Skip to main content
SpringerLink
Log in

Applications of microorganisms to geotechnical engineering for bioclogging and biocementation of soil in situ

  • Review Paper
  • Published:
Reviews in Environmental Science and Bio/Technology Aims and scope Submit manuscript

Abstract

Microbial Geotechnology is a new branch of geotechnical engineering that deals with the applications of microbiological methods to geological materials used in engineering. The aim of these applications is to improve the mechanical properties of soil so that it will be more suitable for construction or environmental purposes. Two notable applications, bioclogging and biocementation, have been explored. Bioclogging is the production of pore-filling materials through microbial means so that the porosity and hydraulic conductivity of soil can be reduced. Biocementation is the generation of particle-binding materials through microbial processes in situ so that the shear strength of soil can be increased. The most suitable microorganisms for soil bioclogging or biocementation are facultative anaerobic and microaerophilic bacteria, although anaerobic fermenting bacteria, anaerobic respiring bacteria, and obligate aerobic bacteria may also be suitable to be used in geotechnical engineering. The majority of the studies on Microbial Geotechnology at present are at the laboratory stage. Due to the complexity, the applications of Microbial Geotechnology would require an integration of microbiology, ecology, geochemistry, and geotechnical engineering knowledge.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Atmaca S, Elci S, Gul K (1996) Comparison of slime production under aerobic and anaerobic conditions. Cytobios 88:149–152

    CAS  Google Scholar 

  • Bachmeier K, Williams AE, Warmington J, Bang SS (2002) Urease activity in microbiologically-induced calcite precipitation. J Biotechnol 93:171–181

    Article  CAS  Google Scholar 

  • Baveye P, Vandevivere P, Hoyle BL, DeLeo PC, de Lozada DS (1998) Environmental impact and mechanisms of the biological clogging of saturated soils and aquifer materials. Crit Rev Environ Sci Technol 28:123–191

    Article  CAS  Google Scholar 

  • Beccari M, Ramadori R (1996) Filamentous activated sludge bulking. In: Horan N (ed) Environmental waste management: a European perspective. John Wiley & Sons, New York, pp 87–114

    Google Scholar 

  • Bergey’s Manual of Systematic Bacteriology (2001) The Archaea and the deeply branching and phototrophic bacteria, 2nd edn, vol 1. Springer-Verlag, New York

  • Bergey’s Manual of Systematic Bacteriology (2005) The proteobacteria, 2nd edn, vol 2. Springer-Verlag, New York

  • Bonala MVS, Reddi LN (1998) Physicochemical and biological mechanisms of soil clogging: an overview. ASCE Geotech Spec Publ 78:43–68

    Google Scholar 

  • Bouwer H (2002) Artificial recharge of groundwater: hydrogeology and engineering. Hydrogeol J 10:121–142

    Article  CAS  Google Scholar 

  • Buffle J, van Leeuwen HP (Ser eds) (2002) Interactions between soil particles and microorganisms. In: Huand M, Bollag JM, Senesi N (Vol eds) IUPAC series on analytical and physical chemistry of environmental systems, vol 8. John Wiley & Sons, Chichester, UK

  • Castanier S, Le Metayer-Levrel G, Perthuisot JP (1999) Ca-carbonates precipitation and limestone genesis—the microbiogeologist point of view. Sediment Geol 126:9–23

    Article  CAS  Google Scholar 

  • DeJong JT, Fritzges MB, Nusstein K (2006) Microbially induced cementation to control sand response to undrained shear. J Geotech Geoenviron Eng 32:1381–1392

    Article  CAS  Google Scholar 

  • Dniker SW, Rhoton FE, Torrent J, Smeck NE, Lal R (2003) Iron (hydr)oxide crystallinity effects on soil aggregation. Soil Sci Soc Am J 67:606–611

    Article  Google Scholar 

  • Dupin HJ, McCarty PL (2000) Impact of colony morphologies and disinfection on biological clogging in porous media. Environ Sci Technol 34:1513–1520

    Article  CAS  Google Scholar 

  • Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) (2006) The prokaryotes: a handbook on the biology of bacteria, vol 3: Archaea. Bacteria: Firmicutes, Actinomycetes, 3rd edn. Springer-Verlag, New York

    Google Scholar 

  • Etemadi O, Petrisor IG, Kim D, Wan MW, Yen TF (2003) Stabilization of metals in subsurface by biopolymers: laboratory drainage flow studies. Soil Sediment Contam 12:647–661

    Article  CAS  Google Scholar 

  • Ferris FG, Stehmeier LG (1992) Bacteriogenic mineral plugging, United States Patent 5143155

