Survey of High-Affinity H2-Oxidizing Bacteria in Soil Reveals Their Vast Diversity Yet Underrepresentation in Genomic Databases
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.
KeywordsBiogeochemistry 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.
- 1.Pieterse G, Krol MC, Batenburg AM, Brenninkmeijer CAM, Popa ME, O'Doherty S, Grant A, Steele LP, Krummel PB, Langenfelds RL, Wang HJ, Vermeulen AT, Schmidt M, Yver C, Jordan A, Engel A, Fisher RE, Lowry D, Nisbet EG, Reimann S, Vollmer MK, Steinbacher M, Hammer S, Forster G, Sturges WT, Röckmann T (2013) Reassessing the variability in atmospheric H2 using the two-way nested TM5 model J Geophys Res Atmos 118:3764–3780. doi:10.1002/jgrd.50204 CrossRefGoogle Scholar
- 10.Khdhiri M, Piche-Choquette S, Tremblay J, Tringe SG, Constant P (2017) The tale of a neglected energy source: elevated hydrogen exposure affects both microbial diversity and function in soil. Appl Environ Microbiol 83. doi:10.1128/aem.00275-17
- 11.Constant P, Chowdhury SP, Hesse L, Pratscher J, Conrad R (2011) Genome data mining and soil survey for the novel group 5 [NiFe]-hydrogenase to explore the diversity and ecological importance of presumptive high-affinity H2-oxidizing bacteria Appl Environ Microbiol 77:6027–6035. doi:10.1128/aem.00673-11 CrossRefPubMedPubMedCentralGoogle Scholar
- 12.Khdhiri M, Hesse L, Popa ME, Quiza L, Lalonde I, Meredith LK, Röckmann T, Constant P (2015) Soil carbon content and relative abundance of high-affinity H2-oxidizing bacteria predict atmospheric H2 soil uptake activity better than soil microbial community composition Soil Biol Biochem 85:1–9. doi:10.1016/j.soilbio.2015.02.030 CrossRefGoogle Scholar