Nitrite in soils: accumulation and role in the formation of gaseous N compounds

LC-IRMS Persulfate Oxidation: Case Study on Neonicotinoid-Related Structures

RATIONALE

Liquid chromatography-isotope ratio mass spectrometry (LC-IRMS) is used to analyze stable carbon isotope ratios of polar nonvolatile compounds. However, challenges with the persulfate-based oxidation interface have been reported, particularly for molecules with recalcitrant structures like those found in neonicotinoids. This study systematically investigates the oxidation efficiency of neonicotinoid-related structures in a commercial LC-IRMS.

METHODS

Neonicotinoid proxies of varying molecular complexity were evaluated for carbon recovery and stable carbon isotope ratio accuracy. LC-IRMS parameters such as oxidant concentration, reaction time, temperature, acid concentration, and the presence of AgNO3 catalyst were varied. Carbon recoveries and δ13C biases were determined by injecting an oxidation-independent inorganic carbon standard under identical conditions. Elemental analyzer isotope ratio mass spectrometry (EA-IRMS) was used to normalize δ13C values.

RESULTS

Several neonicotinoid derivatives exhibited low carbon recovery and significant δ13C bias. Increasing oxidant concentration, reactor temperature, and reaction time improved recoveries but did not fully mitigate isotopic biases. The addition of AgNO3 improved carbon recoveries for most derivatives but introduced variability in δ13C values, likely due to shifts in reaction mechanisms. A workflow to identify oxidation problems during method development was proposed.

CONCLUSIONS

Optimization of LC-IRMS oxidation parameters is critical for urea, guanidine, and nitroguanidine derivatives and similar compounds. A systematic evaluation of oxidation efficiencies under different conditions is needed for optimal mineralization and thus more accurate δ13C ratios.

Linked nitrogen and carbon dynamics reveal distinct pools and patterns in a deep, weathered bedrock rhizosphere

Nitrogen is one of the most limiting nutrients to forest productivity worldwide. Recently, it has been established that diverse ecosystems source a substantial fraction of their water from weathered bedrock, leading to questions about whether root-driven nitrogen cycling extends into weathered bedrock as well. In this study, we specifically examined nitrogen dynamics using specialized instrumentation distributed across a 16 m weathered bedrock vadose zone (WBVZ) underlying an old growth forest in northern California where the rhizosphere-composed of plant roots and their associated microbiome-extends meters into rock. We documented total dissolved nitrogen (TDN), dissolved organic carbon (DOC), inorganic nitrogen (ammonium and nitrate), and CO2 and O2 gases every 1.5 m to 16 m depth for 2 y. We found that TDN concentrations increased with depth, were an order of magnitude greater at 15 m than in the upper 30 cm, and that the majority of TDN throughout the weathered bedrock vadose zone was organic. We also found that TDN concentrations are influenced by depth, season, and interannual precipitation patterns. Carbon isotope composition of the DOC suggests that dissolved organic matter in the WBVZ is primarily derived from plant sources, and not the nitrogen-rich bedrock. We conclude that nitrogen dynamics in the WBVZ may be driven, in part, by an active rhizosphere, meters below the base of soil, and we argue that weathered bedrock horizons may play a key role in C-N cycling in ecosystems with deep-rooted plants.

Bacterial community assembly processes mediate soil functioning under cadmium stress in the agroecosystem

Elucidating the effects of community assembly processes on soil functioning represents a crucial challenge in theoretical ecology, particularly under cadmium (Cd) stress, where our understanding remains limited. In this study, we therefore used amplicon sequencing and a quantitative-PCR-based chip to analyze the changes in bacterial community characteristics, soil functioning and their interrelationships in agroecosystems under different levels of Cd stress. The results indicated that Cd stress led to a decline in community diversity (Z-score), network complexity and stability, an increase in species turnover, and a regulation of community structure. Cd stress significantly increased the relative importance of dispersal limitation and homogeneous selection, reducing community drift and rendering the community more deterministic. Finally, Cd stress significantly reduced soil functional potential (Z-score) and soil functional stability (Z-score), impairing soil carbon, nitrogen, phosphorus, and sulfur cycling. It is noteworthy that correlation and random forest analyses revealed significant effects of specific community assembly processes, including dispersal limitation, homogeneous selection, drift (and others), on changes in soil functional potential (Z-score). The results emphasize the pivotal role of community assembly processes in dictating soil functioning under Cd stress, thereby offering novel insights into the comprehension of microbial-driven mechanisms governing soil functioning.

Application of a portable ion chromatograph for real-time field analysis of nitrite and nitrate in soils and soil pore waters

Real-time monitoring of nitrite and nitrate is crucial for maintaining soil health and promoting plant growth. In this study, a portable ion-chromatograph (IC, Aquamonitrix) analyser, coupled with a field-applicable ultrasonic-assisted extraction method, was utilised for in-field determination of nitrate and nitrite in soils. This is the first application of this type of analyser to soil nutrients. On-site analysis of soil from a local sports field showed 94.8 ± 4.3 μg g-1 nitrate, with LODs of 32.0 μg g-1 for nitrate and 5.4 μg g-1 for nitrite. The results were in close agreement with those obtained using a conventional lab-based IC. Relative standard deviations (%RSDs) for soil analysis using Aquamonitrix were consistently below 10%. The obtained average recoveries of samples spiked with nitrite were 100% and 104% for the portable IC and conventional IC, respectively. Furthermore, to assess the suitability of portable IC for samples with high organic matter content, various natural organic fertilisers were extracted and analysed. The results showed 16.2 ± 0.7 μg g-1 nitrite and 28.5 ± 5.6 μg g-1 nitrate in sheep manure samples with LODs of 2.0 μg g-1 for nitrite and 12.0 μg g-1 for nitrate. The portable IC system was further demonstrated via real-time on-site analysis of soil pore-water acquired using a portable battery-based ceramic pore-water sampler. A continuous increase in nitrate concentration over time was observed (from 80 to 148 μg mL-1) in the soil pore-water in a vegetable garden four days after heavy rain. Unlike conventionally sampled natural waters, 7-day storage of the studied pore water samples revealed no changes in nitrate concentrations. An average of 558 ± 51 μg mL-1 nitrate was detected in the soil pore-water samples analysed on a spinach farm, immediately after irrigation.

Urea amendment decouples nitrification in hydrocarbon contaminated Antarctic soil

Hydrocarbon contaminated soils resulting from human activities pose a risk to the natural environment, including in the Arctic and Antarctic. Engineered biopiles constructed at Casey Station, Antarctica, have proven to be an effective strategy for remediating hydrocarbon contaminated soils, with active ex-situ remediation resulting in significant reductions in hydrocarbons, even in the extreme Antarctic climate. However, the use of urea-based fertilisers, whilst providing a nitrogen source for bioremediation, has also altered the natural soil chemistry leading to increases in pH, ammonium and nitrite. Monitoring of the urea amended biopiles identified rising levels of nitrite to be of particular interest, which misaligns with the long term goal of reducing contaminant levels and returning soil communities to a 'healthy' state. Here, we combine amplicon sequencing, microfluidic qPCR on field samples and laboratory soil microcosms to assess the impact of persistent nitrite accumulation (up to 60 months) on nitrifier abundances observed within the Antarctic biopiles. Differential inhibition of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) Nitrobacter and Nitrospira in the cold, urea treated, alkaline soils (pH 8.1) was associated with extensive nitrite accumulation (76 ± 57 mg N/kg at 60 months). When the ratio of Nitrospira:AOB dropped below ∼1:1, Nitrobacter was completely inhibited or absent from the biopiles, and nitrite accumulated. Laboratory soil microcosms (incubated at 7 °C and 15 °C for 9 weeks) reproduced the pattern of nitrite accumulation in urea fertilized soil at the lower temperature, consistent with our longer-term observations from the Antarctic biopiles, and with other temperature-controlled microcosm studies. Diammonium phosphate amended soil did not exhibit nitrite accumulation, and could be a suitable alternative biostimulant to avoid excessive nitrite build-up.

