The rate and pathway of ferrihydrite transformation in soil depends on the properties of the soil pore water and diffusion processes.
The present review covers developments in studies of nanomaterials (NMs) in the environment since our much cited review in 2008. We discuss novel insights into fate and behavior, metrology, transformations, bioavailability, toxicity mechanisms, and environmental impacts, with a focus on terrestrial and aquatic systems. Overall, the findings were that: 1) despite substantial developments, critical gaps remain, in large part due to the lack of analytical, modeling, and field capabilities, and also due to the breadth and complexity of the area; 2) a key knowledge gap is the lack of data on environmental concentrations and dosimetry generally; 3) substantial evidence shows that there are nanospecific effects (different from the effects of both ions and larger particles) on the environment in terms of fate, bioavailability, and toxicity, but this is not consistent for all NMs, species, and relevant processes; 4) a paradigm is emerging that NMs are less toxic than equivalent dissolved materials but more toxic than the corresponding bulk materials; and 5) translation of incompletely understood science into regulation and policy continues to be challenging. There is a developing consensus that NMs may pose a relatively low environmental risk, but because of uncertainty and lack of data in many areas, definitive conclusions cannot be drawn. In addition, this emerging consensus will likely change rapidly with qualitative changes in the technology and increased future discharges. Environ Toxicol Chem 2018;37:2029\uffe2\uff80\uff932063. \uffc2\uffa9 2018 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.
", "keywords": ["aquatic and soil organisms", "hazard/risk assessment", "Nanoecotoxicity", "Biological Availability", "Environmental Exposure", "Nanometrology", "Aquatic and soil organisms; Nanometrology; Hazard/risk assessment; Nanoecotoxicity; Nanomaterials", "Ecotoxicology", "nanometrology", "01 natural sciences", "Nanostructures", "nanoecotoxicity", "13. Climate action", "Aquatic and soil organisms", "Oxidation-Reduction", "Hazard/risk assessment", "Ecosystem", "Nanomaterials", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://setac.onlinelibrary.wiley.com/doi/pdf/10.1002/etc.4147"}, {"href": "https://doi.org/10.1002/etc.4147"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Toxicology%20and%20Chemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/etc.4147", "name": "item", "description": "10.1002/etc.4147", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/etc.4147"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-04-06T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2020.140835", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:17:20Z", "type": "Journal Article", "created": "2020-07-12", "title": "A chemical, microbiological and (eco)toxicological scheme to understand the efficiency of UV-C/H2O2 oxidation on antibiotic-related microcontaminants in treated urban wastewater", "description": "An assessment comprising chemical, microbiological and (eco)toxicological parameters of antibiotic-related microcontaminants, during the application of UV-C/H2O2 oxidation in secondary-treated urban wastewater, is presented. The process was investigated at bench scale under different oxidant doses (0-50\u00a0mg\u00a0L-1) with regard to its capacity to degrade a mixture of antibiotics (i.e. ampicillin, clarithromycin, erythromycin, ofloxacin, sulfamethoxazole, tetracycline and trimethoprim) with an initial individual concentration of 100\u00a0\u03bcg\u00a0L-1. The process was optimized with respect to the oxidant dose. Under the optimum conditions, the inactivation of selected bacteria and antibiotic resistant bacteria (ARB) (i.e. faecal coliforms, Enterococcus spp., Pseudomonasaeruginosa and total heterotrophs), and the reduction of the abundance of selected antibiotic resistance genes (ARGs) (e.g. blaOXA, qnrS, sul1, tetM) were investigated. Also, phytotoxicity against three plant species, ecotoxicity against Daphnia magna, genotoxicity, oxidative stress and cytotoxicity were assessed. Apart from chemical actinometry, computational fluid dynamics (CFD) modelling was applied to estimate the fluence rate. For the given wastewater quality and photoreactor type used, 40\u00a0mg\u00a0L-1 H2O2 were required for the complete degradation of the studied antibiotics after 18.9\u00a0J\u00a0cm-2. Total bacteria and ARB inactivation was observed at UV doses <1.5\u00a0J\u00a0cm-2 with no bacterial regrowth being observed after 24\u00a0h. The abundance of most ARGs was reduced at 16\u00a0J\u00a0cm-2. The process produced a final effluent with lower phytotoxicity compared to the untreated wastewater. The toxicity against Daphnia magna was shown to increase during the chemical oxidation. Although genotoxicity and oxidative stress fluctuated during the treatment, the latter led to the removal of these effects. Overall, it was made apparent from the high UV fluence required, that the particular reactor although extensively used in similar studies, it does not utilize efficiently the incident radiation and thus, seems not to be suitable for this kind of