Phenotypic and Genomic Identification of Glyphosate-Herbicide Degrading Bacterial Isolate From the Rhizosphere of Chilli Pepper
DOI:
https://doi.org/10.26740/lenterabio.v13n2.p253-261Keywords:
rhizosphere bacteria, bioremediation, identification, agricultural landAbstract
Bacteria are one of the bioremediation agents to treat pollution in agricultural land. Bacteria can degrade contaminant compounds. Bacterial isolate CF6 is a rhizosphere bacterial isolate from chili pepper agricultural soil which has the potential to degrade glyphosate herbicide. However, it needs to be identified to be applied as a bioremediation agent and its effects on the ecosystem understood. This research aims to identify phenotypically and genomically isolates of rhizosphere bacteria that have the potential to degrade glyphosate herbicides so that they can be applied further. Phenotypic identification methods consisted of motility tests, gram staining, catalase, citrate, urease, endospores, Voges-Proskauer, indole production, methyl red, growth in 5% NaCl, and sugar reduction tests. The genomic identification method was divided into four stages, namely DNA isolation, 16S rRNA gene amplification, electrophoresis, and 16S rRNA gene sequencing. Data from phenotypic and genomic tests were analyzed numerically using NTSys 2.11a and MEGA11, respectively. The dendrogram results in this study showed that the CF6 bacterial isolate belonged to the same clade as bacteria of the genus Klebsiella. Meanwhile, the results of BLASTn analysis showed that the CF6 test isolate had a 16S rRNA gene sequence similarity with Klebsiella quasipneumoniae of 98.62%. From the results of the two identification methods, it can be concluded that the CF6 bacterial isolate is K. quasipneumoniae. Aspects of pathogenicity and bacterial degradation rate need to be tested before implementation.
References
Acinas SG, Marcelino LA, Klepac-Ceraj V, & Polz MF, 2004. Divergence and Redundancy of 16S rRNA Sequences in Genomes with Multiple rrn Operons. Journal of Bacteriology; 186(9): 2629–2635. https://doi.org/10.1128/JB.186.9.2629-2635.2004
Akihary CV, & Kolondam J, 2020. Pemanfaatan Gen 16S rRNA Sebagai Perangkat Identifikasi Bakteri Untuk Penelitian-penelitian di Indonesia. PHARMACONJ: Jurnal Ilmiah Farmasi-UNSRAT; 9(1): 16–22. http://dx.doi.org/10.35799/pha.9.2020.27405
Anggara BS, Yuliani Y, & Lisdiana L, 2014. Isolasi dan Karakterisasi Bakteri Endofit Penghasil Hormon Indole Acetic Acid dari Akar Tanaman Ubi Jalar. LenteraBio; 3(3): 160–167. http://ejournal.unesa.ac.id/index.php/lenterabio
Anwar R, Suzanna E, & Djatmiko D, 2021. Pengujian Efektivitas Herbisida Hayati di Perkebunan Kopi pada Berbagai Kondisi Agroekologi. Jurnal Agroqua; 19(1): 33–41. https://doi.org/10.32663/ja.v
Apriliya I, Prasetyo D, & Remila S, 2020. Isolasi Bakteri Rhizosfer Resisten Pestisida dan Herbisida pada Berbagai Jenis Tutupan Lahan. Agrotekma; 5(1): 64–71. https://doi.org/10.31289/agr.v5i1.4466
Arista AM, Yuliani Y, & Lisdiana L, 2018. Identifikasi Isolat Bakteri Endofit A1 dan B1 dari Akar Tanaman Ubi Jalar Berdasarkan Sekuens 16S rDNA. LenteraBio; 7(1): 9–14. http://ejournal.unesa.ac.id/index.php/lenterabio
Celebi O, Ozdemir U, Buyuk F, Unsul BA, Erpek S, Karahan M, Otlu S, Sahim M, Coskun M, Celik E, Gulmes SA, Buyuk E, & Akca D, 2022. Isolation of Mycoplasma spp. from Geese with Pneumonia and Identification of Microbial Isolates via Molecular Methods. Brazilian Journal of Poultry Science; 24: (eRBCA-2021-1522).
