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This data were created as part of the BonaRes Module A-Project - BonaRes - SIGNAL's research activities.\" Although every care has been taken in preparing and testing the data, the BonaRes Module A-Project - BonaRes - SIGNAL and the BonaRes Data Centre cannot guarantee that the data are correct; neither does the BonaRes Module A-Project - BonaRes - SIGNAL and the BonaRes Data Centre accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The BonaRes Module A-Project - BonaRes - SIGNAL and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data. The access to this data is restricted during embargo time. If prior access is requested, contact the data owner / author.", "updated": "2022-06-30", "type": "Service", "created": "2022-06-02", "language": "eng", "title": "WMS service of the dataset 'Microbial population sizes and soil properties in topsoil and subsoil of two alley-cropping agroforestry systems in Germany'", "description": "This web map service (WMS) includes spatial information used by datasets 'Microbial population sizes and soil properties in topsoil and subsoil of two alley-cropping agroforestry systems in Germany'", "formats": [{"name": "CSV"}], "keywords": ["infoMapAccessService", "Soil", "PCR"], "contacts": [{"name": "Lukas Beule", "organization": "Julius K\u00fchn Institute (JKI) \u2013 Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Berlin, Germany", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "lukas.beule@julius-kuehn.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0003-1107-7540", "name_url": "", "description": "https://orcid.org/", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Lukas Beule", "organization": "Julius K\u00fchn Institute (JKI) \u2013 Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Berlin, Germany", "position": null, "roles": ["projectLeader"], "phones": [{"value": null}], "emails": [{"value": "lukas.beule@julius-kuehn.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0003-1107-7540", "name_url": "", "description": "https://orcid.org/", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "BonaRes Data Centre", "organization": "Leibniz Centre for Agricultural Landscape Research (ZALF)", "position": "Research Platform 'Data Analysis & Simulation' - WG Geodata", "roles": ["publisher"], "phones": [{"value": "+49 33432 82 171"}], "emails": [{"value": "bonares-datenzentrum@zalf.de"}], "addresses": [{"deliveryPoint": ["Eberswalder Strasse 84"], "city": "M\u00fcncheberg", "administrativeArea": "Brandenburg", "postalCode": "15374", "country": "Germany"}], "links": [{"href": null}]}, {"organization": "Julius K\u00fchn Institute (JKI) \u2013 Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Berlin, Germany", "roles": ["contributor"]}], "themes": [{"concepts": [{"id": "infoMapAccessService"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}, {"concepts": [{"id": "Soil"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}, {"concepts": [{"id": "PCR"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}]}, "links": [{"href": "https://maps.bonares.de/mapapps/resources/apps/bonares/index.html?lang=en&mid=0160f3e2-aa36-431c-96f7-871dc41e5f8c", "rel": "download"}, {"href": "https://maps.bonares.de/wss/service/ags-relay/ags/guest/arcgis/rest/services/Deutschland/MapServer/WMSServer?request=GetCapabilities&service=WMS"}, {"href": "https://maps.bonares.de/wss/service/ags-relay/ags/guest/arcgis/rest/services/Deutschland/MapServer/WMSServer?request=GetCapabilities&service=WMS"}, {"href": "https://maps.bonares.de/wss/service/ags-relay/ags/guest/arcgis/rest/services/Deutschland/MapServer/WMSServer?request=GetCapabilities&service=WMS"}, {"href": "https://maps.bonares.de/wss/service/ags-relay/ags/guest/arcgis/rest/services/Deutschland/MapServer/WMSServer?request=GetCapabilities&service=WMS"}, {"rel": "self", "type": "application/geo+json", "title": "0160f3e2-aa36-431c-96f7-871dc41e5f8c", "name": "item", "description": "0160f3e2-aa36-431c-96f7-871dc41e5f8c", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/0160f3e2-aa36-431c-96f7-871dc41e5f8c"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-06-30T00:00:00Z"}}, {"id": "10.1007/s00374-006-0139-9", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-07-27T16:14:43Z", "type": "Journal Article", "created": "2006-10-10", "title": "Effect Of Intercropping On Crop Yield And Chemical And Microbiological Properties In Rhizosphere Of Wheat (Triticum Aestivum L.), Maize (Zea Mays L.), And Faba Bean (Vicia Faba L.)", "description": "In this study, we investigated crop yield and various chemical and microbiological properties in rhizosphere of wheat, maize, and faba bean grown in the field solely and intercropped (wheat/faba bean, wheat/maize, and maize/faba bean) in the second and third year after establishment of the cropping systems. In both years, intercropping increased crop yield, changed N and P availability, and affected the microbiological properties in rhizosphere of the three species compared to sole cropping. Generally, intercropping increased microbial biomass C, N, and P availability, whereas it reduced microbial biomass N in rhizosphere of wheat. The rhizosphere bacterial community composition was studied by denaturing gradient gel electrophoresis of 16S rRNA. In the third year of different cropping systems, intercropping significantly changed bacterial community composition in rhizosphere compared with sole cropping, and the effects were most pronounced in the wheat/faba bean intercropping system. The effects were less pronounced in the second year. The results show that intercropping has significant effects on microbiological and chemical properties in the rhizosphere, which may contribute to the yield enhancement by intercropping.", "keywords": ["PCR-DGGE", "2. Zero hunger", "Intercropping", "571", "Bacterial community composition", "Rhizosphere", "Microbial biomass", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences"]}, "links": [{"href": "https://doi.org/10.1007/s00374-006-0139-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biology%20and%20Fertility%20of%20Soils", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00374-006-0139-9", "name": "item", "description": "10.1007/s00374-006-0139-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00374-006-0139-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2006-10-11T00:00:00Z"}}, {"id": "10.1007/s00374-011-0539-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:14:45Z", "type": "Journal Article", "created": "2011-01-18", "title": "Effects Of Organic And Inorganic Fertilization On Soil Bacterial And Fungal Microbial Diversity In The Kabete Long-Term Trial, Kenya", "description": "The effects of crop manure and inorganic fertilizers on composition of microbial communities of central high land soils of Kenya are poorly known. For this reason, we have carried out a thirty-two-year-old long-term trial in Kabete, Kenya. These soils were treated with organic (maize stover (MS) at 10 t ha\u22121, farmyard manure (FYM) at 10 t ha\u22121) and inorganic fertilizers 120 kg N, 52.8 kg P (N2P2), N2P2 + MS, N2P2 + FYM, a control, and a fallow for over 30 years. We examined 16S rRNA gene and 28S rRNA gene fingerprints of bacterial and fungal diversity by PCR amplification and denaturing gradient gel electrophoresis separation, respectively. The PCR bacterial community structure and diversity were negatively affected by N2P2 and were more closely related to the bacterial structure in the soils without any addition (control) than that of soils with a combination of inorganic and organic or inorganic fertilizers alone. The effect on fungal diversity by N2P2 was different than the effect on bacterial diversity since the fungal diversity was similar to that of the N2P2 + FYM and N2P2 + MS-treated. However, soils treated with organic inputs clustered away from soils amended with inorganic inputs. Organic inputs had a positive effect on both bacterial and fungal diversity with or without chemical fertilizers. Results from this study suggested that total diversity of bacterial and fungal communities was closely related to agro-ecosystem management practices and may partially explain the yield differences observed between the different treatments.", "keywords": ["[SDV.SA]Life Sciences [q-bio]/Agricultural sciences", "Microbial diversity", "soil microorganisms", "engrais organique", "http://aims.fao.org/aos/agrovoc/c_27870", "Organic and inorganic amendments", "F08 - Syst\u00e8mes et modes de culture", "rendement des cultures", "630", "fertilisation", "biodiversit\u00e9", "http://aims.fao.org/aos/agrovoc/c_4592", "http://aims.fao.org/aos/agrovoc/c_36669", "http://aims.fao.org/aos/agrovoc/c_2018", "inorganic fertilizers", "http://aims.fao.org/aos/agrovoc/c_10795", "http://aims.fao.org/aos/agrovoc/c_34326", "fertility", "2. Zero hunger", "[SDV.SA] Life Sciences [q-bio]/Agricultural sciences", "http://aims.fao.org/aos/agrovoc/c_33949", "g\u00e9n\u00e9tique des populations", "04 agricultural and veterinary sciences", "agro\u00e9cosyst\u00e8me", "6. Clean water", "fertilit\u00e9 du sol", "PCR", "http://aims.fao.org/aos/agrovoc/c_34079", "polymerization", "community structure", "abonos inorg\u00e1nicos", "management", "570", "http://aims.fao.org/aos/agrovoc/c_7170", "http://aims.fao.org/aos/agrovoc/c_7172", "flore microbienne", "soil", "http://aims.fao.org/aos/agrovoc/c_36167", "micro-organisme du sol", "http://aims.fao.org/aos/agrovoc/c_10176", "organic fertilizers", "abonos org\u00e1nicos", "pratique culturale", "microorganismos del suelo", "suelo", "flore du sol", "P35 - Fertilit\u00e9 du sol", "P34 - Biologie du sol", "polimerizaci\u00f3n", "15. Life on land", "engrais min\u00e9ral", "http://aims.fao.org/aos/agrovoc/c_16367", "http://aims.fao.org/aos/agrovoc/c_4086", "0401 agriculture", " forestry", " and fisheries", "F04 - Fertilisation"]}, "links": [{"href": "https://doi.org/10.1007/s00374-011-0539-3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biology%20and%20Fertility%20of%20Soils", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00374-011-0539-3", "name": "item", "description": "10.1007/s00374-011-0539-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00374-011-0539-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-01-19T00:00:00Z"}}, {"id": "10.1007/s00442-012-2578-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:14:50Z", "type": "Journal Article", "created": "2013-01-07", "title": "Effects Of Drought And N-Fertilization On N Cycling In Two Grassland Soils", "description": "Open AccessOecologia, 171 (3)", "keywords": ["[SDE] Environmental Sciences", "N2O fluxes", "550", "functional genes", "Nitrogen", "[SDV]Life Sciences [q-bio]", "Climate", "Climate Change", "Nitrification and denitrification", "enzyme activites", "Urine", "630", "10127 Institute of Evolutionary Biology and Environmental Studies", "Soil", "Quantitative PCR", "Climate change; Enzyme activities; Functional genes; Quantitative PCR; Nitrification and denitrification; N2O fluxes", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "Animals", "Climate change", "Enzyme activities", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "Ecosystem", "Soil Microbiology", "Functional genes", "Nitrogen Cycle", "Plants", "Archaea", "Droughts", "[SDV] Life Sciences [q-bio]", "1105 Ecology", " Evolution", " Behavior and Systematics", "climate change", "Genes", " Bacterial", "[SDE]Environmental Sciences", "quantitative PCR", "Denitrification", "570 Life sciences; biology", "590 Animals (Zoology)", "Cattle", "nitrification and denitrification"]}, "links": [{"href": "https://doi.org/10.1007/s00442-012-2578-3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Oecologia", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00442-012-2578-3", "name": "item", "description": "10.1007/s00442-012-2578-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00442-012-2578-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-01-08T00:00:00Z"}}, {"id": "10.1016/j.envint.2020.106190", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:16:24Z", "type": "Journal Article", "created": "2020-10-26", "title": "Treated wastewater irrigation promotes the spread of antibiotic resistance into subsoil pore-water", "description": "In the present study, we investigated the impact of treated wastewater (TWW) irrigation on the prevalence of antibiotic resistance genes (ARGs) in subsoil pore-water, a so-far under-appreciated matrix. We hypothesized that TWW irrigation increases ARG prevalence in subsoil pore-water. This hypothesis was tested using a multiphase approach, which consisted of sampling percolated subsoil pore-water from lysimeter-wells of a real-scale TWW-irrigated field, operated for commercial farming practices, and controlled, laboratory microcosms irrigated with freshwater or TWW. We monitored the abundance of six selected ARGs (sul1, blaOXA-58, tetM, qnrS, blaCTX-M-32 and blaTEM), the intI1 gene associated with mobile genetic elements and an indicator for anthropogenic pollution and bacterial abundance (16S rRNA gene) by qPCR. The bacterial load of subsoil pore water was independent of both, irrigation intensity in the field study and irrigation water type in the microcosms. Among the tested genes in the field study, sul1 and intI1 exhibited constantly higher relative abundances. Their abundance was further positively correlated with increasing irrigation intensity. Controlled microcosm experiments verified the observed field study results: the relative abundance of several genes, including sul1 and intI1, increased significantly when irrigating with TWW compared to freshwater irrigation. Overall, TWW irrigation promoted the spread of ARGs and intI1 in the subsoil pore-water, while the bacterial load was maintained. The combined results from the real-scale agricultural field and the controlled lab microcosms indicate that the dissemination of ARGs in various subsurface environments needs to be taken into account during TWW irrigation scenarios.", "keywords": ["0301 basic medicine", "2. Zero hunger", "Agricultural Irrigation", "Antibiotic resistance", "Water", "Subsoil pore-water", "Drug Resistance", " Microbial", "Wastewater", "Wastewater reuse", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "Environmental sciences", "qPCR", "Soil", "03 medical and health sciences", "Genes", " Bacterial", "RNA", " Ribosomal", " 16S", "ARGs", "GE1-350", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.envint.2020.106190"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environment%20International", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envint.2020.106190", "name": "item", "description": "10.1016/j.envint.2020.106190", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envint.2020.106190"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-01-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2019.03.176", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:17:13Z", "type": "Journal Article", "created": "2019-03-13", "title": "Effect of digestate application on microbial respiration and bacterial communities' diversity during bioremediation of weathered petroleum hydrocarbons contaminated soils", "description": "Digestate is an organic by-product of biogas production via anaerobic digestion processes and has a great potential as soil fertilizer due to concentrated nutrients. In this study, we examined digestate as a potential nutrient and microbial seeding for bioremediation of weathered (aged) petroleum hydrocarbon contaminated soils. We analysed 6 different treatments in microcosm using two industrial soils having different textures: a clay rich soil and a sandy soil. After 30\u202fdays of incubation, the highest total petroleum hydrocarbons (TPH) removal was observed in microcosms containing digestate together with bulking agent (17.8% and 12.7% higher than control in clay rich soil and sandy soil, respectively) or digestate together with immobilized bacteria (13.4% and 9% higher than control in clay rich soil and sandy soil, respectively). After digestate application microbial respiration was enhanced in sandy soil and inhibited in clay rich soil due to aggregates formation. After bulking agent addition to clay rich soil aggregates size was reduced and oxygen uptake was improved. Application of digestate to soil resulted in the development of distinct microbial groups in amended and non-amended soils. Genera containing species able to degrade TPH like Acinetobacter and Mycobacterium were abundant in digestate and in soil amended with digestate. Quantification of alkB genes, encoding alkane monoxygenase, revealed high concentration of these genes in digestate bacterial community. After application of digestate, the level of alkB genes significantly increased in soils and remained high until the end of the treatment. The study revealed great potential of digestate as a nutrient and bacteria source for soil bioremediation.", "keywords": ["[SDE] Environmental Sciences", "TPH removal", "550", "Soil remediation", "0211 other engineering and technologies", "alkB genes; Organic fertilizers; qPCR; Soil remediation; TPH removal; Biodegradation", " Environmental; Environmental Restoration and Remediation; Hydrocarbons; Petroleum; Petroleum Pollution; Soil; Soil Pollutants; Soil Microbiology", "02 engineering and technology", "01 natural sciences", "7. Clean energy", "630", "Organic fertilizers", "Environmental", "Soil", "alkB genes", "Soil Pollutants", "Petroleum Pollution", "Environmental Restoration and Remediation", "Soil Microbiology", "0105 earth and related environmental sciences", "2. Zero hunger", "[SDE.IE]Environmental Sciences/Environmental Engineering", "15. Life on land", "Hydrocarbons", "6. Clean water", "qPCR", "Biodegradation", " Environmental", "Petroleum", "[SDE]Environmental Sciences", "Biodegradation", "[SDE.IE] Environmental Sciences/Environmental Engineering"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2019.03.176"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2019.03.176", "name": "item", "description": "10.1016/j.scitotenv.2019.03.176", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2019.03.176"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-01T00:00:00Z"}}, {"id": "10.1007/s11104-013-1855-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:15:18Z", "type": "Journal Article", "created": "2013-08-21", "title": "Soil Microorganisms Respond To Five Years Of Climate Change Manipulations And Elevated Atmospheric Co2 In A Temperate Heath Ecosystem", "description": "Soil microbial responses to global change can affect organic matter turnover and nutrient cycling thereby altering the overall ecosystem functioning. In a large-scale experiment, we investigated the impact of 5\u00a0years of climate change and elevated atmospheric CO2 on soil microorganisms and nutrient availability in a temperate heathland. The future climate was simulated by increased soil temperature (+0.3\u00a0\u00b0C), extended