Efficient biodegradation of petroleum n-alkanes and polycyclic aromatic hydrocarbons by polyextremophilic Pseudomonas aeruginosa san ai with multidegradative capacity

Biocatalytic Potential of Pseudomonas Species in the Degradation of Polycyclic Aromatic Hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs), one of the major environmental pollutants, produced from incomplete combustion of materials like coal, oil, gas, wood, and charbroiled meat, that contaminate the air, soil, and water, necessitating urgent remediation. Understanding the metabolic pathways for PAHs degradation is crucial to preventing environmental damage and health issues. Biological methods are gaining increasing interest due to their cost-effectiveness and environmental friendliness. These methods are particularly suitable for remediating PAHs contamination and mitigating associated risks. The paper also outlines the processes for biodegrading PAHs, emphasizing the function of Pseudomonas spp., a kind of bacterium recognized for its capacity to degrade PAHs. To eliminate PAHs from the environment and reduce threats to human health and the environment, Pseudomonas spp. is essential. Understanding the mechanism of PAH breakdown by means of microbes could lead to effective clean-up strategies. The review highlights the enzymatic capabilities, adaptability, and genetic versatility of the genes like nah and phn of Pseudomonas spp., which are involved in PAHs degradation pathways. Scientific evidence supports using Pseudomonas spp. as biocatalysts for PAHs clean-up, offering cost-effective and eco-friendly solutions.

Metagenomic analyses of a consortium for the bioremediation of hydrocarbons polluted soils

A bacterial consortium was isolated from a soil in Noblejas (Toledo, Spain) with a long history of mixed hydrocarbons pollution, by enrichment cultivation. Serial cultures of hydrocarbons polluted soil samples were grown in a minimal medium using diesel (1 mL/L) as the sole carbon and energy source. The bacterial composition of the Noblejas Consortium (NC) was determined by sequencing 16S rRNA gene amplicon libraries. The consortium contained around 50 amplicon sequence variants (ASVs) and the major populations belonged to the genera Pseudomonas, Enterobacter, Delftia, Stenotrophomonas, Achromobacter, Acinetobacter, Novosphingobium, Allorhizobium-Neorhizobium-Rhizobium, Ochrobactrum and Luteibacter. All other genera were below 1%. Metagenomic analysis of NC has shown a high abundance of genes encoding enzymes implicated in aliphatic and (poly) aromatic hydrocarbons degradation, and almost all pathways for hydrocarbon degradation are represented. Metagenomic analysis has also allowed the construction of metagenome assembled genomes (MAGs) for the major players of NC. Metatranscriptomic analysis has shown that several of the ASVs are implicated in hydrocarbon degradation, being Pseudomonas, Acinetobacter and Delftia the most active populations.

Insights into the characteristics of changes in dissolved organic matter fluorescence components on the natural attenuation process of toluene

Natural attenuation (NA) is of great significance for the remediation of contaminated groundwater, and how to identify NA patterns of toluene in aquifers more quickly and effectively poses an urgent challenge. In this study, the NA of toluene in two typical soils was conducted by means of soil column experiment. Based on column experiments, dissolved organic matter (DOM) was rapidly identified using fluorescence spectroscopy, and the relationship between DOM and the NA of toluene was established through structural equation modeling analysis. The adsorption rates of toluene in clay and sandy soil were 39 % and 26 %, respectively. The adsorption capacity and total NA capacity of silty clay were large. The occurrence of fluorescence peaks of protein-like components and specific products indicated the occurrence of biodegradation. Arenimonas, Acidovorax and Brevundimonas were the main degrading bacteria identified in Column A, while Pseudomonas, Azotobacter and Mycobacterium were the main ones identified in Column B. The pH, ORP, and Fe(II) were the most important factors affecting the composition of microbial communities, which in turn affected the NA of toluene. These results provide a new way to quickly identify NA of toluene.

Asphalt dust influence on the distribution of polycyclic aromatic hydrocarbon in crankcase oil stains of a concrete, covered parking structure

Used crankcase oil is an important source of environmental polycyclic aromatic hydrocarbons (PAHs). Here, we use gas chromatography-mass spectrometry (GC-MS) to measure and compare the concentration of PAHs, including alkylated PAHs, in used oil against new and old oil stains and parking dust collected from a concrete, covered, open parking structure to understand the distribution of PAH in crankcase oil stains. PAH concentration in used oils ranges from 606 ng/mg to 1,592 ng/mg. The PAH distribution in used oil does not match that observed in parking oils stains, parking background, or parking dust. A comparison with PAH distributions in traffic related dusts extracted from the literature and dust collected from a neighboring open asphalt-paved parking suggests that covered parking dust includes substantial contributions from asphalt-paved parking dust, road dust, and/or coal tar dust. The parking dust is the most concentrated source of PAHs in the covered parking structure (PAHs up to 4,371 ng/mg), a small contribution of which can alter the distribution of PAHs in oil stains. Even with this contribution, we were able to observe a significant decrease of the ratio of low molecular weight PAHs to high molecular weight PAHs, and a significant increase in values of the phenanthrene/anthracene and fluoranthene/(fluoranthene + pyrene) ratios when oil stains age, suggesting biodegradation is an active attenuation process in covered, open parking structures.

Exploring the diversity and functional profile of microbial communities of Brazilian soils with high salinity and oil contamination

Environmental pollution associated with the petroleum industry is a major problem worldwide. Microbial degradation is extremely important whether in the extractive process or in bioremediation of contaminants. Assessing the local microbiota and its potential for degradation is crucial for implementing effective bioremediation strategies. Herein, contaminated soil samples of onshore oil fields from a semiarid region in the Northeast of Brazil were investigated using metagenomics and metataxonomics. These soils exhibited hydrocarbon contamination and high salinity indices, while a control sample was collected from an uncontaminated area. The shotgun analysis revealed the predominance of Actinomycetota and Pseudomonadota, while 16S rRNA gene amplicon analysis of the samples showed Actinomycetota, Bacillota, and Pseudomonadota as the most abundant. The Archaea domain phylotypes were assigned to Thermoproteota and Methanobacteriota. Functional analysis and metabolic profile of the soil microbiomes exhibited a broader metabolic repertoire in the uncontaminated soil, while degradation pathways and surfactant biosynthesis presented higher values in the contaminated soils, where degradation pathways of xenobiotic and aromatic compounds were also present. Biosurfactant synthetic pathways were abundant, with predominance of lipopeptides. The present work uncovers several microbial drivers of oil degradation and mechanisms of adaptation to high salinity, which are pivotal traits for sustainable soil recovery strategies.

Fungal-bacterial consortia: A promising strategy for the removal of petroleum hydrocarbons

Nowadays, petroleum hydrocarbon pollution is one of the most widespread types of contamination that poses a serious threat to both public health and the environment. Among various physicochemical methods, bioremediation is an eco-friendly and cost-effective way to eliminate petroleum hydrocarbon pollutants. The successful degradation of all hydrocarbon components and the achievement of optimal efficiency are necessary for the success of this process. Using potential microbial consortia with rich metabolic networks is a promising strategy for addressing these challenges. Mixed microbial communities, comprising both fungi and bacteria, exhibit diverse synergistic mechanisms to degrade complex hydrocarbon contaminants, including the dissemination of bacteria by fungal hyphae, enhancement of enzyme and secondary metabolites production, and co-metabolism of pollutants. Compared to pure cultures or consortia of either fungi or bacteria, different studies have shown increased bioremediation of particular contaminants when combined fungal-bacterial treatments are applied. However, antagonistic interactions, like microbial competition, and the production of inhibitors or toxins can observed between members. Furthermore, optimizing environmental factors (pH, temperature, moisture, and initial contaminant concentration) is essential for consortium performance. With the advancements in synthetic biology and gene editing tools, it is now feasible to design stable and robust artificial microbial consortia systems. This review presents an overview of using microbial communities for the removal of petroleum pollutants by focusing on microbial degradation pathways, and their interactions. It also highlights the new strategies for constructing optimal microbial consortia, as well as the challenges currently faced and future perspectives of applying fungal-bacterial communities for bioremediation.

