{"type": "FeatureCollection", "features": [{"id": "10.1002/cbic.202000051", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:14:00Z", "type": "Journal Article", "created": "2020-01-31", "title": "An Engineered E.\u2005coli Strain for Direct in Vivo Fluorination", "description": "Abstract

Selectively fluorinated compounds are found frequently in pharmaceutical and agrochemical products where currently 25\uffe2\uff80\uff9330\uffe2\uff80\uff89% of optimised compounds emerge from development containing at least one fluorine atom. There are many methods for the site\uffe2\uff80\uff90specific introduction of fluorine, but all are chemical and they often use environmentally challenging reagents. Biochemical processes for C\uffe2\uff88\uff92F bond formation are attractive, but they are extremely rare. In this work, the fluorinase enzyme, originally identified from the actinomycete bacterium Streptomyces cattleya, is engineered into Escherichia coli in such a manner that the organism is able to produce 5\uffe2\uff80\uffb2\uffe2\uff80\uff90fluorodeoxyadenosine (5\uffe2\uff80\uffb2\uffe2\uff80\uff90FDA) from S\uffe2\uff80\uff90adenosyl\uffe2\uff80\uff90l\uffe2\uff80\uff90methionine (SAM) and fluoride in live E.\uffe2\uff80\uff85coli cells. Success required the introduction of a SAM transporter and deletion of the endogenous fluoride efflux capacity in order to generate an E.\uffe2\uff80\uff85coli host that has the potential for future engineering of more elaborate fluorometabolites.

", "keywords": ["SAM transporters", "0301 basic medicine", "570", "S-Adenosylmethionine", "0303 health sciences", "Deoxyadenosines", "Halogenation", "DAS", "Fluorine", "Halogenations", "540", "QD Chemistry", "Streptomyces", "3. Good health", "03 medical and health sciences", "Bacterial Proteins", "Isomerism", "Escherichia coli", "QD", "Fluoride channels", "Genetic Engineering", "Oxidoreductases", "Fluorinases"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/cbic.202000051"}, {"href": "https://doi.org/10.1002/cbic.202000051"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/ChemBioChem", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/cbic.202000051", "name": "item", "description": "10.1002/cbic.202000051", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/cbic.202000051"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-03T00:00:00Z"}}, {"id": "10.1016/j.colsurfb.2023.113433", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:16:24Z", "type": "Journal Article", "created": "2023-06-28", "title": "Contrasting transport and fate of hydrophilic and hydrophobic bacteria in wettable and water-repellent porous media: Straining or attachment?", "description": "Bacterial transport and retention likely depend on bacterial and soil surface properties, especially hydrophobicity. We used a controlled experimental setup to explore hydrophilic Escherichia coli (E. coli) and hydrophobic Rhodococcus erythropolis (PTCC1767) (R. erythropolis) transport through dry (-\u00a015,000\u00a0cm water potential) and water saturated (0\u00a0cm water potential) wettable and water-repellent sand columns. A pulse of bacteria (1\u00a0\u00d7\u00a0108 CFU mL-1) and bromide (10\u00a0mmol\u00a0L-1) moved through the columns under saturated flow (0\u00a0cm) for four pore volumes. A second bacteria and bromide pulse was then poured on the column surfaces and leaching was extended six more pore volumes. In dry wettable sand attachment dominated E. coli retention, whereas R. erythropolis was dominated by straining. Once wetted, the dominant retention mechanisms flipped between these bacteria. Attachment by either bacteria decreased markedly in water-repellent sand, so straining was the main retention mechanism. We explain this from capillary potential energy, which enhanced straining under the formation of water films at very early times (i.e., imbibing) and film thinning at much later times (i.e., draining). The interaction between the hydrophobicity of bacteria and soil on transport, retention and release mechanisms needs greater consideration in predictions.", "keywords": ["Bromides", "2040 Environment and Biodiversity", "570", "Supplementary Information", "Wetting characteristics", "Vadose zone", "610", "Soil", "Colloid and Surface Chemistry", "Sand", "Pore-scale processes", "Escherichia coli", "Physical and Theoretical Chemistry", "European Commission", "101026287", "SDG 15 - Life on Land", "Drought", "T", "Water", "Surfaces and Interfaces", "T Technology", "Interfacial processes", "3. Good health", "TC Hydraulic engineering. Ocean engineering", "Marie Sklodowska-Curie grant", "EU Horizon 2020", "SDG 6 - Clean Water and