BACKGROUND: Denitrification is a microbial process that has received considerable attention during the past decade since it can result in losses of added nitrogen fertilisers from agricultural soils. Paddy soil has been known to have strong denitrifying activity, but the denitrifying microorganisms responsible for fertilisers in paddy soil are not well known. The objective of this study was to explore the impacts of 17\uffe2\uff80\uff90year application of inorganic and organic fertiliser (rice straw) on the abundance and composition of a nosZ\uffe2\uff80\uff90denitrifier community in paddy soil. Soil samples were collected from CK plots (no fertiliser), N (nitrogen fertiliser), NPK (nitrogen, phosphorus and potassium fertilisers) and NPK + OM (NPK plus organic matter). The nitrous oxide reductase gene (nosZ) community composition was analysed using terminal restriction fragment length polymorphism, and the abundance was determined by quantitative PCR.
RESULTS: Both the largest abundance of nosZ\uffe2\uff80\uff90denitrifier and the highest potential denitrifying activity (PDA) occurred in the NPK + OM treatment with about four times higher than that in the CK and two times higher than that in the N and NPK treatments (no significant difference). Denitrifying community composition differed significantly among fertilisation treatments except for the comparison between CK and N treatments. Of the measured abiotic factors, total organic carbon was significantly correlated with the observed differences in community composition and abundance (P < 0.01 by Monte Carlo permutation).
CONCLUSION: This study shows that the addition of different fertilisers affects the size and composition of the nosZ\uffe2\uff80\uff90denitrifier community in paddy soil. Copyright \uffc2\uffa9 2011 Society of Chemical Industry
", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Bacteria", "Nitrogen", "0402 animal and dairy science", "Agriculture", "Oryza", "04 agricultural and veterinary sciences", "15. Life on land", "6. Clean water", "Carbon", "Soil", "03 medical and health sciences", "Genes", " Bacterial", "Denitrification", "0405 other agricultural sciences", "Fertilizers", "Oxidoreductases", "Monte Carlo Method", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1002/jsfa.4533"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20the%20Science%20of%20Food%20and%20Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/jsfa.4533", "name": "item", "description": "10.1002/jsfa.4533", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/jsfa.4533"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-07-27T00:00:00Z"}}, {"id": "10.1016/j.envint.2020.106190", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:12Z", "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": "04e12ad1-77b4-45a2-9ed2-2f9aedcc013c", "type": "Feature", "geometry": null, "properties": {"updated": "2025-09-03T08:42:09Z", "type": "Dataset", "language": "de", "title": "INSPIRE-WCS Soil / Konzeptbodenkarten BB", "description": "Der interoperable INSPIRE-WCS ist ein Downloaddienst, der Daten im INSPIRE-Zielschema Boden (abgeleitet aus der origin\u00e4ren Serie: Konzeptbodenkarten Brandenburg) bereitstellt. Er gibt einen \u00dcberblick zum Fl\u00e4chentyp Bodenartgruppe und Fl\u00e4chentyp Genese der B\u00f6den Brandenburgs und ist aktuell das hochaufl\u00f6sendste blattschnittfreie bodenkundliche Kartenwerk des LBGR im Rasterformat, mit einer Aufl\u00f6sung von 10 x 10 m. Datengrundlagen der Karten sind Fl\u00e4chendaten der Bodensch\u00e4tzung, Geologie und verschiedene bodenkundliche Punkt- und Fl\u00e4chendaten. Die Auswertungen liefern die fachliche Basis sowohl f\u00fcr die Planung und Umsetzung bodenkundlicher Kartierungen, als auch f\u00fcr die Synthese und Ableitung der Bodenfunktions- und -gef\u00e4hrdungsbewertungen. Die G\u00fcte der zugrundeliegenden Konzeptbodenkarten (KBK) hat somit einen hohen Einfluss auf die Qualit\u00e4t der abgeleiteten Produkte. Im Land Brandenburg werden die KBK mit einem regelbasierten Ansatz weitgehend automatisiert softwaretechnisch abgeleitet. Das Verfahren implementiert die bislang analog durchgef\u00fchrten Arbeitsschritte und bildet als \u201eExpertensystem\u201c das Verst\u00e4ndnis \u00fcber die Genese und die Verbreitung der B\u00f6den in Brandenburg weitgehend ab. Derzeit wird ein robustes Verfahren zum Abgleich laufender Erhebungen mit den \u201ePrognosen\u201c der Konzeptkarten und darauf fu\u00dfend deren systematische \u00dcberpr\u00fcfung und Bewertung erarbeitet. Zuk\u00fcnftig sollen in diesem Verfahren erkannte Defizite systematisch in einem modifizierten Ableitungsregelwerk ber\u00fccksichtigt und die Konzeptbodenkarten fortlaufend aktualisiert werden. Eine ausf\u00fchrliche Legende sowie die Erl\u00e4uterungen der Werte ist zu finden unter: https://isk.geobasis-bb.de/geodienste/lbgr/KBK_Erlaeuterungen.pdf. Gem\u00e4\u00df der INSPIRE-Datenspezifikation f\u00fcr Soil liegen die Inhalte INSPIRE-konform vor. Der WCS beinhaltet die folgenden Coverages: - SO.SoilTextureClasses:bft, - SO.SoilGenesis:gft, - SO.SoilPedogenesis:pft. --- The compliant INSPIRE-WCS is a download service that delivers data in the INSPIRE target schema Soil (derived from the original data series: Concept pedological maps in the State of Brandenburg). It provides an overview of the soil texture classes and soil genesis in the State of Brandenburg and is currently the highest-resolution pedological map of the LBGR in raster format with a resolution of 10 x 10 meters. The maps are based on data from German Soil taxonomy classification, geology and various pedological spatial data. The evaluations provide the technical basis for the planning and implementation of soil surveys as well as for the synthesis and derivation of soil function and risk assessments. The quality of the underlying Concept pedological maps (KBK) therefore has a major influence on the quality of the derived products. In the State of Brandenburg, the KBK is derived using a largely automated software-based approach. The procedure implements the work steps that have been carried out analogously to date and, as an 'expert system', largely reflects the understanding of the genesis and distribution of soils in Brandenburg. A robust procedure for comparing current surveys with the 'forecasts' of the KBK and, based on this, their systematic review and evaluation is currently being developed. In the future, deficits identified in this procedure will be systematically taken into account in a modified derivation set of rules and the KBK will be continuously updated. A detailed legend and explanations can be found at: https://isk.geobasis-bb.de/geodienste/lbgr/KBK_Erlaeuterungen.pdf. The content is compliant to the INSPIRE Data Specification on Soil. The WCS includes the following coverages: - SO.SoilTextureClasses:bft, - SO.SoilGenesis:gft, - SO.SoilPedogenesis:pft.", "formats": [{"name": "HTML"}], "keywords": ["boden", "bodenart", "bodendaten", "bodenform", "bodengeologie", "bodengesellschaft", "bodenkarte", "bodenkunde", "bodenscha\u0308tzung", "bodensystematische-einheit", "bodentyp", "brandenburg", "de", "fla\u0308chenbodenform", "genese", "geologie", "infocoverageaccessservice", "inspireidentifiziert", "interoperabel", "interoperability", "interoperable-daten", "konzeptbodenkarte", "konzeptkarte", "opendata", "organisch", "pedogenese", "process", "regional", "soil", "soillayer", "soiltexturegroup", "soiltype", "substratsystematische-einheit", "terrestrisch", "wcs"], "contacts": [{"organization": "Landesamt f\u00fcr Bergbau, Geologie und Rohstoffe Brandenburg (LBGR)", "roles": ["creator"]}]}, "links": [{"href": "https://geoportal.brandenburg.de/detailansichtdienst/render?view=gdibb&url=https%3A%2F%2Fgeoportal.brandenburg.de%2Fgs-json%2Fxml%3Ffileid%3D04e12ad1-77b4-45a2-9ed2-2f9aedcc013c"}, {"href": "https://inspire.brandenburg.de/services/so_kbk_wcs?REQUEST=GetCapabilities&SERVICE=WCS"}, {"href": "https://isk.geobasis-bb.de/geodienste/Sonstiges/Hilfe_Nutzung_Downloaddienst.pdf"}, {"href": "http://data.europa.eu/88u/dataset/04e12ad1-77b4-45a2-9ed2-2f9aedcc013c~~1"}, {"rel": "self", "type": "application/geo+json", "title": "04e12ad1-77b4-45a2-9ed2-2f9aedcc013c", "name": "item", "description": "04e12ad1-77b4-45a2-9ed2-2f9aedcc013c", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/04e12ad1-77b4-45a2-9ed2-2f9aedcc013c"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"null": "date"}}, {"id": "0ded8335-2f1c-4985-8cc3-b3c03f5e7e72", "type": "Feature", "geometry": null, "properties": {"updated": "2025-09-03T08:41:38Z", "type": "Dataset", "language": "de", "title": "WMS Konzeptbodenkarten BB (WMS-KBK)", "description": "Der Darstellungsdienst (WMS) Konzeptbodenkarten Brandenburg stellt Daten der Konzeptbodenkarten zu den Bereichen Fl\u00e4chentyp Bodenartengruppe und Fl\u00e4chentyp Genese bereit. Die Konzeptbodenkarten sind aktuell das hochaufl\u00f6sendste, blattschnittfreie bodenkundliche Kartenwerk des LBGR im Rasterformat mit einer Aufl\u00f6sung von 10 x 10 m. Datengrundlagen der Karten sind Fl\u00e4chendaten der Bodensch\u00e4tzung, Geologie und verschiedene bodenkundliche Punkt- und Fl\u00e4chendaten. Der Dienst umfasst die folgenden Layer: 1. Fl\u00e4chentyp Bodenartengruppe, 2. Fl\u00e4chentyp Genese. Die Auswertungen liefern die fachliche Basis sowohl f\u00fcr die Planung und Umsetzung bodenkundlicher Kartierungen, als auch f\u00fcr die Synthese und Ableitung der Bodenfunktions- und -gef\u00e4hrdungsbewertungen. Die G\u00fcte der zugrundeliegenden Konzeptkarten hat somit einen hohen Einfluss auf die Qualit\u00e4t der abgeleiteten Produkte. Im Land Brandenburg werden die Konzeptbodenkarten mit einem regelbasierten Ansatz weitgehend automatisiert softwaretechnisch abgeleitet. Das Verfahren implementiert die bislang analog durchgef\u00fchrten Arbeitsschritte und bildet als \u201eExpertensystem\u201c das Verst\u00e4ndnis \u00fcber die Genese und die Verbreitung der B\u00f6den in Brandenburg weitgehend ab. Ein robustes Verfahren zum Abgleich laufender Erhebungen mit den \u201ePrognosen\u201c der Konzeptkarten und darauf fu\u00dfend deren systematische \u00dcberpr\u00fcfung und Bewertung wird derzeit erarbeitet. Zuk\u00fcnftig sollen in diesem Verfahren erkannte Defizite systematisch in einem modifizierten Ableitungsregelwerk ber\u00fccksichtigt und die Konzeptbodenkarten fortlaufend aktualisiert werden. Eine ausf\u00fchrliche Legende sowie Erl\u00e4uterungen sind zu finden unter: https://isk.geobasis-bb.de/geodienste/lbgr/KBK_Erlaeuterungen.pdf. Der WMS beinhaltet die folgenden Layer: - Fl\u00e4chentyp Bodenartengruppe [bft], - Fl\u00e4chentyp Genese [gft], - Fl\u00e4chentyp Pedogenese [pft].", "formats": [{"name": "HTML"}], "keywords": ["boden", "bodenart", "bodendaten", "bodenform", "bodengeologie", "bodengesellschaft", "bodenkarte", "bodenkunde", "bodenscha\u0308tzung", "bodensystematische-einheit", "bodentyp", "brandenburg", "de", "fla\u0308chenbodenform", "genese", "geologie", "inspireidentifiziert", "konzeptbodenkarte", "konzeptkarte", "opendata", "organisch", "pedogenese", "substratsystematische-einheit", "terrestrisch", "wms"], "contacts": [{"organization": "Landesamt f\u00fcr Bergbau, Geologie und Rohstoffe Brandenburg (LBGR)", "roles": ["creator"]}]}, "links": [{"href": "https://geoportal.brandenburg.de/detailansichtdienst/render?view=gdibb&url=https%3A%2F%2Fgeoportal.brandenburg.de%2Fgs-json%2Fxml%3Ffileid%3D0ded8335-2f1c-4985-8cc3-b3c03f5e7e72"}, {"href": "https://inspire.brandenburg.de/services/kbk_wms?REQUEST=GetCapabilities&SERVICE=WMS"}, {"href": "http://data.europa.eu/88u/dataset/0ded8335-2f1c-4985-8cc3-b3c03f5e7e72"}, {"rel": "self", "type": "application/geo+json", "title": "0ded8335-2f1c-4985-8cc3-b3c03f5e7e72", "name": "item", "description": "0ded8335-2f1c-4985-8cc3-b3c03f5e7e72", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/0ded8335-2f1c-4985-8cc3-b3c03f5e7e72"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"null": "date"}}, {"id": "10.1007/s00128-012-0523-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:33Z", "type": "Journal Article", "created": "2012-01-25", "title": "Effect Of Long-Term Zinc Pollution On Soil Microbial Community Resistance To Repeated Contamination", "description": "The aim of the study was to compare the effects of stress (contamination trials) on the microorganisms in zinc-polluted soil (5,018\u00a0mg Zn\u00a0kg(-1) soil dry weight) and unpolluted soil (141\u00a0mg Zn kg(-1) soil\u00a0dw), measured as soil respiration rate. In the laboratory, soils were subjected to copper contamination (0, 500, 1,500 and 4,500\u00a0mg\u00a0kg(-1) soil\u00a0dw), and then a bactericide (oxytetracycline) combined with a fungicide (captan) along with glucose (10\u00a0mg\u00a0g(-1) soil\u00a0dw each) were added. There was a highly significant effect of soil type, copper treatment and oxytetracycline/captan treatment. The initial respiration rate of chronically zinc-polluted soil was higher than that of unpolluted soil, but in the copper treatment it showed a greater decline. Microorganisms in copper-treated soil were more susceptible to oxytetracycline/captan contamination. After the successive soil contamination trials the decline of soil respiration was greater in zinc-polluted soil than in unpolluted soil.", "keywords": ["Health", " Toxicology and Mutagenesis", "trace metals", "Oxytetracycline", "Toxicology", "01 natural sciences", "Article", "Captan", "Soil", "Stress", " Physiological", "Soil Pollutants", "Soil Microbiology", "combined stressors", "0105 earth and related environmental