{"type": "FeatureCollection", "features": [{"id": "10.1016/j.envint.2020.106190", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:16:39Z", "type": "Journal Article", "created": "2020-10-26", "title": "Treated wastewater irrigation promotes the spread of antibiotic resistance into subsoil pore-water", "description": "In the present study, we investigated the impact of treated wastewater (TWW) irrigation on the prevalence of antibiotic resistance genes (ARGs) in subsoil pore-water, a so-far under-appreciated matrix. We hypothesized that TWW irrigation increases ARG prevalence in subsoil pore-water. This hypothesis was tested using a multiphase approach, which consisted of sampling percolated subsoil pore-water from lysimeter-wells of a real-scale TWW-irrigated field, operated for commercial farming practices, and controlled, laboratory microcosms irrigated with freshwater or TWW. We monitored the abundance of six selected ARGs (sul1, blaOXA-58, tetM, qnrS, blaCTX-M-32 and blaTEM), the intI1 gene associated with mobile genetic elements and an indicator for anthropogenic pollution and bacterial abundance (16S rRNA gene) by qPCR. The bacterial load of subsoil pore water was independent of both, irrigation intensity in the field study and irrigation water type in the microcosms. Among the tested genes in the field study, sul1 and intI1 exhibited constantly higher relative abundances. Their abundance was further positively correlated with increasing irrigation intensity. Controlled microcosm experiments verified the observed field study results: the relative abundance of several genes, including sul1 and intI1, increased significantly when irrigating with TWW compared to freshwater irrigation. Overall, TWW irrigation promoted the spread of ARGs and intI1 in the subsoil pore-water, while the bacterial load was maintained. The combined results from the real-scale agricultural field and the controlled lab microcosms indicate that the dissemination of ARGs in various subsurface environments needs to be taken into account during TWW irrigation scenarios.", "keywords": ["0301 basic medicine", "2. Zero hunger", "Agricultural Irrigation", "Antibiotic resistance", "Water", "Subsoil pore-water", "Drug Resistance", " Microbial", "Wastewater", "Wastewater reuse", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "Environmental sciences", "qPCR", "Soil", "03 medical and health sciences", "Genes", " Bacterial", "RNA", " Ribosomal", " 16S", "ARGs", "GE1-350", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.envint.2020.106190"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environment%20International", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envint.2020.106190", "name": "item", "description": "10.1016/j.envint.2020.106190", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envint.2020.106190"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-01-01T00:00:00Z"}}, {"id": "10.1007/s00128-012-0523-0", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:14:24Z", "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/s00253-020-10982-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:14:26Z", "type": "Journal Article", "created": "2020-11-11", "title": "Living with sulfonamides: a diverse range of mechanisms observed in bacteria", "description": "Sulfonamides are the oldest class of synthetic antibiotics still in use in clinical and veterinary settings. The intensive utilization of sulfonamides has been leading to the widespread contamination of the environment with these xenobiotic compounds. Consequently, in addition to pathogens and commensals, also bacteria inhabiting a wide diversity of environmental compartments have been in contact with sulfonamides for almost 90\u00a0years. This review aims at giving an overview of the effect of sulfonamides on bacterial cells, including the strategies used by bacteria to cope with these bacteriostatic agents. These include mechanisms of antibiotic resistance, co-metabolic transformation, and partial or total mineralization of sulfonamides. Possible implications of these mechanisms on the ecosystems and dissemination of antibiotic resistance are also discussed. KEY POINTS: \u2022 Sulfonamides are widespread xenobiotic pollutants; \u2022 Target alteration is the main sulfonamide resistance mechanism observed in bacteria; \u2022 Sulfonamides can be modified, degraded, or used as nutrients by some bacteria.", "keywords": ["0301 basic medicine", "Sulfonamides", "0303 health sciences", "Bacteria", "Antibiotic resistance", "Drug Resistance", " Microbial", "Anti-Bacterial Agents", "3. Good health", "03 medical and health sciences", "Biodegradation", " Environmental", "Biodegradation", "Xenobiotic", "Biotransformation", "Ecosystem"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s00253-020-10982-5.pdf"}, {"href": "https://doi.org/10.1007/s00253-020-10982-5"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Microbiology%20and%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00253-020-10982-5", "name": "item", "description": "10.1007/s00253-020-10982-5", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00253-020-10982-5"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-11-11T00:00:00Z"}}, {"id": "10.1007/s10123-021-00215-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:14:43Z", "type": "Journal