Characterization of the Phenanthrene-Degrading Sphingobium yanoikuyae SJTF8 in Heavy Metal Co-Existing Liquid Medium and Analysis of Its Metabolic Pathway

Identification of a putative novel polycyclic aromatic hydrocarbon-biodegrading gene cluster in a marine Roseobacteraceae bacterium Sagittula sp. MA-2

The ability to biodegrade polycyclic aromatic hydrocarbons (PAHs) and the catabolic enzymes responsible for PAH biotransformation in marine bacteria belonging to the family Roseobacteraceae remain largely unexplored despite their wide distribution and highly diverse physiological traits. A bacterial isolate within Roseobacteraceae originating from coastal seawater, Sagittula sp. strain MA-2, that biotransformed phenanthrene and utilized it as a growth substrate was found to possess a putative PAH-degrading gene cluster on one of the eight circular plasmids in its genome. Subsequent comprehensive investigations utilizing bacterial genomes in public databases revealed that gene clusters potentially homologous to this newly found cluster are widely but heterogeneously distributed within Roseobacteraceae and a few non-Roseobacteraceae (Paracoccaceae and Rhizobiaceae) strains from saline environments. Catabolic functions of the enzymes encoded in strain MA-2 were predicted through the profiling of phenanthrene biotransformation products by liquid chromatography-electrospray ionization high-resolution mass spectrometry and substrate docking simulations using predicted three-dimensional structures of selected proteins, and phenanthrene biodegradation pathways were proposed. Strain MA-2 appeared to biodegrade phenanthrene via two separated, concurrent pathways, namely the salicylate and phthalate pathways. This study serves as the first investigation into the functional genes potentially responsible for PAH biodegradation conserved in Roseobacteraceae bacteria, expanding scientific understanding of the physiological repertoire evolved in this ubiquitous marine bacterial group.

IMPORTANCE

The ocean is often characterized as the terminal destination for persistent polycyclic aromatic hydrocarbon (PAH) environmental pollutants; however, the ability to biodegrade PAHs and the corresponding enzymes conserved among marine bacteria are less understood compared to their terrestrial counterparts. A marine bacterial isolate, Sagittula sp. strain MA-2, belonging to the family Roseobacteraceae-a widely distributed and physiologically diverse marine bacterial group-was found to possess a functional gene cluster encoding enzymes potentially responsible for PAH biodegradation in its genome and exhibit the ability to biodegrade the three-ring PAH, phenanthrene. Intriguingly, gene clusters potentially homologous to this cluster were also distributed broadly across genomes from different Roseobacteraceae genera in public databases, which has not been previously investigated. The knowledge provided here expands our understanding of the physiology of Roseobacteraceae and may be applied to explore biotechnologically useful bacteria that contribute to the remediation of polluted marine environments or high-salinity wastewater.

A comprehensive Review into Emission Sources, Formation Mechanisms, Ecological Effects, and Biotransformation Routes of Halogenated Polycyclic Aromatic Hydrocarbons (HPAHs)

Halogenated polycyclic aromatic hydrocarbons (HPAHs, H = F, Cl, Br) are a new class of PAHs derivatives that mainly originate from the incomplete combustion of halogen-laden materials and via metallurgical operations. These compounds circulate extensively in various environmental matrices. This survey provides a comprehensive review on governing synthesis routes of HPAHs, their environmental occurrence, and their health and ecological effects. The review comprehensively enlists and presents emission sources of these emerging organic pollutants into the air that serves as their main reservoir. The formation of HPAHs ensues through successive addition reactions of related precursors accompanied by ring cyclization steps; in addition to direct unimolecular fragmentation of parents halogenated. Halogenation of parent PAHs rapidly occurs in saline ecosystems, thus multiplying the availability of these notorious compounds in the environment. Certain HPAHs appear to be more carcinogenic than dioxins. Transmission routes of HPAHs from their emission sources to water bodies, soil, aquatic life, plants, terrestrial animals, and humans are well-documented. Later, the direct and indirect diffusion of HPAHs from air to the biotic (plants, animals, humans) and abiotic components (soil, water, sediments) are described in detail. The study concludes that HPAHs are permeable to the carbon matrices resulting in the alleviation of the source-to-sink interface. As a potential future perspective, understanding the transmission interfaces lays a foundation to intervene in the introduction of these toxicants into the food chain.

