Crude petroleum-oil biodegradation efficiency of Bacillus subtilis and Pseudomonas aeruginosa strains isolated from a petroleum-oil contaminated soil from North-East India

The diversity of prokaryotes and fungi hosted in crude oils

The diversity of prokaryotes and fungi in crude oils has not been understood clearly, though unique microbial communities may be hosted in crude oil. This study investigated the chemical compositions and microbial communities of crude oils from Henan, Bamianhe, and Jianghan oilfields of China. Statistical analysis revealed significant variations of both prokaryotic and fungal communities (P < 0.05) within different oilfields and oils with different biodegradation levels. Diversity analysis showed little difference in prokaryotic, but a significant difference in fungal (P < 0.05). Prokaryotic diversity was higher in heavily biodegraded oils than those in unaltered and slightly biodegraded oils; the opposite was true for fungal diversity (P < 0.05). Moreover, thermophilic prokaryotes were detected mainly in biodegraded heavy oils produced by the practice of thermal recovery from Henan and Bamianhe oilfields, and halophilic prokaryotes were detected mainly in oils from sandstone reservoirs containing hypersaline formation water from Jianghan Oilfield. Accordingly, microbial communities in oils are affected by oil biodegradation, extraction practices, and natural environments of native inhabitants in subsurface petroleum reservoirs.IMPORTANCEThe biological activities of endogenous microorganisms in crude oil play an important role in the production and development of crude oil. Although there have been many microbiological investigations of crude oil-contaminated sites, our understanding of the phylogenetic diversity, metabolic capabilities, and community dynamics of microbial communities within crude oil is far from complete. In this paper, the prokaryotic and fungal communities of three oil fields in different regions of China were analyzed, and several factors affecting microbial degradation were further identified. This study provides a new direction for the subsequent investigation of microbial activities inside crude oil.

Fate of dissolved organics in oil sands process water during long-term storage: Mechanistic insights into toxicity removal and microbial processes

Refining oil sand process water (OSPW), a byproduct of bitumen extraction from oil sands in Canada, presents significant environmental challenges due to its complex makeup. This complexity is mainly due to the presence of naphthenic acids (NAs), which play a substantial role in contributing to the toxicity of OSPW. Although various treatment technologies have been explored, the long-term behaviour of OSPW dissolved organics under different storage conditions has not been studied extensively. This study is the first to delve deeply into the natural attenuation of OSPW under diverse controlled conditions, focusing on the effects of temperature, dissolved oxygen, and ozone pretreatment on water quality, NAs degradation, toxicity, and bioavailability. Our results revealed the critical role of temperature in OSPW characteristics, with long-term storage at 4 °C demonstrating minimal degradation of dissolved organics, providing the first empirical support for current OSPW storage practices. In contrast, at 20 °C, ozoned OSPW exhibited maximum reduction in the following parameters: total NAs, 72.6 %; chemical oxygen demand, 25.3 %; acute toxicity towards A. fischeri by 60.7 %; and bioavailability of organics by 35.2 %. This suggests that ozone pretreatment facilitates the biodegradation process by breaking down NAs into more readily metabolized compounds, which are further degraded by microbial activity over time. Furthermore, the study identified evolving microbial communities during OSPW storage, highlighting the presence of Bacillus and Fontimonas genera, which may play a role in organics degradation but require further investigation into their specific functions. These findings provide critical insights into the long-term dynamics of organics in OSPW and provide a foundation for optimizing management strategies.

Enhanced anaerobic bioremediation of oil-contaminated intertidal sediment with a combination of anaerobically-synthesized rhamnolipids and sulfate

Oil pollution in intertidal sediments is a serious environmental issue. The anoxic environment of the sediment hinders the decomposition of hydrophobic organic pollutants. Conventional bioremediation methods, such as the sole addition of electron acceptors, have struggled to achieve high efficiencies because of the low solubility of oil pollutants. Herein, the combination of anaerobically-synthesized rhamnolipids and electron acceptor was evaluated for the bioremediation of oil-polluted sediments. Meanwhile, the key genes involved in CNPS cycling were detected to understand the biogeochemical processes and the complex interactions between microbial metabolism, nutrient availability, and pollutant degradation. After the bioremediation, the combination of rhamnolipids and sulfate significantly enhanced the removal of polycyclic aromatic hydrocarbons (74.8 ± 1.4%). On day 270, the polyphenol oxidase activity of rhamnolipids and sulfate with rhamnolipids treatments reached 20870.1 ± 1988.7 mg/(kg·h) and 22373.8 ± 970.1 mg/(kg·h), respectively, which was significantly higher (P < 0.05) than other treatments. The sulfate consumption rate in the treatment with both sulfate and rhamnolipids consistently exceeded that of treatment with sulfate alone. Moreover, on day 60, the abundances of functional genes mediating sulfur oxidation (yedZ and soxY) were significantly higher in the combined treatment than in the sulfate group. The results revealed that the addition of rhamnolipids favored the growth of microorganisms and promoted S cycling, and the combination with sulfate dramatically enhanced the removal of polycyclic aromatic hydrocarbons. This study demonstrated that the combination of sulfate and rhamnolipids exhibited great potential on the anaerobic bioremediation of oil-contaminated intertidal zones.

Nutrient amendments enrich microbial hydrocarbon degradation metagenomic potential in freshwater coastal wetland microcosm experiments

Biostimulating native microbes with fertilizers has proven to be a highly effective strategy to speed up biodegradation rates in microbial communities. This study investigates the genetic potential of microbes to degrade light synthetic crude oil in a freshwater coastal wetland. Experimental sediment microcosms were exposed to a variety of conditions (biological control, a light synthetic crude oil amendment, and light synthetic crude oil with nutrient amendment) and incubated for 30 days before volatile organic compounds (BTEX) were quantified and DNA was sequenced for metagenomic analysis. The resulting DNA sequences were binned into metagenome-assembled genomes (MAGs). Analyses of MAGs uncovered a 13-fold significant increase in the abundance of rate-limiting hydrocarbon degrading monooxygenases and dioxygenases, identified only in MAGs from the light synthetic crude oil with nutrient amendments. Further, complete degradation pathways for BTEX compounds were found only in MAGs resulting from the light synthetic crude with nutrient amendment. Moreover, volatile organic compounds (BTEX, cyclohexane, and naphthalene) analyses of microcosm sediments in the presence of nutrients documented that benzene was degraded below detection limits, toluene (98%) and ethylbenzene (67%) were predominantly reduced within 30 days. Results indicate that the genetic potential to degrade BTEX compounds in this freshwater wetland can be linked to the functional potential for bioremediation. BTEX compounds are typically more recalcitrant and tougher to degrade than alkanes. This study demonstrated that stimulating a microbial community with nutrients to enhance its ability to biodegrade hydrocarbons, even in a relatively nutrient-rich habitat like a freshwater wetland, is an effective remediation tactic.

IMPORTANCE

The impact of oil spills in a freshwater aquatic environment can pose dire social, economic, and ecological effects on the region. An oil spill in the Laurentian Great Lakes region has the potential to affect the drinking water of more than 30 million people. The light synthetic crude oil used in this experimental microcosm study is transported through an underground pipeline crossing the waterway between two Laurentian Great Lakes. This study collected metagenomic data (experiments in triplicate) and assessed the quantity of BTEX compounds, which connected microbial degradation function to gene potential. The resulting data documented the bioremediation capabilities of native microbes in a freshwater coastal wetland. This study also provided evidence for this region that bioremediation can be a viable remediation strategy instead of invasive physical methods.

