{"type": "FeatureCollection", "features": [{"id": "10.1002/biot.202000165", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:14:09Z", "type": "Journal Article", "created": "2020-10-21", "title": "Engineering Native and Synthetic Pathways in Pseudomonas putida for the Production of Tailored Polyhydroxyalkanoates", "description": "Abstract<p>Growing environmental concern sparks renewed interest in the sustainable production of (bio)materials that can replace oil\uffe2\uff80\uff90derived goods. Polyhydroxyalkanoates (PHAs) are isotactic polymers that play a critical role in the central metabolism of producer bacteria, as they act as dynamic reservoirs of carbon and reducing equivalents. PHAs continue to attract industrial attention as a starting point toward renewable, biodegradable, biocompatible, and versatile thermoplastic and elastomeric materials. Pseudomonas species have been known for long as efficient biopolymer producers, especially for medium\uffe2\uff80\uff90chain\uffe2\uff80\uff90length PHAs. The surge of synthetic biology and metabolic engineering approaches in recent years offers the possibility of exploiting the untapped potential of Pseudomonas cell factories for the production of tailored PHAs. In this article, an overview of the metabolic and regulatory circuits that rule PHA accumulation in Pseudomonas putida is provided, and approaches leading to the biosynthesis of novel polymers (e.g., PHAs including nonbiological chemical elements in their structures) are discussed. The potential of novel PHAs to disrupt existing and future market segments is closer to realization than ever before. The review is concluded by pinpointing challenges that currently hinder the wide adoption of bio\uffe2\uff80\uff90based PHAs, and strategies toward programmable polymer biosynthesis from alternative substrates in engineered P. putida strains are proposed.</p>", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Biopolymer", "PHA", "Pseudomonas putida", "Polyhydroxyalkanoates", "Carbon", "12. Responsible consumption", "03 medical and health sciences", "/dk/atira/pure/sustainabledevelopmentgoals/affordable_and_clean_energy; name=SDG 7 - Affordable and Clean Energy", "Metabolic Engineering", "Pseudomonas", "Pathway engineering", "Metabolic engineering", "Synthetic biology"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/biot.202000165"}, {"href": "https://doi.org/10.1002/biot.202000165"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biotechnology%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/biot.202000165", "name": "item", "description": "10.1002/biot.202000165", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/biot.202000165"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-11-09T00:00:00Z"}}, {"id": "10.1007/s00253-020-10811-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:14:30Z", "type": "Journal Article", "created": "2020-08-13", "title": "Industrial biotechnology of Pseudomonas putida: advances and prospects", "description": "Abstract<p>Pseudomonas putidais a Gram-negative, rod-shaped bacterium that can be encountered in diverse ecological habitats. This ubiquity is traced to its remarkably versatile metabolism, adapted to withstand physicochemical stress, and the capacity to thrive in harsh environments. Owing to these characteristics, there is a growing interest in this microbe for industrial use, and the corresponding research has made rapid progress in recent years. Hereby, strong drivers are the exploitation of cheap renewable feedstocks and waste streams to produce value-added chemicals and the steady progress in genetic strain engineering and systems biology understanding of this bacterium. Here, we summarize the recent advances and prospects in genetic engineering, systems and synthetic biology, and applications ofP. putidaas a cell factory.</p>Key points<p>\uffe2\uff80\uffa2 Pseudomonas putida advances to a global industrial cell factory.</p><p>\uffe2\uff80\uffa2 Novel tools enable system-wide understanding and streamlined genomic engineering.</p><p>\uffe2\uff80\uffa2 Applications of P. putida range from bioeconomy chemicals to biosynthetic drugs.</p>", "keywords": ["0301 basic medicine", "ddc:500", "0303 health sciences", "Pseudomonas putida", "EDEMP cycle", "PHA", "Systems Biology", "500", "Genomics", "Mini-Review", "Bioeconomy", "Bacterial chassis", "Lignin", "03 medical and health sciences", "/dk/atira/pure/sustainabledevelopmentgoals/affordable_and_clean_energy; name=SDG 7 - Affordable and Clean Energy", "Microbial cell factory", "13. Climate action", "Biocatalysis", "Synthetic Biology", "KT2440", "Metabolic engineering", "Biotransformation", "Synthetic biology", "Biotechnology"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s00253-020-10811-9.pdf"}, {"href": "https://doi.org/10.1007/s00253-020-10811-9"}, {"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/s00253-020-10811-9", "name": "item", "description": "10.1007/s00253-020-10811-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00253-020-10811-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-13T00:00:00Z"}}, {"id": "10.1016/j.envpol.2016.11.048", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:16:09Z", "type": "Journal Article", "created": "2016-11-19", "title": "Influence of bacterial extracellular polymeric substances on the sorption of Zn on \u03b3-alumina: A combination of FTIR and EXAFS studies", "description": "Extracellular polymeric substances (EPS) isolated from bacteria, are abound of functional groups which can react with metals and consequently influence the immobilization of metals. In this study, we combined with Zn K-edge Extended X-ray Absorption Fine Structure (EXAFS), Fourier Transform Infrared (FTIR) spectroscopy, and High-Resolution Transmission Electron Microscopy (HRTEM) techniques to study the effects of EPS isolated from Bacillus subtilis and Pseudomonas putida on Zn sorption on \u03b3-alumina. The results revealed that Zn sorption on aluminum oxide was pH-dependent and significantly influenced by bacterial EPS. At pH 7.5, Zn sorbed on \u03b3-alumina was in the form of Zn-Al layered doubled hydroxide (LDH) precipitates, whereas at pH 5.5, Zn sorbed on \u03b3-alumina was as a Zn-Al bidentate mononuclear surface complex. The amount of sorbed Zn at pH 7.5 was 1.3-3.7 times higher than that at pH 5.5. However, in the presence of 2\u00a0g\u00a0L-1 EPS, regardless of pH conditions and EPS source, Zn\u00a0+\u00a0EPS + \u03b3-alumina ternary complex was formed on the surface of \u03b3-alumina, which resulted in decreased Zn sorption (reduced by 8.4-67.8%) at pH 7.5 and enhanced Zn sorption (increased by 10.0-124.7%) at pH 5.5. The FTIR and EXAFS spectra demonstrated that both the carboxyl and phosphoryl moieties of EPS were crucial in this process. These findings highlight EPS effects on Zn interacts with \u03b3-alumina.", "keywords": ["Polymers", "Pseudomonas putida", "0211 other engineering and technologies", "02 engineering and technology", "Hydrogen-Ion Concentration", "01 natural sciences", "Zinc", "X-Ray Absorption Spectroscopy", "Spectroscopy", " Fourier Transform Infrared", "Aluminum Oxide", "Hydroxides", "Adsorption", "Bacillus subtilis", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.envpol.2016.11.048"}, {"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.2016.11.048", "name": "item", "description": "10.1016/j.envpol.2016.11.048", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envpol.2016.11.048"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-01-01T00:00:00Z"}}, {"id": "10.1016/j.envpol.2018.09.128", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:16:09Z", "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.2022.120472", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:16:10Z", "type": "Journal Article", "created": "2022-10-19", "title": "Comparative toxicological assessment of three soils polluted with different levels of hydrocarbons and heavy metals using in vitro and in vivo approaches", "description": "The biological effects induced by the pollutants present in soils, together with the chemical and physical characterizations, are good indicators to provide a general overview of their quality. However, the existence of studies where the toxicity associated to soils contaminated with mixtures of pollutants applying both in vitro and in vivo models are scarce. In this work, three soils (namely, Soil 001, Soil 002 and Soil 013) polluted with different concentrations of hydrocarbons and heavy metals were evaluated using different organisms representative of human (HepG2 human cell line) and environmental exposure (the yeast Saccharomyces cerevisiae, the Gram-negative bacterium Pseudomonas putida and, for the in vivo evaluation, the annelid Enchytraeus crypticus). In vitro assays showed that the soluble fraction of the Soil 001, which presented the highest levels of heavy metals, represented a great impact in the viability of the HepG2 cells and S. cerevisiae, while organic extracts from Soils 002 and 013 caused a slight decrease in the viability of HepG2 cells. In addition, in vivo experiments showed that Soils 001 and 013 affected the survival and the reproduction of E. crypticus. Altogether, these results provide a general overview of the potential hazards associated to three specific contaminated sites in a variety of organisms, showing how different concentrations of similar pollutants affect them, and highlights the relevance of testing both organic and soluble extracts when in vitro safety assays of soils are performed.", "keywords": ["Pseudomonas putida", "Enchytraeus crypticus", "Qu\u00edmica anal\u00edtica", "Saccharomyces cerevisiae", "Analytic", "01 natural sciences", "Hydrocarbons", "6. Clean water", "HepG2 cellsSaccharomyces cerevisiaePseudomonas putidaEnchytraeus crypticusSoil contamination", "Chemistry", "Soil", "Soil contamination", "13. Climate action", "Metals", " Heavy", "Humans", "Soil Pollutants", "Chemistry", " Analytic", "HepG2 cells Saccharomyces cerevisiae Pseudomonas putida Enchytraeus crypticus Soil contamination", "HepG2 cells", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.envpol.2022.120472"}, {"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.2022.120472", "name": "item", "description": "10.1016/j.envpol.2022.120472", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envpol.2022.120472"}, {"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.mec.2020.e00126", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:16:43Z", "type": "Journal Article", "created": "2020-03-19", "title": "Synthetic control of plasmid replication enables target- and self-curing of vectors and expedites genome engineering of Pseudomonas putida", "description": "Genome engineering of non-conventional microorganisms calls for the development of dedicated synthetic biology tools. Pseudomonas putida is a Gram-negative, non-pathogenic soil bacterium widely used for metabolic engineering owing to its versatile