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Petroleum pollution poses a critical environmental concern. Bioremediation has gained prominence as an eco-friendly approach for mitigating hydrocarbon pollution. This study reports the isolation and comprehensive characterization of a novel petroleum-degrading bacterium, Rhodococcus indonesiensis SARSHI1. Whole-genome sequencing was performed using a hybrid approach, integrating Oxford Nanopore Technologies (PromethION) and Illumina (NovaSeq 6000) platforms. The complete genome spans 5.7 Mbp and an additional plasmid of 159,118 bp, together encoding 5,150 coding sequences. Structural annotation identified 5220 genes, including 5094 protein-coding genes, one non-coding RNA, one CRISPR array, 56 pseudogenes, and 243 hypothetical proteins. Sequencing yielded 13,900,477 Illumina and 2,539,063 ONT reads, with 13,169,190 and 1,567,736 retained after quality processing, respectively. The assembly achieved 100% completeness with a coding density of 91.4%. Functional annotation revealed key hydrocarbon-degradation genes alkB , ahyA , and almA for long-chain alkanes, and bph , ben , and xylC for aromatics. Additionally, the presence of genes conferring multiple antibiotic resistances and those involved in secondary metabolite synthesis highlighted the strain’s remarkable metabolic adaptability. The complete genome and plasmid sequences have been deposited in GenBank under accession numbers CP180630 and CP180631, respectively. The raw reads are available in the NCBI Sequence Read Archive (SRA) under accession numbers SRX27520007 (Illumina) and SRX27520006 (ONT).

Background Sustainable management of voluminous and hazardous oily sludge produced by petroleum refineries remains a challenging problem worldwide. Characterization of microbial communities of petroleum contaminated sites has been considered as the essential prerequisite for implementation of suitable bioremediation strategies. Three petroleum refinery sludge samples from North Eastern India were analyzed using next-generation sequencing technology to explore the diversity and functional potential of inhabitant microorganisms and scope for their on-site bioremediation. Results All sludge samples were hydrocarbon rich, anaerobic and reduced with sulfate as major anion and several heavy metals. High throughput sequencing of V3-16S rRNA genes from sludge metagenomes revealed dominance of strictly anaerobic, fermentative, thermophilic, sulfate-reducing bacteria affiliated to Coprothermobacter , Fervidobacterium , Treponema , Syntrophus , Thermodesulfovibrio , Anaerolinea , Syntrophobacter, Anaerostipes, Anaerobaculum, etc., which have been well known for hydrocarbon degradation. Relatively higher proportions of archaea were detected by qPCR. Archaeal 16S rRNA gene sequences showed presence of methanogenic Methanobacterium , Methanosaeta , Thermoplasmatales , etc. Detection of known hydrocarbon utilizing aerobic/facultative anaerobic ( Mycobacterium, Pseudomonas, Longilinea, Geobacter , etc.), nitrate reducing ( Gordonia , Novosphigobium, etc.) and nitrogen fixing ( Azovibrio, Rhodobacter , etc.) bacteria suggested niche specific guilds with aerobic, facultative anaerobic and strict anaerobic populations. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predicted putative genetic repertoire of sludge microbiomes and their potential for hydrocarbon degradation; lipid-, nitrogen-, sulfur- and methane- metabolism. Methyl coenzyme M reductase A ( mcr A) and dissimilatory sulfite reductase beta-subunit ( dsr B) genes phylogeny confirmed methanogenic and sulfate-reducing activities within sludge environment endowed by hydrogenotrophic methanogens and sulfate-reducing Deltaproteobacteria and Firmicutes members. Conclusion Refinery sludge microbiomes were comprised of hydrocarbon degrading, fermentative, sulfate-reducing, syntrophic, nitrogen fixing and methanogenic microorganisms, which were in accordance with the prevailing physicochemical nature of the samples. Analysis of functional biomarker genes ascertained the activities of methanogenic and sulfate-reducing organisms within sludge environment. Overall data provided better insights on microbial diversity and activity in oil contaminated environment, which could be exploited suitably for in situ bioremediation of refinery sludge.

