Irrigation according to reliable estimates of crop water requirements (CWR) is one of the key strategies to ensure long-term sustainability of irrigated agriculture. In southern Mediterranean regions, during the irrigation season, CWR is almost totally controlled by the potential evapotranspiration of the irrigated crop. An innovative system for forecasting crop potential evapotranspiration (ETp) has been implemented recently in the Campania region (southern Italy). The system produces ETp forecasts with a lead time of up to 5 days, by coupling the visible and near-infrared crop imagery with numerical weather prediction outputs of a limited area model. The forecasts are delivered to farmers with a simple and intuitive web app interface, which makes daily real-time ETp maps accessible from desktop computers, tablets and smartphones. Forecast performances were evaluated for maize fields of two farms in two irrigation seasons (2014\uffe2\uff80\uff932015). The mean absolute bias of the forecasted ETp was <0.3 mm/day and the RMSE was <0.6 mm/day, both for lead times up to 5 days.
", "keywords": ["2. Zero hunger", "Earth observation", "Crop water requirements", "0207 environmental engineering", "forecasting", "02 engineering and technology", "15. Life on land", "01 natural sciences", "numerical weather predictions", "13. Climate action", "potential evapotranspiration", "11. Sustainability", "Genetics", "Animal Science and Zoology", "Agronomy and Crop Science", "Crop water requirements; Earth observation; forecasting; numerical weather predictions; potential evapotranspiration; Animal Science and Zoology; Agronomy and Crop Science; Genetics", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1017/s0021859618000084"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20Journal%20of%20Agricultural%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1017/s0021859618000084", "name": "item", "description": "10.1017/s0021859618000084", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1017/s0021859618000084"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-28T00:00:00Z"}}, {"id": "10.1016/j.plantsci.2023.111919", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:16:35Z", "type": "Journal Article", "created": "2023-11-20", "title": "Phytosiderophore pathway response in barley exposed to iron, zinc or copper starvation", "description": "Efficient micronutrient acquisition is a critical factor in selecting micronutrient dense crops for human consumption. Enhanced exudation and re-uptake of metal chelators, so-called phytosiderophores, by roots of graminaceous plants has been implicated in efficient micronutrient acquisition. We compared PS biosynthesis and exudation as a response mechanism to either Fe, Zn or Cu starvation. Two barley (Hordeum vulgare L.) lines with contrasting micronutrient grain yields were grown hydroponically and PS exudation (LC-MS) and root gene expression (RNAseq) were determined after either Fe, Zn, or Cu starvation. The response strength of the PS pathway was micronutrient dependent and decreased in the order Fe >\u00a0Zn >\u00a0Cu deficiency. We observed a stronger expression of PS pathway genes and greater PS exudation in the barley line with large micronutrient grain yield suggesting that a highly expressed PS pathway might be an important trait involved in high micronutrient accumulation. In addition to several metal specific transporters, we also found that the expression of IRO2 and bHLH156 transcription factors was not only induced under Fe but also under Zn and Cu deficiency. Our study delivers important insights into the role of the PS pathway in the acquisition of different micronutrients.", "keywords": ["2. Zero hunger", "Phytosiderophore", "/dk/atira/pure/subjectarea/asjc/1300/1311", "/dk/atira/pure/subjectarea/asjc/1100/1102", "Root exudation", "name=Genetics", "Iron", "/dk/atira/pure/subjectarea/asjc/1100/1110", "Hordeum", "Copper deficiency", "Plant Roots", "630", "Mugineic acid", "name=Agronomy and Crop Science", "Zinc", "Barley", "Humans", "Micronutrients", "name=Plant Science", "Biofortification", "Copper"]}, "links": [{"href": "https://doi.org/10.1016/j.plantsci.2023.111919"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.plantsci.2023.111919", "name": "item", "description": "10.1016/j.plantsci.2023.111919", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.plantsci.2023.111919"}, {"rel": "collection", "type": 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\u0645\u0646 \u0627\u0644\u0623\u0634\u062c\u0627\u0631 \u0625\u0644\u0649 \u0627\u0633\u062a\u0642\u0631\u0627\u0631 \u0623\u0643\u0628\u0631 \u0644\u0644\u062a\u0631\u0628\u0629 \u0627\u0644\u0645\u0639\u062f\u0646\u064a\u0629 C \u0639\u0646 \u0637\u0631\u064a\u0642 \u062a\u0643\u0648\u064a\u0646 OM \u0627\u0644\u0645\u0631\u062a\u0628\u0637 \u0628\u0627\u0644\u0645\u0639\u0627\u062f\u0646 \u0648\u062a\u0645\u0639\u062f\u0646 \u0645\u064a\u0643\u0631\u0648\u0628\u064a \u0623\u0643\u0628\u0631 \u0644\u0640 SOM \u0645\u0639 \u0627\u0631\u062a\u0641\u0627\u0639 \u0627\u0644\u0637\u0644\u0628 \u0639\u0644\u0649 \u0627\u0644\u0645\u0648\u0627\u0631\u062f \u0627\u0644\u0645\u064a\u0643\u0631\u0648\u0628\u064a\u0629. \u062a\u0634\u064a\u0631 \u0627\u0644\u0646\u062a\u0627\u0626\u062c \u0625\u0644\u0649 \u0623\u0646 EA \u0628\u0648\u0633\u0627\u0637\u0629 \u0623\u0646\u0648\u0627\u0639 \u0627\u0644\u0623\u0634\u062c\u0627\u0631\u060c \u0648\u0627\u0644\u062d\u062f \u0645\u0646 \u0627\u0644\u0645\u0648\u0627\u0631\u062f \u0627\u0644\u0645\u064a\u0643\u0631\u0648\u0628\u064a\u0629 \u0648\u062a\u0643\u0648\u064a\u0646 \u0627\u0644\u0645\u062c\u062a\u0645\u0639 \u0627\u0644\u0645\u064a\u0643\u0631\u0648\u0628\u064a \u0647\u064a \u0645\u062d\u0631\u0643\u0627\u062a \u0645\u0647\u0645\u0629 \u0644\u0644\u0645\u062e\u0632\u0648\u0646\u0627\u062a \u0648\u0627\u0644\u062a\u0648\u0632\u064a\u0639 \u0627\u0644\u0631\u0623\u0633\u064a \u0644\u0645\u062e\u0632\u0648\u0646 \u0627\u0644\u0643\u0631\u0628\u0648\u0646 \u0627\u0644\u0639\u0636\u0648\u064a \u0641\u064a \u0627\u0644\u062a\u0631\u0628\u0629 \u0628\u064a\u0646 \u0623\u0646\u0648\u0627\u0639 \u0627\u0644\u0623\u0634\u062c\u0627\u0631 \u0648\u0628\u064a\u0646 \u0646\u0648\u0639\u064a\u0646 \u0645\u0646 \u0627\u0644\u062c\u0630\u0648\u0631 \u0627\u0644\u0641\u0637\u0631\u064a\u0629 \u0627\u0644\u0645\u0631\u062a\u0628\u0637\u0629 \u0628\u0647\u0627.", "keywords": ["Biomass (ecology)", "Microbial population biology", "Fagus sylvatica", "Soil Science", "Plant Science", "Plant litter", "Agricultural and Biological Sciences", "Mycorrhizal Fungi and Plant Interactions", "Soil water", "Genetics", "Monoculture", "Forest floor", "Saproxylic Insect Ecology and Forest Management", "Biology", "Beech", "Soil organic matter", "Soil Fertility", "Ecology", "Bacteria", "Picea abies", "Botany", "Life Sciences", "04 agricultural and veterinary sciences", "Soil carbon", "Agronomy", "Insect Science", "FOS: Biological sciences", "0401 agriculture", " forestry", " and fisheries", "Soil Carbon Dynamics and Nutrient Cycling in Ecosystems", "Nutrient"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2022.108754"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2022.108754", "name": "item", "description": "10.1016/j.soilbio.2022.108754", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2022.108754"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-09-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2022.108918", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:16:58Z", "type": "Journal Article", "created": "2022-12-22", "title": "Litter chemistry of common European tree species drives the feeding preference and consumption rate of soil invertebrates, and shapes the diversity and structure of gut and faecal microbiomes", "description": "Open AccessTerrestrial isopods and millipedes are key drivers of a litter decomposition in terrestrial ecosystems but the effects of litter chemistry on feeding preference and litter consumption rate as well as on the diversity and composition of gut and faecal microbiome still entails several challenges. We established a mesocosm experiment with terrestrial isopods (Oniscus asellus) and millipedes (Glomeris marginata) fed by leaf litter from six common European tree species (ash, maple, lime, beech, oak and Norway spruce) to reveal the effect of litter chemistry on consumption rate and feeding preference as well as on the compositions of gut and faecal microbiomes. The total percentage of consumed litter showed that O. asellus preferred nutrient-rich and labile-C litter of ash over more recalcitrant litter of oak, beech, and Norway spruce, while G. marginata preferred calcium-rich ash, maple and lime litter over beech and Norway spruce. Consumption of litter by O. asellus and G. marginata increased with concentrations of magnesium, sulphur and potassium but decreased with concentrations of iron, phosphorus, lignin, cellulose and TOC. The millipede G. marginata harboured higher bacterial OTU richness (73.5 \u00b1 12.5) than the isopod O. asellus (49.1 \u00b1 15.9), but fungal OTU richness was similar with 25.8 \u00b1 6.7 in O. asellus and 25.7 \u00b1 2.7 in G. marginata. In total, faeces of both animals hosted higher diversity than gut. In gut and faeces of O. asellus, the fungal OTU richness was highest for individuals fed by litter of Norway spruce, while lowest OTU richness was recorded for individuals fed by litter of more palatable ash. In contrast, the highest diversity of the fungal community in gut and faeces of G. marginata was recorded for individuals fed by palatable lime litter, while the lowest OTUs richness was recorded when millipedes were fed by maple and spruce. The structures of bacterial and fungal communities generally separated between O. asellus and G. marginata. The fungal community structure in gut and faeces differed between animals fed by different foliar litters, while the bacterial community structure mainly differed between gut and faeces regardless of the offered type of litter. The fungal community structure in gut and faeces of O. asellus and G. marginata were shaped by concentrations of magnesium, sulphur, lignin and cellulose. The bacterial communities in gut and