Active fluid with Acidithiobacillus ferrooxidans: correlations between swimming and the oxidation route

  • Juan D. Torrenegra
  • Liliam C. Agudelo-Morimitsu
  • Marco A. Márquez-Godoy
  • Juan P. Hernández-OrtizEmail author
Original Paper


To explore engineering platforms towards ‘active bacterial baths’, we grow and characterize native and commercial strains of Acidithiobacillus ferrooxidans to promote swimming locomotion. Three different energy sources were used, namely elemental sulfur, ferrous sulfate, and pyrite. The characteristics of the culture, such as pH, Eh, and the concentration of cells and ions, are monitored to seek correlations between the oxidation route and the transport mechanism. We found that only elemental sulfur induces swimming mobility in the commercial DSMZ – 24,419 strain, while ferrous sulfate and the sulfide mineral, pyrite, did not activate swimming on any strain. The bacterial mean squared displacement and the mean velocity are measured to provide a quantitative description of the bacterial mobility. We found that, even if the A. ferrooxidans strain is grown in a sulfur-rich environment, it preferentially oxidizes iron when an iron-based material is included in the media. Similar to other species, once the culture pH decreases below 1.2, the active locomotion is inhibited. The engineering control and activation of swimming in bacterial cultures offer fertile grounds towards applications of active suspensions such as energy-efficient bioleaching, mixing, drug delivery, and bio-sensing.


Active fluid Bacterial mobility Mean squared displacement Acidithiobacillus ferrooxidans 



The authors acknowledge the financial support from the Universidad Nacional de Colombia and its Faculty of Mines. They are also grateful to the Biological Hydro-Metallurgy Laboratory at the Faculty of Mines, part of the Material Characterization Laboratory, at the Universidad Nacional de Colombia, Sede Medellín. This research is embedded in the UW-Madison/UN/Ruta N agreement for the Colombia/Wisconsin One-Health Consortium at the Universidad Nacional de Colombia.

Compliance with ethical standards

Conflict of interest

All the authors declare that they have no conflicts of interest.

Research involving human and animal rights

This article does not contain any studies with human participants or animals performed by any of the authors.


