Microbial Degradation of Hydrocarbons-Basic Principles for Bioremediation: A Review

Functional and structural responses of a halophilic consortium to oily sludge during biodegradation

Biotreatment of oily sludge and the involved microbial communities, particularly in saline environments, have been rarely investigated. We enriched a halophilic bacterial consortium (OS-100) from petroleum refining oily sludge, which degraded almost 86% of the aliphatic hydrocarbon (C10-C30) fraction of the oily sludge within 7 days in the presence of 100 g/L NaCl. Two halophilic hydrocarbon-degrading bacteria related to the genera Chromohalobacter and Halomonas were isolated from the OS-100 consortium. Hydrocarbon degradation by the OS-100 consortium was relatively higher compared to the isolated bacteria, indicating potential synergistic interactions among the OS-100 community members. Exclusion of FeCl2, MgCl2, CaCl2, trace elements, and vitamins from the culture medium did not significantly affect the hydrocarbon degradation efficiency of the OS-100 consortium. To the contrary, hydrocarbon biodegradation dropped from 94.1 to 54.4% and 5% when the OS-100 consortium was deprived from phosphate and nitrogen sources in the culture medium, respectively. Quantitative PCR revealed that alkB gene expression increased up to the 3rd day of incubation with 11.277-fold, consistent with the observed increments in hydrocarbon degradation. Illumina-MiSeq sequencing of 16 S rRNA gene fragments revealed that the OS-100 consortium was mainly composed of the genera Halomonas, Idiomarina, Alcanivorax and Chromohalobacter. This community structure changed depending on the culturing conditions. However, remarkable changes in the community structure were not always associated with remarkable shifts in the hydrocarbonoclastic activity and vice versa. The results show that probably synergistic interactions between community members and different subpopulations of the OS-100 consortium contributed to salinity tolerance and hydrocarbon degradation.

Improved chickpea growth, physiology, nutrient assimilation and rhizoremediation of hydrocarbons by bacterial consortia

BACKGROUND

Soil pollution by petroleum hydrocarbons (PHCs) reduces yield by changing the physico-chemical properties of soil and plants due to PHCs' biotoxicity and persistence. Thus, removing PHCs from the soil is crucial for ecological sustainability. Microbes-assisted phytoremediation is an economical and eco-friendly solution. The current work aimed to develop and use bacterial consortia (BC) for PHCs degradation and plant growth enhancement in hydrocarbon-contaminated soil. Initially, the enriched microbial cultures (that were prepared from PHCs-contaminated soils from five distinct regions) were obtained via screening through microcosm experiments. Afterward, two best microbial cultures were tested for PHCs degradation under various temperature and pH ranges. After culture optimization, isolation and characterization of bacterial strains were done to construct two BC. These constructed BC were tested in a pot experiment for hydrocarbons degradation and chickpea growth in PHCs contaminated soil.

RESULTS

Findings revealed that PHCs exerted significant phytotoxic effects on chickpea growth and physiology when cultivated in PHCs contaminated soil, reducing agronomic and physiological traits by 13-29% and 12-43%, respectively. However, in the presence of BC, the phytotoxic impacts of PHCs on chickpea plants were reduced, resulting in up to 24 - 35% improvement in agronomic and physiological characteristics as compared to un-inoculated contaminated controls. Furthermore, the bacterial consortia boosted chickpea's nutritional absorption and antioxidant mechanism. Most importantly, chickpea plants phytoremediated 52% of the initial PHCs concentration; however, adding BC1 and BC2 with chickpea plants further increased this removal and remediated 74% and 80% of the initial PHCs concentration, respectively.

CONCLUSION

In general, BC2 outperformed BC1 (with few exceptions) in promoting plant growth and PHCs elimination. Therefore, using multi-trait BC for PHCs degradation and plant growth improvement under PHCs stress may be an efficient and environmentally friendly strategy to deal with PHCs pollution and toxicity.

Indigenous fungi with the ability to biodegrade hydrocarbons in diesel-contaminated soil are isolated and selected using a simple methodology

Soil contamination by hydrocarbons is a problem that causes severe damage to the environment and public health. Technologies such as bioremediation using native microbial species represent a promising and environmentally friendly alternative for decontamination. This study aimed to isolate indigenous fungi species from the State of Rio de Janeiro, Brazil and evaluate their diesel degrading capacity in soils contaminated with crude oil. Seven filamentous fungi were isolated after enrichment cultivation from soils collected from contaminated sites and subjected to growth analysis on diesel nutrient media. Two fungal species were pre-selected and identified by morphological genus analysis and molecular techniques as Trichoderma asperellum and Penicillium pedernalense. The microdilution test showed that T. asperellum presented better fungal growth in high diesel concentrations than P. pedernalense. In addition, T. asperellum was able to degrade 41 and 54% of the total petroleum hydrocarbon (TPH) content present in soil artificially contaminated with diesel (10 g/kg of soil) in 7 and 14 days of incubation, respectively. In higher diesel concentration (1000 g of diesel/kg of soil) the TPH degradation reached 26%, 45%, and 48%, in 9, 16, and 30 d, respectively. The results demonstrated that the selected species was suitable for diesel degradation. We can also conclude that the isolation and selection process proposed in this work was successful and represents a simple alternative for obtaining native species with hydrocarbon degradation capacity, for use in the bioremediation process in the recovery of contaminated areas in an ecologically acceptable way.

Yarrowia lipolytica growth, lipids, and protease production in medium with higher alkanes and alkenes

Two strains of Yarrowia lipolytica (CBS 2075 and DSM 8218) were first studied in bioreactor batch cultures, under different controlled dissolved oxygen concentrations (DOC), to assess their ability to assimilate aliphatic hydrocarbons (HC) as a carbon source in a mixture containing 2 g·L-1 of each alkane (dodecane and hexadecane), and 2 g·L-1 hexadecene. Both strains grew in the HC mixture without a lag phase, and for both strains, 30 % DOC was sufficient to reach the maximum values of biomass and lipids. To enhance lipid-rich biomass and enzyme production, a pulse fed-batch strategy was tested, for the first time, with the addition of one or three pulses of concentrated HC medium. The addition of three pulses of the HC mixture (total of 24 g·L-1 HC) did not hinder cell proliferation, and high protease (> 3000 U·L-1) and lipids concentrations of 3.4 g·L-1 and 4.3 g·L-1 were achieved in Y. lipolytica CBS 2075 and DSM 8218 cultures, respectively. Lipids from the CBS 2075 strain are rich in C16:0 and C18:1, resembling the composition of palm oil, considered suitable for the biodiesel industry. Lipids from the DSM 8218 strain were predominantly composed of C16:0 and C16:1, the latter being a valuable monounsaturated fatty acid used in the pharmaceutical industry. Y. lipolytica cells exhibited high intrinsic surface hydrophobicity (> 69 %), which increased in the presence of HC. A reduction in surface tension was observed in both Y. lipolytica cultures, suggesting the production of extracellular biosurfactants, even at low amounts. This study marks a significant advancement in the valorization of HC for producing high-value products by exploring the hydrophobic compounds metabolism of Y. lipolytica.

Survival strategies and assembly mechanisms of microbial communities in petroleum-contaminated soils

This study analyzed petroleum-contaminated soils from south and north locations in China to explore the structure, diversity, functional genes and assembly processes of microbial communities' . Compared with soils from south locations, soils from northern regions exhibited elevated pH, total nitrogen (TN), and total petroleum hydrocarbon (TPH) levels. Among these, TN and TPH were the most influential on the microbial community. The dominant phyla for bacteria, archaea, and fungi were Proteobacteria, Thaumarchaeota, and Ascomycota, respectively. Among them, Proteobacteria was strongly correlated with various functional genes including alkB and many aromatics degradation and denitrification genes (r > 0.9, p < 0.01), suggesting that Proteobacteria play an important role in petroleum-contaminated soils. Metabolism in northern regions was more active than that in southern regions. The northern regions showed a pronounced tendency for denitrification, while the southern regions were characterized by acetoclastic methanogenesis. The assembly of microbial communities exhibited regional patterns, the deterministic assembly was more prominent in the northern soils, while the stochastic assembly was evident in the southern soils. Overall, these findings provide a new conceptual framework to understand the biosphere in petroleum-contaminated soil, potentially guiding improved management practices in the environmental remediation.

