Mineralogical Observation of Calcium Carbonate Precipitation Properties by Bacterial and Plant Ureases

doi:10.12972/ksmer.2016.53.5.398

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2016 Vol.53, Issue 5 Preview Page Next Page

Research Paper (Special Issue)

Mineralogical Observation of Calcium Carbonate Precipitation Properties by Bacterial and Plant Ureases 미생물과 식물에 의해 생성된 탄산칼슘의 광물학적 특성 관찰: 남인현·전철민·김재곤
In-Hyun Nam, Chul-Min Chon and Jae-Gon Kim

31 October 2016. pp. 398-406

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Abstract

Calcium carbonate(CaCO3) can be precipitated by urea hydrolysis by bacterial and plant ureases.Sporosarcina sp. KM-01, KM-07, and KM-12 strains were shown to be able to precipitate CaCO3 using urea amended with calcium chloride. Also, an extract of the plant, Canavalia ensiformis, was shown to produce CaCO3 as an effective biomaterial. The mineralogical formation of CaCO3 using bacteria was compared to that of plant urease in this study. The results revealed that urease in the Canavalia ensiformis extracts precipitated mainly calcite, however, the ureases in the bacterial strains produced vaterite in liquid-state cultures. Considering acidic habitats of the isolated bacterial strains,these results could be attributed to their evolutionary capabilities or the addition of specific amino acid. This makes the general application of biomineralization process based on stimulation of urea hydrolysis and potentially useful for a variety of soil bioengineering and environmental bioremediation.

Keywords

Calcium carbonate

Urease

Bacteria and plant

Calcite

Vaterite

본 연구에서는 미생물과 식물이 가지는 요소분해효소 작용에 의해 침전되는 탄산칼슘(CaCO3)의 광물학적 특성을 관찰하고 비교하였다. 중금속으로 오염된 산성 토양에서 분리한 Sporosarcina sp. KM-01, KM-07, KM-12 등의 박테리아 균주 및 Canavalia ensiformis 식물 추출액에 의해 침전되는 CaCO3를 X-선회절분석(XRD) 및 전자현미경(SEM) 분석을 통해 확인하였다. 박테리아 균주로부터 침전되는 CaCO3은 바테라이트가 주 광물상이었으나, 식물에 의해 생성되는 CaCO3의 주 광물상은 방해석으로 확인되었고, 일부 바테라이트가 검출되었다. 박테리아의 경우 진화적 요인에 의해 낮은 pH에 잘 적응된 균주의 요소분해효소 특이적 활성의 차이로 바테라이트가 생성되고, 아직 명확하게 규명되지 않은 바테라이트 결정 구조와 특정 아미노산의 영향으로 해당 구조가 유지되었을 가능성을 예상할 수 있다. 이러한 결과는 생광물화작용 및 토양환경복원 등의 분야에 적용 시 유용한 자료로 활용될 것을 기대한다.