metabolism and high levels of tolerance to different types of stress. Genome editing of P. putida largely relies on homologous recombination events, assisted by helper plasmid-based expression of genes encoding DNA modifying enzymes. Plasmid curing from selected isolates is the most tedious and time-consuming step of this procedure, and implementing commonly used methods to this end in P. putida (e.g. temperature-sensitive replicons) is often impractical. To tackle this issue, we have developed a toolbox for both target- and self-curing of plasmid DNA in Pseudomonas species. Our method enables plasmid-curing in a simple cultivation step by combining in vivo digestion of vectors by the I-SceI homing nuclease with synthetic control of plasmid replication, triggered by the addition of a cheap chemical inducer (3-methylbenzoate) to the medium. The system displays an efficiency of vector curing >90% and the screening of plasmid-free clones is greatly facilitated by the use of fluorescent markers that can be selected according to the application intended. Furthermore, quick genome engineering of P. putida using self-curing plasmids is demonstrated through genome reduction of the platform strain EM42 by eliminating all genes encoding \u03b2-lactamases, the catabolic ben gene cluster, and the pyoverdine synthesis machinery. Physiological characterization of the resulting streamlined strain, P. putida SEM10, revealed advantageous features that could be exploited for metabolic engineering.", "keywords": ["Genome engineering", "0301 basic medicine", "0303 health sciences", "Pseudomonas putida", "QH301-705.5", "Plasmid curing", "3. Good health", "03 medical and health sciences", "Special issue on Non-conventional microbes edited by Ian Wheeldon and Aindrila Mukhopadhyay", "Biology (General)", "Metabolic engineering", "Synthetic biology", "TP248.13-248.65", "Biotechnology"]}, "links": [{"href": "https://doi.org/10.1016/j.mec.2020.e00126"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Metabolic%20Engineering%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.mec.2020.e00126", "name": "item", "description": "10.1016/j.mec.2020.e00126", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.mec.2020.e00126"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-06-01T00:00:00Z"}}, {"id": "10.1016/j.tim.2020.02.015", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:17:21Z", "type": "Journal Article", "created": "2020-03-31", "title": "Pseudomonas putida", "description": "Pseudomonas putida is a ubiquitous rhizosphere saprophytic bacterium and soil colonizer that belongs to the wide group of fluorescent Pseudomonas species. P. putida strain KT2440, the best-characterized member of the group, became a model laboratory species that attracted considerable attention as a cell host for synthetic biology and metabolic engineering due to its remarkable and versatile metabolism, which has evolved to withstand harsh environmental conditions and physicochemical stress. This species has also retained the ability to survive and thrive in natural soil environments. P. putida mt-2 and other isolates have been recognized and used as agents for bioremediation due to their ability to grow on complex substrates, including aromatic compounds (e.g., toluene and xylenes). The absence of pathogenic determinants is another key feature of strain KT2440 that facilitated its adoption for both fundamental and applied research in microbiology.", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Metabolic Engineering", "Pseudomonas putida", "Synthetic Biology"]}, "links": [{"href": "https://doi.org/10.1016/j.tim.2020.02.015"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Trends%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.tim.2020.02.015", "name": "item", "description": "10.1016/j.tim.2020.02.015", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.tim.2020.02.015"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-06-01T00:00:00Z"}}, {"id": "10.1021/acs.est.2c03149", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:17:28Z", "type": "Journal Article", "created": "2022-09-14", "title": "Chemotactic Bacteria Facilitate the Dispersion of Nonmotile Bacteria through Micrometer-Sized Pores in Engineered Porous Media", "description": "Recent research has demonstrated that chemotactic bacteria can disperse inside microsized pores while traveling toward favorable conditions. Microbe-microbe cotransport might enable nonmotile bacteria to be carried with motile partners to enhance their dispersion and reduce their deposition in porous systems. The aim of this study was to demonstrate the enhancement in the dispersion of nonmotile bacteria (Mycobacterium gilvum VM552, a polycyclic aromatic hydrocarbon-degrader, and Sphingobium sp. D4, a hexachlorocyclohexane-degrader, through micrometer-sized pores near the exclusion-cell-size limit, in the presence of motile Pseudomonas putida G7 cells. For this purpose, we used bioreactors equipped with two chambers that were separated with membrane filters with 3, 5, and 12 \u03bcm pore sizes and capillary polydimethylsiloxane (PDMS) microarrays (20 \u03bcm \u00d7 35 \u03bcm \u00d7 2.2 mm). The cotransport of nonmotile bacteria occurred exclusively in the presence of a chemoattractant concentration gradient, and therefore, a directed flow of motile cells. This cotransport was more intense in the presence of larger pores (12 \u03bcm) and strong chemoeffectors (\u03b3-aminobutyric acid). The mechanism that governed cotransport at the cell scale involved mechanical pushing and hydrodynamic interactions. Chemotaxis-mediated cotransport of bacterial degraders and its implications in pore accessibility opens new avenues for the enhancement of bacterial dispersion in porous media and the biodegradation of heterogeneously contaminated scenarios.", "keywords": ["Chemotactic Factors", "Pseudomonas putida", "Chemotaxis", "Bioaccessibility", "01 natural sciences", "Microbe-microbe cotransport", "Dimethylpolysiloxanes", "Polycyclic Aromatic Hydrocarbons", "Micrometer-sized pores", "Porosity", "Hexachlorocyclohexane", "gamma-Aminobutyric Acid", "Hitchhiking", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://pubs.acs.org/doi/pdf/10.1021/acs.est.2c03149"}, {"href": "https://doi.org/10.1021/acs.est.2c03149"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20%26amp%3B%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1021/acs.est.2c03149", "name": "item", "description": "10.1021/acs.est.2c03149", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1021/acs.est.2c03149"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-09-14T00:00:00Z"}}, {"id": "10.1038/ismej.2016.169", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:17:45Z", "type": "Journal Article", "created": "2017-01-03", "title": "The Pseudomonas putida T6SS is a plant warden against phytopathogens", "description": "Abstract                <p>Bacterial type VI secretion systems (T6SSs) are molecular weapons designed to deliver toxic effectors into prey cells. These nanomachines have an important role in inter-bacterial competition and provide advantages to T6SS active strains in polymicrobial environments. Here we analyze the genome of the biocontrol agent Pseudomonas putida KT2440 and identify three T6SS gene clusters (K1-, K2- and K3-T6SS). Besides, 10 T6SS effector\uffe2\uff80\uff93immunity pairs were found, including putative nucleases and pore-forming colicins. We show that the K1-T6SS is a potent antibacterial device, which secretes a toxic Rhs-type effector Tke2. Remarkably, P. putida eradicates a broad range of bacteria in a K1-T6SS-dependent manner, including resilient phytopathogens, which demonstrates that the T6SS is instrumental to empower P. putida to fight against competitors. Furthermore, we observed a drastically reduced necrosis on the leaves of Nicotiana benthamiana during co-infection with P. putida and Xanthomonas campestris. Such protection is dependent on the activity of the P. putida T6SS. Many routes have been explored to develop biocontrol agents capable of manipulating the microbial composition of the rhizosphere and phyllosphere. Here we unveil a novel mechanism for plant biocontrol, which needs to be considered for the selection of plant wardens whose mission is to prevent phytopathogen infections.</p>", "keywords": ["PROTEIN SECRETION", "Nicotiana", "0301 basic medicine", "570", "INTESTINAL INFLAMMATION", "05 Environmental Sciences", "VIBRIO-CHOLERAE", "Environmental Sciences & Ecology", "VI SECRETION SYSTEM", "Xanthomonas campestris", "Microbiology", "03 medical and health sciences", "Bacterial Proteins", "10 Technology", "Plant Diseases", "0303 health sciences", "Science & Technology", "Ecology", "Pseudomonas putida", "ROOT MICROBIOME", "Gene Expression Regulation", " Bacterial", "06 Biological Sciences", "Type VI Secretion Systems", "GENOMIC ANALYSIS", "Biological Control Agents", "ESCHERICHIA-COLI", "EFFECTORS", "IMMUNITY PROTEINS", "Original Article", "HOST-RANGE", "Life Sciences & Biomedicine"]}, "links": [{"href": "http://www.nature.com/articles/ismej2016169.pdf"}, {"href": "https://doi.org/10.1038/ismej.2016.169"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/ismej.2016.169", "name": "item", "description": "10.1038/ismej.2016.169", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/ismej.2016.169"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-01-03T00:00:00Z"}}, {"id": "10.1111/1462-2920.13956", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:18:43Z", "type": "Journal Article", "created": "2017-10-13", "title": "Type VI secretion systems in plant-associated bacteria", "description": "Summary<p>The type VI secretion system (T6SS) is a bacterial nanomachine used to inject effectors into prokaryotic or eukaryotic cells and is thus involved in both host manipulation and interbacterial competition. The T6SS is widespread among Gram\uffe2\uff80\uff90negative bacteria, mostly within the Proteobacterium Phylum. This secretion system is commonly found in commensal and pathogenic plant\uffe2\uff80\uff90associated bacteria. Phylogenetic analysis of phytobacterial T6SS clusters shows that they are distributed in the five main clades previously described (group 1\uffe2\uff80\uff935). The even distribution of the system among commensal and pathogenic phytobacteria suggests that the T6SS provides fitness and colonization advantages in planta and that the role of the T6SS is not restricted to virulence. This manuscript reviews the phylogeny and biological roles of the T6SS in plant\uffe2\uff80\uff90associated bacteria, highlighting a remarkable diversity both in terms of mechanism and function.