Email this article 
Studi Metagenomik Sampel Perairan yang Diperkaya dari Wilayah Hilir Sungai Citarum dan Potensinya sebagai Agen Bioremediasi
Abstract
Abstrak
Perairan Sungai Citarum banyak memperoleh limpasan limbah antropogenik dari darat yang dapat menimbulkan pencemaran lingkungan. Untuk mengatasi masalah pencemaran tersebut, bakteri dapat dimanfaatkan sebagai agen bioremediasi. Hingga saat ini belum tersedia informasi komunitas bakteri di Perairan Sungai Citarum, khususnya dari wilayah hilir Muara Gembong. Penelitian ini bertujuan untuk mengidentifikasi komunitas, kelimpahan, dan keanekaragaman bakteri dari Perairan Muara Gembong yang telah diperkaya dengan pendekatan metagenomik, serta analisis fungsional dengan melihat profil protein yang dimiliki dari bakteri yang teridentifikasi yang berpotensi sebagai agen bioremediasi. Pengambilan sampel air dilakukan di dua lokasi (A1 dan A2) dengan karateristik perairan yang berbeda. Sampel air estuari diperkaya dengan 0,2x Nutrient Broth. Sekuensing dilakukan dengan metode Next Generation Sequencing (NGS) menggunakan amplikon sekuensing platform Novaseq Illumina, dengan primer 16S rRNA region V3–V4 (341F dan 806R). Hasil identifikasi menunjukkan terdapat 37 genera, 19 famili, 13 ordo, 7 kelas, dan 4 filum bakteri dengan 49 OTU untuk sampel A1 dan 48 OTU untuk sampel A2. Kelimpahan tertinggi diperoleh pada kelas Gammaproteobacteria (99,82%) yang didominasi oleh genus Vibrio. Keanekaragaman bakteri pada kedua sampel diperkaya ini tergolong sedang dengan dominasi tinggi. Analisis fungsional menunjukkan kemampuan bakteri yang teridentifikasi mampu mendegradasi benzoate, dioxin, asam lemak, metana, naftalen, nitrotoluene, PAH, dan sulfur dengan protein dan enzim yang terlibat dalam metabolisme tersebut. Penelitian ini menunjukkan bakteri yang teridentifikasi pada Perairan Muara Gembong mempunyai potensi bioremediasi untuk cemaran lingkungan, seperti polutan organik dari logam berat.
Abstract
Muara Gembong waters is a downstream region of the Citarum watershed that receives anthropogenic runoff and affects water pollution. To overcome the problem of pollution, bacteria can be used as a bioremediation agent. Until now, information on the bacterial community in Citarum River waters has not been obtained, especially in the downstream area of Muara Gembong. This study aims to identify the community, abundance, and diversity of bacteria from Muara Gembong waters that have been enriched with a metagenomic approach, as well as functional analysis by looking at the protein profiles of the identified bacteria that have the potential as bioremediation agents. Water samples were taken at two locations (A1 and A2) with different water characteristics. Estuary water samples were enriched with 0.2x Nutrient Broth (NB). Amplicon sequencing of NGS by Novaseq Illumina platform was used in this research, using 16S rRNA primer region V3-V4 (341F and 806R). The results showed that 37 genera, 19 families, 13 orders, 7 classes, and 4 bacterial phyla were identified with 49 OTUs for A1 and 48 OTUs for A2. The highest abundance was obtained by the Gammaproteobacteria class (99.82%) which dominated by the Vibrio genera. The diversity level is classified as medium diversity with high dominance. Functional analysis showed the ability of the identified bacteria to degrade benzoate, dioxin, fatty acid, methane, naphthalene, nitrotoluene, PAH, and sulfur with proteins and enzymes involved in the metabolism. This study shows that identified bacteria in Muara Gembong waters are potentially appicable for bioremediation of the environment contaminants, such as organic pollutants and heavy metals.
