Chitinolytic Assay and Identification of Bacteria Isolated from Shrimp Waste Based on 16S rDNA Sequences

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Chitinolytic Assay and Identification of Bacteria Isolated from Shrimp Waste Based on 16S rDNA Sequences ()

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DOI: 10.4236/aim.2015.57056 3,909 Downloads 5,086 Views Citations

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Imanda N. Setia, Suharjono

Affiliation(s)

Biology Department, Faculty of Mathematics and Natural Sciences, Brawijaya University, Malang, Indonesia.

ABSTRACT

Shrimp waste contains 20% - 60% chitin and possible to be source of chitinolytic bacteria. Chitinolytic bacteria are capable of hydrolyzing of chitin progressively to produce N-acetylglucosamine monomer which can be used to overcome the shrimp waste. The objectives of this research were to identify species of bacteria with high activity of chitin degradation in shrimp waste and to analyze their potency as chitin degradation agent. The research consists of screening of chitinolytic bacteria based on chitinolytic index, activity assay of chitinase using colorimetric method, and molecular identification of bacteria based on 16S rDNA sequences. Two of eighteen isolates of chitinolytic bacteria (PBK 2 and SA 1.2 isolates) showed the highest chitinolytic index, which were 2.069 and 2.084, whereas chitinase activity was 0.213 and 0.219 U/ml respectively. Based on 16S rDNA sequences, isolate of PBK 2 was identified as Acinetobacter johnsonii 3-1, whereas SA 1.2 was identified as Bacillus amyloliquefaciens GR53 with 99.78% similarity.

KEYWORDS

Chitinolytic Bacteria, Chitin, Shrimp, Shrimp Waste

Cite this paper

Setia, I. and , S. (2015) Chitinolytic Assay and Identification of Bacteria Isolated from Shrimp Waste Based on 16S rDNA Sequences. Advances in Microbiology, 5, 541-548. doi: 10.4236/aim.2015.57056.

Conflicts of Interest

The authors declare no conflicts of interest.

References

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[2] Sachindra, N.M., Bhaskar, N. and Mahendrakar, N.S. (2005) Carotenoids in Different Body Components of Indian Shrimps. Journal of Science Food and Agriculture, 85, 167-172. http://dx.doi.org/10.1002/jsfa.1977

[3] Haliza, W. and dan Suhartono, M.T. (2012) Karakteristik Kitinase dari Mikroba. Balai Teknologi Pascapanen Pertanian, 8.

[4] Knorr, D. (1984) Use of Chitinous Polymers in Food—A Challenge for Food Research and Development. Food Technology, 38, 85-97.

[5] Saima, M.K. and Roohi, I.Z. (2013) Isolation of Novel Chitinolytic Bacteria and Production Optimization of Extracellular Chitinase. Journal of Genetic Engineering and Biotechnology, 11, 39-46. http://dx.doi.org/10.1016/j.jgeb.2013.03.001

[6] Shanmugaiah, V., Mathivanan, N., Balasubramanian, N. and Manoharan, P.T. (2008) Optimization of Cultural Conditions for Production of Chitinase by Bacillus laterosporous MML2270 Isolated from Rice Rhizosphere Soil. African Journal of Biotechnology, 7, 2562-2568.

[7] Sato, K., Kato, Y., Fukamachi, A., Nogawa, M., Taguchi, G. and Shimosaka, M. (2010) Construction and Analysis of a Bacterial Community Exhibiting Strong Chitinolytic Activity. Bioscience, Biotechnology, and Biochemistry, 74, 636-640. http://dx.doi.org/10.1271/bbb.90856

[8] Frandberg, E. (1997) Antifungal Compounds of Chitinolytic Bacteria from Grain Ecosystems. Doctor’s Dissertation.