Sanitation", "TC", "Porosity", "Hydrophobic and Hydrophilic Interactions", "Biotechnology"]}, "links": [{"href": "https://doi.org/10.1016/j.colsurfb.2023.113433"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Colloids%20and%20Surfaces%20B%3A%20Biointerfaces", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.colsurfb.2023.113433", "name": "item", "description": "10.1016/j.colsurfb.2023.113433", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.colsurfb.2023.113433"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-08-01T00:00:00Z"}}, {"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.scitotenv.2024.176196", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:17:34Z", "type": "Journal Article", "created": "2024-09-13", "title": "Modeling bacterial transport and fate: Insight into the cascading consequences of soil water repellency and contrasting hydraulic conditions", "description": "The mechanisms governing bacteria transport and fate rely on their hydrophobicity and the wettability of porous media across a wide range of soil moisture conditions, extending from extreme dryness to highly saturated states. However, it largely remains unknown how transport, retention, and release mechanisms change in natural soil systems in such conditions. We thus optimized our previously published unique transport data for hydrophilic Escherichia coli (E. coli) and hydrophobic Rhodococcus erythropolis (R. erythropolis) bacteria, and bromide (Br-) in two distinct wettable and water-repellent soils at column scale. The soils were initially dry, followed by injecting influents in two pulses followed by a flushing step under saturated flow conditions for six pore volumes. We conducted simulations for each pulse separately and simultaneously for soils. There were differences in hydraulic properties of the soils due to their contrasting wetting characteristic in separate and simultaneously modeling of each pulse affecting Br- and bacteria transport fate. Bacteria attachment was the dominant retention mechanism in both soils in these conditions. Notably, the 82.4\u00a0min-1 attachment rate in wettable soil was almost 10\u00d7 greater than in the water-repellent soil and it governed optimization of bacteria die-off. Physicochemical detachment and physical release unraveled the effect of bacteria size and hydrophobicity interacting with soil wettability. The smaller and hydrophobic R. erythropolis detached more easily while hydrophilic E. coli released; the rates were enhanced by soil water repellency. Further research is needed to reveal the effects of surface wettability properties on bacteria survival especially at the nanoscale.", "keywords": ["690", "Bromides", "Bacteria", "QH301 Biology", "Transport processes", "610", "Attachment", "Water", "QH301", "Water repellency", "Soil", "Straining", "Escherichia coli", "Wettability", "Rhodococcus", "Hydrophobic and Hydrophilic Interactions", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2024.176196"}, {"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.2024.176196", "name": "item", "description": "10.1016/j.scitotenv.2024.176196", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2024.176196"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-12-01T00:00:00Z"}}, {"id": "10.1016/j.ultsonch.2022.105919", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:18:07Z", "type": "Journal Article", "created": "2022-01-18", "title": "Bacterial cell wall material properties determine E. coli resistance to sonolysis", "description": "The applications of bacterial sonolysis in industrial settings are plagued by the lack of the knowledge of the exact mechanism of action of sonication on bacterial cells, variable effectiveness of cavitation on bacteria, and inconsistent data of its efficiency. In this study we have systematically changed material properties of E. coli cells to probe the effect of different cell wall layers on bacterial resistance to ultrasonic irradiation (20\u00a0kHz, output power 6,73\u00a0W, horn type, 3\u00a0mm probe tip diameter, 1\u00a0ml sample volume). We have determined the rates of sonolysis decay for bacteria with compromised major capsular polymers, disrupted outer membrane, compromised peptidoglycan layer, spheroplasts, giant spheroplasts, and in bacteria with different cell physiology. The non-growing bacteria were 5-fold more resistant to sonolysis than growing bacteria. The most important bacterial cell wall structure that determined the outcome during sonication was peptidoglycan. If peptidoglycan was remodelled, weakened, or absent the cavitation was very efficient. Cells with removed peptidoglycan had