An optimum condition of MICP indigenous bacteria with contaminated wastes of heavy metal


Heavy metals are naturally occurring trace elements present in the environment, including soil, water, and air. However, high heavy metal concentration contamination from waste is a serious environmental problem brought on by industrial activities. The research in this study evaluated different biomineralized CaCO3 forms from individual bacteria species in heavy-metal-contaminated soils and mine tailings. Scanning electron microscope (SEM) images of the crystals were used to characterize the precipitated CaCO3. Generally, urea-hydrolysis bacteria form minerals via a microbiologically induced calcite precipitation (MICP) process. These bacteria produce the urease enzyme, which leads to urea-hydrolysis. These bacteria were isolated from heavy-metal-contaminated soils and characterized for their potential utilization in the S/S process. Optimum conditions for indigenous bacterial growth were 30 °C and a pH range of 7–8; and growth patterns were further affected by the growth medium salinity. SEM and X-ray diffraction (XRD) analyses demonstrated that bioaccumulated heavy metal ions were deposited around the cell envelope as rhombohedral and sphere shaped crystalline carbonate minerals in optimum conditions. In this study, the authors hypothesize that the indigenous bacteria can effectively precipitate heavy metals in soil and mine tailing with the urea-hydrolysis enzyme, and play an important role in heavy metal stabilization.

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  1. 1.

    Zhuang P, Zou B, Li NY, Li ZA (2009) Heavy metal contamination in soils and food crops around Dabaoshan mine in Guangdong, China: implication for human health. Environ Geochem Health 31:707–715

    Article  Google Scholar 

  2. 2.

    Olayinka KO, Oyeyiola AO, Odujebe FO, Oboh B (2011) Uptake of potentially toxic metals by vegetable plants grown on contaminated soil and their potential bioavailability using sequential extraction. J Soil Sci Environ 2(8):220–227

    Google Scholar 

  3. 3.

    Pruvot C, Douay F, Herve F, Waterlot C (2006) Heavy metals in soil, crops and grass as a source of human exposure in the former mining areas. J Soils Sediments 6:215–220

    Article  Google Scholar 

  4. 4.

    Chen QY, Tayrer M, Hills CD, Yang XM, Carey P (2009) Immobilisation of heavy metal in cement-based solidification/stabilisation: a review. Waste Manag 29:390–403

    Article  Google Scholar 

  5. 5.

    Jang A, Kim IS (2000) Solidification and stabilization of Pb, Zn, Cd and Cu intailing wastes using cemnet and fly ash. Miner Eng 13(14–15):1659–1662

    Article  Google Scholar 

  6. 6.

    Alpaslan B, Yukselen MA (2000) Remediation of lead contaminated soils by stabilization/solidification. Water Air Soil Pollut 133:253–263

    Article  Google Scholar 

  7. 7.

    Cheung KH, Lai HY, Gu J-D (2006) Membrane-associated hexavalent chromium reductase of Bacillus megaterium TKW 3 with induced expression. J Microbiol Biotechnol 16:855–862

    Google Scholar 

  8. 8.

    DeJong JT, Fritzges MB, Nusslein K (2006) Microbially induced cementation to control sand response to undrained shear. J Geotech Geoenviron Eng 132:1381–1392

    Article  Google Scholar 

  9. 9.

    Cheung KH, Gu JD (2007) Mechanisms of hexavalent chromium detoxification by bacteria and bioremediation applications. Int Biodeterior Biodegrad 59:8–15

    Article  Google Scholar 

  10. 10.

    Sarda D, Choonia HS, Sarode DD, Lele SS (2009) Biocalcification by Bacillus pasteurii urease: a novel application. J Ind Microbiol Biotechnol 36:1111–1115

    Article  Google Scholar 

  11. 11.

    Ramachandran SK, Ramakrishnan V, Bang SS (2001) Remediation of concrete using microorganisms. ACI Mater J 98:3–9

    Google Scholar 

  12. 12.

    Ivanov V, Chu J (2008) Applications of microorganisms to geotechnical engineering for bioclogging and biocementation of soil in situ. Rev Environ Sci Biotechnol 7:139–153

    Article  Google Scholar 

  13. 13.

    Mary SR, Williams, Seraphin S (1998) Heavy metal biomineralization in free-living nematodes, Panagrolaimus spp. Mater Sci Eng 6:47–51

    Article  Google Scholar 

  14. 14.

    Bang SS, Galinat JK, Ramakrishnan V (2001) Calcite precipitation induced by polyurethane-immobilized Bacillus pasteurii. Enzyme Microb Technol 28:404–409

    Article  Google Scholar 

  15. 15.

