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Taxonomic Characterization and Antagonistic Efficacy of Streptomyces Cavourensis SKCMM1 Isolated from Sediment of Pichavaram Mangrove Forest

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Taxonomic Characterization and Antagonistic Efficacy of Streptomyces Cavourensis SKCMM1 Isolated from Sediment of Pichavaram Mangrove Forest Madheslu et al. J Pure Appl Microbiol, 12(4), 1975-1984 Dec. 2018 http://dx.doi.org/10.22207/JPAM.12.4.34 Print ISSN: 0973-7510; Online ISSN: 2581-690X RESEARCH ARTICLE Taxonomic Characterization and Antagonistic Efficacy of Streptomyces cavourensis SKCMM1 Isolated from Sediment of Pichavaram Mangrove Forest Manikandan Madheslu1, Ashok Kumar Marimuthu1, Vaishnavi Jagannathan1, Duraimurugan Kasiviswanathan2, Baby Shakila Parimelazhagan1 and Narendhran Sadasivam1* 1Department of Biotechnology, Sri Krishna Arts and Science College, Coimbatore - 641 008, Tamil Nadu, India. 2School of Community Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur - 711 103, India. Abstract Genus Streptomyces under phylum actinobacteria has been recognized as a prolific source for production of bioactive secondary metabolites. Actinobacterial strain designated as SKCMM1 isolated from Pichavaram Mangrove forest sediment was identified as Streptomyces cavourensis using polyphasic taxonomic approach. This strain shares 99% sequence similarity with Streptomyces cavourensis NBRC 13026T. Ethyl acetate fraction of the strain SKCMM1 exhibited highest biological activity. FTIR and GCMS analysis of crude compounds isolated from the active ethyl acetate fraction states the presence of several phenolic, hydrocarbon and fatty acid compounds with various bioactivities. This study will be an attempt to understand that the strain holds significant antimicrobial activity against test pathogens and antiproliferative activity against HeLa cell lines 50(IC value of 8.9µg/ml). Keywords: Streptomyces, Polyphasic Taxonomy, Liquid – liquid extraction, Spectral analysis, Bioactive compounds. *Correspondence: [email protected]; +91-9043669722 (Received: 25 August 2018; accepted: 10 October 2018) Citation:Manikandan Madheslu, Ashok Kumar Marimuthu, Vaishnavi Jagannathan, Duraimurugan Kasiviswanathan, Baby Shakila Parimelazhagan and Narendhran Sadasivam, Taxonomic Characterization and Antagonistic Efficacy of Streptomyces cavourensis SKCMM1 Isolated from Sediment of Pichavaram Mangrove Forest, J Pure Appl Microbiol., 2018; 12(4):1975-1984. http://dx.doi. org/10.22207/JPAM.12.4.34 © The Author(s) 2018. Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License which permits unrestricted use, sharing, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Journal of Pure and Applied Microbiology 1975 www.microbiologyjournal.org Madheslu et al. J Pure Appl Microbiol, 12(4), 1975-1984 | Dec. 2018 | http://dx.doi.org/10.22207/JPAM.12.4.34 INTRODUCTION Marine ecosystem is a resplendent choice Actinobacteria are present in various for the isolation of novel microbes that confer ecological habitats such as soil, fresh water, splendid outcome in identification, characterization backwater, lake, sewage and marine environment1. and application of secondary metabolites7. Earlier, These bacteria are bounteous group of Streptomyces sp. VITMK1 was isolated from microorganisms that produce a wide array Pichavaram region of Tamil Nadu and it yielded a of secondary metabolites such as antibiotics, potent antibacterial compound diketopiperazine5. antitumor agents, immunosuppressive agents, Similarly, ethyl acetate crude extract obtained from vitamins, enzymes and even cosmetics2. On Streptomyces strain CH54-4 was reported for best contemplating the microbes of the same region, antimicrobial and anti proliferative activity8. In the the marine Actinobacteria are unique for their current study, Streptomyces SKCMM1 is isolated antibiotic production in fluctuating physical, from Pichavaram Mangrove forest of Tamil Nadu chemical and biological factors3. In recent years and identified through polyphasic taxonomic the escalating diligence is towards the exploration characterization approach. The antagonistic ability of novel microbes that manufacture metabolites of the isolate was assayed through shake flask to combat drug resistant pathogenic microbes4-6. fermentation and spectral studies (Fig. 1). Fig. 1. Schematic representation of the present study MATERIALS AND METHODS 10 days. Characteristic tough leathery colonies of Actinomycetes with a clear zone of inhibition were Isolation and Identification of Potential selected and preserved in SCA slants for further Actinomycete use. Isolates were grown in 50 ml of starch casein Five marine sediment samples were broth by submerged culture method (32°C for collected from Pichavaram Mangrove forest, Tamil 7 days), centrifugation was carried out at 