Panduan Pengelolaan Koleksi Mikroorganisme Indonesian Culture Collection InaCC

Authors

Atit Kanti, Muhammad Ilyas, Arif Nurkanto, Tri Ratna Sulistiyani, dan Siti Meliah

Keywords:

Panduan, Pengelolaan, Koleksi, Mikroorganisme, Indonesian, Culture, Collection, InaCC

Synopsis

Penulis :  Atit Kanti, Muhammad Ilyas, Arif Nurkanto, Tri Ratna Sulistiyani, dan Siti Meliah            

Indonesian Culture Collection (lnaCC) merupakan pusat depositori koleksi mikroorganisme Indonesia dibangun untuk memperkuat fungsi otoritas ilmiah LIPI sebagai pusat acuan dalam pengelolaan sumber daya hayati nasional. Melalui buku panduan ini. lnaCC berupaya mendokumentasikan dan membagi informasi yang terkait dengan sistem manajemen mutu koleksi mikroorganisme. mulai dari sistem administrasi hingga pemeliharaan koleksi yang berstandar internasional berdasarkan panduan World Federation for Culture Collections (WFCC) dan siste manajemen ISO 9001:2008.

Buku ini dapat menjadi referensi dasar, baik bagi mahasiswa, peneliti, teknisi laboratorium, maupun staf administrasi yang terkait dengan pengelolaan koleksi mikroorganisme di Indonesia. Diharapkan buku panduan ini dapat memenuhi kebutuhan akan danya metode baku dan sistematis dalam pengelolaan koleksi mikroorganisme yang berstandar internasional untuk tetap mempertahankan kekayaan mikroo ganisme Indonesia.

 

Copyeditor :  Fadly Suhendra dan M. Sidik Layouter : Siti Qomariyah dan Meita Safitr Cover designer  : Dhevi EIR Mahelingga Registrasi : ISBN 978-979-799-982-7 Halaman : xxiii + 191 hlm. Dimensi : A5 (14,8 x 21 cm)

©2018 Lembaga Ilmu Pengetahuan Indonesia (LIPI)

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References

Atschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403–410.

Bappenas. (2003). Strategi dan rencana aksi keanekaragaman hayati Indo- nesia 2003–2020. Dalam Dokumen Indonesian Biodiversity Strategy and Action Plan (IBSAP) 2003–2020. Bappenas, Jakarta.

Day, J. G., Watanabe, M. M., Morris, G. J., Fleck, R. A., & McLellan, M. R. (1997). Long-term viability of preserved eukaryotic algae. J. Appl. Phycol. 9, 121–127.

Davis, L. G., Kuehl, W. M., & Battey, J. F. (1994). Basic methods in molecular biology. 2nd ed. Norwolk: Appleton & Lange.

Emmert, E. A. (2013). Biosafety guidelines for handling microorganisms in the teaching laboratory: Development and rationale. J. Microb. Biol. Educ. 14(1), 78–83.

Erlich, H. A. (1989). PCR technology: Principle and applications for DNA ampli cation. London: Stockton Press.

Flink, J. M, & Knudsen, H. (1983). An introduction to freeze drying. Denmark: Strandberg Bogtryk O set.

Giri, D. (2016). Gram staining: Principle, procedure, interpretation, and animation. Diakses pada 28 Juli 2017 dari http://laboratoryinfo.com/ gram-staining-principle-procedure-interpretation-and-animation/.

Grima, E. M., Perez, J. A. S, Camacho, F. G., Fernandez, F. G. A., Alonso, D. L., & del Castillo, C. I. S. (1994). Preservation of the marine microalgae, Isochrysis galbana: In uence on the fatty acid pro le. Aquaculture 123, 377–385.

Hall, T. A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser 41, 95–98.

Hamada, M., Shibata, C., Nurkanto, A., Ratnakomala, S., Lisdiyanti, P., Tamura, T., & Suzuki, K. I. (2015). Tropicihabitans avus gen. nov., sp. nov., a new member of the family Cellulomonadaceae. Anton van Lee 107, 1299–1306.

