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Beneficial applications of biofilms

Abstract

Many microorganisms live in the form of a biofilm. Although they are feared in the medical sector, biofilms that are composed of non-pathogenic organisms can be highly beneficial in many applications, including the production of bulk and fine chemicals. Biofilm systems are natural retentostats in which the biocatalysts can adapt and optimize their metabolism to different conditions over time. The adherent nature of biofilms allows them to be used in continuous systems in which the hydraulic retention time is much shorter than the doubling time of the biocatalysts. Moreover, the resilience of organisms growing in biofilms, together with the potential of uncoupling growth from catalytic activity, offers a wide range of opportunities. The ability to work with continuous systems using a potentially self-advancing whole-cell biocatalyst is attracting interest from a range of disciplines, from applied microbiology to materials science and from bioengineering to process engineering. The field of beneficial biofilms is rapidly evolving, with an increasing number of applications being explored, and the surge in demand for sustainable and biobased solutions and processes is accelerating advances in the field. This Review provides an overview of the research topics, challenges, applications and future directions in beneficial and applied biofilm research.

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Fig. 1: Prevalent biofilm reactor configurations.
Fig. 2: Aerosol reactor with illumination unit for the cultivation of phototrophic terrestrial biofilms.
Fig. 3: Different applications of productive biofilms on inactive substrata.
Fig. 4: Dependency of biofilm height, pH gradient and activity of cells in anodic systems.
Fig. 5: Impact of biofilms on crops and soil procurement.
Fig. 6: Different approaches to using biofilms as engineered materials.

References

  1. Muffler, K. & Ulber, R. Productive biofilms. Adv. Biochem. Eng. Biotechnol. 146, 264 (2014).

    Google Scholar 

  2. Jo, J., Price-Whelan, A. & Dietrich, L. E. P. Gradients and consequences of heterogeneity in biofilms. Nat. Rev. Microbiol. 20, 593–607 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Halan, B., Buehler, K. & Schmid, A. Biofilms as living catalysts in continuous chemical syntheses. Trends Biotechnol. 30, 453–465 (2012).

    Article  CAS  PubMed  Google Scholar 

  4. Schmeckebier, A., Zayed, A. & Ulber, R. Productive biofilms: from prokaryotic to eukaryotic systems. J. Chem. Technol. Biotechnol. 97, 3049–3064 (2022).

    Article  CAS  Google Scholar 

  5. Rosche, B., Li, X. Z., Hauer, B., Schmid, A. & Buehler, K. Microbial biofilms: a concept for industrial catalysis? Trends Biotechnol. 27, 636–643 (2009).

    Article  CAS  Google Scholar 

  6. Alvarez, A. L., Weyers, S. L., Goemann, H. M., Peyton, B. M. & Gardner, R. D. Microalgae, soil and plants: a critical review of microalgae as renewable resources for agriculture. Algal Res. 54, 102200 (2021).

    Article  Google Scholar 

  7. Nguyen, P. Q., Botyanszki, Z., Tay, P. K. R. & Joshi, N. S. Programmable biofilm-based materials from engineered curli nanofibres. Nat. Commun. 5, 4945 (2014).

    Article  CAS  PubMed  Google Scholar 

  8. Park, H., Schwartzman, A. F., Tang, T.-C., Wang, L. & Lu, T. K. Ultra-lightweight living structural material for enhanced stiffness and environmental sensing. Mater. Today Bio 18, 100504 (2023).

    Article  CAS  PubMed  Google Scholar 

  9. Karygianni, L., Ren, Z., Koo, H. & Thurnheer, T. Biofilm matrixome: extracellular components in structured microbial communities. Trends Microbiol. 28, 668–681 (2020).

    Article  CAS  PubMed  Google Scholar 

  10. Flemming, H. C. et al. The biofilm matrix: multitasking in a shared space. Nat. Rev. Microbiol. 21, 70–86 (2022).

    Article  PubMed  Google Scholar 

  11. Edwards, S. J. & Kjellerup, B. V. Applications of biofilms in bioremediation and biotransformation of persistent organic pollutants, pharmaceuticals/personal care products, and heavy metals. Appl. Microbiol. Biotechnol. 97, 9909–9921 (2013).

    Article  CAS  PubMed  Google Scholar 

  12. Härrer, D., Elreedy, A., Ali, R., Hille-Reichel, A. & Gescher, J. Probing the robustness of Geobacter sulfurreducens against fermentation hydrolysate for uses in bioelectrochemical systems. Bioresour. Technol. 369, 128363 (2023).

    Article  PubMed  Google Scholar 

  13. Morgan-Sagastume, F. Biofilm development, activity and the modification of carrier material surface properties in moving-bed biofilm reactors (MBBRs) for wastewater treatment. Crit. Rev. Env. Sci. Technol. 48, 439–470 (2018).

    Article  CAS  Google Scholar 

  14. Grießmeier, V., Wienhöfer, J., Horn, H. & Gescher, J. Assessing and modeling biocatalysis in field denitrification beds reveals key influencing factors for future constructions. Water Res. 188, 116467 (2021).