faeces of both O. asellus and G. marginata were dominated by copiotrophic bacteria, while fungal communities were dominated by unspecified saprotrophs. Our study suggest that litter quality is a strong driver of feeding preference and consumption rates as well as composition of bacterial and fungal communities in gut and faeces of two species representing the main groups of litter feeding soil fauna in European forests.", "keywords": ["0301 basic medicine", "Genomic Insights into Social Insects and Symbiosis", "Plant Science", "Plant litter", "Agricultural and Biological Sciences", "03 medical and health sciences", "Biochemistry", " Genetics and Molecular Biology", "Litter", "Genetics", "Ecological Niche", "Biology", "Ecosystem", "Beech", "0303 health sciences", "Species Distribution Modeling and Climate Change Impacts", "Ecology", "Ecological Modeling", "Botany", "Life Sciences", "15. Life on land", "Plant-Parasitic Nematodes in Molecular Plant Pathology", "Detritus", "FOS: Biological sciences", "Detritivore", "Environmental Science", "Physical Sciences", "Species richness"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2022.108918"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2022.108918", "name": "item", "description": "10.1016/j.soilbio.2022.108918", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2022.108918"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-02-01T00:00:00Z"}}, {"id": "10.1038/s41467-020-15622-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:38Z", "type": "Journal Article", "created": "2020-05-05", "title": "Sustained fluvial deposition recorded in Mars\u2019 Noachian stratigraphic record", "description": "AbstractOrbital observation has revealed a rich record of fluvial landforms on Mars, with much of this record dating 3.6\uffe2\uff80\uff933.0 Ga. Despite widespread geomorphic evidence, few analyses of Mars\uffe2\uff80\uff99 alluvial sedimentary-stratigraphic record exist, with detailed studies of alluvium largely limited to smaller sand-bodies amenable to study in-situ by rovers. These typically metre-scale outcrop dimensions have prevented interpretation of larger scale channel-morphology and long-term basin evolution, vital for understanding the past Martian climate. Here we give an interpretation of a large sedimentary succession at Izola mensa within the NW Hellas Basin rim. The succession comprises channel and barform packages which together demonstrate that river deposition was already well established >3.7 Ga. The deposits mirror terrestrial analogues subject to low-peak discharge variation, implying that river deposition at Izola was subject to sustained, potentially perennial, fluvial flow. Such conditions would require an environment capable of maintaining large volumes of water for extensive time-periods, necessitating a precipitation-driven hydrological cycle.
", "keywords": ["550", "Science", "General Biochemistry", "Genetics and Molecular Biology", "Q", "500", "General Physics and Astronomy", "Geomorphology", "General Chemistry", "15. Life on land", "01 natural sciences", "Article", "12. Responsible consumption", "Sedimentology", " Stratigraphy", " Fluvial Deposits", " Mars", " Sedimentary Deposits", "[SDU.STU.PL]Sciences of the Universe [physics]/Earth Sciences/Planetology", "13. Climate action", "Inner planets", "[SDU.STU.PL] Sciences of the Universe [physics]/Earth Sciences/Planetology", "0105 earth and related environmental sciences"]}, "links": [{"href": "http://oro.open.ac.uk/70442/1/70442.pdf"}, {"href": "https://www.nature.com/articles/s41467-020-15622-0.pdf"}, {"href": "https://doi.org/10.1038/s41467-020-15622-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-020-15622-0", "name": "item", "description": "10.1038/s41467-020-15622-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-020-15622-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-05T00:00:00Z"}}, {"id": "10.1017/s0021859617000193", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:16Z", "type": "Journal Article", "created": "2017-03-27", "title": "Maize\u2013Common Bean Intercropping To Optimize Maize-Based Crop Production", "description": "SUMMARYMaize (Zea maysL.)\uffe2\uff80\uff93common bean (Phaseolus vulgarisL.) intercropping is a recent practice in north-western Ethiopia and there is limited information on its productivity. A field experiment was conducted at South Achefer and Mecha in north-western Ethiopia during the 2012 and 2013 crop growing seasons to determine combinations of intercrop planting arrangement (IPA) with nitrogen (N) and phosphorus (P) rates for optimizing maize\uffe2\uff80\uff93common bean intercrop productivity and profitability. Treatments consisted of factorial combinations of two IPA (single row of common bean between maize rows and paired rows of common bean between paired rows of maize), two N rates (92 and 128 kg N/ha) and two P rates (20 and 40 kg P/ha). A sole crop maize with recommended fertilizer rate of 128/40 kg N/P/ha was used as a control treatment. The treatments were laid out in a randomized complete block design with three replications. Results indicated that land equivalent ratio was more than unity, and the intercrop system was 20% more productive relative to the sole crop. Maize equivalent yields were highest for most of the intercrop treatments relative to mono-crop maize with yield advantage of 14% from single row IPA with 128/20 kg N/P/ha. Single row IPA with 128/20 kg N/P/ha and paired row IPA with 92/20 kg N/P/ha increased financial returns by 16 and 8% relative to sole crop maize, respectively. Smallholder maize-based cropping of north-western Ethiopia could be nutritionally, agronomically and financially improved through maize\uffe2\uff80\uff93common bean intercropping of single row IPA with appropriate nutrient management.
", "keywords": ["2. Zero hunger", "0106 biological sciences", "0401 agriculture", " forestry", " and fisheries", "farming systems", "genetics", "04 agricultural and veterinary sciences", "15. Life on land", "crops", "maize", "01 natural sciences"], "contacts": [{"organization": "Alemayehu, A., Tamado, T., Nigussie, D., Yigzaw, D., Kinde, T., Wortmann, Charles S.,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1017/s0021859617000193"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20Journal%20of%20Agricultural%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1017/s0021859617000193", "name": "item", "description": "10.1017/s0021859617000193", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1017/s0021859617000193"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-03-27T00:00:00Z"}}, {"id": "10.3390/genes10010068", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:20:52Z", "type": "Journal Article", "created": "2019-01-22", "title": "Convergent Evolution of the Seed Shattering Trait", "description": "Loss of seed shattering is a key trait in crop domestication, particularly for grain crops. For wild plants, seed shattering is a crucial mechanism to achieve greater fitness, although in the agricultural context, this mechanism reduces harvesting efficiency, especially under dry conditions. Loss of seed shattering was acquired independently in different monocotyledon and dicotyledon crop species by \uffe2\uff80\uff98convergent phenotypic evolution\uffe2\uff80\uff99, leading to similar low dehiscent and indehiscent phenotypes. Here, the main aim is to review the current knowledge about seed shattering in crops, in order to highlight the tissue modifications that underlie the convergent phenotypic evolution of reduced shattering in different types of fruit, from the silique of Brassicaceae species, to the pods of legumes and spikes of cereals. Emphasis is given to legumes, with consideration of recent data obtained for the common bean. The current review also discusses to what extent convergent phenotypes arose from parallel changes at the histological and/or molecular levels. For this reason, an overview is included of the main findings relating to the genetic control of seed shattering in the model species Arabidopsis thaliana and in other important crops.
", "keywords": ["QTL mapping", "common bean", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "legumes", "Quantitative Trait Loci", "Common bean; Crop domestication; Gene expression; Legumes; Pod anatomy; QTL mapping; Genetics; Genetics (clinical)", "legume", "Review", "QH426-470", "pod anatomy", "15. Life on land", "Evolution", " Molecular", "crop domestication", "Magnoliopsida", "03 medical and health sciences", "Seed Dispersal", "Seeds", "Genetics", "gene expression"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/1/68/pdf"}, {"href": "https://doi.org/10.3390/genes10010068"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/genes10010068", "name": "item", "description": "10.3390/genes10010068", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes10010068"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-01-19T00:00:00Z"}}, {"id": "10.1038/s41467-018-05824-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:37Z", "type": "Journal Article", "created": "2018-08-20", "title": "Biogenic volatile release from permafrost thaw is determined by the soil microbial sink", "description": "AbstractWarming in the Arctic accelerates thawing of permafrost-affected soils, which leads to a release of greenhouse gases to the atmosphere. We do not know whether permafrost thaw also releases non-methane volatile organic compounds that can contribute to both negative and positive radiative forcing on climate. Here we show using proton transfer reaction\uffe2\uff80\uff93time of flight\uffe2\uff80\uff93mass spectrometry that substantial amounts of ethanol and methanol and in total 316 organic ions were released from Greenlandic permafrost soils upon thaw in laboratory incubations. We demonstrate that the majority of this release is taken up in the active layer above. In an experiment using 14C-labeled ethanol and methanol, we demonstrate that these compounds are consumed by microorganisms. Our findings highlight that the thawing permafrost soils are not only a considerable source of volatile organic compounds but also that the active layer regulates their release into the atmosphere.