pre-summer drought (excluding 5\u20138\u00a0% of the annual precipitation) and elevated CO2 (+130\u00a0ppm) in a factorial design. Soil organic matter and nutrient pools were analysed and linked to microbial measures by quantitative PCR of bacteria and fungi, chloroform fumigation extraction, and substrate-induced respiration to assess their impact of climate change on nutrient availability. Warming resulted in higher measures of fungi and bacteria, of microbial biomass and of microbial growth potential, however, this did not reduce the availability of nitrogen or phosphorus in the soil. Elevated CO2 did not directly affect the microbial measures or nutrient pools, whereas drought shifted the microbial community towards a higher fungal dominance. Although we were not able to show strong interactive effects of the global change factors, warming and drought changed both nutrient availability and microbial community composition in the heathland soil, which could alter the ecosystem carbon and nutrient flow in the long-term.", "keywords": ["Bacterial abundance", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Soil nutrient pools", "Elevated carbon dioxide", "CLIMAITE", "Fungal abundance", "15. Life on land", "Real-time quantitative PCR", "6. Clean water", "Long-term ecosystem manipulation", "03 medical and health sciences", "13. Climate action", "11. Sustainability", "Deschampsia flexuosa"]}, "links": [{"href": "https://doi.org/10.1007/s11104-013-1855-1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11104-013-1855-1", "name": "item", "description": "10.1007/s11104-013-1855-1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-013-1855-1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-08-22T00:00:00Z"}}, {"id": "10.1016/j.apsoil.2010.04.006", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:15:56Z", "type": "Journal Article", "created": "2010-05-22", "title": "Effect Of The Endogeic Earthworm Pontoscolex Corethrurus On The Microbial Structure And Activity Related To Co2 And N2o Fluxes From A Tropical Soil (Madagascar)", "description": "Abstract   The objective of this laboratory study was to determine the influence of a tropical endogeic earthworm,  Pontoscolex corethrurus , on CO 2  and N 2 O fluxes from a tropical Ferralsol and microorganisms potentially involved in these gases emissions. CO 2  and N 2 O fluxes were measured during 35 days from soil mesocosms with and without earthworms. At the end of the incubation, 7% of soil was egested as cast in the earthworm treatment. Then, casts which may be aged from few hours to 35 days old were isolated from non-ingested soil. Different descriptive parameters (activity, density, and structure) of the microbial communities were investigated in the control, the non-ingested soils, and the casts. Quantitative PCR of denitrification genes encoding the nitrite ( nirK ) and nitrous oxide ( nosZ ) reductases was used to study denitrifier density in the earthworm casts. The presence of  P. corethrurus  induced a significant increase in CO 2  emissions but did not affect N 2 O fluxes when measured at mesocosm level. Despite the absence of significant differences in C and N contents between soils and casts, the near infra-red spectra analysis clearly underlined a specific organic signature for the casts. Fungal and bacterial biomass significantly decreased (\u223c2-fold) in casts compared to parent soil, but the fungal-to-bacterial ratio was not modified by the earthworm casting activity. Data suggested that bacterial communities, especially denitrifiers, were modified in casts. The relative abundance of  nirK  and  nosZ  genes increased in the casts while the genetic structures of total bacteria and denitrifying communities were slightly modified in the casts. This study highlighted the importance of earthworm casts as a specific soil habitat where a subset of soil functional bacterial communities (such as denitrifiers) found favourable condition for their growth. However the effect of  P. corethrurus  was less evident when up-scaling from casts to mesocosm level.", "keywords": ["Pontoscolex corethrurus", "Quantitative PCR", "Denitrification genes", "Madagascar", "0401 agriculture", " forestry", " and fisheries", "Microbial activity potentials", "04 agricultural and veterinary sciences", "01 natural sciences", "630", "FAME", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.apsoil.2010.04.006"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Soil%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.apsoil.2010.04.006", "name": "item", "description": "10.1016/j.apsoil.2010.04.006", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.apsoil.2010.04.006"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-07-01T00:00:00Z"}}, {"id": "10.1016/j.apsoil.2010.12.003", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:15:56Z", "type": "Journal Article", "created": "2011-01-14", "title": "Denitrification In A Vertisol Under Long-Term Tillage And No-Tillage Management In Dryland Agricultural Systems: Key Genes And Potential Rates", "description": "Open AccessThis work was partly funded by the \u201cCommision Interministerial de Ciencia y Tecnologia (CICYT)\u201d through the project AGL2005-2423 and by the Spanish Ministry of Education and Science through the project INIA RTA2006-00058-CO3-01. Dr. Melero thanks the Spanish Ministry of Science and Education for financial support through the \u201cJos\u00e9 Castillejo National Human Resources Mobility Program (I+D+I 2008\u20132011)\u201d and the Spanish CSIC through the contract program \u201cJAE-DOC\u201d.", "keywords": ["2. Zero hunger", "0301 basic medicine", "03 medical and health sciences", "NirS", "N2O/N2 ratio", "NosZ", "0401 agriculture", " forestry", " and fisheries", "NirK", "04 agricultural and veterinary sciences", "15. Life on land", "6. Clean water", "Real-time PCR"]}, "links": [{"href": "https://doi.org/10.1016/j.apsoil.2010.12.003"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Soil%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.apsoil.2010.12.003", "name": "item", "description": "10.1016/j.apsoil.2010.12.003", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.apsoil.2010.12.003"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-03-01T00:00:00Z"}}, {"id": "10.1016/j.biocontrol.2025.105723", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:16:02Z", "type": "Journal Article", "created": "2024-10-01", "title": "Advancing Strain-Specific Taqman Assays for Trichoderma Asperellum Detection in Commercial Agricultural Settings", "description": "The global agricultural sector is facing significant challenges in achieving higher sustainability, which has increased interest in using biological control agents (BCAs) to manage plant diseases. However, it is essential to ensure that microbial-based products, such as BCAs, are utilised in a manner that does not harm soil quality and fertility while decreasing reliance on synthetic pesticides. To accomplish this, it is crucial to monitor the fate and persistence of bioinoculants in the soil, which is essential for optimising their application over time, as well as for regulatory and commercial purposes and environmental risk assessment. A qPCR detection method utilising TaqMan chemistry is proposed, which has demonstrated high specificity and sensitivity in detecting Trichoderma asperellum, a common BCA species, in soil. The primers and probe were designed based on the \u03b2tubulin2 gene. The TaqMan-based assay was applied and validated on soils where tomatoes and strawberries were grown after a previous application of T. asperellum FC80 strain over three years. The TaqMan-based assay was able to detect the target strain accurately, meeting the stringent requirements for commercial and regulatory applications. Significance and impact of the study: The TaqMan assay developed here has the potential to impact the agricultural sector significantly. It can be used for regulatory, commercial, and scientific purposes to track, monitor, and determine the presence and fate of T. asperellum under field crop conditions, thereby contributing to adopting more sustainable and efficient agricultural practices.", "keywords": ["traceability qPCR", "Soil", "TaqMan Assay", "S", "QH301-705.5", "Fungi Trichoderma asperellum", "Agriculture", "Biology (General)", "Biological control agent"]}, "links": [{"href": "https://doi.org/10.1016/j.biocontrol.2025.105723"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biological%20Control", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.biocontrol.2025.105723", "name": "item", "description": "10.1016/j.biocontrol.2025.105723", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.biocontrol.2025.105723"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-01T00:00:00Z"}}, {"id": "10.1016/j.ecolind.2024.111796", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:16:16Z", "type": "Journal Article", "created": "2024-02-29", "title": "Ascomycota and Basidiomycota fungal phyla as indicators of land use efficiency for soil organic carbon accrual with woody plantations", "description": "As soil fungi are major players in the carbon accumulation process, the two main fungal degraders in topsoil, Ascomycetes and Basidiomycetes, were investigated as indicators of land use effectiveness in increasing soil carbon accumulation and soil function. The study focused on the soil organic carbon content increase in a 20-year short rotation forest cycle with broadleaf woody plantations compared to a nearby arable cropping system. Total fungi, Ascomycota and Basidiomycota, were quantified in terms of DNA copy number, with specific probes using SYBR\u00ae Green I dye on the QuantStudio\u2122 3D digital PCR system (dPCR). Previously, next generation sequencing analysis using a general primer confirmed that Ascomycota and Basidiomycota were the most represented phyla and that fungal community composition significantly differed between treatments. A range of key soil enzyme activities for the C-cycle were also assessed. Total organic carbon content (TOC), microbial biomass in term of dsDNA and enzyme activities significantly increased in woody plantations compared to arable soil. The TOC increase differed significantly also between wood species, Salix and Robina gave the greatest increase (+30 and 20\u00a0% respectively), followed by Populus (+12), microbial biomass highly correlated with TOC showing the same trend. Total fungi, Ascomycota and Basidiomycota increased significantly in three woody plantations compared to the arable soil system. Ascomycota in the woody plantations increased two to four times (average 3144 n copies \u00b5l\u22121 of DNA) compared to the arable soil (1419 n copies \u00b5l\u22121); Basidiomycota were almost absent in arable soil (av. 94n copies \u00b5l\u22121) and increased five to six times in woody plantations (av. 490 n copies \u00b5l\u22121). Total fungi and ascomycetes correlated strongly with microbial biomass and TOC, whereas basidiomycetes did not. These findings showed that Ascomycota represent the largest portion of fungi in agricultural soils even after a 20-years short rotation forest cycle and they can be taken as indicators of carbon accumulation processes. Therefore, this study suggests that joining the Ascomycetes quantity in the topsoil to the Ascomycota:Basidiomycota ratio seems a good option when setting regional strategies for improving C accrual in farmland with the short-term afforestation.", "keywords": ["Carbon sequestration", "2. Zero hunger", "Ecology", "04 agricultural and veterinary sciences", "15. Life on land", "Topsoil", "01 natural sciences", "Saproptrophic soil fungi", "Land use", "0401 agriculture", " forestry", " and fisheries", "Short rotation forest", "Digital PCR", "QH540-549.5", "0105 earth and related environmental sciences"], "contacts": [{"organization": "Manici, Luisa M., Caputo, Francesco, Fornasier, Flavio, Paletto, Alessandro, Ceotto, Enrico, De Meo, Isabella,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1016/j.ecolind.2024.111796"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecological%20Indicators", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.ecolind.2024.111796", "name": "item", "description": "10.1016/j.ecolind.2024.111796", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.ecolind.2024.111796"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-03-01T00:00:00Z"}}, {"id": "10.1016/j.envpol.2018.09.128", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:16:25Z", "type": "Journal Article", "created": "2018-09-28", "title": "A rationale for the high limits of quantification of antibiotic resistance genes in soil", "description": "The determination of values of abundance of antibiotic resistance genes (ARGs) per mass of soil is extremely useful to assess the potential impacts of relevant sources of antibiotic resistance, such as irrigation with treated wastewater or manure application. Culture-independent methods and, in particular, quantitative PCR (qPCR), have been regarded as suitable approaches for such a purpose. However, it is arguable if these methods are sensitive enough to measure ARGs abundance at levels that may represent a risk for environmental and human health. This study aimed at demonstrating the range of values of ARGs quantification that can be expected based on currently used procedures of DNA extraction and qPCR analyses. The demonstration was based on the use of soil samples spiked with known amounts of wastewater antibiotic resistant bacteria (ARB) (Enterococcus faecalis, Escherichia coli, Acinetobacter johnsonii, or Pseudomonas aeruginosa), harbouring known ARGs, and also on the calculation of expected values determined based on qPCR. The limits of quantification (LOQ) of the ARGs (vanA, qnrS, blaTEM, blaOXA, blaIMP, blaVIM) were observed to be approximately 4 log-units per gram of soil dry weight, irrespective of the type of soil tested. These values were close to the theoretical LOQ values calculated based on currently used DNA extraction methods and qPCR procedures. The observed LOQ values can be considered extremely high to perform an accurate assessment of the impacts of ARGs discharges in soils. A key message is that ARGs accumulation will be noticeable only at very high doses. The assessment of the impacts of ARGs discharges in soils, of associated risks of propagation and potential transmission to humans, must take into consideration this type of evidence, and avoid the simplistic assumption that no detection corresponds to risk absence.", "keywords": ["0301 basic medicine", "2. Zero hunger", "LOD - Limit of detection", "0303 health sciences", "Acinetobacter", "Drug Resistance", " Microbial", "Wastewater", "Real-Time Polymerase Chain Reaction", "6. Clean water", "Anti-Bacterial Agents", "3. Good health", "Manure", "Quantitative PCR", "Soil", "03 medical and health sciences", "Genes", " Bacterial", "13. Climate action", "Pseudomonas aeruginosa", "Enterococcus faecalis", "Escherichia coli", "LOQ - Limit of quantification", "Soil Microbiology", "Risk assessment"]}, "links": [{"href": "https://doi.org/10.1016/j.envpol.2018.09.128"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Pollution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envpol.2018.09.128", "name": "item", "description": "10.1016/j.envpol.2018.09.128", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envpol.2018.09.128"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-12-01T00:00:00Z"}}, {"id": "10.1016/j.envres.2019.108608", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:16:26Z", "type": "Journal Article", "created": "2019-07-26", "title": "Antibiotic resistance gene distribution in agricultural fields and crops. A soil-to-food analysis", "description": "Despite the social concern about the generalization of antibiotic resistance hotspots worldwide, very little is known about the contribution of different potential sources to the global risk. Here we present a quantitative analysis of the distribution of Antibiotic Resistance Genes (ARGs) in soil, rhizospheric soil, roots, leaves and beans in tomato, lettuce and broad beans crops (165 samples in total), grown in nine commercial plots distributed in four geographical zones in the vicinity of Barcelona (North East Spain). We also analyzed five soil samples from a nearby forest, with no record of agricultural activities. DNA samples were analyzed for their content in the ARGs sul1, tetM, qnrS1, blaCTX-M-32, blaOXA-58, mecA, and blaTEM, plus the integron intI1, using qPCR methods. In addition, soil microbiomes from the different plots were analyzed by amplicon-targeted 16S rRNA gene sequencing. Our data show a decreasing gradient of ARG loads from soil to fruits and beans, the latter showing only from 0.1 to 0.01% of the abundance values in soil. The type of crop was the main determinant for both ARG distribution and microbiome composition among the different plots, with minor contributions of geographic location and irrigation water source. We propose that soil amendment and/or fertilization, more than irrigation water, are the main drivers of ARG loads on the edible parts of the crop, and that they should therefore be specifically controlled.", "keywords": ["0301 basic medicine", "2. Zero hunger", "Microbiomes", "Agriculture", "Drug Resistance", " Microbial", "Irrigation water", "15. Life on land", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "3. Good health", "qPCR", "Soil", "03 medical and health sciences", "Antibiotic resistance genes", "Genes", " Bacterial", "Spain", "RNA", " Ribosomal", " 16S", "Rhizosphere", "Endophytes", "Food Analysis", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.envres.2019.108608"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envres.2019.108608", "name": "item", "description": "10.1016/j.envres.2019.108608", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envres.2019.108608"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-10-01T00:00:00Z"}}, {"id": "10.1016/j.ijfoodmicro.2021.109504", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:16:50Z", "type": "Journal Article", "created": "2021-12-21", "title": "Development of a rapid qPCR method to quantify lactic acid bacteria in cold-smoked salmon", "description": "Quantification of lactic acid bacteria (LAB) is essential to control quality of seafood products like cold-smoked salmon (CSS). In the present study, we report the design and optimization of a dual-labelled TaqMan \u2122 probe targeting the V7 region of 16S rRNA gene for the detection of LAB in CSS. This quantitative PCR (qPCR) assays is useful for the simultaneous detection of the ten LAB genera communally encountered in CSS as Aerococcus, Carnobacterium, Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Macrococcus, Streptococcus, Vagococcus and Weissella. The specificity of this method was demonstrated against 14 genera (44 isolates, 35 species) of Gram-positive bacteria and 19 genera of Gram-negative (40 isolates, 34 species). Calibration of the method was performed in CSS matrix using a mix of equimolar cultured solution of five LAB. Quantification with the qPCR method range from 3.5 to 8.5 Log CFU/g in CSS matrix, covering 5 orders of magnitude. On these artificially contaminated CSS slices, PCR method results correlated successfully (R2\u00a0=\u00a00.9945) with the conventional enumeration on Elliker medium. In addition, the new method was successful on commercial CSS from five different origins with a quantification range from 3.7 Log CFU/g to 8.0 Log CFU/g. This one-step quantitative methodology is proposed as a rapid and complementary tool of the cultural methods to investigate the LAB microbiota and biodiversity of CSS.", "keywords": ["LAB", "0301 basic medicine", "0303 health sciences", "Colony Count", " Microbial", "Real-Time Polymerase Chain Reaction", "Lactobacillus", "03 medical and health sciences", "Seafood", "TaqMan TM probe", "Lactobacillales", "Salmon", "RNA", " Ribosomal", " 16S", "Food Microbiology", "Animals", "Real-time PCR"]}, "links": [{"href": "https://doi.org/10.1016/j.ijfoodmicro.2021.109504"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/International%20Journal%20of%20Food%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.ijfoodmicro.2021.109504", "name": "item", "description": "10.1016/j.ijfoodmicro.2021.109504", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.ijfoodmicro.2021.109504"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-02-01T00:00:00Z"}}, {"id": "10.1016/j.jece.2018.02.022", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:16:56Z", "type": "Journal Article", "created": "2018-02-14", "title": "Inter-laboratory calibration of quantitative analyses of antibiotic resistance genes", "description": "Backgrounds: Antibiotic resistant bacteria and antibiotic resistance genes (ARGs) are major human-health threats, widely distributed in the environment. Quantitative PCR (qPCR) is a standard approach to detect and quantify ARGs in environmental compartments. However, the comparison of gene quantification reported by different laboratories is challenging since data are predominantly obtained under non- harmonized conditions, using different qPCR protocols. Objectives: The aim of this study was to develop and calibrate standardized qPCR procedures for quantification of key ARGs, analyzing the same samples with common protocols and distinct equipment, reagents batches and operators. Methods: Treated wastewater from three European countries were processed immediately after collection and transported to the laboratory for total DNA extraction. DNA extracts from each sample were pooled and aliquots were distributed by five partners involved in the calibration procedure. The genes 16S rRNA, vanA, blaTEM, qnrS, sul1, blaCTXM-32 and intI1 were analyzed using harmonized qPCR protocols and the constructed pNORM1 plasmid, which contains fragments of the seven targeted genes, was used for generating standard curves. Conclusions: The 16S rRNA gene was the most abundant, followed by sul1, intI1, qnrS and blaTEM. Quantifications made by different partners were reproducible and inter-laboratory variation was &lt; 20%. The notorious exception was for the qnrS gene, and therefore protocol improvement is recommended. The genes blaCTXM-32 and vanA were below the limit of quantification in most or all of the samples analyzed. The inter-laboratory calibration is an adequate approach to reliably assess ARG abundance and environmental contamination in different environments and geographic locations.", "keywords": ["Life sciences; biology", "info:eu-repo/classification/ddc/570", "0301 basic medicine", "570", "biology", "Inter-laboratory calibration", "Antibiotic resistance gene", "Wastewater", "Life sciences", "01 natural sciences", "6. Clean water", "3. Good health", "Quantitative PCR", "03 medical and health sciences", "ddc:570", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.jece.2018.02.022"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Environmental%20Chemical%20Engineering", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jece.2018.02.022", "name": "item", "description": "10.1016/j.jece.2018.02.022", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jece.2018.02.022"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-02-01T00:00:00Z"}}, {"id": "10400.5/23455", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:26:00Z", "type": "Journal Article", "created": "2022-02-13", "title": "The Analysis of Partial Sequences of the Flavonone 3 Hydroxylase Gene in Lupinus mutabilis Reveals Differential Expression of Two Paralogues Potentially Related to Seed Coat Colour", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Flavonone 3 hydroxylases (EC 1.14.11.9) are key enzymes in the synthesis of anthocyanins and other flavonoids. Such compounds are involved in seed coat colour and stem pigmentation. Lupinus mutabilis (tarwi) is a legume crop domesticated in the Andean region, valued for the high protein and oil content of its seeds. Tarwi accessions are being selected for cultivation in Europe under defined breeding criteria. Seed coat colour patterns are relevant breeding traits in tarwi, and these are conditioned by anthocyanin content. We identified and isolated part of the tarwi flavonone 3-hydroxylase gene (LmF3h) from two accessions with distinct seed coat colour patterns. Two partial LmF3h paralogues, with predicted 20% amino-acid changes but little predicted tertiary structure alterations, were identified in the coloured seed genotype, while only one was present in the white seed genotype. Upon selection and validation of appropriate reference genes, a RT-qPCR analysis showed that these paralogues have different levels of expression during seed development in both genotypes, although they follow the same expression patterns. DNA and transcription analyses enabled to highlight potential F3H paralogues relatable to seed coat pigmentation in tarwi and, upon biochemical and genetic confirmation, prompt marker-assisted breeding for relevant phenotypic traits associated with flavonoid synthesis.</p></article>", "keywords": ["0301 basic medicine", "2. Zero hunger", "<i>F3H</i>", "0303 health sciences", "S", "Agriculture", "<i>Lupinus mutabilis</i>", "03 medical and health sciences", "F3H", "seed coat", "gene expression", "Lupinus mutabilis", "<i>Lupinus mutabilis</i>; <i>F3H</i>; seed coat; gene expression; RT-qPCR reference genes", "RT-qPCR reference genes"]}, "links": [{"href": "http://www.mdpi.com/2073-4395/12/2/450/pdf"}, {"href": "https://repositorio.ulisboa.pt/bitstream/10400.5/23455/1/PTALHINHAS-agronomy-12-00450.pdf"}, {"href": "https://doi.org/10400.5/23455"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10400.5/23455", "name": "item", "description": "10400.5/23455", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10400.5/23455"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-02-11T00:00:00Z"}}, {"id": "10.3390/genes13050850", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:21:50Z", "type": "Journal Article", "created": "2022-05-11", "title": "Short-Term Responses of Soil Microbial Communities to Changes in Air Temperature, Soil Moisture and UV Radiation", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>We analyzed the effects on a soil microbial community of short-term alterations in air temperature, soil moisture and ultraviolet radiation and assessed the role of invertebrates (species Enchytraeus crypticus) in modulating the community\u2019s response to these factors. The reference soil, Lufa 2.2, was incubated for 48 h, with and without invertebrates, under the following conditions: standard (20 \u00b0C + 50% water holding capacity (WHC)); increased air temperature (15\u201325 \u00b0C or 20\u201330 \u00b0C + 50% WHC); flood (20 \u00b0C + 75% WHC); drought (20 \u00b0C + 25% WHC); and ultraviolet radiation (UV) (20 \u00b0C + 50% WHC + UV). BIOLOG EcoPlates and 16S rDNA sequencing (Illumina) were used to assess the microbial community\u2019s physiological profile and the bacterial community\u2019s structure, respectively. The bacterial abundance (estimated by 16S rDNA qPCR) did not change. Most of the conditions led to an increase in microbial activity and a decrease in diversity. The structure of the bacterial community was particularly affected by higher air temperatures (20\u201330 \u00b0C, without E. crypticus) and floods (with E. crypticus). Effects were observed at the class, genera and OTU levels. The presence of invertebrates mostly resulted in the attenuation of the observed effects, highlighting the importance of considering microbiome\u2013invertebrate interactions. Considering future climate changes, the effects described here raise concern. This study provides fundamental knowledge to develop effective strategies to mitigate these negative outcomes. However, long-term studies integrating biotic and abiotic factors are needed.</p></article>", "keywords": ["0301 basic medicine", "Soil invertebrates", "Ultraviolet Rays", "drought", "microbial activity", "DNA", " Ribosomal", "Flood", "Article", "Quantitative PCR", "Soil", "03 medical and health sciences", "soil microbiome", "2. Zero hunger", "metagenomics", "increased temperature; drought; flood; UV exposure; microbial activity; bacterial diversity; metagenomics; quantitative PCR; soil microbiome; soil invertebrates", "Soil microbiome", "0303 health sciences", "Drought", "Bacteria", "Microbiota", "bacterial diversity", "Temperature", "Water", "flood", "15. Life on land", "soil invertebrates", "6. Clean water", "UV exposure", "Microbial activity", "Bacterial diversity", "13. Climate action", "quantitative PCR", "Metagenomics", "Increased temperature", "increased temperature"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/13/5/850/pdf"}, {"href": "https://doi.org/10.3390/genes13050850"}, {"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/genes13050850", "name": "item", "description": "10.3390/genes13050850", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes13050850"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-05-10T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2018.10.268", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:17:12Z", "type": "Journal Article", "created": "2018-10-22", "title": "Antibiotic resistance genes distribution in microbiomes from the soil-plant-fruit continuum in commercial Lycopersicon esculentum fields under different agricultural practices", "description": "While the presence of antibiotic resistance genes (ARGs) in agricultural soils and products has been firmly established, their distribution among the different plant parts and the contribution of agricultural practices, including irrigation with reclaimed water, have not been adequately addressed yet. To this end, we analyzed the levels of seven ARGs (sul1, blaTEM, blaCTX-M-32, mecA, qnrS1, tetM, blaOXA-58), plus the integrase gene intl1, in soils, roots, leaves, and fruits from two commercial tomato fields irrigated with either unpolluted groundwater or from a channel impacted by treated wastewater, using culture-independent, quantitative real-time PCR methods. ARGs and intl1 sequences were found in leaves and fruits at levels representing from 1 to 10% of those found in roots or soil. The relative abundance of intl1 sequences correlated with tetM, blaTEM, and sul1 levels, suggesting a high horizontal mobility potential for these ARGs. High-throughput 16S rDNA sequencing revealed microbiome differences both between sample types (soil plus roots versus leaves plus fruits) and sampling zones, and a correlation between the prevalence of Pseudomonadaceae and the levels of different ARGs, particularly in fruits and leaves. We concluded that both microbiome composition and ARGs levels in plants parts, including fruits, were likely influenced by agricultural practices.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Antibiotic resistance", "Microbiota", "Microbiomes", "Agriculture", "Drug Resistance", " Microbial", "Horizontal gene transfer", "Irrigation water", "15. Life on land", "6. Clean water", "qPCR", "Soil", "03 medical and health sciences", "Solanum lycopersicum", "Genes", " Bacterial", "Fruit", "Soil Microbiology", "Environmental Monitoring"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2018.10.268"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2018.10.268", "name": "item", "description": "10.1016/j.scitotenv.2018.10.268", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2018.10.268"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-02-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2006.05.017", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:17:19Z", "type": "Journal Article", "created": "2006-07-11", "title": "Hydrolase Activities, Microbial Biomass And Bacterial Community In A Soil After Long-Term Amendment With Different Composts", "description": "Open AccessThe use of composts in agricultural soils is a widespread practice and the positive effects on soil and plants are known from numerous studies. However, there have been few attempts to compare the effects of different kinds of composts in one single study. The aim of this paper is to investigate to what extent and to which soil depth four major types of composts would affect the soil and its microbiota. In a crop-rotation field experiment, composts produced from (i) urban organic wastes, (ii) green wastes, (iii) manure and (iv) sewage sludge were applied at a rate equivalent to 175 kg N ha\u22121 yr\u22121 for 12 years. General (total organic C (Corg), total N (Nt), microbial biomass C (Cmic), and basal respiration), specific (enzyme activities related to C, N and P cycles), biochemical properties and bacterial genetic diversity (based on DGGE analysis of 16S rDNA) were analyzed at different depths (0\u201310, 10\u201320 and 20\u201330 cm). Compost treatment increased Corg at all depths from 11 g kg\u22121 for control soil to 16.7 g kg\u22121 for the case of sewage sludge compost. Total N increased with compost treatment at 0\u201310 cm and 10\u201320 cm depths, but not at 20\u201330 cm. Basal respiration and Cmic declined with depth, and the composts resulted in an increase of Cmic and basal respiration. Enzyme activities were different depend on the enzyme and among compost treatments, but in general, the enzyme activities were higher in the upper layers (0\u201310 and 10\u201320 cm) than in the 20\u201330 cm layer. Diversity of ammonia oxidizers and bacteria was lower in the control than in the compost soils. The type of compost had less influence on the composition of the microbial communities than did soil depth.", "keywords": ["PCR-DGGE", "2. Zero hunger", "Microbial activity", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Composts", "Hydrolase activities", "04 agricultural and veterinary sciences", "15. Life on land", "Bacterial communities", "6. Clean water", "Ammonia oxidizers", "12. Responsible consumption"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2006.05.017"}, {"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.2006.05.017", "name": "item", "description": "10.1016/j.soilbio.2006.05.017", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2006.05.017"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2006-12-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2018.05.016", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:17:29Z", "type": "Journal Article", "created": "2018-05-19", "title": "Experimentally testing the species-habitat size relationship on soil bacteria: A proof of concept", "description": "Abstract   The species-area relationship is one of the most widely reported ecological theories accounting for biodiversity of plants and animals. However, we lack solid experimental data demonstrating whether this key ecological theorem also applies in the microbial world. Here, we conducted a microcosm study to evaluate the role of habitat area in driving the diversity, abundance, composition and functioning (i.e., four enzyme activities linked to organic matter decomposition) of soil bacterial communities. Thus, we aim to evaluate whether the principle of species-area relationship is potentially applicable to soil microbes. We established a fully factorial experimental design of three island sizes (\u223c9, 50 and 150\u202fcm2) by two sterile soils (low, high resources). After six months of glasshouse incubation, habitat-area was positively related to bacterial richness, relative abundance of Chloroflexi, Verrucomicrobia and \u03b4-proteobacteria, and soil functions in both soils. Soil with higher resources always had the greatest bacterial richness and functions. Our findings provide a proof of concept by demonstrating the potential importance of both habitat-area and resource availability in driving soil bacterial biodiversity and functioning.", "keywords": ["2. Zero hunger", "habitat (ecology)", "XXXXXX - Unknown", "Bacterial diversity; Decomposition; Ecological theory; Miseq Illumina; Extracellular enzyme activities; quantitative PCR.", "soil biodiversity", "15. Life on land", "biodegradation", "soil microbiology"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2018.05.016"}, {"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.2018.05.016", "name": "item", "description": "10.1016/j.soilbio.2018.05.016", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2018.05.016"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-08-01T00:00:00Z"}}, {"id": "10.1016/j.still.2005.08.001", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:17:34Z", "type": "Journal Article", "created": "2005-09-09", "title": "Soil Aggregation And Bacterial Community Structure As Affected By Tillage And Cover Cropping In The Brazilian Cerrados", "description": "<p>Microbial-based indicators of soil quality are believed to be more dynamic than those based on physical and chemical properties. Recent developments in molecular biology based techniques have led to rapid and reliable tools to characterize microbial community structures. We determined the effects of conventional and no-tillage in cropping systems with and without cover crops on bacterial community structure, total organic carbon (TOC) and soil aggregation. Tillage and rotation did not affect TOC from bulk soil. However, TOC was greater in the largest aggregate size class (7.98-19 mm), and had greater mean-weight diameter under no-tillage than under conventional tillage in the 0-5 cm soil layer. Soil bacterial community structure, based on denaturing gradient gel electrophoresis of polymerase chain reaction amplified DNA (PCR/DGGE) using two different genes as biomarkers, 16S rRNA and rpoB genes, indicated different populations in response to cultivation, tillage and depth, but not due to cover cropping. Soil bacterial community structure and meanweight diameter of soil aggregates indicated alterations in soil conditions due to tillage system. (c) 2005 Elsevier B.V. All rights reserved.