CO2 SEQUESTRATION AND CREATION OF CALCIUM CARBONATES THROUGH MICROBIAL INDUCED CARBONATE PRECIPITATION

Abstract

A method for sequestering CO.sub.2 and creating precipitated calcium carbonates includes: (a) providing a liquid calcification medium including: a nutrient broth including water and a yeast extract, a carbon source selected from calcium carboxylic acids and calcium dicarboxylic acids and mixtures thereof, and bacteria that naturally express the chaA gene; (b) introducing CO.sub.2 to the liquid calcification medium; and (c) allowing microbial induced carbonate precipitation of calcium carbonate, thereby sequestering at least some of the CO.sub.2 introduced in said step of introducing

Claims

1. A method for sequestering CO.sub.2 and creating precipitated calcium carbonates, the method comprising the steps of: (a) providing a liquid calcification medium including: a nutrient broth including water and yeast extract, a carbon source selected from calcium carboxylic acids and calcium dicarboxylic acids and mixtures thereof, and bacteria that naturally express the chaA gene; (b) introducing CO.sub.2 to the liquid calcification medium; and (c) allowing microbial induced carbonate precipitation of calcium carbonate, thereby sequestering at least some of the CO.sub.2 introduced in said step of introducing.

2. The method of claim 1, wherein the liquid calcification medium includes from 1 g to 10 g of the yeast extract per 1 L of water; and from 1 g to 50 g of the carbon source per 1 L of water.

3. The method of claim 2, wherein the liquid calcification medium includes from 2 g/L to 7.5 g/L yeast extract, and from 2.5 g/L to 30 g/L of the carbon source.

4. The method of claim 1, wherein the carbon source is a metabolizable carbon source.

5. The method of claim 1, wherein the carbon source is selected from calcium formate, calcium acetate, calcium propionate, calcium butyrate, calcium succinate, and calcium citrate.

6. The method of claim 5, wherein the carbon source is calcium succinate.

7. The method of claim 1, wherein the nutrient broth is devoid of urea.

8. The method of claim 1, wherein the nutrient broth is devoid of acidifying carbohydrate sources that drive one or more of: metabolic overflow, acetogenesis, and mixed acid fermentation.

9. The method of claim 1, wherein the bacteria are selected from the genera Bacillus, Microbacterium, and Escherichia.

10. The method of claim 9, wherein the bacteria are selected from Eschericia coli, Escherichia coli K12, Bacillus sp., and Microbacterium sp.

11. The method of claim 1, wherein said step of providing a liquid calcification medium comprises the steps of: adjusting the nutrient broth to a pH of from pH 6 or more to pH 9 or less and sterilizing the nutrient broth, both prior to providing the bacteria.

12. The method of claim 11, wherein, after the step of sterilizing the nutrient broth, the step of providing a liquid calcification medium comprises the steps of: cooling the nutrient broth to room temperature and adding the carbon source, both prior to providing the bacteria.

13. The method of claim 12, wherein adding the carbon source includes suspending the carbon source in water to form a suspended carbon source and filter-sterilizing the suspended carbon source.

14. The method of claim 1, wherein said step of introducing CO.sub.2 includes agitating the liquid calcification medium to expose it to CO.sub.2 within the surrounding atmosphere.

15. The method of claim 1, wherein said step of introducing carbon dioxide includes bubbling CO.sub.2 through the liquid calcification medium.

16. The method of claim 1, wherein said step of allowing precipitation of calcium carbonate includes maintaining the liquid calcification medium at a temperature providing aeration for growth of the bacteria.

17. The method of claim 16, wherein temperature of the liquid calcification medium is maintained at from 10° C. or more to 42° C. or less.

18. The method of claim 1, wherein the bacteria have a carbonic anhydrase gene, yadF, and the method further comprises the step of engineering yadF into an inducible, overexpression plasmid vector under control of a propionate inducible promotor.