  1. 1.
    Goodrich, C.P., Brenner, M.P.: Using active colloids as machines to weave and braid on the micrometer scale. Proc. Natl. Acad. Sci. U.S.A. 114, 257–262 (2017).
  2. 2.
    Keber, F., Loiseau, E., Sanchez, T., DeCamp, S., Giomi, L., Bowick, M., Marchetti, M.C., Dogic, Z., Bausch, A.: Topology and dynamics of active nematic vesicles. Science 345, 1135–1139 (2014).
  3. 3.
    Thampi, S.P., Doostmohammadi, A., Shendruk, T.N., Golestanian, R., Yeomans, J.M.: Active micromachines: microfluidics powered by mesoscale turbulence. Sci. Adv. 2, e1501854 (2016). ADSCrossRefGoogle Scholar
  4. 4.
    Takatori, S.C., Brady, J.F.: Towards a thermodynamics of active matter. Phys. Rev. E. 91, (2015).
  5. 5.
    Takatori, S.C., Brady, J.F.: Swim stress, motion, and deformation of active matter: effect of an external field. Soft Matter 10, 9433–9445 (2014). ADSCrossRefGoogle Scholar
  6. 6.
    Takatori, S.C., Yan, W., Brady, J.F.: Swim pressure: stress generation in active matter. Phys. Rev. Lett. 113, 1–5 (2014). CrossRefGoogle Scholar
  7. 7.
    Saintillan, D., Shelley, M.J.: Instabilities, pattern formation, and mixing in active suspensions. Phys. Fluids 20, 123304 (2008). ADSCrossRefzbMATHGoogle Scholar
  8. 8.
    Ezhilan, B., Pahlavan, A.A., Saintillan, D.: Chaotic dynamics and oxygen transport in thin films of aerotactic bacteria. Phys. Fluids 24, (2012).
  9. 9.
    Saintillan, D., Shelley, M.J.: Emergence of coherent structures and large-scale flows in motile suspensions. J. R. Soc. Interface 9, 571–585 (2012). CrossRefGoogle Scholar
  10. 10.
    Wensink, H.H., Dunkel, J., Heidenreich, S., Drescher, K., Goldstein, R.E., Lowen, H., Yeomans, J.M.: Meso-scale turbulence in living fluids. Proc. Natl. Acad. Sci. U.S.A. 109, 14308–14313 (2012).
  11. 11.
    Alexander, G.P., Yeomans, J.M.: Dumb-bell swimmers. Europhys. Lett. 83, (2008).
  12. 12.
    Dunkel, J., Putz, V.B., Zaid, I.M., Yeomans, J.M.: Swimmer–tracer scattering at low Reynolds number. Soft Matter 6, 4268–4276 (2010).
  13. 13.
    Hernandez-Ortiz, J.P., Stoltz, C.G., Graham, M.D.: Transport and collective dynamics in suspensions of confined swimming particles. Phys. Rev. Lett. 95, 1–4 (2005). CrossRefGoogle Scholar
  14. 14.
    Underhill, P.T., Hernandez-Ortiz, J.P., Graham, M.D.: Diffusion and spatial correlations in suspensions of swimming particles. Phys. Rev. Lett. 100, 1–4 (2008). CrossRefGoogle Scholar
  15. 15.
    Hernandez-Ortiz, J.P., Underhill, P.T., Graham, M.D.: Dynamics of confined suspensions of swimming particles. J. Phys. Condens. Matter. 21, (2009).
  16. 16.
    Kolmakov, G.V., Schaefer, A., Aranson, I., Balazs, A.C.: Designing mechano-responsive microcapsules that undergo self-propelled motion. Soft Matter 8, 180–190 (2012). ADSCrossRefGoogle Scholar
  17. 17.
    Guasto, J.S., Rusconi, R., Stocker, R.: Fluid mechanics of planktonic microorganisms. Annu. Rev. Fluid Mech. 44, 373–400 (2012). ADSMathSciNetCrossRefzbMATHGoogle Scholar
  18. 18.
    Sokolov, A., Aranson, I.S.: Physical properties of collective motion in suspensions of bacteria. Phys. Rev. Lett. 109, 1–5 (2012). CrossRefGoogle Scholar
  19. 19.
    Zhou, S., Sokolov, A., Lavrentovich, O.D., Aranson, I.S.: Living liquid crystals. Proc. Natl. Acad. Sci. U.S.A. 111, 1265–1270 (2014).
  20. 20.
    Miño, G.L., Dunstan, J., Rousselet, A., Clément, E., Soto, R.: Induced diffusion of tracers in a bacterial suspension: theory and experiments. J. Fluid Mech. 729, 423–444 (2013). ADSCrossRefzbMATHGoogle Scholar