Phytoremediation of crude oil-contaminated soil using Vigna Unguiculata and associated rhizosphere bacteria

Persistent crude oil contamination poses a significant environmental challenge. In this study, the efficacy of Vigna unguiculata (L.) and associated rhizospheric microorganisms in remediating crude oil-contaminated soil within a microcosm setting was investigated. A randomized block design was employed, and soil samples were subjected to varying degrees of contamination: 0% (UR), 2.5% (CR2), 5.0% (CR5), 7.5% (CR7), and 10.0% (CR10) w/w crude oil. The investigation aimed to assess the potential of Vigna unguiculata (L.) in mitigating crude oil contamination across these defined contamination gradients. The plant growth and crude oil removal were monitored concurrently post-emergence. Plant emergence and growth were significantly affected due to contamination, especially among plants in CR5 and CR10. The bacterial population was higher in the rhizosphere, and the treatments with lower hydrocarbon contamination. It was shown that plant density encouraged the growth of bacterial communities. Significant reduction in soil TPH was observed in CR2 (76.61%) and CR7 (65.88%). There was a strong correlation between plant growth and oil-utilizing bacterial population (r2 = 0.966) and plant growth and hydrocarbon reduction (r2 = 0.956), signifying the role of plant-bacterial synergy. Saturate fractions (C30 - C32) were significantly degraded to lower molecular weight compounds (C11 - C14). Except in CR5 and CR10, the remediation within the cowpea rhizosphere was effective even at regulatory standards. Understanding the rhizosphere ecological dynamics would further highlight the role the bacteria played; hence, it is recommended.

Diversity of hydrocarbon-degrading bacteria in mangroves rhizosphere as an indicator of oil-pollution bioremediation in mangrove forests

Mangrove ecosystems, characterized by high levels of productivity, are susceptible to anthropogenic activities, notably oil pollution arising from diverse origins including spills, transportation, and industrial effluents. Owing to their role in climate regulation and economic significance, there is a growing interest in developing mangrove conservation strategies. In the Arabian Gulf, mangroves stand as the sole naturally occurring green vegetation due to the region's hot and arid climate. However, they have faced persistent oil pollution for decades. This review focuses on global mangrove distribution, with a specific emphasis on Qatar's mangroves. It highlights the ongoing challenges faced by mangroves, particularly in relation to the oil industry, and the impact of oil pollution on these vital ecosystems. It outlines major oil spill incidents worldwide and the diverse hydrocarbon-degrading bacterial communities within polluted areas, elucidating their potential for bioremediation. The use of symbiotic interactions between mangrove plants and bacteria offers a more sustainable, cost-effective and environmentally friendly alternative. However, the success of these bioremediation strategies depends on a deep understanding of the dynamics of bacterial communities, environmental factors and specific nature of the pollutants.

Unveiling the capacity of bioaugmentation application, in comparison with biochar and rhamnolipid for TPHs degradation in aged hydrocarbons polluted soil

Persistent, aged hydrocarbons in soil hinder remediation, posing a significant environmental threat. While bioremediation offers an environmentally friendly and cost-effective approach, its efficacy for complex contaminants relies on enhancing pollutant bioavailability. This study explores the potential of immobilized bacterial consortia combined with biochar and rhamnolipids to accelerate bioremediation of aged total petroleum hydrocarbon (TPH)-contaminated soil. Previous research indicates that biochar and biosurfactants can increase bioremediation rates, while mixed consortia offer sequential degradation and higher hydrocarbon mineralization. The present investigation aimed to assess whether combining these strategies could further enhance degradation in aged, complex soil matrices. The bioaugmentation (BA) with bacterial consortium increased the TPHs degradation in aged soil (over 20% compared to natural attenuation - NA). However, co-application of BA with biochar and rhamnolipid higher did not show a statistically prominent synergistic effect. While biochar application facilitated the maintenance of hydrocarbon degrading bacterial consortium in soil, the present study did not identify a direct influence in TPHs degradation. The biochar application in contaminated soil contributed to TPHs adsorption. Rhamnolipid alone slightly increased the TPHs biodegradation with NA, while the combined bioaugmentation treatment with rhamnolipid and biochar increased the degradation between 27.5 and 29.8%. These findings encourage further exploration of combining bioaugmentation with amendment, like biochar and rhamnolipid, for remediating diverse environmental matrices contaminated with complex and aged hydrocarbons.

Physiology and comparative genomics of the haloalkalitolerant and hydrocarbonoclastic marine strain Rhodococcus ruber MSA14

Marine hydrocarbonoclastic bacteria can use polycyclic aromatic hydrocarbons as carbon and energy sources, that makes these bacteria highly attractive for bioremediation in oil-polluted waters. However, genomic and metabolic differences between species are still the subject of study to understand the evolution and strategies to degrade PAHs. This study presents Rhodococcus ruber MSA14, an isolated bacterium from marine sediments in Baja California, Mexico, which exhibits adaptability to saline environments, a high level of intrinsic pyrene tolerance (> 5 g L- 1), and efficient degradation of pyrene (0.2 g L- 1) by 30% in 27 days. Additionally, this strain demonstrates versatility by using naphthalene and phenanthrene as individual carbon sources. The genome sequencing of R. ruber MSA14 revealed a genome spanning 5.45 Mbp, a plasmid of 72 kbp, and three putative megaplasmids, lengths between 110 and 470 Kbp. The bioinformatics analysis of the R. ruber MSA14 genome revealed 56 genes that encode enzymes involved in the peripheral and central pathways of aromatic hydrocarbon catabolism, alkane, alkene, and polymer degradation. Within its genome, R. ruber MSA14 possesses genes responsible for salt tolerance and siderophore production. In addition, the genomic analysis of R. ruber MSA14 against 13 reference genomes revealed that all compared strains have at least one gene involved in the alkanes and catechol degradation pathway. Overall, physiological assays and genomic analysis suggest that R. ruber MSA14 is a new haloalkalitolerant and hydrocarbonoclastic strain toward a wide range of hydrocarbons, making it a promising candidate for in-depth characterization studies and bioremediation processes as part of a synthetic microbial consortium, as well as having a better understanding of the catabolic potential and functional diversity among the Rhodococci group.

Assessing Diesel Tolerance of Chromobacterium violaceum: Insights from Growth Kinetics, Substrate Utilization, and Implications for Microbial Adaptation

This study aimed to determine the tolerance of Chromobacterium violaceum ATCC 12472 to diesel. The growth of the strain was evaluated through exposure to various diesel concentrations (1, 2.5, 5, 7.5, and 10% v/v), with continuous monitoring of growth via optical density measurements until the death phase was reached. Employing a logistic model, we analyzed the growth kinetics of C. violaceum and compared them with five other models to comprehend substrate utilization dynamics. Our results indicate that optimal bacterial growth occurred at 2.5% (v/v) or 18,125 mg/L diesel, while both higher and lower concentrations manifested inhibitory and increasingly stressful effects. The Aiba model emerged as the most fitting representation of substrate utilization by C. violaceum. In addition, our findings underscore the remarkable diesel tolerance of C. violaceum ATCC 12472, despite the inherently stressful nature of the medium. This study contributes to the understanding of microbial responses to environmental stressors and highlights the pivotal role of the substrate concentration in influencing microbial growth. These insights have implications for bioremediation strategies and enhance our understanding of bacterial ecological resilience in the presence of hydrocarbon pollutants.

