Microbial degradation of petroleum hydrocarbons

In situ bioelectrochemical remediation of contaminated soil and groundwater: A review

Contamination of the subsurface environment poses a serious hazard to the environment and human health. Recently, the bioelectrochemical system (BES) has drawn great attention in soil and groundwater remediation as it does not necessitate the addition of chemicals and exhibits minimal energy consumption to facilitate microbial degradation of pollutants. However, the complexity of the subsurface environment and the design parameters of the BES significantly affect the remediation performance and the current literature on BES primarily concentrates on its application in wastewater treatment, with a lack of summary of that in the subsurface environment. Therefore, the purpose of this review was to provide the current status, challenges, and outlooks of BES in situ treatment of pollutants from soil and groundwater. Firstly, the principles and efficacies of BES in treating the typical pollutants from the subsurface environment were discussed. Secondly, the factors that impact the BES treatment efficiencies, especially soil properties, the distinctive and pivotal factors for BES in situ application, were discussed specifically. Finally, the challenges and outlooks of BES for the in situ remediation of the contaminated soil and groundwater were addressed. BES is a green and sustainable in situ remediation technology and future advancements may necessitate the integration with complementary technologies and innovative system configurations to advance the practical implementation of BES.

Exploring Halophiles for Reclamation of Saline Soils: Biotechnological Interventions for Sustainable Agriculture

Soil salinization is a major constraint on agricultural productivity, particularly in arid and semi-arid regions where limited rainfall cannot wash salts from plant root zones. This leads to disruptions in water uptake, ion balance, photosynthesis, respiration, nutrient absorption, hormone regulation and rhizosphere microbiome disturbances in plants. Chemical and biological methods can help mitigate soil salinity, but biological approaches, like using halophytes and salt-tolerant microorganisms, are preferred for environmental sustainability. Halophytes, however, represent only about 1% of flora and are habitat specific, so halophilic plant growth-promoting (PGP) microbes have emerged as a key eco-friendly solution. Halophilic PGP bacteria have shown promise in remediating saline soils, enhancing fertility and boosting crop resilience by inducing salinity tolerance (IST) and promoting plant growth traits. In the era of modern agriculture where chemical inputs are at their peak of application rendering the soil infertile, halophilic PGP bacteria represent a promising, sustainable approach to support food security, aligning with Sustainable Development Goals for zero hunger.

Bioremediation of alkane-containing saline soils using the long-chain alkane-degrading bacterium Pseudomonas aeruginosa DL: Effects, communities, and networks

Remediation of soil contaminated with long-chain hydrocarbons and affected by salinization poses a considerable challenge. The isolation of a bacterial strain, identified as Pseudomonas aeruginosa DL, from petroleum-contaminated saline-alkali soil has been reported in this study. The strain demonstrated a high capacity to degrade long-chain alkanes and exhibited adaptability to saline-alkali conditions. Gene annotation and analysis of degradation products revealed that the strain DL employed a step-by-step chain-breaking mechanism to degrade long-chain alkanes. Following 160 days of bioaugmented remediation of contaminated soil using the strain DL, 81.36 % degradation of long-chain alkanes, initially present at a concentration of 30,000 mg/kg, was achieved. The activities of soil enzymes, including dehydrogenase, lipase, catalase, and urease, were significantly increased (p < 0.05). Community structure analysis revealed that Pseudomonas aeruginosa DL successfully colonized the contaminated soil, achieving a relative abundance of 69 %. In addition, alkane-degrading bacterial genera, such as Salinimicrobium, Isoptericola, Gordonia, Achromobacter and Ochrobactrum, emerged as new dominant genera. Microbial cooccurrence networks confirmed that bioaugmentation with the strain DL could streamline interpopulation interactions within the community and enhance associative networks, thereby guiding community evolution toward improved alkane degradation. This study offers valuable strain resources and data support for the bioremediation of saline-alkali soils contaminated with long-chain alkanes.

Comparative Genomic and Transcriptomic Analysis Provides New Insights into the Aflatoxin B1 Biodegradability by Kocuria rosea from Deep Sea

As a mycotoxin, aflatoxin B1 (AFB1) has attracted increasing attention due to its highly toxic effects, such as teratogen, carcinogen, and mutagen. AFB1-producing fungi have been found in both terrestrial and marine sources. Over the last two years, the marine-derived bacteria Kocuria rosea has shown the ability to degrade AFB1. However, no studies have yet explored the aflatoxin degradation potential in the genus Kocuria, and the molecular basis of aflatoxin metabolisms by strain has not yet been investigated. In this study, we first compared and analyzed the genomic features of 13 bacteria of the genus Kocuria by comparative genomic analysis and investigated the evolutionary patterns (evolutionary selection pressure analysis and gene family expansion analysis) and pan and core genomes of Kocuria strains. It was found that Kocuria genus strains showed high potential in the bioremediation of aromatic compounds and aflatoxin degradation. In addition, this study revealed 1421 differentially expressed genes and 752 upregulated genes between the aflatoxin group and the control group through transcriptome analysis and conducted functional annotation and analysis of functional enrichment. According to the expression and functional analysis of upregulated genes, the enzymes and genes (cytochrome P450, oxidoreductase, intradiol ring-cleavage dioxygenase, hydrolase, and monooxygenase) involved in the aflatoxin degradation of Kocuria rosea were screened. These findings indicate the potential of Kocuria rosea in the remediation of aflatoxin contamination and provide a foundation and direction for the further excavation of novel degradation genes, exploration of degradation mechanisms, and genomic modification.

The GntR/VanR transcription regulator AlkR represses AlkB2 monooxygenase expression and regulates n-alkane degradation in Pseudomonas aeruginosa SJTD-1

Transmembrane alkane monooxygenase (AlkB)-type monooxygenases, especially AlkB2 monooxygenases, are crucial for aerobic degradation of the medium-to-long-chain n-alkanes in hydrocarbon-utilizing microorganisms. In this study, we identified a GntR/VanR transcription regulator AlkR of Pseudomonas aeruginosa SJTD-1 involved in the negative regulation of AlkB2 and deciphered its nature of DNA binding and ligand release. The deletion of alkR enhanced the transcription levels of the alkB2 gene and the utilization efficiency of the medium-to-long-chain n-alkanes by strain SJTD-1. The dimer of AlkR recognizes and binds to a conserved palindromic motif in the promoter of the alkB2 gene, and structural symmetry is vital for DNA binding and transcription repression. The long-chain fatty acyl coenzyme A compounds can release AlkR and stimulate transcription of alkB2, reflecting the effect of alkane catabolic metabolites. Structural insights unveiled that the arginine residues and scaffold residues of AlkR are critical for DNA binding. Further bioinformatics analysis of AlkR revealed the widespread VanR-AlkB couples distributed in Pseudomonadaceae with high conservation in the sequences of functional genes and intergenic regions, highlighting a conserved regulatory pattern for n-alkane utilization across this family. These findings demonstrate the regulatory mechanism and structural basis of GntR/VanR transcription regulators in modulating n-alkane biodegradation and provide valuable insights in improving the bioremediation efficiency of hydrocarbon pollution.

Innovative strategy for the treatment of oily wastewater by in-situ synthesis of nitrogen-doped biochar supported FeS for activation of peroxymonosulfate

Disposing of oily wastewater poses a significant challenge in treating oilfield-produced wastewater treatment. This study developed a FeSNC-9/PMS system for the effective degradation of total petroleum hydrocarbons (TPHs) in oily wastewater, while increasing the value of excess sludge, thus achieving the dual purpose of waste treatment. This work involved the in-situ preparation of a porous nitrogen-doped biochar-supported iron sulphide catalyst material using surplus sludge from SBR. Compared to undoped FeS (NC-9), FeSNC-9 exhibited excellent pore structure and abundant functional groups. Fe-Nx served as an effective connecting site between FeS species and the graphite network of biochar. The FeSNC-9/PMS system significantly degraded 74.21% of TPHs within 300 min. The FeSNC-9/PMS system demonstrated remarkable TPHs degradation efficiency across a wide temperature range and under both weak acidity and near-neutral conditions The dominant reactive oxygen species were identified as SO4•- and •OH, with O2•- and 1O2 also confirmed as active species. Gas chromatography semi-quantitative analysis showed that the long-chain alkanes of C20-C30 in total petroleum hydrocarbons were significantly degraded into short-chain alkanes or completely mineralized. This work provides new insights for the low-cost and high-efficiency treatment of TPHs in oilfield-produced water, and delves into the activation mechanism of PMS and the degradation pathways of TPHs.

