Soil hydraulic properties are required in various modelling schemes. We propose a consistent spatial soil hydraulic database at 7 soil depths up to 2\uffc2\uffa0m calculated for Europe based on SoilGrids250m and 1\uffc2\uffa0km datasets and pedotransfer functions trained on the European Hydropedological Data Inventory. Saturated water content, water content at field capacity and wilting point, saturated hydraulic conductivity and Mualem\uffe2\uff80\uff90van Genuchten parameters for the description of the moisture retention, and unsaturated hydraulic conductivity curves have been predicted. The derived 3D soil hydraulic layers (EU\uffe2\uff80\uff90SoilHydroGrids ver1.0) can be used for environmental modelling purposes at catchment or continental scale in Europe. Currently, only EU\uffe2\uff80\uff90SoilHydroGrids provides information on the most frequently required soil hydraulic properties with full European coverage up to 2\uffc2\uffa0m depth at 250\uffc2\uffa0m resolution.For a sustainable production of food, research on agricultural soil microbial communities is inevitable. Due to its immense complexity, soil is still some kind of black box. Soil study designs for identifying microbiome members of relevance have various scopes and focus on particular environmental factors. To identify common features of soil microbiomes, data from multiple studies should be compiled and processed. Taxonomic compositions and functional capabilities of microbial communities associated with soils and plants have been identified and characterized in the past few decades. From a fertile Loess\uffe2\uff80\uff93Chernozem-type soil located in Germany, metagenomically assembled genomes (MAGs) classified as members of the phylum Thaumarchaeota/Thermoproteota were obtained. These possibly represent keystone agricultural soil community members encoding functions of relevance for soil fertility and plant health. Their importance for the analyzed microbiomes is corroborated by the fact that they were predicted to contribute to the cycling of nitrogen, feature the genetic potential to fix carbon dioxide and possess genes with predicted functions in plant-growth-promotion (PGP). To expand the knowledge on soil community members belonging to the phylum Thaumarchaeota, we conducted a meta-analysis integrating primary studies on European agricultural soil microbiomes.
ResultsTaxonomic classification of the selected soil metagenomes revealed the shared agricultural soil core microbiome of European soils from 19 locations. Metadata reporting was heterogeneous between the different studies. According to the available metadata, we separated the data into 68 treatments. The phylum Thaumarchaeota is part of the core microbiome and represents a major constituent of the archaeal subcommunities in all European agricultural soils. At a higher taxonomic resolution, 2074 genera constituted the core microbiome. We observed that viral genera strongly contribute to variation in taxonomic profiles. By binning of metagenomically assembled contigs, Thaumarchaeota MAGs could be recovered from several European soil metagenomes. Notably, many of them were classified as members of the family Nitrososphaeraceae, highlighting the importance of this family for agricultural soils. The specific Loess-Chernozem Thaumarchaeota MAGs were most abundant in their original soil, but also seem to be of importance in other agricultural soil microbial communities. Metabolic reconstruction of Switzerland_1_MAG_2 revealed its genetic potential i.a. regarding carbon dioxide (CO$$_2$$ 2 ) fixation, ammonia oxidation, exopolysaccharide production and a beneficial effect on plant growth. Similar genetic features were also present in other reconstructed MAGs. Three Nitrososphaeraceae MAGs are all most likely members of a so far unknown genus.
ConclusionsOn a broad view, European agricultural soil microbiomes are similarly structured. Differences in community structure were observable, although analysis was complicated by heterogeneity in metadata recording. Our study highlights the need for standardized metadata reporting and the benefits of networking open data. Future soil sequencing studies should also consider high sequencing depths in order to enable reconstruction of genome bins. Intriguingly, the family Nitrososphaeraceae commonly seems to be of importance in agricultural microbiomes.
