Biodegradation of High Concentrations of Aliphatic Hydrocarbons in Soil from a Petroleum Refinery: Implications for Applicability of New Actinobacterial Strains

Bioremediation of petroleum-contaminated soil based on both toxicity risk control and hydrocarbon removal-progress and prospect

Petroleum contamination remains a worldwide issue requiring cost-effective bioremediation techniques. However, establishing a universal bioremediation strategy for all types of oil-polluted sites is challenging. This difficulty arises from the heterogeneity of soil textures, the complexity of oil products, and the variations in local climate and environment across different oil-contaminated regions. Several factors can impede bioremediation efficacy: (i) differences in bioavailability and biodegradability between aliphatic and aromatic fractions of crude oil; (ii) inconsistencies between hydrocarbon removal efficiency and toxicity attenuation during remediation; (iii) varying adverse effect of aliphatic and aromatic fractions on soil microorganisms. This review examines the ecotoxicity risk of petroleum contamination to soil fauna and flora. It also discusses three primary bioremediation strategies: biostimulation with nutrients, bioaugmentation with petroleum degraders, and phytoremediation with plants. Based on current research and state-of-the-art challenges, we highlighted future research scopes should focus on (i) exploring the ecotoxicity differentiation of aliphatic and aromatic fractions of crude oil, (ii) establishing unified risk factors and indicators for evaluating oil pollution toxicity, (iii) determining the fate and transformation of aliphatic and aromatic fractions of crude oil using advanced analytical techniques, and (iv) developing combined bioremediation techniques that improve petroleum removal and ecotoxicity attenuation.

A tailored cytochrome P450 monooxygenase from Gordonia rubripertincta CWB2 for selective aliphatic monooxygenation

Cytochrome P450 monooxygenases are recognized as versatile biocatalysts due to their broad reaction capabilities. One important reaction is the hydroxylation of non-activated C-H bonds. The subfamily CYP153A is known for terminal hydroxylation reactions, giving access to functionalized aliphatics. Whilst fatty derivatives may be converted by numerous enzyme classes, midchain aliphatics are seldomly accepted, a prime property of CYP153As. We report here on a new CYP153A member from the genome of the mesophilic actinobacterium Gordonia rubripertincta CWB2 as an efficient biocatalyst. The gene was overexpressed in Escherichia coli and fused with a surrogate electron transport system from Acinetobacter sp. OC4. This chimeric self-sufficient whole-cell system could perform hydroxylation and epoxidation reactions: conversions of C6-C14 alkanes, alkenes, alcohols and of cyclic compounds were observed, yielding production rates of, e.g., 2.69 mM h-1 for 1-hexanol and 4.97 mM h-1 for 1,2-epoxyhexane. Optimizing the linker compositions between the protein units led to significantly altered activity. Balancing linker length and flexibility with glycine-rich and helix-forming linker units increased 1-hexanol production activity to 350 % compared to the initial linker setup with entirely helical linkers. The study shows that strategic coupling of efficient electron supply and a selective enzyme enables previously challenging monooxygenation reactions of midchain aliphatics.

Biofilm formation promoted biodegradation of polyethylene in Gordonia polyisoprenivorans B251 isolated from bacterial enrichment acclimated by hexadecane for two years

Polyethylene (PE) mulch films have been widely used in agriculture and led to a significant pollution in cultivated soils. It is desirable to develop the sustainable method for the degradation of PE. As an environment friendly approach, microbial or enzymatic degradation of PE could meet this demanding. Thus, more microbial strains are required for illustrating biodegrading pathway and developing efficient biological method. In this study, Gordonia polyisoprenivorans B251 capable of degrading PE was isolated from bacterial enrichment with hexadecane as a sole carbon source for two years, in which genus Gordonia had dominated. As revealed by microbial growth curve, the strain B251 had the highest growth rate than other tested strains in the mediums either with hexadecane or PE particles as sole carbon source. The formation of biofilms in both enriched culture and G. polyisoprenivorans B251 pure culture attached to PE film was observed. The capability for PE degradation of individual strain was screened by 30-day incubation with PE film and confirmed by the presence of hydroxyl, carbonyl, carbon-carbon double bond and ether groups in FT-IR analysis and cracks on the surface of PE film observed by scanning electron microscopy (SEM). Therefore, Gordonia polyisoprenivorans, reported as their degradation of environmental contaminants in previous study, were also identified in current study as a candidate for polyethylene biodegradation.