Alkane degradation coupled to Fe(III) reduction mediated by Gram-positive bacteria

Petroleum hydrocarbon contamination, such as n-alkanes, poses a significant global threat to ecosystems and human health. Microbial remediation emerges as a promising strategy for addressing this issue through both aerobic and anaerobic processes. Notably, the majority of anaerobic hydrocarbon degraders identified to date are Gram-negative bacteria. In this study, two electroactive Gram-positive strains, Lysinibacillus spp. strains SL-6A and SL-12A, were isolated from oil-contaminated soils in the Shengli Oilfield, China. Our experiments demonstrated that these strains effectively degraded n-hexadecane (n-C16) through extracellular Fe(III) reduction. When ferric citrate was used as the electron acceptor, strains SL-6A and SL-12A degraded 94.2 % and 87.4 % of n-C16, respectively, within 72 hours. This process was further confirmed using Fe(III)-containing minerals. Surface-enhanced Raman spectroscopy, UV-vis spectroscopy, and cyclic voltammetry data collectively indicated that surface-associated c-type cytochromes (c-Cyts) were crucial for extracellular electron transfer (EET), facilitating Fe(III) reduction. In addition, our strains were capable of producing flavin mononucleotide (FMN), a well-known redox-active organic molecule involved in EET processes, particularly in the presence of Fe(III). Whole-genome sequencing confirmed the pathways for n-alkane degradation and the synthesis of c-Cyts and FMN in our strains. This research highlights the potential of electroactive Gram-positive bacteria in hydrocarbon degradation in contaminated soils.

Unlocking the transcriptional profiles of an oily waste-degrading bacterial consortium

This study investigates the transcriptional profile of a novel oil-degrading microbial consortium (MC1) composed of four bacterial isolates from Brazilian oil reservoirs: Acinetobacter baumannii subsp. oleum ficedula, Bacillus velezensis, Enterobacter asburiae, and Klebsiella pneumoniae. Genomic analysis revealed an enrichment of genes associated with xenobiotic degradation, particularly for aminobenzoate, atrazine, and aromatic compounds, compared to reference genomes. The consortium demonstrated superior growth and complete oil degradation relative to individual strains. Transcriptional profiling during growth on oil indicated that key subsystems involved membrane transport, stress response, and dehydrogenase complexes, crucial for hydrocarbon uptake. Notably, genes for degrading aromatics, naphthalene, and chloroalkanes were significantly expressed during the initial oil growth phase. The dominant gene expressed was alkane 1-monooxygenase, particularly in the late growth phase. While A. baumannii exhibited the highest transcriptional activity, B. velezensis showed lower activity despite possessing numerous hydrocarbon degradation genes. The synergistic interactions among strains, confirmed by complementary gene expression patterns, position MC1 as a promising bioremediation agent for hydrocarbon-contaminated environments. However, more than collaboration, competition for nutrient uptake and resistance to stress drive gene expression and adaptation in the presence of oil as the carbon source.

Investigating the Potential of Native Soil Bacteria for Diesel Biodegradation

In countries with a long petroleum extraction and processing history, such as Romania, extensive soil areas are often polluted with petroleum and its derivatives, posing significant environmental and human health risks. This study explores the diesel biodegradation potential of two native bacterial consortia isolated from hydrocarbon-polluted soils, focusing on their phenotypic and molecular characteristics, growth kinetics, alkane hydroxylase activity, hydrolase production, and biosurfactant synthesis capabilities. The bacterial consortia, CoP1 and CoP2, were successfully obtained using the standard successive enrichment culture method from two soil samples collected from a region affected by petroleum pollution. The CoP1 and CoP2 consortia demonstrated efficient diesel-degrading capabilities, achieving 50.81-84.32% degradation when cultured in a minimal medium containing 1-10% (v/v) diesel as the sole carbon and energy source. This biodegradation potential was corroborated by their significant alkane hydroxylase activity and the detection of multiple catabolic genes in their genomes. The CoP1 consortium contains at least four catabolic genes (alkB, alkM, todM, ndoM) as well as rhamnosyltransferase 1 genes (rhlAB), while the CoP2 consortium contains only two catabolic genes (ndoM, C23DO). The RND transporter gene (HAE1) was present in both consortia. Secondary metabolites, such as glycolipid-type biosurfactants, as well as extracellular hydrolases (protease, amylase, cellulase, and lipase), were produced by both consortia. The CoP1 and CoP2 consortia demonstrate exceptional efficiency in diesel degradation and biosurfactant production, making them well suited for the bioremediation of soils contaminated with petroleum and its derivatives.

A modified iChip for in situ cultivation of bacteria in arid environments

Antimicrobial resistance is an ever-increasing problem for human health, and with only a few novel antimicrobials discovered in recent decades, an extraordinary effort is needed to circumvent this crisis. A promising source of new microbial-derived antimicrobial compounds resides in the large fraction of microbes that are not readily cultured by standard cultivation. It has previously been shown that nests of the social spider Stegodyphus dumicola contain a diverse bacterial community, where only a small fraction of the microbes could be recovered by standard cultivation. To improve the recovery of the bacterial diversity cultured from nests, we modified the previously described isolation chip (iChip) to fit the natural arid environment of S. dumicola nests. Here we provide a comprehensive analysis of the modified iChip's performance. We found that the modified iChip improved the overall culturability, performed equally or better at recovering the bacterial diversity from individual nests, and improved the recovery of rare isolates compared to standard cultivation. Furthermore, we show that the modified iChip can be used in the field. In addition, we observed that the nests contain volatile organic compounds (VOCs) that could serve as substrate for the selective enrichment of rare and iChip-specific isolates. Our modified iChip can be applied for in situ cultivation in a broad range of arid habitats that can be exploited for future drug discovery.IMPORTANCEThe demand for novel antimicrobial compounds is an ever-increasing problem due to the rapid spread of antibiotic-resistant microbes. Therefore, exploring new habitats for microbial-derived antimicrobial compounds is crucial. The nest microbiome of Stegodyphus dumicola remains largely unexplored and could potentially serve as a new source of antimicrobial compounds. To access the nest's microbial diversity, we designed a modified iChip for in situ cultivation inside spider nests and tested its applications in both field and laboratory settings. Our study shows that the iChip's ability to recover in situ abundant genera was comparable or superior to standard cultivation, while the recovery of rare (low-abundant genera) was higher. We argue that these low-abundant and iChip-specific isolates are enriched from naturally occurring nest volatile organic compounds (VOCs) during iChip incubation.

Migration of stable release high concentration toluene vapor and microbial activity varies in silty sand soil

Vapor intrusion (VI) happens when volatile organic compounds (VOCs) migrate from subsurface sources into buildings, harming indoor air quality and occupants' health. To investigate the migration and biodegradation of volatile organic compounds (VOCs) originating from subsurface sources, a soil column experiment was performed. In this experiment, high-concentration vapor from the liquid phase of toluene was steadily released into silty sand soil, aiming to simulate the conceptual model of a specific site. The experimental findings revealed that, within the silty sand soil, it took 36 h for toluene vapors to diffuse through a 120-cm-long soil column. During this process, the volume fractions of O₂ and CO₂ within the soil column varied. The level of microbial activity in the soil column first rose and then declined, as did the abundance of the dominant degrading toluene bacteria group. The experiment demonstrated that covering a certain thickness of silty sand soil could effectively retard the migration of toluene vapor. In addition, biodegradation occurred during the migration of the toluene vapor. However, long-term exposure to high-concentration toluene vapors inhibited both the activity and growth of microorganisms within the soil column.

Research progress of micro-nano bubbles in environmental remediation: Mechanisms, preparation methods, and applications

Micro-nano bubble technology, with its unique physicochemical properties, has demonstrated remarkable application potential in the field of environmental remediation. Compared to traditional macro-bubbles, micro-nano bubbles exhibit exceptional stability in solutions due to their minute size, superior mass transfer efficiency, and pronounced interfacial potential characteristics, effectively resisting coalescence and rupture, thereby prolonging their persistence in environmental media. Currently, the pressurized dissolution of micro-nano bubbles stands as an outstanding approach in environmental governance. This process not only fosters the generation of free radicals and the release of energy but also significantly enhances gas transfer efficiency, effectively disrupting the oxidative structures of pollutants and facilitating the transport and transformation of pollutant residues as a carrier. Micro-nano bubbles play pivotal roles across multiple domains of environmental remediation. In the realm of oil contamination, whether it be soil or oily sludge remediation, micro-nano bubbles demonstrate formidable degradation capabilities. In terms of water pollution treatment, ranging from surface water, groundwater, to industrial wastewater, micro-nano bubble technology proves effective, markedly enhancing water purification efficiency. In the field of agricultural remediation, micro-nano bubbles can save water, increase production, clean and decontaminate. In addition, it also plays an important role in the fields of material modification and membrane fouling remediation. Finally, the economic benefits of micro-nano bubbles and the existing research gaps are further analyzed, and its development direction is speculated: pollution control lacks long-term tracking, and there is a lack of attention to the possible secondary pollution caused by catalysts. The behavior and mechanism of micro-nano bubbles under different environmental conditions are further explored. Optimize its preparation and application methods, pay attention to the energy consumption and economic possibilities of the process, and promote its application in actual environmental remediation.