[9] Al-Ahmadi, K.J., Yazdi, M.T., Najafi, M.F., Shahverdi, A.R., Faramarzi, M.A., Zarrini, G. and Behravan, J. (2008) Optimization of Medium and Cultivation Conditions for Chitinase Production by the Newly Isolated: Aeromonas sp. Biotechnology, 7, 266-272. http://dx.doi.org/10.3923/biotech.2008.266.272

[10] Jabeen, F. and Qazi, J.I. (2014) Isolation of Chitinase Yielding Bacillus cereus JF68 from Soil Employing an Edible Crab Shell Chitin. Journal of Science and Industrial Research, 73, 771-776.

[11] Faramarzi, M.A., Fazeli, M., Yazdi, M.T., Adrangi, S., Al-Ahmadi, K.J., Tasharrofi, N. and Mohseni, F.A. (2009) Optimization of Cultural Condition for Production Chitinase by Soil Isolate of Massilia timonae. Biotechnology, 8, 93-99. http://dx.doi.org/10.3923/biotech.2009.93.99

[12] Jiang, L. (2009) Comparison of Disk Diffusion, Agar Dilution, and Broth Microdilution for Antimicrobial Susceptibility Testing of Five Chitosans. Master’s Thesis, Fujian Agricultural and Forestry University, Fuzhou.

[13] Monreal, J. and Reese, E.T. (1969) The Chitinase of Serratia marcescens. Canadian Journal of Microbiology, 15, 689-696. http://dx.doi.org/10.1139/m69-122

[14] Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A. and Struhl, K. (1997) Current Protocols in Molecular Biology. John Wiley & Sons, Inc., Hoboken.

[15] Suharjono, Sembiring, L., Subagja, Y. and Widayati, W.E. (2010) Sistematik Filogenetik Pseudomonas Strain Indigenous Pendegradasi Liniar Alkilbenzen Sulfonat. Biota, 15, 41-50.

[16] iNtRON Biotechnology (2011) 2x PCR Master mix Solution (i-Taq). http://eng.intronbio.com/

[17] Mulhardt, C. (2010) Molecular Biology and Genomics. Academic Press, Waltham.

[18] Zarei, M., Aminzadeh, S., Ghoroghi, A., Motalebi, A.A., Alikhajeh, J. and Daliri, M. (2012) Chitinase Isolated from Water and Soil Bacteria in Shrimp Farming Ponds. Iranian Journal of Fisheries Sciences, 11, 911-925.

[19] Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. (2011) MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution, 10, 2731-2739. http://dx.doi.org/10.1093/molbev/msr121

[20] Metcalf, L., Eddy, H.P., Tchobanoglous, G., Burton, F.L. and Stensel, H.D. (2003) Wastewater Engineering. 4th Edition, McGraw Hill International Editions, New York.

[21] Suryanto, D., Munir, E. and Yurnaliza (2005) Eksplorasi Bakteri Kitinolitik: Keragaman Genetik Gen Penyandi Kitinase pada Berbagai Jenis Bakteri dan Pemanfaatannya. USU Repository.

[22] Bailly, J.E. and Ollis, D.F. (1986) Biochemical Engineering Fundamentals. McGraw-Hill, New York.

[23] Keyhani, N.O. and Roseman, S. (1999) Physiological Aspect of Chitin Catabolism in Marine Bacteria. Biochimica et Biophysica Acta, 1473, 108-122. http://dx.doi.org/10.1016/S0304-4165(99)00172-5

[24] Lamine, B.M., Lamine, B.M. and Bouziane, A. (2012) Optimization of the Chitinase Production by Serratia Marcescens DSM 30121Tand Biological Control of Locusts. Journal of Biotechnology and Biomaterials, 2, 13-138. http://dx.doi.org/10.4172/2155-952X.1000133

[25] Saleem, F., Younas, A., Bashir, R., Naz, S., Munir, N. and Shakoori, A.R. (2014) Molecular Cloning and Characterization of Exochitinase A Gene of Indigenous Bacillus thuringiensis Isolates. Pakistan Journal of Zoology, 46, 1491-1501.

