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  2. Jurnal Kimia VALENSI Volume 9, No. 2, November 2023
  3. Qodriyah

Exploration The Candidates of Xenobiotic Degrading Indigenous Bacteria from Probolinggo City Landfill by Using Next Generation Sequencing (NGS)

Nur Romadhona Lailatul Qodriyah, Eli Hendrik Sanjaya, Roswanira Abdul Wahab, Evi Susanti

Abstract


Soil bacteria from tropical environments play a significant role in resolving various environmental issues, including biodegradation. Exploratory research on biodiversity is crucial to develop and harness the potential of different types of soil bacteria that are highly abundant. The bacterial diversity in landfills is typically high due to the decomposition of organic and inorganic waste, creating a favorable medium for the growth and development of soil bacteria. This study aims to assess the candidates of xenobiotic degrading indigenous bacteria from the Probolinggo City landfill using Next Generation Sequencing (NGS) method. The research stages include: 1) sampling, 2) isolation of genomic DNA from samples using the ZymoBIOMICS DNA MiniPrep Kit from Zymo Research, 3) amplification of isolated DNA with primers 16S 27F – 1429R, 4) sequencing the results of DNA amplification with NGS, 5) downstream analysis of the results using software Pavian Krona Tools, and 6) narrative analysis review to identify the candidates of xenobiotic degrading indigenous bacteria. The results show that soil samples from the Probolinggo City landfill exhibited a high diversity of bacterial communities. Based on NGS analysis, 2400 bacterial species were identified, comprising 56 genera, 17 orders, 4 classes, and 4 phyla, with respective abundances of Proteobacteria (70%), Firmicutes (15%), Planctomycetes (2%), and Cyanobacteria (0,3%). Based on the narrative analysis review, several bacteria in the Probolinggo City landfill exhibited potential as: 1) polypropylene-degrading bacteria, including Bacillus cereus, B. licheniformis and B. thuringiensis. 2) styrofoam degrading bacteria, namely Bacillus amyloliquefaciens, Bacillus cereus, Bacillus firmus and Pseudomonas aeruginosa. 3) total ammonia nitrogen (TAN) reducing bacteria, including Bacillus megaterium. 4) pesticide degrading bacteria Profenofos and Chlorantraniliprole, including Bacillus stearothermophilus. and 5) tannic acid degrading bacteria, including Pantoea dispersa. These results indicate that the Probolinggo City landfill is a good habitat for various xenobiotic-degrading bacteria, then the isolation of specific bacteria can be designed using an appropriate selective medium.

Keywords


NGS; indigenous bacteria; xenobiotic degrading; landfill

References


Malla MA, Dubey A, Yadav S, Kumar A, Hashem A, Abd-Allah EF. Understanding and designing the strategies for the microbe-mediated remediation of environmental contaminants using omics approaches. Front Microbiol. 2018;9(JUN). doi:10.3389/fmicb.2018.01132

Singh A, Prasad SM, Singh RP, Eds. Plant responses to xenobiotics. In: Singapore: Springer; 2016:Vol 362.

Datta S, Singh S, Kumar V, et al. Endophytic Bacteria in Xenobiotic Degradation. Elsevier Inc.; 2019. doi:10.1016/B978-0-12-818734-0.00006-1

Tétard-Jones C, Edwards R. Potential roles for microbial endophytes in herbicide tolerance in plants. Pest Manag Sci. 2016;72(2):203-209.

doi:10.1002/ps.4147

Miglani R, Parveen N, Kumar A, et al. Degradation of Xenobiotic Pollutants: An Environmentally Sustainable Approach. Metabolites. 2022;12(9). doi:10.3390/metabo12090818

Tsauri S. Isolasi Mikroba Penghasil Antibiotika Dari Tanah Tempat Pengolahan Ayam Di Jalan Abu Bakar Lambogo, Kota Makassar. Universitas Islam Negeri Alauddin Makassar; 2012.

Komala O, Sugiharti D, Darda RI. Pengolahan Sampah Organik Menggunakan Mikroorganisme. Ekologia. 2012;12(2):1-8. https://journal.unpak.ac.id/index.php/ekologia/article/view/239/163

Lestari DA, Imam Muchlissin S, Mukaromah AH, Darmawati S, Ethica SN. Isolasi Bakteri Penghasil Enzim Protease Bacillus Amyloliquefaciens Irod2 Pada Oncom Merah Pasca Fermentasi 48 Jam. Semin Nas Edusainstek. Published online 2018:40-46.