sciences", "soil pollution", "Drug Resistance", " Microbial", "04 agricultural and veterinary sciences", "Pollution", "Adaptation", " Physiological", "soil respiration rate", "6. Clean water", "Anti-Bacterial Agents", "Fungicides", " Industrial", "Zinc", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Copper"], "contacts": [{"organization": "Klimek, Beata", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1007/s00128-012-0523-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bulletin%20of%20Environmental%20Contamination%20and%20Toxicology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00128-012-0523-0", "name": "item", "description": "10.1007/s00128-012-0523-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00128-012-0523-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-01-26T00:00:00Z"}}, {"id": "10.1007/s00248-003-0229-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:34Z", "type": "Journal Article", "created": "2005-06-17", "title": "Methanogen Communities In A Drained Bog: Effect Of Ash Fertilization", "description": "Forestry practises such has drainage have been shown to decrease emissions of the greenhouse gas methane (CH(4)) from peatlands. The aim of the study was to examine the methanogen populations in a drained bog in northern Finland, and to assess the possible effect of ash fertilization on potential methane production and methanogen communities. Peat samples were collected from control and ash fertilized (15,000 kg/ha) plots 5 years after ash application, and potential CH(4) production was measured. The methanogen community structure was studied by DNA isolation, PCR amplification of the methyl coenzyme-M reductase (mcr) gene, denaturing gradient gel electrophoresis (DGGE), and restriction fragment length polymorphism (RFLP) analysis. The drained peatland showed low potential methane production and methanogen diversity in both control and ash-fertilized plots. Samples from both upper and deeper layers of peat were dominated by three groups of sequences related to Rice cluster-I hydrogenotroph methanogens. Even though pH was marginally greater in the ash-treated site, the occurrence of those sequences was not affected by ash fertilization. Interestingly, a less common group of sequences, related to the Fen cluster, were found only in the fertilized plots. The study confirmed the depth related change of methanogen populations in peatland.", "keywords": ["0301 basic medicine", "0303 health sciences", "Bacteria", "tuhkalannoitus", "metanogeeniset mikrobit", "Biodiversity", "15. Life on land", "03 medical and health sciences", "Genes", " Bacterial", "ojitetut suot", "Fertilizers", "Methane", "Ecosystem", "Phylogeny", "Polymorphism", " Restriction Fragment Length"]}, "links": [{"href": "https://doi.org/10.1007/s00248-003-0229-2"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-003-0229-2", "name": "item", "description": "10.1007/s00248-003-0229-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-003-0229-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2005-02-01T00:00:00Z"}}, {"id": "10.1007/s00248-011-9897-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:34Z", "type": "Journal Article", "created": "2011-06-29", "title": "Impacts Of Organic And Inorganic Fertilizers On Nitrification In A Cold Climate Soil Are Linked To The Bacterial Ammonia Oxidizer Community", "description": "The microbiology underpinning soil nitrogen cycling in northeast China remains poorly understood. These agricultural systems are typified by widely contrasting temperature, ranging from -40 to 38\u00b0C. In a long-term site in this region, the impacts of mineral and organic fertilizer amendments on potential nitrification rate (PNR) were determined. PNR was found to be suppressed by long-term mineral fertilizer treatment but enhanced by manure treatment. The abundance and structure of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities were assessed using quantitative polymerase chain reaction and denaturing gradient gel electrophoresis techniques. The abundance of AOA was reduced by all fertilizer treatments, while the opposite response was measured for AOB, leading to a six- to 60-fold reduction in AOA/AOB ratio. The community structure of AOA exhibited little variation across fertilization treatments, whereas the structure of the AOB community was highly responsive. PNR was correlated with community structure of AOB rather than that of AOA. Variation in the community structure of AOB was linked to soil pH, total carbon, and nitrogen contents induced by different long-term fertilization regimes. The results suggest that manure amendment establishes conditions which select for an AOB community type which recovers mineral fertilizer-suppressed soil nitrification.", "keywords": ["DNA", " Bacterial", "2. Zero hunger", "China", "Bacteria", "04 agricultural and veterinary sciences", "15. Life on land", "Cold Climate", "Archaea", "Nitrification", "6. Clean water", "Genes", " Archaeal", "Soil", "DNA", " Archaeal", "Ammonia", "Genes", " Bacterial", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Oxidoreductases", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-011-9897-5"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-011-9897-5", "name": "item", "description": "10.1007/s00248-011-9897-5", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-011-9897-5"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-06-29T00:00:00Z"}}, {"id": "10.1007/s00442-012-2578-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:14:44Z", "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": "10.1007/s10745-012-9538-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:03Z", "type": "Journal Article", "created": "2012-11-19", "title": "Effects Of Landscape Segregation On Livelihood Vulnerability: Moving From Extensive Shifting Cultivation To Rotational Agriculture And Natural Forests In Northern Laos", "description": "This study investigates four decades of socio-economic and environmental change in a shifting cultivation landscape in the northern uplands of Laos. Historical changes in land cover and land use were analyzed using a chronological series of remote sensing data. Impacts of landscape change on local livelihoods were investigated in seven villages through interviews with various stakeholders. The study reveals that the complex mosaics of agriculture and forest patches observed in the study area have long constituted key assets for the resilience of local livelihood systems in the face of environmental and socio-economic risks. However, over the past 20 years, a process of segregating agricultural and forest spaces has increased the vulnerability of local land users. This process is a direct outcome of policies aimed at increasing national forest cover, eradicating shifting cultivation and fostering the emergence of more intensive and commercial agricultural practices. We argue that agriculture-forest segregation should be buffered in such a way that a diversity of livelihood opportunities and economic development pathways can be maintained.", "keywords": ["http://aims.fao.org/aos/agrovoc/c_195", "550", "F08 - Syst\u00e8mes et modes de culture", "t\u00e9l\u00e9d\u00e9tection", "0211 other engineering and technologies", "02 engineering and technology", "2739 Public Health", "910", "630", "couverture v\u00e9g\u00e9tale", "conservation des for\u00eats", "http://aims.fao.org/aos/agrovoc/c_3062", "for\u00eat", "K01 - Foresterie - Consid\u00e9rations g\u00e9n\u00e9rales", "11. Sustainability", "910 Geography & travel", "intensification", "http://aims.fao.org/aos/agrovoc/c_6498", "2. Zero hunger", "landscape mosaics", "resettlement", "sustainability", "Livelihood vulnerability", "Southeast Asia", "rotation culturale", "330 Economics", "E11 - \u00c9conomie et politique fonci\u00e8res", "moyens d'existence durables", "2307 Health", "Laos", "protection de la for\u00eat", "http://aims.fao.org/aos/agrovoc/c_25409", "http://aims.fao.org/aos/agrovoc/c_4182", "P01 - Conservation de la nature et ressources fonci\u00e8res", "ecology", "3306 Health (social science)", "Multifunctional landscapes", "http://aims.fao.org/aos/agrovoc/c_24420", "culture itin\u00e9rante", "gestion des ressources naturelles", "utilisation des terres", "politique fonci\u00e8re", "http://aims.fao.org/aos/agrovoc/c_12076", "Ecosystem services", "http://aims.fao.org/aos/agrovoc/c_28075", "http://aims.fao.org/aos/agrovoc/c_1374158672853", "Toxicology and Mutagenesis", "Environmental and Occupational Health", "15. Life on land", "shifting cultivation", "http://aims.fao.org/aos/agrovoc/c_7038", "http://aims.fao.org/aos/agrovoc/c_9000157", "http://aims.fao.org/aos/agrovoc/c_9000115", "Land sparing", "Shifting cultivation", "impact sur l'environnement", "ecosystem services", "2303 Ecology", "http://aims.fao.org/aos/agrovoc/c_6662"]}, "links": [{"href": "https://boris.unibe.ch/17755/1/Castella2013_Article_EffectsOfLandscapeSegregationO.pdf"}, {"href": "https://doi.org/10.1007/s10745-012-9538-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Human%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s10745-012-9538-8", "name": "item", "description": "10.1007/s10745-012-9538-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s10745-012-9538-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-11-20T00:00:00Z"}}, {"id": "10.1007/s11356-015-4557-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:18Z", "type": "Journal Article", "created": "2015-04-26", "title": "Effects Of Winter Covering Crop Residue Incorporation On Ch4 And N2o Emission From Double-Cropped Paddy Fields In Southern China", "description": "Residue management in cropping systems is useful to improve soil quality. However, the studies on the effects of residue management on methane (CH(4)) and nitrous oxide (N(2)O) emission from paddy field in southern China are few. Therefore, the emissions of CH(4) and N(2)O were investigated in double cropping rice (Oryza sativa L.) systems with different winter covering crops using the static chamber-gas chromatography technique to assess the effects of different covering crops on the emissions of greenhouse gases. The experiment was established in 2004 in Hunan Province, China. Three winter cropping systems were used: rice\u2013rice\u2013rape (Brassica napus L.) (T1), rice\u2013rice\u2013potato with straw mulching (Solanum tuberosum L.) (T2), and rice\u2013rice with winter fallow (CK). A randomized block design was adopted in plots, with three replications. The results showed that T2 plots had the largest CH(4) emissions during the early and late rice growing season with 12.506 and 32.991\u00a0g\u00a0m(\u22122), respectively. When compared to CK, total N(2)O emissions in the early rice growth period and the emissions of the gas increased by 0.013\u00a0g\u00a0m(\u22122) in T1 and 0.045\u00a0g\u00a0m(\u22122) in T2, respectively. Similar results were obtained in the late rice growth period; the total N(2)O emissions increased by 0.027\u00a0g\u00a0m(\u22122) in T1 and 0.084\u00a0g\u00a0m(\u22122) in T2, respectively. The mean value of global warming potentials (GWPs) of CH(4) and N(2)O emissions over 100\u00a0years was in the order of T2\u2009>\u2009T1\u2009>\u2009CK, which indicated CK and T1 was significantly lower than T2 (P\u2009<\u20090.05). This suggests that adoption of T1 would be beneficial for greenhouse gas emission mitigation and could be a good option cropping pattern in double rice cropped regions.", "keywords": ["2. Zero hunger", "13. Climate action", "Health", " Toxicology and Mutagenesis", "Environmental Chemistry", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "15. Life on land", "Pollution", "Research Article"], "contacts": [{"organization": "Weiyan Li, Xiaoping Xiao, Guang-Li Yang, Tang Wenguang, Jimin Sun, Ke Wang, Haiming Tang,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1007/s11356-015-4557-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20and%20Pollution%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11356-015-4557-9", "name": "item", "description": "10.1007/s11356-015-4557-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11356-015-4557-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-04-28T00:00:00Z"}}, {"id": "10.1007/s11356-020-10918-6", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:18Z", "type": "Journal Article", "created": "2020-10-03", "title": "Study of pig manure digestate pre-treatment for subsequent valorisation by struvite", "description": "AbstractThis work evaluates the release of phosphorus contained in the digestate from the anaerobic digestion of pig manure, through an acidification process. The objective of this acidification is to increase the amount of phosphorus available in the digestate liquid fraction and, subsequently, recover this element by chemical precipitation in the form of struvite or calcium phosphate. Two digestate samples (one fresh and one old) were studied and treated by adding various amounts of sulphuric acid to the different digestate fractions (raw digestate, solid fraction and liquid fraction). For the raw digestate, phosphorus releases higher than 95% were obtained for pH 4.0. In the last part of the experiment, the influence of acid pre-treatment on the reaction yield of phosphorus precipitation, in the form of struvite or calcium phosphate, was determined. Improvements in reaction yield were obtained up to 15% for struvite and 80% for calcium phosphate, increasing also in 7.5 times the amount of phosphorus available in the digestate liquid fraction, for both cases.
", "keywords": ["Biofertiliser", "FEASIBILITY", "NUTRIENT RECOVERY", "PH", "Struvite", "Swine", "SWINE WASTE-WATER", "0211 other engineering and technologies", "02 engineering and technology", "7. Clean energy", "01 natural sciences", "CALCIUM", "Acidification", "ANAEROBIC-DIGESTION", "Environmental Chemistry", "PHOSPHORUS REMOVAL", "Animals", "Chemical Precipitation", "Toxicology and Mutagenesis", "Anaerobiosis", "Organic waste", "SLUDGE", "0105 earth and related environmental sciences", "Phosphorus", "General Medicine", "Pollution", "6. Clean water", "Manure", "Nutrient recovery", "Health", "Earth and Environmental Sciences", "Release", "PRECIPITATION", "Waste and Biomass Management & Valorization", "CRYSTALLIZATION"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s11356-020-10918-6.pdf"}, {"href": "https://doi.org/10.1007/s11356-020-10918-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20and%20Pollution%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11356-020-10918-6", "name": "item", "description": "10.1007/s11356-020-10918-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11356-020-10918-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-10-03T00:00:00Z"}}, {"id": "10.1016/j.apsoil.2010.04.006", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:47Z", "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.ijheh.2019.01.004", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:37Z", "type": "Journal Article", "created": "2019-02-06", "title": "The impact of on-site hospital wastewater treatment on the downstream communal wastewater system in terms of antibiotics and antibiotic resistance genes", "description": "This study quantified antibiotic and antibiotic resistance gene (ARG) concentrations in hospital and communal wastewaters as well as the influents and effluents of the receiving urban wastewater treatment plants (UWWTP) in two Dutch cities. In only one city, hospital wastewater was treated on-site using advanced technologies, including membrane bioreactor treatment (MBR), ozonation, granulated activated carbon (GAC) and UV-treatment. On-site hospital wastewater (HWW) treatment reduced gene presence of hospital-related antibiotic resistance genes and antibiotic concentrations in the receiving urban wastewater treatment plant. These findings support the need for on-site treatment of high-risk point sources of antibiotic resistance genes. 13 antibiotic resistance genes, Integrase Class 1 and 16S rRNA concentrations were quantified using multiplex quantitative real-time PCR (qPCR) assays and the presence and/or concentration of 711 antibiotics were analyzed. Hospital wastewater contained approximately 25% more antibiotics and gene concentrations between 0.4 log to 1.8-fold higher than communal wastewater (CWW). blaKPC and vanA could be identified as hospital-related genes and were reduced to under the limit of detection (LOD) during on-site treatment. Advanced on-site treatment removed between 0.5 and 3.6-fold more genes than conventional biological urban wastewater treatment (activated sludge). Advanced on-site treatment was able to eliminate 12 out of 19 detected antibiotics, while urban waste water treatment eliminated up to 1 (out of 21 detected). Different advanced treatment technologies were able to target different pollutants to varying extents, making sequential alignment more effective. MBR treatment was most efficient in antibiotic resistance gene reduction and ozonation in antibiotic reduction. blaKPC could only be detected in the influent of the urban wastewater treatment plant receiving untreated hospital wastewater. Similarly, vanA was only consistently detected in this treatment plant. These results indicate a positive effect of on-site treatment of hospital wastewater on the communal sewage system.", "keywords": ["0301 basic medicine", "0303 health sciences", "Drug Resistance", " Microbial", "Wastewater", "Waste Disposal", " Fluid", "Hospitals", "6. Clean water", "Anti-Bacterial Agents", "12. Responsible consumption", "3. Good health", "03 medical and health sciences", "Genes", " Bacterial", "13. Climate action", "11. Sustainability", "Water Pollutants", "Advanced wastewater treatment Contaminants of emerging concern Pharmafilter Antibiotic resistance"]}, "links": [{"href": "https://doi.org/10.1016/j.ijheh.2019.01.004"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/International%20Journal%20of%20Hygiene%20and%20Environmental%20Health", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.ijheh.2019.01.004", "name": "item", "description": "10.1016/j.ijheh.2019.01.004", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.ijheh.2019.01.004"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-05-01T00:00:00Z"}}, {"id": "10.1016/j.biortech.2019.122728", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:55Z", "type": "Journal Article", "created": "2020-01-02", "title": "Effects of copper salts on performance, antibiotic resistance genes, and microbial community during thermophilic anaerobic digestion of swine manure", "description": "This study investigated methane production and ARGs reduction during thermophilic AD of swine manure with the addition of different Cu salts (cupric sulfate, cupric glycinate, and the 1:1 mixture of these two salts). Results showed methane production was increased by 28.78% through adding mixed Cu salts. The mixed Cu group effectively reduced total ARGs abundance by 26.94%, suggesting mixed Cu salts did not promote the potential ARGs risk. The positive effects of mixed Cu salts on AD performance and ARGs removal might be ascribed to the low bioavailability. Microbial community analysis indicated the highest abundances of Clostridia_MBA03 and Methanobacterium in the mixed Cu group might cause the increased methane production. Spearman's rank correlation analysis elucidated the succession in microbial community induced by environmental factors was the main driver for shaping ARGs profiles. Thus, mixed Cu salts could be an alternative to replace the inorganic Cu salt in animal feed additives.", "keywords": ["Manure", "Genes", " Bacterial", "Swine", "Microbiota", "Animals", "Drug Resistance", " Microbial", "Anaerobiosis", "01 natural sciences", "Copper", "6. Clean water", "Anti-Bacterial Agents", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.biortech.2019.122728"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioresource%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.biortech.2019.122728", "name": "item", "description": "10.1016/j.biortech.2019.122728", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.biortech.2019.122728"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-01T00:00:00Z"}}, {"id": "10.1016/j.cell.2021.04.024", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:15:58Z", "type": "Journal Article", "created": "2021-05-18", "title": "Innovation, conservation, and repurposing of gene function in root cell type development", "description": "Plant species have evolved myriads of solutions, including complex cell type development and regulation, to adapt to dynamic environments. To understand this cellular diversity, we profiled tomato root cell type translatomes. Using xylem differentiation in tomato, examples of functional innovation, repurposing, and conservation of transcription factors are described, relative to the model plant Arabidopsis. Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function. Comparative translatome analyses of rice, tomato, and Arabidopsis cell populations suggest increased expression conservation of root meristems compared with other homologous populations. In addition, the functions of constitutively expressed genes are more conserved than those of cell type/tissue-enriched genes. These observations suggest that higher order properties of cell type and pan-cell type regulation are evolutionarily conserved between plants and animals.", "keywords": ["root development", "translatomes", "General Biochemistry", "Genetics and Molecular Biology", "Green Fluorescent Proteins", "Meristem", "Arabidopsis", "cell types; evolution; exodermis; gene regulation; rice; root development; tomato; translatomes; xylem", "tomato", "xylem", "Genes", " Plant", "Plant Roots", "Inventions", "Solanum lycopersicum", "Species Specificity", "Gene Expression Regulation", " Plant", "Xylem", "evolution", "Gene Regulatory Networks", "Promoter Regions", " Genetic", "Plant Proteins", "2. Zero hunger", "exodermis", "rice", "15. Life on land", "Protein Biosynthesis", "cell types", "gene regulation", "Transcription Factors"]}, "links": [{"href": "https://www.research.unipd.it/bitstream/11577/3392826/2/PIIS0092867421005043.pdf"}, {"href": "https://doi.org/10.1016/j.cell.2021.04.024"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Cell", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.cell.2021.04.024", "name": "item", "description": "10.1016/j.cell.2021.04.024", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.cell.2021.04.024"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-06-01T00:00:00Z"}}, {"id": "10.1016/j.chemosphere.2014.06.094", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:00Z", "type": "Journal Article", "created": "2014-08-13", "title": "Influence of tetracycline on the microbial community composition and activity of nitrifying biofilms", "description": "The present work aims to evaluate the bacterial composition and activity (carbon and nitrogen removal) of nitrifying biofilms exposed to 50 \u03bcg L(-1) of tetracycline. The tetracycline removal efficiency and the occurrence of tetracycline resistance (tet) genes were also studied. Two sequencing batch biofilm reactors (SBBRs) fed with synthetic wastewater were operated without (SBBR1) and with (SBBR2) the antibiotic. Both SBBRs showed similar organic matter biodegradation and nitrification activity. Tetracycline removal was about 28% and biodegradation was probably the principal removal mechanism of the antibiotic. Polymerase chain reaction-denaturing gradient gel electrophoresis analysis of the bacterial community showed shifts leading to not only the fading of some ribotypes, but also the emergence of new ones in the biofilm with tetracycline. The study of the tet genes showed that tet(S) was only detected in the biofilm with tetracycline, suggesting a relationship between its occurrence and the presence of the antibiotic.", "keywords": ["Science & Technology", "Polymers", "Microbiota", "Molecular Sequence Data", "Tetracycline Resistance", "0211 other engineering and technologies", "Resistance genes", "Sequence Analysis", " DNA", "02 engineering and technology", "Tetracycline", "Nitrification", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "Tetracycline removal", "Nitrifying biofilms", "Bacterial Proteins", "Antibiotics", "Biofilms", "11. Sustainability", "Bacterial community", "Adsorption", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.chemosphere.2014.06.094"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Chemosphere", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.chemosphere.2014.06.094", "name": "item", "description": "10.1016/j.chemosphere.2014.06.094", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.chemosphere.2014.06.094"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-12-01T00:00:00Z"}}, {"id": "10.1016/j.ecoenv.2020.111380", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:03Z", "type": "Journal Article", "created": "2020-10-01", "title": "Effect of the growth medium composition on nitrate accumulation in the novel protein crop Lemna minor", "description": "Duckweed is a potential alternative protein source for food and feed. However, little is known about the nitrate accumulation in this plant. A high nitrate level in vegetables can indirectly lead to an elevated intake of nitrites and N-nitroso compounds, increasing the risk of diseases for humans and animals. This research hypothesizes that the nitrate accumulation of Lemna minor differs between growing media. Additionally, it evaluates whether legal safety levels of nitrate for human and animal intake are exceeded. The duckweed was grown on (i) rainwater, and (ii) three synthetic media containing different nutrient levels. Furthermore, (iii) biological effluent of swine manure treatment and (iv) aquaculture effluent from pikeperch production were used, as these are potential media for closing nutrient loops in the agriculture sector. It was found that nitrate levels increased with the increasing availability of macronutrients in the water, and pH showed a particularly strong negative correlation with the nitrate levels in the plant. Nevertheless, nitrate content never exceeded 530\u00a0mg NO3 kg-1 fresh weight. To conclude, Lemna minor's nitrate content was below safety limits for human consumption in all tested growing media; however, a potential risk for ruminants was observed as these are more sensitive to nitrate conversions in their gastro-intestinal track.", "keywords": ["Agriculture and Food Sciences", "0106 biological sciences", "0301 basic medicine", "SAMPLES", "Wastewater", "NUTRIENTS", "01 natural sciences", "Food safety", "BIOMASS", "03 medical and health sciences", "Crude protein", "Vegetables", "Lemnaceae", "Animals", "Araceae", "Humans", "Toxicology and Mutagenesis", "PLANT", "FRUITS", "VEGETABLES", "2. Zero hunger", "Nitrates", "Environmental and Occupational Health", "Agricultural effluents", "NITRITE CONTENT", "Agriculture", "General Medicine", "Hydrogen-Ion Concentration", "Pollution", "DUCKWEEDS LEMNACEAE", "6. Clean water", "Culture Media", "NITROGEN", "Feed safety", "Health", "Public Health", "Dietary Proteins"]}, "links": [{"href": "https://doi.org/10.1016/j.ecoenv.2020.111380"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecotoxicology%20and%20Environmental%20Safety", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.ecoenv.2020.111380", "name": "item", "description": "10.1016/j.ecoenv.2020.111380", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.ecoenv.2020.111380"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-12-01T00:00:00Z"}}, {"id": "10.1016/j.envint.2019.03.060", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:12Z", "type": "Journal Article", "created": "2019-04-05", "title": "Characterization of wastewater effluents in the Danube River Basin with chemical screening, in vitro bioassays and antibiotic resistant genes analysis", "description": "Averaged 7-day composite effluent wastewater samples from twelve wastewater treatment plants (WWTPs) in nine countries (Romania, Serbia, Hungary, Slovenia, Croatia, Slovakia, Czechia, Austria, Germany) in the Danube River Basin were collected. WWTPs' selection was based on countries' dominant technology and a number of served population with the aim to get a representative holistic view of the pollution status. Samples were analyzed for 2248 chemicals of emerging concern (CECs) by wide-scope target screening employing LC-ESI-QTOF-MS. 280 compounds were detected at least in one sample and quantified. Spatial differences in the concentrations and distribution of the compounds classes were discussed. Additionally, samples were analyzed for the possible agonistic/antagonistic potencies using a panel of in vitro transactivation reporter gene CALUX\u00ae bioassays including ER\u03b1 (estrogenics), anti-AR (anti-androgens), GR (glucocorticoids), anti-PR (anti-progestins), PPAR\u03b1 