A widely distributed hydrogenase oxidises atmospheric H₂during bacterial growth

Abstract

18 19 Diverse aerobic bacteria persist by consuming atmospheric hydrogen (H2) using group 20 1h [NiFe]-hydrogenases. However, other hydrogenase classes are also distributed in 21 aerobes, including the group 2a [NiFe]-hydrogenase. Based on studies focused on 22 Cyanobacteria, the reported physiological role of the group 2a [NiFe]-hydrogenase is to 23 recycle H2 produced by nitrogenase. However, given this hydrogenase is also present in 24 various heterotrophs and lithoautotrophs lacking nitrogenases, it may play a wider role in 25 bacterial metabolism. Here we investigated the role of this enzyme in three species from 26 different phylogenetic lineages and ecological niches: Acidithiobacillus ferrooxidans 27 (phylum Proteobacteria), Chloroflexus aggregans (phylum Chloroflexota), and 28 Gemmatimonas aurantiaca (phylum Gemmatimonadota). qRT-PCR analysis revealed 29 that the group 2a [NiFe]-hydrogenase of all three species is significantly upregulated 30 during exponential growth compared to stationary phase, in contrast to the profile of the 31 persistence-linked group 1h [NiFe]-hydrogenase. Whole-cell biochemical assays 32confirmed that all three strains aerobically respire H2 to sub-atmospheric levels, and 33 oxidation rates were much higher during growth. Moreover, the oxidation of H2 supported 34 mixotrophic growth of the carbon-fixing strains C. aggregans and A. ferrooxidans. Finally, 35 we used phylogenomic analyses to show that this hydrogenase is widely distributed and 36 is encoded by 13 bacterial phyla. These findings challenge the current persistence-centric 37 model of the physiological role of atmospheric H2 oxidation and extends this process to 38 two more phyla, Proteobacteria and Gemmatimonadota. In turn, these findings have 39 broader relevance for understanding how bacteria conserve energy in different 40 environments and control the biogeochemical cycling of atmospheric trace gases. 41 42 43 Aerobic bacteria mediate the biogeochemically and ecologically important process of 44 atmospheric hydrogen (H2) oxidation [1]. Terrestrial bacteria constitute the largest sink 45 of this gas and mediate the net consumption of approximately 70 million tonnes of 46 atmospheric H2 per year [2, 3]. The energy derived from this process appears to be 47 critical for sustaining the productivity and biodiversity of ecosystems with low organic 48 carbon inputs [4-9]. Atmospheric H2 oxidation is thought to be primarily mediated by 49 group 1h [NiFe]-hydrogenases, a specialised oxygen-tolerant, high-affinity class of 50 hydrogenases [4, 10-13]. To date, aerobic heterotrophic bacteria from four distinct 51 bacterial phyla, the Actinobacteriota [10, 12, 14, 15], Acidobacteriota [16, 17], 52 Chloroflexota [18], and Verrucomicrobiota [19], have been experimentally shown to 53 consume atmospheric H2 using this enzyme. This process has been primarily linked 54 to energy conservation during persistence. Reflecting this, the expression and activity 55 of the group 1h hydrogenase is induced by carbon starvation across a wide...

Distinct hydrogenotrophic bacteria are stimulated by elevated H2levels in upland and wetland soils

“…S4) and RuBisCO ( (1), in line with recent inferences of a diverse and abundant H2 sink in soils [3,17,78]. However, a range of taxa also encoded hydrogenases implicated in hydrogenotrophic growth, such as the group 1d and 2a [NiFe]-hydrogenases [37,82], as well as the functionally enigmatic group 1c and 1f [NiFe]-hydrogenases [3,45] ( Fig. S4).…”

“…Classical studies have shown numerous Proteobacteria, for example Ralstonia eutropha and Bradyrhizobium japonicum, grow efficiently on high levels of H2 using the low-affinity group 1d [NiFe]-hydrogenases [27][28][29][30][31][32][33][34]. More recently, diverse taxa have been shown to use group 2a [NiFe]-hydrogenases to grow on H2 at a wide range of concentrations [35][36][37][38][39]. Some bacteria use H2 for multiple purposes; for example, some Mycobacterium species switch between synthesising the growthsupporting 2a hydrogenase and persistence-supporting 1h hydrogenase in response to organic carbon availability [40][41][42].…”

Soil Microbiomes With the Genetic Capacity for Atmospheric Chemosynthesis Are Widespread Across the Poles and Are Associated With Moisture, Carbon, and Nitrogen Limitation

“…Here, we also revealed the presence of high numbers of hhyL genes (4.18 × 10 6 –3.39 × 10 7 copies/g soil) in cold desert soils from across the three poles, many of which contained extremely low levels of carbon and nitrogen. We note here that although the qPCR primer are widely implemented ( Constant et al, 2010 , 2011 ; Meredith et al, 2014 ; Khdhiri et al, 2015 ; Piché-Choquette et al, 2016 ), the discovery of high-affinity hydrogenases beyond group 1 h (D. Cowan, personal communication; Greening et al, 2014 ; Islam et al, 2020 ) suggests that the high-affinity hydrogenase gene abundances quantified here are underestimations.…”

Technical Note: Inexpensive modification of Exetainers for the reliable storage of trace-level hydrogen and carbon monoxide gas samples

“…The level of contamination was proportional to the volume of the vial and the mass of rubber (a proxy for the specific surface area in contact with the enclosed gas phase); therefore, form factor and volume of vials have to be considered. For example, serum vials with an increased volume of >100 mL and thus lower exposed surface area relative to volume may still be suitable for gas storage or incubation experiments lasting a few weeks, if treated stoppers are used (Islam et al, 2019(Islam et al, , 2020Kessler et al, 2019).…”