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.
", "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": "2026-05-02T16:14:45Z", "type": "Journal Article", "created": "2020-08-13", "title": "Industrial biotechnology of Pseudomonas putida: advances and prospects", "description": "AbstractPseudomonas 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.
Key points\uffe2\uff80\uffa2 Pseudomonas putida advances to a global industrial cell factory.
\uffe2\uff80\uffa2 Novel tools enable system-wide understanding and streamlined genomic engineering.
\uffe2\uff80\uffa2 Applications of P. putida range from bioeconomy chemicals to biosynthetic drugs.
", "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.tim.2020.02.015", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-02T16:17:30Z", "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": "10.1016/j.envpol.2016.11.048", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-02T16:16:21Z", "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.2022.120472", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-02T16:16:22Z", "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": "2026-05-02T16:16:53Z", "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": "10.1021/acs.est.2c03149", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-02T16:17:37Z", "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": "2026-05-02T16:17:54Z", "type": "Journal Article", "created": "2017-01-03", "title": "The Pseudomonas putida T6SS is a plant warden against phytopathogens", "description": "AbstractBacterial 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.
", "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": "10.1111/1751-7915.13383", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-02T16:18:49Z", "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": "SummaryMost 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.
", "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": "10.1111/1751-7915.13396", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-02T16:18:49Z", "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": "SummaryPseudomonas 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.
", "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": "2026-05-02T16:18:49Z", "type": "Journal Article", "created": "2020-02-11", "title": "An expanded CRISPRi toolbox for tunable control of gene expression in Pseudomonas putida", "description": "SummaryOwing 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.
", "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": "10259/7490", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-02T16:24:43Z", "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": "2026-05-02T16:24:47Z", "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": "PMC9535858", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-02T16:28:29Z", "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"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Pseudomonas+putida&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Pseudomonas+putida&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Pseudomonas+putida&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Pseudomonas+putida&offset=14", "hreflang": "en-US"}], "numberMatched": 14, "numberReturned": 14, "distributedFeatures": [], "timeStamp": "2026-05-03T08:43:43.539255Z"}