Dovichi NJ, & Zhang J, 2000. How Capillary Electrophoresis Sequenced the Human Genome. Angewandte Chemie (International Ed. in English); 39(24): 4463–4468. https://doi.org/10.1002/1521-3773(20001215)39:24<4463::aid-anie4463>3.0.co;2-8
Elarabi NI, Abdelhadi AA, Ahmed RH, Saleh I, Arif IA, Osman G, & Ahmed DS, 2020. Bacillus aryabhattai FACU: A Promising Bacterial Strain Capable of Manipulate The Glyphosate Herbicide Residues. Saudi Journal of Biological Sciences; 27(9): 2207–2214. https://doi.org/10.1016/j.sjbs.2020.06.050
Emerson D, Agulto L, Liu H, & Liu L, 2008. Identifying and Characterizing Bacteria in An Era of Genomics and Proteomics. BioScience; 58(10): 925–936. https://doi.org/10.1641/B581006
Fan J, Yang G, Zhao H, Shi G, Geng Y, Haou T, & Ke T, 2012. Isolation, Identification and Characterization of a Glyphosate Degrading Bacterium Bacillus cereus CB4 from Soil. J. Gen. Appl. Microbiol: 58: 263–271.
Faqihhudin MD, Haryadi H, & Purnamawati H, 2014. Penggunaan Herbisida IPA-Glifosat Terhadap Pertumbuhan, Hasil Residu pada Jagung. Ilmu Pertanian; 17(1): 1–12.
Hagström Å, Pommier T, Rohwer F, Simu K, Stolte W, Svensson D, & Zweifel UL, 2002. Use of 16S Ribosomal DNA for Delineation of Marine Bacterioplankton Species. Applied and Environmental Microbiology: 68(7): 3628–3633. https://doi.org/10.1128/AEM.68.7.3628-3633.2002
Hernández-Alomia F, Ballesteros I, & Castillejo P, 2022. Bioremediation Potential of Glyphosate-Degrading Microorganisms in Eutrophicated Ecuadorian Water Bodies. Saudi Journal of Biological Sciences; 29(3): 1550–1558. https://doi.org/10.1016/j.sjbs.2021.11.013
Kononova SV, & Nesmeyanova MA, 2002. Phosphonates and Their Degradation by Microorganisms. Biochemistry (Moscow); 67(2): 184–195.
Kryuchkova YV, Burygin GL, Gogoleva NE, Gogolev YV, Chernyshova MP, Makarov OE, Fedorov EE, & Turkovskaya OV, 2014. Isolation and Characterization of A Glyphosate-Degrading Rhizosphere Strain, Enterobacter cloacae K7. Microbiological Research; 169(1): 99–105. https://doi.org/10.1016/j.micres.2013.03.002
Kuklinsky-Sobral J, Araújo WL, Mendes R, Pizzirani-Kleiner AA, & Azevedo JL, 2005. Isolation and Characterization of Endophytic Bacteria From Soybean (Glycine max) Grown in Soil Treated with Glyphosate Herbicide. Plant and Soil; 273(1–2): 91–99. https://doi.org/10.1007/s11104-004-6894-1
Manogaran M, Shukor MY, Yasid NA, Johari WLW, & Ahmad SA, 2017. Isolation and Characterisation of Glyphosate-Degrading Bacteria Isolated From Local Soils in Malaysia. Rendiconti Lincei; 28(3): 471–479. https://doi.org/10.1007/s12210-017-0620-4
Nikmah AL, & Lisdiana L, 2024. Penapisan Bakteri Rizosfer Pendegradasi Herbisida Glifosat dari Tanah Pertanian Cabai Rawit (Capsicum frutescent L.). LenteraBio: Berkala Ilmiah Biologi; 13(1): 24–31.
Noer S, 2021. Identifikasi Bakteri Secara Molekular Menggunakan 16S rRNA. EduBiologia: Biological Science and Education Journal; 1(1): 1. https://doi.org/10.30998/edubiologia.v1i1.8596
Nuritasari D, Sarjono PR, & Aminin ALN, 2017. Isolasi Bakteri Termofilik Sumber Air Panas Gedongsongo dengan Media Pengaya MB (Minimal Broth) dan TS (Taoge Sukrosa) serta Identifikasi Fenotip dan Genotip. Jurnal Kimia Sains dan Aplikasi; 20(2): 84–91. https://doi.org/10.14710/jksa.20.2.84-91
Nursulistyarini F, & Ainy EQ, 2014. Isolation and Identification of Endophytic Bacteria Producing Antibacteria Compounds From Anredera cordifolia (Ten.) Steenis Leaf Fenni. Proceeding Biology Education Conference: Biology, Science, Enviromental, and Learning; 11(1): 114–120.