키워드

탄산칼슘

요소분해효소

박테리아와 식물

칼사이트

바테라이트

References

Achal, V., Pan, X. and Zhang, D., 2011, “Remediation of copper-contaminated soil by Kocuria flava CR1, based on microbially induced calcite precipitation,” Ecol. Eng., Vol. 37, No. 10, pp. 1601-1605.
Bremner, J.M. and Douglas, L.A., 1971, “Inhibition of urease activity in soil,” Soil Biol. Biochem., Vol. 3, No. 4, pp. 297-307.
Chen, Y.Y., Clancy, K.A. and Burne, R.A., 1996, “Streptococcus salivarius urease: genetic and biochemical characterization and expression in a dental plaque Streptococcus,” Infect Immun., Vol. 64, No. 2, pp. 585-592.
DeJong, J.T., Fritzges, M.B. and Nüslein, K., 2006, “Microbially induced cementation to control sand response to undrained shear,” J. Geotech. Geoenviron. Eng., Vol. 132, No. 11, pp. 1381-1392.
De Koning-Ward T.F., Ward, A.C. and Robins-Browne, R.M., 1994, “Characterization of the urease-encoding gene complex of Yersinia enterocolitica,” Gene, Vol. 145, No. 1, pp. 25-32.
De Muynck, W., De Belie, N. and Verstraete, W., 2010, “Microbial carbonate precipitation in construction materials: A review,” Ecol. Eng., Vol. 36, No. 2, pp. 118-136.
Grasham, T.L.T. and Sheridan, P.P., 2007, “Design and validation of ureC-based primers for groundwater detection of urea-hydrolyzing bacteria,” Geomicrobiol. J., Vol. 24, No. 3, pp. 353-364.
Gu, C.H., Victor, Y.J., David, J. and Grant, W., 2001, “Polymorph Screening: Influence of Solvents on the Rate of Solvent-mediated Polymorphic Transformation,” J. Pharm. Sci., Vol. 90, No. 11, pp. 1878-1890.
Jones, B.D. and Mobley, H.L., 1989, “Proteus mirabilis urease: nucleotide sequence determination and comparison with Jack bean urease,” J. Bacteriol., Vol. 171, No. 12, pp. 6414-6422.
Kabalah-Amitai, L., Mayzel, B., Kauffmann, Y., Fitch, A.N., Bloch, L., Gilbert, P.U.P.A. and Pokroy, B., 2013, “Vaterite crystals contain two interspersed crystal structures,” Science, Vol. 340, pp. 454-457.
Kawasaki, S., Ogata, S., Hiroyoshi, N., Tsunekawa, M., Kaneko, K. and Terajima, R., 2010, “Effect of temperature on precipitation of calcium carbonate using soil microorganisms,” J. Japan Soc. Eng. Geol., Vol. 51, No. 1, pp. 10-18.
Kim, K.J., No, A.R. and Park, K.S., 2009, “Isolation and identification of urease-positive Photobacterium sp. strain HA-2 from sea water,” Kor. J. Fish Aquat. Sci., Vol. 42, No. 6, pp. 531-536.
Koper, T.E., El-Sheikh, A.F., Norton, J.M. and Klotz, M.G., 2004, “Urease-encoding genes in ammonia-oxidizing bacteria,” Appl. Environ. Microbiol., Vol. 70, No. 4, pp. 2342-2348.
Labigne, A., Cussac, V. and Courcoux, P., 1991, “Shuttle cloning and nucleotide sequences of Helicobacter pylori genes responsible for urease activity,” J. Bacteriol, Vol. 173, No. 6, pp. 1920-1931.
Lee, M.N. and Park, H.D., 2012, “Isolation and characterization of acidophilic yeasts producing urease from Korean traditional Nuruk,” Korean J. Food Preserv., Vol. 19, No. 2, pp. 308-314.
Manoli, F. and Dalas, E., 2001, “Calcium carbonate crystallization in the presence of Glutamic Acid,” J. Cryst. Growth, Vol. 222, pp. 293-297.
Min, S.H. and Lee, M.H., 2007, “Purification and characterization of the Staphylococcus epidermidis urease,” J. Life Sci., Vol. 17, No. 4, pp. 581-586.
Mitchell, J.K. and Santamarina, J.C., 2005, “Biological considerations in geotechnical engineering,” J. Geotech. Geoenviron. Eng., Vol. 131, No. 10, pp. 1222-1233.
Mobley, H.L. and Hausinger, R.P., 1989, “Microbial ureases: significance, regulation, and molecular characterization,” Microbial. Rev., Vol. 53, No. 1, pp. 85-108.
Mulrooney, S.B. and Hausinger, R.P., 1990, “Sequence of the Klebsiella aerogenes urease genes and evidence for accessory proteins facilitating nickel incorporation,” J. Bacteriol., Vol. 172, No. 10, pp. 5837-5843.