Methane-dependent complete denitrification by a single Methylomirabilis bacterium

Methane-dependent nitrate and nitrite removal in anoxic environments is thought to rely on syntrophy between ANME-2d archaea and bacteria in the genus 'Candidatus Methylomirabilis'. Here we enriched and purified a single Methylomirabilis from paddy soil fed with nitrate and methane, which is capable of coupling methane oxidation to nitrate reduction via nitrite to dinitrogen independently. Isotope labelling showed that this bacterium we name 'Ca. Methylomirabilis sinica' stoichiometrically performed methane-dependent complete nitrate reduction to dinitrogen gas. Multi-omics analyses collectively demonstrated that 'M. sinica' actively expressed a well-established pathway for this process, especially including nitrate reductase Nap. Furthermore, 'M. sinica' exhibited a higher nitrate affinity than most denitrifiers, implying its competitive fitness under oligotrophic nitrogen-limited conditions. Our findings revise the paradigm of methane-dependent denitrification performed by two organisms, and the widespread presence of 'M. sinica' in public databases suggests that the coupling of methane oxidation and complete denitrification in single cells substantially contributes to global methane and nitrogen budgets.

Does the application of biogas slurry reduce soil N2O emissions and increase crop yield?-A systematic review

The use of organic fertilizer for agricultural production can reduce the use of chemical fertilizer (CF), reduce greenhouse gas emissions, and maintain crop production. However, biogas slurry (BS), a liquid with a high moisture content and a low C/N ratio, differs from commercial organic fertilizer and manure in terms of its impact on the soil N cycle. Replacing CF with BS needs to be reconsidered regarding soil nitrous oxide (N₂O) emissions and crop production in terms of fertilization, agricultural land type, and soil characteristics. For this systematic review, the results of 92 published studies worldwide were collected. Based on the findings, the combined application of BS and CF can significantly increase soil total N (TN), microbial biomass N (MBN), and soil organic matter (SOM) levels. The Chaol and ACE index values of soil bacteria were increased by 13.58% and 18.53%, whereas those of soil fungi were decreased by 10.45% and 14.53%, respectively. At a replacement ratio (rr) ≤ 70%, crop yield was promoted by 2.20%-12.17%, and soil N₂O emissions were reduced by 1.94%-21.81%. A small rr (≤30%) was more conducive to growth, and a moderate rr (30% < rr ≤ 70%) was more favorable for N₂O emission reduction, especially in the dryland crop system. However, at rr = 100%, soil N₂O emissions in neutral and alkaline dryland soil were increased by 28.56%-32.22%. The importance analysis of the influencing factors showed that the proportion of BS, the N application rate, and the temperature were the factors affecting soil N₂O emissions. Our results provide a scientific basis for the safe use of BS in agricultural systems.

Unchanged nitrate and nitrite isotope fractionation during heterotrophic and Fe(II)-mixotrophic denitrification suggest a non-enzymatic link between denitrification and Fe(II) oxidation

Natural-abundance measurements of nitrate and nitrite (NO_x) isotope ratios (δ¹⁵N and δ¹⁸O) can be a valuable tool to study the biogeochemical fate of NO_x species in the environment. A prerequisite for using NO_x isotopes in this regard is an understanding of the mechanistic details of isotope fractionation (¹⁵ε, ¹⁸ε) associated with the biotic and abiotic NO_x transformation processes involved (e.g., denitrification). However, possible impacts on isotope fractionation resulting from changing growth conditions during denitrification, different carbon substrates, or simply the presence of compounds that may be involved in NO_x reduction as co-substrates [e.g., Fe(II)] remain uncertain. Here we investigated whether the type of organic substrate, i.e., short-chained organic acids, and the presence/absence of Fe(II) (mixotrophic vs. heterotrophic growth conditions) affect N and O isotope fractionation dynamics during nitrate (NO₃^–) and nitrite (NO₂^–) reduction in laboratory experiments with three strains of putative nitrate-dependent Fe(II)-oxidizing bacteria and one canonical denitrifier. Our results revealed that ¹⁵ε and ¹⁸ε values obtained for heterotrophic (¹⁵ε-NO₃^–: 17.6 ± 2.8‰, ¹⁸ε-NO₃^–:18.1 ± 2.5‰; ¹⁵ε-NO₂^–: 14.4 ± 3.2‰) vs. mixotrophic (¹⁵ε-NO₃^–: 20.2 ± 1.4‰, ¹⁸ε-NO₃^–: 19.5 ± 1.5‰; ¹⁵ε-NO₂^–: 16.1 ± 1.4‰) growth conditions are very similar and fall within the range previously reported for classical heterotrophic denitrification. Moreover, availability of different short-chain organic acids (succinate vs. acetate), while slightly affecting the NO_x reduction dynamics, did not produce distinct differences in N and O isotope effects. N isotope fractionation in abiotic controls, although exhibiting fluctuating results, even expressed transient inverse isotope dynamics (¹⁵ε-NO₂^–: –12.4 ± 1.3 ‰). These findings imply that neither the mechanisms ordaining cellular uptake of short-chain organic acids nor the presence of Fe(II) seem to systematically impact the overall N and O isotope effect during NO_x reduction. The similar isotope effects detected during mixotrophic and heterotrophic NO_x reduction, as well as the results obtained from the abiotic controls, may not only imply that the enzymatic control of NO_x reduction in putative NDFeOx bacteria is decoupled from Fe(II) oxidation, but also that Fe(II) oxidation is indirectly driven by biologically (i.e., via organic compounds) or abiotically (catalysis via reactive surfaces) mediated processes co-occurring during heterotrophic denitrification.

Dirammox Is Widely Distributed and Dependently Evolved in Alcaligenes and Is Important to Nitrogen Cycle

Nitrogen cycle is an essential process for environmental health. Dirammox (direct ammonia oxidation), encoded by the dnfT1RT2ABCD cluster, was a novel pathway for microbial N2 production defined in Alcaligenes ammonioxydans HO-1. Here, a copy of the cluster dnfT1RT2ABCD as a whole was proved to have existed and very conserved in all Alcaligenes genomes. Phylogenetic analyses based on 16S rRNA gene sequences and amino acid sequences of DnfAs, together with G + C content data, revealed that dnf cluster was evolved associated with the members of the genus Alcaligenes. Under 20% O2 conditions, 14 of 16 Alcaligenes strains showed Dirammox activity, which seemed likely taxon-related. However, the in vitro activities of DnfAs catalyzing the direct oxidation of hydroxylamine to N2 were not taxon-related but depended on the contents of Fe and Mn ions. The results indicated that DnfA is necessary but not sufficient for Dirammox activity. The fact that members of the genus Alcaligenes are widely distributed in various environments, including soil, water bodies (both freshwater and seawater), sediments, activated sludge, and animal-plant-associated environments, strongly suggests that Dirammox is important to the nitrogen cycle. In addition, Alcaligenes species are also commonly found in wastewater treatment plants, suggesting that they might be valuable resources for wastewater treatment.

Role of chemical reactions in the nitrogenous trace gas emissions and nitrogen retention: A meta-analysis

Increasing evidence has been found that chemical reactions affect significantly the terrestrial nitrogen (N) cycle, which was previously assumed to be mainly dominated by biological processes. Due to the limitation of knowledge and analytical techniques, it is currently challenging to discern the contribution of biotic and abiotic processes to the terrestrial N cycle for geobiologists and biogeochemists alike. To better understand the role of abiotic reactions in the terrestrial N cycle, it is necessary to comprehend the chemical controls on nitrogenous trace gas emissions and N retention in soil under various environmental conditions. In this manuscript, we assess the role of abiotic reactions in nitrous oxide (N₂O) and nitric oxide (NO) emissions as well as N retention through a meta-analysis using all related peer-reviewed publications before August 2020. Results show that abiotic reactions contributed 29.3-37.7% and 44.0-57.0% to the total N₂O emission and N retention, representing 3.7-4.7 and 4.0-6.0 Tg year^-1 of global terrestrial N₂O emission and N retention, respectively. Much higher NO production was observed in sterilized soils than that in unsterilized treatments indicating the major contribution of chemical reactions to NO emission and rapid microbial reduction of NO to N₂O and N₂. Chemical hydroxylamine oxidation accounts for the largest abiotic contribution to N₂O emission, while chemical nitrite reduction and fixation represent for the largest contribution to abiotic NO production and soil N retention, respectively. Factors influencing the abiotic processes include pH, total organic carbon (TOC), total nitrogen (TN), the ratio of carbon to nitrogen (C/N), and transition metals. These results broadened our knowledge about the mechanisms involved in chemical N reactions and provided a simplified estimation about their contribution to nitrogenous trace gas emission and N retention, which is meaningful to further study interactions of biologically and chemically mediated reactions in biogeochemical N cycle.

Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N2O emissions and nitrite accumulation in soil

Soil pH is a key controller of denitrification. We analysed the metagenomics/transcriptomics and phenomics of two soils from a long-term liming experiment, SoilN (pH 6.8) and un-limed SoilA (pH 3.8). SoilA had severely delayed N2O reduction despite early transcription of nosZ (mainly clade I), encoding N2O reductase, by diverse denitrifiers. This shows that post-transcriptionally hampered maturation of the NosZ apo-protein at low pH is a generic phenomenon. Identification of transcript reads of several accessory genes in the nos cluster indicated that enzymes for NosZ maturation were present across a range of organisms, eliminating their absence as an explanation for the failure to produce a functional enzyme. nir transcript abundances (for NO2- reductase) in SoilA suggest that low NO2- concentrations in acidic soils, often ascribed to abiotic degradation, are primarily due to biological activity. The accumulation of NO2- in neutral soil was ascribed to high nar expression (nitrate reductase). The -omics results revealed dominance of nirK over nirS in both soils while qPCR showed the opposite, demonstrating that standard primer pairs only capture a fraction of the nirK pool. qnor encoding NO reductase was strongly expressed in SoilA, implying an important role in controlling NO. Production of HONO, for which some studies claim higher, others lower, emissions from NO2- accumulating soil, was estimated to be ten times higher from SoilA than from SoilN. The study extends our understanding of denitrification-driven gas emissions and the diversity of bacteria involved and demonstrates that gene and transcript quantifications cannot always reliably predict community phenotypes.

Biogas slurry application could potentially reduce N2O emissions and increase crop yield

The huge excrement quantity from the increasing large-scale livestock stressed the ecological, environmental deterioration. As a major benefit for handling livestock manure, the slurry of biogas (BS) is developed during the production of biogas that might increase plant productivity. However, nitrous oxide (N₂O) emissions from BS are considered a significant danger to the environment due to global warming potential. Furthermore, applying different proportions of BS combined with chemical fertilizer (CF) on N₂O productions in the North China Plain (NCP) remains unclear. Herein, two sequential field trials were performed by maize-wheat rotations to substitute the CF by BS and reduce N₂O emissions while keeping the crop yield stable. Four treatments were conducted, including T1, T3, T6, and CK. A total of 226.5 kg N ha^-1 used in the maize-wheat rotation system. Additionally, different ratios of BS (100%, 80%, and 50%) combined with CF were used in wheat season in the tillering stage. Results showed integrated applications of BS with CF have potential for reducing N₂O emission. Our findings showed that the maximum grain yield of CF was 6250 kg ha^-1, which might be achieved by applying 38% BS and 62% of CF. This ratio yielded 1.03 kg ha^-1 N₂O emissions, which was 15% lesser than the N₂O emission of CK, 1.21 kg ha^-1. Considering whole growing period of wheat biogas treatments significantly reduced the cumulative N₂O emissions from 17% to 26% compared to CF. To achieve maximum yield and minimum N₂O emissions, an optimum 38% BS ratio has been suggested. The integrated use of BS and CF provided the greatest grain yield because of necessary nutrients provided by both slurry and CF. Consequently, N₂O emissions reduced based on frequency and type of fertilizer. In conclusion, 38% ratio of BS combined with 62% CF would be a suitable approach to mitigate N₂O emission and simultaneously increase crop yield in NCP.

Microbial Communities and Interactions of Nitrogen Oxides With Methanogenesis in Diverse Peatlands of the Amazon Basin

Tropical peatlands are hotspots of methane (CH₄) production but present high variation and emission uncertainties in the Amazon region. This is because the controlling factors of methane production in tropical peats are not yet well documented. Although inhibitory effects of nitrogen oxides (NO_x) on methanogenic activity are known from pure culture studies, the role of NO_x in the methane cycling of peatlands remains unexplored. Here, we investigated the CH₄ content, soil geochemistry and microbial communities along 1-m-soil profiles and assessed the effects of soil NO_x and nitrous oxide (N₂O) on methanogenic abundance and activity in three peatlands of the Pastaza-Marañón foreland basin. The peatlands were distinct in pH, DOC, nitrate pore water concentrations, C/N ratios of shallow soils, redox potential, and ¹³C enrichment in dissolved inorganic carbon and CH₄ pools, which are primarily contingent on H₂-dependent methanogenesis. Molecular 16S rRNA and mcrA gene data revealed diverse and novel methanogens varying across sites. Importantly, we also observed a strong stratification in relative abundances of microbial groups involved in NO_x cycling, along with a concordant stratification of methanogens. The higher relative abundance of ammonia-oxidizing archaea (Thaumarchaeota) in acidic oligotrophic peat than ammonia-oxidizing bacteria (Nitrospira) is noteworthy as putative sources of NO_x. Experiments testing the interaction of NO_x species and methanogenesis found that the latter showed differential sensitivity to nitrite (up to 85% reduction) and N₂O (complete inhibition), which would act as an unaccounted CH₄ control in these ecosystems. Overall, we present evidence of diverse peatlands likely differently affected by inhibitory effects of nitrogen species on methanogens as another contributor to variable CH₄ fluxes.

Application of acidic conditions and inert-gas sparging to achieve high-efficiency nitrous oxide recovery during nitrite denitrification

Nitrogen removal with energy recovery through denitrification dependent N₂O production is garnering recent attention due to its cost advantages. The most effective current method requires alternating COD and nitrite to achieve high N₂O production making it incompatible with typical wastewaters and consequently difficult to use in most settings. The work described here introduces a robust and highly efficient N₂O recovery approach which has the potential to work with wastewaters containing COD and nitrite simultaneously. This method relies on low pH incubation and inert gas sparging (IGS) to shift a community of mainly N₂ producing nitrite denitrifiers to a community that accumulates N₂O when incubated in the absence of IGS. Before experiencing IGS, samples from activated sludge incubated at a pH of 4.5 and 6.0 only achieved a maximum N₂O production efficiency (PE_N₂O) of ∼26%. After IGS the PE_N₂O values increased to ∼97.5% and ∼80.2% for samples from these same pH 4.5 and pH 6.0 reactors, respectively. IGS did not lead to N₂O production in a pH 7.5 bioreactor. Meta-omics analysis revealed that IGS resulted in an increase in bacteria utilizing the clade I nitrous oxide reductase (nosZ_I) relative to bacteria utilizing the clade II nitrous oxide reductase (nosZ_II). This likely results from IGS flushing out N₂O leaving nitrite as the principal nitrogen oxide available for respiration, favoring nosZ_I utilizing bacteria which are more likely to be complete denitrifiers. Metatranscriptomic analysis suggested that the high PE_N₂O values that occurred after stopping IGS result from the NO generated by chemodenitrification accumulating to levels that inactivate [4Fe:4S] clusters in the NosR protein essential for N₂O reduction in the nosZ_I denitrifiers. This study provides an efficient and straightforward method for N₂O recovery, widening the options for energy recovery from nitrogen-based wastes.

Evaluation of Effects of Municipal Sludge Leachates on Water Quality

Biosolids made from municipal sludge are an attractive solution instead of chemical fertilization. Nevertheless, their effects on the ecosystem should always be considered. In the present study, anaerobically digested sludge was subjected to two leaching methods (EN 12457-2 and NEN 7341) and the main physicochemical parameters were measured in the leachates. The aquatic organisms Daphnia magna and Vibrio fischeri were exposed to the leachates in order to test for adverse effects. Mixtures of biosolid/solid, simulating the high dose of 80 tn/ha, were also created, and the same parameters were measured for EN 12457-2 leachates. The results show a strong seasonal variation for the results for the municipal sludge, even though the sludge did not originate from a touristic area. The biosolid/solid mixtures did not produce toxic responses to the organism tested. Nevertheless, the parameters nitrites and nitrates in the leachates were increased in relation to control and they continued to increase even at Day 40 post-application. This increase was soil-type-dependent. The biosolids in question could be used for field fertilization, however measures should be taken against underground water nitrate pollution.

Dynamics of nitrite in acidic soil during extraction with potassium chloride studied using 15 N tracing

RATIONALE

Nitrite is well known to be unstable, including during soil extraction with KCl (especially in acidic soils), but the source and fate of NO₂ ^- in the short duration of the extraction process remain unclear.

METHODS

A series of ¹⁵ N-tracing studies explored NO₂ ^- transformations during KCl extraction in acidic and alkaline soils. Tests considering multiple factors assessed the interactions of such factors as soil sterilization, extraction time, and pH adjustment. After addition of ¹⁵ NO₂ ^- , ¹⁵ NH₄ ⁺ , and ¹⁵ NO₃ ^- tracers, the concentrations and isotopic compositions of N₂ O, N₂ , NH₄ ⁺ , NO₃ ^- , NO₂ ^- , and dissolved organic nitrogen (DON) were measured to investigate the production and consumption of NO₂ ^- .