and PPAR\u03b3 (peroxisome proliferators) and PAH assays. The potency of the wastewater samples to cause oxidative stress and induce xenobiotic metabolism was determined using the Nrf2 and PXR CALUX\u00ae bioassays, respectively. The signals from each of the bioassays were compared with the recently developed effect-based trigger values (EBTs) and thus allowed for allocating the wastewater effluents into four categories based on their measured toxicity, proposing a putative action plan for wastewater operators. Moreover, samples were analyzed for antibiotics and 13 antibiotic-resistant genes (ARGs) and one mobile genetic element (intl1) with the aim to assess the potential for antibiotic resistance. All data collected from these various types of analysis were stored in an on-line database and can be viewed via interactive map at https://norman-data.eu/EWW_DANUBE.", "keywords": ["0211 other engineering and technologies", "500", "Drug Resistance", " Microbial", "02 engineering and technology", "Wide-scope target screening", "Wastewater", "01 natural sciences", "Bioassays", "6. Clean water", "Anti-Bacterial Agents", "Environmental sciences", "Rivers", "13. Climate action", "Emerging substances", "Antibiotic resistant genes", "Effluent wastewater", "GE1-350", "Biological Assay", "Danube River Basin", "Emerging substances Wide-scope target screening Effluent wastewater Bioassays Antibiotic resistant genes Danube River Basin", "Water Pollutants", " Chemical", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.envint.2019.03.060"}, {"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.2019.03.060", "name": "item", "description": "10.1016/j.envint.2019.03.060", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envint.2019.03.060"}, {"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": "10.1016/j.envpol.2018.09.128", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:14Z", "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.envpol.2010.10.040", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:13Z", "type": "Journal Article", "created": "2011-01-24", "title": "Processes And Factors Controlling N2o Production In An Intensively Managed Low Carbon Calcareous Soil Under Sub-Humid Monsoon Conditions", "description": "An automated system for continuous measurement of N\u2082O fluxes on an hourly basis was employed to study N\u2082O emissions in an intensively managed low carbon calcareous soil under sub-humid temperate monsoon conditions. N\u2082O emissions occurred mainly within two weeks of application of NH\u2084(+) based fertilizer and total N\u2082O emissions in wheat (average 0.35 or 0.21 kg N ha\u207b\u00b9 season\u207b\u00b9) and maize (average 1.47 or 0.49 kg N ha\u207b\u00b9 season\u207b\u00b9) under conventional and optimum N fertilization (300 and 50-122 kg N ha\u207b\u00b9, respectively) were lower than previously reported from low frequency measurements. Results from closed static chamber showed that N\u2082O was produced mainly from nitrification of NH\u2084(+)-based fertilizer, with little denitrification occurring due to limited readily oxidizable carbon and low soil moisture despite consistently high soil nitrate-N concentrations. Significant reductions in N\u2082O emissions can be achieved by optimizing fertilizer N rates, using nitrification inhibitors, or changing from NH\u2084(+)- to NO\u2083(-)-based fertilizers.", "keywords": ["/dk/atira/pure/subjectarea/asjc/2300/2307", "13. Climate action", "Health", " Toxicology and Mutagenesis", "/dk/atira/pure/subjectarea/asjc/3000/3005", "/dk/atira/pure/subjectarea/asjc/2300/2310", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "Toxicology", "Pollution", "01 natural sciences", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.envpol.2010.10.040"}, {"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.2010.10.040", "name": "item", "description": "10.1016/j.envpol.2010.10.040", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envpol.2010.10.040"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-04-01T00:00:00Z"}}, {"id": "10.1016/j.envpol.2017.04.062", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:14Z", "type": "Journal Article", "created": "2017-04-29", "title": "Ecological impacts of atmospheric pollution and interactions with climate change in terrestrial ecosystems of the Mediterranean Basin: Current research and future directions", "description": "Mediterranean Basin ecosystems, their unique biodiversity, and the key services they provide are currently at risk due to air pollution and climate change, yet only a limited number of isolated and geographically-restricted studies have addressed this topic, often with contrasting results. Particularities of air pollution in this region include high O3 levels due to high air temperatures and solar radiation, the stability of air masses, and dominance of dry over wet nitrogen deposition. Moreover, the unique abiotic and biotic factors (e.g., climate, vegetation type, relevance of Saharan dust inputs) modulating the response of Mediterranean ecosystems at various spatiotemporal scales make it difficult to understand, and thus predict, the consequences of human activities that cause air pollution in the Mediterranean Basin. Therefore, there is an urgent need to implement coordinated research and experimental platforms along with wider environmental monitoring networks in the region. In particular, a robust deposition monitoring network in conjunction with modelling estimates is crucial, possibly including a set of common biomonitors (ideally cryptogams, an important component of the Mediterranean vegetation), to help refine pollutant deposition maps. Additionally, increased attention must be paid to functional diversity measures in future air pollution and climate change studies to establish the necessary link between biodiversity and the provision of ecosystem services in Mediterranean ecosystems. Through a coordinated effort, the Mediterranean scientific community can fill the above-mentioned gaps and reach a greater understanding of the mechanisms underlying the combined effects of air pollution and climate change in the Mediterranean Basin.", "keywords": ["air pollution; climate change; coordinated research networks; environmental monitoring; functional diversity; Mediterranean ecosystems; toxicology; pollution", "570", "Coordinated research networks", "550", "Nitrogen", "Climate", "Climate Change", "Air pollution", "Functional diversity", "01 natural sciences", "Air Pollution", "11. Sustainability", "Climate change", "Humans", "14. Life underwater", "Ecosystem", "0105 earth and related environmental sciences", "2. Zero hunger", "Air Pollutants", "Atmosphere", "Research", "Aquatic Ecology", "Environmental monitoring", "Biodiversity", "15. Life on land", "Medio Ambiente", "13. Climate action", "Air pollution; Climate change; Coordinated research networks; Environmental monitoring; Functional diversity; Mediterranean ecosystems; Air Pollutants; Air Pollution; Atmosphere; Biodiversity; Climate; Humans; Nitrogen; Research; Climate Change; Ecosystem; Environmental Monitoring", "Mediterranean ecosystems", "Air pollution; Climate change; Coordinated research networks; Environmental monitoring; Functional diversity; Mediterranean ecosystems; Toxicology; Pollution; Health", " Toxicology and Mutagenesis", "Air pollution; Climate change; Coordinated research networks; Environmental monitoring; Functional diversity; Mediterranean ecosystems; Air Pollutants; Air Pollution; Atmosphere; Biodiversity; Climate; Humans; Nitrogen; Research; Climate Change; Ecosystem; Environmental Monitoring; Toxicology; Pollution; Health", " Toxicology and Mutagenesis", "Environmental Monitoring"]}, "links": [{"href": "https://eprints.lancs.ac.uk/id/eprint/86451/1/CAPERMed06042017_F.pdf"}, {"href": "https://doi.org/10.1016/j.envpol.2017.04.062"}, {"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.2017.04.062", "name": "item", "description": "10.1016/j.envpol.2017.04.062", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envpol.2017.04.062"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-08-01T00:00:00Z"}}, {"id": "10.1016/j.envpol.2023.121325", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:15Z", "type": "Journal Article", "created": "2023-02-22", "title": "Extracellular DNA includes an important fraction of high-risk antibiotic resistance genes in treated wastewaters", "description": "Wastewater treatment plants are among the main hotspots for the release of antibiotic resistance genes (ARGs) into the environment. ARGs in treated wastewater can be found in the intracellular DNA (iDNA) and in the extracellular DNA (eDNA). In this study, we investigated the fate and the distribution (either in eDNA or in iDNA) of ARGs in the treated wastewaters pre and post-disinfection by shotgun metagenomics. The richness of the intracellular resistome was found to be higher than the extracellular one. However, the latter included different high risk ARGs. About 11% of the recovered metagenome assembled genomes (MAGs) from the extracted DNA was positive for at least one ARG and, among them, several were positive for more ARGs. The high-risk ARG bacA was the most frequently detected gene among the MAGs. The disinfection demonstrated to be an important driver of the composition of the antibiotic resistomes. Our results demonstrated that eDNA represents an important fraction of the overall ARGs, including a number of high-risk ARGs, which reach the environment with treated wastewater effluents. The studied disinfections only marginally affect the whole antibiotic resistome but cause important shifts from intracellular to extracellular DNA, potentially threating human health.", "keywords": ["0301 basic medicine", "0303 health sciences", "Drug Resistance", " Microbial", "DNA", "Wastewater", "Antimicrobial resistance", "6. Clean water", "MAG", "Anti-Bacterial Agents", "Disinfection", "03 medical and health sciences", "13. Climate action", "Extracellular DNA", "Genes", " Bacterial", "Humans", "Metagenomics"]}, "links": [{"href": "https://doi.org/10.1016/j.envpol.2023.121325"}, {"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.2023.121325", "name": "item", "description": "10.1016/j.envpol.2023.121325", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envpol.2023.121325"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-04-01T00:00:00Z"}}, {"id": "10.1016/j.envres.2018.12.007", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:15Z", "type": "Journal Article", "created": "2018-12-06", "title": "Distribution of antibiotic resistance genes in soils and crops. A field study in legume plants (Vicia faba L.) grown under different watering regimes", "description": "Social concern has raised during the last years due to the development of antibiotic resistance hotspots in different environmental compartments, including the edible parts of crops. To assess the influence of the water quality used for watering, we collected samples from soil, roots, leaves and beans from the legume plant Vicia faba (broad beans) in three agricultural peri-urban plots (Barcelona, NE Spain), irrigated with either groundwater, river water, or reclaimed water. Antibiotic resistance genes (ARGs) sul1, tetM, qnrS1, blaCTX-M-32,blaOXA-58, mecA, and blaTEM were quantified by real-time PCR, along with 16S rDNA and intl1 sequences, as proxies for bacterial abundance and integron prevalence, respectively. Microbiome composition of all samples were analyzed by high-throughput DNA sequencing. Results show a gradient of bacterial species diversity and of ARG prevalence from highly diverse soil samples to microbially-poor beans and leaves, in which Rhizobiales essentially displaced all other groups, and that presented very small loads of ARGs and integron sequences. The data suggest that the microbiome and the associated resistome were likely influenced by agricultural practices and water quality, and that future irrigation water legal standards should consider the specific Physiology of the different crop plants.", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Agriculture", "Drug Resistance", " Microbial", "Fabaceae", "Wastewater", "15. Life on land", "6. Clean water", "Anti-Bacterial Agents", "Vicia faba", "Soil", "03 medical and health sciences", "Genes", " Bacterial", "Spain", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1016/j.envres.2018.12.007"}, {"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.2018.12.007", "name": "item", "description": "10.1016/j.envres.2018.12.007", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envres.2018.12.007"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-03-01T00:00:00Z"}}, {"id": "10.1016/j.envres.2019.108608", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:15Z", "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.envres.2024.118395", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:15Z", "type": "Journal Article", "created": "2024-02-01", "title": "Sustainable strategies: Nature-based solutions to tackle antibiotic resistance gene proliferation and improve agricultural productivity and soil quality", "description": "The issue of antibiotic resistance is now recognized by the World Health Organisation (WHO) as one of the major problems in human health. Although its effects are evident in the healthcare settings, the root cause should be traced back to the One Health link, extending from animals to the environment. In fact, the use of organic fertilizers in agroecosystems represents one, if not the primary, cause of the introduction of antibiotics and antibiotic-resistant bacteria into the soil. Since the concentrations of antibiotics introduced into the soil are residual, the agroecosystem has become a perfect environment for the selection and proliferation of antibiotic resistance genes (ARGs). The continuous influx of these emerging contaminants (i.e., antibiotics) into the agroecosystem results in the selection and accumulation of ARGs in soil bacteria, occasionally giving rise to multi-resistant bacteria. These bacteria may harbour ARGs related to various antibiotics on their plasmids. In this context, these bacteria can potentially enter the human sphere when individuals consume food from contaminated agroecosystems, leading to the acquisition of multi-resistant bacteria. Once introduced into the nosocomial environment, these bacteria pose a significant threat to human health. In this review, we analyse how the use of digestate as an organic fertilizer can mitigate the spread of ARGs in agroecosystems. Furthermore, we highlight how, according to European guidelines, digestate can be considered a Nature-Based Solution (NBS). This NBS not only has the ability to mitigate the spread of ARGs in agroecosystems but also offers the opportunity to further improve Microbial-Based Solutions (MBS), with the aim of enhancing soil quality and productivity.", "keywords": ["Manure", "Soil", "Bacteria", "Genes", " Bacterial", "agroecosystem; digestate; one health; microbial-based solutions", "Animals", "Humans", "Drug Resistance", " Microbial", "Soil Microbiology", "Anti-Bacterial Agents", "Cell