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Review

Bio-Remediation of Heavy Metal-Contaminated Soil by Microbial-Induced Carbonate Precipitation (MICP)—A Critical Review

1
School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
2
School of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China
3
Institute of Materials Engineering, Nanjing University, Nantong 226000, China
*
Authors to whom correspondence should be addressed.
Sustainability 2023, 15(9), 7622; https://doi.org/10.3390/su15097622
Submission received: 28 March 2023 / Revised: 27 April 2023 / Accepted: 28 April 2023 / Published: 6 May 2023

Abstract

:
Biomineralization processes utilizing microbial-induced carbonate precipitation (MICP) have recently shown promise as an effective approach for remediating heavy metal contamination. This article offers a comprehensive review of the latest research on MICP-mediated heavy metal remediation, with a focus on the characteristics of heavy metals in the treated environment, such as copper, cadmium, lead, nickel, zinc, chromium, and mixed heavy metals. The review summarizes experimental results from various heavy metals treated by MICP, including the enrichment and screening of new urease-positive bacteria, the mineral structure of different heavy metal precipitates, and the efficiency of the MICP technology. Recent advancements in the MICP technology regarding heavy metal removal, long-term stability, and practical applications are also discussed. Additionally, the limitations of the technique and existing solutions are reviewed. In addition, it provides insights on future directions for further research and development of the MICP approach for heavy metal remediation, in order to optimize the technique and improve its efficiency. Overall, the review highlights the potential of MICP as a viable method for heavy metal remediation, offering promising results for the removal of a variety of heavy metal contaminants from contaminated environments.

1. Introduction

Due to domestic and industrial pollution, our environment is plagued with increasing heavy metal (HM) problems, especially in soil and water resources [1]. HMs of particular concern include copper (Cu), cadmium (Cd), lead (Pb), mercury (Hg), zinc (Zn), nickel (Ni), arsenic (As), and chromium (Cr). The HMs in the environment mainly come from the combustion of municipal waste, pesticides, sewage, fossil fuels, mining, and smelting, among others (Figure 1A) [2]. A study reported that due to mining and metallurgical activities, a large amount of Cd and Ni was found in fishes in the river between Norway and Russia [3]. There are also varying levels of HM pollution in Taihu Lake and the East Sea, China [4,5]. These HMs would eventually enter the food chain and accumulate in biological tissues, causing damage to multiple organs, such as the lungs, kidneys, liver, and heart, by causing the production of reactive oxygen species generation, weakening of the antioxidant defense, enzyme inactivation, and oxidative stress [6]. Therefore, environmental protection and HM remediation approaches are urgently needed. The specific sources of HMs, their toxicities, and threats to humans are summarized in Table 1.
In recent times, the traditional technologies of HM remediation (Figure 1B) include physical methods (physical adsorption [24], leaching [25], and electrokinetic remediation [26]), chemical methods (flocculation precipitation [27], electrolysis [28], ion exchange adsorption [29] and chemical precipitation [30]), and biological methods (phytoremediation [31], microbial adsorption [32], microbial fuel cell [33] and biomineralization [34]). Among the proposed methods, biological or microbiological methods have the advantages of relative sustainability, environmental benignity, and low cost [35,36,37]. Lately, biomineralization has been regarded as a high-efficiency, long-term stability, and eco-friendly method, showing great potential in the field of environmental modification [38,39,40]. Biomineralization is a process by which organisms induce minerals [41], and through microorganisms (such as bacteria, fungi, etc.), to conduct bioinduced mineralization and influence the occurrence of mineralization with the mediation of nonliving organic substrates to produce HM precipitation, so as to achieve the purpose of HM remediation [42]. It includes the formation of silicate in algae and diatoms [43], carbonate in invertebrates [44], calcium phosphate and carbonate in hard tissues of vertebrates [45], as well as carbonate [46] and phosphate [47] produced in microbial metabolic activities. So far, most of the applications of biomineralization in engineering belong to the category of microbial mineralization [48]. Remediating HMs with microbial-induced carbonate precipitation (MICP) through the urea hydrolysis pathway (one type of microbial mineralization) has attracted much attention [1,49].
Figure 1. (A) Diagrammatic explanation about heavy metal pollution in the environment [50]. Copyright 2022 Elsevier. (B) Traditional HMs treatment technology.
Figure 1. (A) Diagrammatic explanation about heavy metal pollution in the environment [50]. Copyright 2022 Elsevier. (B) Traditional HMs treatment technology.
Sustainability 15 07622 g001
Although a variety of HM treatment technologies based on MICP have been developed, the remediation of HMs by MICP in practical applications still needs to be explored. Therefore, this review aims to provide an overview of the urea hydrolysis-induced carbonate mineralization approach for heavy metal remediation, including its advantages and limitations, and discuss its potential for practical application in the future.