Bioremediation offers a sustainable and eco-friendly approach for addressing petroleum contamination. In this study, we investigated the hydrocarbon-degrading potential of Microbacter sp. EMBS2025, a strain previously isolated and characterized for its biosurfactant-producing capabilities. The strain was cultivated using varying concentrations of crude oil as the sole carbon source, where it demonstrated robust growth and efficient degradation of both alkanes and aromatic hydrocarbons. Whole-genome sequencing was performed using the Illumina Novaseq 6000 platform, yielding approximately 33.4 million high-quality reads with a sequencing depth (~ 1482 ×). The assembled genome spans 3.52 Mb and comprises 3237 coding sequences (CDS), 19 miscellaneous RNAs, 3 rRNAs, 51 tRNAs, and 1 tmRNA. The genome assembly achieved 100% completeness, providing a fully reconstructed genome. Functional annotation revealed a metabolically versatile profile, including key genes involved in biosurfactant synthesis ( ppsC, treS, treY, mmpL3, otsA , and rhlG_1/rhlG_2) and hydrocarbon degradation ( alkB, sadH, yghA, nuo, gap , BVMO, cat, pca , and ben ) , highlighting its strong oxidation potential. Orthogroup analysis identified unique orthologous groups within the strain, while Average Nucleotide Identity (ANI) analysis suggests that Microbacter sp. EMBS2025 may represent a novel species within the Microbacterium genus. Variant annotation revealed a genome enriched with high-impact variants, with SNPs accounting for 66–68% of the total. The demonstrated bioremediation potential of Microbacter sp. EMBS2025 offers a sustainable solution for oil pollution, contributing to cleaner environments, reduced health risks, and enhanced water quality. The application of this strain in oil-contaminated environments holds significant promise for protecting public health by reducing toxic exposure risks, restoring clean water sources, and supporting agricultural and economic activities in affected communities.

Remediation of persistent organic pollutants in soil especially total petroleum hydrocarbon (TPH) is of global concern due to its toxicity and health implications. Soil flushing has been considered a promising technique among in-situ technologies for treating non-volatile TPH-contaminated soils because it weakens the interaction between hydrocarbons and soil particles to enhance pollutant mobilization efficiency. It is still challenging to optimize the soil flushing treatment because the overall efficacy significantly depends on the environmental characteristics of the subsurface. Advanced soil flushing strategies (e.g., integrating with oxidation, air sparging, and nanoparticles) and novel flushing solutions are discussed to overcome the limitations of the existing process during the remediation of soil systems contaminated with recalcitrant TPH. The flushed-out toxic chemicals comprise a large amount of waste solution, creating another pollutant. The present review summarizes the enhanced soil flushing techniques, and critically discusses their advantages and disadvantages, and addresses follow-up remediation of the generated wash solution containing toxic substances for its safe discharge. Fundamental information on soil flushing is discussed to overcome the challenges encountered during field application such as poor efficiency, high operating cost, and a large amount of generated secondary wastewater.

Petroleum is a vital and strategic energy resource for boosting a country’s GDP. Despite its high economic value, it is considered a primary factor in environmental deterioration. Bioremediation strategies employ indigenous microbial strains to propose an economical and sustainable alternative to conventional remediation practices. The current study investigates the isolation, identification, and characterization of five novel biosurfactant-producing and petroleum hydrocarbon-degrading bacterial species: Rhodococcus indonesiensis strain SARSHI1, Pseudomonas aeruginosa strain SARSHI2, Pseudomonas argentinensis strain SARSHI3, Acinetobacter baumannii strain SARSHI4, and Rhodococcus qingshengii strain SARSHI5. Molecular identification was determined via 16S rRNA sequencing, and their taxonomic identities were validated through biochemical assessments. Their partial sequences were deposited in NCBI with accession numbers: ‘PV034287’, ‘OP597529’, ‘OP584476’, ‘OQ711779’, and ‘OQ711775’ respectively. Amongst them, R. indonesiensis exhibited the highest biosurfactant and hydrocarbon-degrading potential with a critical micelle concentration of 70 mg/L, reduced surface tension of 27 mN/m, an emulsification index (E 24 ) of 85.34%, and hydrocarbon-degrading potency of up to 90%. Gravimetric analysis revealed up to 84% hydrocarbon degradation when supplemented with glycerol, and GC-MS analysis confirmed the selective degradation of n-alkanes (C18–C24). Structural studies employing NMR established the biosurfactant as a lipopeptide. Statistical optimization utilizing RSM - Box-Behnken design obtained the optimized conditions for enhanced biosurfactant and biodegradation activity. Microcosm studies further assessed SARSHI1’s bioremediation potential under field-simulated treatments, achieving up to 95% degradation rates under the combined treatment of Bioaugmentation + Biostimulation + Biosurfactant (BA + BS + B), signifying the amplified bioavailability of hydrocarbons. Phytotoxicity tests confirmed the environmental impact of the bacterial strain. The results govern a robust framework for advancing microbial applications in environmental remediation and further support R. indonesiensis SARSHI1 for large-scale biotechnological paradigms.

