The impact of phenanthrene on membrane phospholipids and its biodegradation by Sphingopyxis soli

Unveiling the synergistic mechanism of autochthonous fungal bioaugmentation and ammonium nitrogen biostimulation for enhanced phenanthrene degradation in oil-contaminated soils

Autochthonous bioaugmentation and nutrient biostimulation are promising bioremediation methods for polycyclic aromatic hydrocarbons (PAHs) in contaminated agricultural soils, but little is known about their combined working mechanism. In this study, a microcosm trial was conducted to explore the combined mechanism of autochthonous fungal bioaugmentation and ammonium nitrogen biostimulation, using DNA stable-isotope-probing (DNA-SIP) and microbial network analysis. Both treatments significantly improved phenanthrene (PHE) removal, with their combined application producing the best results. The microbial community composition was notably altered by all bioremediation treatments, particularly the PHE-degrading bacterial and fungal taxa. Fungal bioaugmentation removed PAHs through extracellular enzyme secretion but reduced soil microbial diversity and ecological stability, while nitrogen biostimulation promoted PAH dissipation by stimulating indigenous soil degrading microbes, including fungi and key bacteria in the soil co-occurrence networks, ensuring the ecological diversity of soil microorganisms. The combination of both approaches proved to be the most effective strategy, maintaining a high degradation efficiency and relatively stable soil biodiversity through the secretion of lignin hydrolytic enzymes by fungi, and stimulating the reproduction of soil native degrading microbes, especially the key degraders in the co-occurrence networks. Our findings provide a fresh perspective of the synergy between fungal bioaugmentation and nitrogen biostimulation, highlighting the potential of this combined bioremediation approach for in situ PAH-contaminated soils.

Biosurfactants-based mixed polycyclic aromatic hydrocarbon degradation: From microbial community structure toward non-targeted metabolomic profile determination

Biosurfactants-based bioremediation is considered an efficient technology to eliminate environmental pollutants including polycyclic aromatic hydrocarbons (PAHs). However, the precise role of rhamnolipids or lipopeptide-biosurfactants in mixed PAH dissipation, shaping microbial community structure, and influencing metabolomic profile remained unclear. In this study, results showed that the maximum PAH degradation was achieved in lipopeptide-assisted treatment (SPS), where the pyrene and phenanthrene were substantially degraded up to 74.28 % and 63.05 % respectively, as compared to rhamnolipids (SPR) and un-aided biosurfactants (SP). Furthermore, the high throughput sequencing analysis revealed a significant change in the PAH-degrading microbial community, with Proteobacteria being the predominant phylum (>98 %) followed by Bacteroidota and Firmicutes in all the treatments. Moreover, Pseudomonas and Pannonibacter were found as highly potent bacterial genera for mixed PAH degradation in SPR, SPS, and SP treatments, nevertheless, the abundance of the genus Pseudomonas was significantly enhanced (>97 %) in SPR treatment groups. On the other hand, the non-targeted metabolomic profile through UHPLC-MS/MS exhibited a remarkable change in the metabolites of amino acids, carbohydrates, and lipid metabolisms by the input of rhamnolipids or lipopeptide-biosurfactants whereas, the maximum intensities of metabolites (more than two-fold) were observed in SPR treatment. The findings of this study suggested that the aforementioned biosurfactants can play an indispensable role in mixed PAH degradation as well as seek to offer new insights into shifts in PAH-degrading microbial communities and their metabolic function, which can guide the development of more efficient and targeted strategies for complete removal of organic pollutants such as PAH from the contaminated environment.

