skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


This content will become publicly available on December 24, 2025

Title: Ecological dynamics explain modular denitrification in the ocean
Microorganisms in marine oxygen minimum zones (OMZs) drive globally impactful biogeochemical processes. One such process is multistep denitrification (NO3–→NO2–→NO→N2O→N2), which dominates OMZ bioavailable nitrogen (N) loss and nitrous oxide (N2O) production. Denitrification-derived N loss is typically measured and modeled as a single step, but observations reveal that most denitrifiers in OMZs contain subsets (“modules”) of the complete pathway. Here, we identify the ecological mechanisms sustaining diverse denitrifiers, explain the prevalence of certain modules, and examine the implications for N loss. We describe microbial functional types carrying out diverse denitrification modules by their underlying redox chemistry, constraining their traits with thermodynamics and pathway length penalties, in an idealized OMZ ecosystem model. Biomass yields of single-step modules increase along the denitrification pathway when organic matter (OM) limits growth, which explains the viability of populations respiring NO2–and N2O in a NO3–-filled ocean. Results predict denitrifier community succession along environmental gradients: Pathway length increases as the limiting substrate shifts from OM to N, suggesting a niche for the short NO3–→NO2–module in free-living, OM-limited communities, and for the complete pathway in organic particle-associated communities, consistent with observations. The model captures and mechanistically explains the observed dominance and higher oxygen tolerance of the NO3–→NO2–module. Results also capture observations that NO3–is the dominant source of N2O. Our framework advances the mechanistic understanding of the relationship between microbial ecology and N loss in the ocean and can be extended to other processes and environments.  more » « less
Award ID(s):
2138890 2142998
PAR ID:
10561777
Author(s) / Creator(s):
; ; ; ; ;
Publisher / Repository:
Proceedings of the National Academy of Sciences USA
Date Published:
Journal Name:
Proceedings of the National Academy of Sciences
Volume:
121
Issue:
52
ISSN:
0027-8424
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; (, ISME Communications)
    null (Ed.)
    Abstract Oxygen minimum zones (OMZs) are unique marine regions where broad redox gradients stimulate biogeochemical cycles. Despite the important and unique role of OMZ microbes in these cycles, they are less characterized than microbes from the oxic ocean. Here we recovered 39 high- and medium-quality metagenome-assembled genomes (MAGs) from the Eastern Tropical South Pacific OMZ. More than half of these MAGs were not represented at the species level among 2631 MAGs from global marine datasets. OMZ MAGs were dominated by denitrifiers catalyzing nitrogen loss and especially MAGs with partial denitrification metabolism. A novel bacterial genome with nitrate-reducing potential could only be assigned to the phylum level. A Marine-Group II archaeon was found to be a versatile denitrifier, with the potential capability to respire multiple nitrogen compounds including N 2 O. The newly discovered denitrifying MAGs will improve our understanding of microbial adaptation strategies and the evolution of denitrification in the tree of life. 
    more » « less
  2. ; ; ; ; (, Applied and Environmental Microbiology)
    Bose, Arpita (Ed.)
    ABSTRACT Denitrification is a form of anaerobic respiration wherein nitrate (NO3−) is sequentially reduced via nitrite (NO2−), nitric oxide, and nitrous oxide (N2O) to dinitrogen gas (N2) by four reductase enzymes. Partial denitrifying bacteria possess only one or some of these four reductases and use them as independent respiratory modules. However, it is unclear if partial denitrifiers sense and respond to denitrification intermediates outside of their reductase repertoire. Here, we tested the denitrifying capabilities of two purple nonsulfur bacteria,Rhodopseudomonas palustrisCGA0092 andRhodobacter capsulatusSB1003. Each had denitrifying capabilities that matched their genome annotation; CGA0092 reduced NO2−to N2, and SB1003 reduced N2O to N2. For each bacterium, N2O reduction could be used both for electron balance during growth on electron-rich organic compounds in light and for energy transformation via respiration in darkness. However, N2O reduction required supplementation with a denitrification intermediate, including those for which there was no associated denitrification enzyme. For CGA0092, NO3−served as a stable, non-catalyzable molecule that was sufficient to activate N2O reduction. Using a β-galactosidase reporter, we found that NO3−acted, at least in part, by stimulating N2O reductase gene expression. In SB1003, NO2−but not NO3−activated N2O reduction, but NO2−was slowly removed, likely by a promiscuous enzyme activity. Our findings reveal that partial denitrifiers can still be subject to regulation by denitrification intermediates that they cannot use. IMPORTANCEDenitrification is a form of microbial respiration wherein nitrate is converted via several nitrogen oxide intermediates into harmless dinitrogen gas. Partial denitrifying bacteria, which individually have some but not all denitrifying enzymes, can achieve complete denitrification as a community by cross-feeding nitrogen oxide intermediates. However, the last intermediate, nitrous oxide (N2O), is a potent greenhouse gas that often escapes, motivating efforts to understand and improve the efficiency of denitrification. Here, we found that at least some partial denitrifying N2O reducers can sense and respond to nitrogen oxide intermediates that they cannot otherwise use. The regulatory effects of nitrogen oxides on partial denitrifiers are thus an important consideration in understanding and applying denitrifying bacterial communities to combat greenhouse gas emissions. 
