{"type": "FeatureCollection", "features": [{"id": "10.1016/j.envexpbot.2020.104095", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:12Z", "type": "Journal Article", "created": "2020-04-25", "title": "Alternation of wet and dry sides during partial rootzone drying irrigation enhances leaf ethylene evolution", "description": "Soil drying increases endogenous ABA and ACC concentrations in planta, but how these compounds interact to regulate stomatal responses to soil drying and re-watering is still unclear. To determine the temporal dynamics and physiological significance of root, xylem and leaf ABA and ACC concentrations in response to deficit irrigation (DI) or partial rootzone drying (PRD-F) and re-watering, these variables were measured in plants exposed to similar whole pot soil water contents. Both DI and PRD-F plants received only a fraction of the irrigation supplied to well-watered (WW) plants, either to all (DI) or part (PRD-F) of the rootzone of plants grown in split-pots. Both DI and PRD-F induced partial stomatal closure, increased root ABA and ACC accumulation consistent with local soil water content, but did not affect xylem or leaf concentrations of these compounds compared to WW plants. Two hours after re-watering all (DI-RW) or part of the rootzone (PRD-A) to the same soil water content, stomatal conductance returned to WW values or further decreased respectively. Re-watering the whole rootzone had no effect on xylem and leaf ABA and ACC concentrations, while re-watering the dry side of the pot in PRD plants had no effect on xylem and leaf ABA concentrations but increased xylem and leaf ACC concentrations and leaf ethylene evolution. Leaf water potential was similar between all irrigation treatments, with stomatal conductance declining as xylem ABA concentrations and leaf ACC concentrations increased. Prior to re-watering PRD plants, accounting for the spatial differences in soil water uptake best explained variation in xylem ACC concentration suggesting root-to-shoot ACC signalling, but this model did not account for variation in xylem ACC concentration after re-watering the dry side of PRD plants. Thus local (foliar) and long-distance (root-to-shoot) variation in ACC status both seem important in regulating the temporal dynamics of foliar ethylene evolution in plants exposed to PRD.", "keywords": ["0106 biological sciences", "Irrigation", "Stomatal conductance", "Root-to-shoot signalling", "Ethylene", "Physiological significance", "Deficit irrigation", "Plant Science", "Leaf water", "F06 Irrigation", "01 natural sciences", "ACC", "Ecology", " Evolution", " Behavior and Systematics", "580", "2. Zero hunger", "Xylem", "15. Life on land", "F60 Plant physiology and biochemistry", "6. Clean water", "Horticulture", "13. Climate action", "Soil water", "Agronomy and Crop Science", "Soil moisture heterogeneity", "Partial rootzone drying"]}, "links": [{"href": "https://eprints.lancs.ac.uk/id/eprint/144510/1/Juan_EEB_Manuscript_final.pdf"}, {"href": "https://doi.org/10.1016/j.envexpbot.2020.104095"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20and%20Experimental%20Botany", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envexpbot.2020.104095", "name": "item", "description": "10.1016/j.envexpbot.2020.104095", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envexpbot.2020.104095"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-01T00:00:00Z"}}, {"id": "10.1016/j.jplph.2012.02.014", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:46Z", "type": "Journal Article", "created": "2012-04-24", "title": "Drought Stress Has Contrasting Effects On Antioxidant Enzymes Activity And Phenylpropanoid Biosynthesis In Fraxinus Ornus Leaves: An Excess Light Stress Affair?", "description": "The experiment was conducted using Fraxinus ornus plants grown outside under full sunlight irradiance, and supplied with 100% (well-watered, WW), 40% (mild drought, MD), or 20% (severe drought, SD) of the daily evapotranspiration demand, with the main objective of exploring the effect of excess light stress on the activity of antioxidant enzymes and phenylpropanoid biosynthesis. Net CO\u2082 assimilation rate at saturating light and daily assimilated CO\u2082 were significantly smaller in SD than in WW and MD plants. Xanthophyll-cycle pigments supported nonphotochemical quenching to a significantly greater extent in SD than in MD and WW leaves. As a consequence, the actual efficiency of PSII (\u03a6(PSII)) was smaller, while the excess excitation-energy in the photosynthetic apparatus was greater in SD than in WW or MD plants. The concentrations of violaxanthin-cycle pigments relative to total chlorophyll (Chl(tot)) exceeded 200 mmol mol\u207b\u00b9 Chl(tot) in SD leaves at the end of the experiment. This leads to hypothesize for zeaxanthin a role not only as nonphotochemical quencher, but also as chloroplast antioxidant. Reductions in ascorbate peroxidase and catalase activities, as drought-stress progressed, were paralleled by greater accumulations of esculetin and quercetin 3-O-glycosides, both phenylpropanoids having effective capacity to scavenge H\u2082O\u2082. The drought-induced accumulation of esculetin and quercetin 3-O-glycosides in the vacuoles of mesophyll cells is consistent with their putative functions as reducing agents for H\u2082O\u2082 in excess light-stressed leaves. Nonetheless, the concentration of H\u2082O\u2082 and the lipid peroxidation were significantly greater in SD than in MD and WW leaves. It is speculated that vacuolar phenylpropanoids may constitute a secondary antioxidant system, even on a temporal basis, activated upon the depletion of primary antioxidant defences, and aimed at keeping whole-cell H\u2082O\u2082 within a sub-lethal concentration range.", "keywords": ["0301 basic medicine", "Analysis of Variance", "Principal Component Analysis", "0303 health sciences", "Time Factors", "Light", "Propanols", "Antioxidant enzymes Drought stress Phenylpropanoids Water relations Violaxanthin-cycle pigments", "Hydrogen Peroxide", "Pigments", " Biological", "Carbon Dioxide", "15. Life on land", "Antioxidants", "6. Clean water", "Antioxidant enzymes; Drought stress; Phenylpropanoids; Violaxanthin-cycle pigments; Water relations; Analysis of Variance; Antioxidants; Carbon Dioxide; Fraxinus; Hydrogen Peroxide; Malondialdehyde; Mesophyll Cells; Microscopy", " Fluorescence; Photosynthesis; Pigments", " Biological; Plant Leaves; Principal Component Analysis; Propanols; Stress", " Physiological; Time Factors; Droughts; Light; Plant Science; Physiology; Agronomy and Crop Science", "Droughts", "Plant Leaves", "03 medical and health sciences", "Fraxinus", "Microscopy", " Fluorescence", "Stress", " Physiological", "Antioxidant enzymes; drought stress; flavonoids", "Malondialdehyde", "Photosynthesis", "Mesophyll Cells"]}, "links": [{"href": "https://doi.org/10.1016/j.jplph.2012.02.014"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Plant%20Physiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jplph.2012.02.014", "name": "item", "description": "10.1016/j.jplph.2012.02.014", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jplph.2012.02.014"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-07-01T00:00:00Z"}}, {"id": "10.1007/s00442-007-0750-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:44Z", "type": "Journal Article", "created": "2007-05-09", "title": "Mangrove Growth In New Zealand Estuaries: The Role Of Nutrient Enrichment At Sites With Contrasting Rates Of Sedimentation", "description": "Mangrove forest coverage is increasing in the estuaries of the North Island of New Zealand, causing changes in estuarine ecosystem structure and function. Sedimentation and associated nutrient enrichment have been proposed to be factors leading to increases in mangrove cover, but the relative importance of each of these factors is unknown. We conducted a fertilization study in estuaries with different sedimentation histories in order to determine the role of nutrient enrichment in stimulating mangrove growth and forest development. We expected that if mangroves were nutrient-limited, nutrient enrichment would lead to increases in mangrove growth and forest structure and that nutrient enrichment of trees in our site with low sedimentation would give rise to trees and sediments that converged in terms of functional characteristics on control sites in our high sedimentation site. The effects of fertilizing with nitrogen (N) varied among sites and across the intertidal zone, with enhancements in growth, photosynthetic carbon gain, N resorption prior to leaf senescence and the leaf area index of canopies being significantly greater at the high sedimentation sites than at the low sedimentation sites, and in landward dwarf trees compared to seaward fringing trees. Sediment respiration (CO(2) efflux) was higher at the high sedimentation site than at the low one sedimentation site, but it was not significantly affected by fertilization, suggesting that the high sedimentation site supported greater bacterial mineralization of sediment carbon. Nutrient enrichment of the coastal zone has a role in facilitating the expansion of mangroves in estuaries of the North Island of New Zealand, but this effect is secondary to that of sedimentation, which increases habitat area and stimulates growth. In estuaries with high sediment loads, enrichment with N will cause greater mangrove growth and further changes in ecosystem function.", "keywords": ["nutrient resorption efficiency", "Whangapoua", "0106 biological sciences", "Geologic Sediments", "Nitrogen", "Performance", "soil respiration", "01 natural sciences", "Rhizophora-mangle", "C1", "Oxygen Consumption", "Plant-growth", "Herbivory", "Photosynthesis", "Deposition", "Ecosystem", "580", "photosynthesis", "Avicenna marina", "Ecology", "leaf area index", "Plant Stems", "Phosphorus", "Soil respiration", "Limitation", "15. Life on land", "Carbon", "Plant Leaves", "Leaf area index", "770400 Coastal and Estuarine Environment", "Nutrient resorption efficiency", "Waikopua", "Avicennia", "Seasons", "270402 Plant Physiology", "New Zealand"]}, "links": [{"href": "https://doi.org/10.1007/s00442-007-0750-y"}, {"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/s00442-007-0750-y", "name": "item", "description": "10.1007/s00442-007-0750-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00442-007-0750-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-05-10T00:00:00Z"}}, {"id": "10.1007/s11104-023-06301-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:15Z", "type": "Journal Article", "created": "2023-10-04", "title": "Root phenotypes for improved nitrogen capture", "description": "Abstract Background

Suboptimal nitrogen availability is a primary constraint for crop production in low-input agroecosystems, while nitrogen fertilization is a primary contributor to the energy, economic, and environmental costs of crop production in high-input agroecosystems. In this article we consider avenues to develop crops with improved nitrogen capture and reduced requirement for nitrogen fertilizer.