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.

Regulation mechanism of the long-chain n-alkane monooxygenase gene almA in Acinetobacter venetianus RAG-1

As toxic pollutants, n-alkanes are pervasively distributed in most environmental matrices. Although the alkane monooxygenase AlmA plays a critical role in the metabolic pathway of solid long-chain n-alkanes (≥C20) that are extremely difficult to degrade, the mechanism regulating this process remains unclear. Here, we characterized the function of AlmA in Acinetobacter venetianus RAG-1, which was mainly involved in the degradation of long-chain n-alkanes (C26-C38), among which, n-C32 induced the almA promoter activity most. APR1 (AlmA Positive Regulator) that it is an AraC/XylS-type transcription regulator, a potential transcriptional regulator of almA, was screened by DNA-pull down, which was determined by conserved domain analysis. The deletion of apR1 severely reduced the capacity of strain RAG-1 to utilize long-chain n-alkanes (C22-C38), indicating the involvement of APR1 in n-alkanes degradation. The results of the APR1-dependent reporter system, electrophoretic mobility shift assay, and microscale thermophoresis further proved that APR1 was able to directly bind to the almA promoter region, thus activating the almA transcription. Furthermore, APR1 could inhibit self-expression through autoregulation in the absence of long-chain n-alkanes. n-C32 acted as a ligand of APR1, and the amino acid residues Val10, Gln50, Ala99, and Ile106 at the N-terminus of APR1 were necessary for binding n-C32. In addition, the key amino acid residues of APR1 within the C-terminal helix-turn-helix motif that bound to the downstream promoter region were confirmed by multiple sequence alignment and site-directed mutagenesis. The homologs of AlmA and APR1 shared a similar evolutionary course in the Proteobacteria; thus, this mode of regulation might be relatively conserved.

IMPORTANCE

The extreme hydrophobicity of long-chain n-alkanes ({greater than or equal to}C20) presents a significant challenge to their degradation in natural environments. It is, therefore, imperative to elucidate the regulatory mechanisms of the metabolic pathways of long-chain n-alkanes, which will be of great significance for the future application of hydrocarbon-degrading bacteria to treat oil spills. However, the majority of current studies have focused on the regulatory mechanisms of short- and medium-chain n-alkanes, with long-chain n-alkanes receiving comparatively little attention. In this study, we identified APR1, a transcriptional regulator of the alkane monooxygenase AlmA in Acinetobacter venetianus RAG-1, and characterized its function and regulatory mechanism. In the presence of ligand n-C32, APR1 could directly activate the transcription of almA, which was involved in the n-C32 metabolism. The amino acid residue unique to the C-terminal DNA-binding domain of AraC/XylS type n-alkanes transcription regulators was also identified. These findings further improved our understanding of the long-chain n-alkanes degradation mechanism, which is important for the management of petroleum pollution.

Bioremediation Potential of Indigenous Bacterial Isolates for Treating Petroleum Hydrocarbons-Induced Environmental Pollution

This study isolates oil-degrading bacteria from contaminated soil in automobile workshops, aiming to address environmental pollution from petroleum spills. Nineteen bacterial isolates were screened, with three isolates S4 (Lysinibacillus macroides), M8 (Serratia marcescens), and M9 (S. marcescens), showing significant oil degradation potency. In shake flask assays, S4 degraded 57.8%, M8 60.2%, and M9 58.1% of oil at a 5% concentration. Molecular identification through 16S rRNA gene sequencing confirmed these strains. Plate assays also supported the degradation potential, with growth zones of 38.4 ± 1.3 mm (S4), 39.7 ± 1.9 mm (M8), and 41.2 ± 1.7 mm (M9). Gas chromatography-mass spectrometry analysis of treated oil indicated the presence of hydrocarbons, phenolic compounds, and esters, suggesting microbial interactions, potentially involving the breakdown or transformation of complex hydrocarbons into simpler compounds by bacterial enzymes. These results highlight the potential of these bacterial strains, particularly S4, for the bioremediation of petroleum-contaminated sites.

Innovative microbial activators for enhanced bioremediation of oil-contaminated soils: mechanistic insights

This paper developed an efficient microbial activator formula and conducted an in-depth study on its efficacy and mechanism in promoting the degradation of petroleum hydrocarbons in oil-contaminated soil. A 60-day microbial remediation experiment conducted on oily soil revealed that the microbial activators significantly boosted the activities of dehydrogenase and catalase, subsequently speeding up the degradation of petroleum hydrocarbons in the soil. The overall degradation rate reached as high as 71.23%, with the most significant degradation effect observed in asphaltenes, achieving a degradation rate of 93.98%. This was followed by aromatic hydrocarbons (90.45%), saturated hydrocarbons (84.39%), and asphaltenes (65%). Compared to traditional microbial stimulation methods, this activator demonstrated significant superiority. Microbial diversity analysis reveals that microbial activators can effectively activate microbial activity in soil targeting refractory petroleum hydrocarbon components. By comparing the changes in microbial community structure before and after the addition of microbial activators, we found that the activators promoted an increase in the abundance of microorganisms belonging to the Bacillota, Pseudomonadota, and Bacteroidetes, which have petroleum hydrocarbon degradation functions, and facilitated the evolution of microbial community structure towards a direction more conducive to petroleum hydrocarbon degradation. KEGG metabolic pathway analysis revealed that the degradation pathways for alkanes, aromatic hydrocarbons, and PAHs are primarily present in these bacterial phylum. This research not only clarifies the degradation mechanism but also supports future bioremediation efforts.

Microaerobic biodegradation of aromatic hydrocarbon mixtures: strategies for efficient nitrate and oxygen dosage

The biodegradation of organic aromatic compounds in subsurface environments is often hindered by limited dissolved oxygen. While oxygen supplementation can enhance in situ biodegradation, it poses financial and technical challenges. This study explores introducing low-oxygen concentrations in anaerobic environments for efficient contaminant removal, particularly in scenarios where coexisting pollutants are present. An innovative strategy of alternating nitrate-reducing and microaerobic conditions to stimulate biodegradation is proposed, utilizing nitrate initially to degrade easily-degradable compounds, and potentially reducing the need for additional oxygen. Batch experiments were conducted to assess the biodegradation of a BTEX, indene, indane, and naphthalene mixture using groundwater and sediments from an anaerobic contaminated aquifer. Two set-ups were incubated for 98 days to assess the redox transitions between microaerobic (oxygen concentrations < 0.5 mg O2 L-1) and nitrate-reducing conditions, aiming to minimize external electron acceptor usage while maximizing degradation. Comparative experiments under fully aerobic and fully anaerobic (nitrate-reducing) conditions were conducted, revealing that under microaerobic conditions, all compounds were completely degraded, achieving removal efficiencies comparable to fully aerobic conditions. A pre-treatment phase involving nitrate-reducing conditions followed by microaerobic conditions showed more effective utilization of oxygen specifically for contaminant degradation compared to fully aerobic conditions. Contrarily, under fully anaerobic conditions, without oxygen addition, partial degradation of ethylbenzene was observed after 400 days, while other compounds remained. The outcomes of this study can provide valuable insights for refining strategies involving oxygen and nitrate dosages, thereby enhancing the efficacy of in situ bioremediation approaches targeting complex hydrocarbon mixtures within anaerobic subsurface environments. KEY POINTS: • BTEX, indene, indane, and naphthalene mix biodegraded under microaerobic conditions • Subsurface microorganisms swiftly adapt from nitrate to microaerobic conditions • More oxygen directed to hydrocarbon biodegradation via a pre-anaerobic treatment.

High-efficiency biodegradation of crude oil and p-hydroxybenzoic acid by Acinetobacter haemolyticus JS-1: Integrated characterization and genomic analysis

Crude oil contamination is a major threat to both the environment and human health. Acinetobacter haemolyticus strain JS-1 was isolated from oil-contaminated soil in Jiangsu Oilfield, China, which exhibits exceptional biodegradation capabilities for crude oil and p-hydroxybenzoic acid (PHBA). This strain can degrade 70-80 % of crude oil at concentrations of 10-20 g/L within 15 days at 30 °C. Strain JS-1 does not produce surfactants but absorbs crude oil through cell surface hydrophobicity. RT-qPCR analysis has identified five types of alkane hydroxylase genes in strain JS-1, including two AlkB-types, one AlmA-type, one LadA-type, and a cytochrome P450 monooxygenase. These genes are likely contributed to its high degradation efficiency. Notably, the CYP153 enzyme is crucial for metabolizing hexadecane and octadecane. We further investigated the PHBA degradation pathway, revealing both the protocatechuate ortho-cleavage pathway and a potential ubiquinone biosynthesis pathway. The remarkable efficiency of strain JS-1 in crude oil biodegradation positions it as a promising candidate for mitigating crude oil pollution. Moreover, its effective PHBA degradation provides new opportunities for the application of microorganism in agricultural management.