  21. 21.
    Calle-Castañeda, S.M., Márquez-Godoy, M.A., Hernández-Ortiz, J.P.: Solubilization of phosphorus from phosphate rocks with Acidithiobacillus thiooxidans following a growing-then-recovery process. World J. Microbiol. Biotechnol. 34, (2018).
  22. 22.
    Calle-Castañeda, S.M., Márquez-Godoy, M.A., Hernández-Ortiz, J.P.: Phosphorus recovery from high concentrations of low-grade phosphate rocks using the biogenic acid produced by the acidophilic bacteria Acidithiobacillus thiooxidans. Miner. Eng. 115, 97–105 (2018). CrossRefGoogle Scholar
  23. 23.
    Drescher, K., Dunkel, J., Cisneros, L.H., Ganguly, S., Goldstein, R.E.: Fluid dynamics and noise in bacterial cell–cell and cell–surface scattering. Proc. Natl. Acad. Sci. 108, 10940–10945 (2011). ADSCrossRefGoogle Scholar
  24. 24.
    Gyrya, V., Aranson, I.S., Berlyand, L.V., Karpeev, D.: A model of hydrodynamic interaction between swimming bacteria. Bull. Math. Biol. 72, 148–183 (2010). MathSciNetCrossRefzbMATHGoogle Scholar
  25. 25.
    Berke, A.P., Turner, L., Berg, H.C., Lauga, E.: Hydrodynamic attraction of swimming microorganisms by surfaces. Phys. Rev. Lett. 101, 1–5 (2008). CrossRefGoogle Scholar
  26. 26.
    Micali, G., Endres, R.G.: Bacterial chemotaxis: information processing, thermodynamics, and behavior. Curr. Opin. Microbiol. 30, 8–15 (2016). CrossRefGoogle Scholar
  27. 27.
    Carlsen, R.W., Sitti, M.: Bio-hybrid cell-based actuators for microsystems. Small 10, 3831–3851 (2014).
  28. 28.
    Aghaie, E., Pazouki, M., Hosseini, M.R., Ranjbar, M.: Kinetic modeling of the bioleaching process of iron removal from kaolin. Appl. Clay Sci. 65–66, 43–47 (2012). CrossRefGoogle Scholar
  29. 29.
    Tuncuk, A., Ciftlik, S., Akcil, A.: Factorial experiments for iron removal from kaolin by using single and two-step leaching with sulfuric acid. Hydrometallurgy 134–135, 80–86 (2013). CrossRefGoogle Scholar
  30. 30.
    Sun, L.X., Zhang, X., Tan, W.S., Zhu, M.L.: Effect of agitation intensity on the biooxidation process of refractory gold ores by Acidithiobacillus ferrooxidans. Hydrometallurgy 127–128, 99–103 (2012). CrossRefGoogle Scholar
  31. 31.
    Zammit, C.M., Cook, N., Brugger, J., Ciobanu, C.L., Reith, F.: The future of biotechnology for gold exploration and processing. Miner. Eng. 32, 45–53 (2012). CrossRefGoogle Scholar
  32. 32.
    Henao, D.M.O., Godoy, M.A.M.: Jarosite pseudomorph formation from arsenopyrite oxidation using Acidithiobacillus ferrooxidans. Hydrometallurgy 104, 162–168 (2010).
  33. 33.
    Rodríguez, Y., Ballester, A., Blázquez, M.L., González, F., Muñoz, J.A.: New information on the pyrite bioleaching mechanism at low and high temperature. Hydrometallurgy 71, 37–46 (2003).
  34. 34.
    Berg, H.C., Brown, D.A.: Chemotaxis in Escherichia coli analysed by three-dimensional tracking. Nature 239, 500–504 (1972).
  35. 35.
    Berg, H.C.: E. coli in Motion. Springer, New York (2003)Google Scholar
  36. 36.
    Berg, H.C.: Random Walks in Biology. Princeton University Press, Princeton (1993)Google Scholar
  37. 37.
    Janssen, P.J.A., Graham, M.D.: Coexistence of tight and loose bundled states in a model of bacterial flagellar dynamics. Phys. Rev. E Stat. Nonlinear Soft Matter Phys. 84, 1–9 (2011). CrossRefGoogle Scholar
  38. 38.
    Copeland, M.F., Weibel, D.B.: Bacterial swarming: a model system for studying dynamic self-assembly. Soft Matter 5, 1174 (2009). ADSCrossRefGoogle Scholar
  39. 39.