Biodegradation Study of Used Engine Oil by Free and Immobilized Cells of the Pseudomonas oleovorans Strain NMA and Their Growth Kinetics

Used engine oil is considered to be one of the high-risk pollutants, and if introduced untreated in the environment, it threatens the whole ecosystem. Therefore, there is a need to find some rapid and efficient methods for the remediation of used engine oil. The present study aimed to isolate indigenous bacterial strains having the capability to degrade used engine oil. The enrichment technique was employed for the isolation of bacterial strains, which were identified by the 16S rRNA technique. As biosurfactants play a vital role in the degradation process, the activity was determined by standard protocols. The bacterial strain was isolated by the enrichment technique and identified as the Pseudomonas oleovorans strain NMA. The bacterial isolate has the ability to utilize used engine oil as the sole source of energy. The biodegradation experiment revealed that both free and immobilized cells degrade used engine oil, but immobilized cells showed the best biodegradation result, with 98-99% degradation efficiency in 7 days of incubation irrespective of all oil concentrations. For the analysis of degraded products, gas chromatography-mass spectrometry (GC-MS) was performed, which indicates that the treated samples do not carry the major engine components, i.e., methyl hexane, pyrene, and phytane, which confirmed that these were transformed by the bacterial activity. Monod kinetics further confirmed that the isolated bacterium utilizes used engine oil as the sole source of energy. These findings clearly indicate the potential of the bacterium NMA to degrade used engine oil with high kinetics, converting it into nontoxic products, and thus be a potential candidate for remediation at contaminated sites.

Diesel-degradation by indigenous bacteria of petroleum-contaminated soils

Relying on native microorganisms is crucial for bioremediating petroleum-contaminated soils within this oil field. This study aimed to isolate native bacteria and investigate their ability to degrade petroleum hydrocarbons in contaminated soils. Flame ionization detector gas chromatography analyzed the capacity of Indigenous bacterial isolates to break down diesel fuel in an aquatic environment. Soil samples were collected from the Naft-Shahr area. Initially, 126 bacterial isolates were obtained from these soils, of which only 48 species could grow on a diesel-containing medium. Further analysis identified the top 8 isolates with high diesel removal potential. Results showed that the diesel removal percentage ranged from 26 to 76% at an initial diesel concentration of 3.7 g. L - 1 after 48 h, without adding any supplementary surface-active agent. Four top isolates were selected based on their degradation activity, removal yield, and biodegradation rate and were identified using 16S rRNA gene sequencing and phylogenetic analysis. Sequence alignment revealed that isolates B11Pet, B19Pet, B27Pet, and B48Pet belong to Staphylococcus gallinarum, Paenarthrobacter nitroguajacolicus, Arthrobacter citreus, and Bacillus thuringiensis, respectively. Among these, Bacillus thuringiensis (B48Pet), with a specific growth rate of 0.211 h⁻1, could uniformly remove all diesel hydrocarbon fractions at 58.81 mg. L⁻1. h⁻1. This strain, alone or in consortia, represents a promising strategy for the bioremediation of petroleum-contaminated soils.

Mechanism of A. oleivorans S4 treating soluble phosphorus deficiency and hydrocarbon contamination simultaneously

Both soluble phosphorus (P) deficiency and petroleum hydrocarbon contamination represent challenges in soil environments. While phosphate-solubilizing bacteria and hydrocarbon-degrading bacteria have been identified and employed in environmental bioremediation, the bacteria co-adapted to soluble P deficiency and hydrocarbon contamination has rarely been reported. This study explored the ability of Acinetobacter oleivorans S4 (A. oleivorans S4) to solubilize phosphate using n-hexadecane (H), glucose (G), and a mixed carbon source (HG) in tricalcium phosphate (TCP) medium. A. oleivorans S4 exhibited robust growth in H-TCP, releasing 31 mg L-1 of soluble P. Conversely, A. oleivorans S4 barely grew in G-TCP, releasing 654 mg L-1 of soluble P. In HG-TCP, biomass surpassed that in H-TCP, with phosphate release comparable to that in G-TCP. HPLC analysis revealed a small amount of TCA cycle acids in H-TCP and a large amount of gluconate in G-TCP and HG-TCP. Transcriptomic analysis showed elevated expression of genes associated with alkane degradation, P starvation, N utilization, and trehalose synthesis in H-TCP, revealing the molecular co-adaptation mechanism of A. oleivorans S4. Furthermore, the addition of glucose enhanced alkane degradation, P and N utilization, and reduced trehalose synthesis. It indicated that incomplete glucose metabolism may provide energy for other reactions, and the increase in soluble P mediated by gluconate may alleviate oxidative stress. Overall, A. oleivorans S4 proves promising for remediating soluble P-deficient and hydrocarbon-contaminated environments, and glucose stimulates its transformation into a super phosphate-solubilizing bacterium.

N-Alkane Assimilation by Pseudomonas aeruginosa and Its Interactions with Virulence and Antibiotic Resistance

Pseudomonas aeruginosa strains with potential for degrading n-alkanes are frequently cultured from hydrocarbon-contaminated sites. The initial hydroxylation step of long-chain n-alkanes is mediated by the chromosomally encoded AlkB1 and AlkB2 alkane hydroxylases. The acquisition of an additional P. putida GPo1-like alkane hydroxylase gene cluster can extend the substrate range assimilated by P. aeruginosa to Collapse

Key Words

• AlkB
• MexAB-OprM
• P. aeruginosa
• alkane hydroxylase
• antibiotic resistance
• hydrocarbon pollution
• solvent tolerance

Collapse

MESH Headings Collapse

Grants Collapse

Affiliation(s)

Balázs Libisch Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary

Collapse

Collaborators Collapse

Enhancing soil petrochemical contaminant remediation through nutrient addition and exogenous bacterial introduction

Biostimulation (providing favorable environmental conditions for microbial growth) and bioaugmentation (introducing exogenous microorganisms) are effective approaches in the bioremediation of petroleum-contaminated soil. However, uncertainty remains in the effectiveness of these two approaches in practical application. In this study, we constructed mesocosms using petroleum hydrocarbon-contaminated soil. We compared the effects of adding nutrients, introducing exogenous bacterial degraders, and their combination on remediating petroleum contamination in the soil. Adding nutrients more effectively accelerated total petroleum hydrocarbon (TPH) degradation than other treatments in the initial 60 days' incubation. Despite both approaches stimulating bacterial richness, the community turnover caused by nutrient addition was gentler than bacterial degrader introduction. As TPH concentrations decreased, we observed a succession in microbial communities characterized by a decline in copiotrophic, fast-growing bacterial r-strategists with high rRNA operon (rrn) copy numbers. Ecological network analysis indicated that both nutrient addition and bacterial degrader introduction enhanced the complexity and stability of bacterial networks. Compared to the other treatment, the bacterial network with nutrient addition had more keystone species and a higher proportion of negative associations, factors that may enhance microbial community stability. Our study demonstrated that nutrient addition effectively regulates community succession and ecological interaction to accelerate the soil TPH degradation.

Transcriptome analysis of Acinetobacter calcoaceticus HX09 strain with outstanding crude-oil-degrading ability

Microbial remediation plays a pivotal role in the elimination of petroleum pollutants, making it imperative to investigate the capabilities of microorganisms in degrading petroleum. The present study describes the isolation of a promising strain, Acinetobacter sp. HX09, from petroleum-contaminated water. GC-MS analysis revealed a remarkable removal efficiency for short and medium-chain alkanes, with a rate of approximately 64% after a 7-days incubation at 30 °C. Transcriptome analysis of HX09 exhibited a predominant upregulation in gene expression levels by the induce of crude oil. Notably, genes such as alkane 1-monooxygenase, dehydrogenases and fatty acid metabolic enzymes exhibited fold changes range from 3.16 to 1.3. Based on the alkB gene sequences in HX09, the Phyre2 algorithm generated a three-dimensional structure that exhibited similarity to segments of acyl coenzyme desaturases and acyl lipid desaturases. Furthermore, three biodegradation-related gene clusters were predicted in HX09 based on the reference genome sequence. These findings contribute to our understanding of the hydrocarbon-degrading mechanisms employed by Acinetobacter species and facilitate the development of effective remediation strategies for crude oil- polluted environments.