Hamada, M., Shibata, C., Nurkanto, A., Ratnakomala, S., Lisdiyanti, P., Tamura, T., & Suzuki, K. I. (2015). Serinibacter tropicus sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove, and emended description of the genus Serinibacter. Int. J. Sys. Evol. Micro- biol. 65, 1151–1154.

Hamada, M., Shibata, C., Tamura, T., Nurkanto, A., Ratnakomala, S., Lisdiyanti, P., Suzuki, K. I. (2016). Cellulosimicrobium marinum sp. nov., an actinobacterium isolated from sea sediment. Arch. Microbiol. 198, 439–444.

Hidayat, I., Meeboon, J., & To-Anun, C. (2007). Anthostomella and Fasci- atispora species (Xylariaceae) from palms including F. ujungkulonensis sp. nov. Mycotaxon. 102, 347–354.

Hiraishi, A., Kamagata, Y., & Nakamura, N. (1995). Polymerase chain reaction ampli cation andrestriction fragment length polymorphism analysis of 16S rRNAgenes from methanogens. J. Ferment. Bioeng. 79, 523–529.

Hubalek, Z. (2003). Protectants used in the cryopreservation of microor- ganisms. Cryobiology 46, 205–229.

Kimura, M. (1980). A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequenc- es. J. Mol. Evol. 16, 111–120.

Kobayashi, R., Kanti, A., & Kawasaki, H. (2016). Pichia chibodasensis sp. nov., a novel Pichia species isolated in Indonesia. Int. J. Syst. Evol. Microbiol. 67, 1024–1027.

Leslie, S. B., Israeli, E., Lighthart, B., Crowe, J. H., & Crowe, L. M. (1995). Trehalose and sucrose protect both membranes and proteins in intact bacteria during drying. Appl. Env. Microbiol. 61, 3592–3597.

Lisdiyanti, P., Kawasaki, H., Seki, T., Yamada, Y., Uchimura, T., & Komagata, K. (2000). Systematic study of the genus Acetobacter with descriptions of Acetobacter indonesiensis sp. nov., Acetobacter tropicalis sp. nov., Acetobacter orleanensis (Henneberg 1906) comb. nov., Acetobacter lovaniensis (Frateur 1950) comb. nov., and Acetobacter estunensis (Carr 1958) comb. nov. J. Gen. Appl. Microbiol. 46, 147–165.

Lisdiyanti, P., Kawasaki, H., Seki, T., Yamada, Y., Uchimura, T., & Komaga- ta, K. (2001). Identi cation of Acetobacter strains isolated from Indo- nesian sources, and proposals of Acetobacter syzygii sp. nov., Acetobacter cibinongensis sp. nov., and Acetobacter orientalis sp. nov. Int. J. Syst. Evol. Microbiol. 47, 119–131.

Lisdiyanti, P., Kawasaki, H., Widyastuti, Y., Saono, S., Seki, T., Yamada, Y., Uchimura, T., & Komagata, K. (2002). Kozakia baliensis gen. nov., sp. nov., a novel acetic acid bacterium in the α-Proteobacteria. Int. J. Syst. Evol. Microbiol. 52, 813–818.

Lisdiyanti, P., Navarro, R. R., Uchimura, T., & Komagata, K. (2006). Re- classi cation of Gluconacetobacter hansenii strains and proposals of Gluconacetobacter saccharivorans sp. nov. and Gluconacetobacter natai- cola sp. nov. Int. J. Syst. Evol. Microbiol. 56, 2101–2111.

Lisdiyanti, P., Otoguro, M., Ratnakomala, S., Lestari, Y., Hastuti, R. D., Triana, E., Katsuhiko, A., & Widyastuti, Y. (2010). Actinokineospora baliensis sp. nov., Actinokineospora cibodasensis sp. nov. and Actinoki- neospora cianjurensis sp. nov., isolated from soil and plant litter. Int. J. Syst. Evol. Microbiol. 60, 2331–2335.