2. Microbial-Induced Carbonate Precipitation

2.1. Mechanism of HM Mineralization with MICP

Due to the rich variety of microorganisms, the MCIP process can be achieved through photosynthesis, ammoniation, denitrification, sulfate reduction, anaerobic sulfide oxidation, and methane oxidation [51,52,53,54,55,56]. Firstly, microorganisms utilize metabolites produced by their metabolic processes, such as ammonia, sulfate, and amino acids, or compounds absorbed from the environment, such as carbon dioxide (CO2), as carbon and energy sources. During metabolism, microorganisms catalyze the conversion of these compounds into CO2, which is a prerequisite for the production of carbonate precipitation [46]. Then, microorganisms further utilize CO2 to participate in the formation process of carbonate precipitation, thereby achieving different metabolic pathways that induce carbonate precipitation (Figure 2).
The most common and effective MICP process is caused by the hydrolysis of urea by urease. Urea is decomposed by urease to form ammonium salt and carbonate ions, which are conducive to the combination and existence of HMs and carbonate [57,58]. The process of MICP is as follows: firstly, urease-positive bacteria (UPB) produce urease [59]; secondly, the urease hydrolyze the urea to produce ammonium and carbonate ions [60]; finally, the produced carbonate ions react with metal ions (M2+) to form carbonate precipitates [61]. The main biologically mediated process of MICP can be summarized into the following four parts: (a) urea hydrolysis (Equations (1) and (2)) [59,62]; (b) chemical equilibrium (Equations (3)–(5)) [62,63]; (c) heterogeneous nucleation (Equation (6)) [64]; and (d) successive stratification [65,66].
CO NH 2 2 +   H 2 O   Urease NH 2 COOH   + NH 3
NH 2 COOH +   H 2 O   Spontaneous   H 2 CO 3 +   NH 3
2 NH 3 + 2 H 2 O     2 NH 4 + + 2 OH
H 2 CO 3   HCO 3 +   H +
HCO 3 +   H + + 2 OH     CO 3 2 + 2 H 2 O
CO 3 2 + Cell M 2 + Cell MCO 3 s
The mechanism through which HMs are removed in the biological induction process can be summarized as the following three points:
(1)
HM elements (such as lead and cadmium, etc.) can be directly captured by biosorption processes, such as transport across the cell membrane, complexation, ion exchange, rain, and physical adsorption [67,68]. Then, the captured HMs react with the microbially produced carbonate and form the corresponding carbonate precipitates;
(2)
in the presence of calcium, the microbially induced calcite can also adsorb HMs (such as Cd and Pb) [69], and co-precipitation of CaCO3 and MCO3 (M = Cd, Pb, etc.) can occur during HM removal;
(3)
the MICP process induced by special bacteria that can produce urease and reductase at the same time (such as Bacillus thuringiensis T124) cannot only reduce Cr (VI) but also increase the pH of the microenvironment and make Cr reach the precipitation condition [70]. These proven effective mechanisms provide many references for MICP technology in HM removal.

2.2. Microorganisms

In addition to the previously discovered fungi [71,72], actinomycetes [73], yeast species [74], and bacteria [75,76,77], recent five-year studies have isolated and identified lots of new UPB (Table 2) [67,70,78,79,80,81,82,83,84,85,86,87,88,89,90].
The genus Bacillus, shown in Table 2, is the main UPB isolated in recent years. The isolated Bacillus strains exhibited a wide range of urease activity, from 6–13 to 1082–1120 U/mL (where 1U denotes the amount of enzyme that can hydrolyze 1 μmol of urea per minute), with activity being a crucial factor in enhancing the yield efficiency of urease production [91]. Among them, Sporosarcina pasteurii has been widely used in various applications, including crack repair [92], soil improvement [93], bio-bricks [94,95,96], and remediation of various HMs [90,97] and radionuclides [98].
Table 2. Recent studies on urease-producing microorganisms.
Table 2. Recent studies on urease-producing microorganisms.
MicroorganismActivity (U/mL)Isolation SiteIsolation Time (Year)Ref.
Bacillus sp. WA-Metal-contaminated soil, Shantou, China2022[99]
Acinetobacter sp. H12-Sludge from Qujiang artificial lake, Shaanxi, China2021[78]
Achromobacter sp. L3-Sediments in Datang Industrial Park, Foshan, Guangdong, China2021[79]
Bacillus thuringiensis T12466.4Cr-contaminated soils, Jiangsu, China2021[70]
Lysinibacillus sp.; Pseudochrobactrum sp.; Sporosarcina sp.-Pyrite station, Sichuan, China2021[67]
Arthrobacter sp. MF-2; Curvibacter sp. HJ-1-Soil, Nanjing Agricultural University, China2020[81]
Bacillus cereus D2194.6Ni mine, Hongqiling, Jilin Province, China2020[83]
Enterobacter sp. CJW-1-Paddy soil, Sichuan, China2020[86]
Bacillus lysine-Pb-contaminated soil, Hubei, China2020[85]
Sporosarcina luteola1082–1120Alkaline and acidic tailings soil, Guerrero State, Mexico 2020[89]
Sporosarcina pasteurii11.08Rhizosphere soil, Zanjan, Iran 2020[90]
Bacillus amyloliquefaciens HU-48; Bacillus atrophaeus HU-11; Bacillus aryabhattai HU-39; Proteus mirabilis HU-57; Bacillus subtilis HU-346–13Barn horse’s soil, College of Agriculture, Al-Jadriya horsemanship club and Baghdad University, Iraq 2019[82]
Bacillus cereus NS4-Industrial soil, Shanghai, China 2019[84]
Paecilomyces inflatus; Plectosphaerella cucumerina-Perovskite straw stalactites on the concrete ceiling2019[88]
Alcaligenes aquatili-Seawater 2019[80]
Bacillus cereus P95–55Peat soil, Miri, Malaysia2018[100]