Pseudomonas aeruginosa PR23 isolated from oil contaminated soil tolerate and degrades mixture of polyaromatic hydrocarbons and express novel proteins

Pseudomonas aeruginosa PR23 isolated from the hydrocarbon contaminated soil can tolerate and degrade mixture of polyaromatic hydrocarbons (PAHs) at an initial concentration of 1300 ppm. The degradation and intermediates formed were assessed by gas chromatography-mass spectrometry (GC-MS) analysis. The isolated strain was able to degrade 59.2% of the mixture of PAHs in 3 days and 71.6% by day 15. Effect of PAHs on protein expression in Pseudomonas aeruginosa PR23 was studied using nano LC-MS/MS. Thirty-six proteins showed a more than 2-fold increase in expression in the presence of mixture of PAHs. Out of these proteins, 7 proteins have been reported for their role in degradation of naphthalene, phenanthrene, and pyrene. The data revealed the presence of 16 proteins that were uniquely expressed in the presence of mixture of PAHs. A twin-arginine translocation signal peptide (Tat system), known for the transportation of folded proteins across the cell membrane, showed more than 8-fold increased expression in the presence of mixture of PAHs. These results indicate that the isolated strain adopts the conditions in the presence of mixture of PAHs by modulating its metabolic and physiological processes. These findings suggest that Pseudomonas aeruginosa PR23 may be a suitable candidate for use in the development of strategies for bioremediation of mixtures of PAHs.

N-alkane shape distinctive microbial patterns in Kuroshio Extension

Marine microorganisms are primary drivers of the elemental cycling. The interaction between heterotrophic prokaryotes and biomarker (n-alkane) in Kuroshio Extension (KE) remains unclear. Here, we categorize KE into three characteristic areas based on ocean temperatures and nutrient conditions: Cold Water Area (CWA), Mixed Area (MA), and Warm Water Area (WWA). A total of 49 samples were collected during two-year voyage to identify the source of n-alkane and associated degrading microorganisms. Total n-alkane concentrations (Σn-Alk) in surface water (SW) spanned from 1,308 ng L-1 to 1,890 ng L-1, it was significantly higher (Tukey-Kramer test, p < 0.05) in MA than CWA and WWA. The Σn-Alk in surface sediments (SS) gradually increased from north to south, ranging from 5,982 ng g-1 to 37,857 ng g-1. Bacteria and algae were the primary sources of n-alkane in both SW and SS. Proteobacteria was the most widely distributed among three areas. The presence of Rhodobacteraceae with alkB was the primary reason affecting n-alkane concentrations in SW. The Gammaproteobacteria with alkB and alkR chiefly affected n-alkane concentrations in SS. In summary, n-alkane s serve as an energy source for particular microorganisms, shaping the unique oceanographic patterns.

Recognizing Functional Groups of MES/APG Mixed Surfactants for Enhanced Solubilization toward Benzo[a]pyrene

Benzo[a]pyrene is difficult to remove from soil due to its high octanol/water partition coefficient. The use of mixed surfactants can increase solubility but with the risk of secondary soil contamination, and the compounding mechanism is still unclear. This study introduced a new approach using environmentally friendly fatty acid methyl ester sulfonate (MES) and alkyl polyglucoside (APG) to solubilize benzo[a]pyrene. The best result was obtained when the ratio of MES/APG was 7:1 under 6 g/L total concentration, with an apparent solubility (Sw) of 8.58 mg/L and a molar solubilization ratio (MSR) of 1.31 for benzo[a]pyrene, which is comparable to that of Tween 80 (MSR, 0.95). The mechanism indicates that the hydroxyl groups (-OH) in APG form "O-H···OSO2-" hydrogen bonding with the sulfonic acid group (-SO3-) of MES, which reduces the electrostatic repulsion between MES molecules, thus facilitating the formation of large and stable micelles. Moreover, the strong solubilizing effect on benzo[a]pyrene should be ascribed to the low polarity of ester groups (-COOCH3) in MES. Functional groups capable of forming hydrogen bonds and having low polarity are responsible for the enhanced solubilization of benzo[a]pyrene. This understanding helps choose suitable surfactants for the remediation of PAH-contaminated soils.

Functional amyloid fibrils of biofilm-forming marine bacterium Pseudomonas aeruginosa PFL-P1 interact spontaneously with pyrene and augment the biodegradation

Bacteria thrive in biofilms embedding in the three-dimensional extracellular polymeric substances (EPS). Functional Amyloid in Pseudomonas (Fap), a protein in EPS, efficiently sequesters polycyclic aromatic hydrocarbons (PAHs). Present study reports the characterization of Fap fibrils from Pseudomonas aeruginosa PFL-P1 and describes the interaction with pyrene to assess the impact on pyrene degradation. Overexpression of fap in E. coli BL21(DE3) cells significantly enhances biofilm formation (p < 0.0001) and amyloid production (p = 0.0002), particularly with pyrene. Defibrillated Fap analysis reveals FapC monomers and increased fibrillation with pyrene. Circular Dichroism (CD), Fourier Transform Infrared Spectroscopy (FTIR), and X-ray Diffraction (XRD) unveil characteristic amyloid peaks and structural changes in Fap fibrils upon pyrene exposure. 3D-EEM analysis identifies a protein-like fluorophore in Fap fibrils, exhibiting pyrene-induced fluorescence quenching. Binding constants range from 5.23 to 7.78 M-1, with ΔG of -5.10 kJ mol-1 at 298 K, indicating spontaneous and exothermic interaction driven by hydrophobic forces. Exogenous Fap fibrils substantially increased the biofilm growth and pyrene degradation by P. aeruginosa PFL-P1 from 46 % to 64 % within 7 days (p = 0.0236). GC-MS identifies diverse metabolites, implying phthalic acid pathway in pyrene degradation. This study deepens insights into structural dynamics of Fap fibrils when exposed to pyrene, offering potential application in environmental bioremediation.

Effect of ultra-violet light radiation on Scenedesmus vacuolatus growth kinetics, metabolic performance, and preliminary biodegradation study

This study presents the effect of ultra-violet (UV) light radiation on the process kinetics, metabolic performance, and biodegradation capability of Scenedesmus vacuolatus. The impact of the UV radiation on S. vacuolatus morphology, chlorophyll, carotenoid, carbohydrates, proteins, lipid accumulation, growth rate, substrate affinity and substrate versatility were evaluated. Thereafter, a preliminary biodegradative potential of UV-exposed S. vacuolatus on spent coolant waste (SCW) was carried out based on dehydrogenase activity (DHA) and total petroleum hydrocarbon degradation (TPH). Pronounced structural changes were observed in S. vacuolatus exposed to UV radiation for 24 h compared to the 2, 4, 6, 12 and 48 h UV exposure. Exposure of S. vacuolatus to UV radiation improved cellular chlorophyll (chla = 1.89-fold, chlb = 2.02-fold), carotenoid (1.24-fold), carbohydrates (4.62-fold), proteins (1.44-fold) and lipid accumulations (1.40-fold). In addition, the 24 h UV exposed S. vacuolatus showed a significant increase in substrate affinity (1/Ks) (0.959), specific growth rate (µ) (0.024 h-1) and biomass accumulation (0.513 g/L) by 1.50, 2 and 1.9-fold respectively. Moreover, enhanced DHA (55%) and TPH (100%) degradation efficiency were observed in UV-exposed S. vacuolatus. These findings provided major insights into the use of UV radiation to enhance S. vacuolatus biodegradative performance towards sustainable green environment negating the use of expensive chemicals and other unfriendly environmental practices.

Bacteria degrading both n-alkanes and aromatic hydrocarbons are prevalent in soils

This study was undertaken to determine the distribution of soil bacteria capable of utilizing both n-alkanes and aromatic hydrocarbons. These microorganisms have not been comprehensively investigated so far. Ten contaminated (4046-43,861 mg of total petroleum hydrocarbons (TPH) kg-1 of dry weight of soil) and five unpolluted (320-2754 mg TPH kg-1 of dry weight of soil) soil samples from temperate, arid, and Alpine soils were subjected to isolation of degraders with extended preferences and shotgun metagenomic sequencing (selected samples). The applied approach allowed to reveal that (a) these bacteria can be isolated from pristine and polluted soils, and (b) the distribution of alkane monooxygenase (alkB) and aromatic ring hydroxylating dioxygenases (ARHDs) encoding genes is not associated with the contamination presence. Some alkB and ARHD genes shared the same taxonomic affiliation; they were most often linked with the Rhodococcus, Pseudomonas, and Mycolicibacterium genera. Moreover, these taxa together with the Paeniglutamicibacter genus constituted the most numerous groups among 132 culturable strains growing in the presence of both n-alkanes and aromatic hydrocarbons. All those results indicate (a) the prevalence of the hydrocarbon degraders with extended preferences and (b) the potential of uncontaminated soil as a source of hydrocarbon degraders applied for bioremediation purposes.