    Article  PubMed  Google Scholar 

  15. Lepine, C., Christianson, L., Davidson, J. & Summerfelt, S. Woodchip bioreactors as treatment for recirculating aquaculture systems’ wastewater: a cost assessment of nitrogen removal. Aquacult. Eng. 83, 85–92 (2018).

    Article  Google Scholar 

  16. Rittmann, B. E. Biofilms, active substrata, and me. Water Res. 132, 135–145 (2018).

    Article  CAS  PubMed  Google Scholar 

  17. Bruin, L. M. M., de, Kreuk, M. K., de, Roest, H. F. R., van der, Uijterlinde, C. & van Loosdrecht, M. C. M. Aerobic granular sludge technology: an alternative to activated sludge? Water Sci. Technol. 49, 1–7 (2004).

    Article  PubMed  Google Scholar 

  18. Tang, C. et al. Performance of high-loaded ANAMMOX UASB reactors containing granular sludge. Water Res. 45, 135–144 (2011).

    Article  CAS  PubMed  Google Scholar 

  19. van de Graaf, A. A. et al. Anaerobic oxidation of ammonium is a biologically mediated process. Appl. Environ. Microbiol. 61, 1246–1251 (1995).

    Article  PubMed  PubMed Central  Google Scholar 

  20. Liu, C. et al. Rapid formation of granules coupling n-DAMO and anammox microorganisms to remove nitrogen. Water Res. 194, 116963 (2021).

    Article  CAS  PubMed  Google Scholar 

  21. Dorias, B., Hauber, G. & Baumann, P. in Biotechnology: Environmental Processes I Vol. 11, 2nd edn, Ch. 16 (eds Rehm, H.-J. & Reed, G.) (Wiley, 1999)

  22. Wang, J., Liang, J., Ning, D., Zhang, T. & Wang, M. A review of biomass immobilization in anammox and partial nitrification/anammox systems: advances, issues, and future perspectives. Sci. Total. Environ. 821, 152792 (2022).

    Article  CAS  PubMed  Google Scholar 

  23. Ebner, H., Sellmer, S. & Follmann, H. in Biotechnology: Products of Primary Metabolism 2nd edn, Ch. 12 (eds Rehm, H.‐J. & Reed, G.) 381–401 (Wiley, 1996).

  24. König, H. in Biotechnology Set 2nd edn (eds Rehm, H.‐J. & Reed, G.) 249–264 (Wiley, 2001).

  25. Yuan, Q., Jia, Z., Roots, P. & Wells, G. A strategy for fast anammox biofilm formation under mainstream conditions. Chemosphere 318, 137955 (2023).

    Article  CAS  PubMed  Google Scholar 

  26. Riesenberg, D. & Guthke, R. High-cell-density cultivation of microorganisms. Appl. Microbiol. Biotechnol. 51, 422–430 (1999).

    Article  CAS  PubMed  Google Scholar 

  27. Shiloach, J. & Fass, R. Growing E. coli to high cell density—a historical perspective on method development. Biotechnol. Adv. 23, 345–357 (2005).

    Article  CAS  PubMed  Google Scholar 

  28. Shukla, S. K., Manobala, T., Rao, T. S., Shukla, S. K. & Rao, T. S. in Immobilization Strategies (eds Tripathi, A. & Melo, J. S.) 535–555 (Springer, 2021).

  29. Morgan-Sagastume, J. M. & Noyola, A. Evaluation of an aerobic submerged filter packed with volcanic scoria. Bioresour. Technol. 99, 2528–2536 (2008).

    Article  CAS  PubMed  Google Scholar 

  30. Cuny, L. et al. Evaluation of productive biofilms for continuous lactic acid production. Biotechnol. Bioeng. 116, 2687–2697 (2019).

    Article  CAS  PubMed  Google Scholar 

  31. Zhang, Q. et al. Mechanical resilience of biofilms toward environmental perturbations mediated by extracellular matrix. Adv. Funct. Mater. 32, 2110699 (2022).

    Article  CAS  Google Scholar 

  32. Ciofu, O., Moser, C., Jensen, P. Ø. & Høiby, N. Tolerance and resistance of microbial biofilms. Nat. Rev. Microbiol. 20, 621–635 (2022).

    Article  CAS  PubMed  Google Scholar 

  33. Halan, B., Schmid, A. & Buehler, K. Real-time solvent tolerance analysis of Pseudomonas sp. strain VLB120ΔC catalytic biofilms. Appl. Environ. Microb. 77, 1563–1571 (2011).

    Article  CAS  Google Scholar 

  34. Mishra, S. et al. Biofilm-mediated bioremediation is a powerful tool for the removal of environmental pollutants. Chemosphere 294, 133609 (2022).

    Article  CAS  Google Scholar 

  35. Darmon, E. & Leach, D. R. F. Bacterial genome instability. Microbiol. Mol. Biol. Rev. 78, 1–39 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  36. Fraser, C., Alm, E. J., Polz, M. F., Spratt, B. G. & Hanage, W. P. The bacterial species challenge: making sense of genetic and ecological diversity. Science 323, 741–746 (2009).