2.3. Current Applications of MICP

MICP is an efficient and environmentally friendly technology that has been mainly applied to civil engineering and the ecological restoration process in recent years, particularly for the solidification and restoration of HMs [86,98,101]. Figure 3A shows the schematic diagram of bacteria adsorption of HMs and biomineralization in soil. In the process of biomineralization, the bacterial cell surface has negatively charged groups that can bind divalent cations to the cell surface at neutral pH, which can provide good nucleation sites for various types of carbonic precipitate formation (Figure 3B) [78,102,103,104,105]. This highlights the significant role played by bacteria in carbonic precipitate formation, which may have implications for HM mineralization or rock formation processes in the environment. Moreover, this biomineralization process can provide a novel approach for material synthesis in biotechnological applications, such as the production of biomineralized materials and biomineral catalysts. Thus, investigating biomineralization has both theoretical and practical significance, and the types of UPB and cell surface or extracellular polymers (EPS) directly or indirectly affect the formation of minerals [48]. Furthermore, the composition of the medium, temperature, pH, saturation index, dissolved organic carbon release, and [M2+]/[CO32−] ratio also play an important role in the formation of the final crystals [106]. Table 3 summarizes the morphology and size of the crystals of HMs in the MICP process.

3. HM Stabilization Using MICP

The MICP technology based on UPB has the advantages of low-energy consumption and environmental friendliness. Hence, it can be developed and applied to the removal of HMs [38]. Therefore, based on the theoretical foundations above, several research studies on the removal of HMs using MICP have been reported in recent years (Table 4). These prominent HMs will be categorically elaborated in this segment.

3.1. Copper

Cu pollution in nature is mainly due to the discharge of agricultural and industrial wastewater into water and soil [110]. In the remediation of Cu pollution by MICP, it generally shows a low removal efficiency due to the toxicity of Cu ions towards UPB. Chuang et al. [112] found that the free Cu ion could reduce the urease activity of Sporosarcina pasteurii by 98% at a free Cu ion concentration of 150 mg/L. In addition, the fitting results of the four-parameter logistic function showed that the half-maximal inhibition concentration (IC50) was 0.39 mg/L based on free Cu concentration in soil solution and urea hydrolyzed amount, as displayed in Figure 4. Furthermore, Duarte-Nass et al. [113] realized that the co-effect of the Cu ion and ammonium end product from urea hydrolysis could synergistically reduce the removal efficiency by 10%. This is because the Cu ion has a high affinity for ammonia, and the end product keeps the metal soluble, thereby impeding the formation of copper carbonate and subsequent precipitation of Cu.
Compared with most MICP-related research works, which are limited to additional microorganisms, Chen and Achal [114] were the first to utilize bio-stimulation in immobilizing Cu in situ in the soil. The bio-stimulation reduced the soluble exchange fraction of Cu by 96.60%, which greatly improved the low removal rate (10%).

3.2. Cadmium

Cd is a highly toxic HM and is widely used in industry, mainly for the manufacture of Ni-Cd batteries, pigments, electroplating, and the like [11,115]. Zhao et al. [109] isolated and screened Cupriavidus sp. and Bacillus sp. strains with high urease activity to dispose of cadmium-contaminated wastewater and soil, with removal rates of 80.10% and 53.8%, respectively. From another report [116], Sporosarcina pasteurii, which also has high urease activity, decreased exchangeable Cd by 85.% and 89.3% after being used to treat Cd-contaminated sandy and clay soil, respectively. This is higher than the earlier study. The concentration of Cd affects the normal metabolic activities of UPB [65]. Studies have shown that the presence of Ca could increase the removal rate of Cd [117]. The presence of Ca could increase the tolerance of bacteria towards Cd, which is consistent with the previous study that Ca protects bacteria from Cd stress [118]. Aside from protecting bacteria by adding Ca, Peng et al. [86] directly screened Enterobacter CJW-1 with high Cd tolerance and found that using oyster shell waste to replace urea as a nutrient source to drive MCIP offered unexpected effects. Given the limited tolerance of a single strain, Yin et al. [101] constructed a bacterial consortium that could adapt to different environmental conditions (temperature, Cd concentration, and pH) and experimented with efficient mineralization of Cd. The mineralization mechanism diagram is shown in Figure 5.

3.3. Lead

Lead is one of the “three major” HMs, with a density of more than 5 g/cm3. A small amount can cause harm to the human system, especially affecting the development of children [119]. Sharma et al. [120] reported the use of blue-green algae alone or in combination with Bacillus sphaericus and Sporosarcina pasteurii to remediate Pb-contaminated sand. The mineralized amount of Pb was 94–99.2%. Most of the previous studies only focused on the relatively low concentrations of Pb. For instance, Jiang et al. [121] used Sporosarcina pasteurii strain to inoculate a nutrient solution containing 0–50 mM Pb(NO3)2 and found that 30 mM of Pb is a marginal value for the influence of bacterial growth and related urease activity. Different from the urea hydrolysis drive, Eltarahony et al. [119] used Proteus 10B for nitrate reduction-driven calcium carbonate precipitation to remediate Pb and Hg in aerobic and anaerobic conditions.

3.4. Nickel

Aside from Ni affecting seed germination, seedling growth, nutrient absorption, cell oxidation, and metabolism, it can also change membrane permeability, protein content, and structure [122]. Given that biochar is a common carrier in biochemical experiments, Zhang et al. [84] combined the biochar of Cinnamomum leaves with MICP to immobilize Ni. However, the result was opposite to the effect of biochar in increasing microbial activity [123]. Recently, Do et al. [83] isolated a psychrotolerant Ni-resistant (400 mg/L) bacterial strain, which can immobilize Ni at a low temperature of 10 °C

3.5. Zinc

Zinc is one of the essential trace elements for plants and animals, but when its amount exceeds 1165 μg/g or 0.008–0.125 mg/L, its toxicity will gradually threaten the modeling of biological communities [124,125,126]. Therefore, Aoki et al. [127] isolated an aerobic denitrifying bacterial strain (Acinetobacter sp. WKDN) with the ability of carbonate biomineralization, which effectively removed dissolved zinc in groundwater.