    Stocks-Fischer S, Galinat JK, Bang SS (1999) Microbiological precipitation of CaCO3. Soil Biol Biochem 31:1563–1571

    Article  Google Scholar 

  16. 16.

    Gollapudi UK, Knutson CL, Bang SS, Islam MR (1995) A new method for controlling leaching through permeable channels. Chemosphere 30:695–705

    Article  Google Scholar 

  17. 17.

    Dick J, De Windt W, De Graef B, Saveyn H, Van der Meeren P, De Belie N, Verstraete W (2006) Bio-deposition of a calcium carbonate layer on degraded limestone by Bacillus species. Biodegradation 17:357–367

    Article  Google Scholar 

  18. 18.

    Lee JR (2011) A study of stabilization methods using minerals for arsenic contaminated soil near Samkwang mine area at Cheongyang-gun, Chungcheongnam-do. Ph.D. Dissertation, Graduated School Pusan National University

  19. 19.

    Ahn JS, Kim JY, Chon CM, Moon HS (2003) Mineralogical and chemical characterization of arsenic solid phases in weathered mine tailings and their leaching potential. Econ Environ Geol 36(1):27–38

    Google Scholar 

  20. 20.

    Hwang BS (2005) Assessment of arsenic and heavy metals leaching behavior in contaminated soils of abandoned metalliferous mines. M.S. Dissertation, Semyung University Graduated School

  21. 21.

    Weaver RW, Angle TS, Bottomley PS (1994) Methods of soil analysis, Part 2. Microbiological and biochemical properties. Soil Science Society of America, USA

    Google Scholar 

  22. 22.

    Nindy Tupple Miller (1982) Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 16(3):584–586

    Google Scholar 

  23. 23.

    Lee JY, Koo JK, Kim KS, Dong JI, Park YH, Bae WK, Yang JW, Yeom IT, Yoon SP, Lee JS, Jang YY, Chung JC, Choi SI, Hwang KY, Hwang JS (2001) Soil environmental engineering. Hyangmunsa, Korea

    Google Scholar 

  24. 24.

    Phae CG, Oh JM (2002) Soil contamination measurement analysis. Sinkwang-munhwasa, Korea

    Google Scholar 

  25. 25.

    Lee S, Kim TH, Lee JH (2007) Soil test method. Goomibook, Korea

    Google Scholar 

  26. 26.

    Liu D, Yates MZ (2006) Formation of rod-shaped calcite crystals by microemulsion-based synthesis. Langmuir 22(13):5566–5569

    Article  Google Scholar 

  27. 27.

    Dhami NK, Reddy MS, Mukherjee A (2014) Synergistic role of bacterial urease and carbonic anhydrase in carbonate mineralization. Appl Biochem Biotechnol 172:2552–2561

    Article  Google Scholar 

  28. 28.

    Siddique R, Achal V, Reddy M, Mukherjee A (2008) Improvement in the compressive strength of cement mortar by the use of a microorganism—Bacillus megaterium. In: Limbachiya MC, Kew H (eds) Excellence in concrete construction through innovation. Taylor and Francis, London, pp 27–30

    Google Scholar 

  29. 29.

    Soon NW, Lee LM, Khun TC, Ling HS (2013) Improvements in engineering properties of soils through microbial-induced calcite precipitation. KSCE J Civil Eng 17:718–728

    Article  Google Scholar 

  30. 30.

    Achal V, Pan X, Zhang D, Fu Q (2012) Bioremediation of Pb-contaminated soil based on microbially induced calcite precipitation. J Microbiol Biotechnol 22(2):244–347

    Article  Google Scholar 

  31. 31.

    Kang CH, Han SH, Shin YJ, Oh SJ, So JS (2014) Bioremediation of Cd by microbially induced calcite precipitation. Appl Biochem Biotechnol 172:1929–1937

    Article  Google Scholar 

  32. 32.

    De Yoreo JJ, Vekilov PG (2003) Principles of crystal nucleation and growth. Rev Mineral Geochem 54:57–93

    Article  Google Scholar 

  33. 33.

    Favre N, Christ ML, Pierre AC (2009) Biocatalytic capture of CO2 with carbonic anhydrase and its transformation to solid carbonate. J Mol Catal B Enzym 60:163–170

    Article  Google Scholar 

  34. 34.

    Gorospe CM, Han SH, Kim SG, Park JY, Kang CH, Jeong JH, So JS (2013) Effects of different calcium salts on calcium carbonate crystal formation by Sporosarcina pasteurii KCTC 3558. Biotechnol Bioprocess Eng 18:903–908

    Article  Google Scholar 

  35. 35.

    Tai CY, Chen FB (1998) Polymorphism of CaCO3 precipitated in a constant-composition environment. Am Inst Chem Eng 44:1790–1798

    Article  Google Scholar 

  36. 36.

