-
BMC Microbiology Jan 2021Pseudomonas putida KT2440 is a metabolically versatile, HV1-certified, genetically accessible, and thus interesting microbial chassis for biotechnological applications....
BACKGROUND
Pseudomonas putida KT2440 is a metabolically versatile, HV1-certified, genetically accessible, and thus interesting microbial chassis for biotechnological applications. However, its obligate aerobic nature hampers production of oxygen sensitive products and drives up costs in large scale fermentation. The inability to perform anaerobic fermentation has been attributed to insufficient ATP production and an inability to produce pyrimidines under these conditions. Addressing these bottlenecks enabled growth under micro-oxic conditions but does not lead to growth or survival under anoxic conditions.
RESULTS
Here, a data-driven approach was used to develop a rational design for a P. putida KT2440 derivative strain capable of anaerobic respiration. To come to the design, data derived from a genome comparison of 1628 Pseudomonas strains was combined with genome-scale metabolic modelling simulations and a transcriptome dataset of 47 samples representing 14 environmental conditions from the facultative anaerobe Pseudomonas aeruginosa.
CONCLUSIONS
The results indicate that the implementation of anaerobic respiration in P. putida KT2440 would require at least 49 additional genes of known function, at least 8 genes encoding proteins of unknown function, and 3 externally added vitamins.
Topics: Anaerobiosis; Bacterial Proteins; Computer Simulation; Databases, Genetic; Fermentation; Gene Expression Profiling; Metabolic Engineering; Microbial Viability; Pseudomonas putida; Pyrimidines
PubMed: 33407113
DOI: 10.1186/s12866-020-02058-1 -
Journal of Contaminant Hydrology May 2023The clopidogrel bisulfate was degraded under aerobic conditions by two bacterial strains isolated from industrial effluents in El-Harrach, Algeria. The sequencing of...
The clopidogrel bisulfate was degraded under aerobic conditions by two bacterial strains isolated from industrial effluents in El-Harrach, Algeria. The sequencing of their 16S rRNA revealed that these two strains are Pseudomonas aeruginosa and Pseudomonas putida. The experiments showed that this consortium could remove clopidogrel bisulfate at high concentrations (5-1500 mg·L) within 96 h incubation period. The HPLC analysis recorded 75.23% degradation of clopidogrel bisulfate at an initial concentration of 100 mg·L after five days of incubation at pH 7.0 and a temperature of 30 °C. Also, a maximum degradation of 99.08% was carried out at a more basic pH (8.5). While only 41% was degraded at a temperature of 20 °C. Moreover, the presence of supplemental sources of carbon and nitrogen in the mixed culture media effectively improved the biodegradation of clopidogrel bisulfate by the stains. Finally, the morphology of the strains and the properties of the cell's surface were studied using a scanning electron microscope (SEM). This study reports, for the first time, the viability of the aerobic biodegradation of clopidogrel bisulfate in water in a wide range of concentrations.
Topics: Clopidogrel; Pseudomonas aeruginosa; Pseudomonas putida; Wastewater; RNA, Ribosomal, 16S; Biodegradation, Environmental
PubMed: 37167785
DOI: 10.1016/j.jconhyd.2023.104198 -
Nature Communications Oct 2020Non-model bacteria like Pseudomonas putida, Lactococcus lactis and other species have unique and versatile metabolisms, offering unique opportunities for Synthetic... (Review)
Review
Non-model bacteria like Pseudomonas putida, Lactococcus lactis and other species have unique and versatile metabolisms, offering unique opportunities for Synthetic Biology (SynBio). However, key genome editing and recombineering tools require optimization and large-scale multiplexing to unlock the full SynBio potential of these bacteria. In addition, the limited availability of a set of characterized, species-specific biological parts hampers the construction of reliable genetic circuitry. Mining of currently available, diverse bacteriophages could complete the SynBio toolbox, as they constitute an unexplored treasure trove for fully adapted metabolic modulators and orthogonally-functioning parts, driven by the longstanding co-evolution between phage and host.
Topics: Bacteriophages; Gene Editing; Lactococcus lactis; Pseudomonas putida; Synthetic Biology
PubMed: 33082347
DOI: 10.1038/s41467-020-19124-x -
FEMS Microbiology Letters May 2020Pseudomonas putida and closely-related species such as Pseudomonas fluorescens and Pseudomonas brassicacearum have been reported as potential biocontrol agents and plant...