3.6. Arsenic

As, referred to as the “king of poisons”, has been one of the most notorious poisons since ancient times [128,129]. However, the behavior of As during the transformation process is unclear. Given this, Wang et al. [20] reported the mechanism of arsenic immobilization and migration in the above process. The stability of HMs containing calcite should be considered when removing HMs through the conversion of calcite to hydroxyapatite. Furthermore, the immobilization effect of hydroxyapatite on HMs such as As should not be overestimated (Figure 6).

3.7. Chromium

Cr mainly exists in nature in two stable forms: Cr (III) and Cr (VI) [22]. Cr (III) produces stable metal–organic complexes with several amines and carboxylates [130]. In contrast, Cr (VI) may be more easily contacted and used by organisms due to its high mobility and high toxicity, causing diseases such as body mutagenesis and carcinogenesis [131,132]. The focus of the treatment of Cr pollution is to restore hexavalent Cr to a state of lower toxicity [133]. Zhao et al. [70] screened a Cr-resistant mineralization strain, Bacillus thuringiensis T124, which can biologically reduce Cr (VI) to lessen its toxicity and afford mineralization. Besides the reductase acting on the cell wall, the underlying mechanism of Cr mineralization was that Cr replaced part of the CaCO3 crystal lattice to mineralize Cr, thereby forming Ca-Cr co-precipitates (CaCO3 and Ca10Cr6O24 (CO3)) (Figure 7).

