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Microbiological Research Aug 2023Polycyclic aromatic hydrocarbons (PAHs) are diverse pollutants of significant environmental concerns, requiring effective biodegradation. This study used different...
Polycyclic aromatic hydrocarbons (PAHs) are diverse pollutants of significant environmental concerns, requiring effective biodegradation. This study used different bioinformatics tools to conduct whole-genome sequencing of two novel bacterial strains, Klebsiella michiganensis EF4 and K. oxytoca ETN19, to improve our understanding of their many genomic functions and degradation pathways of phenanthrene and pyrene. After 28 days of cultivation, strain EF4 degraded approximately 80% and 60% of phenanthrene and pyrene, respectively. However, their combinations (EF4 +ETN19) showed tremendous phenanthrene degradation efficiency, supposed to be at the first-level kinetic model with a t value of approximately 6 days. In addition, the two bacterial genomes contained carbohydrate-active enzymes and secondary metabolites biosynthetic gene clusters associated with PAHs degradation. The two genomes contained the bZIP superfamily of transcription factors, primarily the cAMP-response element-binding protein (CREB), which could regulate the expression of several PAHs degradation genes and enzymes. Interestingly, the two genomes were found to uniquely degrade phenanthrene through a putative pathway that catabolizes 2-carboxybenzalpyruvate into the TCA cycle. An operon containing multicomponent proteins, including a novel gene (JYK05_14550) that could initiate the beginning step of phenanthrene and pyrene degradation, was found in the EF4 genome. However, the degradation pathway of ETN19 showed that the yhfP gene encoding putative quinone oxidoreductase was associated with phenanthrene and pyrene catabolic processes. Furthermore, the significant expression of catechol 1,2-dioxygenase and quinone oxidoreductase genes in EF4 +ETN19 and ETN19 following the quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis confirmed the ability of the bacteria combination to degrade pyrene and phenanthrene effectively. These findings present new insight into the possible co-metabolism of the two bacterial species in the rapid biodegradation of phenanthrene and pyrene in soil environments.
Topics: Klebsiella oxytoca; Phenanthrenes; Polycyclic Aromatic Hydrocarbons; Pyrenes; Bacteria; Biodegradation, Environmental; Oxidoreductases; Sequence Analysis; Quinones
PubMed: 37178499
DOI: 10.1016/j.micres.2023.127410 -
The Science of the Total Environment May 2022The levels of organic pollutants, in particular polycyclic aromatic hydrocarbons (PAHs), are increasing worldwide, yet we lack clarity on how these pollutants affect...
The levels of organic pollutants, in particular polycyclic aromatic hydrocarbons (PAHs), are increasing worldwide, yet we lack clarity on how these pollutants affect microbial communities of different trophic levels, including protists, fungi, and bacteria. Herein, we conducted soil microcosm incubation experiments to investigate the effects of pyrene, a typical PAH, on microbial communities along concentration gradients from 0 to 500 mg kg soil. Protistan communities were more sensitive to pollutants than fungal and bacterial communities, and protistan consumers and phototrophs were the dominant trophic functional groups. In addition, by assessing changes in the diversity and structure of the soil microbiome and ecological networks, we found that the microbial communities, including the protistan community and the two trophic communities composed of protists and their prey, were destabilized with increasing stress and pyrene concentrations. We identified links and complicated relationships between phototrophs, bacteria, and consumers in food webs, which explain the importance of protists in stabilizing the microbial community. Collectively, our work provides novel evidence that protists are considerably sensitive to pollution stress, and caution should be exercised in future evaluations of the protistan and multitrophic communities in polluted soil ecosystems.
Topics: Bacteria; Fungi; Microbiota; Polycyclic Aromatic Hydrocarbons; Pyrenes; Soil; Soil Microbiology; Soil Pollutants
PubMed: 35104532
DOI: 10.1016/j.scitotenv.2022.153539 -
Environmental Science and Pollution... Mar 2024The environment in India is contaminated with polycyclic aromatic hydrocarbons (PAHs) due to the occurrence of large anthropogenic activities, i.e., fuel combustion,...