Malik, K. A. (1991). Maintenance of microorganisms by simple methods. Dalam B. E. Kirshop & A. Doyle (eds.), Maintenance of microorganisms and cultured cells: A Manual of laboratory methods. 2nd ed. London: Academic Press.

Meeboon, J., Hidayat, I., Nakashima, C., & To-anum, C. (2007). Cerco- spora habenariicola sp. nov. and some new records of cercosporoid fungi from ailand. Mycotaxon 99, 117–121.

Meeboon, J., Hidayat, I., To-anun, C., & Nakashima, C. (2008). Cerco- sporoid fungi from ailand II. New species of Cercospora and Passa- lora. Sydowia 60, 253–260.

Meeboon, J., Hidayat, I., Takamatsu, S. (2012). Erysiphe javanica sp. nov., a new tropical powdery mildew from Indonesia. Mycotaxon 120, 189–194.

Meeboon, J., Hidayat, I., Takamatsu, S. (2013a). Pseudoidium javanicum, a new species of powdery mildew on Acalypha spp. from Indonesia. Mycoscience 54 : 183–187.

Meeboon, J., Hidayat, I., Takamatsu, S. (2013b). Setoidium castanopsidis, a new species of anamorphic Cystotheca (Ascomycota, Erysiphales) from Indonesia. Mycoscience 54, 274–278.

Mikata, K. (1999). Preservation of yeast culture by L-drying: Viability after 15 years storage at 5o C. IFO Research Communications 19, 71–82.

Mitic, S., Otekhajmer, I., & Damjanovic, V. (1974). Predicting the stabil- ities of freeze-dried suspensions of Lactobacillus acidophilus by the ac- celerated storage test. Cryobiology 11, 116–120.

Miyamoto-Shinohara, Y., Sukenobe, J., Imaizumi, T., & Nakahara, T. (2006). Survival curves for microbial species stored by freeze-drying. Cryobiology 52, 27–32.

Moore, D., & Frazer, L. N. (2002). Essential fungal genetics. New York: Springer-Verlag.

Morgan, C. A., Herman, N., White, P. A., & Vesey, G. (2006). Preservation of microorganisms by drying: A review. J. Microbiol. Meth. 66, 183–193.

Morgulis, A., Coulouris, G., Raytselis, Y., Madden, T. L., Agarwala, R., & Scha er, A. A. (2008). Database indexing for producing MegaBLAST searches. Bioinformatics 24, 1757–1764.

Mori, K., Nurcahyanto, D. A., Kawasaki, H., Lisdiyanti, P., Suzuki, K. I. (2016a). Haloarchaeobius baliensis sp. nov., Isolated from a solar saltern. Int. J. Syst. Evol. Microbiol. 66, 38–43.

Mori, K., Nurcahyanto, D. A., Kawasaki, H., Lisdiyanti, P., Suzuki, K. I. (2016b). Halobium palmae gen. nov., sp. nov., an extremely halophil- ic archaeon isolated from a solar saltern. Int. J. Syst. Evol. Microbiol. 66, 3799–3804.

Myers, E. W., & Miller, W. (1988). Optimal alignments in linear space. Comput. Appl. Biosci. 4, 11–17.

Nagai, T., Tomoika, K., Takeuchi, K., Iida, M., Kawada, M., & Sato, T. (2005). Evaluation of preservation techniques of microorganisms re- sources in the MAAF Genebank. JARQ 39, 19–27.

Nakagiri, A. (2005). Preservation of fungi and freezing methods. Dalam Workshop on preservation of microorganisms. Biotechnology Center- NITE & Research and Development Center for Biotechnology LIPI. Cibinong: 17–18 Oktober 2005.

National Institute of Technology and Evaluation [NITE]. (2008). Methods for recovering the frozen and thawed fungal culture (Cryotube)/ Opening of ampules and revival of L-dried specimens. Diakses pada 28 Juli 2017 dari www.nite.go.jp/data/000003154.pdf.