Lipid Biomarkers in Urban Soils of the Alluvial Area near Sava River, Belgrade, Serbia

This study focused on the investigation of soil samples from the alluvial zone of the Sava River, located near the heating plant in New Belgrade, Serbia. Using gas chromatography with flame ionization detection (GC-FID), a broad range of alkanes, including linear n-alkanes (C10 to C33) and isoprenoids, was analyzed in all samples. The obtained datasets were effectively made simpler by applying multivariate statistical analysis. Various geochemical indices (CPI, ACL, AI, TAR, etc.) and ratios (S/L, Paq, Pwax, etc.) were calculated and used to distinguish between biogenic and anthropogenic contributions. This approach added a higher level of precision to the source identification of hydrocarbons and provided a detailed geochemical characterization of the investigated soil. The results showed that the topsoil had a high content of TPH (average value, 90.65 mg kg-1), potentially related to an accidental oil spill that occurred repeatedly over extended periods. The uncommon n-alkane profiles reported for the investigated soil samples are probably the result of inputs related to anthropogenic sources, emphasizing that petroleum was the main source of the short-chain n-alkanes. The methodology developed in this study was proven to be efficient for the assessment of the environmental quality of the soil in an urban part of New Belgrade, but it can also be a useful tool for soil monitoring and for a pollution assessment in other (sub)urban areas.

Dual-purpose elemental sulfur for capturing and accelerating biodegradation of petroleum hydrocarbons in anaerobic environment

Hydrophobic organic pollutants in aqueous environments are challenging to biodegrade due to limited contact between microorganisms, the pollutants and the electron acceptor, particularly under anaerobic or anoxic conditions. Here, we propose a novel strategy that uses inexpensive, dual-function elemental sulfur (S0) to enhance biodegradation. Using petroleum hydrocarbons as the target pollutants, we demonstrated that hydrophobic and nonpolar S° can concentrate hydrocarbons while simultaneously serving as an electron acceptor to enrich hydrocarbon-degrading bacteria. The permeable reactive barrier filled with S0 effectively removed petroleum hydrocarbons. In addition to rapid adsorption, we discovered, for the first time, that petroleum hydrocarbons underwent efficient biodegradation through the reduction of S0. Specifically, n-alkanes were degraded by 80 % to 90 % and polycyclic aromatic hydrocarbons by 40 % to 95 %. These degradation rates were 17 % to 30 % and 26 % to 43 % higher, respectively, compared to those observed without S0. Consecutive subcultures combined with untargeted metabolomics analysis revealed that bacteria capable of dissimilatory sulfur reduction enhanced the fermentation process. These bacteria provided electrons to the metabolic network, which facilitated the mineralization of petroleum hydrocarbons. Our findings highlight the significant potential of S° for removing hydrophobic organic pollutants in oxygen-free environments, demonstrate the feasibility of integrating adsorption, biodegradation, and electron supply to enhance pollutant removal.

Degradation behaviors of asphalt by microorganisms in asphalt pavement structure

Pseudomonas and Bacillus are dominant microorganisms to widely distributes in asphalt pavement structure. Microbial degradation leads to asphalt aging, and causes its performance deterioration, reducing the durability of asphalt pavement. To better understand the degradation behaviors of dominant microorganisms on asphalt, and reveals their microbial aging mechanisms on asphalt, the effects of microbial degradation on micromorphology, chemical functional group, component and microstructure of asphalt were discussed. Results indicate that main damages of microbial degradation start from asphalt surface and then permeates into its interior. Microorganisms degrade light components of asphalt as nutrients and decompose them into CO2 and H2O through oxidation reactions, but exhibit limited degradation ability to macromolecular components. Microbial degradation causes the content changes of asphalt components, altering the colloidal structure of asphalt. Microorganisms destroy the continuity of asphalt surface and increase surface roughness of asphalt. This study provides a new insight into microbial aging mechanism of asphalt.

Degradation of aliphatic and aromatic hydrocarbon mixture by a Rhodococcus sp

Rhodococcus sp. strain p52, an aerobic dioxin degrader, was capable of utilizing petroleum hydrocarbons as the sole sources of carbon and energy for growth. In the present study, the degradation of the mixture of aliphatic hydrocarbons (hexadecane and tetradecane) and aromatic hydrocarbons (phenanthrene and anthracene) by strain p52 was examined. The results showed that the degradation of phenanthrene was enhanced in the presence of hexadecane or tetradecane due to increased bioavailability and improved cell surface hydrophobicity, which facilitated better substrate uptake. Conversely, the degradation of hexadecane and tetradecane decreased in the presence of aromatic hydrocarbons, likely due to the cometabolic effect, metabolic regulation, substrate competition, and the shift in enzyme activity. Moreover, the removal of 4.4 g L-1 diesel fuel, a complex mixture of aliphatic hydrocarbons and aromatic hydrocarbons, was investigated and 63.7% of oil contents were depleted within 96 h. Therefore, strain p52 showed the potential to remove petroleum pollutants.

Simultaneous bioremediation of diesel-contaminated soil and water ecosystems using mixed culture of Acinetobacter baumannii IITG19 and Providencia vermicola IITG20

Diesel degradation and bacterial growth were investigated in soil, marine water, and freshwater ecosystems using Acinetobacter baumannii IITG19, Providencia vermicola IITG20, and their mixed culture. Both bacteria were found to be effective in all three ecosystems, with the best degradation occurring in freshwater. Acinetobacter baumannii IITG19 showed higher degradation (59%, 62%, and 76%) than Providencia vermicola IITG20 (31%, 57%, and 67%) in soil, marine water, and freshwater, respectively. Alkanes showed higher degradation than naphthenes and aromatics for both strains. The mixed culture showed higher diesel degradation efficiency than individual strains in all ecosystems. The overall degradation was similar in soil and marine water (66%), while freshwater showed the highest degradation of 81%. In the presence of the mixed culture, the degradation of alkanes was more than 90%. Bacterial growth was highest in freshwater and lowest in soil for both bacteria and the mixed culture. Metabolite analysis confirmed alcoholic degradation for alkanes and cyclo-alcoholic degradation for naphthenes. The degradation rate for mixed culture was higher than that of both the individual strains. The mixed culture had highest degradation rate constant in freshwater at 0.11 day-1 followed by that in marine ecosystem at 0.078 day-1. The rate constant was lowest for soil ecosystem at 0.066 day-1. Thus the mixed culture showed effectiveness in all three ecosystems, with its highest effectiveness observed in the freshwater ecosystem.

Application of xylene-degrading bacteria in the treatment of soil contaminated with petroleum hydrocarbons - A comprehensive laboratory to pilot-scale analysis

Petroleum hydrocarbons, including both aliphatic (gasoline, mineral oil) and aromatic compounds (BTEX), are known for their harmful effects on ecosystems and human health. Despite many studies, large-scale treatment of contaminated soils continues to be challenging, especially at lower temperatures. The use of metabolically-versatile, psychrotolerant, cold-active microorganisms, seems a promising, cost-effective and eco-friendly solution to boost remediation rates. In this study, a suitable microbial consortium was prepared and tested both in lab- and pilot-scale. To achieve the best bioremediation results, bacterial strains were isolated from BTEX-contaminated soil and then tested for the desired traits over a wide range of conditions. Of 5 preselected strains, 3 Pseudomonas strains capable of denitrification and aerobic/anaerobic degradation of hydrocarbons (up to 41.53±7.39 %), further characterized by a broad temperature (4-37 °C), pH (3-4 to 11) and salinity (0-8 %) tolerance, as well as resistance to freezing, were selected. Physiological studies were supported by genetic analyses, which indicated the presence of both alkB and xylM genes, and excluded similarity of the strains to the known opportunistic pathogens. To further confirm the applicability of the consortium, lab-scale analyses were followed by comprehensive pilot-scale tests on ~5 m3 biopile/biocell, at different conditions. The results revealed increased efficacy of the consortium in bioremediation, when compared to biostimulated indigenous strains, for volatile hydrocarbons (93 % vs 88 %) and mineral oil (23 % vs 15 %), as well as 175 % and 136 % acceleration of remediation for the respective compounds in terms of time needed to complete the process. Moreover, the high survivability and metabolic activity of the consortium at different temperatures indicate the possibility of its year-round use for bioremediation of soil contaminated with petroleum hydrocarbons. The study proves the potential of specialized bacteria in the removal of pollutants, and emphasizes the role of bio-based strategies in addressing complex environmental challenges and remediation of contaminated sites.