RESULTS

Nitrite was stable in alkaline soils during KCl extraction. In contrast, changes did occur in acidic soils during KCl extraction: NO₂ ^- declined rapidly in the first 10 min of extraction although the subsequent rate of decrease lessened as the extraction time progressed. Significant dilution of ¹⁵ NO₂ ^- suggested high rates of NO₂ ^- production and even higher rates of consumption. The soil's organic N was the only source of NO₂ ^- and also its main destination. Soil sterilization showed that NO₂ ^- processes during extraction were chemical, not microbial. The pH adjustment of acidic soil stabilized its NO₂ ^- .

CONCLUSIONS

Overall, the pH adjustment of KCl solution appears favorable for investigating NO₂ ^- dynamics. For example, this work recommends an extraction solution comprising a 4:1 mixture of 2.5 M KCl solution and pH 8.4 buffer, which was more convenient to operate than the method reported by Stevens and Laughlin.

Crab Bioturbation and Seasonality Control Nitrous Oxide Emissions in Semiarid Mangrove Forests (Ceará, Brazil)

Seasonality and crab activity affects the nutrients and physicochemical parameters in mangrove soils, thus, affecting the emissions of greenhouse gases, such as nitrous oxide (N2O). Climate change may intensify rainfall and/or enhance droughts, affecting mangroves and associated biota. Crabs are natural soil bioturbators responsible for soil aeration and turnover. We evaluated the effect of Ucides cordatus crab on N2O emissions from mangrove soils under a semiarid climate in Northeastern Brazil. Soil and gas samples were collected over the rainy and dry seasons in crab-naturally-bioturbated and crab-exclusion mangrove plots. We measured the soil’s pH, redox potential, and the total contents of carbon, nitrogen, and sulfur. We found higher N2O emissions in the crab-exclusion sites compared to the bioturbated sites, as well as higher N2O emissions in the rainy season compared to the dry season. The fluxes of N2O (µg m−2 h−1) were 47.3 ± 9.7 and 8.9 ± 0.5 for the crab-exclusion sites, and 36.5 ± 7.8 and 4.5 ± 2.1 for the bioturbated sites (wet and dry seasons, respectively). The soil turning over by macrofauna led to lower N2O fluxes in natural crab-bioturbated areas, and seasonality was the environmental factor that contributed the most to the changes in N2O emissions. Broadly, anthropic activities and seasonality influence nitrogen fate, N2O emissions, and ecological services in coastal ecosystems.

NO and N2 O transformations of diverse fungi in hypoxia: evidence for anaerobic respiration only in Fusarium strains

Fungal denitrification is claimed to produce non-negligible amounts of N₂ O in soils, but few tested species have shown significant activity. We hypothesized that denitrifying fungi would be found among those with assimilatory nitrate reductase, and tested 20 such batch cultures for their respiratory metabolism, including two positive controls, Fusarium oxysporum and Fusarium lichenicola, throughout the transition from oxic to anoxic conditions in media supplemented with NO 2 - . Enzymatic reduction of NO 2 - (NIR) and NO (NOR) was assessed by correcting measured NO- and N₂ O-kinetics for abiotic NO- and N₂ O-production (sterile controls). Significant anaerobic respiration was only confirmed for the positive controls and for two of three Fusarium solani cultures. The NO kinetics in six cultures showed NIR but not NOR activity, observed through the accumulation of NO. Others had NOR but not NIR activity, thus reducing abiotically produced NO to N₂ O. The presence of candidate genes (nirK and p450nor) was confirmed in the positive controls, but not in some of the NO or N₂ O accumulating cultures. Based on our results, we conclude that only the Fusarium cultures were able to sustain anaerobic respiration and produced low amounts of N₂ O as a response to an abiotic NO production from the medium.

Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies

Oxidation of ammonia to nitrite by bacteria and archaea is responsible for global emissions of nitrous oxide directly and indirectly through provision of nitrite and, after further oxidation, nitrate to denitrifiers. Their contributions to increasing N₂ O emissions are greatest in terrestrial environments, due to the dramatic and continuing increases in use of ammonia-based fertilizers, which have been driven by requirement for increased food production, but which also provide a source of energy for ammonia oxidizers (AO), leading to an imbalance in the terrestrial nitrogen cycle. Direct N₂ O production by AO results from several metabolic processes, sometimes combined with abiotic reactions. Physiological characteristics, including mechanisms for N₂ O production, vary within and between ammonia-oxidizing archaea (AOA) and bacteria (AOB) and comammox bacteria and N₂ O yield of AOB is higher than in the other two groups. There is also strong evidence for niche differentiation between AOA and AOB with respect to environmental conditions in natural and engineered environments. In particular, AOA are favored by low soil pH and AOA and AOB are, respectively, favored by low rates of ammonium supply, equivalent to application of slow-release fertilizer, or high rates of supply, equivalent to addition of high concentrations of inorganic ammonium or urea. These differences between AOA and AOB provide the potential for better fertilization strategies that could both increase fertilizer use efficiency and reduce N₂ O emissions from agricultural soils. This article reviews research on the biochemistry, physiology and ecology of AO and discusses the consequences for AO communities subjected to different agricultural practices and the ways in which this knowledge, coupled with improved methods for characterizing communities, might lead to improved fertilizer use efficiency and mitigation of N₂ O emissions.

Long-term impact of poultry manure on crop yield, soil and water quality, and crop revenue

A long-term poultry manure fertilizer study was initiated in 1998 and continued until 2009 under corn-soybean (CS) rotation. To match changing landscape trends, the plots were switched to continuous corn (CC) from 2010 to 2017. In both CS and CC phases, poultry manure (PM) was applied at the crop rotation recommended agronomic N rate and either half (CC phase) or double (CS phase) the recommended rate. Urea-ammonium nitrate (UAN) was applied to comparison plots at the crop recommended application rate (168 kg N ha^-1 and 224 kg N ha^-1 for the CS and CC phases, respectively) throughout the study. The objectives of this study include evaluation of the economic benefits of long-term PM application at various rates (PM2, PM, and PM0.5), and the impact of poultry manure application on soil health and nutrient levels, crop yield, and drainage water quality. Lower NO₃-N concentrations were reported in drainage from PM treated plots when compared to UAN fertilizer applied at the same agronomic rate. Of the parameters tested for soil health analysis after twenty years of repeat application, particulate organic matter (POM) present was significantly greater in the PM treated soils (6.1-6.7 g kg soil^-1) when compared to UAN plots (4.6 g kg soil^-1), showing potential for stabilized soil particles, increased infiltration and water-holding capacity. The results show a consistent positive impact of manure application on corn and soybean yields when compared to yields observed in UAN treated plots. During the CS phase, we estimated the same average revenue per dollar spent for PM and UAN treatments, while the average return rate for PM2 was 1% lower; during CC phase,15% increased return rates were observed when PM0.5 and PM were compared against the UAN treatment. When managed properly, PM application to cropland is a sustainable option for diversifying agroecosystems, improving soil health and improving farm economics.

The coupling interaction of NO2- with NH4+ or NO3- as an important source of N2O emission from agricultural soil in the North China Plain

NO₂^- plays a crucial role in regulating N₂O formation from the soil, while how it affects the production of soil N₂O is still not well understood. In this study, N₂O and NO emissions from an agricultural field of the North China Plain (NCP) were comparatively investigated under five different fertilizer treatments (NH₄⁺, NO₃^-, NO₂^-, NH₄⁺ + NO₂^- and NO₃^- + NO₂^-). Additionally, soil NH₄⁺, NO₂^- and NO₃^- concentrations and the abundance of functional genes associated with nitrogen cycling were also analyzed in the incubation experiment. The results showed that the N₂O average fluxes from the complex treatments of NO₂^- + NO₃^- were 1.4-2.4 times the sum of those from the separate treatments of NO₂^- and NO₃^- whereas from the complex treatments of NO₂^- + NH₄⁺ were a factor of 1-1.4 larger than those from the separate treatments of NO₂^- and NH₄⁺, indicating the coupling interaction of NO₂^- with NH₄⁺ or NO₃^- makes a remarkable contribution to N₂O emission from the soil. Significant reduction of the activity of N₂O reductase was found in the soil with the addition of NO₂^-, which favored the accumulation of N₂O formed through nitrification of NH₄⁺ and denitrification of NO₂^-, resulting in relatively high N₂O emissions from the complex treatments. As the intermediate product of nitrification and denitrification, NO₂^- produced is also expected to interact with NH₄⁺ or NO₃^- to promote N₂O emission from the soil, especially during fertilization events when NO₂^- is easily accumulated due to the acceleration of the nitrification and denitrification processes.

