Applied Microbiology and Biotechnology

, Volume 103, Issue 13, pp 5095–5103 | Cite as

Biofilm systems as tools in biotechnological production

  • Miriam Edel
  • Harald Horn
  • Johannes GescherEmail author


The literature provides more and more examples of research projects that develop novel production processes based on microorganisms organized in the form of biofilms. Biofilms are aggregates of microorganisms that are attached to interfaces. These viscoelastic aggregates of cells are held together and are embedded in a matrix consisting of multiple carbohydrate polymers as well as proteins. Biofilms are characterized by a very high cell density and by a natural retentostat behavior. Both factors can contribute to high productivities and a facilitated separation of the desired end-product from the catalytic biomass. Within the biofilm matrix, stable gradients of substrates and products form, which can lead to a differentiation and adaptation of the microorganisms’ physiology to the specific process conditions. Moreover, growth in a biofilm state is often accompanied by a higher resistance and resilience towards toxic or growth inhibiting substances and factors. In this short review, we summarize how biofilms can be studied and what most promising niches for their application can be. Moreover, we highlight future research directions that will accelerate the advent of productive biofilms in biology-based production processes.


Biofilm Biotechnology Microbiology Bacteria 



Thanks to Dirk Weuster-Botz (Technische Universität München) for discussing the simulation of acetotrophic bacteria growing on membranes.


The research of Harald Horn is supported by the German Research Foundation (DFG HO 1910/16-1).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