Biodegradation of benzo[a]pyrene by a marine Chlorella vulgaris LH-1 with heterotrophic ability

In this study, a microalga, Chlorella vulgaris LH-1, with heterotrophic ability to degrade BaP was explored. The effect of BaP concentration on microalga growth was investigated, and the possible biodegradation mechanism of BaP was proposed. Results showed that low BaP concentration (<5 mg/L) had less negative influence on the growth of this microalga under mixotrophic condition, but high BaP concentration (>5 mg/L) had a significant inhibitory effect on its growth. During heterotrophic cultivation, low BaP concentration (<20 mg/L) promoted the growth of C. vulgaris LH-1, whereas high BaP concentration (>20 mg/L) inhibited its growth significantly. The degradation rates of mixotrophic and heterotrophic C. vulgaris LH-1 were 62.56 %-74.13 % and 52.07 %-71.67 %, respectively, when the BaP concentration ranged from 0.5 mg/L to 2 mg/L. The expression of functional enzyme genes of C. vulgaris LH-1 such as phenol 2-monooxygenase activity, protocatechuate 3,4-dioxygenase activity, catechol 1,2-dioxygenase activity, styrene degradation, and benzoate degradation were upregulated in the process of BaP degradation. C. vulgaris LH-1 may degrade BaP by monooxygenase and dioxygenase simultaneously. The degradation of BaP by this microalga under mixotrophic condition goes through the degradation pathway of phthalic acid, whereas it goes through the degradation pathway of benzoic acid under heterotrophic condition.

Bioremediation of environmental organic pollutants by Pseudomonas aeruginosa: Mechanisms, methods and challenges

The development of the chemical industry has led to a boom in daily consumption and convenience, but has also led to the release of large amounts of organic pollutants, such as petroleum hydrocarbons, plastics, pesticides, and dyes. These pollutants are often recalcitrant to degradation in the environment, whereby the most problematic compounds may even lead to carcinogenesis, teratogenesis and mutagenesis in animals and humans after accumulation in the food chain. Microbial degradation of organic pollutants is efficient and environmentally friendly, which is why it is considered an ideal method. Numerous studies have shown that Pseudomonas aeruginosa is a powerful platform for the remediation of environmental pollution with organic chemicals due to its diverse metabolic networks and its ability to secrete biosurfactants to make hydrophobic substrates more bioavailable, thereby facilitating degradation. In this paper, the mechanisms and methods of the bioremediation of environmental organic pollutants (EOPs) by P. aeruginosa are reviewed. The challenges of current studies are highlighted, and new strategies for future research are prospected. Metabolic pathways and critical enzymes must be further deciphered, which is significant for the construction of a bioremediation platform based on this powerful organism.

Taxonomic and Predictive Functional Profile of Hydrocarbonoclastic Bacterial Consortia Developed at Three Different Temperatures

Microbial community exhibit shift in composition in response to temperature variation. We report crude oil-degrading activity and high-throughput 16S rRNA gene sequencing (metagenome) profiles of four bacterial consortia enriched at three different temperatures in crude oil-amended Bushnell-Hass Medium from an oily sludge sediment. The consortia were referred to as O (4 ± 2 ℃ in 3% w/v crude oil), A (25 ± 2 ℃ in 1% w/v crude oil), H (25 ± 2 ℃ in 3% w/v crude oil), and X (45 ± 2 ℃ in 3% w/v crude oil). The hydrocarbon-degrading activity was highest for consortium A and H and lowest for consortium O. The metagenome profile revealed the predominance of Proteobacteria (62.12-1.25%) in each consortium, followed by Bacteroidota (18.94-37.77%) in the consortium O, A, and H. Contrarily, consortium X comprised 7.38% Actinomycetota, which was essentially low (< 0.09%) in other consortia, and only 0.41% Bacteroidota. The PICRUSt-based functional analysis predicted major functions associated with the metabolism and 5060 common KEGG Orthology (KOs). A total of 296 KOs were predicted exclusively in consortium X. Additionally, 247 KOs were predicted from xenobiotic biodegradation pathways. This study found that temperature had a stronger influence on the composition and function of the bacterial community than crude oil concentration.

Natural surfactant mediated bioremediation approaches for contaminated soil

The treatment of environmental pollution by employing microorganisms is a promising technology, termed bioremediation, which has several advantages over the other established conventional remediation techniques. Consequently, there is an urgent inevitability to develop pragmatic techniques for bioremediation, accompanied by the potency of detoxifying soil environments completely. The bioremediation of contaminated soils has been shown to be an alternative that could be an economically viable way to restore polluted soil. The soil environments have long been extremely polluted by a number of contaminants, like agrochemicals, polyaromatic hydrocarbons, heavy metals, emerging pollutants, etc. In order to achieve a quick remediation overcoming several difficulties the utility of biosurfactants became an excellent advancement and that is why, nowadays, the biosurfactant mediated recovery of soil is a focus of interest to the researcher of the environmental science field specifically. This review provides an outline of the present scenario of soil bioremediation by employing a microbial biosurfactant. In addition to this, a brief account of the pollutants is highlighted along with how they contaminate the soil. Finally, we address the future outlook for bioremediation technologies that can be executed with a superior efficiency to restore a polluted area, even though its practical applicability has been cultivated tremendously over the few decades.

Biodegradation of Benzo[a]pyrene by a White-Rot Fungus Phlebia acerina: Surfactant-Enhanced Degradation and Possible Genes Involved

Polycyclic aromatic hydrocarbons (PAHs) are persistent environmental pollutants that pose a threat to human health. Among these PAHs, benzo[a]pyrene (BaP), a five-ring compound, exhibits high resistance to biodegradation. White-rot fungus Phlebia acerina S-LWZ20190614-6 has demonstrated higher BaP degradation capabilities compared with Phanerochaete chrysosporium and P. sordida YK-624, achieving a degradation rate of 57.7% after 32 days of incubation under a ligninolytic condition. To further enhance the biodegradation rate, three nonionic surfactants were used, and the addition of 1 or 2 g·L-1 of polyethylene glycol monododecyl ether (Brij 30) resulted in nearly complete BaP biodegradation by P. acerina S-LWZ20190614-6. Interestingly, Brij 30 did not significantly affect the activity of manganese peroxidase and lignin peroxidase, but it did decrease laccase activity. Furthermore, the impact of cytochrome P450 on BaP degradation by P. acerina S-LWZ20190614-6 was found to be relatively mild. Transcriptomic analysis provided insights into the degradation mechanism of BaP, revealing the involvement of genes related to energy production and the synthesis of active enzymes crucial for BaP degradation. The addition of Brij 30 significantly upregulated various transferase and binding protein genes in P. acerina S-LWZ20190614-6. Hence, the bioremediation potential of BaP by the white-rot fungus P. acerina S-LWZ20190614-6 holds promise and warrants further exploration.

Microbial Consortium HJ-SH with Very High Degradation Efficiency of Phenanthrene

Phenanthrene (PHE) is one of the model compounds of polycyclic aromatic hydrocarbons (PAHs). In this study, a natural PHE-degrading microbial consortium, named HJ-SH, with very high degradation efficiency was isolated from soil exposed to long-term PHE contamination. The results of GC analysis showed that the consortium HJ-SH degraded 98% of 100 mg/L PHE in 3 days and 93% of 1000 mg/L PHE in 5 days, an efficiency higher than that of any other natural consortia, and even most of the engineered strains and consortia reported so far. Seven dominating strains were isolated from the microbial consortium HJ-SH, named SH-1 to SH-7, which were identified according to morphological observation and 16S rDNA sequencing as Pseudomonas sp., Stenotrophomonas sp., Delftia sp., Pseudomonas sp., Brevundimonas sp., Curtobacterium sp., and Microbacterium sp., respectively. Among all the seven single strains, SH-4 showed the strongest PHE degradation ability, and had the biggest degradation contribution. However, it is very interesting that the microbial consortium can hold its high degradation ability only with the co-existence of all these seven single strains. Moreover, HJ-SH exhibited a very high tolerance for PHE, up to 4.5 g/L, and it can degrade some other typical organic pollutants such as biphenyl, anthracene, and n-hexadecane with the degradation ratios of 93%, 92% and 70%, respectively, under 100 mg/L initial concentration in 5 days. Then, we constructed an artificial consortium HJ-7 consisting of the seven single strains, SH-1 to SH-7. After comparing the degradation ratios, cell growth, and relative degradation rates, it was concluded that the artificial consortium HJ-7 with easier reproducibility, better application stability, and larger room for modification can largely replace the natural consortium HJ-SH. In conclusion, this research provided novel tools and new insights for the bioremediation of PHE and other typical organic pollutants using microbial consortia.

Effects of marine diesel on microbial diversity and activity in high Arctic beach sediments

Global warming induced sea ice loss increases Arctic maritime traffic, enhancing the risk of ecosystem contamination from fuel spills and nutrient loading. The impact of marine diesel on bacterial metabolic activity and diversity, assessed by colorimetric assay, 16S rRNA and metagenomic sequencing, of Northwest Passage (Arctic Ocean) beach sediments was assessed with nutrient amendment at environmentally relevant temperatures (5 and 15 °C). Higher temperature and nutrients stimulated microbial activity, while diesel reduced it, with metabolism inhibited at and above 0.01 % (without nutrients) and at 1 % (with nutrients) diesel inclusions. Diesel exposure significantly decreased microbial diversity and selected for Psychrobacter genus. Microbial hydrocarbon degradation, organic compound metabolism, and exopolysaccharide production gene abundances increased under higher diesel concentrations. Metagenomic binning recovered nine MAGs/bins with hydrocarbon degradation genes. We demonstrate a nutrients' rescue-type effect in diesel contaminated microbial communities via enrichment of microorganisms with stress response, aromatic compound, and ammonia assimilation metabolisms.

Bioremediation of polycyclic aromatic hydrocarbons: An updated microbiological review

A class of organic priority pollutants known as PAHs is of critical public health and environmental concern due to its carcinogenic properties as well as its genotoxic, mutagenic, and cytotoxic properties. Research to eliminate PAHs from the environment has increased significantly due to awareness about their negative effects on the environment and human health. Various environmental factors, including nutrients, microorganisms present and their abundance, and the nature and chemical properties of the PAH affect the biodegradation of PAHs. A large spectrum of bacteria, fungi, and algae have ability to degrade PAHs with the biodegradation capacity of bacteria and fungi receiving the most attention. A considerable amount of research has been conducted in the last few decades on analyzing microbial communities for their genomic organization, enzymatic and biochemical properties capable of degrading PAH. While it is true that PAH degrading microorganisms offer potential for recovering damaged ecosystems in a cost-efficient way, new advances are needed to make these microbes more robust and successful at eliminating toxic chemicals. By optimizing some factors like adsorption, bioavailability and mass transfer of PAHs, microorganisms in their natural habitat could be greatly improved to biodegrade PAHs. This review aims to comprehensively discuss the latest findings and address the current wealth of knowledge in the microbial bioremediation of PAHs. Additionally, recent breakthroughs in PAH degradation are discussed in order to facilitate a broader understanding of the bioremediation of PAHs in the environment.

Medium-chain alkane biodegradation and its link to some unifying attributes of alkB genes diversity

Hydrocarbon footprints in the environment, via biosynthesis, natural seepage, anthropogenic activities and accidents, affect the ecosystem and induce a shift in the healthy biogeochemical equilibrium that drives needed ecological services. In addition, these imbalances cause human diseases and reduce animal and microorganism diversity. Microbial bioremediation, which capitalizes on functional genes, is a sustainable mitigation option for cleaning hydrocarbon-impacted environments. This review focuses on the bacterial alkB functional gene, which codes for a non-heme di‑iron monooxygenase (AlkB) with a di‑iron active site that catalyzes C₈-C₁₆ medium-chain alkane metabolism. These enzymes are ubiquitous and share common attributes such as being controlled by global transcriptional regulators, being a component of most super hydrocarbon degraders, and their distributions linked to horizontal gene transfer (HGT) events. The phylogenetic approach used in the HGT detection suggests that AlkB tree topology clusters bacteria functionally and that a preferential gradient dictates gene distribution. The alkB gene also acts as a biomarker for bioremediation, although it is found in pristine environments and absent in some hydrocarbon degraders. For instance, a quantitative molecular method has failed to link alkB copy number to contamination concentration levels. This limitation may be due to AlkB homologues, which have other functions besides n-alkane assimilation. Thus, this review, which focuses on Pseudomonas putida GPo1 alkB, shows that AlkB proteins are diverse but have some unifying trends around hydrocarbon-degrading bacteria; it is erroneous to rely on alkB detection alone as a monitoring parameter for hydrocarbon degradation, alkB gene distribution are preferentially distributed among bacteria, and the plausible explanation for AlkB affiliation to broad-spectrum metabolism of hydrocarbons in super-degraders hitherto reported. Overall, this review provides a broad perspective of the ecology of alkB-carrying bacteria and their directed biodegradation pathways.

Cell surface hydrophobicity and petroleum hydrocarbon degradation by biofilm-forming marine bacterium Pseudomonas furukawaii PPS-19 under different physicochemical stressors

Biofilm-forming marine bacterium Pseudomonas furukawaii PPS-19 showed strong hydrophobicity under different physicochemical stressors, such as pH and salinity. Strong aggregation of P. furukawaii PPS-19 was observed at hydrophobic interfaces of n-dodecane and crude oil, while uptake of pyrene resulted in blue fluorescence of the bacterium. Changes in biofilm microcolonies were observed under different physicochemical stressors with maximum biofilm thickness of 15.15 µm and 15.77 µm at pH 7% and 1% salinity, respectively. Relative expression analysis of alkB2 gene revealed the maximum expression in n-dodecane (10.5 fold) at pH 7 (1 fold) and 1% salinity (8.3 fold). During the degradation process, a significant drop in surface tension resulted in increased emulsification activity. P. furukawaii PPS-19 showed the respective n-dodecane and pyrene degradation of 94.3% and 81.5% at pH 7% and 94.5% and 83% at 1% salinity. A significant positive correlation was obtained between cell surface hydrophobicity (CSH), biofilm formation, and PHs degradation (P < 0.05) under all the physicochemical stressors, with the highest value at pH 7% and 1% salinity. Analysis of metabolites indicated that mono-terminal oxidation and multiple pathways were followed for n-dodecane and pyrene biodegradation, respectively. Thus, P. furukawaii PPS-19 is an efficient hydrocarbonoclastic bacterium that may be exploited for large-scale oil pollution abatement.

Microbial degradation of petroleum characteristic pollutants in hypersaline environment, emphasizing n-hexadecane and 2,4 di-tert-butylphenol

In this paper, nine strains of salt-tolerant petroleum-degrading bacteria were applied to an biological aerated filter. Simulating the degradation of high-salinity petroleum wastewater with n-hexadecane and 2,4-ditert-butylphenol as the primary pollutants and analyzing the structure of the biofilm at various salt concentrations. According to the results, when the salinity was 4%, the COD removal efficiency reached 74.34%. Various halotolerant microorganisms have adapted to various salt concentrations. At a salinity of 3%, n-hexadecane exhibited the best degradation effect, with a rate of 83.21%. Shewanella, Acinetobacter, and Marinobacter were the predominant bacterial groups at the time. At 4% salinity, Acinetobacter and Pseudomonas were the predominant bacteria, and the average 2,4-ditert-butylphenol degradation rate was the highest at 63.02%. This study provided an experimental basis for further studying the biological treatment of high-salinity petroleum wastewater.

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.

Catalytic resilience of multicomponent aromatic ring-hydroxylating dioxygenases in Pseudomonas for degradation of polycyclic aromatic hydrocarbons

Hydrophobic organic compounds, either natural or introduced through anthropogenic activities, pose a serious threat to all spheres of life, including humankind. These hydrophobic compounds are recalcitrant and difficult to degrade by the microbial system; however, microbes have also evolved their metabolic and degradative potential. Pseudomonas species have been reported to have a multipotential role in the biodegradation of aromatic hydrocarbons through aromatic ring-hydroxylating dioxygenases (ARHDs). The structural complexity of different hydrophobic substrates and their chemically inert nature demands the explicit role of evolutionary conserved multicomponent enzyme ARHDs. These enzymes catalyze ring activation and subsequent oxidation by adding two molecular oxygen atoms onto the vicinal carbon of the aromatic nucleus. This critical metabolic step in the aerobic mode of degradation of polycyclic aromatic hydrocarbons (PAHs) catalyzed by ARHDs can also be explored through protein molecular docking studies. Protein data analysis enables an understanding of molecular processes and monitoring complex biodegradation reactions. This review summarizes the molecular characterization of five ARHDs from Pseudomonas species already reported for PAH degradation. Homology modeling for the amino acid sequences encoding the catalytic α-subunit of ARHDs and their docking analyses with PAHs suggested that the enzyme active sites show flexibility around the catalytic pocket for binding of low molecular weight (LMW) and high molecular weight (HMW) PAH substrates (naphthalene, phenanthrene, pyrene, benzo[α]pyrene). The alpha subunit harbours variable catalytic pockets and broader channels, allowing relaxed enzyme specificity toward PAHs. ARHD's ability to accommodate different LMW and HMW PAHs demonstrates its 'plasticity', meeting the catabolic demand of the PAH degraders.

Biodegradation of benzo(a)pyrene by Pseudomonas strains, isolated from petroleum refinery effluent: Degradation, inhibition kinetics and metabolic pathway

Benzo(a)pyrene, a five-ring polyaromatic hydrocarbon, originating from coal tar, crude oil, tobacco, grilled foods, car exhaust etc, is highly persistent in the environment. It has been classified as a Group I carcinogen, as on its ingestion in human body, diol epoxide metabolites are generated, which bind to DNA causing mutations and eventual cancer. Among various removal methods, bioremediation is most preferred as it is a sustainable approach resulting in complete mineralization of benzo(a)pyrene. Therefore, in this study, biodegradation of benzo(a)pyrene was performed by two strains of Pseudomonas, i. e WDE11 and WD23, isolated from refinery effluent. Maximum benzo(a)pyrene tolerance was 250 mg/L and 225 mg/L against Pseudomonas sp. WD23 and Pseudomonas sp. WDE11 correspondingly. Degradation rate constants varied between 0.0468 and 0.0513/day at 50 mg/L with half-life values between 13.5 and 14.3 days as per first order kinetics, while for 100 mg/L, the respective values varied between 0.006 and 0.007 L/mg. day and 15.28-16.67 days, as per second order kinetics. The maximum specific growth rate of strains WDE11 and WD23 was 0.3512/day and 0.38/day accordingly, while concentrations over 75 mg/L had an inhibitory effect on growth. Major degradation metabolites were identified as dihydroxy-pyrene, naphthalene-1,2-dicarboxylic acid, salicylic acid, and oxalic acid, indicating benzo(a)pyrene was degraded via pyrene intermediates by salicylate pathway through catechol meta-cleavage. The substantial activity of the catechol 2,3 dioxygenase enzyme was noted during the benzo(a)pyrene metabolism by both strains with minimal catechol 1,2 dioxygenase activity. This study demonstrates the exceptional potential of indigenous Pseudomonas strains in complete metabolism of benzo(a)pyrene.

The role of microorganisms in petroleum degradation: Current development and prospects

Petroleum hydrocarbon compounds are persistent organic pollutants, which can cause permanent damage to ecosystems due to their biomagnification. Bioremediation of oil is currently the main solution for the remediation of petroleum hydrocarbon pollutants in ecosystems. Despite several lab studies on oil microbial biodegradation efficiency, still there are various challenges for microorganisms to perform efficiently in outside environments. Herewith, investigating efficient biodegradation technologies through discovering new microorganisms, biodegradation pathways modification, and new bioremediations technologies are in great demand. The degradation of petroleum pollutants by microorganisms and the remediation of contaminated soils are achieved through their key enzymes and metabolic pathways. Although, several challenges hinder the effective biodegradation processes such as the toxic environment, long chains and versatility of petroleum hydrocarbons and the existence of the full metabolism pathways in a single microorganism. There are several developed oil biodegradation strategies by microorganisms such as synthetic biology, biofilm, recombinant technology and microbial consortia. Herewith, the application of multi-omics technology to discover oil-contaminated environments microbial communities, synthetic biology, microbial consortia, and other technologies would help improve the efficiency of microbial remediation.

A comprehensive proteomics analysis of the response of Pseudomonas aeruginosa to nanoceria cytotoxicity

The increased commercial use and spread of nanoceria raises concerns about the risks associated with its effects on living organisms. Although Pseudomonas aeruginosa may be ubiquitous in nature, it is largely found in locations closely linked with human activity. P. aeruginosa san ai was used as a model organism for a deeper understanding of the interaction between biomolecules of the bacteria with this intriguing nanomaterial. A comprehensive proteomics approach along with analysis of altered respiration and production of targeted/specific secondary metabolites was conducted to study the response of P. aeruginosa san ai to nanoceria. Quantitative proteomics found that proteins associated with redox homeostasis, biosynthesis of amino acids, and lipid catabolism were upregulated. Proteins from outer cellular structures were downregulated, including transporters responsible for peptides, sugars, amino acids and polyamines, and the crucial TolB protein of the Tol-Pal system, required for the structural formation of the outer membrane layer. In accordance with the altered redox homeostasis proteins, an increased amount of pyocyanin, a key redox shuttle, and the upregulation of the siderophore, pyoverdine, responsible for iron homeostasis, were found. Production of extracellular molecules, e.g. pyocyanin, pyoverdine, exopolysaccharides, lipase, and alkaline protease, was significantly increased in P. aeruginosa san ai exposed to nanoceria. Overall, nanoceria at sublethal concentrations induces profound metabolic changes in P. aeruginosa san ai and provokes increased secretion of extracellular virulence factors, revealing the powerful influence this nanomaterial has on the vital functions of the microorganism.

Petroleum Hydrocarbon Catabolic Pathways as Targets for Metabolic Engineering Strategies for Enhanced Bioremediation of Crude-Oil-Contaminated Environments

Anthropogenic activities and industrial effluents are the major sources of petroleum hydrocarbon contamination in different environments. Microbe-based remediation techniques are known to be effective, inexpensive, and environmentally safe. In this review, the metabolic-target-specific pathway engineering processes used for improving the bioremediation of hydrocarbon-contaminated environments have been described. The microbiomes are characterised using environmental genomics approaches that can provide a means to determine the unique structural, functional, and metabolic pathways used by the microbial community for the degradation of contaminants. The bacterial metabolism of aromatic hydrocarbons has been explained via peripheral pathways by the catabolic actions of enzymes, such as dehydrogenases, hydrolases, oxygenases, and isomerases. We proposed that by using microbiome engineering techniques, specific pathways in an environment can be detected and manipulated as targets. Using the combination of metabolic engineering with synthetic biology, systemic biology, and evolutionary engineering approaches, highly efficient microbial strains may be utilised to facilitate the target-dependent bioprocessing and degradation of petroleum hydrocarbons. Moreover, the use of CRISPR-cas and genetic engineering methods for editing metabolic genes and modifying degradation pathways leads to the selection of recombinants that have improved degradation abilities. The idea of growing metabolically engineered microbial communities, which play a crucial role in breaking down a range of pollutants, has also been explained. However, the limitations of the in-situ implementation of genetically modified organisms pose a challenge that needs to be addressed in future research.

Mechanisms of biostimulant-enhanced biodegradation of PAHs and BTEX mixed contaminants in soil by native microbial consortium

Despite the co-occurrence of polycyclic aromatic hydrocarbons (PAHs) and benzene, toluene, ethylbenzene, and xylene (BTEX) in the field, to date, knowledge on the bioremediation of benzene and benzo[a]pyrene (BaP) mixed contaminants is limited. In this study, the mechanisms underlying the biodegradation of benzene and BaP under individual and co-contaminated conditions followed by the enhanced biodegradation using methanol, ethanol, and vegetable oil as biostimulants were investigated. The results demonstrated that the benzene biodegradation was highly reduced under the co-contaminated condition compared to the individual benzene contamination, whereas the BaP biodegradation was slightly enhanced with the co-contamination of benzene. Moreover, biostimulation significantly improved the biodegradation of both contaminants under co-contaminated conditions. A trend of significant reduction in the bioavailable BaP contents was observed in all biostimulant-enhanced groups, implying that the bioavailable BaP was the preferred biodegradable BaP fraction. Furthermore, the enzymatic activity analysis revealed a significant increase in lipase and dehydrogenase (DHA) activities, as well as a reduction in the catalase and polyphenol oxidase, suggesting that the increased hydrolysis of fats and proton transfer, as well as the reduced oxidative stress, contributed to the enhanced benzene and BaP biodegradation in the vegetable oil treatment. In addition, the microbial composition analysis results demonstrated that the enriched functional genera contributed to the increased biodegradation efficiency, and the functional genera in the microbial consortium responded differently to different biostimulants, and competitive growth was observed in the biostimulant-enhanced treatments. In addition, the enrichment of Pseudomonas and Rhodococcus species was noticed during the biostimulation of benzene and BaP co-contamination soil, and was positively correlated with the DHA enzyme activities, indicating that these species encode DHA genes which contributed to the higher biodegradation. In conclusion, multiple lines of evidence were provided to shed light on the mechanisms of biostimulant-enhanced biodegradation of PAHs and BTEX co-contamination with native microbial consortiums.