Scope

Intraspecific variation for an array of root phenotypes has been associated with improved nitrogen capture in cereal crops, including architectural phenotypes that colocalize root foraging with nitrogen availability in the soil; anatomical phenotypes that reduce the metabolic costs of soil exploration, improve penetration of hard soil, and exploit the rhizosphere; subcellular phenotypes that reduce the nitrogen requirement of plant tissue; molecular phenotypes exhibiting optimized nitrate uptake kinetics; and rhizosphere phenotypes that optimize associations with the rhizosphere microbiome. For each of these topics we provide examples of root phenotypes which merit attention as potential selection targets for crop improvement. Several cross-cutting issues are addressed including the importance of soil hydrology and impedance, phenotypic plasticity, integrated phenotypes, in silico modeling, and breeding strategies using high throughput phenotyping for co-optimization of multiple phenes.

Conclusions

Substantial phenotypic variation exists in crop germplasm for an array of root phenotypes that improve nitrogen capture. Although this topic merits greater research attention than it currently receives, we have adequate understanding and tools to develop crops with improved nitrogen capture. Root phenotypes are underutilized yet attractive breeding targets for the development of the nitrogen efficient crops urgently needed in global agriculture.

", "keywords": ["2. Zero hunger", "0106 biological sciences", "0301 basic medicine", "Plasticity", "Marschner Review", "Nitrogen", "Physiology", "Nitrogen; Root; Anatomy; Architecture; Soil; Crop breeding; Root phenotyping; Modeling; Rhizosphere; Plasticity; Physiology", "Modeling", "Root phenotyping", "15. Life on land", "01 natural sciences", "Soil", "03 medical and health sciences", "Root", "FOS: Biological sciences", "Architecture", "Rhizosphere", "Crop breeding", "Anatomy", "FOS: Civil engineering"]}, "links": [{"href": "https://doi.org/10.1007/s11104-023-06301-2"}, {"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/s11104-023-06301-2", "name": "item", "description": "10.1007/s11104-023-06301-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-023-06301-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-10-04T00:00:00Z"}}, {"id": "10.1016/j.agee.2022.108124", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:39Z", "type": "Journal Article", "created": "2022-08-18", "title": "Assessing almond response to irrigation and soil management practices using vegetation indexes time-series and plant water status measurements", "description": "Open AccessThis research was funded in the frame of the projects PRECIRIEGO RTC-2017\u20136365-2 financed by Agencia Estatal de Investigaci\u00f3n with European Regional Development Fund co-funds; and the European Union H2020 project SHUI GA 773903. The research was supported also by the CajaMar Caja Rural Contract \u201cEfficient use of water resources under climate change scenarios\u201d. I. Buesa and J.M. Ram\u00edrez-Cuesta acknowledge the postdoctoral financial support received from Juan de la Cierva Spanish Postdoctoral Program (FJC2019\u2013042122-I and IJC2020\u2013043601-I, respectively). Authors acknowledge David Hortelano and Jos\u00e9 Luis Ru\u00edz Garc\u00eda for the help provided in the field measurements acquisition. This work represents a contribution to CSIC Thematic Interdisciplinary Platform PTI TELEDETECT.", "keywords": ["0106 biological sciences", "Soil management", "Almonds", "F06 Irrigation", "01 natural sciences", "12. Responsible consumption", "Vegetation index", "Sentinel 2", "Remote sensing sustainable agriculture", "P33 Soil chemistry and physics", "F40 Plant ecology", "2. Zero hunger", "precision agriculture", "Precision agriculture", "Sustainable agriculture", "Water use efficiency", "Vegetation cover", "F07 Soil cultivation", "04 agricultural and veterinary sciences", "Remote sensing", "15. Life on land", "Tree canopy", "F60 Plant physiology and biochemistry", "6. Clean water", "Water management", "P30 Soil science and management", "P10 Water resources and management", "0401 agriculture", " forestry", " and fisheries", "Remote sensing", " sustainable agriculture", "Sentinel-2"]}, "links": [{"href": "https://www.iris.unict.it/bitstream/20.500.11769/552491/2/Agriculture%2c%20ecosystems%20and%20environment%202022.pdf"}, {"href": "https://doi.org/10.1016/j.agee.2022.108124"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agriculture%2C%20Ecosystems%20%26amp%3B%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.agee.2022.108124", "name": "item", "description": "10.1016/j.agee.2022.108124", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.agee.2022.108124"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-11-01T00:00:00Z"}}, {"id": "10.1016/j.agrformet.2017.10.013", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:40Z", "type": "Journal Article", "created": "2017-10-19", "title": "Climate-Smart Agroforestry: Faidherbia Albida Trees Buffer Wheat Against Climatic Extremes In The Central Rift Valley Of Ethiopia", "description": "Abstract Faidherbia albida parklands cover a large area of the Sudano-Sahelian zone of Africa, a region that suffers from soil fertility decline, food insecurity and climate change. The parklands deliver multiple benefits, including fuelwood, soil nutrient replenishment, moisture conservation, and improved crop yield underneath the canopy. Its microclimate modification may provide an affordable climate adaptation strategy which needs to be explored. We carried out an on-farm experiment for three consecutive seasons in the Ethiopian Central Rift Valley with treatments of Faidherbia trees with bare soil underneath, wheat grown beneath Faidherbia and wheat grown in open fields. We tested the sensitivity of wheat yield to tree-mediated variables of photosynthetically active radiation (PAR), air temperature and soil nitrogen, using APSIM-wheat model. Results showed that soil moisture in the sub-soil was the least for wheat with tree, intermediate for sole tree and the highest for open field. Presence of trees resulted in 35\u201355% larger available N close to tree crowns compared with sole wheat. Trees significantly reduced PAR reaching the canopy of wheat growing underneath to optimum levels. Midday air temperature was about 6\u00a0\u00b0C less under the trees than in the open fields. LAI, number of grains spike\u22121, plant height, total aboveground biomass and wheat grain yield were all significantly higher (P", "keywords": ["Crop physiology", "2. Zero hunger", "Competition", "13. Climate action", "Local adaptation", "Climate change", "0401 agriculture", " forestry", " and fisheries", "Facilitation", "04 agricultural and veterinary sciences", "15. Life on land", "Heat stress", "6. Clean water"]}, "links": [{"href": "https://doi.org/10.1016/j.agrformet.2017.10.013"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agricultural%20and%20Forest%20Meteorology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.agrformet.2017.10.013", "name": "item", "description": "10.1016/j.agrformet.2017.10.013", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.agrformet.2017.10.013"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-01-01T00:00:00Z"}}, {"id": "10.1016/j.envexpbot.2011.04.011", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:12Z", "type": "Journal Article", "created": "2011-04-25", "title": "Experimental Warming Had Little Effect On Carbon-Based Secondary Compounds, Carbon And Nitrogen In Selected Alpine Plants And Lichens", "description": "Accepted version of an article published in the journal: Environmental and Experimental Botany. Published version available on Science Direct: http://dx.doi.org/10.1016/j.envexpbot.2011.04.011", "keywords": ["VDP::Mathematics and natural science: 400::Zoology and botany: 480::Ecology: 488", "VDP::Mathematics and natural science: 400::Zoology and botany: 480::Plant physiology: 492", "13. Climate action", "15. Life on land"], "contacts": [{"organization": "Kari Klanderud, Kari Klanderud, Sylvi M. Sandvik, Line Nybakken, Line Nybakken,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1016/j.envexpbot.2011.04.011"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20and%20Experimental%20Botany", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envexpbot.2011.04.011", "name": "item", "description": "10.1016/j.envexpbot.2011.04.011", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envexpbot.2011.04.011"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-10-01T00:00:00Z"}}, {"id": "10.1016/j.isci.2019.10.043", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:38Z", "type": "Journal Article", "created": "2019-10-25", "title": "Genetic Loci Associated with Early Salt Stress Responses of Roots", "description": "Salinity is a devastating abiotic stress accounting for major crop losses yearly. Plant roots can strikingly grow away from high-salt patches. This response is termed halotropism and occurs through auxin redistribution in roots in response to a salt gradient. Here, a natural variation screen for the early and NaCl-specific halotropic response of 333 Arabidopsis accessions revealed quantitative differences in the first 24 h. These data were successfully used to identify genetic components associated with the response through Genome-Wide Association Study (GWAS). Follow-up characterization of knockout mutants in Col-0 background confirmed the role of transcription factor WRKY25, cation-proton exchanger CHX13, and a gene of unknown function DOB1 (Double Bending 1) in halotropism. In chx13 and dob1 mutants, ion accumulation and shoot biomass under salt stress were also affected. Thus, our GWAS has identified genetic components contributing to main root halotropism that provide insight into the genetic architecture underlying plant salt responses.", "keywords": ["580", "2. Zero hunger", "0301 basic medicine", "570", "0303 health sciences", "Science", "Q", "Plant Biology", "Biological Sciences", "15. Life on land", "Plant Genetics", "Article", "03 medical and health sciences", "Plant Physiology"]}, "links": [{"href": "https://doi.org/10.1016/j.isci.2019.10.043"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/iScience", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.isci.2019.10.043", "name": "item", "description": "10.1016/j.isci.2019.10.043", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.isci.2019.10.043"}, {"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": "10.1016/j.jafr.2023.100732", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:39Z", "type": "Journal Article", "created": "2023-08-07", "title": "Aeromycological studies in the crops of the main cereals: A systematic review", "description": "Open AccessLes \u00e9tudes a\u00e9romycologiques sur les cultures c\u00e9r\u00e9ali\u00e8res permettent de d\u00e9terminer la variation temporelle des agents pathog\u00e8nes des plantes affectant la culture et de d\u00e9terminer le moment appropri\u00e9 pour appliquer les fongicides. Cependant, ce sujet n'a pas \u00e9t\u00e9 syst\u00e9matiquement revu. L'objectif de ce travail \u00e9tait d'analyser syst\u00e9matiquement toutes les \u00e9tudes a\u00e9romycologiques r\u00e9alis\u00e9es sur le ma\u00efs, le bl\u00e9, le riz, l'avoine, l'orge, le seigle, le sorgho et le millet. Une recherche syst\u00e9matique a \u00e9t\u00e9 effectu\u00e9e dans Scopus depuis le d\u00e9but de la base de donn\u00e9es jusqu'au 1er ao\u00fbt 2022. Les crit\u00e8res d'inclusion \u00e9taient qu'il s'agissait d'\u00e9tudes a\u00e9romycologiques sur le bl\u00e9 ou le riz ou le ma\u00efs ou l'avoine ou le sorgho ou le seigle ou l'orge ou le millet et d'\u00e9tudes publi\u00e9es dans des revues \u00e0 comit\u00e9 de lecture index\u00e9es dans Journal Citation Reports et r\u00e9dig\u00e9es en anglais ou en espagnol. Quarante-trois \u00e9tudes (21 sur le bl\u00e9, 15 sur le riz, 5 sur le ma\u00efs, 1 sur le sorgho et 2 sur l'orge) r\u00e9pondant \u00e0 tous les crit\u00e8res d'\u00e9ligibilit\u00e9 ont \u00e9t\u00e9 incluses (une des \u00e9tudes sur le ma\u00efs a \u00e9galement \u00e9t\u00e9 men\u00e9e sur le bl\u00e9). Aucune \u00e9tude a\u00e9romycologique n'a \u00e9t\u00e9 trouv\u00e9e chez l'avoine, le seigle et le millet. Il a \u00e9t\u00e9 not\u00e9 que la plupart des recherches a\u00e9romycologiques ont \u00e9t\u00e9 men\u00e9es sur les cultures de bl\u00e9 et principalement dans les pays des Am\u00e9riques. De plus, les propagules fongiques sont principalement collect\u00e9es par des m\u00e9thodes non viables, en utilisant divers types de collecteurs. En g\u00e9n\u00e9ral, les \u00e9tudes visaient \u00e0 identifier un agent pathog\u00e8ne sp\u00e9cifique et non \u00e0 la diversit\u00e9 des agents pathog\u00e8nes qui peuvent \u00eatre trouv\u00e9s. La relation des champignons identifi\u00e9s avec les param\u00e8tres m\u00e9t\u00e9orologiques \u00e9tait variable dans les diff\u00e9rentes \u00e9tudes. Cette revue syst\u00e9matique permet de r\u00e9sumer les \u00e9tudes a\u00e9romycologiques qui ont \u00e9t\u00e9 men\u00e9es sur les cultures de bl\u00e9, de riz, de ma\u00efs, de sorgho et d'orge. Il sugg\u00e8re \u00e9galement o\u00f9 les futures \u00e9tudes dans ce domaine devraient \u00eatre dirig\u00e9es, en fonction des limites rencontr\u00e9es.", "keywords": ["Impacts of Elevated CO2 and Ozone on Plant Physiology", "Agriculture (General)", "Health", " Toxicology and Mutagenesis", "Plant Science", "Crop", "S1-972", "Agricultural and Biological Sciences", "Barley", "Biochemistry", " Genetics and Molecular Biology", "TX341-641", "10. No inequality", "Biology", "Sorghum", "2. Zero hunger", "Corn", "Airborne spores", "Nutrition. Foods and food supply", "Life Sciences", "Phylogenetic Analysis", "Cell Biology", "15. Life on land", "2414.06 Hongos", "Agronomy", "3. Good health", "Wheat", "Environmental Science", "Physical Sciences", "Rice", "Indoor Air Quality and Health Effects", "Diversity and Evolution of Fungal Pathogens", "Biotechnology"]}, "links": [{"href": "https://doi.org/10.1016/j.jafr.2023.100732"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Agriculture%20and%20Food%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jafr.2023.100732", "name": "item", "description": "10.1016/j.jafr.2023.100732", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jafr.2023.100732"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-01T00:00:00Z"}}, {"id": "10.1111/nph.15014", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:24Z", "type": "Journal Article", "created": "2018-02-09", "title": "Native soils with their microbiotas elicit a state of alert in tomato plants", "description": "Summary