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


  1. Asimakopoulos K, Gavala HN, Skiadas IV (2018) Reactor systems for syngas fermentation processes: a review. Chem Eng J 348:732–744CrossRefGoogle Scholar
  2. Azeredo J, Azevedo NF, Briandet R, Cerca N, Coenye T, Costa AR, Desvaux M, Di Bonaventura G, Hébraud M, Jaglic Z, Kacániová M, Knochel S, Lourenco A, Mergulhao F, Meyer RL, Nychas G, Simones M, Tresse O, Sternberg C (2017) Critical review on biofilm methods. Crit Rev Microbiol 43:313–351CrossRefGoogle Scholar
  3. Beblawy S, Bursac T, Paquete C, Louro R, Clarke TA, Gescher J (2018) Extracellular reduction of solid electron acceptors by Shewanella oneidensis. Mol Microbiol 109:571–583CrossRefGoogle Scholar
  4. Bennetto HP, Delaney GM, Mason JR, Roller SD, Stirling JL and Thurston CF (1988) Applications of microbial electrochemistry. In Resources and applications of biotechnology. Palgrave Macmillan UK, London. pp. 363–374Google Scholar
  5. Beyenal H and Babauta J (2013) Microsensors and microscale gradients in biofilms. Springer, Adv Biochem Eng Biotechnol, pp. 235–256.Google Scholar
  6. Biffinger JC, Ray R, Little BJ, Fitzgerald LA, Ribbens M, Finkel SE, Ringeisen BR (2009) Simultaneous analysis of physiological and electrical output changes in an operating microbial fuel cell with Shewanella oneidensis. Biotechnol Bioeng 103:524–531CrossRefGoogle Scholar
  7. Blauert F, Horn H, Wagner M (2015) Time-resolved biofilm deformation measurements using optical coherence tomography. Biotechnol Bioeng 112:1893–1905CrossRefGoogle Scholar
  8. Bosire EM, Rosenbaum MA (2017) Electrochemical potential influences phenazine production, electron transfer and consequently electric current generation by Pseudomonas aeruginosa. Front Microbiol 8:892CrossRefGoogle Scholar
  9. Bouwer EJ, Crowe PB (1988) Biological processes in drinking water treatment. J Am Water Works Assoc 80:82–93CrossRefGoogle Scholar
  10. Bursac T, Gralnick JA, Gescher J (2017) Acetoin production via unbalanced fermentation in Shewanella oneidensis. Biotechnol Bioeng 114:1283–1289CrossRefGoogle Scholar
  11. Cheng K-C, Demirci A, Catchmark JM (2010) Advances in biofilm reactors for production of value-added products. Appl Microbiol Biotechnol 87:445–456CrossRefGoogle Scholar
  12. Demler M, Weuster-Botz D (2011) Reaction engineering analysis of hydrogenotrophic production of acetic acid by Acetobacterium woodii. Biotechnol Bioeng 108:470–474CrossRefGoogle Scholar
  13. Doll K, Rückel A, Kämpf P, Wende M, Weuster-Botz D (2018) Two stirred-tank bioreactors in series enable continuous production of alcohols from carbon monoxide with Clostridium carboxidivorans. Bioprocess Biosyst Eng 41:1403–1416CrossRefGoogle Scholar
  14. Flemming H-C (2002) Biofouling in water systems – cases, causes and countermeasures. Appl Microbiol Biotechnol 59:629–640CrossRefGoogle Scholar
  15. Flemming H-C, Wingender J (2010) The biofilm matrix. Nat Rev Microbiol 8:623–633CrossRefGoogle Scholar
  16. Flemming H-C, Wingender J, Szewzyk U, Steinberg P, Rice SA, Kjelleberg S (2016) Biofilms: an emergent form of bacterial life. Nat Rev Microbiol 14:563–575CrossRefGoogle Scholar
  17. Förster AH, Beblawy S, Golitsch F, Gescher J (2017) Electrode-assisted acetoin production in a metabolically engineered Escherichia coli strain. Biotechnol Biofuels 10:65CrossRefGoogle Scholar
  18. Fu C, Yue X, Shi X, Ng KK, Ng HY (2017) Membrane fouling between a membrane bioreactor and a moving bed membrane bioreactor: effects of solids retention time. Chem Eng J 309:397–408CrossRefGoogle Scholar
  19. Groher A, Weuster-Botz D (2016) Comparative reaction engineering analysis of different acetogenic bacteria for gas fermentation. J Biotechnol 228:82–94CrossRefGoogle Scholar
  20. Gross R, Schmid A, Buehler K (2012) Catalytic biofilms: a powerful concept for future bioprocesses. In: Lear G, L. G (eds) Microbial biofilms. Caister Academic Press, Norfolk, pp 193–222Google Scholar