3.8. Mixed HMs

Compared with single HM pollution, actual soil pollution is more complicated [134]. Khadim et al. [82] selected two Bacillus strains with a high tolerance towards toxic HMs to remove Cd and Ni. After 48 h of incubation in the initial concentration of Cd and Ni at 500 mg/L, the removal rates of Cd and Ni were 96 and 89%, respectively. Furthermore, Qiao et al. [67] selected Sporosarcina kp-4 and kp-22 for the biomineralization of Cu, Zn, Ni, and Cd. They confirmed that UPB can co-precipitate multiple HMs even without tolerance. By inducing the mineralization of soil containing Pb, Zn, and Cd, Pasteurella bioremediation is superior to chemical precipitation technology in terms of long-term stability [90,97]. Furthermore, MICP is used for metal ion mineralization in high-salt produced water or the seawater desalination process [80,135].
Table 4. Application of MICP to HM removal in recent years.
Table 4. Application of MICP to HM removal in recent years.
HMBacterium/BacterialCulture
Medium
Initial Key Test
Condition/Variables
Removal Rate (%)Advantages/ImprovementsRef.
CuMixed flora:
Bacillus genus;
Actinobacteria phyla
Nutrient Broth of Urea (NBU) and Calcium SourceThe background value in the soil is 14.25 mg/kg;
mixed with 25 and 50 mg/kg
More than 90Avoid adding UPB bacteria to the soil, and domesticating UPB through in situ biological stimulation.[114]
Sporosarcina pasteuriiUrea, calcium, tryptic soy broth (TSB)The background value in the soil is 250 mg/kg-Relationship between the Cu concentration in the soil solution and the hydrolysis of urea was established, and the IC50 of the free Cu ion concentration in the soil solution was determined to be 0.39 mg/L.[112]
Sporosarcina pasteuriiNH4-YE medium32 mg/L10Show that the low removal rate of Cu is due to the complexation of Cu2+ with ammonia due to the hydrolysis of urea, and the sequential process of bacterial growth and Cu precipitation decoupling to achieve effective control of urea demand.[113]
CdAchromobacter sp. L3Basal media (BM)10 mg/L100Separate the high-efficiency Sulfamethoxazole degradation, and Cd mineralization strains from wastewater at the same time.[79]
Cupriavidus sp. CZW-2;
Bacillus sp. CZW-5;
Bacillus sp. CZW-9;
Bacillus sp. CZW-12
Lysogeny broth media225 mg/L80.10,
72.64,
76.70
73.40
Research on the crystallinity, size, bioavailability, and stability of Cd-mineralized precipitates in the MICP process has been perfected.[109]
Enterobacter sp. CJW-1Luria Broth (LB) liquid medium20, 40, 60, 80, 100 mg/L (LB medium);
20 mg/kg (soil)
99.50, 64.86, 51.83, 40.95 and 10.82;
56.10
Combination of urea-decomposing bacteria and oyster shell waste may have a better mineralization effect on Cd in the soil. At the same time, it solves the pollution problem of oyster shell waste, the problem of ammonium root treatment, and the economic pressure caused by urea.[86]
Serratia marcescens (NCIM2919);
Enterobacter cloacae EMB19 (MTCC10649)
Nutrient medium containing 25 mM of CaCl2 and 2% urea50 mg/LWith calcium (98, 53); without calcium (16, 8)Calcium–cadmium co-crystallization is beneficial to the removal of Cd, and the addition of calcium can effectively improve the removal rate of cadmium.[117]
Sporosarcina pasteuriiNutrient Broth of Urea (NBU) and Calcium Source56, 112, and 225 mg/L;
10, 20, 40, and 50 mg/kg (sandy and clay soils)
99.6, 99.8, and 99.8;
Sandy soils: 85.9, 61.1, 74.3, and 80.3.
Clay soils: 89.3, 86.6, 76, and 75.6
Reports on the application of MICP in clay and its research on the immobilization of HMs.
The minimum inhibitory concentration (MIC) of bacteria to Cd is 2 mM.
[116]
Mixed flora:
Klebsiella pneumoniae;
Escherichia coli
Brain heart infusion (BHI) medium3710 mg/L97.4 ± 1.1It proves that there is a carbonate precipitation process induced by microorganisms in anaerobic granular sludge.[136]
Urease-producing consortium (UPC):
Sporosarcina;
norank_f_Bacillaceae;
unclassified_f_Bacillaceae
NBU media100 mg/L92.87Construct a bacterial consortium with high urease activity that can adapt to different environmental conditions; characterize the urease gene and bacterial community succession during the adaptation process.[101]
Cr (VI)Bacillus thuringiensis T124LB mediumThe background value is 39.89 mg/kg;
mixed with 100 mg/L
-By screening Bacillus thuringiensis T124, which produces reductase and urease, it first reduces Cr(VI) to a state of low toxicity and then undergoes stable mineralization.[70]
PbSporosarcina pasteuriiNH4-YE medium2072, 4144, 6216, 8288, and 10,360 mg/L-A hypothetical multilayer precipitation structure is proposed; it is found that a lead concentration of 30 mM is the marginal value that Sporosarcina pasteurii (OD600 = 1.5) can tolerate.[121]
Bacillus sphaericus;
Sporosarcina pasteurii
BG11 broth and nutrient brothAround 225 mg/L94–99.2Use cyanobacteria and bacteria to enhance the strength of artificially polluted sand and immobilize pollutants.[120]
Lysinibacillus fusiformisLB medium200 mg/LpH = 3, <40;
pH = 4, around 90
The acidophilic UPB that can adjust the pH value of the solution is screened out, and then the Pb in the acid wastewater can be removed.[85]
NiBacillus cereus NS4NBU media50 and 100 mg/L89 and 66Apply biochar to the MICP process to remediate Ni.[78]
Bacillus cereus D2Nutrient broth (NB) medium50 mg/L73.47Bacillus cereus D2, which is resistant to low temperatures (10 °C), was selected, which can mineralize Ni in low-temperature areas.
Acinetobacter sp. H12Basal medium3 mg/L56.67Use denitrifying bacteria Acinetobacter sp. H12 to study its ability to remove F and Ni2+.[78]
Cd and PbMicrococcus sp. NCTC-1716Urease broth medium½ MIC of each HMCd: 60.66;
Pb: 97.20
Select Micrococcus sp. NCTC-1716 from calcareous soil proved to be useful for HMs removal.[137]
Cd and NiBacillus and Proteus speciesNB medium500 mg/L of eachCd:96;
Ni:89
The precipitation of metal carbonates induced by microorganisms with and without calcium precipitation is reported.[82]
Cu, Zn, Ni, and CdSporosarcina kp-4;
Sporosarcina kp-22
BPU fluid medium160 mg/L of each75.10, 98.03, 59.46 and 96.18Explore the precipitation modes of different HMs and the role of bacteria in biomineralization.[67]
Pb and HgProteus mirabilis 10BBasal medium350 mg/L of eachAerobic: (Pb: 95.2 and Hg: 91.1);
Anaerobic (Pb: 92 and Hg: 88.3)
Proteus mirabilis 10B was first used to reduce nitrate, which drives calcium carbonate precipitation to remediate Pb and Hg in aerobic and anaerobic conditions.[119]
Pb and CuPaecilomyces inflatus;
Plectosphaerella cucumerina
NB medium100 mg/LPb: 100 and 100;
Cu: 13 and 10
Isolated fungal strains can induce carbonate precipitation.[88]
Pb, Zn, and CdSporosarcina pasteuriiNutrient solution recommended by German strain Center342 mg/kg;
6.79 mg/kg;
235 mg/kg
Pb: 33.3–85.9;
Zn: 21.4–66.0;
Cd: 13.6–29.9
It is proposed to pre-mix the required UPB, nutrient substrate, and calcium salt into the contaminated soil through a mixing method to realize the one-time efficient solidification of HM ions in the soil.[97]
Pb, Cd, and ZnStenotrophomonas rhizophila A323;
Variovorax boronicumulans C113;
Sporosarcina pasteurii DSM33
BPU broth medium20,720, 62,160 and 103,600 mg/L;
11,240, 33,720 and 56,200 mg/L;
6540, 19,620, and 32,700 mg/L
Pb: 96.25, 95.93 and 98.71;
Cd: 71.3, 73.45 and 97.15;
Zn: 63.91, 73.81, and 94.83
Stenotrophomonas rhizophila and boronicumulans ariovorax were firstly reported as ureolytic bacteria for metal biomineralization.[90]
Mn, Pb, Cd, Sr, Ba, and ZnSporosarcina luteola UB3;
Sporosarcina luteola UB5
NB medium NH4-YE medium--Evaluate its ability to produce bio-carbonate, reduce porosity and permeability, and fix biologically effective toxic elements.[89]
As, Cd, Mn, Ni, Ba, and SrUreolytic bacterial consortium:
Sporosarcina;
Arthrobacter
NB medium1.091 mg/L,
0.011 mg/L,
0.4623 mg/L,
0.041 mg/L,
1.074 mg/L and
342 mg/L, respectively
As, Cd, Mn, Ni: 100;
Ba: 92.2;
Sr: 94.2
MICP is applied to the shale oil and gas industry to remove calcium in the produced water to reduce the possibility of clogging the wellbore and damaging the formation.[135]