Genome analysis for the identification of genes involved in phenanthrene biodegradation pathway in Stenotrophomonas indicatrix CPHE1. Phenanthrene mineralization in soils assisted by integrated approaches

Phenanthrene (PHE) is a highly toxic compound, widely present in soils. For this reason, it is essential to remove PHE from the environment. Stenotrophomonas indicatrix CPHE1 was isolated from an industrial soil contaminated by polycyclic aromatic hydrocarbons (PAHs) and was sequenced to identify the PHE degrading genes. Dioxygenase, monooxygenase, and dehydrogenase gene products annotated in S. indicatrix CPHE1 genome were clustered into different trees with reference proteins. Moreover, S. indicatrix CPHE1 whole-genome sequences were compared to genes of PAHs-degrading bacteria retrieved from databases and literature. On these basis, reverse transcriptase-polymerase chain reaction (RT-PCR) analysis pointed out that cysteine dioxygenase (cysDO), biphenyl-2,3-diol 1,2-dioxygenase (bphC), and aldolase hydratase (phdG) were expressed only in the presence of PHE. Therefore, different techniques have been designed to improve the PHE mineralization process in five PHE artificially contaminated soils (50 mg kg^-1), including biostimulation, adding a nutrient solution (NS), bioaugmentation, inoculating S. indicatrix CPHE1 which was selected for its PHE-degrading genes, and the use of 2-hydroxypropyl-β-cyclodextrin (HPBCD) as a bioavailability enhancer. High percentages of PHE mineralization were achieved for the studied soils. Depending on the soil, different treatments resulted to be successful; in the case of a clay loam soil, the best strategy was the inoculation of S. indicatrix CPHE1 and NS (59.9% mineralized after 120 days). In sandy soils (CR and R soils) the highest percentage of mineralization was achieved in presence of HPBCD and NS (87.3% and 61.3%, respectively). However, the combination of CPHE1 strain, HPBCD, and NS showed to be the most efficient strategy for sandy and sandy loam soils (LL and ALC soils showed 35% and 74.6%, respectively). The results indicated a high degree of correlation between gene expression and the rates of mineralization.

Accelerated PAH Transformation in the Presence of Dye Industry Landfill Leachate Combined with Fungal Membrane Lipid Changes

The ascomycete fungus Nectriella pironii, previously isolated from soil continuously contaminated by dye industry waste, was used for the biodegradation of phenanthrene (PHE), benz[a]anthracene (B[a]A), and benz[a]pyrene (B[a]P). The degradation of polycyclic aromatic hydrocarbons (PAHs) by N. pironii was accelerated in the presence of landfill leachate (LL) collected from the area of fungus isolation. The rate of cometabolic elimination of PHE and B[a]P in the presence of LL was, respectively, 75% and 94% higher than in its absence. LC-MS/MS analysis revealed that PAHs were converted to less-toxic derivatives. The parallel lipidomic study showed changes in membrane lipids, including a significant increase in the content of phosphatidylcholine (PC) (almost double) and saturated phospholipid fatty acids (PLFAs) and a simultaneous reduction (twofold) in the content of phosphatidylethanolamine (PE) and unsaturated PLFAs, which may have promoted the fungus to PHE + LL adaptation. In the presence of PHE, an intense lipid peroxidation (fivefold) was observed, confirming the stabilization of the cell membrane and its extended integrity. Determining the course of elimination and adaptation to harmful pollutants is essential for the design of efficient bioremediation systems in the future.

Opposite selection effects of nZVI and PAHs on bacterial community composition revealed by universal and sphingomonads-specific 16S rRNA primers

Next-generation sequencing method employing the sphingomonads-specific and universal 16s rRNA primers were applied to analyze the response of soil bacterial community to continuous stress of nanoscale zero-valent iron (nZVI) and/or polycyclic aromatic hydrocarbons (PAHs) under suspended conditions. The group specific primer greatly improves taxonomic resolution, the overall OTU numbers increased from 12 by universal primer to 42 by sphingomonads-specific primer. It was found that nZVI and PAHs had opposite selection effects on bacterial community composition, furthermore, the abundance of Sphingopyxis was positively related to nZVI while negatively related to PAHs, whereas abundances of Sphingobium and Sphingosinicella were positively related to PAHs (p < 0.01). The improved taxonomic resolution helps identify the potential keystone taxa, which provides valuable information for future bioremediation technology such as synthetic microbiome.

