microbiologically induced calcite precipitation

All three principal kinds of bacteria that are involved in autotrophic production of carbonate obtain carbon from gaseous or dissolved carbon dioxide.{{cite book|editor1=Riding, E.|editor2=Awramik, S.M.|date=2000|title=Microbial Sediments}} These pathways include non-methylotrophic methanogenesis, anoxygenic photosynthesis, and oxygenic photosynthesis. Non-methylotrophic methanogenesis is carried out by methanogenic archaebacteria, which use CO₂ and H₂ in anaerobiosis to give CH₄.

Two separate and often concurrent heterotrophic pathways that lead to calcium carbonate precipitation may occur, including active and passive carbonatogenesis. During active carbonatogenesis, the carbonate particles are produced by ionic exchanges through the cell membrane{{Cite journal|last1=Chu|first1=Jian|last2=Ivanov|first2=Volodymyr|last3=Naeimi|first3=Maryam|last4=Stabnikov|first4=Viktor|last5=Liu|first5=Han-Long|date=2014-04-01|title=Optimization of calcium-based bioclogging and biocementation of sand|url=https://doi.org/10.1007/s11440-013-0278-8|journal=Acta Geotechnica|language=en|volume=9|issue=2|pages=277–285|doi=10.1007/s11440-013-0278-8|hdl=10220/39693 |s2cid=73640508 |issn=1861-1133|hdl-access=free}} by activation of calcium and/or magnesium ionic pumps or channels, probably coupled with carbonate ion production. During passive carbonatogenesis, two metabolic cycles can be involved, the nitrogen cycle and the sulfur cycle. Three different pathways can be involved in the nitrogen cycle: ammonification of amino acids, dissimilatory reduction of nitrate, and degradation of urea or uric acid.Monty, C.L.V., Bosence, D.W.J, Bridges, P.H., Pratt, B.R. (eds.)(1995). Carbonate Mud-Mounds: Their Origin and Evolution. Wiley-Blackwell In the sulfur cycle, bacteria follow the dissimilatory reduction of sulfate.

The microbial urease catalyzes the hydrolysis of urea into ammonium and carbonate. One mole of urea is hydrolyzed intracellularly to 1 mol of ammonia and 1 mole of carbamic acid (1), which spontaneously hydrolyzes to form an additional 1 mole of ammonia and carbonic acid (2).{{cite journal | last1 = Hammes | first1 = F. | last2 = Seka | first2 = A. | last3 = de Knijf | first3 = S. | last4 = Verstraete | first4 = W. | year = 2003 | title = A novel approach to calcium removal from calcium-rich industrial wastewater | journal = Water Research | volume = 37 | issue = 3| pages = 699–704 | doi=10.1016/s0043-1354(02)00308-1| pmid = 12688705 | bibcode = 2003WatRe..37..699H }}

:CO(NH₂)₂ + H₂O → NH₂COOH + NH₃ (1)

:NH₂COOH + H₂O → NH₃ + H₂CO₃ (2)

Ammonium and carbonic acid form bicarbonate and 2 moles of ammonium and hydroxide ions in water (3 &4).

:2NH₃ + 2H₂O ↔ 2NH⁺₄ +2OH⁻ (3)

:H₂CO₃ ↔ HCO⁻₃ + H⁺ (4)

The production of hydroxide ions results in the increase of pH,{{Cite journal|last1=Seifan|first1=Mostafa|last2=Samani|first2=Ali Khajeh|last3=Berenjian|first3=Aydin|date=2017-04-01|title=New insights into the role of pH and aeration in the bacterial production of calcium carbonate (CaCO3)|journal=Applied Microbiology and Biotechnology|language=en|volume=101|issue=8|pages=3131–3142|doi=10.1007/s00253-017-8109-8|pmid=28091788|issn=1432-0614|hdl=10289/11243|s2cid=22539692|hdl-access=free}} which in turn can shift the bicarbonate equilibrium, resulting in the formation of carbonate ions (5)

:HCO⁻₃ + H⁺ + 2NH⁺₄ +2OH⁻ ↔ CO₃⁻² + 2NH⁺₄ + 2H₂O (5)

The produced carbonate ions precipitate in the presence of calcium ions as calcium carbonate crystals (6).