Heat and mass transfer based on the low-temperature thermal treatment of hydrocarbons-impacted soil: A numerical simulation and sandbox validation

Thermal treatment can be an effective method for soil remediation, and numerical models play a crucial role in elucidating the underlying processes that affect efficacy. In this study, experiments were conducted to examine the low-temperature thermal treatment for removing n-hexane and n-octane from soil. The results showed that the removal of two alkanes followed the pseudo-first-order kinetics. Additionally, a quantitative relationship between kinetics constant and temperature was established. Based on experimental results, a simple mathematical model was presented via COMSOL Multiphysics 6.0. The processes considered in the model incorporated conductive and convective heat transfer, the vaporization latent heat, and the removal of organic contaminants which was quantified using an advection-dispersion equation combined with a pseudo-first-order kinetic. The developed model was first validated by a thermal treatment in a soil column, demonstrating conformity with the measured temperature and concentration values. Subsequently, the temporal and spatial changes in soil temperature and contaminant levels were evaluated for different heating temperatures. It was found that thermal conduction dominated heat transfer, whereas thermal convection caused by the migration of liquid water intensified when the temperature was higher than the boiling point. The completion time exhibited a correlation with the heating temperature. It was predicted that the time required to achieve a 90% removal efficiency could be shortened from 14 h to 9.5 h by elevating the heating temperature from 80 ℃ to 120 ℃. The study also investigated the impact of the initial water content on heat transfer. It was observed that the saturated soil showed the slowest heating rate and the longest boiling stage.

Biodegradation capabilities of filamentous fungi in high-concentration heavy crude oil environments

In this comprehensive study, we delved into the capabilities of five fungal strains: Aspergillus flavus, Aspergillus niger, Penicillium chrysogenum, Penicillium glabrum, and Penicillium rubens (the latter isolated from heavy crude oil [HCO]) in metabolizing HCO as a carbon source. Employing a meticulously designed experimental approach, conducted at room temperature (25 °C), we systematically explored various culture media and incubation periods. The results unveiled the exceptional resilience of all these fungi to HCO, with A. flavus standing out as the top performer. Notably, A. flavus exhibited robust growth, achieving a remarkable 59.1% expansion across the medium's surface, accompanied by distinctive macroscopic traits, including a cottony appearance and vibrant coloration. In an effort to further scrutinize its biotransformation prowess, we conducted experiments in a liquid medium, quantifying CO2 production through gas chromatography, which reached its zenith at day 30, signifying substantial bioconversion with a 38% increase in CO2 production. Additionally, we monitored changes in surface tension using the Du Noüy ring method, revealing a reduction in aqueous phase tension from 72.3 to 47 mN/m. This compelling evidence confirms that A. flavus adeptly metabolizes HCO to fuel its growth, while concurrently generating valuable biosurfactants. These findings underscore the immense biotechnological potential of A. flavus in addressing challenges related to HCO, thereby offering promising prospects for bioremediation and crude oil bioupgrading endeavors.

Biosurfactant and biopolymer producing microorganisms from West Kazakhstan oilfield

Microbiological enhanced oil recovery (MEOR) uses indigenous or exogenous microorganisms and nutrients to enhance oil production through synthesis of metabolites reducing oil viscosity and surface tension. In order to find bacteria suitable for MEOR, we studied 26 isolates from wells in the Akingen oilfield in West Kazakhstan. Six of them were selected for further analysis based on their ability to reduce surface tension to less than 40 mN/m, with the A9 isolate exhibiting tension reduction values of 32.76 ± 0.3 mN/m. Based on the morphological features, biochemical activities, and the 16S rRNA gene, the isolates were classified to the Bacillus subtilis group. In the phylogenetic analysis the isolates grouped into two main clusters. Genes encoding the surfactin synthetase subunits were found in A2, A8, A9, A12, PW2, only the PW2 strain had lchAA encoding lichenysin, while sacB encoding levan was noted in A2, A8, A9, and A12. The expression of srfAB, srfAC, and sacB tested with qPCR varied among strains. Nevertheless, whereas temperature moderately affects the expression level, with the highest level recorded at 40 °C, salinity significantly impacts the expression of the genes encoding biosurfactants. B. subtilis strains isolated in the study, especially A9, are promising for microbial-enhanced oil recovery.

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

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

Holistic approach to waste mobil oil bioremediation: Valorizing waste through biosurfactant production for soil restoration

The combustion of mobil oil leads to the emission of toxic compounds in the environment. In this study, the aromatic and aliphatic hydrocarbon fractions present in a waste mobil oil collected from automobile market were comprehensively identified and their toxicity was evaluated using wheat grain. Lysinibacillus sphaericus strain IITR51 isolated and characterized previously could degrade 30-80% of both aliphatic and aromatic hydrocarbons in liquid culture. Interestingly, the strain IITR51 produced 627 mg/L of rhamnolipid biosurfactant by utilizing 3% (v/v) of waste mobil oil in the presence of 1.5% glycerol as additional carbon source. In a soil microcosm study by employing strain IITR51, 50-86% of 3-6 ring aromatic hydrocarbons and 63-98% of aliphatic hydrocarbons (C8 to C22) were degraded. Addition of 60 μg/mL rhamnolipid biosurfactant enhanced the degradation of both aliphatic and aromatic hydrocarbons from 76.88% to 61.21%-94.11% and 78.27% respectively. The degradation of mobil oil components improved the soil physico-chemical properties and increased soil fertility to 64% as evident by the phytotoxicity assessments. The findings indicate that strain IITR51 with degradation capability coupled with biosurfactant production could be a candidate for restoring hydrocarbon contaminated soils.

Unleashing synergistic potential of microbially enhanced anaerobic co-digestion of petroleum refinery biosludge and yard waste: Impact of nutrient balance and microbial diversity

Petroleum refinery sludge, an egregious solid residue generated from the wastewater treatment plants poses an environmental hazard owing to its intricate hydrocarbon composition, necessitating competent treatment for secure disposal. The study proposes a green solution through anaerobic co-digestion of nitrogen-rich petroleum refinery sludge (PS) with carbon-rich yard waste (YW), balancing the nutrients and moisture content for efficient microbial proliferation. Using Central Composite Design-Response Surface Methodology, 1 L batch experiments were conducted with varying carbon/nitrogen (C/N) ratios and pH to achieve maximum biogas yield within 50 days of co-digestion. However, the sluggish biogas recovery (40%) indicated a slow rate-limiting hydrolysis, necessitating pretreatment. Feedstock incubation with Bacillus subtilis IH1 strain, isolated from the microbially-enriched PS, at 108 colony forming units (CFU) per mL for 5 days maximized the soluble chemical oxygen demand and volatile fatty acids by 2.2 and 1.4 folds respectively compared to untreated feedstock. Scale-up Bacillus subtilis aided co-digestion studies further augmented biogas by 76% against untreated monodigestion of PS with significant total petroleum hydrocarbons, emulsions, and lignocellulosic degradation. Further identification of major organic pollutants in the batch digestate revealed significant degradation of the toxic organic hydrocarbon pollutants apotheosizing the efficacy of the synergistic sustainable technique for the management of PS. ENVIRONMENTAL IMPLICATION: The effluent treatment plants (ETPs) of petroleum refining industries generate sludge which is a complex mixture of petroleum hydrocarbons, oil-water (O/W) emulsions and heavy metals. These petroleum hydrocarbon constituents can be linear/cyclic alkanes, polyaromatics, resins and asphaltenes, whose intricate composition is reportedly carcinogenic, cytogenic and mutagenic, classifying it as hazardous waste. Biological treatment of these sludge through anaerobic digestion leads to utilization of petroleum hydrocarbons with subsequent energy recovery. Co-digestion of these sludge with competent co-substrates leads to nutrient balance, diverse microbial proliferation and toxicant dilution. Microbially aided co-digestion further augments methane rendering a digestate with utmost pollutant degradation.

