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.


  • NSF Public Access
  • Search Results
  • Nitrous oxide reduction by two partial denitrifying bacteria requires denitrification intermediates that cannot be respired
Title: Nitrous oxide reduction by two partial denitrifying bacteria requires denitrification intermediates that cannot be respired
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 palustris CGA0092 and Rhodobacter capsulatus SB1003. 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 for both electron balance during growth on electron-rich organic compounds in light and for energy transformation via respiration in the dark. 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.  more » « less
Award ID(s):
1749489
PAR ID:
10384166
Author(s) / Creator(s):
; ; ; ;
Publisher / Repository:
Cold Spring Harbor Laboratory
Date Published:
Journal Name:
bioRxiv
ISSN:
2692-8205
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; (, 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
  2. ; ; ; ; ; (, ISME Communications)
    Abstract Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO3− to N2. This process may be performed entirely by complete denitrifiers capable of all four enzymatic steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Metagenomics and marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes co-occur within complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. We assemble genomes from metagenomes spanning the ETNP and Arabian Sea, and map these metagenome-assembled genomes (MAGs) to 56 metagenomes from all three major ODZs to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 MAGs presents the largest collection of pelagic ODZ microorganisms and reveals a clearer picture of the nitrogen cycling community within this environment. 
    more » « less
  3. ; ; ; ; ; ; ; ; ; ; et al (, The ISME Journal)
    Abstract Anthropogenic perturbations to the nitrogen cycle, primarily through use of synthetic fertilizers, is driving an unprecedented increase in the emission of nitrous oxide (N2O), a potent greenhouse gas and an ozone depleting substance, causing urgency in identifying the sources and sinks of N2O. Microbial denitrification is a primary contributor to biotic production of N2O in anoxic regions of soil, marine systems, and wastewater treatment facilities. Here, through comprehensive genome analysis, we show that pathway partitioning is a ubiquitous mechanism of complete denitrification within microbial communities. We have investigated mechanisms and consequences of process partitioning of denitrification through detailed physiological characterization and kinetic modeling of a synthetic community of Rhodanobacter thiooxydans FW510-R12 and Acidovorax sp. GW101-3H11. We have discovered that these two bacterial isolates, from a heavily nitrate (NO3−) contaminated superfund site, complete denitrification through the exchange of nitrite (NO2−) and nitric oxide (NO). The process partitioning of denitrification and other processes, including amino acid metabolism, contribute to increased cooperativity within this denitrifying community. We demonstrate that certain contexts, such as high NO3−, cause unbalanced growth of community members, due to differences in their substrate utilization kinetics. The altered growth characteristics of community members drives accumulation of toxic NO2−, which disrupts denitrification causing N2O off gassing. 
    more » « less
  4. ; ; ; ; (, Journal of hydrology)
    null (Ed.)
    The increased environmental abundance of anthropogenic reactive nitrogen species (Nr = ammonium [NH4+], nitrite [NO2−] and nitrate [NO3−]) may increase atmospheric nitrous oxide (N2O) concentrations, and thus global warming and stratospheric ozone depletion. Nitrogen cycling and N2O production, reduction, and emissions could be amplified in carbonate karst aquifers because of their extensive global range, susceptibility to nitrogen contamination, and groundwater-surface water mixing that varies redox conditions of the aquifer. The magnitude of N2O cycling in karst aquifers is poorly known, however, and thus we sampled thirteen springs discharging from the karstic Upper Floridan Aquifer (UFA) to evaluate N2O cycling. The springs can be separated into three groups based on variations in subsurface residence times, differences in surface–groundwater interactions, and variable dissolved organic carbon (DOC) and dissolved oxygen (DO) concentrations. These springs are oxic to sub-oxic and have NO3− concentrations that range from < 0.1 to 4.2 mg N-NO3−/L and DOC concentrations that range from < 0.1 to 50 mg C/L. Maximum spring water N2O concentrations are 3.85 μg N-N2O/L or ~ 12 times greater than water equilibrated with atmospheric N2O. The highest N2O concentrations correspond with the lowest NO3− concentrations. Where recharge water has residence times of a few days, partial denitrification to N2O occurs, while complete denitrification to N2 is more prominent in springs with longer subsurface residence times. Springs with short residence times have groundwater emission factors greater than the global average of 0.0060, reflecting N2O production, whereas springs with residence times of months to years have groundwater emission factors less than the global average. These findings imply that N2O cycling in karst aquifers depends on DOC and DO concentrations in recharged surface water and subsequent time available for N processing in the subsurface. 
    more » « less
  5. (, Journal of hydrology)
    null (Ed.)
    The increased environmental abundance of anthropogenic reactive nitrogen species (Nr = ammonium [NH4+], nitrite [NO2􀀀 ] and nitrate [NO3􀀀 ]) may increase atmospheric nitrous oxide (N2O) concentrations, and thus global warming and stratospheric ozone depletion. Nitrogen cycling and N2O production, reduction, and emissions could be amplified in carbonate karst aquifers because of their extensive global range, susceptibility to nitrogen contamination, and groundwater-surface water mixing that varies redox conditions of the aquifer. The magnitude of N2O cycling in karst aquifers is poorly known, however, and thus we sampled thirteen springs discharging from the karstic Upper Floridan Aquifer (UFA) to evaluate N2O cycling. The springs can be separated into three groups based on variations in subsurface residence times, differences in surface–groundwater interactions, and variable dissolved organic carbon (DOC) and dissolved oxygen (DO) concentrations. These springs are oxic to sub-oxic and have NO3􀀀 concentrations that range from < 0.1 to 4.2 mg N-NO3􀀀 /L and DOC concentrations that range from < 0.1 to 50 mg C/L. Maximum spring water N2O concentrations are 3.85 μg N-N2O/L or ~ 12 times greater than water equilibrated with atmospheric N2O. The highest N2O concentrations correspond with the lowest NO3􀀀 concentrations. Where recharge water has residence times of a few days, partial denitrification to N2O occurs, while complete denitrification to N2 is more prominent in springs with longer subsurface residence times. Springs with short residence times have groundwater emission factors greater than the global average of 0.0060, reflecting N2O production, whereas springs with residence times of months to years have groundwater emission factors less than the global average. These findings imply that N2O cycling in karst aquifers depends on DOC and DO concentrations in recharged surface water and subsequent time available for N processing in the subsurface. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email