Cover image: Beech forest in the Vienna Woods (Austria). Image credit: Stephanie A. Eichorst.

Soils harbor a diverse collection of microorganisms with estimates of 10⁹-10¹⁰ cells per gram of soil, and within that gram containing upwards of 1,000 species. Yet the majority (estimates of up to ~80%) of these microorganisms are in a state of non-growth or dormancy for extended periods of time¹. Atmospheric gas scavenging is proposed to be a strategy to survive these periods of non-growth², presumably stemming from carbon deprivation. As such soils are often referred to as “sinks” for atmospheric gases³, namely molecular hydrogen (H₂).

Microorganisms are responsible for the uptake of atmospheric H₂ through the activity of high-affinity enzymes, such as the group 1h [NiFe]-hydrogenase⁴. Significant rates of atmospheric H₂ consumption have been observed in temperate soils such as forests, grasslands and pasture soils, due to the activity of these high-affinity enzymes⁴. Various taxonomic groups have been implicated in this atmospheric H₂ consumption⁵, one of them being members of the phylum Acidobacteria.

Acidobacteria represent one of the most abundant soil phyla based on the 16S rRNA gene in soils⁶. They constitute a large, physiologically and phylogenetically diverse phylum, yet we are just beginning to understand the extent of this extensive diversity regarding their physiological potential and environment function. Our recent large-scale comparative genomic study of mesophilic soil acidobacteria identified the structural and maturation genes for the group 1h [NiFe]-hydrogenase – implicating them as mediators in trace gas scavenging (Eichorst, Trojan et al., 2018).

Our research group (Head: Dr. Dagmar Woebken) at the University of Vienna integrated culture-independent approaches to identify a diverse H₂-scavenging community in temperate soils - an effort led by the co-first authors, Drs. Andrew T. Giguere and Stephanie A. Eichorst (Giguere, Eichorst et al., 2020). We identified new mediators in this biogeochemically and ecologically important process of atmospheric H₂ oxidation through the development of broadly inclusive primers for long-read sequencing of the group 1h [NiFe]-hydrogenase gene. Acidobacteria were prevalent members of this community, notably in temperate soils where H₂ consumption was observed. In culture-based experiments conducted in collaboration with Dr. Chris Greening at Monash University (Australia), we further demonstrated that mesophilic soil acidobacteria consumed H₂ to below atmospheric levels during carbon limitation due to the expression of their group 1h [NiFe]-hydrogenase genes (hhyL and hhyS). We also detected expressed acidobacterial hhyL in temperate soils, illustrating that acidobacteria are active in soils that consume H₂, presumably contributing to the “H₂ sink” in soils. Taken together, our data support the growing evidence that trace gases might be widely used as energy source enabling bacterial persistence.

Useful links:

Our paper can be found here.

Details on our research group at the University of Vienna can be found here.

References:

¹Lennon JT, Jones SE. Microbial seed banks: the ecological and evolutionary implications of dormancy. Nat Rev Microbiol 9:119-30 (2011).

²Morita RY. Is H₂ the universal energy source for long-term survival? Micro Ecol. 38:307-20 (1999).

³Conrad R. Soil microorganisms as controllers of atmospheric trace gases (H₂, CO, CH₄, OCS, N₂O, and NO). Microbiol Rev. 60:609-40 (1996).

⁴Greening C, Constant P, Hards K, Morales SE, Oakeshott JG, Russell RJ et al. Atmospheric hydrogen scavenging: from enzyme to ecosystems. Appl Environ Microbiol. 81:1190-9 (2015).

⁵Greening C, Biswas A, Carere CR, Jackson CJ, Taylor MC, Stott MB et al. Genomic and metagenomic surveys of hydrogenase distribution indicates H₂ is a widely utilized energy source for microbial growth and survival. ISME J. 10:761-77 (2016).

⁶Fierer N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol. 10:579-90 (2017).