Increasing food demand coupled with climate change pose a great challenge to agricultural systems. In this review we summarize recent advances in our knowledge of how plants, together with their associated microbiota, shape rhizosphere processes. We address (molecular) mechanisms operating at the plant\uffe2\uff80\uff93microbe-soil interface and aim to link this knowledge with actual and potential avenues for intensifying agricultural systems, while at the same time reducing irrigation water, fertilizer inputs and pesticide use. Combining in-depth knowledge about above and belowground plant traits will not only significantly advance our mechanistic understanding of involved processes but also allow for more informed decisions regarding agricultural practices and plant breeding. Including belowground plant-soil-microbe interactions in our breeding efforts will help to select crops resilient to abiotic and biotic environmental stresses and ultimately enable us to produce sufficient food in a more sustainable agriculture in the upcoming decades. MIN\u00a0>\u00a0ORG, indicating a higher N2O consumption potential in the NT-ORG treatment, which was confirmed in terms of cumulative emissions. The AOB/16S ratio was strongly affected by fertilisation and was higher in the MIN than in the ORG and CON treatments, regardless of the tillage system. Multiple regression has revealed that this ratio is one of the most important variables explaining cumulative N2O emissions, possibly reflecting the role of bacterial ammonia oxidisers in minerally fertilised soil. Although the AOB/16S ratio aligned well with the measured N2O emissions in our experimental field, the higher genetic potential for denitrification expressed by the (nirK\u00a0+\u00a0nirS)/(nosZI\u00a0+\u00a0nosZII) ratio in NT than CT was not realized in the form of increased emissions. Our results suggest that organic fertilisation in combination with NT shows a promising combination for mitigating N2O emissions; however, addressing the yield gap is necessary before incorporating it in recommendations for farmers.", "keywords": ["du\u0161ik", "2. Zero hunger", "compost", "denitrification", "denitrifikacija", "N$_2$O", "kompost", "15. Life on land", "sonaravno kmetijstvo", "nitrifikacija", "nitrification", "6. Clean water", "conservation agriculture", "conservation agriculture", " compost", " N$_2$O", " N-cycle", " nitrification", " denitrification", "N-cycle", "13. Climate action", "ohranitveno kmetijstvo", "ohranitveno kmetijstvo", " sonaravno kmetijstvo", " kompost", " du\u0161ik", " nitrifikacija", " denitrifikacija", "info:eu-repo/classification/udc/631.4"], "contacts": [{"organization": "Govednik, Anton, Eler, Klemen, Miheli\u010d, Rok, Suhadolc, Marjetka,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2024.172054"}, {"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.2024.172054", "name": "item", "description": "10.1016/j.scitotenv.2024.172054", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2024.172054"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-06-01T00:00:00Z"}}, {"id": "10.1023/a:1004383015778", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-09-20T16:16:35Z", "type": "Journal Article", "title": "The Effect Of Different N Substrates On Biological N2o Production From Forest And Agricultural Light Textured Soils", "description": "N2O emissions from two slightly alkaline sandy soils, from arable land and a woodland, were determined in a laboratory experiment in which the soils were incubated with different sources of nitrogen, with or without glucose, and with 0, 1 and 100 mL C2H2 L-1. Large differences in the rate of N2O production were observed between the two soils and between the different N treatments. The arable soil showed very low N2O emissions derived from reduced forms of N as compared with the N2O which was produced when the soil was provided with NO2- or NO3- and a C source, suggesting a very active denitrifier population. In contrast, the woodland soil showed a very low denitrification activity and a much higher N2O production derived from the oxidation of NH4+ and reduction of NO2- by some processes probably mediated by autotrophic or heterotrophic nitrifiers or dissimilatory NO2- reducers. In both soils, the highest N2O emissions were induced by NO2- addition. Those emissions were demonstrated to have a biological origin, as no significant N2O emissions were measured when the soil was autoclaved.", "keywords": ["Acetylene; Denitrification; N sources; N; 2; O; Nitrification;"]}, "links": [{"href": "https://doi.org/10.1023/a:1004383015778"}, {"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": "10.1023/a:1004383015778", "name": "item", "description": "10.1023/a:1004383015778", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1023/a:1004383015778"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "1998-01-01T00:00:00Z"}}, {"id": "10.1038/s41396-021-01064-z", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:16:46Z", "type": "Journal Article", "created": "2021-07-27", "title": "Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities", "description": "Abstract
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.In the present work, post-burning soil N2O fluxes and related microbial processes were investigated in a Mediterranean shrubland subjected to experimental fires. Nine plots were selected, of which three were used as controls, three were burned with low-intensity fire and three with higher intensity fire. N2O fluxes, soil humidity and temperature were measured starting 2 days before burning and for 1 year after fire. Potential net nitrification, denitrification enzyme activity, mineral N and organic C were measured from soil samples collected periodically after burning. Cumulative data indicate a doubling of N2O production in burned plots over 1 year. Burned plots showed an increase of frequency of hot spots of N2O production. A slight detrimental effect of fire on the analysed biological activities was detected only immediately after burning. After 3 months, both potential net nitrification and denitrification enzyme activity had mostly recovered and potential net nitrification further increased over control levels in the following months. Fire seemed to induce a change in the main source of N2O, which in control plots was represented by heterotrophic activity (50\uffe2\uff80\uff9375%), whereas in burned plots it was mostly of autotrophic origin, most probably due to the significant increase of soil NH4+ after burning.