Molecular response of Anoxybacillus sp. PDR2 under azo dye stress: An integrated analysis of proteomics and metabolomics

Treating azo dye wastewater using thermophilic bacteria is considered a more efficient bioremediation strategy. In this study, a thermophilic bacterial strain, Anoxybacillus sp. PDR2, was regarded as the research target. This strain was characterized at different stages of azo dye degradation by using TMT quantitative proteomic and non-targeted metabolome technology. A total of 165 differentially expressed proteins (DEPs) and 439 differentially metabolites (DMs) were detected in comparisons between bacteria with and without azo dye. It was found that Anoxybacillus sp. PDR2 can degrade azo dye Direct Black G (DBG) through extracellular electron transfer with glucose serving as electron donors. Most proteins related to carbohydrate metabolism, including acetoacetate synthase, and malate synthase G, were overexpressed to provide energy. The bacterium can also self-synthesize riboflavin as a redox mediator of in vitro electron transport. These results lay a theoretical basis for industrial bioremediation of azo dye wastewater.

Phenanthrene biodegradation in a fed-batch reactor treating a spent sediment washing solution: Techno-economic implications for the recovery of ethanol as extracting agent

The continuous dredging of sediments contaminated by polycyclic aromatic hydrocarbons such as phenanthrene (PHE) has required the employment of high-efficiency technologies, including sediment washing (SW). However, the large amount of generated spent SW effluents requires the development of effective, eco-friendly and cost-saving approaches, which can tackle the waste formation in favor of the recovery of chemicals. This study proposes the treatment of a spent SW solution containing ethanol (EtOH) as extracting agent, by testing different initial PHE concentrations (i.e. 20-140 mg L^-1) within six consecutive cycles in a fed-batch bioreactor under aerobic conditions. The biological process achieved a PHE removal of 63-91% after the enrichment of PHE-degrading bacteria and the proper supplementation of nutrients, and was mainly affected by the initial PHE concentration value and the excessive decrease of pH and dissolved oxygen. Achromobacter, Sphingobacterium and Dysgonomonas genera were mainly involved in PHE degradation, which followed a first-order kinetic model (R² = 0.652-0.928) with a degradation rate and half-life time of 0.127-1.177 d^-1 and 0.589-2.912 d, respectively. A techno-economic assessment revealed that a virtuous operation of SW, EtOH recovery and biodegradation of the SW solution can allow the recovery of up to 1.35 tons of EtOH per ton of remediated sediment and the decrease of the overall costs by 50%.

Assembly of fungal mycelium-carbon nanotube composites and their application in pyrene removal

Polycyclic aromatic hydrocarbons (PAHs) have been known for decades to threaten human health. Various physical, chemical and biological methods have been developed to remove PAHs from different matrices. Microbial biodegradation processes are thought to be effective and environmentally friendly, but the low bioavailability of PAHs and their slow removal rate often limit the application of biodegradation. In this study, novel self-assembled PAH-degrading fungal mycelium (Penicillium oxalicum SYJ-1)-carbon nanotube (CNT) composites were applied for pyrene removal. The addition of CNTs did not affect the growth of strain SYJ-1 and promoted the total PAH removal efficiency. The composite could completely remove pyrene at 20 mg L^-1 within 48 h, while the sole fungus and CNTs alone could only remove 72% and 80% of pyrene at 72 h, respectively. A cytochrome P450 inhibition experiment, together with degradation product identification and transcriptomic analysis, suggested that an intracellular PAH transformation pathway was employed by strain SYJ-1. The versatility of this assembly approach was also confirmed by adding different nanomaterials and using them to remove different pollutants. This study provides a strategy of coupling the chemical adsorption and biodegradation capacity of inorganic nanomaterials and microorganisms as composites to treat hydrophobic substrates in restricted bioreactor.