Several studies have investigated soil microbial biodiversity, but understanding of the mechanisms underlying plant responses to soil microbiota remains in its infancy. Here, we focused on tomato (Solanum lycopersicum), testing the hypothesis that plants grown on native soils display different responses to soil microbiotas.

Using transcriptomics, proteomics, and biochemistry, we describe the responses of two tomato genotypes (susceptible or resistant to Fusarium oxysporum f. sp. lycopersici) grown on an artificial growth substrate and two native soils (conducive and suppressive to Fusarium).

Native soils affected tomato responses by modulating pathways involved in responses to oxidative stress, phenol biosynthesis, lignin deposition, and innate immunity, particularly in the suppressive soil. In tomato plants grown on steam\uffe2\uff80\uff90disinfected soils, total phenols and lignin decreased significantly. The inoculation of a mycorrhizal fungus partly rescued this response locally and systemically. Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil.

The \uffe2\uff80\uff98state of alert\uffe2\uff80\uff99 detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses.

", "keywords": ["0301 basic medicine", "Proteome", "Propanols", "Arbuscular mycorrhizal fungi", "arbuscular mycorrhizal fungi", "tomato", "Lignin", "Models", " Biological", "Plant Roots", "defence responses", "Tomato", "Soil", "03 medical and health sciences", "Solanum lycopersicum", "Gene Expression Regulation", " Plant", "Stress", " Physiological", "microbiota", "Plant Immunity", "Soil Microbiology", "suppressive and conducive soils", "susceptible and resistant genotypes", "2. Zero hunger", "0303 health sciences", "Defence responses", "Microbiota", "15. Life on land", "Lignin biosynthesis", "Gene Ontology", "Susceptible and resistant genotypes", "Arbuscular mycorrhizal fungi; Defence responses; Lignin biosynthesis; Microbiota; Suppressive and conducive soils; Susceptible and resistant genotypes; Tomato; Physiology; Plant Science", "Suppressive and conducive soils", "Transcriptome", "lignin biosynthesis"]}, "links": [{"href": "https://iris.unito.it/bitstream/2318/1660820/1/Chialva%20et%20al%20Iris.pdf"}, {"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15014"}, {"href": "https://doi.org/10.1111/nph.15014"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Phytologist", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/nph.15014", "name": "item", "description": "10.1111/nph.15014", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.15014"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-09T00:00:00Z"}}, {"id": "10.1038/nature02403", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:54Z", "type": "Journal Article", "created": "2004-04-21", "title": "The Worldwide Leaf Economics Spectrum", "description": "Bringing together leaf trait data spanning 2,548 species and 175 sites we describe, for the first time at global scale, a universal spectrum of leaf economics consisting of key chemical, structural and physiological properties. The spectrum runs from quick to slow return on investments of nutrients and dry mass in leaves, and operates largely independently of growth form, plant functional type or biome. Categories along the spectrum would, in general, describe leaf economic variation at the global scale better than plant functional types, because functional types overlap substantially in their leaf traits. Overall, modulation of leaf traits and trait relationships by climate is surprisingly modest, although some striking and significant patterns can be seen. Reliable quantification of the leaf economics spectrum and its interaction with climate will prove valuable for modelling nutrient fluxes and vegetation boundaries under changing land-use and climate.", "keywords": ["leaf traits", "0106 biological sciences", "INVESTMENT", "Climate", "Rain", "CLIMATE CHANGE", "SEED PRODUCTION", "01 natural sciences", "spectrum", "BIOMASS", "dry mass", "Biologie/Milieukunde (BIOL)", "MODELS", " BIOLOGICAL", "CLIMATE EFFECT", "Nutritional Physiological Phenomena", "Biomass", "Photosynthesis", "LAND USE", "PRIORITY JOURNAL", "functional-groups", "biodiversity", "ALLOMETRY", "2. Zero hunger", "INVESTMENTS", "Geography", "BIOME", "HUMAN", "04 agricultural and veterinary sciences", "INFORMATION SCIENCE", "Life sciences", "tree", "NUTRITION PHYSIOLOGY", "leaf economics", "LEAF ECONOMICS SPECTRUM", "leaves", "ECONOMIC AND SOCIAL EFFECTS", "GEOGRAPHY", "Models", " Biological", "photosynthesis-nitrogen relations", "LEAF", "PLANT LEAF", "nutrients", "high-rainfall", "DATA REDUCTION", "NONHUMAN", "PLANT LEAVES", "NUTRIENT AVAILABILITY", "ARTICLE", "PHYSIOLOGY", "Ecosystem", "580", "life-span", "ECONOMICS", "PHOTOSYNTHESIS", "RAIN", "nutrient", "land use", "area", "use efficiency", "15. Life on land", "PLANT GROWTH", "CLIMATE", "Plant Leaves", "SPECTRUM ANALYSIS", "DRY MASS", "ECOSYSTEM", "0401 agriculture", " forestry", " and fisheries", "BIODIVERSITY", "VEGETATION"]}, "links": [{"href": "https://doi.org/10.1038/nature02403"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/nature02403", "name": "item", "description": "10.1038/nature02403", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/nature02403"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2004-04-01T00:00:00Z"}}, {"id": "10.1029/2021JG006593", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:50Z", "type": "Journal Article", "created": "2021-12-07", "title": "Identifying Data Needed to Reduce Parameter Uncertainty in a Coupled Microbial Soil C and N Decomposition Model", "description": "Abstract