Keywords
Full Text:
PDF (Bahasa Indonesia)References
Androga, D.D., Özgür, E., Eroglu, I., Yücel, M., & Gündüz, U. (2012). Photofermentative hydrogen production in outdoor conditions. Croatia: INTECH Open Access Publisher. https://www.intechopen.com/chapters/40241
Aravindraja, C., Viszwapriya, D., & Karutha, P.S. (2013). Ultradeep 16S rRNA Sequencing Analysis of Geographically Similar but Diverse Unexplored Marine Samples Reveal Varied Bacterial Community Composition. PLoS ONE, 8(10), e76724.
Azmuda, N., Fakruddin, M., Khan, S.I., Birkeland, N.K. (2019). Bacterial Community Profiling of Tropical Freshwaters in Bangladesh. Front. Public Health, https://doi.org/10.3389/fpubh.2019.00115
Balachandran, C., Duraipandiyan, V., Balakrishna, K., & Ignacimuthu, S. (2012). Petroleum and polycyclic aromatic hydrocarbons (PAHs) degradation and naphthalene metabolism in Streptomyces sp. (ERI-CPDA-1) isolated from oil contaminated soil. Bioresource Technology, 112, 83–90. doi:10.1016/j.biortech.2012.02.059
Bara’padang, B., Fahrudin, A., & Effendi, I. (2019). Analisis Spasial Beban Limbah Budidaya Tambak Terhadap Lingkungan Perairan Pesisir Holtekamp Kota Jayapura, Provinsi Papua. Jurnal Ilmu Kelautan dan Perikanan Papua, 2(2), 75-81
BSN (Badan Standar Nasional). (2019). Air dan air limbah – Bagian 3: Cara uji padatan tersuspensi total (Total Suspended Solids, TSS) secara gravimetri. http://sispk.bsn.go.id/sni/DetailSNI/12245# di
Chen, J.-S. (2004). Nitrogen Fixation in the Clostridia. Nitrogen Fixation: Origins, Applications, and Research Progress, 53–64. doi:10.1007/1-4020-2179-8_3
Costa, R.A., Silva, G.C., Peixoto, J.R., Vieira, G.H.F., Vieira, R.H.S.F. (2010). Quantification and distribution of vibrio species in water from an estuary in Ceará-Brazil impacted by shrimp farming. Brazilian Journal of Oceanography, 58(3).
Departemen Pertanian. (2005, 15 Oktober). Petunjuk Teknis: Analisis Kimia Tanah, Tanaman, Air, Dan Pupuk – N-total. https://balittanah.litbang.pertanian.go.id/ind/dokumentasi/juknis/juknis_kimia.pdf
Deshmukh, K. B., Pathak, A. P., & Karuppayil, M. S. (2011). Bacterial diversity of Lonar soda lake of India. Indian journal of Microbiology, 51(1), 107-111.
Danczak, R. E., Johnston, M. D., Kenah, C., Slattery, M., Wrighton, K. C. & Wilkins, M. J. (2017). Members of the candidate phyla radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities. Microbiome, 5(1),112.
Ederer, M. M., Lewis, T. A., & Crawford, R. L. (1997). 2,4,6-Trinitrotoluene (TNT) transformation by clostridia isolated from a munition-fed bioreactor: comparison with non-adapted bacteria.
Journal of Industrial Microbiology Biotechnology, 18(2-3),82-8.
Esteve-Núñez, A., Caballero, A., & Ramos, J. L. (2001). Biological degradation of 2, 4, 6-trinitrotoluene. Microbiology and molecular biology reviews, 65(3), 335-352.