", "keywords": ["2. Zero hunger", "Nitrous oxide", "denitrification; fire intensity; nitrification; soil nitrogen;", "13. Climate action", "Nitrous oxide; soil; fire", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "15. Life on land", "fire", "soil"]}, "links": [{"href": "https://doi.org/10.1071/wf10120"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/International%20Journal%20of%20Wildland%20Fire", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1071/wf10120", "name": "item", "description": "10.1071/wf10120", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1071/wf10120"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-01-01T00:00:00Z"}}, {"id": "10.1111/1365-2435.12475", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-09-20T16:17:24Z", "type": "Journal Article", "created": "2015-05-12", "title": "Nitrogen Saturation In Humid Tropical Forests After 6years Of Nitrogen And Phosphorus Addition: Hypothesis Testing", "description": "Summary
Nitrogen (N) saturation hypothesis suggests that when an ecosystem reaches N\uffe2\uff80\uff90saturation, continued N input will cause increased N leaching, nitrous oxide (N2O) emission, and N mineralization and nitrification rates. It also suggests that a different element will become the main limiting factor when N saturation has been reached. Although this hypothesis has been tested in temperate forests, whether they can be directly applied to N\uffe2\uff80\uff90saturated tropical forests remain poorly addressed.
To test this hypothesis, soil inorganic N, soil N mineralization and nitrification rate, soil N2O emission rate and nitrate () leaching rate were measured in an N\uffe2\uff80\uff90saturated old\uffe2\uff80\uff90growth tropical forest in southern China, after 6\uffc2\uffa0years of N and P addition. We hypothesized that N addition would stimulate further N saturation, but P addition might alleviate N saturation.
As expected, our results showed that six continuous years of experimental N addition did cause further N saturation, which was indicated by significant increases in soil inorganic N concentration, N2O emission and nitrate () leaching. However, in contrast to our expectations, N addition significantly decreased in\uffc2\uffa0situ rates of net N mineralization and nitrification, which could be related to associated changes in enzyme activity and microbial community composition. On the other hand, P addition mitigated N saturation, as expected. Soil inorganic N concentration, N2O emission and leaching decreased significantly after P addition, but the net rates of N mineralization and nitrification were significantly increased.
Our results provide a new understanding of the N saturation hypothesis, suggesting that the effects of long\uffe2\uff80\uff90term N deposition on net N mineralization and nitrification rates in N\uffe2\uff80\uff90saturated tropical forests can be negative and that P addition can alleviate N saturation in such tropical systems.