</p>", "keywords": ["PROTEIN SECRETION", "0301 basic medicine", "570", "VIBRIO-CHOLERAE", "PATHOGENIC BACTERIA", "Microbiology", "03 medical and health sciences", "Bacterial Proteins", "Proteobacteria", "Phylogeny", "Plant Diseases", "2. Zero hunger", "0303 health sciences", "Science & Technology", "Virulence", "PSEUDOMONAS-AERUGINOSA", "Minireviews", "Plants", "Type VI Secretion Systems", "IN-SILICO ANALYSIS", "AGROBACTERIUM-TUMEFACIENS", "INTERBACTERIAL COMPETITION", "GENOMIC ANALYSIS", "EFFECTORS", "VIRULENCE", "Life Sciences & Biomedicine", "0605 Microbiology"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.13956"}, {"href": "https://doi.org/10.1111/1462-2920.13956"}, {"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": "10.1111/1462-2920.13956", "name": "item", "description": "10.1111/1462-2920.13956", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.13956"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-11-10T00:00:00Z"}}, {"id": "10.1111/1751-7915.13396", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:18:43Z", "type": "Journal Article", "created": "2019-03-12", "title": "Accelerated genome engineering of Pseudomonas putida by I\u2010 Sce I\u2015mediated recombination and CRISPR \u2010Cas9 counterselection", "description": "Summary<p>Pseudomonas species have become reliable platforms for bioproduction due to their capability to tolerate harsh conditions imposed by large\uffe2\uff80\uff90scale bioprocesses and their remarkable resistance to diverse physicochemical stresses. The last few years have brought forth a variety of synthetic biology tools for the genetic manipulation of pseudomonads, but most of them are either applicable only to obtain certain types of mutations, lack efficiency, or are not easily accessible to be used in different Pseudomonas species (e.g. natural isolates). In this work, we describe a versatile, robust and user\uffe2\uff80\uff90friendly procedure that facilitates virtually any kind of genomic manipulation in Pseudomonas species in 3\uffe2\uff80\uff935\uffc2\uffa0days. The protocol presented here is based on DNA recombination forced by double\uffe2\uff80\uff90stranded DNA cuts (through the activity of the I\uffe2\uff80\uff90SceI homing meganuclease from yeast) followed by highly efficient counterselection of mutants (aided by a synthetic CRISPR\uffe2\uff80\uff90Cas9 device). The individual parts of the genome engineering toolbox, tailored for knocking genes in and out, have been standardized to enable portability and easy exchange of functional gene modules as needed. The applicability of the procedure is illustrated both by eliminating selected genomic regions in the platform strain P.\uffc2\uffa0putida KT2440 (including difficult\uffe2\uff80\uff90to\uffe2\uff80\uff90delete genes) and by integrating different reporter genes (comprising novel variants of fluorescent proteins) into a defined landing site in the target chromosome.</p>", "keywords": ["Gene Editing", "Recombination", " Genetic", "0301 basic medicine", "03 medical and health sciences", "Pseudomonas putida", "Brief Reports", "Clustered Regularly Interspaced Short Palindromic Repeats", "CRISPR-Cas Systems", "TP248.13-248.65", "Biotechnology", "3. Good health"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1751-7915.13396"}, {"href": "https://doi.org/10.1111/1751-7915.13396"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1751-7915.13396", "name": "item", "description": "10.1111/1751-7915.13396", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1751-7915.13396"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-03-12T00:00:00Z"}}, {"id": "10.1111/1751-7915.13533", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:18:43Z", "type": "Journal Article", "created": "2020-02-11", "title": "An expanded CRISPRi toolbox for tunable control of gene expression in Pseudomonas putida", "description": "Summary<p>Owing to its wide metabolic versatility and physiological robustness, together with amenability to genetic manipulations and high resistance to stressful conditions, Pseudomonas putida is increasingly becoming the organism of choice for a range of applications in both industrial and environmental applications. However, a range of applied synthetic biology and metabolic engineering approaches are still limited by the lack of specific genetic tools to effectively and efficiently regulate the expression of target genes. Here, we present a single\uffe2\uff80\uff90plasmid CRISPR\uffe2\uff80\uff90interference (CRISPRi) system expressing a nuclease\uffe2\uff80\uff90deficient cas9 gene under the control of the inducible XylS/Pm expression system, along with the option of adopting constitutively expressed guide RNAs (either sgRNA or crRNA and tracrRNA). We showed that the system enables tunable, tightly controlled gene repression (up to 90%) of chromosomally expressed genes encoding fluorescent proteins, either individually or simultaneously. In addition, we demonstrate that this method allows for suppressing the expression of the essential genes pyrF and ftsZ, resulting in significantly low growth rates or morphological changes respectively. This versatile system expands the capabilities of the current CRISPRi toolbox for efficient, targeted and controllable manipulation of gene expression in P. putida.</p>", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Pseudomonas putida", "Life Science", "Gene Expression", "Clustered Regularly Interspaced Short Palindromic Repeats", "CRISPR-Cas Systems", "RNA", " Guide", " CRISPR-Cas Systems", "TP248.13-248.65", "Research Articles", "Biotechnology"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1751-7915.13533"}, {"href": "https://doi.org/10.1111/1751-7915.13533"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1751-7915.13533", "name": "item", "description": "10.1111/1751-7915.13533", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1751-7915.13533"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-02-11T00:00:00Z"}}, {"id": "10.1111/1751-7915.13383", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:18:43Z", "type": "Journal Article", "created": "2019-03-13", "title": "Physical decoupling of XylS/ Pm regulatory elements and conditional proteolysis enable precise control of gene expression in Pseudomonas putida", "description": "Summary<p>Most of the gene expression systems available for Gram\uffe2\uff80\uff90negative bacteria are afflicted by relatively high levels of basal (i.e. leaky) expression of the target gene(s). This occurrence affects the system dynamics, ultimately reducing the output and productivity of engineered pathways and synthetic circuits. In order to circumvent this problem, we have designed a novel expression system based on the well\uffe2\uff80\uff90known XylS/Pm transcriptional regulator/promoter pair from the soil bacterium Pseudomonas putida mt\uffe2\uff80\uff902, in which the key functional elements are physically decoupled. By integrating the xylS gene into the chromosome of the platform strain KT2440, while placing the Pm promoter into a set of standard plasmid vectors, the inducibility of the system (i.e. the output difference between the induced and uninduced state) improved up to 170\uffe2\uff80\uff90fold. We further combined this modular system with an extra layer of post\uffe2\uff80\uff90translational control by means of conditional proteolysis. In this setup, the target gene is tagged with a synthetic motif dictating protein degradation. When the system features were characterized using the monomeric superfolder GFP as a model protein, the basal levels of fluorescence were brought down to zero (i.e. below the limit of detection). In all, these novel expression systems constitute an alternative tool to altogether suppress leaky gene expression, and they can be easily adapted to other vector formats and plugged\uffe2\uff80\uff90in into different Gram\uffe2\uff80\uff90negative bacterial species at the user's will.</p>", "keywords": ["0301 basic medicine", "0303 health sciences", "Pseudomonas putida", "Gene Expression", "Gene Expression Regulation", " Bacterial", "03 medical and health sciences", "Bacterial Proteins", "Proteolysis", "Trans-Activators", "Brief Reports", "Promoter Regions", " Genetic", "TP248.13-248.65", "Biotechnology", "Plasmids"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1751-7915.13383"}, {"href": "https://doi.org/10.1111/1751-7915.13383"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1751-7915.13383", "name": "item", "description": "10.1111/1751-7915.13383", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1751-7915.13383"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-03-12T00:00:00Z"}}, {"id": "10.3390/microorganisms11030735", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:21:11Z", "type": "Journal Article", "created": "2023-03-13", "title": "Inorganic Carbon Assimilation and Electrosynthesis of Platform Chemicals in Bioelectrochemical Systems (BESs) Inoculated with Clostridium saccharoperbutylacetonicum N1-H4", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>The need for greener processes to satisfy the demand of platform chemicals together with the possibility of reusing CO2 from human activities has recently encouraged research on the set-up, optimization, and development of bioelectrochemical systems (BESs) for the electrosynthesis of organic compounds from inorganic carbon (CO2, HCO3\u2212). In the present study, we tested the ability of Clostridium saccharoperbutylacetonicum N1-4 (DSMZ 14923) to produce acetate and D-3-hydroxybutyrate from inorganic carbon present in a CO2:N2 gas mix. At the same time, we tested the ability of a Shewanella oneidensis MR1 and Pseudomonas aeruginosa PA1430/CO1 consortium to provide reducing power to sustain carbon assimilation at the cathode. We tested the performance of three different systems with the same layouts, inocula, and media, but with the application of 1.5 V external voltage, of a 1000 \u2126 external load, and without any connection between the electrodes or external devices (open circuit voltage, OCV). We compared both CO2 assimilation rate and production of metabolites (formate, acetate 3-D-hydroxybutyrate) in our BESs with the values obtained in non-electrogenic control cultures and estimated the energy used by our BESs to assimilate 1 mol of CO2. Our results showed that C. saccharoperbutylacetonicum NT-1 achieved the maximum CO2 assimilation (95.5%) when the microbial fuel cells (MFCs) were connected to the 1000 \u2126 external resistor, with the Shewanella/Pseudomonas consortium as the only source of electrons. Furthermore, we detected a shift in the metabolism of C. saccharoperbutylacetonicum NT-1 because of its prolonged activity in BESs. Our results open new perspectives for the utilization of BESs in carbon capture and electrosynthesis of platform chemicals.