Nurkanto, A., Lisdiyanti, P., Hamada, M., Ratnakomala, S., Shibata, C., & Tamura, T. (2015a). Actinoplanes tropicalis sp. nov. and Actinoplanes cibodasensis sp. nov., Isolated from leaf litter. Int. J. Syst. Evol. Microbiol. 65, 3824–3829.

Nurkanto, A., Lisdiyanti, P., Hamada, M., Ratnakomala, S., Shibata, C., & Tamura, T. (2015b). Cryptosporangium cibodasense sp. nov., isolated from leaf litter in Indonesia. Int. J. Syst. Evol. Microbiol. 65, 4632–4637.

Nurkanto, A., Lisdiyanti, P., Hamada, M., Ratnakomala, S., Shibata, C., & Tamura, T. (2016). Actinoplanes bogoriensis sp. nov., a novel Actino- mycete isolated from leaf litter. J. Antibiotics 69, 26–30.

O`Donnell, K. (1993). Fusarium and its near relatives. Dalam D. R. Reynolds & J.W. Taylor (eds), e fungal holomorph: Mitotic, meiotic, and pleomorphic speci cation in fungal systematics. Wallingford: CAB International.

OECD. (2007). OECD best practice guidelines for biological resource centres. Diakses pada 28 Juli 2017 dari https://www.oecd.org/sti/ biotech/38777417.pdf.

Otero, M. C., Espeche, M. C., & Nader-Macias, M. E. (2007). Optimiza- tion of the freeze-drying media and survival throughout storage of freeze-dried Lactobacillus gasseri and Lactobacillus delbrueckii subsp. Delbrueckii for veterinarian probiotic applications. Process Biochemistry 42, 1406–1411.

Otoguro, M., Ratnakomala, S., Lestari, Y., Hastuti, R. D., Triana, E., Widyastuti, Y., & Ando, K. (2009). Streptomyces baliensis sp. nov., isolated from Balinese soil. Int. J. Syst. Evol. Microbiol. 59, 2158–2161.

Otoguro, M., Yamamura, H., Tamura, T., Irzaldi, R., Ratnakomala, S., Ridwan, R., ... & Ando, K. (2011). Actinophytocola timorensis sp. nov. and Actinophytocola corallina sp. nov., isolated from soil. Int J. Syst. Evol. Microbiol. 61, 834–838.

Pitcher, D. G., Saunders, A., & Owe, R. J. (1989). Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett. Appl. Mi- crobiol. 8, 151–156.

Prakash, O., Nimonkar, Y., & Shouche, Y. S. (2012). Practice and prospect of microbial preservation. FEMS Microbiol. Lett 339, 1–9.

Ryan, M. J., Je ries, P., Bridge, P. D., & Smith, D. (2001). Developing cryopreservation protocols to secure fungal gene function. Cryo-Letters 22, 115–124.

Sakane, T., & Kuroshima, K. (1997). Viabilities of dried cultures of various bacteria after preservation for over 20 years and their prediction by the accelerated strorage test. Microbiol. Cult. Coll. 1–7.

Sato, H. (2007). Workshop on molecular approaches for the identi cation of microorganisms. NITE & Research Center for Biotechnology LIPI, Cibinong: 11–13 July 2007.

Siahaan, S. A., Hidayat, I., Kramadibrata, K., Meeboon, J., & Takamatsu, S. (2015). Phyllactinia poinsettiae sp. nov.: A new species of powdery mildew on poinsettia from Indonesia. Mycoscience 56, 580–583.

Siahaan, S. A., Kramadibrata, K., Hidayat, I., Meeboon, J., Takamatsu, S. (2016). Erysiphe baliensis and E. sidae, two new species of anamorphic Erysiphe (powdery mildew) from Indonesia. Mycoscience 57, 35–41.

Sjamsuridzal, W., Oetari, A., Nakashima, C., Kanti, A., Saraswati, R., Widyastuti, Y., & Ando, K. (2013). New species of the genus Met- schnikowia isolated from owers in Indonesia, Metschnikowia ciboda- sensis sp. nov. J. Microbiol. Biotechnol. 23, 905–912.