Fondriest Environmental Learning Center. (2021, 18 Juni). Turbidity, Total Suspended Solids & Water Clarity. Internet. https://www.fondriest.com/environmental-measurements/parameters/water-quality/turbidity-total-suspended-solids-water-clarity/
Field, J. A., & Sierra-Alvarez, R. (2008). Microbial degradation of chlorinated dioxins. Chemosphere, 71(6), 1005–1018. doi:10.1016/j.chemosphere.2007.10.039
Ghosh, A., & Bhadury, P. (2018). Exploring Biogeographic Patterns of Bacterioplankton Communities Across Global Estuaries. Wiley Microbiology Open. https://pubmed.ncbi.nlm.nih.gov/30303297/
Ghosh, A., Mehta, A., & Khan A. M. 2018. Metagenomic Analysis and Its Applicantions. Reference Module in Life Science. https://doi.org/10.1016/B978-0-12-809633-8.20178-7
Glaring, M. A., Vester, J. K., Lylloff, J. E., Abu Al-Soud, W., Sørensen, S. J., & Stougaard, P. (2015). Microbial diversity in a permanently cold and alkaline environment in Greenland. PloS one, 10(4), e0124863.
Guerra, A. B., Oliveira, J. S., Silva-Portela, R. C. B., Araújo, W., Carlos, A. C., Vasconcelos, A. T. R., & Agnez-Lima, L. F. (2018). Metagenome enrichment approach used for selection of oil-degrading bacteria consortia for drill cutting residue bioremediation. Environmental Pollution, 235, 869–880. doi:10.1016/j.envpol.2018.01.014
Guerinot, M.L., West, P.A., Lee, J.V., & Colwell, R.R. (1982). Vibrio diazotrophicus sp. nov., a Marine Nitrogen-Fixing Bacterium. International Journal of Systematic Bacteriology, 350-357.
Gutiérrez-Lucas, L. , Montor-Antonio, J. , Cortés-López, N. and del Moral, S. (2014) Strategies for the Extraction, Purification and Amplification of Metagenomic DNA from Soil Growing Sugarcane. Advances in Biological Chemistry, 4, 281-289. doi: 10.4236/abc.2014.44034
Harvell, C. D., Garren, M., Work, T.M., Rosenberg, E., Smith, G.W. & Bourne, D.G. (2010). Microbial disease and coral holobiont. Trend in Microbiology, 12, 554-562.
Hidayatullah, I., Subardjo, P., & Satriadi, A. (2016). Pemetaan genanagan ROB di Pesisir Muara Gembong Kabupaten Bekasi Dengan Menggunakan Sistem Informasi Geografis. Jurnal Oseanografi, 5(3), 359 – 367
Holmström, C., & S. Kjelleberg. (1999). Marine Pseudoalteromonas species are associated with higher organisms and produce biologically active extracellular agents. FEMS microbiology ecology, 30(4), 285-293.
Huang, S., Lindahl, P. A., Wang, C., Bennett, G. N., Rudolph, F. B., & Hughes, J. B. (2000). 2,4,6-trinitrotoluene reduction by carbon monoxide dehydrogenase from Clostridium thermoaceticum. Applied and Environmental Microbiology, 66(4):1474-8.
Hughes J B, Wang C, Yesland K, Bhadra R, Richardson A, Bennet G, Rudolph F. (1998). Reduction of 2,4,6-trinitrotoluene by Clostridium acetobutylicum through hydroxylamino intermediates. Environmental Toxicology and Chemistry: An International Journal, 17(3), 343-348.
Ibekwe, A.M., Ma, J., & Murinda, S.E. (2016). Bacterial community composition and structure in an Urban River impacted by different pollutant sources. Journal Science of the Total Environment. 1, 566-567:1176-1185. doi: 10.1016/j.scitotenv.2016.05.168.
Jeffries, T.C., Schmitz Fontes, M.L., Harrison, D.P., Van-Dongen-Vogels, V., Eyre, B.D., Ralph, P.J., & Seymour, J.R. (2016). Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary. Journal Frontiers in Microbiology, 6. https://doi.org/10.3389/fmicb.2015.01438
Jurtshuk, P. (1996). Medical Microbiology. 4th edition: Bacterial Metabolism. Galveston (TX): University of Texas Medical Branch at Galveston
Kalinovskaya, N.I., Ivanova, E.P., Alexeeva, Y.V., & Gorshkova, N.M. (2004). Low-molecular-weight, biologically active compounds from marine Pseudoalteromonas species. Current Microbiology 48, 441–6.