Advancements in microbially explicit ecosystem models incorporate increasingly accurate representations of microbial physiology and enzyme\uffe2\uff80\uff90mediated depolymerization of soil organic matter in predicting biogeochemical responses to global change. However, a major challenge with model structural improvements is the requirement for additional parameters, which are often poorly constrained sources of uncertainty. Furthermore, it is often unclear how to best focus data collection efforts toward reducing model uncertainty. Here, we use Dual Arrhenius Michaelis\uffe2\uff80\uff90Menten Microbial Carbon and Nitrogen Physiology, a microbially mediated, coupled soil C and N cycling model, as a tool to explore the influence of microbial physiological and enzyme kinetic parameters on model estimates. We first quantify the potential for constraining model parameters using empirical measurements of soil respiration. We then use simulated data to identify which additional sources of data collection from the field would provide the greatest impact for constraining model estimates. We find that modeled soil C and N pools and fluxes are disproportionately sensitive to only a few parameters (e.g., activation energies and microbial CUE), while others exert less influence (e.g., Michaelis\uffe2\uff80\uff90Menten half\uffe2\uff80\uff90saturation constants). While some parameters can be constrained by the available data on heterotrophic respiration, the collection of additional data on dissolved organic C and N pools in the soil is identified as a high\uffe2\uff80\uff90priority data need. Improving our ability to model the interactions of soil microbial physiology, soil chemistry, enzyme activities, and environmental factors on C and N cycling will require closely considering model uncertainties and prioritizing future data collection opportunities based on their impact on model performance.Advancements in microbially explicit ecosystem models incorporate increasingly accurate representations of microbial physiology and enzyme\uffe2\uff80\uff90mediated depolymerization of soil organic matter in predicting biogeochemical responses to global change. However, a major challenge with model structural improvements is the requirement for additional parameters, which are often poorly constrained sources of uncertainty. Furthermore, it is often unclear how to best focus data collection efforts toward reducing model uncertainty. Here, we use Dual Arrhenius Michaelis\uffe2\uff80\uff90Menten Microbial Carbon and Nitrogen Physiology, a microbially mediated, coupled soil C and N cycling model, as a tool to explore the influence of microbial physiological and enzyme kinetic parameters on model estimates. We first quantify the potential for constraining model parameters using empirical measurements of soil respiration. We then use simulated data to identify which additional sources of data collection from the field would provide the greatest impact for constraining model estimates. We find that modeled soil C and N pools and fluxes are disproportionately sensitive to only a few parameters (e.g., activation energies and microbial CUE), while others exert less influence (e.g., Michaelis\uffe2\uff80\uff90Menten half\uffe2\uff80\uff90saturation constants). While some parameters can be constrained by the available data on heterotrophic respiration, the collection of additional data on dissolved organic C and N pools in the soil is identified as a high\uffe2\uff80\uff90priority data need. Improving our ability to model the interactions of soil microbial physiology, soil chemistry, enzyme activities, and environmental factors on C and N cycling will require closely considering model uncertainties and prioritizing future data collection opportunities based on their impact on model performance.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.Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia fabaL.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13\uffe2\uff80\uff89Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the\uffc2\uffa0improvement of sustainable protein production across the\uffc2\uffa0Mediterranean, subtropical and northern temperate agroecological zones.The present work aims to quantify the impact of climate change (CC) on the grain yields of irrigated cereals and their water requirements in the Tensift region of Morocco. The Med-CORDEX (MEDiterranean COordinated Regional Climate Downscaling EXperiment) ensemble runs under scenarios RCP4.5 (Representative Concentration Pathway) and RCP8.5 are first evaluated and disaggregated using the quantile-quantile approach. The impact of CC on the duration of the main wheat phenological stages based on the degree-day approach is then analyzed. The results show that the rise in air temperature causes a shortening of the development cycle of up to 50 days. The impacts of rising temperature and changes in precipitation on wheat yields are next evaluated, based on the AquaCrop model, both with and without taking into account the fertilizing effect of CO2. As expected, optimal wheat yields will decrease on the order of 7 to 30% if CO2 concentration rise is not considered. The fertilizing effect of CO2 can counterbalance yield losses, since optimal yields could increase by 7% and 13% respectively at mid-century for the RCP4.5 and RCP8.5 scenarios. Finally, water requirements are expected to decrease by 13 to 42%, mainly in response to the shortening of the cycle. This decrease is associated with a change in temporal patterns, with the requirement peak coming two months earlier than under current conditions.

", "keywords": ["Water resources", "Atmospheric sciences", "Agricultural Irrigation", "environment/Bioclimatology", "550", "Representative Concentration Pathways", "Adaptation to Climate Change in Agriculture", "Arid", "Rain", "[SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy", "Climate Change and Variability Research", "Plant Science", "Precipitation", "02 engineering and technology", "01 natural sciences", "Agricultural and Biological Sciences", "Downscaling", "Climate change", "Quantile", "Triticum", "Climatology", "2. Zero hunger", "Global and Planetary Change", "Ecology", "Geography", "Temperature", "Life Sciences", "Geology", "Morocco", "Phenology", "[SDV.EE.BIO]Life Sciences [q-bio]/Ecology", "Seeds", "Physical Sciences", "Metallurgy", "Desert Climate", "Impacts of Elevated CO2 and Ozone on Plant Physiology", "Climate Change", "0207 environmental engineering", "Yield (engineering)", "Climate model", "Article", "Environmental science", "FOS: Economics and business", "Meteorology", "FOS: Mathematics", "Econometrics", "[SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology", "Biology", "Ecology", " Evolution", " Behavior and Systematics", "0105 earth and related environmental sciences", "[SDV.SA.AGRO] Life Sciences [q-bio]/Agricultural sciences/Agronomy", "Water", "FOS: Earth and related environmental sciences", "Carbon Dioxide", "15. Life on land", "Agronomy", "Materials science", "[SDV.EE.BIO] Life Sciences [q-bio]/Ecology", " environment/Bioclimatology", "13. Climate action", "FOS: Biological sciences", "Environmental Science", "[SDU.STU.HY] Sciences of the Universe [physics]/Earth Sciences/Hydrology", "Crop Yield", "Mediterranean climate", "Mathematics", "Climate Modeling"]}, "links": [{"href": "https://www.nature.com/articles/s41598-019-55251-2.pdf"}, {"href": "https://doi.org/10.1038/s41598-019-55251-2"}, {"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/s41598-019-55251-2", "name": "item", "description": "10.1038/s41598-019-55251-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-019-55251-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-16T00:00:00Z"}}, {"id": "10.1071/fp14125", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:16Z", "type": "Journal Article", "created": "2014-12-03", "title": "Intraspecific Variation In Leaf Growth Of Wheat (Triticum Aestivum) Under Australian Grain Free Air Co2 Enrichment (Agface): Is It Regulated Through Carbon And/Or Nitrogen Supply?", "description": "

Underlying physiological mechanisms of intraspecific variation in growth response to elevated CO2 concentration [CO2] were investigated using two spring wheat (Triticum aestivum L.) cultivars: Yitpi and H45. Leaf blade elongation rate (LER), leaf carbon (C), nitrogen (N) in the expanding leaf blade (ELB, sink) and photosynthesis (A) and C and N status in the last fully expanded leaf blade (LFELB, source) were measured. Plants were grown at ambient [CO2] (~384\uffc2\uffb5molmol\uffe2\uff80\uff931) and elevated [CO2] (~550\uffc2\uffb5molmol\uffe2\uff80\uff931) in the Australian Grains Free Air CO2 Enrichment facility. Elevated [CO2] increased leaf area and total dry mass production, respectively, by 42 and 53% for Yitpi compared with 2 and 13% for H45. Elevated [CO2] also stimulated the LER by 36% for Yitpi compared with 5% for H45. Yitpi showed a 99% increase in A at elevated [CO2] but no A stimulation was found for H45. There was a strong correlation (r2=0.807) between LER of the ELB and soluble carbohydrate concentration in LFELB. In ELB, the highest spatial N concentration was observed in the cell division zone, where N concentrations were 67.3 and 60.6mg g\uffe2\uff80\uff931 for Yitpi compared with 51.1 and 39.2mg g\uffe2\uff80\uff931 for H45 at ambient and elevated [CO2]. In contrast, C concentration increased only in the cell division and cell expansion zone of the ELB of Yitpi. These findings suggest that C supply from the source (LFELB) is cultivar dependent and well correlated with LER, leaf area expansion and whole-plant growth response to elevated [CO2].