Description

DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

[0027] The present invention provides methods for CO.sub.2 sequestration and creation of precipitated calcium carbonates, promoting calcification through a previously unexplored microorganism capability previously described in Banks, E. D., Taylor, N. M., Gulley, J., Lubbers, B. R., Giarrizo, J. G., Bullen, H. A., Hoehler, T. M. and Barton, H. A. 2010. Bacterial Calcium Carbonate Precipitation in Cave Environments: A Function of Calcium Homeostasis. Geomicrobiology Journal 27(5): 444-454. Functionally, this approach is similar to published work in calcification and pore closing in the subsurface to seal CO.sub.2 reservoirs using bacterial ureolysis (e.g., WO2010075503); however, it is mechanistically different. The present method relies on the toxic nature of intracellular Ca.sup.2+ ions in bacteria to promote precipitation to remove excess Ca.sup.2+ by bicarbonate ions sourced from atmospheric CO.sub.2, as demonstrated through stable isotope probing. CO.sub.2 fixation is promoted by manipulating cell physiology using calcium carboxylate salts as a source of energy. In some embodiments, the process in enhanced by over-expression of the carbonic anhydrase enzyme. CO.sub.2 is thus sequestered, being fixed in precipitated calcium carbonates. Through different process conditions and/or ingredient selection, the precipitated calcium carbonates can be of nanometer and micron-scale. These small-scale carbonates, termed precipitated calcium carbonates (PCC) are recoverable from the bacterial-liquid cultures (suspensions) used in the CO.sub.2 fixation process and can have a number of industrial uses.

[0028] In some embodiments, the present invention provides a method for sequestering CO.sub.2 and creating precipitated calcium carbonates, the method including providing a liquid calcification medium; introducing CO.sub.2 to the liquid calcification medium; and allowing microbial induced carbonate precipitation (MICP) of calcium carbonate, thereby sequestering at least some of the CO.sub.2 and creating a precipitated calcium carbonate for collection and use. The liquid calcification medium is formulated to achieve the desired MICP and includes (a) a nutrient broth including water and a yeast extract, (b) a carbon source selected from calcium carboxylic acids and calcium dicarboxylic acids and mixtures thereof, and (c) bacteria that naturally express the chaA gene.

[0029] In some embodiments, the liquid calcification medium includes a yeast extract. In some embodiments, the liquid calcification medium includes 1 g or more of a yeast extract per 1 L of water; and 1 g or more of the carbon source per 1 L of water. In some embodiments, the liquid calcification medium includes from 1 g/L to 10 g/L yeast extract, and from 1 g/L to 50 g/L of the carbon source; in other embodiments, from 2 g/L to 7.5 g/L yeast extract, and from 2.5 g/L to 30 g/L of the carbon source; and, in other embodiments, from 3 g/L to 5 g/L yeast extract, and from 5 g/L to 10 g/L of the carbon source. In one embodiment, the liquid calcification medium includes 4 g/L yeast extract and 7.5 g/L of the carbon source.

[0030] In some embodiments, the carbon source used is calcium salt (wherein the salt refers to the ionic assembly of the Ca.sup.2+ cation with a carboxylic or dicarboxylic anion), allowing the calcium to be taken up with the carbon source by the bacteria for growth. This metabolic pathway uses the uptake of the Ca.sup.2+ cation by the bacterial cell to cause precipitation and cannot be initiated by simply increasing Ca.sup.2+ concentrations in the surrounding media. For example, this process does not occur if the media containing a carbon source is simply amended with CaCl.sub.2.

[0031] In some embodiments, the carbon source is selected from calcium formate, calcium acetate, calcium propionate, calcium butyrate, calcium succinate, and calcium citrate, and mixtures thereof. In some embodiments, the carbon source is calcium succinate. As can be appreciated by a skilled artisan, a liquid culture of the invention can be created by adding exogenous microbes to a liquid culture where growth is initiated by the presence of a calcium carboxylate or dicarboxylic salt, which serves as a carbon source. The carboxylic acid salts that promote CaCO.sub.3 precipitation include calcium formate, calcium acetate, calcium propionate, and calcium butyrate. The dicarboxylic acid salts are calcium succinate and calcium citrate.

