Ice Nucleation Active bacteria in Mount Lawu forest, Indonesia: 2. Identification and characterization of ina gene bacteria isolated from lichens
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Abstract. Arifin TN, Susilowati A, Sutarno. 2018. Ice Nucleation Active bacteria in Mount Lawu forest, Indonesia: 2. Identification and characterization of ina gene bacteria isolated from lichens. Asian J For 2: 39-46. Ice nucleation active (INA) bacteria can catalyze ice formation. Moreover, these bacteria cause frost injury in plants. This study aimed to determine the ina bacteria species of Mount Lawu forest, Java, Indonesia, based on the 16S rRNA gene and the characters of ice nucleation active gene coding of ina bacteria on lichens used ina gene primer. First, the isolates of ina bacteria were grown in NAG, and the DNA could be isolated. After that, genes coding for 16S rRNA and ina were amplified, and the amplification products were sequenced. Furthermore, the sequences were analyzed with BLAST program to know the similarity of bacteria species and ina gene characters. The result showed that the isolated ina bacteria had similarities with Pantoea, Pseudomonas, and Rahnella. The ina gene from N.2.1.B-13 isolate consists of 189 amino acids, dominated by a common amino acid found in other ina genes, like Alanine, Glycine, Tyrosine, Serine, Leucine, and Threonine. N terminal and C terminal are not found because ina gene from N.2.1.B-13 isolate is similar to the ice nucleation protein gene Pseudomonas borealis from bases 2947 bp to 3491 bp or 871 to 1060 amino acids.
2017-01-01
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References
Abe K, Watabe Y, Emori M, Watanabe S, Arai S. 1989. An Ice Nucleation Active gene of Erwinia ananas: Sequence similarity to those of Pseudomonas species and regions required for Ice Nucleation Activity. FEBS Lett 258: 297-300. DOI: 10.1016/0014-5793(89)81678-3.
Andrews JS, Harris RF. 2000. The ecology and biogeography of microorganism on plant surface. Ann Rev Phytopathol 38:145-180. DOI: 10.1146/annurev.phyto.38.1.145.
Christner BC, Morris CE, Foreman CM, Cai R, Sands DC. 2008. Ubiquity of biological ice nucleators in snowfall. Science 319: 1214. DOI: 10.1126/science.1149757.
Edwards AR, Ronald A, Wichman HA, Orser CS. 1994. Unusal pattern of bacterial Ice Nucleation gene evolution. Mol Biol Evol 11: 911-920.
Fatchiyah, Arumaningtyas EL, Widyarti S, Rahayu S. 2011. Biologi Molekuler: Prinsip Dasar Analisis. Erlangga, Jakarta. [Indonesian]
Felsenstein J. 1988. Phylogenies from molecular sequences: Inferences and realibility. Ann Rev Genet 22: 521-556. DOI: 10.1146/annurev.ge.22.120188.002513.
Fu’adah K. 2014. Isolasi dan Estimasi Jumlah Bakteri Ice Nucleation Active (INA) pada Lichenes di Jalur Pendakian Cemara Sewu Gunung Lawu. [Skripsi]. Universitas Sebelas Maret, Surakarta. [Indonesian]
Green RL, Warren GJ. 1985. Physical and functional repetition in a bacterial Ice Nucleation gene. Nature 317: 645-648. DOI: 10.1038/317645a0.
Gurian-Sherman D, Lindow SE. 1993. Bacterial Ice Nucleation: Significance and molecular basis. FASEB J 7: 1338-1343. DOI: 10.1096/fasebj.7.14.8224607.
Hirano SS, Baker LT, Christen DU. 1985. Ice Nucleation of individual leaves in relation to population sizes of Ice Nucleation Active bacteria and frost injury. Plant Physiol 77: 259-265. DOI: 10.1104/pp.77.2.259.