  • Ferris FG, Stehmeier LG, Kantzas A, Mourits FM (1996) Bacteriogenic mineral plugging. Can J Petrol Technol 35:56–61

    CAS  Google Scholar 

  • Fredrickson JK, Gorby YA (1996) Environmental processes mediated by iron-reducing bacteria. Curr Opin Biotechnol 7:287–294

    Article  CAS  Google Scholar 

  • Fujita Y, Ferris FG, Lawson RD, Colwell FS, Smith RW (2000) Calcium carbonate precipitation by ureolytic subsurface bacteria. Geomicrobiol J 17:305–318

    CAS  Google Scholar 

  • Geets J, Boon N, Verstraete W (2006) Strategies of aerobic ammonia-oxidizing bacteria for coping with nutrient and oxygen fluctuations. FEMS Microbiol Ecol 58:1–13

    Article  CAS  Google Scholar 

  • Gioia F, Ciriello PP (2006) The containment of oil spills in porous media using xanthan/aluminium solutions, gelled by gaseous CO2 or by AlCl3 solutions. J Hazard Mater 138:500–506

    Article  CAS  Google Scholar 

  • Hajra MG, Reddi LN, Marchin GL, Mutyala J (2000) Biological clogging in porous media. In: Zimme TF (ed) Environ Geotech ASCE geotechnical special publication 105, New York, pp 151–165

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

    Article  CAS  Google Scholar 

  • Harada T (1983) Special bacterial polysaccharides and polysaccharases. Biochem Soc Symp 48:97–116

    CAS  Google Scholar 

  • Indraratna B, Chu J (Eds) (2005) Ground improvement – case histories. Elsevier, Oxford, UK

    Google Scholar 

  • Ivanov V (2006) Structure of aerobically grown microbial granules. In: Tay JH, Tay STL, Liu Y, Show KY, Ivanov V (eds) Biogranulation technologies for wastewater treatment. Elsevier, Amsterdam, pp 115–134

    Chapter  Google Scholar 

  • Ivanov V, Tay STL (2006a) Seeds for aerobic microbial granules. In: Tay JH, Tay STL, Liu Y, Show KY, Ivanov V (eds) Biogranulation technologies for wastewater treatment. Elsevier, Amsterdam, pp 213–244

    Chapter  Google Scholar 

  • Ivanov V, Tay STL (2006b) Microorganisms of aerobic microbial granules. In: Tay JH, Tay STL, Liu Y, Show KY, Ivanov V (eds) Biogranulation technologies for wastewater treatment. Elsevier, Amsterdam, pp 135–162

    Chapter  Google Scholar 

  • Ivanov V, Wang JY, Stabnikova O, Krasinko V, Stabnikov V, Tay STL, Tay JH (2004) Iron-mediated removal of ammonia from strong nitrogenous wastewater of food processing. Water Sci Technol 49:421–431

    CAS  Google Scholar 

  • Ivanov V, Stabnikov V, Zhuang WQ, Tay ST L, Tay JH (2005) Phosphate removal from return liquor of municipal wastewater treatment plant using iron-reducing bacteria. J Appl Microbiol 98:1152–1161

    Article  CAS  Google Scholar 

  • Ivanov V, Stabnikova O, Sihanonth P, Menasveta P (2006a) Aggregation of ammonia-oxidizing bacteria in microbial biofilm on oyster shell surface. World J Microbiol Biotechnol 22:807–812

    Article  CAS  Google Scholar 

  • Ivanov V, Wang XH, Tay STL, Tay JH (2006b) Bioaugmentation and enhanced formation of microbial granules used in aerobic wastewater treatment. Appl Microbiol Biotechnol 70:374–381

    Article  CAS  Google Scholar 

  • James GA, Warwood BK, Hiebert R., Cunningham AB (2000) Microbial barriers to the spread of pollution. In: Bioremediation. Kluwer Academic, Amsterdam, pp 1–14

  • Jones AL, Brown JM, Mishra V, Perry JD, Steigerwalt AG, Goodfellow M (2004) Rhodococcus gordoniae sp. nov., an actinomycete isolated from clinical material and phenol-contaminated soil. Int J Syst Evol Microbiol 54:407–411

    Article  CAS  Google Scholar 

  • Johnson-Green PC, Crowder AA (1991) Iron oxide deposition on axenic and non-axenic roots of rice seedlings (Oryza sativa L.). J Plant Nutr 14:375–386

    Article  CAS  Google Scholar 

  • Karol RH (2003) Chemical grouting and soil stabilization, 3rd edn. M. Dekker, New York