Petroleum products have contaminated groundwater with harmful organic compounds, such as benzene, toluene, ethylbenzene, and xylenes (BTEX). Collecting and analyzing polluted groundwater samples is expensive and undertaken infrequently. However, quick remedial action in case of unexpected events requires continuous monitoring. In‐situ water quality sensors (pH, EC, DO, ORP) may show correlations with the components of dissolved petroleum hydrocarbon (PHC) such as aromatics and non‐volatile mobile fractions. Correlations are prerequisite to ultimately develop real‐time prediction models. Since suitable field data sets are limited, we simulated the fate of hydrocarbons in groundwater under various realistic conditions using a reactive transport model as novel approach to explore when, where, and why correlations occur. A stationary oil source zone continuously dissolved at the top of a heterogeneous and shallow sandy aquifer over a two‐dimensional cross‐section. Our model considered transient conditions (fluctuating water table) and spatially uniform hydrogeochemical composition. We observed a strong correlation between PHCs and water quality sensors (rolling Spearman's correlation > |0.8|) at varying periods. These correlations are strongly affected by the location of observation wells, the aquifer's hydraulic conductivity, and the availability of calcite and oxide minerals, and other electron acceptors. DO and ORP are significant for the early detection of hydrocarbon contamination, whereas pH and EC are important features for the long‐term monitoring of hydrocarbons. Our findings lay the foundation for the subsequent development of a data analysis model to detect and estimate in real time PHC levels in groundwater using in‐situ water quality sensors. Plain Language Summary Groundwater contamination by petroleum products, including benzene, toluene, ethylbenzene, and xylenes (BTEX), is a serious environmental concern. However, the collection and analysis of polluted groundwater samples are expensive and infrequently conducted. In the event of unexpected contamination, quick remedial action is crucial, which requires continuous monitoring of groundwater quality. We investigated whether in‐situ water quality sensors like pH, electrical conductivity (EC), dissolved oxygen (DO), and oxidation‐reduction potential (ORP) can predict the concentration of dissolved petroleum hydrocarbons (PHC) in groundwater. Understanding the correlations between these sensors and PHC levels is essential for developing real‐time prediction models. Since field data is scarce, we developed a reactive transport model that simulates the movement of PHC in groundwater under different conditions. Our model simulated a scenario where oil continuously dissolves at the top of a sandy aquifer. The correlation between PHC levels and water quality sensors varies depending on the location and timing of measurements. DO and ORP are particularly useful for detecting early signs of contamination, while pH and EC are important for long‐term monitoring. Our findings provide the foundation for developing data analysis models capable of real‐time detection and estimation of PHC levels in groundwater using water quality sensors. Key Points In‐situ water quality sensors are highly correlated with petroleum hydrocarbons in groundwater when spatiotemporal variability is considered DO and ORP are important for early detection, while pH and EC for long‐term prediction of hydrocarbon contamination in groundwater The aquifer's hydrogeology impacts hydrocarbon‐water quality correlations by influencing buffering capacity and flow velocity, among others

Oily sludge is a residue from the petroleum industry composed of a mixture of sand, water, metals, and high content of hydrocarbons (HCs). The heavy oily sludge used in this study originated from Colombian crude oil with high density and low American Petroleum Institute (API) gravity. The residual waste from heavy oil processing was subject to thermal and centrifugal extraction, resulting in heavy oily sludge with very high density and viscosity. Biodegradation of the total petroleum hydrocarbons (TPH) was tested in microcosms using several bioremediation approaches, including: biostimulation with bulking agents and nutrients, the surfactant Tween 80, and bioaugmentation. Select HC degrading bacteria were isolated based on their ability to grow and produce clear zones on different HCs. Degradation of TPH in the microcosms was monitored gravimetrically and with gas chromatography (GC). The TPH removal in all treatments ranged between 2 and 67%, regardless of the addition of microbial consortiums, amendments, or surfactants within the tested parameters. The results of this study demonstrated that bioremediation of heavy oily sludge presents greater challenges to achieve regulatory requirements. Additional physicochemical treatments analysis to remediate this recalcitrant material may be required to achieve a desirable degradation rate.

Phytoremediation is a cost-effective and environmentally friendly method, offering a suitable alternative to chemical and physical approaches for the removal of pollutants from soil. This research explored the phytoremediation potential of Alhagi camelorum , a plant species, for total petroleum hydrocarbons (TPHs) and heavy metals (HMs), specifically lead (Pb), chromium (Cr), nickel (Ni), and cadmium (Cd), in oil-contaminated soil. A field-scale study spanning six months was conducted, involving the cultivation of A. camelorum seeds in a nursery and subsequent transplantation of seedlings onto prepared soil plots. Control plots, devoid of any plants, were also incorporated for comparison. Soil samples were analyzed throughout the study period using inductively coupled plasma-optical emission spectroscopy (ICP‒OES) for HMs and gas chromatography‒mass spectrometry (GC‒MS) for TPHs. The results showed that after six months, the average removal percentage was 53.6 ± 2.8% for TPHs and varying percentages observed for the HMs (Pb: 50 ± 2.1%, Cr: 47.6 ± 2.5%, Ni: 48.1 ± 1.6%, and Cd: 45.4 ± 3.5%). The upward trajectory in the population of heterotrophic bacteria and the level of microbial respiration, in contrast to the control plots, suggests that the presence of the plant plays a significant role in promoting soil microbial growth ( P  < 0.05). Moreover, kinetic rate models were examined to assess the rate of pollutant removal. The coefficient of determination consistently aligned with the first-order kinetic rate model for all the mentioned pollutants (R 2  > 0.8). These results collectively suggest that phytoremediation employing A. camelorum can effectively reduce pollutants in oil-contaminated soils.

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.