Resistant Rhodococcus for Biodegradation of Diesel Fuel at High Concentration and Low Temperature

The resistance of 16 Rhodococcus strains to diesel fuel was studied. The minimal inhibitory concentrations of diesel fuel against Rhodococcus were 4.0-64.0 vol. % and 0.5-16.0 vol. % after 7 days of incubation in Luria-Bertani broth and a mineral "Rhodococcus-surfactant" medium, respectively. The three most resistant strains (R. ruber IEGM 231, IEGM 442 and Rhodococcus sp. IEGM 1276) capable of overcoming the toxicity of diesel fuel at a high (8.0 vol. %) concentration and at a low (4 °C) temperature were selected. Respiration activities, growth kinetics, and changes in the diesel fuel composition during the biodegradation process were elucidated using gas chromatography with mass spectrometry, respirometry, and Bradford analysis. Growth conditions were optimised for the improved biodegradation of diesel fuel by Rhodococcus cells using multifactor analysis. They included the simultaneous addition of 1.3 g·L-1 of granular sugar and 0.25 g·L-1 of yeast extract. The twofold stimulation of the biodegradation of individual hydrocarbons in diesel fuel (n-pentadecane, n-hexadecane and n-heptadecane) was demonstrated when glycolipid Rhodococcus-biosurfactants were added at a concentration of 1.4 g·L-1. A total removal of 71-91% of diesel fuel was achieved in this work.

New insight in the biotreatment of produced water: Pre-oxidation paves a rapid pathway for substrate selection in microbial community

The deep treatment of produced water (PW) had emerged as a formidable challenge due to the coexistence of hydrocarbons, surfactants, ammonium nitrogen, and other refractory organics. On the basis of the pre-oxidation coupled heterotrophic ammonia assimilation (PHAA) system constructed in previous research, this work refined the catalyst selection and reduced the hydraulic retention time. The stable running PHAA system removed 96.2 % of total organic carbon (TOC). The study simulated the effects of organic loading fluctuations on the system and dissected the mechanism of pre-oxidation process and its contribution to microbial community. Pre-oxidation significantly improved the ability of microbial community to handle loading shocks and improved organic degradation efficiency in PW during long-term reactor operation. The PHAA process effectively removed medium to long chain alkanes above C24 in PW and proposed potential degradation pathways and direction. The determination of hydrocarbon enzymes activity showed that pre-oxidation changed the substrate selection, making more aldehydes available as auxiliary carbon sources for microorganisms. Pre-oxidation also enriched and preserved microbial diversity, facilitating the accumulation of functional microorganisms in the PHAA process.

Fungi from Antarctic marine sediment: characterization and assessment for textile dye decolorization and detoxification

Cold-adapted microorganisms can produce enzymes with activity at low and mild temperatures, which can be applied to environmental biotechnology. This study aimed to characterize 20 Antarctic fungi to identify their genus (ITS rDNA marker) and growth temperatures and evaluate their ability to decolorize and detoxify the textile dye indigo carmine (IC). An individual screening was performed to assess the decolorization and detoxification of IC by the isolates, as well as in consortia with other fungi. The isolates were affiliated with seven ascomycete genera: Aspergillus (n = 4), Cosmospora (n = 2), Leuconeurospora (n = 2), Penicillium (n = 3), Pseudogymnoascus (n = 6), Thelebolus (n = 2), and Trichoderma (n = 1). The two isolates from the genus Leuconeurospora were characterized as psychrophilic, while the others were psychrotolerant. The Penicillium isolates were able to decolorize between 60 and 82% of IC. The isolates identified as Pseudogymnoascus showed the best detoxification capacity, with results varying from 49 to 74%. The consortium using only Antarctic ascomycetes (C1) showed 45% of decolorization, while the consortia with the addition of basidiomycetes (C1 + Peniophora and C1 + Pholiota) showed 40% and 50%, respectively. The consortia C1 with the addition of the basidiomycetes presented a lower toxicity after the treatments. In addition, a higher fungal biomass was produced in the presence of dye when compared with the experiment without the dye, which can be indicative of dye metabolization. The results highlight the potential of marine-derived Antarctic fungi in the process of textile dye degradation. The findings encourage further studies to elucidate the degradation and detoxification pathways of the dye IC by these fungal isolates.

Fungal community dynamics in a hyper-arid ecosystem after 7 and 47 years of petroleum contamination

This study investigates the impact of crude oil contamination on the fungal community dynamics in the Evrona Nature Reserve, situated in Israel's hyper-arid Arava Valley. The reserve experienced petroleum-hydrocarbon-spill pollution at two neighboring sites in 1975 and 2014. The initial contamination was left untreated, providing a unique opportunity to compare its effects to those of the second contamination event. In 2022, soil samples were collected from both contaminated areas and nearby clean (control) sites, 47 and 7 years after the spills. The taxonomic diversity of fungal community and functional guilds, as well as various properties of the soil, were analyzed. We focused on three functional groups within fungal communities: saprotrophs, symbiotrophs, and pathotrophs. The results revealed a significant decrease in number of fungal species in the contaminated samples over time. Consequently, prolonged effect of crude oil-contaminated soils can facilitate the development of a distinct fungal community, which has adapted to the conditions of oil contamination. This study aims to elucidate the dynamics of fungal communities in oil-contaminated soils, contributing to a better understanding of their behavior and adaptation in such environments.

Metagenomic and isotopic insights into carbon fixation by autotrophic microorganisms in a petroleum hydrocarbon impacted red clay aquifer

Autotrophic microorganisms, the pivotal carbon fixers, exhibit a broad distribution across diverse environments, playing critical roles in the process of carbon sequestration. However, insights into their distribution characteristics in aquifers, particularly in those petroleum-hydrocarbon-contaminated (PHC) aquifers that were known for rich in heterotrophs, have been limited. In the study, groundwater samples were collected from red clay aquifers in the storage tank leakage area of a PHC site, a prevalent aquifer type in southern China and other regions. Metagenomics combined with hydrochemical and inorganic carbon isotope analyses were employed to elucidate the presence of microbial carbon fixation and its driving forces. Results showed that there were hundreds of autotrophic microorganisms participating in distinct carbon fixation processes in the red clay PHC aquifers. Reductive tricarboxylic acid (rTCA) and dicarboxylate/4-hydroxybutyrate (DC/4HB), as well as 3-hydroxypropionate (3HP or/and 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB)) were the predominant carbon fixation pathways. The abundances of carbon fixation genes and autotrophic microorganisms were significantly and positively correlated with hydrocarbon concentrations and δ13C of dissolved inorganic carbon (δ13C-DIC) values. This finding indicated that the petroleum hydrocarbon significantly promoted the proliferation of carbon fixation microorganisms, leading to a substantial uptake of inorganic carbon. Therefore, we deduce that this process holds considerable potential for carbon sequestration in PHC-contaminated aquifers.

Bioremediation by Brevibacterium sediminis: a prospective pyrene degrading agent to eliminate environmental polycyclic aromatic hydrocarbons

Environmental abuses and subsequent array of health hazards by petroleum products have emerged as a global concern that warrants proper remediation. Pyrene (PYR), a polycyclic aromatic hydrocarbon, is a xenobiotic by-product during crude petroleum processing. Biodegradation potential of two bacterial isolates (MK4 and MK9) of Brevibacterium sediminis from oil contaminated sites was explored. MK4 and MK9 could degrade PYR up to 23 and 59% (1000 mg.L- 1), respectively. A first-order formalism with the rate constant for MK4 and MK9 were found to be 0.022 ± 0.001 and 0.081 ± 0.005 day- 1, respectively with the corresponding half life period of 31.4 ± 1.4 and 8.6 ± 0.60 days respectively. Both the isolates produce biosurfactants as established by drop collapse assay, oil spreading and emulsification activity studies. Decrease in pH, change in absorbance (bacterial growth), and catechol formation support adaptation capability of the isolates to degrade PYR by using it as a source of carbon. PYR ring cleavage was induced by the ring hydroxylating dioxogenase enzyme present in the strains, as identified by PCR assay. In silico analyses of the PYR degrading enzyme revealed its higher binding affinity (-7.6 kcal.mol- 1) and stability (Eigen value:1.655763 × 10- 04) to PYR, as further supported by other thoeroretical studies. MK9 strain was more efficient than the MK4 strain in PYR degradation. Studies gain its prominence as it reports for the first time on the aptitude of B. sediminis as novel PYR-degrading agent that can efficiently be used in the bioremediation of petroleum product pollution with a greener approach.