4. Challenges and Prospects of MICP in Removing HMs

4.1. Improvement of HM Removal

Biomineralization is aimed at immobilizing free HM ions using biological methods. However, a low fixation rate (<20%) can occur during the process of biomineralization [113,117]. Improving the removal of HMs can be achieved by including urea, bacteria, and other techniques. In a related study, Sun et al. [138] found that copper tends to complex with ammonium as the pH increases, thereby reducing the formation of CuCO3. Nonetheless, the reduction in the amount of urea added can minimize the generation of ammonium and eventually improve the removal of Cu. The tolerance of UPB to HMs will directly affect the decomposition of urea and the precipitation of HMs. The screening of UPB that can tolerate high concentrations of HMs has become the first choice for MICP processes. Bhattacharya et al. [117] found that the removal rate of Cd increased from 16% to 98% by supplementing with Ca. Moreover, Fang et al. [107] further found that supplementing Ca improves bacterial tolerance and cadmium removal by reducing the Cd on the surface of the bacteria. This increase in resistance is equally applicable to Cu, Mn, Zn, and Ni. Furthermore, porous materials (including biochar, alginate, metakaolin, expanded clay, granular-activated carbon, and zeolite), as well as colloidal substances (such as calcium alginate, agarose, whey protein concentrate, and gelatin), all have varying degrees of protection against bacteria [139,140,141]. These materials may be used in MICP to remediate HM pollution. Many protection measures can provide several ideas and references for the research of MICP in the mineralization of HMs.

4.2. Long-Term Stability of MICP-Treated Soil

The long-term stability of contaminated soil is an indicator for evaluating the effect of MICP on HM fixation. To some extent, the persistence of the biomineral deposits generated determines the overall long-term stability of the soil matrix. Acid leaching and freeze–thaw (FT) tests are often used to identify this stability [97,142].
Chen and Achal [143] found that simulated acid rain (SAR) with a pH of 3.5 would limit soil microbial activity and biomass, but not affect the stability of biominerals. Furthermore, it is reported that under the SAR with a pH of 3.5, the dissolved Cu and Pb contents of contaminated soil increased by 16 and 15%, respectively. When the SAR pH was 2.5, the increase was 27.2 and 23.6%, respectively. Interestingly, the acid resistance of the different deposited HMs was almost non-differentiable in the acid attack test, but the lowest acid resistance value was 2.0 [144]. Han et al. [34] found that after 60 FT cycles, the average exchangeable content of Cu and Pb in contaminated soil treated by MICP only increased by 12.2 and 8.2%, respectively.
In summary, the dissolution of HMs does not exceed 20% when treated by acid rain with pH not lower than 3.5 and 60 FT cycles. Although the above research data show that only a small amount of HMs are eluted, these small amounts may still cause harm to humans and nature. Furthermore, these studies are only limited to laboratory conditions, and the stability of the contaminated soil treated may be affected by not only a single factor in the actual environment. Therefore, it is necessary to study the changes of various soil indicators under the conditions of mixed factors and conduct large-scale experimental studies.

4.3. Large-Scale Practical Application of MICP in Contaminated Soil

MICP has made great achievements in repairing HM-contaminated soil under laboratory conditions, but large-scale applications can reflect the application prospects of this technology in practical situations. The success of large-scale cultivation of UPB under non-sterile conditions provides a sufficient source of bacteria for practical applications of MICP [145]. There have been many practical applications in large-scale civil engineering, such as 5 m sand pillar cementation, 100 m3 sand biological grouting, 1000 m3 gravel wellbore biological grouting, and windbreak as well as fixation [57,146,147,148], but the practical application of MICP in contaminated soil is rarely reported.
Although most of the potential applications of MICP technology in the remediation of various HMs pollution have been discussed, there are still some questions that need to be answered before MICP can be widely used on a practical commercial scale. To make MICP large-scale commercial applications, it is necessary to further improve or perfect MCIP research, including but not limited to the following:
(1)
During the process of MICP, urea will produce not only carbonate but also ammonium during the decomposition process. Therefore, determining the optimal substrate balance (e.g., urea and Ca) for various MICP applications to optimize the precipitation efficiency of HMs, may increase economic feasibility and reduce the production of harmful by-products.
(2)
The MICP process is more complicated than simple chemical processes and controlled by many factors, such as microbial tolerance, pH, and temperature. Compared with MICP based on suspension cells, MICP based on protective materials has greater potential.
(3)
The nutritional source of laboratory-grade MICP is economically limited in practical applications. Urea-containing wastewater produced by fertilizer plants, the urea synthesis industry, or human activities (sewage) seems to be the simplest solution [149,150]. Seeking more low-cost sources of nutrition can make the application of MICP more economical.
(4)
Due to the influence of the traditional mindset, the behavior of adding microorganisms (albeit harmless microorganisms) into the environment is not accepted by most people. Therefore, in situ simulation to induce bacteria with urease decomposition is an idea worth considering.
(5)
Carry out large-scale experiments and construct mathematical models related to the large-scale experiment process (e.g., urea decomposition and growth kinetics, precipitation kinetics, crystal growth, and microbial–mineral interactions, etc.), which can help evaluate the transportation process—important in controlling MICP for engineering field applications.
(6)
Develop induced polarization (geophysical method) detection tools to detect and evaluate the propagation of MICP in the treatment area in space and time.
The large-scale commercial application of MICP involves many disciplines and technologies. The cooperation of various discipline teams is required to promote the transition of MICP-based technology from the laboratory to the field.