Unraveling the functional instability of bacterial consortia in crude oil degradation via integrated co-occurrence networks

Introduction

Soil ecosystems are threatened by crude oil contamination, requiring effective microbial remediation. However, our understanding of the key microbial taxa within the community, their interactions impacting crude oil degradation, and the stability of microbial functionality in oil degradation remain limited.

Methods

To better understand these key points, we enriched a crude oil-degrading bacterial consortium generation 1 (G1) from contaminated soil and conducted three successive transfer passages (G2, G3, and G4). Integrated Co-occurrence Networks method was used to analyze microbial species correlation with crude oil components across G1-G4.

Results and discussion

In this study, G1 achieved a total petroleum hydrocarbon (TPH) degradation rate of 32.29% within 10 days. Through three successive transfer passages, G2-G4 consortia were established, resulting in a gradual decrease in TPH degradation to 23.14% at the same time. Specifically, saturated hydrocarbon degradation rates ranged from 18.32% to 14.17% among G1-G4, and only G1 exhibited significant aromatic hydrocarbon degradation (15.59%). Functional annotation based on PICRUSt2 and FAPROTAX showed that functional potential of hydrocarbons degradation diminished across generations. These results demonstrated the functional instability of the bacterial consortium in crude oil degradation. The relative abundance of the Dietzia genus showed the highest positive correlation with the degradation efficiency of TPH and saturated hydrocarbons (19.48, 18.38, p < 0.05, respectively), Bacillus genus demonstrated the highest positive correlation (21.94, p < 0.05) with the efficiency of aromatic hydrocarbon degradation. The key scores of Dietzia genus decreased in successive generations. A significant positive correlation (16.56, p < 0.05) was observed between the Bacillus and Mycetocola genera exclusively in the G1 generation. The decline in crude oil degradation function during transfers was closely related to changes in the relative abundance of key genera such as Dietzia and Bacillus as well as their interactions with other genera including Mycetocola genus. Our study identified key bacterial genera involved in crude oil remediation microbiome construction, providing a theoretical basis for the next step in the construction of the oil pollution remediation microbiome.

An overview of bioelectrokinetic and bioelectrochemical remediation of petroleum-contaminated soils

The global problem of petroleum contamination in soils seriously threatens environmental safety and human health. Current studies have successfully demonstrated the feasibility of bioelectrokinetic and bioelectrochemical remediation of petroleum-contaminated soils due to their easy implementation, environmental benignity, and enhanced removal efficiency compared to bioremediation. This paper reviewed recent progress and development associated with bioelectrokinetic and bioelectrochemical remediation of petroleum-contaminated soils. The working principles, removal efficiencies, affecting factors, and constraints of the two technologies were thoroughly summarized and discussed. The potentials, challenges, and future perspectives were also deliberated to shed light on how to overcome the barriers and realize widespread implementation on large scales of these two technologies.

Unique Raoultella species isolated from petroleum contaminated soil degrades polystyrene and polyethylene

Polyolefin plastics, such as polyethylene (PE) and polystyrene (PS), are the most widely used synthetic plastics in our daily life. However, the chemical structure of polyolefin plastics is composed of carbon-carbon (C-C) bonds, which is extremely stable and makes polyolefin plastics recalcitrant to degradation. The growing accumulation of plastic waste has caused serious environmental pollution and has become a global environmental concern. In this study, we isolated a unique Raoultella sp. DY2415 strain from petroleum-contaminated soil that can degrade PE and PS film. After 60 d of incubation with strain DY2415, the weight of the UV-irradiated PE (UVPE) film and PS film decreased by 8% and 2%, respectively. Apparent microbial colonization and holes on the surface of the films were observed by scanning electron microscopy (SEM). Furthermore, the Fourier transform infrared spectrometer (FTIR) results showed that new oxygen-containing functional groups such as -OH and -CO were introduced into the polyolefin molecular structure. Potential enzymes that may be involved in the biodegradation of polyolefin plastics were analyzed. These results demonstrate that Raoultella sp. DY2415 has the ability to degrade polyolefin plastics and provide a basis for further investigating the biodegradation mechanism.

Accurate noise-robust classification of Bacillus species from MALDI-TOF MS spectra using a denoising autoencoder

Bacillus strains are ubiquitous in the environment and are widely used in the microbiological industry as valuable enzyme sources, as well as in agriculture to stimulate plant growth. The Bacillus genus comprises several closely related groups of species. The rapid classification of these remains challenging using existing methods. Techniques based on MALDI-TOF MS data analysis hold significant promise for fast and precise microbial strains classification at both the genus and species levels. In previous work, we proposed a geometric approach to Bacillus strain classification based on mass spectra analysis via the centroid method (CM). One limitation of such methods is the noise in MS spectra. In this study, we used a denoising autoencoder (DAE) to improve bacteria classification accuracy under noisy MS spectra conditions. We employed a denoising autoencoder approach to convert noisy MS spectra into latent variables representing molecular patterns in the original MS data, and the Random Forest method to classify bacterial strains by latent variables. Comparison of the DAE-RF with the CM method using the artificially noisy test samples showed that DAE-RF offers higher noise robustness. Hence, the DAE-RF method could be utilized for noise-robust, fast, and neat classification of Bacillus species according to MALDI-TOF MS data.

Biotechnological potential of microbial bio-surfactants, their significance, and diverse applications

Globally, there is a huge demand for chemically available surfactants in many industries, irrespective of their detrimental impact on the environment. Naturally occurring green sustainable substances have been proven to be the best alternative for reducing reliance on chemical surfactants and promoting long-lasting sustainable development. The most frequently utilized green active biosurfactants, which are made by bacteria, yeast, and fungi, are discussed in this review. These biosurfactants are commonly originated from contaminated sites, the marine ecosystem, and the natural environment, and it holds great potential for environmental sustainability. In this review, we described the importance of biosurfactants for the environment, including their biodegradability, low toxicity, environmental compatibility, and stability at a wide pH range. In this review, we have also described the various techniques that have been utilized to characterize and screen the generation of microbial biosurfactants. Also, we reviewed the potential of biosurfactants and its emerging applications in the foods, cosmetics, pharmaceuticals, and agricultural industries. In addition, we also discussed the ways to overcome problems with expensive costs such as low-cost substrate media formulation, gravitational techniques, and solvent-free foam fractionation for extraction that could be employed during biosurfactant production on a larger scale.

Employing salt-tolerant bacteria Serratia marcescens subsp. SLS for biodegradation of oily kitchen waste

The high oil and salt content of kitchen waste (KW) inhibit bioconversion and humus production. To efficiently degrade oily kitchen waste (OKW), a halotolerant bacterial strain, Serratia marcescens subsp. SLS which could transform various animal fats and vegetable oils, was isolated from KW compost. Its identification, phylogenetic analysis, lipase activity assays, and oil degradation in liquid medium were assessed, and then it was employed to carry out a simulated OKW composting experiment. In liquid medium, the 24 h degradation rate of mixed oils (soybean oil: peanut oil: olive oil: lard = 1:1:1:1, v/v/v/v) was up to 87.37% at 30 °C, pH 7.0, 280 rpm, 2% oil concentration and 3% NaCl concentration. The ultra-performance liquid chromatography/tandem mass spectrometry (UPLC-MS) method demonstrated that the mechanism of SLS strain metabolizing long-chain triglycerides (TAGs) (C53-C60), especially the biodegradation of TAG (C18:3/C18:3/C18:3) by the strain can reach more than 90%. Degradation of 5, 10, 15% concentrations of total mixed oil were also calculated to be 64.57, 71.25, 67.99% respectively after a simulated composting duration of 15 days. The results suggest that the isolated strain of S. marcescens subsp. SLS is suitable for OKW bioremediation in high NaCl concentration within a reasonably short period of time. The findings introduced a salt-tolerant and oil-degrading bacteria, providing insights into the mechanism of oil biodegradation and offering new avenues of study for OKW compost and oily wastewater treatment.