[0032] In some embodiments, the carbon source is added in one or more batch runs, with the carbon being added at 1-10 g/L or added continuously to the culture, to maintain the levels of carbon source at the same rate.

[0033] The present MICP process is not urea-dependent and thus can be carried out in a nutrient broth devoid of urea.

[0034] The methods of this invention mineralize atmospheric CO.sub.2 into CaCO.sub.3 by bacterial activity including calcium stress induced by growth on calcium carboxylic and dicarboxylic acid salts. Calcium is an important co-factor in a number of bacterial enzymes; however, the ability of Ca.sup.2+ to displace other critical divalent metal cations (Fe.sup.2+, Mg.sup.2+, etc), requires cellular Ca.sup.2+ levels to be tightly regulated by the Ca.sup.2+/H+ anti-porter protein, chaA. Nonetheless, once extracellular Ca.sup.2+ ion concentrations exceed the thermodynamic export capacity of chaA, Ca.sup.2+ may leak back into the cell, reaching potentially toxic levels. In order to overcome this, the cell mediates a precipitation reaction by using the carbonic anhydrase (yadF) gene to fix atmospheric CO.sub.2 as HCO.sub.3-(12, 37), increasing extracellular pH. Not only does this pH rise initiate calcification, but it also pulls Ca.sup.2+ ions out of solution that might otherwise overcome the thermodynamic limits of chaA. This is confirmed by knocking out chaA using site-directed mutagenesis, which demonstrates the loss of the calcification phenotype, while cells grow poorly in the presence of CaCO.sub.3. Cellular Ca.sup.2+ homeostasis is therefore critical to growth in the presence of excess Ca.sup.2+. This is confirmed by knocking-out the yadF gene, which was found lethal to bacterial growth in the presence of Ca.sup.2+, while stable isotope probing using C.sup.13O.sub.2 demonstrated that the source of the carbonates in MICP was atmospheric CO.sub.2.

[0035] Previous work has examined CaCO.sub.3 precipitation on B4 media that has been solidified using 1.4% agar. This media contains 2.5 g/L of calcium acetate (as the Ca.sup.2+ ion source), 5.0 g/L of glucose (otherwise known as dextrose) and 4.0 g/L of yeast extract, which serves as a source of amino acids and other trace nutrients to enhance microbial growth. Growth in the presence of glucose leads cells to produce carboxylic and other organic acids, produced through a combination of glucose metabolic overflow, acetogenesis, and mixed acid fermentation. As CaCO.sub.3 precipitation is related to the pH and saturation index, the presence of glucose leads to the acidification of the media, which reduces the pH and prevents CaCO.sub.3 precipitation, which occurs when the pH of the media exceeds the pKa of HCO.sub.3−.fwdarw.CO.sub.3.sup.2− due to the presence of these organic acids.

[0036] Thus, in some embodiments, the nutrient broth is devoid of acidifying carbohydrate sources that drive one or more of glucose metabolic overflow, acetogenesis, and mixed acid fermentation that would create organic acids and increase acidification. In some embodiments, the nutrient broth is devoid of acidifying carbohydrate sources that would lower pH below 8.2. The removal of these carbohydrates removes the metabolic by-products that would otherwise acidify the media, reducing the likelihood of reaching the pK.sub.a of HCO.sub.3.sup.−/CO.sub.3.sup.2− and limiting the precipitation of PCCs.

[0037] In some embodiments, the bacteria that naturally express the chaA gene are selected from one or more of the genera Bacillus, Microbacterium, and Escherichia. In some embodiments, the bacteria are Bacillus sp. In some embodiments, bacteria are Microbacterium sp. In some embodiments, the bacteria are Escherichia sp., and in yet other embodiments, Escherichia coli K12.

