Denitrification in aquatic environments: a cross-system analysis

A meta-analysis was conducted on 136 data sets of denitrification rates (DR) recorded both during the period of highest water temperature and monthly in five types of aquatic ecosystems: oceans, coastal environments, estuaries, lakes and rivers. There was a gradual increase of DR from the ocean to rivers and lakes at both scales, with the rivers showing the highest DR variability. Denitrification peaked during summertime and showed highest seasonal variability in lakes and rivers. High concentrations of nitrate and interstitially-dissolved organic carbon as well as low oxygen concentration in the overlying water enhanced DR both during summer and at a seasonal scale whereas total phosphorus did at the seasonal scale only. There was a positive linear relationship between overlying nitrate and DR over the range of 1–970 lmol NO3 (r2 = 0.86, P = 0.001). DR in lakes and rivers might reach values doubling those in the more denitrifying terrestrial ecosystems (e.g. agrosystems). Discrepancies in DR and its controlling factors between site-specific studies and this meta-analysis may arise from environmental variability at two, often confounded, scales of observation: the habitat and the ecosystem level. Future studies on denitrification in aquatic environments should address the topic of spatial heterogeneity more thoroughlyPeer reviewe

Genome Analysis Coupled with Physiological Studies Reveals a Diverse Nitrogen Metabolism in Methylocystis sp Strain SC2

Dam B, Dam S, Blom J, Liesack W. Genome Analysis Coupled with Physiological Studies Reveals a Diverse Nitrogen Metabolism in Methylocystis sp Strain SC2. Plos One. 2013;8(10): e74767.Background: Methylocystis sp. strain SC2 can adapt to a wide range of methane concentrations. This is due to the presence of two isozymes of particulate methane monooxygenase exhibiting different methane oxidation kinetics. To gain insight into the underlying genetic information, its genome was sequenced and found to comprise a 3.77 Mb chromosome and two large plasmids. Principal Findings: We report important features of the strain SC2 genome. Its sequence is compared with those of seven other methanotroph genomes, comprising members of the Alphaproteobacteria, Gammaproteobacteria, and Verrucomicrobia. While the pan-genome of all eight methanotroph genomes totals 19,358 CDS, only 154 CDS are shared. The number of core genes increased with phylogenetic relatedness: 328 CDS for proteobacterial methanotrophs and 1,853 CDS for the three alphaproteobacterial Methylocystaceae members, Methylocystis sp. strain SC2 and strain Rockwell, and Methylosinus trichosporium OB3b. The comparative study was coupled with physiological experiments to verify that strain SC2 has diverse nitrogen metabolism capabilities. In correspondence to a full complement of 34 genes involved in N-2 fixation, strain SC2 was found to grow with atmospheric N-2 as the sole nitrogen source, preferably at low oxygen concentrations. Denitrification-mediated accumulation of 0.7 nmol N-30(2)/hr/mg dry weight of cells under anoxic conditions was detected by tracer analysis. N-2 production is related to the activities of plasmid-borne nitric oxide and nitrous oxide reductases. Conclusions/Perspectives: Presence of a complete denitrification pathway in strain SC2, including the plasmid-encoded nosRZDFYX operon, is unique among known methanotrophs. However, the exact ecophysiological role of this pathway still needs to be elucidated. Detoxification of toxic nitrogen compounds and energy conservation under oxygen-limiting conditions are among the possible roles. Relevant features that may stimulate further research are, for example, absence of CRISPR/Cas systems in strain SC2, high number of iron acquisition systems in strain OB3b, and large number of transposases in strain Rockwell