Proliferation"]}, "links": [{"href": "https://doi.org/10.1016/j.envres.2024.118395"}, {"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.2024.118395", "name": "item", "description": "10.1016/j.envres.2024.118395", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envres.2024.118395"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-05-01T00:00:00Z"}}, {"id": "10.1016/j.fpsl.2020.100620", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:28Z", "type": "Journal Article", "created": "2021-01-10", "title": "Combination of ferulic acid with Aloe vera gel or alginate coatings for shelf-life prolongation of fresh-cut apples", "description": "Open AccessWeight loss, microbial spoilage and enzymatic browning are the main quality-determining processes which limit the shelf-life of fresh-cut apples. In this study, two edible coatings based on Aloe vera gel (AV) and sodium alginate cross-linked with calcium lactate (AC), with the addition of 10 mg/mL ferulic acid (FA) as a functional ingredient, were developed in order to prolong the quality and safety of fresh-cut apple discs. Texture parameters, pH and Brix values and water activity did not undergo relevant changes related to the treatments. Except for weight loss, which was significantly lower for the coated samples, the addition of FA was found to be the most relevant factor for the other investigated parameters, including the total phenolic content and the antioxidant activity measured by ferric reducing antioxidant power (FRAP). Browning was delayed by the addition of FA and also by the AV coating, while non-coated and alginate coated samples showed the highest values in early stages. Although no effect on Saccharomyces cerevisiae was observed, FA treatments and alginate were effective in reducing Listeria monocytogenes populations by 2.3 \u00b1 0.4 log CFU / g, which contributes to an enhanced product safety.", "keywords": ["2. Zero hunger", "Weight loss", "0404 agricultural biotechnology", "Browning", "Fresh-cut fruit", "Ferulic acid", "04 agricultural and veterinary sciences", "Edible coatings", "Listeria monocytogenes", "Preservation", "631"]}, "links": [{"href": "https://doi.org/10.1016/j.fpsl.2020.100620"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Food%20Packaging%20and%20Shelf%20Life", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.fpsl.2020.100620", "name": "item", "description": "10.1016/j.fpsl.2020.100620", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.fpsl.2020.100620"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-01T00:00:00Z"}}, {"id": "10.1016/j.ijfoodmicro.2021.109043", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:37Z", "type": "Journal Article", "created": "2021-01-08", "title": "Unraveling the emergence and population diversity of Listeria monocytogenes in a newly built meat facility through whole genome sequencing", "description": "The food processing environments of a newly opened meat processing facility were sampled in ten visits carried out during its first 1.5\u00a0years of activity and analyzed for the presence of Listeria monocytogenes. A total of 18 L. monocytogenes isolates were obtained from 229 samples, and their genomes were sequenced to perform comparative genomic analyses. An increase in the frequency of isolation of L. monocytogenes and in the diversity of sequence types (STs) detected was observed along time. Although the strains isolated belonged to six different STs (ST8, ST9, ST14, ST37, ST121 and ST155), ST9 was the most abundant (8 out of 18 strains). Low (0 and 2) single nucleotide polymorphism (SNP) distances were found between two pairs of ST9 strains isolated in both cases 3\u00a0months apart from the same processing room (Lm-1267 and Lm-1705, with a 2 SNPs distance in the core genome; Lm-1265 and Lm-1706, with a 0 SNPs distance), which suggests that these strains may be persistent L. monocytogenes strains in the food processing environment. Most strains showed an in silico attenuated virulence potential either through the truncation of InlA (in 67% of the isolates) or the absence of other virulence factors involved in cell adhesion or invasion. Twelve of the eighteen L. monocytogenes isolates contained a plasmid, which ranged in size from 4 to 87 Kb and harbored stress survival, in addition to heavy metals and biocides resistance determinants. Identical or highly similar plasmids were identified for various sets of L. monocytogenes ST9 isolates, which suggests the clonal expansion and persistence of plasmid-containing ST9 strains in the processing environments of the meat facility. Finally, the analysis of the L. monocytogenes genomes available in the NCBI database, and their associated metadata, evidenced that strains from ST9 are more frequently reported in Europe, linked to foods, particularly to meat and pork products, and less represented among clinical isolates than other L. monocytogenes STs. It also showed that the ST9 strains here isolated were more closely related to the European isolates, which clustered together and separated from ST9 North American isolates.", "keywords": ["0301 basic medicine", "Meat", "Food Handling", "Swine", "Virulence Factors", "Tecnolog\u00eda de los alimentos", "Food processing environment", "Persistence", "03 medical and health sciences", "Manufacturing and Industrial Facilities", "Floors and Floorcoverings", "Animals", "2. Zero hunger", "0303 health sciences", "Virulence", "Whole Genome Sequencing", "Genetic Variation", "Gen\u00e9tica", "Listeria monocytogenes", "Europe", "Genes", " Bacterial", "Whole genome sequencing", "Food Microbiology", "Equipment Contamination", "Disinfectants", "Plasmids"]}, "links": [{"href": "https://doi.org/10.1016/j.ijfoodmicro.2021.109043"}, {"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.2021.109043", "name": "item", "description": "10.1016/j.ijfoodmicro.2021.109043", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.ijfoodmicro.2021.109043"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-01T00:00:00Z"}}, {"id": "10.1016/j.jafr.2023.100732", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:39Z", "type": "Journal Article", "created": "2023-08-07", "title": "Aeromycological studies in the crops of the main cereals: A systematic review", "description": "Open AccessLes \u00e9tudes a\u00e9romycologiques sur les cultures c\u00e9r\u00e9ali\u00e8res permettent de d\u00e9terminer la variation temporelle des agents pathog\u00e8nes des plantes affectant la culture et de d\u00e9terminer le moment appropri\u00e9 pour appliquer les fongicides. Cependant, ce sujet n'a pas \u00e9t\u00e9 syst\u00e9matiquement revu. L'objectif de ce travail \u00e9tait d'analyser syst\u00e9matiquement toutes les \u00e9tudes a\u00e9romycologiques r\u00e9alis\u00e9es sur le ma\u00efs, le bl\u00e9, le riz, l'avoine, l'orge, le seigle, le sorgho et le millet. Une recherche syst\u00e9matique a \u00e9t\u00e9 effectu\u00e9e dans Scopus depuis le d\u00e9but de la base de donn\u00e9es jusqu'au 1er ao\u00fbt 2022. Les crit\u00e8res d'inclusion \u00e9taient qu'il s'agissait d'\u00e9tudes a\u00e9romycologiques sur le bl\u00e9 ou le riz ou le ma\u00efs ou l'avoine ou le sorgho ou le seigle ou l'orge ou le millet et d'\u00e9tudes publi\u00e9es dans des revues \u00e0 comit\u00e9 de lecture index\u00e9es dans Journal Citation Reports et r\u00e9dig\u00e9es en anglais ou en espagnol. Quarante-trois \u00e9tudes (21 sur le bl\u00e9, 15 sur le riz, 5 sur le ma\u00efs, 1 sur le sorgho et 2 sur l'orge) r\u00e9pondant \u00e0 tous les crit\u00e8res d'\u00e9ligibilit\u00e9 ont \u00e9t\u00e9 incluses (une des \u00e9tudes sur le ma\u00efs a \u00e9galement \u00e9t\u00e9 men\u00e9e sur le bl\u00e9). Aucune \u00e9tude a\u00e9romycologique n'a \u00e9t\u00e9 trouv\u00e9e chez l'avoine, le seigle et le millet. Il a \u00e9t\u00e9 not\u00e9 que la plupart des recherches a\u00e9romycologiques ont \u00e9t\u00e9 men\u00e9es sur les cultures de bl\u00e9 et principalement dans les pays des Am\u00e9riques. De plus, les propagules fongiques sont principalement collect\u00e9es par des m\u00e9thodes non viables, en utilisant divers types de collecteurs. En g\u00e9n\u00e9ral, les \u00e9tudes visaient \u00e0 identifier un agent pathog\u00e8ne sp\u00e9cifique et non \u00e0 la diversit\u00e9 des agents pathog\u00e8nes qui peuvent \u00eatre trouv\u00e9s. La relation des champignons identifi\u00e9s avec les param\u00e8tres m\u00e9t\u00e9orologiques \u00e9tait variable dans les diff\u00e9rentes \u00e9tudes. Cette revue syst\u00e9matique permet de r\u00e9sumer les \u00e9tudes a\u00e9romycologiques qui ont \u00e9t\u00e9 men\u00e9es sur les cultures de bl\u00e9, de riz, de ma\u00efs, de sorgho et d'orge. Il sugg\u00e8re \u00e9galement o\u00f9 les futures \u00e9tudes dans ce domaine devraient \u00eatre dirig\u00e9es, en fonction des limites rencontr\u00e9es.", "keywords": ["Impacts of Elevated CO2 and Ozone on Plant Physiology", "Agriculture (General)", "Health", " Toxicology and Mutagenesis", "Plant Science", "Crop", "S1-972", "Agricultural and Biological Sciences", "Barley", "Biochemistry", " Genetics and Molecular Biology", "TX341-641", "10. No inequality", "Biology", "Sorghum", "2. Zero hunger", "Corn", "Airborne spores", "Nutrition. Foods and food supply", "Life Sciences", "Phylogenetic Analysis", "Cell Biology", "15. Life on land", "2414.06 Hongos", "Agronomy", "3. Good health", "Wheat", "Environmental Science", "Physical Sciences", "Rice", "Indoor Air Quality and Health Effects", "Diversity and Evolution of Fungal Pathogens", "Biotechnology"]}, "links": [{"href": "https://doi.org/10.1016/j.jafr.2023.100732"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Agriculture%20and%20Food%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jafr.2023.100732", "name": "item", "description": "10.1016/j.jafr.2023.100732", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jafr.2023.100732"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-01T00:00:00Z"}}, {"id": "10.1016/j.jhazmat.2020.123208", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:45Z", "type": "Journal Article", "created": "2020-06-17", "title": "Effects of prescription antibiotics on soil- and root-associated microbiomes and resistomes in an agricultural context", "description": "The use of treated wastewater for crop irrigation is rapidly increasing to respond to the ever-growing demands for water and food resources. However, this practice may contribute to the spread of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in agricultural settings. To evaluate this potential risk, we analyzed microbiomes and resistomes of soil and Lactuca sativa L. (lettuce) root samples from pots irrigated with tap water spiked with 0, 20, or 100 \u03bcg L-1 of a mixture of three antibiotics (Trimethoprim, Ofloxacin, Sulfamethoxazole). The presence of antibiotics induced changes in bacterial populations, particularly in soil, as revealed by 16S rDNA sequence analysis. Parallel shotgun sequencing identified a total of 56 different ARGs conferring resistance against 14 antibiotic families. Antibiotic -treated samples showed increased loads of ARGs implicated in mutidrug resistance or in both direct and indirect acquired resistance. These changes correlated with the prevalence of Xantomonadales species in the root microbiomes. We interpret these data as indicating different strategies of soil and root microbiomes to cope with the presence of antibiotics, and as a warning that their presence may increase the loads of ARBs and ARGs in edible plant parts, therefore constituting a potential risk for human consumers.", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Microbiota", "Angiotensin-Converting Enzyme Inhibitors", "Drug Resistance", " Microbial", "6. Clean water", "Anti-Bacterial Agents", "Angiotensin Receptor Antagonists", "Soil", "03 medical and health sciences", "Prescriptions", "Genes", " Bacterial", "Humans", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1016/j.jhazmat.2020.123208"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Hazardous%20Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jhazmat.2020.123208", "name": "item", "description": "10.1016/j.jhazmat.2020.123208", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jhazmat.2020.123208"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-12-01T00:00:00Z"}}, {"id": "10.1016/j.jhazmat.2021.126527", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:45Z", "type": "Journal Article", "created": "2021-06-29", "title": "Reduction of antibiotic resistance determinants in urban wastewater by ozone: Emphasis on the impact of wastewater matrix towards the inactivation kinetics, toxicity and bacterial regrowth", "description": "This study investigated the impact of bench-scale ozonation on the inactivation of total cultivable and antibiotic-resistant bacteria (faecal coliforms, Escherichia coli, Pseudomonas aeruginosa, Enterococcus spp., and total heterotrophs), and the reduction of gene markers (16S rRNA and intl1) and antibiotic resistance genes (qacE\u03941, sul1, aadA1 and dfrA1) indigenously present in wastewater effluents treated by membrane bioreactor (MBR) or conventional activated sludge (CAS). The Chick-Watson model-predicted ozone exposure (CT) requirements, showed that higher CT values were needed for CAS- than MBR-treated effluents to achieve a 3-log reduction of each microbial group, i.e., ~30 and 10 gO3 min gDOC-1 respectively. Ozonation was efficient in inactivating the examined antibiotic-resistant bacteria, and no bacterial regrowth was observed after 72\u00a0h. The genes abundance decreased significantly by ozone, but an increase in their abundance was detected 72\u00a0h after storage of the treated samples. A very low removal of DOC was achieved and at the same time phyto- and eco-toxicity increased after the ozonation treatment in both wastewater matrices. The gene abundance, regrowth and toxicity results of this study may be of high environmental significance for comprehensive evaluation of ozone and may guide future studies in assessing these parameters for other oxidants/disinfectants.", "keywords": ["Bacteria", "0211 other engineering and technologies", "Drug Resistance", " Microbial", "02 engineering and technology", "Wastewater", "Waste Disposal", " Fluid", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "Disinfection", "Kinetics", "Ozone", "Genes", "13. Climate action", "Ozonation", "Phytotoxicity", "RNA", " Ribosomal", " 16S", "11. Sustainability", "Ecotoxicity", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.jhazmat.2021.126527"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Hazardous%20Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jhazmat.2021.126527", "name": "item", "description": "10.1016/j.jhazmat.2021.126527", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jhazmat.2021.126527"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-10-01T00:00:00Z"}}, {"id": "10.1016/j.jhazmat.2021.127155", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:45Z", "type": "Journal Article", "created": "2021-09-09", "title": "Elevated levels of antibiotic resistance in groundwater during treated wastewater irrigation associated with infiltration and accumulation of antibiotic residues", "description": "Treated wastewater irrigation (TWW) releases antibiotics and antibiotic resistance genes (ARGs) into the environment and might thus promote the dissemination of antibiotic resistance in groundwater (GW). We hypothesized that TWW irrigation increases ARG abundance in GW through two potential mechanisms: the contamination of GW with resistant bacteria and the accumulation of