Pseudomonas putida and closely-related species such as Pseudomonas fluorescens and Pseudomonas brassicacearum have been reported as potential biocontrol agents and plant growth-promoters. Recently, we have described the biocontrol activity of P. putida B2017 against several phytopathogens of agricultural relevance. In this study, its ability to produce potential antibiotic / toxic metabolites was assessed by functional, chromatography-mass spectrometry and genomic analysis. Our results show that B2017 is not able to synthesize surfactants and common antibiotics produced by Pseudomonas spp., i.e. pyrrolnitrin, 2,4-diacetylphloroglucinol, pyoluteorin and pyocyanin, but it produces pyoverdine, a siderophore which is involved in its biocontrol activity. The non-production of other metabolites, such as cyanide, safracin, promysalin and lipopeptides between others, is also discussed. Our data suggest that the mode of action of B2017 is not mainly due to the production of antimicrobial / toxic metabolites. Moreover, these features make P. putida B2017 a promising biocontrol microorganism for plant protection without side effects on environment, non-target organisms and human health.
Topics: Anti-Bacterial Agents; Bacteria; Bacterial Proteins; Biological Control Agents; Fungi; Genome, Bacterial; Oligopeptides; Plant Diseases; Pseudomonas putida; Siderophores; Surface-Active Agents
PubMed: 32347922
DOI: 10.1093/femsle/fnaa075 -
Environmental Microbiology Feb 2023The Pseudomonas putida group in the Gammaproteobacteria has been intensively studied for bioremediation and plant growth promotion. Members of this group have recently...
The Pseudomonas putida group in the Gammaproteobacteria has been intensively studied for bioremediation and plant growth promotion. Members of this group have recently emerged as promising hosts to convert intermediates derived from plant biomass to biofuels and biochemicals. However, most strains of P. putida cannot metabolize pentose sugars derived from hemicellulose. Here, we describe three isolates that provide a broader view of the pentose sugar catabolism in the P. putida group. One of these isolates clusters with the well-characterized P. alloputida KT2440 (Strain BP6); the second isolate clustered with plant growth-promoting strain P. putida W619 (Strain M2), while the third isolate represents a new species in the group (Strain BP8). Each of these isolates possessed homologous genes for oxidative xylose catabolism (xylDXA) and a potential xylonate transporter. Strain M2 grew on arabinose and had genes for oxidative arabinose catabolism (araDXA). A CRISPR interference (CRISPRi) system was developed for strain M2 and identified conditionally essential genes for xylose growth. A glucose dehydrogenase was found to be responsible for initial oxidation of xylose and arabinose in strain M2. These isolates have illuminated inherent diversity in pentose catabolism in the P. putida group and may provide alternative hosts for biomass conversion.
Topics: Pentoses; Xylose; Arabinose; Pseudomonas putida; Oxidative Stress
PubMed: 36465038
DOI: 10.1111/1462-2920.16296 -
Medium-chain alkane biodegradation and its link to some unifying attributes of alkB genes diversity.The Science of the Total Environment Jun 2023Hydrocarbon footprints in the environment, via biosynthesis, natural seepage, anthropogenic activities and accidents, affect the ecosystem and induce a shift in the... (Review)
Review
Hydrocarbon footprints in the environment, via biosynthesis, natural seepage, anthropogenic activities and accidents, affect the ecosystem and induce a shift in the healthy biogeochemical equilibrium that drives needed ecological services. In addition, these imbalances cause human diseases and reduce animal and microorganism diversity. Microbial bioremediation, which capitalizes on functional genes, is a sustainable mitigation option for cleaning hydrocarbon-impacted environments. This review focuses on the bacterial alkB functional gene, which codes for a non-heme di‑iron monooxygenase (AlkB) with a di‑iron active site that catalyzes C-C medium-chain alkane metabolism. These enzymes are ubiquitous and share common attributes such as being controlled by global transcriptional regulators, being a component of most super hydrocarbon degraders, and their distributions linked to horizontal gene transfer (HGT) events. The phylogenetic approach used in the HGT detection suggests that AlkB tree topology clusters bacteria functionally and that a preferential gradient dictates gene distribution. The alkB gene also acts as a biomarker for bioremediation, although it is found in pristine environments and absent in some hydrocarbon degraders. For instance, a quantitative molecular method has failed to link alkB copy number to contamination concentration levels. This limitation may be due to AlkB homologues, which have other functions besides n-alkane assimilation. Thus, this review, which focuses on Pseudomonas putida GPo1 alkB, shows that AlkB proteins are diverse but have some unifying trends around hydrocarbon-degrading bacteria; it is erroneous to rely on alkB detection alone as a monitoring parameter for hydrocarbon degradation, alkB gene distribution are preferentially distributed among bacteria, and the plausible explanation for AlkB affiliation to broad-spectrum metabolism of hydrocarbons in super-degraders hitherto reported. Overall, this review provides a broad perspective of the ecology of alkB-carrying bacteria and their directed biodegradation pathways.
