., Afroz, F., Rony, S. R., Sharmin, S., Moni, F., Akhter, S. et al. (2022). Isolation and Identification of endophytic Fungi from Syzygium cumini Linn and Investigation of Their Pharmacological Activities. doi:10.1155/2022/9529665. The Scientific World Journal, 2022, Article 9529665.
Santoyo, G., Moreno-Hagelsieb, G., Orozco-Mosqueda, M. C., & Glick, B. R. (2016). Plant growth promoting bacterial endophytes. Microbiological Research, 183, 92–99. doi:10.1016/j.micres.2015.11.008.
Singh, R., Pandey, K. D., Singh, M., Singh, S. K., Hashem, A., Al-Arjani, A. F. et al. (2022). Isolation and characterization of endophytes bacterial strains of Momordica charantia L. and their possible approach in stress management. Microorganisms, 10(2), 290. doi:10.3390/microorganisms10020290.
Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA 11: Molecular evolutionary genetics analysis (version 11). Molecular Biology Evolution. doi:10.1093/molbev/msab120.
Wei, R.-B., Xi, T., Li, J., Wang, P., Li, F.-C., Lin, Y.-C. et al. (2011). Lobophorin C and D, new kijanimicin derivatives from a marine sponge‐associated actinomycetal strain AZS17. Marine Drugs, 9(3), 359–368. doi:10.3390/md9030359.
Wu, T., Xu, J., Liu, J., Guo, W.-H., Li, X.-B., Xia, J.-B. et al. (2019). Characterization and initial application of endophytic Bacillus safensis Strain ZY16 for improving phytoremediation of oil-contaminated saline soils. Frontiers in Microbiology, doi:10.3389/fmicb.2019.00991.
Zotchev, S. B. (2024). Unlocking the potential of bacterial endophytes from medicinal plants for drug discovery. Microbial Biotechnology, 17(2), Article e14382. doi:10.1111/1751-7915.14382.

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
This work is licensed under Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) © Author (s)