Slow-release microencapsulates containing nanoliposomes for bioremediation of soil hydrocarbons contaminated

Encapsulation and nutrient addition in bacterial formulations have disadvantages concerning cell viability during release, storage, and under field conditions. Then, the objective of this work was to encapsulate a bacterial consortium with hydrocarbon-degrading capacities in different matrices composed of cross-linked alginate/ polyvinyl alcohol /halloysite beads (M1, M2, and M3) containing nanoliposomes loaded with or without nutrients and evaluate their viability and release in a liquid medium, and soil (microcosmos). Also, evaluate their capacity to remove total petroleum hydrocarbons (TPH) for 165 days and matrices characterization. The encapsulate consortium showed a quick adaptation to contaminated soil and a percentage of removal (PR) of TPH up to 30% after seven days. All the matrices displayed a PR of up to 90% after 165 days. The matrix M2 displayed significant resistance to degradation and higher cell viability with a PR of 94%. This result supports the encapsulation of bacteria in a sustainable matrix supplemented with nutrients as a well-looked strategy for improving viability and survival and, therefore, enhancing their effectiveness in the remediation of hydrocarbon-contaminated soils.

A potential bioaerosol source from kitchen chimneys in restaurants

Bioaerosols are ubiquitous and have a substantial impact on the atmosphere and human health. Despite the identification of numerous bioaerosol emission sources, the contribution of anthropogenic sources remains inadequately understood. In kitchens, oil stains accumulated at the vent may discharge microorganisms into the environment with airflow, potentially discharging bioaerosol pollution. This putative anthropogenic source of bioaerosols has been long ignored. To investigated whether kitchen chimneys can be a potential source for bioaerosols, air samples, oil stains from in/out chimneys, and surface sand samples were collected near several commercial restaurants. PCoA showed that sampling sites significantly impacted microbiomes, whereas SourceTracker analysis led to the finding that waste grease significantly contributed to bioaerosol composition. Both findings agree with the kitchen chimney as a source of microbes in bioaerosols in the surrounding environment. Furthermore, despite the low biodiversity, a high proportion of stress-tolerant and potential pathogenic bacteria and fungi were found in residual culinary grease, which may escape into the air causing potential risks to human beings. These results led to the proposal that airborne microbiota can originate from cooking waste grease. Immediate actions should be taken into account to enhance disinfection and sterilization aimed at fume vents.

Resting for viability: Gordonia polyisoprenivorans ZM27, a robust generalist for petroleum bioremediation under hypersaline stress

The intrinsic issue associated with the application of microbes for practical pollution remediation involves maintaining the expected activity of engaged strains or consortiums as effectively as that noted under laboratory conditions. Faced with various stress factors, degraders with dormancy ability are more likely to survive and exhibit degradation activity. In this study, a hydrocarbonoclastic and halotolerant strain, Gordonia polyisoprenivorans ZM27, was isolated via stimulation with resuscitation-promoting factor (Rpf). Long-term exposure to dual stresses of 10% NaCl and starvation induced ZM27 to enter a viable but nonculturable (VBNC)-like state, and ZM27 cells could be resuscitated upon Rpf stimulation. Notable changes in both morphological and physiological characteristics between VBNC-like ZM27 cells and resuscitated cells confirmed the response to Rpf and their robust resistance against harsh environments. Whole-genome sequencing and analysis indicated ZM27 could be a generalist degrader with dormancy ability. Subsequently, VBNC-like ZM27 was applied in a soil microcosm experiment to investigate the practical application potential under harsh conditions. VBNC-like ZM27 combined with Rpf stimulation exhibited the most effective biodegradation performance, and the initial n-hexadecane content (1000 mg kg-1) decreased by 63.29% after 14-day incubation. Based on 16S rRNA amplicon sequencing and analysis, Gordonia exhibited a positive response to Rpf stimulation. The relative abundance of genus Gordonia was negatively correlated with that of Alcanivorax, a genus of obligate hydrocarbon degrader with the greatest abundance during soil incubation. Based on the degradation profile and community analysis, generalist Gordonia may be more efficient in hydrocarbon degradation than specialist Alcanivorax under harsh conditions. The characteristics of ZM27, including its sustainable culturability under long-term stress, response to Rpf and robust performance in soil microcosms, are valuable for the remediation of petroleum pollution under stressful conditions. Our work validated the importance of dormancy and highlighted the underestimated role of low-activity degraders in petroleum remediation.

Non-target analysis of organic pollutants in oil-production wastewater treatment stations and surrounding soils: Their profiles, electro-transformation, and environmental risks

Although pollution during crude oil production has been paid attention, there is lack of studies on organic pollutants generated/emitted from oil-production wastewater (OPW) treatment processes, especially advanced oxidation process. Based on GC-Q-Orbitrap-HRMS, the present study performed non-target analysis of volatile/semi-volatile organic compounds in physical and electro-oxidation units of OPW treatment stations located in Shengli Oilfield of China. Overall, 64-227 organic compounds were respectively identified in different units, and electro-oxidation was found elevating (by 2.7-66 times) specie numbers (25-71) of CHO, CHNO and halogenated compounds as well as inducing generation of 38 alkanes and 6 alkyl-PAHs in wastewater, indicating the important roles of reactive oxygen and halogen species in pollutant transformation. In soils (n = 22) closed to OPW treatment stations, 580 compounds were identified with hydrocarbons (45%), esters (24.3%), and others (30.7%, including aldehydes, ketones, phenols, amines, nitriles and heteroatomic compounds), while esters had largest concentration contribution (up to 53.0%) to total compounds. The calculated hazard quotients (HQ) showed 55 compounds in OPW effluents and 314 compounds in soils having medium-high risks, considerable portions of which (23.6% for effluent and 12.7% for soil) were generated from electro-oxidation process, especially including esters and halogenated hydrocarbons, highlighting the contribution of OPW electro-oxidation treatment to ecological risk in oil-production areas.

Depletion of hydrocarbons and concomitant shift in bacterial community structure of a diesel-spiked tropical agricultural soil

Bacterial community of a diesel-spiked agricultural soil was monitored over a 42-day period using the metagenomic approach in order to gain insight into key phylotypes impacted by diesel contamination and be able to predict end point of bioattenuation. Soil physico-chemical parameters showed significant differences (P < 0.05) between the Polluted Soil (PS) and the Unpolluted control (US)across time points. After 21 days, the diesel content decreased by 27.39%, and at the end of 42 days, by 57.11%. Aromatics such as benzene, anthanthrene, propylbenzene, phenanthrenequinone, anthraquinone, and phenanthridine were degraded to non-detected levels within 42 days, while some medium range alkanes and polyaromatics such as acenaphthylene, naphthalene, and anthracene showed significant levels of degradation. After 21 days (LASTD21), there was a massive enrichment of the phylum Proteobacteria (72.94%), a slight decrease in the abundance of phylum Actinobacteriota (12.74%), and > 500% decrease in the abundance of the phylum Acidobacteriodota (5.26%). Day 42 (LASTD42) saw establishment of the dominance of the Proteobacteria (34.95%), Actinobacteriota, (21.71%), and Firmicutes (32.14%), and decimation of phyla such as Gemmatimonadota, Planctomycetota, and Verrucromicrobiota which play important roles in the cycling of elements and soil health. Principal component analysis showed that in PS moisture contents, phosphorus, nitrogen, organic carbon, had greater impacts on the community structure in LASTD21, while acidity, potassium, sodium, calcium and magnesium impacted the control sample. Recovery time of the soil based on the residual hydrocarbons at Day 42 was estimated to be 229.112 d. Thus, additional biostimulation may be required to achieve cleanup within one growing season.

Co-pollution risk of petroleum hydrocarbons and heavy metals in typically polluted estuarine wetlands: Insights from the Xiaoqing River

Excessive accumulation of total petroleum hydrocarbons (TPH) and heavy metals (HMs) in sediments poses a significant threat to the estuarine ecosystem. In this study, the spatial and temporal distribution, ecological risks, sources, and their impacts on the microbial communities of TPH and nine HMs in the estuarine sediments of the Xiaoqing River were determined. Results showed that the spatial distribution of TPH and HMs were similar but opposite in temporal. Ni, Cr, Pb, and Co concentrations were similar to the reference values (RVs). However, the other five HMs (Cu, Zn, Cd, As, and Hg) and TPH concentrations were 2.00-763.44 times higher than RVs; hence, this deserves attention, particularly for Hg. Owing to the water content of the sediments, Hg was mainly concentrated on the surface during the wet season and on the bottom during the dry season. Moreover, because of weak hydrodynamics and upstream pollutant sinks, TPH-HMs in the river were higher than those in the estuary. TPH and HM concentrations were negatively correlated with microbial diversity. Structural equation modeling showed that HMs (path coefficient = -0.50, p < 0.001) had a negative direct effect on microbial community structure and a positive indirect effect on TPH. The microbial community (path coefficient = 0.31, 0.01 < p < 0.05) was significantly correlated with TPH. In summary, this study explores both the chemical analysis of pollutants and their interaction with microbial communities, providing a better understanding of the co-pollution of TPH and HMs in estuarine sediments.