    Article  CAS  PubMed  Google Scholar 

  37. Tenaillon, O. et al. Tempo and mode of genome evolution in a 50,000-generation experiment. Nature 536, 165–170 (2016).

    Article  CAS  PubMed Central  Google Scholar 

  38. Renda, B. A., Hammerling, M. J. & Barrick, J. E. Engineering reduced evolutionary potential for synthetic biology. Mol. BioSyst. 10, 1668–1678 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Akeno, Y., Ying, B. W., Tsuru, S. & Yomo, T. A reduced genome decreases the host carrying capacity for foreign DNA. Microb. Cell Fact. 13, 49 (2014).

    Article  Google Scholar 

  40. Lieder, S., Nikel, P. I., Lorenzo, Vde & Takors, R. Genome reduction boosts heterologous gene expression in Pseudomonas putida. Microb. Cell Fact. 14, 23 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  41. Umenhoffer, K. et al. Reduced evolvability of Escherichia coli MDS42, an IS-less cellular chassis for molecular and synthetic biology applications. Microb. Cell Fact. 9, 38 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  42. Csörgo, B., Fehér, T., Tímár, E., Blattner, F. R. & Pósfai, G. Low-mutation-rate, reduced-genome Escherichia coli: an improved host for faithful maintenance of engineered genetic constructs. Microb. Cell Fact. 11, 11 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  43. Xia, Y. et al. Coupled CFD‐DEM modeling to predict how EPS affects bacterial biofilm deformation, recovery and detachment under flow conditions. Biotechnol. Bioeng. 119, 2551 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Lewandowski, Z. & Beyenal, H. Fundamentals of Biofilm Research (CRC Press, 2017).

  45. Waharte, F., Steenkeste, K., Briandet, R. & Fontaine-Aupart, M. P. Diffusion measurements inside biofilms by image-based fluorescence recovery after photobleaching (FRAP) analysis with a commercial confocal laser scanning microscope. Appl. Environ. Microbiol. 76, 5860–5869 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Axelrod, D., Koppel, D. E., Schlessinger, J., Elson, E. & Webb, W. W. Mobility measurement by analysis of fluorescence photobleaching recovery kinetics. Biophys. J. 16, 1055–1069 (1976).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Hauth, J., Chodorski, J., Wirsen, A. & Ulber, R. Improved FRAP measurements on biofilms. Biophys. J. 118, 2354–2365 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. van den Berg, L., van Loosdrecht, M. C. M. & de Kreuk, M. K. How to measure diffusion coefficients in biofilms: a critical analysis. Biotechnol. Bioeng. 118, 1273–1285 (2021).

    Article  PubMed  Google Scholar 

  49. Kumar, A. et al. Enhanced CO2 fixation and biofuel production via microalgae: recent developments and future directions. Trends Biotechnol. 28, 371–380 (2010).

    Article  CAS  PubMed  Google Scholar 

  50. Lee, S. H. et al. Higher biomass productivity of microalgae in an attached growth system, using wastewater. J. Microbiol. Biotechnol. 24, 1566–1573 (2014).

    Article  CAS  PubMed  Google Scholar 

  51. Scherer, K., Stiefelmaier, J., Strieth, D., Wahl, M. & Ulber, R. Development of a lightweight multi-skin sheet photobioreactor for future cultivation of phototrophic biofilms on facades. J. Biotechnol. 320, 28–35 (2020).

    Article  CAS  PubMed  Google Scholar 

  52. Al-Kaidy, H. et al. Biotechnology and bioprocess engineering – from the first Ullmann’s article to recent trends. ChemBioEng Rev. 2, 175–184 (2015).

    Article  Google Scholar 

  53. Kashid, M. N., Harshe, Y. M. & Agar, D. W. Liquid–liquid slug flow in a capillary: an alternative to suspended drop or film contactors. Ind. Eng. Chem. Res. 46, 8420–8430 (2007).

    Article  CAS  Google Scholar 

  54. Karande, R., Halan, B., Schmid, A. & Buehler, K. Segmented flow is controlling growth of catalytic biofilms in continuous multiphase microreactors. Biotechnol. Bioeng. 111, 1831–1840 (2014).

    Article  CAS  PubMed  Google Scholar 

  55. Gross, R., Buehler, K. & Schmid, A. Engineered catalytic biofilms for continuous large scale production of n-octanol and (S)-styrene oxide. Biotechnol. Bioeng. 110, 424–436 (2013).

    Article  CAS  PubMed  Google Scholar 

  56. Hoschek, A. et al. Mixed-species biofilms for high-cell-density application of Synechocystis sp. PCC 6803 in capillary reactors for continuous cyclohexane oxidation to cyclohexanol. Bioresour. Technol. 282, 171–178 (2019).

