Microbial Ecology

, Volume 74, Issue 4, pp 771–775 | Cite as

Survey of High-Affinity H2-Oxidizing Bacteria in Soil Reveals Their Vast Diversity Yet Underrepresentation in Genomic Databases

  • Sarah Piché-Choquette
  • Mondher Khdhiri
  • Philippe Constant


While high-affinity H2-oxidizing bacteria (HA-HOB) serve as the main sink of atmospheric H2, the ecology of this specialist functional group is rather unknown due to its recent discovery. The main purpose of our study is to provide the first extensive survey of HA-HOB in farmland, larch, and poplar soils exposed to 0.5 and 10,000 ppmv H2. Using qPCR and qRT-PCR assays along with PCR amplicon high-throughput sequencing of hhyL gene encoding for the large subunit of high-affinity [NiFe]-hydrogenases (HAH), we found that hhyL gene expression ratio explained better variation in measured H2 oxidation rates than HA-HOB species richness. Carbon, nitrogen, pH, and bacterial species richness appeared as the most important drivers of HA-HOB community structure. Our study also highlights the need to cultivate HA-HOB due to the huge gap in current genomic databases.


Biogeochemistry H2-oxidizing bacteria High-throughput sequencing Trace gas 



This work was supported by a Natural Sciences and Engineering Research Council of Canada Discovery grant to P.C. The authors acknowledge use of McGill University and Génome Québec Innovation Centre for the preparation of hhyL gene libraries and sequencing services. S.P.-C. and M.K. are grateful to the Fondation Universitaire Armand-Frappier INRS for their Ph.D. scholarship.

Supplementary material

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Copyright information

© Springer Science+Business Media, LLC 2017

Authors and Affiliations

  1. 1.INRS-Institut Armand-FrappierLavalCanada

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