Biosurfactants production by marine yeasts isolated from zoanthids and characterization of an emulsifier produced by Yarrowia lipolytica LMS 24B

The present study investigates the potential for biosurfactant production of 19 marine yeast species obtained from zoanthids. Using the emulsification index test to screen the samples produced by the marine yeasts, we verified that five isolates exhibited an emulsification index ≥50%. Additional tests were performed on such isolates, including oil displacement, drop collapse, Parafilm M assay, and surface tension measurement. The tolerance of produced biosurfactants for environmental conditions was also analyzed, especially considering the media's temperature, pH, and salinity. Moreover, the surfactant's ability to emulsify different hydrocarbon sources and to metabolize kerosene as the sole carbon source was evaluated in vitro. Our results demonstrate that yeast biosurfactants can emulsify hydrocarbon sources under different physicochemical conditions and metabolize kerosene as a carbon source. Considering the Yarrowia lipolytica LMS 24B as the yeast model for biosurfactant production from the cell's wall biomass, emulsification indexes of 61.2% were obtained, even at a high temperature of 120 °C. Furthermore, the Fourier-transform middle infrared spectroscopy (FTIR) analysis of the biosurfactant's chemical composition revealed the presence of distinct functional groups assigned to a glycoprotein complex. Considering the status of developing new bioproducts and bioprocesses nowadays, our findings bring a new perspective to biosurfactant production by marine yeasts, especially Y. lipolytica LMS 24B. In particular, the presented results validate the relevance of marine environments as valuable sources of genetic resources, i.e., yeast strains capable of metabolizing and emulsifying petroleum derivatives.

Microorganism-mediated bioremediation of dyes from contaminated soil: Mechanisms, recent advances, and future perspectives

Many methods have been proposed for the remediation of dye-contaminated soils, a widespread form of environment pollution. Bioremediation, it is hoped, can combine ecological benefits with efficiency of dye decontamination. We review the types and sources of dye contaminants; their possible effects on plant, animal, and human health; and emerging strategies for microbial bioremediation. Challenges, limitations, recommendations for future research, and prospects for large-scale commercialization of microbial bioremediation are discussed.

The remediation of polycyclic aromatic hydrocarbon contaminated soil by immobilized microorganisms using distiller's grains

Polycyclic aromatic hydrocarbons are a persistent organic pollutant, and their biodegradation in the soil is often limited due to the limited degradation ability of indigenous bacteria and the low activity of exogenous PAH degrading bacteria. Immobilized microbial technology can protect microorganisms from the impact of harsh environments, and distiller's grains have the potential as carriers for microbial immobilization. This study aims to use distiller's grains as a microbial carrier, investigate the feasibility of immobilized microorganisms using distiller's grains for remediation of PAH contaminated soil; explore the relationship between soil nutrient content, consumption, and PAH degradation rate; and reveal the mechanism of bioremediation from the perspective of soil enzyme activity and microbial community composition. The results showed that after 72 days of remediation, the removal rates of phenanthrene and pyrene in the treatment of immobilized microorganisms in distiller grains reached 91.78% and 58.59%, respectively. Distiller grains can serve as a carrier for microorganisms, providing them with shelter and nutrients to enhance their chance of survival. Additionally, they can regulate the composition of soil particles and improve aeration, thereby increasing the efficiency of PAH degradation in soil.

Simultaneous removal of aliphatic and aromatic crude oil hydrocarbons by Pantoea agglomerans isolated from petroleum-contaminated soil in the west of Iran

Hydrocarbons are considered as one of the most common and harmful environmental pollutants affecting human health and the environment. Bioremediation as an environmentally friendly, highly efficient, and cost-effective method in remediating oil-contaminated environments has been interesting in recent decades. In this study, hydrocarbon degrader bacterial strains were isolated from the highly petroleum-contaminated soils in the Dehloran oil field in the west of Iran. Out of 37 isolates, 15 can grow on M9 agar medium that contains 1.5 g L-1 of crude oil as the sole carbon source. The morphological, biochemical, and 16SrRNA sequencing analyses were performed for the isolates. The choosing of the isolates as the hydrocarbon degrader was examined by evaluating the efficacy of their crude oil removal at a concentration of 10 g L-1 in an aqueous medium. The results showed that five isolates belonging to Pseudomonas sp., Pseudomonas oryzihabitans, Roseomonas aestuarii, Pantoea agglomerans, and Arthrobacter sp. had a hyper hydrocarbon-degrading activity and they could remove more than 85% of the total petroleum hydrocarbon (TPH) after 96 h. The highest TPH removal of about 95.75% and biodegradation rate of 0.0997 g L-1 h-1 was observed for P. agglomerans. The gas chromatography-mass spectroscopy (GC-MS) analysis was performed during the biodegradation process by P. agglomerans to detect the degradation intermediates and final products. The results confirmed the presence of intermediates such as alcohols and fatty acids in the terminal oxidation pathway of alkanes in this biodegradation process. A promising P. agglomerans NB391 strain can remove aliphatic and aromatic hydrocarbons simultaneously.

Bacterial crude oil and polyaromatic hydrocarbon degraders from Kazakh oil fields as barley growth support

Bacterial strains of the genera Arthrobacter, Bacillus, Dietzia, Kocuria, and Micrococcus were isolated from oil-contaminated soils of the Balgimbaev, Dossor, and Zaburunye oil fields in Kazakhstan. They were selected from 1376 isolated strains based on their unique ability to use crude oil and polyaromatic hydrocarbons (PAHs) as sole source of carbon and energy in growth experiments. The isolated strains degraded a wide range of aliphatic and aromatic components from crude oil to generate a total of 170 acid metabolites. Eight metabolites were detected during the degradation of anthracene and of phenanthrene, two of which led to the description of a new degradation pathway. The selected bacterial strains Arthrobacter bussei/agilis SBUG 2290, Bacillus atrophaeus SBUG 2291, Bacillus subtilis SBUG 2285, Dietzia kunjamensis SBUG 2289, Kocuria rosea SBUG 2287, Kocuria polaris SBUG 2288, and Micrococcus luteus SBUG 2286 promoted the growth of barley shoots and roots in oil-contaminated soil, demonstrating the enormous potential of isolatable and cultivable soil bacteria in soil remediation. KEY POINTS: • Special powerful bacterial strains as potential crude oil and PAH degraders. • Growth on crude oil or PAHs as sole source of carbon and energy. • Bacterial support of barley growth as resource for soil remediation.

Bioremediation of hydrocarbon by co-culturing of biosurfactant-producing bacteria in microbial fuel cell with Fe2O3-modified anode

The most common type of environmental contamination is petroleum hydrocarbons. Sustainable and environmentally friendly treatment strategies must be explored in light of the increasing challenges of toxic and critical wastewater contamination. This paper deals with the bacteria-producing biosurfactant and their employment in the bioremediation of hydrocarbon-containing waste through a microbial fuel cell (MFC) with Pseudomonas aeruginosa (exoelectrogen) as co-culture for simultaneous power generation. Staphylococcus aureus is isolated from hydrocarbon-contaminated soil and is effective in hydrocarbon degradation by utilizing hydrocarbon (engine oil) as the only carbon source. The biosurfactant was purified using silica-gel column chromatography and characterised through FTIR and GCMS, which showed its glycolipid nature. The isolated strains are later employed in the MFCs for the degradation of the hydrocarbon and power production simultaneously which has shown a power density of 6.4 W/m3 with a 93% engine oil degradation rate. A biogenic Fe2O3 nanoparticle (NP) was synthesized using Bambusa arundinacea shoot extract for anode modification. It increased the power output by 37% and gave the power density of 10.2 W/m3. Thus, simultaneous hydrocarbon bioremediation from oil-contamination and energy recovery can be achieved effectively in MFC with modified anode.

