Microbial degradation of petroleum hydrocarbons

Hydrocarbon Degradation and Enzyme Activities of Aspergillus oryzae and Mucor irregularis Isolated from Nigerian Crude Oil-Polluted Sites

Many free-living saprobic fungi are nature recruited organisms for the degradation of wastes, ranging from lignocellulose biomass to organic/inorganic chemicals, aided by their production of enzymes. In this study, fungal strains were isolated from contaminated crude-oil fields in Nigeria. The dominant fungi were selected from each site and identified as Aspergillus oryzae and Mucor irregularis based on morphological and molecular characterization, with site percentage incidences of 56.67% and 66.70%, respectively. Selected strains response/tolerance to complex hydrocarbon (used engine oil) was studied by growing them on Bushnell Haas (BH) mineral agar supplemented with the hydrocarbon at different concentrations, i.e., 5%, 10%, 15%, and 20%, with a control having dextrose. Hydrocarbon degradation potentials of these fungi were confirmed in BH broth culture filtrates pre-supplemented with 1% engine oil after 15 days of incubation using GC/MS. In addition, the presence of putative enzymes, laccase (Lac), manganese peroxidase (MnP), and lignin peroxidase (LiP) was confirmed in culture filtrates using appropriate substrates. The analyzed fungi grew in hydrocarbon supplemented medium with no other carbon source and exhibited 39.40% and 45.85% dose inhibition response (DIR) respectively at 20% hydrocarbon concentration. An enzyme activity test revealed that these two fungi produced more Lac than MnP and LiP. It was also observed through the GC/MS analyses that while A. oryzae acted on all hydrocarbon components in the used engine oil, M. irregularis only degraded the long-chain hydrocarbons and BTEX. This study confirms that A. oryzae and M. irregularis have the potential to be exploited in the bio-treatment and removal of hydrocarbons from polluted soils.

Enhanced Growth of Mungbean and Remediation of Petroleum Hydrocarbons by Enterobacter sp. MN17 and Biochar Addition in Diesel Contaminated Soil

Petroleum hydrocarbon (PHC) contamination of soil is a widespread global environmental concern due to the persistence and recalcitrant nature of PHCs. The PHCs are highly toxic and their removal from the terrestrial ecosystem is necessary to maintain soil as well as human health. Here, a pot experiment was performed to examine the impact of Enterobacter sp. MN17 and biochar addition on the growth of mungbean plants and PHCs removal from diesel-polluted soil. For this purpose, soil was contaminated artificially with diesel to achieve a final concentration of 5000 mg kg−1. Untreated and Enterobacter sp. MN17 treated mungbean seeds were sown in pots. Sugarcane bagasse biochar was applied as an amendment in respective pots along with the recommended levels of essential nutrients. Results showed that PHCs significantly suppressed the seedling emergence as well as agronomic and physiological attributes of mungbean as compared to un-contaminated controls. However, the co-application of Enterobacter sp. MN17 and biochar significantly reduced the phytotoxicity of PHCs to mungbean plants and effectively increased the seedling emergence, shoot and root length, shoot fresh and dry biomass, root fresh and dry biomass of plants up to 24%, 54%, 52%, 52%, 54%, 55% and 60%, respectively as compared to controls. Similarly, 30%, 57%, 64%, 36% and 57% increase in chlorophylls contents, transpiration rate, stomatal conductance, sub-stomatal conductance, and photosynthetic rate, respectively were observed in their combined application as compared to respective controls. Furthermore, the co-addition of biochar and Enterobacter sp. MN17 could remove 69% and 85% higher PHCs from unplanted and planted pots, respectively, than that of their respective controls. Our results suggest that the co-application of biochar and Enterobacter sp. MN17 may be useful in enhancing plant growth and eliminating PHCs from contaminated soil.

Oilfield waste treatment using novel hydrocarbon utilizing bacterial consortium - A microcosm approach

Oily sludge is a hazardous waste generated through petroleum producing and processing industrial units. Due to its harmful environmental impacts, it needs to be treated in sustainable manner. The present study aimed to evaluate influence of bioaugmentation on oily sludge biodegradation efficiency of a novel hydrocarbon utilizing bacterial consortium (HUBC) using microcosms. Three approaches (bioaugmentation, natural attenuation and abiotic factors) were used for microcosm studies. Bioaugmentation treatment showed best results for oily sludge degradation than natural attenuation and abiotic factors, resulting 82.13 ± 1.21% oily sludge degradation in 56 days. In bioaugmented microcosm on 56th day 0.30 ± 0.07 × 10⁸ CFU/g hydrocarbon utilizing bacteria were noted. Results showed that HUBC could be used to remediate soil polluted with oily sludge. This study imparts a notable approach for farming application(s).

Microbial Polyethylene Terephthalate Hydrolases: Current and Future Perspectives

Plastic has rapidly transformed our world, with many aspects of human life now relying on a variety of plastic materials. Biological plastic degradation, which employs microorganisms and their degradative enzymes, has emerged as one way to address the unforeseen consequences of the waste streams that have resulted from mass plastic production. The focus of this review is microbial hydrolase enzymes which have been found to act on polyethylene terephthalate (PET) plastic. The best characterized examples are discussed together with the use of genomic and protein engineering technologies to obtain PET hydrolase enzymes for different applications. In addition, the obstacles which are currently limiting the development of efficient PET bioprocessing are presented. By continuing to study the possible mechanisms and the structural elements of key enzymes involved in microbial PET hydrolysis, and by assessing the ability of PET hydrolase enzymes to work under practical conditions, this research will help inform large-scale waste management operations. Finally, the contribution of microbial PET hydrolases in creating a potential circular PET economy will be explored. This review combines the current knowledge on enzymatic PET processing with proposed strategies for optimization and use, to help clarify the next steps in addressing pollution by PET and other plastics.

Bacterial diversity in aqueous/sludge phases within diesel fuel storage tanks

Diesel fuel storage tanks are not hostile environments for microorganisms and tend to form sludges in the water deposited at the bottom of the tanks. The lack of nutrient, carbon and energy limitations within these habitats boost the abundance and the metabolic activity of microorganisms providing microbial hotspots with high growing rates of diesel degradation (0.10 ± 0.021 d^-1). Five different Phyla (Thermotogae, Spirochaetes, Firmicutes, Bacteroidetes Proteobacteria) were identified within the aqueous/sludge phase from in situ diesel storage tanks, by cultured independent molecular surveys using the 16S rDNA gene fragment. The identified dominant strains were Geotoga aestuarianus, Flavobacterium ceti, Spirochaeta thermophila, Propionispira arboris, Sporobacterium olearium and Dysgonomonas genera. The altitude where the storage tanks are located and the organic carbon concentration within the aqueous/sludge phases affected the bacterial diversity. Therefore, the more diverse the microbial communities are, the more probability of the presence of bacteria with capacity to metabolized diesel and eliminate organic matter. Despite, only phosphate showed an effect on the bacterial distribution within the storage tanks, there was an apparent lack of deterministic process in structuring microbial communities. Consequently, preventative protocols are a priority to avoid the microbial growth within diesel fuel storage tanks. A new focus of this worldwide problem within the oil industry would be to explore deeply the wide range of metabolic and adaptive capacities of these microorganisms. These microbial consortia are potential tools with new specific services to apply in bioremediation among others.

Enhancing anaerobic degradation of oily sludge using subcritical hydrothermal pretreatment

AIMS

Oily sludge is a kind of mixture that is extremely harmful to the environment. Anaerobic digestion (AD) is a commonly used method for biodegrading oily sludge. However, the AD treatment cycle is usually long and inefficient. Here, we developed an approach to improve the degradation rate of oily sludge by integrating subcritical hydrothermal pretreatment (SHP) and AD.