Phenanthrene-Degrading and Nickel-Resistant Neorhizobium Strain Isolated from Hydrocarbon-Contaminated Rhizosphere of Medicago sativa L

Pollutant degradation and heavy-metal resistance may be important features of the rhizobia, making them promising agents for environment cleanup biotechnology. The degradation of phenanthrene, a three-ring polycyclic aromatic hydrocarbon (PAH), by the rhizobial strain Rsf11 isolated from the oil-polluted rhizosphere of alfalfa and the influence of nickel ions on this process were studied. On the basis of whole-genome and polyphasic taxonomy, the bacterium Rsf11 represent a novel species of the genus Neorhizobium, so the name Neorhizobium phenanthreniclasticum sp. nov. was proposed. Analysis of phenanthrene degradation by the Rsf1 strain revealed 1-hydroxy-2-naphthoic acid as the key intermediate and the activity of two enzymes apparently involved in PAH degradation. It was also shown that the nickel resistance of Rsf11 was connected with the extracellular adsorption of metal by EPS. The joint presence of phenanthrene and nickel in the medium reduced the degradation of PAH by the microorganism, apparently due to the inhibition of microbial growth but not due to the inhibition of the activity of the PAH degradation enzymes. Genes potentially involved in PAH catabolism and nickel resistance were discovered in the microorganism studied. N. phenanthreniclasticum strain Rsf11 can be considered as a promising candidate for use in the bioremediation of mixed PAH-heavy-metal contamination.

Proteogenomic Characterization of Pseudomonas veronii SM-20 Growing on Phenanthrene as Only Carbon and Energy Source

In this study, we conducted an extensive investigation of the biodegradation capabilities and stress response of the newly isolated strain Pseudomonas veronii SM-20 in order, to assess its potential for bioremediation of sites contaminated with polycyclic aromatic hydrocarbons (PAHs). Initially, phenotype microarray technology demonstrated the strain's proficiency in utilizing various carbon sources and its resistance to certain stressors. Genomic analysis has identified numerous genes involved in aromatic hydrocarbon metabolism. Biodegradation assay analyzed the depletion of phenanthrene (PHE) when it was added as a sole carbon and energy source. We found that P. veronii strain SM-20 degraded approximately 25% of PHE over a 30-day period, starting with an initial concentration of 600 µg/mL, while being utilized for growth. The degradation process involved PHE oxidation to an unstable arene oxide and 9,10-phenanthrenequinone, followed by ring-cleavage. Comparative proteomics provided a comprehensive understanding of how the entire proteome responded to PHE exposure, revealing the strain's adaptation in terms of aromatic metabolism, surface properties, and defense mechanism. In conclusion, our findings shed light on the promising attributes of P. veronii SM-20 and offer valuable insights for the use of P. veronii species in environmental restoration efforts targeting PAH-impacted sites.

Phenanthrene removal from a spent sediment washing solution in a continuous-flow stirred-tank reactor

The issue of polycyclic aromatic hydrocarbons (PAHs) is widespread in marine sediments involving ecological systems and human health. Sediment washing (SW) has proven to be the most effective remediation approach for sediments polluted by PAHs, such as phenanthrene (PHE). However, SW still raises waste handling concerns due to a considerable amount of effluents generated downstream. In this context, the biological treatment of a PHE- and ethanol-containing spent SW solution can represent a highly efficient and environmentally-friendly strategy, but its knowledge is still scarce in scientific literature and no studies have so far been conducted in continuous mode. Therefore, a synthetic PHE-polluted SW solution was biologically treated in a 1 L aerated continuous-flow stirred-tank reactor for 129 days by evaluating the effect of different pH values, aeration flowrates and hydraulic retention times as operating parameters over five successive phases. A PHE removal efficiency of up to 75-94% was achieved by an acclimated PHE-degrading consortium mainly composed of Proteobacteria, Bacteroidota and Firmicutes phyla through biodegradation following the adsorption mechanism. PHE biodegradation, mainly occurring via the benzoate route due to the presence of PAH-related-degrading functional genes and a phthalate accumulation up to 46 mg/L, was also accompanied by a reduction of dissolved organic carbon and ammonia nitrogen above 99% in the treated SW solution.

Surfactant-enhanced bioremediation of petroleum-contaminated soil and microbial community response: A field study

Surfactant-enhanced bioremediation (SEBR) is frequently employed to clean up soil polluted with petroleum hydrocarbons, but few studies have focused on how surfactants affect microbial communities and different fractions of petroleum hydrocarbons, particularly in the field. Here, the surfactants sodium dodecyl benzene sulfonate (SDBS), alpha olefin sulfonate (AOS), Triton X-100 (TX-100), Tween80, and rhamnolipid were combined with the oil-degrading bacterium Pseudomonas sp. SB to remediate oil-contaminated soil in the laboratory. AOS gave the highest removal efficiency (65.1%) of total petroleum hydrocarbons (TPHs). Therefore, AOS was used in a field experiment with Pseudomonas sp. SB and the removal efficiency of TPHs and long-chain hydrocarbons C21-C40 reached 57.4 and 53.0%, respectively, significantly higher than the other treatments. During bioremediation the addition of Pseudomonas sp. SB significantly stimulated the growth of bacterial genera such as Alcanivorax, Luteimonas, Parvibaculum, Stenotrophomonas, and Pseudomonas and AOS further stimulated the growth of Sphingobacterium, Pseudomonas and Alcanivorax. This study validates the feasibility of surfactant-enhanced bioremediation in the field and partly reveals the mechanism of surfactant-enhanced bioremediation from the perspective of changes in different fractions of petroleum and microbial community dynamics.