Functional materials contributing to the removal of chlorinated hydrocarbons from soil and groundwater: Classification and intrinsic chemical-biological removal mechanisms

Chlorinated hydrocarbons (CHs) are the main contaminants in soil and groundwater and have posed great challenge on the remediation of soil and ground water. Different remediation materials have been developed to deal with the environmental problems caused by CHs. Remediation materials can be classified into three main categories according to the corresponding technologies: adsorption materials, chemical reduction materials and bioaugmentation materials. In this paper, the classification and preparation of the three materials are briefly described in terms of synthesis and properties according to the different types. Then, a detailed review of the remediation mechanisms and applications of the different materials in soil and groundwater remediation is presented in relation to the various properties of the materials and the different challenges encountered in laboratory research or in the environmental application. The removal trends in different environments were found to be largely similar, which means that composite materials tend to be more effective in removing CHs in actual remediation. For instance, adsorbents were found to be effective when combined with other materials, due to the ability to take advantage of the respective strengths of both materials. The rapid removal of CHs while minimizing the impact of CHs on another material and the material itself on the environment. Finally, suggestions for the next research directions are given in conjunction with this paper.

Advanced bioremediation by an amalgamation of nanotechnology and modern artificial intelligence for efficient restoration of crude petroleum oil-contaminated sites: a prospective study

Crude petroleum oil spillage is becoming a global concern for environmental pollution and poses a severe threat to flora and fauna. Bioremediation is considered a clean, eco-friendly, and cost-effective process to achieve success among the several technologies adopted to mitigate fossil fuel pollution. However, due to the hydrophobic and recalcitrant nature of the oily components, they are not readily bioavailable to the biological components for the remediation process. In the last decade, nanoparticle-based restoration of oil-contaminated, owing to several attractive properties, has gained significant momentum. Thus, intertwining nano- and bioremediation can lead to a suitable technology termed 'nanobioremediation' expected to nullify bioremediation's drawbacks. Furthermore, artificial intelligence (AI), an advanced and sophisticated technique that utilizes digital brains or software to perform different tasks, may radically transfer the bioremediation process to develop an efficient, faster, robust, and more accurate method for rehabilitating oil-contaminated systems. The present review outlines the critical issues associated with the conventional bioremediation process. It analyses the significance of the nanobioremediation process in combination with AI to overcome such drawbacks of a traditional approach for efficiently remedying crude petroleum oil-contaminated sites.

Contemporary updates on bioremediation applications of graphene and its composites

Graphene, a 2D single-layered carbon sp² hybrid substance set in a honeycomb network, is widespread in many carbon-based materials. Due to its extraordinary optical, electrical, thermal, mechanical, and magnetic competences as well as its significant specific surface area, it has attracted a lot of interest recently. Synthesizing graphene refers to any process for creating or extracting the material, depending on the desired purity, size, and efflorescence of the finished good. Numerous methods have been employed for graphene synthesis categorized as top-down procedures and bottom-up procedures. Graphene finds its implementations in various industries such as electronics, energy, chemical, transport, defence, and biomedical areas such as accurate biosensing. It has been widely used in water treatment as a binder for organic contaminants and heavy metals. Many researches have fixated on creating various modified graphene, graphene oxide composites, graphene nanoparticle composites and semiconductor hybrids of graphene for contaminant removal from water. In this review, we have tried to address various production methods for graphene and its composites along with their advantages and disadvantages. Furthermore, we have presented a summary on graphene's outstanding immobilization of a variety of contaminants like toxic heavy metals, organic dyes, inorganic pollutants and pharmaceutical wastes. Additionally, a development of graphene-based microbial fuel cell (MFC) has been evaluated in an effort to produce ecological wastewater treatment and bioelectricity.

A novel dehydrocoenzyme activator combined with a composite microbial agent TY for enhanced bioremediation of crude oil-contaminated soil

Bioaugmentation (BA) and biostimulation (BS) synergistic remediation is an effective remediation strategy for oil-contaminated soil. In this study, the optimal combination system of composite microbial agent TY (Achromobacter: Pseudomona = 2:1) and dehydrocoenzyme activator (NaNO₃ (7.0 g/L), (NH₄)₂HPO₄ (1.0 g/L), riboflavin (6.0 mg/L)) was screened. Under the best combination system, the degradation rate of crude oil in oil-contaminated soil reached 79.44% after 60 d, which was 1.74 times and 1.23 times higher than that of compound microbial agent TY treatment and dehydrogenase activator treatment, respectively. In addition, a highly efficient combination system was found to target the degradation of oil C₁₀-C₂₈ fractions by gas chromatography (GC). The increased abundance of dehydrogenase coenzymes such as flavin nucleotides (FAD and FMN), coenzyme I (NAD⁺, Co I) and coenzyme II (NADP⁺, Co II) as well as dioxygenases and monooxygenases promote the degradation of crude oil. Furthermore, the dominant genera at the genus level in soil were analyzed by high-throughput sequencing, which were Nocardioides (46.48%-56.07%), Gordonia (11.40%-14.61%), Intrasporangiaceae (5.05%-10.58%), Pseudomonas (1.39%-1.92%) and Dietzia (0.64%-2.77%). Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis showed that the abundance of genes associated with crude oil degradation such as ABC transporters (2.89%), fatty acid (1.04%), carbon metabolism (4.5%) and aromatic compound (0.92%) was assigned enhanced after 60 d of remediation. These results indicated that the combination system of the compound bacterium TY and the dehydrocoenzyme activator is a propective option for the bioremediation of oil-contaminated soil.

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

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

Surfactant-enhanced mobilization of persistent organic pollutants: Potential for soil and sediment remediation and unintended consequences

This review aims to provide an overview of the sources and reactions of persistent organic pollutants (POPs) and surfactants in soil and sediments, the surfactant-enhanced solubilisation of POPs, and the unintended consequences of surfactant-induced remediation of soil and sediments contaminated with POPs. POPs include chemical compounds that are recalcitrant to natural degradation through photolytic, chemical, and biological processes in the environment. POPs are potentially toxic compounds mainly used in pesticides, solvents, pharmaceuticals, or industrial applications and pose a significant and persistent risk to the ecosystem and human health. Surfactants can serve as detergents, wetting and foaming compounds, emulsifiers, or dispersants, and have been used extensively to promote the solubilization of POPs and their subsequent removal from environmental matrices, including solid wastes, soil, and sediments. However, improper use of surfactants for remediation of POPs may lead to unintended consequences that include toxicity of surfactants to soil microorganisms and plants, and leaching of POPs, thereby resulting in groundwater contamination.