", "keywords": ["0301 basic medicine", "Ethanol", "Science", "Climate", "Methanol", "General Biochemistry", "Genetics and Molecular Biology", "Q", "General Physics and Astronomy", "Permafrost", "General Chemistry", "15. Life on land", "01 natural sciences", "Article", "03 medical and health sciences", "13. Climate action", "11. Sustainability", "SDG 13 - Climate Action", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://www.nature.com/articles/s41467-018-05824-y.pdf"}, {"href": "https://doi.org/10.1038/s41467-018-05824-y"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-018-05824-y", "name": "item", "description": "10.1038/s41467-018-05824-y", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-018-05824-y"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-08-24T00:00:00Z"}}, {"id": "10.1038/s41467-018-05980-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:37Z", "type": "Journal Article", "created": "2018-08-29", "title": "Land use driven change in soil pH affects microbial carbon cycling processes", "description": "AbstractSoil microorganisms act as gatekeepers for soil\uffe2\uff80\uff93atmosphere carbon exchange by balancing the accumulation and release of soil organic matter. However, poor understanding of the mechanisms responsible hinders the development of effective land management strategies to enhance soil carbon storage. Here we empirically test the link between microbial ecophysiological traits and topsoil carbon content across geographically distributed soils and land use contrasts. We discovered distinct pH controls on microbial mechanisms of carbon accumulation. Land use intensification in low-pH soils that increased the pH above a threshold (~6.2) leads to carbon loss through increased decomposition, following alleviation of acid retardation of microbial growth. However, loss of carbon with intensification in near-neutral pH soils was linked to decreased microbial biomass and reduced growth efficiency that was, in turn, related to trade-offs with stress alleviation and resource acquisition. Thus, less-intensive management practices in near-neutral pH soils have more potential for carbon storage through increased microbial growth efficiency, whereas in acidic soils, microbial growth is a bigger constraint on decomposition rates.White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin (2n\uffe2\uff80\uff89=\uffe2\uff80\uff8950, 451\uffe2\uff80\uff89Mb), as well as de novo assemblies of a landrace and a wild relative. We describe a modern accession displaying increased soil exploration capacity through early establishment of lateral and cluster roots. We also show how seed quality may have been impacted by domestication in term of protein profiles and alkaloid content. The availability of a high-quality genome assembly together with companion genomic and transcriptomic resources will enable the development of modern breeding strategies to increase and stabilize white lupin yield.
", "keywords": ["Repetitive Sequences", " Nucleic Acid/genetics", "0301 basic medicine", "[SDV]Life Sciences [q-bio]", "Plant Roots/genetics", "Gene Dosage", "Plant Science", "Crop", "Alkaloids/chemistry", "Plant Roots", "Gene", "Repetitive Sequences", "630", "Agricultural and Biological Sciences", "Domestication", "Soil", "Models", "Symbiotic Nitrogen Fixation in Legumes", "Gene Duplication", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "http://aims.fao.org/aos/agrovoc/c_3224", "Plant Proteins/metabolism", "Plant Proteins", "2. Zero hunger", "0303 health sciences", "Genome", "Q", "http://aims.fao.org/aos/agrovoc/c_27583", "Life Sciences", "Transcriptome/genetics", "http://aims.fao.org/aos/agrovoc/c_92382", "Polymorphism", " Single Nucleotide/genetics", "Lupinus", "[SDV] Life Sciences [q-bio]", "Protein Crop", "Seeds", "http://aims.fao.org/aos/agrovoc/c_5956", "White (mutation)", "Single Nucleotide/genetics", "Sequence Analysis", "Genome", " Plant", "expression des g\u00e8nes", "http://aims.fao.org/aos/agrovoc/c_4464", "Synteny/genetics", "Evolution", "Lupin Seeds", "Science", "Centromere", "Lupinus/genetics", "Polymorphism", " Single Nucleotide", "Article", "g\u00e9nomique", "Evolution", " Molecular", "Evolution and Nutritional Properties of Lupin Seeds", "physiologie v\u00e9g\u00e9tale", "03 medical and health sciences", "Alkaloids", "Genetic", "Nucleic Acid/genetics", "Seeds/physiology", "Centromere/genetics", "Genetics", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "Polymorphism", "Biology", "Ecology", " Evolution", " Behavior and Systematics", "Repetitive Sequences", " Nucleic Acid", "Sequence assembly", "http://aims.fao.org/aos/agrovoc/c_25189", "Ecotype", "Models", " Genetic", "g\u00e9nome", "Botany", "Molecular", "Genetic Variation", "Molecular Sequence Annotation", "Plant", "DNA", "Sequence Analysis", " DNA", "s\u00e9quence nucl\u00e9otidique", "15. Life on land", "http://aims.fao.org/aos/agrovoc/c_27527", "Agronomy", "Plant Leaves", "Evolution and Ecology of Endophyte-Grass Symbiosis", "Lupinus albus", "FOS: Biological sciences", "Genomic Structural Variation", "Plant Leaves/metabolism", "Gene expression", "Transcriptome", "am\u00e9lioration des plantes"]}, "links": [{"href": "https://www.nature.com/articles/s41467-019-14197-9.pdf"}, {"href": "https://doi.org/10.1038/s41467-019-14197-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-019-14197-9", "name": "item", "description": "10.1038/s41467-019-14197-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-019-14197-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-24T00:00:00Z"}}, {"id": "10.1038/s41467-022-29161-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:38Z", "type": "Journal Article", "created": "2022-03-17", "title": "Structure and function of the soil microbiome underlying N2O emissions from global wetlands", "description": "AbstractWetland soils are the greatest source of nitrous oxide (N2O), a critical greenhouse gas and ozone depleter released by microbes. Yet, microbial players and processes underlying the N2O emissions from wetland soils are poorly understood. Using in situ N2O measurements and by determining the structure and potential functional of microbial communities in 645 wetland soil samples globally, we examined the potential role of archaea, bacteria, and fungi in nitrogen (N) cycling and N2O emissions. We show that N2O emissions are higher in drained and warm wetland soils, and are correlated with functional diversity of microbes. We further provide evidence that despite their much lower abundance compared to bacteria, nitrifying archaeal abundance is a key factor explaining N2O emissions from wetland soils globally. Our data suggest that ongoing global warming and intensifying environmental change may boost archaeal nitrifiers, collectively transforming wetland soils to a greater source of N2O.Diversified cropping systems, especially those including legumes, have been proposed to enhance food production with reduced inputs and environmental impacts. However, the impact of legume pre-crops on main crop yield and its drivers has never been systematically investigated in a global context. Here, we synthesize 11,768 yield observations from 462 field experiments comparing legume-based and non-legume cropping systems and show that legumes enhanced main crop yield by 20%. These yield advantages decline with increasing N fertilizer rates and crop diversity of the main cropping system. The yield benefits are consistent among main crops (e.g., rice, wheat, maize) and evident across pedo-climatic regions. Moreover, greater yield advantages (32% vs. 7%) are observed in low- vs. high-yielding environments, suggesting legumes increase crop production with low inputs (e.g., in Africa or organic agriculture). In conclusion, our study suggests that legume-based rotations offer a critical pathway for enhancing global crop production, especially when integrated into low-input and low-diversity agricultural systems.Legume-rhizobium signaling during establishment of symbiotic nitrogen fixation restricts rhizobium colonization to specific cells. A limited number of root hair cells allow infection threads to form, and only a fraction of the epidermal infection threads progress to cortical layers to establish functional nodules. Here we use single-cell analysis to define the epidermal and cortical cell populations that respond to and facilitate rhizobium infection. We then identify high-confidence nodulation gene candidates based on their specific expression in these populations, pinpointing genes stably associated with infection across genotypes and time points. We show that one of these, which we name SYMRKL1, encodes a protein with an ectodomain predicted to be nearly identical to that of SYMRK and is required for normal infection thread formation. Our work disentangles cellular processes and transcriptional modules that were previously confounded due to lack of cellular resolution, providing a more detailed understanding of symbiotic interactions.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.Humans modify ecosystems and biodiversity worldwide, with negative consequences for ecosystem functioning. Promoting plant diversity is increasingly suggested as a mitigation strategy. However, our mechanistic understanding of how plant diversity affects the diversity of heterotrophic consumer communities remains limited. Here, we disentangle the relative importance of key components of plant diversity as drivers of herbivore, predator, and parasitoid species richness in experimental forests and grasslands. We find that plant species richness effects on consumer species richness are consistently positive and mediated by elevated structural and functional diversity of the plant communities. The importance of these diversity components differs across trophic levels and ecosystems, cautioning against ignoring the fundamental ecological complexity of biodiversity effects. Importantly, plant diversity effects on higher trophic-level species richness are in many cases mediated by modifications of consumer abundances. In light of recently reported drastic declines in insect abundances, our study identifies important pathways connecting plant diversity and consumer diversity across ecosystems.
