6.2 Applications of Microbially Induced Mineral Precipitation
The precipitation of minerals by groundwater microorganisms can be applied in several different ways, depending foremost on the chemical reactivity and physical properties of the mineral precipitates. Hydrous ferric oxides, sulfide, and carbonate minerals are frequently targeted for use because of their capacity to immobilize inorganic contaminants through surface adsorption and co-precipitation reactions. Carbonate minerals are also known to be effective cementing agents that will adhere to and bind unconsolidated mineral grains together.
As products of lithotrophic bacterial Fe(II)-oxidation, hydrous ferric oxides are recognized as potent adsorbent solids that have a high chemical affinity for dissolved ions (Langmuir, 1997). This reactivity contributes to the removal of metal cations such as Sr2+, Cd2+, Pb2+, and UO22+ from solution. Anionic solutes such as arsenate (AsO43-), chromate (CrO42-), phosphate (PO43-), and iodide (I –) are also adsorbed by hydrous ferric oxides (Katsoyiannis and Zouboulis, 2006). The ubiquitous environmental distribution of Fe(II)-oxidizing bacteria makes bacteriogenic hydrous ferric oxide precipitation a strong candidate for natural attention of inorganic contaminants in groundwater systems.
Sulfide is produced as a conjugate reductant in anaerobic microbial respiration with sulfate as the terminal electron acceptor. This can trigger oversaturation and precipitation of sulfide mineral phases incorporating contaminants such as Cd2+, Pb2+, Hg2+, and As3+. The availability of organic matter as an electron donor for bacterial sulfate reduction is essential for sulfide production. If organic matter (or sulfate) concentrations are too low, biostimulation involving injection of one or both limiting nutrients can be used to induce sulfide mineral precipitation.
A major distinction between applications of microbial precipitation of hydrous ferric oxides and metal sulfides relates to differences in groundwater redox conditions. Bacterial oxidation of Fe(II) and precipitation of hydrous ferric oxides requires relatively oxidizing conditions using oxygen or nitrate as electron acceptors, whereas reducing conditions are needed for metal sulfide precipitation by microorganisms that use sulfate as an electron acceptor. In the intermediate redox zone, metabolic production of Fe(II) in response to microbial Fe(III)-reduction contributes to the transformation of hydrous ferric oxides into Fe(II)/Fe(III) “green rust” minerals (Figure 22). These mixed oxidation state mineral phases not only retain the adsorptive properties of hydrous ferric oxides (Parmar et al., 2001; Perez et al., 2021) but also behave as solid phase reductants for contaminants such as nitrate, chromate, selenate (SeO42-), and carbon tetrachloride (Erbs et al., 1999; Genin et al., 2001).

Figure 22 – Scanning electron micrograph showing platy crystals of green rust (GR) that have formed from the reduction of hydrous ferric oxide (HFO) in a culture of the Fe(III)-reducing bacterium Shewanella algae strain BrY. The bacteria are visible as an unorganized mass of elongated rods between the mineral precipitates. Scale bar = 10 μm.
Applications of microbially induced calcium carbonate precipitation commonly rely on the activity of ureolytic bacteria (Ferris and Stehmeier, 1992; Ferris et al., 1996; Fujita et al., 2000). Both aerobic and anaerobic bacterial species catalyze the hydrolysis of urea using the urease enzyme to produce ammonium ions and dissolved inorganic carbon (DIC), which give rise to an increase in pH (Ferris et al., 2003). In the presence of dissolved calcium, which is often injected together with urea, the higher DIC concentrations and pH lead to oversaturation and precipitation of calcium carbonate minerals (Figure 23). Denitrification, ammonification, sulfate reduction, and methane oxidation have also been implicated in microbially induced carbonate mineral precipitation (Anbu et al., 2016; Zhu and Dittrich, 2016; Eltarahony et al., 2020).

Figure 23 – Scanning electron micrograph of a growing calcite crystal precipitated in artificial groundwater by the ureolytic bacterium Sporoscarcina ureae. The bacteria appear as rod-shaped cells that are surrounding and adhering to the surface of the calcite crystal. Scale bar = 3.0 μm.
The precipitation of carbonate minerals by microorganisms is advantageous for the capture and immobilization of contaminants with an ionic radius similar to Ca2+. This reactivity extends from coprecipitation and isomorphic replacement of Ca2+ during crystal growth (Langmuir, 1997; Mitchell and Ferris, 2005). Groundwater contaminants identified as candidates for mitigation by microbially induced mineral precipitation include Cd2+, Pb2+, Zn2+, and Hg2+ as well as radionuclides 90Sr and 60Co (Mitchell and Ferris 2005; Eltarahony et al., 2020).
Another useful aspect of microbial carbonate mineral precipitation is the effectiveness of the process in cementing unconsolidated sediments (biocementation/bioconsolidation) and infilling of empty pore spaces (biomineral plugging/grouting). Practical applications in geomechanics include improvement of shear strength and stiffness of loose (uncompacted) deposits of alluvium, whereas permeability reduction is the primary goal in hydrogeological engineering to reduce groundwater invasion into tunnels, oil field production operations, and other underground works (Jack et al., 1991, 1993; Ferris and Stehmeier, 1992; Ferris et al., 1996; Anbu et al., 2016; Minto et al., 2016).
In comparison to traditional chemical-based grouts, the precipitation of carbonate minerals by microorganisms through biostimulation or bioaugmentation not only requires lower injection pressures but also penetrates deeper into smaller pores and fracture apertures (Minto et al., 2016). This is because the nutrient and mineralizing solutions needed to induce microbial carbonate mineral precipitation have a viscosity close to that of water (near 1.0 mPa · s), whereas the viscosity of chemical cements tends to be much higher (approximately 50 mPa · s).