The environment in India is contaminated with polycyclic aromatic hydrocarbons (PAHs) due to the occurrence of large anthropogenic activities, i.e., fuel combustion, mineral roasting, and biomass burning. Hence, 13 toxic PAHs were detected: phenanthrene, anthracene, fluoranthene, pyrene, and benz(a) anthracene, ben-zo; (b) fluoranthene, benzo(k) fluoranthene, benzo(a) pyrene, benzo(ghi)perylene, dibenz (ah) anthracene, indeno1,2,3-(cd) pyrene, coronene and coronene in the environment (i.e., ambient particulate matter, road dust, sludge, and sewage) of the most industrialized area. Pollutants such as heavy metals and polycyclic aromatic hydrocarbons co-contaminate the soil and pose a significant hazard to the ecosystem because these pollutants are harmful to both humans and the environment. Phytoremediation is an economical plant-based natural approach for soil clean-up that has no negative impact on ecosystems. The aim of this study was to investigate the effects of pyrene (500 mg kg), Zn (150 mg kg), Pb (150 mg kg), and Cd (150 mg kg) alone and in combination on the phytoextraction efficiency of Medicago sativa growing in contaminated soil. Plant biomass, biochemical activities, translocation factors, accumulation of heavy metals, and pyrene removal were determined. After 60 days of planting, compared with those of the control plants, the growth parameters, biomass, and chlorophyll content of the M. sativa plants were significantly lower, and the reactive oxygen species activity, such as proline and polyphenol content and metallothionein protein content, was markedly greater in the pyrene and heavy metal-polluted soils. Furthermore, the combined toxicity of pyrene and all three metals on M. sativa growth and biochemical parameters was significantly greater than that of pyrene, Zn, Pb, or Cd alone, indicating the synergistic effect of pyrene and heavy metals on cytotoxicity. Pyrene stress increased Cd accumulation in M. sativa. After pyrene exposure alone or in combination with Zn-pyrene, a greater pyrene removal rate (85.5-81.44%) was observed than that in Pb-pyrene, Cd-pyrene, and Zn-Pb-Cd-pyrene polluted soils (62.78-71.27%), indicating that zinc can enhance the removal of pyrene from contaminated soil. The resulting hypotheses demonstrated that Medicago sativa can be used as a promising phytoremediation agent for co-contaminated soil.
Topics: Humans; Medicago sativa; Biodegradation, Environmental; Ecosystem; Lead; Soil Pollutants; Metals, Heavy; Pyrenes; Zinc; Polycyclic Aromatic Hydrocarbons; Environmental Pollutants; Anthracenes; Soil; Fluorenes
PubMed: 38383928
DOI: 10.1007/s11356-024-32499-4 -
Environmental Science and Pollution... Sep 2021Hexavalent chromium (Cr(VI)) and pyrene are toxic pollutants that are difficult to remediate from soils and wastewater. Serratia sp. strains have been previously...
Hexavalent chromium (Cr(VI)) and pyrene are toxic pollutants that are difficult to remediate from soils and wastewater. Serratia sp. strains have been previously demonstrated to remove either Cr(VI) or pyrene and here a new isolate, called the Z6 strain, was demonstrated to remove both simultaneously. The removal occurs primarily by Cr(VI) reduction and pyrene biodegradation, and genome analysis suggests the removal mechanisms are the putative chromate reductase and two assumable pathways of pyrene degradation. The Z6 strain effectively removed most Cr(VI) (up to approximately 86%) and pyrene (up to approximately 57%) in seven different types of wastewater after 7 days of biotreatment. Additionally, the carrier loofa used for bacteria immobilization did not change the kinetics of Cr(VI) reduction or pyrene degradation. The carrier loofa was also effective for multiple uses, with removal capacity not being significantly affected over the first seven cycles with the same carrier loofa. These results provide data for developing practical biotreatment applications of Cr(VI) and pyrene contaminated sites.
Topics: Biodegradation, Environmental; Chromium; Pyrenes; Serratia; Water Pollution
PubMed: 33871775
DOI: 10.1007/s11356-021-13893-8 -
International Journal of... 2024Polycyclic aromatic hydrocarbons (PAHs) are a serious threat to the health of the environment. This study investigated the potential of for the uptake, accumulation,...
Polycyclic aromatic hydrocarbons (PAHs) are a serious threat to the health of the environment. This study investigated the potential of for the uptake, accumulation, and biodegradation of phenanthrene and pyrene. plants were treated with 10 and 30 mg L concentrations of phenanthrene and pyrene for the experimental duration of ten days. Phenanthrene and pyrene concentrations were measured using the high-performance liquid chromatography (HPLC) technique. Identification of the intermediate by-products resulting from the biological degradation of PAHs was performed by gas chromatography-mass spectrometry (GC/MS). The quantities of phenanthrene and pyrene in the ten-day treatments with 10 and 30 mg L were 0.007 and 0.011 mg g FW, and 0.048 and 0.079 mg g FW, respectively. The growth parameters in the plants such as fresh weight, dry weight and RFN as well as the content of photosynthetic pigment of the plant decreased significantly compared to the control sample ( < 0.05). Ten compounds were identified from the plant tissue during the decomposition of pyrene and phenanthrene, and none of the PAHs were identified in the aquatic environment. Therefore, the use of for phytoremediation of water resources contaminated with PAHs is an effective and promising method.