Oxidization of benzo[a]pyrene by CYP102 in a novel PAHs-degrader Pontibacillus sp. HN14 with potential application in high salinity environment

Benzo [a]pyrene (BaP) is a type of high-molecular-weight polycyclic aromatic hydrocarbons (PAHs) with potent carcinogenicity; however, there are limited studies on its degradation mechanism. Here, a strain of Pontibacillus sp. HN14 with BaP degradation ability was isolated from mangrove sediments in Dongzhai Port, Hainan Province. Our study showed that biodegradation efficiencies reached 42.15% after Pontibacillus sp. HN14 was cultured with 20 mg L^-1 BaP as the sole carbon source for 25 days and still had degradability of BaP at a 25% high salinity level. Moreover, 9,10-dihydrobenzo [a]pyrene-7(8H)-one, an intermediate metabolite, was detected during BaP degradation in the HN14 strain. Genome analysis identified a gene encoding the CYP102(HN14) enzyme. The results showed that the E. coli strain with CYP102(HN14) overexpression could transfer BaP to 9,10-dihydrobenzo [a]pyrene-7(8H)-one with a conversion rate of 43.5%, indicating that CYP102(HN14) played an essential role in BaP degradation in Pontibacillus sp. HN14. Thus, our results provide a novel BaP biodegradation molecule, which could be used in BaP bioremediation in high salinity conditions. This study is the first to show that CYP102(HN14) had the BaP oxidization ability in bacteria. CYP102(HN14) could be essential in removing PAHs in saline-alkali soil and other high salt environments through enzyme immobilization.

Coupling of desorption of phenanthrene from marine sediments and biodegradation of the sediment washing solution in a novel biochar immobilized-cell reactor

The recurrent dredging of marine sediments needs the use of ex-situ technologies such as sediment washing (SW) to effectively remove polycyclic aromatic hydrocarbons. Notwithstanding, the large volumes of generated spent SW effluents require adequate treatment by employing highly-efficient, inexpensive and environmentally-friendly solutions. This study proposes the phenanthrene (PHE) desorption from sediments using Tween® 80 (TW80) as extracting agent and the treatment of the resulting spent SW solution in a biochar (BC) immobilized-cell bioreactor. The SW process reached the highest PHE removal of about 91% using a surfactant solution containing 10,800 mg L^-1 of TW80. The generated amount of spent PHE-polluted SW solution can be controlled by keeping a solid to liquid ratio of 1:4. A PHE degradation of up to 96% was subsequently achieved after 43 days of continuous reactor operation, aerobically treating the TW80 solution in the BC immobilized-cell bioreactor with a hydraulic retention time of 3.5 days. Brevundimonas, Chryseobacterium, Dysgonomonas, Nubsella, and both uncultured Weeksellaceae and Xanthobacteraceae genera were mainly involved in PHE biodegradation. A rough economic study showed a total cost of 342.60 € ton^-1 of sediment, including the SW operations, TW80 and BC supply and the biological treatment of the SW solution.

Kinetic and statistical perspectives on the interactive effects of recalcitrant polyaromatic and sulfur heterocyclic compounds and in-vitro nanobioremediation of oily marine sediment at microcosm level

A halotolerant biosurfactant producer Pseudomonas aeruginosa strain NSH3 (NCBI Gene Bank Accession No. MN149622) was isolated to degrade high concentrations of recalcitrant polyaromatic hydrocarbons (PAHs) and polyaromatic heterocyclic sulfur compounds (PASHs). In biphasic batch bioreactors, the biodegradation and biosurfactant-production activities of NSH3 have been significantly enhanced (p < 0.0001) by its decoration with eco-friendly prepared magnetite nanoparticles (MNPs). On an artificially contaminated sediment microcosm level, regression modeling and statistical analysis based on a 2³ full factorial design of experiments were trendily applied to provide insights into the interactive impacts of such pollutants. MNPs-coated NSH3 were also innovatively applied for nanobioremediation (NBR) of in-vitro diesel oil-polluted sediment microcosms. Gravimetric, chromatographic, and microbial respiratory analyses proved the significantly enhanced biodegradation capabilities of MNPs-coated NSH3 (p < 0.001) and the complete mineralization of various recalcitrant diesel oil components. Kinetic analyses showed that the biodegradation of iso- and n-alkanes was best fitted with a second-order kinetic model equation. Nevertheless, PAHs and PASHs in biphasic batch bioreactors and sediment microcosms followed the first-order kinetic model equation. Sustainable NBR overcome the toxicity of low molecular weight hydrocarbons, mass transfer limitation, and steric hindrance of hydrophobic recalcitrant high molecular weight hydrocarbons and alkylated polyaromatic compounds.