sonolysis resistance equal to lipid vesicles and were extremely sensitive to sonolysis. The results suggest that bacterial physiological state as well as cell wall architecture are major determinants that influence the outcome of bacterial sonolysis.", "keywords": ["sonication", "0301 basic medicine", "cell envelope", "Cell envelope", "ultrazvo\u010dna sonikacija", "Short Communication", "celi\u010dna ovojnica", "QC221-246", "Peptidoglycan", "viability", " bacteria", " Escherichia coli", " sonication", " cell envelope", "Sonication", "03 medical and health sciences", "Cell Wall", "bakterijske celice", "Escherichia coli", "bacteria", "QD1-999", "info:eu-repo/classification/udc/579.23:577.352:544.57", "0303 health sciences", "liza celic", "Bacteria", "viability", "sonoliza", "Escherichia coli Proteins", "Acoustics. Sound", "bakterijske celice", " Escherichia coli", " celi\u010dna ovojnica", " liza celic", " ultrazvo\u010dna sonikacija", " sonoliza", "info:eu-repo/classification/udc/579", "Chemistry", "Viability"]}, "links": [{"href": "https://doi.org/10.1016/j.ultsonch.2022.105919"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ultrasonics%20Sonochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.ultsonch.2022.105919", "name": "item", "description": "10.1016/j.ultsonch.2022.105919", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.ultsonch.2022.105919"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-01-01T00:00:00Z"}}, {"id": "10.1016/j.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 (Bacillus sp. MEP218, a soil bacterium with high potential as a source of bioactive molecules, produces mostly C16\uffe2\uff80\uff93C17 fengycin and other cyclic lipopeptides (CLP) when growing under previously optimized culture conditions. This work addressed the elucidation of the genome sequence of MEP218 and its taxonomic classification. The genome comprises 3,944,892\uffc2\uffa0bp, with a total of 3474 coding sequences and a G\uffe2\uff80\uff89+\uffe2\uff80\uff89C content of 46.59%. Our phylogenetic analysis to determine the taxonomic position demonstrated that the assignment of the MEP218 strain to Bacillus velezensis species provides insights into its evolutionary context and potential functional attributes. The in silico genome analysis revealed eleven gene clusters involved in the synthesis of secondary metabolites, including non-ribosomal CLP (fengycins and surfactin), polyketides, terpenes, and bacteriocins. Furthermore, genes encoding phytase, involved in the release of phytic phosphate for plant and animal nutrition, or other enzymes such as cellulase, xylanase, and alpha 1\uffe2\uff80\uff934 glucanase were detected. In vitro antagonistic assays against Salmonella typhimurium, Acinetobacter baumanii, Escherichia coli, among others, demonstrated a broad spectrum of C16\uffe2\uff80\uff93C17 fengycin produced by MEP218. MEP218 genome sequence analysis expanded our understanding of the diversity and genetic relationships within the Bacillus genus and updated the Bacillus databases with its unique trait to produce antibacterial fengycins and its potential as a resource of biotechnologically useful enzymes.The effects of two kinds ofEscherichia coli(E. coli) strain, wild-typeE. coliW3110 andE. colinir-Ptac, which has enhanced NO2reduction activity, on oral CH4emission and NO3toxicity in NO3-treated sheep were assessed in a respiratory hood system in a 4\uffc3\uff976 Youden square design. NO3(1\uffc2\uffb73g NaNO3/kg0\uffc2\uffb775body weight) and/orE. colistrains were delivered into the rumen through a fistula as a single dose 30min after the morning meal.Escherichia colicells were inoculated for sheep to provide an initialE. colicell density of optical density at 660nm of 2, which corresponded to 2\uffc3\uff971010cells/ml. The six treatments consisted of saline,E. coliW3110,E. colinir-Ptac, NO3, NO3plusE. coliW3110, and NO3plusE. colinir-Ptac. CH4emission from sheep was reduced by the inoculation ofE. coliW3110 orE. colinir-Ptac by 6% and 12%, respectively. NO3markedly inhibited CH4emission from sheep. Compared with sheep given NO3alone, the inoculation ofE. coliW3110 to NO3-infused sheep lessened ruminal and plasma toxic NO2accumulation and blood methaemoglobin production, while keeping ruminal methanogenesis low. Ruminal and plasma toxic NO2accumulation and blood methaemoglobin production in sheep were unaffected by the inoculation ofE. colinir-Ptac. These results suggest that ruminal methanogenesis may be reduced by the inoculation ofE. coliW3110 orE. colinir-Ptac. The inoculation ofE. coliW3110 may abate NO3toxicity when NO3is used to inhibit CH4emission from ruminants.

