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Microorganisms Nov 2021Integrative and conjugative elements (ICEs) are chromosomally integrated self-transmissible mobile genetic elements. Although some ICEs are known to carry genes for the...
A New ICE Subfamily Integrative and Conjugative Element Responsible for Horizontal Transfer of Biphenyl and Salicylic Acid Catabolic Pathway in the PCB-Degrading Strain KF716.
Integrative and conjugative elements (ICEs) are chromosomally integrated self-transmissible mobile genetic elements. Although some ICEs are known to carry genes for the degradation of aromatic compounds, information on their genetic features is limited. We identified a new member of the ICE family carrying biphenyl catabolic genes and salicylic acid catabolic genes from the PCB-degrading strain KF716. The 117-kb ICEKF716 contains common core regions exhibiting homology with those of degradative ICE from B13 and ICE from sp. CIB. A comparison of the gene loci collected from the public database revealed that several putative ICEs from B6-2 JAB1, AN10 and 2A20 had highly conserved core regions with those of ICEKF716, along with the variable region that encodes the catabolic genes for biphenyl, naphthalene, toluene, or phenol. These data indicate that this type of ICE subfamily is ubiquitously distributed within aromatic compound-degrading bacteria. ICEKF716 was transferred from KF716 to PAO1 via a circular extrachromosomal intermediate form. In this study, we describe the structure and genetic features of ICEKF716 compared to other catabolic ICEs.
PubMed: 34946064
DOI: 10.3390/microorganisms9122462 -
Journal of Bacteriology Oct 2019A1501 is a versatile nitrogen-fixing bacterium capable of living in diverse environments and coping with various oxidative stresses. NfiS, a regulatory noncoding RNA...
A1501 is a versatile nitrogen-fixing bacterium capable of living in diverse environments and coping with various oxidative stresses. NfiS, a regulatory noncoding RNA (ncRNA) involved in the control of nitrogen fixation in A1501, was previously shown to be required for optimal resistance to HO; however, the precise role of NfiS and the target genes involved in the oxidative stress response is entirely unknown. In this work, we systematically investigated the NfiS-based mechanisms underlying the response of this bacterium to HO at the cellular and molecular levels. A mutant strain carrying a deletion of showed significant downregulation of oxidative stress response genes, especially , a catalase gene, and , an essential regulator for transcription of catalase genes. Secondary structure prediction revealed two binding sites in NfiS for mRNA. Complementation experiments using truncated genes showed that each of two sites is functional, but not sufficient, for NfiS-mediated regulation of oxidative stress resistance and nitrogenase activities. Microscale thermophoresis assays further indicated direct base pairing between mRNA and NfiS at both sites 1 and 2, thus enhancing the half-life of the transcript. We also demonstrated that expression is dependent on OxyR and that both OxyR and KatB are essential for optimal oxidative stress resistance and nitrogenase activities. HO at low concentrations was detoxified by KatB, leaving O as a by-product to support nitrogen fixation under O-insufficient conditions. Moreover, our data suggest that the direct interaction between NfiS and mRNA is a conserved and widespread mechanism among strains. Protection against oxygen damage is crucial for survival of nitrogen-fixing bacteria due to the extreme oxygen sensitivity of nitrogenase. This work exemplifies how the small ncRNA NfiS coordinates oxidative stress response and nitrogen fixation via base pairing with mRNA and mRNA. Hence, NfiS acts as a molecular link to coordinate the expression of genes involved in oxidative stress response and nitrogen fixation. Our study provides the first insight into the biological functions of NfiS in oxidative stress regulation and adds a new regulation level to the mechanisms that contribute to the oxygen protection of the MoFe nitrogenase.
Topics: Bacterial Proteins; Base Pairing; Catalase; Gene Expression Regulation, Bacterial; Hydrogen Peroxide; Mutation; Nitrogen Fixation; Oxidative Stress; Pseudomonas stutzeri; RNA, Bacterial; RNA, Untranslated; Repressor Proteins
PubMed: 31262840
DOI: 10.1128/JB.00334-19 -
Frontiers in Microbiology 2022The impact of high concentrations of heavy metals and the loss of functional microorganisms usually affect the nitrogen removal process in wastewater treatment systems....