[26] Saadoun, I., Al-Omari, R., Jadarat, Z. and Ababneh, Q. (2009) Influence of Culture Conditions of Streptomyces sp. (Strain S242) on Chitinase Production. Polish Journal of Microbiology, 58, 339-345.

[27] Nocker, A., Lepo, J.E. and Synder, R.A. (2004) Influence of an Oyster Reef on Development of the Microbial Heterotrophic Community of an Estuarine Biofilm. Applied and Environtal Microbiology, 70, 6834-6845. http://dx.doi.org/10.1128/AEM.70.11.6834-6845.2004

[28] Drancourt, M., Bollet, C., Carlioz, A., Martelin, R., Gayral, J.P. and Raoult, D. (2000) 16S Ribosomal DNA Sequence Analysis of Large Collection of Enviromental and Clinical Unidentifiable Bacterial Isolate. Journal of Clinical Microbiology, 3, 3623-3630.

[29] Bitton, G. (2005) Wastewater Microbiology. 3rd Edition, John Wiley & Sons, Inc., Canada. http://dx.doi.org/10.1002/0471717967

[30] Wiedmann-Al-Ahmad, M., Tichy, H.V. and Schon, G. (1994) Characterization of Acinetobacter Type Strains and Isolates Obtained from Wastewater Treatment Plants by PCR Fingerprinting. Applied and Environtal Microbiology, 60, 4066-4071.

[31] Ohtake, H., Takahashi, K., Tsuzuki, Y. and Toda, K. (1985) Uptake and Release of Phosphate by a Pure Culture of Acinetobacter calcoaceticus. Water Research, 19, 1587-1594. http://dx.doi.org/10.1016/0043-1354(85)90404-X

[32] Sabry, S.A. (1992) Microbial Degradation of Shrimp-Shell Waste. Journal of Basic Microbiology, 32, 107-111. http://dx.doi.org/10.1002/jobm.3620320207

[33] Wang, S., Shih, I., Liang, T. and Wang, C. (2002) Purification and Characterization of Two Antifungal Chitinases Extracellularly Produced by Bacillus amyloliquefaciens V656 in a Shrimp and Crab Shell Powder Medium. Journal of Agricultural and Food Chemistry, 50, 2241-2248. http://dx.doi.org/10.1021/jf010885d

[34] Askarian, F., Zhou, Z., Olsen, R.E., Sperstad, S. and Ringo, E. (2012) Culturable Autochthonous Gut Bacteria in Atlantic Salmon (Salmo salar L.) Fed Diets with or without Chitin. Characterisation by 16S rRNA Gene Sequencing, Ability to Produce Enzymes and in Vitro Growth Inhibition of Four Fish Pathogens. Aquaculture, 326, 1-8. http://dx.doi.org/10.1016/j.aquaculture.2011.10.016

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[1]	Irianto, H.E. (2011) Strategi Pengembangan Produk Indikasi Geografis berbasis Komoditas Perikanan Budaya. Prosiding Forum Inovasi Teknik Akuakultur.

[2]	Sachindra, N.M., Bhaskar, N. and Mahendrakar, N.S. (2005) Carotenoids in Different Body Components of Indian Shrimps. Journal of Science Food and Agriculture, 85, 167-172. http://dx.doi.org/10.1002/jsfa.1977

[3]	Haliza, W. and dan Suhartono, M.T. (2012) Karakteristik Kitinase dari Mikroba. Balai Teknologi Pascapanen Pertanian, 8.

[4]	Knorr, D. (1984) Use of Chitinous Polymers in Food—A Challenge for Food Research and Development. Food Technology, 38, 85-97.