", "keywords": ["Male", "2. Zero hunger", "Nitrates", "Rumen", "Sheep", "Metabolic Clearance Rate", "0402 animal and dairy science", "04 agricultural and veterinary sciences", "Carbon Dioxide", "Nitrate Reductase", "3. Good health", "Oxygen Consumption", "Fermentation", "Escherichia coli", "Animals", "Infusions", " Parenteral", "Methane", "Methemoglobin", "Nitrites"], "contacts": [{"organization": "Junichi Takahashi, I. Shinzato, Y. Asakura, C. Sar, B. Pen, R. Morikawa, B. Mwenya, A. Tsujimoto, K. Kuwaki, K. Takaura, N. Isogai, Yasuhiko Toride,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1079/bjn20051517"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/British%20Journal%20of%20Nutrition", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1079/bjn20051517", "name": "item", "description": "10.1079/bjn20051517", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1079/bjn20051517"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2005-11-01T00:00:00Z"}}, {"id": "10.1111/1462-2920.15751", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:19:48Z", "type": "Journal Article", "created": "2021-09-28", "title": "Novel Alcaligenes ammonioxydans sp. nov. from wastewater treatment sludge oxidizes ammonia to N2 with a previously unknown pathway", "description": "Summary

Heterotrophic nitrifiers are able to oxidize and remove ammonia from nitrogen\uffe2\uff80\uff90rich wastewaters but the genetic elements of heterotrophic ammonia oxidation are poorly understood. Here, we isolated and identified a novel heterotrophic nitrifier, Alcaligenes ammonioxydans sp. nov. strain HO\uffe2\uff80\uff901, oxidizing ammonia to hydroxylamine and ending in the production of N2 gas. Genome analysis revealed that strain HO\uffe2\uff80\uff901 encoded a complete denitrification pathway but lacks any genes coding for homologous to known ammonia monooxygenases or hydroxylamine oxidoreductases. Our results demonstrated strain HO\uffe2\uff80\uff901 denitrified nitrite (not nitrate) to N2 and N2O at anaerobic and aerobic conditions respectively. Further experiments demonstrated that inhibition of aerobic denitrification did not stop ammonia oxidation and N2 production. A gene cluster (dnfT1RT2ABCD) was cloned from strain HO\uffe2\uff80\uff901 and enabled E. coli accumulated hydroxylamine. Sub\uffe2\uff80\uff90cloning showed that genetic cluster dnfAB or dnfABC already enabled E. coli cells to produce hydroxylamine and further to 15N2 from (15NH4)2SO4. Transcriptome analysis revealed these three genes dnfA, dnfB and dnfC were significantly upregulated in response to ammonia stimulation. Taken together, we concluded that strain HO\uffe2\uff80\uff901 has a novel dnf genetic cluster for ammonia oxidation and this dnf genetic cluster encoded a previously unknown pathway of direct ammonia oxidation (Dirammox) to N2.