</p></article>", "keywords": ["570", "CO<sub>2</sub> capture", "PCA", "[SDV.BIO]Life Sciences [q-bio]/Biotechnology", "QH301-705.5", "Pseudomonas aeruginosa PA1430/CO1", "3-D-hydroxybutyrate; CO2 capture; Clostridium saccharoperbutylacetonicum NT-1; PCA; Pseudomonas aeruginosa PA1430/CO1; Shewanella oneidensis MR1; electrosynthesis", "<i>Shewanella oneidensis</i> MR1", "Article", "[SDV.BIO] Life Sciences [q-bio]/Biotechnology", "electrosynthesis", "CO<sub>2</sub> capture; <i>Clostridium saccharoperbutylacetonicum</i> NT-1; electrosynthesis; 3-D-hydroxybutyrate; PCA; <i>Shewanella oneidensis</i> MR1; <i>Pseudomonas aeruginosa</i> PA1430/CO1", "[CHIM.OTHE] Chemical Sciences/Other", "13. Climate action", "Clostridium saccharoperbutylacetonicum NT-1", "Shewanella oneidensis MR1", "3-D-hydroxybutyrate; CO2 capture; clostridium saccharoperbutylacetonicum NT-1; PCA; pseudomonas aeruginosa PA1430/CO1; shewanella oneidensis MR1; electrosynthesis", "CO$_2$ capture", "3-Dhydroxybutyrate", "3-D-hydroxybutyrate", "Biology (General)", "[CHIM.OTHE]Chemical Sciences/Other", "<i>Clostridium saccharoperbutylacetonicum</i> NT-1"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/11/3/735/pdf"}, {"href": "https://doi.org/10.3390/microorganisms11030735"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/microorganisms11030735", "name": "item", "description": "10.3390/microorganisms11030735", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/microorganisms11030735"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-03-13T00:00:00Z"}}, {"id": "10.3389/fmicb.2025.1372302", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:20:55Z", "type": "Journal Article", "created": "2025-02-25", "title": "Bio-electrosynthesis of polyhydroxybutyrate and surfactants in microbial fuel cells: a preliminary study", "description": "<p>Microbial Electrochemical Technology (MET) offers a promising avenue for CO2 utilization by leveraging the ability of chemolithotrophic microorganisms to use inorganic carbon in biosynthetic processes. By harnessing the power of electroactive bacteria, METs can facilitate the conversion of inorganic carbon into organic compounds. Therefore, this work combines biosurfactant production at the anode and PHB production at the cathode of Microbial Fuel Cells (MFCs), while testing the efficiency of Microbial Electrosynthesis Cells (MECs), and traditional culture in liquid media. This study employed a consortium of Pseudomonas aeruginosa PA1430/CO1 and Shewanella oneidensis MR-1, to provide reducing equivalents to Cupriavidus necator DSM428 for CO2 fixation and polyhydroxybutyrate (PHB) production. Glycerol was used as a carbon source by the anode consortium to investigate biosurfactant production. Additionally, Adaptive Laboratory Evolution (ALE) was employed to enhance the efficiency of this process to develop biofilms capable of synthesizing PHB from CO2 in MFCs under a controlled gas atmosphere (10% CO2, 10% O2, 2% H2, 78% N2). Observed results showed a higher direct CO2 removal from the gas mix in MECs (73%) than in MFCs (65%) compared to control cultures. Anionic (18.8 mg/L) and non-ionic (14.6 mg/L) surfactants were primarily present at the anodes of MFCs. Confocal microscope analysis revealed that the accumulation of PHBs in C. necator was significantly higher in MFCs (73% of cell volume) rather than in MECs (23%) and control cultures (40%). Further analyses on metabolites in the different systems are ongoing. Our data gave evidence that the anode consortium was able to provide enough electrons to sustain the chemolithotrophic growth of C. necator and the biosynthesis of PHBs at the cathode of MFCs, in a mechanism suggestive of the direct interspecies electron transfer (DIET), naturally occurring in natural environment.</p", "keywords": ["PHBs electrosynthesis", "Cupravidus necator DSM 428", "Pseudomonas aeruginosa PA1430/CO1", "CO2 capture", "Microbiology", "Shewanella oneidensis-MR1", "bioelectrochemical systems", "QR1-502", "CO2 capture; Cupravidus necator DSM 428; PHBs electrosynthesis; Pseudomonas aeruginosa PA1430/CO1; Shewanella oneidensis-MR1; bioelectrochemical systems; biosurfactants"], "contacts": [{"organization": "Nastro, Rosa Anna, Kuppam, Chandrasekhar, Toscanesi, Maria, Trifuoggi, Marco, Pietrelli, Andrea, Pasquale, Vincenzo, Avignone-Rossa, Claudio,", "roles": ["creator"]}]}, "links": [{"href": "https://iris.uniroma1.it/bitstream/11573/1735928/2/Nastro%2c%20Rosa%20Anna_Bio-electrosynthesis_2025.pdf"}, {"href": "https://doi.org/10.3389/fmicb.2025.1372302"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fmicb.2025.1372302", "name": "item", "description": "10.3389/fmicb.2025.1372302", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2025.1372302"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-02-25T00:00:00Z"}}, {"id": "10.3390/genes10080601", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:21:07Z", "type": "Journal Article", "created": "2019-08-09", "title": "Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>The genus Pseudomonas comprises many known plant-associated microbes with plant growth promotion and disease suppression properties. Genome-based studies allow the prediction of the underlying mechanisms using genome mining tools and the analysis of the genes unique for a strain by implementing comparative genomics. Here, we provide the genome sequence of the strain Pseudomonas brassicacearum 3Re2-7, formerly known as P. trivialis and P. reactans, elucidate its revised taxonomic classification, experimentally verify the gene predictions by transcriptome sequencing, describe its genetic biocontrol potential and contextualize it to other known Pseudomonas biocontrol agents. The P. brassicacearum 3Re2-7 genome comprises a circular chromosome with a size of 6,738,544 bp and a GC-content of 60.83%. 6267 genes were annotated, of which 6113 were shown to be transcribed in rich medium and/or in the presence of Rhizoctonia solani. Genome mining identified genes related to biocontrol traits such as secondary metabolite and siderophore biosynthesis, plant growth promotion, inorganic phosphate solubilization, biosynthesis of lipo- and exopolysaccharides, exoproteases, volatiles and detoxification. Core genome analysis revealed, that the 3Re2-7 genome exhibits a high collinearity with the representative genome for the species, P. brassicacearum subsp. brassicacearum NFM421. Comparative genomics allowed the identification of 105 specific genes and revealed gene clusters that might encode specialized biocontrol mechanisms of strain 3Re2-7. Moreover, we captured the transcriptome of P. brassicacearum 3Re2-7, confirming the transcription of the predicted biocontrol-related genes. The gene clusters coding for 2,4-diacetylphloroglucinol (phlABCDEFGH) and hydrogen cyanide (hcnABC) were shown to be highly transcribed. Further genes predicted to encode putative alginate production enzymes, a pyrroloquinoline quinone precursor peptide PqqA and a matrixin family metalloprotease were also found to be highly transcribed. With this study, we provide a basis to further characterize the mechanisms for biocontrol in Pseudomonas species, towards a sustainable and safe application of P. brassicacearum biocontrol agents.</p></article>", "keywords": ["COMPARATIVE GENOMICS", "0301 basic medicine", "570", "Antifungal Agents", "Plant-growth promotion", "Biolog\u00eda", "comparative genomics", "Phloroglucinol", "PLANT-GROWTH PROMOTION", "Article", "Rhizoctonia", "12. Responsible consumption", "transcriptomics", "03 medical and health sciences", "https://purl.org/becyt/ford/1.6", "Genome mining", "Hydrogen Cyanide", "Pseudomonas", "genome mining", "RNA SEQUENCING", "TRANSCRIPTOMICS", "biocontrol", "GENOME MINING", "PSEUDOMONASBRASSICACEARUM", "https://purl.org/becyt/ford/1", "Transcriptomics", "2. Zero hunger", "0303 health sciences", "Comparative genomics", "Biocontrol", "RNA sequencing", "<i>Pseudomonas brassicacearum</i>", "3. Good health", "BIOCONTROL", "Pseudomonas brassicacearum", "Biological Control Agents", "Genes", " Bacterial", "Transcriptome", "plant-growth promotion"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/8/601/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/8/601/pdf"}, {"href": "https://doi.org/10.3390/genes10080601"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/genes10080601", "name": "item", "description": "10.3390/genes10080601", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes10080601"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-09T00:00:00Z"}}, {"id": "10.3390/genes10060456", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:21:07Z", "type": "Journal Article", "created": "2019-06-14", "title": "Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.</p></article>", "keywords": ["0301 basic medicine", "TPH", "consortium", "Article", "diesel", "03 medical and health sciences", "PAHs", "rhizoremediation", "Pseudomonas", "RNA", " Ribosomal", " 16S", "11. Sustainability", "Soil Pollutants", "Polycyclic Aromatic Hydrocarbons", "bacteria", "Phylogeny", "Soil Microbiology", "Chryseobacterium", "2. Zero hunger", "metagenomics", "rhizoremediation; diesel; bacteria; consortium; metagenomics; PAHs; TPH", "0303 health sciences", "Microbiota", "Biodiversity", "15. Life on land", "Biolog\u00eda y Biomedicina / Biolog\u00eda", "Rhizoremediation", "Biodegradation", " Environmental", "Petroleum", "13. Climate action", "Metagenome"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://doi.org/10.3390/genes10060456"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/genes10060456", "name": "item", "description": "10.3390/genes10060456", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes10060456"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-14T00:00:00Z"}}, {"id": "10.5281/zenodo.14626839", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:22:52Z", "type": "Dataset", "title": "Data set of soil microbial components in response to extreme spring events at variable temperatures", "description": "The soil microbial response to prolonged soil drought (20% field capacity FC), wetness (above FC) and moderate drought (common at 50% FC) was simulated in pots at two spring temperatures - 2\u00b0C and +2.5\u00b0C colder and warmer, respectively, compared to the average in the central-eastern Po Valley, Italy (decade 2014-2024).\u00a0   Two soils (a ploughed soil and an adjacent renatured soil) were subjected to two 60-day cycles (cold and warm spring) at three levels of soil water content. The climate simulation started after the wheat seedlings had reached the two-leaf stage in all pots. Soil samples were taken from the wheat rhizome at the end of each experiment.  The response of microbial biomass was evaluated in terms of double-stranded DNA (dsDNA), total bacteria quantified as 16S gene copy number using Real Time PCR and total fungi quantified as 18S gene copy number using Digital PCR.   Three major bacterial groups, Pseudomonas, Actinomycetes and Bacillus, were quantified by real-time PCR using specific primers of the 16S region (F968/Ps-r; F243/518r; BacF/518).   Twenty-two enzyme activities were also quantified in soil samples. The data set contains a total of twenty-eight variables.", "keywords": ["climate change", "microbial biomass", "soil bacteria", "Pseudomonas", "actinomycetes", "estreme events", "soil fungi", "microrganisms", "Bacillus", "metabolic activity", "soil"], "contacts": [{"organization": "Manici, Luisa M.", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.14626839"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.14626839", "name": "item", "description": "10.5281/zenodo.14626839", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.14626839"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2026-01-10T00:00:00Z"}}, {"id": "10486/713957", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:25:01Z", "type": "Journal Article", "created": "2019-06-14", "title": "Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.</p></article>", "keywords": ["0301 basic medicine", "TPH", "consortium", "Article", "diesel", "03 medical and health sciences", "PAHs", "rhizoremediation", "Pseudomonas", "RNA", " Ribosomal", " 16S", "11. Sustainability", "Soil Pollutants", "Polycyclic Aromatic Hydrocarbons", "bacteria", "Phylogeny", "Soil Microbiology", "Chryseobacterium", "2. Zero hunger", "metagenomics", "rhizoremediation; diesel; bacteria; consortium; metagenomics; PAHs; TPH", "0303 health sciences", "Microbiota", "Biodiversity", "15. Life on land", "Biolog\u00eda y Biomedicina / Biolog\u00eda", "Rhizoremediation", "Biodegradation", " Environmental", "Petroleum", "13. Climate action", "Metagenome"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://doi.org/10486/713957"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10486/713957", "name": "item", "description": "10486/713957", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10486/713957"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-14T00:00:00Z"}}, {"id": "10259/7490", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:24:46Z", "type": "Journal Article", "created": "2022-10-19", "title": "Comparative toxicological assessment of three soils polluted with different levels of hydrocarbons and heavy metals using in vitro and in vivo approaches", "description": "The biological effects induced by the pollutants present in soils, together with the chemical and physical characterizations, are good indicators to provide a general overview of their quality. However, the existence of studies where the toxicity associated to soils contaminated with mixtures of pollutants applying both in vitro and in vivo models are scarce. In this work, three soils (namely, Soil 001, Soil 002 and Soil 013) polluted with different concentrations of hydrocarbons and heavy metals were evaluated using different organisms representative of human (HepG2 human cell line) and environmental exposure (the yeast Saccharomyces cerevisiae, the Gram-negative bacterium Pseudomonas putida and, for the in vivo evaluation, the annelid Enchytraeus crypticus). In vitro assays showed that the soluble fraction of the Soil 001, which presented the highest levels of heavy metals, represented a great impact in the viability of the HepG2 cells and S. cerevisiae, while organic extracts from Soils 002 and 013 caused a slight decrease in the viability of HepG2 cells. In addition, in vivo experiments showed that Soils 001 and 013 affected the survival and the reproduction of E. crypticus. Altogether, these results provide a general overview of the potential hazards associated to three specific contaminated sites in a variety of organisms, showing how different concentrations of similar pollutants affect them, and highlights the relevance of testing both organic and soluble extracts when in vitro safety assays of soils are performed.", "keywords": ["Pseudomonas putida", "Enchytraeus crypticus", "Qu\u00edmica anal\u00edtica", "Saccharomyces cerevisiae", "Analytic", "01 natural sciences", "Hydrocarbons", "6. Clean water", "Chemistry", "Soil", "Soil contamination", "13. Climate action", "Metals", " Heavy", "Humans", "Soil Pollutants", "Chemistry", " Analytic", "HepG2 cells Saccharomyces cerevisiae Pseudomonas putida Enchytraeus crypticus Soil contamination", "HepG2 cells", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10259/7490"}, {"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": "10259/7490", "name": "item", "description": "10259/7490", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10259/7490"}, {"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": "10261/281764", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:24:50Z", "type": "Journal Article", "created": "2022-09-14", "title": "Chemotactic Bacteria Facilitate the Dispersion of Nonmotile Bacteria through Micrometer-Sized Pores in Engineered Porous Media", "description": "Recent research has demonstrated that chemotactic bacteria can disperse inside microsized pores while traveling toward favorable conditions. Microbe-microbe cotransport might enable nonmotile bacteria to be carried with motile partners to enhance their dispersion and reduce their deposition in porous systems. The aim of this study was to demonstrate the enhancement in the dispersion of nonmotile bacteria (Mycobacterium gilvum VM552, a polycyclic aromatic hydrocarbon-degrader, and Sphingobium sp. D4, a hexachlorocyclohexane-degrader, through micrometer-sized pores near the exclusion-cell-size limit, in the presence of motile Pseudomonas putida G7 cells. For this purpose, we used bioreactors equipped with two chambers that were separated with membrane filters with 3, 5, and 12 \u03bcm pore sizes and capillary polydimethylsiloxane (PDMS) microarrays (20 \u03bcm \u00d7 35 \u03bcm \u00d7 2.2 mm). The cotransport of nonmotile bacteria occurred exclusively in the presence of a chemoattractant concentration gradient, and therefore, a directed flow of motile cells. This cotransport was more intense in the presence of larger pores (12 \u03bcm) and strong chemoeffectors (\u03b3-aminobutyric acid). The mechanism that governed cotransport at the cell scale involved mechanical pushing and hydrodynamic interactions. Chemotaxis-mediated cotransport of bacterial degraders and its implications in pore accessibility opens new avenues for the enhancement of bacterial dispersion in porous media and the biodegradation of heterogeneously contaminated scenarios.", "keywords": ["Chemotactic Factors", "Pseudomonas putida", "Chemotaxis", "Bioaccessibility", "01 natural sciences", "Microbe-microbe cotransport", "Dimethylpolysiloxanes", "Polycyclic Aromatic Hydrocarbons", "Micrometer-sized pores", "Porosity", "Hexachlorocyclohexane", "gamma-Aminobutyric Acid", "Hitchhiking", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://pubs.acs.org/doi/pdf/10.1021/acs.est.2c03149"}, {"href": "https://doi.org/10261/281764"}, {"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": "10261/281764", "name": "item", "description": "10261/281764", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10261/281764"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-09-14T00:00:00Z"}}, {"id": "11336/151981", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:25:11Z", "type": "Journal Article", "created": "2019-08-09", "title": "Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>The genus Pseudomonas comprises many known plant-associated microbes with plant growth promotion and disease suppression properties. Genome-based studies allow the prediction of the underlying mechanisms using genome mining tools and the analysis of the genes unique for a strain by implementing comparative genomics. Here, we provide the genome sequence of the strain Pseudomonas brassicacearum 3Re2-7, formerly known as P. trivialis and P. reactans, elucidate its revised taxonomic classification, experimentally verify the gene predictions by transcriptome sequencing, describe its genetic biocontrol potential and contextualize it to other known Pseudomonas biocontrol agents. The P. brassicacearum 3Re2-7 genome comprises a circular chromosome with a size of 6,738,544 bp and a GC-content of 60.83%. 6267 genes were annotated, of which 6113 were shown to be transcribed in rich medium and/or in the presence of Rhizoctonia solani. Genome mining identified genes related to biocontrol traits such as secondary metabolite and siderophore biosynthesis, plant growth promotion, inorganic phosphate solubilization, biosynthesis of lipo- and exopolysaccharides, exoproteases, volatiles and detoxification. Core genome analysis revealed, that the 3Re2-7 genome exhibits a high collinearity with the representative genome for the species, P. brassicacearum subsp. brassicacearum NFM421. Comparative genomics allowed the identification of 105 specific genes and revealed gene clusters that might encode specialized biocontrol mechanisms of strain 3Re2-7. Moreover, we captured the transcriptome of P. brassicacearum 3Re2-7, confirming the transcription of the predicted biocontrol-related genes. The gene clusters coding for 2,4-diacetylphloroglucinol (phlABCDEFGH) and hydrogen cyanide (hcnABC) were shown to be highly transcribed. Further genes predicted to encode putative alginate production enzymes, a pyrroloquinoline quinone precursor peptide PqqA and a matrixin family metalloprotease were also found to be highly transcribed. With this study, we provide a basis to further characterize the mechanisms for biocontrol in Pseudomonas species, towards a sustainable and safe application of P. brassicacearum biocontrol agents.</p></article>", "keywords": ["COMPARATIVE GENOMICS", "0301 basic medicine", "570", "Antifungal Agents", "Plant-growth promotion", "Biolog\u00eda", "comparative genomics", "Phloroglucinol", "PLANT-GROWTH PROMOTION", "Article", "Rhizoctonia", "12. Responsible consumption", "transcriptomics", "03 medical and health sciences", "https://purl.org/becyt/ford/1.6", "Genome mining", "Hydrogen Cyanide", "Pseudomonas", "genome mining", "RNA SEQUENCING", "TRANSCRIPTOMICS", "biocontrol", "GENOME MINING", "PSEUDOMONASBRASSICACEARUM", "https://purl.org/becyt/ford/1", "Transcriptomics", "2. Zero hunger", "0303 health sciences", "Comparative genomics", "Biocontrol", "RNA sequencing", "<i>Pseudomonas brassicacearum</i>", "3. Good health", "BIOCONTROL", "Pseudomonas brassicacearum", "Biological Control Agents", "Genes", " Bacterial", "Transcriptome", "plant-growth promotion"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/8/601/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/8/601/pdf"}, {"href": "https://doi.org/11336/151981"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11336/151981", "name": "item", "description": "11336/151981", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11336/151981"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-09T00:00:00Z"}}, {"id": "11367/116840", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:25:12Z", "type": "Journal Article", "created": "2023-03-13", "title": "Inorganic Carbon Assimilation and Electrosynthesis of Platform Chemicals in Bioelectrochemical Systems (BESs) Inoculated with Clostridium saccharoperbutylacetonicum N1-H4", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>The need for greener processes to satisfy the demand of platform chemicals together with the possibility of reusing CO2 from human activities has recently encouraged research on the set-up, optimization, and development of bioelectrochemical systems (BESs) for the electrosynthesis of organic compounds from inorganic carbon (CO2, HCO3\u2212). In the present study, we tested the ability of Clostridium saccharoperbutylacetonicum N1-4 (DSMZ 14923) to produce acetate and D-3-hydroxybutyrate from inorganic carbon present in a CO2:N2 gas mix. At the same time, we tested the ability of a Shewanella oneidensis MR1 and Pseudomonas aeruginosa PA1430/CO1 consortium to provide reducing power to sustain carbon assimilation at the cathode. We tested the performance of three different systems with the same layouts, inocula, and media, but with the application of 1.5 V external voltage, of a 1000 \u2126 external load, and without any connection between the electrodes or external devices (open circuit voltage, OCV). We compared both CO2 assimilation rate and production of metabolites (formate, acetate 3-D-hydroxybutyrate) in our BESs with the values obtained in non-electrogenic control cultures and estimated the energy used by our BESs to assimilate 1 mol of CO2. Our results showed that C. saccharoperbutylacetonicum NT-1 achieved the maximum CO2 assimilation (95.5%) when the microbial fuel cells (MFCs) were connected to the 1000 \u2126 external resistor, with the Shewanella/Pseudomonas consortium as the only source of electrons. Furthermore, we detected a shift in the metabolism of C. saccharoperbutylacetonicum NT-1 because of its prolonged activity in BESs. Our results open new perspectives for the utilization of BESs in carbon capture and electrosynthesis of platform chemicals.