:Ca⁺² + CO₃⁻² ↔ CaCO₃ (6)

The formation of a monolayer of calcite further increases the affinity of the bacteria to the soil surface, resulting in the production of multiple layers of calcite.

MICP has been reported as a long-term remediation technique that has been exhibited high potential for crack cementation of various structural formations such as granite and concrete.{{cite journal | last1 = Jagadeesha Kumar | first1 = B.G. | last2 = Prabhakara | first2 = R. | last3 = Pushpa | first3 = H. | year = 2013 | title = Bio mineralization of calcium carbonate by different bacterial strains and their application in concrete crack remediation | journal = International Journal of Advances in Engineering & Technology | volume = 6 | issue = 1| pages = 202–213 }}

MICP has been shown to prolong concrete service life due to calcium carbonate precipitation. The calcium carbonate heals the concrete by solidifying on the cracked concrete surface, mimicking the process by which bone fractures in human body are healed by osteoblast cells that mineralize to reform the bone. Two methods are currently being studied: injection of calcium carbonate precipitating bacteria.{{cite journal | last1 = Achal | first1 = V. | last2 = Mukherjee | first2 = A. | last3 = Basu | first3 = P.C. | last4 = Reddy | first4 = M.S. | year = 2009 | title = Strain improvement of Sporosarcina pasteurii for enhanced urease and calcite production | journal = Journal of Industrial Microbiology and Biotechnology | volume = 36 | issue = 7| pages = 981–988 | doi=10.1007/s10295-009-0578-z| pmid = 19408027 | s2cid = 29667294 | doi-access = free }}Wang, J. (2013). Self-healing concrete by means of immobilized carbonate precipitating bacteria. Ghent University. Faculty of Engineering and Architecture, Ghent, Belgium and by applying bacteria and nutrients as a surface treatment.{{cite journal | last1 = De Muynck | first1 = W. | last2 = Debrouwer | first2 = D. | last3 = Belie | first3 = N. | last4 = Verstraete | first4 = W. | year = 2008 | title = Bacterial carbonate precipitation improves durability of cementitious materials | journal = Cement and Concrete Research | volume = 38 | issue = 7| pages = 1005–1014 | doi=10.1016/j.cemconres.2008.03.005}}{{Cite journal|last1=Bergh|first1=John Milan van der|last2=Miljević|first2=Bojan|last3=Šovljanski|first3=Olja|last4=Vučetić|first4=Snežana|last5=Markov|first5=Siniša|last6=Ranogajec|first6=Jonjaua|last7=Bras|first7=Ana|date=2020-07-10|title=Preliminary approach to bio-based surface healing of structural repair cement mortars|url=https://www.sciencedirect.com/science/article/pii/S0950061820305626|journal=Construction and Building Materials|language=en|volume=248|pages=118557|doi=10.1016/j.conbuildmat.2020.118557|s2cid=216414601 |issn=0950-0618}} Increase in strength and durability of MICP treated cement mortar and concrete has been reported.{{cite journal | last1 = Reddy | first1 = S. | last2 = Achyutha Satya | first2 = K. | last3 = Seshagiri Rao | first3 = M.V. | last4 = Azmatunnisa | first4 = M. | year = 2012 | title = A biological approach to enhance strength and durability in concrete structures | journal = International Journal of Advances in Engineering & Technology | volume = 4 | issue = 2| pages = 392–399 }}

Architect Ginger Krieg Dosier won the 2010 Metropolis Next Generation Design Competition for her work using microbial-induced calcite precipitation to manufacture bricks while lowering carbon dioxide emissions.{{cite magazine|author=Suzanne LaBarre|url=http://www.metropolismag.com/May-2010/The-Better-Brick-2010-Next-Generation-Winner/|title=The Better Brick: 2010 Next Generation Winner|magazine=Metropolis Magazine|date=May 1, 2010}} She has since founded Biomason, Inc., a company that employs microorganisms and chemical processes to manufacture building materials.