4.4. Efficient Removal of Heavy Metals from Contaminated Soil

HMs can be stabilized in the soil for a long time using MICP technology, but still remain in the soil. It is a huge challenge to completely separate or extract them from the contaminated soil. Furthermore, the prevalence of acid rain presents a significant threat to the presence of HM sediments. As acidification increases, the previously immobilized HMs may be reactivated. This reactivation could potentially result in significant environmental consequences [143]. Therefore, this work supplements a method for UPB to collaborate with the phytoremediation for isolating HMs from heavy metal-contaminated soil. Because microbial synergistic phytoremediation is an effective alternative method for the in situ treatment of heavy metal-contaminated soil, microorganisms can promote plant growth and further enhance phytoremediation capacity [151]. In the meantime, plants can provide beneficial nutrients or organic matter to microorganisms [152]. Furthermore, the application of UPB in sandy soils has shown good plant compatibility [153]. The MICP technology quickly inactivates HMs, which can reduce the risk of Cd migration due to environmental changes (such as rainfall, etc.) that are inevitable in traditional phytoremediation or solve the problem of plant survival under high concentrations of HMs. Combining with the use of genetically modified super-enriched plants for continuous repair can solve the long-term durability problem of mineralized HMs.

5. Conclusions

In this work, the basic mechanism of MICP removal of HMs and the latest research progress were summarized by comparing extensive study results. Research progress includes screening new UPB and their application together with the improvement of MCIP technology in the field of HM pollution control.
Based on the findings, the following recommendations are proposed for the repair of MICP technology. Firstly, further research is necessary to determine the optimal conditions for the release of ammonium during MICP treatment. This is a critical factor that affects the effectiveness of the technology in removing harmful HMs. Secondly, developing more sustainable and cost-effective sources of urea could significantly reduce the environmental impact of MICP treatment, making it more commercially viable. Lastly, it is crucial to enhance our understanding of the activity and sensitivity of microorganisms involved in the MICP process. This understanding can lead to the development of more efficient and effective treatment strategies.
This article discusses the prospects and ideas of the large-scale application of MICP and supplements the method of complete HM removal. Hence, researchers will be inspired in solving the key development issues necessary to promote MICP technology to save HM-contaminated soil and offer commercial-scale applications.

Author Contributions

Conceptualization, L.C. and Q.N.; methodology, L.C.; writing—original draft preparation, S.W. and L.F.; writing—review and editing, L.C. and S.W.; investigation and software S.W.; supervision and project administration, Q.N. and M.F.D. All authors have read and agreed to the published version of the manuscript.

Funding

The authors would like to thank the support from the Jiangsu Province ‘‘Six Talent Peak’’ program (XCL-111), Jiangsu Province Key Project of Research and Development Plan (BE2020676), the program of the Nantong Science and Technology Project (Grant no. MS22021006), and the China Postdoctoral Science Foundation (Grant no. 2022T150275 and 2020M671359).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The data presented in this study are available on request from the corresponding author.

Conflicts of Interest

The authors declare no conflict of interest.

Abbreviations

The following abbreviations are used in this manuscript:
UPBUrease-producing bacteria
EPSExtracellular polymers
SARSimulated acid rain
MICPMicrobial-induced carbonate precipitation
HMHeavy metal
IC50Half-maximal inhibition concentration
UPCUrease-producing consortium
NBUNutrient broth of urea
TSBTryptic soy broth
BMBasal media
LBLuria broth
MICMinimum inhibitory concentration
BHIBrain heart infusion
NBNutrient broth
FTFreeze–thaw
CMMCarbonate-mineralized microorganisms