", "keywords": ["China", "Nitrogen mineralization and nitrification", "Tropical forest", "Nitrogen saturation", "13. Climate action", "Phosphorus addition", "0401 agriculture", " forestry", " and fisheries", "N 2 O emission", "04 agricultural and veterinary sciences", "15. Life on land", "Nitrogen deposition"]}, "links": [{"href": "https://doi.org/10.1111/1365-2435.12475"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Functional%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1365-2435.12475", "name": "item", "description": "10.1111/1365-2435.12475", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1365-2435.12475"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-06-06T00:00:00Z"}}, {"id": "10.1111/1462-2920.15751", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:17:25Z", "type": "Journal Article", "created": "2021-09-28", "title": "Novel Alcaligenes ammonioxydans sp. nov. from wastewater treatment sludge oxidizes ammonia to N2 with a previously unknown pathway", "description": "SummaryHeterotrophic 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": "10.1128/msystems.00562-19", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:17:51Z", "type": "Journal Article", "created": "2020-01-13", "title": "Transcriptomic Response of Nitrosomonas europaea Transitioned from Ammonia- to Oxygen-Limited Steady-State Growth", "description": "Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea , growing under oxygen-limited conditions. Large areas in the tropics receive elevated atmospheric nutrient inputs. Presently, little is known on how nitrogen (N) cycling in tropical montane forest soils will respond to such increased nutrient inputs. We assessed how gross rates of mineral N production (N mineralization and nitrification) and microbial N retention (NH4+ and NO3\uffe2\uff88\uff92 immobilization and dissimilatory NO3\uffe2\uff88\uff92 reduction to NH4+ [DNRA]) change with elevated N and phosphorus (P) inputs in montane forest soils at 1000\uffe2\uff80\uff90, 2000\uffe2\uff80\uff90, and 3000\uffe2\uff80\uff90m elevations in south Ecuador. At each elevation, four replicate plots (20 \uffc3\uff97 20 m each) of control, N (added at 50 kg N\uffc2\uffb7ha\uffe2\uff88\uff921\uffc2\uffb7yr\uffe2\uff88\uff921), P (added at 10 kg P\uffc2\uffb7ha\uffe2\uff88\uff921\uffc2\uffb7yr\uffe2\uff88\uff921), and combined N + P additions have been established since 2008. We measured gross N cycling rates in 2010 and 2011, using 15N pool dilution techniques with in situ incubation of intact soil cores taken from the top 5 cm of soil. In control plots, gross soil\uffe2\uff80\uff90N cycling rates decreased with increase in elevation, and microbial N retention was tightly coupled with mineral N production. At 1000 m and 2000 m, four\uffe2\uff80\uff90year N and combined N + P additions increased gross mineral N production but decreased NH4+ and NO3\uffe2\uff88\uff92 immobilization and DNRA compared to the control. At 3000 m, four\uffe2\uff80\uff90year N and combined N + P additions increased gross N mineralization rates and decreased DNRA compared to the control; although NH4+ and NO3\uffe2\uff88\uff92 immobilization in the N and N + P plots were not different from the control, these were lower than their respective mineral N production. At all elevations, decreased microbial N retention was accompanied by decreased microbial biomass C and C:N ratio. P addition did not affect any of the soil\uffe2\uff80\uff90N cycling processes. Our results signified that four years of N addition, at a rate expected to occur at these sites, uncoupled the soil\uffe2\uff80\uff90N cycling processes, as indicated by decreased microbial N retention. This fast response of soil\uffe2\uff80\uff90N cycling processes across elevations implies that greater attention should be paid to the biological implications on montane forests of such uncoupled soil\uffe2\uff80\uff90N cycling.
", "keywords": ["2. Zero hunger", "Altitude", "Phosphorus", "04 agricultural and veterinary sciences", "Forests", "Nitrogen Cycle", "15. Life on land", "dissimilatory nitrate reduction to ammonium; gross N mineralization; gross nitrification; microbial N immobilization;nitrogen and phosphorus additions; nutrient manipulation experiment; tropical Andes ;tropical montane forests", "Random Allocation", "Soil", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Ecuador", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1890/14-0295.1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1890/14-0295.1", "name": "item", "description": "10.1890/14-0295.1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1890/14-0295.1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-03-01T00:00:00Z"}}, {"id": "10.1590/s1516-35982011000700024", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:18:16Z", "type": "Journal Article", "created": "2017-02-03", "title": "Impact Of Different Grazing Systems For Bovine Cattle On The Soil Microbiological And Chemical Characteristics", "description": "The objective of this work was to study the effect