in

Mineralogy of microbially induced calcium carbonate precipitates formed using single cell drop-based microfluidics

  • 1.

    Dong, H. L. & Lu, A. H. Mineral-microbe interactions and implications for remediation. Elements 8, 95–100. https://doi.org/10.2113/gselements.8.2.95 (2012).

    CAS  Article  Google Scholar 

  • 2.

    Li, X. B. et al. Spatial patterns of carbonate biomineralization in biofilms. Appl. Environ. Microbiol. 81, 7403–7410. https://doi.org/10.1128/aem.01585-15 (2015).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 3.

    Miot, J., Benzerara, K. & Kappler, A. In Annual Review of Earth and Planetary Sciences, Vol. 42 Annual Review of Earth and Planetary Sciences (ed R. Jeanloz) 271–289 (Annual Reviews, 2014).

  • 4.

    Brookshaw, D., Pattrick, R., Lloyd, J. & Vaughan, D. Microbial effects on mineral–radionuclide interactions and radionuclide solid-phase capture processes. Mineral. Mag. 76, 200. https://doi.org/10.1180/minmag.2012.076.3.25 (2012).

    CAS  Article  Google Scholar 

  • 5.

    Li, J. et al. Biomineralization, crystallography and magnetic properties of bullet-shaped magnetite magnetosomes in giant rod magnetotactic bacteria. Earth Planet. Sci. Lett. 293, 368–376. https://doi.org/10.1016/j.epsl.2010.03.007 (2010).

    ADS  CAS  Article  Google Scholar 

  • 6.

    Douglas, S. & Beveridge, T. J. Mineral formation by bacteria in natural microbial communities. FEMS Microbiol. Ecol. 26, 79–88. https://doi.org/10.1111/j.1574-6941.1998.tb00494.x (1998).

    CAS  Article  Google Scholar 

  • 7.

    Dick, G. et al. The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats. Front. Microbiol. https://doi.org/10.3389/fmicb.2013.00124 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  • 8.

    Hatzenpichler, R., Krukenberg, V., Spietz, R. L. & Jay, Z. J. Next-generation physiology approaches to study microbiome function at single cell level. Nat. Rev. Microbiol. https://doi.org/10.1038/s41579-020-0323-1 (2020).

    Article  PubMed  Google Scholar 

  • 9.

    Phillips, A. J. et al. Engineered applications of ureolytic biomineralization: a review. Biofouling 29, 715–733. https://doi.org/10.1080/08927014.2013.796550 (2013).

    CAS  Article  PubMed  Google Scholar 

  • 10.

    Cuthbert, M. O. et al. Controls on the rate of ureolysis and the morphology of carbonate precipitated by S. pasteurii biofilms and limits due to bacterial encapsulation. Ecol. Eng. 41, 32–40 (2012).

    Article  Google Scholar 

  • 11.

    De Muynck, W., Verbeken, K., De Belie, N. & Verstraete, W. Influence of urea and calcium dosage on the effectiveness of bacterially induced carbonate precipitation on limestone. Ecol. Eng. 36, 99–111. https://doi.org/10.1016/j.ecoleng.2009.03.025 (2010).

    Article  Google Scholar 

  • 12.

    Ferris, F. G., Fyfe, W. S. & Beveridge, T. J. Bacteria as nucleation sites for authigenic minerals in a metal-contaminated lake sediment. Chem. Geol. 63, 225–232. https://doi.org/10.1016/0009-2541(87)90165-3 (1987).

    ADS  CAS  Article  Google Scholar 

  • 13.

    Hammes, F. & Verstraete, W. Key roles of pH and calcium metabolism in microbial carbonate precipitation. Rev. Environ. Sci. Biotechnol. 1, 3–7. https://doi.org/10.1023/a:1015135629155 (2002).

    CAS  Article  Google Scholar 

  • 14.

    van Paassen, L. Biogrout, Ground Improvement by Microbial Induced Carbonate Precipitation. Doctoral Thesis. (Delft University of Technology, Delft, Netherlands, 2009).

  • 15.

    Zhang, W., Ju, Y., Zong, Y., Qi, H. & Zhao, K. In situ real-time study on dynamics of microbially induced calcium carbonate precipitation at a single-cell level. Environ. Sci. Technol. https://doi.org/10.1021/acs.est.8b02660 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  • 16.

    Dohnalkova, A. C. et al. Imaging hydrated microbial extracellular polymers: comparative analysis by electron microscopy. Appl. Environ. Microbiol. 77, 1254–1262. https://doi.org/10.1128/aem.02001-10 (2011).

    CAS  Article  PubMed  Google Scholar 

  • 17.

    Kaminski, T. S., Scheler, O. & Garstecki, P. Droplet microfluidics for microbiology: techniques, applications and challenges. Lab Chip 16, 2168–2187. https://doi.org/10.1039/c6lc00367b (2016).