Surfactants Influencing the Biocatalytic Performance of Natural Alkane-Degrading Bacteria via Interfacial Biocatalysis in Pickering Emulsions

Setting superhydrophobic Mycobacterium sp. as an example, the hydrophobic bacteria acting as demulsifying agents of surfactant-stabilized conventional emulsions, vice versa, the synergistic/antagonistic influence of nonionic surfactants (Tween 80 or Span 80) on the stability of the bacteria-stabilized Pickering emulsions was investigated. At the same time, the activated/suppression effect of nonionic surfactants on microbial degradation of tetradecane, which exhibited a dose-response relationship, was also found. The hydrophobic bacteria acting as demulsifying agents and the suppression influence of nonionic surfactants on the biocatalytic performance (indexing as biomass) of natural alkane-degrading bacteria, believed to be totally separated concepts previously, are for the first time found to be closely related to in situ surface modification of bacteria with nonionic surfactants. During the degradation of tetradecane by Mycobacterium sp. in the presence of nonionic surfactants, demulsification due to the bacteria acting as demulsifying agents and interfacial biocatalysis in the bacteria-stabilized Pickering emulsions are involved, which provides useful information to select optimal dispersants for marine oil spills.

Laccase-mediated degradation of petroleum hydrocarbons in historically contaminated soil

Laccases (EC1.10.3.2) have attracted growing attention in bioremediation research due to their high reactivity and substrate versatility. In this study, three genes for potential novel laccases were identified in an enrichment culture from contaminated field soil and recombinantly expressed in E. coli. Two of them, designated as PlL and BaL, were biochemically characterized regarding their optimal pH and temperature, kinetic parameters, and substrate versatility. In addition, lacasse PlL from Parvibaculum lavamentivorans was tested on historically contaminated soil. Treatment with PlL led to a significantly higher reduction of total petroleum hydrocarbons (83% w/w) compared to the microbial control (74% w/w). Hereby, PlL was especially effective in degrading hydrocarbons > C17. Their residual concentration was by 43% w/w lower than in the microbial treatment. In comparison to the laccase from Myceliophthora thermophila (MtL), PlL treatment was not significantly different for the fraction > C17 but resulted in a 30% (w/w) lower residual concentration for hydrocarbons < C18. In general, PlL can promote the degradation of petroleum hydrocarbons. As a consequence, it can be applied to reduce remediation time by duly achieving remediation target concentrations needed for site closure.

Crude Oil Degradation in Temperatures Below the Freezing Point by Bacteria from Hydrocarbon-Contaminated Arctic Soils and the Genome Analysis of Sphingomonas sp. AR_OL41

Intensive human activity in the Arctic region leads to hydrocarbon pollution of reservoirs and soils. Isolation of bacteria capable of growing at low temperatures and degrading oil and petroleum products is of scientific and practical value. The aim of this work was to study the physiology and growth in oil at temperatures below 0 °C of four strains of bacteria of the genera Pseudomonas, Rhodococcus, Arthrobacter, and Sphingomonas-previously isolated from diesel-contaminated soils of the Franz Josef Land archipelago-as well as genomic analysis of the Sphingomonas sp. AR_OL41 strain. The studied strains grew on hydrocarbons at temperatures from -1.5 °C to 35 °C in the presence of 0-8% NaCl (w/v). Growth at a negative temperature was accompanied by visual changes in the size of cells as well as a narrowing of the spectrum of utilized n-alkanes. The studied strains were psychrotolerant, degraded natural biopolymers (xylan, chitin) and n-alkanes of petroleum, and converted phosphates into a soluble form. The ability to degrade n-alkanes is rare in members of the genus Sphingomonas. To understand how the Sphingomonas sp. AR_OL41 strain has adapted to a cold, diesel-contaminated environment, its genome was sequenced and analyzed. The Illumina HiSeq 2500 platform was used for AR_OL41 genome strain sequencing. The genome analysis of the AR_OL41 strain showed the presence of genes encoding enzymes of n-alkane oxidation, pyruvate metabolism, desaturation of membrane lipids, and the formation of exopolysaccharides, confirming the adaptation of the strain to hydrocarbon pollution and low habitat temperature. Average nucleotide identity and digital DNA-DNA hybridization values for genomes of the AR_OL41 strain with that of the phylogenetically relative Sphingomonas alpine DSM 22537T strain were 81.9% and 20.9%, respectively, which allows the AR_OL41 strain to be assigned to a new species of the genus Sphingomonas. Phenomenological observations and genomic analysis indicate the possible participation of the studied strains in the self-purification of Arctic soils from hydrocarbons and their potential for biotechnological application in bioremediation of low-temperature environments.

Long-term effects of oil contamination on soil quality and metabolic function

Widespread soil contamination with oil and the toxicity of petroleum hydrocarbons to soil biota make it extremely important to study microbial responses to oil stress. Soil metabolites reflect the main metabolic pathways in the soil microbial community. The examination of changes in the soil metabolic profile and metabolic function is essential for a better understanding of the nature of the pollution and restoration of the disturbed soils. The present study aimed to assess the long-term effect of oil on the ecological state of the soil, evaluate quantitative and qualitative differences in metabolite composition between soil contaminated with oil and non-contaminated soil, and reveal biologically active metabolites that are related to oil contamination and can be used for contamination assessment. A long-term field experiment was conducted to examine the effects of various oil concentrations on the biochemical properties and metabolic profile of the soil. Podzolic soil contaminated with oil demonstrated the long-term inhibition of soil biological activity and vegetation. Oil affected the metabolic activity of soil fungi increasing the production of toxic metabolites. A metabolomic approach was employed to determine soil metabolites. The metabolite profile was found to vary greatly between oil-contaminated and non-contaminated soils. Carbohydrates had the largest number of metabolites negatively affected by oil, while the content of organic acids, phenolic compounds, and terpenoids was mainly increased in oil-contaminated soil. The evaluation of the long-term impact of oil on microbial metabolism can make a valuable contribution to the assessment of soil quality and the activity of soil microorganisms being under stress from oil pollution. The results contribute to a further understanding of the role of microorganisms in the ecological functions of contaminated soil, which can be useful in the development of rehabilitation strategies for disturbed sites.

Biofilm formation in xenobiotic-degrading microorganisms

The increased presence of xenobiotics affects living organisms and the environment at large on a global scale. Microbial degradation is effective for the removal of xenobiotics from the ecosystem. In natural habitats, biofilms are formed by single or multiple populations attached to biotic/abiotic surfaces and interfaces. The attachment of microbial cells to these surfaces is possible via the matrix of extracellular polymeric substances (EPSs). However, the molecular machinery underlying the development of biofilms differs depending on the microbial species. Biofilms act as biocatalysts and degrade xenobiotic compounds, thereby removing them from the environment. Quorum sensing (QS) helps with biofilm formation and is linked to the development of biofilms in natural contaminated sites. To date, scant information is available about the biofilm-mediated degradation of toxic chemicals from the environment. Therefore, we review novel insights into the impact of microbial biofilms in xenobiotic contamination remediation, the regulation of biofilms in contaminated sites, and the implications for large-scale xenobiotic compound treatment.

Ribosomal RNA gene operon copy number, a functional trait indicating the hydrocarbon degradation level of bacterial communities

The lack of universal indicators for predicting microbial biodegradation potential and assessing remediation effects limits the generalization of bioremediation. The community-level ribosomal RNA gene operon (rrn) copy number, an important functional trait, has the potential to serve as a key indicator of the bioremediation of organic pollutants. A meta-analysis based on 1275 samples from 26 hydrocarbon-related studies revealed a positive relationship between the microbial hydrocarbon biodegradation level and the community-level rrn copy number in soil, seawater and culture. Subsequently, a microcosm experiment was performed to decipher the community-level rrn copy number response mechanism during total petroleum hydrocarbon (TPH) biodegradation. The treatment combining straw with resuscitation-promoting factor (Rpf) exhibited the highest community-level rrn copy number and the most effective biodegradation compared with other treatments, and the initial TPH content (20,000 mg kg-1) was reduced by 67.67% after 77 days of incubation. TPH biodegradation rate was positively correlated with the average community-level rrn copy number (p = 0.001, R2 = 0.5781). Both meta and community analyses showed that rrn copy number may reflect the potential of hydrocarbon degradation and microbial dormancy. Our findings provide insight into the applicability of the community-level rrn copy number to assess bacterial biodegradation for pollution remediation.