studies.", "keywords": ["Life sciences; biology", "info:eu-repo/classification/ddc/570", "570", "biology", "0211 other engineering and technologies", "Hydrogen Peroxide", "02 engineering and technology", "Wastewater", "Life sciences", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "13. Climate action", "616", "11. Sustainability", "Animals", "ddc:570", "Oxidation-Reduction", "Water Pollutants", " Chemical", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2020.140835"}, {"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.2020.140835", "name": "item", "description": "10.1016/j.scitotenv.2020.140835", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2020.140835"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-11-01T00:00:00Z"}}, {"id": "10.1007/s00128-020-02835-8", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-05-30T16:14:49Z", "type": "Journal Article", "created": "2020-03-28", "title": "Fate of 2,4,6-tribromophenol in soil under different redox conditions.", "description": "Fate of 2,4,6-tribromophenol (TBP) in environmental matrices is obscure. We used 14C-tracer to investigated mineralization, transformation, and non-extractable residue (NER)-formation of TBP in a soil under continuously oxic, continuously anoxic, and anoxic-oxic alteration conditions. In all cases, TBP rapidly dissipated, mineralized to CO2, and formed NERs in the soil. Considerable amounts of transformation products (2-12%) were detected during the incubation. Marked mineralization (13-26%) indicated that soil microorganisms used TBP as their energy source. About 62-70% of the initial radioactivity was transformed into NERs, being mainly attributed to binding to humic and fulvic acid fractions. TBP transformation was significantly faster under oxic conditions than under anoxic conditions, and was boosted when the soil redox changed from anoxic to oxic state. The results provide new insights into fate of TBP in soil and suggest the importance to evaluate the stability of NERs for risk assessment of TBP in soil.", "keywords": ["Minerals", "Soil", "Phenols", "0211 other engineering and technologies", "Soil Pollutants", "Benzopyrans", "02 engineering and technology", "Oxidation-Reduction", "01 natural sciences", "Humic Substances", "6. Clean water", "0105 earth and related environmental sciences"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s00128-020-02835-8.pdf"}, {"href": "https://doi.org/10.1007/s00128-020-02835-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bulletin%20of%20Environmental%20Contamination%20and%20Toxicology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00128-020-02835-8", "name": "item", "description": "10.1007/s00128-020-02835-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00128-020-02835-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-28T00:00:00Z"}}, {"id": "10.1007/s00253-011-3535-5", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "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": "10.1016/j.soilbio.2012.04.019", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-05-30T16:17:31Z", "type": "Journal Article", "created": "2012-05-03", "title": "Ammonia Volatilization Losses From Surface-Applied Urea With Urease And Nitrification Inhibitors", "description": "Abstract Urease inhibitor (UI) and nitrification inhibitor (NI) have the potential to improve N-use efficiency of applied urea and minimize N losses via gaseous emissions of ammonia (NH3) to the atmosphere and nitrate ( NO 3 \u2212 ) leaching into surface and ground water bodies. There is a growing interest in the formulations of coating chemical fertilizers with both UI and NI. However, limited information is available on the combined use of UI and NI applied with urea fertilizer. Therefore the aim of this study was to investigate the effects of treating urea with both UI and NI to minimize NH3 volatilization. Two experiments were set up in volatilization chambers under controlled conditions to examine this process. In the first experiment, UR was treated with the urease inhibitor NBPT [N-(n-butyl) thiophosphoric acid triamide] at a rate of 1060\u00a0mg\u00a0kg\u22121 urea and/or with the nitrification inhibitor DCD (dicyandiamide) at rates equivalent to 5 or 10% of the urea N. A randomized experimental design with five treatments and five replicates was used: 1) UR, 2) UR\u00a0+\u00a0NBPT, 3) UR\u00a0+\u00a0DCD 10%, 4) UR\u00a0+\u00a0NBPT\u00a0+\u00a0DCD 5%, and 5) UR\u00a0+\u00a0NBPT\u00a0+\u00a0DCD 10%. The fertilizer treatments were applied to the surface of an acidic Red Latosol soil moistened to 60% of the maximum water retention and placed inside volatilization chambers. Controls chambers were added to allow for NH3 volatilized from unfertilized soil or contained in the air that swept over the soil surface. The second experiment had an additional treatment with surface-applied DCD. The chambers were glass vessels (1.5\u00a0L) fit with air inlet and outlet tubings to allow air to pass over the soil. Ammonia volatilized was swept and carried to a flask containing a boric acid solution to trap the gas and then measured daily by titration with a standardized H2SO4 solution. Continuous measurements were recorded for 19 and 23 days for the first and second