    Suzuki, I., Lee, D., Mackay, B., Harahuc, L.: Effect of various ions, pH, and osmotic pressure on oxidation of elemental sulfur by Thiobacillus thiooxidans effect of various ions, pH, and osmotic pressure on oxidation of elemental sulfur by Thiobacillus thiooxidans. Appl. Environ. Microbiol. 65, 5163–5168 (1999)Google Scholar
  40. 40.
    Kearns, D.B.: A field guide to bacterial swarming motility. Nat. Rev. Microbiol. 8, 634–644 (2010). CrossRefGoogle Scholar
  41. 41.
    Amouric, A., Brochier-Armanet, C., Johnson, D.B., Bonnefoy, V., Hallberg, K.B.: Phylogenetic and genetic variation among Fe(II)- oxidizing acidithiobacilli supports the view that these comprise multiple species with different ferrous iron oxidation pathways. Microbiology 157, 111–122 (2011). CrossRefGoogle Scholar
  42. 42.
    Patteson, A.E., Gopinath, A., Goulian, M., Arratia, P.E.: Running and tumbling with E. coli in polymeric solutions. Sci. Rep. 5, 1–11 (2015). CrossRefGoogle Scholar
  43. 43.
    Mendelson, N.H., Bourque, A., Wilkening, K., Anderson, K.R., Watkins, J.C.: Organized cell swimming motions in Bacillus subtilis colonies: patterns of short-lived whirls and jets. J. Bacteriol. 181, 600–609 (1999)Google Scholar
  44. 44.
    Leptos, K.C., Guasto, J.S., Gollub, J.P., Pesci, A.I., Goldstein, R.E.: Dynamics of enhanced tracer diffusion in suspensions of swimming eukaryotic microorganisms. Phys. Rev. Lett. 103, (2009).
  45. 45.
    Sokolov, A., Aranson, I.S.: Reduction of viscosity in suspension of swimming bacteria. Phys. Rev. Lett. 103, 2–5 (2009). Google Scholar
  46. 46.
    Sand, W., Gehrke, T., Jozsa, P.G., Schippers, A.: (Bio)chemistry of bacterial leaching - direct vs. indirect bioleaching. Hydrometallurgy 59, 159–175 (2001).
  47. 47.
    Ponce, J.S., Moinier, D., Byrne, D., Amouric, A., Bonnefoy, V.: Acidithiobacillus ferrooxidans oxidizes ferrous iron before sulfur likely through transcriptional regulation by the global redox responding RegBA signal transducing system. Hydrometallurgy 127–128, 187–194 (2012). CrossRefGoogle Scholar
  48. 48.
    Suzuki, I., Takeuchi, T.L., Yuthasastrakosol, T.D., Oh, J.K.: Ferrous iron and sulfur oxidation and ferric Iron reduction activities of Thiobacillus ferrooxidans are affected by growth on ferrous iron, sulfur, or a sulfide ore ferrous iron and sulfur oxidation and ferric iron reduction activities of Thiobacillus f. Appl. Environ. Microbiol. 56, 1620–1626 (1990)Google Scholar
  49. 49.
    Tributsch, H.: Direct versus indirect bioleaching. Hydrometallurgy 59, 177–185 (2001). CrossRefGoogle Scholar
  50. 50.
    Caicedo, G., Prada, M., Pelaez, H., Moreno, C., Marquez, M.: Evaluation of a coal biodesulfurization process (semi-continuous mode) on the pilot plant level. Dyna 79, 114–118 (2012)Google Scholar
  51. 51.
    Márquez, M.A., Ospina, J.D., Morales, A.L.: New insights about the bacterial oxidation of arsenopyrite: a mineralogical scope. Miner. Eng. 39, 248–254 (2012). CrossRefGoogle Scholar
  52. 52.
    Mousavi, S.M., Yaghmaei, S., Salimi, F., Jafari, A.: Influence of process variables on biooxidation of ferrous sulfate by an indigenous Acidithiobacillus ferrooxidans. Part I: flask experiments. Fuel 85, 2555–2560 (2006). CrossRefGoogle Scholar
  53. 53.
    Ohmura, N., Tsugita, K., Koizumi, J.I., Saika, H.: Sulfur-binding protein of flagella of Thiobacillus ferrooxidans. J. Bacteriol. 178, 5776–5780 (1996)CrossRefGoogle Scholar
  54. 54.
    Li, Y., Li, H.: Type IV pili of Acidithiobacillus ferrooxidans can transfer electrons from extracellular electron donors. J. Basic Microbiol. 53, 1–6 (2013). CrossRefGoogle Scholar
