Isolation and characterisation of crude oil sludge degrading bacteria

Simultaneous production of biosurfactant and extracellular unspecific peroxygenases by Moesziomyces aphidis XM01 enables an efficient strategy for crude oil degradation

Crude oil is a hazardous pollutant that poses significant and lasting harm to human health and ecosystems. In this study, Moesziomyces aphidis XM01, a biosurfactant mannosylerythritol lipids (MELs)-producing yeast, was utilized for crude oil degradation. Unlike most microorganisms relying on cytochrome P450, XM01 employed two extracellular unspecific peroxygenases, MaUPO.1 and MaUPO.2, with preference for polycyclic aromatic hydrocarbons (PAHs) and n-alkanes respectively, thus facilitating efficient crude oil degradation. The MELs produced by XM01 exhibited a significant emulsification activity of 65.9% for crude oil and were consequently supplemented in an "exogenous MELs addition" strategy to boost crude oil degradation, resulting in an optimal degradation ratio of 72.3%. Furthermore, a new and simple "pre-MELs production" strategy was implemented, achieving a maximum degradation ratio of 95.9%. During this process, the synergistic up-regulation of MaUPO.1, MaUPO.1 and the key MELs synthesis genes contributed to the efficient degradation of crude oil. Additionally, the phylogenetic and geographic distribution analysis of MaUPO.1 and MaUPO.1 revealed their wide occurrence among fungi in Basidiomycota and Ascomycota, with high transcription levels across global ocean, highlighting their important role in biodegradation of crude oil. In conclusion, M. aphidis XM01 emerges as a novel yeast for efficient and eco-friendly crude oil degradation.

Metataxonomic Characterization of Enriched Consortia Derived from Oil Spill-Contaminated Sites in Guimaras, Philippines, Reveals Major Role of Klebsiella sp. in Hydrocarbon Degradation

Oil spills are major anthropogenic disasters that cause serious harm to marine environments. In the Philippines, traditional methods of rehabilitating oil-polluted areas were proven to be less efficient and cause further damage to the environment. Microbial degradation has poised itself to be a promising alternative to those traditional methods in remediating oil spills. Hence, the present study aimed to enrich and characterize hydrocarbon-degrading microbial consortia from oil-contaminated regions in Guimaras Island for potential use in bioremediation. A total of 75 soil samples were obtained and used as inoculum for the enrichment for hydrocarbon degraders. Afterwards, 32 consortia were recovered and subjected to the 2,6-DCPIP assay for biodegradation ability on four types of hydrocarbons: diesel, xylene, hexane, and hexadecane. The consortia that obtained the highest percent degradation for each of the four hydrocarbons were "B2" (92.34% diesel degraded), "A5" (85.55% hexadecane degraded), "B1" (74.33% hexane degraded), and "B7" (63.38% xylene degraded). Illumina MiSeq 16S rRNA gene amplicon sequencing revealed that the dominant phyla in all consortia are Pseudomonadota (previously Proteobacteria), followed by Bacillota (previously Firmicutes). Overall, the amplicon sequence variants (ASVs) retrieved were mainly from the Gammaproteobacteria class, in which many hydrocarbon-degrading bacteria are found. Predictive functional profiling of the consortium showed the presence of genes involved in the degradation of recalcitrant hydrocarbon pollutants. Fatty acid metabolism, which includes alkB (alkane-1-monooxygenase) and genes for beta oxidation, was inferred to be the most abundant amongst all hydrocarbon degradation pathways. Klebsiella sp. is the predominant ASV in all the sequenced consortia as well as the major contributor of hydrocarbon degradation genes. The findings of the study can serve as groundwork for the development of hydrocarbon-degrading bacterial consortia for the bioremediation of oil spill-affected areas in the Philippines. Likewise, this paper provides a basis for further investigation into the role of Klebsiella sp. in the bioremediation of hydrocarbon pollutants.