Topics: Animals; Humans; Alkanes; Biodegradation, Environmental; Ecosystem; Hydrocarbons; Iron; Phylogeny; Pseudomonas putida; Genes, Bacterial
PubMed: 36948313
DOI: 10.1016/j.scitotenv.2023.162951 -
Current Microbiology Feb 2021Brassica napus L. is a main oilseed crop cultivated around the world. Plant growth-promoting rhizobacteria (PGPR) are generally applied to a wide range of agricultural...
Brassica napus L. is a main oilseed crop cultivated around the world. Plant growth-promoting rhizobacteria (PGPR) are generally applied to a wide range of agricultural crops for the growth enhancement. In this study, an I-plate technique was used to investigate the plant growth-promoting activity of Pseudomonas putida (strain ATCC12633) on B. napus plants. The volatile organic compounds (VOCs) produced by P. putida were determined by gas chromatography-mass spectrometric (GC-MS) analysis. Furthermore, P. putida were evaluated for its efficacy to induce resistance-related enzymes like peroxidase (POD), phenylalanine ammonia-lyase (PAL), catalase (CAT), and other biochemical compounds such as proline (Pro) and hydrogen peroxide (HO) in B. napus plants. According to the results, P. putida significantly increased the growth of B. napus compared to control. The major VOCs released by P. putida were 2-Butynedioic acid, dimethyl ester, Dimethyl ester of 4,7-dimethylnaphthalene-1,2-dicarboxylic acid, N-[3-Methylaminopropyl]aziridine, Cyclododecane, and Hexadecanoic acid. B. napus seeds treatment with P. putida caused enhanced activities of POD, PAL, CAT, Pro, and HO compared to control. So, the results of the present study showed that inoculation of B. napus with P. putida could serve as a useful tool for promoting the plant growth and inducing systemic resistance.
Topics: Brassica napus; Hydrogen Peroxide; Pseudomonas putida; Seeds; Volatile Organic Compounds
PubMed: 33403487
DOI: 10.1007/s00284-020-02335-2 -
Genome Biology and Evolution Jun 2024Many nonsporulating bacterial species survive prolonged resource exhaustion, by entering a state termed long-term stationary phase. Here, we performed long-term...
Many nonsporulating bacterial species survive prolonged resource exhaustion, by entering a state termed long-term stationary phase. Here, we performed long-term stationary phase evolutionary experiments on the bacterium Pseudomonas putida, followed by whole-genome sequencing of evolved clones. We show that P. putida is able to persist and adapt genetically under long-term stationary phase. We observed an accumulation of mutations within the evolving P. putida populations. Within each population, independently evolving lineages are established early on and persist throughout the 4-month-long experiment. Mutations accumulate in a highly convergent manner, with similar loci being mutated across independently evolving populations. Across populations, mutators emerge, that due to mutations within mismatch repair genes developed a much higher rate of mutation than other clones with which they coexisted within their respective populations. While these general dynamics of the adaptive process are quite similar to those we previously observed in the model bacterium Escherichia coli, the specific loci that are involved in adaptation only partially overlap between P. putida and E. coli.
Topics: Pseudomonas putida; Adaptation, Physiological; Mutation; Genome, Bacterial; Evolution, Molecular
PubMed: 38849986
DOI: 10.1093/gbe/evae117 -
Bulletin of Entomological Research Oct 2020The cabbage aphid, Brevicoryne brassicae L. (Hem: Aphididae), is one of the most serious pests of canola worldwide. In this research, the effects of Pseudomonas putida,...