Simultaneous action of microbial phospholipase C and lipase on model bacterial membranes - Modeling the processes crucial for bioaugmentation

Bioaugmentation is a promising method of the remediation of soils polluted by persistent organic pollutants (POP). Unfortunately, it happens frequently that the microorganisms inoculated into the soil die out due to the presence of enzymes secreted by autochthonous microorganisms. Especially destructive are here phospholipases C (PLC) and lipases which destruct the microorganism's cellular membrane. The composition of bacterial membranes differs between species, so it is highly possible that depending on the membrane constitution some bacteria are more resistant to PLCs and lipases than other. To shed light on these problems we applied phospholipid Langmuir monolayers as model microbial membranes and studied their interactions with α-toxin (model bacterial PLC) and the lipase isolated from soil fungus Candida rugosa. Membrane phospholipids differing in their headgroup (phosphatidylcholines, phosphatidylethanolamines, phosphatidylglycerols and cardiolipins) and in their tail structure were applied. The monolayers were characterized by the Langmuir technique, visualized by Brewster angle microscopy, and the packing mode of the phospholipid molecules was verified by the application of the diffraction of synchrotron radiation. We also studied the mutual miscibility of diacylglycerols and the native phospholipids as their interaction is crucial for the understanding of the PLC and lipase activity. It turned out that all the investigated phospholipid classes can be hydrolyzed by PLC; however, they differ profoundly in the hydrolysis degree. Depending on the effects of the initial PLC action and the mutual organization of the diacylglycerol and phospholipid molecules the lipase can ruin the model membranes or can be completely neutral to them.

The genus Sphingopyxis: Systematics, ecology, and bioremediation potential - A review

The genus Sphingopyxis was first reported in the year 2001. Phylogenetically, Sphingopyxis is well delineated from other genera Sphingobium, Sphingomonas and Novosphingobium of sphingomonads group, family Sphingomonadaceae of Proteobacteria. To date (at the time of writing), the genus Sphingopyxis comprises of twenty validly published species available in List of Prokaryotic Names with Standing in Nomenclature. Sphingopyxis spp. have been isolated from diverse niches including, agricultural soil, marine and fresh water, caves, activated sludge, thermal spring, oil and pesticide contaminated soil, and heavy metal contaminated sites. Sphingopyxis species have drawn considerable attention not only for their ability to survive under extreme environments, but also for their potential to degrade number of xenobiotics and other environmental contaminants that impose serious threat to human health. At present, genome sequence of both cultivable and non-cultivable strains (metagenome assembled genome) are available in the public databases (NCBI) and genome wide studies confirms the presence of mobile genetic elements and plethora of degradation genes and pathways making them a potential candidate for bioremediation. Beside genome wide predictions there are number of experimental evidences confirm the degradation potential of bacteria belonging to genus Sphingopyxis and also the production of different secondary metabolites that help them interact and survive in their ecological niches. This review provides detailed information on ecology, general characteristic and the significant implications of Sphingopyxis species in environmental management along with the bio-synthetic potential.

Microbial vanadate reduction coupled to co-metabolic phenanthrene biodegradation in groundwater

Vanadate [V(V)] and phenanthrene (PHE) commonly coexist in groundwater aquifer, posing potential threats to ecological environment and public health. However, little is known about the complicated biogeochemical processes involving microbial V(V) reduction coupled with co-metabolic PHE biodegradation. Herein we demonstrated that synchronous removal of V(V) and PHE could be realized under anaerobic condition. Complete V(V) removal and PHE degradation efficiency of 82.0 ± 0.8% were achieved in 7-d operation in batch experiment. 250-d continuous column experiment implied that hydrochemical condition affected V(V) and PHE removals. V(V) was reduced to insoluble vanadium (IV) and PHE was degraded into small molecule organics (e.g. salicylic acid). Geobacter and Acetobacterium used methanol and intermediates from PHE degradation as electron donors for V(V) reduction. PHE was decomposed by Mycobacterium and Clostridium with methanol as co-metabolic substrate and V(V) as electron acceptor. Genes encoding proteins for V(V) reduction (omcA, omcB and mtrC) and PHE degradation (phnAc) were upregulated. Cytochrome c and nicotinamide adenine dinucleotide promoted electron transfer for V(V) and PHE detoxification. Extracellular polymeric substances could bind V(V) and improve the bioavailability of PHE. Our findings provide a robust strategy for remediation of V(V) and PHE co-contaminated groundwater.