High-throughput bioamphiphile production by ethyl methane sulphonate induced mutant of hydrocarbonoclastic Enterobacter xiangfangensis STP-3: In depth structural elucidation and application to petroleum refinery oil sludge bioremediation

The environmental release of noxious petroleum hydrocarbons (PHCs) from the petroleum refining industries is an intractable global challenge. Indigenous PHCs degrading microbes produce insufficient yield of amphiphilic biomolecules with trivial efficiency makes the bioremediation process ineffective. In this concern, the present study is focused on the production of high yield multi-functional amphiphilic biomolecule through the genetic modification of Enterobacter xiangfangensis STP-3 strain using Ethyl methane sulphonate (EMS) induced mutagenesis. Mutant M9_{E.xiangfangensis} showed 2.32-fold increased yield of bioamphiphile than wild-type strain. Novel bioamphiphile produced by M9_{E.xiangfangensis} exhibited improved surface and emulsification activities which ensure the maximum degradation of petroleum oil sludge (POS) by 86% than wild-type (72%). SARA, FT-IR, and GC-MS analyses confirmed the expedited degradation of POS and ICP-MS analysis indicated the enhanced removal of heavy metals in connection with the ample production of functionally improved bioamphiphile. FT-IR NMR, MALDI-TOF, GC-MS and LC-MS/MS analyses portrayed the lipoprotein nature of bioamphiphile comprising pentameric fatty acid moiety conjugated with the catalytic esterase moiety. Further, homology modelling and molecular docking revealed the stronger interaction of hydrophobic amino acids, leucine and isoleucine with the PHCs in the case of wild-type esterase moiety, whereas in the mutant, aromatic amino acids were majorly interacted with the long chain and branched chain alkanes, thereby exhibited better efficiency. This is the first report on the adoption of EMS induced mutagenesis strategy to ameliorate the amphiphilic biomolecules for their sustainable applications in diverse biotechnological, environmental and industrial arenas.

Assessment of oily sludge biodegradation in lab scale composting and slurry bioreactor by bacterial consortium

The present study aimed to investigate biodegradability of oily sludge in lab scale composting and slurry bioreactor using a potential bacterial consortium isolated from petroleum-contaminated sites. The consortium used in the study consisted of bacterial genera, including Enterobacter, Bacillus, Microbacterium, Alcaligenes Pseudomonas, Ochrobactrum, Micrococcus, and Shinella which were obtained after rigorous screening using different hydrocarbons. The meticulously designed lab scale composting experiments were carried out and showed that the combination of 10% oily sludge (A1) exhibited the highest total carbon (TC) removal, which was 40.33% within 90 days. To assess the composting experiments' efficiency, the first (k₁) and second (k₂) order rate constants were evaluated and was found to be 0.0004-0.0067 per day and second (k₂) 0.0000008-0.00005 g/kg. day respectively. To further enhance the biodegradation rate of A1 combination, a slurry bioreactor was used. The maximum total petroleum hydrocarbon (TPH) removals in a slurry bioreactor for cycle-I and -II were 48.8% and 46.5%, respectively, on the 78th and 140th days of the treatment. The results obtained in the study will be a technological platform for the development of slurry phase treatment of petroleum waste in a sustainable and eco-friendly manner.

Bioaugmentation potential of inoculum derived from anaerobic digestion feedstock for enhanced methane production using water hyacinth

The utilisation of water hyacinth for production of biogas is considered to be a solution to both its control and the global renewable energy challenge. In this instance, an investigation was conducted to evaluate the potential of water hyacinth inoculum to enhance methane production during anaerobic digestion (AD). Chopped whole water hyacinth (10% (w/v)) was digested to prepare an inoculum consisting mainly of water hyacinth indigenous microbes. The inoculum was incorporated in the AD of freshly chopped whole water hyacinth to set up different ratios of water hyacinth inoculum and water hyacinth mixture with appropriate controls. The results of batch tests with water hyacinth inoculum showed a maximal cumulative volume of 211.67 ml of methane after 29 days of AD as opposed to 88.6 ml of methane generated from the control treatment without inoculum. In addition to improving methane production, inclusion of water hyacinth inoculum reduced the electrical conductivity (EC) values of the resultant digestate, and, amplification of nifH and phoD genes in the digestate accentuates it as a potential soil ameliorant. This study provides an insight into the potential of water hyacinth inoculum to enhance methane production and contribute to the feasibility of the digestate as a soil fertility enhancer.