[5]	Saima, M.K. and Roohi, I.Z. (2013) Isolation of Novel Chitinolytic Bacteria and Production Optimization of Extracellular Chitinase. Journal of Genetic Engineering and Biotechnology, 11, 39-46. http://dx.doi.org/10.1016/j.jgeb.2013.03.001

[6]	Shanmugaiah, V., Mathivanan, N., Balasubramanian, N. and Manoharan, P.T. (2008) Optimization of Cultural Conditions for Production of Chitinase by Bacillus laterosporous MML2270 Isolated from Rice Rhizosphere Soil. African Journal of Biotechnology, 7, 2562-2568.

[7]	Sato, K., Kato, Y., Fukamachi, A., Nogawa, M., Taguchi, G. and Shimosaka, M. (2010) Construction and Analysis of a Bacterial Community Exhibiting Strong Chitinolytic Activity. Bioscience, Biotechnology, and Biochemistry, 74, 636-640. http://dx.doi.org/10.1271/bbb.90856

[8]	Frandberg, E. (1997) Antifungal Compounds of Chitinolytic Bacteria from Grain Ecosystems. Doctor’s Dissertation.

[9]	Al-Ahmadi, K.J., Yazdi, M.T., Najafi, M.F., Shahverdi, A.R., Faramarzi, M.A., Zarrini, G. and Behravan, J. (2008) Optimization of Medium and Cultivation Conditions for Chitinase Production by the Newly Isolated: Aeromonas sp. Biotechnology, 7, 266-272. http://dx.doi.org/10.3923/biotech.2008.266.272

[10]	Jabeen, F. and Qazi, J.I. (2014) Isolation of Chitinase Yielding Bacillus cereus JF68 from Soil Employing an Edible Crab Shell Chitin. Journal of Science and Industrial Research, 73, 771-776.

[11]	Faramarzi, M.A., Fazeli, M., Yazdi, M.T., Adrangi, S., Al-Ahmadi, K.J., Tasharrofi, N. and Mohseni, F.A. (2009) Optimization of Cultural Condition for Production Chitinase by Soil Isolate of Massilia timonae. Biotechnology, 8, 93-99. http://dx.doi.org/10.3923/biotech.2009.93.99

[12]	Jiang, L. (2009) Comparison of Disk Diffusion, Agar Dilution, and Broth Microdilution for Antimicrobial Susceptibility Testing of Five Chitosans. Master’s Thesis, Fujian Agricultural and Forestry University, Fuzhou.

[13]	Monreal, J. and Reese, E.T. (1969) The Chitinase of Serratia marcescens. Canadian Journal of Microbiology, 15, 689-696. http://dx.doi.org/10.1139/m69-122

[14]	Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A. and Struhl, K. (1997) Current Protocols in Molecular Biology. John Wiley & Sons, Inc., Hoboken.

[15]	Suharjono, Sembiring, L., Subagja, Y. and Widayati, W.E. (2010) Sistematik Filogenetik Pseudomonas Strain Indigenous Pendegradasi Liniar Alkilbenzen Sulfonat. Biota, 15, 41-50.

[16]	iNtRON Biotechnology (2011) 2x PCR Master mix Solution (i-Taq). http://eng.intronbio.com/

[17]	Mulhardt, C. (2010) Molecular Biology and Genomics. Academic Press, Waltham.

[18]	Zarei, M., Aminzadeh, S., Ghoroghi, A., Motalebi, A.A., Alikhajeh, J. and Daliri, M. (2012) Chitinase Isolated from Water and Soil Bacteria in Shrimp Farming Ponds. Iranian Journal of Fisheries Sciences, 11, 911-925.

[19]	Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. (2011) MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution, 10, 2731-2739. http://dx.doi.org/10.1093/molbev/msr121

[20]	Metcalf, L., Eddy, H.P., Tchobanoglous, G., Burton, F.L. and Stensel, H.D. (2003) Wastewater Engineering. 4th Edition, McGraw Hill International Editions, New York.

[21]	Suryanto, D., Munir, E. and Yurnaliza (2005) Eksplorasi Bakteri Kitinolitik: Keragaman Genetik Gen Penyandi Kitinase pada Berbagai Jenis Bakteri dan Pemanfaatannya. USU Repository.