[0038] In order to initiate growth, a colony of the bacterial species is inoculated into a small (<25 mL) culture of standard nutrient broth that contains 5.0 g/L of a pancreatic digest of gelatin and 3.0 g/L of beef extract. This broth is incubated at 20-37° C. with shaking at 200 rpm for 16-24 hours. This starter culture is then inoculated into the calcification media at 1:1,000-10,000 dilution.

[0039] In some embodiments, the liquid calcification medium is formed by adding the carbon source to the nutrient broth, and thereafter inoculating with the bacteria. In some embodiments, the liquid calcification medium is formed by sterilizing the nutrient broth before adding the carbon source to the nutrient broth, and thereafter inoculating with the bacteria. In some embodiments, the liquid calcification medium is formed by sterilizing the nutrient broth and adjusting its pH to from pH 6 or more to pH 9 or less before adding the carbon source to the nutrient broth, and thereafter inoculating with the bacteria. In some embodiments, the liquid calcification medium is formed by sterilizing the nutrient broth before adding the carbon source to the nutrient broth, cooling the nutrient broth and carbon source (in some embodiments to 25° C. or less), and thereafter inoculating with the bacteria. In some embodiments, the carbon source is added by first suspending the carbon source in water to form a suspended carbon source and filter sterilizing the suspended carbon source with a 0.2 micrometer cellulose filter.

[0040] The provision of the liquid calcification medium can be in any suitable vessel, whether adapted for batch or continuous process. In some embodiments, the CO.sub.2 is introduced by agitating the liquid calcification medium, thus exposing it to CO.sub.2 in the general environment or general atmosphere. In some embodiments, the CO.sub.2 is bubbled through the liquid calcification medium.

[0041] In some embodiments, to facilitate the microbially induced precipitation of calcium carbonate, the liquid calcification medium is maintained at a suitable temperature for growth of the bacteria. In some embodiments, the liquid calcification medium is maintained with suitable aeration for growth of the bacteria. In some embodiments, the temperature of the liquid calcification medium is maintained at from 10° C. or more to 42° C. or less and in yet other embodiments the temperature of the liquid calcification medium is maintained at from 25° C. or more to 37° C. or less.

[0042] The PCCs are separated from the liquid media via filtration, including membrane filtration or tangential flow filtration.

[0043] Reductions to practice have demonstrated that the calcium salt chemistry influences the type of calcite polymorph that is formed. On calcium acetate, lactate, and propionate, the unstable polymorph vaterite was the dominant form of CaCO.sub.3. On succinate, a combination of vaterite and calcite was produced, while on pyruvate, calcite was the dominant mineral. The metabolism of the carboxylic acids will influence the metabolic products produced, which in turn sorb to the surface of the mineral and influence the type of polymorph produced. This may also allow tailoring of the final precipitate chemistry.

[0044] Per the forgoing, CO.sub.2 can be sequestered and PCCs created in the various sizes and shapes. Particulate (μm scale) calcium carbonate has a number of industrial uses: in paper, carbonates are used as a filler and coating, which can increase the smoothness, brightness and help preserve paper; in thermoplastics, carbonates are used as a filler to reduce polymer volume (and cost), modulate elasticity to increase impact resistance, while their thermal conductivity accelerates product manufacturing; in sealants and adhesives, carbonates serves as a filler, thixotropic agent, and reduce shrinkage and sag as polymers set; in coatings (paints), carbonates can serve as an extender and rheology agent, and play an important role in opacity, brightness, gloss and durability; powders are also important in a number of sports, where they reduce hand sweat, such as climbing and gymnastics. Over 130,000 kilotons of carbonate were produced worldwide in 2019 using energy mining extraction technologies. Current industrial PCC production also requires sintering of limestone rock to create lime (CaO). This CaO is then slaked with water and CO.sub.2, a process which contributes up to 2% of global CO.sub.2 emissions annually (the CO.sub.2 liberated from sintering has been calculated at 0.62 tons CO.sub.2 per ton PCCs). The invention described herein is the first green alternative for PCC production, with net-negative CO.sub.2 release during production.