Article", "created": "2021-10-23", "title": "Novel methods of microbiome analysis in the food industry", "description": "The study of the food microbiome has gained considerable interest in recent years, mainly due to the wide range of applications that can be derived from the analysis of metagenomes. Among these applications, it is worth mentioning the possibility of using metagenomic analyses to determine food authenticity, to assess the microbiological safety of foods thanks to the detection and tracking of pathogens, antibiotic resistance genes and other undesirable traits, as well to identify the microorganisms responsible for food processing defects. Metataxonomics and metagenomics are currently the gold standard methodologies to explore the full potential of metagenomes in the food industry. However, there are still a number of challenges that must be solved in order to implement these methods routinely in food chain monitoring, and for the regulatory agencies to take them into account in their opinions. These challenges include the difficulties of analysing foods and food-related environments with a low microbial load, the lack of validated bioinformatics pipelines adapted to food microbiomes and the difficulty of assessing the viability of the detected microorganisms. This review summarizes the methods of microbiome analysis that have been used, so far, in foods and food-related environments, with a specific focus on those involving Next-Generation Sequencing technologies.", "keywords": ["2. Zero hunger", "0301 basic medicine", "Food metagenome", "0303 health sciences", "Food microbiome", "3309 Tecnolog\u00eda de Los Alimentos", "Tecnolog\u00eda de los alimentos", "Metataxonomics", "Microbiota", "3309.90 Microbiolog\u00eda de Alimentos", "Drug Resistance", " Microbial", "Resistome", "03 medical and health sciences", "Food Industry", "Metagenome", "Metagenomics"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s10123-021-00215-8.pdf"}, {"href": "https://doi.org/10.1007/s10123-021-00215-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/International%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s10123-021-00215-8", "name": "item", "description": "10.1007/s10123-021-00215-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s10123-021-00215-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-10-23T00:00:00Z"}}, {"id": "10.1016/j.ijheh.2019.01.004", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:17:07Z", "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": "2026-04-03T16:16:16Z", "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"], "contacts": [{"organization": "Wu, Xiayuan, Tian, Zhenzhen, Lv, Zuopeng, Chen, Zixuan, Liu, Yongdi, Yong, Xiaoyu, Zhou, Jun, Xie, Xinxin, Jia, Honghua, Wei, Ping,", "roles": ["creator"]}]}, "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.envint.2018.03.044", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:16:39Z", "type": "Journal Article", "created": "2018-04-06", "title": "Antibiotic resistance in wastewater treatment plants: Tackling the black box", "description": "Wastewater is among the most important reservoirs of antibiotic resistance in urban environments. The abundance of carbon sources and other nutrients, a variety of possible electron acceptors such as oxygen or nitrate, the presence of particles onto which bacteria can adsorb, or a fairly stable pH and temperature are examples of conditions favouring the remarkable diversity of microorganisms in this peculiar habitat. The wastewater microbiome brings together bacteria of environmental, human and animal origins, many harbouring antibiotic resistance genes (ARGs). Although numerous factors contribute, mostly in a complex interplay, for shaping this microbiome, the effect of specific potential selective pressures such as antimicrobial residues or metals, is supposedly determinant to dictate the fate of antibiotic resistant bacteria (ARB) and ARGs during wastewater treatment. This paper aims to enrich the discussion on the ecology of ARB&ARGs in urban wastewater treatment plants (UWTPs), intending to serve as a guide for wastewater engineers or other professionals, who may be interested in studying or optimizing the wastewater treatment for the removal of ARB&ARGs. Fitting this aim, the paper overviews and discusses: i) aspects of the complexity of the wastewater system and/or treatment that may affect the fate of ARB&ARGs; ii) methods that can be used to explore the resistome, meaning the whole ARB&ARGs, in wastewater habitats; and iii) some frequently asked questions for which are proposed addressing modes. The paper aims at contributing to explore how ARB&ARGs behave in UWTPs having in mind that each plant is a unique system that will probably need a specific procedure to maximize ARB&ARGs removal.", "keywords": ["0301 basic medicine", "Bacteria", "Microbiota", "SWOT analysis", "Wastewater", "15. Life on land", "Wastewater treatment optimization", "01 natural sciences", "6. Clean water", "Water Purification", "12. Responsible