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Figure 2. Microbial carbonate precipitation induced by different metabolisms [46]. Copyright 2016 Frontiers Media SA.
Figure 2. Microbial carbonate precipitation induced by different metabolisms [46]. Copyright 2016 Frontiers Media SA.
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Figure 3. (A). Soil solidification and HM stabilization [34]. Copyright 2020 Elsevier. (B) Schematic diagram of bacteria adsorption of heavy HMs and biomineralization [58,107].
Figure 3. (A). Soil solidification and HM stabilization [34]. Copyright 2020 Elsevier. (B) Schematic diagram of bacteria adsorption of heavy HMs and biomineralization [58,107].
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Figure 4. Prediction of the inhibitory effect of free Cu concentration in soil solution on urea hydrolysis [112]. The study shows the amount of urea hydrolyzed at each free Cu concentration of the soil solution fitted using a four-parameter logistic function, with the dashed line representing the fit and the black dots representing the experimental data. Copyright 2020 Elsevier.
Figure 4. Prediction of the inhibitory effect of free Cu concentration in soil solution on urea hydrolysis [112]. The study shows the amount of urea hydrolyzed at each free Cu concentration of the soil solution fitted using a four-parameter logistic function, with the dashed line representing the fit and the black dots representing the experimental data. Copyright 2020 Elsevier.
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Figure 5. Cadmium mineralization mechanism with bacterial consortium [101]. Copyright 2021 Elsevier.
Figure 5. Cadmium mineralization mechanism with bacterial consortium [101]. Copyright 2021 Elsevier.
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Figure 6. Arsenic immobilization and migration mechanism in microbial-induced calcium carbonate conversion to hydroxyapatite [20]. Copyright 2021 Elsevier.
Figure 6. Arsenic immobilization and migration mechanism in microbial-induced calcium carbonate conversion to hydroxyapatite [20]. Copyright 2021 Elsevier.
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Figure 7. Hexavalent chromium remediation mechanism in the microbial-reduction mineralization synergistic process [70]. Copyright 2021 Elsevier.
Figure 7. Hexavalent chromium remediation mechanism in the microbial-reduction mineralization synergistic process [70]. Copyright 2021 Elsevier.
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Table 1. Sources of various HMs and their negative impact on humans.
Table 1. Sources of various HMs and their negative impact on humans.
HMsPermissible Limit (mg/L)SourcesSymptoms/DiseaseSeverityRef.
AgencyLimits
Cu (II)WHO a-Textile, paper, paint manufacturing, leather tanning, battery manufacturing, automobile radiator manufacturing, and agricultural resources (wide use of chemical fertilizers and fungicides), etc.Vomiting, anemia, cramps, convulsions, and even death, etc.Average[7,8,9,10]
FAO b0.2
EPA c1.3
Cd (II)WHO0.003Galvanizing and electroplating, manufacturing of batteries, electrical conductors, alloys, pigments, and plastics, stabilization of phosphate fertilizers, etc.Damage to kidneys, gill epithelium, cardiovascular system, and musculoskeletal system, and even death, etc.High[9,10,11]
FAO0.01
EPA0.005
Pb (II)WHO0.001Lead mining, smelting, coal combustion, use of lead-based paint and lead-containing pipes in water supply systems, food canned solder, ceramic glazes, lead-containing batteries, and cosmetics, etc.Damage to the kidneys, central nervous system, liver and reproductive system, basic cell processes, and brain function. Symptoms of poisoning are anemia, insomnia, headache, dizziness, irritability, muscle weakness, hallucinations, and kidney damage.High[9,10,12,13]
FAO0.01
EPA0.015
Hg (II)WHO0.001Natural activities, such as degassing of the earth’s crust, emissions of volcanoes, evaporation of the ocean, gold mining and refining, coal-fired power plants, etc.Cause kidney dysfunction, nervous system problems, sleep disorders, hearing loss, impaired reproductive function, heart problems, etc.High[9,14,15]
FAO-
EPA0.002
Zn (II)WHO-Rock, mineral, steel production and coal or waste burning, etc.Cause stomach cramps, skin irritation, vomiting, nausea, anemia, etc.Low[10,16,17]
FAO2
EPA-
Ni (II)WHO0.02Electroplating, batteries, electronic equipment, alloys (such as stainless steel), pesticides, fertilizers, and herbicides, etc.Allergies, kidney and liver diseases, infertility, dermatitis, stomach pain, gingivitis, migraine, insomnia, and nausea, etc.High[9,10,18,19]
FAO0.2
EPA0.1
As (III),
As(V)
WHO-Coal-fired power plants, mining, smelting, agricultural pesticides, and volcanic activities, etc.Cause cardiovascular disease, chronic bronchitis, liver and kidney damage, etc.High[20,21]
FAO-
EPA-
Cr (VI), Cr (III)WHO0.005Alloy manufacturing, dyes and pigments, electroplating, metal finishing, petroleum refining, leather tanning, wood preservation, corrosion inhibitors in conventional and nuclear power plants, etc.Damage the liver and kidneys, cause skin lesions or rashes, and be mutagenic, carcinogenic, and teratogenic.High[9,10,22,23]
FAO0.1
EPA0.1
a Drinking water quality guidelines of the World Health Organization (WHO). b Irrigation water quality guidelines of the Food and Agriculture Organization (FAO). c Drinking water threshold of the Environmental Protection Agency (EPA).
Table 3. Morphology and size of the crystals of HMs in the MICP process.
Table 3. Morphology and size of the crystals of HMs in the MICP process.
TypesHMs SourceMorphology of PrecipitationSize (µm)Ref.
AsNaAsO2, Na2HAsO4Rhombus, spherical, or double pyramid0.2–2[20]
CdCdSO4, CdCl2 Sparsely soluble, irregular shape, sphere0.5–50[82,108,109]
CrK2Cr2O7SphereApproximately 0.1[70]
CuCuCl2Sphere5–10[110]
MnMnCl2Sphere<3[89]
NiNiCl2Irregular shape, rhombus10–40[82]
PbPbCl2Sphere, platy5–50[89,111]
ZnZnCl2Acicular, fibro-radial1–100[89,111]
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Wang, S.; Fang, L.; Dapaah, M.F.; Niu, Q.; Cheng, L. Bio-Remediation of Heavy Metal-Contaminated Soil by Microbial-Induced Carbonate Precipitation (MICP)—A Critical Review. Sustainability 2023, 15, 7622. https://doi.org/10.3390/su15097622

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Wang S, Fang L, Dapaah MF, Niu Q, Cheng L. Bio-Remediation of Heavy Metal-Contaminated Soil by Microbial-Induced Carbonate Precipitation (MICP)—A Critical Review. Sustainability. 2023; 15(9):7622. https://doi.org/10.3390/su15097622

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Wang, Sheng, Longyang Fang, Malcom Frimpong Dapaah, Qijian Niu, and Liang Cheng. 2023. "Bio-Remediation of Heavy Metal-Contaminated Soil by Microbial-Induced Carbonate Precipitation (MICP)—A Critical Review" Sustainability 15, no. 9: 7622. https://doi.org/10.3390/su15097622

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