Using digital polymerase chain reaction to characterize microbial communities in wetland mesocosm soils under different vegetation and seasonal nutrient loadings

Constructed wetlands are multi-functional systems that can effectively store and transform pollutants primarily through natural processes. However, the removal of nitrogen pollutant by wetlands is highly variable, likely due to a combination of factors such as plant species-specific assimilation behavior, the effects of soil microbial diversity, and variable nitrogen inputs. In this study, the effects of plant species richness (i.e., number of plant species in a system) and seasonal nutrient loading (i.e., nitrogen fertilization) on the microbial community responsible for regulating nitrogen turnover in wetland mesocosm soils was investigated. Digital polymerase chain reaction was used to quantify bacterial abundance. Principal component analysis was employed to identify dominant patterns within the data, and resampling-based analysis of variance was used to assess statistical significance of any observed differences caused by fertilization, season, and/or plant species richness. Results indicated that fertilization or season, which was convolved with fertilization, was the dominant factor influencing the microbial community in the study environment. The effects of plant species richness were more nuanced. Its greater richness significantly impacted the abundance of only a subset of bacterial groups (i.e., the ammonia oxidizing bacteria, Nitrospira spp. of nitrite-oxidizing bacteria, and comammox, but not the denitrifying bacteria).

Impact of nitrogen compounds on fungal and bacterial contributions to codenitrification in a pasture soil

Ruminant urine patches on grazed grassland are a significant source of agricultural nitrous oxide (N₂O) emissions. Of the many biotic and abiotic N₂O production mechanisms initiated following urine-urea deposition, codenitrification resulting in the formation of hybrid N₂O, is one of the least understood. Codenitrification forms hybrid N₂O via biotic N-nitrosation, co-metabolising organic and inorganic N compounds (N substrates) to produce N₂O. The objective of this study was to assess the relative significance of different N substrates on codenitrification and to determine the contributions of fungi and bacteria to codenitrification. ¹⁵N-labelled ammonium, hydroxylamine (NH₂OH) and two amino acids (phenylalanine or glycine) were applied, separately, to sieved soil mesocosms eight days after a simulated urine event, in the absence or presence of bacterial and fungal inhibitors. Soil chemical variables and N₂O fluxes were monitored and the codenitrified N₂O fluxes determined. Fungal inhibition decreased N₂O fluxes by ca. 40% for both amino acid treatments, while bacterial inhibition only decreased the N₂O flux of the glycine treatment, by 14%. Hydroxylamine (NH₂OH) generated the highest N₂O fluxes which declined with either fungal or bacterial inhibition alone, while combined inhibition resulted in a 60% decrease in the N₂O flux. All the N substrates examined participated to some extent in codenitrification. Trends for codenitrification under the NH₂OH substrate treatment followed those of total N₂O fluxes (85.7% of total N₂O flux). Codenitrification fluxes under non-NH₂OH substrate treatments (0.7-1.2% of total N₂O flux) were two orders of magnitude lower, and significant decreases in these treatments only occurred with fungal inhibition in the amino acid substrate treatments. These results demonstrate that in situ studies are required to better understand the dynamics of codenitrification substrates in grazed pasture soils and the associated role that fungi have with respect to codenitrification.

Intense rainfalls trigger nitrite leaching in agricultural soils depleted in organic matter

Nitrate and ammonium are common inorganic contaminants of anthropogenic origin in many shallow aquifers around the world, while nitrite is less common, but it is most harmful than nitrate and ammonium due to its high reactivity. This paper presents evidence of nitrite accumulation after intense rainfalls in soil samples collected in an agricultural field characterized by organic matter chronic depletion. Moreover, an intact core from the same site was also collected to perform an unsaturated column experiment (60 cm long and 20 cm outer diameter) mimicking heavy rainfalls (230 mm in 2 days). Results from the field site showed nitrite accumulation (up to 0.45 mmol/kg) at 50-70 cm depth, just below the plough layer. The column experiment showed very high initial concentrations of nitrate and nitrite in the leachate and a progressive decrease of nitrate due to denitrification. The numerical flow model was calibrated versus the observed volumetric water contents and leachate flow rates. The numerical reactive transport model was calibrated versus the leachate concentrations of six dissolved species (ammonium, nitrate, nitrite, dissolved organic carbon, chloride and bromide). The optimized model resulted to be robustly calibrated providing insights on the kinetic rates driving the production, accumulation and leakage of nitrite, showing that incomplete denitrification is the source of nitrite. As far as the authors are aware, this is the first study reporting a clear link between high nitrite leaching rates and extreme rainfall events in lowland agricultural soils depleted in organic matter. The proposed methodology could be applied to quantify nitrite cycling processes in many other agricultural areas of the world affected by extreme rainfall events.

Manganese Oxide Biomineralization Provides Protection against Nitrite Toxicity in a Cell-Density-Dependent Manner

Manganese biomineralization is a widespread process among bacteria and fungi. To date, there is no conclusive experimental evidence for how and if this process impacts microbial fitness in the environment. Here, we show how a model organism for manganese oxidation is growth inhibited by nitrite, and that this inhibition is mitigated in the presence of manganese. We show that such manganese-mediated mitigation of nitrite inhibition is dependent on the culture inoculum size, and that manganese oxide (MnOX) forms granular precipitates in the culture, rather than sheaths around individual cells. We provide evidence that MnOX protection involves both its ability to catalyze nitrite oxidation into (nontoxic) nitrate under physiological conditions and its potential role in influencing processes involving reactive oxygen species (ROS). Taken together, these results demonstrate improved microbial fitness through MnOX deposition in an ecological setting, i.e., mitigation of nitrite toxicity, and point to a key role of MnOX in handling stresses arising from ROS.IMPORTANCE We present here a direct fitness benefit (i.e., growth advantage) for manganese oxide biomineralization activity in Roseobacter sp. strain AzwK-3b, a model organism used to study this process. We find that strain AzwK-3b in a laboratory culture experiment is growth inhibited by nitrite in manganese-free cultures, while the inhibition is considerably relieved by manganese supplementation and manganese oxide (MnOX) formation. We show that biogenic MnOX interacts directly with nitrite and possibly with reactive oxygen species and find that its beneficial effects are established through formation of dispersed MnOX granules in a manner dependent on the population size. These experiments raise the possibility that manganese biomineralization could confer protection against nitrite toxicity to a population of cells. They open up new avenues of interrogating this process in other species and provide possible routes to their biotechnological applications, including in metal recovery, biomaterials production, and synthetic community engineering.

A potential central role of Thaumarchaeota in N-Cycling in a semi-arid environment, Fort Stanton Cave, Snowy River passage, New Mexico, USA

Low biomass and productivity of arid-land caves with limited availability of nitrogen (N) raises the question of how microbes acquire and cycle this essential element. Caves are ideal environments for investigating microbial functional capabilities, as they lack phototrophic activity and have near constant temperatures and high relative humidity. From the walls of Fort Stanton Cave (FSC), multicolored secondary mineral deposits of soil-like material low in fixed N, known as ferromanganese deposits (FMD), were collected. We hypothesized that within FMD samples we would find the presence of microbial N cycling genes and taxonomy related to N cycling microorganisms. Community DNA were sequenced using Illumina shotgun metagenomics and 16S rRNA gene sequencing. Results suggest a diverse N cycle encompassing several energetic pathways including nitrification, dissimilatory nitrate reduction and denitrification. N cycling genes associated with assimilatory nitrate reduction were also identified. Functional gene sequences and taxonomic findings suggest several bacterial and archaeal phyla potentially play a role in nitrification pathways in FSC and FMD. Thaumarchaeota, a deep-branching archaeal division, likely play an essential and possibly dominant role in the oxidation of ammonia. Our results provide genomic evidence for understanding how microbes are potentially able to acquire and cycle N in a low-nutrient subterranean environment.