Batubara UM, Susilawati IO, Riany H. Isolasi dan Karakterisasi Bakteri Indigenous Tanah di Kawasan Kampus Universitas Jambi. Pros Semirata 2015 Bid MIPA BKS-PTN Bara. Published online 2015:243-250.

Hidayat YP. Interpretasi Zona Pencemaran Air Lindi Di Sekitar Tempat Pembuangan Akhir (TPA) Pasir Bajing Daerah Sukaraja, Kecamatan Banyuresmi Kabupaten Garut Menggunakan Metode Geolistrik Konfigurasi Wenner Beta. UIN Sunan Gunung Djati Bandung; 2020.

Ristiati NP, Suryanti IAP, Indrawan IMY. Isolasi Dan Karakterisasi Bakteri Tanah Pada Tempat Pemrosesan Akhir Di Desa Bengkala Kabupaten Buleleng. J Mat Sains, dan Pembelajarannya. 2018;12(1):64-77.

Jain K, Bhunia H, Sudhakara Reddy M. Degradation of polypropylene–poly-L-lactide blend by bacteria isolated from compost.

Bioremediat J. 2018;22(3-4):73-90. doi:10.1080/10889868.2018.1516620

Vollmers J, Wiegand S, Kaster AK. Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters! Vol 12.; 2017. doi:10.1371/journal.pone.0169662

Barone R, De Santi C, Esposito FP, et al. Marine metagenomics, a valuable tool for enzymes and bioactive compounds discovery. Front Mar Sci. 2014;1(SEP):1-6. doi:10.3389/fmars.2014.00038

Nuro F. Metagenomik: penelusuran makhluk tak kasat mata dalam tanah. Bio Trends. 2017;8(2):7-14. http://lipi.go.id/publikasi/metagenomik-penelusuran-makhluk-tak-kasat-mata-dalam-tanah/5334

Purwoko D, Cartealy IC, Tajuddin T, Dinarti D, Sudarsono S. Analisis Bioinformatika Berbasis Web Pada Sekuen Genom Parsial Sagu (Metroxylon sagu Rottb.). J Bioteknol Biosains Indones. 2018;5(1):98.

doi:10.29122/jbbi.v5i1.2878

Tasma IM. Pemanfaatan Teknologi Sekuensing Genom untuk Mempercepat Program Pemuliaan Tanaman Utilization of Genome Sequencing Technology to Accelerate Plant Breeding Program. J Litbang Pertan. 2015;34(2):159–168.

Kim J, Kim JG, Kang Y, et al. Quorum sensing and the LysR-type transcriptional activator ToxR regulate toxoflavin biosynthesis and transport in Burkholderia glumae. Mol Microbiol. 2004;54(4):921-934.

doi:10.1111/j.1365-2958.2004.04338.x

Vinje H, Liland KH, Almøy T, Snipen L. Comparing K-mer based methods for improved classification of 16S sequences. BMC Bioinformatics. 2015;16(1):1-13. doi:10.1186/s12859-015-0647-4

Akinsanya MA, Goh JK, Lim SP, Ting ASY. Metagenomics study of endophytic bacteria in Aloe vera using next-generation technology. Genomics Data. 2015;6:159-163. doi:https://doi.org/10.1016/j.gdata.2015.09.004

Wang R, Zhang H, Sun L, Qi G, Chen S, Zhao X. Microbial community composition is related to soil biological and chemical properties and bacterial wilt outbreak. Sci Rep. 2017;7(1):1-10.

doi:10.1038/s41598-017-00472-6

Wangka M, Wullur S, Angkouw D. E, Mamuaja M. J, Tumbol A. R, Ginting L. E. Analisis Komunitas Bakteri Pada Sedimen Dari Pulau Bangka Sulawesi Utara. J Ilm Platax. 2020;8(2):196-203.

Dong Y, Gao M, Qiu W, Song Z. Effect of microplastics and arsenic on nutrients and microorganisms in rice rhizosphere soil. Ecotoxicol Environ Saf. 2021;211:111899. doi:10.1016/j.ecoenv.2021.111899

Pratiwi WM, Asri MT. Isolasi dan Identifikasi Bakteri Indigenous Pendegradasi Pestisida Profenofos dan Klorantraniliprol di Jombang Jawa Timur. LenteraBio Berk Ilm Biol. 2022;11(2):300-309. doi:10.26740/lenterabio.v11n2.p300-309

Devi M, Prijambada ID, Widianto D. Isolasi Dan Identifikasi Bakteri Pendegradasi Asam Tanat, Serta Uji Kemampuannya Dalam Mendegradasi Plastik PET (Polyethylene Terephthalate). Universitas Gadjah Mada; 2021.


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DOI: 10.15408/jkv.v9i2.34316

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