Kementerian Lingkungan Hidup Republik Indonesia. (2019). Keputusan Menteri Negara Lingkungan Hidup Nomor 51 Tahun 2004 Tentang Baku Mutu Air Laut. Jakarta.
Kopejtka, K., Tomasch, J., Zeng, Y., Tichý, M., Sorokin, D.Y., & Koblížek, M. (2017). Genomic Analysis of the Evolution of Phototrophy among Haloalkaliphilic Rhodobacterales. Genome Biol Evol, 9(7). 1950–1962.
Kurniama, S.S., Naila, M.M., Listyorini, D., & Sri, S.E. (2014). Optimization of DNA Isolation and Purification Technique from Chili Pepper (Capsicum frutescens) Using Genomic DNA Mini Kit (Plant) Geneaid. Semnas. XI Pendidik. Biol. FKIP UNS, 65–70.
Nakatsu, C. H., Byappanahalli, M. N., & Nevers, M. B. (2019). Bacterial Community 15S rRNA Gene Sequencing Charaterizes Riverine Microbial Impact on Lake Michigan. Frontiers in Microbiology, 10.996
Nogales, J., García, J. L., & Díaz, E. (2017). Degradation of Aromatic Compounds in Pseudomonas: A Systems Biology View. Aerobic Utilization of Hydrocarbons, Oils and Lipids, 1-49. doi:10.1007/978-3-319-39782-5_32-1
Novogene. (2020). Novogene 16S Analysis Report. https://filgen.jp/Product/Bioscience5-seq/Novogene_Demo_Report_16S-V2.pdf
Novogene. (2022, 21 Juni). 16S/18S/ITS Amplicon Metagenomic Sequencing. https://en.novogene.com/services/research-services/metagenome-sequencing/16s-18s-its-amplicon-metagenomic-sequencing/ .
Omeroglu, E. E., Sudagidan, M., Yurt, M. N. Z., Tasbasi, B. B., Acar, E. E., & Ozalp, V. C (2021). Microbial community of soda Lake Van as obtained from direct and enriched water, sediment and fish samples. Scientific Reports, 11(1), 1-13. https://doi.org/10.1038/s41598-021-97980-3
Othman, N., Abdul-Talib, S., & Tay, C. C. (2016). Optimization of low ring polycylic aromatic biodegradation. IOP Conference Series: Materials Science and Engineering Journal, 136, 012054. doi:10.1088/1757-899x/136/1/012054
Parulekar, N. N., Kolekar, P., Jenkins, A., Kleiven, S., Utkillen, H., Johansen, A., Sawant, S., Kale, U.K., Kale, M., & Saebo, M. (2017). Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis. PloS one, 12(3), e0173408 https://doi.org/10.1371/journal.pone.0173408
Praditya, T. (2011). Pengaruh Perubahan Tata Guna Lahan dan Aktivitas Manusia Terhadap Kualitas Air Sub DAS Saluran Tarum Barat. Skripsi. Departemen Suberdaya Hutan dan Ekowisata IPB.
Prisentria, S. (2018). Keanekaragaman Bakteri Pada Terumbu Karang Acropora sp. di Pulau Biawak, Indramayu. Skripsi. Jatinangor: Prodi Ilmu Kelautan FPIK Unpad
Putri, F.D.M., Widyastuti, E., & Christiani. (2014). Hubungan Perbandingan Total Nitrogen dan Total Fosfor dengan Kelimpahan Chrysophyta di Perairan Waduk Panglima Besar Soedirman, Banjarnegara. Journal Scripta Biologica, 1(1).
Rastina. (2012). Strategi Pengelolaan Lingkungan Berdasarkan Pemodelan Kualitas Air di Perairan Estuaria Tallo Sulawesi Selatan. Disertasi. Sekolah Pascasarjana Institut Pertanian Bogor.
Respati, N. Y. (2017). Optimasi Suhu dan pH Media Pertumbuhan Bakteri Pelarut Fosfat dari Isolat Bakteri Termofilik. Jurnal Prodi Biologi, 6(7).
