{"type": "FeatureCollection", "features": [{"id": "10.1016/j.scitotenv.2018.11.010", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:17:20Z", "type": "Journal Article", "created": "2018-11-03", "title": "\u03b415N of lichens reflects the isotopic signature of ammonia source", "description": "Although it is generally accepted that \u03b415N in lichen reflects predominating N isotope sources in the environment, confirmation of the direct correlation between lichen \u03b415N and atmospheric \u03b415N is still missing, especially under field conditions with most confounding factors controlled. To fill this gap and investigate the response of lichens with different tolerance to atmospheric N deposition, thalli of the sensitive Evernia prunastri and the tolerant Xanthoria parietina were exposed for ten weeks to different forms and doses of N in a field manipulation experiment where confounding factors were minimized. During this period, several parameters, namely total N, \u03b415N and chlorophyll a fluorescence, were measured. Under the experimental conditions, \u03b415N in lichens quantitatively responded to the \u03b415N of released gaseous ammonia (NH3). Although a high correlation between the isotopic signatures in lichen tissue and supplied N was found both in tolerant and sensitive species, chlorophyll a fluorescence indicated that the sensitive species very soon lost its photosynthetic functionality with increasing N availability. The most damaging response to the different N chemical forms was observed with dry deposition of NH3, although wet deposition of ammonium ions had a significant observable physiological impact. Conversely, there was no significant effect of nitrate ions on chlorophyll a fluorescence, implying differential sensitivity to dry deposition versus wet deposition and to ammonium versus nitrate in wet deposition. Evernia prunastri was most sensitive to NH3, then NH4+, with lowest sensitivity to NO3-. Moreover, these results confirm that lichen \u03b415N can be used to indicate the \u03b415N of atmospheric ammonia, providing a suitable tool for the interpretation of the spatial distribution of NH3 sources in relation to their \u03b415N signal.", "keywords": ["Air Pollutants", "Nitrates", "Lichens", "Nitrogen Isotopes", "Chlorophyll A", "0211 other engineering and technologies", "02 engineering and technology", "Models", " Theoretical", "chlorophyll a fluorescence", "01 natural sciences", "nitrogen deposition", "Xanthoria parietina", "Species Specificity", "Ammonia", "13. Climate action", "source spatial distribution", "biomonitoring", "physiological response", "Photosynthesis", "Environmental Monitoring", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2018.11.010"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2018.11.010", "name": "item", "description": "10.1016/j.scitotenv.2018.11.010", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2018.11.010"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-02-01T00:00:00Z"}}, {"id": "10.1002/jsfa.11205", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:14:33Z", "type": "Journal Article", "created": "2021-03-12", "title": "A novel ammoniation treatment of barley as a strategy to optimize rumen pH, feed degradability and microbial protein synthesis", "description": "AbstractBACKGROUND

Meeting the energy and nitrogen (N) requirements of high\uffe2\uff80\uff90performing ruminants at the same time as avoiding digestive disturbances (i.e. rumen acidosis) is a key priority in ruminant nutrition. The present study evaluated the effect of a cereal ammoniation treatment, in which barley grains are combined with urea and enzymes that catalyze the conversion of urea to ammonia to optimize rumen function. Twelve rumen cannulated sheep were randomly divided into two groups and fed a diet containing 60% of ammoniated barley (AMM) or untreated barley supplemented with urea (CTL) to investigate the impact on rumen fermentation and feed utilization.

RESULTS

AMM had higher total N content and effective rumen degradable N than untreated barely. AMM sheep had a consistently higher rumen pH throughout the day (6.31 versus 6.03) and tended to have a lower post\uffe2\uff80\uff90prandial ammonia peak and higher acetate molar proportion (+5.1%) than CTL sheep. The rumen environment in AMM sheep favored the colonization and utilization of agro\uffe2\uff80\uff90industrial by\uffe2\uff80\uff90products (i.e. orange pulp) by the rumen microbes leading to a higher feed degradability. AMM sheep also had higher total tract apparent N digestibility (+21.7%) and urinary excretion of purine derivatives (+34%), suggesting a higher N uptake and microbial protein synthesis than CTL sheep.

CONCLUSION

The inclusion of AMM in the diet of ruminants represents a valid strategy for maintaining rumen pH within a physiological range and improving N utilization by the rumen microbes, which could have positive effects on the health and productivity of animals in intensive production systems. These findings warrant further studies under conventional farm conditions. \uffc2\uffa9 2021 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

