University of Oulu

Aho, V.T.E., Tolonen, T., Haverinen, J. et al. Survey of microbes in industrial-scale second-generation bioethanol production for better process knowledge and operation. Appl Microbiol Biotechnol 104, 8049–8064 (2020).

Survey of microbes in industrial-scale second-generation bioethanol production for better process knowledge and operation

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Author: Aho, Velma T. E.1,2; Tolonen, Tiina3; Haverinen, Jasmiina3;
Organizations: 1Institute of Biotechnology, University of Helsinki, Helsinki, Finland
2Department of Neurology, Helsinki University Hospital, Helsinki, Finland
3Unit of Measurement Technology, Kajaani University Consortium, University of Oulu, Kajaani, Finland
4St1 Oy, Helsinki, Finland
Format: article
Version: accepted version
Access: open
Online Access: PDF Full Text (PDF, 0.5 MB)
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Language: English
Published: Springer Nature, 2020
Publish Date: 2022-03-02


The microbes present in bioethanol production processes have been previously studied in laboratory-scale experiments, but there is a lack of information on full-scale industrial processes. In this study, the microbial communities of three industrial bioethanol production processes were characterized using several methods. The samples originated from second-generation bioethanol plants that produce fuel ethanol from biowaste, food industry side streams, or sawdust. Amplicon sequencing targeting bacteria, archaea, and fungi was used to explore the microbes present in biofuel production and anaerobic digestion of wastewater and sludge. Biofilm-forming lactic acid bacteria and wild yeasts were identified in fermentation samples of a full-scale plant that uses biowaste as feedstock. During the 20-month monitoring period, the anaerobic digester adapted to the bioethanol process waste with a shift in methanogen profile indicating acclimatization to high concentrations of ammonia. Amplicon sequencing does not specifically target living microbes. The same is true for indirect parameters, such as low pH, metabolites, or genes of lactic acid bacteria. Since rapid identification of living microbes would be indispensable for process management, a commercial method was tested that detects them by measuring the rRNA of selected microbial groups. Small-scale testing indicated that the method gives results comparable with plate counts and microscopic counting, especially for bacterial quantification. The applicability of the method was verified in an industrial bioethanol plant, inspecting the clean-in-place process quality and detecting viability during yeast separation. The results supported it as a fast and promising tool for monitoring microbes throughout industrial bioethanol processes.

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Series: Applied microbiology and biotechnology
ISSN: 0175-7598
ISSN-E: 1432-0614
ISSN-L: 0175-7598
Volume: 104
Issue: 18
Pages: 8049 - 8064
DOI: 10.1007/s00253-020-10818-2
Type of Publication: A1 Journal article – refereed
Field of Science: 116 Chemical sciences
Funding: This study was funded by The Finnish Funding Agency for Innovation (grant number 2591/31/2013), by The Centre for Economic, Development, Transport and the Environment, North Ostrobothnia (grant number S12370), and by St1 Oy.
Copyright information: © Springer-Verlag GmbH Germany, part of Springer Nature 2020. This is a post-peer-review, pre-copyedit version of an article published in Applied Microbiology and Biotechnology. The final authenticated version is available online at: