{"type": "FeatureCollection", "features": [{"id": "3146683732", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:27:20Z", "type": "Dataset", "title": "Yedoma domain Mineral Concentrations Assessment (YMCA)", "description": "Mineral elements play a crucial role for organic carbon stabilization, which is key for organic carbon mineralization rates in soils. With thawing permafrost, especially in ice-rich regions such as the Yedoma domain, vast amounts of organic carbon previously stored in deep frozen deposits are unlocked and therefore available to undergo microbial mineralization leading to potential carbon dioxide and methane emissions. Mineral elements interfere with organic carbon degradation through various processes: i) mineral protection (aggregation, adsorption, and complexation) stabilizes organic carbon and mitigates its mineralization, and ii) change in mineral nutrients availability affects microorganisms growth and metabolic activity. Despite huge efforts to assess organic carbon stocks and lability in permafrost regions, there is a lack of studies on the mineral component assessment, which we aim to close with this dataset. Here, we provide a large-scale Yedoma domain Mineral Concentrations Assessment (YMCA) dataset of never thawed (since deposition) ice-rich Yedoma permafrost and previously thawed and partly refrozen Alas deposits. We used a portable X-ray fluorescence device (pXRF) for Si, Al, Fe, Ca, K, Ti, Mn, Zn, Sr and Zr concentration measurements on 1,292 sediment samples. Portable XRF measured concentrations trueness was calibrated using standard alkaline fusion and ICP-OES measurement from a subset of 144 samples (R\u00b2 from 0.725 to 0.996). This methodology lead to the creation of the Yedoma domain Mineral Concentration Assessment (YMCA) dataset, a necessary step to estimate mineral element stocks in never thawed Yedoma and previously thawed Alas deposits. Practically, the YMCA dataset is organized as follow: (i) all site and sample properties: sample ID, type of deposit, site location, profile ID, GPS coordinates, country, lithology, unconsolidated sediment type, geological epoch, samples depth below surface level (b.s.l) or height above sea/river level (a.s.l), sediment characteristics, bulk density, gravimetric and absolute ice content, total organic carbon content; (ii) the Si, Al, Fe, Ca, K, Ti, Mn, Zn, Sr and Zr concentrations (corrected based on linear regressions) in Yedoma and Alas deposits (n=1292).", "keywords": ["Density", "Permafrost", "Profile ID", "gravimetric", "Density", " bulk", " permafrost", "Aluminium", "total", "Sample code/label", "Portable X ray fluorescence device", "Titanium", "Mineral element", "Yedoma", "Portable X-ray fluorescence device", "Description", "Number", "Lithology/composition/facies", "Sample code label", "6. Clean water", "Deposit type", "Country", "sediment rock", "Zinc", "Earth System Research", "Alas", "Profile", "Silicon", "Lithology composition facies", "Height above sea level", "organic", "Iron", "Site", "DEPTH", " sediment/rock", "bulk", "Ice content", " gravimetric", "LONGITUDE", "Organic carbon", "Manganese", "Sediment type", "organic carbon", "15. Life on land", "Ice content", "Carbon", "Epoch", "Sample ID", "13. Climate action", "Strontium", "DEPTH", "LATITUDE", "Potassium", "Calcium", "Zirconium", "permafrost", "Carbon", " organic", " total"]}, "links": [{"href": "https://doi.org/3146683732"}, {"rel": "self", "type": "application/geo+json", "title": "3146683732", "name": "item", "description": "3146683732", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3146683732"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-01T00:00:00Z"}}, {"id": "31591727", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-23T16:27:20Z", "type": "Journal Article", "created": "2019-10-08", "title": "Root\u2010induced soil deformation influences Fe, S and P: rhizosphere chemistry investigated using synchrotron XRF and XANES", "description": "Summary

Rhizosphere soil has distinct physical and chemical properties from bulk soil. However, besides root\uffe2\uff80\uff90induced physical changes, chemical changes have not been extensively measured in situ on the pore scale.

In this study, we couple structural information, previously obtained using synchrotron X\uffe2\uff80\uff90ray computed tomography (XCT), with synchrotron X\uffe2\uff80\uff90ray fluorescence microscopy (XRF) and X\uffe2\uff80\uff90ray absorption near\uffe2\uff80\uff90edge structure (XANES) to unravel chemical changes induced by plant roots.

Our results suggest that iron (Fe) and sulfur (S) increase notably in the direct vicinity of the root via solubilization and microbial activity. XANES further shows that Fe is slightly reduced, S is increasingly transformed into sulfate (SO42\uffe2\uff88\uff92) and phosphorus (P) is increasingly adsorbed to humic substances in this enrichment zone. In addition, the ferrihydrite fraction decreases drastically, suggesting the preferential dissolution and the formation of more stable Fe oxides. Additionally, the increased transformation of organic S to sulfate indicates that the microbial activity in this zone is increased. These changes in soil chemistry correspond to the soil compaction zone as previously measured via XCT.

The fact that these changes are colocated near the root and the compaction zone suggests that decreased permeability as a result of soil structural changes acts as a barrier creating a zone with increased rhizosphere chemical interactions via surface\uffe2\uff80\uff90mediated processes, microbial activity and acidification.

The ubiquitous occurrence of microplastics (MPs) in the environment and the use of plastics in packaging materials result in the presence of MPs in the food chain and the exposure of consumers. Yet, no fully validated analytical method is available for microplastic (MP) quantification, thereby preventing the reliable estimation of the level of exposure and, ultimately, the assessment of the food safety risks associated with MP contamination. In this study, a novel approach is presented that exploits interactive artificial intelligence tools to enable the automation of MP analysis. An integrated method for the analysis of MPs in bottled water based on Nile Red staining and fluorescent microscopy was developed and validated, featuring a partial interrogation of the filter and a fully automated image processing workflow based on a Random Forest classifier, thereby boosting the analysis speed. The image analysis provided particle count, size and size distribution of the MPs. From these data, a rough estimation of the mass of the individual MPs, and consequently of the MP mass concentration in the sample, could be obtained as well. Critical materials, method performance characteristics, and final applicability were studied in detail. The method showed to be highly sensitive in sizing MPs down to 10 \u00b5m, with a particle count limit of detection and quantification of 28 and 85 items/500 mL, respectively. Linearity of mass concentration determined between 10 ppb and 1.5 ppm showed a regression coefficient of (R2) of 0.99. Method precision was demonstrated by repeatability of 9 - 16% RSD (n = 7) and within-laboratory reproducibility of 15 - 27 % RSD (n = 21). Accuracy based on recovery was 92 \u00b1 15 % and 98 \u00b1 23 % at a level of 0.1 and 1.0 ppm, respectively. The quantitative performance characteristics thus obtained complied with regulatory requirements. Finally, the method was successfully applied to the analysis of twenty commercial samples of bottled water, with and without gas and flavor additives, yielding results ranging from values below the limit of detection to 7237 (95% CI [6456, 8088]) items/500 mL.

", "keywords": ["Fluorescence microscopy", "Artificial intelligence", "Bottled water", "Method validation", "Artificial Intelligence", "Microplastics", "Drinking Water", "Microplastic", "Nile red", "Reproducibility of Results", "Plastics", "6. Clean water"]}, "links": [{"href": "https://doi.org/37487270"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Talanta", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "37487270", "name": "item", "description": "37487270", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/37487270"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-04-10T00:00:00Z"}}, {"id": "4941261d-98ba-4c70-ad52-708e6cae460c", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[10.69, 53.86], [10.69, 53.86], [10.7, 53.86], [10.7, 53.86], [10.69, 53.86]]]}, "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 Other's research activities.\" Although every care has been taken in preparing and testing the data, the Other and the BonaRes Data Centre cannot guarantee that the data are correct; neither does the Other 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 Other and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data.", "updated": "2023-08-02", "type": "Service", "created": "2023-07-26", "language": "eng", "title": "Web Map Service of the dataset 'Chlorophyll-Data of eutrophied urban ponds in L\u00fcbeck (Germany, Schleswig-Holstein)'", "description": "This WMS Map Service includes spatial information used by datasets 'AGIS Map Service of the dataset 'Chlorophyll-Data of eutrophied urban ponds in L\u00fcbeck (Germany, Schleswig-Holstein)''", "formats": [{"name": "CSV"}], "keywords": ["infoMapAccessService", "Soil", "chlorophylls", "chlorophyll fluorescence", "surface water", "urban environment", "eutrophication", "Algae", "Cyanobacteria"], "contacts": [{"name": "Christian Lohaus", "organization": "Technische Hochschule L\u00fcbeck", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "christian.lohaus@th-luebeck.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0009-0002-6950-3952", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Norbert Reintjes", "organization": "Technische Hochschule L\u00fcbeck", "position": null, "roles": ["projectLeader"], "phones": [{"value": null}], "emails": [{"value": "norbert.reintjes@th-luebeck.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": null}]}, {"name": null, "organization": "Leibniz Centre for Agricultural Landscape Research (ZALF)", "position": "Research Platform 'Data Analysis & Simulation' - 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": "Franz Weinland", "organization": "Technische Hochschule L\u00fcbeck", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "franz.weinland@icloud.com"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0002-5071-2271", "name_url": "", "description": "ORCID:", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Tillmann Westphal", "organization": "Technische Hochschule L\u00fcbeck", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "tillmann.westphal@th-luebeck.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": null}]}, {"name": "Fabian M\u00f6ller", "organization": "Technische Hochschule L\u00fcbeck", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "f.moeller@stud.th-luebeck.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": null}]}, {"name": "Norbert Reintjes", "organization": "Technische Hochschule L\u00fcbeck", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "norbert.reintjes@th-luebeck.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": null}]}, {"organization": "Technische Hochschule L\u00fcbeck", "roles": ["contributor"]}], "themes": [{"concepts": [{"id": "infoMapAccessService"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}, {"concepts": [{"id": "Soil"}, {"id": "chlorophylls"}, {"id": "chlorophyll fluorescence"}, {"id": "surface water"}, {"id": "urban environment"}, {"id": "eutrophication"}, {"id": "Algae"}, {"id": "Cyanobacteria"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}]}, "links": [{"href": "https://maps.bonares.de/mapapps/resources/apps/bonares/index.html?lang=en&mid=4941261d-98ba-4c70-ad52-708e6cae460c", "rel": "download"}, {"href": "https://maps.bonares.de/wss/service/ags-relay/ags/guest/arcgis/rest/services/Extern/ID_E114_KMW_CHL_2022_PUB_Geo_point/MapServer/WMSServer?request=GetCapabilities&service=WMS"}, {"href": "https://maps.bonares.de/wss/service/ags-relay/ags/guest/arcgis/rest/services/Extern/Measuring_Point_KMW_chl_2022/MapServer/WMSServer?request=GetCapabilities&service=WMS"}, {"rel": "self", "type": "application/geo+json", "title": "4941261d-98ba-4c70-ad52-708e6cae460c", "name": "item", "description": "4941261d-98ba-4c70-ad52-708e6cae460c", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/4941261d-98ba-4c70-ad52-708e6cae460c"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-08-02T00:00:00Z"}}, {"id": "PMC8640753", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:29:50Z", "type": "Journal Article", "created": "2021-02-13", "title": "Plant-environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere", "description": "Abstract

Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants\uffe2\uff80\uff99 large volume of influence. Here, we present the development of 3D live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor made dual-illumination light-sheet system acquired scattering signals from the plant whilst fluorescence signals were captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm3in size with as good as 5 \uffce\uffbcm resolution at a rate of up to one scan every 30 minutes. The system tracked the movement ofBacillus subtilispopulations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favoured small pore spaces over the surface of soil particles, colonising the root in a pulsatile manner. Migrations appeared to be directed towards the root cap, the point \uffe2\uff80\uff9cfirst contact\uffe2\uff80\uff9d, before subsequent colonisation of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.We have developed a tuneable workflow for the study of soil microbes in an imitative 3D soil environment that is compatible with routine and advanced optical imaging, is chemically customisable, and is reliably refractive index matched based on the metabolic profile of the study organism. We demonstrate our transparent soil pipeline with two representative soil organisms,Bacillus subtilisandStreptomyces coelicolor, and visualise their colonisation behaviours using fluorescence microscopy and mesoscopy. This spatially structured, 3D approach to microbial culture has the potential to further study the behaviour of other difficult-to-culture bacteria in conditions matching their native environment and could be expanded to study microbial interactions, such as interaction, competition, and warfare.

3.Graphical Abstract

A step-by-step method for creating a tailored 3D culture medium for study of soil microbes.

The complete workflow can be split into three parts: Growth and observation, metabolic profiling to provide a stable refractive index matching solution, and production of the 3D soil environment. The 3D culture scaffold was created by cryomilling Nafion\uffe2\uff84\uffa2 resin pellets and size filtration. Chemical processing altered the surface chemistry of Nafion\uffe2\uff84\uffa2 particles and facilitated nutrient binding by titration of a defined liquid culture medium. Metabolic profiling determined non-metabolisable sugars and provided an inert refractive index matching substrate, which was added to the final nutrient titration. Inoculation and growth of the test strain allowed for downstream assessment of colonisation behaviours and community dynamicsin situby, for example, optical microscopy.Microorganisms colonizing plant roots co-exist in complex, spatially structured multispecies biofilm communities. However, little is known about microbial interactions and the underlying spatial organization within biofilm communities established on plant roots. Here, a well-established four-species biofilm model (Stenotrophomonas rhizophila, Paenibacillus amylolyticus, Microbacterium oxydans, and Xanthomonas retroflexus, termed as SPMX) was applied to Arabidopsis roots to study the impact of multispecies biofilm on plant growth and the community spatial dynamics on the roots. SPMX co-culture notably promoted root development and plant biomass. Co-cultured SPMX increased root colonization and formed multispecies biofilms, structurally different from those formed by monocultures. By combining 16S rRNA gene amplicon sequencing and fluorescence in situ hybridization with confocal laser scanning microscopy, we found that the composition and spatial organization of the four-species biofilm significantly changed over time. Monoculture P. amylolyticus colonized plant roots poorly, but its population and root colonization were highly enhanced when residing in the four-species biofilm. Exclusion of P. amylolyticus from the community reduced overall biofilm production and root colonization of the three species, resulting in the loss of the plant growth-promoting effects. Combined with spatial analysis, this led to identification of P. amylolyticus as a keystone species. Our findings highlight that weak root colonizers may benefit from mutualistic interactions in complex communities and hereby become important keystone species impacting community spatial organization and function. This work expands the knowledge on spatial organization uncovering interspecific interactions in multispecies biofilm communities on plant roots, beneficial for harnessing microbial mutualism promoting plant growth. Investigating active participants in the fixation of dinitrogen gas is vital as N is often a limiting factor for primary production. Biological nitrogen fixation is performed by a diverse guild of bacteria and archaea (diazotrophs), which can be free\uffe2\uff80\uff90living or symbionts. Free\uffe2\uff80\uff90living diazotrophs are widely distributed in the environment, yet our knowledge about their identity and ecophysiology is still limited. A major challenge in investigating this guild is inferring activity from genetic data as this process is highly regulated. To address this challenge, we evaluated and improved several 15 N\uffe2\uff80\uff90based methods for detecting N 2 fixation activity (with a focus on soil samples) and studying active diazotrophs. We compared the acetylene reduction assay and the 15 N 2 tracer method and demonstrated that the latter is more sensitive in samples with low activity. Additionally, tracing 15 N into microbial RNA provides much higher sensitivity compared to bulk soil analysis. Active soil diazotrophs were identified with a 15 N\uffe2\uff80\uff90RNA\uffe2\uff80\uff90SIP approach optimized for environmental samples and benchmarked to 15 N\uffe2\uff80\uff90DNA\uffe2\uff80\uff90SIP. Lastly, we investigated the feasibility of using SIP\uffe2\uff80\uff90Raman microspectroscopy for detecting 15 N\uffe2\uff80\uff90labelled cells. Taken together, these tools allow identifying and investigating active free\uffe2\uff80\uff90living diazotrophs in a highly sensitive manner in diverse environments, from bulk to the single\uffe2\uff80\uff90cell level.

Phosphorus (P) is essential for plant growth. Arbuscular mycorrhizal fungi (AMF) aid its uptake by acquiring P from sources distant from roots in return for carbon. Little is known about how AMF colonise soil pore\uffe2\uff80\uff90space, and models of AMF\uffe2\uff80\uff90enhanced P\uffe2\uff80\uff90uptake are poorly validated.

We used synchrotron X\uffe2\uff80\uff90ray computed tomography to visualize mycorrhizas in soil and synchrotron X\uffe2\uff80\uff90ray fluorescence/X\uffe2\uff80\uff90ray absorption near edge structure (XRF/XANES) elemental mapping for P, sulphur (S) and aluminium (Al) in combination with modelling.

We found that AMF inoculation had a suppressive effect on colonisation by other soil fungi and identified differences in structure and growth rate between hyphae of AMF and nonmycorrhizal fungi. Our results showed that AMF co\uffe2\uff80\uff90locate with areas of high P and low Al, and preferentially associate with organic\uffe2\uff80\uff90type P species over Al\uffe2\uff80\uff90rich inorganic P.

We discovered that AMF avoid Al\uffe2\uff80\uff90rich areas as a source of P. Sulphur\uffe2\uff80\uff90rich regions were found to be correlated with higher hyphal density and an increased organic\uffe2\uff80\uff90associated P\uffe2\uff80\uff90pool, whilst oxidized S\uffe2\uff80\uff90species were found close to AMF hyphae. Increased S oxidation close to AMF suggested the observed changes were microbiome\uffe2\uff80\uff90related. Our experimentally\uffe2\uff80\uff90validated model led to an estimate of P\uffe2\uff80\uff90uptake by AMF hyphae that is an order of magnitude lower than rates previously estimated \uffe2\uff80\uff93 a result with significant implications for the modelling of plant\uffe2\uff80\uff93soil\uffe2\uff80\uff93AMF interactions.