Analysis of Bacteria Community in the sediment from Bangka Island, North Sulawesi
DOI:
https://doi.org/10.35800/jip.8.2.2020.29887Abstract
Marine sediments are nutrient-rich and is a suitable habitat of bacteria. This research is a preliminary study of molecular analysis to identify the bacteria in the sediments from the littoral area that covered by mangroves in Bangka Island, North Sulawesi. The purposes of this study are to obtain the uncultivated bacterial DNA genome which is used to identify the bacteria and bacterial community in the sediments. Isolation of DNA genome from uncultured bacterial was carried out by following the genomic DNA extraction procedure using the DNeasy® PowerSoil Extraction Kit. Before isolating the bacterial DNA, sample were went through freezing and thawing processes. The DNA isolation result was subsequently tested using electrophoresis and UV-Vis spectrophotometers. Subsequently the genomic DNA was amplified using Polymerase Chain Reaction and the bacteria were identified using Next Generation Sequencing (NGS) analysis. The results of this study showed that the DNA of uncultured bacteria from sediment have the purity of 1.05 and the DNA amplification band was detected at 1300-1600bp. The bacteria in Bangka Island, North Sulawesi sediments were consisted of Gemmatimonadetes, Acidobacteria, Chioroflexi, Firmicutes, Bacteroidetes, Actinobacteria, Cyanobacteria and Proteobacteria respectively. Phylum Proteobacteria was found has the highest relative abundance in the sediment.
Keywords : Bacteria, Deoxyribo Nucleic Acid, Sediment, Uncultured.
Â
ABSTRAK
Sedimen laut merupakan suatu habitat yang kaya akan nutrient dan merupakan habitat dari bakteri. Penelitian ini merupakan tahapan awal dalam rangkaian analisis molekuler bakteri yang hidup di sedimen dari daerah litoral yang ditumbuhi oleh mangrove pada Pulau Bangka Sulawesi Utara. Tujuan penelitian ini adalah untuk mendapatkan DNA genom bakteri tanpa kultivasi yang digunakan dalam analisis jenis dan komunitas bakteri pada sedimen. Isolasi DNA genom bakteri tanpa kultivasi dilakukan dengan mengikuti prosedur Kit ekstraksi DNA DNeasy® PowerSoil. Sebelum tahap isolasi DNA bakteri, sampel diperlakukan proses freezing and thawing. Hasil isolasi DNA diuji menggunakan elektroforesis dan spektrofotometer UV-Vis. DNA genom diamplifikasi menggunakan Polymerase Chain Reaction dan ditentukan jenis bakteri dengan menggunakan Next Generation Sequencing analysis. Hasil penelitian menujukkan bahwa DNA bakteri tanpa kultivasi memiliki kemurnian 1,05. DNA amplifikasi terdeteksi pada posisi 1300-1600bp. Dan jenis bakteri yang hidup pada sedimen di Pulau Bangka Sulawesi Utara, terdiri dari filum Gemmatimonadetes, Acidobacteria, Chioroflexi, Firmicutes, Bacteroidetes, Actinobacteria, Cyanobacteria dan Proteobacteria. Kelimpahan tertinggi bakteri yang hidup pada sedimen tersebut adalah  filum Proteobacteria.
Kata kunci : Bakteri, Deoxyribo Nucleic Acid, Sedimen, Tanpa kultivasi.References
Abrar, M., T.R. Ferasyi., Amiruddin., Fakhurrazi., Erina., Razali., M. Sabri., H. Abdullah., Zainuddin., A. Haris., Safika., M. Dewi., and R.A. Barus. 2019. Molecular Subtyping and DNA Sequencing Homology of Escherichia Coli O157:H7 isolated from Aceh cattle. Internasional Conference on Biological Sciences and Biotechnology. 305(1):1-7.
Annisaqois, M. 2018. Analisis Molekuler DNA Alga Merah (Rhodophyta) Kappaphycus sp. Skripsi. Fakultas Perikanan dan Ilmu Kelautan Sam Ratulangi, Manado. 44 hal.
Bissett, A., C. Burke., P.L.M Cook., and J.P. Bowman. 2007. Bacterial community shifts in organically perturbed sediments. Environmental Microbiology. 9(1):46-60.
Dahuri, R., J. Rais., S.P. Ginting., dan Sitepu. 2001. Pengolahan Sumber Daya Wilayah Pesisir dan Lautan Secara Terpadu. PT. Pradnya Paramita. Jakarta. 328 hal.
Dewi, K.T., G. Latuputty., Y.A. Priohandono., dan C. Purawanto. 2017. Respon Mikrofauna (Ostracoda) Terhadap Kondisi Lingkungan Sekitar Pulau Bangka, Sulawesi Utara. Jurnal. Geologi Kelautan. 15(1):1-9.
Das, S., P.S. Lyla and S.A. Khan. 2006. Marine Microbial Diversity and Ecology: Importance and Future Perspectives.General Article. Currenct Science. 90(10):1325-1335.
Gao, P., H. Tian., Y. Wang, Y. Li., Xie, J. and T. Ma. 2016. Spatial isolation and environmental factors drive distinct bacterial and archaeal communities in different types of petroleum reservoirs in China. 6(20174):1-12.
Hidayati., E. Saleh., dan T. Aulawi. 2016. Identifikasi Keragaman Gen BMPR-1B (Bone Morphogenetic Protein Receptor IB) Pada Ayam Arab, Ayam Kampung dan Ayam Ras Petelur menggunakan PCR-RFLP. Jurnal Peternakan. 13(1):1-12.