</p>", "keywords": ["2. Zero hunger", "GENES", "Cerrados", "16S RIBOSOMAL-RNA", "no-tillage", "04 agricultural and veterinary sciences", "15. Life on land", "DGGE profiling", "SUSTAINABILITY", "PCR", "16S rDNA", "GRADIENT GEL-ELECTROPHORESIS", "MANAGEMENT", "0401 agriculture", " forestry", " and fisheries", "NO-TILLAGE", "HETEROGENEITY", "DGGE", "soil structure", "rpoB", "MICROBIAL DIVERSITY"]}, "links": [{"href": "https://doi.org/10.1016/j.still.2005.08.001"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20and%20Tillage%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.still.2005.08.001", "name": "item", "description": "10.1016/j.still.2005.08.001", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.still.2005.08.001"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2006-11-01T00:00:00Z"}}, {"id": "10.1080/01490451.2014.908981", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:18:53Z", "type": "Journal Article", "created": "2015-08-19", "title": "Response Of Soil Denitrifying Communities To Long-Term Prescribed Burning In Two Australian Sclerophyll Forests", "description": "Low-intensity prescribed burning is a common forest management tool and plays a major role in modifying biogeochemical cycling through the alteration of substrate availability and microbial communities. In this study, we assessed the response of microbial community to repeated prescribed burning in two sclerophyll forests (the Bauple site, dry, annual rainfall 1000\u00a0mm; and the Peachester site, wet, 1711\u00a0mm) in southeast Queensland, Australia. At the dry sclerophyll forest (the Bauple site), annual and triennial burning did not significantly alter the soil carbon (C) and nitrogen (N) content, while at the wet scleophyll forest (the Peachester site), two yearly burnings resulted in significantly lower soil total C and N contents compared to the long unburnt treatment. In spite of these different responses, prescribed burning regimes did not significantly influence the abundance of 16S rRNA or denitrifying gene (<i>nar</i>G, <i>nir</i>K, <i>nir</i>S, <i>nos</i>Z) at both sites. These results indicated that, long-term prescribed burning has little effect on the denitrifying communities, while it has varying effects on soil chemical properties at the two sites, which are likely to be explained by differences in vegetation type and soil moisture regime.", "keywords": ["580", "550", "FoR 0403 (Geology)", "denitrifying community", "Geology", "04 agricultural and veterinary sciences", "15. Life on land", "long-term repeated burning", "Microbiology", "3. Good health", "FoR 0605 (Microbiology)", "qPCR", "Soil biology", "13. Climate action", "sclerophyll forest", "0401 agriculture", " forestry", " and fisheries", "soil moisture"]}, "links": [{"href": "https://doi.org/10.1080/01490451.2014.908981"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Geomicrobiology%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1080/01490451.2014.908981", "name": "item", "description": "10.1080/01490451.2014.908981", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1080/01490451.2014.908981"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-08-09T00:00:00Z"}}, {"id": "10.1093/jambio/lxac048", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:19:05Z", "type": "Journal Article", "created": "2023-03-17", "title": "Two species-specific TaqMan-based quantitative polymerase chain reaction assays for the detection in soil ofPaenibacillus polymyxainocula", "description": "AbstractAims<p>The increasingly widespread use of beneficial microbial inocula in agriculture gives rise to two primary needs: i) the assessment of the environmental risk, i.e. their impact on local soil microbiome and soil properties; ii) being able to track them and monitor their persistence and fate to both optimize their formulation and application method. In previous years, PCR-based methods have detected bacterial or fungal bioinoculant at the species or strain level. However, the selective detection, quantification, and monitoring of target microbial species in a complex ecosystem such as soil require that the tests possess high specificity and sensitivity.</p>Methods and results<p>The work proposes a quantitative real-time PCR detection method using TaqMan chemistry, showing high specificity and sensitivity for the Paenibacillus polymyxa K16 strain. The primer and probe sets were designed using the polymyxin gene cluster targeting pmxC and pmxE sequences. Validation tests showed that these assays allowed a discriminant and specific detection of P. polymyxa K16 in soil.</p>Conclusion<p>The TaqMan-assay developed could thus ensure the necessary level of discrimination required by commercial and regulatory purposes to detect and monitor the bioinoculant in soil.</p", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "TaqMan probes", "molecular markers", "Bioinoculant", "bioinoculant", "polymyxin gene", "Real-Time Polymerase Chain Reaction", "Sensitivity and Specificity", "6. Clean water", "03 medical and health sciences", "qPCR", "Soil", "TaqMan Probe", "PGPR", "RNA", "Paenibacillus polymyxa", "Paenibacillus", "Ecosystem", "DNA Primers"]}, "links": [{"href": "https://iris.cnr.it/bitstream/20.500.14243/453423/1/FPinzari_Two%20species-specific%20TaqMan-based%20quantitative%20assays_453423_2023.pdf"}, {"href": "https://doi.org/10.1093/jambio/lxac048"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Applied%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/jambio/lxac048", "name": "item", "description": "10.1093/jambio/lxac048", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/jambio/lxac048"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-12-15T00:00:00Z"}}, {"id": "10.3168/jds.2010-3281", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:21:31Z", "type": "Journal Article", "created": "2010-11-21", "title": "Nitrate And Sulfate: Effective Alternative Hydrogen Sinks For Mitigation Of Ruminal Methane Production In Sheep", "description": "Twenty male crossbred Texel lambs were used in a 2 \u00d7 2 factorial design experiment to assess the effect of dietary addition of nitrate (2.6% of dry matter) and sulfate (2.6% of dry matter) on enteric methane emissions, rumen volatile fatty acid concentrations, rumen microbial composition, and the occurrence of methemoglobinemia. Lambs were gradually introduced to nitrate and sulfate in a corn silage-based diet over a period of 4 wk, and methane production was subsequently determined in respiration chambers. Diets were given at 95% of the lowest ad libitum intake observed within one block in the week before methane yield was measured to ensure equal feed intake of animals between treatments. All diets were formulated to be isonitrogenous. Methane production decreased with both supplements (nitrate: -32%, sulfate: -16%, and nitrate+sulfate: -47% relative to control). The decrease in methane production due to nitrate feeding was most pronounced in the period immediately after feeding, whereas the decrease in methane yield due to sulfate feeding was observed during the entire day. Methane-suppressing effects of nitrate and sulfate were independent and additive. The highest methemoglobin value observed in the blood of the nitrate-fed animals was 7% of hemoglobin. When nitrate was fed in combination with sulfate, methemoglobin remained below the detection limit of 2% of hemoglobin. Dietary nitrate decreased heat production (-7%), whereas supplementation with sulfate increased heat production (+3%). Feeding nitrate or sulfate had no effects on volatile fatty acid concentrations in rumen fluid samples taken 24h after feeding, except for the molar proportion of branched-chain volatile fatty acids, which was higher when sulfate was fed and lower when nitrate was fed, but not different when both products were included in the diet. The total number of rumen bacteria increased as a result of sulfate inclusion in the diet. The number of methanogens was reduced when nitrate was fed. Enhanced levels of sulfate in the diet increased the number of sulfate-reducing bacteria. The number of protozoa was not affected by nitrate or sulfate addition. Supplementation of a diet with nitrate and sulfate is an effective means for mitigating enteric methane emissions from sheep.", "keywords": ["Male", "Rumen", "reduction", "in-vitro", "nitrogen", "Random Allocation", "fumaric-acid", "Animals", "Intestinal Mucosa", "real-time pcr", "2. Zero hunger", "rumen", "Nitrates", "Sheep", "Sulfates", "emissions", "0402 animal and dairy science", "methanogenesis", "04 agricultural and veterinary sciences", "Hydrogen-Ion Concentration", "Fatty Acids", " Volatile", "Diet", "Agricultural Land Management", "cattle", "Dietary Supplements", "Fermentation", "Animal Nutritional Physiological Phenomena", "feed-intake", "Methemoglobinemia", "Methane"]}, "links": [{"href": "https://doi.org/10.3168/jds.2010-3281"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Dairy%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3168/jds.2010-3281", "name": "item", "description": "10.3168/jds.2010-3281", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3168/jds.2010-3281"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-12-01T00:00:00Z"}}, {"id": "10.1111/j.1574-6941.2007.00394.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:19:44Z", "type": "Journal Article", "created": "2007-10-19", "title": "Quantitation And Diversity Analysis Of Ruminal Methanogenic Populations In Response To The Antimethanogenic Compound Bromochloromethane", "description": "Methyl coenzyme-M reductase A (mcrA) clone libraries were generated from microbial DNA extracted from the rumen of cattle fed a roughage diet with and without supplementation of the antimethanogenic compound bromochloromethane. Bromochloromethane reduced total methane emissions by c. 30%, with a resultant increase in propionate and branched chain fatty acids. The mcrA clone libraries revealed that Methanobrevibacter spp. were the dominant species identified. A decrease in the incidence of Methanobrevibacter spp. from the clone library generated from bromochloromethane treatment was observed. In addition, a more diverse methanogenic population with representatives from Methanococcales, Methanomicrobiales and Methanosacinales orders was observed for the bromochloromethane library. Sequence data generated from these libraries aided in the design of an mcrA-targeted quantitative PCR (qPCR) assay. The reduction in methane production by bromochloromethane was associated with an average decrease of 34% in the number of methanogenic Archaea when monitored with this qPCR assay. Dissociation curve analysis of mcrA amplicons showed a clear difference in melting temperatures for Methanobrevibacter spp. (80-82 degrees C) and all other methanongens (84-86 degrees C). A decrease in the intensity of the Methanobrevibacter spp. specific peak and an increase for the other peak in the bromochloromethane-treated animals corresponded with the changes within the clone libraries.", "keywords": ["Male", "0301 basic medicine", "Rumen", "Bromochloromethane", "Methanogens", "Molecular Sequence Data", "Euryarchaeota", "Methanobrevibacter", "Polymerase Chain Reaction", "630", "03 medical and health sciences", "2402 Applied Microbiology and Biotechnology", "Animals", "Methyl coenzyme-M reductase", "Phylogeny", "Gene Library", "2. Zero hunger", "0303 health sciences", "Hydrocarbons", " Halogenated", "2404 Microbiology", "Sequence Analysis", " DNA", "mcrA", "qPCR", "DNA", " Archaeal", "Cattle", "Oxidoreductases", "2303 Ecology", "Methane"]}, "links": [{"href": "https://doi.org/10.1111/j.1574-6941.2007.00394.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1574-6941.2007.00394.x", "name": "item", "description": "10.1111/j.1574-6941.2007.00394.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1574-6941.2007.00394.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-12-01T00:00:00Z"}}, {"id": "10.1128/aem.00033-11", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:19:54Z", "type": "Journal Article", "created": "2011-04-23", "title": "Association Of Earthworm-Denitrifier Interactions With Increased Emission Of Nitrous Oxide From Soil Mesocosms Amended With Crop Residue", "description": "ABSTRACT           <p>             Earthworm activity is known to increase emissions of nitrous oxide (N             2             O) from arable soils. Earthworm gut, casts, and burrows have exhibited higher denitrification activities than the bulk soil, implicating priming of denitrifying organisms as a possible mechanism for this effect. Furthermore, the earthworm feeding strategy may drive N             2             O emissions, as it determines access to fresh organic matter for denitrification. Here, we determined whether interactions between earthworm feeding strategy and the soil denitrifier community can predict N             2             O emissions from the soil. We set up a 90-day mesocosm experiment in which             15             N-labeled maize (             Zea mays             L.) was either mixed in or applied on top of the soil in the presence or absence of the epigeic earthworm             Lumbricus rubellus             and/or the endogeic earthworm             Aporrectodea caliginosa             . We measured N             2             O fluxes and tested the bulk soil for denitrification enzyme activity and the abundance of 16S rRNA and denitrifier genes             nirS             and             nosZ             through real-time quantitative PCR. Compared to the control,             L. rubellus             increased denitrification enzyme activity and N             2             O emissions on days 21 and 90 (day 21,             P             = 0.034 and             P             = 0.002, respectively; day 90,             P             = 0.001 and             P             = 0.007, respectively), as well as cumulative N             2             O emissions (76%;             P             = 0.014).             A. caliginosa             activity led to a transient increase of N             2             O emissions on days 8 to 18 of the experiment. Abundance of             nosZ             was significantly increased (100%) on day 90 in the treatment mixture containing             L. rubellus             alone. We conclude that             L. rubellus             increased cumulative N             2             O emissions by affecting denitrifier community activity via incorporation of fresh residue into the soil and supplying a steady, labile carbon source.           </p>", "keywords": ["2. Zero hunger", "agricultural soil", "Bacteria", "nosz genes", "carbon", "Nitrous Oxide", "n2o emission", "n2o-producing microorganisms", "04 agricultural and veterinary sciences", "15. Life on land", "pcr data", "microbial activity", "Animal Feed", "Zea mays", "lumbricus-rubellus", "Soil", "Denitrification", "Animals", "0401 agriculture", " forestry", " and fisheries", "community composition", "Oligochaeta", "organic-matter"]}, "links": [{"href": "https://doi.org/10.1128/aem.00033-11"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/aem.00033-11", "name": "item", "description": "10.1128/aem.00033-11", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.00033-11"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-06-15T00:00:00Z"}}, {"id": "10.3389/fmicb.2018.01176", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:21:36Z", "type": "Journal Article", "created": "2018-06-08", "title": "Enhanced Bacterial Fitness Under Residual Fluoroquinolone Concentrations Is Associated With Increased Gene Expression in Wastewater-Derived qnr Plasmid-Harboring Strains", "description": "Plasmids harboring qnr genes confer resistance to low fluoroquinolone concentrations. These genes are of significant clinical, evolutionary and environmental importance, since they are widely distributed in a diverse array of natural and clinical environments. We previously extracted and sequenced a large (\u223c185 Kbp) qnrB-harboring plasmid, and several small (\u223c8 Kbp) qnrS-harboring plasmids, from Klebsiella pneumoniae isolates from municipal wastewater biosolids, and hypothesized that these plasmids provide host bacteria a selective advantage in wastewater treatment plants (WWTPs) that often contain residual concentrations of fluoroquinolones. The objectives of this study were therefore to determine the effect of residual fluoroquinolone concentrations on the growth kinetics of qnr plasmid-harboring bacteria; and on the copy number of qnr plasmids and expression of qnr genes. Electrotransformants harboring either one of the two types of plasmids could grow at ciprofloxacin concentrations exceeding 0.5 \u03bcg ml-1, but growth was significantly decreased at concentrations higher than 0.1 \u03bcg ml-1. In contrast, plasmid-free strains failed to grow even at 0.05 \u03bcg ml-1. No differences were observed in plasmid copy number under the tested ciprofloxacin concentrations, but qnr expression increased incrementally from 0 to 0.4 \u03bcg ml-1, suggesting that the transcription of this gene is regulated by antibiotic concentration. This study reveals that wastewater-derived qnr plasmids confer a selective advantage in the presence of residual fluoroquinolone concentrations and provides a mechanistic explanation for this phenomenon.", "keywords": ["0301 basic medicine", "0303 health sciences", "qnr genes", "Microbiology", "QR1-502", "6. Clean water", "fitness", "3. Good health", "wastewater treatment", "03 medical and health sciences", "qPCR expression analysis", "plasmid", "11. Sustainability", "qnr genes", " wastewater treatment", " plasmid", " qPCR expression analysis", " fitness"], "contacts": [{"organization": "Roberto B. M. Marano, Roberto B. M. Marano, Edouard Jurkevitch, Eddie Cytryn, Ella Kaplan, Ella Kaplan,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2018.01176"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fmicb.2018.01176", "name": "item", "description": "10.3389/fmicb.2018.01176", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2018.01176"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-06-08T00:00:00Z"}}, {"id": "10.3390/agronomy12020450", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:21:44Z", "type": "Journal Article", "created": "2022-02-14", "title": "The Analysis of Partial Sequences of the Flavonone 3 Hydroxylase Gene in Lupinus mutabilis Reveals Differential Expression of Two Paralogues Potentially Related to Seed Coat Colour", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Flavonone 3 hydroxylases (EC 1.14.11.9) are key enzymes in the synthesis of anthocyanins and other flavonoids. Such compounds are involved in seed coat colour and stem pigmentation. Lupinus mutabilis (tarwi) is a legume crop domesticated in the Andean region, valued for the high protein and oil content of its seeds. Tarwi accessions are being selected for cultivation in Europe under defined breeding criteria. Seed coat colour patterns are relevant breeding traits in tarwi, and these are conditioned by anthocyanin content. We identified and isolated part of the tarwi flavonone 3-hydroxylase gene (LmF3h) from two accessions with distinct seed coat colour patterns. Two partial LmF3h paralogues, with predicted 20% amino-acid changes but little predicted tertiary structure alterations, were identified in the coloured seed genotype, while only one was present in the white seed genotype. Upon selection and validation of appropriate reference genes, a RT-qPCR analysis showed that these paralogues have different levels of expression during seed development in both genotypes, although they follow the same expression patterns. DNA and transcription analyses enabled to highlight potential F3H paralogues relatable to seed coat pigmentation in tarwi and, upon biochemical and genetic confirmation, prompt marker-assisted breeding for relevant phenotypic traits associated with flavonoid synthesis.