", "keywords": ["0106 biological sciences", "2. Zero hunger", "570", "/dk/atira/pure/core/keywords/nachhaltigkeitswissenschaft; name=Sustainability Science", "Science", "/dk/atira/pure/subjectarea/asjc/1600; name=Chemistry(all)", "Q", "/dk/atira/pure/subjectarea/asjc/1300; name=Biochemistry", " Genetics and Molecular Biology(all)", "634", "Biodiversity", "/dk/atira/pure/core/keywords/biology; name=Ecosystems Research", "Plants", "15. Life on land", "/dk/atira/pure/subjectarea/asjc/1000; name=General", "01 natural sciences", "Article", "ddc:", "/dk/atira/pure/subjectarea/asjc/3100; name=Physics and Astronomy(all)", "Species Specificity", "Animals", "14. Life underwater", "Arthropods"]}, "links": [{"href": "https://www.nature.com/articles/s41467-019-09448-8.pdf"}, {"href": "https://doi.org/10.1038/s41467-019-09448-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-019-09448-8", "name": "item", "description": "10.1038/s41467-019-09448-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-019-09448-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-03-29T00:00:00Z"}}, {"id": "10.1038/s41586-022-04737-7", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:41Z", "type": "Journal Article", "created": "2022-05-18", "title": "Tropical tree mortality has increased with rising atmospheric water stress", "description": "Evidence exists that tree mortality is accelerating in some regions of the tropics1,2, with profound consequences for the future of the tropical carbon sink and the global anthropogenic carbon budget left to limit peak global warming below 2\u2009\u00b0C. However, the mechanisms that may be driving such mortality changes and whether particular species are especially vulnerable remain unclear3-8. Here we analyse a 49-year record of tree dynamics from 24 old-growth forest plots encompassing a broad climatic gradient across the Australian moist tropics and find that annual tree mortality risk has, on average, doubled across all plots and species over the last 35\u00a0years, indicating a potential halving in life expectancy and carbon residence time. Associated losses in biomass were not offset by gains from growth and recruitment. Plots in less moist local climates presented higher average mortality risk, but local mean climate did not predict the pace of temporal increase in mortality risk. Species varied in the trajectories of their mortality risk, with the highest average risk found nearer to the upper end of the atmospheric vapour pressure deficit niches of species. A long-term increase in vapour pressure deficit was evident across the region, suggesting that thresholds involving atmospheric water stress, driven by global warming, may be a primary cause of increasing tree mortality in moist tropical forests.", "keywords": ["Risk", "0301 basic medicine", "Carbon Sequestration", "Time Factors", "[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics", "Population dynamics", "Acclimatization", "[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics", " Phylogenetics and taxonomy", "Global Warming", "History", " 21st Century", "333", "[SDV.BV.BOT] Life Sciences [q-bio]/Vegetal Biology/Botanics", "Trees", "03 medical and health sciences", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "Stress", " Physiological", "[SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics", " Phylogenetics and taxonomy", "[SDV.EE.ECO] Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "Community ecology", "Biomass", "580", "Population Density", "Tropical Climate", "0303 health sciences", "Dehydration", "Atmosphere", "Climate-change ecology", "Australia", "Water", "Humidity", "Phylogenetics and taxonomy", "[SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics", "History", " 20th Century", "15. Life on land", "Tropical ecology", "Carbon", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "13. Climate action", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "Forest ecology", "environment/Ecosystems"]}, "links": [{"href": "https://eprints.whiterose.ac.uk/187195/1/Bauman_et_al_ms_Nature_final_AAM.pdf"}, {"href": "https://www.nature.com/articles/s41586-022-04737-7.pdf"}, {"href": "https://doi.org/10.1038/s41586-022-04737-7"}, {"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/s41586-022-04737-7", "name": "item", "description": "10.1038/s41586-022-04737-7", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41586-022-04737-7"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-05-18T00:00:00Z"}}, {"id": "10.1038/s41586-023-05791-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:41Z", "type": "Journal Article", "created": "2023-03-08", "title": "The giant diploid faba genome unlocks variation in a global protein crop", "description": "AbstractIncreasing 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.Bacillus sp. MEP218, a soil bacterium with high potential as a source of bioactive molecules, produces mostly C16\uffe2\uff80\uff93C17 fengycin and other cyclic lipopeptides (CLP) when growing under previously optimized culture conditions. This work addressed the elucidation of the genome sequence of MEP218 and its taxonomic classification. The genome comprises 3,944,892\uffc2\uffa0bp, with a total of 3474 coding sequences and a G\uffe2\uff80\uff89+\uffe2\uff80\uff89C content of 46.59%. Our phylogenetic analysis to determine the taxonomic position demonstrated that the assignment of the MEP218 strain to Bacillus velezensis species provides insights into its evolutionary context and potential functional attributes. The in silico genome analysis revealed eleven gene clusters involved in the synthesis of secondary metabolites, including non-ribosomal CLP (fengycins and surfactin), polyketides, terpenes, and bacteriocins. Furthermore, genes encoding phytase, involved in the release of phytic phosphate for plant and animal nutrition, or other enzymes such as cellulase, xylanase, and alpha 1\uffe2\uff80\uff934 glucanase were detected. In vitro antagonistic assays against Salmonella typhimurium, Acinetobacter baumanii, Escherichia coli, among others, demonstrated a broad spectrum of C16\uffe2\uff80\uff93C17 fengycin produced by MEP218. MEP218 genome sequence analysis expanded our understanding of the diversity and genetic relationships within the Bacillus genus and updated the Bacillus databases with its unique trait to produce antibacterial fengycins and its potential as a resource of biotechnologically useful enzymes.Changes in litterfall dynamics and soil properties due to anthropogenic or natural perturbations have important implications to soil carbon (C) and nutrient cycling via microbial pathway. Here we determine soil microbial responses to contrasting types of litter inputs (leaf vs. fine woody litter) and nitrogen (N) deposition by conducting a multi-year litter manipulation and N addition experiment in a mixed-wood forest. We found significantly higher soil organic C, total N, microbial biomass C (MBC) and N (MBN), microbial activity (MR) and activities of four soil extracellular enzymes, including \uffce\uffb2-glucosidase (BG), N-acetyl-\uffce\uffb2-glucosaminidase (NAG), phenol oxidase (PO) and peroxidase (PER), as well as greater total bacteria biomass and relative abundance of gram-negative bacteria (G-) community, in top soils of plots with presence of leaf litter than of those without litter or with presence of only fine woody litter. No apparent additive or interactive effects of N addition were observed in this study. The occurrence of more labile leaf litter stimulated G-, which may facilitate microbial community growth and soil C stabilization as inferred by findings in literature. A continued treatment with contrasting types of litter inputs is likely to result in divergence in soil microbial community structure and function.
", "keywords": ["Biomass (ecology)", "China", "Biogeochemical Cycling of Nutrients in Aquatic Ecosystems", "Microbial population biology", "Nitrogen", "Soil Science", "Organic chemistry", "Forests", "Nitrogen cycle", "Article", "Plant litter", "Nutrient cycle", "Environmental science", "Microbial Ecology", "Agricultural and Biological Sciences", "Soil", "Soil biology", "Litter", "Soil water", "Genetics", "Environmental Chemistry", "Biomass", "Forest floor", "Biology", "Soil Microbiology", "Ecosystem", "2. Zero hunger", "Ecology", "Bacteria", "Marine Microbial Diversity and Biogeography", "Life Sciences", "04 agricultural and veterinary sciences", "15. Life on land", "Wood", "Soil carbon", "Carbon", "Agronomy", "6. Clean water", "3. Good health", "Chemistry", "FOS: Biological sciences", "Environmental Science", "Physical Sciences", "0401 agriculture", " forestry", " and fisheries", "Soil Carbon Dynamics and Nutrient Cycling in Ecosystems", "Nutrient"]}, "links": [{"href": "https://doi.org/10.1038/srep19536"}, {"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/srep19536", "name": "item", "description": "10.1038/srep19536", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/srep19536"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-01-14T00:00:00Z"}}, {"id": "10.1038/srep34786", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:45Z", "type": "Journal Article", "created": "2016-10-10", "title": "Contrasting Effects Of Nitrogen And Phosphorus Addition On Soil Respiration In An Alpine Grassland On The Qinghai-Tibetan Plateau", "description": "AbstractHigh soil organic carbon content, extensive root biomass, and low nutrient availability make alpine grasslands an important ecosystem for assessing the influence of nutrient enrichment on soil respiration (SR). We conducted a four-year (2009\uffe2\uff80\uff932012) field experiment in an alpine grassland on the Qinghai-Tibetan Plateau to examine the individual and combined effects of nitrogen (N, 100\uffe2\uff80\uff89kg ha\uffe2\uff88\uff921year\uffe2\uff88\uff921) and phosphorus (P, 50\uffe2\uff80\uff89kg ha\uffe2\uff88\uff921year\uffe2\uff88\uff921) addition on SR. We found that both N and P addition did not affect the overall growing-season SR but effects varied by year: with N addition SR increased in the first year but decreased during the last two years. However, while P addition did not affect SR during the first two years, SR increased during the last two years. No interactive effects of N and P addition were observed, and both N addition and P addition reduced heterotrophic respiration during the last year of the experiment. N and P addition affected SR via different processes: N mainly affected heterotrophic respiration, whereas P largely influenced autotrophic respiration. Our results highlight the divergent effects of N and P addition on SR and address the important potential of P enrichment for regulating SR and the carbon balance in alpine grasslands.