[0045] In light of the foregoing, it should be appreciated that the present invention significantly advances the art in a number of ways. While particular embodiments of the invention have been disclosed in detail herein, it should be appreciated that the invention is not limited thereto or thereby inasmuch as variations on the invention herein will be readily appreciated by those of ordinary skill in the art. The scope of the invention shall be appreciated from the claims that follow.

EXAMPLES

[0046] Past investigators have used environmental bacterial isolates to suggest that microorganisms bring about calcification by simply increasing the pH of media containing excess Ca.sup.2+ and dissolved HCO.sub.3.sup.−. Nonetheless, there are no good model organisms to extensively understand the metabolic principles behind calcification or to manipulate the process for industrial application. Demonstrated below is an Escherichia coli (E. coli) system based on the metabolism of calcium acetate and calcium succinate that allows the metabolic limitation to be overcome that have previously prevented a deeper understanding of metabolic calcification.

[0047] Through the use of E. coli, it can be shown that the use of calcium acetate and calcium succinate as carbon sources increases the cellular demand for dissolved CO.sub.2 in the media. Through these metabolic processes, the consumption of HCO.sub.3.sup.− and the rising production of CO.sub.3.sup.2− ions, an increase in the pH of the medium leads to additional precipitation of CO.sub.2-derived carbonates as environmentally stable calcite. By tailoring E. coli calcification using different calcium salt chemistries (calcium acetate, calcium succinate, calcium pyruvate, calcium propionate and calcium lactate), the system can be tuned to produce a number of calcite polymorphs and particulates, for use in a number of industrial processes from paper production, adhesives, food preparation, and pharmaceutical production. The system can also be enhanced by engineering an inducible carbonic anhydrase into a gene over-expression system, allowing for increased calcification and CO.sub.2 fixation in E. coli. It is demonstrated that by using calcium succinate as a Ca.sup.2+ source, the system can be scaled up to allow significant CO.sub.2 fixation as an environmentally stable carbonate.

[0048] Calcification by Escherichia coli.

[0049] Traditionally, researchers have used Boquet B4 media (which contains calcium acetate) to screen environmental isolates for the calcification phenotype. While E. coli has not been shown to precipitate CaCO.sub.3 using this assay, it does precipitate CaCO.sub.3 via ureolysis and in the presence of metastable calcium phosphate, suggesting that calcification is functionally possible. It has previously been demonstrated that E. coli in liquid B4 media produces a number of carboxylic and other organic acids, which are produced through a combination of glucose metabolic overflow, acetogenesis, and mixed acid fermentation. As CaCO.sub.3 precipitation is related to the pH and saturation index, it was considered that the inability of E. coli to calcify on B4 was due to acidification of the media due to the presence of these organic acids. To test this, cultures were set up in B4, with (B4) and without (B4m) the addition of glucose. After one week of growth, no calcification was seen for E. coli on B4 (containing glucose), while in the absence of glucose (B4m), calcification was observed. By calibrating cresol red as a pH indicator, it was demonstrated that the media surrounding the E. coli colonies had dropped below a pH of 5.0 in the presence of glucose but increased to pH of greater than 8.8 in its absence, demonstrating that calcification can proceed in E. coli without the addition of this sugar.

[0050] Environmental work has shown that organic acids produced by E. coli react with CaCO.sub.3 to produce various calcium salts (with acetate as a representative acid in the following reaction):

2CH.sub.3COO.sup.−+2H.sup.++CaCO.sub.3.fwdarw.CO.sub.2+H.sub.2O+Ca(CH.sub.3COO).sub.2.