  21. Halan B, Schmid A, Buehler K (2011) Real-time solvent tolerance analysis of Pseudomonas sp. strain VLB120ΔC catalytic biofilms. Appl Environ Microbiol 77:1563–1571CrossRefGoogle Scholar
  22. Halan B, Buehler K, Schmid A (2012) Biofilms as living catalysts in continuous chemical syntheses. Trends Biotechnol 30:453–465CrossRefGoogle Scholar
  23. Hall-Stoodley L, Costerton JW, Stoodley P (2004) Bacterial biofilms: from the Natural environment to infectious diseases. Nat Rev Microbiol 2:95–108CrossRefGoogle Scholar
  24. Hansen SH, Kabbeck T, Radtke CP, Krause S, Krolitzki E, Peschke T, Gasmi J, Rabe KS, Wagner M, Horn H, Hubbuch J, Gescher J, Niemeyer CM, (2017) Machine-assisted cultivation and analysis of biofilms. bioRxiv 210583.Google Scholar
  25. He Z, Mansfeld F (2009) Exploring the use of electrochemical impedance spectroscopy (EIS) in microbial fuel cell studies. Energy Environ Sci 2:215–219CrossRefGoogle Scholar
  26. Herrling MP, Weisbrodt J, Kirkland CM, Williamson NH, Lackner S, Codd SL, Seymour JD, Guthausen G, Horn H (2017) NMR investigation of water diffusion in different biofilm structures. Biotechnol Bioeng 114:2857–2867CrossRefGoogle Scholar
  27. Horn H, Morgenroth E (2006) Transport of oxygen, sodium chloride, and sodium nitrate in biofilms. Chem Eng Sci 61:1347–1356CrossRefGoogle Scholar
  28. Ivleva NP, Wagner M, Horn H, Niessner R, Haisch C (2009) Towards a nondestructive chemical characterization of biofilm matrix by Raman microscopy. Anal Bioanal Chem 393:197–206CrossRefGoogle Scholar
  29. Ivleva NP, Wagner M, Horn H, Niessner R, Haisch C (2010) Raman microscopy and surface-enhanced Raman scattering (SERS) for in situ analysis of biofilms. J Biophotonics 3:548–556CrossRefGoogle Scholar
  30. Janczewski L, Trusek-Holownia A (2016) Biofilm-based membrane reactors – selected aspects of the application and microbial layer control. Desalin Water Treat 57:22909–22916CrossRefGoogle Scholar
  31. Kipf E, Koch J, Geiger B, Erben J, Richter K, Gescher J, Zengerle R, Kerzenmacher S (2013) Systematic screening of carbon-based anode materials for microbial fuel cells with Shewanella oneidensis MR-1. Bioresour Technol 146:386–392CrossRefGoogle Scholar
  32. Kipf E, Zengerle R, Gescher J, Kerzenmacher S (2014) How does the choice of anode material influence electrical performance? A comparison of two microbial fuel cell model organisms. ChemElectroChem 1:1849–1853CrossRefGoogle Scholar
  33. Klausen M, Heydorn A, Ragas P, Lambertsen L, Aaes-Jørgensen A, Molin S, Tolker-Nielsen T (2003) Biofilm formation by Pseudomonas aeruginosa wild type, flagella and type IV pili mutants. Mol Microbiol 48:1511–1524CrossRefGoogle Scholar
  34. Korneel Rabaey, Nico Boon, Höfte M, Verstraete W (2005) Microbial phenazine production enhances electron transfer in biofuel cells. Environ Sci Technol 39(9):3401–3408CrossRefGoogle Scholar
  35. Kracke F, Lai B, Yu S, Krömer JO (2018) Balancing cellular redox metabolism in microbial electrosynthesis and electro fermentation – a chance for metabolic engineering. Metab Eng 45:109–120CrossRefGoogle Scholar
  36. Krieg T, Sydow A, Schröder U, Schrader J, Holtmann D (2014) Reactor concepts for bioelectrochemical syntheses and energy conversion. Trends Biotechnol 32:645–655CrossRefGoogle Scholar
  37. Lackner S, Terada A, Horn H, Henze M, Smets BF (2010) Nitritation performance in membrane-aerated biofilm reactors differs from conventional biofilm systems. Water Res 44:6073–6084CrossRefGoogle Scholar
  38. Ledezma P, Greenman J, Ieropoulos I (2012) Maximising electricity production by controlling the biofilm specific growth rate in microbial fuel cells. Bioresour Technol 118:615–618CrossRefGoogle Scholar
  39. Li W-W, Sheng G-P (2011) Microbial fuel cells in power generation and extended applications. Adv Biochem Eng/Biotechn 128:165–197Google Scholar