", "keywords": ["Diurnal regulation of LER", "580", "0106 biological sciences", "0301 basic medicine", "2. Zero hunger", "070303 Crop and Pasture Biochemistry and Physiology", "leaf blade elongation rate", "diurnal regulation of LER", "gas exchange", "Growth analysis", "15. Life on land", "01 natural sciences", "Leaf blade elongation rate", "03 medical and health sciences", "Elevated (CO2)", "elevated [CO2]", "Gas exchange", "growth analysis"]}, "links": [{"href": "https://doi.org/10.1071/fp14125"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Functional%20Plant%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1071/fp14125", "name": "item", "description": "10.1071/fp14125", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1071/fp14125"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-01-01T00:00:00Z"}}, {"id": "10.1111/ejss.70078", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:18:58Z", "type": "Journal Article", "created": "2025-03-11", "title": "The Effect of Crop Diversification and Season on Microbial Carbon Use Efficiency Across a European Pedoclimatic Gradient", "description": "ABSTRACT

Microbial transformation of soil organic matter plays a critical role in carbon (C) cycling making it essential to understand how land use and management practices influence microbial physiology and its connection to C dynamics. One factor that is likely to impact soil microbial physiology is crop diversification via its influence on belowground diversity (e.g., chemical heterogeneity of C inputs, microbial community composition). However, the effect of crop diversification measures on microbial physiology and potential effects on C cycling in agricultural soils is still unclear. To address this knowledge gap, we sampled topsoil from eight experimental sites covering different crop diversification measures across Europe (i.e., cover crops, ley farming, vegetation stripes). We used the 18O\uffe2\uff80\uff90labelling method to analyse microbial C use efficiency (CUE), growth, respiration and biomass C. Additionally, a second sampling at five selected sites examined whether the growing season influenced the impact of crop diversification. Meta\uffe2\uff80\uff90analysis revealed no overall effect of crop diversification on CUE, microbial activity, biomass or soil organic C (SOC). However, the effects varied with the type of diversification measure: cover crops did not affect carbon processing, vegetation stripes increased microbial activity, and ley farming enhanced CUE. The largest variation in CUE was observed between samplings at the same sites, indicating seasonal dynamics. Temperature, precipitation and photosynthetically active radiation predicted seasonal variation in CUE (R2\uffe2\uff80\uff89=\uffe2\uff80\uff890.36). While cover crops did not significantly impact C storage in our study, both ley farming and vegetation stripes increased SOC. The overall effect of crop diversification on SOC seems to be decoupled from highly temporally variable CUE in the bulk soil and rather relate to C\uffe2\uff80\uff90inputs.

Ecosystem water\uffe2\uff80\uff90use efficiency (WUE) is an important metric linking the global land carbon and water cycles. Eddy covariance\uffe2\uff80\uff90based estimates of WUE in temperate/boreal forests have recently been found to show a strong and unexpected increase over the 1992\uffe2\uff80\uff932010 period, which has been attributed to the effects of rising atmospheric CO2 concentrations on plant physiology.

To test this hypothesis, we forced the observed trend in the process\uffe2\uff80\uff90based land surface model JSBACH by increasing the sensitivity of stomatal conductance (gs) to atmospheric CO2 concentration. We compared the simulated continental discharge, evapotranspiration (ET), and the seasonal CO2 exchange with observations across the extratropical northern hemisphere.

The increased simulated WUE led to substantial changes in surface hydrology at the continental scale, including a significant decrease in ET and a significant increase in continental runoff, both of which are inconsistent with large\uffe2\uff80\uff90scale observations. The simulated seasonal amplitude of atmospheric CO2 decreased over time, in contrast to the observed upward trend across ground\uffe2\uff80\uff90based measurement sites.

Our results provide strong indications that the recent, large\uffe2\uff80\uff90scale WUE trend is considerably smaller than that estimated for these forest ecosystems. They emphasize the decreasing CO2 sensitivity of WUE with increasing scale, which affects the physiological interpretation of changes in ecosystem WUE.

", "keywords": ["580", "0106 biological sciences", "Time Factors", "plant physiology", "Vapor Pressure", "evapotranspiration", "577", "Water", "04 agricultural and veterinary sciences", "Carbon Dioxide", "15. Life on land", "01 natural sciences", "water efficiency", "3. Good health", "Plant Leaves", "13. Climate action", "atmospheric carbon dioxide", "XXXXXX - Unknown", "0401 agriculture", " forestry", " and fisheries", "Seasons", "ecosystems", "Ecosystem", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.14288"}, {"href": "https://doi.org/10.1111/nph.14288"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Phytologist", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/nph.14288", "name": "item", "description": "10.1111/nph.14288", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.14288"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-11-07T00:00:00Z"}}, {"id": "10.1111/nph.14634", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:24Z", "type": "Journal Article", "created": "2017-06-13", "title": "Circular linkages between soil biodiversity, fertility and plant productivity are limited to topsoil at the continental scale", "description": "Summary

The current theoretical framework suggests that tripartite positive feedback relationships between soil biodiversity, fertility and plant productivity are universal. However, empirical evidence for these relationships at the continental scale and across different soil depths is lacking.

We investigate the continental\uffe2\uff80\uff90scale relationships between the diversity of microbial and invertebrate\uffe2\uff80\uff90based soil food webs, fertility and above\uffe2\uff80\uff90ground plant productivity at 289 sites and two soil depths, that is 0\uffe2\uff80\uff9310 and 20\uffe2\uff80\uff9330\uffc2\uffa0cm, across Australia.

Soil biodiversity, fertility and plant productivity are strongly positively related in surface soils. Conversely, in the deeper soil layer, the relationships between soil biodiversity, fertility and plant productivity weaken considerably, probably as a result of a reduction in biodiversity and fertility with depth. Further modeling suggested that strong positive associations among soil biodiversity\uffe2\uff80\uff93fertility and fertility\uffe2\uff80\uff93plant productivity are limited to the upper soil layer (0\uffe2\uff80\uff9310\uffc2\uffa0cm), after accounting for key factors, such as distance from the equator, altitude, climate and physicochemical soil properties.

These findings highlight the importance of surface soil biodiversity for soil fertility, and suggest that any loss of surface soil could potentially break the links between soil biodiversity\uffe2\uff80\uff93fertility and/or fertility\uffe2\uff80\uff93plant productivity, which can negatively impact nutrient cycling and food production, upon which future generations depend.

", "keywords": ["Soil biodiversity; plant productivity; terrestrial ecosystems; ecosystem functionality; bacteria; eukaryotes.", "0301 basic medicine", "Eukaryotes", "Climate", "Plant Development", "soil biodiversity", "Terrestrial ecosystems", "Soil", "03 medical and health sciences", "eukaryotes", "1110 Plant Science", "XXXXXX - Unknown", "plant productivity", "bacteria", "Ecosystem functionality", "Soil Microbiology", "2. Zero hunger", "0303 health sciences", "Bacteria", "Australia", "terrestrial ecosystems", "1314 Physiology", "Biodiversity", "15. Life on land", "Soil biodiversity", "ecosystem functionality", "Fertility", "ecosystems", "Plant productivity"]}, "links": [{"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.14634"}, {"href": "https://doi.org/10.1111/nph.14634"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Phytologist", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/nph.14634", "name": "item", "description": "10.1111/nph.14634", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.14634"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-06-13T00:00:00Z"}}, {"id": "10.1128/msystems.00859-24", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:31Z", "type": "Journal Article", "created": "2024-09-10", "title": "A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities", "description": "ABSTRACT

Due to recent improvements, Nanopore sequencing has become a promising method for experiments relying on amplicon sequencing. We describe a flexible workflow to generate and annotate high-quality, full-length 16S rDNA amplicons. We evaluated it for two applications, namely, (i) identification of bacterial isolates and (ii) species-level profiling of microbial communities. We assessed the identification of single bacterial isolates by sequencing, using a set of barcoded full-length 16S rRNA gene primer pairs (pair A), on 47 isolates encompassing multiple genera and compared those results with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification. Species-level community profiling was tested with two sets of barcoded full-length 16S primer pairs (A and B) and compared to the results obtained with shotgun Illumina sequencing using 27 stool samples. We developed a Nextflow pipeline to retain high-quality reads and taxonomically annotate them. We found high agreement between our workflow and MALDI-TOF data for isolate identification (positive predictive value = 0.90, Cram\uffc3\uffa9r\uffe2\uff80\uff99s V = 0.857, and Theil\uffe2\uff80\uff99s U = 0.316). For species-level community profiling, we found strong correlations ( r s > 0.6) of alpha diversity indices between the two primer sets and Illumina sequencing. At the community level, we found significant but small differences when comparing sequencing techniques. Finally, we found a moderate to strong correlation when comparing the relative abundances of individual species (average r s = 0.6 and 0.533 for primers A and B). Despite identified shortcomings, the proposed workflow enabled accurate identification of single bacterial isolates and prominent features in microbial communities, making it a worthwhile alternative to MALDI-TOF MS and Illumina sequencing.

IMPORTANCE

A quick, robust, simple, and cost-effective method to identify bacterial isolates and communities in each sample is indispensable in the fields of microbiology and infection biology. Recent technological advances in Oxford Nanopore Technologies sequencing make this technique an attractive option considering the adaptability, portability, and cost-effectiveness of the platform, even with small sequencing batches. Here, we validated a flexible workflow to identify bacterial isolates and characterize bacterial communities using the Oxford Nanopore Technologies sequencing platform combined with the most recent v14 chemistry kits. For bacterial isolates, we compared our nanopore-based approach to matrix-assisted laser desorption ionization-time of flight mass spectrometry-based identification. For species-level profiling of complex bacterial communities, we compared our nanopore-based approach to Illumina shotgun sequencing. For reproducibility purposes, we wrapped the code used to process the sequencing data into a ready-to-use and self-contained Nextflow pipeline.