The impact of high concentrations of heavy metals and the loss of functional microorganisms usually affect the nitrogen removal process in wastewater treatment systems. In the study, a unique auto-aggregating aerobic denitrifier ( strain YC-34) was isolated with potential applications for Cr(VI) biosorption and reduction. The nitrogen removal efficiency and denitrification pathway of the strain were determined by measuring the concentration changes of inorganic nitrogen during the culture of the strain and amplifying key denitrification functional genes. The changes in auto-aggregation index, hydrophobicity index, and extracellular polymeric substances (EPS) characteristic index were used to evaluate the auto-aggregation capacity of the strain. Further studies on the biosorption ability and mechanism of cadmium in the process of denitrification were carried out. The changes in tolerance and adsorption index of cadmium were measured and the micro-characteristic changes on the cell surface were analyzed. The strain exhibited excellent denitrification ability, achieving 90.58% nitrogen removal efficiency with 54 mg/L nitrate-nitrogen as the initial nitrogen source and no accumulation of ammonia and nitrite-nitrogen. Thirty percentage of the initial nitrate-nitrogen was converted to N, and only a small amount of NO was produced. The successful amplification of the denitrification functional genes, , and , further suggested a complete denitrification pathway from nitrate to nitrogen. Furthermore, the strain showed efficient aggregation capacity, with the auto-aggregation and hydrophobicity indices reaching 78.4 and 75.5%, respectively. A large amount of protein-containing EPS was produced. In addition, the strain effectively removed 48.75, 46.67, 44.53, and 39.84% of Cr(VI) with the initial concentrations of 3, 5, 7, and 10 mg/L, respectively, from the nitrogen-containing synthetic wastewater. It also could reduce Cr(VI) to the less toxic Cr(III). FTIR measurements and characteristic peak deconvolution analysis demonstrated that the strain had a robust hydrogen-bonded structure with strong intermolecular forces under the stress of high Cr(VI) concentrations. The current results confirm that the novel denitrifier can simultaneously remove nitrogen and chromium and has potential applications in advanced wastewater treatment for the removal of multiple pollutants from sewage.
PubMed: 35992714
DOI: 10.3389/fmicb.2022.961815 -
Environmental Health and Preventive... Sep 2008The aim of this study is to examine arsenic accumulation by Pseudomonas stutzeri and its response to some thiol chelators, DMPS and MiADMSA.
OBJECTIVE
The aim of this study is to examine arsenic accumulation by Pseudomonas stutzeri and its response to some thiol chelators, DMPS and MiADMSA.
METHODS
Determination of arsenic accumulation by Pseudomonas sp. was carried out using an atomic absorption spectrophotometer, a TEM and an EDAX. Arsenate reductase enzyme assay was carried out from a cell-free extract of Pseudomonas sp. The effect of chelating agents on arsenite accumulation was analyzed. Total cellular proteins were analyzed using 1-D SDS-PAGE.
RESULTS
Pseudomonas sp. exhibited a maximum accumulation of 4 mg As g(-1) (dry weight). TEM and EDAX analysis showed the presence of As-containing electron-dense particles inside the cells. Data on arsenate reductase enzyme kinetics yielded a K (m) of 0.40 mM for arsenate and a V (max) of 5,952 mumol arsenate reduced per minute per milligram of protein. The chelating agents MiADMSA and DMPS were found to reduce the arsenic accumulation by 60 and 35%, respectively, whereas the presence of both chelating agents in medium containing cells pretreated with arsenite reduced it by up to 90%. The total protein profile of the cellular extract, obtained by 1-D SDS-PAGE, indicated five upregulated proteins, and three of these proteins exhibited differential expression when the cells were grown with MiADMSA and DMPS.
CONCLUSION
This study shows a new approach towards arsenic detoxification. A combination treatment with MiADMSA and DMPS may be useful for removing intracellular arsenic. The proteins that were found to be induced in this study may play an important role in the extrusion of arsenic from the cells, and this requires further characterization.
PubMed: 19568912
DOI: 10.1007/s12199-008-0038-9 -
Ecotoxicology and Environmental Safety Jan 2024Silver nanoparticles (AgNPs) are widely used in daily life and industry because of their excellent antibacterial properties. AgNPs can exist in wastewater in various...
Silver nanoparticles (AgNPs) are widely used in daily life and industry because of their excellent antibacterial properties. AgNPs can exist in wastewater in various forms, such as Ag, AgSO, AgCO, AgS, AgO, and AgCl. To assess the potential environmental risk of AgNPs and various forms of Ag, their toxic effects were investigated using the common denitrifier species Pseudomonas stutzeri (P. stutzeri). The inhibitory effect of AgNPs and various forms of Ag on P. stutzeri growth and its denitrification performance occurred in a concentration-dependent manner. The denitrification efficiency of P. stutzeri decreased from 95%∼97% to 89∼95%, 74∼95%, and 56∼85% under low, medium, and high exposure doses, respectively, of AgNPs and various forms of Ag. The changes in cell membrane morphology and increases in lactate dehydrogenase (LDH) release indicated that AgNPs and various forms of Ag damaged the cell membrane of P. stutzeri. Oxidative stress caused by excessive accumulation of reactive oxygen species (ROS) increased superoxide dismutase (SOD) and catalase (CAT) activities and decreased glutathione (GSH) levels. Overall, this study will help elucidate the impact of AgNPs and their transformation products on nitrogen removal efficiency in wastewater biological treatment systems.