", "keywords": ["2. Zero hunger", "Rumen", "Sheep", "Bacteria", "Food Handling", "0402 animal and dairy science", "Hordeum", "04 agricultural and veterinary sciences", "Hydrogen-Ion Concentration", "Animal Feed", "Diet", "Gastrointestinal Microbiome", "Bacterial Proteins", "Ammonia", "Barley", "Rumen fermentation", "Animals", "Urea", "Ammoniation", "Digestion", "Feed utilization", "Research Articles"]}, "links": [{"href": "https://eprints.gla.ac.uk/235892/1/235892.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/jsfa.11205"}, {"href": "https://doi.org/10.1002/jsfa.11205"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20the%20Science%20of%20Food%20and%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jsfa.11205", "name": "item", "description": "10.1002/jsfa.11205", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.11205"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-24T00:00:00Z"}}, {"id": "10.1002/jsfa.4349", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:14:33Z", "type": "Journal Article", "created": "2011-03-29", "title": "Efficiency Of Urease And Nitrification Inhibitors In Reducing Ammonia Volatilization From Diverse Nitrogen Fertilizers Applied To Different Soil Types And Wheat Straw Mulching", "description": "Some authors suggest that the absence of tillage in agricultural soils might have an influence on the efficiency of nitrogen applied in the soil surface. In this study we investigate the influence of no-tillage and soil characteristics on the efficiency of a urease inhibitor (N-(n-butyl)thiophosphoric triamide, NBPT) and a nitrification inhibitor (diciandiamide, DCD) in decreasing ammonia volatilization from urea and ammonium nitrate (AN), respectively.The results indicate that ammonia volatilization in soils amended with urea was significantly higher than in those fertilized with AN. Likewise, the main soil factors affecting ammonia volatilization from urea are clay and sand soil contents. While clay impedes ammonia volatilization, sand favours it. The presence of organic residues on soil surface (no-tillage) tends to increase ammonia volatilization from urea, although this fact depended on soil type. The presence of NBPT in urea fertilizer significantly reduced soil ammonia volatilization. This action of NBPT was negatively affected by acid soil pH and favoured by soil clay content.The presence of organic residues on soil surface amended with urea increased ammonia volatilization, and was particularly high in sandy compared with clay soils. Application of NBPT reduced ammonia volatilization although its efficiency is reduced in acid soils. Concerning AN fertilization, there were no differences in ammonia volatilization with or without DCD in no-tillage soils.", "keywords": ["2. Zero hunger", "Nitrates", "Plant Stems", "Nitrogen", "Agriculture", "04 agricultural and veterinary sciences", "Hydrogen-Ion Concentration", "Silicon Dioxide", "Nitrification", "Urease", "6. Clean water", "Soil", "Organophosphorus Compounds", "Ammonia", "Clay", "Urea", "0401 agriculture", " forestry", " and fisheries", "Aluminum Silicates", "Enzyme Inhibitors", "Volatilization", "Fertilizers", "Humic Substances", "Triticum"]}, "links": [{"href": "https://doi.org/10.1002/jsfa.4349"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20the%20Science%20of%20Food%20and%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jsfa.4349", "name": "item", "description": "10.1002/jsfa.4349", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.4349"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-03-29T00:00:00Z"}}, {"id": "10.1007/s11104-011-0870-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:15:29Z", "type": "Journal Article", "created": "2011-07-05", "title": "Biochar Adsorbed Ammonia Is Bioavailable", "description": "Biochar is produced as a by-product of the low temperature pyrolysis of biomass during bioenergy extraction and its incorporation into soil is of global interest as a potential carbon sequestration tool. Biochar influences soil nitrogen transformations and its capacity to take up ammonia is well recognized. Anthropogenic emissions of ammonia need to be mitigated due to negative environmental impacts and economic losses. Here we use an isotope of nitrogen to show that ammonia-N adsorbed by biochar is stable in ambient air, but readily bioavailable when placed in the soil. When biochars, containing adsorbed 15N labelled ammonia, were incorporated into soil the 15N recovery by roots averaged 6.8% but ranged from 26.1% to 10.9% in leaf tissue due to differing biochar properties with plant 15N recovery greater when acidic biochars were used to capture ammonia. Recovery of 15N as total soil nitrogen (organic+inorganic) ranged from 45% to 29% of 15N applied. We provide a proof of concept for a synergistic mitigation option where anthropogenic ammonia emissions could be captured using biochar, and made bioavailable in soils, thus leading to nitrogen capture by crops, while simultaneously sequestering carbon in soils.", "keywords": ["ryegrass", "550", "ANZSRC::31 Biological sciences", "ANZSRC::0703 Crop and Pasture Production", "ANZSRC::050301 Carbon Sequestration Science", "ANZSRC::30 Agricultural", "04 agricultural and veterinary sciences", "540", "ammonia", "01 natural sciences", "7. Clean energy", "nitrogen", "veterinary and food sciences", "13. Climate action", "ANZSRC::0503 Soil Sciences", "ANZSRC::41 Environmental sciences", "0401 agriculture", " forestry", " and fisheries", "biochar", "ANZSRC::070304 Crop and Pasture Biomass and Bioproducts", "N stable isotope", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1007/s11104-011-0870-3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11104-011-0870-3", "name": "item", "description": "10.1007/s11104-011-0870-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-011-0870-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-07-06T00:00:00Z"}}, {"id": "10.1007/s00248-011-9897-5", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-05-30T16:14:50Z", "type": "Journal Article", "created": "2011-06-29", "title": "Impacts Of Organic And Inorganic Fertilizers On Nitrification In A Cold Climate Soil Are Linked To The Bacterial Ammonia Oxidizer Community", "description": "The microbiology underpinning soil nitrogen cycling in northeast China remains poorly understood. These agricultural systems are typified by widely contrasting temperature, ranging from -40 to 38\u00b0C. In a long-term site in this region, the impacts of mineral and organic fertilizer amendments on potential nitrification rate (PNR) were determined. PNR was found to be suppressed by long-term mineral fertilizer treatment but enhanced by manure treatment. The abundance and structure of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities were assessed using quantitative polymerase chain reaction and denaturing gradient gel electrophoresis techniques. The abundance of AOA was reduced by all fertilizer treatments, while the opposite response was measured for AOB, leading to a six- to 60-fold reduction in AOA/AOB ratio. The community structure of AOA exhibited little variation across fertilization treatments, whereas the structure of the AOB community was highly responsive. PNR was correlated with community structure of AOB rather than that of AOA. Variation in the community structure of AOB was linked to soil pH, total carbon, and nitrogen contents induced by different long-term fertilization regimes. The results suggest that manure amendment establishes conditions which select for an AOB community type which recovers mineral fertilizer-suppressed soil nitrification.", "keywords": ["DNA", " Bacterial", "2. Zero hunger", "China", "Bacteria", "04 agricultural and veterinary sciences", "15. Life on land", "Cold Climate", "Archaea", "Nitrification", "6. Clean water", "Genes", " Archaeal", "Soil", "DNA", " Archaeal", "Ammonia", "Genes", " Bacterial", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Oxidoreductases", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-011-9897-5"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-011-9897-5", "name": "item", "description": "10.1007/s00248-011-9897-5", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-011-9897-5"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-06-29T00:00:00Z"}}, {"id": "10.1007/s00253-011-3535-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:14:50Z", "type": "Journal Article", "created": "2011-08-17", "title": "Methanotrophic Community Structure And Activity Under Warming And Grazing Of Alpine Meadow On The Tibetan Plateau", "description": "Knowledge about methanotrophs and their activities is important to understand the microbial mediation of the greenhouse gas CH(4) under climate change and human activities in terrestrial ecosystems. The effects of simulated warming and sheep grazing on methanotrophic abundance, community composition, and activity were studied in an alpine meadow soil on the Tibetan Plateau. There was high abundance of methanotrophs (1.2-3.4\u2009\u00d7\u200910(8) pmoA gene copies per gram of dry weight soil) assessed by real-time PCR, and warming significantly increased the abundance regardless of grazing. A total of 64 methanotrophic operational taxonomic units (OTUs) were obtained from 1,439 clone sequences, of these OTUs; 63 OTUs (98.4%) belonged to type I methanotrophs, and only one OTU was Methylocystis of type II methanotrophs. The methanotroph community composition and diversity were not apparently affected by the treatments. Warming and grazing significantly enhanced the potential CH(4) oxidation activity. There were significantly negative correlations between methanotrophic abundance and soil moisture and between methanotrophic abundance and NH(4)-N content. The study suggests that type I methanotrophs, as the dominance, may play a key role in CH(4) oxidation, and the alpine meadow has great potential to consume more CH(4) under future warmer and grazing conditions on the Tibetan Plateau.", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Sheep", "Bacteria", "Molecular Sequence Data", "Temperature", "Sequence Analysis", " DNA", "15. Life on land", "Real-Time Polymerase Chain Reaction", "Tibet", "Biota", "Soil", "03 medical and health sciences", "Ammonia", "13. Climate action", "Animals", "Methane", "Oxidation-Reduction", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00253-011-3535-5"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Microbiology%20and%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00253-011-3535-5", "name": "item", "description": "10.1007/s00253-011-3535-5", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00253-011-3535-5"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-08-17T00:00:00Z"}}, {"id": "10.1007/s00374-012-0752-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:14:56Z", "type": "Journal