Nam, I.H., Kim, Y.M., Murugesan, K., Jeon, J.R., Chang, Y.Y. and Chang, Y.S., 2008, “Bioremediation of PCDD/Fs- contaminated municipal solid waste incinerator fly ash by a potent microbial biocatalyst,” J. Hazard. Mater., Vol. 157, pp. 114-121.
Nam, I.H., Kim, Y.M., Schmidt, S. and Chang, Y.S., 2006, “Biotransformation of 1,2,3-tri- and 1,2,3,4,7,8-hexachlorodibenzo-p-dioxin by Sphingomonas wittichii strain RW1,” Appl. Environ. Microbiol., Vol. 72, pp. 112-116.
Nam, I.H., Roh, S.B., Park, M.J., Chon, C.M., Kim, J.G., Jeong, S.W., Song, H. and Yoon, M.H., 2016, “Immobilization of heavy metal contaminated mine wastes using Canavalia ensiformis extract,” Catena, Vol. 136, pp. 53–58.
Okwadha, G.D. and Li, J., 2010, “Optimum conditions for microbial carbonate precipitation,” Chemosphere, Vol. 81, No. 9, pp. 1143-1148.
Park, J.W., Kim, J.S., Ahn, J.W. and Han, C., 2006, “A Study on characteristics of precipitated calcium carbonate prepared by the nozzle spouting method,” J. Korean Ind. Eng. Chem., Vol. 17, No. 1, pp. 67-72.
Park, K.S., Iida, T., Yamaichi, Y., Oyagi, T., Yamamoto, K. and Honda, T., 2000, “Genetic characterization of DNA region containing the trh and ure genes of Vibrio parahaemolyticus,” Infect Immun., Vol. 68, No. 10, pp. 5742-5748.
Park, M.J., Yoon, M.H. and Nam, I.H., 2014, “Characterization of urease-producing bacteria isolated from heavy metal contaminated mine soil,” Korean J. Soil Sci. Fert., Vol. 47, No. 6, pp. 391-397.
Park, S.S., Kim, W.J. and Lee, J.C., 2011, “Effect of biomineralization on the strength of cemented sands,” J. Korean Geotech. Soc., Vol. 27, No. 5, pp. 75-84.
Roh, S.B., Park, M.J., Chon, C.M., Kim, J.G., Song, H., Yoon, M.H. and Nam, I.H., 2015, “Bioremediation of heavy metal contaminated mine wastes using urease based plant extract,” J. Soil Groundw. Environ., Vol. 20, No. 1, pp. 56-64.
Shivkumara, C., Singh, P., Gupta, A. and Hegde, M.S., 2006, “Synthesis of vaterite CaCO₃ by direct precipitation using glycine and L-alanine as directing agents,” Mater. Res. Bull., Vol. 41, No. 8, pp. 1455-1460.
Sondi, I. and Salopek-Sondi, B., 2005, “Influence of the primary structure of enzymes on the formation of CaCO₃ polymorphs: A comparison of plant (Canavalia ensiformis) and bacterial (Bacillus pasteurii) ureases,” Langmuir, Vol. 21, pp. 8876-8882.
Song, S.M., Seong, B.I., Koo, J.H. and Kim, I.H., 2011, “Effect of Aspartic Acid and Lysine on Polymorphism of Calcium Carbonate Crystal Formed by Gas-Liquid Reaction,” Korean Chem. Eng. Res., Vol. 49, No. 1, pp. 109-113.
Tabatabai M.A., 1973, “Michaelis constants of urease in soils and soil fraction,” Soil Sci. Soc. Am. Proc., Vol. 37, No. 5, pp. 701-707.
Terajima, R., Shimada, S., Oyama, T. and Kawasaki, S., 2009, “Fundamental study of siliceous biogrout for eco-friendly soil improvement,” J. Japan Soc. Civil Eng. C., Vol. 65, No. 1, pp. 120-130.
Van Paassen, L.A., Ghose, R., Linden, T.J.M. van der, Star, W.R.L. van der, and Loosdrecht, M.C.M. van, 2010, “Quantifying biomediated ground improvement by ureolysis: large-scale biogrout experiment,” J. Geotech. Geoenviron. Eng., Vol. 136, No. 12, pp. 1721-1728.
Whiffin, V.S., Paassen, L.A. van, and Harkes, M.P., 2007, “Microbial carbonate precipitation as a soil improvement technique,” Geomicrobiol, J. Vo. 24, No. 5, pp. 417-423.
Xie, A.J., Shen, Y.H., Zhang, C.Y., Yuan, Z.W., Zhu, X.M. and Yang, Y.M., 2005, “Crystal growth of calcium carbonate with various morphologies in different amino acid systems,” J. Cryst. Growth, Vol. 285, pp. 436-443.
Young, G.M., Amid, D. and Miller, V.L., 1996, “A bifunctional urease enhances survival of pathogenic Yersinia enterocolitica and Morganella morganii at low pH,” J. Bacteriol., Vol. 178, No. 22, pp. 6487-6495.

