The microbial nitrogen cycle

Nitrogen is an essential element in biological systems, and one that often limits production in both aquatic and terrestrial systems. Due to its requirement in biological macromolecules, its acquisition and cycling have the potential to structure microbial communities, as well as to control productivity on the ecosystem scale. In addition, its versatile redox chemistry is the basis of complex biogeochemical transformations that control the inventory of fixed nitrogen, both in local environments and over geological time. Although many of the pathways in the microbial nitrogen cycle were described more than a century ago, additional fundamental pathways have been discovered only recently. These findings imply that we still have much to learn about the microbial nitrogen cycle, the organisms responsible for it, and their interactions in natural and human environments. Progress in nitrogen cycle research has been facilitated by recent rapid technological advances, especially in genomics and isotopic approaches. In this Research Topic, we reviewed the leading edge of nitrogen cycle research based on these approaches, as well as by exploring microbial processes in modern ecosystems

Global nitrous oxide production determined by oxygen sensitivity of nitrification and denitrification

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 with 15N 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

Aquatic nitrous oxide reductase gene (nosZ) phylogeny and environmental distribution

Nitrous oxide (N2O) is a potent greenhouse gas and a major cause of ozone depletion. One-third of atmospheric N2O originates in aquatic environments. Reduction of N2O to dinitrogen gas (N2) requires the nitrous oxide reductase enzyme, which is encoded by the gene nosZ. Organisms that contain nosZ are the only known biological sinks of N2O and are found in diverse genera and a wide range of environments. The two clades of nosZ (Clade I and II) contain great diversity, making it challenging to study the population structure and distribution of nosZ containing organisms in the environment. A database of over 11,000 nosZ sequences was compiled from NCBI (representing diverse aquatic environments) and unpublished sequences and metagenomes (primarily from oxygen minimum zones, OMZs, where N2O levels are often elevated). Sequences were clustered into archetypes based on DNA and amino acid sequence identity and their clade, phylogeny, and environmental source were determined. Further analysis of the source and environmental distribution of the sequences showed strong habitat separation between clades and phylogeny. Although there are more Clade I nosZ genes in the compilation, Clade II is more diverse phylogenetically and has a wider distribution across environmental sources. On the other hand, Clade I nosZ genes are predominately found within marine sediment and are primarily from the phylum Pseudonomonadota. The majority of the sequences analyzed from marine OMZs represented distinct phylotypes between different OMZs showing that the nosZ gene displays regional and environmental separation. This study expands the known diversity of nosZ genes and provides a clearer picture of how the clades and phylogeny of nosZ organisms are distributed across diverse environments

Nitrogen substrate–dependent nitrous oxide cycling in salt marsh sediments

Nitrous oxide (N2O) is important to Earth\u27s climate because it is a strong absorber of radiation and an important ozone depletion agent. Increasing anthropogenic nitrogen input into the marine environment, especially to coastal waters, has led to increasing N2O emissions. Identifying the nitrogen compounds that serve as substrates for N2O production in coastal waters reveals important pathways and helps us understand their control by environmental factors. In this study, sediments were collected from a long-term fertilization site in Great Sippewissett Marsh, Falmouth, Massachusetts. The 15N tracer incubation time course experiments were conducted and analyzed for potential N2O production and consumption rates. The two nitrogen substrates of N2O production, ammonium and nitrate, correspond to the two production pathways, nitrification and denitrification, respectively. When measurable nitrate was present, despite ambient high ammonium concentrations, denitrification was the major N2O production pathway. When nitrate was absent, ammonium became the dominant substrate for N2O production, via nitrification and coupled nitrification-denitrification. Net N2O consumption was enhanced under low oxygen and nitrate conditions. N2O production and consumption rates increased with increasing levels of nitrogen fertilization in long-term experimental plots. These results indicate that increasing anthropogenic nitrogen input to salt marshes can stimulate sedimentary N2O production via both nitrification and denitrification, whereas episodic oxygen depletion results in net N2O consumption

Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones

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

Diversity, Distribution, and Expression of Diazotroph nifH Genes in Oxygen-Deficient Waters of the Arabian Sea

The Arabian Sea oxygen minimum zone (OMZ), the largest suboxic region in the world\u27s oceans, is responsible for up to half of the global mesopelagic fixed nitrogen ( N ) loss from the ocean via denitrification and anammox. Dinitrogen (N2) fixation is usually attributed to cyanobacteria in the surface ocean. Model prediction and physiological inhibition of N2 fixation by oxygen, however, suggest that N2 fixation should be enhanced near the oxygen-deficient zone (ODZ) of the Arabian Sea. N2 fixation and cyanobacterial nifH genes (the gene encoding dinitrogenase reductase) have been reported in surface waters overlying the Arabian Sea ODZ. Here, water samples from depths above and within the Arabian Sea ODZ were examined to explore the distribution, diversity, and expression of nifH genes. In surface waters, nifH DNA and cDNA sequences related to Trichodesmium, a diazotroph known to occur and fix N2 in the Arabian Sea, were detected. Proteobacterial nifH phylotypes (DNA but not cDNA) were also detected in surface waters. Proteobacterial nifH DNA and cDNA sequences, as well as nifH DNA and cDNA sequences related to strictly anaerobic N -fixers, were obtained from oxygen-deficient depths. This first report of nifH gene expression in subsurface low-oxygen waters suggests that there is potential for active N2 fixation by several phylogenetically and potentially metabolically diverse microorganisms in pelagic OMZs

Nitrite oxidation exceeds reduction and fixed nitrogen loss in anoxic Pacific waters

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Babbin, A. R., Buchwald, C., Morel, F. M. M., Wankel, S. D., & Ward, B. B. Nitrite oxidation exceeds reduction and fixed nitrogen loss in anoxic Pacific waters. Marine Chemistry, 224, (2020): 103814, doi:10.1016/j.marchem.2020.103814.The diversity of nitrogen-based dissimilatory metabolisms in anoxic waters continues to increase with additional studies to the marine oxygen deficient zones (ODZs). Although the microbial oxidation of nitrite (NO2–) has been known for over a century, studies of the pathways and microbes involved have generally proceeded under the assumption that nitrite oxidation to nitrate requires dioxygen (O2). Anaerobic NO2– oxidation until now has been conclusively shown only for anammox bacteria, albeit only as a limited sink for NO2– in their metabolism compared to the NO2– reduced to N2. Here, using direct experimental techniques optimized for replicating in situ anoxic conditions, we show that NO2– oxidation is substantial, widespread, and consistent across the ODZs of the eastern tropical Pacific Ocean. Regardless of the specific oxidant, NO2– oxidation rates are up to an order of magnitude larger than simultaneous N2 production rates for which these zones are known, and cannot be explained by anammox rates alone. Higher rates of NO2– oxidation over reduction in anoxic waters are paradoxical but help to explain how anammox rates can be enhanced over denitrification in shallow anoxic waters (σθ < 26.4) at the edge of the ODZs but not within the ODZ core. Furthermore, nitrite oxidation may be the key to reconciliation of the perceived imbalance of the global fixed nitrogen loss budget.This work was funded by National Science Foundation grants OCE–1029951 to B.B.W, BIO–1402109 to A.R.B., and OCE-1260373 to S.D.W. Additional financial support to A.R.B. was provided by Simons Foundation grant 622065 and the generous contributions of Dr. Bruce L. Heflinger