METHODS AND RESULTS

First, using SHP, the hydrocarbon compounds with long carbon chains that make up oil sludge were decomposed into hydrocarbons with short carbon chains, which are conducive to microbial decomposition and transformation. Then, AD was performed using a variety of temperature and solid-liquid ratio parameters. The results showed that the degradation ratio of oily sludge was higher when SHP was combined with AD than when no pre-treatment was performed. Optimal degradation was reached by performing SHP to obtain CHS8, then performing AD at 30°C using a 1:5 solid-liquid ratio. Under these conditions, maximum degradation ratios of 69·00% of TOC, 59·02% of COD, 44·68% of ammonia and 54·24% of oil content were reached.

CONCLUSIONS

In conclusion, after SHP with 8% dilute sulphuric acid, most of the macromolecular hydrocarbons in the oily sludge were converted into smaller molecules, which facilitated subsequent microbial decomposition. The results showed that this combination of SHP and AD processes promotes more efficient degradation than a conventional single AD process without any hydrothermal pretreatment.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our experiments provide technical support for enhancing the rapid degradation of oily sludge.

Degradation of the mixture of ethyl formate, propionic aldehyde, and acetone by Aeromonas salmonicida: A novel microorganism screened from biomass generated in the citric acid fermentation industry

Microorganisms play important roles in the degradation of volatile organic compounds. Aeromonas salmonicida strain (AEP-3) generated from biomass in the citric acid fermentation industry was screened and subjected to denaturing gradient gel electrophoresis (DGGE) fingerprinting and 16S rDNA gene sequencing. The growth conditions of AEP-3 in Luria-Bertani broth were optimized at 25 °C and approximately pH 7. AEP-3 was used to degrade ethyl formate, propionic aldehyde, or acetone alone and their mixture. The concentrations of ethyl formate, propionic aldehyde, and acetone were below 7500, 600, and 800 mg L^-1, respectively, and their maximum degradation efficiencies were 100%, 92.41%, and 34.75%. AEP-3 first degraded acetone and propionic aldehyde in the mixture, followed by ethyl formate. The degradation pathways of these organic compounds in the mixture and their substrate interactions during degradation were explored. Propionic aldehyde was first converted into propionic acid in the metabolic process and was involved in the subsequent carboxylic acid cycle. By contrast, ethyl formate was first hydrolyzed into formic acid and ethanol. Then, formic acid participated in the cyclic metabolism of carboxylic acid, whereas, ethanol was hydrolyzed into acetaldehyde and acetic acid through alcohol and aldehyde dehydrogenase. Additionally, acetone directly interacted with nitrate in the medium under the action of hydrogen ions and produced carbon dioxide, water, and nitrogen. Overall, this study provides a new degrading bacterium biodegradability toward the exhaust gas of citric acid fermentation.

Production of glycolipid biosurfactant during crude oil degradation by the novel indigenous isolated Achromobacter kerstersii LMG3441

This study aimed to find biosurfactant producing and crude oil-degrading bacteria able to decontaminate crude oil from wastewater. The bacteria that were isolated from contaminated sites in an oil refinery plant in Isfahan, Iran, were identified by 16S rDNA sequencing as Achromobacter kerstersii strain LMG3441, Klebsiella pneumonia strain SKBA6, and Klebsiella variicola strain SKV2. According to the results obtained from different tests for the production of biosurfactant among three strains, only Achromobacter kerstersii strain LMG3441 was selected for further study. The pattern of residual hydrocarbons was analyzed by high-resolution gas chromatography-mass spectrometry (GC-MS). This novel and indigenous strain was capable of producing the highest amount of a glycolipid biosurfactant (7.81 g/L) in MSM (mineral salt medium) with 1% (v/v) crude oil as the only source of carbon and energy. The compound showed high surface activation capacity with reduction of surface tension from 40 mN m^-1 in the control to 23.3 mN m^-1 by the bacterium. The results of GC-MS for assessment of residual hydrocarbons in the MSM and comparison with crude oil as a control showed that 53% of the hydrocarbons in the crude oil were consumed by this novel strain.

Unitary and binary remediations by plant and microorganism on refining oil-contaminated soil

Refining oil contaminants are complex and cause serious harm to the environment. Remediation of refining oil-contaminated soil is challenging but has significant impact in China. Two plant species Agropyron fragile (Roth) P. Candargy and Avena sativa L. and one bacterium Bacillus tequilensis ZJ01 were used to investigate their efficiency in remediating the refining oil-polluted soil sampled from an oil field in northern China. The simulated experiments of remediations by A. fragile or A. sativa alone and A. fragile or A. sativa combined with B. tequilensis ZJ01 for 39 days and by B. tequilensis ZJ01 alone for 7 days were performed in the laboratory, with B. tequilensis ZJ01 added before or after the germination of seeds. Seed germination rates and morphological characteristics of the plants, along with the varieties of oil hydrocarbons in the soil, were recorded to reflect the remediation efficiency. The results showed that the contamination was weakened in all experimental groups. A. sativa was more sensitive to the pollutants than A. fragile, and A. fragile was much more resistant to the oil hydrocarbons, especially to aromatic hydrocarbons. Adding B. tequilensis ZJ01 before the germination of seeds could restrain the plant growth while adding after the germination of A. fragile seeds notably improved the remediation efficiency. The degradation rate of oil hydrocarbons by B. tequilensis ZJ01 alone was also considerable. Together, our results suggest that the unitary remediation by B. tequilensis ZJ01 and the binary remediation by A. fragile combined with B. tequilensis ZJ01 added after the germination of seeds are recommended for future in situ remediations.

Barbero G, Palma M. Characterization of Biodegraded Ignitable Liquids by Headspace-Ion Mobility Spectrometry

The detection of ignitable liquids (ILs) can be crucial when it comes to determining arson cases. Such identification of ILs is a challenging task that may be affected by a number of factors. Microbial degradation is considered one of three major processes that can alter the composition of IL residues. Since biodegradation is a time related phenomenon, it should be studied at different stages of development. This article presents a method based on ion mobility spectroscopy (IMS) which has been used as an electronic nose. In particular, ion mobility sum spectrum (IMSS) in combination with chemometric techniques (hierarchical cluster analysis (HCA) and linear discriminant analysis (LDA)) has been applied for the characterization of different biodegraded ILs. This method intends to use IMSS to identify a range of ILs regardless of their degree of biodegradation. Three ILs (diesel, gasoline and kerosene) from three different commercial brands were evaluated after remaining in a soil substrate for several lengths of time (0, 2, 5, 13 and 38 days). The HCA results showed the samples’ trend to fall into categories characterized by ILs type and biodegradation time. The LDAs allowed a 99% successful classification of the samples according to the IL type. This is the first time that an HS-IMS technique has been used to detect ILs that have undergone biodegradation processes. The results show that IMS may be a promising alternative to the current standard method based on gas-chromatography for the analysis of biodegraded ILs. Furthermore, no pretreatment of the samples nor the use of a solvent is required.