", "keywords": ["Alcaligenes ammonioxydans sp. nov.", "0301 basic medicine", "106014 Genomics", "Nitrogen", "HYDROXYLAMINE OXIDASE", "direct ammonia oxidation (Dirammox)", "OXIDATION", "REDUCTASE", "Water Purification", "THIOSPHAERA-PANTOTROPHA", "PYRUVIC-OXIME", "03 medical and health sciences", "heterotrophic nitrifier", "Ammonia", "106014 Genomik", "Escherichia coli", "Alcaligenes", "wastewater", "Nitrites", "106022 Mikrobiologie", "HETEROTROPHIC NITRIFICATION", "0303 health sciences", "PURIFICATION", "Sewage", "AEROBIC DENITRIFICATION", "Nitrification", "Aerobiosis", "6. Clean water", "NITROGEN", "FAECALIS", "Denitrification", "106022 Microbiology", "Oxidation-Reduction"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.15751"}, {"href": "https://doi.org/10.1111/1462-2920.15751"}, {"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": "10.1111/1462-2920.15751", "name": "item", "description": "10.1111/1462-2920.15751", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.15751"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-09-28T00:00:00Z"}}, {"id": "10.2134/jeq2011.0207", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:21:40Z", "type": "Journal Article", "created": "2012-01-05", "title": "Biochar Pyrolyzed At Two Temperatures Affects Escherichia Coli Transport Through A Sandy Soil", "description": "The incorporation of biochar into soils has been proposed as a means to sequester carbon from the atmosphere. An added environmental benefit is that biochar has also been shown to increase soil retention of nutrients, heavy metals, and pesticides. The goal of this study was to evaluate whether biochar amendments affect the transport of Escherichia coli through a water-saturated soil. We looked at the transport of three E. coli isolates through 10-cm columns packed with a fine sandy soil amended with 2 or 10% (w/w) poultry litter biochar pyrolyzed at 350 or 700\u00b0C. For all three isolates, mixing the high-temperature biochar at a rate of 2% into the soil had no impact on transport behavior. When added at a rate of 10%, a reduction of five orders of magnitude in the amount of E. coli transported through the soil was observed for two of the isolates, and a 60% reduction was observed for the third isolate. Mixing the low-temperature biochar into the soil resulted in enhanced transport through the soil for two of the isolates, whereas no significant differences in transport behavior were observed between the low-temperature and high-temperature biochar amendments for one isolate. Our results show that the addition of biochar can affect the retention and transport behavior of E. coli and that biochar application rate, biochar pyrolysis temperature, and bacterial surface characteristics were important factors determining the transport of E. coli through our test soil.", "keywords": ["2. Zero hunger", "Hot Temperature", "04 agricultural and veterinary sciences", "01 natural sciences", "6. Clean water", "3. Good health", "Soil", "13. Climate action", "Charcoal", "Escherichia coli", "Water Movements", "0401 agriculture", " forestry", " and fisheries", "Adsorption", "Water Microbiology", "Soil Microbiology", "0105 earth and related environmental sciences"], "contacts": [{"organization": "Sergio M. Abit, Carl H. Bolster,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.2134/jeq2011.0207"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Environmental%20Quality", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.2134/jeq2011.0207", "name": "item", "description": "10.2134/jeq2011.0207", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.2134/jeq2011.0207"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-01-01T00:00:00Z"}}, {"id": "10.3390/s18072250", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:22:44Z", "type": "Journal Article", "created": "2018-07-12", "title": "Biosensing System for Concentration Quantification of Magnetically Labeled E. coli in Water Samples", "description": "

Bacterial contamination of water sources (e.g., lakes, rivers and springs) from waterborne bacteria is a crucial water safety issue and its prevention is of the utmost significance since it threatens the health and well-being of wildlife, livestock, and human populations and can lead to serious illness and even death. Rapid and multiplexed measurement of such waterborne pathogens is vital and the challenge is to instantly detect in these liquid samples different types of pathogens with high sensitivity and specificity. In this work, we propose a biosensing system in which the bacteria are labelled with streptavidin coated magnetic markers (MPs\u2014magnetic particles) forming compounds (MLBs\u2014magnetically labelled bacteria). Video microscopy in combination with a particle tracking software are used for their detection and quantification. When the liquid containing the MLBs is introduced into the developed, microfluidic platform, the MLBs are accelerated towards the outlet by means of a magnetic field gradient generated by integrated microconductors, which are sequentially switched ON and OFF by a microcontroller. The velocities of the MLBs and that of reference MPs, suspended in the same liquid in a parallel reference microfluidic channel, are calculated and compared in real time by a digital camera mounted on a conventional optical microscope in combination with a particle trajectory tracking software. The MLBs will be slower than the reference MPs due to the enhanced Stokes\u2019 drag force exerted on them, resulting from their greater volume and altered hydrodynamic shape. The results of the investigation showed that the parameters obtained from this method emerged as reliable predictors for E. coli concentrations.