Dependence of nitrite oxidation on nitrite and oxygen in low-oxygen seawater

Nitrite oxidation is an essential step in transformations of fixed nitrogen. The physiology of nitrite oxidizing bacteria (NOB) implies that the rates of nitrite oxidation should be controlled by concentration of their substrate, nitrite, and the terminal electron acceptor, oxygen. The sensitivities of nitrite oxidation to oxygen and nitrite concentrations were investigated using 15N tracer incubations in the Eastern Tropical North Pacific. Nitrite stimulated nitrite oxidation under low in situ nitrite conditions, following Michaelis-Menten kinetics, indicating that nitrite was the limiting substrate. The nitrite half-saturation constant (Ks = 0.254 ± 0.161 μM) was 1–3 orders of magnitude lower than in cultivated NOB, indicating higher affinity of marine NOB for nitrite. The highest rates of nitrite oxidation were measured in the oxygen depleted zone (ODZ), and were partially inhibited by additions of oxygen. This oxygen sensitivity suggests that ODZ specialist NOB, adapted to low-oxygen conditions, are responsible for apparently anaerobic nitrite oxidation. Key Points: • Nitrite addition stimulated nitrite oxidation in both oxic and anoxic waters • Natural assemblages of marine nitrite-oxidizing bacteria have high affinity for nitrite • Addition of oxygen at μM-level inhibited nitrite oxidation in oxygen depleted water

Multiple Metabolisms Constrain the Anaerobic Nitrite Budget in the Eastern Tropical South Pacific

The Eastern Tropical South Pacific is one of the three major oxygen deficient zones (ODZs) in the global ocean and is responsible for approximately one third of marine water column nitrogen loss. It is the best studied of the ODZs and, like the others, features a broad nitrite maximum across the low oxygen layer. How the microbial processes that produce and consume nitrite in anoxic waters interact to sustain this feature is unknown. Here we used 15N-tracer experiments to disentangle five of the biologically mediated processes that control the nitrite pool, including a high-resolution profile of nitrogen loss rates. Nitrate reduction to nitrite likely depended on organic matter fluxes, but the organic matter did not drive detectable rates of denitrification to N2. However, multiple lines of evidence show that denitrification is important in shaping the biogeochemistry of this ODZ. Significant rates of anaerobic nitrite oxidation at the ODZ boundaries were also measured. Lodate was a potential oxidant that could support part of this nitrite consumption pathway. We additionally observed N2 production from labeled cyanate and postulate that anammox bacteria have the ability to harness cyanate as another form of reduced nitrogen rather than relying solely on ammonification of complex organic matter. The balance of the five anaerobic rates measured—anammox, denitrification, nitrate reduction, nitrite oxidation, and dissimilatory nitrite reduction to ammonium—is sufficient to reproduce broadly the observed nitrite and nitrate profiles in a simple one-dimensional model but requires an additional source of reduced nitrogen to the deeper ODZ to avoid ammonium overconsumption. ©2017. American Geophysical Union. All Rights Reserved

Long-term fertilization alters the relative importance of nitrate reduction pathways in salt marsh sediments

Salt marshes provide numerous valuable ecological services. In particular, nitrogen (N) removal in salt marsh sediments alleviates N loading to the coastal ocean. N removal reduces the threat of eutrophication caused by increased N inputs from anthropogenic sources. It is unclear, however, whether chronic nutrient over-enrichment alters the capacity of salt marshes to remove anthropogenic N. To assess the effect of nutrient enrichment on N cycling in salt marsh sediments, we examined important N cycle pathways in experimental fertilization plots in a New England salt marsh. We determined rates of nitrification, denitrification, and dissimilatory nitrate reduction to ammonium (DNRA) using sediment slurry incubations with 15 N labeled ammonium or nitrate tracers under oxic headspace (20% oxygen / 80% helium). Nitrification and denitrification rates were more than ten-fold higher in fertilized plots compared to control plots. By contrast, DNRA, which retains N in the system, was high in control plots but not detected in fertilized plots. The relative contribution of DNRA to total nitrate reduction largely depends on the carbon/nitrate ratio in the sediment. These results suggest that long-term fertilization shifts N cycling in salt marsh sediments from predominantly retention to removal. Long-term fertilization alters the relative importance of nitrate reduction pathways in salt marsh sediments: NO 3 - reduction in salt marsh sediments (PDF Download Available). Available from: https://www.researchgate.net/publication/305480944_Long-term_fertilization_alters_the_relative_importance_of_nitrate_reduction_pathways_in_salt_marsh_sediments_NO_3_-_reduction_in_salt_marsh_sediments [accessed Jun 6, 2017]