Integrated metabolomics and lipidomics reveals high accumulation of polyunsaturated lysoglycerophospholipids in human lung fibroblasts exposed to fine particulate matter

Exposure to fine particulate matter (PM) comprising toxic compounds arising from air pollution is a major human health concern. It is linked to increased mortality and incidence of various lung diseases. However, the mechanisms underlying the toxic effects of PM on lung fibroblasts have not been fully explored. We used targeted quantitative metabolomics and lipidomics analysis along with cytotoxicity studies to comprehensively characterize the alterations in the metabolite profiles of human lung fibroblasts (HEL 299) upon exposure to PM_2.5 and PM₁₀. This exposure at 50 μg/mL for 72 h induced an abnormally high apoptotic response via triggering intracellular reactive oxygen species (ROS) production and mitochondrial dysfunction through an imbalance between pro- and anti-apoptotic signaling pathways. The cytotoxic effects of PM_2.5 were more severe than those of PM₁₀. Metabolomics and lipidomics analyses revealed that PM exposure triggered substantial changes in the cellular metabolite profile, which involved reduced mitochondria-related metabolites such as tricarboxylic acid (TCA) cycle intermediates, amino acids, and free fatty acids as well as increased lysoglycerophospholipids (LPLs) containing polyunsaturated fatty acids. The decrease in mitochondria-related metabolites suggested that PM exposure led to reduced TCA cycle capacity and energy production. Apoptotic and inflammatory responses as well as mitochondrial dysfunction were likely to be accelerated because of excessive accumulation of LPLs, contributing to the disruption of membrane rafts and Ca²⁺ homeostasis and causing increased mitochondrial ROS formation. These results provide valuable insights regarding the toxic effects of PM exposure. Our study also provides a new direction for research on PM exposure-related health disorders using different cell lines.

Plasma Lipidomics Reveals Insights into Anti-Obesity Effect of Chrysanthemum morifolium Ramat Leaves and Its Constituent Luteolin in High-Fat Diet-Induced Dyslipidemic Mice

The Chrysanthemum morifolium Ramat (CM) is widely used as a traditional medicine and herbal tea by the Asian population for its health benefits related to obesity. However, compared to the flowers of CM, detailed mechanisms underlying the beneficial effects of its leaves on obesity and dyslipidemia have not yet been elucidated. Therefore, to investigate the lipidomic biomarkers responsible for the pharmacological effects of CM leaf extract (CLE) in plasma of mice fed a high-fat diet (HFD), the plasma of mice fed a normal diet (ND), HFD, HFD plus CLE 1.5% diet, and HFD plus luteolin 0.003% diet (LU) for 16 weeks were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) combined with multivariate analysis. In our analysis, the ND, HFD, CLE, and LU groups were clearly differentiated by partial least-squares discriminant analysis (PLS-DA) score plots. The major metabolites contributing to this differentiation were cholesteryl esters (CEs), lysophosphatidylcholines (LPCs), phosphatidylcholines (PCs), ceramides (CERs), and sphingomyelins (SMs). The levels of plasma CEs, LPCs, PCs, SMs, and CERs were significantly increased in the HFD group compared to those in the ND group, and levels of these lipids recovered to normal after administration of CLE or LU. Furthermore, changes in hepatic mRNA expression levels involved in the Kennedy pathway and sphingolipid biosynthesis were also suppressed by treatment with CLE or LU. In conclusion, this study examined the beneficial effects of CLE and LU on obesity and dyslipidemia, which were demonstrated as reduced synthesis of lipotoxic intermediates. These results may provide valuable insights towards evaluating the therapeutic effects of CLE and LU and understanding obesity-related diseases.