</p></article>", "keywords": ["570", "CO<sub>2</sub> capture", "PCA", "[SDV.BIO]Life Sciences [q-bio]/Biotechnology", "QH301-705.5", "Pseudomonas aeruginosa PA1430/CO1", "3-D-hydroxybutyrate; CO2 capture; Clostridium saccharoperbutylacetonicum NT-1; PCA; Pseudomonas aeruginosa PA1430/CO1; Shewanella oneidensis MR1; electrosynthesis", "<i>Shewanella oneidensis</i> MR1", "Article", "[SDV.BIO] Life Sciences [q-bio]/Biotechnology", "electrosynthesis", "CO<sub>2</sub> capture; <i>Clostridium saccharoperbutylacetonicum</i> NT-1; electrosynthesis; 3-D-hydroxybutyrate; PCA; <i>Shewanella oneidensis</i> MR1; <i>Pseudomonas aeruginosa</i> PA1430/CO1", "[CHIM.OTHE] Chemical Sciences/Other", "13. Climate action", "Clostridium saccharoperbutylacetonicum NT-1", "Shewanella oneidensis MR1", "3-D-hydroxybutyrate; CO2 capture; clostridium saccharoperbutylacetonicum NT-1; PCA; pseudomonas aeruginosa PA1430/CO1; shewanella oneidensis MR1; electrosynthesis", "CO$_2$ capture", "3-Dhydroxybutyrate", "3-D-hydroxybutyrate", "Biology (General)", "[CHIM.OTHE]Chemical Sciences/Other", "<i>Clostridium saccharoperbutylacetonicum</i> NT-1"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/11/3/735/pdf"}, {"href": "https://iris.uniroma1.it/bitstream/11573/1717333/3/Nastro_Inorganic-Carbon_2023.pdf"}, {"href": "https://doi.org/11367/116840"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11367/116840", "name": "item", "description": "11367/116840", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11367/116840"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-03-13T00:00:00Z"}}, {"id": "11367/151839", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:25:12Z", "type": "Journal Article", "created": "2025-02-25", "title": "Bio-electrosynthesis of polyhydroxybutyrate and surfactants in microbial fuel cells: a preliminary study", "description": "<p>Microbial Electrochemical Technology (MET) offers a promising avenue for CO2 utilization by leveraging the ability of chemolithotrophic microorganisms to use inorganic carbon in biosynthetic processes. By harnessing the power of electroactive bacteria, METs can facilitate the conversion of inorganic carbon into organic compounds. Therefore, this work combines biosurfactant production at the anode and PHB production at the cathode of Microbial Fuel Cells (MFCs), while testing the efficiency of Microbial Electrosynthesis Cells (MECs), and traditional culture in liquid media. This study employed a consortium of Pseudomonas aeruginosa PA1430/CO1 and Shewanella oneidensis MR-1, to provide reducing equivalents to Cupriavidus necator DSM428 for CO2 fixation and polyhydroxybutyrate (PHB) production. Glycerol was used as a carbon source by the anode consortium to investigate biosurfactant production. Additionally, Adaptive Laboratory Evolution (ALE) was employed to enhance the efficiency of this process to develop biofilms capable of synthesizing PHB from CO2 in MFCs under a controlled gas atmosphere (10% CO2, 10% O2, 2% H2, 78% N2). Observed results showed a higher direct CO2 removal from the gas mix in MECs (73%) than in MFCs (65%) compared to control cultures. Anionic (18.8 mg/L) and non-ionic (14.6 mg/L) surfactants were primarily present at the anodes of MFCs. Confocal microscope analysis revealed that the accumulation of PHBs in C. necator was significantly higher in MFCs (73% of cell volume) rather than in MECs (23%) and control cultures (40%). Further analyses on metabolites in the different systems are ongoing. Our data gave evidence that the anode consortium was able to provide enough electrons to sustain the chemolithotrophic growth of C. necator and the biosynthesis of PHBs at the cathode of MFCs, in a mechanism suggestive of the direct interspecies electron transfer (DIET), naturally occurring in natural environment.</p", "keywords": ["PHBs electrosynthesis", "Cupravidus necator DSM 428", "Pseudomonas aeruginosa PA1430/CO1", "CO2 capture", "Microbiology", "Shewanella oneidensis-MR1", "bioelectrochemical systems", "QR1-502", "CO2 capture; Cupravidus necator DSM 428; PHBs electrosynthesis; Pseudomonas aeruginosa PA1430/CO1; Shewanella oneidensis-MR1; bioelectrochemical systems; biosurfactants"]}, "links": [{"href": "https://iris.uniroma1.it/bitstream/11573/1735928/2/Nastro%2c%20Rosa%20Anna_Bio-electrosynthesis_2025.pdf"}, {"href": "https://doi.org/11367/151839"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11367/151839", "name": "item", "description": "11367/151839", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11367/151839"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-02-25T00:00:00Z"}}, {"id": "11573/1735928", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:25:15Z", "type": "Journal Article", "created": "2025-02-25", "title": "Bio-electrosynthesis of polyhydroxybutyrate and surfactants in microbial fuel cells: a preliminary study", "description": "<p>Microbial Electrochemical Technology (MET) offers a promising avenue for CO2 utilization by leveraging the ability of chemolithotrophic microorganisms to use inorganic carbon in biosynthetic processes. By harnessing the power of electroactive bacteria, METs can facilitate the conversion of inorganic carbon into organic compounds. Therefore, this work combines biosurfactant production at the anode and PHB production at the cathode of Microbial Fuel Cells (MFCs), while testing the efficiency of Microbial Electrosynthesis Cells (MECs), and traditional culture in liquid media. This study employed a consortium of Pseudomonas aeruginosa PA1430/CO1 and Shewanella oneidensis MR-1, to provide reducing equivalents to Cupriavidus necator DSM428 for CO2 fixation and polyhydroxybutyrate (PHB) production. Glycerol was used as a carbon source by the anode consortium to investigate biosurfactant production. Additionally, Adaptive Laboratory Evolution (ALE) was employed to enhance the efficiency of this process to develop biofilms capable of synthesizing PHB from CO2 in MFCs under a controlled gas atmosphere (10% CO2, 10% O2, 2% H2, 78% N2). Observed results showed a higher direct CO2 removal from the gas mix in MECs (73%) than in MFCs (65%) compared to control cultures. Anionic (18.8 mg/L) and non-ionic (14.6 mg/L) surfactants were primarily present at the anodes of MFCs. Confocal microscope analysis revealed that the accumulation of PHBs in C. necator was significantly higher in MFCs (73% of cell volume) rather than in MECs (23%) and control cultures (40%). Further analyses on metabolites in the different systems are ongoing. Our data gave evidence that the anode consortium was able to provide enough electrons to sustain the chemolithotrophic growth of C. necator and the biosynthesis of PHBs at the cathode of MFCs, in a mechanism suggestive of the direct interspecies electron transfer (DIET), naturally occurring in natural environment.</p", "keywords": ["PHBs electrosynthesis", "Cupravidus necator DSM 428", "Pseudomonas aeruginosa PA1430/CO1", "CO2 capture", "Microbiology", "Shewanella oneidensis-MR1", "bioelectrochemical systems", "QR1-502", "CO2 capture; Cupravidus necator DSM 428; PHBs electrosynthesis; Pseudomonas aeruginosa PA1430/CO1; Shewanella oneidensis-MR1; bioelectrochemical systems; biosurfactants"]}, "links": [{"href": "https://iris.uniroma1.it/bitstream/11573/1735928/2/Nastro%2c%20Rosa%20Anna_Bio-electrosynthesis_2025.pdf"}, {"href": "https://doi.org/11573/1735928"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11573/1735928", "name": "item", "description": "11573/1735928", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11573/1735928"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-02-25T00:00:00Z"}}, {"id": "1854/LU-01HGJDFDZ9Q1AC2RW5NYCK987M", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:25:29Z", "type": "Journal Article", "created": "2023-03-13", "title": "Finding optimal microorganisms to increase crop productivity and sustainability under drought \u2013 a structured reflection", "description": "ABSTRACTConsidering the more frequent and longer drought events due to climate change, improving plant drought tolerance became a priority. The search for plant growth promoting rhizobacteria (PGPR) able to improve plant drought tolerance has been long addressed, but with inconsistent results. Here, we summarize the PGPR mechanisms that improve plant drought tolerance, identify the pitfalls in current PGPR isolation and selection routines, and discuss the key points to define new strategies to get optimal PGPR for plant drought tolerance. Drought and host genotype impact rhizo-communities, and host-mediated selection strategies may be used to obtain a drought-adapted rhizomicrobiome that can be a source for PGPR isolation. Alternatively, an integrated omics-level analysis can improve our knowledge on the mechanisms of rhizomicrobiome construction, and a targeted approach can be designed, which will be focused on key PGP traits. New strategies to build PGPR consortia for improvement of plant drought tolerance are also suggested.", "keywords": ["2. Zero hunger", "Drought; PGPR isolation; PGPR screening; Plant- rhizomicrobiome interactions", "Drought", "MICROBIAL COMMUNITY", "BACILLUS-AMYLOLIQUEFACIENS", "PGPR screening", "Biology and Life Sciences", "Plant culture", "THERMOPHILIC BACTERIA", "15. Life on land", "Plant-rhizomicrobiome interactions", "6. Clean water", "SB1-1110", "PSEUDOMONAS-PUTIDA", "13. Climate action", "PLANT-GROWTH", "ARABIDOPSIS-THALIANA", "QK900-989", "WATER-STRESS", "Plant ecology", "ROOT COLONIZATION", "GROWTH-PROMOTING RHIZOBACTERIA", "GENE-EXPRESSION", "PGPR isolation"]}, "links": [{"href": "https://repositorio.ulisboa.pt/bitstream/10451/59998/1/Rosa%20et%20al%202023.pdf"}, {"href": "https://repositorio.ulisboa.pt/bitstream/10451/59563/1/Finding%20optimal%20microorganisms%20to%20increase%20crop%20productivity%20and%20sustainability%20under%20drought%20%20%20a%20structured%20reflection.pdf"}, {"href": "https://www.tandfonline.com/doi/pdf/10.1080/17429145.2023.2178680"}, {"href": "https://doi.org/1854/LU-01HGJDFDZ9Q1AC2RW5NYCK987M"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Plant%20Interactions", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "1854/LU-01HGJDFDZ9Q1AC2RW5NYCK987M", "name": "item", "description": "1854/LU-01HGJDFDZ9Q1AC2RW5NYCK987M", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/1854/LU-01HGJDFDZ9Q1AC2RW5NYCK987M"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-03-12T00:00:00Z"}}, {"id": "2950940967", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:26:15Z", "type": "Journal Article", "created": "2019-06-14", "title": "Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.