Tracking nitrogen allocation to proteome biosynthesis in a marine microbial community

Urea assimilation and oxidation supports the activity of a phylogenetically diverse microbial community in the dark ocean

“…Notably, twelve of the fourteen phyla identified in the contig-based analysis were also identified with the MAG-based analysis. The groups identified as containing ureC in the 50 m samples are generally consistent with previous work in the euphotic zone, especially in the identification of Gammaproteobacteria and Prochlorococcus [14]. The deep-sea analysis revealed that some taxonomic groups with members known to use urea at the surface also have members with the genetic capacity to do so at depth, including Nitrososphaerales, Verrucomicrobiota, and Myxococcota, as well as members of several groups not before reported to utilize urea, including SAR202 and Alphaproteobacteria TMED109.…”

“…Notably, twelve of the fourteen phyla identified in the contig-based analysis were also identified with the MAG-based analysis. The groups identified as containing ureC in the 50 m samples are generally consistent with previous work in the euphotic zone, especially in the identification of Gammaproteobacteria and Prochlorococcus [14].…”

“…Urea is increasingly recognized as a source of nitrogen for cell growth [30] [20,54] and nitrification [17,18] in the sunlit ocean. In the euphotic zone, nitrogen from urea is assimilated by phylogenetically diverse taxa, including Cyanobacteria, Proteobacteria, and Thermoproteota (e.g., Nitrosophaeria) [14, 18, 20] [19, 28, 55], at rates exceeding those for nitrate, leucine, glutamate [14], and even ammonium [56], and it is also oxidized by nitrifying Nitrosophaeria to support chemoautotrophy [57,58]. Our observations in the aphotic zone of the northwest Pacific Ocean indicate that the significance of this molecule not only extends to the aphotic zonewhere an equally broad yet predominantly different set of organisms cleave it-but indicate that its role may be even more central to ecosystem functioning there than in surface waters.…”

“…Nitrogen dynamics have been studied extensively in the euphotic zone (e.g., [5,14] ), but less is known about nitrogen cycling in the deep sea, a region increasingly recognized as hosting a diverse, active, and influential microbiome ( [7,15,16]). Urea, a form of organic nitrogen which can be cleaved enzymatically to create two molecules of ammonia, has been proposed as a key substrate for both anabolism and nitrification in the deep sea [17,18].…”

Dynamic nitrogen fixation in an aerobic endophyte of Populus

“…Peptide search results were processed through the classified Peptide Isotope Enrichment (cPIE) workflow [ 42 ] to determine peptide-specific isotope incorporation (atom% 15 N). This approach involves extracting MS1 intensities to calculate relative abundances of all isotopologue species for each identified peptide, correcting enrichment estimates for potential contaminating signal from NA isotopes, and filtering results through a logit classifier trained on bacterial culture data of known isotopic enrichment to exclude likely false-positive results, all implemented in R v4.0.5 (R Core Team, 2017).…”