Isolation and characterization of crude-oil-dependent bacteria from the coast of Ghana using oxford nanopore sequencing

The utilization and improper use of crude oil can have irreparable damage on the environment and human populations. This study sought to isolate hydrocarbon utilizing bacteria from 1% v/v pristine seawater and 1% v/v crude oil using enrichment culture techniques. Whole genome sequencing of DNA using the Oxford Nanopore sequencing technique with Fastq WIMP as the workflow at 3% abundance was undertaken. The results showed that the most abundant isolates identified using this technique at specific sampling sites were, Acinetobacter junii (51.9%), Alcanivarax pacificus (15.8%), Acinetobacter haemolyticus (21.6%), Pseudomonas aeruginosa (23.4%), Alcanivorax xenomutans (24.7%), Alcanivorax xenomutans (23.0%) Acinetobacter baumannii (40.0%) and Acinetobacter junii (14.2%). Cumulatively, the most abundant isolates in the 8 sampling sites were Acinetobacter junii (17.91%), Alcanivorax xenomutans (11.68%), Pseudomonas aeruginosa (7.68%), Escherichia coli (7.67%), Acinetobacter haemolyticus (3.40%), and Alkanivorax pacificus (3.10%). Spearman's rank correlation analysis to examine the strength of relationship between the physicochemical parameters and type of bacteria isolated, revealed that salinity (0.8046) and pH (0.7252) were the highest. Isolated bacteria from pristine seawater, especially Escherichia coli have shown their capacity for bioremediating oil spill pollution in oceanic environments in Ghana.

Potential Utilization of Bacterial Consortium of Symbionts Marine Sponges in Removing Polyaromatic Hydrocarbons and Heavy Metals, Review

Toxic materials in waste generally contain several components of the global trending pollutant category, especially PAHs and heavy metals. Bioremediation technology for waste management that utilizes microorganisms (bacteria) has not been fully capable of breaking down these toxic materials into simple and environmentally friendly chemical products. This review paper examines the potential application of a consortium of marine sponge symbionts with high performance and efficiency in removing PAHs and heavy metal contaminants. The method was carried out through a review of several related research articles by the author and published by other researchers. The results of the study conclude that the development of global trending pollutant (GTP) bioremediation technology could be carried out to increase the efficiency of remediation. Several types of marine sponge symbiont bacteria, hydrocarbonoclastic (R-1), metalloclastic (R-2), and metallo-hydro-carbonoclastic (R-3), have the potential to be applied to improve waste removal performance. A consortium of crystalline bacterial preparations is required to mobilize into GTP-exposed sites rapidly. Bacterial symbionts of marine sponges can be traced mainly to sea sponges, whose body surface is covered with mucus.

Characterization of biosurfactant produced in response to petroleum crude oil stress by Bacillus sp. WD22 in marine environment

Bacillus sp. WD22, previously isolated from refinery effluent, degraded 71% of C8 hydrocarbons present in 1.0% v/v PCO in seawater (control medium), which reduced to 16.3%, on addition of yeast extract. The bacteria produced a biosurfactant in both media, whose surface was observed to be amorphous in nature under FESEM-EDAX analysis. The biosurfactant was characterized as a linear surfactin by LCMS and FT-IR analysis. The critical micelle concentration was observed as 50 mg/L and 60 mg/L at which the surface tension of water was reduced to 30 mN/m. Purified biosurfactant could emulsify petroleum-based oils and vegetable oils effectively and was stable at all tested conditions of pH, salinity and temperature up to 80 °C. The biosurfactant production was found to be mixed growth associated in control medium, while it was strictly growth associated in medium with yeast extract as studied by the Leudeking-Piret model.

Biodegradation kinetics and metabolism of Benzo(a)fluorene by Pseudomonas strains isolated from refinery effluent

The final sinkers of polyaromatic hydrocarbons are water sources, where they undergo bioaccumulation and biomagnification, leading to adverse mutagenic, carcinogenic, and teratogenic effects on exposure in flora, fauna, and humans. Two indigenous strains, Pseudomonas sp. WDE11 and Pseudomonas sp. WD23, isolated from refinery effluent, degraded over 97.5% of benzo(a)fluorene (10 mg/L) in 7 days. On growth at concentration dependent amounts (50 mg/L and 100 mg/L), the degradation reduced to approximately 90% and 80% respectively in 56 days. Degradation kinetics was concentration dependent, as degradation followed first-order and second-order kinetics for 50 mg/L and 100 mg/L respectively. The half-life for degradation of benzo(a)fluorene ranged between 11.64 - 12.26 days and 13.11-14.5 days for strains WDE11 and WD23 respectively. The values of Andrew-Haldane kinetic parameters i.e. μ_max, K_s, and K_i were 0.306 day^-1, 11.11 mg/L, and 120.41 mg/L for strain WDE11 respectively, while for strain WD23, the respective values were 0.312 day^-1, 9.97 mg/L, and 152 mg/L. Degradation metabolites were identified by their MS patterns as 3,4-dihydroxy fluorene, 2-(1-oxo-2,3-dihydro-1H-inden-2-yl) acetic acid, 3,4-dihydrocoumarin, salicylic acid, catechol, and oxalic acid. Metabolic pathway of degradation constructed, revealed that benzo(a)fluorene was metabolized via the formation of fluorene, further metabolized by salicylate pathway forming catechol. The catechol formed was degraded into simpler metabolites by meta-cleavage pathway, which was validated by catechol 2,3 dioxygenase enzyme activity.

Bacterial Communities Associated with Crude Oil Bioremediation through Composting Approaches with Indigenous Bacterial Isolate

In this study, we aim to investigate the efficiency of crude oil bioremediation through composting and culture-assisted composting. First, forty-eight bacteria were isolated from a crude oil-contaminated soil, and the isolate with the highest crude oil degradation activity, identified as Pseudomonas aeruginosa, was selected. The bioremediation was then investigated and compared between crude oil-contaminated soil (S), the contaminated soil composted with fruit-based waste (SW), and the contaminated soil composted with the same waste with the addition of the selected bacterium (SWB). Both compost-based methods showed high efficiencies of crude oil bioremediation (78.1% and 83.84% for SW and SWB, respectively). However, only a slight difference between the treatments without and with the addition of P. aeruginosa was observed. To make a clear understanding of this point, bacterial communities throughout the 4-week bioremediation period were analyzed. It was found that the community dynamics between both composted treatments were similar, which corresponds with their similar bioremediation efficiencies. Interestingly, Pseudomonas disappeared from the system after one week, which suggests that this genus was not the key degrader or only involved in the early stage of the process. Altogether, our results elaborate that fruit-based composting is an effective approach for crude oil bioremediation.

Biotreatment of oily sludge by a bacterial consortium: Effect of bioprocess conditions on biodegradation efficiency and bacterial community structure

We studied the biodegradation of oily sludge generated by a petroleum plant in Bahrain by a bacterial consortium (termed as AK6) under different bioprocess conditions. Biodegradation of petroleum hydrocarbons in oily sludge (C₁₁-C₂₉) increased from 24% after two days to 99% after 9 days of incubation in cultures containing 5% (w/v) of oily sludge at 40°C. When the nitrogen source was excluded from the batch cultures, hydrocarbon biodegradation dropped to 45% within 7 days. The hydrocarbon biodegradation decreased also by increasing the salinity to 3% and the temperature above 40°C. AK6 tolerated up to 50% (w/v) oily sludge and degraded 60% of the dichloromethane-extractable oil fraction. Illumina-MiSeq analyses revealed that the AK6 consortium was mainly composed of Gammaproteobacteria (ca. 98% of total sequences), with most sequences belonging to Klebsiella (77.6% of total sequences), Enterobacter (16.7%) and Salmonella (5%). Prominent shifts in the bacterial composition of the consortium were observed when the temperature and initial sludge concentration increased, and the nitrogen source was excluded, favoring sequences belonging to Pseudomonas and Stenotrophomonas. The AK6 consortium is endowed with a strong oily sludge tolerance and biodegradation capability under different bioprocess conditions, where Pseudomonas spp. appear to be crucial for hydrocarbon biodegradation.

Pseudomonas in environmental bioremediation of hydrocarbons and phenolic compounds- key catabolic degradation enzymes and new analytical platforms for comprehensive investigation

Pollution of the environment with petroleum hydrocarbons and phenolic compounds is one of the biggest problems in the age of industrialization and high technology. Species of the genus Pseudomonas, present in almost all hydrocarbon-contaminated areas, play a particular role in biodegradation of these xenobiotics, as the genus has the potential to decompose various hydrocarbons and phenolic compounds, using them as its only source of carbon. Plasticity of carbon metabolism is one of the adaptive strategies used by Pseudomonas to survive exposure to toxic organic compounds, so a good knowledge of its mechanisms of degradation enables the development of new strategies for the treatment of pollutants in the environment. The capacity of microorganisms to metabolize aromatic compounds has contributed to the evolutionally conserved oxygenases. Regardless of the differences in structure and complexity between mono- and polycyclic aromatic hydrocarbons, all these compounds are thermodynamically stable and chemically inert, so for their decomposition, ring activation by oxygenases is crucial. Genus Pseudomonas uses several upper and lower metabolic pathways to transform and degrade hydrocarbons, phenolic compounds, and petroleum hydrocarbons. Data obtained from newly developed omics analytical platforms have enormous potential not only to facilitate our understanding of processes at the molecular level but also enable us to instigate and monitor complex biodegradations by Pseudomonas. Biotechnological application of aromatic metabolic pathways in Pseudomonas to bioremediation of environments polluted with crude oil, biovalorization of lignin for production of bioplastics, biofuel, and bio-based chemicals, as well as Pseudomonas-assisted phytoremediation are also considered.