</p></article>", "keywords": ["0301 basic medicine", "TPH", "consortium", "Article", "diesel", "03 medical and health sciences", "PAHs", "rhizoremediation", "Pseudomonas", "RNA", " Ribosomal", " 16S", "11. Sustainability", "Soil Pollutants", "Polycyclic Aromatic Hydrocarbons", "bacteria", "Phylogeny", "Soil Microbiology", "Chryseobacterium", "2. Zero hunger", "metagenomics", "rhizoremediation; diesel; bacteria; consortium; metagenomics; PAHs; TPH", "0303 health sciences", "Microbiota", "Biodiversity", "15. Life on land", "Biolog\u00eda y Biomedicina / Biolog\u00eda", "Rhizoremediation", "Biodegradation", " Environmental", "Petroleum", "13. Climate action", "Metagenome"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://doi.org/2950940967"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2950940967", "name": "item", "description": "2950940967", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2950940967"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-14T00:00:00Z"}}, {"id": "PMC9535858", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:28:48Z", "type": "Journal Article", "created": "2022-09-14", "title": "Chemotactic Bacteria Facilitate the Dispersion of Nonmotile Bacteria through Micrometer-Sized Pores in Engineered Porous Media", "description": "Recent research has demonstrated that chemotactic bacteria can disperse inside microsized pores while traveling toward favorable conditions. Microbe-microbe cotransport might enable nonmotile bacteria to be carried with motile partners to enhance their dispersion and reduce their deposition in porous systems. The aim of this study was to demonstrate the enhancement in the dispersion of nonmotile bacteria (Mycobacterium gilvum VM552, a polycyclic aromatic hydrocarbon-degrader, and Sphingobium sp. D4, a hexachlorocyclohexane-degrader, through micrometer-sized pores near the exclusion-cell-size limit, in the presence of motile Pseudomonas putida G7 cells. For this purpose, we used bioreactors equipped with two chambers that were separated with membrane filters with 3, 5, and 12 \u03bcm pore sizes and capillary polydimethylsiloxane (PDMS) microarrays (20 \u03bcm \u00d7 35 \u03bcm \u00d7 2.2 mm). The cotransport of nonmotile bacteria occurred exclusively in the presence of a chemoattractant concentration gradient, and therefore, a directed flow of motile cells. This cotransport was more intense in the presence of larger pores (12 \u03bcm) and strong chemoeffectors (\u03b3-aminobutyric acid). The mechanism that governed cotransport at the cell scale involved mechanical pushing and hydrodynamic interactions. Chemotaxis-mediated cotransport of bacterial degraders and its implications in pore accessibility opens new avenues for the enhancement of bacterial dispersion in porous media and the biodegradation of heterogeneously contaminated scenarios.", "keywords": ["Chemotactic Factors", "Pseudomonas putida", "Chemotaxis", "Bioaccessibility", "01 natural sciences", "Microbe-microbe cotransport", "Dimethylpolysiloxanes", "Polycyclic Aromatic Hydrocarbons", "Micrometer-sized pores", "Porosity", "Hexachlorocyclohexane", "gamma-Aminobutyric Acid", "Hitchhiking", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://pubs.acs.org/doi/pdf/10.1021/acs.est.2c03149"}, {"href": "https://doi.org/PMC9535858"}, {"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": "PMC9535858", "name": "item", "description": "PMC9535858", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC9535858"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-09-14T00:00:00Z"}}, {"id": "a798d288-eadf-41b5-a9e7-2f31ced8020d", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[52.26, 52.26], [52.26, 52.26], [52.26, 52.26], [52.26, 52.26], [52.26, 52.26]]]}, "properties": {"rights": "Restrictions applied to assure the protection of privacy or intellectual property, and any special restrictions or limitations or warnings on using the resource or metadata. Reports, articles, papers, scientific and non - scientific works of any form, including tables, maps, or any other kind of output, in printed or electronic form, based in whole or in part on the data supplied, must contain an acknowledgement of the form: \"Data reused from the BonaRes Data Centre www.bonares.de. This data were created as part of the BonaRes Module A-Project - BonaRes - DiControl's research activities.\" Although every care has been taken in preparing and testing the data, the BonaRes Module A-Project - BonaRes - DiControl and the BonaRes Data Centre cannot guarantee that the data are correct; neither does the BonaRes Module A-Project - BonaRes - DiControl and the BonaRes Data Centre accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The BonaRes Module A-Project - BonaRes - DiControl and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data.", "updated": "2024-01-31", "type": "Service", "created": "2023-10-18", "language": "eng", "title": "Web Map Service of the dataset 'Growth parameters, nutrient status and colonization density of beneficial microbes in winter rye grown organically and conventionally.'", "description": "This Web Map Service includes spatial information used by datasets 'Web Map Service of the dataset 'Growth parameters, nutrient status and colonization density of beneficial microbes in winter rye grown organically and conventionally.''", "formats": [{"name": "CSV"}], "keywords": ["infoMapAccessService", "Soil", "beneficial organisms", "organic agriculture", "conventional farming", "consortia", "Pseudomonas", "Bacillus", "Trichoderma harzianum", "rye", "Soil", "beneficial organisms", "organic agriculture", "conventional farming", "consortia", "Pseudomonas", "Bacillus", "Trichoderma harzianum", "rye"], "contacts": [{"name": "Jan Helge Behr", "organization": "Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V., Gro\u00dfbeeren, Germany", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "behr@igzev.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0002-8402-9251", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Rita Grosch", "organization": "Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V., Gro\u00dfbeeren, Germany", "position": null, "roles": ["projectLeader"], "phones": [{"value": null}], "emails": [{"value": "grosch@igzev.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0002-7179-5715", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "zalf", "organization": "Leibniz Centre for Agricultural Landscape Research (ZALF)", "position": "Research Platform 'Data Analysis & Simulation' - Workgroup Research Data Management", "roles": ["publisher"], "phones": [{"value": "+49 33432 82 300"}], "emails": [{"value": "dataservice@zalf.de"}], "addresses": [{"deliveryPoint": ["Eberswalder Strasse 84"], "city": "M\u00fcncheberg", "administrativeArea": "Brandenburg", "postalCode": "15374", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Michael Baumecker", "organization": "Berlin Humboldt University, Germany", "position": null, "roles": ["projectMember"], "phones": [{"value": null}], "emails": [{"value": "michael.baumecker@agrar.hu-berlin.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": null}]}, {"organization": "Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V., Gro\u00dfbeeren, Germany", "roles": ["contributor"]}], "themes": [{"concepts": [{"id": "infoMapAccessService"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}, {"concepts": [{"id": "Soil"}, {"id": "beneficial organisms"}, {"id": "organic agriculture"}, {"id": "conventional farming"}, {"id": "consortia"}, {"id": "Pseudomonas"}, {"id": "Bacillus"}, {"id": "Trichoderma harzianum"}, {"id": "rye"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}, {"concepts": [{"id": "Soil"}, {"id": "beneficial organisms"}, {"id": "organic agriculture"}, {"id": "conventional farming"}, {"id": "consortia"}, {"id": "Pseudomonas"}, {"id": "Bacillus"}, {"id": "Trichoderma harzianum"}, {"id": "rye"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}]}, "links": [{"href": "https://maps.bonares.de/mapapps/resources/apps/bonares/index.html?lang=en&mid=31463cb6-8ba6-4e6d-be32-2de9059c85bc", "rel": "download"}, {"href": "https://maps.bonares.de/wss/service/ags-relay/ags/guest/arcgis/rest/services/Dicontrol/ID_4644_LTE_Thyrow_2020_Geodata/MapServer/WMSServer?request=GetCapabilities&service=WMS"}, {"rel": "self", "type": "application/geo+json", "title": "a798d288-eadf-41b5-a9e7-2f31ced8020d", "name": "item", "description": "a798d288-eadf-41b5-a9e7-2f31ced8020d", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/a798d288-eadf-41b5-a9e7-2f31ced8020d"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-31T00:00:00Z"}}, {"id": "31463cb6-8ba6-4e6d-be32-2de9059c85bc", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[52.26, 52.26], [52.26, 52.26], [52.26, 52.26], [52.26, 52.26], [52.26, 52.26]]]}, "properties": {"themes": [{"concepts": [{"id": "farming"}], "scheme": "https://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_TopicCategoryCode"}, {"concepts": [{"id": "Soil"}, {"id": "beneficial organisms"}, {"id": "organic agriculture"}, {"id": "conventional farming"}, {"id": "consortia"}, {"id": "Pseudomonas"}, {"id": "Bacillus"}, {"id": "Trichoderma harzianum"}, {"id": "rye"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}, {"concepts": [{"id": "opendata"}], "scheme": "Individual"}, {"concepts": [{"id": "Boden"}, {"id": "beneficial organism"}, {"id": "organic farming"}, {"id": "above-ground biomass"}, {"id": "Soil"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}], "rights": "Restrictions applied to assure the protection of privacy or intellectual property, and any special restrictions or limitations or warnings on using the resource or metadata. Reports, articles, papers, scientific and non - scientific works of any form, including tables, maps, or any other kind of output, in printed or electronic form, based in whole or in part on the data supplied, must contain an acknowledgement of the form: \"Data reused from the BonaRes Data Centre www.bonares.de. This data were created as part of the BonaRes Module A-Project - BonaRes - DiControl's research activities.