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

Abstract

ABSTRACTHydrogen is an important trace gas in the atmosphere. Soil microorganisms are known to be an important part of the biogeochemical H2cycle, 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 [NiFe]-hydrogenases, including their frequency of horizontal gene transfer, and foundhypDto be an applicable marker for the detection of the different known hydrogenase groups. Investigation of two freshwater lakes showed that [NiFe]-hydrogenases occur in many prokaryotic orders. We found that the respectivehypDgenes cooccur with oxygen-tolerant [NiFe]-hydrogenases (groups 1 and 5) mainly ofActinobacteria,Acidobacteria, andBurkholderiales; cyanobacterial uptake hydrogenases (group 2a) of cyanobacteria; H2-sensing hydrogenases (group 2b) ofBurkholderiales,Rhizobiales, andRhodobacterales; and two groups of multimeric soluble hydrogenases (groups 3b and 3d) ofLegionellalesand cyanobacteria. These findings support and expand a previous analysis of metagenomic data (M. Barz et al., PLoS One 5:e13846, 2010,http://dx.doi.org/10.1371/journal.pone.0013846) and further identify [NiFe]-hydrogenases that could be involved in hydrogen cycling in aquatic surface waters.