  55. 55.
    Li, Y.-Q., Wan, D.-S., Huang, S.-S., Leng, F.-F., Yan, L., Ni, Y.-Q., Li, H.-Y.: Type IV pili of Acidithiobacillus ferrooxidans are necessary for sliding, twitching motility, and adherence. Curr. Microbiol. 60, 17–24 (2010). CrossRefGoogle Scholar
  56. 56.
    Jerez, C.A.: The use of genomics, proteomics and other OMICS technologies for the global understanding of biomining microorganisms. Hydrometallurgy 94, 162–169 (2008). CrossRefGoogle Scholar
  57. 57.
    Valdés, J., Pedroso, I., Quatrini, R., Dodson, R.J., Tettelin, H., Blake, R., Eisen, J.A., Holmes, D.S.: Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics 9, 597 (2008). CrossRefGoogle Scholar
  58. 58.
    Klingl, A., Moissl-Eichinger, C., Wanner, G., Zweck, J., Huber, H., Thomm, M., Rachel, R.: Analysis of the surface proteins of Acidithiobacillus ferrooxidans strain SP5/1 and the new, pyrite-oxidizing Acidithiobacillus isolate HV2/2, and their possible involvement in pyrite oxidation. Arch. Microbiol. 193, 867–882 (2011). CrossRefGoogle Scholar
  59. 59.
    DiSPIRITO, A., Silver, M., Voss, L., Tuovinen, O.: Flagella and pili of iron-oxidizing Thiobacilli isolated from uranium mine in northern Ontario, Canada. Appl. Environ. Microbiol. 43, 1196–1200 (1982)Google Scholar
  60. 60.
    Silverman, M.P., Lundgren, D.G.: Studies on the chemoautotrophic iron bacterium Ferrobacillus ferrooxidans. I. an improved medium and a harvesting procedure for securing high cell yields. J. Bacteriol. 77, 642–647 (1959)Google Scholar
  61. 61.
    Nemati, M., Harrison, S.T.L., Hansford, G.S., Webb, C.: Biological oxidation of ferrous sulphate by Thiobacillus ferrooxidans: a review on the kinetic aspects. Biochem. Eng. J. 1, 171–190 (1998). CrossRefGoogle Scholar
  62. 62.
    Štyriaková, I., Bekényiová, A., Štyriaková, D., Jablonovská, K., Štyriak, I.: Second pilot-plant bioleaching verification of the iron removal from quartz sands. Procedia Earth Planet. Sci. 15, 861–865 (2015). ADSCrossRefGoogle Scholar
  63. 63.
    Chang, R., Goldsby, K.A.: General chemistry: the essential concepts. McGraw-Hill Education - New York, New York (2014)Google Scholar
  64. 64.
    Refait, P., Bon, C., Simon, L., Bourrié, G., Trolard, F., Bessiére, J., Génin, J.-M.R.: Chemical composition and Gibbs standard free energy of formation of Fe(II)-Fe(III) hydroxysulphate green rust and Fe(II) hydroxide. Clay Miner. 34, 499–499 (1999). ADSCrossRefGoogle Scholar
  65. 65.
    Majzlan, J., Navrotsky, A., McCleskey, R.B., Alpers, C.N.: Thermodynamic properties and crystal structure refinement of ferricopiapite, coquimbite, rhomboclase, and F2(SO4)3(H2O)5. Eur. J. Mineral. 18, 175–186 (2006). ADSCrossRefGoogle Scholar
  66. 66.
    Plumb, J.J., Muddle, R., Franzmann, P.D.: Effect of pH on rates of iron and sulfur oxidation by bioleaching organisms. Miner. Eng. 21, 76–82 (2008). CrossRefGoogle Scholar
  67. 67.
    Majzlan, J., Navrotsky, A., Schwertmann, U.: Thermodynamics of iron oxides: part III. Enthalpies of formation and stability of ferrihydrite (∼Fe(OH)3), schwertmannite (∼FeO(OH)3/4(SO4)1/8), and ε-Fe2O3. Geochim. Cosmochim. Acta 68, 1049–1059 (2004).
  68. 68.
    Brock, T.D., Gustafson, J.: Ferric iron reduction by sulfur- and iron-oxidizing bacteria. Appl. Environ. Microbiol. 32, 567–571 (1976)Google Scholar
  69. 69.
    Schrader, J.A., Holmes, D.S.: Phenotypic switching of Thiobacillus ferrooxidans. J. Bacteriol. 170, 3915–3923 (1988). CrossRefGoogle Scholar