    Google Scholar 

  • Kenyon WJ, Esch SW, Buller CS (2005) The curdlan-type exopolysaccharide produced by cellulomonas flavigena KU forms part of an extracellular glycocalyx involved in cellulose degradation. Antonie Van Leeuwenhoek 87:143–148

    Article  CAS  Google Scholar 

  • Kucharski ES, Winchester W, Leeming WA, Cord-Ruwisch R, Muir C, Banjup WA, Whiffin VS, Al-Thawadi S, Mutlaq J (2005) Microbial biocementation. Patent Application WO/2006/066326; International Application No.PCT/AU2005/001927

  • Lovley DR, Holmes DE, Nevin KP (2004) Dissimilatory Fe(III) and Mn(IV) reduction. Adv Microb Physiol 49:219–286

    Article  CAS  Google Scholar 

  • McConkey BG, Reimer CD, Nicholaichuk W (1990) Sealing earthen hydraulic structures with enhanced gleization and sodium carbonate: 2. Application for lining an irrigation canal. C Agr Eng 163–170

  • Mataix-Solera J, Guerrero C, Hernández MT, García-Orenes F, Mataix-Beneyto J, Gómez I, Escalante B (2005) Improving soil physical properties related to hydrological behaviour by inducing microbiological changes after organic amendments. Geophys Res Abs 7, 00341

    Google Scholar 

  • Meadows A, Meadows PS, Wood DM, Murray JMH (1994) Microbiological effects on slope stability: an experimental analysis. Sedimentology 41:423–435

    Article  Google Scholar 

  • Mitchell JK, Santamarina JC (2005) Biological considerations in geotechnical engineering. J Geotech Geoenviron Eng 131:1222–1233

    Article  CAS  Google Scholar 

  • Momemi D, Kamel R, Martin R, Yen TF (1999) Potential use of biopolymer grouts for liquefaction mitigation. In: Leeson A, Alleman BC (eds) Phytoremediation and innovation strategies for specialized remedial applications. Batelle Press, Columbus, pp 175–180

    Google Scholar 

  • Mozley PS, Davis JM (2005) Internal structure and mode of growth of elongate calcite concretions: evidence for small-scale, microbially induced, chemical heterogeneity in groundwater. Geol Soc Am Bull 117:1400–1412

    Article  CAS  Google Scholar 

  • Mulder EG, Deinema MH (1992) The sheathed bacteria. In: Balows A (ed) The prokaryotes: a handbook on the biology of bacteria: ecophysiology, isolation, identification, applications. Springer-Verlag, New York, pp 2613–2624

    Google Scholar 

  • Murphy EM, Ginn TR (2000) Modeling microbial processes in porous media. Hydrogeol J 8:142–158

    Article  Google Scholar 

  • Portilho M, Matioli G, Zanin GM, de Moraes FF, Scamparini AR (2006) Production of insoluble exopolysaccharide Agrobacterium sp. (ATCC 31749 and IFO 13140). Appl Biochem Biotechnol 129–132:864–869

    Article  Google Scholar 

  • Ragusa SR, de Zoysa DS, Rengasamy P (1994) The effect of microorganisms, salinity and turbidity on hydraulic conductivity of irrigation channel soil. Irrigation Sci 15:159–166

    Google Scholar 

  • Ralph DE, Stevenson JM (1995) The role of bacteria in well clogging. Water Res 29:365–369

    Article  CAS  Google Scholar 

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

    CAS  Google Scholar 

  • Ravenscroft N, Walker SG, Dutton GG, Smit J (1991) Identification, isolation, and structural studies of extracellular polysaccharides produced by Caulobacter crescentus. J Bacteriol 173:5677–5684

    CAS  Google Scholar 

  • Reid RP, Visscher PT, Decho AW, Stolz JF, Bebout BM, Dupraz C, Macintyre IG, Paerl HW, Pinckney JL, Prufert-Bebout L, Steppe TF, DesMarais DJ (2000) The role of microbes in accretion, lamination and early lithification of modern marine stromatolites. Nature 406:989–992

    Article  CAS  Google Scholar 

  • Rodgers M, Mulqueen J, Healy MG (2004) Surface clogging in an intermittent stratified sand filter. Soil Sci Soc Am J 68:1827–1832

    Article  CAS  Google Scholar 

  • Ross CW, Mew G, Childs CW (1989) Deep cementation in late quaternary sands near Westport, New Zealand. Aust J Soil Res 27:275–288

    Article  CAS  Google Scholar 

  • Ross N, Villemur R, Deschenes L, Samson R (2001) Clogging of limestone fracture by stimulating groundwater microbes. Water Res 35:2029–2037