Miscanthus x giganteus stress tolerance and phytoremediation capacities in highly diesel contaminated soils

Second generation biofuel crop Miscanthus x giganteus (Mxg) was studied as a candidate for petroleum hydrocarbons (PHs) contaminated soil phytomanagement. The soil was polluted by diesel in wide concentration gradient up to 50 g⋅kg-1 in an ex-situ pot experiment. The contaminated soil/plant interactions were investigated using plant biometric and physiological parameters, soil physico-chemical and microbial community's characteristics. The plant parameters and chlorophyll fluorescence indicators showed an inhibitory effect of diesel contamination; however much lower than expected from previously published results. Moreover, lower PHs concentrations (5 and 10 g⋅kg-1) resulted in positive reinforcement of electron transport as a result of hormesis effect. The soil pH did not change significantly during the vegetation season. The decrease of total organic carbon was significantly lower in planted pots. Soil respiration and dehydrogenases activity increased with the increasing contamination indicating ongoing PHs biodegradation. In addition, microbial biomass estimated by phospholipid fatty acids increased only at higher PHs concentrations. Higher dehydrogenases values were obtained in planted pots compared to unplanted. PHs degradation followed the first-order kinetics and for the middle range of contamination (10-40 g⋅kg-1) significantly lower PHs half-lives were determined in planted than unplanted soil pointing on phytoremediation. Diesel degradation was in range 35-70 % according to pot variant. Results confirmed the potential of Mxg for diesel contaminated soils phytomanagement mainly in PHs concentrations up to 20 g⋅kg-1 where phytoremediation was proved, and biomass yield was reduced only by 29 %.

Whole Genome Analysis and Assessment of the Metabolic Potential of Gordonia rubripertincta Strain 112, a Degrader of Aromatic and Aliphatic Compounds

The application of Gordonia strains in biotechnologies of environmental purification as degraders of pollutants of different chemical structures is an interesting research topic. The strain Gordonia rubripertincta 112 (IEGM112) is capable of utilizing diesel fuel, alkanes, and aromatic compounds. The aim of this work was to study the potential of G. rubripertincta 112 as a degrader of aromatic and aliphatic compounds and analyze its complete genome in comparison with other known G. rubripertincta strains. The genome had a total length of 5.28 Mb and contained 4861 genes in total, of which 4799 were coding sequences (CDS). The genome contained 62 RNA genes in total, of which 50 were tRNAs, three were ncRNAs, and nine were rRNAs. The strain bears plasmid elements with a total length of 189,570 nucleotides (plasmid p1517). The strain can utilize 10.79 ± 1.17% of hexadecane and 16.14 ± 0.16% of decane over 3 days of cultivation. In the genome of the strain, we have found metabolic pathways of alkane (cytochrome P450 hydroxylases) and catechol (ortho- and meta-pathways) degradation. These results will help us to further approach the fundamental study of the processes occurring in the strain cells and to enrich our knowledge of the catabolic capabilities of G. rubripertincta.

Potential and prospects of Actinobacteria in the bioremediation of environmental pollutants: Cellular mechanisms and genetic regulations

Increasing industrialization and anthropogenic activities have resulted in the release of a wide variety of pollutants into the environment including pesticides, polycyclic aromatic hydrocarbons (PAHs), and heavy metals. These pollutants pose a serious threat to human health as well as to the ecosystem. Thus, the removal of these compounds from the environment is highly important. Mitigation of the environmental pollution caused by these pollutants via bioremediation has become a promising approach nowadays. Actinobacteria are a group of eubacteria mostly known for their ability to produce secondary metabolites. The morphological features such as spore formation, filamentous growth, higher surface area to volume ratio, and cellular mechanisms like EPS secretion, and siderophore production in Actinobacteria render higher resistance and biodegradation ability. In addition, these bacteria possess several oxidoreductase systems (oxyR, catR, furA, etc.) which help in bioremediation. Actinobacteria genera including Arthrobacter, Rhodococcus, Streptomyces, Nocardia, Microbacterium, etc. have shown great potential for the bioremediation of various pollutants. In this review, the bioremediation ability of these bacteria has been discussed in detail. The utilization of various genera of Actinobacteria for the biodegradation of organic pollutants, including pesticides and PAHs, and inorganic pollutants like heavy metals has been described. In addition, the cellular mechanisms in these microbes which help to withstand oxidative stress have been discussed. Finally, this review explores the Actinobacteria mediated strategies and recent technologies such as the utilization of mixed cultures, cell immobilization, plant-microbe interaction, utilization of biosurfactants and nanoparticles, etc., to enhance the bioremediation of various environmental pollutants.

