A widely distributed hydrogenase oxidises atmospheric H2 during bacterial growth

Abstract

Diverse aerobic bacteria persist by consuming atmospheric hydrogen (H2) using group 1h [NiFe]-hydrogenases. However, other hydrogenase classes are also distributed in aerobes, including the group 2a [NiFe]-hydrogenase. Based on studies focused on Cyanobacteria, the reported physiological role of the group 2a [NiFe]-hydrogenase is to recycle H2 produced by nitrogenase. However, given this hydrogenase is also present in various heterotrophs and lithoautotrophs lacking nitrogenases, it may play a wider role in bacterial metabolism. Here we investigated the role of this enzyme in three species from different phylogenetic lineages and ecological niches: Acidithiobacillus ferrooxidans (phylum Proteobacteria), Chloroflexus aggregans (phylum Chloroflexota), and Gemmatimonas aurantiaca (phylum Gemmatimonadota). qRT-PCR analysis revealed that the group 2a [NiFe]-hydrogenase of all three species is significantly upregulated during exponential growth compared to stationary phase, in contrast to the profile of the persistence-linked group 1h [NiFe]-hydrogenase. Whole-cell biochemical assays confirmed that all three strains aerobically respire H2 to sub-atmospheric levels, and oxidation rates were much higher during growth. Moreover, the oxidation of H2 supported mixotrophic growth of the carbon-fixing strains C. aggregans and A. ferrooxidans. Finally, we used phylogenomic analyses to show that this hydrogenase is widely distributed and is encoded by 13 bacterial phyla. These findings challenge the current persistence-centric model of the physiological role of atmospheric H2 oxidation and extend this process to two more phyla, Proteobacteria and Gemmatimonadota. In turn, these findings have broader relevance for understanding how bacteria conserve energy in different environments and control the biogeochemical cycling of atmospheric trace gases.

Hydrogen-Oxidizing Bacteria Are Abundant in Desert Soils and Strongly Stimulated by Hydration

“…In energy-deprived desert soils, a key role of this hydrogenase is likely to recycle H 2 endogenously produced by the energetically demanding nitrogenase reaction, as previously reported for other Nostoc strains (71,72). However, given recent discoveries regarding the physiological role of group 2a [NiFe]-hydrogenase (51), it is also plausible that this hydrogenase enables these bacteria to conserve energy by scavenging exogenous H 2 . Together, these genomic inferences provide considerable support for the continual energy-harvesting hypothesis by uncovering flexibility in energy conservation and carbon acquisition pathways, including hydrogenases associated with the most abundant chemoheterotrophic and photoautotrophic taxa.…”

“…These findings are supported by pure culture studies that show high-affinity hydrogenases are most expressed in carbon-limited cells (43)(44)(45)(46)(47) and, when knocked out, result in decreased long-term survival (48)(49)(50). Diverse bacteria can also support mixotrophic growth using atmospheric H 2 (51)(52)(53)(54). Overall, atmospheric H 2 is a highly dependable substrate for bacteria in oligotrophic environments given that it is ubiquitous in the lower atmosphere (mixing ratio, 0.53 ppmv), has a low activation energy, and yields a large amount of free energy when oxidized (55)(56)(57)(58).…”

“…S6). The low-affinity group 1d [NiFe]-hydrogenases and medium-affinity group 2a [NiFe]hydrogenases have dual roles in recycling endogenously produced H 2 and supporting hydrogenotrophic growth on exogenous H 2 (51,67,68), whereas the function of group 1c hydrogenases in aerobes is unresolved (58). Concordantly, group 2a [NiFe]hydrogenases were present in three cyanobacterial MAGs, namely, the nitrogen-fixing filamentous Nostoc and Tolypothrix (Fig.…”

A Model of Aerobic and Anaerobic Metabolism of Hydrogen in the Extremophile Acidithiobacillus ferrooxidans

“…Four distinct bacterial phyla containing a number of acidophiles (Actinobacteriota, Acidobacteriota, Chloroflexota, and Verrucomicrobiota) have been experimentally shown to utilize atmospheric H 2 by the [NiFe] group 2a hydrogenase (Islam et al, 2020). To date, autotrophic growth by dissimilatory H 2 oxidation has been reported only for several acidophiles.…”

“…ferrooxidans ATCC 23270 T genome has been shown to encode four different types of [NiFe] hydrogenases: (i) membrane-bound respiratory [NiFe] group 1 hydrogenase, (ii) cyanobacterial uptake and cytoplasmic [NiFe] group 2 hydrogenase, (iii) bidirectional hetero-multimeric cytoplasmic [NiFe] group 3 hydrogenase, (iv) H 2 -evolving, energy-conserving, membrane-associated [NiFe] group 4 hydrogenase (Valdés et al, 2008). Even though H 2 as an electron donor has several advantages for acidophiles compared to other inorganic substrates, including avoiding generating or consuming acidity and Fe 3+ precipitation, few physiological studies have been reported (Fischer et al, 1996;Ohmura et al, 2002;Islam et al, 2020), and no detailed information on H 2 uptake and metabolic pathways in acidophilic mesophiles is available. Recently, the energy metabolism pathways for autotrophic growth on H 2 in thermoacidophilic methanotrophs of the genus Methylacidiphilum and Methylacidimicrobium (both Verrucomicrobia) from extremely acidic geothermal systems have been proposed (Carere et al, 2017;Mohammadi et al, 2019;Schmitz et al, 2020).…”