Polystyrene-colonizing bacteria are enriched for long-chain alkane degradation pathways

One of the most promising strategies for the management of plastic waste is microbial biodegradation, but efficient degraders for many types of plastics are still lacking, including those for polystyrene (PS). Genomics has emerged as a powerful tool for mining environmental microbes that may have the ability to degrade different types of plastics. In this study, we use 16S rRNA sequencing to analyze the microbiomes for multiple PS samples collected from sites with different vegetation in Taiwan to reveal potential common properties between species that exhibit growth advantages on PS surfaces. Phylum enrichment analysis identified Cyanobacteria and Deinococcus-Thermus as being the most over-represented groups on PS, and both phyla include species known to reside in extreme environments and could encode unique enzymes that grant them properties suitable for colonization on PS surfaces. Investigation of functional enrichment using reference genomes of PS-enriched species highlighted carbon metabolic pathways, especially those related to hydrocarbon degradation. This is corroborated by the finding that genes encoding long-chain alkane hydroxylases such as AlmA are more prevalent in the genomes of PS-associated bacteria. Our analyses illustrate how plastic in the environment support the colonization by different microbes compared to surrounding soil. In addition, our results point to the possibility that alkane hydroxylases could confer growth advantages of microbes on PS.

Adding nanoparticles to improve emulsion efficiency and enhance microbial degradation in Pickering emulsions

Interfacial microbial degradation of alkane in Pickering emulsions stabilized by hydrophobic bacterial cells is a new mechanism for microbial degradation of water-insoluble chemicals, where both water-insoluble chemicals in the oil phase and water-soluble nutrients (such as nitrogen and phosphorus) in the water phase are bio-accessible to living microorganisms anchoring onto the oil-water interfaces. In the present work, super-hydrophobic Mycobacterium sp. (contact angle 168.6°) degradation of tetradecane was set up as a model. Addition of fumed SiO2 particles (Aerosil® R974) as a new strategy was developed to enhance tetradecane degradation where the biodegradation rate (based on the accumulated biomass) increased by approximately 80%. The enhanced effect of SiO2 particles on the tetradecane degradation attributed to the synergistic effect of SiO2 particles on the emulsion efficiency of Pickering emulsions stabilized by bacterial cells and then on the enhancement of interfacial microbial degradation in Pickering emulsions. KEY POINTS: • Interfacial microbial degradation in bacterial cells stabilized Pickering emulsions. • Adding fumed SiO2 particles to enhance microbial degradation of tetradecane. • Correlation relationship between emulsion efficiency and interfacial microbial degradation.

Biodegradation of phenanthrene by piezotolerant Bacillus subtilis EB1 and genomic insights for bioremediation

A marine strain B. subtilis EB1, isolated from Equator water, showed excellent degradation towards a wide range of hydrocarbons. Degradation studies revealed dense growth with 93 % and 83 % removal of phenanthrene within 72 h at 0.1 and 20 MPa, respectively. The identification of phenanthrene degradation metabolites by GC-MS combined with its whole genome analysis provided the pathway involved in the degradation process. Whole genome sequencing indicated a genome size of 3,983,989 bp with 4331 annotated genes. The genome provided the genetic compartments, which includes monooxygenase, dioxygenase, dehydrogenase, biosurfactant synthesis catabolic genes for the biodegradation of aromatic compounds. Detailed COG and KEGG pathway analysis confirmed the genes involved in the oxygenation reaction of hydrocarbons, piezotolerance, siderophores, chemotaxis and transporter systems which were specific to adaptation for survival in extreme marine habitat. The results of this study will be a key to design an optimal bioremediation strategy for oil contaminated extreme marine environment.

Microbial remediation of oil-contaminated shorelines: a review

Frequent marine oil spills have led to increasingly serious oil pollution along shorelines. Microbial remediation has become a research hotspot of intertidal oil pollution remediation because of its high efficiency, low cost, environmental friendliness, and simple operation. Many microorganisms are able to convert oil pollutants into non-toxic substances through their growth and metabolism. Microorganisms use enzymes' catalytic activities to degrade oil pollutants. However, microbial remediation efficiency is affected by the properties of the oil pollutants, microbial community, and environmental conditions. Feasible field microbial remediation technologies for oil spill pollution in the shorelines mainly include the addition of high-efficiency oil degrading bacteria (immobilized bacteria), nutrients, biosurfactants, and enzymes. Limitations to the field application of microbial remediation technology mainly include slow start-up, rapid failure, long remediation time, and uncontrolled environmental impact. Improving the environmental adaptability of microbial remediation technology and developing sustainable microbial remediation technology will be the focus of future research. The feasibility of microbial remediation techniques should also be evaluated comprehensively.

Correlating the succession of microbial communities from Nigerian soils to petroleum biodegradation

Whilst biodegradation of different hydrocarbon components has been widely demonstrated to occur by specialist oil-degrading bacteria, less is known about the impact on microbial communities as a function of oil composition by comparing the biodegradation of chemically complex fuels to synthetic products. The objectives of this study were (i) to assess the biodegradation capacity and succession of microbial communities isolated from Nigerian soils in media with crude oil or synthetic oil as sole sources of carbon and energy, and (ii) to assess the temporal variability of the microbial community size. Community profiling was done using 16 S rRNA gene amplicon sequencing (Illumina), and oil profiling using gas chromatography. The biodegradation of natural and synthetic oil differed probably due to the content of sulfur that may interfere with the biodegradation of hydrocarbons. Both alkanes and PAHs in the natural oil were biodegraded faster than in the synthetic oil. Variable community responses were observed during the degradation of alkanes and more simple aromatic compounds, but at later phases of growth they became more homogeneous. The degradation capacity and the size of the community from the more-contaminated soil were higher than those from the less-contaminated soil. Six abundant organisms isolated from the cultures were found to biodegrade oil molecules in pure cultures. Ultimately, this knowledge may contribute to a better understanding of how to improve the biodegradation of crude oil by optimizing culturing conditions through inoculation or bioaugmentation of specific bacteria during ex-situ biodegradation such as biodigesters or landfarming.

Bacterial enzymatic degradation of recalcitrant organic pollutants: catabolic pathways and genetic regulations

Contamination of soil and natural water bodies driven by increased organic pollutants remains a universal concern. Naturally, organic pollutants contain carcinogenic and toxic properties threatening all known life forms. The conventional physical and chemical methods employed to remove these organic pollutants ironically produce toxic and non-ecofriendly end-products. Whereas microbial-based degradation of organic pollutants provides an edge, they are usually cost-effective and take an eco-friendly approach towards remediation. Bacterial species, including Pseudomonas, Comamonas, Burkholderia, and Xanthomonas, have the unique genetic makeup to metabolically degrade toxic pollutants, conferring their survival in toxic environments. Several catabolic genes, such as alkB, xylE, catA, and nahAc, that encode enzymes and allow bacteria to degrade organic pollutants have been identified, characterized, and even engineered for better efficacy. Aerobic and anaerobic processes are followed by bacteria to metabolize aliphatic saturated and unsaturated hydrocarbons such as alkanes, cycloalkanes, aldehydes, and ethers. Bacteria use a variety of degrading pathways, including catechol, protocatechuate, gentisate, benzoate, and biphenyl, to remove aromatic organic contaminants such as polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and pesticides from the environment. A better understanding of the principle, mechanisms, and genetics would be beneficial for improving the metabolic efficacy of bacteria to such ends. With a focus on comprehending the mechanisms involved in various catabolic pathways and the genetics of the biotransformation of these xenobiotic compounds, the present review offers insight into the various sources and types of known organic pollutants and their toxic effects on health and the environment.