Topics: Silver; Pseudomonas stutzeri; Metal Nanoparticles; Denitrification; Wastewater; Nitrogen; Antioxidants
PubMed: 38056119
DOI: 10.1016/j.ecoenv.2023.115785 -
3 Biotech Feb 2023Toxic polycyclic aromatic hydrocarbons (PAHs) are often released into the environment during the combustion and processing of fossil fuels and are capable of causing...
UNLABELLED
Toxic polycyclic aromatic hydrocarbons (PAHs) are often released into the environment during the combustion and processing of fossil fuels and are capable of causing significant pollution to people and the environment. One of the representative substances of PAHs is phenanthrene, which is often studied as a model compound for PAHs treatment. In this study, we compared the results of transcriptome analysis of in two different culture conditions under phenanthrene-induced culture (test group) and glucose-induced culture (control group), and analysed the key enzymatic mechanisms of in the biodegradation of phenanthrene. In our experiments, the transcriptome results showed that a total of 380 genes were more than twofold differentially expressed in the test group, of which 187 genes were significantly up-regulated in expression under Phenanthrene induction. Among the 380 differentially expressed genes, 90 genes were involved in Phenanthrene biodegradation, mainly including genes involved in biometabolism, cellular chemotaxis, substrate transport, signal induction and other related processes. Based on the transcriptome sequence analysis of at the time of phenanthrene induction, a total of 25 dioxygenase genes were identified, and the related genes were mainly concentrated in two relatively concentrated clusters of PAHs biodegradation genes. The transcriptome analysis resulted in a complete set of enzyme genes related to the phenanthrene biodegradation pathway. The analysis of key enzymes led to the inference of a possible phenanthrene biodegradation pathway: the salicylic acid degradation pathway. The results of this study provide a theoretical basis for in situ remediation of PAHs-contaminated environments using .
SUPPLEMENTARY INFORMATION
The online version contains supplementary material available at 10.1007/s13205-023-03473-7.
PubMed: 36718409
DOI: 10.1007/s13205-023-03473-7 -
Scientific Reports Feb 2021The bacterium Pseudomonas stutzeri SPM-1, obtained from textile wastewater dumping sites of Surat, Gujarat was studied for the degradation of the textile azo dye Procion...
The bacterium Pseudomonas stutzeri SPM-1, obtained from textile wastewater dumping sites of Surat, Gujarat was studied for the degradation of the textile azo dye Procion Red-H3B. The optimization was carried on the phenanthrene enrichment medium followed by exposing it to variable environmental factors and nutritional sources. The complete decolorization of dye (50 mg/L) happened within 20 h of incubation at pH 8 and temperature 32 ± 0.2 °C under microaerophilic conditions. Decolourization was monitored with the shifting of absorbance peak in UV-Vis spectrophotometry and HPLC analysis. The physicochemical studies of effluent before and after the treatment revealed 85%, 90%, and 65% decline in BOD, COD, and TOC levels. The strain showed significant activities of azoreductase (95%), laccase (76%), and NADH-DCIP reductase (88%) at 12 h, 10 h, and 8 h of growth respectively indicating evidence for reductive cleavage of the dye. The changes in the functional groups were confirmed by the presence of new peaks in FT-IR data. GC-MS analysis helped in recognizing the degraded dye compounds thus elucidating the proposed pathway for degradation of Procion Red-H3B. The potential of the bioremediation process was concluded by a phytotoxicity test using two plants, Vigna radiata and Cicer arietinum. Our study demonstrates that the strain Pseudomonas stutzeri SPM-1 has rapid decolorization efficiency and holds a noteworthy perspective in industrial application for textile wastewater treatment.
Topics: Azo Compounds; Biodegradation, Environmental; Gas Chromatography-Mass Spectrometry; Humans; Pseudomonas stutzeri; Spectroscopy, Fourier Transform Infrared; Triazines; Wastewater; Water Pollutants, Chemical; Water Purification
PubMed: 33542307
DOI: 10.1038/s41598-021-82494-9 -
Biotechnology Reports (Amsterdam,... Mar 2020In this work, was used for the optimum biogenic synthesis of antibacterial silver nanoparticles (AgNPs) which were applied for colorimetric detection of platinum ions...