</p></article>", "keywords": ["0301 basic medicine", "2. Zero hunger", "<i>F3H</i>", "0303 health sciences", "S", "Agriculture", "<i>Lupinus mutabilis</i>", "03 medical and health sciences", "F3H", "seed coat", "gene expression", "Lupinus mutabilis", "<i>Lupinus mutabilis</i>; <i>F3H</i>; seed coat; gene expression; RT-qPCR reference genes", "RT-qPCR reference genes"]}, "links": [{"href": "http://www.mdpi.com/2073-4395/12/2/450/pdf"}, {"href": "https://doi.org/10.3390/agronomy12020450"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/agronomy12020450", "name": "item", "description": "10.3390/agronomy12020450", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/agronomy12020450"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-02-11T00:00:00Z"}}, {"id": "10400.14/37827", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:26:00Z", "type": "Journal Article", "created": "2022-05-10", "title": "Short-Term Responses of Soil Microbial Communities to Changes in Air Temperature, Soil Moisture and UV Radiation", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>We analyzed the effects on a soil microbial community of short-term alterations in air temperature, soil moisture and ultraviolet radiation and assessed the role of invertebrates (species Enchytraeus crypticus) in modulating the community\u2019s response to these factors. The reference soil, Lufa 2.2, was incubated for 48 h, with and without invertebrates, under the following conditions: standard (20 \u00b0C + 50% water holding capacity (WHC)); increased air temperature (15\u201325 \u00b0C or 20\u201330 \u00b0C + 50% WHC); flood (20 \u00b0C + 75% WHC); drought (20 \u00b0C + 25% WHC); and ultraviolet radiation (UV) (20 \u00b0C + 50% WHC + UV). BIOLOG EcoPlates and 16S rDNA sequencing (Illumina) were used to assess the microbial community\u2019s physiological profile and the bacterial community\u2019s structure, respectively. The bacterial abundance (estimated by 16S rDNA qPCR) did not change. Most of the conditions led to an increase in microbial activity and a decrease in diversity. The structure of the bacterial community was particularly affected by higher air temperatures (20\u201330 \u00b0C, without E. crypticus) and floods (with E. crypticus). Effects were observed at the class, genera and OTU levels. The presence of invertebrates mostly resulted in the attenuation of the observed effects, highlighting the importance of considering microbiome\u2013invertebrate interactions. Considering future climate changes, the effects described here raise concern. This study provides fundamental knowledge to develop effective strategies to mitigate these negative outcomes. However, long-term studies integrating biotic and abiotic factors are needed.</p></article>", "keywords": ["0301 basic medicine", "Soil invertebrates", "Ultraviolet Rays", "drought", "microbial activity", "DNA", " Ribosomal", "Flood", "Article", "Quantitative PCR", "Soil", "03 medical and health sciences", "soil microbiome", "2. Zero hunger", "metagenomics", "increased temperature; drought; flood; UV exposure; microbial activity; bacterial diversity; metagenomics; quantitative PCR; soil microbiome; soil invertebrates", "Soil microbiome", "0303 health sciences", "Drought", "Bacteria", "Microbiota", "bacterial diversity", "Temperature", "Water", "flood", "15. Life on land", "soil invertebrates", "6. Clean water", "UV exposure", "Microbial activity", "Bacterial diversity", "13. Climate action", "quantitative PCR", "Metagenomics", "Increased temperature", "increased temperature"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/13/5/850/pdf"}, {"href": "https://doi.org/10400.14/37827"}, {"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": "10400.14/37827", "name": "item", "description": "10400.14/37827", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10400.14/37827"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-05-10T00:00:00Z"}}, {"id": "10.3390/microorganisms12051002", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:21:54Z", "type": "Journal Article", "created": "2024-05-16", "title": "Real-Time PCR (qtPCR) to Discover the Fate of Plant Growth-Promoting Rhizobacteria (PGPR) in Agricultural Soils", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>To optimize the application of plant growth-promoting rhizobacteria (PGPR) in field trials, tracking methods are needed to assess their shelf life and to determine the elements affecting their effectiveness and their interactions with plants and native soil microbiota. This work developed a real-time PCR (qtPCR) method which traces and quantifies bacteria when added as microbial consortia, including five PGPR species: Burkholderia ambifaria, Bacillus amyloliquefaciens, Azotobacter chroococcum, Pseudomonas fluorescens, and Rahnella aquatilis. Through a literature search and in silico sequence analyses, a set of primer pairs which selectively tag three bacterial species (B. ambifaria, B. amyloliquefaciens and R. aquatilis) was retrieved. The primers were used to trace these microbial species in a field trial in which the consortium was tested as a biostimulant on two wheat varieties, in combination with biochar and the mycorrhizal fungus Rhizophagus intraradices. The qtPCR assay demonstrated that the targeted bacteria had colonized and grown into the soil, reaching a maximum of growth between 15 and 20 days after inoculum. The results also showed biochar had a positive effect on PGPR growth. In conclusion, qtPCR was once more an effective method to trace the fate of supplied bacterial species in the consortium when used as a cargo system for their delivery.</p></article>", "keywords": ["sustainable agriculture", "0301 basic medicine", "2. Zero hunger", "biostimulants", "0303 health sciences", "03 medical and health sciences", "microbial consortia (MC)", "real-time PCR (qtPCR)", "traceability", "QH301-705.5", "Biology (General)", "plant growth-promoting rhizobacteria (PGPR)", "Article"]}, "links": [{"href": "https://www.mdpi.com/2076-2607/12/5/1002/pdf"}, {"href": "https://doi.org/10.3390/microorganisms12051002"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/microorganisms12051002", "name": "item", "description": "10.3390/microorganisms12051002", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/microorganisms12051002"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-05-16T00:00:00Z"}}, {"id": "10.34894/MIRO5P", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:22:07Z", "type": "Dataset", "title": "Replication Data for: Priming of soil organic matter: chemical structure of added compounds is more important than the energy content", "description": "In March 2014 soil (0-10cm) was collected in Dennenkamp (the Netherlands), a former arable site that has developed into a natural grassland. In the laboratory, fresh soil was sieved (4 mm), homogenized and stored at 4 \u00baC until further use. We report the following data: - CO2 evolution after addition of 13C labelled substrates (glucose, cellobiose and vanillic acid) to the soil. - Abundance of microbial groups (fungi and/or bacteria) that used labeled and non-labeled carbon, measured as increase in 16S rRNA gene copy numbers and 18SrDNA copy numbers, for bacteria and fungi respectively, per g of soil. - Biomass yield (for fungi and bacteria separately) for three substrates (glucose, cellobiose and vanillic acid), used that as a proxy for microbial usable energy", "keywords": ["2. Zero hunger", "Earth and Environmental Science", "qPCR data", "Earth and Environmental Sciences", "Verwerkte data", "Processed data", "15. Life on land", "Environmental Research", "Natural Sciences", "CO2 data", "Geosciences"], "contacts": [{"organization": "Di Lonardo, D.P.", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.34894/MIRO5P"}, {"rel": "self", "type": "application/geo+json", "title": "10.34894/MIRO5P", "name": "item", "description": "10.34894/MIRO5P", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.34894/MIRO5P"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-01-01T00:00:00Z"}}, {"id": "10.5061/dryad.79cnp5htw", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:22:25Z", "type": "Dataset", "title": "Data from: A tipping-point in carbon storage when forest expands into tundra is related to mycorrhizal recycling of nitrogen", "description": "unspecifiedTundra ecosystems are global belowground sinks for atmospheric CO2.  Ongoing warming-induced encroachment by shrubs and trees risks turning  this sink into a CO2 source, resulting in a positive feedback on climate  warming. To advance mechanistic understanding of how shifts in mycorrhizal  types affect long-term carbon (C) and nitrogen (N) stocks, we studied  small-scale soil depth profiles of fungal communities and C-N dynamics  across a subarctic-alpine forest-heath vegetation gradient. Belowground  organic stocks decreased abruptly at the transition from heath to forest,  linked to the presence of certain tree-associateds ectomycorrhizal fungi  that contribute to decomposition when mining N from organic matter. In  contrast, ericoid mycorrhizal plants and fungi were associated with  organic matter accumulation and slow decomposition. If climatic controls  on arctic-alpine forest lines are relaxed, increased decomposition will  likely outbalance increased plant productivity, decreasing the overall C  sink capacity of displaced tundra.", "keywords": ["C-N dynamics", "ectomycorrhizal exploration type", "functional genes", "ergosterol", "ITS2 meta-barcoding", "Fungal community", "Arctic greening", "Climate feedback", "15. Life on land", "litter saprotrophs", "mycorrhizal type", "litter bags", "13. Climate action", "soil solution", "FOS: Biological sciences", "soil carbon storage", "quantitative PCR", "soil profiles", "Ectomycorrhizal fungal community", "Ericoid Mycorrhiza", "treeline ecotone"], "contacts": [{"organization": "Clemmensen, Karina E, Durling, Mikael B, Michelsen, Anders, Hallin, Sara, Finlay, Roger D, Lindahl, Bj\u00f6rn D,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.79cnp5htw"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.79cnp5htw", "name": "item", "description": "10.5061/dryad.79cnp5htw", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.79cnp5htw"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-02-28T00:00:00Z"}}, {"id": "20.500.14243/453423", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:26:49Z", "type": "Journal Article", "created": "2023-03-17", "title": "Two species-specific TaqMan-based quantitative polymerase chain reaction assays for the detection in soil ofPaenibacillus polymyxainocula", "description": "AbstractAims<p>The increasingly widespread use of beneficial microbial inocula in agriculture gives rise to two primary needs: i) the assessment of the environmental risk, i.e. their impact on local soil microbiome and soil properties; ii) being able to track them and monitor their persistence and fate to both optimize their formulation and application method. In previous years, PCR-based methods have detected bacterial or fungal bioinoculant at the species or strain level. However, the selective detection, quantification, and monitoring of target microbial species in a complex ecosystem such as soil require that the tests possess high specificity and sensitivity.</p>Methods and results<p>The work proposes a quantitative real-time PCR detection method using TaqMan chemistry, showing high specificity and sensitivity for the Paenibacillus polymyxa K16 strain. The primer and probe sets were designed using the polymyxin gene cluster targeting pmxC and pmxE sequences. Validation tests showed that these assays allowed a discriminant and specific detection of P. polymyxa K16 in soil.</p>Conclusion<p>The TaqMan-assay developed could thus ensure the necessary level of discrimination required by commercial and regulatory purposes to detect and monitor the bioinoculant in soil.</p", "keywords": ["2. Zero hunger", "TaqMan probes", "molecular markers", "bioinoculant", "polymyxin gene", "Real-Time Polymerase Chain Reaction", "Sensitivity and Specificity", "6. Clean water", "qPCR", "Soil", "PGPR", "RNA", "Paenibacillus polymyxa", "Paenibacillus", "Ecosystem", "DNA Primers"]}, "links": [{"href": "https://iris.cnr.it/bitstream/20.500.14243/453423/1/FPinzari_Two%20species-specific%20TaqMan-based%20quantitative%20assays_453423_2023.pdf"}, {"href": "https://academic.oup.com/jambio/article-pdf/134/1/lxac048/49094737/lxac048.pdf"}, {"href": "https://doi.org/20.500.14243/453423"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Applied%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "20.500.14243/453423", "name": "item", "description": "20.500.14243/453423", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/20.500.14243/453423"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-12-15T00:00:00Z"}}, {"id": "66f7069c84c2db39a5d7deacb4eb3076", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:28:48Z", "type": "Report", "title": "Estudio sobre el valor predictivo de la duraci\u00f3n de los s\u00edntomas, datos anal\u00edticos y las pruebas de imagen en el desarrollo de apendicitis complicada", "description": "Open AccessLa apendicitis aguda es una enfermedad con importante prevalencia en nuestro entorno que, en ocasiones, se puede complicar antes de su tratamiento definitivo. Esto es debido a que no siempre se manifiesta de la misma manera, existiendo gran variabilidad cl\u00ednica y escasos datos anal\u00edticos que apoyen el diagn\u00f3stico. Por eso, es importante la estratificaci\u00f3n de pacientes potencialmente graves de manera precoz para optimizar su manejo quir\u00fargico. Analizar la influencia de estas variables cl\u00ednicas, anal\u00edticas y radiol\u00f3gicas es de vital importancia para identificar y tratar de manera precoz a los pacientes que desarrollan apendicitis complicada. Se ha llevado a cabo un estudio anal\u00edtico retrospectivo de casos y controles realizado sobre las historias cl\u00ednicas de pacientes intervenidos por apendicitis aguda en el Hospital Cl\u00ednico Universitario de Valladolid en los \u00faltimos dos a\u00f1os comparando los resultados aportados por las pruebas preoperatorias con los informes de anatom\u00eda patol\u00f3gica. En el resultado se han encontrado diferencias estad\u00edsticamente significativas a la hora de comparar el grupo anatomopatol\u00f3gico de las apendicitis complicadas con algunas variables como son la edad, los tiempos quir\u00fargicos y valores anal\u00edticos (PCR).", "keywords": ["Apendicitis - Cirug\u00eda", "Diagnostico", "Apendicitis complicada", "PCR", "Grado anatomopatol\u00f3gico", "Tiempo quir\u00fargico"], "contacts": [{"organization": "Abril Garrido, Gonzalo", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/66f7069c84c2db39a5d7deacb4eb3076"}, {"rel": "self", "type": "application/geo+json", "title": "66f7069c84c2db39a5d7deacb4eb3076", "name": "item", "description": "66f7069c84c2db39a5d7deacb4eb3076", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/66f7069c84c2db39a5d7deacb4eb3076"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-01T00:00:00Z"}}, {"id": "7f2a5656-d850-4081-9fc5-474263e2631d", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[6.29, 47.59], [6.29, 54.33], [14.51, 54.33], [14.51, 47.59], [6.29, 47.59]]]}, "properties": {"license": "CC BY", "rights": "Restrictions applied to assure the protection of privacy or intellectual property, and any special restrictions or limitations or warnings on using the resource or metadata. Reports, articles, papers, scientific and non - scientific works of any form, including tables, maps, or any other kind of output, in printed or electronic form, based in whole or in part on the data supplied, must contain an acknowledgement of the form: \"Data reused from the BonaRes Data Centre www.bonares.de. This data were created as part of the BonaRes Module A-Project - BonaRes - ORDIAmur's research activities.\" Although every care has been taken in preparing and testing the data, the BonaRes Module A-Project - BonaRes - ORDIAmur and the BonaRes Data Centre cannot guarantee that the data are correct; neither does the BonaRes Module A-Project - BonaRes - ORDIAmur and the BonaRes Data Centre accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The BonaRes Module A-Project - BonaRes - ORDIAmur and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data.", "updated": "2026-01-30", "type": "Service", "created": "2026-01-27", "language": "eng", "title": "Web Map Service of the  ORDIAmur Central Experiment 12", "description": "This Web Map Service includes spatial information used by datasets from the ORDIAmur Central Experiment 12", "keywords": ["infoMapAccessService", "Soil", "replanting", "PCR", "replanting", "genetic techniques", "roots", "leaves", "Germany"], "contacts": [{"name": "Leibniz Centre for Agricultural Landscape Research", "organization": "ZALF", "position": "Computation and Data Service Platform - Workgroup Research Data Management", "roles": ["publisher"], "phones": [{"value": "+49 33432 82 300"}], "emails": [{"value": "dataservice@zalf.de"}], "addresses": [{"deliveryPoint": ["Eberswalder Strasse 84"], "city": "M\u00fcncheberg", "administrativeArea": "Brandenburg", "postalCode": "15374", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Luisa Baader", "organization": "Julius K\u00fchn-Institut, Insitut f\u00fcr Z\u00fcchtungsforschung an Obst", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "luisa.baader@julius-kuehn.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": null}]}, {"name": "Susan Schr\u00f6pfer", "organization": "Julius K\u00fchn-Institut, Insitut f\u00fcr Z\u00fcchtungsforschung an Obst", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "susan.schroepfer@julius-kuehn.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": null}]}, {"name": "Stefanie Reim", "organization": "Julius K\u00fchn-Institut, Insitut f\u00fcr Z\u00fcchtungsforschung an Obst", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "stefanie.reim@julius-kuehn.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": null}]}, {"name": "Nils Orth", "organization": "Leibniz Universit\u00e4t Hannover", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "orth@baum.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0009-0006-1026-9881", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Jiem Kr\u00fcger", "organization": "Leibniz Universit\u00e4t Hannover", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "krueger@ifbk.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0003-4148-0461", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Georg Guggenberger", "organization": "Leibniz Universit\u00e4t Hannover", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "guggenberger@ifbk.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0002-6962-8264", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Jens Boy", "organization": "Leibniz Universit\u00e4t Hannover", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "boy@ifbk.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0002-2751-957X", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Jecqueline Kaldun", "organization": "Universit\u00e4t Bayreuth", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "jacqueline.kaldun@uni-bayreuth.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": null}]}, {"name": "Eva Lehndorff", "organization": "Universit\u00e4t Bayreuth", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "eva.lehndorff@uni-bayreuth"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": null}]}, {"name": "Nele Meyer", "organization": "Goethe Universit\u00e4t Frankfurt", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "nele.meyer@em.uni-frankfurt.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": null}]}, {"name": "Kristin Hauschild", "organization": "Julius K\u00fchn-Institut, Insitut f\u00fcr Epidemiologie und Pathogendiagnostik", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "kristin.hauschild@julius-kuehn.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": null}]}, {"name": "Henryk Flachowsky", "organization": "Julius K\u00fchn-Institut, Insitut f\u00fcr Z\u00fcchtungsforschung an Obst", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "henryk.flachowsky@julius-kuehn.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": null}]}, {"name": "Traud Winkelmann", "organization": "Leibniz Universit\u00e4t Hannover", "position": null, "roles": ["projectLeader"], "phones": [{"value": null}], "emails": [{"value": "traud.winkelmann@zier.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0002-2509-1418", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"organization": "Julius K\u00fchn-Institut, Insitut f\u00fcr Z\u00fcchtungsforschung an Obst;Leibniz Universit\u00e4t Hannover;Goethe Universit\u00e4t Frankfurt;Julius K\u00fchn-Institut, Insitut f\u00fcr Epidemiologie und Pathogendiagnostik;Universit\u00e4t Bayreuth", "roles": ["contributor"]}], "themes": [{"concepts": [{"id": "infoMapAccessService"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}, {"concepts": [{"id": "Soil"}, {"id": "replanting"}, {"id": "PCR"}, {"id": "replanting"}, {"id": "genetic techniques"}, {"id": "roots"}, {"id": "leaves"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}, {"concepts": [], "scheme": "free keywords"}, {"concepts": [{"id": "Germany"}], "scheme": "individual"}]}, "links": [{"href": "https://maps.bonares.de/mapapps/resources/apps/bonares/index.html?lang=en&mid=7f2a5656-d850-4081-9fc5-474263e2631d", "rel": "information"}, {"href": "https://maps.bonares.de/wss/service/ags-relay/ags/guest/arcgis/rest/services/Ordiamur/ID_6075_Central_Experiment_12/MapServer/WMSServer?request=GetCapabilities&service=WMS"}, {"rel": "self", "type": "application/geo+json", "title": "7f2a5656-d850-4081-9fc5-474263e2631d", "name": "item", "description": "7f2a5656-d850-4081-9fc5-474263e2631d", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/7f2a5656-d850-4081-9fc5-474263e2631d"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2026-01-30T00:00:00Z"}}, {"id": "e512d7a4-fe58-4d6e-8b2b-31c607174a7f", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[8.93, 51.85], [8.93, 54.38], [10.75, 54.38], [10.75, 51.85], [8.93, 51.85]]]}, "properties": {"themes": [{"concepts": [{"id": "farming"}], "scheme": "https://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_TopicCategoryCode"}, {"concepts": [{"id": "Soil"}, {"id": "replanting"}, {"id": "planting"}, {"id": "PCR"}, {"id": "genetic techniques"}, {"id": "roots"}, {"id": "plant vegetative organs"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}, {"concepts": [{"id": "opendata"}], "scheme": "Individual"}, {"concepts": [{"id": "Boden"}, {"id": "Apfelnachbaukrankheit"}, {"id": "Bodenm\u00fcdigkeit"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}, {"concepts": [{"id": "Boden"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}], "license": "CC BY", "rights": "Restrictions applied to assure the protection of privacy or intellectual property, and any special restrictions or limitations or warnings on using the resource or metadata. Reports, articles, papers, scientific and non - scientific works of any form, including tables, maps, or any other kind of output, in printed or electronic form, based in whole or in part on the data supplied, must contain an acknowledgement of the form: \"Data reused from the BonaRes Data Centre www.bonares.de. This data were created as part of the BonaRes Module A-Project - ORDIAmur's research activities.\"\n\nAlthough every care has been taken in preparing and testing the data, the BonaRes Module A-Project - ORDIAmur and  the BonaRes Data Centre cannot guarantee that the data are correct; neither does the BonaRes Module A-Project - ORDIAmur and the BonaRes Data Centre accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The BonaRes Module A-Project - ORDIAmur and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data.", "updated": "2020-09-11", "type": "Dataset", "created": "2020-07-13", "language": "eng", "title": "ARD Biomarkers: qPCR data", "description": "This dataset contains raw data of RT-qPCR runs from two experiments, which aimed at the identification and characterization of candidate genes for ARD biomarkers in roots of the ARD sensitive apple rootstock M26. The experiments underlying this study are presented in DOI 10.1371/journal.pone.0238876. This dataset is a continuation of DOI 10.20387/bonares-kvak-frbf. \n\nIn the first experiment, plants of M26 were grown in a biotest, including untreated and disinfected ARD soil from the three ORDIAmur reference sites Ellerhoop, Heidgraben and Ruthe. Plant shoot length was recorded over a course of eight weeks. After 0, 1, 3 and 7 days, root samples for gene expression analysis were taken. The expression of the previously identified candidate genes 1-aminocyclopropane-1-carboxylate oxidase homolog 1-like (ACO1), ethylene-responsive transcription factor RAP2-11-like (ERF RAP2.11), ethylene-responsive transcription factor 1B-like (ERF1B), gibberellin-regulated protein 1-like (GASA1), zinc finger domain-containing protein 10-like (GATAD10), biphenyl synthase 3 (BIS3) and biphenyl 4-hydroxylase (B4Hb) was investigated. As reference genes elongation factor 1-alpha (EF1a), elongation factor 1-beta 2-like (EF1b) and tubulin beta chain (TUBB) were selected after their expression stability was tested. The genes biphenyl synthase 3 (BIS3), biphenyl 4-hydroxylase (B4Hb) and ethylene-responsive transcription factor 1B (ERF1B) showed a strong and uniform regulation amongst the three soils tested and were identified as candidates for further testing in experiment 2. \n\nIn experiment 2, the expression of BIS3, B4Hb and ERF1B was investigated in M26 in response to the stressors heat, high salinity and nutrient starvation, which were applied in peat substrate (heat salt) or quartz sand (nutrient starvation). Furthermore, grass soil from Heidgraben with no previous apple culture was tested. ARD soil from Heidgraben and peat substrate served as controls. Gene expression was investigated in the roots after 0, 7 and 14 days and phytoalexin contents were analyzed after 14 days. The second experiment revealed a response of ERF1B to heat stress. All three genes responded to grass soil but to a lesser extent than to ARD soil after two weeks.\n\nResearch domain: Plant Breeding\n\nResearch question: This study aimed at the identification and characterization biomarkers for apple replant disease (ARD). The first experiment aimed at narrowing down a set of previously identified set of candidate genes by studying their expression in apple roots in a biotest with soil from three ARD sites. These genes were further characterized in the second experiment by studying their expression in response to common unspecific stressors. The identified candidates may serve to improve our understanding of the disease and upon further characterization aid in the breeding of ARD tolerant apple rootstocks.", "formats": [{"name": "CSV"}], "keywords": ["Soil", "replanting", "planting", "PCR", "genetic techniques", "roots", "plant vegetative organs", "opendata", "Boden", "Apfelnachbaukrankheit", "Bodenm\u00fcdigkeit", "Boden"], "contacts": [{"name": "Annmarie-Deetja Rohr", "organization": "Leibniz Universit\u00e4t Hannover", "position": null, "roles": ["author"], "phones": [{"value": "0049 511 762 4017"}], "emails": [{"value": "rohr@baum.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": "Hannover", "administrativeArea": null, "postalCode": "30419", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Traud Winkelmann", "organization": "Leibniz Universit\u00e4t Hannover", "position": "Professorin", "roles": ["projectLeader"], "phones": [{"value": "0049 511 762 3602"}], "emails": [{"value": "traud.winkelmann@zier.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": "Hannover", "administrativeArea": "ORDIAmur", "postalCode": "30419", "country": "Germany"}], "links": [{"href": null}]}, {"name": "BonaRes Data Centre", "organization": "Leibniz Centre for Agricultural Landscape Research (ZALF)", "position": "Research Platform 'Data Analysis & Simulation' - WG Geodata", "roles": ["publisher"], "phones": [{"value": "+49 33432 82 171"}], "emails": [{"value": "bonares-datenzentrum@zalf.de"}], "addresses": [{"deliveryPoint": ["Eberswalder Strasse 84"], "city": "M\u00fcncheberg", "administrativeArea": "Brandenburg", "postalCode": "15374", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Benye Liu", "organization": "Institute of Pharmaceutical Biology", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "b.liu@tu-braunschweig.de"}], "addresses": [{"deliveryPoint": ["Mendelssohnstrasse 1"], "city": "Braunschweig", "administrativeArea": null, "postalCode": "38106", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Ludger Beerhues", "organization": "Institute of Pharmaceutical Biology", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "l.beerhues@tu-braunschweig.de"}], "addresses": [{"deliveryPoint": ["Mendelssohnstrasse 1"], "city": "Braunschweig", "administrativeArea": null, "postalCode": "38106", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Jessical Schimmel", "organization": "Leibniz Universit\u00e4t Hannover", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "schimmel@ifbk.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": "Hannover", "administrativeArea": "ORDIAmur", "postalCode": "30419", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Georg Guggenberger", "organization": "Leibniz Universit\u00e4t Hannover", "position": "Professor", "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "guggenberger@ifbk.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": "Hannover", "administrativeArea": "ORDIAmur", "postalCode": "30419", "country": "Germany"}], "links": [{"href": null}]}, {"organization": "Institute of Pharmaceutical Biology;Leibniz Universit\u00e4t Hannover", "roles": ["contributor"]}]}, "links": [{"href": "https://maps.bonares.de/mapapps/resources/apps/bonares/index.html?lang=en&mid=e512d7a4-fe58-4d6e-8b2b-31c607174a7f", "rel": "download"}, {"rel": "self", "type": "application/geo+json", "title": "e512d7a4-fe58-4d6e-8b2b-31c607174a7f", "name": "item", "description": "e512d7a4-fe58-4d6e-8b2b-31c607174a7f", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/e512d7a4-fe58-4d6e-8b2b-31c607174a7f"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-09-11T00:00:00Z"}}, {"id": "26f8e218-ae63-43a5-b566-b968bd7a2137", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[9.68, 53.7], [9.68, 53.7], [9.68, 53.7], [9.68, 53.7], [9.68, 53.7]]]}, "properties": {"themes": [{"concepts": [{"id": "farming"}], "scheme": "https://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_TopicCategoryCode"}, {"concepts": [{"id": "Soil"}, {"id": "qPCR"}, {"id": "Streptomyces"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}, {"concepts": [{"id": "opendata"}, {"id": "apple replant disease"}, {"id": "M.26"}, {"id": "EMR.2"}, {"id": "G.935"}, {"id": "Illumina-MiSeq"}], "scheme": "Individual"}, {"concepts": [{"id": "Boden"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}, {"concepts": [{"id": "Europe"}, {"id": "Germany"}, {"id": "Schleswig-Holstein"}], "scheme": "individual"}], "license": "CC BY", "rights": "Restrictions applied to assure the protection of privacy or intellectual property, and any special restrictions or limitations or warnings on using the resource or metadata. Reports, articles, papers, scientific and non - scientific works of any form, including tables, maps, or any other kind of output, in printed or electronic form, based in whole or in part on the data supplied, must contain an acknowledgement of the form: \"Data reused from the BonaRes Data Centre www.bonares.de. This data were created as part of the BonaRes Module A-Project - BonaRes - ORDIAmur's research activities.\" Although every care has been taken in preparing and testing the data, the BonaRes Module A-Project - BonaRes - ORDIAmur and the BonaRes Data Centre cannot guarantee that the data are correct; neither does the BonaRes Module A-Project - BonaRes - ORDIAmur and the BonaRes Data Centre accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The BonaRes Module A-Project - BonaRes - ORDIAmur and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data.", "updated": "2026-01-15", "type": "Dataset", "created": "2025-12-02", "language": "eng", "title": "ORDIAmur Central Experiment 10 - Rhizosphere Bacteria Reads", "description": "Illumina-MiSeq sequencing was performed using the primer pair 515F/806R to amplify a bacterial fragment of the 16S rRNA gene (V4 region). The sequences were bioinformatically processed, annotated and reads were rarefied to 14,401 reads. The raw sequences are available at NCBI.\n\nGeneral description see mother table: (https://doi.org/10.20387/bonares-r5cg-rx85); Related datasets are listed in the metadata element 'Related Identifier'.\nDataset version 1.0", "formats": [{"name": "CSV"}], "keywords": ["Soil", "qPCR", "Streptomyces", "opendata", "apple replant disease", "M.26", "EMR.2", "G.935", "Illumina-MiSeq", "Boden", "Europe", "Germany", "Schleswig-Holstein"], "contacts": [{"name": "Leibniz Centre for Agricultural Landscape Research", "organization": "ZALF", "position": "Computation and Data Service Platform - Workgroup Research Data Management", "roles": ["publisher"], "phones": [{"value": "+49 33432 82 300"}], "emails": [{"value": "dataservice@zalf.de"}], "addresses": [{"deliveryPoint": ["Eberswalder Strasse 84"], "city": "M\u00fcncheberg", "administrativeArea": "Brandenburg", "postalCode": "15374", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Nils Orth", "organization": "Leibniz University Hannover", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "orth@baum.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0009-0006-1026-9881", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Kristin Hauschild", "organization": "Julius K\u00fchn Institute", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "kristin.hauschild@ufz.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0001-5261-9583", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Silvia Gschwendtner", "organization": "Helmholtz Munich", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "silvia.gschwendtner@helmholtz-munich.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0002-6379-3728", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Fatma M. Mahmoud", "organization": "Helmholtz Munich", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "fatma.mahmoud@helmholtz-muenchen.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0002-2997-4242", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Sarah Benning", "organization": "Helmholtz Munich", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "sarahmabenning@gmail.com"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0009-0002-2025-9645", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Traud Winkelmann", "organization": "Leibniz University Hannover", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "winkelmann@zier.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0002-2509-1418", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Traud Winkelmann", "organization": "Leibniz University Hannover", "position": null, "roles": ["projectLeader"], "phones": [{"value": null}], "emails": [{"value": "winkelmann@zier.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0002-2509-1418", "name_url": "", "description": "0000-0002-2509-1418", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"organization": "Julius K\u00fchn Institute;Helmholtz Munich;Leibniz University Hannover", "roles": ["contributor"]}], "title_alternate": "Data collection: Part 2/4, table: Rhizosphere Bacteria Reads"}, "links": [{"href": "https://maps.bonares.de/mapapps/resources/apps/bonares/index.html?lang=en&mid=26f8e218-ae63-43a5-b566-b968bd7a2137", "rel": "information"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/8bcd5787-19b2-4fa2-8af7-45a7c8c5533f", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "26f8e218-ae63-43a5-b566-b968bd7a2137", "name": "item", "description": "26f8e218-ae63-43a5-b566-b968bd7a2137", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/26f8e218-ae63-43a5-b566-b968bd7a2137"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2026-01-15T00:00:00Z"}}, {"id": "PMC11124357", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:30:19Z", "type": "Journal Article", "created": "2024-05-16", "title": "Real-Time PCR (qtPCR) to Discover the Fate of Plant Growth-Promoting Rhizobacteria (PGPR) in Agricultural Soils", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>To optimize the application of plant growth-promoting rhizobacteria (PGPR) in field trials, tracking methods are needed to assess their shelf life and to determine the elements affecting their effectiveness and their interactions with plants and native soil microbiota. This work developed a real-time PCR (qtPCR) method which traces and quantifies bacteria when added as microbial consortia, including five PGPR species: Burkholderia ambifaria, Bacillus amyloliquefaciens, Azotobacter chroococcum, Pseudomonas fluorescens, and Rahnella aquatilis. Through a literature search and in silico sequence analyses, a set of primer pairs which selectively tag three bacterial species (B. ambifaria, B. amyloliquefaciens and R. aquatilis) was retrieved. The primers were used to trace these microbial species in a field trial in which the consortium was tested as a biostimulant on two wheat varieties, in combination with biochar and the mycorrhizal fungus Rhizophagus intraradices. The qtPCR assay demonstrated that the targeted bacteria had colonized and grown into the soil, reaching a maximum of growth between 15 and 20 days after inoculum. The results also showed biochar had a positive effect on PGPR growth. In conclusion, qtPCR was once more an effective method to trace the fate of supplied bacterial species in the consortium when used as a cargo system for their delivery.