Distribution Analysis of Hydrogenases in Surface Waters of Marine and Freshwater Environments

Abstract

BackgroundSurface waters of aquatic environments have been shown to both evolve and consume hydrogen and the ocean is estimated to be the principal natural source. In some marine habitats, H2 evolution and uptake are clearly due to biological activity, while contributions of abiotic sources must be considered in others. Until now the only known biological process involved in H2 metabolism in marine environments is nitrogen fixation.Principal FindingsWe analyzed marine and freshwater environments for the presence and distribution of genes of all known hydrogenases, the enzymes involved in biological hydrogen turnover. The total genomes and the available marine metagenome datasets were searched for hydrogenase sequences. Furthermore, we isolated DNA from samples from the North Atlantic, Mediterranean Sea, North Sea, Baltic Sea, and two fresh water lakes and amplified and sequenced part of the gene encoding the bidirectional NAD(P)-linked hydrogenase. In 21% of all marine heterotrophic bacterial genomes from surface waters, one or several hydrogenase genes were found, with the membrane-bound H2 uptake hydrogenase being the most widespread. A clear bias of hydrogenases to environments with terrestrial influence was found. This is exemplified by the cyanobacterial bidirectional NAD(P)-linked hydrogenase that was found in freshwater and coastal areas but not in the open ocean.SignificanceThis study shows that hydrogenases are surprisingly abundant in marine environments. Due to its ecological distribution the primary function of the bidirectional NAD(P)-linked hydrogenase seems to be fermentative hydrogen evolution. Moreover, our data suggests that marine surface waters could be an interesting source of oxygen-resistant uptake hydrogenases. The respective genes occur in coastal as well as open ocean habitats and we presume that they are used as additional energy scavenging devices in otherwise nutrient limited environments. The membrane-bound H2-evolving hydrogenases might be useful as marker for bacteria living inside of marine snow particles.

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).…”

Induction of Photosynthetic Carbon Fixation in Anoxia Relies on Hydrogenase Activity and Proton-Gradient Regulation-Like1-Mediated Cyclic Electron Flow in Chlamydomonas reinhardtii

“…In cyanobacteria, the bidirectional Ni-Fe hydrogenase might also work as an electron valve for disposal of electrons generated at the onset of illumination of cells (Cournac et al, 2004) or when excess electrons are generated during photosynthesis, preventing the slowing of the electron transport chain under stress conditions (Appel et al, 2000;Carrieri et al, 2011). The bidirectional Ni-Fe hydrogenase could also dispose of excess of reducing equivalents during fermentation in dark anaerobic conditions, helping to generate ATP and maintaining homeostasis (Barz et al, 2010). A similar role for hydrogenase in setting the redox poise in the chloroplast of C. reinhardtii in anoxia has been recently uncovered (Clowez et al, 2015).…”

Bacterial Diversity of a Microbial Mat from Hot Spring at Wartawan Beach, Lampung and Its Potential as a Source of Hydrogenases

“…Universal primer was used for amplification of 16S rRNA gene, forward: 52 AGAGTTTGATCMTGGCTCAG32 and reverse primer 52 AAGGAGGTGATCCANCCRCA3 (Xu et al, 2013) and FeFe (FeFe-272F: 5-GCHGA YMTBACHAT WATGGARGA-3 and FeFe-427R: 5-GCNGCYT CCATDACDCCDCCNGT-3), NiFe (HoxH-f GTATYTGY GGYATTTGTCCTGT and HoxH-r GGCATTTG TCCTRCTGYATGTGT) for hydrogenase genes (Barz et al, 2010;Schmidt, Drake, & Horn, 2010 …”

“…On the other hand, hydrogenase gene related to Cyanobacteria dominated in NiFe hydrogenase followed by NiFe genes related to Bacteroidetes and Proteobacteria. Cyanobacteria were known as a NiFe hydrogenase provider (Barz et al, 2010). They play two different NiFe types: fixing nitrogen strain that an uptake enzyme and bidirectional group strains (Tamagnini et al, 2007).…”

“…The isolation and studies of microbial hydrogenases diversity have been well studied from several environments, including from saline mat (Boyd et al, 2009), hot spring (Karadag et al, 2009;Minnan et al, 2005), marine and fresh waters (Barz et al, 2010; Kot hari , Pot raf ka, & Garci a-Pi chel, 2012), anaerobically-digested sludge (Quéméneur et al, 2011), acidophilic sludge (Fang, Zhang, & Li, 2006), acidophilic ethanol-H2-coproducing system (Xing, Ren, & Rittmann, 2008). Those microorganisms include anaerobes (Clostridia, Methylotrophs, methanogenic bacteria, Rumen bacteria, archaea), facultative anaerobes (Escherichia and Enterobacter), aerobes (Alcaligenes and Bacillus), photosynthetic bacteria, and Cyanobacteria (Nandi & Sengupta, 1998).…”