Casciotti, K. L. | Search bioRxiv

bioRxiv2025

Denitrification genes in SAR11 and other ubiquitous lineages of marine bacteria isolated from the northern Benguela Upwelling System

Denitrification is a microbial process that leads to nitrogen loss from marine oxygen minimum zones (OMZs). The complete metabolic pathway for denitrification reduces nitrate to dinitrogen gas in four sequential steps. Many anaerobic and facultatively anaerobic bacteria are capable of the initial step of nitrate reduction to nitrite. Far fewer reduce nitrite to nitric oxide, nitrous oxide, or dinitrogen gas. In this study, we cultured and sequenced the complete genomes of 24 bacteria isolated from low dissolved oxygen waters (DO = 24 {micro}M) in the northern Benguela Upwelling System (nBUS) OMZ to identify facultatively anaerobic bacteria with the genetic potential to contribute to denitrification. Most of the isolates obtained from the nBUS have denitrification genes (79%). They include several new species in the order Pelagibacterales (SAR11), as well as representatives from a previously uncultured family of Arenicellales (UBA868), a previously uncultured genus of Paracoccaceae, and a previously undescribed genus of Porticoccaceae. All ten nBUS SAR11 have a previously unidentified genomic region that codes for a copper-containing nitrite reductase (nirK), suggesting that they have the potential to contribute to nitrogen loss by respiring nitrite to nitric oxide. Significance StatementVast genomic diversity has confounded sequencing efforts to identity the potential for marine bacteria to contribute to denitrification in marine oxygen minimum zones (OMZs). To identify facultatively anaerobic microbes with the genetic potential to contribute to marine nitrogen loss, we cultured and sequenced the complete genomes of bacteria from low-oxygen waters of the northern Benguela Upwelling System. Complete genomes allowed for a comprehensive analysis of denitrification. Most bacterial isolates, including all ten SAR11, have the genetic potential to contribute to denitrification. This suggests that some of the most abundant lineages of marine bacteria in the oceans are adapted to anoxic conditions in OMZs and may have a more direct role in marine nitrogen loss than previously suspected.

microbiology↗

bioRxiv2024

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

Urea is hypothesized to be an important source of nitrogen and chemical energy to microorganisms in the deep sea; however, direct evidence for urea use below the epipelagic ocean is lacking. Here, we explore urea utilization from 50 to 4000 meters depth in the northeastern Pacific Ocean using metagenomics, nitrification rates, and single-cell stable-isotope-uptake measurements with nanoscale secondary ion mass spectrometry (nanoSIMS). We find that the majority (>60%) of active cells across all samples assimilated urea-derived N, and that cell-specific nitrogen-incorporation rates from urea were higher than that from ammonium. Both urea concentrations and assimilation rates relative to ammonium generally increased below the euphotic zone. We detected ammonia- and urea-based nitrification at all depths at one of two sites analyzed, demonstrating their potential to support chemoautotrophy in the mesopelagic and bathypelagic regions. Using newly generated metagenomes we find that the ureC gene, encoding the catalytic subunit of urease, is found within 39% of deep-sea cells in this region, including the Nitrosophaerota (likely for nitrification) as well as thirteen other phyla such as Proteobacteria, Verrucomicrobia, Plantomycetota, Nitrospinota, and Chloroflexota (likely for assimilation). Analysis of public metagenomes revealed ureC within 10-46% of deep-sea cells around the world, with higher prevalance below the photic zone, suggesting urea is widely available to the deep-sea microbiome globally. Our results demonstrate that urea is a nitrogen source to abundant and diverse microorganisms in the dark ocean, as well as a significant contributor to deep-sea nitrification and therefore fuel for chemoautotrophy.

microbiology↗