Representing Organic Matter Thermodynamics in Biogeochemical Reactions via Substrate-Explicit Modeling

Predictive biogeochemical modeling requires data-model integration that enables explicit representation of the sophisticated roles of microbial processes that transform substrates. Data from high-resolution organic matter (OM) characterization are increasingly available and can serve as a critical resource for this purpose, but their incorporation into biogeochemical models is often prohibited due to an over-simplified description of reaction networks. To fill this gap, we proposed a new concept of biogeochemical modeling-termed substrate-explicit modeling-that enables parameterizing OM-specific oxidative degradation pathways and reaction rates based on the thermodynamic properties of OM pools. Based on previous developments in the literature, we characterized the resulting kinetic models by only two parameters regardless of the complexity of OM profiles, which can greatly facilitate the integration with reactive transport models for ecosystem simulations by alleviating the difficulty in parameter identification. The two parameters include maximal growth rate (μmax) and harvest volume (Vh) (i.e., the volume that a microbe can access for harvesting energy). For every detected organic molecule in a given sample, our approach provides a systematic way to formulate reaction kinetics from chemical formula, which enables the evaluation of the impact of OM character on biogeochemical processes across conditions. In a case study of two sites with distinct OM thermodynamics using ultra high-resolution metabolomics datasets derived from Fourier transform ion cyclotron resonance mass spectrometry analyses, our method predicted how oxidative degradation is primarily driven by thermodynamic efficiency of OM consistent with experimental rate measurements (as shown by correlation coefficients of up to 0.61), and how biogeochemical reactions can vary in response to carbon and/or oxygen limitations. Lastly, we showed that incorporation of enzymatic regulations into substrate-explicit models is critical for more reasonable predictions. This result led us to present integrative biogeochemical modeling as a unifying framework that can ideally describe the dynamic interplay among microbes, enzymes, and substrates to address advanced questions and hypotheses in future studies. Altogether, the new modeling concept we propose in this work provides a foundational platform for unprecedented predictions of biogeochemical and ecosystem dynamics through enhanced integration with diverse experimental data and extant modeling approaches.

Biodegradation of petroleum refining industry oil sludge by microbial-assisted biocarrier matrix: process optimization using response surface methodology

Safe disposal of petroleum oil sludge generated from crude oil storage tank bottom is a major challenge for petroleum refineries across the globe. The presence of long chain hydrocarbons in petroleum oil sludge are known to have effects on the environment through bioaccumulation or biosorption. The present study was focused to develop a modified bioremediation process using hydrocarbonoclastic microbial-assisted biocarrier matrix (MABC) mediated through biosurfactants and biocatalysts for the efficient treatment of petroleum industrial oily sludge. The development of hydrocarbonoclastic microbial-assisted biocarrier matrix was confirmed by scanning electron microscopy analysis. The biocatalysts such as lipase, laccase, esterase and biosurfactant produced by MABC system were found to be 40 U/mg, 18 U/mg, 36 U/mg and 220 mg/g of oil sludge respectively using one variable at a time approach. Further, the response surface methodology was used to determine the optimum treatment conditions (Time, pH, Mass of biocarrier matrix and Amount of oil sludge) for the enhanced removal of total petroleum hydrocarbons (TPH) present in the oil sludge and TPH was degraded by 88.78% at Hydraulic Retention Time of 7 days. The biodegradation of oil sludge was confirmed using Gas Chromatography-Mass Spectrometry analysis.

Effects of chronic exposure to water accommodated fraction (WAF) of light crude oil on gut microbiota composition of the lined sole (Achirus lineatus)

Exposure of marine fish to hydrocarbon compounds from crude oil can cause physiological and ecological alterations that can result in several cytotoxic, genotoxic, and teratogenic damages. One consequence of this exposure is the dysbiosis of the gut microbiota, where the normal bacterial composition is modified. Herein, we assessed the effect of the exposure to water accommodated fraction (WAF) of a light crude oil into the gut microbiota of a native species, the lined sole Achirus lineatus, a benthonic fish widely distributed in the Gulf of Mexico (GoM). We performed a chronic bioassay using two WAF concentrations (5 and 10% v/v), collecting lined sole entire gastrointestinal tracts for microbiota analyses at two timepoints, 14 and 28 days. Changes in the gut microbiota composition were determined by high throughput amplicon sequencing of the gene 16S rRNA. Diversity analyses showed that WAF exposure produced similar changes in the microbiota composition at both concentrations. Metagenomic functional prediction showed that these alterations could result in a shift in the gut redox status, towards a more anoxygenic environment. Enrichment of bacteria capable of use hydrocarbon as carbon source seems to be fast regardless time of exposure or WAF concentrations. Our results suggest that chronic WAF exposure can cause a dysbiosis in this benthic native species from the GoM.

Bioremediation of oily sludge polluted soil employing a novel strain of Pseudomonas aeruginosa and phytotoxicity of petroleum hydrocarbons for seed germination

Agricultural land pollution is key a problem globally, which is linked with growth of industries. Petroleum industrial sector is one of the major industrial sectors and the activities of petroleum industry lead to the agricultural land pollution. Oily sludge is a type of solid and hazardous waste generated from petroleum industrial activities. Hence, there is an urgent need to find remediation methods of the oily sludge contaminated agricultural land. Thus, the aim of this work was to study bioremediation of oily sludge polluted soil employing a novel strain of Pseudomonas aeruginosa and evaluation of phytotoxicity on germination of Vigna radiata seed in pots. Five different approaches were adopted for the bioremediation studies, which included Bioaugmentation + Biostimulation, bioaugmentation, biostimulation, natural attenuation and abiotic factors. Simultaneous application of P. aeruginosa NCIM 5514 and nutrients in microcosm showed 92.97 ± 0.92% decrease in oily sludge with good hydrocarbon utilizing bacterial count and decreased nutrient level in 56 days. Pot experiments on seed germination of mung beans (Vigna radiata) seeds was performed by pot experiments. 80.95% germination in five days in treated soil. From the results it was concluded that simultaneous use of oily sludge degraders and nutrient supplement could revive seed germination ability of oily sludge polluted soil effectively. This is first report of comparing five techniques to bioremediate oily sludge polluted soil using Pseudomonas aeruginosa, followed by pot study using V. radiata seeds, showing that P. aeruginosa can be an efficient bioremediation agent and can be effectively used for remediation of oily sludge contaminated soil.

Bacterial Community Composition in Produced Water of Diyarbakır Oil Fields in Turkey : Bacterial communities in produced waters of south-eastern Turkey reported in detail for the first time

Oil fields harbour a wide variety of microorganisms with different metabolic capabilities. To examine the microbial ecology of petroleum reservoirs, a molecular-based approach was used to assess the composition of bacterial communities in produced water of Diyarbakır oil fields in Turkey. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rRNA gene fragments was performed to characterise the bacterial community structure of produced water samples and to identify predominant community members after sequencing of separated DGGE bands. The majority of bacterial sequences retrieved from DGGE analysis of produced water samples belonged to unclassified bacteria (50%). Among the classified bacteria, Proteobacteria (29.2%), Firmicutes (8.3%), Bacteroidetes (8.3%) and Actinobacteria (4.2%) groups were identified. Pseudomonas was the dominant genus detected in the produced water samples. The results of this research provide, for the first time, insight into the complexity of microbial communities in the Diyarbakır oil reservoirs and their dominant constituents.

Microbial degradation of dyes: An overview

Industrialization increases use of dyes due to its high demand in paper, cosmetic, textile, leather and food industries. This in turn would increase wastewater generation from dye industrial activities. Various dyes and its structural compounds present in dye industrial wastewater have harmful effects on plants, animals and humans. Synthetic dyes are more resistant than natural dyes to physical and chemical methods for remediation which makes them more difficult to get decolorize. Microbial degradation has been researched and reviewed largely for quicker dye degradation. Genetically engineered microorganisms (GEMs) play important role in achieving complete dye degradation. This paper provides scientific and technical information about dyes & dye intermediates and biodegradation of azo dye. It also compiles information about factors affecting dye(s) biodegradation, role of genetically modified organisms (GMOs) in process of dye(s) degradation and perspectives in this field of research.