", "keywords": ["Biomass (ecology)", "0106 biological sciences", "Mechanics and Transport in Unsaturated Soils", "Nitrogen", "Soil Science", "Organic chemistry", "Plant Science", "Thermal Effects on Soil", "01 natural sciences", "Article", "Environmental science", "Agricultural and Biological Sciences", "Engineering", "Soil water", "Genetics", "Biology", "Ecosystem", "Civil and Structural Engineering", "2. Zero hunger", "Soil Fertility", "Ecology", "Bacteria", "Respiration", "Botany", "Life Sciences", "Plant Nutrient Uptake and Signaling Pathways", "Phosphorus", "Soil respiration", "04 agricultural and veterinary sciences", "15. Life on land", "Grassland", "Soil carbon", "Agronomy", "Chemistry", "13. Climate action", "FOS: Biological sciences", "Physical Sciences", "Heterotroph", "Growing season", "0401 agriculture", " forestry", " and fisheries", "Soil Carbon Dynamics and Nutrient Cycling in Ecosystems", "Animal science", "Nutrient"]}, "links": [{"href": "https://doi.org/10.1038/srep34786"}, {"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/srep34786", "name": "item", "description": "10.1038/srep34786", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/srep34786"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-10-10T00:00:00Z"}}, {"id": "10.1051/e3sconf/20199212014", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:17:52Z", "type": "Journal Article", "created": "2019-06-25", "title": "Multi-scale effects on the hydraulic behaviour of a root-permeated and compacted soil", "description": "While roots have been generally proved to be beneficial to soil mechanical behaviour, different and counterposed results have been found when investigating their effects on soil hydraulic response. Roots affect the hydro-mechanical and chemical properties of soils at different scales. In this regard, the paper focuses on studying the macroscopic hydraulic properties of root-permeated and compacted soils considering microstructural features coming from mercury intrusion porosimetry and X-ray micro-tomography. The results are interpreted bearing in mind the influence of the different soil hydraulic states on roots structure and physiology. The analysis of the results shows that roots growing in a compacted soil at low stresses are opening fissures while decreasing micropore volume inside aggregates due to chemical effects. This response has important effects on the hydraulic behaviour of the soil.
", "keywords": ["0106 biological sciences", "[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics", "550", "0211 other engineering and technologies", "Soil hydraulic", "02 engineering and technology", "01 natural sciences", "[SDV.BV.BOT] Life Sciences [q-bio]/Vegetal Biology/Botanics", "[SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics", " Phylogenetics and taxonomy", "[SDV.EE.ECO] Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "GE1-350", "Soil compaction", "\u00c0rees tem\u00e0tiques de la UPC::Enginyeria civil::Geot\u00e8cnia::Mec\u00e0nica de s\u00f2ls", "621", "Phylogenetics and taxonomy", "[SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics", "Roots", "6. Clean water", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "Environmental sciences", "S\u00f2ls -- Compactaci\u00f3", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "environment/Ecosystems", ":Enginyeria civil::Geot\u00e8cnia::Mec\u00e0nica de s\u00f2ls [\u00c0rees tem\u00e0tiques de la UPC]", "Macroscopic hydraulic properties"]}, "links": [{"href": "https://www.e3s-conferences.org/10.1051/e3sconf/20199212014/pdf"}, {"href": "https://doi.org/10.1051/e3sconf/20199212014"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/E3S%20Web%20of%20Conferences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1051/e3sconf/20199212014", "name": "item", "description": "10.1051/e3sconf/20199212014", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1051/e3sconf/20199212014"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-01-01T00:00:00Z"}}, {"id": "10.1093/plcell/koac263", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:18:19Z", "type": "Journal Article", "created": "2022-08-26", "title": "Burning questions for a warming and changing world: 15 unknowns in plant abiotic stress", "description": "AbstractWe present unresolved questions in plant abiotic stress biology as posed by 15 research groups with expertise spanning eco-physiology to cell and molecular biology. Common themes of these questions include the need to better understand how plants detect water availability, temperature, salinity, and rising carbon dioxide (CO2) levels; how environmental signals interface with endogenous signaling and development (e.g. circadian clock and flowering time); and how this integrated signaling controls downstream responses (e.g. stomatal regulation, proline metabolism, and growth versus defense balance). The plasma membrane comes up frequently as a site of key signaling and transport events (e.g. mechanosensing and lipid-derived signaling, aquaporins). Adaptation to water extremes and rising CO2 affects hydraulic architecture and transpiration, as well as root and shoot growth and morphology, in ways not fully understood. Environmental adaptation involves tradeoffs that limit ecological distribution and crop resilience in the face of changing and increasingly unpredictable environments. Exploration of plant diversity within and among species can help us know which of these tradeoffs represent fundamental limits and which ones can be circumvented by bringing new trait combinations together. Better defining what constitutes beneficial stress resistance in different contexts and making connections between genes and phenotypes, and between laboratory and field observations, are overarching challenges.Rhizobial infection of legume roots during development of nitrogen fixing root nodules occurs either intracellularly though plant derived infection threads traversing the epidermal and cortical cell layers to deliver the bacteria or intercellularly via bacterial entry between epidermal plant cells. Although, around 25% of all legume genera are postulated to be intercellularly infected, the pathways and mechanisms supporting this process has remained virtually unexplored due to lack of genetically amenable legumes that have this infection mode. In this study, we report that the model legume Lotus japonicus is infected intercellularly by Rhizobium sp. IRBG74 and demonstrate that the resources available in Lotus enable insight into the genetic requirements and the fine-tuning of the pathway governing intercellular infection. Inoculation of Lotus mutants shows that Ern1 and RinRK1 are dispensable for intercellular infection in contrast to intracellular infection. Other symbiotic genes, including Nfr5, SymRK, CCaMK, Epr3, Cyclops, Nin, Nsp1, Nsp2, Cbs and Vpy1 are equally important for both entry modes. Comparative RNAseq analysis of roots inoculated with IRBG74 revealed a distinctive transcriptome response compared to intracellular colonization. In particular, a number of cytokinin-related genes were differentially regulated. Corroborating this observation cyp735A and ipt4 cytokinin biosynthesis mutants were significantly affected in their nodulation with IRBG74 while lhk1 cytokinin receptor mutants did not form any nodules. These results indicate that a differential requirement for cytokinin signalling conditions intercellular rhizobial entry and highlight the distinct modalities of the inter- and intra-cellular infection mechanisms.Plant roots integrate environmental signals and developmental programs using exquisite spatiotemporal control. This is apparent in the deposition of suberin, an apoplastic diffusion barrier, which regulates the entry and exit of water, solutes and gases, and is environmentally plastic. Suberin is considered a hallmark of endodermal differentiation, but we find that it is absent in the tomato endodermis during normal development. Instead, suberin is present in the exodermis, a cell type that is absent in the model organismArabidopsis thaliana. Here, we uncover genes driving exodermal suberization and describe its effects on drought responses in tomato, unravelling the similarities and differences with the paradigmatic Arabidopsis endodermis. Cellular resolution imaging, gene expression, and mutant analyses reveal loss of this program from the endodermis, and its co-option in the exodermis. Functional genetic analyses of the tomato MYB92 transcription factor and ASFT enzyme demonstrate the importance of exodermal suberin for a plant water-deficit response. Controlling the degree of exodermal suberization could be a new strategy for breeding climate-resilient plants.Ongoing global warming is expected to augment soil respiration by increasing the microbial activity, driving self-reinforcing feedback to climate change. However, the compensatory thermal adaptation of soil microorganisms and substrate depletion may weaken the effects of rising temperature on soil respiration. To test this hypothesis, we collected soils along a large-scale forest transect in eastern China spanning a natural temperature gradient, and we incubated the soils at different temperatures with or without substrate addition. We combined the exponential thermal response function and a data-driven model to study the interaction effect of thermal adaptation and substrate availability on microbial respiration and compared our results to those from two additional continental and global independent datasets. Modeled results suggested that the effect of thermal adaptation on microbial respiration was greater in areas with higher mean annual temperatures, which is consistent with the compensatory response to warming. In addition, the effect of thermal adaptation on microbial respiration was greater under substrate addition than under substrate depletion, which was also true for the independent datasets reanalyzed using our approach. Our results indicate that thermal adaptation in warmer regions could exert a more pronounced negative impact on microbial respiration when the substrate availability is abundant. These findings improve the body of knowledge on how substrate availability influences the soil microbial community\uffe2\uff80\uff93temperature interactions, which could improve estimates of projected soil carbon losses to the atmosphere through respiration.Climate oscillations in the Quaternary forced species to major latitudinal or altitudinal range shifts. It has been suggested that adaptation concomitant with range shifts plays key roles in species responses during climate oscillations, but the role of selection for local adaptation to climatic changes remains largely unexplored. Here, we investigated population structure, demographic history and signatures of climate-driven selection based on genome-wide polymorphism data of 141 Japanese Arabidopsis halleri individuals, with European ones as outgroups. Coalescent-based analyses suggested a genetic differentiation between Japanese subpopulations since the Last Glacial Period (LGP), which would have contributed to shaping the current pattern of population structure. Population demographic analysis revealed the population size fluctuations in the LGP, which were particularly prominent since the subpopulations started to diverge (\uffe2\uff88\uffbc50, 000 years ago). The ecological niche modeling predicted the geographic or distribution range shifts from southern coastal regions to northern coastal and mountainous areas, possibly in association with the population size fluctuations. Through genome-wide association analyses of bioclimatic variables and selection scans, we investigated whether climate-associated loci are enriched in the extreme tails of selection scans, and demonstrated the prevailing signatures of selection, particularly toward a warmer climate in southern subpopulations and a drier environment in northern subpopulations, which may have taken place during or after the LGP. Our study highlights the importance of integrating climate associations, selection scans and population demographic analyses for identifying genomic signatures of population-specific adaptation, which would also help us predict the evolutionary responses to future climate changes.Rhizobial infection of legume roots during development of nitrogen fixing root nodules occurs either intracellularly though plant derived infection threads traversing the epidermal and cortical cell layers to deliver the bacteria or intercellularly via bacterial entry between epidermal plant cells. Although, around 25% of all legume genera are postulated to be intercellularly infected, the pathways and mechanisms supporting this process has remained virtually unexplored due to lack of genetically amenable legumes that have this infection mode. In this study, we report that the model legume Lotus japonicus is infected intercellularly by Rhizobium sp. IRBG74 and demonstrate that the resources available in Lotus enable insight into the genetic requirements and the fine-tuning of the pathway governing intercellular infection. Inoculation of Lotus mutants shows that Ern1 and RinRK1 are dispensable for intercellular infection in contrast to intracellular infection. Other symbiotic genes, including Nfr5, SymRK, CCaMK, Epr3, Cyclops, Nin, Nsp1, Nsp2, Cbs and Vpy1 are equally important for both entry modes. Comparative RNAseq analysis of roots inoculated with IRBG74 revealed a distinctive transcriptome response compared to intracellular colonization. In particular, a number of cytokinin-related genes were differentially regulated. Corroborating this observation cyp735A and ipt4 cytokinin biosynthesis mutants were significantly affected in their nodulation with IRBG74 while lhk1 cytokinin receptor mutants did not form any nodules. These results indicate that a differential requirement for cytokinin signalling conditions intercellular rhizobial entry and highlight the distinct modalities of the inter- and intra-cellular infection mechanisms.
