-
Plants (Basel, Switzerland) Nov 2020The signaling pathways induced by in rice plants at the early plant-rhizobacteria interaction stages, with and without inoculation of pv. , were studied. In the...
The signaling pathways induced by in rice plants at the early plant-rhizobacteria interaction stages, with and without inoculation of pv. , were studied. In the absence of pathogen, reduced ethylene (ET) production, and promoted root and stem elongation. Interestingly, gene , which plays an important role in root formation, was found significantly up-regulated in the presence of the rhizobacterium. Although pv. inoculation enhanced ET production in rice plants, treatment repressed ET-, jasmonic acid (JA)- and salicylic acid (SA)-mediated defense pathways, and induced the biosynthesis of abscisic acid (ABA), and the overexpression of and some pathogenesis-related proteins (PRs), which in turn increased the susceptibility of the rice plants against the pathogen. Collectively, this is the first work on the defense signaling induced by plant growth-promoting rhizobacteria in plants at the early interaction stages, and suggests that rhizobacteria stimulate an alternative defense mechanism in plants based on ABA accumulation and signaling.
PubMed: 33255501
DOI: 10.3390/plants9121641 -
Frontiers in Bioengineering and... 2021Crude glycerol has emerged as a suitable feedstock for the biotechnological production of various industrial chemicals given its high surplus catalyzed by the biodiesel...
Crude glycerol has emerged as a suitable feedstock for the biotechnological production of various industrial chemicals given its high surplus catalyzed by the biodiesel industry. bacteria metabolize the polyol into several biopolymers, including alginate and medium-chain-length poly(3-hydroxyalkanoates) (PHAs). Although is a suited platform to derive these polyoxoesters from crude glycerol, the attained concentrations in batch and fed-batch cultures are still low. In this study, we employed KT2440 and the hyper-PHA producer Δ mutant in two different fed-batch modes to synthesize -PHAs from raw glycerol. Initially, the cells grew in a batch phase (μ 0.21 h) for 22 h followed by a carbon-limiting exponential feeding, where the specific growth rate was set at 0.1 (h), resulting in a cell dry weight (CDW) of nearly 50 (g L) at 40 h cultivation. During the PHA production stage, we supplied the substrate at a constant rate of 50 (g h), where the KT2440 and the Δ produced 9.7 and 12.7 gPHA L, respectively, after 60 h cultivation. We next evaluated the PHA production ability of the strains using a DO-stat approach under nitrogen depletion. Citric acid was the main by-product secreted by the cells, accumulating in the culture broth up to 48 (g L) under nitrogen limitation. The mutant Δ amassed 38.9% of the CDW as -PHA and exhibited a specific PHA volumetric productivity of 0.34 (g L h), 48% higher than the parental KT2440 under the same growth conditions. The biosynthesized PHAs had average molecular weights ranging from 460 to 505 KDa and a polydispersity index (PDI) of 2.4-2.6. Here, we demonstrated that the DO-stat feeding approach in high cell density cultures enables the high yield production of -PHA in strains using the industrial crude glycerol, where the fed-batch process selection is essential to exploit the superior biopolymer production hallmarks of engineered bacterial strains.
PubMed: 33796510
DOI: 10.3389/fbioe.2021.642023 -
BMC Veterinary Research Apr 2024The present study aimed to determine the major cause of the high mortality affecting farmed gilthead seabream (Sparus aurata) and controlling this disease condition....
The present study aimed to determine the major cause of the high mortality affecting farmed gilthead seabream (Sparus aurata) and controlling this disease condition. Fifteen diseased S. aurata were sampled from a private fish farm located at Eldeba Triangle, Damietta, fish showed external skin hemorrhages, and ulceration. Bacterial isolates retrieved from the diseased fish were identified biochemically as Pseudomonas putida and then confirmed by phylogenetic analysis of the 16 S rRNA gene sequence. P. putida was also isolated from three batches of tilapia-trash feed given to S. aurata. Biofilm and hemolytic assay indicated that all P. putida isolates produced biofilm, but 61.11% can haemolyse red blood cells. Based on the antibiotic susceptibility test results, P. putida was sensitive to florfenicol with minimum inhibitory concentrations ranging between 0.25 and 1.0 µg mL, but all isolates were resistant to ampicillin and sulfamethoxazole-trimethoprim. Pathogenicity test revealed that P. putida isolate (recovered from the tilapia-trash feed) was virulent for S. aurata with LD equal to 4.67 × 10 colony forming unit (CFU) fish. After intraperitoneal (IP) challenge, fish treated with 10 mg kg of florfenicol showed 16.7% mortality, while no mortality was recorded for the fish group that received 20 mg kg. The non-treated fish group showed 46.7% mortality after bacterial challenge. HPLC analysis of serum florfenicol levels reached 1.07 and 2.52 µg mL at the 5th -day post-drug administration in the fish groups received 10 and 20 mg kg, respectively. In conclusion, P. putida was responsible for the high mortality affecting cultured S. aurata, in-feed administration of florfenicol (20 mg kg) effectively protected the challenged fish.