Catalase and superoxide dismutase response and the underlying molecular mechanism for naphthalene

Naphthalene, a naturally-occurring polyaromatic hydrocarbon, pose potential threats to health for its wide exposures in environment. Naphthalene could disrupt the redox equilibrium resulting in oxidative damage. Antioxidant enzymes catalase (CAT) and superoxide dismutase (SOD) are considered to be the efficient defense barriers to protect organisms from negative impacts of toxicants. Limited information is available regarding the underlying molecular mechanism between antioxidant enzymes and naphthalene. In this paper, structural and functional alterations of CAT and SOD for low dose (1.6-25.6 mg/L) naphthalene exposure have been investigated at the molecular and cellular levels. The enzyme activity responses of CAT and SOD in hepatocytes for naphthalene were consistent with the molecular, in which the activity of CAT increased and the activity of SOD slightly inhibited. Spectroscopy methods and molecular docking were carried out to investigate the underlying binding mechanisms. Naphthalene exposure significantly changed the conformation of CAT with secondary structure alteration (α-helix increase) but only changed the skeleton structure of SOD without secondary structure alteration. Naphthalene could bind to CAT and SOD primarily via H-binding force accompanied with the particle size of CAT/SOD agglomerates decreasing. Naphthalene preferentially bound to the surface of CAT and SOD. Besides, naphthalene could also bind directly to the active center of CAT with the key residues Arg364 and Tyr 357 for activity. This paper provides a combined cellular and molecular strategy to research biomarker responses for toxicants exposure. Besides, this study offers detailed basic data for the comprehensive understanding of naphthalene toxicity.

Metagenomic Insights Into the Mechanisms for Biodegradation of Polycyclic Aromatic Hydrocarbons in the Oil Supply Chain

Petroleum is a very complex and diverse organic mixture. Its composition depends on reservoir location and in situ conditions and changes once crude oil is spilled into the environment, making the characteristics associated with every spill unique. Polycyclic aromatic hydrocarbons (PAHs) are common components of the crude oil and constitute a group of persistent organic pollutants. Due to their highly hydrophobic, and their low solubility tend to accumulate in soil and sediment. The process by which oil is sourced and made available for use is referred to as the oil supply chain and involves three parts: (1) upstream, (2) midstream and (3) downstream activities. As consequence from oil supply chain activities, crude oils are subjected to biodeterioration, acidification and souring, and oil spills are frequently reported affecting not only the environment, but also the economy and human resources. Different bioremediation techniques based on microbial metabolism, such as natural attenuation, bioaugmentation, biostimulation are promising approaches to minimize the environmental impact of oil spills. The rate and efficiency of this process depend on multiple factors, like pH, oxygen content, temperature, availability and concentration of the pollutants and diversity and structure of the microbial community present in the affected (contaminated) area. Emerging approaches, such as (meta-)taxonomics and (meta-)genomics bring new insights into the molecular mechanisms of PAH microbial degradation at both single species and community levels in oil reservoirs and groundwater/seawater spills. We have scrutinized the microbiological aspects of biodegradation of PAHs naturally occurring in oil upstream activities (exploration and production), and crude oil and/or by-products spills in midstream (transport and storage) and downstream (refining and distribution) activities. This work addresses PAH biodegradation in different stages of oil supply chain affecting diverse environments (groundwater, seawater, oil reservoir) focusing on genes and pathways as well as key players involved in this process. In depth understanding of the biodegradation process will provide/improve knowledge for optimizing and monitoring bioremediation in oil spills cases and/or to impair the degradation in reservoirs avoiding deterioration of crude oil quality.

Fungal bioremediation of soil co-contaminated with petroleum hydrocarbons and toxic metals

Abstract

Much research has been carried out on the bacterial bioremediation of soil contaminated with petroleum hydrocarbons and toxic metals but much less is known about the potential of fungi in sites that are co-contaminated with both classes of pollutants. This article documents the roles of fungi in soil polluted with both petroleum hydrocarbons and toxic metals as well as the mechanisms involved in the biotransformation of such substances. Soil characteristics (e.g., structural components, pH, and temperature) and intracellular or excreted extracellular enzymes and metabolites are crucial factors which affect the efficiency of combined pollutant transformations. At present, bioremediation of soil co-contaminated with petroleum hydrocarbons and toxic metals is mostly focused on the removal, detoxification, or degradation efficiency of single or composite pollutants of each type. Little research has been carried out on the metabolism of fungi in response to complex pollutant stress. To overcome current bottlenecks in understanding fungal bioremediation, the potential of new approaches, e.g., gradient diffusion film technology (DGT) and metabolomics, is also discussed.

Key points

• Fungi play important roles in soil co-contaminated with TPH and toxic metals.

• Soil characteristics, enzymes, and metabolites are major factors in bioremediation.

• DGT and metabolomics can be applied to overcome current bottlenecks.

Emerging Trends in Biological Treatment of Wastewater From Unconventional Oil and Gas Extraction

Unconventional oil and gas exploration generates an enormous quantity of wastewater, commonly referred to as flowback and produced water (FPW). Limited freshwater resources and stringent disposal regulations have provided impetus for FPW reuse. Organic and inorganic compounds released from the shale/brine formation, microbial activity, and residual chemicals added during hydraulic fracturing bestow a unique as well as temporally varying chemical composition to this wastewater. Studies indicate that many of the compounds found in FPW are amenable to biological degradation, indicating biological treatment may be a viable option for FPW processing and reuse. This review discusses commonly characterized contaminants and current knowledge on their biodegradability, including the enzymes and organisms involved. Further, a perspective on recent novel hybrid biological treatments and application of knowledge gained from omics studies in improving these treatments is explored.

Impact of necrophytoremediation on petroleum hydrocarbon degradation, ecotoxicity and soil bacterial community composition in diesel-contaminated soil

Hydrocarbon degradation is usually measured in laboratories under controlled conditions to establish the likely efficacy of a bioremediation process in the field. The present study used greenhouse-based bioremediation to investigate the effects of natural attenuation (NA) and necrophytoremediation (addition of pea straw (PS)) on hydrocarbon degradation, toxicity and the associated bacterial community structure and composition in diesel-contaminated soil. A significant reduction in total petroleum hydrocarbon (TPH) concentration was detected in both treatments; however, PS-treated soil showed more rapid degradation (87%) after 5 months together with a significant reduction in soil toxicity (EC50 = 91 mg diesel/kg). Quantitative PCR analysis revealed an increase in the number of 16S rRNA and alkB genes in the PS-amended soil. Substantial shifts in soil bacterial community were observed during the bioremediation, including an increased abundance of numerous hydrocarbon-degrading bacteria. The bacterial community shifted from dominance by Alphaproteobacteria and Gammaproteobacteria in the original soil to Actinobacteria during bioremediation. The dominance of two genera of bacteria, Sphingobacteria and Betaproteobacteria, in both NA- and PS-treated soil demonstrated changes occurring within the soil bacterial community through the incubation period. Additionally, pea straw itself was found to harbour a diverse hydrocarbonoclastic community including Luteimonas, Achromobacter, Sphingomonas, Rhodococcus and Microbacterium. At the end of the experiment, PS-amended soil exhibited reduced ecotoxicity and increased bacterial diversity as compared with the NA-treated soil. These findings suggest the rapid growth of species stimulated by the bioremediation treatment and strong selection for bacteria capable of degrading petroleum hydrocarbons during necrophytoremediation. Graphical abstract.

Biogas slurry as an activator for the remediation of petroleum contaminated soils through composting mediated by humic acid

Soil pollution caused by petroleum hydrocarbons is a widespread environmental problem. Composting is one of the cost-effective solutions for petroleum hydrocarbons removal but limited by low efficiency of bioremediation, leading to high phytotoxicity. Given that biogas slurry as nutrients can alter the microbial activity, the aim of this study was to investigate the role of biogas slurry on the remediation of petroleum contaminated soils in composting. Herein, we added biogas slurry into the composting of hydrocarbon contaminated soil to investigate its effect on the biodegradation of petroleum hydrocarbons, humic acid (HA) transformation and the safety of product. The results showed that biogas slurry addition improved the degradation of organic matter and total petroleum hydrocarbons (TPH) (especially C > 16), but also increased 18.0% of germination index and the humification degree of HA. The estrone from biogas slurry was removed during composting and did not affect the phytotoxicity level of compost. Redundancy analysis and structural equation modeling indicated that TPH degradation was significantly related to the humification of HA components and total nitrogen from biogas slurry, which contributed to composting safety. Therefore, biogas slurry could be a possible activator for the remediation of petroleum contaminated soils through composting mediated by HA transformation, which is beneficial to obtain the composts with a lower phytotoxicity and higher maturity for soil application.