Article", "created": "2012-11-22", "title": "Nitrogen Dynamics Of Anaerobically Digested Slurry Used To Fertilize Paddy Fields", "description": "To determine nitrogen (N) fate and environmental impact of applying anaerobic digestion slurry (ADS) to rice paddy (Oryza sativa L.), a field experiment was established using three treatments based on contrasting N application rate. The ADS (with ammonium-N accounting for >80 % of total N) treatment at a conventional application rate of 270 kg N ha\u22121 was compared to a negative control (no N fertilizer) and a positive control of urea applied at 270 kg N ha\u22121. The N budget showed the following distribution of applied N from ADS and urea: 41.3 \u00b1 5.1 % for ADS and 36.6 \u00b1 4.4 % for urea recovered by the rice plant (including straw, grain, and root), 16.4 \u00b1 3.7 % for ADS and 7.4 \u00b1 1.8 % for urea lost via ammonia volatilization, 0.26 \u00b1 0.15 % for ADS and 0.15 \u00b1 0.12 % for urea lost by direct N2O emission, 1.9 \u00b1 0.5 % for ADS and 2.3 \u00b1 0.8 % for urea leached downward, 0.70 \u00b1 0.15 % for ADS and 0.67 \u00b1 0.12 % for urea discharged with floodwater drainage, and 39.4 \u00b1 8.4 % for ADS and 53.0 \u00b1 9.1 % for urea retained by soil or lost by N2 emission. Compared to urea application, ADS application impacts the environment mainly through gaseous N losses rather than water N losses. ADS application had a positive impact on rice grain yield and reduced chemical fertilizer use. Considering the wide distribution of paddy fields and the ever-increasing quantities of ADS, ADS may serve as a valuable N source for rice cultivation, although mitigating ammonia and N2O losses should be further investigated.", "keywords": ["2. Zero hunger", "Agricultural and Veterinary Sciences", "Agronomy & Agriculture", "04 agricultural and veterinary sciences", "Ammonia volatilization", "Biological Sciences", "7. Clean energy", "Nitrogen-use efficiency", "6. Clean water", "Anaerobically digested slurry", "Denitrification", "Paddy field", "0401 agriculture", " forestry", " and fisheries", "Zero Hunger", "Environmental Sciences"]}, "links": [{"href": "https://escholarship.org/content/qt3d16p0gn/qt3d16p0gn.pdf"}, {"href": "https://doi.org/10.1007/s00374-012-0752-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biology%20and%20Fertility%20of%20Soils", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00374-012-0752-8", "name": "item", "description": "10.1007/s00374-012-0752-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00374-012-0752-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-11-22T00:00:00Z"}}, {"id": "10.1007/s00425-017-2647-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:14:59Z", "type": "Journal Article", "created": "2017-01-04", "title": "The cost of surviving nitrogen excess: energy and protein demand in the lichen Cladonia portentosa as revealed by proteomic analysis", "description": "Different nitrogen forms affect different metabolic pathways in lichens. In particular, the most relevant changes in protein expression were observed in the fungal partner, with NO 3- mostly affecting the energetic metabolism and NH 4+ affecting transport and regulation of proteins and the energetic metabolism much more than NO 3- did. Excess deposition of reactive nitrogen is a well-known agent of stress for lichens, but which symbiont is most affected and how, remains a mystery. Using proteomics can expand our understanding of stress effects on lichens. We investigated the effects of different doses and forms of reactive nitrogen, with and without supplementary phosphorus and potassium, on the proteome of the lichen Cladonia portentosa growing in a 'real-world' simulation of nitrogen deposition. Protein expression changed with the nitrogen treatments but mostly in the fungal partner, with NO3- mainly affecting the energetic metabolism and NH4+ also affecting the protein synthesis machinery. The photobiont mainly responded overexpressing proteins involved in energy production. This suggests that in response to nitrogen stress, the photobiont mainly supports the defensive mechanisms initiated by the mycobiont with an increased energy production. Such surplus energy is then used by the cell to maintain functionality in the presence of NO3-, while a futile cycle of protein production can be hypothesized to be induced by NH4+ excess. External supply of potassium and phosphorus influenced differently the responses of particular enzymes, likely reflecting the many processes in which potassium exerts a regulatory function.", "keywords": ["Chlorophyll", "Proteomics", "0301 basic medicine", "570", "mycobiont", "Lichens", "Nitrogen", "Cell Respiration", "Nitrate", "Mass Spectrometry", "Molecular mechanism", "03 medical and health sciences", "nitrate", "Ammonia", "Electrophoresis", " Gel", " Two-Dimensional", "Photosynthesis", "Ammonium", " Molecular mechanism", " Mycobiont", " Nitrate", " Photobiont", " Stress response", "Ammonium; Molecular mechanism; Mycobiont; Nitrate; Photobiont; Stress response; Genetics; Plant Science", "0303 health sciences", "Nitrates", "Stress response", "Chlorophyll A", "stress response", "Mycobiont", "ammonium", "Photobiont", "photobiont", "molecular mechanism", "Energy Metabolism", "Ammonium"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s00425-017-2647-2.pdf"}, {"href": "https://doi.org/10.1007/s00425-017-2647-2"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Planta", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00425-017-2647-2", "name": "item", "description": "10.1007/s00425-017-2647-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00425-017-2647-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-01-04T00:00:00Z"}}, {"id": "10.1007/s00442-002-1130-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:14:59Z", "type": "Journal Article", "created": "2014-12-22", "title": "Responses Of Soil Nitrogen Dynamics In A Mojave Desert Ecosystem To Manipulations In Soil Carbon And Nitrogen Availability", "description": "We investigated the effects of changes in soil C and N availability on N mineralization, nitrification, denitrification, NH(3) volatilization, and soil respiration in the Mojave Desert. Results indicate a C limitation to microbial N cycling. Soils from underneath the canopies of Larrea tridentata (DC.) Cov., Pleuraphis rigida Thurber, and Lycium spp. exhibited higher rates of CO(2 ) flux, lower rates of NH(3) volatilization, and a decrease in inorganic N (NH(4)(+)-N and NO(3)(-)-N) with C addition. In addition to C limitation, soils from plant interspaces also exhibited a N limitation. Soils from all locations had net immobilization of N over the course of a 15-day laboratory incubation. However, soils from interspaces had lower rates of net nitrification and potential denitrification compared to soils from under plant canopies. The response to changes in C availability appears to be a short-term increase in microbial immobilization of inorganic N. Under controlled conditions, and over a longer time period, the effects of C and N availability appear to give way to larger differences due to spatial location. These findings have implications for ecosystems undergoing changes in soil C and N availability due to such processes as desertification, exotic species invasions, or elevated atmospheric CO(2) concentration.", "keywords": ["Nitrogen", "Biological Availability", "04 agricultural and veterinary sciences", "Carbon Dioxide", "15. Life on land", "01 natural sciences", "California", "Carbon", "Soil", "Ammonia", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Desert Climate", "Volatilization", "Ecosystem", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1007/s00442-002-1130-2"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Oecologia", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00442-002-1130-2", "name": "item", "description": "10.1007/s00442-002-1130-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00442-002-1130-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2003-01-25T00:00:00Z"}}, {"id": "10.1007/s00442-005-0222-1", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-05-30T16:15:00Z", "type": "Journal Article", "created": "2005-10-04", "title": "Variations In Soil N Cycling And Trace Gas Emissions In Wet Tropical Forests", "description": "We used a previously described precipitation gradient in a tropical montane ecosystem of Hawai'i to evaluate how changes in mean annual precipitation (MAP) affect the processes resulting in the loss of N via trace gases. We evaluated three Hawaiian forests ranging from 2200 to 4050 mm year-1 MAP with constant temperature, parent material, ecosystem age, and vegetation. In situ fluxes of N2O and NO, soil inorganic nitrogen pools (NH4+ and NO3-), net nitrification, and net mineralization were quantified four times over 2 years. In addition, we performed 15N-labeling experiments to partition sources of N2O between nitrification and denitrification, along with assays of nitrification potential and denitrification enzyme activity (DEA). Mean NO and N2O emissions were highest at the mesic end of the gradient (8.7+/-4.6 and 1.1+/-0.3 ng N cm-2 h-1, respectively) and total oxidized N emitted decreased with increased MAP. At the wettest site, mean trace gas fluxes were at or below detection limit (This study aims to evaluate the application of ultrafiltration technology for the separation of particles and oil droplets and the recovery of ammonia from hydrothermal liquefaction (HTL) wastewater. Real HTL wastewater from the hydrothermal liquefaction of municipal sewage sludge was used in this study. Experiments were carried out using a submerged polyethersulfone ultrafiltration membrane with molecular weight cutoff of 100 kDa in combination with air stripping and addition to acid and base traps for recovery of volatiles. Results showed, that the best operation mode of ultrafiltration is with backwash cycles of the permeate, maintaining a flux lower than the critical flux of 6 L/h\u00b7m2. The setup led to fast stripping of ammonia, which was successfully recovered by 88% in the acid trap. This application can be considered an adequate first stage treatment of the HTL wastewater. The importance of this work is that it proves that membrane technology can be successful in treating complex real HTL wastewater, and is not only limited for applications using model solutions.

