“Anaerobic” nitrite oxidation
Nitrite is a transient intermediate that rarely accumulates in the ocean but is the critical pivot point between loss of fixed nitrogen (during denitrification) and its retention as a nutrient (by oxidation to nitrate). Nitrite oxidation is an obligately aerobic process, but many years ago, we measured high rates of nitrite oxidation in water collected from anoxic depth in the oxygen minimum zone off Peru (Lipschultz et al. 1990). More recently, we found metagenomic evidence for clades of nitrite oxidizing bacteria that occur only in low oxygen water (Sun et al. 2021). Distinct responses of nitrite oxidation rate to oxygen concentration indicate that the physiology of NOB acclimated to anoxic environments (Sun et al., 2019) is different from those living in oxygenated waters (Figure 1, Sun et al., 2023). These novel OMZ NOB clades are most likely responsible for observed high nitrite oxidation rates in very low/zero oxygen water (Figure 2, Fortin et al. 2024). Current efforts at sea (Figure 3) in the lab are investigating the mechanism of the process and the metabolism of the microbes that are responsible for it.
Figure 1. a. A schematic of marine nitrogen cycling processes consuming or producing nitrite. b. Potential mechanisms of nitrite oxidation and schematic responses of nitrite oxidation to oxygen additions in the oxic layer, oxic-anoxic interface, and the anoxic layer. (Sun et al. 2023, Nitrite oxidation across the full oxygen spectrum in the ocean)
Figure 2. Nitrite oxidation rate (nM/day), DNA and cDNA based nxrB gene abundance (gene copies/mL seawater), and the relative abundance (RPKM) of NOB groups at a station in the ETNP OMZ, plotted against depth (m) from the surface. NOB 1 – 10 represent metagenome assembled genomes (draft genomes or MAGs) that appear to be restricted to low oxygen waters (Fortin et al. 2024, Nitrite-oxidizing bacteria adapted to low oxygen conditions dominate nitrite oxidation in marine oxygen minimum zones)
Figure 3. Samantha Fortin setting up incubations of oxygen minimum zone samples in a glove bag in the ETSP aboard R/V Roger Revelle.
Nitrous oxide (N2O) in surface waters
Nitrous oxide consumption is usually associated with anoxic environments where denitrification is the microbial process involved. We have detected both production and consumption of N2O in surface waters that cannot be attributed to the known microbial processes. Therefore, we are currently isolating N2O respiring microbes from surface water and characterizing their metabolic potential (especially carbon and nitrogen transformations) based on their genomes and metagenomes of the natural assemblage (Figure 4). We hope to use this information to figure out how and why biological nitrous oxide consumption occurs in surface water. We are also investigating the mechanism and global significance of abiotic photoproduction of N2O in surface waters (Leon-Palmero et al. 2024), which may support a branch of a possible cryptic N2O cycle whose net effect on global emissions is totally unexplored.
Figure 4. Moriah Kunes and Catherine Hexter setting up incubations/isolations for nitrous oxide consuming microbes in the ETSP aboard R/V Roger Revelle.
Urea as a substrate for nitrification
Ammonium oxidation, the first step in nitrification, produces nitrite that can be further oxidized to nitrate, and it also produces the potent greenhouse gas, nitrous oxide, as a side product. Rates of nitrite oxidation often exceed the rates of ammonium oxidation, implying that there must be another source of nitrite in oxic waters. Urea oxidation by ammonia oxidizing microbes might supply some of that missing nitrite. It turns out that different clades of ammonia oxidizers have different preferences for urea vs ammonium, and that many of them are able to oxidize urea directly to nitrite. In the open ocean, urea can support nearly half of the total nitrite production (Figure 5, Wan et al. 2024). Urea oxidation also leads to the production of nitrous oxide, a previously unappreciated implication of the metabolic diversity of ammonia oxidizers.
Fig. 5. In-situ rates of ammonia oxidation, urea-N oxidation and nitrite oxidation, respectively in the South China Sea and the western North Pacific Subtropical Gyre stations, respectively. The error bars denote one standard deviation of triplicate rate measurements; in some cases, the error bars are smaller than the symbols. The insert panels depict the rate in the mesopelagic zone. Note the concentrations and rates are shown in different scales, and the rates in the insert panels are shown in log scale. (Wan et al. 2024, Significance of urea in sustaining nitrite production by ammonia oxidizers in the oligotrophic ocean)