</p></article>", "keywords": ["sustainable agriculture", "0301 basic medicine", "2. Zero hunger", "biostimulants", "0303 health sciences", "03 medical and health sciences", "microbial consortia (MC)", "real-time PCR (qtPCR)", "traceability", "QH301-705.5", "Biology (General)", "plant growth-promoting rhizobacteria (PGPR)", "Article"]}, "links": [{"href": "https://www.mdpi.com/2076-2607/12/5/1002/pdf"}, {"href": "https://doi.org/PMC11124357"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC11124357", "name": "item", "description": "PMC11124357", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC11124357"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-05-16T00:00:00Z"}}, {"id": "869bffc1-c0c0-408e-adc9-2d1d863b1415", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[8.93, 51.85], [8.93, 54.38], [10.75, 54.38], [10.75, 51.85], [8.93, 51.85]]]}, "properties": {"themes": [{"concepts": [{"id": "farming"}], "scheme": "https://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_TopicCategoryCode"}, {"concepts": [{"id": "Soil"}, {"id": "replanting"}, {"id": "planting"}, {"id": "PCR"}, {"id": "genetic techniques"}, {"id": "roots"}, {"id": "plant vegetative organs"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}, {"concepts": [{"id": "opendata"}], "scheme": "Individual"}, {"concepts": [{"id": "Boden"}, {"id": "Apfelnachbaukrankheit"}, {"id": "Bodenm\u00fcdigkeit"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}, {"concepts": [{"id": "Boden"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}], "license": "CC BY", "rights": "Restrictions applied to assure the protection of privacy or intellectual property, and any special restrictions or limitations or warnings on using the resource or metadata. Reports, articles, papers, scientific and non - scientific works of any form, including tables, maps, or any other kind of output, in printed or electronic form, based in whole or in part on the data supplied, must contain an acknowledgement of the form: \"Data reused from the BonaRes Data Centre www.bonares.de. This data were created as part of the BonaRes Module A-Project - ORDIAmur's research activities.\"\n\nAlthough every care has been taken in preparing and testing the data, the BonaRes Module A-Project - ORDIAmur and  the BonaRes Data Centre cannot guarantee that the data are correct; neither does the BonaRes Module A-Project - ORDIAmur and the BonaRes Data Centre accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The BonaRes Module A-Project - ORDIAmur and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data.", "updated": "2020-09-11", "type": "Dataset", "created": "2020-07-09", "language": "eng", "title": "ARD Biomarkers", "description": "This dataset includes data from two experiments, which aimed at the identification and characterization of candidate genes for ARD biomarkers in roots of the ARD sensitive apple rootstock M26. It is a supplement to the research article DOI 10.1371/journal.pone.0238876. \n\nIn the first experiment, plants of M26 were grown in a biotest, including untreated and disinfected ARD soil from the three ORDIAmur reference sites Ellerhoop, Heidgraben and Ruthe. Plant shoot length was recorded over a course of eight weeks. After 0, 1, 3 and 7 days, root samples for gene expression analysis were taken. Further root samples for phytoalexin analysis were taken after 3, 7, 10 and 56 days. After 8 weeks, shoot and root fresh and dry masses were determined from the remaining plants to assess ARD severity in the soils. The genes biphenyl synthase 3 (BIS3), biphenyl 4-hydroxylase (B4Hb) and ethylene-responsive transcription factor 1B (ERF1B) were identified for further testing. \n\nIn experiment 2, the expression of BIS3, B4Hb and ERF1B was investigated in M26 in response to the stressors heat, high salinity and nutrient starvation, which were applied in peat substrate (heat, salt) or quartz sand (nutrient starvation). Furthermore, grass soil from Heidgraben with no previous apple culture was tested. ARD soil from Heidgraben and peat substrate served as controls. Gene expression was investigated in the roots after 7 and 14 days and phytoalexin contents were analyzed after 14 days. Shoot lengths were recorded weekly and after 8 weeks and fresh and dry masses of shots and roots were taken. A nutrient analysis was conducted with the shoot material to investigate the effects of the nutrient starvation. The second experiment revealed a response of ERF1B to heat stress. All three genes responded to grass soil but to a lesser extent than to ARD soil after two weeks.\n\nResearch domain: Plant Breeding\n\nResearch question: This study aimed at the identification and characterization biomarkers for apple replant disease (ARD). The first experiment aimed at narrowing down a set of previously identified set of candidate genes by studying their expression in apple roots in a biotest with soil from three ARD sites. These genes were further characterized in the second experiment by studying their expression in response to common unspecific stressors. The identified candidates may serve to improve our understanding of the disease and upon further characterization aid in the breeding of ARD tolerant apple rootstocks.", "formats": [{"name": "CSV"}], "keywords": ["Soil", "replanting", "planting", "PCR", "genetic techniques", "roots", "plant vegetative organs", "opendata", "Boden", "Apfelnachbaukrankheit", "Bodenm\u00fcdigkeit", "Boden"], "contacts": [{"name": "Annmarie-Deetja Rohr", "organization": "Leibniz Universit\u00e4t Hannover", "position": null, "roles": ["author"], "phones": [{"value": "0049 511 762 4017"}], "emails": [{"value": "rohr@baum.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": "Hannover", "administrativeArea": null, "postalCode": "30419", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Traud Winkelmann", "organization": "Leibniz Universit\u00e4t Hannover", "position": "Professorin", "roles": ["projectLeader"], "phones": [{"value": "0049 511 762 3602"}], "emails": [{"value": "traud.winkelmann@zier.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": "Hannover", "administrativeArea": "ORDIAmur", "postalCode": "30419", "country": "Germany"}], "links": [{"href": null}]}, {"name": "BonaRes Data Centre", "organization": "Leibniz Centre for Agricultural Landscape Research (ZALF)", "position": "Research Platform 'Data Analysis & Simulation' - WG Geodata", "roles": ["publisher"], "phones": [{"value": "+49 33432 82 171"}], "emails": [{"value": "bonares-datenzentrum@zalf.de"}], "addresses": [{"deliveryPoint": ["Eberswalder Strasse 84"], "city": "M\u00fcncheberg", "administrativeArea": "Brandenburg", "postalCode": "15374", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Benye Liu", "organization": "Institute of Pharmaceutical Biology", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "b.liu@tu-braunschweig.de"}], "addresses": [{"deliveryPoint": ["Mendelssohnstrasse 1"], "city": "Braunschweig", "administrativeArea": null, "postalCode": "38106", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Ludger Beerhues", "organization": "Institute of Pharmaceutical Biology", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "l.beerhues@tu-braunschweig.de"}], "addresses": [{"deliveryPoint": ["Mendelssohnstrasse 1"], "city": "Braunschweig", "administrativeArea": null, "postalCode": "38106", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Jessical Schimmel", "organization": "Leibniz Universit\u00e4t Hannover", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "schimmel@ifbk.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": "Hannover", "administrativeArea": "ORDIAmur", "postalCode": "30419", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Georg Guggenberger", "organization": "Leibniz Universit\u00e4t Hannover", "position": "Professor", "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "guggenberger@ifbk.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": "Hannover", "administrativeArea": "ORDIAmur", "postalCode": "30419", "country": "Germany"}], "links": [{"href": null}]}, {"organization": "Institute of Pharmaceutical Biology;Leibniz Universit\u00e4t Hannover", "roles": ["contributor"]}], "title_alternate": "apple replant disease (ARD): Biomarkers"}, "links": [{"href": "https://maps.bonares.de/mapapps/resources/apps/bonares/index.html?lang=en&mid=869bffc1-c0c0-408e-adc9-2d1d863b1415", "rel": "download"}, {"rel": "self", "type": "application/geo+json", "title": "869bffc1-c0c0-408e-adc9-2d1d863b1415", "name": "item", "description": "869bffc1-c0c0-408e-adc9-2d1d863b1415", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/869bffc1-c0c0-408e-adc9-2d1d863b1415"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-09-11T00:00:00Z"}}, {"id": "cc59dbb4-6f59-4709-a3b4-72e7dff1935e", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[8.93, 51.85], [8.93, 54.38], [10.75, 54.38], [10.75, 51.85], [8.93, 51.85]]]}, "properties": {"license": "CC BY", "rights": "Restrictions applied to assure the protection of privacy or intellectual property, and any special restrictions or limitations or warnings on using the resource or metadata. Reports, articles, papers, scientific and non - scientific works of any form, including tables, maps, or any other kind of output, in printed or electronic form, based in whole or in part on the data supplied, must contain an acknowledgement of the form: \"Data reused from the BonaRes Data Centre www.bonares.de. This data were created as part of the BonaRes Module A-Project - ORDIAmur's research activities.\" Although every care has been taken in preparing and testing the data, the BonaRes Module A-Project - ORDIAmur and the BonaRes Data Centre cannot guarantee that the data are correct; neither does the BonaRes Module A-Project - ORDIAmur and the BonaRes Data Centre accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The BonaRes Module A-Project - ORDIAmur and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data.", "updated": "2021-03-16", "type": "Service", "created": "2020-07-09", "language": "eng", "title": "WMS Service of the dataset 'ARD Biomarkers'", "description": "This WMS Service includes spatial information used by datasets 'WMS Service of the dataset 'ARD Biomarkers'''", "keywords": ["infoMapAccessService", "Soil", "replanting", "planting", "PCR", "genetic techniques", "roots", "plant vegetative organs"], "contacts": [{"name": "Annmarie-Deetja Rohr", "organization": "Leibniz Universit\u00e4t Hannover", "position": null, "roles": ["author"], "phones": [{"value": "0049 511 762 4017"}], "emails": [{"value": "rohr@baum.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": "Hannover", "administrativeArea": null, "postalCode": "30419", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Traud Winkelmann", "organization": "Leibniz Universit\u00e4t Hannover", "position": "Professorin", "roles": ["projectLeader"], "phones": [{"value": "0049 511 762 3602"}], "emails": [{"value": "traud.winkelmann@zier.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": "Hannover", "administrativeArea": "ORDIAmur", "postalCode": "30419", "country": "Germany"}], "links": [{"href": null}]}, {"name": "BonaRes Data Centre", "organization": "Leibniz Centre for Agricultural Landscape Research (ZALF)", "position": "Research Platform 'Data Analysis & Simulation' - 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Reports, articles, papers, scientific and non - scientific works of any form, including tables, maps, or any other kind of output, in printed or electronic form, based in whole or in part on the data supplied, must contain an acknowledgement of the form: \"Data reused from the BonaRes Data Centre www.bonares.de. This data were created as part of the BonaRes Module A-Project - BonaRes - ORDIAmur's research activities.\" Although every care has been taken in preparing and testing the data, the BonaRes Module A-Project - BonaRes - ORDIAmur and the BonaRes Data Centre cannot guarantee that the data are correct; neither does the BonaRes Module A-Project - BonaRes - ORDIAmur and the BonaRes Data Centre accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The BonaRes Module A-Project - BonaRes - ORDIAmur and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data.", "updated": "2026-01-09", "type": "Service", "created": "2025-12-02", "language": "eng", "title": "Web Map Service of the dataset 'ORDIAmur Central Experiment 10 '", "description": "This Web Map Service includes spatial information used by datasets 'ORDIAmur Central Experiment 10'", "keywords": ["infoMapAccessService", "Soil", "qPCR", "Streptomyces"], "contacts": [{"name": "Leibniz Centre for Agricultural Landscape Research", "organization": "ZALF", "position": "Computation and Data Service Platform - Workgroup Research Data Management", "roles": ["publisher"], "phones": [{"value": "+49 33432 82 300"}], "emails": [{"value": "dataservice@zalf.de"}], "addresses": [{"deliveryPoint": ["Eberswalder Strasse 84"], "city": "M\u00fcncheberg", "administrativeArea": "Brandenburg", "postalCode": "15374", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Nils Orth", "organization": "Leibniz University Hannover", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "orth@baum.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0009-0006-1026-9881", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Kristin Hauschild", "organization": "Julius K\u00fchn Institute", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "kristin.hauschild@ufz.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0001-5261-9583", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Silvia Gschwendtner", "organization": "Helmholtz Munich", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "silvia.gschwendtner@helmholtz-munich.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0002-6379-3728", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Fatma M. Mahmoud", "organization": "Helmholtz Munich", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "fatma.mahmoud@helmholtz-muenchen.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0002-2997-4242", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Sarah Benning", "organization": "Helmholtz Munich", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "sarahmabenning@gmail.com"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0009-0002-2025-9645", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Traud Winkelmann", "organization": "Leibniz University Hannover", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "winkelmann@zier.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0002-2509-1418", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Traud Winkelmann", "organization": "Leibniz University Hannover", "position": null, "roles": ["projectLeader"], "phones": [{"value": null}], "emails": [{"value": "winkelmann@zier.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0002-2509-1418", "name_url": "", "description": "0000-0002-2509-1418", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"organization": "Julius K\u00fchn Institute;Helmholtz Munich;Leibniz University Hannover", "roles": ["contributor"]}], "themes": [{"concepts": [{"id": "infoMapAccessService"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}, {"concepts": [{"id": "Soil"}, {"id": "qPCR"}, {"id": "Streptomyces"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}, {"concepts": [], "scheme": "individual"}]}, "links": [{"href": "https://maps.bonares.de/mapapps/resources/apps/bonares/index.html?lang=en&mid=d5a4ef96-cd8e-4fed-bfa6-457e85f1ff19", "rel": "information"}, {"href": "https://maps.bonares.de/wss/service/ags-relay/ags/guest/arcgis/rest/services/Ordiamur/Ordimur_ID_6074/MapServer/WMSServer?request=GetCapabilities&service=WMS"}, {"rel": "self", "type": "application/geo+json", "title": "d5a4ef96-cd8e-4fed-bfa6-457e85f1ff19", "name": "item", "description": "d5a4ef96-cd8e-4fed-bfa6-457e85f1ff19", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/d5a4ef96-cd8e-4fed-bfa6-457e85f1ff19"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2026-01-09T00:00:00Z"}}, {"id": "d5a54fad-8856-4726-9919-685a8f0c5c58", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[6.72, 50.79], [6.72, 52.62], [9.99, 52.62], [9.99, 50.79], [6.72, 50.79]]]}, "properties": {"themes": [{"concepts": [{"id": "farming"}], "scheme": "https://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_TopicCategoryCode"}, {"concepts": [{"id": "Soil"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}, {"concepts": [{"id": "opendata"}], "scheme": "Individual"}, {"concepts": [{"id": "Boden"}, {"id": "Soil"}, {"id": "Apple replant disease (ARD)"}, {"id": "Gene Expression"}, {"id": "BioMark HD microfluidic system"}, {"id": "high-throughput qRT-PCR"}, {"id": "phytoalexins"}, {"id": "Greenhouse bio-test"}, {"id": "soil properties"}, {"id": "Malus genotypes"}, {"id": "rootstock"}, {"id": "biomarker"}, {"id": "central experiment 5"}, {"id": "CE5"}, {"id": "ORDIAmur"}, {"id": "M26"}, {"id": "M9"}, {"id": "Malus x robusta"}, {"id": "B63"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}, {"concepts": [{"id": "Boden"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}], "rights": "Reports, articles, papers, scientific and non-scientific works of any form, including tables, maps, or any other kind of output, in printed or electronic form, based in whole or in part on the data supplied, must contain an acknowledgement of the form: \"Data re-used from the BonaRes Data Centre (www.bonares.de). This data were created as part of BonaRes Module A-Project - ORDIAmur's research activities. Although every care has been taken in preparing and testing the data, BonaRes Module A-Project - ORDIAmur and BonaRes Data Centre cannot guarantee that the data are correct; neither does BonaRes Module A-Project - ORDIAmur and BonaRes Data Centre accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The BonaRes Module A-Project - ORDIAmur and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data. The access to this data is restricted during embargo time. If prior access is requested, contact the data owner / author.", "updated": "2020-04-30", "type": "Dataset", "created": "2020-01-07", "language": "eng", "title": "Apple Replant Disease Greenhouse Bio-Test Plant Growth", "description": "Apple replant disease (ARD) is a soil-borne disease, which is of particular importance for fruit tree nurseries and fruit growers. The disease manifests by a poor vegetative development, stunted growth and reduced yield in terms of quantity and quality, if apple plants (usually rootstocks) are replanted several times at the same site. Genotype-specific differences in the reaction of apple plants to ARD are documented, but less is known about the genetic mechanisms behind this symptomatology. Recent transcriptome analyses resulted in a number of candidate genes possibly involved in the plant response. In the present study, the expression of 108 selected candidate genes was investigated in root and leaf tissue of four different apple genotypes grown in untreated ARD soil and ARD soil disinfected by \u03b3-irradiation originating from two different sites in Germany. Thirty-nine out of the 108 candidate genes were differentially expressed in roots by taking a p-value of  0.05 and a fold change of  1.5 as cutoff. Sixteen genes were more than 4.5-fold upregulated in roots of plants grown in ARD soil. The four genes MNL2 (putative mannosidase), ALF5 (multi antimicrobial extrusion protein), UGT73B4 (UDP-glycosyltransferase 73B4) and ECHI (chitin-binding) were significantly upregulated in roots. These genes seem to be related to the host plant response to ARD, although they have never been described in this context before. Six of the highly upregulated genes belong to the phytoalexin biosynthesis pathway. Their genotype-specific gene expression pattern was consistent with the phytoalexin content measured in roots. The biphenyl synthase (BIS) genes were found to be useful as early biomarkers for ARD, because their expression pattern correlated well with the phenotypic reaction of the Malus genotypes investigated.