    Article  CAS  PubMed  Google Scholar 

  57. Dong, H., Zhang, W., Zhou, S., Ying, H. & Wang, P. Rational design of artificial biofilms as sustainable supports for whole-cell catalysis through integrating extra- and intracellular catalysis. ChemSusChem 15, e202200850 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Gunes, B. A critical review on biofilm-based reactor systems for enhanced syngas fermentation processes. Renew. Sustain. Energy Rev. 143, 110950 (2021).

    Article  CAS  Google Scholar 

  59. Sun, X., Atiyeh, H. K., Huhnke, R. L. & Tanner, R. S. Syngas fermentation process development for production of biofuels and chemicals: a review. Bioresour. Technol. Rep. 7, 100279 (2019).

    Article  Google Scholar 

  60. Stoll, I. K. et al. The complex way to sustainability: petroleum-based processes versus biosynthetic pathways in the formation of c4 chemicals from syngas. Ind. Eng. Chem. Res. 58, 15863–15871 (2019).

    Article  CAS  Google Scholar 

  61. Zhang, F. et al. Fatty acids production from hydrogen and carbon dioxide by mixed culture in the membrane biofilm reactor. Water Res. 47, 6122–6129 (2013).

    Article  CAS  PubMed  Google Scholar 

  62. Mohammadi, M. et al. Bioconversion of synthesis gas to second generation biofuels: a review. Renew. Sustain. Energy Rev. 15, 4255–4273 (2011).

    Article  CAS  Google Scholar 

  63. Riegler, P. et al. Continuous conversion of CO2/H2 with Clostridium aceticum in biofilm reactors. Bioresour. Technol. 291, 121760 (2019).

    Article  CAS  PubMed  Google Scholar 

  64. Ning, X. et al. Emerging bioelectrochemical technologies for biogas production and upgrading in cascading circular bioenergy systems. iScience 24, 102998 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Chavez, B. A., Raghavan, V. & Tartakovsky, B. A comparative analysis of biopolymer production by microbial and bioelectrochemical technologies. RSC Adv. 12, 16105–16118 (2022).

    Article  Google Scholar 

  66. Ahmad, A., Priyadarshani, M., Das, S. & Ghangrekar, M. M. Role of bioelectrochemical systems for the remediation of emerging contaminants from wastewater: a review. J. Basic. Microbiol. 62, 201–222 (2021).

    Article  PubMed  Google Scholar 

  67. Roy, M., Aryal, N., Zhang, Y., Patil, S. A. & Pant, D. Technological progress and readiness level of microbial electrosynthesis and electrofermentation for carbon dioxide and organic wastes valorization. Curr. Opin. Green. Sustain. Chem. 35, 100605 (2022).

    Article  CAS  Google Scholar 

  68. Conners, E. M., Rengasamy, K. & Bose, A. Electroactive biofilms: how microbial electron transfer enables bioelectrochemical applications. J. Ind. Microbiol. Biotechnol. 49, 12 (2022).

    Article  Google Scholar 

  69. Hackbarth, M. et al. Monitoring and quantification of bioelectrochemical Kyrpidia spormannii biofilm development in a novel flow cell setup. Chem. Eng. J. 390, 124604 (2020).

    Article  CAS  Google Scholar 

  70. Renslow, R. S. et al. Metabolic spatial variability in electrode-respiring Geobacter sulfurreducens biofilms. Energy Environ. Sci. 6, 1827–1836 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Lichtervelde, A. C. L., de, Heijne, A., ter, Hamelers, H. V. M., Biesheuvel, P. M. & Dykstra, J. E. Theory of ion and electron transport coupled with biochemical conversions in an electroactive biofilm. Phys. Rev. Appl. 12, 014018 (2019).

    Article  Google Scholar 

  72. Fujikawa, T. et al. Unexpected genomic features of high current density-producing Geobacter sulfurreducens strain YM18. Fems. Microbiol. Lett. 368, fnab119 (2021).

    Article  CAS  PubMed  Google Scholar 

  73. Jiang, X. et al. Probing single- to multi-cell level charge transport in Geobacter sulfurreducens DL-1. Nat. Commun. 4, 2751 (2013).

    Article  Google Scholar 

  74. Liu, X., Walker, D. J. F., Nonnenmann, S. S., Sun, D. & Lovley, D. R. Direct observation of electrically conductive pili emanating from Geobacter sulfurreducens. mBio 12, e02209–e02221 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Gu, Y. et al. Structure of Geobacter pili reveals secretory rather than nanowire behaviour. Nature 597, 430–434 (2021).

    Article  CAS  PubMed Central  Google Scholar 

  76. Philipp, L.-A., Edel, M. & Gescher, J. Chapter one genetic engineering for enhanced productivity in bioelectrochemical systems. Adv. Appl. Microbiol. 111, 1–31 (2020).

    Article  CAS  PubMed  Google Scholar 

  77. Lovley, D. R. Powering microbes with electricity: direct electron transfer from electrodes to microbes. Env. Microbiol. Rep. 3, 27–35 (2011).

