Antimicrobial activities and phylogenetic study of bacteria associated with Cyperus rotundus rhizosphere from Cemoro Sewu Plateau, Indonesia
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Abstract. Ambarwati A, Wahyuono S, Moeljopawiro S, Sembiring L, Yuwono T. 2019. Antimicrobial activities and phylogenetic study of bacteria associated with Cyperus rotundus rhizosphere from Cemoro Sewu Plateau, Indonesia. Biodiversitas 20: 2206-2212. A study has been conducted to investigate the activity of bacteria isolated from the rhizosphere of Purple Nut Sedge (Cyperus rotundus) from Cemoro Sewu Plateu, Indonesia as antimicrobial agent and the molecular relatedness between the isolates with other bacteria based on phylogenetic tree analysis. A total of six bacteria were obtained and tested for their capability to inhibit the growth of test organisms using agar block method and characterized molecularly using 16S rDNA sequence analysis. It was observed that the six isolates demonstrated the ability to inhibit at least one of four test microorganisms growth, with a diameter of inhibition zone ranging from 8-35 mm. The CRC32 isolate was the best isolate in inhibiting Staphylococcus aureus ATCC 25923 with a diameter inhibition zone of 26 mm (strong), while isolate CRA8 was the best anti-Candida (showing 35 mm of inhibition zone). The phylogenetic tree analysis resulted in two genera, four isolates belonging to Bacillus, while the other two isolates were known related to Paenibacillus genus. BLAST analysis on the CRC 32 isolate revealed that it is closely related with Paenibacillus peroriae strain 3763 with 99% sequence similarities and CRA8 isolates demonstrated the highest similarity with Paenibacillus sonchi strain X19-5 (97%). The results of this study demonstrated that the bacterial isolates from plant rhizosphere of Cemoro Sewu Plateau were the members of the Bacillus and Paenibacillus genera and demonstrated the potential as antimicrobial agent.
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References
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Romanenko LA, Uchino M, Kalinovskaya NI, Mikhailov VV. 2008. Isolation, phylogenetic analysis and screening of marine mollusc-associated bacteria for antimicrobial, hemolytic and surface activities. Microbiol Res. 163: 633-644.
Shaheen M, Li J, Ross AC, Vederas JC, Jensen SE. 2011. Paenibacillus polymyxa PKBI produces variants of polymyxin B-type antibiotics. Chem Biol. 18(12): 1640-8.
Susilowati R, Sabdono A, Widowati I. 2015. Isolation and characterization of bacteria associated with brown algae Sargassum spp. from Pajang Island and their antibacterial activities. Prosedia Environ Sci. 23: 240-246.
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The CLUSTAL_X windows interface: flex- ible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 4876–82.
Ullah I, Arshed M, Noureen U, Chuadhry MJI, Jadoon MA. 2010. Isolation of Streptomyces from the sediments of selected thermal springs of northern Pakistan and its interinsic susceptibility and resistance. Rec Zool Surv Pak. 21:47-50.
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Wilson GS, Raftos DA, Nair S.V. 2011. Antimicrobial activity of surface attached marin bacteria in biofilm. Microbiol Res J Int. 166: 437-448.
Wu X, Shen X, Ding R, Qian C, Fang H, Li O. 2010. Isolation and partial characterization of antibiotics produced by Paenibacillus elgii B69. FEMS Microbiol Lett. 310: 32-38.
Zhao L, Xu Y, Lai X. 2018. Antagonistic endophytic bacteria associated with nodule of soybean (Glycine max L.) and plant growth-promoting properties. Braz J Microbiol. 49(2): 269-278.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215: 403–10.
Amin A, Khan MA, Ehsanullah M, Haroon U, Azam SM, Hameed A. 2012. Production of peptide antibiotics by Bacillus sp. GU 057 indigenously isolated from saline soil. Braz J Microbiol. 43(4): 1340–1346. DOI:10.1590/S1517-838220120004000015.