MICP technique may be applied to produce a material that can be used as a filler in rubber and plastics, fluorescent particles in stationery ink, and a fluorescent marker for biochemistry applications, such as western blot.{{cite journal | last1 = Yoshida | first1 = N. | last2 = Higashimura | first2 = E. | last3 = Saeki | first3 = Y. | year = 2010 | title = Catalytic biomineralization of fluorescent calcite by the thermophilic bacterium Geobacillus thermoglucosidasius | journal = Applied and Environmental Microbiology | volume = 76 | issue = 21| pages = 7322–7327 | doi=10.1128/aem.01767-10 | pmid=20851984 | pmc=2976237| bibcode = 2010ApEnM..76.7322Y }}

Microbial induced calcium carbonate precipitation has been proposed as an alternative cementation technique to improve the properties of potentially liquefiable sand. The increase in shear strength, confined compressive strength, stiffness and liquefaction resistance was reported due to calcium carbonate precipitation resulting from microbial activity. The increase of soil strength from MICP is a result of the bonding of the grains and the increased density of the soil. Research has shown a linear relationship between the amount of carbonate precipitation and the increase in strength and porosity.{{Cite journal|title = Factors Affecting Improvement in Engineering Properties of Residual Soil through Microbial-Induced Calcite Precipitation|journal = Journal of Geotechnical and Geoenvironmental Engineering|date = 2014-01-13|volume = 140|issue = 5|doi = 10.1061/(asce)gt.1943-5606.0001089|first1 = Ng Wei|last1 = Soon|first2 = Lee Min|last2 = Lee|first3 = Tan Chew|last3 = Khun|first4 = Hii Siew|last4 = Ling|pages=04014006|s2cid = 129723650}}{{Cite journal|title = Stress-deformation and compressibility responses of bio-mediated residual soils|journal = Ecological Engineering|date = 2013-11-01|pages = 142–149|volume = 60|doi = 10.1016/j.ecoleng.2013.07.034|first1 = Min Lee|last1 = Lee|first2 = Wei Soon|last2 = Ng|first3 = Yasuo|last3 = Tanaka}} A 90% decrease in porosity has also been observed in MICP treated soil. Light microscopic imaging suggested that the mechanical strength enhancement of cemented sandy material is caused mostly due to point-to-point contacts of calcium carbonate crystals and adjacent sand grains.{{cite thesis |author=Al-Thawadi |year=2008 |title=High strength in-situ biocementation of soil by calcite precipitating locally isolated ureolytic bacteria |type=Ph.D. dissertation |publisher=Murdoch University, Western Australia}}

One-dimensional column experiments allowed the monitoring of treatment progration by the means of change in pore fluid chemistry.{{cite journal|last1=Al Qabany|first1=Ahmed|last2=Soga|first2=Kenichi|last3=Santamarina|first3=Carlos|title=Factors affecting efficiency of microbially induced calcite precipitation |journal=Journal of Geotechnical and Geoenvironmental Engineering |date=August 2012 |volume=138 |issue=8 |pages=992–1001 |doi=10.1061/(ASCE)GT.1943-5606.0000666}} Triaxial compression tests on untreated and bio-cemented Ottawa sand have shown an increase in shear strength by a factor of 1.8.{{cite journal | last1 = Tagliaferri | first1 = F. | last2 = Waller | first2 = J. | last3 = Ando | first3 = E. | last4 = Hall | first4 = S.A. | last5 = Viggiani | first5 = G. | last6 = Besuelle | first6 = P. | last7 = DeJong | first7 = J.T. | year = 2011 | title = Observing strain localization processes in bio-cemented sand using X-ray imaging | url = https://hal.archives-ouvertes.fr/hal-01570995/file/Tagliaferri_etal_postreview-04.pdf| journal = Granular Matter | volume = 13 | issue = 3| pages = 247–250 | doi=10.1007/s10035-011-0257-4| s2cid = 121636099 }} Changes in pH and concentrations of urea, ammonium, calcium and calcium carbonate in pore fluid with the distance from the injection point in 5-meter column experiments have shown that bacterial activity resulted in successful hydrolysis of urea, increase in pH and precipitation of calcite. However, such activity decreased as the distance from the injection point increased. Shear wave velocity measurements demonstrated that positive correlation exists between shear wave velocity and the amount of precipitated calcite.Weil, M.H., DeJong, J.T., Martinez, B.C., Mortensen, B.M., Waller, J.T. (2012). Seismic and resistivity measurements for real-time monitoring of microbially induced calcite precipitation in sand. ASTM J. Geotech. Testing, In Press.