    Article  CAS  Google Scholar 

  78. Edel, M., Horn, H. & Gescher, J. Biofilm systems as tools in biotechnological production. Appl. Microbiol. Biotechnol. 103, 5095–5103 (2019).

    Article  CAS  Google Scholar 

  79. Jourdin, L., Sousa, J., van Stralen, N. & Strik, D. P. B. T. B. Techno-economic assessment of microbial electrosynthesis from CO2 and/or organics: an interdisciplinary roadmap towards future research and application. Appl. Energ. 279, 115775 (2020).

    Article  CAS  Google Scholar 

  80. Prévoteau, A., Carvajal-Arroyo, J. M., Ganigué, R. & Rabaey, K. Microbial electrosynthesis from CO2: forever a promise? Curr. Opin. Biotech. 62, 48–57 (2020).

    Article  PubMed  Google Scholar 

  81. Walter, X. A. et al. From the lab to the field: self-stratifying microbial fuel cells stacks directly powering lights. Appl. Energ. 277, 115514 (2020).

    Article  CAS  Google Scholar 

  82. Cao, B. et al. Silver nanoparticles boost charge-extraction efficiency in Shewanella microbial fuel cells. Science 373, 1336–1340 (2021).

    Article  CAS  PubMed  Google Scholar 

  83. Wang, D. et al. Surface modification of Shewanella oneidensis MR-1 with polypyrrole-dopamine coating for improvement of power generation in microbial fuel cells. J. Power Sources 483, 229220 (2021).

    Article  CAS  Google Scholar 

  84. Knoll, M. T., Fuderer, E. & Gescher, J. Sprayable biofilm—agarose hydrogels as 3D matrix for enhanced productivity in bioelectrochemical systems. Biofilm 4, 100077 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Krieg, T., Sydow, A., Schröder, U., Schrader, J. & Holtmann, D. Reactor concepts for bioelectrochemical syntheses and energy conversion. Trends Biotechnol. 32, 645–655 (2014).

    Article  CAS  PubMed  Google Scholar 

  86. Kerzenmacher, S. Engineering of microbial electrodes. Adv. Biochem. Eng. Biotechnol. 167, 135–180 (2017).

  87. Asensio, Y. et al. Upgrading fluidized bed bioelectrochemical reactors for treating brewery wastewater by using a fluid-like electrode. Chem. Eng. J. 406, 127103 (2021).

    Article  CAS  Google Scholar 

  88. Hackbarth, M., Gescher, J., Horn, H. & Reiner, J. E. A scalable, rotating disc bioelectrochemical reactor (RDBER) suitable for the cultivation of both cathodic and anodic biofilms. Bioresour. Technol. Rep. 21, 101357 (2023).

    Article  CAS  Google Scholar 

  89. Nerenberg, R. The membrane-biofilm reactor (MBfR) as a counter-diffusional biofilm process. Curr. Opin. Biotech. 38, 131–136 (2016).

    Article  CAS  PubMed  Google Scholar 

  90. Martin, K. J. & Nerenberg, R. The membrane biofilm reactor (MBfR) for water and wastewater treatment: principles, applications, and recent developments. Bioresour. Technol. 122, 83–94 (2012).

    Article  CAS  PubMed  Google Scholar 

  91. Elisiário, M. P., Wever, H. D., Hecke, W. V., Noorman, H. & Straathof, A. J. J. Membrane bioreactors for syngas permeation and fermentation. Crit. Rev. Biotechnol. 42, 856–872 (2022).

    Article  PubMed  Google Scholar 

  92. Yasin, M. et al. Microbial synthesis gas utilization and ways to resolve kinetic and mass-transfer limitations. Bioresour. Technol. 177, 361–374 (2015).

    Article  CAS  PubMed  Google Scholar 

  93. Asimakopoulos, K., Gavala, H. N. & Skiadas, I. V. Reactor systems for syngas fermentation processes: a review. Chem. Eng. J. 348, 732–744 (2018).

    Article  CAS  Google Scholar 

  94. Dong, K. et al. Nitrogen removal from nitrate-containing wastewaters in hydrogen-based membrane biofilm reactors via hydrogen autotrophic denitrification: biofilm structure, microbial community and optimization strategies. Front. Microbiol. 13, 924084 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  95. Nangle, S. N. et al. Valorization of CO2 through lithoautotrophic production of sustainable chemicals in Cupriavidus necator. Metab. Eng. 62, 207–220 (2020).

    Article  CAS  PubMed  Google Scholar 

  96. Windhorst, C. & Gescher, J. Efficient biochemical production of acetoin from carbon dioxide using Cupriavidus necator H16. Biotechnol. Biofuels 12, 163 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Stiefelmaier, J. et al. Characterization of terrestrial phototrophic biofilms of cyanobacterial species. Algal Res. 50, 101996 (2020).

    Article  Google Scholar 

  98. Bolhuis, H., Cretoiu, M. S. & Stal, L. J. Molecular ecology of microbial mats. FEMS Microbiol. Ecol. 90, 335–350 (2014).