Biodegradation of monocrotophos by Brucella intermedia Msd2 isolated from cotton plant

Widespread and inadequate use of Monocrotophos has led to several environmental issues. Biodegradation is an ecofriendly method used for detoxification of toxic monocrotophos. In the present study, Msd2 bacterial strain was isolated from the cotton plant growing in contaminated sites of Sahiwal, Pakistan. Msd2 is capable of utilizing the monocrotophos (MCP) organophosphate pesticide as its sole carbon source for growth. Msd2 was identified as Brucella intermedia on the basis of morphology, biochemical characterization and 16S rRNA sequencing. B. intermedia showed tolerance of MCP up to 100 ppm. The presence of opd candidate gene for pesticide degradation, gives credence to B. intermedia as an effective bacterium to degrade MCP. Screening of the B. intermedia strain Msd2 for plant growth promoting activities revealed its ability to produce ammonia, exopolysaccharides, catalase, amylase and ACC-deaminase, and phosphorus, zinc and potassium solubilization. The optimization of the growth parameters (temperatures, shaking rpm, and pH level) of the MCP-degrading isolate was carried out in minimal salt broth supplemented with MCP. The optimal pH, temperature, and rpm for Msd2 growth were observed as pH 6, 35 °C, and 120 rpm, respectively. Based on optimization results, batch degradation experiment was performed. Biodegradation of MCP by B. intermedia was monitored using HPLC and recorded 78% degradation of MCP at 100 ppm concentration within 7 days of incubation. Degradation of MCP by Msd2 followed the first order reaction kinetics. Plant growth promoting and multi-stress tolerance ability of Msd2 was confirmed by molecular analysis. It is concluded that Brucella intermedia strain Msd2 could be beneficial as potential biological agent for an effective bioremediation for polluted environments.

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

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

Bioremediation of heavy oily sludge: a microcosms study

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.

Effect of moisture content on the evolution of bacterial communities and organic matter degradation during bioaugmented biogas residues composting

Composting is an excellent way to recycle biogas residues into a stable, non-toxic agricultural end product. In this study, the dynamic changes of physical-chemical parameters and bacterial community in three groups of bioaugmentation composting systems at different moisture contents (MC) of 50% (MC50), 60% (MC60) and 70% (MC70) were monitored. The differences of bacterial communities in composts with different initial MC were compared, and the interaction between biological and non-biological parameters was also explored. The results revealed that after 30 days of composting, the biogas residues compost in MC60 reached highest temperature of 64 °C, total Kjeldahl nitrogen (TKN) of 2%, seed germination index (GI) of 110%, and the longest thermophilic period duration of 5 days (55 °C). Additionally, the result of high-throughput sequencing showed that the diversity of bacterial communities in MC60 was the highest, and the abundance of Actinobacteria (16.93-52.63%), Firmicutes (8.71-56.75%), and Proteobacteria (16.88-46.95%) in all groups were the highest at phylum level. The LEfSe analysis indicated that the abundance of Ochrobactrum and Cellulomonadaceae in MC60 was significantly (p < 0.05) higher than with other treatments. Moreover, canonical correspondence analysis (CCA) indicated thermophilic period duration is significantly (p < 0.05) positively correlated with Paenibacillus. Besides, it was found the relative abundance of Nocardiopsis and Georgenia has a significant (p < 0.01) correlation with the fertilizer efficiency of compost. These results showed that controlling the initial moisture content at 60% can improve the maturity and fertilizer efficiency of compost, and enable the bacteria beneficial to composting to gain the advantage of proliferation.

A comparative study on chemical characterization and properties of surface active compounds from Gram-positive Bacillus and Gram-negative Ochrobactrum strains utilizing pure hydrocarbons and waste mineral lubricating oils

Mineral lubricating oils are widely used in various industrial sectors for their applications in maintenance and functioning of machineries. However, indiscriminate dumping of these used oils have resulted in polluting the natural reservoirs which subsequently destroys ecological balance. Bacteria can emulsify or lower surface tension between phases of immiscible substrates and can acquire them as their carbon and energy sources. Such a phenomenon is mediated by production of extracellular polymers which can function as eminent surface active compounds based on their surfactant or emulsifying nature. The comparison between bacterial strains (Gram-positive Bacillus stratosphericus A15 and Gram-negative Ochrobactrum pseudintermedium C1) on utilization of pure straight chain hydrocarbons, waste mineral lubricating oils as sole carbon source and chemical characterization of the synthesized surface active compounds were studied. Characterization analysis by Ultraviolet Visible spectrophotometry, Fourier transform infrared spectroscopy, Nuclear Magnetic Resonance spectroscopy, Carbon-Hydrogen-Nitrogen analysis has given detailed structural elucidation of surface active compounds. The contrasting nature of bacterial strains in utilization of different hydrocarbons of waste mineral lubricating oils was observed in Gas Chromatography-Mass Spectroscopy analysis. The variation between both strains in utilization of hydrocarbons can be manifested in chemical structural differences and properties of the produced surface active compounds. Scanning Electron Microscopy has given detailed insight into the microstructural difference of the compounds. The utilization of lubricating oils can address waste disposal problem and offer an economical feasible approach for bacterial production of surface active compounds. Our results suggest that these surface active compounds can maneuver applications in environmental bioremediation and agriculture, pharmaceuticals and food as functional biomaterials.

Biocatalytic lipoprotein bioamphiphile induced treatment of recalcitrant hydrocarbons in petroleum refinery oil sludge through transposon technology

The present investigation employed transposon technology to enhance the degradation of recalcitrant petroleum hydrocarbons present in petroleum oil sludge by using biosurfactant hyper-producing strain Enterobacter xiangfangensis STP-3. Out of 2500 transposon induced mutants, mutants M_{257E.xiangfangensis} and M_{916E.xiangfangensis} hyper-produce biocatalytic lipoprotein biosurfactant by1.98 and 2.34 fold higher than wild-type strain. Transposon induced mutation also modified the amino acid composition which improved the hydrophobicity and thermal stability of the biosurfactants produced by mutants, compared to the wild-type biosurfactant. GC-MS and LC-MS-MS revealed that biosurfactants have pentameric lipid moiety and esterase as protein moiety. Increased biosurfactant hydrophobicity and yield by the mutants resulted in the enhanced bioavailability of petroleum hydrocarbons, thereby mutants M_{257E.xiangfangensis} and M_{916E.xiangfangensis} demonstrated better petroleum oil sludge degradation by 82% and 88% respectively, than wild-type (72%). Disrupted genes vgr G and pgm M in M257_{E.xiangfangensis} and M916_{E.xiangfangensis} respectively hyper-produce biosurfactant by competitive pathway inhibition and increased precursor availability mechanism. Hyper-production of biosurfactant was also validated by comparing the expression of biosynthetic genes ent E, ent F and est using qPCR. This is the first report on the application of transposon technology to hyper-produce biosurfactant for the effective bioremediation of hydrocarbon contaminated environments.

Transcriptome Profiling Reveals Differential Gene Expression of Laccase Genes in Aspergillus terreus KC462061 during Biodegradation of Crude Oil

Fungal laccases have high catalytic efficiency and are utilized for the removal of crude oil because they oxidize various aliphatic and aromatic hydrocarbons and convert them into harmless compounds or less toxic compounds, thus accelerating the biodegradation potential of crude oil. Laccases are important gene families and the function of laccases genes varied widely based on transcription and function. Biodegradation of crude oil using Aspergillus terreus KC462061 was studied in the current study beside the transcription level of eight laccase (Lcc) genes have participated in biodegradation in the presence of aromatic compounds, and metal ions. Time-course profiles of laccase activity in the presence of crude oil indicated that the five inducers individual or combined have a very positive on laccase activity. In the status of the existence of crude oil, the synergistic effect of Cu-ABTS compound caused an increase in laccase yields up to 22-fold after 10 days than control. The biodegradation efficiencies of A. terreus KC462061 for aliphatic and aromatic hydrocarbons of crude oil were 82.1 ± 0.2% and 77.4 ± 0.6%, respectively. The crude oil biodegradation efficiency was improved by the supplemented Cu-ABTS compound in A. terreus KC462061. Gas chromatography-mass spectrometry was a very accurate tool to demonstrate the biodegradation efficiencies of A. terreus KC462061 for crude oil. Significant differences were observed in the SDS-PAGE of A. terreus KC462061 band intensities of laccase proteins after the addition of five inducers, but the Cu-ABTS compound highly affects very particular laccase electrophoresis. Quantitative real-time polymerase chain reaction (qPCR) was used for the analysis of transcription profile of eight laccase genes in A. terreus KC462061 with a verified reference gene. Cu²⁺ ions and Cu-ABTS were highly effective for efficient laccase expression profiling, mainly via Lcc11 and 12 transcription induction. The current study will explain the theoretical foundation for laccase transcription in A. terreus KC462061, paving the road for commercialization and usage.