Topics: Animals; Thiamphenicol; Fish Diseases; Pseudomonas putida; Anti-Bacterial Agents; Animal Feed; Sea Bream; Pseudomonas Infections; Microbial Sensitivity Tests; Tilapia; Phylogeny; RNA, Ribosomal, 16S; Biofilms
PubMed: 38664683
DOI: 10.1186/s12917-024-04004-z -
International Journal of Molecular... Aug 2023A novel group of conjugative plasmids of is characterized. The prototype plasmid pPPUT-Tik1-1 (153,663 bp), isolated from a permafrost strain of Tik1, carries a...
A novel group of conjugative plasmids of is characterized. The prototype plasmid pPPUT-Tik1-1 (153,663 bp), isolated from a permafrost strain of Tik1, carries a defective mercury transposon, Tn, and a streptomycin resistance transposon, Tn Ten plasmids and 34 contigs with backbone regions closely related to pPPUT-Tik1-1 have been found in GenBank. Two of these plasmids from clinical strains of and are almost identical to the ancient plasmid. A characteristic feature of this group of plasmids is the presence of two genes encoding the initiators of replication ( and ). None of these genes have high similarity with plasmid replication genes belonging to known incompatibility groups. It has been demonstrated that while pPPUT-Tik1-1-like plasmids have homologous backbone regions, they significantly differ by the molecular structure and the predicted functions of their accessory regions. Some of the pPPUT-Tik1-1-related plasmids carry determinants of antibiotic resistance and/or heavy metal salts. Some plasmids are characterized by the ability to degrade xenobiotics. Plasmids related to pPPUT-Tik1-1 are characterized by a narrow host range and are found in various species of the genus. Interestingly, we also found shorter plasmid variants containing the same replication module, but lacking conjugation genes and containing other structural changes that strongly distinguish them from plasmids related to pPPUT-Tik1-1, indicating that the structure of the replication module cannot be used as the sole criterion for classifying plasmids. Overall, the results suggest that the plasmids of the novel group can be spread using conjugation in environmental and clinical strains of and may play diverse adaptive functions due to the presence of various accessory regions.
Topics: Pseudomonas putida; Permafrost; Pseudomonas; Databases, Nucleic Acid; Host Specificity
PubMed: 37686323
DOI: 10.3390/ijms241713518 -
Nature Microbiology Oct 2022Many bacteria utilize contact-dependent killing machineries to eliminate rivals in their environmental niches. Here we show that the plant root colonizer Pseudomonas...
Many bacteria utilize contact-dependent killing machineries to eliminate rivals in their environmental niches. Here we show that the plant root colonizer Pseudomonas putida strain IsoF is able to kill a wide range of soil and plant-associated Gram-negative bacteria with the aid of a type IVB secretion system (T4BSS) that delivers a toxic effector into bacterial competitors in a contact-dependent manner. This extends the range of targets of T4BSSs-so far thought to transfer effectors only into eukaryotic cells-to prokaryotes. Bioinformatic and genetic analyses showed that this killing machine is entirely encoded by the kib gene cluster located within a rare genomic island, which was recently acquired by horizontal gene transfer. P. putida IsoF utilizes this secretion system not only as a defensive weapon to kill bacterial competitors but also as an offensive weapon to invade existing biofilms, allowing the strain to persist in its natural environment. Furthermore, we show that strain IsoF can protect tomato plants against the phytopathogen Ralstonia solanacearum in a T4BSS-dependent manner, suggesting that IsoF can be exploited for pest control and sustainable agriculture.