Corksorb Enhances Alkane Degradation by Hydrocarbonoclastic Bacteria

Biosorbent materials are effective in the removal of spilled oil from water, but their effect on hydrocarbonoclastic bacteria is not known. Here, we show that corksorb, a cork-based biosorbent, enhances growth and alkane degradation by Rhodococcus opacus B4 (Ro) and Alcanivorax borkumensis SK2 (Ab). Ro and Ab degraded 96 ± 1% and 72 ± 2%, respectively, of a mixture of n-alkanes (2 g L-1) in the presence of corksorb. These values represent an increase of 6 and 24%, respectively, relative to the assays without corksorb. The biosorbent also increased the growth of Ab by 51%. However, no significant changes were detected in the expression of genes involved in alkane uptake and degradation in the presence of corksorb relative to the control without the biosorbent. Nevertheless, transcriptomics analysis revealed an increased expression of rRNA and tRNA coding genes, which confirms the higher metabolic activity of Ab in the presence of corksorb. The effect of corksorb is not related to the release of soluble stimulating compounds, but rather to the presence of the biosorbent, which was shown to be essential. Indeed, scanning electron microscopy images and downregulation of pili formation coding genes, which are involved in cell mobility, suggest that cell attachment on corksorb is a determinant for the improved activity. Furthermore, the existence of native alkane-degrading bacteria in corksorb was revealed, which may assist in situ bioremediation. Hence, the use of corksorb in marine oil spills may induce a combined effect of sorption and stimulated biodegradation, with high potential for enhancing in situ bioremediation processes.

Miscanthus x giganteus role in phytodegradation and changes in bacterial community of soil contaminated by petroleum industry

The second generation energy crop Miscanthus x giganteus (Mxg) was cultivated in pots with mixtures of clean and petroleum industry contaminated soil affected by petroleum, Pb, Zn contamination and high salinity. The survival rate reached 100%, nevertheless the biomass parameters were negatively affected even in the lowest proportion of contaminated soil. In the lowest contamination, where the plant grew still quite successfully, C10-C40 degradation was significantly enhanced compared to the unplanted control with degradation of 58 ± 14%. The plant contribution to aliphatics degradation was significantly correlated with biomass, thus it was negligible in higher contamination. A similar pattern was documented in development of the soil bacterial community. The shift in community structure after Mxg cultivation was observed mainly in the soil with the lowest contaminant proportion, though an increase of bacterial diversity in the miscanthus rhizosphere was observed in all cases. Relative abundance of Actinobacteria was reduced on behalf of several less abundant phyla (Verrucomicrobia, Bacterioides, Acidobacteria). The majority of genera identified as potential petroleum degraders (Pseudomonas, Shinella, Altererythrobacter, Azospirillum, Mesorhizobium, Dyella) were more abundant in contaminated soil with miscanthus, suggesting that Mxg could be a promising crop for phytomanagement of petroleum contaminated soils but salt phytotoxicity needs to be mitigated first.

Bioremediation of Total Petroleum Hydrocarbons (TPH) by Bioaugmentation and Biostimulation in Water with Floating Oil Spill Containment Booms as Bioreactor Basin

A crude oil spill is a common issue during offshore oil drilling, transport and transfer to onshore. Second, the production of petroleum refinery effluent is known to cause pollution due to its toxic effluent discharge. Sea habitats and onshore soil biota are affected by total petroleum hydrocarbons (TPH) as a pollutant in their natural environment. Crude oil pollution in seawater, estuaries and beaches requires an efficient process of cleaning. To remove crude oil pollutants from seawater, various physicochemical and biological treatment methods have been applied worldwide. A biological treatment method using bacteria, fungi and algae has recently gained a lot of attention due to its efficiency and lower cost. This review introduces various studies related to the bioremediation of crude oil, TPH and related petroleum products by bioaugmentation and biostimulation or both together. Bioremediation studies mentioned in this paper can be used for treatment such as emulsified residual spilled oil in seawater with floating oil spill containment booms as an enclosed basin such as a bioreactor, for petroleum hydrocarbons as a pollutant that will help environmental researchers solve these problems and completely clean-up oil spills in seawater.