Arifuzzaman M, Khatun MR, Rahman H. 2010. Isolation and screening of Actinomycetes from Sundarbans soil for antibacterial activity. Afr. J. Biotechnol. 9(29): 4615-4619.
Asagabaldan MA, Ayuningrum D, Kristiana R, Sabdono A, Radjasa K, Trianto A. 2017. Identification and antibacterial activity of bacteria isolated from marine sponge Haliclona (Reniera) sp. against Multi-Drug Resistant Human Pathogen. IOP Conf. Ser.Earth. Environ. Sci. 55(1): 012019.
Balcazar JL, Loureiro S, Silva YJD, Pintado J, Planas M. 2010. Identification and characterization of bacteria with antibacterial activities isolated from seahorses (Hippocampus guttulatus). J Antibiot. 63: 271-274.
Chelossi E, Milanese M, Milano A, Pronzato R, Riccardi G. 2004. Caharacterisation and antimicrobial activity of epibiotic bacteria from Petrosia ficiformis (Porifera, Demospongiae). J. Exp. Mar. Biol. Ecol. 309: 21-33.
Cherif A, Ouzari H, Daffonchio D, Cherif H, Ben SK, Hassen A, Jaoua S, Boudabous A. 2001. Thuricin 7: a novel bacteriocin produced by Bacillus thuringiensis BMG1.7, a new strain isolated from soil. J. Appl. Microbiol. 32(4) : 243-247.
Cita YP, Suhermanto A, Radjasa OK, Sudharmono P. 2017. Antibacterial activities of marine bacteria isolated from sponge Xestospongia testudinaria from Sorong, Papua. Asian Pac. J Trop. Biomed. 7(50): 450-454.
Deng Y, Lu Z, Bi H, Lu F, Zhang C, Bie X. 2011. Ioslation and characterization of peptide antibiotics LI-F04 and Polymyxin B6 produced by Paenibacillus polymyxa strain Jsa-9. J Peptides. 32(9): 1917-1923.
Ebrahimipour GH, Khosravibabadi Z, Sadeghi H, Aliahmadi A. 2014. Isolation, partial purification and characterization of an antimicrobial compound, produced by Bacillus atrophaeus. Jundishapur J Microbiol. 7(9): e11802.
Fitri DS, Pangastuti A, Susilowati A, Sutarno. 2017. Endophytic bacteria producing antibacterial against methicillin-resistant Staphylococcus aureus (MRSA) in seagrass from Rote Ndao, East Nusa Tenggara, Indonesia. Biodiversitas. 18(2): 733-740.
Florey HW. 1947. Antibiotics produced by bacteria. J. Intern. Med. 128: 495-504.
Foster JW, Woodruff HB. 2010. Antibiotic substances produced by bacteria. Ann. N.Y. Acad. Sci. 12(13): 125-136.
Gopi M, Kumaran S, Kumar TTA, Deivasigamani B, Alagappan K, Prasad SG. 2012. Antibacterial potential of sponge endosymbiont marine Enterobacter sp at Kavaratti Island, Lakshadweep archipelago. Asian Pac J Trop Med. 5(2): 42-146.
Guo Y, Huang E, Yuan C, ZhangL, Yousef E. 2012. Isolation of a Paenibacillus sp. strain and structural elucidation of its broad-spectrum lipopeptide antibiotic. Appl. Environ. Microbiol. 78(9): 3156-3165.
Hong Y, Ma Y, Zhou Y, Gao F, Liu H, Chen S. 2009. Paenibacillus sonchi sp. nov., a nitrogen-fixing spesies isolated from the rizhosphere of Sonchus oleraceus. Int. J. Syst. Evol. Microbiol. 59: 2656-2661.
Kai H, Yamashita M, Takase S, Hashimoto M, Muramatsu H, Nakamura I, Yoshikawa K, Ezaki M, Nitta K, Watanabe M, Inamura N, Fujie A. 2013. KB425796-A, a novel antifungal antibiotic produced by Paenibacillus sp. 530603. J Antibiot. 66: 465-471.