", "keywords": ["name=Physiology", "580", "0301 basic medicine", "/dk/atira/pure/subjectarea/asjc/1300/1314", "0303 health sciences", "/dk/atira/pure/subjectarea/asjc/1300/1311", "571", "Regular Issue", "name=Genetics", "/dk/atira/pure/subjectarea/asjc/1100/1110", "Plant Roots", "03 medical and health sciences", "Gene Expression Regulation", " Plant", "Calcium-Calmodulin-Dependent Protein Kinases", "Lotus", "name=Plant Science", "Root Nodules", " Plant", "Plant Proteins", "Rhizobium", "Signal Transduction"]}, "links": [{"href": "http://academic.oup.com/plphys/article-pdf/185/3/1131/37166752/kiaa049.pdf"}, {"href": "https://doi.org/10.1093/plphys/kiaa049"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Physiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/plphys/kiaa049", "name": "item", "description": "10.1093/plphys/kiaa049", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/plphys/kiaa049"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-31T00:00:00Z"}}, {"id": "10.1098/rstb.2020.0169", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:18:23Z", "type": "Journal Article", "created": "2021-08-08", "title": "The role of soils in delivering Nature's Contributions to People", "description": "This theme issue provides an assessment of the contribution of soils to Nature's Contributions to People (NCP). The papers in this issue show that soils can contribute positively to the delivery of all NCP. These contributions can be maximized through careful soil management to provide healthy soils, but poorly managed, degraded or polluted soils may contribute negatively to the delivery of NCP. Soils are also shown to contribute positively to the UN Sustainable Development Goals. Papers in the theme issue emphasize the need for careful soil management. Priorities for soil management must include: (i) for healthy soils in natural ecosystems, protect them from conversion and degradation, (ii) for managed soils, manage in a way to protect and enhance soil biodiversity, health, productivity and sustainability and to prevent degradation, and (iii) for degraded soils, restore to full soil health. Our knowledge of what constitutes sustainable soil management is mature enough to implement best management practices, in order to maintain and improve soil health. The papers in this issue show the vast potential of soils to contribute to NCP. This is not only desirable, but essential to sustain a healthy planet and if we are to deliver sustainable development in the decades to come.
This article is part of the theme issue \uffe2\uff80\uff98The role of soils in delivering Nature\uffe2\uff80\uff99s Contributions to People\uffe2\uff80\uff99.Ammonia\uffe2\uff80\uff90oxidising archaea (AOA) are important microorganisms contributing towards the nitrogen flux in the environment. Unlike archaea from other major phyla, genetic tools are yet to be developed for the AOA, and identification of antibiotic resistance markers for selecting mutants is required for a genetic system. The aim of this study was to test the effects of selected antibiotics (hygromycin B, neomycin, apramycin, puromycin, novobiocin) on pure cultures of three well studied AOA strains, \uffe2\uff80\uff98Candidatus Nitrosocosmicus franklandianus C13\uffe2\uff80\uff99, Nitrososphaera viennensis EN76 and Nitrosopumilus maritimus SCM1. Puromycin, hygromycin B and neomycin inhibited some but not all tested archaeal strains. All strains were resistant to apramycin and inhibited by novobiocin to various degrees. As N. viennensis EN76 was relatively more resistant to the tested antibiotics, a wider range of concentrations and compounds (chloramphenicol, trimethoprim, statins) was tested against this strain. N. viennensis EN76 was inhibited by trimethoprim, but not by chloramphenicol, and growth recovered within days in the presence of simvastatin, suggesting either degradation of, or spontaneous resistance against, this compound. This study highlights the physiological differences between different genera of AOA and has identified new candidate antibiotics for selective enrichment and the development of selectable markers for genetic systems in AOA.Site occupancy\uffe2\uff80\uff90detection models (SODMs) are statistical models widely used for biodiversity surveys where imperfect detection of species occurs. For instance, SODMs are increasingly used to analyse environmental DNA (eDNA) data, taking into account the occurrence of both false\uffe2\uff80\uff90positive and false\uffe2\uff80\uff90negative errors. However, species occurrence data are often characterized by spatial and temporal autocorrelation, which might challenge the use of standard SODMs. Here we reviewed the literature of eDNA biodiversity surveys and found that most of studies do not take into account spatial or temporal autocorrelation. We then demonstrated how the analysis of data with spatial or temporal autocorrelation can be improved by using a conditionally autoregressive SODM, and show its application to environmental DNA data. We tested the autoregressive model on both simulated and real data sets, including chronosequences with different degrees of autocorrelation, and a spatial data set on a virtual landscape. Analyses of simulated data showed that autoregressive SODMs perform better than traditional SODMs in the estimation of key parameters such as true\uffe2\uff80\uff90/false\uffe2\uff80\uff90positive rates and show a better discrimination capacity (e.g., higher true skill statistics). The usefulness of autoregressive SODMs was particularly high in data sets with strong autocorrelation. When applied to real eDNA data sets (eDNA from lake sediment cores and freshwater), autoregressive SODM provided more precise estimation of true\uffe2\uff80\uff90/false\uffe2\uff80\uff90positive rates, resulting in more reasonable inference of occupancy states. Our results suggest that analyses of occurrence data, such as many applications of eDNA, can be largely improved by applying conditionally autoregressive specifications to SODMs.