  40. Liu T, Yu Y-Y, Deng X-P, Ng CK, Cao B, Wang J-Y, Scott AR, Kjelleberg S, Song H (2015) Enhanced Shewanella biofilm promotes bioelectricity generation. Biotechnol Bioeng 112:2051–2059CrossRefGoogle Scholar
  41. Lovley DR, Nevin KP (2013) Electrobiocommodities: powering microbial production of fuels and commodity chemicals from carbon dioxide with electricity. Curr Opin Biotechnol 24:385–390CrossRefGoogle Scholar
  42. Martinez CM, Alvarez LH (2018) Application of redox mediators in bioelectrochemical systems. Biotechnol Adv 36:1412–1423CrossRefGoogle Scholar
  43. Mayer A, Schädler T, Trunz S, Stelzer T, Weuster-Botz D (2018) Carbon monoxide conversion with Clostridium aceticum. Biotechnol Bioeng 115:2740–2750CrossRefGoogle Scholar
  44. Melkus G, Rolletschek H, Fuchs J, Radchuk V, Grafahrend-Belau E, Sreenivasulu N, Rutten T, Weier D, Heinzel N, Schreiber F, Altmann T, Jakob PM, Borisjuk L (2011) Dynamic 13C/1H NMR imaging uncovers sugar allocation in the living seed. Plant Biotechnol J 9:1022–1037CrossRefGoogle Scholar
  45. Muffler K, Lakatos M, Schlegel C, Strieth D, Kuhne S and Ulber R (2014) Application of biofilm bioreactors in white biotechnology. In Productive Biofilms 123–161.Google Scholar
  46. Neu TR and Lawrence JR (2014) Investigation of microbial biofilm structure by laser scanning microscopy. In Productive Biofilms pp. 1–51.Google Scholar
  47. Neu TR, Lawrence JR (2015) Innovative techniques, sensors, and approaches for imaging biofilms at different scales. Trends Microbiol 23:233–242CrossRefGoogle Scholar
  48. Nielsen PH, Daims H and Lemmer H (2009) FISH handbook for biological wastewater treatment : identification and quantification of microorganisms in activated sludge and biofilms by FISH, FISH Handbook for Biological Wastewater Treatment.Google Scholar
  49. Percival SL, Vuotto C, Donelli G, Lipsky BA (2015) Biofilms and wounds: an identification algorithm and potential treatment options. Adv Wound Care 4:389–397CrossRefGoogle Scholar
  50. Picioreanu C, Blauert F, Horn H, Wagner M (2018) Determination of mechanical properties of biofilms by modelling the deformation measured using optical coherence tomography. Water Res 145:588–598CrossRefGoogle Scholar
  51. Reguera G, Nevin KP, Nicoll JS, Covalla SF, Woodard TL, Lovley DR (2006) Biofilm and nanowire production leads to increased current in Geobacter sulfurreducens fuel cells. Appl Environ Microbiol 72:7345–7348CrossRefGoogle Scholar
  52. Reichert P (1995) Design techniques of a computer program for the identification of processes and the simulation of water quality in aquatic systems. Environ Softw 10:199–210CrossRefGoogle Scholar
  53. Rittmann BE (2018) Biofilms, active substrata, and me. Water Res 132:135–145CrossRefGoogle Scholar
  54. Rollefson JB, Stephen CS, Tien M, Bond DR (2011) Identification of an extracellular polysaccharide network essential for cytochrome anchoring and biofilm formation in Geobacter sulfurreducens. J Bacteriol 193:1023–1033CrossRefGoogle Scholar
  55. Rosche B, Li XZ, Hauer B, Schmid A, Buehler K (2009) Microbial biofilms: a concept for industrial catalysis? Trends Biotechnol 27:636–643CrossRefGoogle Scholar
  56. Santoro C, Arbizzani C, Erable B, Ieropoulos I (2017) Microbial fuel cells: from fundamentals to applications. A review. J Power Sources 356:225–244CrossRefGoogle Scholar
  57. Seviour T, Derlon N, Dueholm MS, Flemming H-C, Girbal-Neuhauser E, Horn H, Kjelleberg S, Loosdrecht MCM, Lotti T, Malpei MF, Nerenberg R, Neu TR, Paul E, Yu H, Lin Y (2019) Extracellular polymeric substances of biofilms: suffering from an identity crisis. Water Res 151(1–7):1–7CrossRefGoogle Scholar
  58. Shen Y, Brown R, Wen Z (2014) Syngas fermentation of Clostridium carboxidivoran P7 in a hollow fiber membrane biofilm reactor: evaluating the mass transfer coefficient and ethanol production performance. Biochem Eng J 85:21–29CrossRefGoogle Scholar