Enhanced bioremediation of oil-contaminated soil in a slurry bioreactor by H2O2-stimulation of oil-degrading/biosurfactant-generating bacteria: performance optimization and bacterial metagenomics

Oil-contaminated soil is the main challenge for oil-rich countries, and this study aimed to investigate the performance of the H₂O₂-stimulated slurry bioreactor for the bioremediation of real oil-contaminated soil. The effect of biomass concentration, soil to water (S/W) ratio, slurry temperature, pH, and H₂O₂ concentration were optimized for the removal of total petroleum hydrocarbons (TPH) from oil-contaminated soil. TPH removal efficiency, biosurfactants production, and peroxidase and dehydrogenase activities were measured. The optimum conditions for the complete biodegradation of 32 [Formula: see text] in the slurry bioreactor during 6 days were biomass of 2250 mg/L, S/W ratio of 20%, the temperature of 30 °C, pH of 7, and an H₂O₂ concentration of 120 mg/L. The highest peroxidase, dehydrogenase, surfactin, and rhamnolipid formation were also obtained under optimum conditions. The results pointed out that complete biodegradation of 32 g/kg of TPH in oil-contaminated soil at a short reaction time of 6 days is achievable in the developed process operated under optimum conditions. The GC/FID analysis of solid and liquid phases showed that the bioprocess completely biodegraded the different TPH fractions. H₂O₂ efficiently stimulated the biosurfactant-generating bacteria to produce peroxidase and thereby accelerating the bioremediation rate. Accordingly, an H₂O₂-mediated slurry bioreactor inoculated with biosurfactant/peroxidase-generating bacteria is a promising technique for cleaning up oil-contaminated soils.

The ecological response and distribution characteristics of microorganisms and polycyclic aromatic hydrocarbons in a retired coal gas plant post-thermal remediation site

Thermal remediation is one of the most common approaches of removing organic pollutants in the retired contamination sites. However, little is known about the performance of bacterial community characteristics after in situ thermal remediation. In this study, the ecological response and spatial distributional characteristics of microorganisms and polycyclic aromatic hydrocarbons (PAHs) were investigated using a high throughput sequencing method in a retired coal gas plant site after in situ thermal remediation in Nanjing, China. Combination of Venn, clustering-correlation heatmap and two - factor correlation network analysis revealed that, microbial communities were obviously affected and classified by soil depths, temperature, and contamination level, respectively. The common and endemic microorganisms of each group were identified. The relative abundances of Thermaerobacter, Calditerricola, Brevibacillus, Ralstonia and Rhodococcus (aerobic bacteria) gradually declined with the increase of soil depth, while those of Bacillus, Fictibacillus, Paenibacillus, Rheinheimera presented opposite tendency. Some thermophilic degradation bacteria of PAHs, including Thermaerobacter, Calditerricola, Bacillus, Rhodococcus, unclassified_p__Firmicutes, Arthrobacter and Deinococcus, were identified and increased in the abundance at heavily polluted sites. Additionally, Proteobacteria, Bacteroidota, Deinococcota, Chloroflexi, Acidobacteriota, and Actinobacteriota showed negative response to the increase of soil depth, temperature and pollution level, while Firmicutes presented a positive response. This implied that Firmicutes has better stress resistance and adaptability to thermal remediation condition. The key environmental factors affecting microorganism composition and distribution were Temperature, Total nitrogen, Oxidation-Reduction Potential, Organic matters, and PAHs concentrations, which explains the dominant driving mechanism of soil depth, temperature, and contamination level on microbial characteristics in thermal remediation site. Our study could contribute to a better understanding of the resilience and adaptation mechanisms of microbial community at the contaminated site after the in situ thermal remediation.

Falsochrobactrum&nbsp;tianjinense sp. nov., a New Petroleum-Degrading Bacteria Isolated from Oily Soils

The microbial remediation technology had great potential and attracted attention to total petroleum hydrocarbon pollution (TPH) remediation, but its efficiency is limited by its application in the field. In this study, a new TPH-degrading strain, TDYN1, was isolated from contaminated oil soil in Dagang Oilfield in Tianjin, China, and identified as Falsochrobactrum sp. by 16S rRNA sequence analysis. The physiological characterization of the isolate was observed. The orthogonal experiment was carried out for the optimum degradation conditions to improve its biodegradation efficiency. The strain was the gram-stain-negative, short rod-shaped, non-spore-forming, designated Falsochrobactrum tianjinense sp. nov (strain TDYN1); it had 3.51 Mb, and the DNA G + C content of the strain was 56.0%. The degradation rate of TDYN1 was 69.95% after 7 days of culture in optimal degradation conditions (temperature = 30 °C, pH = 8, salinity = 10 g L^-1, petroleum concentration = 1 g L^-1, and the inoculation dose of strain TDYN1 = 6%) and also reached more than 30% under other relatively extreme conditions. It suggested that the TDYN1 has great potential for TPH remediation in the soils of North China.

A review on biosurfactant producing bacteria for remediation of petroleum contaminated soils

The discharge of potentially toxic petroleum hydrocarbons into the environment has been a matter of concern, as these organic pollutants accumulate in many ecosystems due to their hydrophobicity and low bioavailability. Petroleum hydrocarbons are neurotoxic and carcinogenic organic pollutants, extremely harmful to human and environmental health. Traditional treatment methods for removing hydrocarbons from polluted areas, including various mechanical and chemical strategies, are ineffective and costly. However, many indigenous microorganisms in soil and water can utilise hydrocarbon compounds as sources of carbon and energy and hence, can be employed to degrade hydrocarbon contaminants. Therefore, bioremediation using bacteria that degrade petroleum hydrocarbons is commonly viewed as an environmentally acceptable and effective method. The efficacy of bioremediation can be boosted further by using potential biosurfactant-producing microorganisms, as biosurfactants reduce surface tension, promote emulsification and micelle formation, making hydrocarbons bio-available for microbial breakdown. Further, introducing nanoparticles can improve the solubility of hydrophobic hydrocarbons as well as microbial synthesis of biosurfactants, hence establishing a favourable environment for microbial breakdown of these chemicals. The review provides insights into the role of microbes in the bioremediation of soils contaminated with petroleum hydrocarbons and emphasises the significance of biosurfactants and potential biosurfactant-producing bacteria. The review partly focusses on how nanotechnology is being employed in different critical bioremediation processes.

Development of Rhizophora mangle (Rhizophoraceae) and Avicennia schaueriana (Avicenniaceae) in the presence of a hydrocarbon-degrading bacterial consortium and marine diesel oil

The development of Rhizophora mangle and Avicennia schaueriana seedlings impacted by marine diesel oil (MDO) was evaluated in the presence or absence of a hydrocarbon-degrading bacterial consortium (HBC). The bioassays were conducted in a greenhouse during 6 months and consisted of three different treatments (control, MDO only and MDO + HBC). The bacterial consortium was mainly composed of Bacillus spp. (73%), but Rhizobium spp., Pseudomonas spp., Ochrobactrum spp., and Brevundimonas spp. were also present. After 6 months, A. schaueriana seedlings showed higher mortality compared to those of R. mangle; R. mangle exhibited 68% (control), 44% (MDO alone) and 50% (MDO + HBC) seedlings survivorship compared to 42% (control), 0% (MDO alone) and 4% (MDO + HBC) for A. schaueriana. This variability may be due to differences in species physiology. Stem growth, diameter and number of leaves remained constant during the 6 months of the experiment with marine diesel oil and hydrocarbon-degrading bacterial consortium (MDO + BBC). For both mangrove species, bacterial enzymatic activity in the sediments was sufficient to maintain cell counts of 10⁷ cells cm^-3 in the rhizospheric soil and possibly synthetize the extracellular polymeric substances (EPS) that may emulsify and solubilize oil products.