", "keywords": ["0301 basic medicine", "0303 health sciences", "magnetophoresis", "magnetic microparticles", "Chemical technology", "magnetic labeling", "Microfluidics", "TP1-1185", "Biosensing Techniques", "Article", "6. Clean water", "particle tracking", "Magnetics", "03 medical and health sciences", "bacteria quantification", "13. Climate action", "Escherichia coli", "biosensing", "Water Microbiology"]}, "links": [{"href": "http://www.mdpi.com/1424-8220/18/7/2250/pdf"}, {"href": "https://doi.org/10.3390/s18072250"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Sensors", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/s18072250", "name": "item", "description": "10.3390/s18072250", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/s18072250"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-07-12T00:00:00Z"}}, {"id": "11336/226991", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:27:09Z", "type": "Journal Article", "created": "2023-12-13", "title": "Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis", "description": "Abstract

Bacillus sp. MEP218, a soil bacterium with high potential as a source of bioactive molecules, produces mostly C16\uffe2\uff80\uff93C17 fengycin and other cyclic lipopeptides (CLP) when growing under previously optimized culture conditions. This work addressed the elucidation of the genome sequence of MEP218 and its taxonomic classification. The genome comprises 3,944,892\uffc2\uffa0bp, with a total of 3474 coding sequences and a G\uffe2\uff80\uff89+\uffe2\uff80\uff89C content of 46.59%. Our phylogenetic analysis to determine the taxonomic position demonstrated that the assignment of the MEP218 strain to Bacillus velezensis species provides insights into its evolutionary context and potential functional attributes. The in silico genome analysis revealed eleven gene clusters involved in the synthesis of secondary metabolites, including non-ribosomal CLP (fengycins and surfactin), polyketides, terpenes, and bacteriocins. Furthermore, genes encoding phytase, involved in the release of phytic phosphate for plant and animal nutrition, or other enzymes such as cellulase, xylanase, and alpha 1\uffe2\uff80\uff934 glucanase were detected. In vitro antagonistic assays against Salmonella typhimurium, Acinetobacter baumanii, Escherichia coli, among others, demonstrated a broad spectrum of C16\uffe2\uff80\uff93C17 fengycin produced by MEP218. MEP218 genome sequence analysis expanded our understanding of the diversity and genetic relationships within the Bacillus genus and updated the Bacillus databases with its unique trait to produce antibacterial fengycins and its potential as a resource of biotechnologically useful enzymes.

Bacterial contamination of water sources (e.g., lakes, rivers and springs) from waterborne bacteria is a crucial water safety issue and its prevention is of the utmost significance since it threatens the health and well-being of wildlife, livestock, and human populations and can lead to serious illness and even death. Rapid and multiplexed measurement of such waterborne pathogens is vital and the challenge is to instantly detect in these liquid samples different types of pathogens with high sensitivity and specificity. In this work, we propose a biosensing system in which the bacteria are labelled with streptavidin coated magnetic markers (MPs\u2014magnetic particles) forming compounds (MLBs\u2014magnetically labelled bacteria). Video microscopy in combination with a particle tracking software are used for their detection and quantification. When the liquid containing the MLBs is introduced into the developed, microfluidic platform, the MLBs are accelerated towards the outlet by means of a magnetic field gradient generated by integrated microconductors, which are sequentially switched ON and OFF by a microcontroller. The velocities of the MLBs and that of reference MPs, suspended in the same liquid in a parallel reference microfluidic channel, are calculated and compared in real time by a digital camera mounted on a conventional optical microscope in combination with a particle trajectory tracking software. The MLBs will be slower than the reference MPs due to the enhanced Stokes\u2019 drag force exerted on them, resulting from their greater volume and altered hydrodynamic shape. The results of the investigation showed that the parameters obtained from this method emerged as reliable predictors for E. coli concentrations.

