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Concept: Nitrogen cycle


Agricultural soils represent the main source of anthropogenic N2O emissions. Recently, interactions of black carbon with the nitrogen cycle have been recognized and the use of biochar is being investigated as a means to reduce N2O emissions. However, the mechanisms of reduction remain unclear. Here we demonstrate the significant impact of biochar on denitrification, with a consistent decrease in N2O emissions by 10-90% in 14 different agricultural soils. Using the (15)N gas-flux method we observed a consistent reduction of the N2O/(N2 + N2O) ratio, which demonstrates that biochar facilitates the last step of denitrification. Biochar acid buffer capacity was identified as an important aspect for mitigation that was not primarily caused by a pH shift in soil. We propose the function of biochar as an “electron shuttle” that facilitates the transfer of electrons to soil denitrifying microorganisms, which together with its liming effect would promote the reduction of N2O to N2.

Concepts: PH, Metabolism, Bioremediation, Buffer solution, Carbon dioxide, Nitrogen cycle, Denitrification, Nitrogen


Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially-mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups contributing to nitrogen cycling and a reproducible network of decomposers that emerge on predictable timescales. The results show this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development and the process of decomposition is sufficiently reproducible that it offers unique opportunities for forensic investigations.

Concepts: Denitrification, Embalming, Nitrogen cycle, Enzyme, Bacteria, Oxygen, Metabolism, Nitrogen


Human activities have doubled the pre-industrial supply of reactive nitrogen on Earth, and future rates of increase are expected to accelerate. Yet little is known about the capacity of the biosphere to buffer increased nitrogen influx. Past changes in global ecosystems following deglaciation at the end of the Pleistocene epoch provide an opportunity to understand better how nitrogen cycling in the terrestrial biosphere responded to changes in carbon cycling. We analysed published records of stable nitrogen isotopic values (δ(15)N) in sediments from 86 lakes on six continents. Here we show that the value of sedimentary δ(15)N declined from 15,000 years before present to 7,056 ± 597 years before present, a period of increasing atmospheric carbon dioxide concentrations and terrestrial carbon accumulation. Comparison of the nitrogen isotope record with concomitant carbon accumulation on land and nitrous oxide in the atmosphere suggests millennia of declining nitrogen availability in terrestrial ecosystems during the Pleistocene-Holocene transition around 11,000 years before present. In contrast, we do not observe a consistent change in global sedimentary δ(15)N values during the past 500 years, despite the potential effects of changing temperature and nitrogen influx from anthropogenic sources. We propose that the lack of a single response may indicate that modern increases in atmospheric carbon dioxide and net carbon sequestration in the biosphere have the potential to offset recent increased supplies of reactive nitrogen in some ecosystems.

Concepts: Quaternary, Oxide, Nitrogen cycle, Earth, Holocene calendar, Nitrogen, Oxygen, Carbon dioxide


This study attempts to elucidate the emission sources and mechanisms of nitrous oxide (N2O) during simultaneous nitrification and denitrification (SND) process under oxygen-limiting condition. The results indicated that N2O emitted during low-oxygen SND process was 0.8±0.1mgN/gMLSS, accounting for 7.7% of the nitrogen input. This was much higher than the reported results from conventional nitrification and denitrification processes. Batch experiments revealed that nitrifier denitrification was attributed as the dominant source of N2O production. This could be well explained by the change of ammonia-oxidizing bacteria (AOB) community caused by the low-oxygen condition. It was observed that during the low-oxygen SND process, AOB species capable of denitrification, i.e., Nitrosomonas europaea and Nitrosomonas-like, were enriched whilst the composition of denitrifiers was only slightly affected. N2O emission by heterotrophic denitrification was considered to be limited by the presence of oxygen and unavailability of carbon source.

