Applied Microbiology and Biotechnology

, Volume 103, Issue 19, pp 8241–8253 | Cite as

Enriched hydrogen-oxidizing microbiomes show a high diversity of co-existing hydrogen-oxidizing bacteria

  • Elham Ehsani
  • Charles Dumolin
  • Jan B. A. Arends
  • Frederiek-Maarten Kerckhof
  • Xiaona Hu
  • Peter Vandamme
  • Nico BoonEmail author
Environmental biotechnology


While numerous reports exist on the axenic culturing of different hydrogen-oxidizing bacteria (HOB), knowledge about the enrichment of microbial communities growing on hydrogen, oxygen, and carbon dioxide as sole carbon and energy sources remains negligible. We want to elucidate if in such enrichments, most enriched populations are HOBs or heterotrophic organisms. In the present study, bacteria enriched from a soil sample and grown over 5 transfers using a continuous supply of hydrogen, oxygen, and carbon dioxide to obtain an enriched autotrophic hydrogen-oxidizing microbiome. The success of the enrichment was evaluated by monitoring ammonium consumption and biomass concentration for 120 days. The shift in the microbial composition of the original soil inoculum and all transfers was observed based on 16S rRNA amplicon sequencing. The hydrogen-oxidizing facultative chemolithoautotroph Hydrogenophaga electricum was isolated and found to be one of the abundant species in most transfers. Moreover, Achromobacter was isolated both under heterotrophic and autotrophic conditions, which was characterized as a hydrogen-oxidizing bacterium. The HOB enrichment condition constructed in this study provided an environment for HOB to develop and conquer in all transfers. In conclusion, we showed that enrichments on hydrogen, oxygen, and carbon dioxide as sole carbon and energy sources contain a diverse mixture of HOB and heterotrophs that resulted in a collection of culturable isolates. These isolates can be useful for further investigation for industrial applications.


Hydrogen-oxidizing bacteria HOB enrichment HOB isolation Microbial composition Heterotrophs 



The authors kindly acknowledge Dr. Silvio Matassa for assistance and scientific guidance. Dr. Ruben Props is warmly thanked for his interest and help with flow cytometry. EE would also like to express gratitude to Xu Zhang for her advice and help during the experiment. The research leading to results presented in this publication was carried out with infrastructure funded by EMBRC Belgium - FWO project GOH3817N. Dr. Marta Calatayud Arroyo and Lotte Van Peteghem are appreciated for their critical comments on this manuscript.

Funding Information

EE, CD, PV, and NB received funding for this work from the Geconcerteerde Onderzoeksactie (GOA) of Ghent University (BOF15/GOA/006). JA was supported by the European Research Council via Starter Grant no. 310023 ‘ELECTROTALK.’ The research leading to results presented in this publication was carried out with infrastructure funded by EMBRC Belgium - FWO project GOH3817N.

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.

Supplementary material

253_2019_10082_MOESM1_ESM.pdf (476 kb)
ESM 1 (PDF 475 kb)


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Copyright information

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

Authors and Affiliations

  • Elham Ehsani
    • 1
  • Charles Dumolin
    • 2
  • Jan B. A. Arends
    • 1
  • Frederiek-Maarten Kerckhof
    • 1
  • Xiaona Hu
    • 1
  • Peter Vandamme
    • 2
  • Nico Boon
    • 1
    Email author
  1. 1.Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
  2. 2.Laboratory for Microbiology (LM-UGent), Faculty of SciencesGhent UniversityGhentBelgium

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