Topics: Biofilms; Solanum lycopersicum; Pseudomonas putida; Ralstonia solanacearum; Soil
PubMed: 36123439
DOI: 10.1038/s41564-022-01209-6 -
Frontiers in Bioengineering and... 2021Polyhydroxyalkanoates (PHAs) have attracted much attention as a good substitute for petroleum-based plastics, especially mcl-PHA due to their superior physical and...
Polyhydroxyalkanoates (PHAs) have attracted much attention as a good substitute for petroleum-based plastics, especially mcl-PHA due to their superior physical and mechanical properties with broader applications. Artificial microbial consortia can solve the problems of low metabolic capacity of single engineered strains and low conversion efficiency of natural consortia while expanding the scope of substrate utilization. Therefore, the use of artificial microbial consortia is considered a promising method for the production of mcl-PHA. In this work, we designed and constructed a microbial consortium composed of engineered MG1655 and KT2440 based on the "nutrition supply-detoxification" concept, which improved mcl-PHA production from glucose-xylose mixtures. An engineered that preferentially uses xylose was engineered with an enhanced ability to secrete acetic acid and free fatty acids (FFAs), producing 6.44 g/L acetic acid and 2.51 g/L FFAs with 20 g/L xylose as substrate. The mcl-PHA producing strain of in the microbial consortium has been engineered to enhance its ability to convert acetic acid and FFAs into mcl-PHA, producing 0.75 g/L mcl-PHA with mixed substrates consisting of glucose, acetic acid, and octanoate, while also reducing the growth inhibition of by acetic acid. The further developed artificial microbial consortium finally produced 1.32 g/L of mcl-PHA from 20 g/L of a glucose-xylose mixture (1:1) after substrate competition control and process optimization. The substrate utilization and product synthesis functions were successfully divided into the two strains in the constructed artificial microbial consortium, and a mutually beneficial symbiosis of "nutrition supply-detoxification" with a relatively high mcl-PHA titer was achieved, enabling the efficient accumulation of mcl-PHA. The consortium developed in this study is a potential platform for mcl-PHA production from lignocellulosic biomass.
PubMed: 35083203
DOI: 10.3389/fbioe.2021.794331 -
Frontiers in Microbiology 2020Plastics, in all forms, are a ubiquitous cornerstone of modern civilization. Although humanity undoubtedly benefits from the versatility and durability of plastics, they...
Plastics, in all forms, are a ubiquitous cornerstone of modern civilization. Although humanity undoubtedly benefits from the versatility and durability of plastics, they also cause a tremendous burden for the environment. Bio-upcycling is a promising approach to reduce this burden, especially for polymers that are currently not amenable to mechanical recycling. Wildtype KT2440 is able to grow on 1,4-butanediol as sole carbon source, but only very slowly. Adaptive laboratory evolution (ALE) led to the isolation of several strains with significantly enhanced growth rate and yield. Genome re-sequencing and proteomic analysis were applied to characterize the genomic and metabolic basis of efficient 1,4-butanediol metabolism. Initially, 1,4-butanediol is oxidized to 4-hydroxybutyrate, in which the highly expressed dehydrogenase enzymes encoded within the PP_2674-2680 gene cluster play an essential role. The resulting 4-hydroxybutyrate can be metabolized through three possible pathways: (i) oxidation to succinate, (ii) CoA activation and subsequent oxidation to succinyl-CoA, and (iii) beta oxidation to glycolyl-CoA and acetyl-CoA. The evolved strains were both mutated in a transcriptional regulator (PP_2046) of an operon encoding both beta-oxidation related genes and an alcohol dehydrogenase. When either the regulator or the alcohol dehydrogenase is deleted, no 1,4-butanediol uptake or growth could be detected. Using a reverse engineering approach, PP_2046 was replaced by a synthetic promotor (14g) to overexpress the downstream operon (PP_2047-2051), thereby enhancing growth on 1,4-butanediol. This work provides a deeper understanding of microbial 1,4-butanediol metabolism in , which is also expandable to other aliphatic alpha-omega diols. It enables the more efficient metabolism of these diols, thereby enabling biotechnological valorization of plastic monomers in a bio-upcycling approach.
PubMed: 32256468
DOI: 10.3389/fmicb.2020.00382 -
Journal of Hazardous Materials May 2022The β-lactam antibiotic meropenem (MEM) is widely used in infectious disease treatment and consequently can be released into the environment, causing environmental...