Concepts: Nitrogen dioxide, Carbon dioxide, Oxygen, Nitrous oxide, Nitrogen cycle, Denitrification, Bacteria, Nitrogen


The intensive application of fertilizers during agricultural practices has led to an unprecedented perturbation of the nitrogen cycle, illustrated by the growing accumulation of nitrates in soils and waters, and of nitrogen oxides in the atmosphere. Besides increasing use efficiency of current N fertilizers, priority should be given to put on value the process of biological nitrogen fixation, through more sustainable technologies that reduce the undesired effects of chemical N fertilization of agricultural crops. Wider legume adoption, supported by coordinated legume breeding and inoculation programs are approaches at hand. Also available are biofertilizers based on microbes that help to reduce the needs of N fertilization in important crops like cereals. Engineering in cereals the capacity to fix nitrogen, either by themselves or in symbiosis with nitrogen-fixing microbes, are attractive future options that nevertheless require more intensive and internationally coordinated research efforts. Although nitrogen-fixing plants may be less productive, at some point agriculture must significantly reduce the use of warming (chemically synthesized) N and give priority to the biological nitrogen fixation, if it is to sustain both food production and environmental health for a continuously growing human population.

Concepts: Fertilizer, Denitrification, Nitrification, Nitrogen cycle, Ammonia, Agriculture, Nitrogen fixation, Nitrogen


Removal of excess nitrogen (N) can best be achieved through denitrification processes that transform N in water and terrestrial ecosystems to di-nitrogen (N2) gas. The greenhouse gas nitrous oxide (N2O) is considered an intermediate or end-product in denitrification pathways. Both abiotic and biotic denitrification processes use a single N source to form N2O. However, N2 can be formed from two distinct N sources (known as hybrid N2) through biologically mediated processes of anammox and codenitrification. We questioned if hybrid N2 produced during fungal incubation at neutral pH could be attributed to abiotic nitrosation and if N2O was consumed during N2 formation. Experiments with gas chromatography indicated N2 was formed in the presence of live and dead fungi and in the absence of fungi, while N2O steadily increased. We used isotope pairing techniques and confirmed abiotic production of hybrid N2 under both anoxic and 20% O2 atmosphere conditions. Our findings question the assumptions that (1) N2O is an intermediate required for N2 formation, (2) production of N2 and N2O requires anaerobiosis, and (3) hybrid N2 is evidence of codenitrification and/or anammox. The N cycle framework should include abiotic production of N2.

Concepts: Carbon dioxide, Biology, Nitrogen cycle, Internal combustion engine, Denitrification, Greenhouse gas, Nitrous oxide, Nitrogen


It has been hypothesized that nitrogen fixation occurs in the human gut. However, whether the gut microbiota truly has this potential remains unclear. We investigated the nitrogen-fixing activity and diversity of the nitrogenase reductase (NifH) genes in the faecal microbiota of humans, focusing on Papua New Guinean and Japanese individuals with low to high habitual nitrogen intake. A (15)N2 incorporation assay showed significant enrichment of (15)N in all faecal samples, irrespective of the host nitrogen intake, which was also supported by an acetylene reduction assay. The fixed nitrogen corresponded to 0.01% of the standard nitrogen requirement for humans, although our data implied that the contribution in the gut in vivo might be higher than this value. The nifH genes recovered in cloning and metagenomic analyses were classified in two clusters: one comprising sequences almost identical to Klebsiella sequences and the other related to sequences of Clostridiales members. These results are consistent with an analysis of databases of faecal metagenomes from other human populations. Collectively, the human gut microbiota has a potential for nitrogen fixation, which may be attributable to Klebsiella and Clostridiales strains, although no evidence was found that the nitrogen-fixing activity substantially contributes to the host nitrogen balance.

Concepts: Nitrogen cycle, Molybdenum, Bacteria, Nitrogen fixation, Nitrogenase, Rhizobia, Nitrogen, Gut flora


Reactive nitrogen species have a strong influence on atmospheric chemistry and climate, tightly coupling the Earth’s nitrogen cycle with microbial activity in the biosphere. Their sources, however, are not well constrained, especially in dryland regions accounting for a major fraction of the global land surface. Here, we show that biological soil crusts (biocrusts) are emitters of nitric oxide (NO) and nitrous acid (HONO). Largest fluxes are obtained by dark cyanobacteria-dominated biocrusts, being ∼20 times higher than those of neighboring uncrusted soils. Based on laboratory, field, and satellite measurement data, we obtain a best estimate of ∼1.7 Tg per year for the global emission of reactive nitrogen from biocrusts (1.1 Tg a(-1) of NO-N and 0.6 Tg a(-1) of HONO-N), corresponding to ∼20% of global nitrogen oxide emissions from soils under natural vegetation. On continental scales, emissions are highest in Africa and South America and lowest in Europe. Our results suggest that dryland emissions of reactive nitrogen are largely driven by biocrusts rather than the underlying soil. They help to explain enigmatic discrepancies between measurement and modeling approaches of global reactive nitrogen emissions. As the emissions of biocrusts strongly depend on precipitation events, climate change affecting the distribution and frequency of precipitation may have a strong impact on terrestrial emissions of reactive nitrogen and related climate feedback effects. Because biocrusts also account for a large fraction of global terrestrial biological nitrogen fixation, their impacts should be further quantified and included in regional and global models of air chemistry, biogeochemistry, and climate.