", "keywords": ["0106 biological sciences", "Genetics", " Population", "Spatio-Temporal Analysis", "330", "DNA", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "Biostatistics", "15. Life on land", "Biota", "01 natural sciences", "conditionally autoregressive model; sedimentary DNA; spatial autocorrelation; species occupancy-detection model; temporal autocorrelation; true skill statistics; Biostatistics; DNA; Spatio-Temporal Analysis; Biota; Genetics", " Population; Biotechnology; Ecology", " Evolution", " Behavior and Systematics; Genetics"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/635968/2/Chen_et_al-2019-Molecular_Ecology_Resources.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12949"}, {"href": "https://doi.org/10.1111/1755-0998.12949"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Molecular%20Ecology%20Resources", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1755-0998.12949", "name": "item", "description": "10.1111/1755-0998.12949", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1755-0998.12949"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-11-01T00:00:00Z"}}, {"id": "10.1111/brv.12949", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:18:33Z", "type": "Journal Article", "created": "2023-03-14", "title": "Trade\u2010offs in carbon\u2010degrading enzyme activities limit long\u2010term soil carbon sequestration with biochar addition", "description": "ABSTRACTBiochar amendment is one of the most promising agricultural approaches to tackle climate change by enhancing soil carbon (C) sequestration. Microbial\uffe2\uff80\uff90mediated decomposition processes are fundamental for the fate and persistence of sequestered C in soil, but the underlying mechanisms are uncertain. Here, we synthesise 923 observations regarding the effects of biochar addition (over periods ranging from several weeks to several years) on soil C\uffe2\uff80\uff90degrading enzyme activities from 130 articles across five continents worldwide. Our results showed that biochar addition increased soil ligninase activity targeting complex phenolic macromolecules by 7.1%, but suppressed cellulase activity degrading simpler polysaccharides by 8.3%. These shifts in enzyme activities explained the most variation of changes in soil C sequestration across a wide range of climatic, edaphic and experimental conditions, with biochar\uffe2\uff80\uff90induced shift in ligninase:cellulase ratio correlating negatively with soil C sequestration. Specifically, short\uffe2\uff80\uff90term (<1\uffc2\uffa0year) biochar addition significantly reduced cellulase activity by 4.6% and enhanced soil organic C sequestration by 87.5%, whereas no significant responses were observed for ligninase activity and ligninase:cellulase ratio. However, long\uffe2\uff80\uff90term (\uffe2\uff89\uffa51\uffc2\uffa0year) biochar addition significantly enhanced ligninase activity by 5.2% and ligninase:cellulase ratio by 36.1%, leading to a smaller increase in soil organic C sequestration (25.1%). These results suggest that shifts in enzyme activities increased ligninase:cellulase ratio with time after biochar addition, limiting long\uffe2\uff80\uff90term soil C sequestration with biochar addition. Our work provides novel evidence to explain the diminished soil C sequestration with long\uffe2\uff80\uff90term biochar addition and suggests that earlier studies may have overestimated soil C sequestration with biochar addition by failing to consider the physiological acclimation of soil microorganisms over time.Retreating glaciers, icons of climate change, release new potential habitats for both aquatic and terrestrial organisms. High\uffe2\uff80\uff90elevation species are threatened by temperature increases and the upward migration of lowlands species. Improving our understanding of successional processes after glacier retreat becomes urgent, especially in the tropics, where glacier shrinkage is particularly fast. We examined the successional patterns of aquatic invertebrates, ground beetles, terrestrial plants, soil eukaryotes (algae, invertebrates, plants) in an equatorial glacier foreland (Carihuairazo, Ecuador). Based on both taxonomical identification and eDNA metabarcoding, we analysed the effects of both environmental conditions and age of deglacierization on community composition. Except for algae, diversity increased with time since deglacierization, especially among passive dispersers, suggesting that dispersal was a key driver structuring the glacier foreland succession. Spatial \uffce\uffb2\uffe2\uff80\uff90diversity was mainly attributed to nestedness for aquatic invertebrates, terrestrial plants and soil algae, likely linked to low environmental variability within the studied glacier foreland; and to turnover for soil invertebrates, suggesting competition exclusion at the oldest successional stage. Pioneer communities were dominated by species exhibiting flexible feeding strategies and high dispersal ability (mainly transported by wind), probably colonising from lower altitudes, or from the glacier in the case of algae. Overall, glacier foreland colonisation in the tropics exhibit common characteristics to higher latitudes. High\uffe2\uff80\uff90elevation species are nevertheless threatened, as the imminent extinction of many tropical glaciers will affect species associated to glacier\uffe2\uff80\uff90influenced habitats but also prevent cold\uffe2\uff80\uff90adapted and hygrophilous species from using these habitats as refuges in a warming world.
", "keywords": ["Colonization", "[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics", "550", "Early succession", "glacier retreat", "Sociology", "[SDV.EE.ECO] Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "Environmental DNA Sequencing", "Glacier", "Ecology", "Geography", "early succession", "Life Sciences", "Phylogenetics and taxonomy", "Biodiversity", "[SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics", "Threatened species", "FOS: Sociology", "Multiple-taxa", "multiple-taxa", "Habitat", "[SDE]Environmental Sciences", "Physical Sciences", "environment/Ecosystems", "570", "Physical geography", "Population", "Global Diversity of Microbial Eukaryotes and Their Evolution", "[SDV.BV.BOT] Life Sciences [q-bio]/Vegetal Biology/Botanics", "Ecological succession", "Biochemistry", " Genetics and Molecular Biology", "Biological dispersal", "[SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics", " Phylogenetics and taxonomy", "equatorial glacier foreland", "Equatorial glacier foreland", "Glacier retreat", "Molecular Biology", "Biology", "Demography", "Marine Microbial Diversity and Biogeography", "Colonisation", "South America", "15. Life on land", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "13. Climate action", "FOS: Biological sciences", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", "Environmental Science", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "early succession; equatorial glacier foreland; glacier retreat; multiple-taxa", "Environmental DNA in Biodiversity Monitoring"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/851699/2/rosero%202021.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/ecog.05478"}, {"href": "https://doi.org/10.1111/ecog.05478"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecography", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/ecog.05478", "name": "item", "description": "10.1111/ecog.05478", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/ecog.05478"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-05-06T00:00:00Z"}}, {"id": "10.1111/gcb.15496", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:18:39Z", "type": "Journal Article", "created": "2020-12-20", "title": "Topsoil organic matter build\u2010up in glacier forelands around the world", "description": "AbstractSince the last glacial maximum, soil formation related to ice\uffe2\uff80\uff90cover shrinkage has been one major sink of carbon accumulating as soil organic matter (SOM), a phenomenon accelerated by the ongoing global warming. In recently deglacierized forelands, processes of SOM accumulation, including those that control carbon and nitrogen sequestration rates and biogeochemical stability of newly sequestered carbon, remain poorly understood. Here, we investigate the build\uffe2\uff80\uff90up of SOM during the initial stages (up to 410\uffc2\uffa0years) of topsoil development in 10 glacier forelands distributed on four continents. We test whether the net accumulation of SOM on glacier forelands (i) depends on the time since deglacierization and local climatic conditions (temperature and precipitation); (ii) is accompanied by a decrease in its stability and (iii) is mostly due to an increasing contribution of organic matter from plant origin. We measured total SOM concentration (carbon, nitrogen), its relative hydrogen/oxygen enrichment, stable isotopic (13C, 15N) and carbon functional groups (C\uffe2\uff80\uff90H, C=O, C=C) compositions, and its distribution in carbon pools of different thermal stability. We show that SOM content increases with time and is faster on forelands experiencing warmer climates. The build\uffe2\uff80\uff90up of SOM pools shows consistent trends across the studied soil chronosequences. During the first decades of soil development, the low amount of SOM is dominated by a thermally stable carbon pool with a small and highly thermolabile pool. The stability of SOM decreases with soil age at all sites, indicating that SOM storage is dominated by the accumulation of labile SOM during the first centuries of soil development, and suggesting plant carbon inputs to soil (SOM depleted in nitrogen, enriched in hydrogen and in aromatic carbon). Our findings highlight the potential vulnerability of SOM stocks from proglacial areas to decomposition and suggest that their durability largely depends on the relative contribution of carbon inputs from plants.
", "keywords": ["[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics", "550", "Nitrogen", "Chronosequence", "551", "01 natural sciences", "[SDV.BV.BOT] Life Sciences [q-bio]/Vegetal Biology/Botanics", "Soil", "soil organic matter", "carbon stability; chronosequence; climate sensitivity; soil organic matter; topsoil development; Carbon; Nitrogen; Temperature; Ice Cover; Soil", "[SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics", " Phylogenetics and taxonomy", "[SDV.EE.ECO] Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "Ice Cover", "topsoil development", "Carbon stability", "0105 earth and related environmental sciences", "2. Zero hunger", "Soil organic matter", "Temperature", "Phylogenetics and taxonomy", "04 agricultural and veterinary sciences", "[SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics", "15. Life on land", "Climate sensitivity", "Primary Research Articles", "Carbon", "chronosequence", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "13. Climate action", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", "[SDE]Environmental Sciences", "Topsoil development", "climate sensitivity", "carbon stability; chronosequence; climate sensitivity; soil organic matter; topsoil development;", "0401 agriculture", " forestry", " and fisheries", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "environment/Ecosystems", "carbon stability"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/851691/2/khedim%202021%20submitted.pdf"}, {"href": "https://air.unimi.it/bitstream/2434/851691/3/khedim%202021%20Global%20Change%20Biol.pdf"}, {"href": "https://boa.unimib.it/bitstream/10281/300214/2/10281-300214_VoR.