Given the ability to detect these salts in the environment, E. coli growth was tested on other calcium salts (calcium propionate, calcium lactate, calcium pyruvate, and calcium succinate) as a mechanism to similarly drive calcification in E. coli. As E. coli only expresses the citrate transporter under anaerobic conditions, calcium citrate was used to differentiate active calcium metabolism from passive pH effects on calcification in culture. The results demonstrate that when E. coli is grown on B4 media with calcium acetate replaced by other calcium salts, there is a distinct pattern of calcification: no calcification was observed when glucose was present but occurred readily on all the provided calcium salts in the absence of glucose. Cresol red indicated that in all cases, the presence of glucose led to acidification of the surrounding media, while in its absence the media became alkali. The exception to this was calcium citrate; E. coli grew on the media and produced alkali conditions in the absence of glucose, but the lack of calcification demonstrates the need for a metabolizable calcium salt in promoting calcification.

[0051] The amount of calcification observed in the colonies varied depending on both pH and the calcium salt added, although this observation was only qualitative; to date there have been no methods that have allowed quantification of calcification on bacterial colonies. To overcome this limitation and allow a direct comparison of pH versus calcite, a machine learning approach was used to train image analysis software to identify and measure calcite crystal production. The TWS plugin image feature recognition algorithm was used to identify carbonate crystals using a set of colony training images, followed by manually designating areas as crystal, colony, or background. The plugin analyzed subsequent images using this training set and calculated a probability map showing coverage of colonies by calcite crystals. Once the calcite was identified and segmented, percent coverage was calculated using the Analyze Particles function built into ImageJ, making it possible to quantify and compare coverage of calcification in single colonies of E. coli. Using this approach, calcification on calcium pyruvate, succinate, lactate, acetate, and propionate was quantified. The data indicated that calcification was more pronounced when calcium acetate and succinate were used for growth: about 46% coverage, compared to about 30% coverage for calcium propionate, calcium lactate, and calcium pyruvate (p<0.05 in a Student's T-test). Beyond calcification levels, there did not appear to be any differences between colony count, size, or growth rate between the various media. There was no direct correlation between pH and total calcification, confirming the hypothesis that calcification is not entirely pH dependent and metabolism and the type of calcium salt each play an important role.

[0052] The role of acetate as a driver of calcification has been well described: the glyoxylic acid bypass for acetate utilization requires higher CO.sub.2 uptake by the cell to synthesize fatty acids in the absence of CO.sub.2 produced by the reduction of isocitrate and a-ketoglutarate. This increased utilization of CO.sub.2 presumably pulls dissolved HCO.sub.3.sup.− out of the surrounding media, increasing the pH and the saturation index for calcification. Succinate utilization in E. coli occurs from the reduction of succinate to fumarate, allowing succinate to directly feed into the citric acid cycle, similarly bypassing needed CO.sub.2 produced from the full cycle; this bypass does not occur in metabolism of the weaker calcium salts: pyruvate, lactate, and propionate. To provide a more quantifiable estimation of the role of pH and saturation index in calcification, a liquid culture assay was developed. Liquid cultures were grown and monitored for microbial growth (via an increase in opacity at OD.sub.600) and insoluble Ca.sup.2+ ion concentrations as a proxy for calcification. This assay allowed for observation of the onset of calcification with pH changes and indicated that the amount of calcification depended on the calcium source, with the highest amount of calcification occurring with calcium succinate (about 42 ppm Ca.sup.2+). The amount of calcification was increased with calcium acetate, but not to the same extent (17 ppm Ca.sup.2+). The data indicated that the calcium salts that induce the highest calcification also demonstrate a rapid pH rise and the onset of calcification (at about 7 hours), although again pH alone was not diagnostic of the onset of calcification. By engineering the E. coli carbonic anhydrase gene into an inducible, overexpression plasmid vector, the liquid growth system was used to demonstrate that calcification could be dramatically increased in E. coli in a controllable manner.