The cabbage aphid, Brevicoryne brassicae L. (Hem: Aphididae), is one of the most serious pests of canola worldwide. In this research, the effects of Pseudomonas putida, salicylic acid (SA), and integrated application of both inducers were studied on the resistance of canola to B. brassicae. In free-choice situation, the number of B. brassicae attracted on canola plants under treatments containing P. putida and SA was significantly lower compared to control plants. In the life table study, pre-adult survival, longevity, reproductive period, and fecundity of this aphid were lowest on plants treated with P. putida + SA. The net reproductive rate (R0), intrinsic rate of population increase (r), and finite rate of increase (λ) of B. brassicae decreased significantly in the following order: control (47.19 offspring, 0.293 and 1.340 day-1), P. putida (16.7 offspring, 0.238 and 1.269 day-1), SA (6.37 offspring, 0.163 and 1.178 day-1), and P. putida + SA (3.24 offspring, 0.112 and 1.119 day-1). Moreover, the beneficial effect of the integrated application of P. putida and SA on plant growth parameters was significantly evident in our study. The highest values of glucosinolates, total phenol, and flavonoids were recorded in P. putida + SA treatment. We concluded that canola plants treated with P. putida + SA are more resistant to the cabbage aphid. These findings demonstrated that SA integrated with P. putida on canola plants act effectively for reducing the population of B. brassicae and can be used in integrated management programs of this pest.
Topics: Animals; Antibiosis; Aphids; Brassica napus; Female; Fertility; Pseudomonas putida; Salicylic Acid
PubMed: 32252840
DOI: 10.1017/S0007485320000097 -
Medicine Nov 2019The aim of this study was to analyze the risk factors, clinical features, and antimicrobial resistance of Pseudomonas putida (P putida) isolated from Tongji Hospital in... (Observational Study)
Observational Study
The aim of this study was to analyze the risk factors, clinical features, and antimicrobial resistance of Pseudomonas putida (P putida) isolated from Tongji Hospital in Wuhan, China.The data of 44 patients with P putida infections were retrospectively reviewed in this study. All cases of P putida strains were detected by the clinical laboratory of Tongji Hospital in the period of January 2010 to December 2017. Antimicrobial susceptibility testing was conducted using Kirby-Bauer method.Forty-four effective strains of P putida were isolated, including 32 inpatients and 12 outpatients. The 32 inpatients cases were obtained from various departments, which were urosurgery wards (n = 5, 15.6%), pediatrics wards (n = 4, 12.5%), hepatic surgery wards (n = 4, 12.5%), among others. The isolates had been discovered from urine specimens (28.2%), blood specimens (21.9%), sputum specimens (12.5%), and so on. Twenty-five patients had histories of catheterization before the isolation of P putida. Twenty-four patients were in immunocompromised states, 5 patients had undergone surgery, catheterization and were taking immunosuppressive therapy simultaneously. Polymicrobial infections were found in some P putida cases, especially Stenotrophomonas maltophilia, Pseudomonas aeruginosa, and Escherichia coli. All the patients had treated by antimicrobial before culture. Multi-drug-resistant strains were detected in 75% of P putida isolates. The P putida strains were resistant to trimethoprim/sulfamethoxazole (97.7%), aztreonam (88.6%), minocyline (74.3%), ticarcillin/clavulanic acid (72.7%), and sensitive to amikacin (86.4%), imipenem (62.8%), gentamicin (56.8%).Catheterization or other invasive procedures, immunocompromised states, and underlying diseases increased the risks of P putida infections. Moreover, the P putida strains were highly resistant to trimethoprim/sulfamethoxazole, aztreonam, minocyline, ticarcillin/clavulanic acid.
Topics: Adult; Aged; Aged, 80 and over; Anti-Bacterial Agents; Child; Child, Preschool; China; Drug Resistance, Bacterial; Female; Humans; Male; Microbial Sensitivity Tests; Middle Aged; Pseudomonas Infections; Pseudomonas putida; Retrospective Studies; Risk Factors; Young Adult
PubMed: 31689866
DOI: 10.1097/MD.0000000000017812