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.15496"}, {"href": "https://doi.org/10.1111/gcb.15496"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Global%20Change%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/gcb.15496", "name": "item", "description": "10.1111/gcb.15496", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/gcb.15496"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-01-16T00:00:00Z"}}, {"id": "10.1371/journal.pone.0038858", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:19:26Z", "type": "Journal Article", "created": "2012-06-11", "title": "Decline In Topsoil Microbial Quotient, Fungal Abundance And C Utilization Efficiency Of Rice Paddies Under Heavy Metal Pollution Across South China", "description": "Open AccessLos suelos agr\u00edcolas han estado cada vez m\u00e1s sujetos a la contaminaci\u00f3n por metales pesados en todo el mundo. Sin embargo, los impactos en la estructura y actividad de la comunidad microbiana del suelo de los suelos de campo a\u00fan no se han caracterizado bien. En 2009 se recolectaron muestras de tierra vegetal de campos de arroz contaminados con metales pesados (PS) y sus campos de fondo (BGS) en cuatro sitios del sur de China. Los cambios con la contaminaci\u00f3n met\u00e1lica en relaci\u00f3n con el BGS en el tama\u00f1o y la estructura de la comunidad de los microorganismos del suelo se examinaron con m\u00faltiples ensayos microbiol\u00f3gicos de medici\u00f3n de carbono de biomasa (MBC) y nitr\u00f3geno (MBN), recuento en placa de colonias cultivables y an\u00e1lisis de \u00e1cidos grasos fosfol\u00edpidos (PLFA) junto con el perfil de electroforesis en gel de gradiente desnaturalizante (DGGE) del gen de ARNr 16S y ARNr 18S y ensayo de PCR en tiempo real. Adem\u00e1s, se llev\u00f3 a cabo una incubaci\u00f3n de laboratorio de 7 d\u00edas a una temperatura constante de 25 \u00b0C para realizar un seguimiento adicional de los cambios en la actividad metab\u00f3lica. Si bien la disminuci\u00f3n de la contaminaci\u00f3n por metales en MBC y MBN, as\u00ed como en el tama\u00f1o de la poblaci\u00f3n cultivable, el contenido total de PLFA y el n\u00famero de bandas DGGE de bacterias no se observaron de manera significativa y consistente, de hecho se observ\u00f3 una reducci\u00f3n significativa de la contaminaci\u00f3n por metales en el cociente microbiano, en el tama\u00f1o de la poblaci\u00f3n f\u00fangica cultivable y en la proporci\u00f3n de PLFA f\u00fangicos a bacterianos de manera consistente en todos los sitios en una medida que var\u00eda de 6% a 74%. Adem\u00e1s, se observ\u00f3 un aumento consistentemente significativo en el cociente metab\u00f3lico de hasta un 68% bajo contaminaci\u00f3n en todos los sitios. Estas observaciones apoyaron un cambio de la comunidad microbiana con disminuci\u00f3n en su abundancia, disminuci\u00f3n en la proporci\u00f3n de hongos y, por lo tanto, en la eficiencia de utilizaci\u00f3n de C bajo contaminaci\u00f3n en los suelos. Adem\u00e1s, las proporciones de cociente microbiano, de hongos a bacterias y qCO2 son mejores indicativas de los impactos de los metales pesados en la estructura y actividad de la comunidad microbiana. Los efectos potenciales de estos cambios en el ciclo del carbono y la producci\u00f3n de CO2 en los arrozales contaminados merecen m\u00e1s estudios de campo.", "keywords": ["Microbial population biology", "Colony Count", " Microbial", "Agricultural and Biological Sciences", "Sociology", "Soil water", "Soil Pollutants", "Soil Microbiology", "2. Zero hunger", "Principal Component Analysis", "Temperature gradient gel electrophoresis", "Ecology", "Q", "Fatty Acids", "R", "Life Sciences", "Agriculture", "04 agricultural and veterinary sciences", "Biota", "Pollution", "6. Clean water", "FOS: Sociology", "Chemistry", "Physical Sciences", "Environmental chemistry", "Medicine", "Research Article", "Environmental Monitoring", "16S ribosomal RNA", "China", "Microorganism", "Environmental Impact of Heavy Metal Contamination", "Nitrogen", "Science", "Population", "Soil Science", "Real-Time Polymerase Chain Reaction", "Environmental science", "Microbial Ecology", "12. Responsible consumption", "Metals", " Heavy", "Genetics", "Biology", "Demography", "Bacteria", "Denaturing Gradient Gel Electrophoresis", "Marine Microbial Diversity and Biogeography", "Oryza", "15. Life on land", "Topsoil", "Carbon", "Agronomy", "RNA", " Ribosomal", "13. Climate action", "FOS: Biological sciences", "Environmental Science", "0401 agriculture", " forestry", " and fisheries", "Soil Carbon Dynamics and Nutrient Cycling in Ecosystems"]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0038858"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLoS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0038858", "name": "item", "description": "10.1371/journal.pone.0038858", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0038858"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-06-11T00:00:00Z"}}, {"id": "10.1371/journal.pone.0200979", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:19:29Z", "type": "Journal Article", "created": "2019-04-11", "title": "Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR", "description": "AbstractSoil DNA extraction encounters numerous challenges that can affect both yield and purity of the recovered DNA. Clay particles lead to reduced DNA extraction efficiency, and PCR inhibitors from the soil matrix can negatively affect downstream analyses when applying DNA sequencing. Further, these effects impede molecular analysis of bacterial community compositions in lower biomass samples, as often observed in deeper soil layers. Many studies avoid these complications by using indirect DNA extraction with prior separation of the cells from the matrix, but such methods introduce other biases that influence the resulting microbial community composition.
To address these issues, a direct DNA extraction method was applied in combination with the use of a commercial product, the G2 DNA/RNA Enhancer\uffc2\uffae, marketed as being capable of improving the amount of DNA recovered after the lysis step. The results showed that application of G2 increased DNA yields from the studied clayey soils from layers between 1.00 and 2.20 m below ground level.
Importantly, the use of G2 did not introduce bias, as it did not result in any significant differences in the biodiversity of the bacterial community measured in terms of alpha and beta diversity and taxonomical composition.
Finally, this study considered a set of customised lysing tubes for evaluating possible influences on the DNA yield. Tubes customization included different bead sizes and amounts, along with lysing tubes coming from two suppliers. Results showed that the lysing tubes with mixed beads allowed greater DNA recovery compared to the use of either 0.1 or 1.4 mm beads, irrespective of the tube supplier.
These outcomes may help to improve commercial products in DNA/RNA extraction kits, besides raising awareness about the optimal choice of additives, offering opportunities for acquiring a better understanding of topics such as vertical microbial characterisation and environmental DNA recovery in low biomass samples.
", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Science", "Microbial Consortia", "DIVERSITY", "SOFTWARE", "Real-Time Polymerase Chain Reaction", "BACILLUS-SUBTILIS", "BIOMASS", "03 medical and health sciences", "BIOAUGMENTATION", "DNA", " Bacterial/chemistry", "MICROBIAL COMMUNITIES", "Soil Microbiology", "2. Zero hunger", "0303 health sciences", "16S RIBOSOMAL-RNA", "Q", "R", "PROFILES", "ACIDS", "TRANSFORMATION", "6. Clean water", "Microbial Consortia/genetics", "Enhancer Elements", " Genetic", "13. Climate action", "Medicine", "Research Article"]}, "links": [{"href": "https://www.biorxiv.org/content/10.1101/365395v1.full.pdf"}, {"href": "https://doi.org/10.1371/journal.pone.0200979"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLOS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0200979", "name": "item", "description": "10.1371/journal.pone.0200979", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0200979"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-07-09T00:00:00Z"}}, {"id": "10.1371/journal.pone.0029642", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-25T16:19:25Z", "type": "Journal Article", "created": "2012-01-04", "title": "Carbon Stocks And Fluxes In Tropical Lowland Dipterocarp Rainforests In Sabah, Malaysian Borneo", "description": "Deforestation in the tropics is an important source of carbon C release to the atmosphere. To provide a sound scientific base for efforts taken to reduce emissions from deforestation and degradation (REDD+) good estimates of C stocks and fluxes are important. We present components of the C balance for selectively logged lowland tropical dipterocarp rainforest in the Malua Forest Reserve of Sabah, Malaysian Borneo. Total organic C in this area was 167.9 Mg C ha\u207b\u00b9\u00b13.8 (SD), including: Total aboveground (TAGC: 55%; 91.9 Mg C ha\u207b\u00b9\u00b12.9 SEM) and belowground carbon in trees (TBGC: 10%; 16.5 Mg C ha\u207b\u00b9\u00b10.5 SEM), deadwood (8%; 13.2 Mg C ha\u207b\u00b9\u00b13.5 SEM) and soil organic matter (SOM: 24%; 39.6 Mg C ha\u207b\u00b9\u00b10.9 SEM), understory vegetation (3%; 5.1 Mg C ha\u207b\u00b9\u00b11.7 SEM), standing litter (<1%; 0.7 Mg C ha\u207b\u00b9\u00b10.1 SEM) and fine root biomass (<1%; 0.9 Mg C ha\u207b\u00b9\u00b10.1 SEM). Fluxes included litterfall, a proxy for leaf net primary productivity (4.9 Mg C ha\u207b\u00b9 yr\u207b\u00b9\u00b10.1 SEM), and soil respiration, a measure for heterotrophic ecosystem respiration (28.6 Mg C ha\u207b\u00b9 yr\u207b\u00b9\u00b11.2 SEM). The missing estimates necessary to close the C balance are wood net primary productivity and autotrophic respiration.Twenty-two years after logging TAGC stocks were 28% lower compared to unlogged forest (128 Mg C ha\u207b\u00b9\u00b113.4 SEM); a combined weighted average mean reduction due to selective logging of -57.8 Mg C ha\u207b\u00b9 (with 95% CI -75.5 to -40.2). Based on the findings we conclude that selective logging decreased the dipterocarp stock by 55-66%. Silvicultural treatments may have the potential to accelerate the recovery of dipterocarp C stocks to pre-logging levels.", "keywords": ["0106 biological sciences", "1000 Multidisciplinary", "Tropical Climate", "Science", "Rain", "Q", "R", "1100 General Agricultural and Biological Sciences", "Biodiversity", "15. Life on land", "01 natural sciences", "Carbon", "Dipterocarpaceae", "Trees", "10127 Institute of Evolutionary Biology and Environmental Studies", "Soil", "1300 General Biochemistry", " Genetics and Molecular Biology", "Borneo", "Seedlings", "13. Climate action", "570 Life sciences; biology", "590 Animals (Zoology)", "Medicine", "Biomass", "Research Article"], "contacts": [{"organization": "Saner, Philippe, Loh, Yen Yee, Ong, Robert C., Hector, Andy,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0029642"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLoS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0029642", "name": "item", "description": "10.1371/journal.pone.0029642", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0029642"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-01-03T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Genetics&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Genetics&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Genetics&", "hreflang": "en-US"}, {"rel": "next", "type": "application/geo+json", "title": "items (next)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Genetics&offset=50", "hreflang": "en-US"}], "numberMatched": 146, "numberReturned": 50, "distributedFeatures": [], "timeStamp": "2026-05-26T00:15:26.342624Z"}