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.
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.
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- Award ID(s):
- 1749489
- NSF-PAR ID:
- 10384166
- Publisher / Repository:
- Cold Spring Harbor Laboratory
- Date Published:
- Journal Name:
- bioRxiv
- ISSN:
- 2692-8205
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract -
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
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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
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Removing excessive nitrate (NO3−) from wastewater has increasingly become an important research topic in light of the growing concerns over the related environmental problems and health issues. In particular, catalytic/electrocatalytic approaches are attractive for NO3− removal, because NO3− from wastewater can be converted to N2 and released back to the atmosphere using renewable H2 or electricity, closing the loop of the global N cycle. However, achieving high product selectivity towards the desirable N2 has proven challenging in the direct NO3−-to-N2 reaction. In this presentation, we will report our finding on unique and ultra-high electrochemical NO3−-to-NO2−activity on an oxide-derived silver electrode (OD-Ag). Up to 98% selectivity and 95% faradaic efficiency of NO2− were observed and maintained under a wide potential window. Benefiting from overcoming the rate-determining barrier of NO3−-to-NO2−during nitrate reduction, further reduction of accumulated NO2− to NH4+ can be well regulated by the cathodic potential on OD-Ag to achieve a faradaic efficiency of 89%. These indicated the potential controllable pathway to the key nitrate reduction products (NO2−or NH4+) on OD-Ag. DFT computations provided insights into the unique NO2−selectivity on Ag electrodes compared with Cu, showing the critical role of a proton-assisted mechanism. Based on the ultra-high NO3−-to-NO2−activity on OD-Ag, we designed a novel electrocatalytic-catalytic combined process for denitrifying real-world NO3−-containing agricultural wastewater, leading to 95+% of NO3− conversion to N2 with minimal NOX gases. In addition to the wastewater treatment process to N2 and electrochemical synthesis of NH3, NO2− derived from electrocatalytic NO3− conversion can serve as a reactive platform for distributed production of various nitrogen products. Our new research progress along this direction will be briefly presented.more » « less
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