consumption", "03 medical and health sciences", "Anti-Infective Agents", "13. Climate action", "Drug Resistance", " Bacterial", "11. Sustainability", "Animals", "Humans", "Antibiotic resistance monitoring", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.envint.2018.03.044"}, {"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.2018.03.044", "name": "item", "description": "10.1016/j.envint.2018.03.044", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envint.2018.03.044"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-06-01T00:00:00Z"}}, {"id": "10.1016/j.envint.2019.03.060", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:16:39Z", "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": "2026-04-03T16:16:41Z", "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.2022.120873", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:16:41Z", "type": "Journal Article", "created": "2022-12-15", "title": "Comparative selective pressure potential of antibiotics in the environment", "description": "To guide both environmental and public health policy, it is important to assess the degree of antibiotic resistance selection pressure under measured environmental concentrations (MECs), and to compare the efficacy of different mitigation strategies to minimize the spread of resistance. To this end, the resistance selection and enrichment potential due to antibiotic emissions into the environment must be analysed from a life cycle perspective, for a wide range of antibiotics, and considering variations in the underlying fitness costs between different resistance mutations and genes. The aim of this study is to consistently derive fitness cost-dependent minimum selective concentrations (MSCs) from readily available bacterial inhibition data and to build MSC-based species sensitivity distributions (SSDs). These are then used to determine antibiotic-specific resistance selection concentrations predicted to promote resistance in 5% of exposed bacterial species (RSC5). Using a previously developed competition model, we provide estimated MSC10 endpoints for 2,984 antibiotic and bacterial species combinations; the largest set of modelled MSCs available to date. Based on constructed SSDs, we derive RSC5 for 128 antibiotics with four orders of magnitude difference in their 'selective pressure potential' in the environment. By comparing our RSC5 to MECs, we highlight specific environmental compartments (e.g. hospital and wastewater effluents, lakes and rivers), as well as several antibiotics (e.g. ciprofloxacin, norfloxacin, enrofloxacin, and tetracycline), to be scrutinized for their potential role in resistance selection and dissemination. In addition to enabling comparative risk screening of the selective pressure potential of multiple antibiotics, our SSD-derived RSC5 provide the point of departure for calculating new life cycle-based characterization factors for antibiotics to compare mitigation strategies, thereby contributing towards a 'One-Health' approach to tackling the global antibiotic resistance crisis.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Bacteria", "Antibiotic resistance", "Drug Resistance", " Microbial", "Tetracycline", "6. Clean water", "Anti-Bacterial Agents", "3. Good health", "Selection coefficient", "03 medical and health sciences", "Ciprofloxacin", "Species sensitivity distribution", "Fitness cost", "Life cycle impact assessment", "/dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being; name=SDG 3 - Good Health and Well-being", "Minimum selective concentration", "Norfloxacin"]}, "links": [{"href": "https://doi.org/10.1016/j.envpol.2022.120873"}, {"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.2022.120873", "name": "item", "description": "10.1016/j.envpol.2022.120873", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envpol.2022.120873"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-02-01T00:00:00Z"}}, {"id": "10.1016/j.envpol.2016.01.007", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:16:40Z", "type": "Journal Article", "created": "2016-01-16", "title": "Effects Of Manure And Mineral Fertilization Strategies On Soil Antibiotic Resistance Gene Levels And Microbial Community In A Paddy-Upland Rotation System", "description": "This work investigated the responses of antibiotic resistance genes (ARGs) and the soil microbial community in a paddy-upland rotation system to mineral fertilizer (NPK) and different application dosages of manure combined with NPK. The occurrence of five tetracycline ARGs (tetA, tetB, tetC, tetG and tetW), two sulfonamide ARGs (sul1 and sul2) and one genetic element (IntI1) was quantified. NPK application showed only slight or no impact on soil ARGs abundances compared with the control without fertilizer. Soil ARGs abundances could be increased by manure-NPK application but was related to manure dosage (2250-9000 kg ha(-1)). Principal component analysis (PCA) showed that the soil ARG profile of the treatment with 9000 kg ha(-1) manure separated clearly from the other treatments; the ARGs that contributed most to the discrimination of this treatment were tetA, tetG, tetW, sul1, sul2 and IntI1. Community level physiological profile (CLPP) analysis showed that increasing manure dosage from 4500 kg ha(-1) to 9000 kg ha(-1) induced a sharp increase in almost all of the detected ARGs but would not change the microbial community at large. However, 9000 kg ha(-1) manure application produced a decline in soil microbial activity. Determination of antibiotics and heavy metals in soils suggested that the observed bloom of soil ARGs might associate closely with the accumulation of copper and zinc in soil.", "keywords": ["2. Zero hunger", "Minerals", "Rotation", "Agriculture", "Drug Resistance", " Microbial", "Oryza", "15. Life on land", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "Manure", "Soil", "Metals", " Heavy", "8. Economic growth", "Fertilizers", "Soil Microbiology", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.envpol.2016.01.007"}, {"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.2016.01.007", "name": "item", "description": "10.1016/j.envpol.2016.01.007", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envpol.2016.01.007"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-04-01T00:00:00Z"}}, {"id": "10.1016/j.envpol.2023.121325", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:16:42Z", "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": {"license": "Open Access", "updated": "2026-04-03T16:16:42Z", "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": "2026-04-03T16:16:42Z", "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": "2026-04-03T16:16:42Z", "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.foodres.2022.112202", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:16:47Z", "type": "Journal Article", "created": "2022-11-19", "title": "Evidence of virulence and antibiotic resistance genes from the microbiome mapping in minimally processed vegetables producing facilities", "description": "Daily consumption of fresh vegetables is highly recommended by international health organizations, because of their high content of nutrients. However, fresh vegetables might harbour several pathogenic microorganisms or contribute to spread antibiotic resistance, thus representing a hazard for consumers. In addition, little is known about the transmission routes of the residential microbiome from the food handling environment to vegetables. Therefore, we collected environmental and food samples from three manufactures producing fresh vegetables to estimate the relevance of the built environment microbiome on that of the finished products. Our results show that food contact surfaces sampled after routine cleaning and disinfection procedures host a highly diverse microbiome, including pathogens such as the enterotoxigenic Bacillus cereus sensu stricto. In addition, we provide evidence of the presence of a wide range of antibiotic resistance and virulence genes on food contact surfaces associated with multiple taxa, thus supporting the hypothesis that selection of resistant and pathogenic taxa might occur on sanitized surfaces. This study also highlights the potential of microbiome mapping routinely applied in food industries monitoring programs to ensure food safety.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Food industry", "Virulence", "3309 Tecnolog\u00eda de Los Alimentos", "Antimicrobials", "Biolog\u00eda", "Tecnolog\u00eda de los alimentos", "Biofilm", "Microbiota", "Drug Resistance", " Microbial", "Anti-Bacterial Agents", "03 medical and health sciences", "Bacillus cereus", "Vegetables", "Antimicrobials; Bacillus cereus; Biofilm; Food industry; Metagenomics", "Metagenomics", "2414 Microbiolog\u00eda"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/903001/1/1-s2.0-S0963996922012601-main.pdf"}, {"href": "https://doi.org/10.1016/j.foodres.2022.112202"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Food%20Research%20International", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.foodres.2022.112202", "name": "item", "description": "10.1016/j.foodres.2022.112202", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.foodres.2022.112202"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-12-01T00:00:00Z"}}, {"id": "10.1016/j.jhazmat.2020.123208", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:17:16Z", "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": "2026-04-03T16:17:16Z", "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": "2026-04-03T16:17:16Z", "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": "2026-04-03T16:17:16Z", "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": "2026-04-03T16:17:30Z", "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.2019.135733", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:17:31Z", "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.watres.2017.10.007", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:18:07Z", "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.2019.05.025", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:18:07Z", "type": "Journal Article", "created": "2019-05-09", "title": "Continuous ozonation of urban wastewater: Removal of antibiotics, antibiotic-resistant Escherichia coli and antibiotic resistance genes and phytotoxicity", "description": "This work evaluated the removal of a mixture