Stress Response of Miscanthus Plants and Soil Microbial Communities: A Case Study in Metals and Hydrocarbons Contaminated Soils

Second-generation biofuel crop miscanthus is one of the most promising plants tested for phytomanagement of contaminated sites. In this preliminary pot case study, the most used hybrid Miscanthus x giganteus was cultivated in three different real contaminated soils: agricultural soil contaminated with Cd; post-military soil slightly contaminated with Zn, Pb and Cd; and soil contaminated by petroleum industry with metals and hydrocarbons. The stress response of plants and soil microbial communities was monitored to receive data that are important for successful phytomanagement application. With metals only, the plant grew well, and chlorophyll fluorescence measurement proved their good vitality. Changes in leaf anatomy (leaf thickness and sclerenchyma cells area) were additionally determined in post-military soil compared to agricultural. On the contrary, in petroleum-contaminated soil, the biomass yield was too reduced and also physiological parameters were significantly decreased. The response of microbial communities also differed. In agricultural soil, no microbial stress was determined. In post-military soil, it became reduced during the experiment, and in petroleum contamination, it increased year-on-year. It could be concluded that miscanthus is suitable for cultivation in metals contaminated soils with potential for microbial communities support, but in soil contaminated by the petroleum industry, its application did not seem meaningful.

Hydrocarbon Removal by Two Differently Developed Microbial Inoculants and Comparing Their Actions with Biostimulation Treatment

Bioremediation of soils polluted with petroleum compounds is a widely accepted environmental technology. We compared the effects of biostimulation and bioaugmentation of soil historically contaminated with aliphatic and polycyclic aromatic hydrocarbons. The studied bioaugmentation treatments comprised of the introduction of differently developed microbial inoculants, namely: an isolated hydrocarbon-degrading community C1 (undefined-consisting of randomly chosen degraders) and a mixed culture C2 (consisting of seven strains with well-characterized enhanced hydrocarbon-degrading capabilities). Sixty days of remedial treatments resulted in a substantial decrease in total aliphatic hydrocarbon content; however, the action of both inoculants gave a significantly better effect than nutrient amendments (a 69.7% decrease for C1 and 86.8% for C2 vs. 34.9% for biostimulation). The bioaugmentation resulted also in PAH removal, and, again, C2 degraded contaminants more efficiently than C1 (reductions of 85.2% and 64.5%, respectively), while biostimulation itself gave no significant results. Various bioassays applying different organisms (the bacterium Vibrio fischeri, the plants Sorghum saccharatum, Lepidium sativum, and Sinapis alba, and the ostracod Heterocypris incongruens) and Ames test were used to assess, respectively, potential toxicity and mutagenicity risk after bioremediation. Each treatment improved soil quality, however only bioaugmentation with the C2 treatment decreased both toxicity and mutagenicity most efficiently. Illumina high-throughput sequencing revealed the lack of (C1) or limited (C2) ability of the introduced degraders to sustain competition from indigenous microbiota after a 60-day bioremediation process. Thus, bioaugmentation with the bacterial mixed culture C2, made up of identified, hydrocarbon-degrading strains, is clearly a better option for bioremediation purposes when compared to other treatments.

Simultaneous Application of Biosurfactant and Bioaugmentation with Rhamnolipid-Producing Shewanella for Enhanced Bioremediation of Oil-Polluted Soil

In the present study, a combined treatment strategy involving the addition of rhamnolipid, rhamnolipid-producing bacteria (Shewanella sp. BS4) and a native soil microbial community for the remediation of hydrocarbon-contaminated soil under pilot-scale conditions was adopted. The isolate BS4 (rhl+), demonstrating the highest emulsification activity and surface tension reduction efficiency, was identified based on 16 S rDNA sequencing as Shewanella sp. strain. Growth conditions for rhamnolipid production were optimized based on Central Composite Design (CCD) as 2.9% crude oil, a 54 × 106 CFU g−1 inoculation load of soil, a temperature of 30.5 °C, and a pH of 6.7. In situ bioremediation experiments, conducted using hydrocarbon-contaminated soil treated with the combination of rhamnolipid and rhamnolipid-producing bacteria, showed that the inoculated Shewanella sp. BS4, along with the indigenous soil microbial community, supported the highest hydrocarbon-degrading bacterial population and soil respiration activity, and this treatment resulted in 75.8% hydrocarbon removal efficiency, which was higher compared to contaminated soil devoid of any treatment.