Genomics and Ecophysiology of Heterotrophic Nitrogen-Fixing Bacteria Isolated from Estuarine Surface Water

Abstract

The ability to reduce atmospheric nitrogen (N2) to ammonia, known as N2 fixation, is a widely distributed trait among prokaryotes that accounts for an essential input of new N to a multitude of environments. Nitrogenase reductase gene (nifH) composition suggests that putative N2-fixing heterotrophic organisms are widespread in marine bacterioplankton, but their autecology and ecological significance are unknown. Here, we report genomic and ecophysiology data in relation to N2 fixation by three environmentally relevant heterotrophic bacteria isolated from Baltic Sea surface water: Pseudomonas stutzeri strain BAL361 and Raoultella ornithinolytica strain BAL286, which are gammaproteobacteria, and Rhodopseudomonas palustris strain BAL398, an alphaproteobacterium. Genome sequencing revealed that all were metabolically versatile and that the gene clusters encoding the N2 fixation complex varied in length and complexity between isolates. All three isolates could sustain growth by N2 fixation in the absence of reactive N, and this fixation was stimulated by low concentrations of oxygen in all three organisms (≈4 to 40 µmol O2 liter−1). P. stutzeri BAL361 did, however, fix N at up to 165 µmol O2 liter−1, presumably accommodated through aggregate formation. Glucose stimulated N2 fixation in general, and reactive N repressed N2 fixation, except that ammonium (NH4+) stimulated N2 fixation in R. palustris BAL398, indicating the use of nitrogenase as an electron sink. The lack of correlations between nitrogenase reductase gene expression and ethylene (C2H4) production indicated tight posttranscriptional-level control. The N2 fixation rates obtained suggested that, given the right conditions, these heterotrophic diazotrophs could contribute significantly to in situ rates.

Metabolic versatility of a novel N2‐fixing Alphaproteobacterium isolated from a marine oxygen minimum zone

“…2) but very little is known about their potential to fix N 2 (Dai et al ., ; Im Jeong et al ., ). The conserved nucleotide identity and synteny of the compared N 2 fixation gene clusters implies that this region was subject to lateral gene transfer, which has previously been reported for other heterotrophic diazotrophs (e.g., Cantera et al ., ; Bentzon‐Tilia et al ., ).…”

Basin‐wide N2 fixation in the deep waters of the Mediterranean Sea

“…Alternatively, their abundance and activity may fluctuate according to DOM dynamics. A pioneering genomics study targeting diazotrophic Alphaproteobacteria and Gammaproteobacteria isolated from coastal Denmark waters showed that these organisms devoted an important part of their genome to aromatic hydrocarbon metabolism, although diverse systems related to carbohydrate and fatty acid metabolism were also found [ Bentzon‐Tilia et al ., ], suggesting a flexible metabolism. Conversely, Severin et al .…”

Diversity and Activity of Diazotrophs in Great Barrier Reef Surface Waters

“…Conversely, when DIN concentrations were ≤0.09 μM we observed the highest rates of N 2 fixation (∼68 nmol L -1 d -1 ), associated with less diverse diazotroph communities (H′ = ∼1.5), typically dominated by Trichodesmium (at 30–50% of the diazotroph assemblage). In culture, cyanobacterial and proteobacterial diazotrophs have been shown to significantly decrease N 2 fixation with increasing DIN concentrations (Knapp et al, 2012; Bentzon-Tilia et al, 2015), indicating a switch to DIN supported growth (Kustka et al, 2003; Masuda et al, 2013; Bentzon-Tilia et al, 2015), which may reduce the demand for dissolved iron (Kustka et al, 2003). However, in the environment N 2 fixation is increasingly being found to occur outside of the classical ecological niche of low DIN waters (Fernandez et al, 2011; Knapp, 2012; Farnelid et al, 2013), and can even increase in response to simulated (mesocosm) and natural (mesoscale processes) co-additions of N with other nutrients (Dekaezemacker et al, 2013; Loscher et al, 2016).…”