Lazzarini A, Cavaletti L, Toppo G, Marinelli F. 2000. Rare genera of Actinomycetes as potential producer of new antibiotics. Anton Leeuw Int J G. 78(3-4): 399-405.
Madigan MT, Martinko JM, Parker J. 2003. Brock Biology of Microorganisms. Tent Edition. Prentice Hall, USA.
Magarvey NA, Keller JM, Bernan V, Dworkin M, Sherman DH. 2004. Isolation and characterization of novel marine-derivated Actinomycete taxa rich in bioactive metabolites. Appl Environ Microbiol.. 70(12): 7520-7529.
Malanicheva IA, Kozlov DG, Efimenko TA, Zenkova VA, Kastrukha GS, Reznikova MI, Korolev AM, Borshchevskaia LN, Tarasova OD, Sineoki? SP, Efremenkova OV. 2014. New antibiotics produced by Basillus subtilis strains. Mikrobiologiia. 83(4):445-50.
Mardhiana, Pradana AP, Adiwena M, Santoso D, Wijaya R, Murtilaksono A. 2017. Use of endophytic bacteria from roots of Cyperus rotundus for biocontrol of Meloidogyne incognita. Biodiversitas. 18(4): 1308-1315.
Mohan G, Thangappanpillai AKT, Ramasamy B. 2016. Antimicrobial activities of secondary metabolites and phylogenetic study of sponge endosymbiotic bacteria, Bacillus sp. at agatti Island, Lakshadweep Archipelago. Biotechnol Rep. 11:44-52.
Nedialkova D, Naidenova M. 2005. Screening the antimicrobial activity of Actinomycetes strains isolated from antarctica. J Cult Collect. 4: 29-35.
Nithya C, Pandian SK. 2010. Isolation of heterotrophic bacteria from Palk Bay sediments showing heavy metal tolerance and antibiotic production. Microbiol Res. 165: 578-593.
Romanenko LA, Uchino M, Kalinovskaya NI, Mikhailov VV. 2008. Isolation, phylogenetic analysis and screening of marine mollusc-associated bacteria for antimicrobial, hemolytic and surface activities. Microbiol Res. 163: 633-644.
Shaheen M, Li J, Ross AC, Vederas JC, Jensen SE. 2011. Paenibacillus polymyxa PKBI produces variants of polymyxin B-type antibiotics. Chem Biol. 18(12): 1640-8.
Susilowati R, Sabdono A, Widowati I. 2015. Isolation and characterization of bacteria associated with brown algae Sargassum spp. from Pajang Island and their antibacterial activities. Prosedia Environ Sci. 23: 240-246.
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The CLUSTAL_X windows interface: flex- ible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 4876–82.
Ullah I, Arshed M, Noureen U, Chuadhry MJI, Jadoon MA. 2010. Isolation of Streptomyces from the sediments of selected thermal springs of northern Pakistan and its interinsic susceptibility and resistance. Rec Zool Surv Pak. 21:47-50.
Wilson GS, Raftos DA, Corrigan SL, Nair SV. 2010. Diversity and antimicrobial activities of surface-attached marine bacteria from Sydney Harbour, Australia. Microbiol Res J Int. 165: 300-311.
Wilson GS, Raftos DA, Nair S.V. 2011. Antimicrobial activity of surface attached marin bacteria in biofilm. Microbiol Res J Int. 166: 437-448.
Wu X, Shen X, Ding R, Qian C, Fang H, Li O. 2010. Isolation and partial characterization of antibiotics produced by Paenibacillus elgii B69. FEMS Microbiol Lett. 310: 32-38.
Zhao L, Xu Y, Lai X. 2018. Antagonistic endophytic bacteria associated with nodule of soybean (Glycine max L.) and plant growth-promoting properties. Braz J Microbiol. 49(2): 269-278.
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