experiment, respectively. The soil samples were then analyzed for UR\u2013, NH 4 + \u2013 , and NO 3 \u2212 \u2013 N . Losses of NH3 by volatilization with unamended UR ranged from 28 to 37% of the applied N, with peak of losses observed the third day after fertilization. NBPT delayed the peak of NH3 losses due to urease inhibition and reduced NH3 volatilization between 54 and 78% when compared with untreated UR. Up to 10 days after the fertilizer application, NH3 losses had not been affected by DCD in the UR or the UR\u00a0+\u00a0NBPT treatments; thereafter, NH3 volatilization tended to decrease, but not when DCD was present. As a consequence, the addition of DCD caused a 5\u201316% increase in NH3 volatilization losses of the fertilizer N applied as UR from both the UR and the UR\u00a0+\u00a0NBPT treatments. Because the effectiveness of NBPT to inhibit soil urease activity was strong only in the first week, it could be concluded that DCD did not affect the action of NBPT but rather, enhanced volatilization losses by maintaining higher soil NH 4 + concentration and pH for a longer time. Depending on the combination of factors influencing NH3 volatilization, DCD could even offset the beneficial effect of NBPT in reducing NH3 volatilization losses.", "keywords": ["soil chemistry", "Urease inhibitors", "Surface treatment", "nutrient use efficiency", "Ammonia volatilization", "01 natural sciences", "630", "Ammonia", "Oxidation", "DCD", "Urea", "Urea fertilizers", "Fertilizers", "volatilization", "Groundwater", "0105 earth and related environmental sciences", "soil surface", "coating", "fertilizer application", "Urease inhibitor", "04 agricultural and veterinary sciences", "Nitrification inhibitor", "Nitrification", "Inorganic acids", "6. Clean water", "enzyme activity", "inhibitor", "pH effects", "Metabolism", "NBPT", "Denitrification", "Leaching", "Soils", "0401 agriculture", " forestry", " and fisheries", "Experiments", "Stabilized fertilizer"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2012.04.019"}, {"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.2012.04.019", "name": "item", "description": "10.1016/j.soilbio.2012.04.019", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2012.04.019"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-09-01T00:00:00Z"}}, {"id": "10.1016/j.chemosphere.2019.02.158", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-05-30T16:16:22Z", "type": "Journal Article", "created": "2019-02-25", "title": "Bioreduction of selenate in an anaerobic biotrickling filter using methanol as electron donor", "description": "The anaerobic bioreduction of selenate, fed in step (up to 60\u202fmg.L-1) or continuous (\u223c7\u202fmg.L-1) trickling mode, in the presence of gas-phase methanol (4.3-50\u202fg\u202fm-3.h-1) was evaluated in a biotrickling filter (BTF). During the 48\u202fd of step-feed and 41\u202fd of continuous-feed operations, average selenate removal efficiencies (RE)\u202f>\u202f90% and \u223c68% was achieved, corresponding to a selenate reduction rate of, respectively, 7.3 and 4.5\u202fmg.L-1.d-1. During the entire period of BTF operation, 65.6% of the total Se fed as SeO42- was recovered. Concerning gas-phase methanol, the maximum elimination capacity (ECmax) was 46.4\u202fg\u202fm-3.h-1, with a RE\u202f>\u202f80%. Methanol was mainly utilized for acetogenesis and converted to volatile fatty acids (VFA) in the liquid-phase. Up to 5000\u202fmg.L-1 of methanol and 800\u202fmg.L-1 of acetate accumulated in the trickling liquid of the BTF.", "keywords": ["Bacteria", "Sewage", "Methanol", "0211 other engineering and technologies", "02 engineering and technology", "Selenic Acid", "Fatty Acids", " Volatile", "Archaea", "01 natural sciences", "6. Clean water", "Biodegradation", " Environmental", "Bioreactors", "Oxidation-Reduction", "Filtration", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.chemosphere.2019.02.158"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Chemosphere", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.chemosphere.2019.02.158", "name": "item", "description": "10.1016/j.chemosphere.2019.02.158", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.chemosphere.2019.02.158"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-01T00:00:00Z"}}, {"id": "10.1016/j.biortech.2018.12.056", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:16:16Z", "type": "Journal Article", "created": "2018-12-17", "title": "Assessing arsenic redox state evolution in solution and solid phase during As(III) sorption onto chemically-treated sewage sludge digestate biochars", "description": "This work aimed to determine the arsenic redox state distribution during As(III) sorption onto chemically-modified biochars. A solid-liquid extraction protocol using phosphoric (0.3\u202fM) and ascorbic (0.5\u202fM) acids at 80\u202f\u00b0C for 20\u202fmin was established to ensure a quantitative recovery and stability of As(III) during the extraction. During sorption experiments, the redox conversions of As occurred and As(III) was either stable or partially oxidized in solution. The As distribution strongly varied depending on the biochar chemical treatment performed as well as the selected washing procedures (batch versus column washings). As(III) oxidation