A Review on Biotechnological Approaches Applied for Marine Hydrocarbon Spills Remediation

The increasing demand for petroleum products generates needs for innovative and reliable methods for cleaning up crude oil spills. Annually, several oil spills occur around the world, which brings numerous ecological and environmental disasters on the surface of deep seawaters like oceans. Biological and physico-chemical remediation technologies can be efficient in terms of spill cleanup and microorganisms—mainly bacteria—are the main ones responsible for petroleum hydrocarbons (PHCs) degradation such as crude oil. Currently, biodegradation is considered as one of the most sustainable and efficient techniques for the removal of PHCs. However, environmental factors associated with the functioning and performance of microorganisms involved in hydrocarbon-degradation have remained relatively unclear. This has limited our understanding on how to select and inoculate microorganisms within technologies of cleaning and to optimize physico-chemical remediation and degradation methods. This review article presents the latest discoveries in bioremediation techniques such as biostimulation, bioaugmentation, and biosurfactants as well as immobilization strategies for increasing the efficiency. Besides, environmental affecting factors and microbial strains engaged in bioremediation and biodegradation of PHCs in marines are discussed.

Physiological changes in Rhodococcus ruber S103 immobilized on biobooms using low-cost media enhance stress tolerance and crude oil-degrading activity

For economic feasibility, sugarcane molasses (0.5%, w/v) containing K₂HPO₄ (0.26%, w/v) and mature coconut water, low value byproducts, were used in cultivation of Rhodococcus ruber S103 for inoculum production and immobilization, respectively. Physiological changes of S103 grown in low-cost media, including cell hydrophobicity, saturated/unsaturated ratio of cellular fatty acids and biofilm formation activity, enhanced stress tolerance and crude oil biodegradation in freshwater and even under high salinity (5%, w/v). Biobooms comprised of S103 immobilized on polyurethane foam (PUF) was achieved with high biomass content (10¹⁰ colony-forming units g^-1 PUF) via a scale-up process in a 5-L modified fluidized-bed bioreactor within 3 days. In a 500-L mesocosm, natural freshwater was spiked with crude oil (72 g or 667 mg g^-1 dry biobooms), and a simulated wave was applied. Biobooms could remove 100% of crude oil within only 3 days and simultaneously biodegraded 60% of the adsorbed oil after 7 days when compared to boom control with indigenous bacteria. In addition, biobooms had a long shelf-life (at least 100 days) with high biodegradation activity (85.2 ± 2.3%) after storage in 10% (w/v) skimmed milk at room temperature. This study demonstrates that the low-cost production of biobooms has potential for future commercial bioremediation.

Recent advancements in hydrocarbon bioremediation and future challenges: a review

Petrochemicals are important hydrocarbons, which are one of the major concerns when accidently escaped into the environment. On one hand, these cause soil and fresh water pollution on land due to their seepage and leakage from automobile and petrochemical industries. On the other hand, oil spills occur during the transport of crude oil or refined petroleum products in the oceans around the world. These hydrocarbon and petrochemical spills have not only posed a hazard to the environment and marine life, but also linked to numerous ailments like cancers and neural disorders. Therefore, it is very important to remove or degrade these pollutants before their hazardous effects deteriorate the environment. There are varieties of mechanical and chemical methods for removing hydrocarbons from polluted areas, but they are all ineffective and expensive. Bioremediation techniques provide an economical and eco-friendly mechanism for removing petrochemical and hydrocarbon residues from the affected sites. Bioremediation refers to the complete mineralization or transformation of complex organic pollutants into the simplest compounds by biological agents such as bacteria, fungi, etc. Many indigenous microbes present in nature are capable of detoxification of various hydrocarbons and their contaminants. This review presents an updated overview of recent advancements in various technologies used in the degradation and bioremediation of petroleum hydrocarbons, providing useful insights to manage such problems in an eco-friendly manner.

Complete genome sequence of Pseudomonas stutzeri S116 owning bifunctional catalysis provides insights into affecting performance of microbial fuel cells

Background

Pseudomonas stutzeri S116 is a sulfur-oxidizing bacteria isolated from marine sludge. It exhibited excellent electricity generation as bioanode and biocathode applied in microbial fuel cells (MFCs). Complete genome sequencing of P. stutzeri and cyclic voltammetry method were performed to reveal its mechanism in microbial fuel cells system.

Results

This study indicated that the MFCs generated a maximum output voltage of 254.2 mV and 226.0 mV, and maximum power density of 765 mW/m² and 656.6 mW/m² respectively. Complete genome sequencing of P. stutzeri S116 was performed to indicate that most function genes showed high similarities with P. stutzeri, and its primary annotations were associated with energy production and conversion (6.84%), amino acid transport and metabolism (6.82%) and inorganic ion transport and metabolism (6.77%). Homology of 36 genes involved in oxidative phosphorylation was detected, which suggests the strain S116 possesses an integrated electron transport chain. Additionally, many genes encoding pilus-assembly proteins and redox mediators (riboflavin and phenazine) were detected in the databases. Thiosulfate oxidization and dissimilatory nitrate reduction were annotated in the sulfur metabolism pathway and nitrogen metabolism pathway, respectively. Gene function analysis and cyclic voltammetry indicated that P. stutzeri probably possesses cellular machinery such as cytochrome c and redox mediators and can perform extracellular electron transfer and produce electricity in MFCs.

Conclusion

The redox mediators secreted by P. stutzeri S116 were probably responsible for performance of MFCs. The critical genes and metabolic pathways involved in thiosulfate oxide and nitrate reduction were detected, which indicated that the strain can treat wastewater containing sulfide and nitrite efficiently.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02552-8.

Biosurfactant production by Bacillus subtilis SL and its potential for enhanced oil recovery in low permeability reservoirs

Microbial enhanced oil recovery (MEOR) technology is an environmental-friendly EOR method that utilizes the microorganisms and their metabolites to recover the crude oil from reservoirs. This study aims to research the potential application of strain SL in low permeability reservoirs. Strain SL is identified as Bacillus subtilis by molecular methods. Based on the mass spectrometry, the biosurfactant produced by strain SL is characterized as lipopeptide, and the molecular weight of surfactin is 1044, 1058, 1072, 1084 Da. Strain SL produces 1320 mg/L of biosurfactant with sucrose as the sole carbon source after 72 h. With the production of biosurfactant, the surface tension of cell-free broth considerably decreases to 25.65 ± 0.64 mN/m and the interfacial tension against crude oil reaches 0.95 ± 0.22 mN/m. The biosurfactant exhibits excellent emulsification with crude oil, kerosene, octane and hexadecane. In addition, the biosurfactant possesses splendid surface activity at pH 5.0–12.0 and NaCl concentration of 10.0% (w/v), even at high temperature of 120 °C. The fermentation solution of strain SL is applied in core flooding experiments under reservoir conditions and obtains additional 5.66% of crude oil. Hence, the presented strain has tremendous potential for enhancing the oil recovery from low-permeability reservoirs.

Optimization of biomass production by autochthonous Pseudomonas sp. MT1A3 as strategy to apply bioremediation in situ in a chronically hydrocarbon-contaminated soil

These days, petroleum hydrocarbon pollution has become a global problem, because of this, bioremediation is presented as a strategy for cleaning up sites contaminated with organic pollutants, and it has an increasing role in relation to the potential it presents as a non-invasive and cost-effective technology. The aim of this study is to optimize the biomass production of Pseudomonas sp. MT1A3 strain as a soil bioremediation approach for petroleum hydrocarbon polluted environments. Factorial experimental designs were employed to study the effect of several factors of composition medium and incubation conditions on biomass production. Agro-industrial wastes such as peanut oil as carbon source, NaNO₃ as nitrogen source and incubation temperature were found to be significant independent variables. These factors were further optimized using Box-Behnken design. Combination of peanut oil 18.69 g/L, NaNO₃ 2.39 g/L and 26.06 °C incubation temperature was optimum for maximum biomass production of MT1A3 and the model validated in a bioreactor allowed to obtain 9.67 g/L. Based on these results, this autochthonous strain was applied in bioaugmentation as a bioremediation strategy through microcosm designs, reaching 93.52% of total hydrocarbon removal at 60 days. This constitutes a promising alternative for hydrocarbon-contaminated soil.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03183-6.