Coming Late for Dinner: Localized Digestate Depot Fertilization for Extensive Cultivation of Marginal Soil With Sida hermaphrodita

Improving fertility of marginal soils for the sustainable production of biomass is a strategy for reducing land use conflicts between food and energy crops. Digestates can be used as fertilizer and for soil amelioration. In order to promote plant growth and reduce potential adverse effects on roots because of broadcast digestate fertilization, we propose to apply local digestate depots placed into the rhizosphere. We grew Sida hermaphrodita in large mesocosms outdoors for three growing seasons and in rhizotrons in the greenhouse for 3 months both filled with marginal substrate, including multiple sampling dates. We compared digestate broadcast application with digestate depot fertilization and a mineral fertilizer control. We show that depot fertilization promotes a deep reaching root system of S. hermaphrodita seedlings followed by the formation of a dense root cluster around the depot-fertilized zone, resulting in a fivefold increased biomass yield. Temporal adverse effects on root growth were linked to high initial concentrations of ammonium and nitrite in the rhizosphere in either fertilizer application, followed by a high biomass increase after its microbial conversion to nitrate. We conclude that digestate depot fertilization can contribute to an improved cultivation of perennial energy-crops on marginal soils.

Effect of rice-straw biochar on nitrous oxide emissions from paddy soils under elevated CO2 and temperature

In paddy ecosystems, the feedback of N₂O emissions on climate change as well as the effects of biochar on N₂O emissions will have a profound impact on global warming and rice production. In order to investigate the effect of biochar amendment on N₂O emissions from paddy soils under elevated atmospheric CO₂ concentration (700ppm) and air temperature (ambient +3°C), a microcosm study was performed in plant growth chambers with rice plant and rice-straw-derived biochar. N₂O emissions from urea-fertilized paddy soils had a significant increase with the biochar amendment during midseason drainage under ambient CO₂ concentration and air temperature. However, N₂O emissions was suppressed under simultaneous elevated CO₂ concentration and air temperature, regardless of whether biochar was amended; under this condition the stimulating effect of biochar was attenuated. Reduced mineral N concentrations and increased DOC concentrations could inhibit N₂O emission at simultaneously elevated CO₂ concentration and air temperature. Increased soil pH and variation in the abundance of archaeal and bacterial amoA genes indicated that biochar amendment could stimulate ammonia oxidation-induced N₂O emission during nitrification. Moreover, the liming effect of biochar was lessened under elevated CO₂ concentration and temperature, which may contribute to the attenuated stimulating effect of biochar on N₂O emissions. More attention should to be paid to the effect of soil pH-induced changes in ammonia oxidation, when mitigating N₂O emissions in urea-fertilized paddy soils with biochar amendment at elevated CO₂ concentrations and air temperatures.

Nitrite-Oxidizing Bacteria Community Composition and Diversity Are Influenced by Fertilizer Regimes, but Are Independent of the Soil Aggregate in Acidic Subtropical Red Soil

Nitrification is the two-step aerobic oxidation of ammonia to nitrate via nitrite in the nitrogen-cycle on earth. However, very limited information is available on how fertilizer regimes affect the distribution of nitrite oxidizers, which are involved in the second step of nitrification, across aggregate size classes in soil. In this study, the community compositions of nitrite oxidizers (Nitrobacter and Nitrospira) were characterized from a red soil amended with four types of fertilizer regimes over a 26-year fertilization experiment, including control without fertilizer (CK), swine manure (M), chemical fertilization (NPK), and chemical/organic combined fertilization (MNPK). Our results showed that the addition of M and NPK significantly decreased Nitrobacter Shannon and Chao1 index, while M and MNPK remarkably increased Nitrospira Shannon and Chao1 index, and NPK considerably decreased Nitrospira Shannon and Chao1 index, with the greatest diversity achieved in soils amended with MNPK. However, the soil aggregate fractions had no impact on that alpha-diversity of Nitrobacter and Nitrospira under the fertilizer treatment. Soil carbon, nitrogen and phosphorus in the soil had a significant correlation with Nitrospira Shannon and Chao1 diversity index, while total potassium only had a significant correlation with Nitrospira Shannon diversity index. However, all of them had no significant correlation with Nitrobacter Shannon and Chao1 diversity index. The resistance indices for alpha-diversity indexes (Shannon and Chao1) of Nitrobacter were higher than those of Nitrospira in response to the fertilization regimes. Manure fertilizer is important in enhancing the Nitrospira Shannon and Chao1 index resistance. Principal co-ordinate analysis revealed that Nitrobacter- and Nitrospira-like NOB communities under four fertilizer regimes were differentiated from each other, but soil aggregate fractions had less effect on the nitrite oxidizers community. Redundancy analysis and Mantel test indicated that soil nitrogen, carbon, phosphorus, and available potassium content were important environmental attributes that control the Nitrobacter- and Nitrospira-like NOB community structure across different fertilization treatments under aggregate levels in the red soil. In general, nitrite-oxidizing bacteria community composition and alpha-diversity are depending on fertilizer regimes, but independent of the soil aggregate.

Water quality of surface runoff and lint yield in cotton under furrow irrigation in Northeast Arkansas

Use of furrow irrigation in row crop production is a common practice through much of the Midsouth US and yet, nutrients can be transported off-site through surface runoff. A field study with cotton (Gossypium hirsutum, L.) was conducted to understand the impact of furrow tillage practices and nitrogen (N) fertilizer placement on characteristics of runoff water quality during the growing season. The experiment was designed as a randomized complete block design with conventional (CT) and conservation furrow tillage (FT) in combination with either urea (URN) broadcast or 32% urea ammonium nitrate (UAN) injected, each applied at 101kgNha^-1. Concentrations of ammonium (NH₄-N), nitrate (NO₃-N), nitrite (NO₂-N), and dissolved phosphorus (P) in irrigation runoff water and lint yields were measured in all treatments. The intensity and chemical form of nutrient losses were primarily controlled by water runoff volume and agronomic practice. Across tillage and fertilizer N treatments, median N concentrations in the runoff were <0.3mgNL^-1, with NO₃-N being relatively the highest among N forms. Concentrations of runoff dissolved P were <0.05mgPL^-1 and were affected by volume of runoff water. Water pH, specific electrical conductivity, alkalinity and hardness were within levels that common to local irrigation water and less likely to impair pollution in waterways. Lint yields averaged 1111kgha^-1 and were higher (P-value=0.03) in FT compared to CT treatments. Runoff volumes across irrigation events were greater (P-value=0.02) in CT than FT treatments, which increased NO₃-N mass loads in CT treatments (394gNO₃-Nha^-1season^-1). Nitrate-N concentrations in CT treatments were still low and pose little threat to N contaminations in waterways. The findings support the adoption of conservation practices for furrow tillage and N fertilizer placement that can reduce nutrient runoff losses in furrow irrigation systems.

Denitrification by Anaeromyxobacter dehalogenans, a Common Soil Bacterium Lacking the Nitrite Reductase Genes nirS and nirK

The versatile soil bacterium Anaeromyxobacter dehalogenans lacks the hallmark denitrification genes nirS and nirK (encoding NO₂ ^-→NO reductases) and couples growth to NO₃ ^- reduction to NH₄ ⁺ (respiratory ammonification) and to N₂O reduction to N₂ A. dehalogenans also grows by reducing Fe(III) to Fe(II), which chemically reacts with NO₂ ^- to form N₂O (i.e., chemodenitrification). Following the addition of 100 μmol of NO₃ ^- or NO₂ ^- to Fe(III)-grown axenic cultures of A. dehalogenans, 54 (±7) μmol and 113 (±2) μmol N₂O-N, respectively, were produced and subsequently consumed. The conversion of NO₃ ^- to N₂ in the presence of Fe(II) through linked biotic-abiotic reactions represents an unrecognized ecophysiology of A. dehalogenans The new findings demonstrate that the assessment of gene content alone is insufficient to predict microbial denitrification potential and N loss (i.e., the formation of gaseous N products). A survey of complete bacterial genomes in the NCBI Reference Sequence database coupled with available physiological information revealed that organisms lacking nirS or nirK but with Fe(III) reduction potential and genes for NO₃ ^- and N₂O reduction are not rare, indicating that NO₃ ^- reduction to N₂ through linked biotic-abiotic reactions is not limited to A. dehalogenans Considering the ubiquity of iron in soils and sediments and the broad distribution of dissimilatory Fe(III) and NO₃ ^- reducers, denitrification independent of NO-forming NO₂ ^- reductases (through combined biotic-abiotic reactions) may have substantial contributions to N loss and N₂O flux.IMPORTANCE Current attempts to gauge N loss from soils rely on the quantitative measurement of nirK and nirS genes and/or transcripts. In the presence of iron, the common soil bacterium Anaeromyxobacter dehalogenans is capable of denitrification and the production of N₂ without the key denitrification genes nirK and nirS Such chemodenitrifiers denitrify through combined biotic and abiotic reactions and have potentially large contributions to N loss to the atmosphere and fill a heretofore unrecognized ecological niche in soil ecosystems. The findings emphasize that the comprehensive understanding of N flux and the accurate assessment of denitrification potential can be achieved only when integrated studies of interlinked biogeochemical cycles are performed.