\" Although every care has been taken in preparing and testing the data, the BonaRes Module A-Project - BonaRes - DiControl and the BonaRes Data Centre cannot guarantee that the data are correct; neither does the BonaRes Module A-Project - BonaRes - DiControl and the BonaRes Data Centre accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The BonaRes Module A-Project - BonaRes - DiControl and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data.", "updated": "2023-11-21", "type": "Dataset", "created": "2023-10-18", "language": "eng", "title": "Growth parameters, nutrient status and colonization density of beneficial microbes in winter rye grown organically and conventionally.", "description": "The study focuses on the impact of a beneficial microbial consortium on the plant performance of winter rye under different farming practices during the vegetation period, including the winter growing season. Winter rye plants grown in a long-time field trial (Thy_ABS; 52\u00b015\u2019 N, 13\u00b014\u2019 E, 44 m a.s.l.)  under conventional or organic farming practices were inoculated after plant emergence in autumn 2020 with a beneficial microbial consortium containing Pseudomonas sp. (RU47, drench inoculation with 2 L per m\u00b2 of 7.5 x 107 CFU mL-1), Bacillus atrophaeus (ABi03, drench inoculation with 2 L per m\u00b2 of 7.5 x 107 CFU mL-1) and Trichoderma harzianum (OMG16, soil inoculation with 100 mg inoculum per m\u00b2). The density of the microbial inoculants in the rhizosphere and root-associated soil as well as the plant performance and nutrient status was quantified in autumn and the following spring. Selective plating demonstrated that the beneficial microbes successfully colonized the rhizosphere and root-associated soil of winter rye throughout its early growth cycle. The inoculation with a beneficial microbial consortium enhanced the biomass of winter rye, especially under organic farming practices at the second sampling in spring. The consortium significantly improved the nutrient status of the winter rye plants, providing an effective way to overcome nutrient limitations often found in organic farming.\n\nResearch domain: Plant Cultivation and Agricultural Technology\n\nResearch question: We hypothesized that (i) early inoculation of winter rye enables sufficient colonization of each BMc member at\nearly plant developmental stage, supporting its persistence in the rhizosphere throughout the vegetation period; (ii) the application of BMc shapes the composition of the rhizosphere bacterial community depending on the farming practice and thus differentially affects the plant performance.", "formats": [{"name": "CSV"}], "keywords": ["Soil", "beneficial organisms", "organic agriculture", "conventional farming", "consortia", "Pseudomonas", "Bacillus", "Trichoderma harzianum", "rye", "opendata", "Boden", "beneficial organism", "organic farming", "above-ground biomass", "Soil"], "contacts": [{"name": "Jan Helge Behr", "organization": "Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V., Gro\u00dfbeeren, Germany", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "behr@igzev.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0002-8402-9251", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Rita Grosch", "organization": "Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V., Gro\u00dfbeeren, Germany", "position": null, "roles": ["projectLeader"], "phones": [{"value": null}], "emails": [{"value": "grosch@igzev.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0002-7179-5715", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "zalf", "organization": "Leibniz Centre for Agricultural Landscape Research (ZALF)", "position": "Research Platform 'Data Analysis & Simulation' - Workgroup Research Data Management", "roles": ["publisher"], "phones": [{"value": "+49 33432 82 300"}], "emails": [{"value": "dataservice@zalf.de"}], "addresses": [{"deliveryPoint": ["Eberswalder Strasse 84"], "city": "M\u00fcncheberg", "administrativeArea": "Brandenburg", "postalCode": "15374", "country": "Germany"}], "links": [{"href": null}]}, {"name": "Michael Baumecker", "organization": "Berlin Humboldt University, Germany", "position": null, "roles": ["projectMember"], "phones": [{"value": null}], "emails": [{"value": "michael.baumecker@agrar.hu-berlin.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": null}]}, {"organization": "Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V., Gro\u00dfbeeren, Germany", "roles": ["contributor"]}]}, "links": [{"href": "https://maps.bonares.de/mapapps/resources/apps/bonares/index.html?lang=en&mid=31463cb6-8ba6-4e6d-be32-2de9059c85bc", "rel": "download"}, {"href": "https://metadata.bonares.de:443/smartEditor/preview/Field.jpg", "name": "preview", "description": "Web image thumbnail (URL)", "protocol": "WWW:LINK-1.0-http--image-thumbnail", "rel": "preview"}, {"rel": "self", "type": "application/geo+json", "title": "31463cb6-8ba6-4e6d-be32-2de9059c85bc", "name": "item", "description": "31463cb6-8ba6-4e6d-be32-2de9059c85bc", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/31463cb6-8ba6-4e6d-be32-2de9059c85bc"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-11-21T00:00:00Z"}}, {"id": "d841a5fd-a161-473a-a851-8d2b34702f8b", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[52.26, 52.26], [52.26, 52.26], [52.26, 52.26], [52.26, 52.26], [52.26, 52.26]]]}, "properties": {"themes": [{"concepts": [{"id": "farming"}], "scheme": "https://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_TopicCategoryCode"}, {"concepts": [{"id": "Soil"}, {"id": "beneficial organisms"}, {"id": "organic agriculture"}, {"id": "conventional farming"}, {"id": "consortia"}, {"id": "Pseudomonas"}, {"id": "Bacillus"}, {"id": "Trichoderma harzianum"}, {"id": "rye"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}, {"concepts": [{"id": "opendata"}], "scheme": "Individual"}, {"concepts": [{"id": "Boden"}, {"id": "beneficial organism"}, {"id": "organic farming"}, {"id": "above-ground biomass"}, {"id": "Soil"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}], "rights": "Restrictions applied to assure the protection of privacy or intellectual property, and any special restrictions or limitations or warnings on using the resource or metadata. Reports, articles, papers, scientific and non - scientific works of any form, including tables, maps, or any other kind of output, in printed or electronic form, based in whole or in part on the data supplied, must contain an acknowledgement of the form: \"Data reused from the BonaRes Data Centre www.bonares.de. This data were created as part of the BonaRes Module A-Project - BonaRes - DiControl's research activities.\" Although every care has been taken in preparing and testing the data, the BonaRes Module A-Project - BonaRes - DiControl and the BonaRes Data Centre cannot guarantee that the data are correct; neither does the BonaRes Module A-Project - BonaRes - DiControl and the BonaRes Data Centre accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The BonaRes Module A-Project - BonaRes - DiControl and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data.", "updated": "2023-11-21", "type": "Dataset", "created": "2023-10-18", "language": "eng", "title": "Growth parameters, nutrient status and colonization density of beneficial microbes in winter rye grown organically and conventionally - Plant traits", "description": "The study focuses on the impact of a beneficial microbial consortium on the plant performance of winter rye under different farming practices during the vegetation period, including the winter growing season. Winter rye plants grown in a long-time field trial (Thy_ABS; 52\u00b015\u2019 N, 13\u00b014\u2019 E, 44 m a.s.l.)  under conventional or organic farming practices were inoculated after plant emergence in autumn 2020 with a beneficial microbial consortium containing Pseudomonas sp. (RU47, drench inoculation with 2 L per m\u00b2 of 7.5 x 107 CFU mL-1), Bacillus atrophaeus (ABi03, drench inoculation with 2 L per m\u00b2 of 7.5 x 107 CFU mL-1) and Trichoderma harzianum (OMG16, soil inoculation with 100 mg inoculum per m\u00b2). The density of the microbial inoculants in the rhizosphere and root-associated soil as well as the plant performance and nutrient status was quantified in autumn and the following spring. Selective plating demonstrated that the beneficial microbes successfully colonized the rhizosphere and root-associated soil of winter rye throughout its early growth cycle. The inoculation with a beneficial microbial consortium enhanced the biomass of winter rye, especially under organic farming practices at the second sampling in spring. The consortium significantly improved the nutrient status of the winter rye plants, providing an effective way to overcome nutrient limitations often found in organic farming.\n\nResearch domain: Plant Cultivation and Agricultural Technology\n\nResearch question: We hypothesized that (i) early inoculation of winter rye enables sufficient colonization of each BMc member at\nearly plant developmental stage, supporting its persistence in the rhizosphere throughout the vegetation period; (ii) the application of BMc shapes the composition of the rhizosphere bacterial community depending on the farming practice and thus differentially affects the plant performance.", "formats": [{"name": "CSV"}], "keywords": ["Soil", "beneficial organisms", "organic agriculture", "conventional farming", "consortia", "Pseudomonas", "Bacillus", "Trichoderma harzianum", "rye", "opendata", "Boden", "beneficial organism", "organic farming", "above-ground biomass", "Soil"], "contacts": [{"name": "Jan Helge Behr", "organization": "Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V., Gro\u00dfbeeren, Germany", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "behr@igzev.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0002-8402-9251", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "Rita Grosch", "organization": "Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V., Gro\u00dfbeeren, Germany", "position": null, "roles": ["projectLeader"], "phones": [{"value": null}], "emails": [{"value": "grosch@igzev.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": {"url": null, "protocol": null, "protocol_url": "", "name": "0000-0002-7179-5715", "name_url": "", "description": "ORCID", "description_url": "", "applicationprofile": null, "applicationprofile_url": "", "function": null}}]}, {"name": "zalf", "organization": "Leibniz Centre for Agricultural Landscape Research (ZALF)", "position": "Research Platform 'Data Analysis & Simulation' - 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