Aromatic Hydrocarbon Removal by Novel Extremotolerant Exophiala and Rhodotorula Spp. from an Oil Polluted Site in Mexico

Since Aromatic hydrocarbons are recalcitrant and toxic, strategies to remove them are needed. The aim of this work was to isolate fungi capable of using aromatic hydrocarbons as carbon sources. Two isolates from an oil polluted site in Mexico were identified through morphological and molecular markers as a novel Rhodotorula sp. and an Exophiala sp. Both strains were able to grow in a wide range of pH media, from 4 to 12, showing their optimal growth at alkaline pH's and are both halotolerant. The Exophiala strain switched from hyphae to yeast morphotype in high salinity conditions. To the best of our knowledge, this is the first report of salt triggering dimorphism. The Rhodotorula strain, which is likely a new undescribed species, was capable of removing singled ringed aromatic compounds such as benzene, xylene, and toluene, but could not remove benzo[a] pyrene nor phenanthrene. Nevertheless, these hydrocarbons did not impair its growth. The Exophiala strain showed a different removal capacity. It could remove the polyaromatic hydrocarbons but performed poorly at removing toluene and xylene. Nevertheless, it still could grow well in the presence of the aromatic compounds. These strains could have a potential for aromatic compounds removal.

Biodegradation of Tetrahydrofuran by the Newly Isolated Filamentous Fungus Pseudallescheria boydii ZM01

Tetrahydrofuran (THF) is widely used as a precursor for polymer syntheses and a versatile solvent in industries. THF is an environmental hazard and carcinogenic to humans. In the present study, a new THF-degrading filamentous fungus, Pseudallescheria boydii ZM01, was isolated and characterized. Strain ZM01 can tolerate a maximum THF concentration of 260 mM and can completely degrade 5 mM THF in 48 h, with a maximum THF degradation rate of 133.40 mg THF h⁻¹ g⁻¹ dry weight. Growth inhibition was not observed when the initial THF concentration was below 150 mM, and the maximum THF degradation rate was still maintained at 118.21 mg THF h⁻¹ g⁻¹ dry weight at 50 mM THF, indicating the great potential of this strain to degrade THF at high concentrations. The initial key metabolic intermediate 2-hydroxytetrahydrofuran was detected and identified by gas chromatography (GC) analyses for the first time during the THF degradation process. Analyses of the effects of initial pH, incubation temperature, and heavy metal ions on THF degradation revealed that strain ZM01 can degrade THF under a relatively wide range of conditions and has good degradation ability under low pH and Cu²⁺ stress, suggesting its adaptability and applicability for industrial wastewater treatment.

Bioremediation of intertidal zones polluted by heavy oil spilling using immobilized laccase-bacteria consortium

Heavy oil pollution in the intertidal zones has become a worldwide environmental problem. In this study, bioremediation on heavy oil pollutants in the intertidal zones using an immobilized laccase-bacteria consortium system was evaluated with the aid of intertidal experimental pools built in the coastal area. It is found that degradation efficiency of the immobilized laccase-bacteria consortium for heavy oil was 66.5% after 100 days remediation, with the reaction rate constant of 0.018 d^-1. Gas Chromatograph-Mass Spectrometer analysis shows that degradation efficiency of saturated hydrocarbons and aromatic hydrocarbons were 79.2% and 78.7%, which were 64.9% and 65.1% higher than control. It is further seen that degradation of long-chain n-alkanes of C26-C35 and polycyclic aromatic hydrocarbons with more than three rings were significant. Metagenomic analysis indicates that the immobilized laccase-bacterial consortium has not only increased the biodiversity of heavy oil degrading bacteria, but also accelerated the degradation of heavy oil.

Treatment of wastewater from petroleum industry: current practices and perspectives

Petroleum industry is one of the fastest growing industries, and it significantly contributes to economic growth in developing countries like India. The wastewater from a petroleum industry consist a wide variety of pollutants like petroleum hydrocarbons, mercaptans, oil and grease, phenol, ammonia, sulfide, and other organic compounds. All these compounds are present as very complex form in discharged water of petroleum industry, which are harmful for environment directly or indirectly. Some of the techniques used to treat oily waste/wastewater are membrane technology, photocatalytic degradation, advanced oxidation process, electrochemical catalysis, etc. In this review paper, we aim to discuss past and present scenario of using various treatment technologies for treatment of petroleum industry waste/wastewater. The treatment of petroleum industry wastewater involves physical, chemical, and biological processes. This review also provides scientific literature on knowledge gaps and future research directions to evaluate the effect(s) of various treatment technologies available.

Potential Enhancement of the In-Situ Bioremediation of Contaminated Sites through the Isolation and Screening of Bacterial Strains in Natural Hydrocarbon Springs

Petroleum hydrocarbon contamination (PHC) is an issue of major concern worldwide. These compounds represent the most common environmental pollutants and their cleaning up is mandatory. The main goal of this research was to analyze microbial communities in a site in southern Italy characterized by the presence of hydrocarbons of natural origin by using a multidisciplinary approach based on microbiological, geological and hydrological investigations. Bacterial communities of two springs, the surrounding soils, and groundwater were studied through a combination of molecular and culture-dependent methodologies to explore the biodiversity at the study site, to isolate microorganisms with degradative abilities, and to assess their potential to develop effective strategies to restore the environmental quality. Next-generation sequencing revealed the dominance of species of the Proteobacteria phylum but also the presence of other autochthonous hydrocarbon-oxidizing microorganisms affiliated to other phyla (e.g., species of the genera Flavobacterium and Gordonia). The traditional cultivation-based approach led to the isolation and identification of 11 aerobic hydrocarbon-oxidizing proteobacteria, some of which were able to grow with phenanthrene as the sole carbon source. Seven out of the 11 isolated bacterial strains produced emulsion with diesel fuel (most of them showing emulsifying capacity values greater than 50%) with a high stability after 24 h and, in some cases, after 48 h. These results pave the way for further investigations finalized at (1) exploiting both the degradation ability of the bacterial isolates and/or microbial consortia to remediate hydrocarbon-contaminated sites and (2) the capability to produce molecules with a promoting effect for oil polluted matrices restoration.

Microbial eco-physiological strategies for salinity-mediated crude oil biodegradation

Salinity variability strongly affects the behaviors of oil degrading bacteria for spilled oil biodegradation in the marine environment. However, limited studies explored the strategies of microbes on salinity-mediated crude oil biodegradation. In this study, a halotolerant bio-emulsifier producer, Exiguobacterium sp. N41P, was examined as a model strain for Alaska North Slope (ANS) crude oil (0.5%, v/v) biodegradation. Results indicated that Exiguobacterium sp. N41P could tolerant a wide range of salinity (0-120 g/L NaCl) and achieve the highest degradation efficiency under the salinity of 15 g/L NaCl due to the highest biofilm formation ability. Moreover, increased salinity induced decreased cell surface hydrophobicity and a migration of microbial growth from oil phase to aqueous phase, leading to limited bio-emulsifier productivity and depressed degradation of insoluble long-chain n-alkanes while enhancing the degradation of relative soluble naphthalene. Research findings illustrated the microbial eco-physiological mechanism for spilled oil biodegradation under diverse salinities and advanced the understanding of sophisticated marine crude oil biodegradation process.