Polycyclic Aromatic Hydrocarbon Degradation in the Sea-Surface Microlayer at Coastal Antarctica

As much as 400 Tg of carbon from airborne semivolatile aromatic hydrocarbons is deposited to the oceans every year, the largest identified source of anthropogenic organic carbon to the ocean. Microbial degradation is a key sink of these pollutants in surface waters, but has received little attention in polar environments. We have challenged Antarctic microbial communities from the sea-surface microlayer (SML) and the subsurface layer (SSL) with polycyclic aromatic hydrocarbons (PAHs) at environmentally relevant concentrations. PAH degradation rates and the microbial responses at both taxonomical and functional levels were assessed. Evidence for faster removal rates was observed in the SML, with rates 2.6-fold higher than in the SSL. In the SML, the highest removal rates were observed for the more hydrophobic and particle-bound PAHs. After 24 h of PAHs exposure, particle-associated bacteria in the SML showed the highest number of significant changes in their composition. These included significant enrichments of several hydrocarbonoclastic bacteria, especially the fast-growing genera Pseudoalteromonas, which increased their relative abundances by eightfold. Simultaneous metatranscriptomic analysis showed that the free-living fraction of SML was the most active fraction, especially for members of the order Alteromonadales, which includes Pseudoalteromonas. Their key role in PAHs biodegradation in polar environments should be elucidated in further studies. This study highlights the relevant role of bacterial populations inhabiting the sea-surface microlayer, especially the particle-associated habitat, as relevant bioreactors for the removal of aromatic hydrocarbons in the oceans.

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.

Short-Term Biodegradation of Crude Petroleum Oil in Water by Photostimulated Janibacter terrae Strain S1N1

Biodegradation is a sustainable green strategy that gives the opportunity for remediation of water contaminated with petroleum products. In this study, 12 bacterial isolates were recovered from River Nile, Egypt and screened for their potential to degrade a mixture of paraffinic petroleum crude oil. The most promising isolate was identified according to 16S rRNA sequencing as Janibacter terrae strain S1N1 (GenBank accession No. KX570955.1). In order to boost the biodegradation efficiency, the bacterial suspension was photostimulated by exposure to different irradiation doses using a low-power helium-neon (He-Ne) laser (λ = 632.8 nm). Maximum biodegradation was achieved after 4 min of exposure (134.07 J cm^-2) at optimized pH value (6) and temperature (35 °C). The gas chromatography-mass spectrometry (GC-MS) analysis revealed the biodegradation of 96.5% of the substrate after only 48 h of incubation. The n-C₁₇/Pr and n-C₁₈/Ph ratios indicated a preferential biodegradation of iso-paraffines over normal ones. Meanwhile, pristane/phytane (Pr/Ph) ratios were indicative of selective biodegradation for pristane. The carbon preference index (CPI) was nearly around unity indicating the ability of Janibacter terrae to attack the odd and even n-alkanes simultaneously. These results support the superiority of irradiated bacteria in optimizing the biodegradation efficiency and shortening the time of treatment, thus proposing an eco-friendly technique in water bioremediation programs.

Significance of both alkB and P450 alkane-degrading systems in Tsukamurella tyrosinosolvens: proteomic evidence

The Tsukamurella tyrosinosolvens PS2 strain was isolated from hydrocarbons-contaminated petrochemical sludge as a long chain alkane-utilizing bacteria. Complete genome analysis showed the presence of two alkane oxidation systems: alkane 1-monooxygenase (alkB) and cytochrome P450 monooxygenase (P450) genes with established high homology to the well-known alkane-degrading actinobacteria. According to the comparative genome analysis, both systems have a wide distribution among environmental and clinical isolates of the genus Tsukamurella and other members of Actinobacteria. We compared the expression of different proteins during the growth of Tsukamurella on sucrose and on hexadecane. Both alkane monooxygenases were upregulated on hexadecane: AlkB-up to 2.5 times, P450-up to 276 times. All proteins of the hexadecane oxidation pathway to acetyl-CoA were also upregulated. Accompanying proteins for alkane degradation involved in biosurfactant synthesis and transport of organic and inorganic molecules were increased. The change in the carbon source affected the pathways for the regulation of translation and transcription. The proteomic profile showed that hexadecane is an adverse factor causing activation of general and universal stress proteins as well as shock and resistance proteins. Differently expressed proteins of Tsukamurella tyrosinosolvens PS2 shed light on the alkane degradation in other members of Actinobacteria class. KEY POINTS: • alkB and P450 systems have a wide distribution among the genus Tsukamurella. • alkB and P450 systems have coexpression with the predominant role of P450 protein. • Hexadecane causes significant changes in bacterial proteome.

Current research on simultaneous oxidation of aliphatic and aromatic hydrocarbons by bacteria of genus Pseudomonas

One of the most frequently used methods for elimination of oil pollution is the use of biological preparations based on oil-degrading microorganisms. Such microorganisms often relate to bacteria of the genus Pseudomonas. Pseudomonads are ubiquitous microorganisms that often have the ability to oxidize various pollutants, including oil hydrocarbons. To date, individual biochemical pathways of hydrocarbon degradation and the organization of the corresponding genes have been studied in detail. Almost all studies of this kind have been performed on degraders of individual hydrocarbons belonging to a single particular class. Microorganisms capable of simultaneous degradation of aliphatic and aromatic hydrocarbons are very poorly studied. Most of the works on such objects have been devoted only to phenotype characteristic and some to genetic studies. To identify the patterns of interaction of several metabolic systems depending on the growth conditions, the most promising are such approaches as transcriptomics and proteomics, which make it possible to obtain a comprehensive assessment of changes in the expression of hundreds of genes and proteins at the same time. This review summarizes the existing data on bacteria of the genus Pseudomonas capable of the simultaneous oxidation of hydrocarbons of different classes (alkanes, monoaromatics, and polyaromatics) and presents the most important results obtained in the studies on the biodegradation of hydrocarbons by representatives of this genus using methods of transcriptomic and proteomic analyses.

A study of the flexibility of the carbon catabolic pathways of extremophilic P. aeruginosa san ai exposed to benzoate versus glucose as sole carbon sources by multi omics analytical platform

Polyextremophilic, hydrocarbonoclastic Pseudomonas aeruginosa san ai can survive under extreme environmental challenges in the presence of a variety of pollutants such as organic solvents and hydrocarbons, particularly aromatics, heavy metals, and high pH. To date, the metabolic plasticity of the extremophilic P. aeruginosa, has not been sufficiently studied in regard to the effect of changing carbon sources. Therefore, the present study explores the carbon metabolic pathways of polyextremophilic P. aeruginosa san ai grown on sodium benzoate versus glucose and its potential for aromatic degradation. P. aeruginosa san ai removed/metabolised nearly 430 mg/L of benzoate for 48 h, demonstrating a high capacity for aromatic degradation. Comparative functional proteomics, targeted metabolomics and genomics analytical approaches were employed to study the carbon metabolism of the P. aeruginosa san ai. Functional proteomic study of selected enzymes participating in the β-ketoadipate and the Entner-Doudoroff pathways revealed a metabolic reconfiguration induced by benzoate compared to glucose. Metabolome analysis implied the existence of both catechol and protocatechuate branches of the β-ketoadipate pathway. Enzymatic study of benzoate grown cultures confirmed the activity of the ortho- catechol branch of the β-ketoadipate pathway. Even high concentrations of benzoate did not show increased stress protein synthesis, testifying to its extremophilic nature capable of surviving in harsh conditions. This ability of Pseudomonas aeruginosa san ai to efficiently degrade benzoate can provide a wide range of use of this strain in environmental and agricultural application.