Information

Publisher :The Korean Society of Mineral and Energy Resources Engineers
Publisher(Ko) :한국자원공학회
Journal Title :Journal of the Korean Society of Mineral and Energy Resources Engineers
Journal Title(Ko) :한국자원공학회지
Volume : 53
No :5
Pages :398-406
DOI :https://doi.org/10.12972/ksmer.2016.53.5.398

[1] Achal, V., Pan, X. and Zhang, D., 2011, “Remediation of copper-contaminated soil by Kocuria flava CR1, based on microbially induced calcite precipitation,” Ecol. Eng., Vol. 37, No. 10, pp. 1601-1605.

[2] Bremner, J.M. and Douglas, L.A., 1971, “Inhibition of urease activity in soil,” Soil Biol. Biochem., Vol. 3, No. 4, pp. 297-307.

[3] Chen, Y.Y., Clancy, K.A. and Burne, R.A., 1996, “Streptococcus salivarius urease: genetic and biochemical characterization and expression in a dental plaque Streptococcus,” Infect Immun., Vol. 64, No. 2, pp. 585-592.

[4] DeJong, J.T., Fritzges, M.B. and Nüslein, K., 2006, “Microbially induced cementation to control sand response to undrained shear,” J. Geotech. Geoenviron. Eng., Vol. 132, No. 11, pp. 1381-1392.

[5] De Koning-Ward T.F., Ward, A.C. and Robins-Browne, R.M., 1994, “Characterization of the urease-encoding gene complex of Yersinia enterocolitica,” Gene, Vol. 145, No. 1, pp. 25-32.

[6] De Muynck, W., De Belie, N. and Verstraete, W., 2010, “Microbial carbonate precipitation in construction materials: A review,” Ecol. Eng., Vol. 36, No. 2, pp. 118-136.

[7] Grasham, T.L.T. and Sheridan, P.P., 2007, “Design and validation of ureC-based primers for groundwater detection of urea-hydrolyzing bacteria,” Geomicrobiol. J., Vol. 24, No. 3, pp. 353-364.

[8] Gu, C.H., Victor, Y.J., David, J. and Grant, W., 2001, “Polymorph Screening: Influence of Solvents on the Rate of Solvent-mediated Polymorphic Transformation,” J. Pharm. Sci., Vol. 90, No. 11, pp. 1878-1890.

[9] Jones, B.D. and Mobley, H.L., 1989, “Proteus mirabilis urease: nucleotide sequence determination and comparison with Jack bean urease,” J. Bacteriol., Vol. 171, No. 12, pp. 6414-6422.

[10] Kabalah-Amitai, L., Mayzel, B., Kauffmann, Y., Fitch, A.N., Bloch, L., Gilbert, P.U.P.A. and Pokroy, B., 2013, “Vaterite crystals contain two interspersed crystal structures,” Science, Vol. 340, pp. 454-457.