The β-lactam antibiotic meropenem (MEM) is widely used in infectious disease treatment and consequently can be released into the environment, causing environmental pollution. In this study, Pseudomonas putida strain R51 was isolated from the wastewater of a poultry farm and found to efficiently degrade MEM. The genome of strain R51 contains a variety of heavy metal and antibiotic resistance genes, including the metallo-β-lactamase gene (JQN61_03315) and cadmium resistance gene cadA (JQN61_19995). Under cadmium stress, the degradation rate of MEM increased significantly in strain R51. Transcriptional analysis revealed that the expression of JQN61_03315 and cadA significantly increased under cadmium stress and that the expression of many genes associated with heavy metal and antibiotic resistance also changed significantly. Molecular docking analysis suggested that metallo-β-lactamase JQN61_03315 binds to MEM. In addition, no plasmid was found in strain R51, and no mobile genetic elements were found nearby JQN61_03315. In conclusion. we proposed that JQN61_03315 was responsible for the degradation of MEM, that the expression of this gene was induced under cadmium stress, and that strain R51 can be used for bioremediation of MEM without the risk for the transmission of the MEM resistance gene. These findings will have importance for studying the microbial degradation of MEM in the presence of heavy metal pollutants.
Topics: Anti-Bacterial Agents; Cadmium; Meropenem; Microbial Sensitivity Tests; Molecular Docking Simulation; Pseudomonas putida; beta-Lactamases
PubMed: 35123130
DOI: 10.1016/j.jhazmat.2022.128354 -
Genes Sep 2023strain U can be grown using, as sole carbon sources, the biogenic amines putrescine or cadaverine, as well as their catabolic intermediates, ɣ-aminobutyrate or...
strain U can be grown using, as sole carbon sources, the biogenic amines putrescine or cadaverine, as well as their catabolic intermediates, ɣ-aminobutyrate or δ-aminovalerate, respectively. Several paralogs for the genes that encode some of the activities involved in the catabolism of these compounds, such as a putrescine-pyruvate aminotransferase ( and genes) and a ɣ-aminobutyrate aminotransferase ( and genes) have been identified in this bacterium. When the expression pattern of these genes is analyzed by qPCR, it is drastically conditioned by supplying the carbon sources. Thus, is upregulated by putrescine, whereas seems to be exclusively induced by cadaverine. However, increases its expression in response to different polyamines or aminated catabolic derivatives from them (i.e., ɣ-aminobutyrate or δ-aminovalerate), although does not change its expression level concerning no-amine unrelated carbon sources (citrate). These results reveal differences between the mechanisms proposed for polyamine catabolism in and concerning strain U, as well as allow a deeper understanding of the enzymatic systems used by this last strain during polyamine metabolism.
Topics: Cadaverine; Putrescine; Pseudomonas putida; Polyamines; Pseudomonas aeruginosa; Escherichia coli; Aminobutyrates; Carbon; Gene Expression
PubMed: 37895246
DOI: 10.3390/genes14101897 -
Engineering in Life Sciences Jul 2021KT2440 is emerging as a promising microbial host for biotechnological industry due to its broad range of substrate affinity and resilience to physicochemical stresses....
KT2440 is emerging as a promising microbial host for biotechnological industry due to its broad range of substrate affinity and resilience to physicochemical stresses. Its natural tolerance towards aromatics and solvents qualifies this versatile microbe as promising candidate to produce next generation biofuels such as isobutanol. In this study, we scaled-up the production of isobutanol with from shake flask to fed-batch cultivation in a 30 L bioreactor. The design of a two-stage bioprocess with separated growth and production resulted in 3.35 g L. Flux analysis revealed that the NADPH expensive formation of isobutanol exceeded the cellular catabolic supply of NADPH finally causing growth retardation. Concomitantly, the cell counteracted to the redox imbalance by increased formation of 2-ketogluconic thereby providing electrons for the respiratory ATP generation. Thus, partially uncoupled ATP formation from the availability of NADH. The quantitative analysis of intracellular pyridine nucleotides NAD(P) and NAD(P)H revealed elevated catabolic and anabolic reducing power during aerobic production of isobutanol. Additionally, the installation of micro-aerobic conditions during production doubled the integral glucose-to-isobutanol conversion yield to 60 mg g while preventing undesired carbon loss as 2-ketogluconic acid.
PubMed: 34257629
DOI: 10.1002/elsc.202000116