Assessment of oily sludge biodegradation in lab scale composting and slurry bioreactor by bacterial consortium

The present study aimed to investigate biodegradability of oily sludge in lab scale composting and slurry bioreactor using a potential bacterial consortium isolated from petroleum-contaminated sites. The consortium used in the study consisted of bacterial genera, including Enterobacter, Bacillus, Microbacterium, Alcaligenes Pseudomonas, Ochrobactrum, Micrococcus, and Shinella which were obtained after rigorous screening using different hydrocarbons. The meticulously designed lab scale composting experiments were carried out and showed that the combination of 10% oily sludge (A1) exhibited the highest total carbon (TC) removal, which was 40.33% within 90 days. To assess the composting experiments' efficiency, the first (k₁) and second (k₂) order rate constants were evaluated and was found to be 0.0004-0.0067 per day and second (k₂) 0.0000008-0.00005 g/kg. day respectively. To further enhance the biodegradation rate of A1 combination, a slurry bioreactor was used. The maximum total petroleum hydrocarbon (TPH) removals in a slurry bioreactor for cycle-I and -II were 48.8% and 46.5%, respectively, on the 78th and 140th days of the treatment. The results obtained in the study will be a technological platform for the development of slurry phase treatment of petroleum waste in a sustainable and eco-friendly manner.

Multi-Approach Characterization of Novel Pyrene-Degrading Mycolicibacterium austroafricanum Isolates Lacking nid Genes

Polycyclic aromatic hydrocarbons (PAHs) are chemical compounds that are widespread in the environment, arising from the incomplete combustion of organic material, as well as from human activities involving petrol exploitation, petrochemical industrial waste, gas stations, and environmental disasters. PAHs of high molecular weight, such as pyrene, have carcinogenic and mutagenic effects and are considered pollutants. The microbial degradation of PAHs occurs through the action of multiple dioxygenase genes (nid), which are localized in genomic island denominate region A, and cytochrome P450 monooxygenases genes (cyp) dispersed in the bacterial genome. This study evaluated pyrene degradation by five isolates of Mycolicibacterium austroafricanum using 2,6-dichlorophenol indophenol (DCPIP assay), gas chromatography/mass spectrometry (CG/MS), and genomic analyses. Two isolates (MYC038 and MYC040) exhibited pyrene degradation indexes of 96% and 88%, respectively, over a seven-day incubation period. Interestingly, the genomic analyses showed that the isolates do not have nid genes, which are involved in PAH biodegradation, despite their ability to degrade pyrene, suggesting that degradation may occur due to the presence of cyp150 genes, or even genes that have not yet been described. To the best of our knowledge, this is the first report of isolates without nid genes demonstrating the ability to degrade pyrene.

Petroleum-Degrading Fungal Isolates for the Treatment of Soil Microcosms

The main purpose of this study was to degrade total petroleum hydrocarbons (TPHs) from contaminated soil in batch microcosm reactors. Native soil fungi isolated from the same petroleum-polluted soil and ligninolytic fungal strains were screened and applied in the treatment of soil-contaminated microcosms in aerobic conditions. The bioaugmentation processes were carried out using selected hydrocarbonoclastic fungal strains in mono or co-cultures. Results demonstrated the petroleum-degrading potential of six fungal isolates, namely KBR1 and KBR8 (indigenous) and KBR1-1, KB4, KB2 and LB3 (exogenous). Based on the molecular and phylogenetic analysis, KBR1 and KB8 were identified as Aspergillus niger [MW699896] and tubingensis [MW699895], while KBR1-1, KB4, KB2 and LB3 were affiliated with the genera Syncephalastrum sp. [MZ817958], Paecilomyces formosus [MW699897], Fusarium chlamydosporum [MZ817957] and Coniochaeta sp. [MW699893], respectively. The highest rate of TPH degradation was recorded in soil microcosm treatments (SMT) after 60 days by inoculation with Paecilomyces formosus 97 ± 2.54%, followed by bioaugmentation with the native strain Aspergillus niger (92 ± 1.83%) and then by the fungal consortium (84 ± 2.21%). The statistical analysis of the results showed significant differences.

A comprehensive review on the potential of microbial enzymes in multipollutant bioremediation: Mechanisms, challenges, and future prospects

Industrialization and other human activity represent significant environmental hazards. Toxic contaminants can harm a comprehensive platform of living organisms in their particular environments. Bioremediation is an effective remediation process in which harmful pollutants are eliminated from the environment using microorganisms or their enzymes. Microorganisms in the environment often create a variety of enzymes that can eliminate hazardous contaminants by using them as a substrate for development and growth. Through their catalytic reaction mechanism, microbial enzymes may degrade and eliminate harmful environmental pollutants and transform them into non-toxic forms. The principal types of microbial enzymes which can degrade most hazardous environmental contaminants include hydrolases, lipases, oxidoreductases, oxygenases, and laccases. Several immobilizations, genetic engineering strategies, and nanotechnology applications have been developed to improve enzyme performance and reduce pollution removal process costs. Until now, the practically applicable microbial enzymes from various microbial sources and their ability to degrade multipollutant effectively or transformation potential and mechanisms are unknown. Hence, more research and further studies are required. Additionally, there is a gap in the suitable approaches considering toxic multipollutants bioremediation using enzymatic applications. This review focused on the enzymatic elimination of harmful contaminants in the environment, such as dyes, polyaromatic hydrocarbons, plastics, heavy metals, and pesticides. Recent trends and future growth for effectively removing harmful contaminants by enzymatic degradation are also thoroughly discussed.

Recent innovations and challenges in the eradication of emerging contaminants from aquatic systems

Presence of emerging pollutants (EPs), aka Micropollutants (MPs) in the freshwater environments is a severe threat to the environment and human beings. They include pharmaceuticals, insecticides, industrial chemicals, natural hormones, and personal care items and the pollutants are mostly present in wastewater generated from urbanization and increased industrial growth. Even concentrations as low as ngL^-1 or mgL^-1 have proven ecologically lethal to aquatic biota. For several years, the biodegradation of various Micropollutants (MPs) in aquatic ecosystems has been a significant area of research worldwide, with many chemical compounds being discovered in various water bodies. As aquatic biota spends most of their formative phases in polluted water, the impacts on aquatic biota are obvious, indicating that the environmental danger is substantial. In contrast, the impact of these contaminants on aquatic creatures and freshwater consumption is more subtle and manifests directly when disrupting the endocrine system. Research and development activities are expected to enable the development of ecologically sustainable, cost-effective, and efficient treatments for practical systems in the near future. Therefore, this review aims to understand recent emerging pollutants discovered and the available treatment technologies and suggest an innovative and cost-effective method to treat these EPs, which is sustainable and follows the circular bioeconomy.

Effects of Dispersant on the Petroleum Hydrocarbon Biodegradation and Microbial Communities in Seawater from the Baltic Sea and Norwegian Sea

Dispersants have been used in several oil spill accidents, but little information is available on their effectiveness in Baltic Sea conditions with low salinity and cold seawater. This study investigated the effects of dispersant use on petroleum hydrocarbon biodegradation rates and bacterial community structures. Microcosm experiments were conducted at 5 °C for 12 days with North Sea crude oil and dispersant Finasol 51 with open sea Gulf of Bothnia and coastal Gulf of Finland and Norwegian Sea seawater. Petroleum hydrocarbon concentrations were analysed with GC-FID. Bacterial community structures were studied using 16S rDNA gene amplicon sequencing, and the abundance of genes involved in hydrocarbon degradation with quantitative PCR. The highest oil degradation gene abundances and oil removal were observed in microcosms with coastal seawater from the Gulf of Bothnia and Gulf of Finland, respectively, and the lowest in the seawater from the Norwegian Sea. Dispersant usage caused apparent effects on bacterial communities in all treatments; however, the dispersant’s effect on the biodegradation rate was unclear due to uncertainties with chemical analysis and variation in oil concentrations used in the experiments.