Hirano SS, Upper CD. 2000. Bacteria in the leaf ecosystems with emphasis on Pseudomonas syringae a pathogen, ice nucleus, and epiphyte. Mol Microbiol Biol Rev 64: 624-653. DOI: 10.1128/MMBR.64.3.624-653.2000.
Kieft TL. 1988. Ice Nucleation Activity in lichens. Appl Environ Microbiol 54: 1678-1681. DOI: 10.1128/aem.54.7.1678-1681.1988.
Lee MR, Lee RE, Strong-Gunderson JM, Minges SR. 1995. Isolation of Ice-Nucleating Active bacteria from the freeze-tolerant frog, Rana sylvatica. Cryobiology 32: 358-365. DOI: 10.1006/cryo.1995.1036.
Li JK, Izquierdo MP, Lee TC. 1997. Effects of Ice-Nucleation Active bacteria on the freezing of some model food systems. Intl J Food Sci Technol 32: 41-49. DOI: 10.1046/j.1365-2621.1997.00380.x.
Lindermann J, Constantinidou HA, Barchet WR, Upper CD. 1982. Plants as sources of airborne bacteria, including Ice Nucleation bacteria. Appl Environ Microbiol 44: 1059-1063. DOI: 10.1128/aem.44.5.1059-1063.1982.
Lindow SE, Amy DC, Upper CD. 1978. Distribution of Ice Nucleation Active bacteria on plants in nature. Appl Environ Microbiol 36: 831-838. DOI: 10.1128/aem.36.6.831-838.1978.
Lindow SE, Arny DC, Upper CD. 1982a. Bacterial Ice-Nucleation: A factor in frost injury to plants. Plant Physiol 70: 1084-1089. DOI: 10.1104/pp.70.4.1084.
Lindow SE, Brandl MT. 2003. Microbiology of the phylosphere. Appl Environ Microbiol 69: 1875-1883. DOI: 10.1128/AEM.69.4.1875-1883.2003.
Lindow SE, Hirano SS, Barchet WR, Arny DC, Upper CD. 1982b. Relationship between Ice Nucleation frequency of bacteria and frost injury. Plant Physiology 70: 1090-1093. DOI: 10.1104/pp.70.4.1090.
Lindow SE. 1990. Bacterial Ice nucleation Activity. In: Clement Z, Rudolp K, Sand DC (eds). Methods in Phytobacteriology. Academiai Kiodo, Budapest.
Loper JE, Lindow SE. 1994. A biological sensor for iron available to bacteria in their habitats on plant surfaces. Appl Environ Microbiol 60: 1934-1941. DOI: 10.1128/aem.60.6.1934-1941.1994.
Madigan MT, Martinko JM, Parker J. 1997. Brock, the Biology of Microorganisms. 8th Edition. Prentice Hall, Upper Saddle River, New Jersey.
Maki LR, Galyon EL, Chang-Chien M, Caldwell DR. 1974. Ice Nucleation induced by Pseudomonas syringae. Appl Microbiol 28: 456-459. DOI: 10.1128/am.28.3.456-459.1974.
Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ, Wade WG. 1998. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64: 2333. DOI: 10.1128/aem.64.6.2333-2333.1998.
Morris CE, Georgakopoulos DG, Sands DC. 2004. Ice Nucleation Active bacteria and their potential role in precipitation. J Phys IV France 121: 87-103. DOI: 10.1051/jp4:2004121004.
Nejad P, Ramstedt M, Granhall U, Roos S, Mcivor I. 2006. Biochemical characterization and identification of Ice-Nucleation-Active (INA) willow phatogens by means of BIOLOG® Microplate, ina gene primers and pcr based 16S rRNA gene analyses. J Plant Dis Prot 113: 97-106. DOI: 10.1007/BF03356165.
Obata H, Nakai T, Tanishita J, Tokuyama T. 1989. Identification of an Ice-Nucleating bacterium and its Ice Nucleation properties. J Ferment Bioeng 67: 143-147. DOI: 10.1016/0922-338X(89)90111-6.
