Characterization and identification of three thermophilic Bacillus strain isolated from Domas Crater, Mt. Tangkuban Perahu, Indonesia
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Abstract. Safitri R, Kusumawardhani PD, Annisa, Partasasmita R, Asharina S, Maskoen AM. 2020. Characterization and identification of three thermophilic Bacillus strains isolated from Domas Crater, Mt. Tangkuban Perahu, Indonesia. Biodiversitas 21: 3444-3453. A community of thermophiles within the hot spring of Domas Crater, Mount Tangkuban West Java, has been cultivated and identified based on the 16S ribosomal RNA gene sequence. The hot spring has a temperature of 45°C-76 °C, pH 1-2, the isolate has been cultivated in Thermus medium at a temperature of 70 and pH 6. The three isolated strains were L61A, TS61A, and D41A identified based on the 16S ribosomal RNA gene sequence refer to the GenBank database and all of them belong to the Phylum Firmicutes, which are clustered within the taxonomic groups of Bacillus, the Bacillus, and Geobacillus genera. Nucleotide sequences were compared for homology with BLASTN search at the NCBI Web-site revealed that strains (L61A) had 99.93% similarity with Geobacillus uzenensis. TS61A strain has a 99.24% similarity with Bacillus wiedmannii. Whereas D41A has 99.79% similarity with Bacillus paramycoides. The characterization also includes the phenotypic and biochemical of strains. The bacillus genera were known as a source of thermostable enzymes, plant growth-promoting, probiotics, decomposers of various polysaccharide materials, and bioremediation.
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References
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Zhou JF, Pei-Ke G, Xiao-Hui D, Xiao-Yu C, Hui-Mei T, Jun-Jie X, Guo-Qiang L, Ting M. 2016. Heavy Hydrocarbon Degradation of Crude Oil by A Novel Thermophilic Geobacillus stearothermophilus strain A-2. International Biodeterioration and Biodegradation. Elsevier Ltd, 126: 224–230
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25: 3389–402.
Aliyu H, Lebre PH, Blom J, Cowan DA, De Maayer P. 2016. Phylogenomic re-assessment of the thermophilic genus Geobacillus. Syst Appl Microbiol. 39: 527-533.
BPPT. 2019. Stages of microbial identification work based on the Gen 16s rRNA area using PCR and DNA sequence analysis, Tangerang: Agency for Assessment and Application of Technology. [Indonesian]
Filippidou S, Thomas J, Tina W, Wafa MK, Ilona P, Andrej AD, Veronica M, Reto L, Jorge ES, Shannon LJ, Patrick SGC, Cristina D, Pilar J. 2019. Adaptive strategies in a poly-extreme environment: differentiation of vegetative cells in Serratia ureilytica and resistance to extreme conditions. Frontiers Microbiol 10 (102): 1-13
Fujiwara S. 2002. Extremophiles: developments of their special functions and potential resources. J Biosci Bioeng. 94: 518-525.
Habib N, Inam UK, Firasat H, Zhou E, Xiao M, Dong L, Zhi XY, Li WJ. 2017. Meiothermus luteus sp. nov., a slightly thermophilic bacterium isolated from a hot spring Int J Syst Evol Microbiol 67: 2910–2914.
Handayani S, Iman S, Freisleben HJ, Harald H, Andi, Fery A, Cenmi M, Zessinda L, Rosari S, Seruni KUF, Septelia IW, Michael T. 2012. Archaeal Life on Tangkuban Perahu-Sampling and Culture Growth in Indonesian Laboratories. HAYATI J Biosci, 19 (3): 150-154.
Hartanti. 2010. Isolation and Selection of Thermophilic Cellulolytic Bacteria from Gunung Pancar Hot Crater, Bogor. [Skription], Institut Pertanian Bogor. [Indonesian]
Kanza A, 2016. Characterization of Bacillus and LactoBacillus Probiotics Encapsulated in Several Carriers and Their Effects on Vannamei Shrimp Performance. [Skription]. Universitas Padjadjaran [Indonesian]
Komalasari K. 2009. Effect of Comparison of Blood Volume and Buffer Lysis and Speed of Centrifugation on the Quality of DNA Products in Holstein Frequency Cattle (FH). [Skription]. Institut Pertanian Bogor. Bogor [Indonesian]
Kumar S, Glen S, Michael L, Christina K, Koichiro T. 2018 Mega X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol, 35 (6): 1547–1549
Kusnadi, Peristiwati, Syulasmi, Ammi, Rochnintaniawati D. 2003. Common text book microbiology. Bandung: JICA – IMSTEP FMIPA Universitas Pendidikan Indonesia. Bandung.
Lane, D. J. 1991. 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics 115–175.
Mahmudah R, Maswati B, Sappawali. 2016. Identification of thermophilic bacterial isolates from Lejja hot springs, Kabupaten Soppeng. Al-Kimia, 4(1): 31-42.
Malik A, Iman S, Andi Y, Seruni KUF, Septelia IW, Harald H, Zessinda L, Rosari S, Freisleben HJ. 2014. Characterization of tthermoplasma species cultured from sampling on Tangkuban Perahu, Indonesia. Microbiol Indonesia, 8 (1): 16-23.
Nazina T, Tourova TP, Poltaraus AB, Novikova EV, Grigoryan AA, Ivanova AE, Lysenko AM, Petrunyaka VV, Osipov GA, Belyaev SS, Ivanov MV. 2001. Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of B. stearothermophilus, B. thermocatenulatus, Inter J Syst Evol Microbiol 51(2): 433–446.
Nealon K, Iain DN, Mark KK. 1996. Characterization of the DNA polymerase requirement of human base excision repair. Nucleic Acids Res 24 (19): 3763–3770
Niederberger T. 2016. Extremophile. https://www.britannica.com/science/extre mophile (Accessed on March 14, 2019 at 19:17 WIB)
Ratnawati L, Salim T, Agustina W, Sriharti. 2015. Isolation of thermophilic microbes resistant to ethanol from Ciater Hot Springs, Subang-West Java. Procedia Chemistry, 16: 548-554.
Sambrook J, Russell DW. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold spring harbor laboratory press, cold spring harbor, NY.
Tominaga Y, Ohshiro T, Suzuki H. 2016. Conjugative plasmid transfer from Escherichia coli is a versatile approach for genetic transformation of thermophilic Bacillus and Geobacillus species. Extremophiles. Springer Japan 20(3): 375–381.
Zhou JF, Pei-Ke G, Xiao-Hui D, Xiao-Yu C, Hui-Mei T, Jun-Jie X, Guo-Qiang L, Ting M. 2016. Heavy Hydrocarbon Degradation of Crude Oil by A Novel Thermophilic Geobacillus stearothermophilus strain A-2. International Biodeterioration and Biodegradation. Elsevier Ltd, 126: 224–230
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