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


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


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


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


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


Pairing denitrifying woodchip bioreactors and phosphorus-sorbing filters provides a unique, engineered approach for dual nutrient removal from waters impaired with both nitrogen (N) and phosphorus (P). This column study aimed to test placement of two P-filter media (acid mine drainage treatment residuals and steel slag) relative to a denitrifying system to maximize N and P removal and minimize pollution swapping under varying flow conditions (i.e., woodchip column hydraulic retention times (HRTs) of 7.2, 18, and 51 h; P-filter HRTs of 7.6-59 min). Woodchip denitrification columns were placed either upstream or downstream of P-filters filled with either medium. The configuration with woodchip denitrifying systems placed upstream of the P-filters generally provided optimized dissolved P removal efficiencies and removal rates. The P-filters placed upstream of the woodchip columns exhibited better P removal than downstream-placed P-filters only under overly long (i.e., N-limited) retention times when highly reduced effluent exited the woodchip bioreactors. The paired configurations using mine drainage residuals provided significantly greater P removal than the steel slag P-filters (e.g., 25-133 versus 8.8-48 g P removed m(-3) filter media d(-1), respectively), but there were no significant differences in N removal between treatments (removal rates: 8.0-18 g N removed m(-3) woodchips d(-1); N removal efficiencies: 18-95% across all HRTs). The range of HRTs tested here resulted in various undesirable pollution swapping by-products from the denitrifying bioreactors: nitrite production when nitrate removal was not complete and sulfate reduction, chemical oxygen demand production and decreased pH during overly long retention times. The downstream P-filter placement provided a polishing step for removal of chemical oxygen demand and nitrite.

Concepts: Eutrophication, Redox, Biotechnology, Nitrogen, Denitrification, Acid mine drainage, Nitrogen cycle, Slag


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, Nitrous oxide, Greenhouse gas, Denitrification, Internal combustion engine, Nitrogen cycle


Abiotic stresses impact negatively on plant growth, profoundly affecting yield and quality of crops. Although much is known about plant responses, very little is understood at the molecular level about the initial sensing of environmental stress. In plants, hypoxia (low oxygen, which occurs during flooding) is directly sensed by the Cys-Arg/N-end rule pathway of ubiquitin-mediated proteolysis, through oxygen-dependent degradation of group VII Ethylene Response Factor transcription factors (ERFVIIs) via amino-terminal (Nt-) cysteine [1, 2]. Using Arabidopsis (Arabidopsis thaliana) and barley (Hordeum vulgare), we show that the pathway regulates plant responses to multiple abiotic stresses. In Arabidopsis, genetic analyses revealed that response to these stresses is controlled by N-end rule regulation of ERFVII function. Oxygen sensing via the Cys-Arg/N-end rule in higher eukaryotes is linked through a single mechanism to nitric oxide (NO) sensing [3, 4]. In plants, the major mechanism of NO synthesis is via NITRATE REDUCTASE (NR), an enzyme of nitrogen assimilation [5]. Here, we identify a negative relationship between NR activity and NO levels and stabilization of an artificial Nt-Cys substrate and ERFVII function in response to environmental changes. Furthermore, we show that ERFVIIs enhance abiotic stress responses via physical and genetic interactions with the chromatin-remodeling ATPase BRAHMA. We propose that plants sense multiple abiotic stresses through the Cys-Arg/N-end rule pathway either directly (via oxygen sensing) or indirectly (via NO sensing downstream of NR activity). This single mechanism can therefore integrate environment and response to enhance plant survival.

Concepts: Photosynthesis, Oxygen, Plant, Nitrogen, Arabidopsis thaliana, Arabidopsis, Annual plant, Nitrogen cycle


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


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