    CAS  PubMed  Google Scholar 

  99. Angermayr, S. A., Rovira, A. G. & Hellingwerf, K. J. Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends Biotechnol. 33, 352–361 (2015).

    Article  CAS  PubMed  Google Scholar 

  100. Fisher, M. L., Allen, R., Luo, Y. & Curtiss, R. Export of extracellular polysaccharides modulates adherence of the cyanobacterium Synechocystis. PLoS One 8, e74514 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Agostoni, M., Waters, C. M. & Montgomery, B. L. Regulation of biofilm formation and cellular buoyancy through modulating intracellular cyclic di-GMP levels in engineered cyanobacteria. Biotechnol. Bioeng. 113, 311–319 (2016).

    Article  CAS  PubMed  Google Scholar 

  102. Rosenbaum, M., He, Z. & Angenent, L. T. Light energy to bioelectricity: photosynthetic microbial fuel cells. Curr. Opin. Biotechnol. 21, 259–264 (2010).

    Article  CAS  PubMed  Google Scholar 

  103. Obileke, K. C., Onyeaka, H., Meyer, E. L. & Nwokolo, N. Microbial fuel cells, a renewable energy technology for bio-electricity generation: a mini-review. Electrochem. Commun. 125, 107003 (2021).

    Article  CAS  Google Scholar 

  104. Tschörtner, J., Lai, B. & Krömer, J. O. Biophotovoltaics: green power generation from sunlight and water. Front. Microbiol. 10, 866 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  105. McCormick, A. J. et al. Photosynthetic biofilms in pure culture harness solar energy in a mediatorless bio-photovoltaic cell (BPV) system. Energy Environ. Sci. 4, 4699–4709 (2011).

    Article  CAS  Google Scholar 

  106. Miranda, A. F. et al. Applications of microalgal biofilms for wastewater treatment and bioenergy production. Biotechnol. Biofuels 10, 1–23 (2017).

    Article  Google Scholar 

  107. Kollmen, J. & Strieth, D. The beneficial effects of cyanobacterial co-culture on plant growth. Life 12, 223 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Mutale-Joan, C., Sbabou, L. & Hicham, E. A. Microalgae and cyanobacteria: how exploiting these microbial resources can address the underlying challenges related to food sources and sustainable agriculture: a review. J. Plant. Growth Regul. 42, 1–20 (2022).

    Article  Google Scholar 

  109. Stirk, W. A., Ördög, V., Staden, J. V. & Jäger, K. Cytokinin- and auxin-like activity in Cyanophyta and microalgae. J. Appl. Phycol. 14, 215–221 (2002).

    Article  CAS  Google Scholar 

  110. Han, X., Zeng, H., Bartocci, P., Fantozzi, F. & Yan, Y. Phytohormones and effects on growth and metabolites of microalgae: a review. Fermentation 4, 25 (2018).

    Article  Google Scholar 

  111. Shariatmadari, Z., Riahi, H., Hashtroudi, M. S., Ghassempour, A. R. & Aghashariatmadary, Z. Plant growth promoting cyanobacteria and their distribution in terrestrial habitats of Iran. Soil. Sci. Plant. Nutr. 59, 535–547 (2013).

    Article  CAS  Google Scholar 

  112. Kumar, G., Teli, B., Mukherjee, A., Bajpai, R. & Sarma, B. K. in Secondary Metabolites of Plant Growth Promoting Rhizomicroorganisms (eds Singh, H., Keswani, C., Reddy, M., Sansinenea, E. & García-Estrada, C.) 239–252 (Springer, 2019).

  113. Irisarri, P., Gonnet, S. & Monza, J. Cyanobacteria in Uruguayan rice fields: diversity, nitrogen fixing ability and tolerance to herbicides and combined nitrogen. J. Biotechnol. 91, 95–103 (2001).

    Article  CAS  PubMed  Google Scholar 

  114. Prasanna, R., Joshi, M., Rana, A., Shivay, Y. S. & Nain, L. Influence of co-inoculation of bacteria-cyanobacteria on crop yield and C–N sequestration in soil under rice crop. World J. Microbiol. Biotechnol. 28, 1223–1235 (2012).

    Article  CAS  PubMed  Google Scholar 

  115. Roeselers, G., Loosdrecht, M. C. M. V. & Muyzer, G. Phototrophic biofilms and their potential applications. J. Appl. Phycol. 20, 227–235 (2008).

    Article  CAS  PubMed  Google Scholar 

  116. Fischer, S. E., Fischer, S. I., Magris, S. & Mori, G. B. Isolation and characterization of bacteria from the rhizosphere of wheat. World J. Microbiol. Biotechnol. 23, 895–903 (2007).

    Article  CAS  Google Scholar 

  117. Karthikeyan, N., Prasanna, R., Nain, L. & Kaushik, B. D. Evaluating the potential of plant growth promoting cyanobacteria as inoculants for wheat. Eur. J. Soil. Biol. 43, 23–30 (2007).