was favored with the KOH-modified biochar washed in batch mode. This oxidation was mostly induced by the biochar solid compounds rather than by soluble compounds released in solution. The As redox state distribution of As sorbed onto the biochars was successfully assessed using the extraction procedure. Arsenic was predominantly sorbed as As(III) (76-92%) onto the biochars.", "keywords": ["550", "Sewage", "[SPI.GPROC] Engineering Sciences [physics]/Chemical and Process Engineering", "Charcoal", "[SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering", "Adsorption", "540", "Oxidation-Reduction", "01 natural sciences", "6. Clean water", "Arsenic", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.biortech.2018.12.056"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioresource%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.biortech.2018.12.056", "name": "item", "description": "10.1016/j.biortech.2018.12.056", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.biortech.2018.12.056"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-03-01T00:00:00Z"}}, {"id": "10.1016/j.ecolmodel.2023.110507", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:16:27Z", "type": "Journal Article", "created": "2023-10-10", "title": "Interactive effects of microbial functional diversity and carbon availability on decomposition \u2013 A theoretical exploration", "description": "Microbial functional diversity in litter and soil has been hypothesized to affect the rate of decomposition of organic matter and other soil ecosystem functions. However, there are no clear theoretical expectations on how these effects might change with substrate availability, heterogeneity in the substrate chemistry, and different aspects of functional diversity itself (number of microbial groups vs. distribution of functional traits). To explore how these factors shape the decomposition-diversity relation, we carry out numerical experiments using a flexible reaction network comprising microbial processes and interactions with bioavailable carbon (extracellular degradation, uptake, respiration, growth, and mortality), and ecological processes (competition among the different groups). We also considered diverse carbon substrates, in terms of varying nominal oxidation state of carbon (NOSC). The reaction network was used to test the effects of (i) number of microbial groups, (ii) number of carbon pools, (iii) microbial functional diversity, and (iv) amount of bioavailable carbon. We found that the decomposition rate constant increases with increasing substrate concentration and heterogeneity, as well as with increasing microbial functional diversity or variance of microbial traits, albeit these biological factors are less important. The multivariate dependence of the decomposition rate constant (and other decomposition and microbial growth metrics) on substrate and microbial factors can be described using power laws with exponents lower than one, indicating that diversity effects on decomposition and microbial growth are reduced at high substrate concentration and heterogeneity, or at high microbial diversity.
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.Significant rates of atmospheric dihydrogen (H2) consumption have been observed in temperate soils due to the activity of high-affinity enzymes, such as the group 1h [NiFe]-hydrogenase. We designed broadly inclusive primers targeting the large subunit gene (hhyL) of group 1h [NiFe]-hydrogenases for long-read sequencing to explore its taxonomic distribution across soils. This approach revealed a diverse collection of microorganisms harboring hhyL, including previously unknown groups and taxonomically not assignable sequences. Acidobacterial group 1h [NiFe]-hydrogenase genes were abundant and expressed in temperate soils. To support the participation of acidobacteria in H2 consumption, we studied two representative mesophilic soil acidobacteria, which expressed group 1h [NiFe]-hydrogenases and consumed atmospheric H2 during carbon starvation. This is the first time mesophilic acidobacteria, which are abundant in ubiquitous temperate soils, have been shown to oxidize H2 down to below atmospheric concentrations. As this physiology allows bacteria to survive periods of carbon starvation, it could explain the success of soil acidobacteria. With our long-read sequencing approach of group 1h [NiFe]-hydrogenase genes, we show that the ability to oxidize atmospheric levels of H2 is more widely distributed among soil bacteria than previously recognized and could represent a common mechanism enabling bacteria to persist during periods of carbon deprivation.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": {"license": "Open Access", "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": "AbstractWe 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": "10.1039/d2em00290f", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:18:28Z", "type": "Journal Article", "created": "2022-09-22", "title": "Ferrihydrite transformations in flooded paddy soils: rates, pathways, and product spatial distributions", "description": "The rate and pathway of ferrihydrite transformation in soil depends on the properties of the soil pore water and diffusion processes.