Concepts: Nitrogen fixation, Precipitation, Nitrogen cycle, Nitric acid, Nitric oxide, Dinitrogen trioxide, Earth, Nitrogen


Nitrogen stable isotope ratio (δ(15)N) in Greenland snow nitrate and in North American remote lake sediments has decreased gradually beginning as early as ∼1850 Christian Era. This decrease was attributed to increasing atmospheric deposition of anthropogenic nitrate, reflecting an anthropogenic impact on the global nitrogen cycle, and the impact was thought to be amplified ∼1970. However, our subannually resolved ice core records of δ(15)N and major ions (e.g., $$\mathrm{N}{\mathrm{O}}_{\mathrm{3}}^{-}$$, $$\mathrm{S}{\mathrm{O}}_{4}^{2-}$$) over the last ∼200 y show that the decrease in δ(15)N is not always associated with increasing $$\mathrm{N}{\mathrm{O}}_{\mathrm{3}}^{-}$$ concentrations, and the decreasing trend actually leveled off ∼1970. Correlation of δ(15)N with H(+), $$\mathrm{N}{\mathrm{O}}_{\mathrm{3}}^{-}$$, and HNO3 concentrations, combined with nitrogen isotope fractionation models, suggests that the δ(15)N decrease from ∼1850-1970 was mainly caused by an anthropogenic-driven increase in atmospheric acidity through alteration of the gas-particle partitioning of atmospheric nitrate. The concentrations of $$\mathrm{N}{\mathrm{O}}_{\mathrm{3}}^{-}$$ and $$\mathrm{S}{\mathrm{O}}_{4}^{2-}$$ also leveled off ∼1970, reflecting the effect of air pollution mitigation strategies in North America on anthropogenic NOx and SO2 emissions. The consequent atmospheric acidity change, as reflected in the ice core record of H(+) concentrations, is likely responsible for the leveling off of δ(15)N ∼1970, which, together with the leveling off of $$\mathrm{N}{\mathrm{O}}_{\mathrm{3}}^{-}$$ concentrations, suggests a regional mitigation of anthropogenic impact on the nitrogen cycle. Our results highlight the importance of atmospheric processes in controlling δ(15)N of nitrate and should be considered when using δ(15)N as a source indicator to study atmospheric flux of nitrate to land surface/ecosystems.

Concepts: Oxygen, Isotopes, Greenland, Ammonia, Eutrophication, Ice core, North America, Nitrogen cycle


The processes that convert bioavailable inorganic nitrogen to inert nitrogen gas are prominent in continental shelf sediments and represent a critical global sink, yet little is known of these pathways in the Arctic where 18% of the world’s continental shelves are located. Moreover, few data from the Arctic exist that separate loss processes like denitrification and anaerobic ammonium oxidation (anammox) from recycling pathways like dissimilatory nitrate reduction to ammonium (DNRA) or source pathways like nitrogen fixation. Here we present measurements of these co-occurring processes using (15)N tracers. Denitrification was heterogeneous among stations and an order of magnitude greater than anammox and DNRA, while nitrogen fixation was undetectable. No abiotic factors correlated with interstation variability in biogeochemical rates; however, bioturbation potential explained most of the variation. Fauna-enhanced denitrification is a potentially important but overlooked process on Arctic shelves and highlights the role of the Arctic as a significant global nitrogen sink.

Concepts: Ammonia, Nitrogen metabolism, Metabolism, Nitrogen fixation, Redox, Nitrogen cycle, Denitrification, Nitrogen