", "keywords": ["DNA", " Bacterial", "1303 Biochemistry", "gut microbiome", "610 Medicine & health", "Microbiology", "Workflow", "1311 Genetics", "RNA", " Ribosomal", " 16S", "1312 Molecular Biology", "1706 Computer Science Applications", "DNA Barcoding", " Taxonomic", "Humans", "DNA sequencing", "Bacteria", "10179 Institute of Medical Microbiology", "Microbiota", "2404 Microbiology", "1314 Physiology", "bioinformatics", "QR1-502", "Nanopore Sequencing", "1105 Ecology", " Evolution", " Behavior and Systematics", "Spectrometry", " Mass", " Matrix-Assisted Laser Desorption-Ionization", "570 Life sciences; biology", "2611 Modeling and Simulation", "Research Article"]}, "links": [{"href": "https://doi.org/10.1128/msystems.00859-24"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSystems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/msystems.00859-24", "name": "item", "description": "10.1128/msystems.00859-24", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/msystems.00859-24"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-04-11T00:00:00Z"}}, {"id": "10.3389/fpls.2015.00574", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:21:11Z", "type": "Journal Article", "created": "2015-08-11", "title": "Leaf \u03b415N as a physiological indicator of the responsiveness of N2-fixing alfalfa plants to elevated [CO2], temperature and low water availability", "description": "The natural (15)N/(14)N isotope composition (\u03b4(15)N) of a tissue is a consequence of its N source and N physiological mechanisms in response to the environment. It could potentially be used as a tracer of N metabolism in plants under changing environmental conditions, where primary N metabolism may be complex, and losses and gains of N fluctuate over time. In order to test the utility of \u03b4(15)N as an indicator of plant N status in N2-fixing plants grown under various environmental conditions, alfalfa (Medicago sativa L.) plants were subjected to distinct conditions of [CO2] (400 vs. 700 \u03bcmol mol(-1)), temperature (ambient vs. ambient +4\u00b0C) and water availability (fully watered vs. water deficiency-WD). As expected, increased [CO2] and temperature stimulated photosynthetic rates and plant growth, whereas these parameters were negatively affected by WD. The determination of \u03b4(15)N in leaves, stems, roots, and nodules showed that leaves were the most representative organs of the plant response to increased [CO2] and WD. Depletion of heavier N isotopes in plants grown under higher [CO2] and WD conditions reflected decreased transpiration rates, but could also be related to a higher N demand in leaves, as suggested by the decreased leaf N and total soluble protein (TSP) contents detected at 700 \u03bcmol mol(-1) [CO2] and WD conditions. In summary, leaf \u03b4(15)N provides relevant information integrating parameters which condition plant responsiveness (e.g., photosynthesis, TSP, N demand, and water transpiration) to environmental conditions.", "keywords": ["0106 biological sciences", "0301 basic medicine", "Physiology", "growth", "Climate Change", "Plant physiology", "Plantes", "Growth", "Plant Science", "01 natural sciences", "SB1-1110", "03 medical and health sciences", "Climate change", "2. Zero hunger", "Alfalfa", "Plant culture", "Plants", "15. Life on land", "delta15N", "6. Clean water", "climate change", "Fisiologia vegetal", "Carbon dioxide", "physiology", "Di\u00f2xid de carboni", "alfalfa", "\u03b415N"]}, "links": [{"href": "https://doi.org/10.3389/fpls.2015.00574"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fpls.2015.00574", "name": "item", "description": "10.3389/fpls.2015.00574", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fpls.2015.00574"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-08-11T00:00:00Z"}}, {"id": "10.3390/app11062746", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:21:17Z", "type": "Journal Article", "created": "2021-03-19", "title": "Halophyte Plants and Their Residues as Feedstock for Biogas Production\u2014Chances and Challenges", "description": "

The importance of green technologies is steadily growing. Salt-tolerant plants have been proposed as energy crops for cultivation on saline lands. Halophytes such as Salicornia europaea, Tripolium pannonicum, Crithmum maritimum and Chenopodium quinoa, among many other species, can be cultivated in saline lands, in coastal areas or for treating saline wastewater, and the biomass might be used for biogas production as an integrated process of biorefining. However, halophytes have different salt tolerance mechanisms, including compartmentalization of salt in the vacuole, leading to an increase of sodium in the plant tissues. The sodium content of halophytes may have an adverse effect on the anaerobic digestion process, which needs adjustments to achieve stable and efficient conversion of the halophytes into biogas. This review gives an overview of the specificities of halophytes that needs to be accounted for using their biomass as feedstocks for biogas plants in order to expand renewable energy production. First, the different physiological mechanisms of halophytes to grow under saline conditions are described, which lead to the characteristic composition of the halophyte biomass, which may influence the biogas production. Next, possible mechanisms to avoid negative effects on the anaerobic digestion process are described, with an overview of full-scale applications. Taking all these aspects into account, halophyte plants have a great potential for biogas and methane production with yields similar to those produced by other energy crops and the simultaneous benefit of utilization of saline soils.

", "keywords": ["anaerobic digestion", "0301 basic medicine", "Technology", "Inoculum adaptation", "QH301-705.5", "QC1-999", "Plant physiology", "Salicornia europaea", "Co-digestion", "7. Clean energy", "biogas production", "03 medical and health sciences", "Anaerobic digestion", "co-digestion", "Biology (General)", "Chenopodium quinoa", "QD1-999", "Crithmum maritimum", "2. Zero hunger", "0303 health sciences", "T", "Physics", "Sa-linity", "Crithmum maritimum", "Tripolium pannonicum", "15. Life on land", "Engineering (General). Civil engineering (General)", "Biogas production", "Dewey Decimal Classification::600 | Technik", "6. Clean water", "Chenopodium quinoa", "Chemistry", "13. Climate action", "TA1-2040", "Halophyte composition", "halophyte composition"]}, "links": [{"href": "https://www.mdpi.com/2076-3417/11/6/2746/pdf"}, {"href": "https://doi.org/10.3390/app11062746"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/app11062746", "name": "item", "description": "10.3390/app11062746", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/app11062746"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-18T00:00:00Z"}}, {"id": "10.5061/dryad.cvdncjt2t", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:21:56Z", "type": "Dataset", "title": "Carbohydrate depletion in roots impedes phosphorus nutrition of forest trees", "description": "unspecifiedThe aim of the study was to determine the effect of belowground plant-derived carbohydrates on P uptake, P concentrations and enzymes activities related to P mobilization in roots, ectomycorrhizas and soil and on the abundances of P-related genes in soil bacteria. We report data from a girdling experiment in two temperate beech forest with contrasting soil phosphorus concentrations. We used soil cores and the fractions of the organic layer and mineral topsoil separately one and eight weeks after the girdling treatment. We collected bulk soil, rhizosphere and root. We provide data on soil for pH, water extractable organic carbon mineral elements in soil, and soil enzyme activities. Enzyme activities are shown for the bulk soil and the rhizosphere We provide data for microbial P, microbial biomass, gene abundances of P-related genes for soil bacteria, and phospholipid fatty acids. We provide data on root biomass, carbohydrates, total P, soluble, other root mineral nutrients, and phopphatase and enzyme activities. The data set further contain 33P labelling data for P uptake into roots.", "keywords": ["2. Zero hunger", "Forest Botany and Tree Physiology", "15. Life on land"], "contacts": [{"organization": "Clausing, Simon, Pena, Rodica, Song, Bin, M\u00fcller, Karolin, Mayer-Gruner, Paula, Marhan, Sven, Grafe, Martin, Schulz, Stefanie, Kr\u00fcger, Jaane, Lang, Friederike, Schloter, Michael, Kandeler, Ellen, Polle, Andrea,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.cvdncjt2t"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.cvdncjt2t", "name": "item", "description": "10.5061/dryad.cvdncjt2t", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.cvdncjt2t"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-10-05T00:00:00Z"}}, {"id": "10.5061/dryad.s87008d", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:22:01Z", "type": "Dataset", "title": "Data from: Cross-biome patterns in soil microbial respiration predictable from evolutionary theory on thermal adaptation", "description": "unspecifiedClimate warming may stimulate microbial metabolism of soil carbon, causing a carbon cycle-climate feedback whereby carbon is redistributed from soil to atmospheric CO2. The magnitude of this feedback is uncertain, in part because warming-induced shifts in microbial physiology and/or community composition could retard or accelerate soil carbon losses. Here, we measure microbial respiration rates for soils collected from 22 sites in each of three years, at locations spanning boreal to tropical climates. Respiration was measured in the laboratory with standard temperatures, moisture and excess carbon substrate, to allow physiological and community effects to be detected independent from the influence of these abiotic controls. Patterns in respiration for soils collected across the climate gradient are consistent with evolutionary theory on physiological responses that compensate for positive effects of temperature on metabolism. Respiration rates per unit microbial biomass were as much as 2.6-times higher for soils sampled from sites with a mean annual temperature (MAT) of -2.0 versus 21.7\u00baC. Subsequent 100-day incubations suggested differences in the plasticity of the thermal response among microbial communities, with communities sampled from sites with higher MAT having a more plastic response. Our findings are consistent with adaptive metabolic responses to contrasting thermal regimes that are also observed in plants and animals. These results may help build confidence in soil carbon-climate feedback projections by improving understanding of microbial processes represented in biogeochemical models.", "keywords": ["2. Zero hunger", "soil organic carbon", "Thermal acclimation", "Microbial physiology", "13. Climate action", "soil biogeochemical models", "Earth system models", "Soil respiration", "15. Life on land", "Soil carbon", "soil microbial biomass"], "contacts": [{"organization": "Bradford, Mark A., McCulley, Rebecca L., Crowther, Thomas W., Oldfield, Emily E., Wood, Stephen A., Fierer, Noah,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.s87008d"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.s87008d", "name": "item", "description": "10.5061/dryad.s87008d", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.s87008d"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-01-18T00:00:00Z"}}, {"id": "10138/356895", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:25:03Z", "type": "Journal Article", "created": "2023-03-08", "title": "The giant diploid faba genome unlocks variation in a global protein crop", "description": "Abstract

Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity 1 . However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value 2 . Faba bean ( Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13\uffe2\uff80\uff89Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the\uffc2\uffa0improvement of sustainable protein production across the\uffc2\uffa0Mediterranean, subtropical and northern temperate agroecological zones. 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.