[11] Kawasaki, S., Ogata, S., Hiroyoshi, N., Tsunekawa, M., Kaneko, K. and Terajima, R., 2010, “Effect of temperature on precipitation of calcium carbonate using soil microorganisms,” J. Japan Soc. Eng. Geol., Vol. 51, No. 1, pp. 10-18.

[12] Kim, K.J., No, A.R. and Park, K.S., 2009, “Isolation and identification of urease-positive Photobacterium sp. strain HA-2 from sea water,” Kor. J. Fish Aquat. Sci., Vol. 42, No. 6, pp. 531-536.

[13] Koper, T.E., El-Sheikh, A.F., Norton, J.M. and Klotz, M.G., 2004, “Urease-encoding genes in ammonia-oxidizing bacteria,” Appl. Environ. Microbiol., Vol. 70, No. 4, pp. 2342-2348.

[14] Labigne, A., Cussac, V. and Courcoux, P., 1991, “Shuttle cloning and nucleotide sequences of Helicobacter pylori genes responsible for urease activity,” J. Bacteriol, Vol. 173, No. 6, pp. 1920-1931.

[15] Lee, M.N. and Park, H.D., 2012, “Isolation and characterization of acidophilic yeasts producing urease from Korean traditional Nuruk,” Korean J. Food Preserv., Vol. 19, No. 2, pp. 308-314.

[16] Manoli, F. and Dalas, E., 2001, “Calcium carbonate crystallization in the presence of Glutamic Acid,” J. Cryst. Growth, Vol. 222, pp. 293-297.

[17] Min, S.H. and Lee, M.H., 2007, “Purification and characterization of the Staphylococcus epidermidis urease,” J. Life Sci., Vol. 17, No. 4, pp. 581-586.

[18] Mitchell, J.K. and Santamarina, J.C., 2005, “Biological considerations in geotechnical engineering,” J. Geotech. Geoenviron. Eng., Vol. 131, No. 10, pp. 1222-1233.

[19] Mobley, H.L. and Hausinger, R.P., 1989, “Microbial ureases: significance, regulation, and molecular characterization,” Microbial. Rev., Vol. 53, No. 1, pp. 85-108.

[20] Mulrooney, S.B. and Hausinger, R.P., 1990, “Sequence of the Klebsiella aerogenes urease genes and evidence for accessory proteins facilitating nickel incorporation,” J. Bacteriol., Vol. 172, No. 10, pp. 5837-5843.

[21] Nam, I.H., Kim, Y.M., Murugesan, K., Jeon, J.R., Chang, Y.Y. and Chang, Y.S., 2008, “Bioremediation of PCDD/Fs- contaminated municipal solid waste incinerator fly ash by a potent microbial biocatalyst,” J. Hazard. Mater., Vol. 157, pp. 114-121.

[22] Nam, I.H., Kim, Y.M., Schmidt, S. and Chang, Y.S., 2006, “Biotransformation of 1,2,3-tri- and 1,2,3,4,7,8-hexachlorodibenzo-p-dioxin by Sphingomonas wittichii strain RW1,” Appl. Environ. Microbiol., Vol. 72, pp. 112-116.

[23] Nam, I.H., Roh, S.B., Park, M.J., Chon, C.M., Kim, J.G., Jeong, S.W., Song, H. and Yoon, M.H., 2016, “Immobilization of heavy metal contaminated mine wastes using Canavalia ensiformis extract,” Catena, Vol. 136, pp. 53–58.

[24] Okwadha, G.D. and Li, J., 2010, “Optimum conditions for microbial carbonate precipitation,” Chemosphere, Vol. 81, No. 9, pp. 1143-1148.