antibiotics in GW. To test this, the GW below a real-scale TWW-irrigated field was sampled for six months. Sampling took place before, during and after high-intensity TWW irrigation. Samples were analysed with 16S rRNA amplicon sequencing, qPCR of six ARGs and the class 1 integron-integrase gene intI1, while liquid chromatography tandem mass spectrometry was performed to detect antibiotic and pharmaceutical residues. Absolute abundance of 16S rRNA in GW decreased rather than increased during long-term irrigation. Also, the relative abundance of TWW-related bacteria did not increase in GW during long-term irrigation. In contrast, long-term TWW irrigation increased the relative abundance of sul1 and intI1 in the GW microbiome. Furthermore, GW contained elevated concentrations of sulfonamide antibiotics, especially sulfamethoxazole, to which sul1 confers resistance. Total sulfonamide concentrations in GW correlated with sul1 relative abundance. Consequently, TWW irrigation promoted sul1 and intI1 dissemination in the GW microbiome, most likely due to the accumulation of drug residues.", "keywords": ["Genes", " Bacterial", "RNA", " Ribosomal", " 16S", "Drug Resistance", " Microbial", "Wastewater", "Groundwater", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.jhazmat.2021.127155"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Hazardous%20Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jhazmat.2021.127155", "name": "item", "description": "10.1016/j.jhazmat.2021.127155", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jhazmat.2021.127155"}, {"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.jhazmat.2024.134885", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:45Z", "type": "Journal Article", "created": "2024-06-12", "title": "Anthropogenic pollution may enhance natural transformation in water, favouring the spread of antibiotic resistance genes", "description": "Aquatic ecosystems are crucial in the antimicrobial resistance cycle. While intracellular DNA has been extensively studied to understand human activity's impact on antimicrobial resistance gene (ARG) dissemination, extracellular DNA is frequently overlooked. This study examines the effect of anthropogenic water pollution on microbial community diversity, the resistome, and ARG dissemination. We analyzed intracellular and extracellular DNA from wastewater treatment plant effluents and lake surface water by shotgun sequencing. We also conducted experiments to evaluate anthropogenic pollution's effect on transforming extracellular DNA (using Gfp-plasmids carrying ARGs) within a natural microbial community. Chemical analysis showed treated wastewater had higher anthropogenic pollution-related parameters than lake water. The richness of microbial community, antimicrobial resistome, and high-risk ARGs was greater in treated wastewaters than in lake waters both for intracellular and extracellular DNA. Except for the high-risk ARGs, richness was significantly higher in intracellular than in extracellular DNA. Several ARGs were associated with mobile genetic elements and located on plasmids. Furthermore, Gfp-plasmid transformation within a natural microbial community was enhanced by anthropogenic pollution levels. Our findings underscore anthropogenic pollution's pivotal role in shaping microbial communities and their antimicrobial resistome. Additionally, it may facilitate ARG dissemination through extracellular DNA plasmid uptake.", "keywords": ["Bacteria", "Antibiotic resistance", "Microbiota", "Water Pollution", "Metagenome assembled genomes", "Drug Resistance", " Microbial", "Horizontal gene transfer", "Wastewater", "extracellular DNA; antibiotic resistance; metagenome assembled genomes; transformation; horizontal gene transfer", "Transformation", "Anti-Bacterial Agents", "Lakes", "Extracellular DNA", "Genes", " Bacterial", "Drug Resistance", " Bacterial", "Water Microbiology", "Plasmids"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/1115155/2/Sivalingam%20et%20al%202024.pdf"}, {"href": "https://doi.org/10.1016/j.jhazmat.2024.134885"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Hazardous%20Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jhazmat.2024.134885", "name": "item", "description": "10.1016/j.jhazmat.2024.134885", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jhazmat.2024.134885"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-08-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2018.10.268", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:58Z", "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.scitotenv.2019.03.176", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:58Z", "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": "10.1016/j.scitotenv.2019.135733", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:16:58Z", "type": "Journal Article", "created": "2019-11-26", "title": "International tempo-spatial study of antibiotic resistance genes across the Rhine river using newly developed multiplex qPCR assays", "description": "The aim of this study was to capture and explain changes in antibiotic resistance gene (ARG) presence and concentration internationally across the Rhine river. Intl1 concentrations and national antibiotic usage were investigated as proxies to predict anthropogenic ARG pollution. Newly-developed multiplex qPCR assays were employed to investigate ARG profiles across 8 locations (L1-L8) in three countries (Switzerland, Germany, the Netherlands) and to detect potential regional causes for variation. Two of these locations were further monitored, over the duration of one month. A total of 13 ARGs, Intl1 and 16S rRNA were quantified. ARG presence and concentrations initially increased from L1(Diepoldsau) to L3(Darmstadt). A continuous increase could not be observed at subsequent locations, with the large river volume likely being a major contributing factor for stability. ARG presence and concentrations fluctuated widely across different locations. L2(Basel) and L3 were the two most polluted locations, coinciding with these locations being well-developed pharmaceutical production locations. We draw attention to the characteristic, clearly distinct ARG profiles, with gene presence being consistent and gene concentrations varying significantly less over time than across different locations. Five genes were Rhine-typical (ermB, ermF, Intl1, sul1 and tetM). Intl1 and sul1 were the genes with highest and second-highest concentration, respectively. Aph(III)a and blaOXA were permanently introduced downstream of L1, indicating no source of these genes prior to L1. We highlight that correlations between Intl1 and ARG concentrations (R2\u00a0=\u00a00.72) were driven by correlations to sul1 and disappeared when excluding sul1 from the analysis (R2\u00a0=\u00a00.05). Intl1 therefore seems to be a good proxy for sul1 concentrations but not necessarily for overall (anthropogenic) ARG pollution. Aminoglycoside usage per country correlated with concentrations of aph(III)a and several unrelated antibiotic resistance genes (blaOXA,ermB, ermF and tetM). This correlation can be explained by co-resistance caused by mobile genetic elements (MGEs), such as Tn1545.", "keywords": ["0301 basic medicine", "03 medical and health sciences", "Rivers", "Genes", " Bacterial", "13. Climate action", "Germany", "RNA", " Ribosomal", " 16S", "Drug Resistance", " Microbial", "01 natural sciences", "Switzerland", "Anti-Bacterial Agents", "Netherlands", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2019.135733"}, {"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.2019.135733", "name": "item", "description": "10.1016/j.scitotenv.2019.135733", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2019.135733"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2007.02.001", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:04Z", "type": "Journal Article", "created": "2007-03-13", "title": "Nitrogen Fertilization Reduces Diversity And Alters Community Structure Of Active Fungi In Boreal Ecosystems", "description": "Nitrogen (N) availability is increasing in many ecosystems due to anthropogenic disturbance. We used a nucleotide analog technique and sequencing of ribosomal RNA genes to test whether N fertilization altered active fungal communities in two boreal ecosystems. In decaying litter from a recently burned spruce forest, Shannon diversity decreased significantly with N fertilization, and taxonomic richness declined from 44 to 33 operational taxonomic units (OTUs). In soils from a mature spruce forest, richness also declined with N fertilization, from 67 to 52 OTUs. Fungal community structure in litter differed significantly with N fertilization, primarily because fungi of the order Ceratobasidiales increased in abundance. We observed similar changes in fungal diversity and community structure with starch addition to litter, suggesting that N fertilization may affect fungal communities by altering plant carbon inputs. These changes could have important consequences for ecosystem processes such as decomposition and nutrient mineralization.", "keywords": ["ribosomal genes", "0301 basic medicine", "nucleotide analog", "carbon", "04 agricultural and veterinary sciences", "15. Life on land", "nitrogen", "diversity", "03 medical and health sciences", "fertilization", "litter quality", "0401 agriculture", " forestry", " and fisheries", "fungi", "boreal forest", "community structure"]}, "links": [{"href": "https://escholarship.org/content/qt2rs399mh/qt2rs399mh.pdf"}, {"href": "https://doi.org/10.1016/j.soilbio.2007.02.001"}, {"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.2007.02.001", "name": "item", "description": "10.1016/j.soilbio.2007.02.001", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2007.02.001"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-08-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2011.03.005", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:08Z", "type": "Journal Article", "created": "2011-04-15", "title": "Experimental Warming Effects On The Microbial Community Of A Temperate Mountain Forest Soil", "description": "Soil microbial communities mediate the decomposition of soil organic matter (SOM). The amount of carbon (C) that is respired leaves the soil as CO(2) (soil respiration) and causes one of the greatest fluxes in the global carbon cycle. How soil microbial communities will respond to global warming, however, is not well understood. To elucidate the effect of warming on the microbial community we analyzed soil from the soil warming experiment Achenkirch, Austria. Soil of a mature spruce forest was warmed by 4\u00a0\u00b0C during snow-free seasons since 2004. Repeated soil sampling from control and warmed plots took place from 2008 until 2010. We monitored microbial biomass C and nitrogen (N). Microbial community composition was assessed by phospholipid fatty acid analysis (PLFA) and by quantitative real time polymerase chain reaction (qPCR) of ribosomal RNA genes. Microbial metabolic activity was estimated by soil respiration to biomass ratios and RNA to DNA ratios. Soil warming did not affect microbial biomass, nor did warming affect the abundances of most microbial groups. Warming significantly enhanced microbial metabolic activity in terms of soil respiration per amount of microbial biomass C. Microbial stress biomarkers were elevated in warmed plots. In summary, the 4\u00a0\u00b0C increase in soil temperature during the snow-free season had no influence on microbial community composition and biomass but strongly increased microbial metabolic activity and hence reduced carbon use efficiency.", "keywords": ["2. Zero hunger", "13. Climate action", "Microbial biomass", "PLFA", "Soil warming", "rRNA genes", "Soil Science", "0401 agriculture", " forestry", " and fisheries", "Microbial community structure", "04 agricultural and veterinary sciences", "15. Life on land", "Microbiology", "Article"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2011.03.005"}, {"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.2011.03.005", "name": "item", "description": "10.1016/j.soilbio.2011.03.005", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2011.03.005"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-07-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2013.05.007", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:10Z", "type": "Journal Article", "created": "2013-05-25", "title": "Tropical Agricultural Land Management Influences On Soil Microbial Communities Through Its Effect On Soil Organic Carbon", "description": "Abstract We analyzed the microbial community that developed after 4 years of testing different soil-crop management systems in the savannah\u2013forest transition zone of Eastern Ghana where management systems can rapidly alter stored soil carbon as well as soil fertility. The agricultural managements were: (i) the local practice of fallow regrowth of native elephant grass ( Pennisetum purpureum ) followed by biomass burning before planting maize in the spring, (ii) the same practice but without burning and the maize receiving mineral nitrogen fertilizer, (iii) a winter crop of a legume, pigeon pea ( Cajanus cajan ), followed by maize, (iv) vegetation free winter period (bare fallow) followed by maize, and (v) unmanaged elephant grass-shrub vegetation. The mean soil organic carbon (SOC) contents of the soils after 4 years were: 1.29, 1.67, 1.54, 0.80 and 1.34%, respectively, differences that should affect resources for the microbial community. From about 290,000 sequences obtained by pyrosequencing the SSU rRNA gene, canonical correspondence analysis showed that SOC was the most important factor that explained differences in microbial community structure among treatments. This analysis as well as phylogenetic ecological network construction indicated that members of the Acidobacteria GP4 and GP6 were more abundant in soils with relatively high SOC whereas Acidobacteria GP1, GP7, and Actinobacteria were more prevalent in soil with lower SOC. Burning of winter fallow vegetation led to an increase in Bacillales, especially those belonging to spore-forming genera. Of the managements, pigeon-pea cultivation during the winter period promoted a higher microbial diversity and also sequestered more SOC, presumably improving soil structure, fertility, and resiliency.", "keywords": ["2. Zero hunger", "Bacillales", "Agricultural and Veterinary Sciences", "Life on Land", "Agronomy & Agriculture", "SSU rRNA genes", "Biological Sciences", "15. Life on land", "Soil organic carbon loss", "Acidobacteria", "Pigeon-pea winter-period cultivation", "13. Climate action", "Microbial community", "Zero Hunger", "Environmental Sciences", "Tropical agricultural practices"]}, "links": [{"href": "https://escholarship.org/content/qt2f60c133/qt2f60c133.pdf"}, {"href": "https://doi.org/10.1016/j.soilbio.2013.05.007"}, {"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.2013.05.007", "name": "item", "description": "10.1016/j.soilbio.2013.05.007", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2013.05.007"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-10-01T00:00:00Z"}}, {"id": "10.1016/j.still.2005.08.001", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:18Z", "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": "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.