Volatile organic compounds (VOCs) in solid waste landfill cover soil: Chemical and isotopic composition vs. degradation processes

Landfills for solid waste disposal release to the atmosphere a large variety of volatile organic compounds (VOCs). Bacterial activity in landfill cover soils can play an important role in mitigating VOC emission. In order to evaluate the effects of degradation processes and characterize VOCs composition in landfill cover soil, gases from 60 sites and along 7 vertical profiles within the cover soil were collected for chemical and isotopic analysis at two undifferentiated urban solid waste disposal sites in Spain: (i) Pinto (Madrid) and (ii) Zurita (Fuerteventura, Canary Islands). The CO₂/CH₄ ratios and δ¹³C-CO₂ and δ¹³C-CH₄ values were controlled by either oxidation or reduction processes of landfill gas (LFG). VOCs were dominated by aromatics, alkanes and O-substituted compounds, with minor cyclics, terpenes, halogenated and S-substituted compounds. Degradation processes, depending on both (i) waste age and (ii) velocity of the uprising biogas through the soil cover, caused (i) an increase of degradation products (e.g., CO₂, O-substituted compounds) and (ii) a decrease of degradable components (e.g., CH₄, alkanes, alkylated aromatics, cyclic and S-substituted compounds). Terpenes, halogenated compounds, phenol and furans were unaffected by degradation processes and only depended on waste composition. These results highlight the fundamental role played by microbial activity in mitigating atmospheric emissions of VOCs from landfills. Nevertheless, the recalcitrant behaviour shown by compounds hazardous for health and environment remarks the importance of a correct landfill management that has to be carried out for years after the waste disposal activity is completed, since LFG emissions can persist for long time.

Ecotoxicological effects of petroleum-contaminated soil on the earthworm Eisenia fetida

Petroleum is an important industrial raw material that enters the soil during production and use and is harmful to soil organisms. To evaluate the toxicity of petroleum-contaminated soil, earthworms (Eisenia fetida) were used as model organisms for soil ecotoxicity studies. We found that earthworm weight and cocoon production decreased significantly after exposure to petroleum-contaminated soil. In addition, soil contaminated with high concentrations of petroleum can cause damage to the DNA within earthworm seminal vesicles. Superoxide dismutase (SOD), catalase, and peroxidase activities were significantly inhibited when earthworms were exposed to petroleum-contaminated soil, indicating that oxidative stress was induced by petroleum pollutants. The mRNA levels of annetocin precursor, a reproduction-related gene, was significantly inhibited after petroleum exposure. The mRNA levels of translationally controlled tumour protein (TCTP) and SOD exhibited a concentration-dependent relationship, and their relative expression increased with petroleum concentration.

The tale of a versatile enzyme: Alpha-amylase evolution, structure, and potential biotechnological applications for the bioremediation of n-alkanes

As the primary source of a wide range of industrial products, the study of petroleum-derived compounds is of pivotal importance. However, the process of oil extraction and refinement is among the most environmentally hazardous practices, impacting almost all levels of the ecological chain. So far, the most appropriate strategy to overcome such an issue is through bioremediation, which revolves around the employment of different microorganisms to degrade hazardous compounds, generating less environmental impact and lower monetary costs. In this sense, a myriad of organisms and enzymes are considered possible candidates for the bioremediation process. Amidst the potential candidates is α-amylase, an evolutionary conserved starch-degrading enzyme. Notably, α-amylase was not only seen to degrade n-alkanes, a subclass of alkanes considered the most abundant petroleum-derived compounds but also low-density polyethylene, a dangerous pollutant produced from petroleum. Thus, due to its high conservation in both eukaryotic and prokaryotic lineages, in addition to the capability to degrade different types of hazardous compounds, the study of α-amylase becomes a rising interest. Nevertheless, there are no studies that review all biotechnological applications of α-amylase for bioremediation. In this work, we critically review the potential biotechnological applications of α-amylase, focusing on the biodegradation of petroleum-derived compounds. Evolutionary aspects are discussed, as well for all structural information and all features that could impact on the employment of this protein in the biotechnological industry, such as pH, temperature, and medium conditions. New perspectives and critical assessments are conducted regarding the application of α-amylase in the bioremediation of n-alkanes.

Fatty acid metabolism and brain mitochondrial performance of juvenile Nile tilapia (Oreochromis niloticus) exposed to the water-accommodated fraction of Maya crude oil

Crude oil and its derivatives are still the primary source of energy for humankind. However, during its transportation and treatment, spills of this resource can occur in aquatic environments. Nile tilapia is one of the most globally widespread fish species. This species is even found in brackish water due to its tolerance to salinity and pollution. In this study, the performance of brain cells (mitochondrial membrane potential [ΔΨm], calcium [Ca²⁺] and O₂ and H₂O₂ levels) exposed to crude oil was assessed. In addition, fatty acid metabolism (cholesterol concentration and fatty acid synthase [FAS], acyl CoA-oxidase [AOX] and catalase [CAT] activities) in the brain, heart, liver and intestine of Nile tilapia exposed to the water-accommodated fraction (WAF) of 0.01, 0.1 or 1 g/L Maya crude oil (MCO) for 96 h were evaluated. After exposure, in brain cells, there were only increases in ROS and slight reductions in ΔΨm. Exposure to WAF of MCO induced and increased the levels of cholesterol and altered FAS and AOX activities in all examined tissues. The brain is the most susceptible organ to alterations in the activity of fatty acid metabolic enzymes and cholesterol levels relative to the heart, liver and intestine. The correlation between inhibition of the activity of CAT and AOX suggests a possible reduction in the proliferation and size of peroxisomes. Most biomarkers were significantly altered in the brains of Nile tilapia exposed to the WAF containing 1 g/L MCO in comparison to the control.

Production of biosurfactant by Bacillus subtilis RSL-2 isolated from sludge and biosurfactant mediated degradation of oil

This study aims to unveil the effect of biosurfactant as stimulant in crude oil bioremediation. Isolated oil-degrading strain, B. subtilis RSL 2 was optimized for the maximum oil degradation and biosurfactant production using Response surface methodology. The produced biosurfactant was characterized and investigated for its effect on microbial oil degradation in two modes (a) sequential and (b) simultaneous. The strain produced 3.5 g/L of biosurfactant at pH 4.0, 25 °C, using 1 g/L crude oil as the only C-source in 7 days, which was characterized as lipopeptide with a critical micelle concentration (CMC) of 0.5 g/L. The biosurfactant improved surface wettability of a hydrophobic substrate i.e. increased surface energy from 30 ± 1 to 35 ± 1 mJ/m². Further, the simultaneous feed of biosurfactant at 0.5 CMC enhanced oil biodegradation (72%) and biosurfactant production (5.2 g/L) by about 1.6 times than the sequential mode due to improvement in mobilization of oil thus making it more bioavailable.

Distribution Characteristics of Bacterial Communities and Hydrocarbon Degradation Dynamics During the Remediation of Petroleum-Contaminated Soil by Enhancing Moisture Content

Microorganisms are the driver of petroleum hydrocarbon degradation in soil micro-ecological systems. However, the distribution characteristics of microbial communities and hydrocarbon degradation dynamics during the remediation of petroleum-contaminated soil by enhancing moisture content are not clear. In this study, polymerase chain reaction and high-throughput sequencing of soil microbial DNA were applied to investigate the compositions of microorganisms and alpha diversity in the oil-polluted soil, and the hydrocarbon removal also being analyzed using ultrasonic extraction and gravimetric method in a laboratory simulated ex-situ experiment. Results showed the distribution of petroleum hydrocarbon degrading microorganisms in the petroleum-contaminated loessal soil mainly was Proteobacteria phylum (96.26%)-Gamma-proteobacteria class (90.03%)-Pseudomonadales order (89.98%)-Pseudomonadaceae family (89.96%)-Pseudomonas sp. (87.22%). After 15% moisture content treatment, Actinobacteria, Proteobacteria, and Firmicutes still were the predominant phyla, but their relative abundances changed greatly. Also Bacillus sp. and Promicromonospora sp. became the predominant genera. Maintaining 15% moisture content increased the relative abundance of Firmicutes phylum and Bacillus sp. As the moisture-treated time increases, the uniformity and the richness of the soil bacterial community were decreased and increased respectively; the relative abundance of Pseudomonas sp. increased. Petroleum hydrocarbon degradation by enhancing soil moisture accorded with the pseudo-first-order reaction kinetic model (correlation coefficient of 0.81; half-life of 56 weeks). The richness of Firmicutes phylum and Bacillus sp. may be a main reason for promoting the removal of 18% petroleum hydrocarbons responded to 15% moisture treatment. Our results provided some beneficial microbiological information of oil-contaminated soil and will promote the exploration of remediation by changing soil moisture content for increasing petroleum hydrocarbon degradation efficiency.