", "keywords": ["info:eu-repo/classification/ddc/660", "550", "660", "ddc:660", "Hydrothermal liquefaction wastewater", "0211 other engineering and technologies", "Ultrafiltration", "Oil and particle removal", "02 engineering and technology", "Ammonia recovery", "01 natural sciences", "6. Clean water", "Chemical engineering", "Air stripping", "628", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.jwpe.2021.102427"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Water%20Process%20Engineering", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jwpe.2021.102427", "name": "item", "description": "10.1016/j.jwpe.2021.102427", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jwpe.2021.102427"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-12-01T00:00:00Z"}}, {"id": "10.1016/j.sbsr.2022.100541", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:17:16Z", "type": "Journal Article", "created": "2022-11-21", "title": "Application of metal oxide semiconductor for detection of ammonia emissions from agricultural sources", "description": "Agricultural emissions of ammonia (NH3) reduce air quality and biodiversity. Measuring the effectiveness of mitigations measures requires rapid monitoring tools, however, conventional methods are labour intensive and costly. This study evaluated the performance of a prototype metal oxide semiconductor (MOS) gas sensor for monitoring NH3. Conventional methods were used to calibrate sensor conductance. The metal oxide semiconductor (MOS) gas sensor was calibrated against NH3 released from a 0.1\u00a0M phosphate buffer spiked with ammonium chloride and NH3 released from recently spread cattle slurry. Field measurements using the MOS sensor were compared with values measuring a Bruker Open Path Air Monitoring System. Sensor conductance and NH3 concentration were described using single site Langmuir adsorption model. Field calibrations suggest a higher detection limit above 0.1\u00a0ppm and coefficients of determination were 0.93 and 0.89 for sensors 1 and 2, respectively. For prototypes deployed under field conditions, sensitivities of 2.2 and 2.4 with nonlinearity constants of 0.53 and 0.51, were found for sensor 1 and 3 respectively. Average R2 values were 0.88 for sensor 1 and 0.92 for sensor 3. The calibrations were used to calculate NH3 concentrations from slurry emissions using MOS sensor conductance. NH3 concentrations between 0.2 and 1\u00a0ppm, were measured with standard deviation of 20% of verified concentrations. The MOS sensor is sensitive enough to detect NH3 emission from agricultural sources with concentrations above 0.2\u00a0ppm. Low power and cost of MOS sensors are an advantage over existing techniques.", "keywords": ["Emission", "Ammonia", "Calibration", "0401 agriculture", " forestry", " and fisheries", "Agriculture", "04 agricultural and veterinary sciences", "TA1-2040", "Engineering (General). Civil engineering (General)", "01 natural sciences", "Metal-oxide semiconductor", "Sensor", "0105 earth and related environmental sciences"], "contacts": [{"organization": "Bastiaan Molleman, Enrico Alessi, Dominika Krol, Phoebe A. Morton, Karen Daly,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1016/j.sbsr.2022.100541"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Sensing%20and%20Bio-Sensing%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.sbsr.2022.100541", "name": "item", "description": "10.1016/j.sbsr.2022.100541", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.sbsr.2022.100541"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-12-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2013.02.018", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-05-30T16:17:17Z", "type": "Journal Article", "created": "2013-03-07", "title": "Impact Of Urease Inhibitor On Ammonia And Nitrous Oxide Emissions From Temperate Pasture Soil Cores Receiving Urea Fertilizer And Cattle Urine", "description": "New Zealand's intensively grazed pastures receive the majority of nitrogen (N) input in the form of urea, which is the major constituent of animal urine and the most common form of mineral N in inorganic N fertilizers. In soil, urea is rapidly hydrolyzed to ammonium (NH4(+)) ions, a part of which may be lost as ammonia (NH3) and subsequently as nitrous oxide (N2O), which is a greenhouse gas. Two glasshouse experiments were conducted to study the effect of a urease inhibitor (UI), N-(n-butyl) thiophosphoric triamide (NBPT), commercially named Agrotain, applied with urine and urea on urea hydrolysis and NH3 and N2O emissions. Treatments included the commercially available products Sustain Yellow (urea+Agrotain+4% sulfur coating), Sustain Green (urea+Agrotain) and urea, and cattle urine (476 kg N ha(-1)) with and without Agrotain applied to intact soil cores of a fine sandy loam soil. The addition of Agrotain to urine and urea (i.e. Sustain Green) reduced NH3 emission by 22% to 47%, respectively. Agrotain was also effective in reducing N2O emissions from urine and Sustain Green by 62% and 48%, respectively. The reduction in N2O emissions varied with the type and amount of N applied and plant N uptake. Plant N uptake was significantly higher in the soil cores receiving Agrotain with urea than urea alone, but the slight increase in dry matter yield was non-significant. Hence, urease inhibitor reduced N losses through NH3 and N2O emissions, thereby increasing plant uptake of N.", "keywords": ["pasture", "2. Zero hunger", "nitrous oxide", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "urea", "04 agricultural and veterinary sciences", "ammonia", "nitrogen", "6. Clean water", "cattle urine", "12. Responsible consumption"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2013.02.018"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2013.02.018", "name": "item", "description": "10.1016/j.scitotenv.2013.02.018", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2013.02.018"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-11-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2013.10.011", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:17:17Z", "type": "Journal Article", "created": "2013-10-26", "title": "Shifts In The Abundance And Community Structure Of Soil Ammonia Oxidizers In A Wet Sclerophyll Forest Under Long-Term Prescribed Burning", "description": "Fire shapes global biome distribution and promotes the terrestrial biogeochemical cycles. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play a vital role in the biogeochemical cycling of nitrogen (N). However, behaviors of AOB and AOA under long-term prescribed burning remain unclear. This study was to examine how fire affected the abundances and communities of soil AOB and AOA. A long-term repeated forest fire experiment with three burning treatments (never burnt, B0; biennially burnt, B2; and quadrennially burnt, B4) was used in this study. The abundances and community structure of soil AOB and AOA were determined using quantitative PCR, restriction fragment length polymorphism and clone library. More frequent fires (B2) increased the abundance of bacterium amoA gene, but tended to decrease archaeal amoA genes. Fire also modified the composition of AOA and AOB communities. Canonical correspondence analysis showed soil pH and dissolved organic C (DOC) strongly affected AOB genotypes, while nitrate-N and DOC shaped the AOA distribution. The increased abundance of bacterium amoA gene by fires may imply an important role of AOB in nitrification in fire-affected soils. The fire-induced shift in the community composition of AOB and AOA demonstrates that fire can disturb nutrient cycles.", "keywords": ["0301 basic medicine", "570", "0303 health sciences", "Bacteria", "Nitrogen", "Forestry", "Biodiversity", "15. Life on land", "Archaea", "Nitrification", "Fires", "Trees", "Soil", "03 medical and health sciences", "Biodegradation", " Environmental", "Soil biology", "Ammonia", "13. Climate action", "Oxidation-Reduction", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2013.10.011"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2013.10.011", "name": "item", "description": "10.1016/j.scitotenv.2013.10.011", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2013.10.011"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-02-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2006.05.017", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:17:26Z", "type": "Journal Article", "created": "2006-07-11", "title": "Hydrolase Activities, Microbial Biomass And Bacterial Community In A Soil After Long-Term Amendment With Different Composts", "description": "Open AccessThe use of composts in agricultural soils is a widespread practice and the positive effects on soil and plants are known from numerous studies. However, there have been few attempts to compare the effects of different kinds of composts in one single study. The aim of this paper is to investigate to what extent and to which soil depth four major types of composts would affect the soil and its microbiota. In a crop-rotation field experiment, composts produced from (i) urban organic wastes, (ii) green wastes, (iii) manure and (iv) sewage sludge were applied at a rate equivalent to 175 kg N ha\u22121 yr\u22121 for 12 years. General (total organic C (Corg), total N (Nt), microbial biomass C (Cmic), and basal respiration), specific (enzyme activities related to C, N and P cycles), biochemical properties and bacterial genetic diversity (based on DGGE analysis of 16S rDNA) were analyzed at different depths (0\u201310, 10\u201320 and 20\u201330 cm). Compost treatment increased Corg at all depths from 11 g kg\u22121 for control soil to 16.7 g kg\u22121 for the case of sewage sludge compost. Total N increased with compost treatment at 0\u201310 cm and 10\u201320 cm depths, but not at 20\u201330 cm. Basal respiration and Cmic declined with depth, and the composts resulted in an increase of Cmic and basal respiration. Enzyme activities were different depend on the enzyme and among compost treatments, but in general, the enzyme activities were higher in the upper layers (0\u201310 and 10\u201320 cm) than in the 20\u201330 cm layer. Diversity of ammonia oxidizers and bacteria was lower in the control than in the compost soils. The type of compost had less influence on the composition of the microbial communities than did soil depth.", "keywords": ["PCR-DGGE", "2. Zero hunger", "Microbial activity", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Composts", "Hydrolase activities", "04 agricultural and veterinary sciences", "15. Life on land", "Bacterial communities", "6. Clean water", "Ammonia oxidizers", "12. Responsible consumption"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2006.05.017"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2006.05.017", "name": "item", "description": "10.1016/j.soilbio.2006.05.017", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2006.05.017"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2006-12-01T00:00:00Z"}}, {"id": "10.1016/j.wasman.2020.05.047", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-05-30T16:17:52Z", "type": "Journal Article", "created": "2020-06-13", "title": "Ammonia recovery from food waste digestate using solar heat-assisted stripping-absorption", "description": "The highest costs of stripping-absorption processes for ammonia recovery are related to energy (for heating and air supply) and chemical addition (for pH adjustment). In this paper, a simplified system that used no chemicals, and a renewable source of energy for heating, was tested to recover nitrogen as ammonium sulfate from food waste digestate. pH adjustment was achieved by CO2 stripping, and vacuum tube solar collectors were used to provide heating. The effect of different temperatures (25\u00a0\u00b0C and 45\u00a0\u00b0C) and gas to liquid ratios (1700 and 2600) on ammonia removal and recovery were assessed. Ammonia removal efficiencies higher than 91% were achieved for all evaluated experimental conditions. The solar heater showed adequate capacity to increase the temperature of the liquid digestate by 21\u00a0\u00b0C and maintain the temperature at 45\u00a0\u00b0C throughout the experiment. Tests carried out at 45\u00a0\u00b0C achieved the highest ammonia removal efficiency (98%) at the lowest evaluated G/L ratio (1700). Better absorption efficiencies could potentially have been achieved if lower inlet airflow rates and packing material had been used in the absorption column.", "keywords": ["Hot Temperature", "Nitrogen", "0211 other engineering and technologies", "02 engineering and technology", "Waste Disposal", " Fluid", "01 natural sciences", "7. Clean energy", "6. Clean water", "Refuse Disposal", "12. Responsible consumption", "Ammonia", "Food", "11. Sustainability", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.wasman.2020.05.047"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Waste%20Management", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.wasman.2020.05.047", "name": "item", "description": "10.1016/j.wasman.2020.05.047", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.wasman.2020.05.047"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-07-01T00:00:00Z"}}, {"id": "10.1016/j.watres.2018.06.016", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:17:52Z", "type": "Journal Article", "created": "2018-06-14", "title": "High-solids anaerobic digestion model for homogenized reactors", "description": "During high-solids anaerobic digestion (HS-AD) of the organic fraction of municipal solid waste (OFMSW), an important total solid (TS) removal occurs, leading to the modification of the reactor content mass/volume, in contrast to 'wet' anaerobic digestion (AD). Therefore, HS-AD mathematical simulations need to be approached differently than 'wet' AD simulations. This study aimed to develop a modelling tool based on the anaerobic digestion model 1 (ADM1) capable of simulating the TS and the reactor mass/volume dynamics in HS-AD of OFMSW. Four hypotheses were used, including the effects of apparent concentrations at high TS. The model simulated adequately HS-AD of OFMSW in batch and continuous mode, particularly the evolution of TS, reactor mass, ammonia and volatile fatty acids. By adequately simulating the reactor content mass/volume and the TS, the HS-AD model might bring further insight about potentially inhibitory mechanisms (i.e. NH3 buildup and/or acidification) occurring in HS-AD of OFMSW.", "keywords": ["[SDE] Environmental Sciences", "ADM1", "570", "[SDV]Life Sciences [q-bio]", "High-solids anaerobic digestion", " ADM1", " Reactor mass simulation", " Total solids", " Apparent concentrations", "0211 other engineering and technologies", "High-solids anaerobic digestion", "02 engineering and technology", "Solid Waste", "01 natural sciences", "7. Clean energy", "Reactor mass simulation", "total solids", "12. Responsible consumption", "high-solids anaerobic digestion", "Bioreactors", "Ammonia", "Apparent concentrations", "reactor mass simulation", "Anaerobiosis", "0105 earth and related environmental sciences", "apparent concentrations", "Total solids", "Models", " Theoretical", "Fatty Acids", " Volatile", "6. Clean water", "Refuse Disposal", "[SDV] Life Sciences [q-bio]", "[SDE]Environmental Sciences"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/718585/1/1-s2.0-S0043135418304603-main.pdf"}, {"href": "https://doi.org/10.1016/j.watres.2018.06.016"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Water%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.watres.2018.06.016", "name": "item", "description": "10.1016/j.watres.2018.06.016", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.watres.2018.06.016"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-10-01T00:00:00Z"}}, {"id": "10.1016/j.watres.2019.114932", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:17:52Z", "type": "Journal Article", "created": "2019-07-30", "title": "Assessing practical identifiability during calibration and cross-validation of a structured model for high-solids anaerobic digestion", "description": "High-solids anaerobic digestion (HS-AD) of the organic fraction of municipal solid waste (OFMSW) is operated at a total solid (TS) content\u202f\u2265\u202f10% to enhance the waste treatment economy, though it might be associated to free ammonia (NH3) inhibition. This study aimed to calibrate and cross-validate a HS-AD model for homogenized reactors in order to assess the effects of high NH3 levels in HS-AD of OFMSW, but also to evaluate the suitability of the reversible non-competitive inhibition function to reproduce the effect of NH3 on the main acetogenic and methanogenic populations. The practical identifiability of structural/biochemical parameters (i.e. 35) and initial conditions (i.e. 32) was evaluated using batch experiments at different TS and/or inoculum-to-substrate ratios. Variance-based global sensitivity analysis and approximate Bayesian computation were used for parameter optimization. The experimental data in this study permitted to estimate up to 8 biochemical parameters, whereas the rest of parameters and biomass contents were poorly identifiable. The study also showed the relatively high levels of NH3 (i.e. up to 2.3\u202fg\u202fN/L) and ionic strength (i.e. up to 0.9\u202fM) when increasing TS in HS-AD of OFMSW. However, the NH3 non-competitive function was unable to capture the acetogenic/methanogenic inhibition. Therefore, the calibration emphasized the need for target-oriented experimental data to enhance the practical identifiability and the predictive capabilities of structured HS-AD models, but also the need for further testing the NH3 inhibition function used in these simulations.", "keywords": ["[SDE] Environmental Sciences", "[SDV]Life Sciences [q-bio]", "0207 environmental engineering", "high-solids anaerobic digestion model", "Bayes Theorem", "02 engineering and technology", "Solid Waste", "01 natural sciences", "7. Clean energy", "6. Clean water", "Refuse Disposal", "12. Responsible consumption", "[SDV] Life Sciences [q-bio]", "High-solids anaerobic digestion model", " ammonia inhibition", " ionic strength", " global sensitivity analysis", " approximate bayesian computation", "Bioreactors", "global sensitivity analysis", "[SDE]Environmental Sciences", "Calibration", "High-solids anaerobic digestion model", "Anaerobiosis", "ionic strength", "Methane", "ammonia inhibition", "approximate bayesian computation", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/757589/1/Post-print%20for%20IRIS.pdf"}, {"href": "https://hal.inrae.fr/hal-02623443/file/S0043135419307067.pdf"}, {"href": "https://doi.org/10.1016/j.watres.2019.114932"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Water%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.watres.2019.114932", "name": "item", "description": "10.1016/j.watres.2019.114932", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.watres.2019.114932"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-11-01T00:00:00Z"}}, {"id": "10.1038/s41396-023-01467-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:18:18Z", "type": "Journal Article", "created": "2023-07-14", "title": "Nitrification and beyond: metabolic versatility of ammonia oxidising archaea", "description": "Abstract

Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.Under controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale.Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major cultivated phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest affinity for both ammonia and total ammonium of any characterized AOA, and these values are similar to previously determined ammonia and total ammonium affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values supports the hypothesis that\uffe2\uff80\uff94like for AOB\uffe2\uff80\uff94ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.Archaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM) and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "Bacteria", "Agriculture", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "15. Life on land", "Archaea", "Biota", "Article", "6. Clean water", "Genes", " Archaeal", "03 medical and health sciences", "Ammonia", "Genes", " Bacterial", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Oxidation-Reduction", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/srep28981"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/srep28981", "name": "item", "description": "10.1038/srep28981", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/srep28981"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-30T00:00:00Z"}}, {"id": "10.1038/srep32791", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:18:26Z", "type": "Journal Article", "created": "2016-09-06", "title": "Responses Of Soil Hydrolytic Enzymes, Ammonia-Oxidizing Bacteria And Archaea To Nitrogen Applications In A Temperate Grassland In Inner Mongolia", "description": "Abstract

We used a seven-year urea gradient applied field experiment to investigate the effects of nitrogen (N) applications on soil N hydrolytic enzyme activity and ammonia-oxidizing microbial abundance in a typical steppe ecosystem in Inner Mongolia. The results showed that N additions inhibited the soil N-related hydrolytic enzyme activities, especially in 392\uffe2\uff80\uff89kg N ha\uffe2\uff88\uff921\uffe2\uff80\uff89yr\uffe2\uff88\uff921 treatment. As N additions increased, the amoA gene copy ratios of ammonia-oxidizing archaea (AOA) to ammonia-oxidizing bacteria (AOB) decreased from 1.13 to 0.65. Pearson correlation analysis showed that the AOA gene copies were negatively related with NH4+-N content. However, the AOB gene copies were positively correlated with NO3\uffe2\uff88\uff92-N content. Moderate N application rates (56\uffe2\uff80\uff93224\uffe2\uff80\uff89kg N ha\uffe2\uff88\uff921\uffe2\uff80\uff89yr\uffe2\uff88\uff921) accompanied by P additions are beneficial to maintaining the abundance of AOB, as opposed to the inhibition of highest N application rate (392\uffe2\uff80\uff89kg N ha\uffe2\uff88\uff921\uffe2\uff80\uff89yr\uffe2\uff88\uff921) on the abundance of AOB. This study suggests that the abundance of AOB and AOA would not decrease unless N applications exceed 224\uffe2\uff80\uff89kg N ha\uffe2\uff88\uff921\uffe2\uff80\uff89yr\uffe2\uff88\uff921 in temperate grasslands in Inner Mongolia.