Intercellular signalling is an indispensable part of multicellular life. Understanding the commonalities and differences in how signalling molecules function in two remote branches of the tree of life may shed light on the reasons these molecules were originally recruited for intercellular signalling. Here we review the plant function of three highly studied animal intercellular signalling molecules, namely glutamate, \u03b3-aminobutyric acid (GABA), and melatonin. By considering both their signalling function in plants and their broader physiological function, we suggest that molecules with an original function as key metabolites or active participants in reactive ion species scavenging have a high chance of becoming intercellular signalling molecules. Naturally, the evolution of machinery to transduce a message across the plasma membrane is necessary. This fact is demonstrated by three other well-studied animal intercellular signalling molecules, namely serotonin, dopamine, and acetylcholine, for which there is currently no evidence that they act as intercellular signalling molecules in plants.

", "keywords": ["0301 basic medicine", "0303 health sciences", "signalling molecules", "plant physiology", "QH301-705.5", "Science", "Q", "R", "Plant Biology", "Glutamic Acid", "Plants", "03 medical and health sciences", "Journal Article", "reactive ion species", "Medicine", "Animals", "comparative biology", "Biology (General)", "metabolism", "gamma-Aminobutyric Acid", "Melatonin", "Signal Transduction"]}, "links": [{"href": "https://doi.org/10.7554/elife.83361"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/eLife", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.7554/elife.83361", "name": "item", "description": "10.7554/elife.83361", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.7554/elife.83361"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-06-20T00:00:00Z"}}, {"id": "10261/276560", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:25:06Z", "type": "Journal Article", "created": "2020-04-24", "title": "Alternation of wet and dry sides during partial rootzone drying irrigation enhances leaf ethylene evolution", "description": "Soil drying increases endogenous ABA and ACC concentrations in planta, but how these compounds interact to regulate stomatal responses to soil drying and re-watering is still unclear. To determine the temporal dynamics and physiological significance of root, xylem and leaf ABA and ACC concentrations in response to deficit irrigation (DI) or partial rootzone drying (PRD-F) and re-watering, these variables were measured in plants exposed to similar whole pot soil water contents. Both DI and PRD-F plants received only a fraction of the irrigation supplied to well-watered (WW) plants, either to all (DI) or part (PRD-F) of the rootzone of plants grown in split-pots. Both DI and PRD-F induced partial stomatal closure, increased root ABA and ACC accumulation consistent with local soil water content, but did not affect xylem or leaf concentrations of these compounds compared to WW plants. Two hours after re-watering all (DI-RW) or part of the rootzone (PRD-A) to the same soil water content, stomatal conductance returned to WW values or further decreased respectively. Re-watering the whole rootzone had no effect on xylem and leaf ABA and ACC concentrations, while re-watering the dry side of the pot in PRD plants had no effect on xylem and leaf ABA concentrations but increased xylem and leaf ACC concentrations and leaf ethylene evolution. Leaf water potential was similar between all irrigation treatments, with stomatal conductance declining as xylem ABA concentrations and leaf ACC concentrations increased. Prior to re-watering PRD plants, accounting for the spatial differences in soil water uptake best explained variation in xylem ACC concentration suggesting root-to-shoot ACC signalling, but this model did not account for variation in xylem ACC concentration after re-watering the dry side of PRD plants. Thus local (foliar) and long-distance (root-to-shoot) variation in ACC status both seem important in regulating the temporal dynamics of foliar ethylene evolution in plants exposed to PRD.", "keywords": ["0106 biological sciences", "Irrigation", "Stomatal conductance", "Root-to-shoot signalling", "Ethylene", "Physiological significance", "Deficit irrigation", "Plant Science", "Leaf water", "F06 Irrigation", "01 natural sciences", "ACC", "Ecology", " Evolution", " Behavior and Systematics", "580", "2. Zero hunger", "Xylem", "15. Life on land", "F60 Plant physiology and biochemistry", "6. Clean water", "Horticulture", "13. Climate action", "Soil water", "Agronomy and Crop Science", "Soil moisture heterogeneity", "Partial rootzone drying"]}, "links": [{"href": "https://eprints.lancs.ac.uk/id/eprint/144510/1/Juan_EEB_Manuscript_final.pdf"}, {"href": "https://doi.org/10261/276560"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20and%20Experimental%20Botany", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10261/276560", "name": "item", "description": "10261/276560", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10261/276560"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-01T00:00:00Z"}}, {"id": "10754/660313", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:25:20Z", "type": "Journal Article", "created": "2019-10-25", "title": "Genetic Loci Associated with Early Salt Stress Responses of Roots", "description": "Salinity is a devastating abiotic stress accounting for major crop losses yearly. Plant roots can strikingly grow away from high-salt patches. This response is termed halotropism and occurs through auxin redistribution in roots in response to a salt gradient. Here, a natural variation screen for the early and NaCl-specific halotropic response of 333 Arabidopsis accessions revealed quantitative differences in the first 24 h. These data were successfully used to identify genetic components associated with the response through Genome-Wide Association Study (GWAS). Follow-up characterization of knockout mutants in Col-0 background confirmed the role of transcription factor WRKY25, cation-proton exchanger CHX13, and a gene of unknown function DOB1 (Double Bending 1) in halotropism. In chx13 and dob1 mutants, ion accumulation and shoot biomass under salt stress were also affected. Thus, our GWAS has identified genetic components contributing to main root halotropism that provide insight into the genetic architecture underlying plant salt responses.", "keywords": ["580", "0301 basic medicine", "2. Zero hunger", "570", "0303 health sciences", "Science", "Q", "Plant Biology", "Biological Sciences", "15. Life on land", "Plant Genetics", "Article", "03 medical and health sciences", "Plant Physiology"]}, "links": [{"href": "https://doi.org/10754/660313"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/iScience", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10754/660313", "name": "item", "description": "10754/660313", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10754/660313"}, {"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": "20.500.11769/552491", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:25:52Z", "type": "Journal Article", "created": "2022-08-18", "title": "Assessing almond response to irrigation and soil management practices using vegetation indexes time-series and plant water status measurements", "description": "Current water scarcity scenario has led to the implementation of sustainable agricultural practices intended to improve water use efficiency. The present work evaluates during three agricultural campaigns (2018-2020) the response of a young almond orchard to two management practices in terms by combining remote sensing indexes (Normalized Difference Vegetation Index, NDVI; and Soil Adjusted Vegetation Indexes, SAVI) and physiological/ morphological measurement (stem water potential, \u03a8stem; trunk perimeter and canopy diameter). The management practices included (I) sustained deficit irrigation and (II) soil management. Severe deficit irrigation resulted in lower vegetation indexes (VI) values, \u03a8stem and tree dimensions (13 %, 23 % and 14 % lower, respectively) than those obtained for full irrigation strategy; whereas moderate deficit irrigation did not affect any of the parameters analysed. The presence of vegetation cover in the inter-row resulted in a VIs increase (19-42 %) and in lower tree dimensions (reductions of 7-8 % for trunk perimeter and 0.34-0.37 m for canopy diameter) when compared to bare soil treatment, but did not have any influence on \u03a8stem. The present study proves the suitability of remote sensing and physiological measurements for assessing almond response to the different management practices.", "keywords": ["0106 biological sciences", "Soil management", "Almonds", "F06 Irrigation", "01 natural sciences", "12. Responsible consumption", "Vegetation index", "Sentinel 2", "Remote sensing sustainable agriculture", "P33 Soil chemistry and physics", "F40 Plant ecology", "2. Zero hunger", "precision agriculture", "Precision agriculture", "Sustainable agriculture", "Water use efficiency", "Vegetation cover", "F07 Soil cultivation", "04 agricultural and veterinary sciences", "Remote sensing", "15. Life on land", "Tree canopy", "F60 Plant physiology and biochemistry", "6. Clean water", "Water management", "P30 Soil science and management", "P10 Water resources and management", "0401 agriculture", " forestry", " and fisheries", "Sentinel-2"]}, "links": [{"href": "https://www.iris.unict.it/bitstream/20.500.11769/552491/2/Agriculture%2c%20ecosystems%20and%20environment%202022.pdf"}, {"href": "https://doi.org/20.500.11769/552491"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agriculture%2C%20Ecosystems%20%26amp%3B%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "20.500.11769/552491", "name": "item", "description": "20.500.11769/552491", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/20.500.11769/552491"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-11-01T00:00:00Z"}}, {"id": "20.500.11850/636573", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:25:55Z", "type": "Journal Article", "created": "2023-10-04", "title": "Root phenotypes for improved nitrogen capture", "description": "Abstract Background

Suboptimal nitrogen availability is a primary constraint for crop production in low-input agroecosystems, while nitrogen fertilization is a primary contributor to the energy, economic, and environmental costs of crop production in high-input agroecosystems. In this article we consider avenues to develop crops with improved nitrogen capture and reduced requirement for nitrogen fertilizer.