Biotransformation of nitro aromatic amines in artificial alkaline habitat by pseudomonas DL17

Nitro-aromatics are listed in carcinogenic, teratogenic, and mutagenic compounds list. p-nitro-aniline is one of them used as a precursor of various chemical compounds in many industries like dyes, drugs, paints and several others. These are mostly given out as an effluent in rivers, lakes or open passage of land which exert several hazards to living creatures and environment. Some of the organic compounds are stable in alkaline condition and persist longer in environment. Very few reports are elaborating bio-remediation in alkaline condition using different hydrocarbons. This study was planned to elaborate mechanism of detoxification and searching the potential of decontamination of p-nitro-aniline in alkaline condition by experimental microbial strain. The bacterial strain pseudomonas DL17 was isolated from alkaline Lake Lonar, Buldana, (MS.) India; and employed in this experiment considering its indigenous property to tolerate the alkaline pH. It also showed resistance to p-nitro-aniline with its raising concentrations on testing after adaptation. The experimental microbial stain showed 100% biodegradation of (500 mg/L) p-nitro-aniline within 48h. On shaking incubator with 110 rpm and at 32 °C optimum temperature. The centrifugate obtained after spinning at 10,000 g by cold centrifuge was used for solvent extraction. Generally, ethyl acetate or DCM was used for solvent extraction. The estimation of residual remains of p-nitro aniline by 6h. intervals was carried after removal of flasks from shaking incubator and centrifugation. At the optimum temperature and pH experiments were carried after knowing the resistance to experimental contaminant range (100–400 mg/L) of p-nitro aniline one month and further extended to 500 mg/L for 15days more.

The residual metabolites were purified by column chromatography and various spectrometric studies such as UV-Vis spectroscopy, HNMR, FTIR and GCMS revealed that p-Phenylenediamine, acetanilide, aniline, acetaminophen, catechol, p-bezoquinone, cis-cis muconate as a metabolites. On the basis of the metabolites isolated and characterized by different spectroscopic studies the bio-catalytic mechanism was deduced. The induced enzymes such as nitroreductase, catalase, peroxidase, acetanilide hydroxylase, super oxide dismutase, catechol 1, 2 dioxygenase, catechol 2, 3 dioxygenase has commercial importance in biochemical industries. Induction of such biotransformation enzymes and consumption of p-nitro aniline concentration in experiments makes sure that this microbial strain pseudomonas DL17 can be employed for decontamination of nitro aniline polluted sites as well as isolation of such metabolites characterized and enzymes studied.

Characterization of bacterial community in oil-contaminated soil and its biodegradation efficiency of high molecular weight (>C40) hydrocarbon

In this study, two biosurfactant producing Pseudomonas aeruginosa sp. were isolated from motor oil contaminated soil for crude oil, alkane and PAH degradation studies. Metagenomics analysis identified as proteobacteria phyla was the dominant. Isolated two bacterial species were well grown in mineral salt medium with 1% of crude oil, alkanes (dotriacontane and tetratetracontane) and PAH (pyrene, benzopyrene and anthracene) as sole carbon sources. Total biodegradation efficiency (BE) of strains PP3 and PP4 in Crude oil degradation evaluated by the analysis of gas chromatography and mass spectrometry was 50% and 86% respectively. BE of PP3, PP4 and mixed consortium in alkane biodegradation were 46%, 47% and 36%, respectively. BE of PP3, PP4 and mixed consortium in PAH biodegradation were 22%, 48% and 35%, respectively. Based on the results revealed that strain pp4 was more efficient bacteria to degrade the crude oil, alkane and PAH than pp3. This was due to the higher production of biosurfactant by PP4 than PP3 and also confirmed in the test of emulsification index (E₂₄). FTIR results showed that the produced biosurfactant could partially solubilize the crude oil hydrocarbons, alkanes and PAH and confirmed as glycolipid (rhamnolipid) in nature. Thus, the obtained results from the GCMS showed that all hydrocarbons were utilized by bacteria as carbon source for biosurfactant production and utilize the high molecular weight hydrocarbons. Based on the present study we can suggest that identified potential biosurfactant producing bacteria are used for biodegradation of high molecular weight hydrocarbon (>C40).

Anthracene and Pyrene Biodegradation Performance of Marine Sponge Symbiont Bacteria Consortium

Every petroleum-processing plant produces sewage sludge containing several types of polycyclic aromatic hydrocarbons (PAHs). The degradation of PAHs via physical, biological, and chemical methods is not yet efficient. Among biological methods, the use of marine sponge symbiont bacteria is considered an alternative and promising approach in the degradation of and reduction in PAHs. This study aimed to explore the potential performance of a consortium of sponge symbiont bacteria in degrading anthracene and pyrene. Three bacterial species (Bacillus pumilus strain GLB197, Pseudomonas stutzeri strain SLG510A3-8, and Acinetobacter calcoaceticus strain SLCDA 976) were mixed to form the consortium. The interaction between the bacterial consortium suspension and PAH components was measured at 5 day intervals for 25 days. The biodegradation performance of bacteria on PAH samples was determined on the basis of five biodegradation parameters. The analysis results showed a decrease in the concentration of anthracene (21.89%) and pyrene (7.71%), equivalent to a ratio of 3:1, followed by a decrease in the abundance of anthracene (60.30%) and pyrene (27.52%), equivalent to a ratio of 2:1. The level of pyrene degradation was lower than that of the anthracene due to fact that pyrene is more toxic and has a more stable molecular structure, which hinders its metabolism by bacterial cells. The products from the biodegradation of the two PAHs are alcohols, aldehydes, carboxylic acids, and a small proportion of aromatic hydrocarbon components.

Efficiency and kinetics of Assam crude oil degradation by Pseudomonas aeruginosa and Bacillus sp

We report kinetics of Assam crude oil degradation by Pseudomonas aeruginosa AKS1 and Bacillus sp. AKS2, both isolated from Assam refinery sediments. The isolates exhibited appreciable degrees of hydrophobicity, emulsification index and biosurfactant production. Crude oil degradation efficiency of isolates was assessed in (1) liquid medium amended with 1% v/v crude oil and (2) microcosm sediments (125 mg crude oil/ 10 g sand). In liquid culture, biodegradation rate (k) and half-life (t_1/2) values were found to be 0.038 day^-1 and 18.09 days for P. aeruginosa AKS1, and 0.020 day^-1 and 33.97 days in case of Bacillus sp. AKS2, respectively. In microcosm sediments, the estimated k and t _1/2 values were 0.014 day^-1 and 50 days for P. aeruginosa AKS1, and 0.011 day^-1 and 61.34 days in case of Bacillus sp. AKS2. The level of nutrient treatment in microcosm sand sediment was 125 µg N and 62.5 µg P/g sediment in case of P. aeruginosa AKS1 and 375 µg N and 37.5 µg P/g sediment in case of Bacillus sp. AKS2. In microcosms without inorganic nutrients, values of k and t_1/2 were found to be 0.007 day^-1 and 100 days for P. aeruginosa AKS1 and for Bacillus sp. AKS2, the respective values were 0.005 day^-1 and 150.68 days. Our data provides important information for predictive hydrocarbon degradation in liquid medium and contaminated sediments.

Application of integrated extremophilic (halo-alkalo-thermophilic) bacterial consortium in the degradation of petroleum hydrocarbons and treatment of petroleum refinery wastewater under extreme condition

Degradation of petroleum hydrocarbon under extreme conditions such as high salinity, temperature and pH was difficult due to unavailability of potential bacterial strains. The present study details the efficiency of extremophilic bacterial consortium in biodegradation of different petroleum hydrocarbons and treatment of petroleum refinery wastewater under extreme condition. Extreme condition for the degradation of petroleum hydrocarbons was optimized at 8% salinity, pH-10 and temperature-60 °C. The consortium recorded complete degradation of low molecular weight (LMW) petroleum hydrocarbons (200 ppm) such as anthracene, phenanthrene, fluorene and naphthalene in 8 days under optimized extreme condition. High molecular weight (HMW) hydrocarbons such as pyrene (100 ppm), benzo(e)pyrene (20 ppm), benzo(k)fluoranthene (20 ppm) and benzo(a)pyrene (20 ppm), revealed 93%, 60%, 55% and 51% degradation by the extremophilic consortium under optimized extreme condition. The extremophilic consortium mineralized fluorene (61%) at high saline condition up to 24%. Addition of yeast extract potently accelerated the biodegradation under extreme condition. Treatment of petroleum refinery wastewater in continuous stirred tank reactor recorded 92% COD removal with complete removal of LMW hydrocarbons in 16 days and 91% of HMW hydrocarbons in 32 days under extreme condition. The hydrocarbons degrading extremophilic consortium possessed Ochrobactrum, Bacillus, Marinobacter, Pseudomonas, Martelella, Stenotrophomonas and Rhodococcus.