    Article  CAS  Google Scholar 

  118. Grzesik, M., Romanowska-Duda, Z. & Kalaji, H. M. Effectiveness of cyanobacteria and green algae in enhancing the photosynthetic performance and growth of willow (Salix viminalis L.) plants under limited synthetic fertilizers application. Photosynthetica 55, 510–521 (2017).

    Article  CAS  Google Scholar 

  119. Saadatnia, H. & Riahi, H. Cyanobacteria from paddy fields in Iran as a biofertilizer in rice plants. Plant. Soil. Env. 55, 207–212 (2009).

    Article  Google Scholar 

  120. Coppens, J. et al. The use of microalgae as a high-value organic slow-release fertilizer results in tomatoes with increased carotenoid and sugar levels. J. Appl. Phycol. 28, 2367–2377 (2016).

    Article  CAS  Google Scholar 

  121. Maqubela, M. P., Mnkeni, P. N. S., Issa, O. M., Pardo, M. T. & D’Acqui, L. P. Nostoc cyanobacterial inoculation in South African agricultural soils enhances soil structure, fertility, and maize growth. Plant. Soil. 315, 79–92 (2009).

    Article  CAS  Google Scholar 

  122. Prasanna, R. et al. Cyanobacteria-based bioinoculants influence growth and yields by modulating the microbial communities favourably in the rhizospheres of maize hybrids. Eur. J. Soil. Biol. 75, 15–23 (2016).

    Article  Google Scholar 

  123. Fedeson, D. T. & Ducat, D. C. Cyanobacterial surface display system mediates engineered interspecies and abiotic binding. ACS Synth. Biol. 6, 367–374 (2017).

    Article  CAS  PubMed  Google Scholar 

  124. Cengic, I., Uhlén, M. & Hudson, E. P. Surface display of small affinity proteins on Synechocystis sp. strain PCC 6803 mediated by fusion to the major type IV pilin PilA1. J. Bacteriol. 200, e00270–e00318 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Quoc, B. N. et al. An investigation into the optimal granular sludge size for simultaneous nitrogen and phosphate removal. Water Res. 198, 117119 (2021).

    Article  Google Scholar 

  126. Bathe, S., Kreuk, M. de, McSwain, B. & Schwarzenbeck, N. (eds) Aerobic Granular Sludge (IWA Publishing, 2015).

  127. Ghosh, S. & Chakraborty, S. Production of polyhydroxyalkanoates (PHA) from aerobic granules of refinery sludge and Micrococcus aloeverae strain SG002 cultivated in oily wastewater. Int. Biodeterior. Biodegrad. 155, 105091 (2020).

    Article  CAS  Google Scholar 

  128. Bahgat, N. T., Wilfert, P., Korving, L. & Loosdrecht, Mvan Integrated resource recovery from aerobic granular sludge plants. Water Res. 234, 119819 (2023).

    Article  CAS  PubMed  Google Scholar 

  129. Nancharaiah, Y. V. & Reddy, G. K. K. Aerobic granular sludge technology: mechanisms of granulation and biotechnological applications. Bioresour. Technol. 247, 1128–1143 (2018).

    Article  CAS  PubMed  Google Scholar 

  130. Jiang, Q. et al. Current progress, challenges and perspectives in the microalgal-bacterial aerobic granular sludge process: a review. Int. J. Environ. Res. Publ. Health 19, 13950 (2022).

    Article  CAS  Google Scholar 

  131. Chen, A. Y. et al. Synthesis and patterning of tunable multiscale materials with engineered cells. Nat. Mater. 13, 515–523 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Cheng, K.-C., Catchmark, J. M. & Demirci, A. Enhanced production of bacterial cellulose by using a biofilm reactor and its material property analysis. J. Biol. Eng. 3, 12 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  133. Lee, Y. S. & Park, W. Current challenges and future directions for bacterial self-healing concrete. Appl. Microbiol. Biotechnol. 102, 3059–3070 (2018).

    Article  CAS  PubMed  Google Scholar 

  134. Dhami, N. K., Reddy, S. M. & Mukherjee, A. in Advanced Topics in Biomineralization (ed. Seto, J.) 137–164 (InTechOpen, 2012).

  135. Saracho, A. C. et al. Controlling the calcium carbonate microstructure of engineered living building materials. J. Mater. Chem. A. 9, 24438–24451 (2021).

    Article  Google Scholar 

  136. Little, B. J., Hinks, J. & Blackwood, D. J. Microbially influenced corrosion: towards an interdisciplinary perspective on mechanisms. Int. Biodeter. Biodegr. 154, 105062 (2020).

    Article  CAS  Google Scholar 

  137. Zuo, R., Kus, E., Mansfeld, F. & Wood, T. K. The importance of live biofilms in corrosion protection. Corros. Sci. 47, 279–287 (2005).

    Article  CAS  Google Scholar 

  138. Liu, T. et al. Marine bacteria provide lasting anticorrosion activity for steel via biofilm-induced mineralization. ACS Appl. Mater. Inter. 10, 40317–40327 (2018).