of eight antibiotics (i.e. ampicillin (AMP), azithromycin (AZM), erythromycin (ERY), clarithromycin (CLA), ofloxacin (OFL), sulfamethoxazole (SMX), trimethoprim (TMP) and tetracycline (TC)) from urban wastewater, by ozonation operated in continuous mode at different hydraulic retention times (HRTs) (i.e. 10, 20, 40 and 60\u202fmin) and specific ozone doses (i.e. 0.125, 0.25, 0.50 and 0.75 gO3 gDOC- 1). As expected, the efficiency of ozonation was highly ozone dose- and contact time-dependent. The removal of the parent compounds of the selected antibiotics to levels below their detection limits was achieved with HRT of 40\u202fmin and specific ozone dose of 0.125 gO3 gDOC- 1. The effect of ozonation was also investigated at a microbiological and genomic level, by studying the efficiency of the process with respect to the inactivation of Escherichia coli and antibiotic-resistant E.\u00a0coli, as well as to the reduction of the abundance of selected antibiotic resistance genes (ARGs). The inactivation of total cultivable E.\u00a0coli was achieved under the experimental conditions of HRT 40\u202fmin and 0.25 gO3 gDOC-1, at which all antibiotic compounds were already degraded. The regrowth examinations revealed that higher ozone concentrations were required for the permanent inactivation of E.\u00a0coli below the Limit of Quantification (Soils 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.There are a multitude of resistance strategies that microbes can apply to avoid inhibition by antimicrobials. One of these strategies is the enzymatic modification of the antibiotic, in a process generally termed inactivation. Furthermore, some microorganisms may not be limited to the mere inactivation of the antimicrobial compounds. They can continue by further enzymatic degradation of the compounds' carbon backbone, taking nutritional and energetic advantage of the former antibiotic. This driving force to harness an additional food source in a complex environment adds another level of complexity to the reasonably well\uffe2\uff80\uff90understood process of antibiotic resistance proliferation on a single cell level: It brings bioprotection into play at the level of microbial community. Despite the possible implications of a resistant community in a host and a lurking antibiotic failure, knowledge of degradation pathways of antibiotics and their connections is scarce. Currently, it is limited to only a few families of antibiotics (e.g. \uffce\uffb2\uffe2\uff80\uff90lactams and sulfonamides). In this article, we discuss the fluctuating nature of the relationship between antibiotic resistance and the biodegradation of antibiotics. This distinction mainly depends on the genetic background of the microbe, as general resistance genes can be recruited to function in a biodegradation pathway.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "Opinion", "Sulfonamides", "0303 health sciences", "03 medical and health sciences", "Biodegradation", " Environmental", "Bacteria", "Drug Resistance", " Bacterial", "Humans", "beta-Lactams", "Anti-Bacterial Agents"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.15018"}, {"href": "https://doi.org/10.1111/1462-2920.15018"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1462-2920.15018", "name": "item", "description": "10.1111/1462-2920.15018", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.15018"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-04-28T00:00:00Z"}}, {"id": "10.1186/s40168-020-00941-7", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:20:42Z", "type": "Journal Article", "created": "2020-11-19", "title": "Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms", "description": "Abstract Background

The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the resistome, not only in the animals but also on the farm environment. Here, we evaluate the resistome footprint of an extensive pig farming system, maintained for decades, as compared to that of industrialized intensive pig farming by analyzing 105 fecal, environmental and slurry metagenomes from 38 farms.

Results

Our results evidence a significantly higher abundance of antimicrobial resistance genes (ARGs) on intensive farms and a link between AMU and AMR to certain antimicrobial classes. We observed differences in the resistome across sample types, with a higher richness and dispersion of ARGs within environmental samples than on those from feces or slurry. Indeed, a deeper analysis revealed that differences among the three sample types were defined by taxa-ARGs associations. Interestingly, mobilome analyses revealed that the observed AMR differences between intensive and extensive farms could be linked to differences in the abundance of mobile genetic elements (MGEs). Thus, while there were no differences in the abundance of chromosomal-associated ARGs between intensive and extensive herds, a significantly higher abundance of integrons in the environment and plasmids, regardless of the sample type, was detected on intensive farms.

Conclusions

Overall, this study shows how AMU, production system, and sample type influence, mainly through MGEs, the profile and dispersion of ARGs in pig production.

", "keywords": ["0301 basic medicine", "Farms", "Sanidad animal", "Swine", "Antimicrobial resistance", "Microbial ecology", "Sustainable farming", "Cerdos", "Feces", "03 medical and health sciences", "Anti-Infective Agents", "Environmental Microbiology", "Animals", "Mobilome", "Antiinfecciosos", "One health", "2. Zero hunger", "Excrementos", "0303 health sciences", "Research", "QR100-130", "Drug Resistance", " Microbial", "15. Life on land", "Farm environment", "6. Clean water", "Genes", " Bacterial", "Animals", " Domestic", "2401.05 desarrollo Animal", "Metagenome", "Veterinaria"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1186/s40168-020-00941-7.pdf"}, {"href": "https://doi.org/10.1186/s40168-020-00941-7"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40168-020-00941-7", "name": "item", "description": "10.1186/s40168-020-00941-7", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40168-020-00941-7"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-11-19T00:00:00Z"}}, {"id": "10.1534/g3.119.400716", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:21:01Z", "type": "Journal Article", "created": "2020-01-10", "title": "Whole Genome Sequencing and Comparative Genomics of Two Nematicidal Bacillus Strains Reveals a Wide Range of Possible Virulence Factors", "description": "Abstract

Bacillus firmus nematicidal bacterial strains are used to control plant parasitic nematode infestation of crops in agricultural production. Proteases are presumed to be the primary nematode virulence factors in nematicidal B. firmus degrading the nematode cuticle and other organs. We determined and compared the whole genome sequences of two nematicidal strains. Comparative genomics with a particular focus on possible virulence determinants revealed a wider range of possible virulence factors in a B. firmus isolate from a commercial bionematicide and a wild type Bacillus sp. isolate with nematicidal activity. The resulting 4.6 Mb B. firmus I-1582 and 5.3 Mb Bacillus sp. ZZV12-4809 genome assemblies contain respectively 18 and 19 homologs to nematode-virulent proteases, two nematode-virulent chitinase homologs in ZZV12-4809 and 28 and 36 secondary metabolite biosynthetic clusters, projected to encode antibiotics, small peptides, toxins and siderophores. The results of this study point to the genetic capability of B. firmus and related species for nematode virulence through a range of direct and indirect mechanisms.

", "keywords": ["2. Zero hunger", "Whole Genome Sequencing", "complete genomes", "Virulence Factors", "Antinematodal Agents", "virulence factors", "bacillus firmus", "biological control", "Bacillus", "bioinformatics", "Genomics", "QH426-470", "Genome Report", "3. Good health", "Bacterial Proteins", "Drug Resistance", " Bacterial", "Genetics", "BACILLUS FIRMUS", " COMPLETE GENOMES", " BIOINFORMATICS", " BIOLOGICAL CONTROL", " NEMATICIDAL ACTIVITY", " VIRULENCE FACTORS", "Bacillus firmus", "nematicidal activity", "Genome", " Bacterial"]}, "links": [{"href": "http://academic.oup.com/g3journal/article-pdf/10/3/881/38825647/g3journal0881.pdf"}, {"href": "https://doi.org/10.1534/g3.119.400716"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/G3%20Genes%7CGenomes%7CGenetics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1534/g3.119.400716", "name": "item", "description": "10.1534/g3.119.400716", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1534/g3.119.400716"}, {"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": "10.2527/jas.2005-652", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:22:08Z", "type": "Journal Article", "created": "2006-08-05", "title": "Efficacy Of Ionophores In Cattle Diets For Mitigation Of Enteric Methane", "description": "Use of ionophores in cattle diets has been proposed as a strategy for mitigation of enteric CH4 emissions. Short- and long-term effects of feeding a single ionophore (monensin) or rotation of 2 ionophores (monensin and lasalocid) on enteric CH4 emissions were evaluated in 36 Angus yearling steers (328 +/- 24.9 kg of BW) over a 16-wk period. Steers were randomly assigned to 6 dietary treatments of 6 steers each. The 6 diets were low-concentrate without ionophore supplementation, low-concentrate with monensin supplementation, low-concentrate with a 2-wk rotation of monensin and lasalocid supplementation, high-concentrate without ionophore supplementation, high-concentrate with monensin supplementation, and high-concentrate with a 2-wk rotation of monensin and lasalocid supplementation. Daily enteric CH4 emissions, as measured using the SF(6) tracer gas technique, ranged from 54.7 to 369.3 L/steer daily. Supplementing ionophores decreased (P < 0.05) enteric CH4 emissions, expressed as liters per kilogram of DMI or percentage of GE intake, by 30% for the first 2 wk and by 27% for the first 4 wk, for cattle receiving the high-concentrate and low-concentrate diets, respectively. Cattle fed a rotation of ionophores did not (P > 0.05) exhibit a greater decrease and did not (P > 0.05) have a longer period