Scope

Intraspecific variation for an array of root phenotypes has been associated with improved nitrogen capture in cereal crops, including architectural phenotypes that colocalize root foraging with nitrogen availability in the soil; anatomical phenotypes that reduce the metabolic costs of soil exploration, improve penetration of hard soil, and exploit the rhizosphere; subcellular phenotypes that reduce the nitrogen requirement of plant tissue; molecular phenotypes exhibiting optimized nitrate uptake kinetics; and rhizosphere phenotypes that optimize associations with the rhizosphere microbiome. For each of these topics we provide examples of root phenotypes which merit attention as potential selection targets for crop improvement. Several cross-cutting issues are addressed including the importance of soil hydrology and impedance, phenotypic plasticity, integrated phenotypes, in silico modeling, and breeding strategies using high throughput phenotyping for co-optimization of multiple phenes.

Conclusions

Substantial phenotypic variation exists in crop germplasm for an array of root phenotypes that improve nitrogen capture. Although this topic merits greater research attention than it currently receives, we have adequate understanding and tools to develop crops with improved nitrogen capture. Root phenotypes are underutilized yet attractive breeding targets for the development of the nitrogen efficient crops urgently needed in global agriculture.

", "keywords": ["2. Zero hunger", "0106 biological sciences", "0301 basic medicine", "Plasticity", "Marschner Review", "Nitrogen", "Physiology", "Nitrogen; Root; Anatomy; Architecture; Soil; Crop breeding; Root phenotyping; Modeling; Rhizosphere; Plasticity; Physiology", "Modeling", "Root phenotyping", "15. Life on land", "01 natural sciences", "Soil", "03 medical and health sciences", "Root", "FOS: Biological sciences", "Architecture", "Rhizosphere", "Crop breeding", "Anatomy", "FOS: Civil engineering"]}, "links": [{"href": "https://doi.org/20.500.11850/636573"}, {"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": "20.500.11850/636573", "name": "item", "description": "20.500.11850/636573", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/20.500.11850/636573"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-10-04T00:00:00Z"}}, {"id": "2440/106807", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:26:15Z", "type": "Journal Article", "created": "2017-06-13", "title": "Circular linkages between soil biodiversity, fertility and plant productivity are limited to topsoil at the continental scale", "description": "Summary

The current theoretical framework suggests that tripartite positive feedback relationships between soil biodiversity, fertility and plant productivity are universal. However, empirical evidence for these relationships at the continental scale and across different soil depths is lacking.

We investigate the continental\uffe2\uff80\uff90scale relationships between the diversity of microbial and invertebrate\uffe2\uff80\uff90based soil food webs, fertility and above\uffe2\uff80\uff90ground plant productivity at 289 sites and two soil depths, that is 0\uffe2\uff80\uff9310 and 20\uffe2\uff80\uff9330\uffc2\uffa0cm, across Australia.

Soil biodiversity, fertility and plant productivity are strongly positively related in surface soils. Conversely, in the deeper soil layer, the relationships between soil biodiversity, fertility and plant productivity weaken considerably, probably as a result of a reduction in biodiversity and fertility with depth. Further modeling suggested that strong positive associations among soil biodiversity\uffe2\uff80\uff93fertility and fertility\uffe2\uff80\uff93plant productivity are limited to the upper soil layer (0\uffe2\uff80\uff9310\uffc2\uffa0cm), after accounting for key factors, such as distance from the equator, altitude, climate and physicochemical soil properties.

These findings highlight the importance of surface soil biodiversity for soil fertility, and suggest that any loss of surface soil could potentially break the links between soil biodiversity\uffe2\uff80\uff93fertility and/or fertility\uffe2\uff80\uff93plant productivity, which can negatively impact nutrient cycling and food production, upon which future generations depend.

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.

Intercellular signalling is an indispensable part of multicellular life. Understanding the commonalities and differences in how signalling molecules function in two remote branches of the tree of life may shed light on the reasons these molecules were originally recruited for intercellular signalling. Here we review the plant function of three highly studied animal intercellular signalling molecules, namely glutamate, \u03b3-aminobutyric acid (GABA), and melatonin. By considering both their signalling function in plants and their broader physiological function, we suggest that molecules with an original function as key metabolites or active participants in reactive ion species scavenging have a high chance of becoming intercellular signalling molecules. Naturally, the evolution of machinery to transduce a message across the plasma membrane is necessary. This fact is demonstrated by three other well-studied animal intercellular signalling molecules, namely serotonin, dopamine, and acetylcholine, for which there is currently no evidence that they act as intercellular signalling molecules in plants.

", "keywords": ["0301 basic medicine", "0303 health sciences", "signalling molecules", "plant physiology", "QH301-705.5", "Science", "Q", "R", "Plant Biology", "Glutamic Acid", "Plants", "03 medical and health sciences", "Journal Article", "reactive ion species", "Medicine", "Animals", "comparative biology", "Biology (General)", "metabolism", "gamma-Aminobutyric Acid", "Melatonin", "Signal Transduction"]}, "links": [{"href": "https://doi.org/PMC10281673"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/eLife", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC10281673", "name": "item", "description": "PMC10281673", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC10281673"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-06-20T00:00:00Z"}}, {"id": "PMC11494973", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:28:58Z", "type": "Journal Article", "created": "2024-09-10", "title": "A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities", "description": "ABSTRACT

Due to recent improvements, Nanopore sequencing has become a promising method for experiments relying on amplicon sequencing. We describe a flexible workflow to generate and annotate high-quality, full-length 16S rDNA amplicons. We evaluated it for two applications, namely, (i) identification of bacterial isolates and (ii) species-level profiling of microbial communities. We assessed the identification of single bacterial isolates by sequencing, using a set of barcoded full-length 16S rRNA gene primer pairs (pair A), on 47 isolates encompassing multiple genera and compared those results with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification. Species-level community profiling was tested with two sets of barcoded full-length 16S primer pairs (A and B) and compared to the results obtained with shotgun Illumina sequencing using 27 stool samples. We developed a Nextflow pipeline to retain high-quality reads and taxonomically annotate them. We found high agreement between our workflow and MALDI-TOF data for isolate identification (positive predictive value = 0.90, Cram\uffc3\uffa9r\uffe2\uff80\uff99s V = 0.857, and Theil\uffe2\uff80\uff99s U = 0.316). For species-level community profiling, we found strong correlations ( r s > 0.6) of alpha diversity indices between the two primer sets and Illumina sequencing. At the community level, we found significant but small differences when comparing sequencing techniques. Finally, we found a moderate to strong correlation when comparing the relative abundances of individual species (average r s = 0.6 and 0.533 for primers A and B). Despite identified shortcomings, the proposed workflow enabled accurate identification of single bacterial isolates and prominent features in microbial communities, making it a worthwhile alternative to MALDI-TOF MS and Illumina sequencing.

IMPORTANCE

A quick, robust, simple, and cost-effective method to identify bacterial isolates and communities in each sample is indispensable in the fields of microbiology and infection biology. Recent technological advances in Oxford Nanopore Technologies sequencing make this technique an attractive option considering the adaptability, portability, and cost-effectiveness of the platform, even with small sequencing batches. Here, we validated a flexible workflow to identify bacterial isolates and characterize bacterial communities using the Oxford Nanopore Technologies sequencing platform combined with the most recent v14 chemistry kits. For bacterial isolates, we compared our nanopore-based approach to matrix-assisted laser desorption ionization-time of flight mass spectrometry-based identification. For species-level profiling of complex bacterial communities, we compared our nanopore-based approach to Illumina shotgun sequencing. For reproducibility purposes, we wrapped the code used to process the sequencing data into a ready-to-use and self-contained Nextflow pipeline.

", "keywords": ["DNA", " Bacterial", "1303 Biochemistry", "gut microbiome", "610 Medicine & health", "Microbiology", "Workflow", "1311 Genetics", "RNA", " Ribosomal", " 16S", "1312 Molecular Biology", "1706 Computer Science Applications", "DNA Barcoding", " Taxonomic", "Humans", "DNA sequencing", "Bacteria", "10179 Institute of Medical Microbiology", "Microbiota", "2404 Microbiology", "1314 Physiology", "bioinformatics", "QR1-502", "Nanopore Sequencing", "1105 Ecology", " Evolution", " Behavior and Systematics", "Spectrometry", " Mass", " Matrix-Assisted Laser Desorption-Ionization", "570 Life sciences; biology", "2611 Modeling and Simulation", "Research Article"]}, "links": [{"href": "https://doi.org/PMC11494973"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSystems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC11494973", "name": "item", "description": "PMC11494973", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC11494973"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-04-11T00:00:00Z"}}, {"id": "PMC8027828", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:29:03Z", "type": "Journal Article", "created": "2020-10-06", "title": "Acidobacteria are active and abundant members of diverse atmospheric H2-oxidizing communities detected in temperate soils", "description": "Abstract

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.