", "keywords": ["2. Zero hunger", "China", "Bacteria", "Nitrogen", "Hydrolysis", "04 agricultural and veterinary sciences", "15. Life on land", "Archaea", "Grassland", "Nitrification", "Article", "Soil", "Ammonia", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Oxidation-Reduction", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/srep32791"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/srep32791", "name": "item", "description": "10.1038/srep32791", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/srep32791"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-09-06T00:00:00Z"}}, {"id": "10.1038/srep43853", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:18:26Z", "type": "Journal Article", "created": "2017-03-08", "title": "A New Urease-Inhibiting Formulation Decreases Ammonia Volatilization And Improves Maize Nitrogen Utilization In North China Plain", "description": "Abstract

Overuse of urea, low nitrogen (N) utilization, and large N losses are common in maize production in North China Plain (NCP). To solve these problems, we conducted two field experiments at Shangzhuang and Quzhou in NCP to test the ability of a newly developed urease inhibitor product Limus\uffc2\uffae to decrease NH3 volatilization from urea applied to maize. Grain yield, apparent N recovery efficiency (REN) and N balance when using urea applied with or without Limus were also measured over two maize growing seasons. Cumulative NH3 loss in the two weeks following urea application without Limus ranged from 9\uffe2\uff80\uff93108\uffe2\uff80\uff89kg N ha\uffe2\uff88\uff921, while Limus addition significantly decreased NH3 loss by a mean of 84%. Urea with Limus did not significantly increase maize yields (P\uffe2\uff80\uff89<\uffe2\uff80\uff890.05) compared with urea alone. However, a significant 11\uffe2\uff80\uff9317% improvement in REN with Limus was observed at QZ. The use of urea-N plus Limus would permit a reduction in N applications of 55\uffe2\uff80\uff9360% compared to farmers\uffe2\uff80\uff99 practice and/or further 20% N saving compared with optimized urea-N rate (150\uffe2\uff80\uff89kg N ha\uffe2\uff88\uff921, based on N requirement by target yield of 7.5 t ha\uffe2\uff88\uff921), and would achieve the same maize yields but with significantly decreased NH3 loss and increased N utilization.

", "keywords": ["2. Zero hunger", "China", "Nitrogen", "Agriculture", "04 agricultural and veterinary sciences", "Urease", "Zea mays", "01 natural sciences", "Article", "Soil", "Ammonia", "Urea", "0401 agriculture", " forestry", " and fisheries", "Biomass", "Seasons", "Volatilization", "Fertilizers", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1038/srep43853"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/srep43853", "name": "item", "description": "10.1038/srep43853", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/srep43853"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-03-08T00:00:00Z"}}, {"id": "10.1039/d1ra03337a", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:18:28Z", "type": "Journal Article", "created": "2021-09-10", "title": "Exploring the performance of a functionalized CNT-based sensor array for breathomics through clustering and classification algorithms: from gas sensing of selective biomarkers to discrimination of chronic obstructive pulmonary disease", "description": "

Extensive application of clustering and classification algorithms shows the potential of a CNT-based sensor array in breathomics.

", "keywords": ["electronic nose", "Linear discriminant analysis", "Principal component analysis", "Breath analysis", "02 engineering and technology", "sensors", "Supported Vectror Machine", "01 natural sciences", "nanotubes", "Ammonia; Biomarkers; Carbon nanotubes; Classification (of information); Clustering algorithms; Molecules; Nitrogen oxides; Principal component analysis; Sulfur compounds; Support vector machines", "0104 chemical sciences", "3. Good health", "breathomics", "Chemistry", "SWCNTs", "COPD", "ta318", "e-nose", "0210 nano-technology", "ta215"]}, "links": [{"href": "https://iris.cnr.it/bitstream/20.500.14243/536855/1/RSC%20Adv._2021.pdf"}, {"href": "https://boa.unimib.it/bitstream/10281/517427/2/d1ra03337a.pdf%3b"}, {"href": "https://publicatt.unicatt.it/bitstream/10807/190102/1/d1ra03337a.pdf"}, {"href": "http://pubs.rsc.org/en/content/articlepdf/2021/RA/D1RA03337A"}, {"href": "https://doi.org/10.1039/d1ra03337a"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/RSC%20Advances", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1039/d1ra03337a", "name": "item", "description": "10.1039/d1ra03337a", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1039/d1ra03337a"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-01-01T00:00:00Z"}}, {"id": "10.1056/nejm199703063361004", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-05-30T16:18:35Z", "type": "Journal Article", "created": "2002-07-27", "title": "Sympathetic Cardioneuropathy in Dysautonomias", "description": "The classification of dysautonomias has been confusing, and the pathophysiology obscure. We examined sympathetic innervation of the heart in patients with acquired, idiopathic dysautonomias using thoracic positron-emission tomography and assessments of the entry rate of the sympathetic neurotransmitter norepinephrine into the cardiac venous drainage (cardiac norepinephrine spillover). We related the laboratory findings to signs of sympathetic neurocirculatory failure (orthostatic hypotension and abnormal blood-pressure responses associated with the Valsalva maneuver), central neural degeneration, and responsiveness to treatment with levodopa-carbidopa (Sinemet).Cardiac scans were obtained after intravenous administration of 6-[18F]fluorodopamine in 26 patients with dysautonomia. Fourteen had sympathetic neurocirculatory failure--three with no signs of central neurodegeneration (pure autonomic failure), two with parkinsonism responsive to treatment with levodopa-carbidopa, and nine with central neurodegeneration unresponsive to treatment with levodopa-carbidopa (the Shy-Drager syndrome). The rates of cardiac norepinephrine spillover were estimated on the basis of concentrations of intravenously infused [3H]norepinephrine during catheterization of the right side of the heart.Patients with pure autonomic failure or parkinsonism and sympathetic neurocirculatory failure had no myocardial 6-[18F]fluorodopamine-derived radioactivity or cardiac norepinephrine spillover, indicating loss of myocardial sympathetic-nerve terminals, whereas patients with the Shy-Drager syndrome had increased levels of 6-[18F]fluorodopamine-derived radioactivity, indicating intact sympathetic terminals and absent nerve traffic. Patients with dysautonomia who did not have sympathetic neurocirculatory failure had normal levels of 6-[18F]fluorodopamine-derived radioactivity in myocardium and normal rates of cardiac norepinephrine spillover.The results of 6-[18F]fluorodopamine positron-emission tomography and neurochemical analyses support a new clinical pathophysiologic classification of dysautonomias, based on the occurrence of sympathetic neurocirculatory failure, signs of central neurodegeneration, and responsiveness to levodopa-carbidopa.", "keywords": ["Adult", "Aged", " 80 and over", "Fluorine Radioisotopes", "Nitrogen Radioisotopes", "Sympathetic Nervous System", "Epinephrine", "Dopamine", "Myocardium", "Shy-Drager Syndrome", "Heart", "Parkinson Disease", "Middle Aged", "3. Good health", "Diagnosis", " Differential", "Levodopa", "Norepinephrine", "Autonomic Nervous System Diseases", "Ammonia", "Parasympathetic Nervous System", "Reference Values", "Coronary Circulation", "Humans", "Aged", "Tomography", " Emission-Computed"], "contacts": [{"organization": "Graeme Eisenhofer, Richard O. Cannon, Irwin J. Kopin, Courtney Holmes, David S. Goldstein,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1056/nejm199703063361004"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20England%20Journal%20of%20Medicine", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1056/nejm199703063361004", "name": "item", "description": "10.1056/nejm199703063361004", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1056/nejm199703063361004"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "1997-01-01T00:00:00Z"}}, {"id": "10.1088/1748-9326/acd709", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:18:58Z", "type": "Journal Article", "created": "2023-05-19", "title": "Fertilization strategies for abating N pollution at the scale of a highly vulnerable and diverse semi-arid agricultural region (Murcia, Spain)", "description": "Abstract