One of the first patents on ground improvement by MICP was the patent “Microbial Biocementation” by Murdoch University (Australia).Kucharski, E.S., Cord-Ruwisch, R., Whiffin, V.S., Al-Thawadi, S.M.J. (2006). Microbial biocementation, World Patent. WO/2006/066326, June. 29. A large scale (100 m³) have shown a significant increase in shear wave velocity was observed during the treatment. Originally MICP was tested and designed for underground applications in water saturated ground, requiring injection and production pumps. Recent work {{cite journal | last1 = Cheng | first1 = L. | last2 = Cord-Ruwisch | first2 = R. | year = 2012 | title = In situ soil cementation with ureolytic bacteria by surface percolation | url = http://researchrepository.murdoch.edu.au/id/eprint/8611/| journal = Ecological Engineering | volume = 42 | pages = 64–72 | doi=10.1016/j.ecoleng.2012.01.013}} has demonstrated that surface percolation or irrigation is also feasible and in fact provides more strength per amount of calcite provided because crystals form more readily at the bridging points between sand particles over which the water percolates.{{cite journal | last1 = Cheng | first1 = L. | last2 = Cord-Ruwisch | first2 = R. | last3 = Shahin | first3 = M.A. | year = 2013 | title = Cementation of sand soil by microbially induced calcite precipitation at various degrees of saturation | url = http://researchrepository.murdoch.edu.au/id/eprint/13837/| journal = Canadian Geotechnical Journal | volume = 50 | issue = 1| pages = 81–90 | doi=10.1139/cgj-2012-0023| hdl = 20.500.11937/33429 | s2cid = 128482595 | hdl-access = free }}

Benefits of MICP for liquefaction prevention

MICP has the potential to be a cost-effective and green alternative to traditional methods of stabilizing soils, such as chemical grouting, which typically involve the injection of synthetic materials into the soil. These synthetic additives are typically costly and can create environmental hazards by modifying the pH and contaminating soils and groundwater. Excluding sodium silicate, all traditional chemical additives are toxic. Soils engineered with MICP meet green construction requirements because the process exerts minimal disturbance to the soil and the environment.

MICP treatment may be limited to deep soil due to limitations of bacterial growth and movement in subsoil. MICP may be limited to the soils containing limited amounts of fines due to the reduction in pore spaces in fine soils. Based on the size of microorganism, the applicability of biocementation is limited to GW, GP, SW, SP, ML, and organic soils.{{cite journal | last1 = Mitchell | first1 = J.K. | last2 = Santamarina | first2 = J.C. | year = 2005 | title = Biological considerations in geotechnical engineering | journal = Journal of Geotechnical and Geoenvironmental Engineering | volume = 131 | issue = 10| pages = 1222–1233 | doi=10.1061/(asce)1090-0241(2005)131:10(1222)}} Bacteria are not expected to enter through pore throats smaller than approximately 0.4 μm. In general, the microbial abundance was found to increase with the increase in particle size.{{cite journal | last1 = Rebata-Landa | first1 = V. | last2 = Santamarina | first2 = J.C. | year = 2006 | title = Mechanical limits to microbial activity in deep sediments | journal = Geochemistry, Geophysics, Geosystems | volume = 7 | issue = 11| pages = 1–12 | doi=10.1029/2006gc001355 | bibcode=2006GGG.....711006R| citeseerx = 10.1.1.652.6863 | s2cid = 129846326 }} On the other hand, the fine particles may provide more favorable nucleation sites for calcium carbonate precipitation because the mineralogy of the grains could directly influence the thermodynamics of the precipitation reaction in the system. The habitable pores and traversable pore throats were found in coarse sediments and some clayey sediments at shallow depth. In clayey soil, bacteria are capable of reorienting and moving clay particles under low confining stress (at shallow depths). However, inability to make these rearrangements under high confining stresses limits bacterial activity at larger depths. Furthermore, sediment-cell interaction may cause puncture or tensile failure of the cell membrane. Similarly, at larger depths, silt and sand particles may crush and cause a reduction in pore spaces, reducing the biological activity. Bacterial activity is also impacted by challenges such as predation, competition, pH, temperature, and nutrient availability. These factors can contribute to the population decline of bacteria. Many of these limitations can be overcome through the use of MICP through bio-stimulation - a process through which indigenous ureolytic soil bacteria are enriched in situ.{{cite journal|last1=Burbank|first1=Malcolm|last2=Weaver|first2=Thomas|last3=Williams|first3=Barbara|last4=Crawford|first4=Ronald|title=Geotechnical Tests of Sands Following Bioinduced Calcite Precipitation Catalyzed by Indigenous Bacteria|journal=Journal of Geotechnical and Geoenvironmental Engineering|date=June 2013|volume=139|issue=6|doi=10.1061/(ASCE)GT.1943-5606.0000781|pages=928–936}} This method is not always possible as not all indigenous soils have enough ureolytic bacteria to achieve successful MICP.