Stimulation of methane production from benzoate with addition of carbon materials

Huge amounts of wastewater that contain aromatic compounds such as benzene and phenols are discharged worldwide. Benzoate is a typical intermediate in the anaerobic transformation of those aromatic compounds. In this study, electrically conductive carbon-based materials of granulated activated carbon (GAC), multiwalled carbon nanotubes (MwCNTs), and graphite were evaluated for the ability to promote the benzoate degradation. The results showed that 82-93% of the electrons were recovered in CH₄ production from benzoate. The carbon materials stimulated benzoate degradation in the sequence of GAC (5 g/L) > MwCNTs (1 g/L) ~ Graphite (0.1 g/L) > Control. Acetate was the only detected intermediate in the process of benzoate degradation. Taxonomic analyses revealed that benzoate was degraded by Syntrophus to acetate and H₂, which were subsequently converted to methane by Methanosarcina (both acetoclastic methanogens and hydrogenotrophic methanogens) and Methanoculleus (hydrogenotrophic methanogens), and direct interspecies electron transfer (DIET) of Desulfovibrio and Methanosarcina. Thus, these results suggest a method to effectively enhance the removal of aromatic compounds and methane recovery.

Sewage enhanced bioelectrochemical degradation of petroleum hydrocarbons in soil environment through bioelectro-stimulation

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Acetate and sewage were evaluated for enhanced hydrocarbons degradation in soil bioelectrochemical systems.

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Sewage has superior function in improving in situ bioelectrochemical degradation.

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Both acetate and sewage improved power density, substrate and sulfate removal.

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Soil contaminated with produced water was remediated by more than 70 %.

The impact of readily biodegradable substrates (sewage and acetate) in bioelectroremediation of hydrocarbons (PW) was evaluated in a bench-scale soil-based hybrid bioelectrochemical system. Addition of bioelectro-stimulants evidenced efficient degradation than control operation. Acetate and sewage were exhibited power density of 1126 mW/m² and 1145 mW/m², respectively, which is almost 15 % higher than control (without stimulant, 974 mW/m²). Increased electrochemical activity was correlated well with total petroleum hydrocarbons (TPH) degradation through addition of acetate (TPH_R, 525 mg/L, 67.4 %) and sewage (TPH_R, 560 mg/L,71.8 %) compared to the control operation (TPH_R, 503 mg/L, 64.5 %). Similarly, chemical oxygen demand (COD) reduction was also enhanced from 69.0 % (control) to 72.1 % and 74.6 % with acetate and sewage, respectively. Sewage and acetate also showed a positive role in sulfates removal, which enhanced from 56.0 % (control) to 62.9 % (acetate) and 72.6 % (sewage). This study signifies the superior function of sewage as biostimulant compared to acetate for the bioelectroremediation of hydrocarbons in contaminated soils.

Bacterial diversity of the green turtle (Chelonia mydas) nest environment

The green turtle is an endangered species that is highly sensitive to environmental pollution that can adversely affect the healthy development of eggs. Moreover, the presence of some bacteria in nests can be regarded as an indicator of the pollution level in nesting areas. In our study, nest sand and egg contents were collected from Sugözü Beaches (Turkey), in the Mediterranean. Phenotypic and genotypic identification of bacteria were carried out by using conventional phenotypic methods, 16S rRNA gene sequencing respectively. The extended-spectrum beta-lactamase presence and carbapenem resistance of bacteria isolated from egg contents were determined. This is the first report of carbapenem resistance in the eggs. All strains were evaluated in three different categories including growth promoters in agriculture and aquaculture, pathogens that are found in human and animal, and biomonitoring aquatic pollution. According to our analysis, 67 bacterial species were identified from samples. This study is the first record of Alcaligenes, Zobellella, Lysinibacillus, Sphingobacterium, Achromobacter, Acinetobacter, Alcanivorax, Ochrobactrum, Microbacterium, Rhodococcus, and Stenotrophomonas isolated from sea turtles. Pathogens detected in the bacterial flora can threaten both sea turtles and field workers. These data can contribute to the development of new conservation strategies on the treatment of sea turtles, nest protection, and pollution detection on nesting beaches.

Baseline for plastic and hydrocarbon pollution of rivers, reefs, and sediment on beaches in Veracruz State, México, and a proposal for bioremediation

Plastic and hydrocarbon pollution in aquatic ecosystems is a worldwide reality and serious concern today. Plastic debris presents a threat to ecosystems and organisms. Hydrocarbons are also considered priority pollutants. The hydrophobicity of the polymer in combination with the high surface area causes plastics to act as a vector for organic contaminants such as hydrocarbons. The first aim of this work was to evaluate the presence of plastic and hydrocarbon pollution in water from two reefs and two rivers and to identify plastic in six sediment beaches in Veracruz State, Mexico. In addition, the second aim was to analyse the ability of a bacterial consortium to biodegrade hydrocarbons in an airlift bioreactor and to identify degrading bacterial strains of polyethylene terephthalate (PET). Microplastics (100 nm-5 mm) were found in four water samples. Fragments of plastic collected from the reefs ranged in size from 0.716 to 32 μm and in rivers from 0.833 to 784 μm. On the sediment beaches, macroplastics of sizes 2-10 cm were detected. A number of hydrocarbons were also detected in the water samples of both reefs and one river, including n-octane, n-nonane, phenanthrene, n-eicosane, n-dotriacontane, n-hexatriacontane, n-triacontane, and n-tetratriacontane. As a biotechnological alternative for remediation of hydrocarbons and plastics, we attempted to produce a collection of native microorganisms able to degrade them. This work shows results from the bioprospection of a bacterial consortium (Xanthomonas, Acinetobacter bouvetii, Shewanella, and Aquamicrobium lusatiense) for hydrocarbon biodegradation in an airlift bioreactor. The tested consortium was able to successfully degrade the maximum diesel concentration (20 g L^-1) tested for 10 days. Also, the first visual evidence of PET degradation by an isolated forest-native bacterial strain showed that Bacillus muralis is the most efficient degrader.

Isolation and characterization of hydrocarbon-degrading bacteria from gas station leaking-contaminated groundwater in the Southern Amazon, Brazil

Abstract Twenty-three hydrocarbon-degrading bacteria strains were isolated from gas station leaking-contaminated groundwater located in the Southern Amazon, Brazil. Based on hydrocarbon (diesel, hexadecane, benzene, toluene and xylene) degradation ability, two strains were selected for further study. The amplification and sequencing of the 16S rRNA gene showed that these two strains belonged to the genus Bacillus (Bacillus sp. L26 and Bacillus sp. L30). GC-MS analysis showed that strain L30 was the most effective in degrading n-alkane (C10-C27) from diesel after 7 days of cultivation in mineral medium. Both strains produced biosurfactants and showed emulsification activity, specially the strain L30. Alkane hydroxylase gene (group III), which is important for alkane biodegradation, was present in strains. As a result, this study indicated that these bacteria could have promising applications in hydrocarbon bioremediation.