", "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": "10.1016/j.syapm.2020.126149", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:28Z", "type": "Journal Article", "created": "2020-09-30", "title": "Genetic diversity and phylogeny of indigenous rhizobia nodulating faba bean (Vicia faba L.) in Greece", "description": "The genetic diversity and phylogeny of fast-growing rhizobia isolated from root nodules of Vicia faba grown in different geographical regions of Greece were assessed. Although Rhizobium leguminosarum sv. viciae is the most common symbiont of Vicia spp. in European soils, there is no available information on native rhizobia nodulating faba bean in Greece. Seventy bacterial strains were isolated and grouped into sixteen distinct profiles based on BOX-PCR fingerprinting. The phylogenetic affiliation was further defined by sequence analysis of the rrs and multilocus sequence analysis (MLSA) of three housekeeping genes (recA, atpD and gyrB). Fifty-eight isolates were affiliated with recently described genospecies gsF-2, represented by R. laguerreae FB206T, whereas six isolates were closely related to gsB and two isolates might belong to gsA. Two isolates assigned to R. hidalgonense and another two non-nodulating strains could not be assigned to any validly defined species and possibly belong to a new rhizobial lineage. Interestingly, R. laguerreae strains were commonly found at all sampling sites, suggesting that they could be the main symbionts of faba beans in Greek soils. According to the phylogenies of two symbiosis-related genes (nodC and nifH), all nodulating isolates belonged to symbiovar (sv.) viciae harboring four distinct nodC gene haplotypes and they were grouped into two clades together with strains assigned to R. laguerreae and genospecies of R. leguminosarum isolated from other countries and continents. This is the first report that R. hidalgonense strains belong to sv. viciae. No correlation was observed between the nodC haplotypes, geographic origin and chromosomal background of the isolates in the study.", "keywords": ["MLSA", "DNA", " Bacterial", "0301 basic medicine", "0303 health sciences", "Genes", " Essential", "Greece", "Viciae", "Sequence Analysis", " DNA", "DNA Fingerprinting", "Vicia faba", "03 medical and health sciences", "Symbiovar", "Genes", " Bacterial", "RNA", " Ribosomal", " 16S", "Root Nodules", " Plant", "Symbiosis", "Phylogeny", "Soil Microbiology", "Multilocus Sequence Typing", "Rhizobium"]}, "links": [{"href": "https://doi.org/10.1016/j.syapm.2020.126149"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Systematic%20and%20Applied%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.syapm.2020.126149", "name": "item", "description": "10.1016/j.syapm.2020.126149", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.syapm.2020.126149"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-11-01T00:00:00Z"}}, {"id": "10.1016/j.watres.2017.10.007", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:30Z", "type": "Journal Article", "created": "2017-10-27", "title": "The role of operating parameters and oxidative damage mechanisms of advanced chemical oxidation processes in the combat against antibiotic-resistant bacteria and resistance genes present in urban wastewater", "description": "An upsurge in the study of antibiotic resistance in the environment has been observed in the last decade. Nowadays, it is becoming increasingly clear that urban wastewater is a key source of antibiotic resistance determinants, i.e. antibiotic-resistant bacteria and antibiotic resistance genes (ARB&ARGs). Urban wastewater reuse has arisen as an important component of water resources management in the European Union and worldwide to address prolonged water scarcity issues. Especially, biological wastewater treatment processes (i.e. conventional activated sludge), which are widely applied in urban wastewater treatment plants, have been shown to provide an ideal environment for the evolution and spread of antibiotic resistance. The ability of advanced chemical oxidation processes (AOPs), e.g. light-driven oxidation in the presence of H2O2, ozonation, homogeneous and heterogeneous photocatalysis, to inactivate ARB and remove ARGs in wastewater effluents has not been yet evaluated through a systematic and integrated approach. Consequently, this review seeks to provide an extensive and critical appraisal on the assessment of the efficiency of these processes in inactivating ARB and removing ARGs in wastewater effluents, based on recent available scientific literature. It tries to elucidate how the key operating conditions may affect the process efficiency, while pinpointing potential areas for further research and major knowledge gaps which need to be addressed. Also, this review aims at shedding light on the main oxidative damage pathways involved in the inactivation of ARB and removal of ARGs by these processes. In general, the lack and/or heterogeneity of the available scientific data, as well as the different methodological approaches applied in the various studies, make difficult the accurate evaluation of the efficiency of the processes applied. Besides the operating conditions, the variable behavior observed by the various examined genetic constituents of the microbial community, may be directed by the process distinct oxidative damage mechanisms in place during the application of each treatment technology. For example, it was shown in various studies that the majority of cellular damage by advanced chemical oxidation may be on cell wall and membrane structures of the targeted bacteria, leaving the internal components of the cells relatively intact/able to repair damage. As a result, further in-depth mechanistic studies are required, to establish the optimum operating conditions under which oxidative mechanisms target internal cell components such as genetic material and ribosomal structures more intensively, thus conferring permanent damage and/or death and preventing potential post-treatment re-growth.", "keywords": ["Titanium", "Photolysis", "Bacteria", "Sewage", "Sulfates", "Ultraviolet Rays", "0211 other engineering and technologies", "Drug Resistance", " Microbial", "Hydrogen Peroxide", "02 engineering and technology", "Wastewater", "Oxidants", "01 natural sciences", "6. Clean water", "Water Purification", "12. Responsible consumption", "Oxidative Stress", "Ozone", "Genes", " Bacterial", "13. Climate action", "Antibiotic resistance Advanced chemical oxidation Inactivation mechanisms Wastewater treatment", "Drug Resistance", " Bacterial", "11. Sustainability", "Oxidation-Reduction", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.watres.2017.10.007"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Water%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.watres.2017.10.007", "name": "item", "description": "10.1016/j.watres.2017.10.007", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.watres.2017.10.007"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-01T00:00:00Z"}}, {"id": "10.1016/j.watres.2019.114916", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:30Z", "type": "Journal Article", "created": "2019-07-25", "title": "Removal of extracellular free DNA and antibiotic resistance genes from water and wastewater by membranes ranging from microfiltration to reverse osmosis", "description": "The final publication is available via https://doi.org/10.1016/j.watres.2019.114916.", "keywords": ["Osmosis", "0211 other engineering and technologies", "membrane filtration", "Wastewater treatment", "02 engineering and technology", "water reuse", "Wastewater", "01 natural sciences", "Water Purification", "12. Responsible consumption", "Water reuse", "antibiotic resistance genes", "free extracellular DNA", "Antibiotic resistance genes", "11. Sustainability", "Humans", "Drinking water treatment", "0105 earth and related environmental sciences", "Water", "Drug Resistance", " Microbial", "DNA", "drinking water treatment", "6. Clean water", "Anti-Bacterial Agents", "wastewater treatment", "Genes", " Bacterial", "Free extracellular DNA", "Membrane filtration"]}, "links": [{"href": "https://doi.org/10.1016/j.watres.2019.114916"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Water%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.watres.2019.114916", "name": "item", "description": "10.1016/j.watres.2019.114916", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.watres.2019.114916"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-11-01T00:00:00Z"}}, {"id": "10.1016/j.watres.2019.114906", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:30Z", "type": "Journal Article", "created": "2019-07-23", "title": "Antibiotic resistance and class 1 integron gene dynamics along effluent, reclaimed wastewater irrigated soil, crop continua: elucidating potential risks and ecological constraints", "description": "Reuse of municipal wastewater is a growing global trend, but currently there is lack of consensus regarding the potential dissemination of antibiotic resistance elements by treated wastewater irrigation. We tracked intI1, a proxy for anthropogenic pollution, and an assemblage of antibiotic resistance genes associated with mobile elements and/or wastewater (blaGES, blaOXA2, blaOXA10, blaTEM, blaCTX-M-32 and qnrS) in treated wastewater effluents, effluent stabilization reservoirs, and along irrigation water-soil-crop continua in experimental lysimeters and large-scale commercial fields. While several of the targeted antibiotic resistance genes were profuse in effluents, there was almost no correlation between gene abundance in irrigation water and those detected in soil, and no evidence of systematic gene transfer to irrigated soil or crops. In contrast, soil intI1 abundance correlated strongly to irrigation water levels in lysimeters and sandy field soils, but this was not the case for clay-rich soils or for most of the analyzed crops, suggesting that intI1 may not always be a reliable marker for tracking the impact of treated wastewater irrigation. We hypothesize that 'ecological boundaries' expedited by biotic and abiotic factors constrain dissemination of antibiotic resistance elements, and assert that a more holistic perception of these factors is crucial for understanding and managing antibiotic resistance dissemination.", "keywords": ["2. Zero hunger", "Soil", "Agricultural Irrigation", "Genes", " Bacterial", "13. Climate action", "Drug Resistance", " Microbial", "Wastewater", "15. Life on land", "Waste Disposal", " Fluid", "01 natural sciences", "6. Clean water", "Integrons", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.watres.2019.114906"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Water%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.watres.2019.114906", "name": "item", "description": "10.1016/j.watres.2019.114906", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.watres.2019.114906"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-11-01T00:00:00Z"}}, {"id": "10.1016/j.watres.2021.116818", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:30Z", "type": "Journal Article", "created": "2021-01-08", "title": "Antibiotic resistance gene load and irrigation intensity determine the impact of wastewater irrigation on antimicrobial resistance in the soil microbiome", "description": "Treated wastewater (TWW) irrigation is a useful counter-measure against the depletion of freshwater (FW) resources. However, TWW contains several contaminants of emerging concern, such as antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs). Thus, TWW irrigation might promote the spread of antimicrobial resistance in soil environments. In the present work, we hypothesized that the ARG load and irrigation intensity define the effect of TWW irrigation on ARG spread dynamics in soil. This hypothesis was tested using a multiphase approach: a) comparing soil from a full-scale, commercially operated, TWW irrigated field with non-irrigated soil, b) long-term sampling of the TWW irrigated field over one year with different irrigation intensities and intercepted by irrigation breaks and c) laboratory-scale soil microcosms irrigated with TWW compared to FW. Six ARGs, the integrase gene intI1 and the 16S rRNA were quantified using qPCR. In addition, effects of TWW irrigation on bacterial community composition of microcosm-samples were analysed with 16S rRNA amplicon sequencing. The genes sul1, qnrS, blaOXA-58, tet(M) and intI1 were significantly more abundant in the TWW irrigated field soil, whereas blaCTX--M-32 and blaTEM, the least abundant genes in the TWW irrigation, showed higher abundance in the non-irrigated soil. The relative abundance of sul1, qnrS, blaOXA-58, tet(M) and intI1 correlated with TWW irrigation intensity and decreased during irrigation breaks. Despite the decrease, the levels of these genes remained consistently higher than the non-irrigated soil indicating persistence upon their introduction into the soil. Microcosm experiments verified observations from the field study: TWW irrigation promoted the spread of ARGs and intI1 into soil at far elevated levels compared to FW irrigation. However, the impact of TWW irrigation on 16S rRNA absolute abundance and the soil microbial community composition was negligible. In conclusion, the impact of TWW irrigation depends mainly on the introduced ARG load and the irrigation intensity.", "keywords": ["0301 basic medicine", "2. Zero hunger", "Agricultural Irrigation", "Microbiota", "Angiotensin-Converting Enzyme Inhibitors", "Wastewater", "15. Life on land", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "Angiotensin Receptor Antagonists", "Soil", "03 medical and health sciences", "Genes", " Bacterial", "RNA", " Ribosomal", " 16S", "Drug