Topics: Biodegradation, Environmental; Soil Pollutants; Phenanthrenes; Pyrenes; Polycyclic Aromatic Hydrocarbons; Plants
PubMed: 37705149
DOI: 10.1080/15226514.2023.2257314 -
Macromolecular Rapid Communications Nov 2023The vibrationally resolved pyrene fluorescence probe method is once popular but now languished, because the vibrationally resolved patterns of pyrene with limited...
The vibrationally resolved pyrene fluorescence probe method is once popular but now languished, because the vibrationally resolved patterns of pyrene with limited sensitivity and concentration independence have not been updated for over 50 years. During investigation on the polymer interdiffusion of a latex film, it is found that a pyrene acylhydrazone whose vibrationally resolved fluorescence pattern contradictory to those reported in pyrene and most pyrene derivatives. The pyrene acylhydrazone has sensitive concentration- and polarity-dependent fluorescence spectra (the sensitivity on polarity is at most 26 times higher than the old vibrationally resolved patterns), and the sensitivity well remains when it is copolymerized in a polymer. The vibrationally resolved spectrum of this pyrene acylhydrazone is a powerful fluorescence probe, which would be as useful as the pyrene excimer probe nowadays popular.
Topics: Fluorescent Dyes; Polymers; Fluorescence; Spectrometry, Fluorescence; Pyrenes
PubMed: 37690003
DOI: 10.1002/marc.202300391 -
International Journal of Molecular... May 2021Newly designed and synthesized diarylethene (DAE) derivatives with aliphatic amine sidearms and one with two pyrenes, revealed excellent photo-switching property of...
Newly designed and synthesized diarylethene (DAE) derivatives with aliphatic amine sidearms and one with two pyrenes, revealed excellent photo-switching property of central DAE core in MeOH and water. The only exception was bis-pyrene analogue, its DAE core very readily photochemically closed, but reversible opening completely hampered by aromatic stacking interaction of pyrene(s) with cyclic DAE. In this process, pyrene fluorescence showed to be a reliable monitoring method, an open form characterized by strong emission at 480 nm (typical for pyrene-aggregate), while closed form emitted weakly at 400 nm (typical for pyrene-DAE quenching). Only open DAE-bis-pyrene form interacted measurably with ds-DNA/RNA by flexible insertion in polynucleotide grooves, while self-stacked closed form did not bind to DNA/RNA. For the same steric reasons, flexible open DAE-bis-pyrene form was bound to at least three different binding sites at bovine serum albumin (BSA), while rigid, self-stacked closed form interacted dominantly with only one BSA site. Preliminary screening of antiproliferative activity against human lung carcinoma cell line A549 revealed that all DAE-derivatives are non-toxic. However, bis-pyrene analogue efficiently entered cells and located in the cytoplasm, whereby irradiation by light (315-400 nm) resulted in a strong, photo-induced cytotoxic effect, typical for pyrene-related singlet oxygen species production.
Topics: A549 Cells; Animals; Cattle; Cell Survival; DNA; Electrons; Humans; Light; Molecular Conformation; Nucleic Acid Denaturation; Photochemical Processes; Pyrenes; RNA; Serum Albumin, Bovine; Spectrometry, Fluorescence; Spectrophotometry, Ultraviolet; Temperature
PubMed: 34066402
DOI: 10.3390/ijms22094916 -
Journal of Environmental Science and... 2023Polycyclic aromatic hydrocarbons (PAHs) are among the most widely spread pollutants in the environment including the agricultural soil. PAH degradation by indigenous...
Polycyclic aromatic hydrocarbons (PAHs) are among the most widely spread pollutants in the environment including the agricultural soil. PAH degradation by indigenous bacteria is an effective and economical means to remove these pollutants from the environment. Here, we report a bacterial consortium (Pdy-1) isolated from paddy rice soil in northern Japan able to degrade polycyclic aromatic hydrocarbons (PAHs) at high rates. Pdy-1 was incubated with a mixture of PAH compounds (fluorene, phenanthrene, and pyrene) in Bushnell Haas Medium at a final concentration of 100 mg/L each. PDY-1 degraded 100% of fluorene, 95% of phenanthrene, and 52% of pyrene in 5 days. Phenanthrene and pyrene were completely degraded at 10 d and 15 d, respectively. Cloning of the 16S rRNA gene revealed that the consortium was composed of 40% and 7% each of , , and , , , , , and were also detected. PCR-DGGE showed the dynamics of the consortium during the incubation period. Real-time PCR revealed that PAH degrading genes such as the gram-positive ring dihydroxylating genes (PAH-RDH) and pyrene dioxygenase () were most abundant at day 5 when the rapid biodegradation of the PAHs was observed. This study improves our understanding on dynamics and characteristics of an effective PAH-degrading bacterial consortium from paddy rice soil.