Production and Characterisation of an Exopolysaccharide by Bacillus amyloliquefaciens: Biotechnological Applications

The Bacillus amyloliquefaciens RT7 strain was isolated from an extreme acidic environment and identified. The biodegradation capabilities of the strain using different carbon sources (glucose, oleic acid, Tween 80, PEG 200, and the combination of glucose-Tween 80) were evaluated via an indirect impedance technique. The glucose-Tween 80 combination was further studied using nuclear magnetic resonance (NMR). The exopolysaccharide (EPS_RT7) that had been produced with the strain when biodegrading glucose-Tween 80 was isolated and characterised using different techniques (GC-MS, HPLC/MSMS, ATR-FTIR, TGA, and DSC), and its molecular weight was estimated. The results show that the average molecular weight of EPS_RT7 was approximately 7.0794 × 10⁴ Da and a heteropolysaccharide composed of mannose, glucose, galactose, and xylose (molar ratio, 1:0.5:0.1:0.1) with good thermostability. EPS_RT7 showed good emulsifying activity against different natural oils and hydrocarbons at high concentrations (2 mg/mL) and at the studied pH range (3.1-7.2). It also presented good emulsifying activity compared to that of commercial emulsifiers. Lastly, EPS_RT7 showed antioxidant capacity for different free radicals, a lack of cytotoxicity, and antioxidant activity at the cellular level. EPS_RT7 has promising applications in bioremediation processes and other industrial applications.

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.

Biodegradation half-lives of biodiesel fuels in aquatic and terrestrial systems: A review

Information on biodegradation kinetics of biodiesel fuels is a key aspect in risk and impact assessment practice and in selection of appropriate remediation strategies. Unfortunately, this information is scattered, while factors influencing variability in biodegradation rates are still not fully understood. Therefore, we systematically reviewed 32 scientific literature sources providing 142 biodegradation and 56 mineralization half-lives of diesel and biodiesel fuels in various experimental systems. The analysis focused on the variability in half-lives across fuels and experimental conditions, reporting sets of averaged half-life values and their statistical uncertainty. Across all data points, biodegradation half-lives ranged from 9 to 62 days, and were 2-5.5 times shorter than mineralization half-lives. Across all fuels, biodegradation and mineralization half-lives were 2.5-8.5 times longer in terrestrial systems when compared to aquatic systems. The half-lives were generally shorter for blends with increasing biodiesel content, although differences in number of data points from various experiments masked differences in half-lives between different fuels. This in most cases resulted in lack of statistically significant effects of the type of blends and experimental system on biodegradation half-lives. Our data can be used for improved characterization of risks and impacts of biodiesel fuels in aerobic aquatic and terrestrial environments, while more experiments are required to quantify biodegradation kinetics in anaerobic conditions. Relatively high biodegradability of biodiesel may suggest that passive approaches to degrade and dissipate contaminants in situ, like monitored natural attenuation, may be appropriate remediation strategies for biodiesel fuels.

Structural characterization and physicochemical properties of the exopolysaccharide produced by the moderately halophilic bacterium Chromohalobacter salexigens, strain 3EQS1

A strain, 3EQS1, was isolated from a salt sample taken from Lake Qarun (Fayoum Province, Egypt). On the basis of physiological, biochemical, and phylogenetic analyses, the strain was classified as Chromohalobacter salexigens. By 72 h of growth at 25 °C, strain 3EQS1 produced large amounts (15.1 g L^-1) of exopolysaccharide (EPS) in a liquid mineral medium (initial pH 8.0) containing 10% sucrose and 10% NaCl. The EPS was precipitated from the cell-free culture medium with chilled ethanol and was purified by gel-permeation and anion-exchange chromatography. The molecular mass of the EPS was 0.9 × 10⁶ Da. Chemical analyses, Fourier transform infrared spectroscopy, and nuclear magnetic resonance spectroscopy showed that the EPS was a linear β-D-(2 → 6)-linked fructan (levan). In aqueous solution, the EPS tended to form supramolecular aggregates with a critical aggregation concentration of 240 µg mL^-1. The EPS had high emulsifying activity (E₂₄, %) against kerosene (31.2 ± 0.4%), sunflower oil (76.9 ± 1.3%), and crude oil (98.9 ± 0.8%), and it also had surfactant properties. A 0.1% (w/v) aqueous EPS solution reduced the surface tension of water by 11.9%. The levan of C. salexigens 3EQS1 may be useful in various biotechnological processes.

Genetic engineering to enhance microalgal-based produced water treatment with emphasis on CRISPR/Cas9: A review

In recent years, the increased demand for and regional variability of available water resources, along with sustainable water supply planning, have driven interest in the reuse of produced water. Reusing produced water can provide important economic, social, and environmental benefits, particularly in water-scarce regions. Therefore, efficient wastewater treatment is a crucial step prior to reuse to meet the requirements for use within the oil and gas industry or by external users. Bioremediation using microalgae has received increased interest as a method for produced water treatment for removing not only major contaminants such as nitrogen and phosphorus, but also heavy metals and hydrocarbons. Some research publications reported nearly 100% removal of total hydrocarbons, total nitrogen, ammonium nitrogen, and iron when using microalgae to treat produced water. Enhancing microalgal removal efficiency as well as growth rate, in the presence of such relevant contaminants is of great interest to many industries to further optimize the process. One novel approach to further enhancing algal capabilities and phytoremediation of wastewater is genetic modification. A comprehensive description of using genetically engineered microalgae for wastewater bioremediation is discussed in this review. This article also reviews random and targeted mutations as a method to alter microalgal traits to produce strains capable of tolerating various stressors related to wastewater. Other methods of genetic engineering are discussed, with sympathy for CRISPR/Cas9 technology. This is accompanied by the opportunities, as well as the challenges of using genetically engineered microalgae for this purpose.

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.

Genetically engineered microorganisms for environmental remediation

In the recent era, the increasing persistence of hazardous contaminants is badly affecting the globe in many ways. Due to high environmental contamination, almost every second species on earth facing the worst issue in their survival. Advances in newer remediation approaches may help enhance bioremediation's quality, while conventional procedures have failed to remove hazardous compounds from the environment. Chemical and physical waste cleanup approaches have been used in current circumstances; however, these methods are costly and harmful to the environment. Thus, there has been a rise in the use of bioremediation due to an increase in environmental contamination, which led to the development of genetically engineered microbes (GEMs). It is safer and more cost-effective to use engineered microorganisms rather than alternative methods. GEMs are created by introducing a stronger protein into bacteria through biotechnology or genetic engineering to enhance the desired trait. Biodegradation of oil spills, halobenzoates naphthalenes, toluenes, trichloroethylene, octanes, xylenes etc. has been accomplished using GEMs such bacteria, fungus, and algae. Biotechnologically induced microorganisms are more powerful than naturally occurring ones and may degrade contaminants faster because they can quickly adapt to new pollutants they encounter or co-metabolize. Genetic engineering is a worthy process that will benefit the environment and ultimately the health of our people.

Growth suppression of bacteria by biofilm deterioration using silver nanoparticles with magnetic doping

Decades of antibiotic use and misuse have generated selective pressure toward the rise of antibiotic-resistant bacteria, which now contaminate our environment and pose a major threat to humanity. According to the evolutionary "Red queen theory", developing new antimicrobial technologies is both urgent and mandatory. While new antibiotics and antibacterial technologies have been developed, most fail to penetrate the biofilm that protects bacteria against external antimicrobial attacks. Hence, new antimicrobial formulations should combine toxicity for bacteria, biofilm permeation ability, biofilm deterioration capability, and tolerability by the organism without renouncing compatibility with a sustainable, low-cost, and scalable production route as well as an acceptable ecological impact after the ineluctable release of the antibacterial compound in the environment. Here, we report on the use of silver nanoparticles (NPs) doped with magnetic elements (Co and Fe) that allow standard silver antibacterial agents to perforate bacterial biofilms through magnetophoretic migration upon the application of an external magnetic field. The method has been proved to be effective in opening micrometric channels and reducing the thicknesses of models of biofilms containing bacteria such as Enterococcus faecalis, Enterobacter cloacae, and Bacillus subtilis. Besides, the NPs increase the membrane lipid peroxidation biomarkers through the formation of reactive oxygen species in E. faecalis, E. cloacae, B. subtilis, and Pseudomonas putida colonies. The NPs are produced using a one-step, scalable, and environmentally low-cost procedure based on laser ablation in a liquid, allowing easy transfer to real-world applications. The antibacterial effectiveness of these magnetic silver NPs may be further optimized by engineering the external magnetic fields and surface conjugation with specific functionalities for biofilm disruption or bactericidal effectiveness.