Hydroxylamine released by nitrifying microorganisms is a precursor for HONO emission from drying soils

Nitrous acid (HONO) is an important precursor of the hydroxyl radical (OH), the atmosphere´s primary oxidant. An unknown strong daytime source of HONO is required to explain measurements in ambient air. Emissions from soils are one of the potential sources. Ammonia-oxidizing bacteria (AOB) have been identified as possible producers of these HONO soil emissions. However, the mechanisms for production and release of HONO in soils are not fully understood. In this study, we used a dynamic soil-chamber system to provide direct evidence that gaseous emissions from nitrifying pure cultures contain hydroxylamine (NH₂OH), which is subsequently converted to HONO in a heterogeneous reaction with water vapor on glass bead surfaces. In addition to different AOB species, we found release of HONO also in ammonia-oxidizing archaea (AOA), suggesting that these globally abundant microbes may also contribute to the formation of atmospheric HONO and consequently OH. Since biogenic NH₂OH is formed by diverse organisms, such as AOB, AOA, methane-oxidizing bacteria, heterotrophic nitrifiers, and fungi, we argue that HONO emission from soil is not restricted to the nitrifying bacteria, but is also promoted by nitrifying members of the domains Archaea and Eukarya.

Insights into Nitrate-Reducing Fe(II) Oxidation Mechanisms through Analysis of Cell-Mineral Associations, Cell Encrustation, and Mineralogy in the Chemolithoautotrophic Enrichment Culture KS

Most described nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOB) are mixotrophic and depend on organic cosubstrates for growth. Encrustation of cells in Fe(III) minerals has been observed for mixotrophic NRFeOB but not for autotrophic phototrophic and microaerophilic Fe(II) oxidizers. So far, little is known about cell-mineral associations in the few existing autotrophic NRFeOB. Here, we investigate whether the designated autotrophic Fe(II)-oxidizing strain (closely related to Gallionella and Sideroxydans) or the heterotrophic nitrate reducers that are present in the autotrophic nitrate-reducing Fe(II)-oxidizing enrichment culture KS form mineral crusts during Fe(II) oxidation under autotrophic and mixotrophic conditions. In the mixed culture, we found no significant encrustation of any of the cells both during autotrophic oxidation of 8 to 10 mM Fe(II) coupled to nitrate reduction and during cultivation under mixotrophic conditions with 8 to 10 mM Fe(II), 5 mM acetate, and 4 mM nitrate, where higher numbers of heterotrophic nitrate reducers were present. Two pure cultures of heterotrophic nitrate reducers (Nocardioides and Rhodanobacter) isolated from culture KS were analyzed under mixotrophic growth conditions. We found green rust formation, no cell encrustation, and only a few mineral particles on some cell surfaces with 5 mM Fe(II) and some encrustation with 10 mM Fe(II). Our findings suggest that enzymatic, autotrophic Fe(II) oxidation coupled to nitrate reduction forms poorly crystalline Fe(III) oxyhydroxides and proceeds without cellular encrustation while indirect Fe(II) oxidation via heterotrophic nitrate-reduction-derived nitrite can lead to green rust as an intermediate mineral and significant cell encrustation. The extent of encrustation caused by indirect Fe(II) oxidation by reactive nitrogen species depends on Fe(II) concentrations and is probably negligible under environmental conditions in most habitats.IMPORTANCE Most described nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOB) are mixotrophic (their growth depends on organic cosubstrates) and can become encrusted in Fe(III) minerals. Encrustation is expected to be harmful and poses a threat to cells if it also occurs under environmentally relevant conditions. Nitrite produced during heterotrophic denitrification reacts with Fe(II) abiotically and is probably the reason for encrustation in mixotrophic NRFeOB. Little is known about cell-mineral associations in autotrophic NRFeOB such as the enrichment culture KS. Here, we show that no encrustation occurs in culture KS under autotrophic and mixotrophic conditions while heterotrophic nitrate-reducing isolates from culture KS become encrusted. These findings support the hypothesis that encrustation in mixotrophic cultures is caused by the abiotic reaction of Fe(II) with nitrite and provide evidence that Fe(II) oxidation in culture KS is enzymatic. Furthermore, we show that the extent of encrustation caused by indirect Fe(II) oxidation by reactive nitrogen species depends on Fe(II) concentrations and is probably negligible in most environmental habitats.

Influence of soil moisture on codenitrification fluxes from a urea-affected pasture soil

Intensively managed agricultural pastures contribute to N₂O and N₂ fluxes resulting in detrimental environmental outcomes and poor N use efficiency, respectively. Besides nitrification, nitrifier-denitrification and heterotrophic denitrification, alternative pathways such as codenitrification also contribute to emissions under ruminant urine-affected soil. However, information on codenitrification is sparse. The objectives of this experiment were to assess the effects of soil moisture and soil inorganic-N dynamics on the relative contributions of codenitrification and denitrification (heterotrophic denitrification) to the N₂O and N₂ fluxes under a simulated ruminant urine event. Repacked soil cores were treated with ¹⁵N enriched urea and maintained at near saturation (−1 kPa) or field capacity (−10 kPa). Soil inorganic-N, pH, dissolved organic carbon, N₂O and N₂ fluxes were measured over 63 days. Fluxes of N₂, attributable to codenitrification, were at a maximum when soil nitrite (NO₂⁻) concentrations were elevated. Cumulative codenitrification was higher (P = 0.043) at −1 kPa. However, the ratio of codenitrification to denitrification did not differ significantly with soil moisture, 25.5 ± 15.8 and 12.9 ± 4.8% (stdev) at −1 and −10 kPa, respectively. Elevated soil NO₂⁻ concentrations are shown to contribute to codenitrification, particularly at −1 kPa.

A Novel Approach to Estimating Nitrous Oxide Emissions during Wetting Events from Single-Timepoint Flux Measurements

Precipitation and irrigation induce pulses of NO emissions in agricultural soils, but the magnitude, duration, and timing of these pulses remain uncertain. This uncertainty makes it difficult to accurately extrapolate emissions from unmeasured time periods between chamber sampling events. Therefore, we developed a modeling protocol to predict NO emissions from data collected daily for 7 d after wetting events. Within a cover crop-based corn ( L.) production system in Beltsville, MD, we conducted the 7-d time series during four time periods representing a range of corn growth stages in 2013 and 2014. Treatments included mixtures and monocultures of grass and legume cover crops that were fertilized with pelletized poultry litter or urea-ammonium nitrate solution (9-276 kg N ha). Most fluxes did not exhibit the expected exponential decay over time (82%); therefore, cumulative emissions were calculated using trapezoidal integration over 7 d after the wetting event. Cumulative 7-d emissions were well correlated with single point gas fluxes on the second day after a wetting event using a generalized linear mixed model (ln[emissions] = 0.809∙ln[flux] + 2.47). Soil chemical covariates before or after a wetting event were weakly associated with cumulative emissions. The ratio of dissolved organic C to total inorganic N was negatively correlated with cumulative emissions ( = 0.23-0.29), whereas nitrate was positively correlated with cumulative emissions ( = 0.23-0.33). Our model is an innovative approach that is calibrated using site-specific time series data, which may then be used to estimate short-term NO emissions after wetting events using only a single flux measurement.

Complex N acquisition by soil diazotrophs: how the ability to release exoenzymes affects N fixation by terrestrial free-living diazotrophs

Terrestrial systems support a variety of free-living soil diazotrophs, which can fix nitrogen (N) outside of plant associations. However, owing to the metabolic costs associated with N fixation, free-living soil diazotrophs likely rely on soil N to satisfy the majority of cellular N demand and only fix atmospheric N under certain conditions. Culture-based studies and genomic data show that many free-living soil diazotrophs can access high-molecular weight organic soil N by releasing N-acquiring enzymes such as proteases and chitinases into the extracellular environment. Here, we formally propose a N acquisition strategy used by free-living diazotrophs that accounts for high-molecular weight N acquisition through exoenzyme release by these organisms. We call this the ‘LAH N-acquisition strategy' for the preferred order of N pools used once inorganic soil N is limiting: (1) low-molecular weight organic N, (2) atmospheric N and (3) high-molecular weight organic N. In this framework, free-living diazotrophs primarily use biological N fixation (BNF) as a short-term N acquisition strategy to offset the cellular N lost in exoenzyme excretion as low-molecular weight N becomes limiting. By accounting for exoenzyme release by free-living diazotrophs within a cost–benefit framework, investigation of the LAH N acquisition strategy will contribute to a process-level understanding of BNF in soil environments.