Monitoring microbial community structure and variations in a full-scale petroleum refinery wastewater treatment plant

This research investigated the process efficiency and microbial communities and their diversity in a full-scale wastewater treatment plant (WWTP) fed with petroleum refining wastewater (PRW) that contained toxic hydrocarbon contaminants and carcinogens. Process parameters and bacterial community structures were monitored for six months to create a link between microbial dynamics and influent characteristics of petrochemical wastewater. The WWTP showed a stable process with efficiencies >70% for both soluble chemical oxygen demand (SCOD) and benzene removal. More than 30 genera were identified by metagenomic analysis, and the bacterial populations changed significantly during the operation period. Among them, genera Sulfuritalea (11.9 ± 3.5%), Ottowia (4.3 ± 2.2%), Thauera (3.1 ± 7.2%) and Hyphomicrobium (1.3 ± 0.7%) were dominant and important bacterial genera that may have been responsible for the degradation of aromatic compounds such as benzene and phenol.

Innovative, ecofriendly biosorbent-biodegrading biofilms for bioremediation of oil- contaminated water

Immobilization of microorganisms capable of degrading specific contaminants significantly promotes bioremediation processes. In this study, innovative and ecofriendly biosorbent-biodegrading biofilms have been developed in order to remediate oil-contaminated water. This was achieved by immobilizing hydrocarbon-degrading gammaproteobacteria and actinobacteria on biodegradable oil-adsorbing carriers, based on polylactic acid and polycaprolactone electrospun membranes. High capacities for adhesion and proliferation of bacterial cells were observed by scanning electron microscopy. The bioremediation efficiency of the systems, tested on crude oil and quantified by gas chromatography, showed that immobilization increased hydrocarbon biodegradation by up to 23 % compared with free living bacteria. The resulting biosorbent biodegrading biofilms simultaneously adsorbed 100 % of spilled oil and biodegraded more than 66 % over 10 days, with limited environmental dispersion of cells. Biofilm-mediated bioremediation, using eco-friendly supports, is a low-cost, low-impact, versatile tool for bioremediation of aquatic systems.

Biofiltration of oil sands process water in fixed-bed biofilm reactors shapes microbial community structure for enhanced degradation of naphthenic acids

Naphthenic acids (NAs) are a complex mixture of carboxylic acids present in oil sands process water (OSPW). Their recalcitrant nature makes them difficult to be removed from the environment using conventional remediation strategies. This study hypothesized that, upon continuous operation, biofiltration of OSPW in fixed-bed biofilm reactors would allow the development of NA-degrading microbial community within the biofilter following successful removal. Both raw and ozonated OSPW were treated in the biofilters and changes in microbial community were tested via 16S/18S amplicon sequencing and metatranscriptomics. Through switch from suspended growth to attached growth, a shift in indigenous microbial community was seen following by an increase in alpha diversity. Concomitantly, improved degradation of NAs was monitored, i.e., 35.8% and 69.4% of NAs were removed from raw and ozonated OSPW, respectively. Metatranscriptomics analysis suggested the presence of genes involved in the degradation of organic acids and petroleum-related compounds. Specifically, functional abundance of aromatic compounds' metabolism improved from 0.05% to 0.76%; whereas abundance of benzoate transport and degradation pathway increased from 0.04% to 0.64%. These changes conclude that continuous operation of OSPW in the bioreactors was in favor of shaping the overall microbiome towards better NA degradation.

Enhanced biodegradation of n-Hexadecane in solid-phase of soil by employing immobilized Pseudomonas Aeruginosa on size-optimized coconut fibers

In this research, biodegradation of hexadecane as a model contaminant in solid soil using both free and immobilized Pseudomonas Aeruginosa, capable of producing biosurfactant, was investigated. Coconut fibers in three mesh sizes were used as a cellulosic biocarrier for immobilization procedure. Bioremediation experiments were monitored for 60 days after incubation at 27 °C in small columns, containing contaminated solid soil, with the capability of aeration from bottom to top. The difference in the number of immobilized bacteria cells on the fibers with different particle sizes, emphasizes the importance of choosing an optimized carrier size. Enhancement in hexadecane degradation up to 50 % at the end of experiments was achieved by immobilized Pseudomonas Aeruginosa on the fibers with a mesh size between 8 and 16 compared to inoculation of free bacteria cells into the soil. Effect of mixing the pretreated fibers with soil and inoculating free cells into this mixture was also investigated compared to free cell experiments without fiber, which led to 28 % decrease in hexadecane degradation. Obtained kinetic equations for experiments confirm the impact of immobilization of bacteria on the enhancement of biodegradation rate and reduction of the half-life of the contaminant is soil.

Coagulation-flocculation and moving bed biofilm reactor as pre-treatment for water recycling in the petrochemical industry

Water recycling and reuse is of important value in water-using sectors like petrochemical industry. The aim of this research was to optimise the pre-treatment of petrochemical wastewater to undergo a further membrane treatment, with the final objective of water recycling within the same industry. Laboratory coagulation-flocculation tests prior to biological treatment were performed using Actiflo® Veolia commercial technology and an optimal coagulant dose of 30 mg/L ferric chloride was obtained. A bench-scale Moving Bed Biofilm Reactor (MBBR) system with two sequential reactors with working volumes of 5 L was filled with Z-carriers at 35% of their working volume. Organic loading rate (OLR) was varied from 0.2 to 3.25 kg/(m³ d) and the hydraulic retention time (HRT) ranged from 23.4 h to 4.5 h. High soluble chemical oxygen demand (sCOD) removals were obtained in stationary states (80-90%) and the calculated maximum sCOD that the system could degrade was 4.96 ± 0.01 kg/(m³ d) at 23 ± 2 °C. Changes in feed composition did not decrease sCOD removals showing that MBBR is a robust technology and the coagulation-flocculation step could be by-passed. Further removal of total suspended solids (TSS) and turbidity from the MBBR effluent would be required before a reverse osmosis (RO) step could be performed. A biofilm-forming genus, Haliscomenobacter spp., and an oil degrading genus Flavobacterium spp. were found in all the attached biomass samples. Acinetobacter spp. was the major bacterial genera found in suspended biomass. Proteobacteria and Bacteroidetes were the major phyla detected in the carrier samples while Proteobacteria the main one detected in the suspended biomass. The lack of fungal annotated sequences in databases led to a major proportion of fungal sequences being categorized as unclassified Fungi. The results obtained indicate that MBBR is an appropriate technology for hydrocarbon-degrading microorganism growth and, thus, for petrochemical wastewater pre-treatment for water regeneration.

Plant-assisted remediation of hydrocarbons in water and soil: Application, mechanisms, challenges and opportunities

Due to the increasing importance of diesel and petroleum for industrial development during the last century, petrochemical effluents have significantly contributed to the pollution of aquatic and soil environments. The contamination generated by petroleum hydrocarbons can endanger not only humans but also the environment. Phytoremediation or plant-assisted remediation can be considered one of the best technologies to manage petroleum product-contaminated water and soil. The main advantages of this method are that it is environmentally-friendly, potentially cost-effective and does not require specialised equipment. The scope of this review includes a description of hydrocarbon pollutants from petrochemical industries, their toxicity impacts and methods of treatment and degradation. The major emphasis is on phytodegradation (phytotransformation) and rhizodegradation since these mechanisms are the most favourable alternatives for soil and water reclamation of hydrocarbons using tropical plants. In addressing these issues, this review also covers challenges to retrieve the environment (soil and water) from petroleum contaminations through phytoremediation, and its opportunities to remove or reduce the negative environmental impacts of petroleum contaminations and restore damaged ecosystems with sustainable ways to keep healthy life for the future.