Topics: Polycyclic Aromatic Hydrocarbons; Oryza; Soil; Microbial Consortia; RNA, Ribosomal, 16S; Soil Pollutants; Phenanthrenes; Fluorenes; Pyrenes; Bacteria; Biodegradation, Environmental; Environmental Pollutants; Soil Microbiology
PubMed: 37122120
DOI: 10.1080/10934529.2023.2204803 -
Environmental Pollution (Barking, Essex... Jul 2022The widely detected pyrene (PYR) is prone to accumulate and pose risks to the soil ecosystem. In this study, an aerobic closed microcosm was constructed to assess the...
The widely detected pyrene (PYR) is prone to accumulate and pose risks to the soil ecosystem. In this study, an aerobic closed microcosm was constructed to assess the effects of PYR at the environmental concentration (12.09 mg kg) on the structure, interactions, and metabolism of carbon sources of soil microbial communities. The results found that half-life of PYR was 37 d and its aerobic biodegradation was mainly implemented by both Gram-negative and Gram-positive bacteria as revealed by the quantitative results. High-throughput sequencing based on 16 S rRNA and ITS genes showed that PYR exposure interfered more significantly with the diversity and abundance of the bacterial community than that of the fungal community. For bacteria, rare species were sensitive to PYR, while Gemmatimonadota, Gaiellales, and Planococcaceae involved in organic pollutants detoxification and degradation were tolerant of PYR stress. Co-occurrence network analysis demonstrated that PYR enhanced the intraspecific cooperation within the bacterial community and altered the patterns of trophic interaction in the fungal community. Furthermore, the keystone taxa and their topological roles were altered, potentially inducing functionality changes. Function annotation suggested PYR inhibited the nitrogen fixation and ammonia oxidation processes but stimulated methylotrophy and methanol oxidation, especially on day 7. For the metabolism, microbial communities accelerated the metabolism of nitrogenous carbon sources (e.g. amine) to meet the physiological needs under PYR stress. This study clarifies the impacts of PYR on the structure, metabolism, and potential N and C cycling functions of soil microbial communities, deepening the knowledge of the environmental risks of PYR.
Topics: Bacteria; Carbon; Microbiota; Pyrenes; Soil; Soil Microbiology
PubMed: 35429592
DOI: 10.1016/j.envpol.2022.119301 -
Langmuir : the ACS Journal of Surfaces... Nov 2021The cationic gemini surfactant PyO-3-12 was designed to include two dimethyl ammonium groups, one dodecyl tail, and 1-pyrenemethyl hexyl ether tail into the structure of...
The cationic gemini surfactant PyO-3-12 was designed to include two dimethyl ammonium groups, one dodecyl tail, and 1-pyrenemethyl hexyl ether tail into the structure of the surfactant. The pyrenyl label ensured that the fluorescence of pyrene could be employed to probe the behavior of PyO-3-12 at the molecular level. The introduction of the oxygen atom in the β-position to pyrene was found to be critical for restoring the sensitivity of the pyrenyl label to the polarity of its environment. The properties of PyO-3-12 were characterized in water by surface tension and a fluorescence methodology that involved the global model-free analysis (MFA) of the pyrene monomer and excimer fluorescence decays to provide quantitative information about the state (unassociated--aggregated) of PyO-3-12. The MFA was combined with a fluorescence quenching study with 2,6-dinitrotoluene to determine the size of the PyO-3-12 micelles. PyO-3-12 was found to behave like a typical gemini surfactant, exhibiting a critical micelle concentration (CMC) of 0.38 (±0.05) mM and an aggregation number () equal to 23 (±2). Besides allowing PyO-3-12 to probe the polarity of its environment, the oxygen atom in the β-position next to pyrene brought some pyrenyl labels closer to the interface between the micellar interior and the aqueous phase, in a process that increased the effective volume of the hydrophobic part of PyO-3-12. This led to an increase in the packing parameter of PyO-3-12 and, consequently, an increase in compared to the value of 14 (±0.2) obtained for Py-3-12, a gemini surfactant, whose chemical structure was similar to that of PyO-3-12 but without the oxygen in the β-position to pyrene. The methodology described in this study to prepare and characterize pyrene-labeled surfactants is general and can be applied to study any pyrene-labeled surfactant and its interactions with oppositely charged macromolecules.
Topics: Hydrophobic and Hydrophilic Interactions; Micelles; Pyrenes; Surface Tension; Surface-Active Agents
PubMed: 34791874
DOI: 10.1021/acs.langmuir.1c01759