[0053] To confirm that the insoluble Ca.sup.2+ ions in the media were present in a stable, mineral form XRD was used. To do this, rather than acidifying the captured, insoluble particulates in the media for ICP-MS, they were collected, dried, and subjected to XRD. The results demonstrated that the calcium salt chemistry influenced the type of calcite polymorph that was formed. On calcium acetate, lactate and propionate, the unstable polymorph vaterite was the dominant form of CaCO.sub.3. On succinate, a combination of vaterite and calcite was produced, while on pyruvate, calcite was the dominant mineral. The data confirmed that the supplied calcium salt is converted to a mineral form, but that the metabolism of the salt used can influence the type of mineral produced and may allow tailoring of the final precipitate chemistry.

Methods

[0054] Growth Conditions and Bacterial Strains

[0055] Unless otherwise noted, all chemicals and growth media were obtained from Fisher Scientific (Pittsburg, Pa.). Calcification was assayed on either solid (with 15 g/L agar) or in liquid calcification B4 media (4 g yeast extract, 10 g glucose), but amended with a variety of different calcium salts [calcium acetate, calcium propionate, calcium L-lactate hydrate, calcium succinate monohydrate, calcium pyruvate, and calcium citrate tribasic tetrahydrate). The basal calcification media was resuspended in 800 mL water, adjusted to pH 7.2 and autoclaved, cooled to 50° C., before 2.5 g of the calcium salt (in 200 mL filter sterilized dH.sub.2O). As calcium citrate and calcium succinate are insoluble in water, they were dissolved in 200 mL 0.1 M HCl and readjusted to pH 7.2 before filtering. The minimal B4 media (B4m) was made as described, but without the addition of glucose. When required, cresol red (8 mg/L) was added as a pH indicator (indicator range pH 6.2-8.8).

[0056] E. coli K-12 type strain MG1655 (F.sup.− lambda.sup.− ΔilvG rfb-50 rph-1) was used to assay calcification phenotypes and grown at 37° C. on LB agar or B4 and amended B4 media plates. A Thermo Fisher Scientific (Waltham, Mass., USA) Orion Micro pH 12Ga. needle tipped electrode combined with a Reed (Wilmington, N.C., USA) SD-230 pH meter was used to confirm the pH of the agar calibrated using Fisher Scientific (Waltham, Mass., USA) pH 7 and 10 buffers. Unless indicated, all assays were carried out in triplicate. An Olympus (Tokyo, Japan) SZX7 stereomicroscope fitted with an Olympus DFPL I.5× objective and Olympus SCI80 color digital camera was used to Image the single colonies of E. coli. Olympus cellSens Standard 2.3 software was used to acquire images with a resolution of 2456×1842 at a standard aspect ratio. For accurate color reproduction the high-quality color image style option was selected and the compartment for insertion of contrast cartridges was left clear.

[0057] Quantification of Calcification: Solid Media

[0058] As calcification occurred very quickly in colonies at 37° C., E. coli MGI655 was grown at room temperature (21° C.) to examine calcification rates. After one week, a minimum of ten individual colonies were chosen at random and imaged using an Olympus SZX7 microscope equipped with an Olympus SCI80 camera. Images were captured using cellSens Standard 2 software (Olympus) and analyzed using the ImageJ plugins Trainable Weka Segmentation (TWS; v3.2.33) and MorphoLibJ (v1.4.1) to measure calcification. The TWS plugin image feature recognition algorithm was used to identify carbonate crystals on the colony using a set of training images of colonies from the same plate, followed by manually designating areas as crystal (red), colony (green), or background (purple) to generate an overlay output. The classification was then scored as .model file for use with other images of similar morphology, which was further refined with additional training images of a series. The plugin analyzed subsequent images using this training set and calculated a probability map showing coverage of colonies by calcite crystals.