Haryogya, A.M., and Ustadi. 2020. Departement of Fhisheries, Faculty of Acriculture, Universitas Gadjah Mada. Isolation and Moleculr Identification of Chitinolytic Bacterium from Ronto. 147(03030). Publis online 10 February 2020. https://doi.org/10.1051/e3sconf/202014703030 .
Hold, J.G., N.R. Krieg., P.H.A. Sneath., J.T. Staley., S.T. Wiliams. 1994. Williams, Bergey’s Manual of Determinative Bacteriology Edition, USA: Williams and Wilkins Pub. 18:787.
Handbook. 2018. Ready to Load. https://www.qiagen.com. Diakses pada tanggal 22 agustus 2019.
Irianto, K. 2016. Pemanfaatan Bakteri Untuk Keselamatan Lingkungan. Artikel. Mikrobiologi Lingkungan Fakultas Pertanian Universitas Warmadewa. 22 hal.
MorÉ, M.I., J.B. Herrick., M.C. Silva., W.C. Ghiorse., and E.I. Madsen. 1994. Quantitative Cell Lysis of Indigenous Microorganisms and Rapid Extraction of Microbial DNA from Sediment. American Society for Microbiologi 60(5):1572-1580.
Kathiresan, K., B.L. Bingham. 2001. Biology of Mangroves and Mangrove Ecosystems. Avances in Marine Biology. 40(40):81-251.
Napitupulu, H.G., I.F.M. Rumengan., S. Wulur., E.L. Ginting., J.R.T.S.L. Rimper., B.H. Toloh. 2019. Identifikasi moleluler bakteri pada media kultur Brachionus rotundiformis yang dimasukkan Ikan mentah sebagai sumber nutrisi. Jurnal. Ilmiah Platax. Fakultas Perikanan dan Ilmu Kelautan Sam Ratulangi, Manado. 7(1):158-169.
Pambudiono, A., E. Suarsini., M. Amin. 2016. Isolasi DNA Genom Bakteri Potensial Pengkelat Logam Berat Kadmium dari Limbah Cair Penapungan Agar. Seminar. Nasional Pendidikan dan Saintek. 103-107.
Riyanto, B., N. Rahmania., dan F. Idham. 2011. Energi Listrik Dari Sedimen Laut Teluk Jakarta Melalui Teknologi Microbial Fuel Cell. Jurnal. Pengolahan Hasil Perikanan Indonesia. 14(1):32-42.
Restu, M., Mukrimin., dan Gusmiaty. 2012. Optimalisasi Teknik Ekstraksi dan Isolasi DNA Tanaman Suren (Toona SureniMerr.) untuk Analisis Keragaman Genetik berdasarkan Random Amplified Polymorphic DNA (RAPD). Jurnal. Natur Indonesia, 14(2):138-142.
Rangian, L., E.L. Ginting., S. Wulur., E. Kaligis., S. Tilaar., dan R. Tumbol. 2018. Amplifikasi Isolat Bakteri SF1 Simbion spons Facaplysynopsis sp. Dari Perairan Tongkakeina, Sulawesi Utara. Jurnal. Ilmiah Platax. Fakultas Perikanan dan Ilmu Kelautan Sam Ratulangi, Manado. 6(2):77-82.
Sulandri S & M.S.A Zein. 2003. Panduan Praktis Laboratorium DNA. Bidang Zoologi LIPI. Bogor
Sambrook, J., E.F Fristsch., and T. Maniatis. 1989. Moleculer Cloning. 2nd ed. Cold Spring Harbor Press. University of Texas South Western Medical Center, Texas. (516):367-8432.
Servin, J.A., C.W. Herbold., R.G. Skophammer., J.A. Lake. 2008. Evidence Excluding the Root of the Tree of Life from the Actinobacteria. Mol. Biol. 25(1):1-4.
Sauer, P., and M.J. Kang. 1998. Quantitation DNA. Qiagen News. 2: 23-26.
Wilson, K.M., and J.M Walker. 2010. Principles and Techniques of Biochemistry and Molecular Biology. 7th edition. Cambridge University Press. New York. The McGraw-Hill Companies, Inc. New York. 101-149.
Wantania, L.L., S. Wullur., E.L Ginting., D.M.H. Mantiri., S.L. Undap., D.A. Sumilat., G.S. Gerung. 2019. Isolasi dan Amplifikasi gen 16S rRNA isolasi mikroba asosiatif pada alga merah Kappaphycus alvarezii dari perairan Desa Belang, kabupaten Minahasa Tenggara, Sulawesi Utara. Jurnal. Ilmiah Platax. Fakultas Perikanan dan Ilmu Kelautan Sam Ratulangi Manado 7(1):220-226.
Downloads
Published
How to Cite
Issue
Section
License
COPYRIGHT
Authors who publish with this journal agree to the following terms:
Authors hold their copyright and grant this journal the privilege of first publication, with the work simultaneously licensed under a Creative Commons Attribution License that permits others to impart the work with an acknowledgment of the work's origin and initial publication by this journal.
Authors can enter into separate or additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (for example, post it to an institutional repository or publish it in a book), with an acknowledgment of its underlying publication in this journal.
Authors are permitted and encouraged to post their work online (for example, in institutional repositories or on their website) as it can lead to productive exchanges, as well as earlier and greater citation of the published work (See The Effect of Open Access).