We studied the transformation of 57Fe-labelled ferrihydrite and lepidocrocite mixed with a flooded paddy soil by using 57Fe-M\uffc3\uffb6ssbauer spectroscopy.Ferrihydrite, a poorly crystalline Fe(iii)-oxyhydroxide, is abundant in soils and is often found associated with organic matter. Siderite is stabilised against oxidation in the presence of Low Molecular Weight Organic Acids (LMWOAs) with implications for iron mineral transformations and therefore contaminant and nutrient cycling.
Microbial soil habitats are characterized by rapid shifts in substrate and nutrient availabilities, as well as chemical and physical parameters. One such parameter that can vary in soil is oxygen; thus, microbial survival is dependent on adaptation to this substrate. To better understand the metabolic abilities and adaptive strategies to oxygen-deprived environments, we combined genomics with transcriptomics of a model organism, Acidobacterium capsulatum, to explore the effect of decreasing, environmentally relevant oxygen concentrations. The decrease from 10 to 0.1\uffc2\uffa0\uffc2\uffb5M oxygen (3.6 to 0.036 pO2% present atmospheric level, respectively) caused the upregulation of the transcription of genes involved in signal transduction mechanisms, energy production and conversion and secondary metabolites biosynthesis, transport, and catabolism based on clusters of orthologous group categories. Contrary to established observations for aerobic metabolism, key genes in oxidative stress response were significantly upregulated at lower oxygen concentrations, presumably due to an NADH/NAD+ redox ratio imbalance as the cells transitioned into nanoxia. Furthermore, A. capsulatum adapted to nanoxia by inducing a respiro-fermentative metabolism and rerouting fluxes of its central carbon and energy pathways to adapt to high NADH/NAD+ redox ratios. Our results reveal physiological features and metabolic capabilities that allowed A. capsulatum to adapt to oxygen-limited conditions, which could expand into other environmentally relevant soil strains.Volatile organic compounds (VOCs) play an essential role in climate change and air pollution by modulating tropospheric oxidation capacity and providing precursors for ozone and aerosol formation. Arctic permafrost buries large quantities of frozen soil carbon, which could be released as VOCs with permafrost thawing or collapsing as a consequence of global warming. However, due to the lack of reported studies in this field and the limited capability of the conventional measurement techniques, it is poorly understood how much VOCs could be emitted from thawing permafrost and the chemical speciation of the released VOCs. Here we apply a Vocus proton-transfer-reaction time-of-flight mass spectrometer (PTR-TOF) in laboratory incubations for the first time to examine the release of VOCs from thawing permafrost peatland soils sampled from Finnish Lapland. The warming-induced rapid VOC emissions from the thawing soils were mainly attributed to the direct release of old, trapped gases from the permafrost. The average VOC fluxes from thawing permafrost were four times as high as those from the active layer (the top layer of soil in permafrost terrain). The emissions of less volatile compounds, i.e. sesquiterpenes and diterpenes, increased substantially with rising temperatures. Results in this study demonstrate the potential for substantive VOC releases from thawing permafrost. We anticipate that future global warming could stimulate VOC emissions from the Arctic permafrost, which may significantly influence the Arctic atmospheric chemistry and climate change.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"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=OXIDATION&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=OXIDATION&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=OXIDATION&", "hreflang": "en-US"}, {"rel": "next", "type": "application/geo+json", "title": "items (next)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=OXIDATION&offset=50", "hreflang": "en-US"}], "numberMatched": 123, "numberReturned": 50, "distributedFeatures": [], "timeStamp": "2026-05-30T17:28:38.493511Z"}