Bacteria-Triggered Mineralization of Silica Shells with Nanochannels for Biocatalysis in Harsh Conditions

Biocatalytic processes using microorganisms are considered efficient and economically and environmentally friendly reactions. However, the viability and function of these microorganisms are prone to being hindered by various practical environments. Here, we reported a bacteria-induced nanochannel structure that endowed the microorganism with biocatalytic ability in harsh conditions. We revealed that the bacteria could trigger the fusion of silica nanoparticles on their surface by the secreted alkaline metabolite, resulting in silica shells with nanochannels on bacteria (bacteria@nSiO2). The nanochannel structure in silica shells endowed bacteria with biocatalytic ability in multiple harsh conditions. We revealed that these nanochannels could influence the mass transfer from the extracellular to the intracellular environment, which protected the bacteria from excessive toxic substance while preserving the mass exchange during biocatalysis. This feature ensured bacteria@nSiO2 with efficient bioactivity under harsh conditions for industrial catalysis and degradation of pollution, which cannot be achieved by corresponding native bacteria. Using the crude oil spill as a practical example, we presented that bacteria@nSiO2 could degrade highly concentrated crude oil, which any reported bacteria cannot achieve. This work emphasized the role of nanochannels in the regulation of cellular functions for enhanced biocatalysis. It also demonstrated a bacteria-triggered nanostructure formation, which is a promising methodology for nanotechnology and provides a strategy for more advanced organism-material hybrids.

Enhancing biodegradation of aged hydrocarbon-contaminated soils through toluene addition: assessing effects on solid and slurry phase treatments

The main challenge in treating aged soils highly contaminated with total petroleum hydrocarbons (TPH) is to enhance their bioavailability for microbial degradation. Hydrocarbons in soils undergo chemical changes that make them more resistant to biodegradation. This study investigates toluene's efficacy in enhancing the biodegradation of aged hydrocarbon-contaminated soil containing 292,000 mg TPH kg-1 dry soil. Toluene's effect was compared between solid phase (SOP) and slurry phase (SLP) treatments using a microbial consortium isolated from Cyperus laxus rhizosphere. TPH biodegradation and microbial respiration were measured, the latter to estimate the respiratory quotient (RQ, the ratio between moles of carbon dioxide released and moles of oxygen absorbed during respiration). Toluene significantly accelerated TPH biodegradation in both treatments, achieving ~ 30% higher removal than in a non-solvent control, possibly through improved bioavailability of aromatic compounds and other low molecular weight compounds. According to the RQ analysis, toluene enhanced microbial respiratory processes and hydrocarbon catabolism with higher hydrocarbon mineralization (RQ =  ~ 0.5) in both SOP and SLP assays. Our results reveal toluene's potential to increase hydrocarbon availability and microbial degradation efficiency in aged contaminated soils; its use in various bioremediation techniques could be of broad applicability across diverse soil types and pollutants.

Microorganisms immobilized hydroxyethyl cellulose/luffa composite sponge for selective adsorption and biodegradation of oils in wastewater

The highly efficient removal of oils such as oils or dyes from wastewater has aroused wide concern and is of great significance for clean production and environmental remediation. The synthesis of a novel aerogel (designated as HEC/LS) is reported herein, achieved through a sol-gel method followed by freeze-drying utilizing loofa and hydroxyethyl cellulose as the raw materials. The new HEC/LS aerogel exhibits excellent porosity and specific surface area, with a porosity of 88.70 %, a total pore area of 0.607 m2 g-1, and a specific surface area of 230 m2 g-1. The prepared HEC/LS aerogel exhibits exceptional hydrophilicity and self-floatability, facilitating its rapid absorption of water up to 21 times its own weight within a mere 3 s. Additionally, it demonstrates good adsorption performance for methylene blue (MB), with a maximum adsorption capacity of 83.30 mg g-1. Subsequently, a new hydrophobic microorganisms-loaded composite aerogel (namely, Bn-HEC/LS) was obtained by doping microorganisms into the as-prepared HEC/LS in multiple enrichment followed by a hydrophobic and oleophilic surface modification. Based on its rich porous structure and oleophilic wettability, the as-synthesized Bn-HEC/LS exhibits excellent selective adsorption and degradation properties for the oil contamination, the diesel oil could be selectively absorbed in the Bn-HEC/LS and degraded by the loaded microorganisms. Among them, B5-HEC/LS displays the highest removal efficiency of 94.50 % within 180 h, while free microorganisms and HEC/LS aerogels show degradation efficiencies of only 21.70 % and 48.10 %, respectively. The fixation of microorganisms in the aerogel increases their number within the material and enhances the relative microorganisms removal capacity. The hydrophobic and lipophilic modifications improve the selective adsorption performance of the aerogel on diesel oil, resulting in a significantly high removal rate of Bn-HEC/LS for diesel oil. The results indicate that the immobilization of microorganisms into aerogel improves the activity of microorganisms, and the hydrophobic and oleophilic modification enhances the selective adsorption performance of aerogel to diesel oil, thus resulting in a very high removal rate of Bn-HEC/LS for diesel oil. This study is expected to provide a now possibility for the green and efficient bioremediation of oils.

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

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

Laccase: Sustainable production strategies, heterologous expression and potential biotechnological applications

Laccase is a multicopper oxidase enzyme that target different types of phenols and aromatic amines. The enzyme can be isolated and characterized from microbes, plants and insects. Its ubiquitous nature and delignification ability makes it a valuable tool for research and development. Sustainable production methods are being employed to develop low cost biomanufacturing of the enzyme while achieving high titers. Laccase have significant industrial application ranging from food industry where it can be used for wine stabilization, texture improvement and detection of phenolic compounds in food products, to cosmetics offering benefits such as skin brightening and hair colouring. Dye decolourization/degradation, removal of pharmaceutical products/emerging pollutants and hydrocarbons from wastewater, biobleaching of textile fabrics, biofuel production and delignification of biomass making laccase a promising green biocatalyst. Innovative methods such as using inducers, microbial co-culturing, recombinant DNA technology, protein engineering have pivotal role in developing laccase with tailored properties. Enzyme immobilization using new age compounds including nanoparticles, carbonaceous components, agro-industrial residues enhance activity, stability and reusability. Commercial formulations of laccase have been prepared and readily available for a variety of applications. Certain challenges including production cost, metabolic stress in response to heterologous expression, difficulty in purification needs to be addressed.

Bioremediation of Polycyclic Aromatic Hydrocarbons by Means of Bacteria and Bacterial Enzymes

Polycyclic aromatic hydrocarbons (PAHs) are widespread, persistent, and toxic environmental pollutants. Many anthropogenic and some natural factors contribute to the spread and accumulation of PAHs in aquatic and soil systems. The effective and environmentally friendly remediation of these chemical compounds is an important and challenging problem that has kept scientists busy over the last few decades. This review briefly summarizes data on the main sources of PAHs, their toxicity to living organisms, and physical and chemical approaches to the remediation of PAHs. The basic idea behind existing approaches to the bioremediation of PAHs is outlined with an emphasis on a detailed description of the use of bacterial strains as individual isolates, consortia, or cell-free enzymatic agents.

Review on biochar as a sustainable green resource for the rehabilitation of petroleum hydrocarbon-contaminated soil

Petroleum pollution is one of the primary threats to the environment and public health. Therefore, it is essential to create new strategies and enhance current ones. The process of biological reclamation, which utilizes a biological agent to eliminate harmful substances from polluted soil, has drawn much interest. Biochars are inexpensive, environmentally beneficial carbon compounds extensively employed to remove petroleum hydrocarbons from the environment. Biochar has demonstrated an excellent capability to remediate soil pollutants because of its abundant supply of the required raw materials, sustainability, affordability, high efficacy, substantial specific surface area, and desired physical-chemical surface characteristics. This paper reviews biochar's methods, effectiveness, and possible toxic effects on the natural environment, amended biochar, and their integration with other remediating materials towards sustainable remediation of petroleum-polluted soil environments. Efforts are being undertaken to enhance the effectiveness of biochar in the hydrocarbon-based rehabilitation approach by altering its characteristics. Additionally, the adsorption, biodegradability, chemical breakdown, and regenerative facets of biochar amendment and combined usage culminated in augmenting the remedial effectiveness. Lastly, several shortcomings of the prevailing methods and prospective directions were provided to overcome the constraints in tailored biochar studies for long-term performance stability and ecological sustainability towards restoring petroleum hydrocarbon adultered soil environments.