of grazing systems: rotational, continuous and the absence of cattle, in pastures of Brachiaria brizantha on microbial activity (respiratory, potential nitrification, solubilizing, and enzymatic) and on the chemical attributes (contents of organic carbon, total nitrogen, organic phosphorus, and moisture) of Eutrustox soil over one year. Eight Canchim breed animals were used. The samples were collected in the four seasons from 2005 to 2006. The average of organic C, organic P, and moisture contents, as well as potential nitrification and solubilizing activity and urease and acid phosphatase activities were significantly higher in the spring and/or summer than in autumn and/or winter. The total nitrogen amounts did not vary among seasons. While the respiratory activity was larger during winter and summer, cellulase activity was smaller during spring than in the other seasons. Except for organic P, higher values of the variables studied were observed in the rotational grazing. The results indicate that the hot and rainy season and the rotational grazing system cause increases in the soil microbiological and chemical attributes.", "keywords": ["urease", "2. Zero hunger", "cellulase", "550", "potential nitrification", "microbial respiratory activity", "04 agricultural and veterinary sciences", "15. Life on land", "SF1-1100", "630", "phosphatase", "Animal culture", "Cellulase", "0401 agriculture", " forestry", " and fisheries"], "contacts": [{"organization": "Garcia, Martha Regina Lucizano, Sampaio, Alexandre Amstalden Moraes, Nahas, Ely,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1590/s1516-35982011000700024"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Revista%20Brasileira%20de%20Zootecnia", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1590/s1516-35982011000700024", "name": "item", "description": "10.1590/s1516-35982011000700024", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1590/s1516-35982011000700024"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-07-01T00:00:00Z"}}, {"id": "10.3389/fenvs.2014.00025", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-09-20T16:18:55Z", "type": "Journal Article", "created": "2014-07-03", "description": "Open AccessPeer reviewed", "keywords": ["2. Zero hunger", "nitrous oxide", "nitrifier-denitrification", "codenitrification", "Nitrous Oxide", "04 agricultural and veterinary sciences", "15. Life on land", "nitrification", "6. Clean water", "Environmental sciences", "nitrogen fertilizers", "13. Climate action", "nitrous oxide", " charcoal", " nitrification", " DCD", " codenitrification", " nitrogen fertilizers", "Charcoal", "Environmental Science", "DCD", "0401 agriculture", " forestry", " and fisheries", "GE1-350", "charcoal", "Nitrogen fertilizers"], "contacts": [{"organization": "S\u00e1nchez-Garc\u00eda, Mar\u00eda, Roig, Asunci\u00f3n, S\u00e1nchez-Monedero, Miguel \u00c1ngel, Cayuela, Mar\u00eda Luz,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.3389/fenvs.2014.00025"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Environmental%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fenvs.2014.00025", "name": "item", "description": "10.3389/fenvs.2014.00025", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fenvs.2014.00025"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-07-03T00:00:00Z"}}, {"id": "10.3390/f7020045", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:19:04Z", "type": "Journal Article", "created": "2016-02-19", "description": "Microbial-mediated decomposition and nutrient mineralization are major drivers of forest productivity. As landscape-scale fuel reduction treatments are being implemented throughout the fire-prone western United States of America, it is important to evaluate operationally how these wildfire mitigation treatments alter belowground processes. We quantified these important belowground components before and after management-applied fuel treatments of thinning alone, thinning combined with prescribed fire, and prescribed fire in ponderosa pine (Pinus ponderosa) stands at the Southwest Plateau, Fire and Fire Surrogate site, Arizona. Fuel treatments did not alter pH, total carbon and nitrogen (N) concentrations, or base cations of the forest floor (O horizon) or mineral soil (0\uffe2\uff80\uff935 cm) during this 2-year study. In situ rates of net N mineralization and nitrification in the surface mineral soil (0\uffe2\uff80\uff9315 cm) increased 6 months after thinning with prescribed fire treatments; thinning only resulted in net N immobilization. The rates returned to pre-treatment levels after one year. Based on phospholipid fatty acid composition, microbial communities in treated areas were similar to untreated areas (control) in the surface organic horizon and mineral soil (0\uffe2\uff80\uff935 cm) after treatments. Soil potential enzyme activities were not significantly altered by any of the three fuel treatments. Our results suggest that a variety of one-time alternative fuel treatments can reduce fire hazard without degrading soil fertility.