    CAS  Article  PubMed  Google Scholar 

  • 18.

    Vincent, M. E., Liu, W. S., Haney, E. B. & Ismagilov, R. F. Microfluidic stochastic confinement enhances analysis of rare cells by isolating cells and creating high density environments for control of diffusible signals. Chem. Soc. Rev. 39, 974–984. https://doi.org/10.1039/b917851a (2010).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 19.

    Taheri-Araghi, S., Brown, S. D., Sauls, J. T., McIntosh, D. B. & Jun, S. In Annual Review of Biophysics, Vol. 44 (ed K. A. Dill) 123–142 (Annual Reviews, 2015).

  • 20.

    Pratt, S. L. et al. DropSOAC: stabilizing microfluidic drops for time-lapse quantification of single-cell bacterial physiology. Front. Microbiol. https://doi.org/10.3389/fmicb.2019.02112 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  • 21.

    Schmitz, C. H. J., Rowat, A. C., Köster, S. & Weitz, D. A. Dropspots: a picoliter array in a microfluidic device. Lab Chip 9, 44–49. https://doi.org/10.1039/B809670H (2009).

    CAS  Article  PubMed  Google Scholar 

  • 22.

    Rodriguez-Ruiz, I. et al. Transient calcium carbonate hexahydrate (ikaite) nucleated and stabilized in confined nano- and picovolumes. Cryst. Growth Des. 14, 792–802. https://doi.org/10.1021/cg401672v (2014).

    CAS  Article  Google Scholar 

  • 23.

    Yashina, A., Meldrum, F. & deMello, A. Calcium carbonate polymorph control using droplet-based microfluidics. Biomicrofluidics 6, 10. https://doi.org/10.1063/1.3683162 (2012).

    CAS  Article  Google Scholar 

  • 24.

    Liu, P. Y., Yao, J., Couples, G. D., Ma, J. S. & Iliev, O. 3-D modelling and experimental comparison of reactive flow in carbonates under radial flow conditions. Sci. Rep. 7, 10. https://doi.org/10.1038/s41598-017-18095-2 (2017).

    ADS  CAS  Article  Google Scholar 

  • 25.

    Connolly, J. et al. Construction of two ureolytic model organisms for the study of microbially induced calcium carbonate precipitation. J. Microbiol. Methods 94, 290–299. https://doi.org/10.1016/j.mimet.2013.06.028 (2013).

    CAS  Article  PubMed  Google Scholar 

  • 26.

    Duffy, D. C., McDonald, J. C., Schueller, O. J. & Whitesides, G. M. Rapid prototyping of microfluidic systems in poly(dimethylsiloxane). Anal. Chem. 70, 4974–4984. https://doi.org/10.1021/ac980656z (1998).

    CAS  Article  PubMed  Google Scholar 

  • 27.

    Holtze, C. et al. Biocompatible surfactants for water-in-fluorocarbon emulsions. Lab Chip 8, 1632–1639. https://doi.org/10.1039/b806706f (2008).

    CAS  Article  PubMed  Google Scholar 

  • 28.

    Jung, D., Biggs, H., Erikson, J. & Ledyard, P. U. New colorimetric reaction for endpoint, continuous-flow, and kinetic measurement of urea. Clin. Chem. 21, 1136–1140 (1975).

    CAS  Article  Google Scholar 

  • 29.

    Phillips, A. J. et al. Fracture sealing with microbially-induced calcium carbonate precipitation: a field study. Environ. Sci. Technol. 50, 4111–4117. https://doi.org/10.1021/acs.est.5b05559 (2016).

    ADS  CAS  Article  PubMed  Google Scholar 

  • 30.

    Yoshida, N., Higashimura, E. & Saeki, Y. Catalytic biomineralization of fluorescent calcite by the thermophilic bacterium Geobacillus thermoglucosidasius. Appl. Environ. Microbiol. 76, 7322–7327. https://doi.org/10.1128/aem.01767-10 (2010).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 31.

    Tinevez, J. Y. et al. TrackMate: an open and extensible platform for single-particle tracking. Methods 115, 80–90. https://doi.org/10.1016/j.ymeth.2016.09.016 (2017).

    CAS  Article  PubMed  Google Scholar 

  • 32.

    Vejborg, R. M. & Klemm, P. Cellular chain formation in Escherichia coli biofilms. Microbiology (Reading, England) 155, 1407–1417. https://doi.org/10.1099/mic.0.026419-0 (2009).

    CAS  Article  Google Scholar 

  • 33.

    Rodriguez-Blanco, J. D., Shaw, S. & Benning, L. G. The kinetics and mechanisms of amorphous calcium carbonate (ACC) crystallization to calcite, via vaterite. Nanoscale 3, 265–271. https://doi.org/10.1039/c0nr00589d (2011).

    ADS  CAS  Article  PubMed  Google Scholar 

  • 34.