Overuse of N fertilizers in crops has induced the disruption of the N cycle, triggering the release of reactive N (Nr) to the environment. Several EU policies have been developed to address this challenge, establishing targets to reduce agricultural Nr losses. Their achievement could be materialized through the introduction of fertilizing innovations such as incorporating fertilizer into soils, using urease inhibitors, or by adjusting N inputs to crop needs that could impact in both yields and environment. The Murcia region (southeastern Spain) was selected as a paradigmatic case study, since overfertilization has induced severe environmental problems in the region in the last decade, to assess the impact of a set of 8 N fertilizing alternatives on crop yields and environmental Nr losses. Some of these practices imply the reduction of N entering in crops. We followed an integrated approach analyzing the evolution of the region in the long-term (1860\uffe2\uff80\uff932018) and considering nested spatial- (from grid to region) and systems scales (from crops to the full agro-food system). We hypothesized that, even despite reduction of N inputs, suitable solutions for the abatement of Nr can be identified without compromising crop yields. The most effective option to reduce Nr losses was removing synthetic N fertilizers, leading to 75% reductions in N surpluses mainly due to a reduction of 64% of N inputs, but with associated yield penalties (31%\uffe2\uff80\uff9335%). The most feasible alternative was the removal of urea, resulting in 19% reductions of N inputs, 15%\uffe2\uff80\uff9321% declines in N surplus, and negligible yield losses. While these measures are applied at the field scale, their potential to produce a valuable change can only be assessed at regional scale. Because of this, a spatial analysis was performed showing that largest Nr losses occurred in irrigated horticultural crops. The policy implications of the results are discussed.Ammonia-oxidising archaea (AOA) are environmentally important microorganisms involved in the biogeochemical cycling of nitrogen. Routine cultivation of AOA is exclusively performed in liquid cultures and reports on their growth on solid medium are scarce. The ability to grow AOA on solid medium would be beneficial for not only the purification of enrichment cultures but also for developing genetic tools. The aim of this study was to develop a reliable method for growing individual colonies from AOA cultures on solid medium. Three phylogenetically distinct AOA strains were tested: \uffe2\uff80\uff98Candidatus Nitrosocosmicus franklandus C13\uffe2\uff80\uff99, Nitrososphaera viennensis EN76 and \uffe2\uff80\uff98Candidatus Nitrosotalea sinensis Nd2\uffe2\uff80\uff99. Of the gelling agents tested, agar and Bacto-agar severely inhibited growth of all three strains. In contrast, both \uffe2\uff80\uff98Ca. N. franklandus C13\uffe2\uff80\uff99 and N. viennensis EN76 tolerated Phytagel\uffe2\uff84\uffa2 while the acidophilic \uffe2\uff80\uff98Ca. N. sinensis Nd2\uffe2\uff80\uff99 was completely inhibited. Based on these observations, we developed a Liquid-Solid (LS) method that involves immobilising cells in Phytagel\uffe2\uff84\uffa2 and overlaying with liquid medium. This approach resulted in the development of visible distinct colonies from \uffe2\uff80\uff98Ca. N. franklandus C13\uffe2\uff80\uff99 and N. viennensis EN76 cultures and lays the groundwork for the genetic manipulation of this group of microorganisms.Ammonia oxidizers are key players in the global nitrogen cycle and are responsible for the oxidation of ammonia to nitrite, which is further oxidized to nitrate by other microorganisms. Their activity can lead to adverse effects on some human-impacted environments, including water pollution through leaching of nitrate and emissions of the greenhouse gas nitrous oxide (N2O). Ammonia monooxygenase (AMO) is the key enzyme in microbial ammonia oxidation and shared by all groups of aerobic ammonia oxidizers. The AMO has not been purified in an active form, and much of what is known about its potential structure and function comes from studies on its interactions with inhibitors. The archaeal AMO is less well studied as ammonia oxidizing archaea were discovered much more recently than their bacterial counterparts. The inhibition of ammonia oxidation by aliphatic alcohols (C1-C8) using the model terrestrial ammonia oxidizing archaeon \uffe2\uff80\uff98Candidatus Nitrosocosmicus franklandus\uffe2\uff80\uff99 C13 and the ammonia oxidizing bacterium Nitrosomonas europaea was examined in order to expand knowledge about the range of inhibitors of ammonia oxidizers. Methanol was the most potent specific inhibitor of the AMO in both ammonia oxidizers, with half-maximal inhibitory concentrations (IC50) of 0.19 and 0.31\uffe2\uff80\uff89mM, respectively. The inhibition was AMO-specific in \uffe2\uff80\uff98Ca. N. franklandus\uffe2\uff80\uff99 C13 in the presence of C1-C2 alcohols, and in N. europaea in the presence of C1-C3 alcohols. Higher chain-length alcohols caused non-specific inhibition and also inhibited hydroxylamine oxidation. Ethanol was tolerated by \uffe2\uff80\uff98Ca. N. franklandus\uffe2\uff80\uff99 C13 at a higher threshold concentration than other chain-length alcohols, with 80\uffe2\uff80\uff89mM ethanol being required for complete inhibition of ammonia oxidation.Heterotrophic nitrifiers are able to oxidize and remove ammonia from nitrogen\uffe2\uff80\uff90rich wastewaters but the genetic elements of heterotrophic ammonia oxidation are poorly understood. Here, we isolated and identified a novel heterotrophic nitrifier, Alcaligenes ammonioxydans sp. nov. strain HO\uffe2\uff80\uff901, oxidizing ammonia to hydroxylamine and ending in the production of N2 gas. Genome analysis revealed that strain HO\uffe2\uff80\uff901 encoded a complete denitrification pathway but lacks any genes coding for homologous to known ammonia monooxygenases or hydroxylamine oxidoreductases. Our results demonstrated strain HO\uffe2\uff80\uff901 denitrified nitrite (not nitrate) to N2 and N2O at anaerobic and aerobic conditions respectively. Further experiments demonstrated that inhibition of aerobic denitrification did not stop ammonia oxidation and N2 production. A gene cluster (dnfT1RT2ABCD) was cloned from strain HO\uffe2\uff80\uff901 and enabled E. coli accumulated hydroxylamine. Sub\uffe2\uff80\uff90cloning showed that genetic cluster dnfAB or dnfABC already enabled E. coli cells to produce hydroxylamine and further to 15N2 from (15NH4)2SO4. Transcriptome analysis revealed these three genes dnfA, dnfB and dnfC were significantly upregulated in response to ammonia stimulation. Taken together, we concluded that strain HO\uffe2\uff80\uff901 has a novel dnf genetic cluster for ammonia oxidation and this dnf genetic cluster encoded a previously unknown pathway of direct ammonia oxidation (Dirammox) to N2.