Study on a Strain of Lysinibacillus sp. with the Potential to Improve the Quality of Oil Sands

A strain of Lysinibacillus sp., named as Y316, can degrade heavy fractions such as resins and asphaltenes in oil sand. We used Y316 to degrade oil sand samples for 35 days. After bacterial degradation, the oil sand degradation efficiency was 5.88%, while the degradation efficiency of the control group was only 0.29% under the same conditions. Compared with the control group, the saturated content of oil sand in the degradation group increased from 9.56 to 14.39%. After degradation, the resin and asphaltene fractions decreased by 5.34 and 4.77%, respectively. The results of the vaporizable fraction analysis also confirmed the degradation of heavy fractions and the formation of light fractions. After 35 days of degradation, the vaporizable fractions of saturates increased by 3.76 times. The results indicate that Y316 has great significance for improving the quality of oil sands and assisting in oil sand exploitation.

Bacterial diversity and competitors for degradation of hazardous oil refining waste under selective pressures of temperature and oxygen

Oil refining waste (ORW) contains complex, hazardous, and refractory components, causing more severe long-term environmental pollution than petroleum. Here, ORW was used to simulate the accelerated domestication of bacteria from oily sludges and polymer-flooding wastewater, and the effects of key factors, oxygen and temperature, on the ORW degradation were evaluated. Bacterial communities acclimated respectively in 30/60 °C, aerobic/anaerobic conditions showed differentiated degradation rates of ORW, ranging from 5% to 34%. High-throughput amplicon sequencing and ORW component analysis revealed significant correlation between bacterial diversity/biomass and degradation efficiency/substrate preference. Under mesophilic and oxygen-rich condition, the high biomass and abundant biodiversity with diverse genes and pathways for petroleum hydrocarbons degradation, effectively promoted the rapid and multi-component degradation of ORW. While under harsh conditions, a few dominant genera still contributed to ORW degradation, although the biodiversity was severely restricted. The typical dominant facultative anaerobes Bacillus (up to 99.8% abundance anaerobically) and Geobacillus (up to 99.9% abundance aerobically and anaerobically) showed oxygen-independent sustainable degradation ability and broad-spectrum of temperature adaptability, making them promising and competitive bioremediation candidates for future application. Our findings provide important strategies for practical bioremediation of varied environments polluted by hazardous ORW.

Fundamental Investigation on a Foam-Generating Microorganism and Its Potential for Mobility Reduction in High-Permeability Flow Channels

This study proposed a novel foam EOR technique using Pseudomonas aeruginosa to generate the foam and investigated the potential of the microbial foam EOR to modify the permeability of a high-permeability porous system. We investigated oxygen nanobubble, carbon dioxide nanobubble and ferrous sulfate concentrations to discover the optimal levels for activating the foam generation of the microorganism through cultivation experiments. We also clarified the behavior of the microbial foam generation and the bioproducts that contribute to the foam generation. The potential of the foam to decrease the permeability of high-permeability porous systems was evaluated through flooding experiments using sand pack cores. The foam generation became more active with the increase in the number of nanobubbles, while there was an optimal concentration of ferrous sulfate for foam generation. The foam was identified as being induced by the proteins produced by the microorganism, which can be expected to bring about several advantages over surfactant-induced foam. The foam successfully decreased the permeability of high-permeability sand pack cores to half of their initial levels. These results demonstrate that the microbial foam EOR has the potential to decrease the permeability of high-permeability porous systems and improve the permeability heterogeneity in oil reservoirs.

Formulation of a Culture Medium to Optimize the Production of Lipopeptide Biosurfactant by a New Isolate of Bacillus sp.: A Soil Heavy Metal Mitigation Approach

This research aimed to optimize a lipopeptide biosurfactant produced from Bacillus sp. SHA302 due to its high efficiency of heavy metal release in soil. The results demonstrated that the metal release capacity of the lipopeptide biosurfactant alone increased with increasing the biosurfactant concentration. Among treatments with different biosurfactant concentrations plus acid, the highest metal release rates of 53.8% ± 1.4 and 39.3% ± 1.7 for Zn and Pb, respectively, were observed in the critical micelle concentration (CMC) + HCl treatment. The results of a factorial experiment designed for optimizing biosurfactant production showed that among five inexpensive carbon sources and six mineral nitrogen sources, sugar beet molasses (1%) and ammonium chloride (0.1%) were the most efficient sources in lowering the surface tension (ST) of the culture media to 32.2 ± 0.76 mN/m. The second step of the experiment was a Plackett-Burman design with 11 factors and showed that the four factors of pH, ammonium chloride, magnesium sulfate, and molasses significantly affected (P < 0.05) the changes in ST and biosurfactant production. The third step of the experiment was done using the response surface methodology (RSM) with a central composite design. The results showed that a pH of 7.3, 1.5 g/l of ammonium chloride, 0.3 g/l of magnesium sulfate, and 10% of sugar beet molasses yielded values of 29.2 ± 0.71 mN/m and 5.74 ± 0.52 g/l for the two variables of ST and biosurfactant production, respectively, which reached their most optimal levels.

Bioremediation of motor oil-contaminated soil and water by a novel indigenous Pseudomonas otitidis strain DU13 and characterization of its biosurfactant

Production of biosurfactant by a novel indigenous isolate Pseudomonas otitidis strain DU13 and its role in bioremediation of petroleum hydrocarbon is reported. The identity of the isolate was confirmed by 16S rDNA gene sequencing analysis (Genbank accession: MK177190). The biosurfactant produced by the isolate could reduce the surface tension of petroleum supplemented medium by 46% just after 7 days of treatment. The emulsification index (E ₂₄ ) of the surfactant was found 37, 35, and 20%, respectively, against used motor oil, diesel, and kerosene. The FTIR spectrum of the crude biosurfactant showed the presence of υ_C-H stretch, υ_CH2, υ_-C=C stretch and υ_C-H bonding. The isolated strain could degrade 26% of TPH content of used motor oil in liquid culture. Whereas, ex situ pilot-scale field trial demonstrated very high bioremediation potential of the isolate in terms of germination rate of Vigna radiata and Cicer arietinum seeds and plant growth just after 20 days of treatment.

Structural and functional characterization of a novel biosurfactant from Bacillus sp. IITD106

Plant saponins are attractive biosurfactants and have been used to enhance phytoremediation. There are only limited reports on saponins produced by bacteria. Here, we report structural and functional characterization of a novel saponin produced by Bacillus sp. IITD106. Biosurfactant production was determined by emulsion index, drop collapse, oil displacement and hemolytic assays. The biosurfactant was stable over a range of temperature (30 °C to 70 °C), salinity (0-150 g liter^-1) and pH (4-10). The surface tension of the medium reduced from 58.89 mN/m to 27.29 mN/m using the isolated biosurfactant. Chromatographic analysis revealed the biosurfactant to be a glycolipid. LCMS, FT-IR and NMR analysis identified the biosurfactant to be a saponin containing two sugar groups and a 5 ringed triterpene sapogenin unit. Genome sequencing of the strain revealed the presence of genes responsible for biosynthesis of saponin. Statistical optimization of culture medium resulted in 9.3-fold increase in biosurfactant production. Kinetics study of biosurfactant production performed in a stirred tank batch bioreactor resulted in 6.04 g liter^-1 and 6.9 g liter^-1 biomass and biosurfactant concentration, respectively. The biosurfactant was found to solubilize polycyclic aromatic hydrocarbons. The potential of cell free biosurfactant containing broth to enhance oil recovery was tested in a sand pack column and recovery of 63% of residual oil was observed. To our knowledge this is the first report of saponin production by any of the strains of Bacillus.

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

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