Deciphering the molecular interaction of extracellular polymeric substances of a marine bacterium Pseudomonas furukawaii PPS-19 with petroleum hydrocarbons and development of bioadsorbent

Petroleum hydrocarbon contamination is a serious hazard to marine environments, affecting ecosystems and marine life. However, extracellular polymeric substances (EPS) of marine bacteria constituting various hydrophilic and hydrophobic functional groups sequester petroleum hydrocarbons (PHs). In this study, interaction of EPS of Pseudomonas furukawaii PPS-19 with PHs such as crude oil, n-dodecane, and pyrene and its impact on PHs adsorption was investigated. Protein component of EPS was increased after treatment with PHs. Red shift of UV-Vis spectra implied change in molecular structure of EPS. Functional groups of proteins (CO, NH2) and polysaccharides (C-C, C-OH, C-O-C) predominantly interacted with PHs. Interaction with PHs affected secondary structure of EPS. Change in binding energies of corresponding functionalities of C 1s, O 1s, and N 1s confirmed the interaction. Disruption of crystalline peaks led to increased pore size in EPS primarily due to the increase in surface electronegativity. Static quenching mechanism unveils formation of complex between fulvic acid of EPS and PHs. Relative expression of alg8 gene was significantly increased in the presence of n-dodecane (6.31 fold) (P < 0.05; One way ANOVA). n-dodecane and pyrene adsorption capacity of Immobilized EPS was significantly higher (356.5 and 338.2 mg g-1, respectively) (P < 0.001; One way ANOVA) than control. Adsorption rate fits into the pseudo-second-order kinetic model. This study establishes that interaction of PHs causes structural and physical changes in EPS and EPS could be used as an adsorbent material for the sequestration of PHs pollution.

A column study: Impact of redox, substrate composition and exposure order on toluene and benzene biodegradation and microbial communities

Aromatic compounds persist as hazardous contaminants in both aquatic and terrestrial environments, needing rapid and effective remediation strategies. This study evaluated toluene and benzene biodegradation under sulfate and nitrate-reducing conditions in column experiments, utilizing aquifer sediments from a contaminated site. Over a period of 36 weeks, four glass columns were operated simultaneously in an alternating flow-batch regime. Each column received either nitrate or sulfate as an electron acceptor while being exposed to different substrate compositions in varied exposure orders. A redox dependent contaminant removal efficiency was observed, with toluene removal efficiency at 81% under sulfate and 55% under nitrate-reducing conditions, and benzene removal efficiency approximately at 44% and 59%, respectively, within 4-6 weeks. The rapid removal under anaerobic conditions was attributed to the alternating flow-batch regime, allowing biomass growth in batch mode, and applying selection pressure to non-specific biodegraders during flow regime. Toluene removal remained unaffected by benzene's presence but exhibited slight inhibition in the presence of an aromatic mixture composed of BTEX, indene, indane, and naphthalene. Benzene removal efficiency dropped to 8% in the presence of toluene but remained unaffected by the mixture. Pre-exposure to a single compound enhanced breakdown efficiency when further faced with a more complex mixture. Additionally, beta-diversity analysis conducted on the four columns revealed distinct microbial community clustering between sulfate and nitrate-reducing conditions, emphasizing the determining role of redox conditions. Findings of this study can be used to develop more effective pollution cleanup strategies, specifically targeting parameters like redox conditions, substrate interactions, and pollution history, thus improving our ability to mitigate contamination across diverse environments.

Methods Using Marine Aquatic Photoautotrophs along the Qatari Coastline to Remediate Oil and Gas Industrial Water

Qatar and other Gulf States have a diverse range of marine vegetation that is adapted to the stressful environmental conditions of seawater. The industrial wastewater produced by oil and gas activities adds further detrimental conditions for marine aquatic photosynthetic organisms on the Qatari coastlines. Thus, these organisms experience severe stress from both seawater and industrial wastewater. This review discusses the biodiversity in seawater around Qatar, as well as remediation methods and metabolic pathways to reduce the negative impacts of heavy metals and petroleum hydrocarbons produced during these activities. The role of microorganisms that are adjacent to or associated with these aquatic marine organisms is discussed. Exudates that are released by plant roots enhance the role of microorganisms to degrade organic pollutants and immobilize heavy metals. Seaweeds may have other roles such as biosorption and nutrient uptake of extra essential elements to avoid or reduce eutrophication in marine environments. Special attention is paid to mangrove forests and their roles in remediating shores polluted by industrial wastewater. Seagrasses (Halodule uninervis, Halophila ovalis, and Thalassia hemprichii) can be used as promising candidates for phytoremediation or bioindicators for pollution status. Some genera among seaweeds that have proven efficient in accumulating the most common heavy metals found in gas activities and biodegradation of petroleum hydrocarbons are discussed.

Valorization of waste engine oil to mono- and di-rhamnolipid in a sustainable approach to circular bioeconomy

This study aims to valorize waste engine oil (WEO) for synthesizing economically viable biosurfactants (rhamnolipids) to strengthen the circular bioeconomy concept. It specifically focuses on investigating the influence of key bioprocess parameters, viz. agitation and aeration rates, on enhancing rhamnolipid yield in a fed-batch fermentation mode. The methodology involves conducting experiments in a stirred tank bioreactor (3 L) using Pseudomonas aeruginosa gi |KP 163922| as the test organism. Central composite design and response surface methodology (CCD-RSM) are employed to design the experiments and analyze the effects of agitation and aeration rates on various parameters, including dry cell biomass (DCBM), surface tension, tensoactivity, and rhamnolipid yield. It is also essential to determine the mechanistic pathway of biosurfactant production followed by the strain using complex hydrophobic substrates such as WEO. The study reveals that optimal agitation and aeration rates of 200 rpm and 1 Lpm result in the highest biosurfactant yield of 29.76 g/L with minimal surface tension (28 mN/m). Biosurfactant characterization using FTIR, 1H NMR, and UPLC-MS/MS confirm the presence of dominant molecular ion peaks m/z 543.9 and 675.1. This suggests that the biosurfactant is a mixture of mono- and di-rhamnolipids (RhaC10C10, RhaRhaC10C12:1, RhaRhaC12:1C10). The findings present a sustainable approach for biosurfactant production in a fed-batch bioreactor. This research opens the possibility of exploring the use of pilot or large-scale bioreactors for biosurfactant production in future investigations.

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

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

Advanced photocatalysis as a viable and sustainable wastewater treatment process: A comprehensive review

In our era, water pollution not only poses a serious threat to human, animal, and biotic life but also causes serious damage to infrastructure and the ecosystem. A set of physical, chemical, and biological technologies have been exploited to decontaminate and/or disinfect water pollutants, toxins, microbes, and contaminants, but none of these could be ranked as sustainable and scalable wastewater technology. The photocatalytic process can harmonize the sunlight to degrade certain toxins, chemicals, microbes, and antibiotics, present in water. For example, transition metal oxides (ZnO, SnO2, TiO2, etc.), when integrated into an organic framework of graphene or nitrides, can bring about more than 90% removal of dyes, microbial load, pesticides, and antibiotics. Similarly, a modified network of graphitic carbon nitride can completely decontaminate petrochemicals. The present review will primarily highlight the mechanistic aspects for the removal and/or degradation of highly concerned contaminants, factors affecting photocatalysis, engineering designs of photoreactors, and pros and cons of various wastewater treatment technologies already in practice. The photocatalytic reactor can be a more viable and sustainable wastewater treatment opportunity. We hope the researcher will find a handful of information regarding the advanced oxidation process accomplished via photocatalysis and the benefits associated with the photocatalytic-type degradation of water pollutants and contaminants.

Bioremediation of petroleum hydrocarbons polluted soil by spent mushroom substrates: Microbiological structure and functionality

Spent mushroom substrate (SMS) holds valuable microbiota that can be useful in remediating polluted soils with hydrocarbons. However, the microorganisms behind the bioremediation process remain uncertain. In this work, a bioremediation assay of total petroleum hydrocarbons (TPHs) polluted soil by SMS application was performed to elucidate the microorganisms and consortia involved in biodegradation by a metabarcoding analysis. Untreated polluted soil was compared to seven bioremediation treatments by adding SMS of Agaricus bisporus, Pleurotus eryngii, Pleurotus ostreatus, and combinations. Soil microbial activity, TPH biodegradation, taxonomic classification, and predictive functional analysis were evaluated in the microbiopiles at 60 days. Different metagenomics approaches were performed to understand the impact of each SMS on native soil microbiota and TPHs biodegradation. All SMSs enhanced the degradation of aliphatic and aromatic hydrocarbons, being A. bisporus the most effective, promoting an efficient consortium constituted by the bacterial families Alcanivoraceae, Alcaligenaceae, and Dietziaceae along with the fungal genera Scedosporium and Aspergillus. The predictive 16 S rRNA gene study partially explained the decontamination efficacy by observing changes in the taxonomic structure of bacteria and fungi, and changes in the potential profiles of estimated degradative genes across the different treatments. This work provides new insights into TPHs bioremediation.