Resistance", " Bacterial", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.watres.2021.116818"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Water%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.watres.2021.116818", "name": "item", "description": "10.1016/j.watres.2021.116818", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.watres.2021.116818"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-04-01T00:00:00Z"}}, {"id": "10.1021/acs.est.1c00612", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:36Z", "type": "Journal Article", "created": "2021-04-28", "title": "Hidden Resistome: Enrichment Reveals the Presence of Clinically Relevant Antibiotic Resistance Determinants in Treated Wastewater-Irrigated Soils", "description": "Treated-wastewater (TW) irrigation transfers antibiotic-resistant bacteria (ARB) to soil, but persistence of these bacteria is generally low due to resilience of the soil microbiome. Nonetheless, wastewater-derived bacteria and associated antibiotic resistance genes (ARGs) may persist below detection levels and potentially proliferate under copiotrophic conditions. To test this hypothesis, we exposed soils from microcosm, lysimeter, and field experiments to short-term enrichment in copiotroph-stimulating media. In microcosms, enrichment stimulated growth of multidrug-resistant Escherichia coli up to 2 weeks after falling below detection limits. Lysimeter and orchard soils irrigated in-tandem with either freshwater or TW were subjected to culture-based, qPCR and shotgun metagenomic analyses prior, and subsequent, to enrichment. Although native TW- and freshwater-irrigated soil microbiomes and resistomes were similar to each other, enrichment resulted in higher abundances of cephalosporin- and carbapenem-resistant Enterobacteriaceae and in substantial differences in the composition of microbial communities and ARGs. Enrichment stimulated ARG-harboring Bacillaceae in the freshwater-irrigated soils, whereas in TWW-irrigated soils, ARG-harboring \u03b3-proteobacterial families Enterobacteriaceae and Moraxellaceae were more profuse. We demonstrate that TW-derived ARB and associated ARGs can persist at below detection levels in irrigated soils and believe that similar short-term enrichment strategies can be applied for environmental antimicrobial risk assessment in the future.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Agricultural Irrigation", "Angiotensin-Converting Enzyme Inhibitors", "Drug Resistance", " Microbial", "Wastewater", "6. Clean water", "Anti-Bacterial Agents", "3. Good health", "Angiotensin Receptor Antagonists", "Soil", "03 medical and health sciences", "Genes", " Bacterial", "Humans", "Soil Microbiology"]}, "links": [{"href": "https://pubs.acs.org/doi/pdf/10.1021/acs.est.1c00612"}, {"href": "https://doi.org/10.1021/acs.est.1c00612"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20%26amp%3B%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1021/acs.est.1c00612", "name": "item", "description": "10.1021/acs.est.1c00612", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1021/acs.est.1c00612"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-04-27T00:00:00Z"}}, {"id": "10.1021/acs.est.1c00811", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:36Z", "type": "Journal Article", "created": "2021-05-12", "title": "Deciphering Potential Roles of Earthworms in Mitigation of Antibiotic Resistance in the Soils from Diverse Ecosystems", "description": "Earthworms are capable of redistributing bacteria and antibiotic resistance genes (ARGs) through soil profiles. However, our understanding of the earthworm gut microbiome and its interaction with the antibiotic resistome is still lacking. Here, we characterized the earthworm gut and soil microbiome and antibiotic resistome in natural and agricultural ecosystems at a national scale, and microcosm studies and field experiments were also employed to test the potential role of earthworms in dynamics of soil ARGs. The diversity and structure of bacterial communities were different between the earthworm gut and soil. A significant correlation between bacterial community dissimilarity and spatial distance between sites was identified in the earthworm gut. The earthworm gut consistently had lower ARGs than the surrounding soil. A significant reduction in the relative abundance of mobile genetic elements and dominant bacterial phylotypes that are the likely hosts of ARGs was observed in the earthworm gut compared to the surrounding soil, which might contribute to the decrease of ARGs in the earthworm gut. The microcosm studies and field experiments further confirmed that the presence of earthworms significantly reduced the number and abundance of ARGs in soils. Our study implies that earthworm-based bioremediation may be a method to reduce risks associated with the presence of ARGs in soils.", "keywords": ["2. Zero hunger", "0301 basic medicine", "Soil", "0303 health sciences", "03 medical and health sciences", "Genes", " Bacterial", "XXXXXX - Unknown", "Animals", "Drug Resistance", " Microbial", "Oligochaeta", "15. Life on land", "Soil Microbiology", "Anti-Bacterial Agents"]}, "links": [{"href": "https://doi.org/10.1021/acs.est.1c00811"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20%26amp%3B%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1021/acs.est.1c00811", "name": "item", "description": "10.1021/acs.est.1c00811", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1021/acs.est.1c00811"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-05-12T00:00:00Z"}}, {"id": "10.1128/aem.03393-12", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:19:30Z", "type": "Journal Article", "created": "2012-12-16", "title": "Functional Gene Differences In Soil Microbial Communities From Conventional, Low-Input, And Organic Farmlands", "description": "ABSTRACTVarious agriculture management practices may have distinct influences on soil microbial communities and their ecological functions. In this study, we utilized GeoChip, a high-throughput microarray-based technique containing approximately 28,000 probes for genes involved in nitrogen (N)/carbon (C)/sulfur (S)/phosphorus (P) cycles and other processes, to evaluate the potential functions of soil microbial communities under conventional (CT), low-input (LI), and organic (ORG) management systems at an agricultural research site in Michigan. Compared to CT, a high diversity of functional genes was observed in LI. The functional gene diversity in ORG did not differ significantly from that of either CT or LI. Abundances of genes encoding enzymes involved in C/N/P/S cycles were generally lower in CT than in LI or ORG, with the exceptions of genes in pathways for lignin degradation, methane generation/oxidation, and assimilatory N reduction, which all remained unchanged. Canonical correlation analysis showed that selected soil (bulk density, pH, cation exchange capacity, total C, C/N ratio, NO 3 \uffe2\uff88\uff92 , NH 4 + , available phosphorus content, and available potassium content) and crop (seed and whole biomass) variables could explain 69.5% of the variation of soil microbial community composition. Also, significant correlations were observed between NO 3 \uffe2\uff88\uff92 concentration and denitrification genes, NH 4 + concentration and ammonification genes, and N 2 O flux and denitrification genes, indicating a close linkage between soil N availability or process and associated functional genes.
", "keywords": ["2. Zero hunger", "Michigan", "Nitrogen", "Agriculture", "Phosphorus", "04 agricultural and veterinary sciences", "15. Life on land", "Microarray Analysis", "Biota", "Carbon", "Soil", "Genes", " Bacterial", "Metagenome", "0401 agriculture", " forestry", " and fisheries", "Metabolic Networks and Pathways", "Soil Microbiology", "Sulfur"]}, "links": [{"href": "https://doi.org/10.1128/aem.03393-12"}, {"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.03393-12", "name": "item", "description": "10.1128/aem.03393-12", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.03393-12"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-02-15T00:00:00Z"}}, {"id": "10.1038/ismej.2010.3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:53Z", "type": "Journal Article", "created": "2010-02-04", "title": "Shifts In Microbial Community Structure Along An Ecological Gradient Of Hypersaline Soils And Sediments", "description": "AbstractStudies of hypersaline ecosystems often yield novel organisms and contribute to our understanding of extreme environments. Soils and sediments from La Sal del Rey, a previously uncharacterized, hypersaline lake located in southern Texas, USA, were surveyed to characterize the structure and diversity of their microbial communities. Samples were collected along a transect that spanned vegetated uplands, exposed lakebed sediments, and water-logged locations, capturing a wide range of environments and physical and chemical gradients. Community quantitative PCR (qPCR) was used in combination with tag-encoded pyrosequencing, 16S rRNA gene cloning, and Sanger sequencing to characterize the lake's soil and sediment microbial communities. Further, we used multivariate statistics to identify the relationships shared between sequence diversity and heterogeneity in the soil environment. The overall microbial communities were surprisingly diverse, harboring a wide variety of taxa, and sharing significant correlations with site water content, phosphorus and total organic carbon concentrations, and pH. Some individual populations, especially of Archaea, also correlated with sodium concentration and electrical conductivity salinity. Across the transect, Bacteria were numerically dominant relative to Archaea, and among them, three phyla\uffe2\uff80\uff94the Proteobacteria, Bacteroidetes, and Firmicutes\uffe2\uff80\uff94accounted for the majority of taxa detected. Although these taxa were detected with similar abundances to those described in other hypersaline ecosystems, the greater depth of sequencing achieved here resulted in the detection of taxa not described previously in hypersaline sediments. The results of this study provide new information regarding a previously uncharacterized ecosystem and show the value of high-throughput sequencing in the study of complex ecosystems.
", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Geologic Sediments", "Salinity", "0303 health sciences", "Bacteria", "Genes", " rRNA", "Sequence Analysis", " DNA", "15. Life on land", "Archaea", "Polymerase Chain Reaction", "Texas", "6. Clean water", "Soil", "03 medical and health sciences", "DNA", " Archaeal", "13. Climate action", "RNA", " Ribosomal", " 16S", "Water Microbiology", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/ismej.2010.3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/ismej.2010.3", "name": "item", "description": "10.1038/ismej.2010.3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/ismej.2010.3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-02-04T00:00:00Z"}}, {"id": "10.1038/nature02053", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:54Z", "type": "Journal Article", "created": "2003-10-22", "title": "Genome-Scale Approaches To Resolving Incongruence In Molecular Phylogenies", "description": "One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes. To systematically investigate the degree of incongruence, and potential methods for resolving it, we screened the genome sequences of eight yeast species and selected 106 widely distributed orthologous genes for phylogenetic analyses, singly and by concatenation. Our results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies. By contrast, analyses of the entire data set of concatenated genes yielded a single, fully resolved species tree with maximum support. Comparable results were obtained with a concatenation of a minimum of 20 genes; substantially more genes than commonly used but a small fraction of any genome. These results have important implications for resolving branches of the tree of life.", "keywords": ["0301 basic medicine", "Saccharomyces", "0303 health sciences", "03 medical and health sciences", "Genes", " Fungal", "Regression Analysis", "Reproducibility of Results", "Genomics", "Genome", " Fungal", "Phylogeny"]}, "links": [{"href": "https://doi.org/10.1038/nature02053"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/nature02053", "name": "item", "description": "10.1038/nature02053", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/nature02053"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2003-10-01T00:00:00Z"}}, {"id": "10.1038/s41396-022-01225-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-04T16:17:56Z", "type": "Journal Article", "created": "2022-03-30", "title": "Cross-biome antibiotic resistance decays after millions of years of soil development", "description": "AbstractSoils harbor the most diverse naturally evolved antibiotic resistance genes (ARGs) on Earth, with implications for human health and ecosystem functioning. How ARGs evolve as soils develop over centuries, to millennia (i.e., pedogenesis), remains poorly understood, which introduces uncertainty in predictions of the dynamics of ARGs under changing environmental conditions. Here we investigated changes in the soil resistome by analyzing 16 globally distributed soil chronosequences, from centuries to millennia, spanning a wide range of ecosystem types and substrate age ranges. We show that ARG abundance and diversity decline only after millions of years of soil development as observed in very old chronosequences. Moreover, our data show increases in soil organic carbon content and microbial biomass as soil develops that were negatively correlated with the abundance and diversity of soil ARGs. This work reveals natural dynamics of soil ARGs during pedogenesis and suggests that such ecological patterns are predictable, which together advances our understanding of the environmental drivers of ARGs in terrestrial environments.