[0059] Once crystals had been identified and segmented, percent coverage was calculated using the Analyze Particles function built into ImageJ. To obtain individual crystal information, a particle analysis was used. The Image] TWS Get probability function was used to generate a probability map of a colony. The image was then formatted as an 8-bit image and the threshold values adjusted until the calcite crystals were selected and the analyze particle function was used, and the minimum size of pixel units was used to mitigate artefact errors. A TWS analysis gave an ROJ overlay allowed measurement of the area, and selections were saved as a .csv file. For the best results, multiple classifiers were produced to account for the change in colony thickness and shadow gradient effects as the colonies grew, changed shape, and became increasingly opaque and occupied by crystals over time. The final overlay of crystal coverage generated by the particle analysis was periodically applied back to the original colony image to check the accuracy of the fit of the classifier and then adjusted where necessary. A detailed description along with ImageJ script was then created.

[0060] Quantification of Calcification: Liquid Media

[0061] For quantification of calcification in liquid media, 50 mL cultures of calcification media were inoculated with 1 mL of an overnight culture of E. coli grown in 4 g/L yeast extract media grown to OD.sub.600 0.75. The cultures were grown in a 250 mL side-arm flask (OWK Life Sciences, Millville, N.J.) at 37° C. with shaking (250 rpm) on an Excella E24 incubated shaker (New Brunswick, Eddison, N.J.). Growth was recorded by taking the optical density (OD.sub.600) every 30 minutes using a OR 2800 spectrophotometer (Hach, Loveland, Colo.). Once the optical density had reached OD.sub.600 0.1, 1 mL samples were taken every hour to quantify any solid CaCO.sub.3. To do this, the 1 mL samples were filtered onto a 25 mm Isopore 0.2 μm black PC membrane (Millipore, Burlington, Mass.) using a micro-syringe 25 mm filter holder (Millipore) and washed 10 mL 20 mM HEPES buffer (adjusted to pH 8.3). The membrane was then submerged in 10 mL of a 5% nitric acid (TraceMetal grade) for 30 minutes to dissolve any calcite and centrifuged for 10 minutes at 2,739 rcf on a Survall LegendXTR Centrifuge (Thermo Scientific, Waltham, Mass.) to remove any cell debris. The calcium concentrations of the resulting HNO.sub.3 acid solution were measured using a 700 Series ICP-OES (Agilent Technologies, Santa Clara Calif.). Wavelength calibrations were completed using 5 ppm Mn calibration solution, with 0, 3, 7 and 10 ppm calcium ion calibration standards prepared from a 10 ppm calcium stock solution (0.1% v/v HNO.sub.3; Inorganic Ventures, Christiansburg, Va.). Analysis of calcium concentration (per mL of culture) was then carried out using ICP Expert II software (Agilent Technologies).

[0062] XRD Analyses

[0063] For XRD analyses of carbonate minerals, 250 μL of overnight cultures of E. coli grown in B4m (OD.sub.600 0.8) was inoculated into 25 mL of liquid media in a 250 mL flask (OWK Life Sciences) and grown for one week at room temperature with shaking at 100 rpm on a SKC-6200 orbital platform shaker (ReioTech, Daejeon, Republic of Korea). Any precipitated minerals were collected by vacuum filtration of the culture onto an MF-Millipore 8.0 μm MCE membrane and washed of cell debris with 15 mL of a 20 mM HEPES buffer at pH 8.3. These filters were allowed to dry for 1 hour at room temperature in a glass Petri plates. The surface of the membranes was then scraped using a metal spatula into a 10 mL glass tube and allowed to dry for an additional 24 hours. This material was then subjected to XRD analysis with an Ultima IV X-ray diffractometer (Rigaku, Tokyo, Japan) operated at 40 KV and 35 mA with a Cu K-alpha energy frequency (wavelength of 1.54 Å). Identification of the diffraction profiles was determined using PDXL 2.1 software package (Rigaku).