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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. 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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3. 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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4. 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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5. Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

   https://doi.org/10.1038/s41396-020-00825-6  

   Gazitúa, M. Consuelo ; Vik, Dean R. ; Roux, Simon ; Gregory, Ann C. ; Bolduc, Benjamin ; Widner, Brittany ; Mulholland, Margaret R. ; Hallam, Steven J. ; Ulloa, Osvaldo ; Sullivan, Matthew B. ( November 2020 , The ISME Journal)

   Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.

    

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