MICP is a promising technique that can be used for containment of various contaminants and heavy metals. The availability of lead in soil may reduced by its chelation with the MICP product, which is the mechanism responsible for lead immobilization.{{cite journal|last1=Achal|first1=Varenyam|last2=Pan|first2=Xiangliang|last3=Zhang|first3=Daoyong|last4=Fu|first4=Qinglong|title=Bioremediation of Pb-contaminated soil based on microbially induced calcite precipitation|journal=Journal of Microbiology and Biotechnology|date= 2012|volume=22|issue=2|pages=244–247|pmid=22370357|doi=10.4014/jmb.1108.08033|s2cid=30168684}} MICP can be also applied to achieve sequestration of heavy metals and radionuclides. Microbially induced calcium carbonate precipitation of radionuclide and contaminant metals into calcite is a competitive co-precipitation reaction in which suitable divalent cations are incorporated into the calcite lattice.Hamdan, N., Kavazanjian, Jr. E., Rittmann, B.E. (2011). Sequestration of radionuclides and metal contaminants through microbially-induced carbonate precipitation. Pan-Am CGS Geotechnical Conference{{cite journal | last1 = Li | first1 = L. | last2 = Qian | first2 = C.X. | last3 = Cheng | first3 = L. | last4 = Wang | first4 = R.X. | year = 2010 | title = A laboratory investigation of microbe-inducing CdCO₃ precipitate treatment in Cd²⁺ contaminated soil | journal = Journal of Soils and Sediments | volume = 10 | issue = 2| pages = 248–254 | doi=10.1007/s11368-009-0089-6| s2cid = 97718866 }} Europium, a trivalent lanthanide, which was used as a homologue for trivalent actinides, such as Pu(III), Am(III), and Cm(III), was shown to incorporate into the calcite phase substituting for Ca(II) as well as in a low-symmetry site within the biomineral.{{cite journal|last1=Johnstone|first1=Erik|last2=Hofmann|first2=Sascha|last3=Cherkouk|first3=Andrea|last4=Schmidt|first4=Moritz|title=Study of the interaction of Eu3+ with Microbially Induced Calcium Carbonate Precipitates Using TRLFS.|journal=Environmental Science and Technology|date= 2016|volume=50|issue=22|pages=12411–12420|doi=10.1021/acs.est.6b03434|pmid=27766852}}

Shewanella oneidensis inhibits the dissolution of calcite under laboratory conditions.{{cite journal|date= November 7, 2006|pages=1075–1079|title=Saving a fragile legacy. Biotechnology and microbiology are increasingly used to preserve and restore the world's cultural heritage|author=Andrea Rinaldi|journal=EMBO Reports|pmc=1679785|pmid=17077862|doi=10.1038/sj.embor.7400844|volume=7|issue=11}}

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