Genome sequencing and in silico analysis of isoprene degrading monooxygenase enzymes of Sphingobium sp. BHU LFT2

The whole genome sequencing of a novel isoprene degrading strain of Sphingobium sp. BHU LFT2, its in silico analysis for identifying and characterizing enzymes, especially isoprene monooxygenases (IsoMO), which initiate the degradation process, and in vitro validation with cell extract of optimal temperature and pH and analysis for utilizing isoprene as the preferential substrate, were conducted. The most efficient monooxygenase was identified through comparative analyses using molecular docking followed by molecular dynamics simulation approach. The in silico results revealed high thermostability for most of the monooxygenases. Most potent monooxygenase with locus ID JQK15_20300 exhibiting high sequence similarity with known monooxygenases of isoprene-degrading Rhodococcus sp. LB1 and SC4 strains was identified. Interaction energy of -17.25 kJ/mol for JQK15_20300 with isoprene, was almost similar as that analysed for above-mentioned similar known counterparts, was exhibited by the molecular docking. Molecular dynamic simulation of 100 ns and free energy analysis of JQK15_20300 in the complex with isoprene gave persistent interaction of isoprene with JQK15_20300 during the simulation with high average binding energy of -47.13 kJ/mol thus proving higher affinity of JQK15_20300 for isoprene. The study revealed that the highly efficient isoprene degrading strain of Sphingobium sp. BHU LFT2 having effective monooxygenase could be utilized for large-scale applications including detoxification of air contaminated with isoprene in closed working systems.Communicated by Ramaswamy H. Sarma.

Insights Into Mechanism of the Naphthalene-Enhanced Biodegradation of Phenanthrene by Pseudomonas sp. SL-6 Based on Omics Analysis

The existence of polycyclic aromatic hydrocarbons (PAHs) in contaminated environment is multifarious. At present, studies of metabolic regulation focus on the degradation process of single PAH. The global metabolic regulatory mechanisms of microorganisms facing coexisting PAHs are poorly understood, which is the major bottleneck for efficient bioremediation of PAHs pollution. Naphthalene (NAP) significantly enhanced the biodegradation of phenanthrene (PHE) by Pseudomonas sp. SL-6. To explore the underlying mechanism, isobaric tags for relative and absolute quantification (iTRAQ) labeled quantitative proteomics was used to characterize the differentially expressed proteins of SL-6 cultured with PHE or NAP + PHE as carbon source. Through joint analysis of proteome and genome, unique proteins were identified and quantified. The up-regulated proteins mainly concentrated in PAH catabolism, Transporters and Electron transfer carriers. In the process, the regulator NahR, activated by salicylate (intermediate of NAP-biodegradation), up-regulates degradation enzymes (NahABCDE and SalABCDEFGH), which enhances the biodegradation of PHE and accumulation of toxic intermediate–1-hydroxy-2-naphthoic acid (1H2Na); 1H2Na stimulates the expression of ABC transporter, which maintains intracellular physiological activity by excreting 1H2Na; the up-regulation of cytochrome C promotes the above process running smoothly. Salicylate works as a trigger that stimulates cell to respond globally. The conjecture was verified at transcriptional and metabolic levels. These new insights contribute to improving the overall understanding of PAHs-biodegradation processes under complex natural conditions, and promoting the application of microbial remediation technology for PAHs pollution.

Isolation and identification of naphthalene degrading bacteria and their degradation characteristics under rainwater environment in heavily polluted areas

This study is screened for naphthalene degrading strains from a heavily polluted area with high naphthalene concentration in the rainwater for the effective removal of naphthalene from rainwater. Recently, naphthalene biodegradation has been achieved in water. However, the influences of organics and inorganics in the rainwater on the biodegradation of naphthalene remains unclear. The naphthalene degrading strain Klebsiella sp. (WJ-1) was identified from sewage sludge. The effects of temperature, pH, inoculum size, and rotation speed on the degradation ability of WJ-1 were studied. The results showed that the naphthalene degradation rates of WJ-1 in rainwater were higher than those in aqueous solution at different experimental conditions. The optimal conditions were 30 °C, 10% inoculum size, pH 7.0, and a rotation speed of 150 rpm. The substances in rainwater might be important co-metabolites of naphthalene degradation. Based on intermediate metabolites detected by gas chromatography-mass spectrometer (GC-MS), the naphthalene biodegradation pathway was identified, as being similar to the phthalic acid pathway. These results suggest WJ-1 as a good candidate for the efficient bioremediation of naphthalene from rainwater in heavily polluted areas.