Atmospheric emission of nitric oxide and processes involved in its biogeochemical transformation in terrestrial environment

Nitric oxide (NO) is an intra- and intercellular gaseous signaling molecule with a broad spectrum of regulatory functions in biological system. Its emissions are produced by both natural and anthropogenic sources; however, soils are among the most important sources of NO. Nitric oxide plays a decisive role in environmental-atmospheric chemistry by controlling the tropospheric photochemical production of ozone and regulates formation of various oxidizing agents such as hydroxyl radical (OH), which contributes to the formation of acid of precipitates. Consequently, for developing strategies to overcome the deleterious impact of NO on terrestrial ecosystem, it is mandatory to have reliable information about the exact emission mechanism and processes involved in its transformation in soil-atmospheric system. Although the formation process of NO is a complex phenomenon and depends on many physicochemical characteristics, such as organic matter, soil pH, soil moisture, soil temperature, etc., this review provides comprehensive updates about the emission characteristics and biogeochemical transformation mechanism of NO. Moreover, this article will also be helpful to understand the processes involved in the consumption of NO in soils. Further studies describing the functions of NO in biological system are also discussed.

Ammonia-Oligotrophic and Diazotrophic Heavy Metal-Resistant Serratia liquefaciens Strains from Pioneer Plants and Mine Tailings

Mine tailings are man-made environments characterized by low levels of organic carbon and assimilable nitrogen, as well as moderate concentrations of heavy metals. For the introduction of nitrogen into these environments, a key role is played by ammonia-oligotrophic/diazotrophic heavy metal-resistant guilds. In mine tailings from Zacatecas, Mexico, Serratia liquefaciens was the dominant heterotrophic culturable species isolated in N-free media from bulk mine tailings as well as the rhizosphere, roots, and aerial parts of pioneer plants. S. liquefaciens strains proved to be a meta-population with high intraspecific genetic diversity and a potential to respond to these extreme conditions. The phenotypic and genotypic features of these strains reveal the potential adaptation of S. liquefaciens to oligotrophic and nitrogen-limited mine tailings with high concentrations of heavy metals. These features include ammonia-oligotrophic growth, nitrogen fixation, siderophore and indoleacetic acid production, phosphate solubilization, biofilm formation, moderate tolerance to heavy metals under conditions of diverse nitrogen availability, and the presence of zntA, amtB, and nifH genes. The acetylene reduction assay suggests low nitrogen-fixing activity. The nifH gene was harbored in a plasmid of ∼60 kb and probably was acquired by a horizontal gene transfer event from Klebsiella variicola.

Neglecting diurnal variations leads to uncertainties in terrestrial nitrous oxide emissions

Nitrous oxide (N₂O) is an important greenhouse gas produced in soil and aquatic ecosystems. Its warming potential is 296 times higher than that of CO₂. Most N₂O emission measurements made so far are limited in temporal and spatial resolution causing uncertainties in the global N₂O budget. Recent advances in laser spectroscopic techniques provide an excellent tool for area-integrated, direct and continuous field measurements of N₂O fluxes using the eddy covariance method. By employing this technique on an agricultural site with four laser-based analysers, we show here that N₂O exchange exhibits contrasting diurnal behaviour depending upon soil nitrogen availability. When soil N was high due to fertilizer application, N₂O emissions were higher during daytime than during the night. However, when soil N became limited, emissions were higher during the night than during the day. These reverse diurnal patterns supported by isotopic analyses may indicate a dominant role of plants on microbial processes associated with N₂O exchange. This study highlights the potential of new technologies in improving estimates of global N₂O sources.

Interference of Nitrite with Pyrite under Acidic Conditions: Implications for Studies of Chemolithotrophic Denitrification

Chemolithotrophic denitrification coupled to pyrite oxidation is regarded a key process in the removal of nitrate in aquifers. A common product is nitrite, which is a strong oxidant under acidic conditions. Nitrite may thus interfere with Fe(II) during acidic extraction, a procedure typically used to quantify microbial pyrite oxidation, in overestimating Fe(III) production. We studied the reaction between pyrite (5-125 mM) and nitrite (40-2000 μM) at pH 0, 5.5, and 6.8 in the absence and presence of oxygen. Significant oxidation of pyrite was measured at pH 0 with a yield of 100 μM Fe(III) after 5 mM pyrite was incubated with 2000 μM nitrite for 24 h. Dissolved oxygen increased the rate at pH 0. No oxidation of pyrite was observed at pH 5.5 and 6.8. Our data imply a cyclic model for pyrite oxidation by Fe(III) on the basis of the oxidation of residual Fe(II) by NO and NO2. Interference by nitrite could be avoided if nitrite was removed from the pyrite suspensions through a washing procedure prior to acidic extraction. We conclude that such interferences should be considered in studies on microbially mediated pyrite oxidation with nitrate.

Stable isotopes and iron oxide mineral products as markers of chemodenitrification

When oxygen is limiting in soils and sediments, microorganisms utilize nitrate (NO3-) in respiration--through the process of denitrification--leading to the production of dinitrogen (N2) gas and trace amounts of nitrous (N2O) and nitric (NO) oxides. A chemical pathway involving reaction of ferrous iron (Fe2+) with nitrite (NO2-), an intermediate in the denitrification pathway, can also result in production of N2O. We examine the chemical reduction of NO2- by Fe(II)--chemodenitrification--in anoxic batch incubations at neutral pH. Aqueous Fe2+ and NO2- reacted rapidly, producing N2O and generating Fe(III) (hydr)oxide mineral products. Lepidocrotite and goethite, identified by synchrotron X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy, were produced from initially aqueous reactants, with two-line ferrihydrite increasing in abundance later in the reaction sequence. Based on the similarity of apparent rate constants with different mineral catalysts, we propose that the chemodenitrification rate is insensitive to the type of Fe(III) (hydr)oxide. With stable isotope measurements, we reveal a narrow range of isotopic fractionation during NO2- reduction to N2O. The location of N isotopes in the linear N2O molecule, known as site preference, was also constrained to a signature range. The coexistence of Fe(III) (hydr)oxide, characteristic 15N and 18O fractionation, and N2O site preference may be used in combination to qualitatively distinguish between abiotic and biogenically emitted N2O--a finding important for determining N2O sources in natural systems.

Nitrite Control over Dissimilatory Nitrate/Nitrite Reduction Pathways in Shewanella loihica Strain PV-4

Shewanella loihica strain PV-4 harbors both a functional denitrification (NO3 (-)→N2) and a respiratory ammonification (NO3 (-)→NH4 (+)) pathway. Batch and chemostat experiments revealed that NO2 (-) affects pathway selection and the formation of reduced products. Strain PV-4 cells grown with NO2 (-) as the sole electron acceptor produced exclusively NH4 (+). With NO3 (-) as the electron acceptor, denitrification predominated and N2O accounted for ∼90% of reduced products in the presence of acetylene. Chemostat experiments demonstrated that the NO2 (-):NO3 (-) ratio affected the distribution of reduced products, and respiratory ammonification dominated at high NO2 (-):NO3 (-) ratios, whereas low NO2 (-):NO3 (-) ratios favored denitrification. The NO2 (-):NO3 (-) ratios affected nirK transcript abundance, a measure of denitrification activity, in the chemostat experiments, and cells grown at a NO2 (-):NO3 (-) ratio of 3 had ∼37-fold fewer nirK transcripts per cell than cells grown with NO3 (-) as the sole electron acceptor. In contrast, the transcription of nrfA, implicated in NO2 (-)-to-NH4 (+) reduction, remained statistically unchanged under continuous cultivation conditions at NO2 (-):NO3 (-) ratios below 3. At NO2 (-):NO3 (-) ratios above 3, both nirK and nrfA transcript numbers decreased and the chemostat culture washed out, presumably due to NO2 (-) toxicity. These findings implicate NO2 (-) as a relevant modulator of NO3 (-) fate in S. loihica strain PV-4, and, by extension, suggest that NO2 (-) is a relevant determinant for N retention (i.e., ammonification) versus N loss and greenhouse gas emission (i.e., denitrification).