  59. Staudt C, Horn H, Hempel D and Neu T (2003) Screening of lectins for staining lectin-specific glycoconjugates in the EPS of biofilms. In Biofilms in industry, medicine & Environmental Biotechnology. pp. 308–327.Google Scholar
  60. Staudt C, Horn H, Hempel DC, Neu TR (2004) Volumetric measurements of bacterial cells and extracellular polymeric substance glycoconjugates in biofilms. Biotechnol Bioeng 88:585–592CrossRefGoogle Scholar
  61. Stewart PS, Franklin MJ (2008) Physiological heterogeneity in biofilms. Nat Rev Microbiol 6:199–210CrossRefGoogle Scholar
  62. Sturm-Richter K, Golitsch F, Sturm G, Kipf E, Dittrich A, Beblawy S, Kerzenmacher S, Gescher J (2015) Unbalanced fermentation of glycerol in Escherichia coli via heterologous production of an electron transport chain and electrode interaction in microbial electrochemical cells. Bioresour Technol 186:89–96CrossRefGoogle Scholar
  63. Subramanian P, Pirbadian S, El-Naggar MY, Jensen GJ (2018) Ultrastructure of Shewanella oneidensis MR-1 nanowires revealed by electron cryotomography. Proc Natl Acad Sci U S A 115:3246–3255CrossRefGoogle Scholar
  64. Sun D, Chen J, Huang H, Liu W, Ye Y, Cheng S (2016) The effect of biofilm thickness on electrochemical activity of Geobacter sulfurreducens. Int J Hydrog Energy 41:16523–16528CrossRefGoogle Scholar
  65. Thorn RMS, Austin AJ, Greenman J, Wilkins JPG, Davis PJ (2009) In vitro comparison of antimicrobial activity of iodine and silver dressings against biofilms. J Wound Care 18:343–346CrossRefGoogle Scholar
  66. Timberlake DL, Strand SE, Williamson KJ (1988) Combined aerobic heterotrophic oxidation, nitrification and denitrification in a permeable-support biofilm. Water Res 22:1513–1517CrossRefGoogle Scholar
  67. van Benthum WAJ, van Loosdrecht MDM, Heijnen JJ (1997) Control of heterotrophic layer formation on nitrifying biofilms in a biofilm airlift suspension reactor. Biotechnol Bioeng 53:397–405CrossRefGoogle Scholar
  68. von Canstein H, Ogawa J, Shimizu S, Lloyd JR (2008) Secretion of flavins by Shewanella species and their role in extracellular electron transfer. Appl Environ Microbiol 74:615–623CrossRefGoogle Scholar
  69. Wagner M, Horn H (2017) Optical coherence tomography in biofilm research: a comprehensive review. Biotechnol Bioeng 114:1386–1402CrossRefGoogle Scholar
  70. Wagner M, Manz B, Volke F, Neu TR, Horn H (2010) Online assessment of biofilm development, sloughing and forced detachment in tube reactor by means of magnetic resonance microscopy. Biotechnol Bioeng 107:172–181CrossRefGoogle Scholar
  71. Wingender J, Neu TR and Flemming H-C (1999) What are bacterial extracellular polymeric substances? In Microbial extracellular polymeric substances. pp. 1–19.Google Scholar
  72. Xiao Y, Zhao F (2017) Electrochemical roles of extracellular polymeric substances in biofilms. Curr Opin Electrochem 4:206–211CrossRefGoogle Scholar
  73. Yong Y-C, Yu Y-Y, Zhang X, Song H (2014) Highly active bidirectional electron transfer by a self-assembled electroactive reduced-graphene-oxide-hybridized biofilm. Angew Chem Int Ed 53:4480–4483CrossRefGoogle Scholar
  74. Zajdel TJ, Baruch M, Méhes G, Stavrinidou E, Berggren M, Maharbiz MM, Simon DT, Ajo-Franklins CM (2018) PEDOT:PSS-based multilayer bacterial-composite films for bioelectronics. Sci Rep 8:15293CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Institute for Biological InterfacesKarlsruhe Institute of Technology (KIT)Eggenstein-LeopoldshafenGermany
  2. 2.Karlsruhe Institute of Technology, Engler-Bunte-InstitutWater Chemistry and Water TechnologyKarlsruheGermany
  3. 3.DVGW Research Laboratories for Water Chemistry and Water TechnologyKarlsruheGermany
  4. 4.Institute for Applied Biology, Department of Applied BiologyKarlsruhe Institute of TechnologyKarlsruheGermany

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