[25] Park, J.W., Kim, J.S., Ahn, J.W. and Han, C., 2006, “A Study on characteristics of precipitated calcium carbonate prepared by the nozzle spouting method,” J. Korean Ind. Eng. Chem., Vol. 17, No. 1, pp. 67-72.

[26] Park, K.S., Iida, T., Yamaichi, Y., Oyagi, T., Yamamoto, K. and Honda, T., 2000, “Genetic characterization of DNA region containing the trh and ure genes of Vibrio parahaemolyticus,” Infect Immun., Vol. 68, No. 10, pp. 5742-5748.

[27] Park, M.J., Yoon, M.H. and Nam, I.H., 2014, “Characterization of urease-producing bacteria isolated from heavy metal contaminated mine soil,” Korean J. Soil Sci. Fert., Vol. 47, No. 6, pp. 391-397.

[28] Park, S.S., Kim, W.J. and Lee, J.C., 2011, “Effect of biomineralization on the strength of cemented sands,” J. Korean Geotech. Soc., Vol. 27, No. 5, pp. 75-84.

[29] Roh, S.B., Park, M.J., Chon, C.M., Kim, J.G., Song, H., Yoon, M.H. and Nam, I.H., 2015, “Bioremediation of heavy metal contaminated mine wastes using urease based plant extract,” J. Soil Groundw. Environ., Vol. 20, No. 1, pp. 56-64.

[30] Shivkumara, C., Singh, P., Gupta, A. and Hegde, M.S., 2006, “Synthesis of vaterite CaCO₃ by direct precipitation using glycine and L-alanine as directing agents,” Mater. Res. Bull., Vol. 41, No. 8, pp. 1455-1460.

[31] Sondi, I. and Salopek-Sondi, B., 2005, “Influence of the primary structure of enzymes on the formation of CaCO₃ polymorphs: A comparison of plant (Canavalia ensiformis) and bacterial (Bacillus pasteurii) ureases,” Langmuir, Vol. 21, pp. 8876-8882.

[32] Song, S.M., Seong, B.I., Koo, J.H. and Kim, I.H., 2011, “Effect of Aspartic Acid and Lysine on Polymorphism of Calcium Carbonate Crystal Formed by Gas-Liquid Reaction,” Korean Chem. Eng. Res., Vol. 49, No. 1, pp. 109-113.

[33] Tabatabai M.A., 1973, “Michaelis constants of urease in soils and soil fraction,” Soil Sci. Soc. Am. Proc., Vol. 37, No. 5, pp. 701-707.

[34] Terajima, R., Shimada, S., Oyama, T. and Kawasaki, S., 2009, “Fundamental study of siliceous biogrout for eco-friendly soil improvement,” J. Japan Soc. Civil Eng. C., Vol. 65, No. 1, pp. 120-130.

[35] Van Paassen, L.A., Ghose, R., Linden, T.J.M. van der, Star, W.R.L. van der, and Loosdrecht, M.C.M. van, 2010, “Quantifying biomediated ground improvement by ureolysis: large-scale biogrout experiment,” J. Geotech. Geoenviron. Eng., Vol. 136, No. 12, pp. 1721-1728.

[36] Whiffin, V.S., Paassen, L.A. van, and Harkes, M.P., 2007, “Microbial carbonate precipitation as a soil improvement technique,” Geomicrobiol, J. Vo. 24, No. 5, pp. 417-423.

[37] Xie, A.J., Shen, Y.H., Zhang, C.Y., Yuan, Z.W., Zhu, X.M. and Yang, Y.M., 2005, “Crystal growth of calcium carbonate with various morphologies in different amino acid systems,” J. Cryst. Growth, Vol. 285, pp. 436-443.

[38] Young, G.M., Amid, D. and Miller, V.L., 1996, “A bifunctional urease enhances survival of pathogenic Yersinia enterocolitica and Morganella morganii at low pH,” J. Bacteriol., Vol. 178, No. 22, pp. 6487-6495.

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