", "keywords": ["2. Zero hunger", "570", "Soil microbial diversity", "Metagenomically assembled genomes", "Research", "European soil", "Open metagenome data analysis", "15. Life on land", "Microbiology", "Thaumarchaeota", "QR1-502", "Environmental sciences", "Agricultural microbiome", "Soil health", "GE1-350"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1186/s40793-023-00479-9.pdf"}, {"href": "https://doi.org/10.1186/s40793-023-00479-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40793-023-00479-9", "name": "item", "description": "10.1186/s40793-023-00479-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40793-023-00479-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-03-30T00:00:00Z"}}, {"id": "10261/406452", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-06-25T16:31:18Z", "type": "Journal Article", "created": "2025-10-14", "title": "Digital Soil Health Assessment: Pedogenon Mapping and Unit\u2010Specific Thresholds for Basque Country Forest Plantations", "description": "ABSTRACTIn Europe, rural landscapes and forests have been subjected to intensive anthropogenic transformations and uses since Antiquity. Since the early 20th century, many traditionally managed forests and mountain pastures were transformed into intensive forestry plantations. Hence, it is important to assess the effects of forest plantations on soil health. The European Soil Monitoring Law (SML) proposes the establishment of soil units for monitoring soil health and soil degradation processes using time\uffe2\uff80\uff90series of several indicators: SOC:clay for soil organic carbon (SOC) loss, pH for acidification and bulk density for compaction, among others. Thresholds that may be local must be defined for these different indicators. We propose an approach in which: (1) we delineate soil units applying unsupervised classification to a set of environmental covariates, proxies of the soil\uffe2\uff80\uff90forming factors (pedogenon mapping) and (2) use semi\uffe2\uff80\uff90natural native forests (i.e., secondary forests of native species with lesser human interventions compared to past decades) as references for setting unit\uffe2\uff80\uff90specific thresholds for soil indicators (reference approach) and (3) assessing and mapping the condition of forest plantations (intensively managed forests). We apply this approach to the Basque Country using soil data from the forest monitoring network Basonet. When considering the threshold suggested by the SML for SOC:clay (<\uffe2\uff80\uff891/13), 61% of plots at 0\uffe2\uff80\uff9320\uffe2\uff80\uff89cm layer and 90% at 20\uffe2\uff80\uff9340\uffe2\uff80\uff89cm layer of plantations were in poor condition (unhealthy), while 37% of plots at 0\uffe2\uff80\uff9320\uffe2\uff80\uff89cm and 79% at 20\uffe2\uff80\uff9340\uffe2\uff80\uff89cm of semi\uffe2\uff80\uff90natural forests would be considered unhealthy. When considering semi\uffe2\uff80\uff90natural forest as references the proportion of plantation plots in poor condition for SOC:clay ranged between 14%\uffe2\uff80\uff9350% depending on the percentile used to set thresholds (5th and 25th percentiles). Forest plantations had lower soil pH compared to semi\uffe2\uff80\uff90natural forests, with 15%\uffe2\uff80\uff9360% of plantation plots with pH lower than the unit\uffe2\uff80\uff90specific thresholds (poor condition). Only 3% of topsoils and 2% of subsoils under plantations were considered unhealthy with a fixed pH threshold of 4.2. All plantation plots were in good condition (healthy) in terms of bulk density with the EU criteria, but 9.6% of semi\uffe2\uff80\uff90natural plots had greater bulk density than the suggested thresholds. Our approach demonstrates the need of considering the context of soil\uffe2\uff80\uff90forming factors when identifying thresholds for soil health indicators.Soil hydraulic properties are required in various modelling schemes. We propose a consistent spatial soil hydraulic database at 7 soil depths up to 2\uffc2\uffa0m calculated for Europe based on SoilGrids250m and 1\uffc2\uffa0km datasets and pedotransfer functions trained on the European Hydropedological Data Inventory. Saturated water content, water content at field capacity and wilting point, saturated hydraulic conductivity and Mualem\uffe2\uff80\uff90van Genuchten parameters for the description of the moisture retention, and unsaturated hydraulic conductivity curves have been predicted. The derived 3D soil hydraulic layers (EU\uffe2\uff80\uff90SoilHydroGrids ver1.0) can be used for environmental modelling purposes at catchment or continental scale in Europe. Currently, only EU\uffe2\uff80\uff90SoilHydroGrids provides information on the most frequently required soil hydraulic properties with full European coverage up to 2\uffc2\uffa0m depth at 250\uffc2\uffa0m resolution.For a sustainable production of food, research on agricultural soil microbial communities is inevitable. Due to its immense complexity, soil is still some kind of black box. Soil study designs for identifying microbiome members of relevance have various scopes and focus on particular environmental factors. To identify common features of soil microbiomes, data from multiple studies should be compiled and processed. Taxonomic compositions and functional capabilities of microbial communities associated with soils and plants have been identified and characterized in the past few decades. From a fertile Loess\uffe2\uff80\uff93Chernozem-type soil located in Germany, metagenomically assembled genomes (MAGs) classified as members of the phylum Thaumarchaeota/Thermoproteota were obtained. These possibly represent keystone agricultural soil community members encoding functions of relevance for soil fertility and plant health. Their importance for the analyzed microbiomes is corroborated by the fact that they were predicted to contribute to the cycling of nitrogen, feature the genetic potential to fix carbon dioxide and possess genes with predicted functions in plant-growth-promotion (PGP). To expand the knowledge on soil community members belonging to the phylum Thaumarchaeota, we conducted a meta-analysis integrating primary studies on European agricultural soil microbiomes.