  70. 70.
    Valdés, J., Pedroso, I., Quatrini, R., Holmes, D.S.: Comparative genome analysis of Acidithiobacillus ferrooxidans, A. thiooxidans and A. caldus: insights into their metabolism and ecophysiology. Hydrometallurgy 94, 180–184 (2008).
  71. 71.
    Abràmoff, M.D., Magalhães, P.J., Ram, S.J.: Image processing with ImageJ. Biophoton. Int. 11, 36–42 (2004)Google Scholar
  72. 72.
    Douarche, C., Buguin, A., Salman, H., Libchaber, A.: E. coli and oxygen: a motility transition. Phys. Rev. Lett. 102, 2–5 (2009). CrossRefGoogle Scholar
  73. 73.
    Wu, X.L., Libchaber, A.: Particle diffusion in a quasi-two-dimensional bacterial bath. Phys. Rev. Lett. 84, 3017–3020 (2000). ADSCrossRefGoogle Scholar
  74. 74.
    Miño, G., Mallouk, T.E., Darnige, T., Hoyos, M., Dauchet, J., Dunstan, J., Soto, R., Wang, Y., Rousselet, A., Clement, E.: Enhanced diffusion due to active swimmers at a solid surface. Phys. Rev. Lett. 106, 1–4 (2011). CrossRefGoogle Scholar
  75. 75.
    Cisneros, L.H., Cortez, R., Dombrowski, C., Goldstein, R.E., Kessler, J.O.: Fluid dynamics of self-propelled microorganisms, from individuals to concentrated populations. In: Taylor, G.K., Triantafyllou, M.S., Tropea, C. (eds.) Animal Locomotion, pp. 99–115. Springer, Berlin, Heidelberg (2010)Google Scholar
  76. 76.
    Rice, E.W., Baird, R.B., Eaton, A.D., Clesceri, L.S.: Standard Methods for the Examination of Water and Wastewater. American Public Health Association, American Water Works Association, Water Environment Federation, Washington DC (1998)Google Scholar
  77. 77.
    Zhang, C., Zhang, R., Xia, J., Zhang, Q., Nie, Z.: Sulfur activation-related extracellular proteins of Acidithiobacillus ferrooxidans. Trans. Nonferrous Metals Soc. China 18, 1398–1402 (2008). CrossRefGoogle Scholar
  78. 78.
    Ramírez, P., Guiliani, N., Valenzuela, L., Beard, S., Jerez, C.A.: Differential protein expression during growth of Acidithiobacillus ferrooxidans on ferrous iron, sulfur compounds, or metal sulfides. Appl. Environ. Microbiol. 70, 4491–4498 (2004). CrossRefGoogle Scholar
  79. 79.
    Yarzábal, A., Appia-Ayme, C., Ratouchniak, J., Bonnefoy, V.: Regulation of the expression of the Acidithiobacillus ferrooxidans Rus operon encoding two cytochromes c, a cytochrome oxidase and rusticyanin. Microbiology 150, 2113–2123 (2004). CrossRefGoogle Scholar
  80. 80.
    Sharma, P.K., Das, A., Hanumantha Rao, K., Forssberg, K.S.E.: Surface characterization of Acidithiobacillus ferrooxidans cells grown under different conditions. Hydrometallurgy 71, 285–292 (2003). CrossRefGoogle Scholar
  81. 81.
    Harrison, A.P., Jarvis, B.W., Johnson, J.L.: Heterotrophic bacteria from cultures of autotrophic Thiobacillus ferrooxidans: relationships as studied by means of deoxyribonucleic acid homology. J. Bacteriol. 143, 448–454 (1980)Google Scholar
  82. 82.
    Son, K., Guasto, J.S., Stocker, R.: Bacteria can exploit a flagellar buckling instability to change direction. Nat. Phys. 9, 494–498 (2013). CrossRefGoogle Scholar

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Authors and Affiliations

  1. 1.Departamento de Materiales y MineralesUniversidad Nacional de Colombia, Sede MedellínMedellínColombia
  2. 2.Colombia/Wisconsin One-Health ConsortiumUniversidad Nacional de Colombia, Sede MedellínMedellínColombia
  3. 3.The Biotechnology CenterUniversity of Wisconsin–MadisonMadisonUSA

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