    Tlili, M. M. et al. Characterization of CaCO3 hydrates by micro-Raman spectroscopy. J. Raman Spectrosc. 33, 10–16. https://doi.org/10.1002/jrs.806 (2002).

    ADS  CAS  Article  Google Scholar 

  • 35.

    Clarkson, J. R., Price, T. J. & Adams, C. J. Role of metastable phases in the spontaneous precipitation of calcium-carbonate. J. Chem. Soc. Faraday Trans. 88, 243–249. https://doi.org/10.1039/ft9928800243 (1992).

    CAS  Article  Google Scholar 

  • 36.

    Gabrielli, C., Jaouhari, R., Joiret, S., Maurin, G. & Rousseau, P. Study of the electrochemical deposition of CaCO3 by in situ Raman spectroscopy—I. Influence of the substrate. J. Electrochem. Soc. 150, C478–C484. https://doi.org/10.1149/1.1579482 (2003).

    CAS  Article  Google Scholar 

  • 37.

    Behrens, G., Kuhn, L. T., Ubic, R. & Heuer, A. H. Raman-spectra of vateritic calcium-carbonate. Spectrosc. Lett. 28, 983–995. https://doi.org/10.1080/00387019508009934 (1995).

    ADS  CAS  Article  Google Scholar 

  • 38.

    Wagner, O. et al. Biocompatible fluorinated polyglycerols for droplet microfluidics as an alternative to PEG-based copolymer surfactants. Lab Chip 16, 65–69. https://doi.org/10.1039/C5LC00823A (2016).

    CAS  Article  PubMed  Google Scholar 

  • 39.

    Gruner, P. et al. Controlling molecular transport in minimal emulsions. Nat. Commun. 7, 10392. https://doi.org/10.1038/ncomms10392 (2016).

    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 40.

    Bai, Y. et al. A double droplet trap system for studying mass transport across a droplet-droplet interface. Lab Chip 10, 1281–1285. https://doi.org/10.1039/b925133b (2010).

    CAS  Article  PubMed  Google Scholar 

  • 41.

    Hoffmann, R. et al. TEM preparation methods and influence of radiation damage on the beam sensitive CaCO3 shell of Emiliania huxleyi. Micron 62, 28–36. https://doi.org/10.1016/j.micron.2014.03.004 (2014).

    CAS  Article  PubMed  Google Scholar 

  • 42.

    Hooley, R., Brown, A. & Brydson, R. Factors affecting electron beam damage in calcite nanoparticles. Micron 120, 25–34. https://doi.org/10.1016/j.micron.2019.01.011 (2019).

    CAS  Article  PubMed  Google Scholar 

  • 43.

    Bentov, S., Weil, S., Glazer, L., Sagi, A. & Berman, A. Stabilization of amorphous calcium carbonate by phosphate rich organic matrix proteins and by single phosphoamino acids. J. Struct. Biol. 171, 207–215. https://doi.org/10.1016/j.jsb.2010.04.007 (2010).

    CAS  Article  PubMed  Google Scholar 

  • 44.

    Rautaray, D., Sanyal, A., Bharde, A., Ahmad, A. & Sastry, M. Biological synthesis of stable vaterite crystals by the reaction of calcium ions with germinating chickpea seeds. Cryst. Growth Des. 5, 399–402. https://doi.org/10.1021/cg0341858 (2005).

    CAS  Article  Google Scholar 

  • 45.

    Kawaguchi, T. & Decho, A. W. A laboratory investigation of cyanobacterial extracellular polymeric secretions (EPS) in influencing CaCO3 polymorphism. J. Cryst. Growth 240, 230–235. https://doi.org/10.1016/s0022-0248(02)00918-1 (2002).

    ADS  CAS  Article  Google Scholar 

  • 46.

    Wang, S.-S., Picker, A., Cölfen, H. & Xu, A.-W. Heterostructured calcium carbonate microspheres with calcite equatorial loops and vaterite spherical cores. Angew. Chem. Int. Ed. 52, 6317–6321. https://doi.org/10.1002/anie.201301184 (2013).

    CAS  Article  Google Scholar 

  • 47.

    Rao, A. & Cölfen, H. Morphology control and molecular templates in biomineralization. Biominer. Biomater. https://doi.org/10.1016/B978-1-78242-338-6.00003-X (2016).

    Article  Google Scholar 

  • 48.

    Aggarwal, K. P., Narula, S., Kakkar, M. & Tandon, C. Nephrolithiasis: molecular mechanism of renal stone formation and the critical role played by modulators. Biomed Res Int 2013, 292953–292953. https://doi.org/10.1155/2013/292953 (2013).

    CAS  Article  Google Scholar 


  • Source: Ecology - nature.com

    Georgina Mace (1953–2020)

    Designing off-grid refrigeration technologies for crop storage in Kenya