", "keywords": ["2. Zero hunger", "Ecology", "Life on Land", "fuel treatments", "13. Climate action", "Forestry Sciences", "fuel treatments; nitrification; nitrogen mineralization; phospholipid fatty acids; soil enzymes", "Plant Biology", "phospholipid fatty acids", "15. Life on land", "soil enzymes", "nitrification", "nitrogen mineralization"], "contacts": [{"organization": "Overby, Steven T, Hart, Stephen C,", "roles": ["creator"]}]}, "links": [{"href": "http://www.mdpi.com/1999-4907/7/2/45/pdf"}, {"href": "https://escholarship.org/content/qt54s4m5pt/qt54s4m5pt.pdf"}, {"href": "https://doi.org/10.3390/f7020045"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Forests", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/f7020045", "name": "item", "description": "10.3390/f7020045", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/f7020045"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-02-18T00:00:00Z"}}, {"id": "10.5424/sjar/2008062-320", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:21:05Z", "type": "Journal Article", "created": "2013-11-21", "description": "The aim of this experiment was to evaluate the effects of adding DMPP (3,4-dimethylpyrazole phosphate) to urea on nitrate leaching and maize (Zea mays L.) yield over two growing seasons. Two nitrogen (N) levels (optimum and excessive) were applied to an irrigated maize crop under Mediterranean conditions. There were five treatments: optimal N (as urea) and the same dose plus DMPP; optimal N (as urea plus 40 kg N/ha) and the same N dose plus DMPP; and a control with no added N fertilizer. The maize was irrigated with an overhead mobile-line sprinkler system. EnviroSCAN probes were used to determine drainage and evapotranspiration and ceramic cups to obtain soil solution samples at a soil depth of 1.4 m. The use of DMPP with urea reduced nitrate leaching. No phytotoxic effects were observed due to the DMPP. There were no differences in grain yield between treatments with and without DMPP at the same rate of N. When DMPP was applied, sodium was displaced from the soil exchange complex due to increased NH4+ concentration, which also increased the electrical conductivity of soil in the drainage zone.
", "keywords": ["ZEA MAYS; APLICACION DE ABONOS; ABONOS NITROGENADOS; UREA; NITRATOS; LIXIVIACION; POLUCION DE AGUAS SUBTERRANEAS; INHIBIDORES DE LA NITRIFICACION; CONTROL DE LA CONTAMINACION; RENDIMIENTO DE CULTIVOS", "NITRIFICATION INHIBITORS", "INHIBIDORES DE LA NITRIFICACION", "NITROGEN FERTILIZERS", "CONTROL DE LA CONTAMINACION", "LEACHING", "POLLUTION CONTROL", "GROUNDWATER POLLUTION", "NITRATES", "Fertilizing", "RENDIMIENTO DE CULTIVOS", "CROP YIELD", "FERTILIZER APPLICATION", "APLICACION DE ABONOS", "ZEA MAYS", "ZEA MAYS; FERTILIZER APPLICATION; NITROGEN FERTILIZERS; UREA; NITRATES; LEACHING; GROUNDWATER POLLUTION; NITRIFICATION INHIBITORS; POLLUTION CONTROL; CROP YIELD", "POLUCION DE AGUAS SUBTERRANEAS", "2. Zero hunger", "ABONOS NITROGENADOS", "0402 animal and dairy science", "04 agricultural and veterinary sciences", "6. Clean water", "NITRATOS", "0401 agriculture", " forestry", " and fisheries", "LIXIVIACION", "UREA"], "contacts": [{"organization": "D\u00edez L\u00f3pez, J.A., Hernaiz, P.,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5424/sjar/2008062-320"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Spanish%20Journal%20of%20Agricultural%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.5424/sjar/2008062-320", "name": "item", "description": "10.5424/sjar/2008062-320", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5424/sjar/2008062-320"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-06-01T00:00:00Z"}}, {"id": "11353/10.1376671", "type": "Feature", "geometry": null, "properties": {"updated": "2026-09-20T16:21:54Z", "type": "Journal Article", "created": "2020-01-13", "title": "Transcriptomic Response of Nitrosomonas europaea Transitioned from Ammonia- to Oxygen-Limited Steady-State Growth", "description": "Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea , growing under oxygen-limited conditions. 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.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.Increasing food demand coupled with climate change pose a great challenge to agricultural systems. In this review we summarize recent advances in our knowledge of how plants, together with their associated microbiota, shape rhizosphere processes. We address (molecular) mechanisms operating at the plant\uffe2\uff80\uff93microbe-soil interface and aim to link this knowledge with actual and potential avenues for intensifying agricultural systems, while at the same time reducing irrigation water, fertilizer inputs and pesticide use. Combining in-depth knowledge about above and belowground plant traits will not only significantly advance our mechanistic understanding of involved processes but also allow for more informed decisions regarding agricultural practices and plant breeding. Including belowground plant-soil-microbe interactions in our breeding efforts will help to select crops resilient to abiotic and biotic environmental stresses and ultimately enable us to produce sufficient food in a more sustainable agriculture in the upcoming decades.