", "keywords": ["0301 basic medicine", "0303 health sciences", "magnetophoresis", "magnetic microparticles", "Chemical technology", "magnetic labeling", "Microfluidics", "TP1-1185", "Biosensing Techniques", "Article", "6. Clean water", "particle tracking", "Magnetics", "03 medical and health sciences", "bacteria quantification", "13. Climate action", "Escherichia coli", "biosensing", "Water Microbiology"]}, "links": [{"href": "http://www.mdpi.com/1424-8220/18/7/2250/pdf"}, {"href": "https://doi.org/2867552234"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Sensors", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2867552234", "name": "item", "description": "2867552234", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2867552234"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-07-12T00:00:00Z"}}, {"id": "50|userclaim___::85c2e6974a364f4a96fdee6d82a5dd41", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:29:26Z", "type": "Other", "title": "Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis", "keywords": ["Bacteriocin", "Gene", "Synteny", "Microbiology", "Agricultural and Biological Sciences", "Biochemistry", " Genetics and Molecular Biology", "Genetics", "Escherichia coli", "RNA Sequencing Data Analysis", "Molecular Biology", "Biology", "GC-content", "Genome", "Acinetobacter", "Bacteria", "Probiotics and Prebiotics", "In silico", "Life Sciences", "Ribosomal RNA", "Whole genome sequencing", "FOS: Biological sciences", "Microbial Enzymes and Biotechnological Applications", "metagenomics assembly", "Biotechnology", "Food Science", "Phylogenetic tree"], "contacts": [{"organization": "Mariano Pistorio, Mar\u00eda Julia Estrella, Edgardo Jofr\u00e9, Gonzalo Torres Tejerizo, Bruno Contreras-Moreira, Daniela Medeot, Anal\u00eda Sannazzaro, Medeot, Daniela, Daniela B. Medeot, Sannazzaro, Anal\u00eda, Anal\u00eda In\u00e9s Sannazzaro, Estrella, Maria Julia, Mar\u00eda Julia Estrella, Torres Tejerizo, Gonzalo, Gonzalo Torres Tejerizo, Contreras\u2011Moreira, Bruno, Bruno Contreras\u2010Moreira, Pistorio, Mariano, Mariano Pistorio, Jofr\u00e9, Edgardo, Edgardo Jofr\u00e9,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/50|userclaim___::85c2e6974a364f4a96fdee6d82a5dd41"}, {"rel": "self", "type": "application/geo+json", "title": "50|userclaim___::85c2e6974a364f4a96fdee6d82a5dd41", "name": "item", "description": "50|userclaim___::85c2e6974a364f4a96fdee6d82a5dd41", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/50|userclaim___::85c2e6974a364f4a96fdee6d82a5dd41"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-13T00:00:00Z"}}, {"id": "85c2e6974a364f4a96fdee6d82a5dd41", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:30:18Z", "type": "Other", "title": "Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis", "keywords": ["Bacteriocin", "Gene", "Synteny", "Microbiology", "Agricultural and Biological Sciences", "Biochemistry", " Genetics and Molecular Biology", "Genetics", "Escherichia coli", "RNA Sequencing Data Analysis", "Molecular Biology", "Biology", "GC-content", "Genome", "Acinetobacter", "Bacteria", "Probiotics and Prebiotics", "In silico", "Life Sciences", "Ribosomal RNA", "Whole genome sequencing", "FOS: Biological sciences", "Microbial Enzymes and Biotechnological Applications", "metagenomics assembly", "Biotechnology", "Food Science", "Phylogenetic tree"], "contacts": [{"organization": "Mariano Pistorio, Mar\u00eda Julia Estrella, Edgardo Jofr\u00e9, Gonzalo Torres Tejerizo, Bruno Contreras-Moreira, Daniela Medeot, Anal\u00eda Sannazzaro, Medeot, Daniela, Daniela B. Medeot, Sannazzaro, Anal\u00eda, Anal\u00eda In\u00e9s Sannazzaro, Estrella, Maria Julia, Mar\u00eda Julia Estrella, Torres Tejerizo, Gonzalo, Gonzalo Torres Tejerizo, Contreras\u2011Moreira, Bruno, Bruno Contreras\u2010Moreira, Pistorio, Mariano, Mariano Pistorio, Jofr\u00e9, Edgardo, Edgardo Jofr\u00e9,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/85c2e6974a364f4a96fdee6d82a5dd41"}, {"rel": "self", "type": "application/geo+json", "title": "85c2e6974a364f4a96fdee6d82a5dd41", "name": "item", "description": "85c2e6974a364f4a96fdee6d82a5dd41", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/85c2e6974a364f4a96fdee6d82a5dd41"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-13T00:00:00Z"}}, {"id": "PMC2569841", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:31:02Z", "type": "Journal Article", "created": "2008-06-03", "title": "Transcription increases methylmethane sulfonate-induced mutations in alkB strains of Escherichia coli", "description": "Methylmethane sulfonate (MMS) produces DNA base lesions, including 3-methylcytosine (m3C), more effectively in single-stranded DNA. The repair of m3C in Escherichia coli is mediated by AlkB through oxidative demethylation and in the absence of repair, m3C leads to base-substitution mutations. We describe here results of experiments that were designed to investigate whether transcription of a gene in E. coli affects the process of mutagenesis by MMS and the roles played