", "keywords": ["Alcaligenes ammonioxydans sp. nov.", "0301 basic medicine", "106014 Genomics", "Nitrogen", "HYDROXYLAMINE OXIDASE", "direct ammonia oxidation (Dirammox)", "OXIDATION", "REDUCTASE", "Water Purification", "THIOSPHAERA-PANTOTROPHA", "PYRUVIC-OXIME", "03 medical and health sciences", "heterotrophic nitrifier", "Ammonia", "106014 Genomik", "Escherichia coli", "Alcaligenes", "wastewater", "Nitrites", "106022 Mikrobiologie", "HETEROTROPHIC NITRIFICATION", "0303 health sciences", "PURIFICATION", "Sewage", "AEROBIC DENITRIFICATION", "Nitrification", "Aerobiosis", "6. Clean water", "NITROGEN", "FAECALIS", "Denitrification", "106022 Microbiology", "Oxidation-Reduction"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.15751"}, {"href": "https://doi.org/10.1111/1462-2920.15751"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1462-2920.15751", "name": "item", "description": "10.1111/1462-2920.15751", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.15751"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-09-28T00:00:00Z"}}, {"id": "10.1111/1462-2920.16316", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:19:16Z", "type": "Journal Article", "created": "2023-01-04", "title": "The effect of methane and methanol on the terrestrial ammonia\u2010oxidizing archaeon \u2018Candidatus Nitrosocosmicus franklandus C13\u2019", "description": "Abstract

The ammonia monooxygenase (AMO) is a key enzyme in ammonia\uffe2\uff80\uff90oxidizing archaea, which are abundant and ubiquitous in soil environments. The AMO belongs to the copper\uffe2\uff80\uff90containing membrane monooxygenase (CuMMO) enzyme superfamily, which also contains particulate methane monooxygenase (pMMO). Enzymes in the CuMMO superfamily are promiscuous, which results in co\uffe2\uff80\uff90oxidation of alternative substrates. The phylogenetic and structural similarity between the pMMO and the archaeal AMO is well\uffe2\uff80\uff90established, but there is surprisingly little information on the influence of methane and methanol on the archaeal AMO and terrestrial nitrification. The aim of this study was to examine the effects of methane and methanol on the soil ammonia\uffe2\uff80\uff90oxidizing archaeon \uffe2\uff80\uff98Candidatus Nitrosocosmicus franklandus C13\uffe2\uff80\uff99. We demonstrate that both methane and methanol are competitive inhibitors of the archaeal AMO. The inhibition constants (Ki) for methane and methanol were 2.2 and 20\uffe2\uff80\uff89\uffce\uffbcM, respectively, concentrations which are environmentally relevant and orders of magnitude lower than those previously reported for ammonia\uffe2\uff80\uff90oxidizing bacteria. Furthermore, we demonstrate that a specific suite of proteins is upregulated and downregulated in \uffe2\uff80\uff98Ca. Nitrosocosmicus franklandus C13\uffe2\uff80\uff99 in the presence of methane or methanol, which provides a foundation for future studies into metabolism of one\uffe2\uff80\uff90carbon (C1) compounds in ammonia\uffe2\uff80\uff90oxidizing archaea.Ammonia\uffe2\uff80\uff90oxidising archaea (AOA) are important microorganisms contributing towards the nitrogen flux in the environment. Unlike archaea from other major phyla, genetic tools are yet to be developed for the AOA, and identification of antibiotic resistance markers for selecting mutants is required for a genetic system. The aim of this study was to test the effects of selected antibiotics (hygromycin B, neomycin, apramycin, puromycin, novobiocin) on pure cultures of three well studied AOA strains, \uffe2\uff80\uff98Candidatus Nitrosocosmicus franklandianus C13\uffe2\uff80\uff99, Nitrososphaera viennensis EN76 and Nitrosopumilus maritimus SCM1. Puromycin, hygromycin B and neomycin inhibited some but not all tested archaeal strains. All strains were resistant to apramycin and inhibited by novobiocin to various degrees. As N. viennensis EN76 was relatively more resistant to the tested antibiotics, a wider range of concentrations and compounds (chloramphenicol, trimethoprim, statins) was tested against this strain. N. viennensis EN76 was inhibited by trimethoprim, but not by chloramphenicol, and growth recovered within days in the presence of simvastatin, suggesting either degradation of, or spontaneous resistance against, this compound. This study highlights the physiological differences between different genera of AOA and has identified new candidate antibiotics for selective enrichment and the development of selectable markers for genetic systems in AOA.Unprecedented nitrogen (N) inputs into terrestrial ecosystems have profoundly altered soil N cycling. Ammonia oxidizers and denitrifiers are the main producers of nitrous oxide (N2O), but it remains unclear how ammonia oxidizer and denitrifier abundances will respond to N loading and whether their responses can predict N\uffe2\uff80\uff90induced changes in soil N2O emission. By synthesizing 101 field studies worldwide, we showed that N loading significantly increased ammonia oxidizer abundance by 107% and denitrifier abundance by 45%. The increases in both ammonia oxidizer and denitrifier abundances were primarily explained by N loading form, and more specifically, organic N loading had stronger effects on their abundances than mineral N loading. Nitrogen loading increased soil N2O emission by 261%, whereas there was no clear relationship between changes in soil N2O emission and shifts in ammonia oxidizer and denitrifier abundances. Our field\uffe2\uff80\uff90based results challenge the laboratory\uffe2\uff80\uff90based hypothesis that increased ammonia oxidizer and denitrifier abundances by N loading would directly cause higher soil N2O emission. Instead, key abiotic factors (mean annual precipitation, soil pH, soil C:N ratio, and ecosystem type) explained N\uffe2\uff80\uff90induced changes in soil N2O emission. Altogether, these findings highlight the need for considering the roles of key abiotic factors in regulating soil N transformations under N loading to better understand the microbially mediated soil N2O emission.Anthropogenic nitrogen (N) loading alters soil ammonia\uffe2\uff80\uff90oxidizing archaea (AOA) and bacteria (AOB) abundances, likely leading to substantial changes in soil nitrification. However, the factors and mechanisms determining the responses of soil AOA:AOB and nitrification to N loading are still unclear, making it difficult to predict future changes in soil nitrification. Herein, we synthesize\uffc2\uffa068 field studies around the world to evaluate the impacts of N loading on soil ammonia oxidizers and nitrification. Across a wide range of biotic and abiotic factors, climate is the most important driver of the responses of AOA:AOB to N loading. Climate does not directly affect the N\uffe2\uff80\uff90stimulation of nitrification, but does so via climate\uffe2\uff80\uff90related shifts in AOA:AOB. Specifically, climate modulates the responses of AOA:AOB to N loading by affecting soil pH, N\uffe2\uff80\uff90availability and moisture. AOB play a dominant role in affecting nitrification in dry climates, while the impacts from AOA can exceed AOB in humid climates. Together, these results suggest that climate\uffe2\uff80\uff90related shifts in soil ammonia\uffe2\uff80\uff90oxidizing community maintain the N\uffe2\uff80\uff90stimulation of nitrification, highlighting the importance of microbial community composition in mediating the responses of the soil N cycle to N loading.