[22]	Bailly, J.E. and Ollis, D.F. (1986) Biochemical Engineering Fundamentals. McGraw-Hill, New York.

[23]	Keyhani, N.O. and Roseman, S. (1999) Physiological Aspect of Chitin Catabolism in Marine Bacteria. Biochimica et Biophysica Acta, 1473, 108-122. http://dx.doi.org/10.1016/S0304-4165(99)00172-5

[24]	Lamine, B.M., Lamine, B.M. and Bouziane, A. (2012) Optimization of the Chitinase Production by Serratia Marcescens DSM 30121Tand Biological Control of Locusts. Journal of Biotechnology and Biomaterials, 2, 13-138. http://dx.doi.org/10.4172/2155-952X.1000133

[25]	Saleem, F., Younas, A., Bashir, R., Naz, S., Munir, N. and Shakoori, A.R. (2014) Molecular Cloning and Characterization of Exochitinase A Gene of Indigenous Bacillus thuringiensis Isolates. Pakistan Journal of Zoology, 46, 1491-1501.

[26]	Saadoun, I., Al-Omari, R., Jadarat, Z. and Ababneh, Q. (2009) Influence of Culture Conditions of Streptomyces sp. (Strain S242) on Chitinase Production. Polish Journal of Microbiology, 58, 339-345.

[27]	Nocker, A., Lepo, J.E. and Synder, R.A. (2004) Influence of an Oyster Reef on Development of the Microbial Heterotrophic Community of an Estuarine Biofilm. Applied and Environtal Microbiology, 70, 6834-6845. http://dx.doi.org/10.1128/AEM.70.11.6834-6845.2004

[28]	Drancourt, M., Bollet, C., Carlioz, A., Martelin, R., Gayral, J.P. and Raoult, D. (2000) 16S Ribosomal DNA Sequence Analysis of Large Collection of Enviromental and Clinical Unidentifiable Bacterial Isolate. Journal of Clinical Microbiology, 3, 3623-3630.

[29]	Bitton, G. (2005) Wastewater Microbiology. 3rd Edition, John Wiley & Sons, Inc., Canada. http://dx.doi.org/10.1002/0471717967

[30]	Wiedmann-Al-Ahmad, M., Tichy, H.V. and Schon, G. (1994) Characterization of Acinetobacter Type Strains and Isolates Obtained from Wastewater Treatment Plants by PCR Fingerprinting. Applied and Environtal Microbiology, 60, 4066-4071.

[31]	Ohtake, H., Takahashi, K., Tsuzuki, Y. and Toda, K. (1985) Uptake and Release of Phosphate by a Pure Culture of Acinetobacter calcoaceticus. Water Research, 19, 1587-1594. http://dx.doi.org/10.1016/0043-1354(85)90404-X

[32]	Sabry, S.A. (1992) Microbial Degradation of Shrimp-Shell Waste. Journal of Basic Microbiology, 32, 107-111. http://dx.doi.org/10.1002/jobm.3620320207

[33]	Wang, S., Shih, I., Liang, T. and Wang, C. (2002) Purification and Characterization of Two Antifungal Chitinases Extracellularly Produced by Bacillus amyloliquefaciens V656 in a Shrimp and Crab Shell Powder Medium. Journal of Agricultural and Food Chemistry, 50, 2241-2248. http://dx.doi.org/10.1021/jf010885d

[34]	Askarian, F., Zhou, Z., Olsen, R.E., Sperstad, S. and Ringo, E. (2012) Culturable Autochthonous Gut Bacteria in Atlantic Salmon (Salmo salar L.) Fed Diets with or without Chitin. Characterisation by 16S rRNA Gene Sequencing, Ability to Produce Enzymes and in Vitro Growth Inhibition of Four Fish Pathogens. Aquaculture, 326, 1-8. http://dx.doi.org/10.1016/j.aquaculture.2011.10.016