Acidobacteria are active and abundant members of diverse atmospheric H2-oxidizing communities detected in temperate soils

• Published in: The ISME Journal 2021-02, Vol.15 (2), p.363-376
• Main Authors: Giguere, Andrew T., Eichorst, Stephanie A., Meier, Dimitri V., Herbold, Craig W., Richter, Andreas, Greening, Chris, Woebken, Dagmar
• Format: Article
• Language: English
• Subjects: 45/43; 631/326/171/1818; 631/326/41/1969; 704/158/670; Acidic soils; Bacteria; Biomedical and Life Sciences; Carbon; Consumption; Deprivation; Ecology; Evolutionary Biology; Genes; Hydrogenase; Intermetallic compounds; Iron compounds; Life Sciences; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Microorganisms; Nickel compounds; Oxidation; Soil bacteria; Soil microorganisms; Soils
• ISSN: 1751-7362; 1751-7370
• DOI: 10.1038/s41396-020-00750-8

Significant rates of atmospheric dihydrogen (H 2 ) consumption have been observed in temperate soils due to the activity of high-affinity enzymes, such as the group 1h [NiFe]-hydrogenase. We designed broadly inclusive primers targeting the large subunit gene ( hhyL ) of group 1h [NiFe]-hydrogenases for long-read sequencing to explore its taxonomic distribution across soils. This approach revealed a diverse collection of microorganisms harboring hhyL , including previously unknown groups and taxonomically not assignable sequences. Acidobacterial group 1h [NiFe]-hydrogenase genes were abundant and expressed in temperate soils. To support the participation of acidobacteria in H 2 consumption, we studied two representative mesophilic soil acidobacteria, which expressed group 1h [NiFe]-hydrogenases and consumed atmospheric H 2 during carbon starvation. This is the first time mesophilic acidobacteria, which are abundant in ubiquitous temperate soils, have been shown to oxidize H 2 down to below atmospheric concentrations. As this physiology allows bacteria to survive periods of carbon starvation, it could explain the success of soil acidobacteria. With our long-read sequencing approach of group 1h [NiFe]-hydrogenase genes, we show that the ability to oxidize atmospheric levels of H 2 is more widely distributed among soil bacteria than previously recognized and could represent a common mechanism enabling bacteria to persist during periods of carbon deprivation.