Sjamsuridzal W., Lisdiyanti, P., Kusmiyati, Rachmatmulya, A., Pratiwi, E., ..., Sujaya, I. N. (2008). FORKOMIKRO catalogue of cultures of Indonesian microorganisms. 1st Ed. Jakarta: Yayasan Obor Indonesia.

Smith, D. (1991). Maintenance of lamentous fungi. Dalam B. E. Kirshop & A. Doyle (eds.), Maintenance of microorganisms and cultured cells: A manual of laboratory methods. 2nd ed. London: Academic Press.

Smith, D. (1993). Tolerance to freezing and thawing. D. H. Jennings (ed.), Stress tolerance in fungi (145–171). New York: Marcel Dekker.

Smith, D. (2003). Culture collections over the world. Int. Microbiol. 6, 95–100.

Smith, D., & Ryan, M. (2012). Review article: Implementing best practices and validation of cryopreservation techniques for microorganisms. e Scienti c World Journal. 9. http://dx.doi.org/10.1100/2012/805659.

Sukara, E. & Lisdiyanti, P. (ed.). (2016). Exploring Indonesian microbial genetic resources for industrial application. Jakarta: LIPI Press.

Sukarno, N., Kurihara, Y., Park, J. Y., Inaba, S., Ando, K., Harayama, S., ... & Yuniarti, E. (2009). Lecanicillium and Verticillium species from Indonesia and Japan including three new species. Mycoscience 50, 369–379.

omson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., & Higgins, D. G. (1997). e Clustal X windows interface: Flexible strategies for multiple sequences allignment aided by quality analysis tools. Nucl. Ac. Res. 25, 4876–4882.

Tommerup, I. C., & Kirby, D. K. (1979). Preservation of spores vesicu- lar-arbuscular endophytes by L-drying. Appl. Environ. Microbiol. 37, 831–835.

Tsuru, S. (1973). Preservation of marine and fresh water algae by means of freezing and freeze-drying. Cryobiology 10, 445–452.

Yamamura, H., Lisdiyanti, P., Ridwan, R., Ratnakomala, S., Sarawati, R., Lestari, Y., ... & Ando, K. (2010). Dietzia timorensis sp. nov., isolated from soil. Int. J. Syst. Evol. Microbiol. 60, 451–454.

Viljoen, G. J., Nei, L. H., & Crowther, J. R. (2005). Molecular diagnostic PCR handbook. Springer: e Netherlands.

Watanabe, M. M., Kawachi, M., Hiroki, M., & Kasai, F. (2000). NIES Collection list of strains. 6th Ed. Japan: NIES.

Wessman, P., Hakansson, S., Leifer, K., & Rubino, S. (2013). Formulations for freeze-drying of bacteria and their in uence on cell survival. Journal of Visualized Experiments 78, 1–5.

WFCC Executive Board. (2010). World federation for culture collections (WFCC) guidelines for the establishment and operation of collections of cultures of microorganisms, 3rd ed. 19 pp. Diakses pada 7 Maret 2018 dari http://www.wfcc.info/pdf/Guidelines_e.pdf.

White, T. J., Bruns, T. D., Lee, S. B., Taylor, J. W. (1990). Ampli cation and direct sequencing of fungal RNA genes for phylogenetics. Dalam M. A. Innis, D. H. Gelfand, J. J. Sninsky, & T. J. White (eds), PCR protocols. San Diego: Academic.

WIPO. (2018). Guide to the deposit of microorganisms under the Budapest Treaty. Diakses pada 7 Maret 2018 dari http://www.wipo.int/treaties/ en/registration/budapest/guide/.

Zayed, G, & Roos, Y. H. (2004). In uence of trehalose and moisture content on survival of Lactobacillus salivarius subjected to freeze-drying and storage. Process Biochemistry 39, 1081–1086.

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Published

September 6, 2018