8000 Nadu using a sterile borer at a depth of 10 to 15 cm rpm for 15 min and the clear supernatant was (Table 1 and Figure 2). The serially diluted (10-1 to challenged against selected bacterial pathogens 10-5) samples were seeded on Starch Casein agar (E.coli MTCC 1698, E.coli ESBL, Bacillus pumilis (SCA) (HiMedia, India) plates supplemented with NCIM2327, Proteus vulgaris, Staphylococcus antibiotics (Cycloheximide 50µg/ml and Nystatin aureus MTCC 3160, Staphylococcus aureus 50µg/ml) and incubated at room temperature for (methicillin resistant), Shigella flexneri MTCC Journal of Pure and Applied Microbiology 1976 www.microbiologyjournal.org Madheslu et al. J Pure Appl Microbiol, 12(4), 1975-1984 | Dec. 2018 | http://dx.doi.org/10.22207/JPAM.12.4.34 1457) by well diffusion method. The potent isolate SKCMM1 were methylated and analyzed Actinobacteria was selected based on the vast by GC-MS, using the standard sherlock microbial zone of inhibition and it was taken for further identification system13. studies. 16s rRNA Gene Sequencing Genomic DNA was extracted and Table 1. Characteristics of samples collected from subjected to polymerase chain reaction14 Pichavaram Mangrove forest, India. targeting 16S rRNA gene using the Sample Latitude Longitude(E) Temp pH 5’-AGAGTTTGATCCTGGCTCAG-3’– forward primer no (N) (E) (o C) and 5’TACGGCTACCTTGTTACGACT-3’ – reverse primer15. The reaction mixture contained 10X Taq MS1 11° 30' 11'’ 79° 46' 37'’ 24 7.9 buffer, 25 mM MgCl2, 4 mM dNTPs, Taq polymerase MS2 11° 28' 37'’ 79° 47' 15'’ 28 7.5 0.5U, template DNA 5-10 ng and primers at 10 MS3 11° 27' 51'’ 79° 47' 24'’ 28 8.2 pmol concentration (Fermentas, Thermo Scientific, MS4 11° 27' 22'’ 79° 47' 17'’ 29 7.7 Vilnius, Lithuania). The PCR conditions comprised MS5 11° 27' 24'’ 79° 46' 46'’ 26 8.1 of initial denaturation at 94oC for 10 min followed MS = Marine Sediment by 23 cycles of denaturation at 94oC for 15 sec, annealing at 55oC for 15 sec, extension at 72oC for 1 min and a final extension of 72oC for 10 min carried out in Master thermal cycler (Eppendorf, Germany). Later, amplicon sequencing was done in ABI 3730xl cycle sequencer (Facility from Sciegenom, Cochin, India) and sequences were deposited in GenBank (NCBI). The dendrogram analysis was done in MEGA 4.0 to study the evolutionary similarity of SKCMM1 strain. Production and Extraction of Bioactive Compound using Streptomyces cavourensis SKCMM1 For production, 125 ml of Starch casein Fig. 2. Schematic representation map showing sampling broth SKCMM1 (500 ml Erlenmeyer flask) was area inoculated with 1 ml Streptomyces cavourensis and incubated at 28oC in a rotary shaker (180 rpm) for 7 Phenotypic Characterization of Strain SKCMM1 days. Then, broth was filtered using Whatmann No Potential Actinobacterial strain 42 aseptically and stored at 4oC. In order to select SKCMM1 was characterized morphologically the best choice of solvent for active compound and physiologically as prescribed in International Streptomyces Project (ISP)9. The micro-morphology of strain was observed under light microscopy and Scanning Electron Microscopy (JEOL JSM- 5610) after incubation at 28°C for 7 days. The pigmentation of aerial mycelium and structure of sporophores were observed on different ISP media 1 – 7, which are an ideal aspect in its classification. Colony morphology was recorded with respect to size, colour, aerial mycelium, substrate mycelium and pigmentation. Addition to that, biochemical and physiological examinations were performed according to standard methodology5, 10. Standard procedures were used to determine the cell wall amino acids11 and cell wall sugars12 of the potent Actinobacterial strain. Fatty acids extracted from Fig. 3. Electron micrograph image of isolate SKCMM1 Journal of Pure and Applied Microbiology 1977 www.microbiologyjournal.org Madheslu et al. J Pure Appl Microbiol, 12(4), 1975-1984 | Dec. 2018 | http://dx.doi.org/10.22207/JPAM.12.4.34 Fig. 4. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences showing the relationships of strain SKCMM1 with related species extraction, an equal volume of various solvents Spectral analysis of ethyl acetate extract (hexane, chloroform, ethyl acetate, n-butanol and The active extract dissolved in methanol propanol) along with filtrate were shaken well was taken for UV Vis and FTIR analysis using for 60-90 mins. The collected solvent fractions Shimadzu – 1601 UV VIS and Shimadzu IR 8000 were concentrated using distillation column and respectively. The functional groups present in the the crude obtained was challenged against test sample were detected in the spectral range of 400 bacterial strains. Based on the zone of inhibition to 4000 cm-1. The ethyl acetate sample extract results, ethyl acetate was selected as the best was analyzed by GC-MS [Thermo GC – Trace
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