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1. Uncultured Nitrospina -like species are major nitrite oxidizing bacteria in oxygen minimum zones

   https://doi.org/10.1038/s41396-019-0443-7  

   Sun, Xin ; Kop, Linnea F. M. ; Lau, Maggie C. Y. ; Frank, Jeroen ; Jayakumar, Amal ; Lücker, Sebastian ; Ward, Bess B. ( May 2019 , The ISME Journal)

   Oxygen minimum zones (OMZs) are marine regions where O2 is undetectable at intermediate depths. Within OMZs, the oxygen-depleted zone (ODZ) induces anaerobic microbial processes that lead to fixed nitrogen loss via denitrification and anammox. Surprisingly, nitrite oxidation is also detected in ODZs, although all known marine nitrite oxidizers (mainly Nitrospina) are aerobes. We used metagenomic binning to construct metagenome-assembled genomes (MAGs) of nitrite oxidizers from OMZs. These MAGs represent two novel Nitrospina-like species, both of which differed from all known Nitrospina species, including cultured species and published MAGs. Relative abundances of different Nitrospina genotypes in OMZ and non-OMZ seawaters were estimated by mapping metagenomic reads to newly constructed MAGs and published high-quality genomes of members from the Nitrospinae phylum. The two novel species were present in all major OMZs and were more abundant inside ODZs, which is consistent with the detection of higher nitrite oxidation rates in ODZs than in oxic seawaters and suggests novel adaptations to anoxic environments. The detection of a large number of unclassified nitrite oxidoreductase genes in the dataset implies that the phylogenetic diversity of nitrite oxidizers is greater than previously thought.

    

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2. Well-Aerated Southern Appalachian Forest Soils Demonstrate Significant Potential for Gaseous Nitrogen Loss

   https://doi.org/10.3390/f10121155  

   Baas, Peter ; Knoepp, Jennifer D. ; Mohan, Jacqueline E. ( December 2019 , Forests)

   null (Ed.)

   Understanding the dominant soil nitrogen (N) cycling processes in southern Appalachian forests is crucial for predicting ecosystem responses to changing N deposition and climate. The role of anaerobic nitrogen cycling processes in well-aerated soils has long been questioned, and recent N cycling research suggests it needs to be re-evaluated. We assessed gross and potential rates of soil N cycling processes, including mineralization, nitrification, denitrification, nitrifier denitrification, and dissimilatory nitrate reduction to ammonium (DNRA) in sites representing a vegetation and elevation gradient in the U.S. Department of Agriculture (USDA) Forest Service Experimental Forest, Coweeta Hydrologic Laboratory in southwestern North Carolina, USA. N cycling processes varied among sites, with gross mineralization and nitrification being greatest in high-elevation northern hardwood forests. Gaseous N losses via nitrifier denitrification were common in all ecosystems but were greatest in northern hardwood. Ecosystem N retention via DNRA (nitrification-produced NO3 reduced to NH4) ranged from 2% to 20% of the total nitrification and was highest in the mixed-oak forest. Our results suggest the potential for gaseous N losses through anaerobic processes (nitrifier denitrification) are prevalent in well-aerated forest soils and may play a key role in ecosystem N cycling. 

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3. Determination of site‐specific nitrogen cycle reaction kinetics allows accurate simulation of in situ nitrogen transformation rates in a large North American estuary

   https://doi.org/10.1002/lno.12628  

   Tang, Weiyi ; Fortin, Samantha_G ; Intrator, Naomi ; Lee, Jenna_A ; Kunes, Moriah_A ; Jayakumar, Amal ; Ward, Bess_B ( July 2024 , Limnology and Oceanography)

   Nitrogen (N) bioavailability affects phytoplankton growth and primary production in the aquatic environment. N bioavailability is partly determined by biological N cycling processes that either transform N species or remove fixed N. Reliable estimates of their kinetic parameters can help understand the distribution of N cycling processes. However, available estimates of kinetic parameters are often derived from microbial isolates and may not be representative of the natural environment. Observations are particularly lacking in estuarine and coastal waters. We conducted isotope tracer addition incubations to evaluate substrate affinities of nitrification, denitrification and anammox in the Chesapeake Bay water column. The half‐saturation constant for ammonia oxidation ranged from 0.38 to 0.75 μM ammonium, substantially higher than observed in the open oceans. Half‐saturation constants for denitrification—0.92–1.86 μM nitrite or 1.15 μM nitrate—were within the lower end or less than those reported for other aquatic environments and for denitrifier isolates. Interestingly, water column denitrification potential was comparable to that of sedimentary denitrification, highlighting the contribution of the water column to N removal during anoxia. Mostly undetectable anammox rates prevented us from deriving the half‐saturation constants, suggesting a low affinity of anammox. Using these substrate kinetics, we were able to predict in situ N cycling rates and explain the vertical distribution of N nutrient concentrations. Our newly derived substrate kinetics parameters can be useful for improving model representation of N nutrient dynamics in estuarine and coastal waters, which is critical for assessing the ecosystem productivity and function.

    

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4. Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones

   https://doi.org/10.1038/s41396-020-00852-3  

   Sun, Xin ; Frey, Claudia ; Garcia-Robledo, Emilio ; Jayakumar, Amal ; Ward, Bess B. ( January 2021 , The ISME Journal)

   Nitrite is a pivotal component of the marine nitrogen cycle. The fate of nitrite determines the loss or retention of fixed nitrogen, an essential nutrient for all organisms. Loss occurs via anaerobic nitrite reduction to gases during denitrification and anammox, while retention occurs via nitrite oxidation to nitrate. Nitrite oxidation is usually represented in biogeochemical models by one kinetic parameter and one oxygen threshold, below which nitrite oxidation is set to zero. Here we find that the responses of nitrite oxidation to nitrite and oxygen concentrations vary along a redox gradient in a Pacific Ocean oxygen minimum zone, indicating niche differentiation of nitrite-oxidizing assemblages. Notably, we observe the full inhibition of nitrite oxidation by oxygen addition and nitrite oxidation coupled with nitrogen loss in the absence of oxygen consumption in samples collected from anoxic waters. Nitrite-oxidizing bacteria, including novel clades with high relative abundance in anoxic depths, were also detected in the same samples. Mechanisms corresponding to niche differentiation of nitrite-oxidizing bacteria across the redox gradient are considered. Implementing these mechanisms in biogeochemical models has a significant effect on the estimated fixed nitrogen budget.

    

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5. Electrocatalytic Reduction of Nitrate to Nitrite and Ammonia over Oxide-Derived Silver Electrodes

   Liu, Hengzhou ; Park, Jaeryl ; Chen, Yifu ; Gu, Shuang ; Roling, Luke ; Li, Wenzhen ( August 2021 , 262nd ACS National Meeting)

   The nitrogen cycle plays a key role biological, energy, environment, and industrial processes. Breaking natural nitrogen cycle is leading to accumulation of reactive nitrogen chemicals in water and atmosphere, therefore, better management of N-cycle has emerged as an urgent research need in energy and environmental science. 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. Importantly, NO2− derived from nitrate may serve as a crucial reactive platform for distributed production of various nitrogen products, such as NO, NH2OH, NH3, and urea. 

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