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Strain dynamics of contaminating bacteria modulate the yield of ethanol biorefineries

Author

Listed:
  • Felipe Senne Oliveira Lino

    (Technical University of Denmark)

  • Shilpa Garg

    (Technical University of Denmark)

  • Simone S. Li

    (Technical University of Denmark
    University of Queensland)

  • Maria-Anna Misiakou

    (Technical University of Denmark)

  • Kang Kang

    (Leibniz Institute for Natural Product Research and Infection Biology)

  • Bruno Labate Vale da Costa

    (Escola de Engenharia de Alimentos da Universidade de Campinas)

  • Tobias Svend-Aage Beyer-Pedersen

    (Technical University of Denmark)

  • Thamiris Guerra Giacon

    (Departamento de Engenharia Química da Escola Politécnica da Universidade de São Paulo. Universidade de São Paulo)

  • Thiago Olitta Basso

    (Departamento de Engenharia Química da Escola Politécnica da Universidade de São Paulo. Universidade de São Paulo)

  • Gianni Panagiotou

    (Leibniz Institute for Natural Product Research and Infection Biology)

  • Morten Otto Alexander Sommer

    (Technical University of Denmark)

Abstract

Bioethanol is a sustainable energy alternative and can contribute to global greenhouse-gas emission reductions by over 60%. Its industrial production faces various bottlenecks, including sub-optimal efficiency resulting from bacteria. Broad-spectrum removal of these contaminants results in negligible gains, suggesting that the process is shaped by ecological interactions within the microbial community. Here, we survey the microbiome across all process steps at two biorefineries, over three timepoints in a production season. Leveraging shotgun metagenomics and cultivation-based approaches, we identify beneficial bacteria and find improved outcome when yeast-to-bacteria ratios increase during fermentation. We provide a microbial gene catalogue which reveals bacteria-specific pathways associated with performance. We also show that Limosilactobacillus fermentum overgrowth lowers production, with one strain reducing yield by ~5% in laboratory fermentations, potentially due to its metabolite profile. Temperature is found to be a major driver for strain-level dynamics. Improved microbial management strategies could unlock environmental and economic gains in this US $ 60 billion industry enabling its wider adoption.

Suggested Citation

  • Felipe Senne Oliveira Lino & Shilpa Garg & Simone S. Li & Maria-Anna Misiakou & Kang Kang & Bruno Labate Vale da Costa & Tobias Svend-Aage Beyer-Pedersen & Thamiris Guerra Giacon & Thiago Olitta Basso, 2024. "Strain dynamics of contaminating bacteria modulate the yield of ethanol biorefineries," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49683-2
    DOI: 10.1038/s41467-024-49683-2
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    References listed on IDEAS

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    1. Felipe Lino & Djordje Bajic & Jean Celestin Charles Vila & Alvaro Sánchez & Morten Otto Alexander Sommer, 2021. "Complex yeast–bacteria interactions affect the yield of industrial ethanol fermentation," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
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