    Article  CAS  Google Scholar 

  • Seki K, Miyazaki T, Nakano M (1998) Effects of microorganisms on hydraulic conductivity decrease in infiltration. Eur J Soil Sci 49:231–236

    Article  Google Scholar 

  • Seki K, Kamiya J, Miyazaki T (2005) Temperature dependence of hydraulic conductivity decrease due to biological clogging under ponded infiltration. Trans Jap Soc Irrigation Drain Reclam Eng 237:13–19

    Google Scholar 

  • Seviour R, Blackall L (Eds) (2007) The microbiology of activated sludge, 2nd edn. IWA Publishing

  • Sharp RR, Cunningham AB, Komlos J, Billmayer J (1999) Observation of thick biofilm accumulation and structure in porous media and corresponding hydrodynamic and mass transfer effects. Water Sci Technol 39:195–201

    Article  Google Scholar 

  • Stabnikov VP, Ivanov VN (2006) The effect of iron hydroxide concentrations on the anaerobic fermentation of sulfate-containing model wastewater. Appl Biochem Microbiol 42:284–288

    Article  CAS  Google Scholar 

  • Stehr G, Zorner S, Bottcher B, Koops HP (1995) Exopolymers: an ecological characteristic of a floc-attached, ammonia-oxidizing bacterium. Microb Ecol 30:15–126

    Article  Google Scholar 

  • Stewart TL, Fogler HS (2001) Biomass plug development and propagation in porous media. Biotechnol Bioeng 72:353–363

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Sutherland IW (1990) Biotechnology of microbial exopolysaccharides. Cambridge University Press, Cambridge

    Google Scholar 

  • Thompson BG, Thomas JR (1984) Method of enhancing oil recovery by use of exopolymer producing microorganisms, United States Patent 4460043

  • Thompson BG, Thomas JR (1985) Method of enhancing oil recovery by use of exopolymer-producing micro-organisms, United States Patent 4561500

  • Tsang PH, Li G, Brun YV, Freund LB, Tang JX (2006) Adhesion of single bacterial cells in the micronewton range. Proc Natl Acad Sci USA 103:11435–11436

    Article  CAS  Google Scholar 

  • Vandevivere P, Baveye P (1992) Relationship between transport of bacteria and their clogging efficiency in sand columns. Appl Environ Microbiol 58:2523–2530

    CAS  Google Scholar 

  • Veenbergen V, Lambert JWM, VanderHoek EE, VanTol AF, Weersma SI (2005) Underground space use, analysis of the past and lessons for the future. In: Proceedings ITA-AITES World Tunnel Congress, 7–12 May 2005, Istanbul

  • Weber KA, Achenbach LA, Coates JD (2006) Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction. Nat Rev Microbiol 4:752–764

    Article  CAS  Google Scholar 

  • Weiss JV, Emerson D, Megonigal JP (2005) Rhizosphere iron (III) deposition and reduction in a Juncus effusus L.-dominated wetland. Soil Sci Soc Am J 69:1861–1870

    Article  CAS  Google Scholar 

  • Wingender J, Neu TR, Flemming HC (eds) (1999) Microbial extracellular polymeric substances: characterization, structure and function. Springer-Verlag Berlin and Heidelberg GmbH & Co

  • Wu JG, Stahl P, Zhang R (1997) Experimental study on the reduction of soil hydraulic conductivity by enhanced biomass growth. Soil Sci 162:741–748

    Article  CAS  Google Scholar 

  • Yamanaka T, Miyasaka H, Aso I, Tanigawa M, Shoji K (2002) Involvement of sulfur- and iron-transforming bacteria in heaving of house foundations. Geomicrobiol J 19:519–528

    Article  CAS  Google Scholar 

  • Yang IC, Li Y, Park JK, Yen TF (1993) Subsurface application of slime—forming bacteria in soil matrices. In: Proceedings of the 2nd international symposium in situ and on site bioreclamation, April 1993, San Diego, CA, Lewis Publishers, Boca Raton, FL

  • Yen TF, Yang ICY, Karimi S, Martin GR (1996) Biopolymers for geotechnical applications. In: Chenchayya TB (ed) North American water and environment congress & destructive water. ASCE, New York, pp 1602–1607

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Block N1, School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore

    Volodymyr Ivanov & Jian Chu

Authors
  1. Volodymyr Ivanov
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jian Chu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Volodymyr Ivanov.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ivanov, V., Chu, J. Applications of microorganisms to geotechnical engineering for bioclogging and biocementation of soil in situ. Rev Environ Sci Biotechnol 7, 139–153 (2008). https://doi.org/10.1007/s11157-007-9126-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11157-007-9126-3

Keywords

Search

Navigation