Obiefuna HO, & Onuorah SC, 2022. Isolation and Characterization of Glyphosate-Degrading Bacteria from Agricultural Soil in Awka, Anambra State, Nigeria. MJSAT; 2(4): 194-198. https://doi.org/10.56532/mjsat.v2i4.81
Oliveira CF, Paim TGS, Reiter KC, Rieger A, & D’Azevedo PA, 2014. Evaluation of Four Different DNA Estraction Methods in Coagulase-Negative Staphylococci Clinical Isolates. Revista Do Instituto de Medicina Tropical de Sao Paulo; 56(1): 29–33. https://doi.org/10.1590/S0036-46652014000100004
Olukanni OD, Albert AA, Farinto M, Awotula AO, & Osuntoki AA, 2023. Tween-80 Enhanced Biodegradation of Naphthalene by Klebsiella quasipneumoniae. Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology; 116(7): 697–709. https://doi.org/10.1007/s10482-023-01839-8
Prastio RA, Isnawati I, & Rahayu DA, 2022. Isolasi, Karakterisasi, dan Identifikasi Bakteri Patogen pada Tumbuhan Kantong Semar (Nepenthes gracillis). LenteraBio : Berkala Ilmiah Biologi; 11(2): 255–262. https://doi.org/10.26740/lenterabio.v11n2.p255-262
Pratama MA, Amin M, & Suarsini E, 2016. Isolasi Bakteri Indigen Pengoksidasi Sulfida (H2S) pada Limbah Cair Industri Pengolahan Ikan di Sungai Kali Mati, Kecamatan Muncar. Prosiding SNPBS; 1(3): 357–362.
Preena PG, Dharmaratnam A, & Swaminathan TR, 2020. Antimicrobial Resistance Analysis of Pathogenic Bacteria Isolated From Freshwater Nile Tilapia (Oreochromis niloticus) Cultured in Kerala, India. Current Microbiology; 77(11): 3278–3287. https://doi.org/10.1007/s00284-020-02158-1
Rosahdi TD, Tafiani N, & Hafsari AR, 2019. Identifikasi Spesies Isolat Bakteri K2Br5 dari Tanah Karst dengan Sistem Kekerabatan Melalui Analisis Urutan Nukleotida Gen 16S rRNA. Al-Kimiya; 5(2): 84–88. https://doi.org/10.15575/ak.v5i2.3836
Shi YW, Yang H, Chu M, Niu XX, Huo XD, Gao Y, Zeng J, Zhang T, Li YG, Outi KE, Lou K, Li XY, Dang WF, & Li C, 2020. Klebsiella. Beneficial Microbes in Agro-Ecology: Bacteria and Fungi; 233–257. https://doi.org/10.1016/B978-0-12-823414-3.00013-7
Sulistyanto WN, & Trimulyono G, 2019. Karakterisasi Fenotip dan Indeks Similaritas Isolat Actinomycetes yang Memiliki Kemampuan Antibakteri Terhadap Escherichia coli dan Staphylococcus aureus. Biotropika: Journal of Tropical Biology; 7(3): 112–120. https://doi.org/10.21776/ub.biotropika.2019.007.03.4
Syah MA, 2022. Isolasi dan Karakterisasi Molekuler Gen 16S rRNA Bakteri Lipolitik Asal Limbah Kulit Biji Jambu Mete. Jurnal Sumberdaya Hayati; 8(1): 20–26. https://doi.org/10.29244/jsdh.8.1.20-26
Teul SM, Rahmawati R, & Ifadatin S, 2023. Identification of Lactic Acid Bacteria from Fermented Kimchi Sawi Ansabi (Brassica juncea L.) using Phenotypic Similarities. Jurnal Biologi Tropis; 23(4): 50–60. https://doi.org/10.29303/jbt.v23i4.5315
Triwahyuni D, 2019. Isolasi dan Karakterisasi Bakteri Indigenous Pendegradasi Residu Herbisida Glifosat dari Lahan Perkebunan Kelapa Sawit Lampung Tengah. Skripsi. Universitas Airlangga.
Wangiyana IGAS, 2019. Comparation of Dendrogram and Cladogram Topology of Gyrinops versteegii and Others Gyrinops Member For Polyphasic Taxonomy. Jurnal Silva Samalas; 2(1): 13–18.
Widowati T, Ginting RCB, Widyastuti U, Nugraha A, & Ardiwinata A, 2017. Isolasi dan Identifikasi Bakteri Resisten Herbisida Glifosat dan Paraquat dari Rizosfer Tanaman Padi. Biopropal Industri; 8(2): 63–70.
Yang L, & Yang K, 2020. Biological Function of Klebsiella variicola and Its Effect On The Rhizosphere Soil of Maize Seedlings. PeerJ; 8: 1–24. https://doi.org/10.7717/peerj.9894
Zhang C, Hao Q, Zhang Z, Zhang X, Pan H, Zhang J, Zhang H, & Sun F, 2019. Whole Genome Sequencing and Analysis of Chlorimuron-Ethyl Degrading Bacteria Klebsiella pneumoniae 2n3. International Journal of Molecular Sciences; 20(12). https://doi.org/10.3390/ijms20123053
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