Ridwan, F. (2014). Pemodelan perubahan penutupan/penggunaan Lahan dengan pendekatan artificial neural network dan logistic regression (Studi kasus: DAS Citarum, Jawa Barat). Skripsi. Fakultas Pertanian IPB.
Rizal, A.C., Ihsan, Y.N., Afrianto, E., & Yuliadi, L.P.S. (2017). Pendekatan Status Nutrien Pada Sedimen Untuk Mengukur Struktur Komunitas Makrozoobentos di Wilayah Muara Sungai dan Pesisir Pantai Rancabuaya, Kabupaten Garut. Jurnal Perikanan dan Kelautan, VIII(2)
Sarhan M.S., Hamza M.A., Yousef H.H., Patz S., Becker M., Elsawey H., Nemer R., Daanaa H.S.A., Mourad E.F., Morsi A.T., Abdelfadeel M.R., Abbas M.T., Fayez M., Rupel S. & Hegazi N.A. (2019). Culturomics of the plant prokaryotic microbiome and the dawn of plant-based culture media – A review. Journal of Advanced Research.19, 15-27.
Schnell S. & Schinck B. (1991). Anaerobic aniline degradation via reductive deamination of 4-aminobenzoyl-CoA in Desulfobacterium anilini. Archives of Microbiology,155,183–190.
Sieber, C.M.K., Paul, B.G., Castelle, C.J., Hu, P., Tringe, S.G., Valentine, D.L., & Banfield, J.F. (2019). Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community. mBio, 10(6).
Simbolon, A.R. (2016). Kandungan Logam Berat Timbal (Pb) di Perairan Cilincing Pesisir DKI Jakarta. Prosiding Seminar Nasional Pendidikan Biologi dan Biologi. Yogyakarta: FMIPA UNY
Supriyati, D. & Rahayu, R.D. (2011). Studi Potensi Bakteri Labrenzia aggregate G3 dan Alpha proteobacterium G4. Berk. Penel. Hayati Edisi Khusus, 4C (13–18).
Susana, T. (2004). Sumber polutan nitrogen dalam air laut. Oseana, XXIX(3). 25-33,
Wang, P., Chen, B., Yuan, R., Li, C., & Li, Y. (2016). Characteristics of aquatic bacterial community and the influencing factors in an urban river. Science of the Total Environment, 569–570 (2016) 382–389.
Wang, W., & Shao, Z. (2012). Diversity of flavin-binding monooxygenase genes (almA) in marine bacteria capable of degradation long-chain alkanes. FEMS Microbiology Ecology, 80(3), 523–533. doi:10.1111/j.1574-6941.2012.01322.x
West, P.A., Brayton, P.R., Twilley, R.R., Bryant, T.N., & Colwell, R.R. (1985). Numerical taxonomy of nitrogen-fixing “decarboxylase-negative” Vibrio species isolated from aquatic environments. International Journal of Systematic Bacteriology, 35198-205.
West, P.A., Lee, J. V., & Bryant, T. N. (1983). Numerical taxonomy of strains of Vibrio species isolated from water and birds in Kent, England. Journal of Applied Bacteriology, 55263-282.
Xing, P., Guo, L., Tian, W., & Wu, Q.L. (2010). Novel clostridium populations involved in the anaerobic degradation of microcystis blooms. ISME Journal, 2011, 5. 792–800
Xu, X.-W., Wu, Y.-H., Wang, C.-S., Gao, X.-H., Wang, X.-G., & Wu, M. (2009). Pseudoalteromonas lipolytica sp. nov., isolated from the Yangtze River estuary. International Journal Of Systematic And Evolutionary Microbiology, 60(9), 2176–2181.
DOI: http://dx.doi.org/10.15578/jpbkp.v17i1.794
Article Metrics
Abstract view : 1331 timesPDF (Bahasa Indonesia) - 410 times
Refbacks
- There are currently no refbacks.
JPBKP adalah Jurnal Ilmiah yang terindeks :
ISSN : 1907-9133(print), ISSN : 2406-9264(online)
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.