    Article  CAS  Google Scholar 

  139. Li, Z. et al. Marine biofilms with significant corrosion inhibition performance by secreting extracellular polymeric substances. ACS Appl. Mater. Inter. 13, 47272–47282 (2021).

    Article  CAS  Google Scholar 

  140. Karande, R. et al. Continuous cyclohexane oxidation to cyclohexanol using a novel cytochrome P450 monooxygenase from Acidovorax sp. CHX100 in recombinant P. taiwanensis VLB120 biofilms. Biotechnol. Bioeng. 113, 52–61 (2016).

    Article  CAS  PubMed  Google Scholar 

  141. Gross, R., Hauer, B., Otto, K. & Schmid, A. Microbial biofilms: new catalysts for maximizing productivity of long‐term biotransformations. Biotechnol. Bioeng. 98, 1123–1134 (2007).

    Article  CAS  PubMed  Google Scholar 

  142. Yang, G., Mai, Q., Zhuang, Z. & Zhuang, L. Buffer capacity regulates the stratification of anode-respiring biofilm during brewery wastewater treatment. Environ. Res. 201, 111572 (2021).

    Article  CAS  PubMed  Google Scholar 

  143. Flemming, H. C. & Wuertz, S. Bacteria and archaea on Earth and their abundance in biofilms. Nat. Rev. Microbiol. 17, 247–260 (2019).

    Article  CAS  PubMed  Google Scholar 

  144. Penesyan, A., Paulsen, I. T., Kjelleberg, S. & Gillings, M. R. Three faces of biofilms: a microbial lifestyle, a nascent multicellular organism, and an incubator for diversity. npj Biofilms Microbiomes 7, 80 (2021).

    Article  CAS  PubMed Central  Google Scholar 

  145. Sauer, K. et al. The biofilm life cycle: expanding the conceptual model of biofilm formation. Nat. Rev. Microbiol. 20, 608–620 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  146. Cai, Y. M. Non-surface attached bacterial aggregates: a ubiquitous third lifestyle. Front. Microbiol. 11, 3106 (2020).

    Article  Google Scholar 

  147. Valentini, M. & Filloux, A. Biofilms and cyclic di-GMP (c-di-GMP) signaling: lessons from Pseudomonas aeruginosa and other bacteria. J. Biol. Chem. 291, 12547–12555 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  148. Baker, A. E. et al. Flagellar stators stimulate c-di-GMP production by Pseudomonas aeruginosa. J. Bacteriol. 201, e00741–e00818 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  149. Webster, S. S., Lee, C. K., Schmidt, W. C., Wong, G. C. L. & O’Toole, G. A. Interaction between the type 4 pili machinery and a diguanylate cyclase fine-tune c-di-GMP levels during early biofilm formation. Proc. Natl Acad. Sci. USA 118, e2105566118 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Baker, A. E. et al. PilZ domain protein FlgZ mediates cyclic di-GMP-dependent swarming motility control in Pseudomonas aeruginosa. J. Bacteriol. 198, 1837–1846 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Thormann, K. M. Dynamic hybrid flagellar motors—fuel switch and more. Front. Microbiol. 13, 867 (2022).

    Article  Google Scholar 

  152. Gerven, N. V., Klein, R. D., Hultgren, S. J. & Remaut, H. Bacterial amyloid formation: structural insights into curli biogensis. Trends Microbiol. 23, 693–706 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  153. Mukherjee, S. & Bassler, B. L. Bacterial quorum sensing in complex and dynamically changing environments. Nat. Rev. Microbiol. 17, 371–382 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. Paula, A. J., Hwang, G. & Koo, H. Dynamics of bacterial population growth in biofilms resemble spatial and structural aspects of urbanization. Nat. Commun. 11, 1354 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  155. Blauert, F., Horn, H. & Wagner, M. Time‐resolved biofilm deformation measurements using optical coherence tomography. Biotechnol. Bioeng. 112, 1893–1905 (2015).

    Article  CAS  Google Scholar 

  156. Rumbaugh, K. P. & Sauer, K. Biofilm dispersion. Nat. Rev. Microbiol. 18, 571–586 (2020).

    Article  CAS  PubMed Central  Google Scholar 

  157. Moore-Ott, J. A., Chiu, S., Amchin, D. B., Bhattacharjee, T. & Datta, S. S. A biophysical threshold for biofilm formation. eLife 11, e76380 (2022).

    Article  CAS  PubMed Central  Google Scholar 

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Acknowledgements

The authors thank J. Kollmen, D. Strieth, J. Stiefelmaier and A. Schmeckebier (funded by the DFG (German Research Foundation), Collaborative Research Center 926, project C03 – Project-ID 172116086) as well as R. Karande and M. Bozan for providing research data and illustrations on the topic of phototropic biofilms and reactor configurations, respectively.

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Philipp, LA., Bühler, K., Ulber, R. et al. Beneficial applications of biofilms. Nat Rev Microbiol (2023). https://doi.org/10.1038/s41579-023-00985-0

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