ResultsTaxonomic classification of the selected soil metagenomes revealed the shared agricultural soil core microbiome of European soils from 19 locations. Metadata reporting was heterogeneous between the different studies. According to the available metadata, we separated the data into 68 treatments. The phylum Thaumarchaeota is part of the core microbiome and represents a major constituent of the archaeal subcommunities in all European agricultural soils. At a higher taxonomic resolution, 2074 genera constituted the core microbiome. We observed that viral genera strongly contribute to variation in taxonomic profiles. By binning of metagenomically assembled contigs, Thaumarchaeota MAGs could be recovered from several European soil metagenomes. Notably, many of them were classified as members of the family Nitrososphaeraceae, highlighting the importance of this family for agricultural soils. The specific Loess-Chernozem Thaumarchaeota MAGs were most abundant in their original soil, but also seem to be of importance in other agricultural soil microbial communities. Metabolic reconstruction of Switzerland_1_MAG_2 revealed its genetic potential i.a. regarding carbon dioxide (CO$$_2$$ 2 ) fixation, ammonia oxidation, exopolysaccharide production and a beneficial effect on plant growth. Similar genetic features were also present in other reconstructed MAGs. Three Nitrososphaeraceae MAGs are all most likely members of a so far unknown genus.
ConclusionsOn a broad view, European agricultural soil microbiomes are similarly structured. Differences in community structure were observable, although analysis was complicated by heterogeneity in metadata recording. Our study highlights the need for standardized metadata reporting and the benefits of networking open data. Future soil sequencing studies should also consider high sequencing depths in order to enable reconstruction of genome bins. Intriguingly, the family Nitrososphaeraceae commonly seems to be of importance in agricultural microbiomes.
", "keywords": ["2. Zero hunger", "570", "Soil microbial diversity", "Metagenomically assembled genomes", "Research", "European soil", "Open metagenome data analysis", "15. Life on land", "Microbiology", "Thaumarchaeota", "QR1-502", "Environmental sciences", "Agricultural microbiome", "Soil health", "GE1-350"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1186/s40793-023-00479-9.pdf"}, {"href": "https://doi.org/PMC10064710"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC10064710", "name": "item", "description": "PMC10064710", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC10064710"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-03-30T00:00:00Z"}}, {"id": "google-earth-files", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[-26.54, 37.55], [-26.54, 70.55], [39.73, 70.55], [39.73, 37.55], [-26.54, 37.55]]]}, "properties": {"themes": [{"concepts": [{"id": "geoscientificInformation"}], "scheme": "https://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_TopicCategoryCode"}, {"concepts": [{"id": "European"}], "scheme": "https://inspire.ec.europa.eu/metadata-codelist/SpatialScope"}, {"concepts": [{"id": "ESDAC"}], "scheme": "Source"}], "updated": "2008-01-01", "type": "Dataset", "created": "2008-01-01", "language": "eng", "title": "Google Earth Files", "description": "Google Earth Files (with \".kmz\" extension) that correspond to 73 attribute maps derived from the European Soil Database v2 (ESDB v2) for EU27 countries.", "formats": [{"name": "metadata"}, {"name": "image/png"}, {"name": "canonical"}], "keywords": ["ESDAC", "European Soil Database and soil properties", "European", "ESDAC"], "contacts": [{"name": null, "organization": "Joint Research 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"https://repository.soilwise-he.eu/cat/collections/metadata:main/items/google-earth-files"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-01-01T00:00:00Z"}}, {"id": "sinfo-esdb-data-adapted-mars-crop-yield-forecasting-system", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[-26.54, 37.55], [-26.54, 70.55], [39.73, 70.55], [39.73, 37.55], [-26.54, 37.55]]]}, "properties": {"themes": [{"concepts": [{"id": "geoscientificInformation"}], "scheme": "https://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_TopicCategoryCode"}, {"concepts": [{"id": "European"}], "scheme": "https://inspire.ec.europa.eu/metadata-codelist/SpatialScope"}, {"concepts": [{"id": "ESDAC"}], "scheme": "Source"}], "updated": "2007-01-01", "type": "Dataset", "created": "2007-01-01", "language": "eng", "externalIds": [{"value": "https://esdac.jrc.ec.europa.eu/node/33970"}], "title": "SINFO: ESDB Data adapted for the MARS Crop Yield Forecasting System", "description": "A database (2007) that is the result of adapting the European Soil Database for the provision of new and specific soil information for the CGMS (Crop Growth Monitoring System) for use in the MARS Crop Yield Forecast Sing System.", "formats": [{"name": "metadata"}, {"name": "image/png"}, {"name": "canonical"}], "keywords": ["ESDAC", "European Soil Database and soil properties", "European", "ESDAC"], "contacts": [{"name": null, "organization": "European Commission - DG JRC", "position": null, "roles": ["pointOfContact"], "phones": [{"value": null}], "emails": [{"value": "ec-esdac@ec.europe.eu"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": "Italy"}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": null, "name_url": "", "description": 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{"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-01-01T00:00:00Z"}}, {"id": "european-soil-database-derived-data", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[-26.54, 37.55], [-26.54, 70.55], [39.73, 70.55], [39.73, 37.55], [-26.54, 37.55]]]}, "properties": {"themes": [{"concepts": [{"id": "geoscientificInformation"}], "scheme": "https://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_TopicCategoryCode"}, {"concepts": [{"id": "European"}], "scheme": "https://inspire.ec.europa.eu/metadata-codelist/SpatialScope"}, {"concepts": [{"id": "ESDAC"}], "scheme": "Source"}], "updated": "2013-01-01", "type": "Dataset", "created": "2013-01-01", "language": "eng", "externalIds": [{"value": "https://esdac.jrc.ec.europa.eu/node/34635"}], "title": "European Soil Database Derived data", "description": "A number of layers for soil properties have been created based on data from the European Soil Database in combination with data from the Harmonized World Soil Database (HWSD) and Soil-Terrain Database (SOTER).", "formats": [{"name": "metadata"}, {"name": "image/png"}, {"name": "canonical"}], "keywords": ["ESDAC", "European Soil Database and soil properties", "European", "ESDAC"], "contacts": [{"name": null, "organization": "European Commission Joint Research Centre", "position": null, "roles": ["pointOfContact"], "phones": [{"value": null}], "emails": [{"value": "ec-esdac@ec.europe.eu"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": "Italy"}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": null, "name_url": "", "description": null, "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}]}, "links": [{"href": "https://esdac.jrc.ec.europa.eu/node/34635", "name": "European Soil Database Derived data", "protocol": "metadata", "rel": null}, {"href": "https://esdac.jrc.ec.europa.eu/public_path//datainventoryitem_img/derived_data.png", "name": "Preview", "protocol": "image/png", "rel": "preview"}, {"href": "https://github.com/ejpsoil/ejpsoildatahub/tree/main/datasets/esdac/european-soil-database-derived-d.yml", "name": "Source of the record", "protocol": "canonical", "rel": "canonical"}, {"rel": "self", "type": "application/geo+json", "title": "european-soil-database-derived-data", "name": "item", "description": "european-soil-database-derived-data", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/european-soil-database-derived-data"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-01-01T00:00:00Z"}}, {"id": "european-soil-database-v20-vector-and-attribute-data", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[-26.54, 37.55], [-26.54, 70.55], [39.73, 70.55], [39.73, 37.55], [-26.54, 37.55]]]}, "properties": {"themes": [{"concepts": [{"id": "geoscientificInformation"}], "scheme": "https://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_TopicCategoryCode"}, {"concepts": [{"id": "European"}], "scheme": "https://inspire.ec.europa.eu/metadata-codelist/SpatialScope"}, {"concepts": [{"id": "ESDAC"}], "scheme": "Source"}], "updated": "2006-01-01", "type": "Dataset", "created": "2006-01-01", "language": "eng", "externalIds": [{"value": "https://esdac.jrc.ec.europa.eu/node/34643"}], "title": "European Soil Database v2.0 (vector and attribute data)", "description": "This database (2004) is the only harmonized soil database for Europe, extending also to Eurasia. It contains a soil geographical database SGDBE (polygons) to which a number of essential soil attributes are attached, and an associate database PTRDB, with attributes which values have been derived through pedotransfer rules. 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