\n\nThe presented data contain growth records from the greenhouse biotest of the Malus genotypes M26, M9, B63 and Malus x robusta MAL0595 potted into untreated of disinfected soil from the ARD sites Heidgraben and Meckenheim. Shoot length was recorded weekly and after four weeks, fresh and dry masses of the shoots and roots were measured. Single plants were pooled for gene expression and phytoalexin analysis. The use and pooling of each individual plant can be traced back within the dataset. \n\nThe experiment is summarized in Reim et al. (2020): \u201cGenes involved in stress response and especially in phytoalexin biosynthesis are up-regulated in four Malus genotypes in response to apple replant disease\u201d, Front. Plant Sci., doi: 10.3389/fpls.2019.01724.\n\nGene expression data is available at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135081.", "formats": [{"name": "CSV"}], "keywords": ["Soil", "opendata", "Boden", "Soil", "Apple replant disease (ARD)", "Gene Expression", "BioMark HD microfluidic system", "high-throughput qRT-PCR", "phytoalexins", "Greenhouse bio-test", "soil properties", "Malus genotypes", "rootstock", "biomarker", "central experiment 5", "CE5", "ORDIAmur", "M26", "M9", "Malus x robusta", "B63", "Boden"], "contacts": [{"name": "Stefanie Reim", "organization": "Julius K\u00fchn-Institut, Insitut f\u00fcr Z\u00fcchtungsforschung an Obst", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "stefanie.reim@julius-kuehn.de"}], "addresses": [{"deliveryPoint": [null], "city": "Dresden", "administrativeArea": "ORDIAmur", "postalCode": "01326", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Annmarie-Deetja Rohr", "organization": "Leibniz Universit\u00e4t Hannover", "position": null, "roles": ["author"], "phones": [{"value": "0049 511 762 4017"}], "emails": [{"value": "rohr@baum.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": "Hannover", "administrativeArea": null, "postalCode": "30419", "country": "Germany"}], "links": [{"href": null}]}, {"name": "BonaRes Data Centre", "organization": "Leibniz Centre for Agricultural Landscape Research (ZALF)", "position": "Research Platform 'Data' - WG Geodata", "roles": ["publisher"], "phones": [{"value": "+49 33432 82 171"}], "emails": [{"value": "bonares-datenzentrum@zalf.de"}], "addresses": [{"deliveryPoint": ["Eberswalder Strasse 84"], "city": "M\u00fcncheberg", "administrativeArea": "Brandenburg", "postalCode": "15374", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Traud Winkelmann", "organization": "Leibniz Universit\u00e4t Hannover", "position": "Professorin", "roles": ["projectLeader"], "phones": [{"value": "0049 511 762 3602"}], "emails": [{"value": "traud.winkelmann@zier.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": "Hannover", "administrativeArea": "ORDIAmur", "postalCode": "30419", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Stefan Wei\u00df", "organization": "Leibniz Universit\u00e4t Hannover", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "weiss@baum.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": "Hannover", "administrativeArea": "ORDIAmur", "postalCode": "30419", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Benye Liu", "organization": "Institute of Pharmaceutical Biology", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "b.liu@tu-braunschweig.de"}], "addresses": [{"deliveryPoint": ["Mendelssohnstrasse 1"], "city": "Braunschweig", "administrativeArea": null, "postalCode": "38106", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Ludger Beerhues", "organization": "Institute of Pharmaceutical Biology", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "l.beerhues@tu-braunschweig.de"}], "addresses": [{"deliveryPoint": ["Mendelssohnstrasse 1"], "city": "Braunschweig", "administrativeArea": null, "postalCode": "38106", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Michaela Schmitz", "organization": "Hochschule Bonn-Rhein-Sieg", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "Michaela.Schmitz@h-brs.de"}], "addresses": [{"deliveryPoint": [null], "city": "Rheinbach", "administrativeArea": null, "postalCode": null, "country": "Germany"}], "links": [{"href": null}]}, {"name": "Magda-Viola Hanke", "organization": "Julius K\u00fchn-Institut, Insitut f\u00fcr Z\u00fcchtungsforschung an Obst", "position": "Institutsleiterin", "roles": ["author"], "phones": [{"value": "+49 351 2616214"}], "emails": [{"value": "magda-viola.hanke@julius-kuehn.de"}], "addresses": [{"deliveryPoint": [null], "city": "Dresden", "administrativeArea": "ORDIAmur", "postalCode": "013260", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Henryk Flachowsky", "organization": "Julius K\u00fchn-Institut, Insitut f\u00fcr Z\u00fcchtungsforschung an Obst", "position": "Wissenschaftlicher Oberrat", "roles": ["author"], "phones": [{"value": "+49 351 2616215"}], "emails": [{"value": "henryk.flachowsky@julius-kuehn.de"}], "addresses": [{"deliveryPoint": [null], "city": "Dresden", "administrativeArea": "ORDIAmur", "postalCode": "01326", "country": "Germany"}], "links": [{"href": null}]}, {"organization": "Julius K\u00fchn-Institut, Insitut f\u00fcr Z\u00fcchtungsforschung an Obst;Institute of Pharmaceutical Biology;Leibniz Universit\u00e4t Hannover;Hochschule Bonn-Rhein-Sieg", "roles": ["contributor"]}], "title_alternate": "ARD Greenhouse Bio-Test Plant Growth"}, "links": [{"href": "https://maps.bonares.de/mapapps/resources/apps/bonares/index.html?lang=en&mid=d5a54fad-8856-4726-9919-685a8f0c5c58", "rel": "download"}, {"rel": "self", "type": "application/geo+json", "title": "d5a54fad-8856-4726-9919-685a8f0c5c58", "name": "item", "description": "d5a54fad-8856-4726-9919-685a8f0c5c58", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/d5a54fad-8856-4726-9919-685a8f0c5c58"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"interval": ["2017-08-09T00:00:00Z", "2017-09-07T00:00:00Z"]}}, {"id": "4c60e19f-0162-4f20-9a0f-d68bfbf867fe", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[6.29, 47.59], [6.29, 54.33], [14.51, 54.33], [14.51, 47.59], [6.29, 47.59]]]}, "properties": {"themes": [{"concepts": [{"id": "farming"}], "scheme": "https://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_TopicCategoryCode"}, {"concepts": [{"id": "Soil"}, {"id": "replanting"}, {"id": "PCR"}, {"id": "replanting"}, {"id": "genetic techniques"}, {"id": "roots"}, {"id": "leaves"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}, {"concepts": [{"id": "opendata"}], "scheme": "Individual"}, {"concepts": [{"id": "Boden"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}], "license": "CC BY", "rights": "Restrictions applied to assure the protection of privacy or intellectual property, and any special restrictions or limitations or warnings on using the resource or metadata. Reports, articles, papers, scientific and non - scientific works of any form, including tables, maps, or any other kind of output, in printed or electronic form, based in whole or in part on the data supplied, must contain an acknowledgement of the form: \"Data reused from the BonaRes Data Centre www.bonares.de. This data were created as part of the BonaRes Module A-Project - BonaRes - ORDIAmur's research activities.\" Although every care has been taken in preparing and testing the data, the BonaRes Module A-Project - BonaRes - ORDIAmur and the BonaRes Data Centre cannot guarantee that the data are correct; neither does the BonaRes Module A-Project - BonaRes - ORDIAmur and the BonaRes Data Centre accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The BonaRes Module A-Project - BonaRes - ORDIAmur and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data.", "updated": "2026-01-30", "type": "Dataset", "created": "2026-01-27", "language": "eng", "title": "ORDIAmur Central Experiment 12 \u2013 gene expression data", "description": "Young M.26 apple plants were grown in the greenhouse for 6 weeks in Apple Replant Disease (ARD) affected soils from 151 different locations in Germany. Samples of each soil that were disinfected through gamma-irradiation served as ARD-unaffected controls. The expression of 90 candidate genes and 4 reference genes (ACT7, EF1a, EF1b, TUBB) was analyzed by RT-qPCR in the roots of plants grown in 151 different soils and the leaves of plants grown in 18 different soils.", "formats": [{"name": "CSV"}], "keywords": ["Soil", "replanting", "PCR", "replanting", "genetic techniques", "roots", "leaves", "opendata", "Boden"], "contacts": [{"name": "Leibniz Centre for Agricultural Landscape Research", "organization": "ZALF", "position": "Computation and Data Service Platform - Workgroup Research Data Management", "roles": ["publisher"], "phones": [{"value": "+49 33432 82 300"}], "emails": [{"value": "dataservice@zalf.de"}], "addresses": [{"deliveryPoint": ["Eberswalder Strasse 84"], "city": "M\u00fcncheberg", "administrativeArea": "Brandenburg", "postalCode": "15374", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Luisa Baader", "organization": "Julius K\u00fchn-Institut, Insitut f\u00fcr Z\u00fcchtungsforschung an Obst", "position": 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Reports, articles, papers, scientific and non - scientific works of any form, including tables, maps, or any other kind of output, in printed or electronic form, based in whole or in part on the data supplied, must contain an acknowledgement of the form: \"Data reused from the BonaRes Data Centre www.bonares.de. This data were created as part of the BonaRes Module A-Project - BonaRes - ORDIAmur's research activities.\" Although every care has been taken in preparing and testing the data, the BonaRes Module A-Project - BonaRes - ORDIAmur and the BonaRes Data Centre cannot guarantee that the data are correct; neither does the BonaRes Module A-Project - BonaRes - ORDIAmur and the BonaRes Data Centre accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The BonaRes Module A-Project - BonaRes - ORDIAmur and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data.", "updated": "2026-01-15", "type": "Dataset", "created": "2025-12-02", "language": "eng", "title": "ORDIAmur Central Experiment 10", "description": "Young apple rootstocks (M.26, EMR.2 and G.935) were grown on apple replant disease affected soil or gamma-irradiated ARD soil (disinfected control) for eight weeks in a greenhouse. Roots were collected, surface disinfected and the genomic DNA was extracted.  This table contains the index of all tables forming this data collection.\n\nRelated datasets are listed in the metadata element 'Related Identifier'.\nDataset version 1.0", "formats": [{"name": "CSV"}], "keywords": ["Soil", "qPCR", "Streptomyces", "opendata", "apple replant disease", "M.26", "EMR.2", "G.935", "Illumina-MiSeq", "Boden", "Europe", "Germany", "Schleswig-Holstein"], "contacts": [{"name": "Leibniz Centre for Agricultural Landscape Research", "organization": "ZALF", "position": "Computation and Data Service Platform - Workgroup Research Data Management", "roles": ["publisher"], "phones": [{"value": "+49 33432 82 300"}], "emails": [{"value": "dataservice@zalf.de"}], "addresses": [{"deliveryPoint": ["Eberswalder Strasse 84"], "city": "M\u00fcncheberg", "administrativeArea": "Brandenburg", "postalCode": "15374", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Nils Orth", "organization": "Leibniz University Hannover", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "orth@baum.uni-hannover.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0009-0006-1026-9881", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Kristin Hauschild", "organization": "Julius K\u00fchn Institute", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "kristin.hauschild@ufz.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0001-5261-9583", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Silvia Gschwendtner", "organization": "Helmholtz Munich", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "silvia.gschwendtner@helmholtz-munich.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0002-6379-3728", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Fatma M. 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Reports, articles, papers, scientific and non - scientific works of any form, including tables, maps, or any other kind of output, in printed or electronic form, based in whole or in part on the data supplied, must contain an acknowledgement of the form: \"Data reused from the BonaRes Data Centre www.bonares.de. This data were created as part of the BonaRes Module A-Project - BonaRes - SIGNAL's research activities.\" Although every care has been taken in preparing and testing the data, the BonaRes Module A-Project - BonaRes - SIGNAL and the BonaRes Data Centre cannot guarantee that the data are correct; neither does the BonaRes Module A-Project - BonaRes - SIGNAL and the BonaRes Data Centre accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The BonaRes Module A-Project - BonaRes - SIGNAL and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data. The access to this data is restricted during embargo time. If prior access is requested, contact the data owner / author.", "updated": "2022-06-30", "type": "Dataset", "created": "2022-06-02", "language": "eng", "title": "Microbial population sizes and soil properties in topsoil and subsoil of two alley-cropping agroforestry systems in Germany", "description": "We quantified bacteria, fungi, and functional groups of microorganisms in the topsoil and subsoil of two alley-cropping systems using real-time PCR. Topsoil and subsoil samples were collected in the tree rows and at multiple distances from the trees within the crop rows of the agroforestry systems as well as at an adjacent monoculture cropland. Soil cores were divided into topsoil (0 \u2013 15 and 15 \u2013 30 cm soil depth) and subsoil (30 \u2013 45 and 45 \u2013 60 cm soil depth).\n\nResearch domain: Soil Sciences\n\nResearch question: This study aimed to recover microbial DNA from topsoil and subsoil of two temperate poplar-based alley-cropping systems and quantify soil bacteria and fungi as well as different functional groups of microorganisms (nitrifying, denitrifying, methanotrophic, and methanogenic microorganisms) at different soil depths using real-time PCR. We hypothesized that i) microbial abundance decreases with soil depth, ii) tree rows promote microbial communities in both the topsoil and subsoil, and iii) the promotion of microorganisms through the tree rows is stronger in the subsoil than topsoil.", "formats": [{"name": "CSV"}], "keywords": ["Soil", "Soil", "nitrogen fixation genes", "genes", "PCR", "nitrogen cycle", "Bacteria", "Basidiomycota", "Ascomycota", "agroforestry", "agroforestry systems", "Alley cropping", "cropping systems", "Microbiological analysis", "Microbiology", "Microbiology", "Boden", "PCR"], "contacts": [{"name": "Lukas Beule", "organization": "Julius K\u00fchn Institute (JKI) \u2013 Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Berlin, Germany", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "lukas.beule@julius-kuehn.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0003-1107-7540", "name_url": "", "description": "https://orcid.org/", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Lukas Beule", "organization": "Julius K\u00fchn Institute (JKI) \u2013 Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Berlin, Germany", "position": null, "roles": ["projectLeader"], "phones": [{"value": null}], "emails": [{"value": "lukas.beule@julius-kuehn.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0003-1107-7540", "name_url": "", "description": "https://orcid.org/", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "BonaRes Data Centre", "organization": "Leibniz Centre for Agricultural Landscape Research (ZALF)", "position": "Research Platform 'Data Analysis & Simulation' - WG Geodata", "roles": ["publisher"], "phones": [{"value": "+49 33432 82 171"}], "emails": [{"value": "bonares-datenzentrum@zalf.de"}], "addresses": [{"deliveryPoint": ["Eberswalder Strasse 84"], "city": "M\u00fcncheberg", "administrativeArea": "Brandenburg", "postalCode": "15374", "country": "Germany"}], "links": [{"href": null}]}, {"organization": "Julius K\u00fchn Institute (JKI) \u2013 Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Berlin, Germany", "roles": ["contributor"]}]}, "links": [{"rel": "self", "type": "application/geo+json", "title": "e662d3de-e5e1-4d8d-b4bf-8597bce04ee3", "name": "item", "description": "e662d3de-e5e1-4d8d-b4bf-8597bce04ee3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/e662d3de-e5e1-4d8d-b4bf-8597bce04ee3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-06-30T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=PCR&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=PCR&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=PCR&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=PCR&offset=45", "hreflang": "en-US"}], "numberMatched": 45, "numberReturned": 45, "distributedFeatures": [], "timeStamp": "2026-07-28T04:00:45.022770Z"}