Effective bioremediation of soil from the Burgan oil field (Kuwait) using compost: A comprehensive hydrocarbon and DNA fingerprinting study

An innovative combination of metagenomic profiling of microbial communities and GC-MS & Pyrolysis-GC-MS fingerprinting methods were used to assess the biodegradation of contaminated soil from the Burgan oil field in Kuwait. The soil was treated with (sludge) compost in microcosms to evaluate the feasibility of this material for bioremediation purposes. The most favourable trial showed a > 80% decrease in TPH, thereby indicating strong potential for full-scale application using a cost-effective technology and thus in line with the principles of the circular economy. The microbial study showed that compost addition enhanced the organic matter and nutrient content of the soil. However, the microorganisms in the compost did not seem to play a relevant role in bioremediation, meaning that compost amendments serve as a biostimulation rather than a bioaugmentation approach. The chemical study of the distinct oil fractions revealed rapidly biodegraded compounds (alkanes, alkyl-aromatics, etc.) and others that were much more refractory (hopanes, benzohopanes, etc.). Of note, although heavy fractions are usually considered recalcitrant to biodegradation, we observed incipient degradation of the asphaltene fraction by means of double-shot thermodesorption and pyrolysis. Finally, chemical fingerprinting also revealed that the treated soil contained some of the compounds found in the compost, such as coprostanol, cholesterol, and plant sterols. This observation would support the use of these compounds as proxies to monitor the effects of compost and to adjust dosages in real-scale bioremediation treatments.

Engineering microbes for enhancing the degradation of environmental pollutants: A detailed review on synthetic biology

Anthropogenic activities resulted in the deposition of huge quantities of contaminants such as heavy metals, dyes, hydrocarbons, etc into an ecosystem. The serious ill effects caused by these pollutants to all living organisms forced in advancement of technology for degrading or removing these pollutants. This degrading activity is mostly depending on microorganisms owing to their ability to survive in harsh adverse conditions. Though native strains possess the capability to degrade these pollutants the development of genetic engineering and molecular biology resulted in engineering approaches that enhanced the efficiency of microbes in degrading pollutants at faster rate. Many bioinformatics tools have been developed for altering/modifying genetic content in microbes to increase their degrading potency. This review provides a detailed note on engineered microbes - their significant importance in degrading environmental contaminants and the approaches utilized for modifying microbes. The genes responsible for degrading the pollutants have been identified and modified fir increasing the potential for quick degradation. The methods for increasing the tolerance in engineered microbes have also been discussed. Thus engineered microbes prove to be effective alternate compared to native strains for degrading pollutants.

Simulation on the Permeability Evaluation of a Hybrid Liner for the Prevention of Contaminant Diffusion in Soils Contaminated with Total Petroleum Hydrocarbon

This study describes the test results to evaluate the impermeability efficiency, according to the total petroleum hydrocarbon (TPH) reaction time of a hybrid liner for preventing the TPH diffusion, and the numerical analysis results, according to the various TPH reaction times of the hybrid liner. The experimental results indicated that the hybrid liner performed effectively as an impermeable material under the condition of a 4 h reaction time between TPH and the hybrid liner. In other words, the permeability of the hybrid liner was lower than 7.64 × 10^-7 cm/s when the reaction time of the TPH and the hybrid liner exceeded 4 h. This means that polynorbornene applied as a reactant becomes completely gelated four hours after it reacts with TPH, demonstrating its applicability as a liner. The numerical analysis results to evaluate the TPH diffusion, according to the hybrid liner-TPH reaction time indicated that the concentration decreased, compared to the initial concentration as the hybrid liner-TPH reaction time increased, regardless of the head-difference and the observation point for all concentration conditions. In addition, the reduction ratio of the concentration, compared to the initial concentration was 99% ~ 100%, when the reaction time of the hybrid liner-TPH was more than 4 h. It was found that the concentration diffusion of TPH reacting with the hybrid liner was decreased when the distance from the hybrid liner and the reaction time of the hybrid liner-TPH were increased. In other words, in the case of a high-TPH condition, the concentration reduction ratio is 12.5~17.8%, 16.9~29.7%, depending on the distance ratio (D/L = 0.06, 0.54, 0.94), respectively, when the reaction time of the hybrid liner-TPH is 0 h and 0.5 h, respectively. In the case of medium- and low-TPH conditions, the concentration reduction ratio, according to the distance ratio is 12.0% to 20.8% and 17.0% to 29.8%, respectively. This result means that a numerical analysis model can be used sufficiently to predict the TPH diffusion, according to the distance from the location where the hybrid liner is installed.

Interaction between indigenous hydrocarbon-degrading bacteria in reconstituted mixtures for remediation of weathered oil in soil

It has been demonstrated that biostimulation is necessary to investigate the interactions between indigenous bacteria and establish an approach for the bioremediation of soils contaminated with weathered oil. This was achieved by adjusting the carbon (C)/nitrogen (N)/phosphorus (P) ratio to 100/10/1 combined with the application of 0.8 mL/kg Tween-80. In addition, three indigenous bacteria isolated from the same soil were introduced solely or combined concomitantly with stimulation. Removal of n-alkanes and the ratios of n-heptadecane to pristane and n-octadecane to phytane were taken to indicate their biodegradation performance over a period of 16 weeks. One strain of Pseudomonas aeruginosa D7S1 improved the efficiency of the process of stimulation. However, another Pseudomonas aeruginosa, D5D1, inhibited the overall process when combined with other bacteria. One strain of Bacillus licheniformis D1D2 did not affect the process significantly. The Fourier transform infrared analysis of the residual hydrocarbons supported the conclusions pertaining to the biodegradation processes when probing the modifications in densities and stretching. The indigenous bacteria cannot mutually benefit from their metabolisms for bioremediation if augmented artificially. However, the strain Pseudomonas. aeruginosa D7S1 was able to perform better alone than in a consortium of indigenous bacteria.

Physiological and microbiological hormesis in sedge Eleocharis palustris induced by crude oil in phytoremediation of flooded clay soil

Soil contamination with petroleum hydrocarbons affects plants and rhizospheric microorganisms. Microbial activity participates in important biochemical processes that stimulate, together with plants, the modification of toxic compounds for organisms. A nine-month experiment was set up to study the effect over time of oil on plant height (cm), formation of new plants, plant matter production (gravimetry), and population of rhizospheric microorganisms (serial dilution) in the sedge Eleocharis palustris. Removal of total petroleum hydrocarbons (soxhlet and gravimetry) from the soil was also evaluated. The means of the evaluated variables registered significant statistical differences (Duncan, p < 0.05) regarding the age of the plant and the amount of crude oil. There was a high correlation between oil and plant height (0.848) and with new plants (0.994). 60 mg oil dose promoted the greatest statistical difference in the amounts of roots and plant biomass (p < 0.05). E. palustris exposed to 60 and 75 mg of oil stimulated high densities of microalgae, actinomycetes, fungi, hydrocarbonoclastic bacteria and Pseudomonas spp; the overall ratio was 2:1 relative to natural attenuation. Plant and microorganism variables evaluated registered physiological and microbiological hormetic indices ≥1, showing a positive linear relationship. Natural attenuation was more efficient in removing crude oil. We conclude that E. palustris is tolerant to oil exposure. It is suggested to combine it with natural attenuation for the optimization of soils contaminated with crude oil.