hypD as a Marker for [NiFe]-Hydrogenases in Microbial Communities of Surface Waters

Abstract

Hydrogen is an important trace gas in the atmosphere. Soil microorganisms are known to be an important part of the biogeochemical H 2 cycle, contributing 80 to 90% of the annual hydrogen uptake. Different aquatic ecosystems act as either sources or sinks of hydrogen, but the contribution of their microbial communities is unknown.[NiFe]-hydrogenases are the best candidates for hydrogen turnover in these environments since they are able to cope with oxygen. As they lack sufficiently conserved sequence motifs, reliable markers for these enzymes are missing, and consequently, little is known about their environmental distribution. We analyzed the essential maturation genes of A tmospheric hydrogen concentrations result from a number of counteracting processes. H 2 is mainly produced due to photooxidation of methane and other hydrocarbons in the upper atmosphere and due to fossil fuel and biomass burning. By far the largest proportion of hydrogen (80 to 90%) is consumed by microorganisms in the soil, whereas the remaining part reacts with OH radicals (1, 2). Since OH radicals are important for the degradation of methane, hydrogen levels indirectly control the amount of this trace gas. Currently, the atmospheric concentration of H 2 is about 0.5 ppm (2).The processes governing hydrogen concentrations and exchange in marine and freshwater environments are poorly described. In general, it seems that tropical surface waters act as hydrogen sources contributing about 6% to the global hydrogen production (2). Possible causes of H 2 evolution are photochemical processes in the surface layers as well as nitrogen fixation (3-6). Thorough flux analysis is still lacking. On the other hand, investigations of temperate surface waters showed net hydrogen uptake that could be assigned to microorganisms (7).Three classes of hydrogenases, the enzymes involved in hydrogen turnover, are known. Their classification is based on their active site metal ions being either a single [Fe] Although they are phylogenetically related, it is not possible to derive degenerated primers for the amplification of [NiFe]-hydrogenase genes, because their signature motifs are too scattered and too short. However, all [NiFe]-hydrogenases ultimately depend on the presence of six maturation genes, hypABCDEF (10). The most promising candidate of all maturation genes is the highly conserved hypD, encoding a protein with a ferredoxin:thioredoxin reductase-like [4Fe-4S] cluster and additional cysteine residues that probably work as a redox cascade. In concert with HypC, it works as a scaffold protein that allows the insertion of the Fe(CN) 2 (CO) in the correct oxidation state into the active site of the [NiFe]-hydrogenases (11-17).Since hydrogen leakage from anaerobic habitats is negligible and does not contribute to a significant extent to H 2 levels in the atmosphere (18)(19)(20), microbial influence on its atmospheric concentration apart from nitrogen fixation mainly relies on [NiFe]-hydrogenases. A few studies already attempted to analyze the occurrence o...

Transition from unclassified Ktedonobacterales to Actinobacteria during amorphous silica precipitation in a quartzite cave environment

“…Total DNA from all the three speleothems under analysis was used as template for PCR amplification reactions targeting the coxL and hypD genes using OmpF-O/Br 85 and hypDfor2-hypDrev 86 primer sets, respectively (Table S1 ). Total DNA extracted from QP was also used for the amplification of full-length 16S rRNA gene using 27F-1492R primers 76 (Table S1 ).…”

[NiFe]-hydrogenases are constitutively expressed in an enriched Methanobacterium sp. population during electromethanogenesis

“…One of these proteins, HypD, is highly conserved and essential for the maturation of hydrogenases. HypD contributes to the insertion of the Fe(CN) 2 (CO) moiety in the correct oxidation state into the active site of different [NiFe]-hydrogenases [14]. Due to this tight relationship, HypD is a good candidate to measure the expression of different soluble [NiFe]-hydrogenases.…”

Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival

“…Furthermore, detailed biochemical information and atomicresolution structures are available for only a subset of hydrogenases (Volbeda et al, 1995;Peters et al, 1998;Shima et al, 2008;Fritsch et al, 2011;Mills et al, 2013). Although the contribution of H 2 metabolism to total ecosystem processes is recognised in some environments (for example, anoxic sediments, animal guts and hydrothermal vents; Vignais and Billoud, 2007;Schwartz et al, 2013), the role of hydrogenases in general soil and aquatic ecosystems remains largely unresolved (Barz et al, 2010;Constant et al, 2011;Beimgraben et al, 2014;Greening et al, 2015b). Consequently, the influence of H 2 evolution and consumption on community structuring and global biogeochemical cycling requires further investigation (Schwartz et al, 2013;Greening et al, 2015b).…”