    more » « less
  3. ; ; ; ; (, Global Biogeochemical Cycles)
    Abstract Oceanic emissions of nitrous oxide (N2O) account for roughly one‐third of all natural sources to the atmosphere. Hot‐spots of N2O outgassing occur over oxygen minimum zones (OMZs), where the presence of steep oxygen gradients surrounding anoxic waters leads to enhanced N2O production from both nitrification and denitrification. However, the relative contributions from these pathways to N2O production and outgassing in these regions remains poorly constrained, in part due to shared intermediary nitrogen tracers, and the tight coupling of denitrification sources and sinks. To shed light on this problem, we embed a new, mechanistic model of the OMZ nitrogen cycle within a three‐dimensional eddy‐resolving physical‐biogeochemical model of the Eastern Tropical South Pacific (ETSP), tracking contributions from remote advection, atmospheric exchange, and local nitrification and denitrification. The model indicates that net N2O production from denitrification is approximately one order of magnitude greater than nitrification within the ETSP OMZ. However, only ∼32% of denitrification‐derived N2O production ultimately outgasses to the atmosphere in this region (contributing ∼36% of the air‐sea N2O flux on an annual basis), while the remaining is exported out of the domain. Instead, remotely produced N2O advected into the OMZ region accounts for roughly half (∼57%) of the total N2O outgassing, with smaller contributions from nitrification (∼7%). Our results suggests that, together with enhanced production by denitrification, upwelling of remotely derived N2O contributes the most to N2O outgassing over the ETSP OMZ. 
    more » « less
  4. ; ; (, Environmental Microbiology Reports)
    Summary Microbial enzymes often occur as distinct variants that share the same substrate but differ in substrate affinity, sensitivity to environmental conditions, or phylogenetic ancestry. Determining where variants occur in the environment helps identify thresholds that constrain microbial cycling of key chemicals, including the greenhouse gas nitrous oxide (N2O). To understand the enzymatic basis of N2O cycling in the ocean, we mined metagenomes to characterize genes encoding bacterial nitrous oxide reductase (NosZ) catalyzing N2O reduction to N2. We examined data sets from diverse biomes but focused primarily on those from oxygen minimum zones where N2O levels are often elevated. With few exceptions, marinenosZdata sets were dominated by ‘atypical’ clade II gene variants. AtypicalnosZhas been associated with low oxygen, enhanced N2O affinity, and organisms lacking enzymes for complete denitrification, i.e., non‐denitrifiers. AtypicalnosZ often occurred in metagenome‐assembled genomes (MAGs) with nitrate or nitrite respiration genes, although MAGs with genes for complete denitrification were rare. We identified atypicalnosZ in several taxa not previously associated with N2O consumption, in addition to known N2O‐associated groups. The data suggest that marine environments generally select for high N2O‐scavenging ability across diverse taxa and have implications for how N2O concentration may affect N2O removal rates. 
    more » « less
  5. ; ; ; ; (, Global Biogeochemical Cycles)
    Abstract The ocean is estimated to contribute up to ~20% of global fluxes of atmospheric nitrous oxide (N2O), an important greenhouse gas and ozone depletion agent. Marine oxygen minimum zones contribute disproportionately to this flux. To further understand the partition of nitrification and denitrification and their environmental controls on marine N2O fluxes, we report new relationships between oxygen concentration and rates of N2O production from nitrification and denitrification directly measured with15N tracers in the Eastern Tropical Pacific. Highest N2O production rates occurred near the oxic‐anoxic interface, where there is strong potential for N2O efflux to the atmosphere. The dominant N2O source in oxygen minimum zones was nitrate reduction, the rates of which were 1 to 2 orders of magnitude higher than those of ammonium oxidation. The presence of oxygen significantly inhibited the production of N2O from both nitrification and denitrification. These experimental data provide new constraints to a multicomponent global ocean biogeochemical model, which yielded annual oceanic N2O efflux of 1.7–4.4 Tg‐N (median 2.8 Tg‐N, 1 Tg = 1012 g), with denitrification contributing 20% to the oceanic flux. Thus, denitrification should be viewed as a net N2O production pathway in the marine environment. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email