    Bäuerlein E (2007) Hand book of biomineralization. Wiley, Weinheim

    Book  Google Scholar 

  37. 37.

    Bazylinski DA, Frankel RB, Konhauser KO (2007) Modes of biomineralization of magnetite by microbes. Geomicrobiology 24:465–475

    Article  Google Scholar 

  38. 38.

    Abo-El-Enein SA, Ali AH, Talkhan FN, Abdel-Gawwad HA (2012) Utilization of microbial induced calcite precipitation for sand consolidation and mortar crack remediation. HBRC J 8:185–192

    Article  Google Scholar 

  39. 39.

    Hammes F, Boon N, de Villiers J, Verstraete W, Siciliano SD (2003) Strain-specific ureolytic microbial calcium carbonate precipitation. Appl Environ Microbiol 69:4901–4909

    Article  Google Scholar 

  40. 40.

    Park SJ, Park YM, Chun WY, Kim WJ, Ghim SY (2010) Calcite-forming bacteria for compressive strength improvement in mortar. J Microbiol Biotechnol 20:782–788

    Google Scholar 

  41. 41.

    Kawaguchi T, Decho AW (2002) A laboratory investigation of cyanobacterial extracellular polymeric secretion (EPS) in influencing CaCO3 polymorphism. J Cryst Growth 240:230–235

    Article  Google Scholar 

  42. 42.

    Dhami NK, Reddy MS, Mukherjee A (2013) Biomineralization of calcium carbonate polymorphs by the bacterial strains isolated from calcareous sites. J Microbiol Biotechnol 23:707–714

    Article  Google Scholar 

  43. 43.

    Ferrer MR, Quevedo-Sarmiento J, Bejar V, Delgado R, Ramos-Cormenzana A, Rivadeneyra MA (1988) Calcium carbonate formation by Deleya halophila: effect on salt concentration and incubation temperature. Geomicrobiol J 6:49–57

    Article  Google Scholar 

  44. 44.

    Hammes F, Verstraete W (2002) Key roles of pH and calcium metabolism in microbial carbonate precipitation. Rev Environ Sci Biotechnol 1:3–7

    Article  Google Scholar 

  45. 45.

    Mitchell AC, Ferris FG (2005) The coprecipitation of Sr into calcite precipitates induced by bacterial ureolysis in artificial groundwater: temperature and kinetics dependence. Geochim Gosmochim Acta 69:4199–4210

    Article  Google Scholar 

  46. 46.

    Okwadha GDO, Li J (2010) Optimum conditions for microbial carbonate precipitation. Chemosphere 81:1143–1148

    Article  Google Scholar 

  47. 47.

    Loewenthal RE, Marais GVR (1978) Carbonate chemistry of aquatic systems: theory and application, vol 1. Ann Arbor Science, Ann Arbor

    Google Scholar 

  48. 48.

    Anne S, Rozen bamuO, Andreazza P, Rouet JL (2010) Evidence of a bacterial carbonate coating on plaster samples subjected to the calcite bioconcept biomineralization techniques. Constr Build Mater 24:1036–1042

    Article  Google Scholar 

  49. 49.

    Ferris FG, Phoenix V, Fujita Y, Smith RW (2003) Kinetics of calcite precipitation induced by ureolytic bacteria at 10 to 20 °C in artificial groundwater. Geochim Cosmochim Acta 67:1701–1710

    Google Scholar 

  50. 50.

    Dupraz S, Menez B, Gouze P, Leprovost R, Benezeth P, Pokrovsky OS, Guyot F (2009) Experimental approach of CO2 biomineralization in deep saline aquifers. Chem Geol 265:54–62

    Article  Google Scholar 

  51. 51.

    Mobley HLT, Island MD, Hausinger RP (1995) Molecular biology of microbial ureases. Microbiol Rev 59:451–580

    Google Scholar 

  52. 52.

    Braissant O, Caillaume G, Dupraz C, Verrecchia EP (2003) Bacterially induced mineralization of calcium carbonate in terrestrial environments: the role of exopolysaccharides and amino acids. J Sediment Res 73(3):485–490

    Article  Google Scholar 

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This study was supported by the Korea Ministry of Environment (MOE) as part of the GAIA Project (Geo-Advanced Innovative Action Project; No. 2015000550007).

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Correspondence to Jai-Young Lee.

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Kim, JH., Lee, JY. An optimum condition of MICP indigenous bacteria with contaminated wastes of heavy metal. J Mater Cycles Waste Manag 21, 239–247 (2019).

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  • CaCO3
  • Heavy metal
  • Soil
  • Mine tailing
  • S/S
  • Indigenous bacteria