Oladoye CO, Olaoye OA, Cornnerton IF. 2013. Isolation and identification of bacteria associated with spoilage of sweet potatoes during postharvest storage. Intl Agric Food Sci 3 (1): 10-15.
Pangastuti A. 2006. Definisi spesies prokaryota berdasarkan urutan basa gen penyandi 16S rRNA dan gen penyandi protein. Biodiversitas 7 (3): 292-296.
Paradis S, Boissinot M, Paquette N, Bélanger SD, Martel EA, Boudreau DK, Picard FJ, Ouellette M, Roy PH, Bergeron MG. 2005. Phylogeny of the Enterobacteriaceae Based on genes encoding elongation factor Tu and F-ATPase ?-subunit. Intl J Syst Evol Microbiol 55: 2013-2025. DOI: 10.1099/ijs.0.63539-0.
Pouleur S, Richard C, Martin JG, Autoun H. 1992. Ice Nucleation Activity in Fusarium acuminatum and Fusarium avenaceum. Appl Environ Microbiol 58: 2960-2964. DOI: 10.1128/aem.58.9.2960-2964.1992.
Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular Cloning. Cold Spring Harbor Press, University of Texas South Western Medical Centre, Texas.
Samsali O. 2008. Medicinal epiphytic plants along trecking line of Cemorosewu, Mount Lawu. [Hon. Thesis]. Faculty of Mathematicsand Natural Sciences, Universitas Sebelas Maret, Surakarta. [Indonesian]
Setyawan AD. 2000. Tumbuhan epifit pada tegakan pohon puspa Schima wallichii (D.C.) Korth. di Gunung Lawu. Biodiversitas 1 (1): 20-25. DOI: 10.13057/biodiv/d010102.
Stephanie, Waturangi DE. 2011. Distribution of Ice Nucleation-Active (INA) bacteria from rain-water and air. Hayati 18: 108-112. DOI: 10.4308/hjb.18.3.108.
Stephen FA, Warren G, Webb M, Eugene WM, David JL. 1990. Basic local alignment search tool. J Mol Biol 215 (3): 403-410. DOI: 10.1016/S0022-2836(05)80360-2.
Wahyudi AT. 1995. Pembekuan inti es oleh bakteri. Hayati 2: 55-59. [Indonesian]
Warren GJ, Corotto L, Wolber P. 1986. Conserved repeats on diverged Ice Nucleation structural genes from two species of Pseudomonas. Nucleic Acids Res 14: 8047-8060. DOI: 10.1093/nar/14.20.8047.
Watanabe K, Sato M. 1998. Detection of variation of the R-domain structure of Ice Nucleation genes in Erwinia herbicola-group bacteria by PCR- RFLP analysis. Curr Microbiol 37 (1): 201-209. 10.1007/s002849900364.
Waturangi DE, Meicy V, Suwanto A. 2008. Isolation and identification of Ice Nucleating Active bacteria from Indonesian edible leafy plant poh-pohan (Pilea glaberina). Microbiol Indones 2 (1): 8-10. DOI: 10.5454/mi.2.1.2.
Waturangi DE, Tjhen A. 2009. Isolation, characterization and genetic diversity of Ice Nucleation Active bacteria on various plant. Hayati 16 (2): 54-58. DOI: 10.4308/hjb.16.2.54.
Wu Z, Qin L, Walker VK. 2009. Characterization and recombinant expression of a divergent Ice Nucleation protein from Pseudomonas borealis. J. Microbiol 155: 1164-1169. DOI: 10.1099/mic.0.025114-0.
Zein, Arifin MS, Prawiradilaga, Malia D. 2013. DNA Barcode Fauna Indonesia. Kencana, Jakarta. [Indonesian]
Zhao J, Orser CS. 1990. Conserved repetition in the Ice Nucleation gene inaX from Xanthomonas campestris pv. translucens. Mol Gen Genet 223:163-166. DOI: 10.1007/BF00315811.