by AlkB and lesion bypass polymerase PolV. Using a genetic reversion assay, we have confirmed that MMS mutagenesis is suppressed by AlkB, but is enhanced by PolV. High transcription of the target gene enhances reversion frequency in an orientation-dependent manner. When the cytosines that are the likely targets of MMS were in the non-template strand (NTS), transcription increased the MMS-induced reversion frequency several fold. This increase was dependent on the presence of PolV. In contrast, when the same cytosines were present in the template strand, transcription had little effect on reversion frequency induced by MMS. These data suggest that MMS creates 3-methylcytosine adducts in the NTS and are consistent with an idea proposed previously that transcription makes the NTS transiently single-stranded and more accessible to chemicals. We propose that this is the underlying cause of its increased sensitivity to MMS and suggest that transcriptionally active DNA may be a preferred target for the action of alkylating agents that prefer single-stranded DNA.", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Transcription", " Genetic", "Mutagenesis", "Escherichia coli Proteins", "Escherichia coli", "Methyl Methanesulfonate", "Mixed Function Oxygenases", "Mutagens", "3. Good health"], "contacts": [{"organization": "Douglas, Fix, Chandrika, Canugovi, Ashok S, Bhagwat,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/PMC2569841"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/DNA%20Repair", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC2569841", "name": "item", "description": "PMC2569841", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC2569841"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-08-01T00:00:00Z"}}, {"id": "PMC6068504", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:31:04Z", "type": "Journal Article", "created": "2018-07-12", "title": "Biosensing System for Concentration Quantification of Magnetically Labeled E. coli in Water Samples", "description": "

Bacterial contamination of water sources (e.g., lakes, rivers and springs) from waterborne bacteria is a crucial water safety issue and its prevention is of the utmost significance since it threatens the health and well-being of wildlife, livestock, and human populations and can lead to serious illness and even death. Rapid and multiplexed measurement of such waterborne pathogens is vital and the challenge is to instantly detect in these liquid samples different types of pathogens with high sensitivity and specificity. In this work, we propose a biosensing system in which the bacteria are labelled with streptavidin coated magnetic markers (MPs\u2014magnetic particles) forming compounds (MLBs\u2014magnetically labelled bacteria). Video microscopy in combination with a particle tracking software are used for their detection and quantification. When the liquid containing the MLBs is introduced into the developed, microfluidic platform, the MLBs are accelerated towards the outlet by means of a magnetic field gradient generated by integrated microconductors, which are sequentially switched ON and OFF by a microcontroller. The velocities of the MLBs and that of reference MPs, suspended in the same liquid in a parallel reference microfluidic channel, are calculated and compared in real time by a digital camera mounted on a conventional optical microscope in combination with a particle trajectory tracking software. The MLBs will be slower than the reference MPs due to the enhanced Stokes\u2019 drag force exerted on them, resulting from their greater volume and altered hydrodynamic shape. The results of the investigation showed that the parameters obtained from this method emerged as reliable predictors for E. coli concentrations.

", "keywords": ["0301 basic medicine", "0303 health sciences", "magnetophoresis", "magnetic microparticles", "Chemical technology", "magnetic labeling", "Microfluidics", "TP1-1185", "Biosensing Techniques", "Article", "6. Clean water", "particle tracking", "Magnetics", "03 medical and health sciences", "bacteria quantification", "13. Climate action", "Escherichia coli", "biosensing", "Water Microbiology"]}, "links": [{"href": "http://www.mdpi.com/1424-8220/18/7/2250/pdf"}, {"href": "https://doi.org/PMC6068504"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Sensors", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC6068504", "name": "item", "description": "PMC6068504", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC6068504"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-07-12T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Escherichia+coli&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Escherichia+coli&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Escherichia+coli&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Escherichia+coli&offset=20", "hreflang": "en-US"}], "numberMatched": 20, "numberReturned": 20, "distributedFeatures": [], "timeStamp": "2026-04-04T13:41:18.302923Z"}