In this work, was used for the optimum biogenic synthesis of antibacterial silver nanoparticles (AgNPs) which were applied for colorimetric detection of platinum ions (Pt). The optimum synthesis conditions were 2 mM AgNO pH 9 and incubation at 60 °C for 24 h. The FTIR spectra indicated that biomolecules such as amino acids, proteins or enzymes from were involved in the synthesis of AgNPs in the size range of 10-50 nm. Among the various metal ions tested and screened initially, the colloidal AgNPs probe-based colorimetric assay selectively detected Pt with 50 ppm as the limit of detection (LOD). The assay demonstrated in the present study quantitatively recovered Pt in the range of 70-150 % with good accuracy and precision. Further, the test of antibacterial activity of AgNPs alone, and in combination with ampicillin showed excellent activity against four of the six tested bacteria.
PubMed: 31867229
DOI: 10.1016/j.btre.2019.e00404 -
Applied and Environmental Microbiology Feb 2021Diazotrophs can produce bioavailable nitrogen from inert N gas by bioelectrochemical nitrogen fixation (-BNF), which is emerging as an energy-saving and highly selective...
Diazotrophs can produce bioavailable nitrogen from inert N gas by bioelectrochemical nitrogen fixation (-BNF), which is emerging as an energy-saving and highly selective strategy for agriculture and industry. However, current -BNF technology is impeded by requirements for NH assimilation inhibitors to facilitate intracellular ammonia secretion and precious metal catalysts to generate H as the energy-carrying intermediate. Here, we initially demonstrate inhibitor- and catalystless extracellular NH production by the diazotroph Pseudomonas stutzeri A1501 using an electrode as the sole electron donor. Multiple lines of evidence revealed that P. stutzeri produced 2.32 ± 0.25 mg/liter extracellular NH at a poised potential of -0.3 V (versus standard hydrogen electrode [SHE]) without the addition of inhibitors or expensive catalysts. The electron uptake mechanism was attributed to the endogenous electron shuttle phenazine-1-carboxylic acid, which was excreted by P. stutzeri and mediated electron transfer from electrodes into cells to directly drive N fixation. The faradaic efficiency was 20% ± 3%, which was 2 to 4 times that of previous -BNF attempts using the H-mediated pathway. This study reports a diazotroph capable of producing secretable NH via extracellular electron uptake, which has important implications for optimizing the performance of -BNF systems and exploring the novel nitrogen-fixing mode of syntrophic microbial communities in the natural environment. Ammonia greatly affects global ecology, agriculture, and the food industry. Diazotrophs with an enhanced capacity of extracellular NH excretion have been proven to be more beneficial to the growth of microalgae and plants, whereas most previously reported diazotrophs produce intracellular organic nitrogen in the absence of chemical suppression and genetic manipulation. Here, we demonstrate that Pseudomonas stutzeri A1501 is capable of extracellular NH production without chemical suppression or genetic manipulation when the extracellular electrode is used as the sole electron donor. We also reveal the electron uptake pathway from the extracellular electron-donating partner to P. stutzeri A1501 via redox electron shuttle phenazines. Since both P. stutzeri A1501 and potential electron-donating partners (such as electroactive microbes and natural semiconductor minerals) are abundant in diverse soils and sediments, P. stutzeri A1501 has broader implications on the improvement of nitrogen fertilization in the natural environment.
Topics: Ammonia; Nitrogen Fixation; Pseudomonas stutzeri
PubMed: 33310714
DOI: 10.1128/AEM.01998-20 -
International Journal of Molecular... Feb 2023In marine environments, biofilm can cause negative impacts, including the biofouling process. In the search for new non-toxic formulations that inhibit biofilm,...
In marine environments, biofilm can cause negative impacts, including the biofouling process. In the search for new non-toxic formulations that inhibit biofilm, biosurfactants (BS) produced by the genus have demonstrated considerable potential. To elucidate the changes that BS from promote in growth inhibition and biofilm formation, this research performed a nuclear magnetic resonance (NMR) metabolomic profile analysis to compare the metabolic differences between planktonic cells and biofilms of , a pioneer fouling bacteria. The multivariate analysis showed a clear separation between groups with a higher concentration of metabolites in the biofilm than in planktonic cells of . When planktonic and biofilm stages were treated with BS, some differences were found among them. In planktonic cells, the addition of BS had a minor effect on growth inhibition, but at a metabolic level, NADP+, trehalose, acetone, glucose, and betaine were up-regulated in response to osmotic stress. When the biofilm was treated with the BS, a clear inhibition was observed and metabolites such as glucose, acetic acid, histidine, lactic acid, phenylalanine, uracil, and NADP+ were also up-regulated, while trehalose and histamine were down-regulated in response to the antibacterial effect of the BS.
Topics: Biofouling; Pseudomonas stutzeri; Plankton; NADP; Trehalose; Biofilms; Bacillus
PubMed: 36835662
DOI: 10.3390/ijms24044249