of depressed enteric CH4 emissions compared with cattle receiving monensin only. Ionophore supplementation did not (P > 0.05) alter total ruminal fluid VFA concentration; however, the acetate:propionate ratio and ammonia-N concentration in ruminal fluid were decreased (P < 0.001) from the time that ionophores were introduced to the time they were removed from the diets. Both monensin and the rotation of monensin and lasalocid decreased (P < 0.001) total ciliate protozoal populations by 82.5% in the first 2 wk and by 76.8% in the first 4 wk during which they were supplemented in the high-concentrate and low-concentrate diets, respectively. Original ciliate protozoal populations were restored by the fourth and sixth week of supplementation when cattle were fed the high- or low-concentrate diets, respectively. No significant change was observed thereafter. These data suggest that the effects of ionophores on enteric CH(4) production are related to ciliate protozoal populations and that ciliate protozoal populations can adapt to the ionophores present in either low- or high-concentrate diets. Rotation of monensin and lasalocid did not (P > 0.05) prevent ciliate protozoal adaptation to ionophores.", "keywords": ["Male", "2. Zero hunger", "Lasalocid", "Time Factors", "Ionophores", "Drug Resistance", "0402 animal and dairy science", "Eukaryota", "04 agricultural and veterinary sciences", "Animal Feed", "Diet", "Gastrointestinal Tract", "Animals", "Animal Nutritional Physiological Phenomena", "Cattle", "Monensin", "Methane"], "contacts": [{"organization": "Denis Kraus\u00e9, K. M. Wittenberg, K. H. Ominski, H. Guan,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.2527/jas.2005-652"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Animal%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.2527/jas.2005-652", "name": "item", "description": "10.2527/jas.2005-652", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.2527/jas.2005-652"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2006-07-01T00:00:00Z"}}, {"id": "1959.7/uws:64278", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:27:32Z", "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/1959.7/uws:64278"}, {"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": "1959.7/uws:64278", "name": "item", "description": "1959.7/uws:64278", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/1959.7/uws:64278"}, {"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": "1959.7/uws:76989", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-04-03T16:27:33Z", "type": "Journal Article", "created": "2022-03-30", "title": "Cross-biome antibiotic resistance decays after millions of years of soil development", "description": "Abstract

Soils 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.Bacillus firmus nematicidal bacterial strains are used to control plant parasitic nematode infestation of crops in agricultural production. Proteases are presumed to be the primary nematode virulence factors in nematicidal B. firmus degrading the nematode cuticle and other organs. We determined and compared the whole genome sequences of two nematicidal strains. Comparative genomics with a particular focus on possible virulence determinants revealed a wider range of possible virulence factors in a B. firmus isolate from a commercial bionematicide and a wild type Bacillus sp. isolate with nematicidal activity. The resulting 4.6 Mb B. firmus I-1582 and 5.3 Mb Bacillus sp. ZZV12-4809 genome assemblies contain respectively 18 and 19 homologs to nematode-virulent proteases, two nematode-virulent chitinase homologs in ZZV12-4809 and 28 and 36 secondary metabolite biosynthetic clusters, projected to encode antibiotics, small peptides, toxins and siderophores. The results of this study point to the genetic capability of B. firmus and related species for nematode virulence through a range of direct and indirect mechanisms.Bacillus firmus nematicidal bacterial strains are used to control plant parasitic nematode infestation of crops in agricultural production. Proteases are presumed to be the primary nematode virulence factors in nematicidal B. firmus degrading the nematode cuticle and other organs. We determined and compared the whole genome sequences of two nematicidal strains. Comparative genomics with a particular focus on possible virulence determinants revealed a wider range of possible virulence factors in a B. firmus isolate from a commercial bionematicide and a wild type Bacillus sp. isolate with nematicidal activity. The resulting 4.6 Mb B. firmus I-1582 and 5.3 Mb Bacillus sp. ZZV12-4809 genome assemblies contain respectively 18 and 19 homologs to nematode-virulent proteases, two nematode-virulent chitinase homologs in ZZV12-4809 and 28 and 36 secondary metabolite biosynthetic clusters, projected to encode antibiotics, small peptides, toxins and siderophores. The results of this study point to the genetic capability of B. firmus and related species for nematode virulence through a range of direct and indirect mechanisms.