ACTIVIDAD ANTIFÚNGICA Y CARACTERÍSTICAS DE PROMOCIÓN DE CRECIMIENTO VEGETAL DE Pseudomonas aeruginosa y Enterobacter sp. DEGRADADORAS DE HIDROCARBUROS AISLADAS DE SUELO CONTAMINADO

El diésel es una mezcla compleja de hidrocarburos alifáticos y aromáticos, que por su amplio uso se ha convertido en un contaminante ambiental muy frecuente. Debido a esto, es imperativo explorar alternativas viables y económicas para la remoción de dicho contaminante. El propósito del presente trabajo fue analizar la degradación de diésel por bacterias aisladas de suelo contaminado con esa mezcla de hidrocarburos, así como evaluar su actividad antagónica sobre hongos fitopatógenos, sus características de promoción del crecimiento vegetal y tolerancia a pesados. A partir del enriquecimiento en diésel como única fuente de carbono, se obtuvieron los aislados bacterianos J3 y S3, cuya identificación bioquímica y molecular reveló que corresponden a Pseudomonas aeruginosa y Enterobacter sp., respectivamente. Además, se observó que el crecimiento bacteriano fue mejor entre 2 y 5 % de diésel, mientras que el pH óptimo fue de 7,0 y 8,0 en presencia de 3 % de diésel. También, S3 mostró buen crecimiento a concentraciones de hasta 4 % de NaCl. Por otro lado, las bacterias mostraron inhibición del crecimiento micelial de los hongos fitopatógenos Alternaria sp., Botrytis cinerea, Colletotrichum siamense y Fusarium proliferatum. Además de características de promoción de crecimiento vegetal como producción de ácido indol acético (AIA), solubilización de fosfato, producción de sideróforos y surfactantes. También, se observó que las bacterias crecieron en presencia de metales como Zn, Cu, Ba y Pb, en concentraciones de entre 1,5 y >10 mM. En conclusión, las bacterias aisladas e identificadas en este estudio presentan características que las hacen excelentes candidatas para la remoción de hidrocarburos solas o mediante fitorremediación por sus características de promoción de crecimiento vegetal.

Unravelling the genetic and functional diversity of dominant bacterial communities involved in manure co-composting bioremediation of complex crude oil waste sludge

The present study aimed to characterize the bacterial community and functional diversity in co-composting microcosms of crude oil waste sludge amended with different animal manures, and to evaluate the scope for biostimulation based in situ bioremediation. Gas chromatography–mass spectrometry (GC–MS) analyses revealed enhanced attenuation (>90%) of the total polyaromatic hydrocarbons (PAHs); the manure amendments significantly enhancing (up to 30%) the degradation of high molecular weight (HMW) PAHs. Microbial community analysis showed the dominance (>99% of total sequences) of sequences affiliated to phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. The core genera enriched were related to hydrocarbon metabolism (Pseudomonas, Delftia, Methylobacterium, Dietzia, Bacillus, Propionibacterium, Bradyrhizobium, Streptomyces, Achromobacter, Microbacterium and Sphingomonas). However, manure-treated samples exhibited high number and heterogeneity of unique operational taxonomic units (OTUs) with enrichment of additional hydrocarbon-degrading bacterial taxa (Proteiniphilum, unclassified Micrococcales, unclassified Lachnospiraceae, Sphingobium and Stenotrophomonas). Thirty-three culturable hydrocarbon-degrading microbes were isolated from the co-composting microcosms and mainly classified into Burkholderia, Sanguibacter, Pseudomonas, Bacillus, Rhodococcus, Lysinibacillus, Microbacterium, Brevibacterium, Geobacillus, Micrococcus, Arthrobacter, Cellulimicrobacterium, Streptomyces Dietzia,etc,. that was additionally affirmed with the presence of catechol 2,3-dioxygenase gene. Finally, enhanced in situ degradation of total (49%), LMW (>75%) and HMW PAHs (>35%) was achieved with an enriched bacterial consortium of these microbes. Overall, these findings suggests that co-composting treatment of crude oil sludge with animal manures selects for intrinsically diverse bacterial community, that could be a driving force behind accelerated bioremediation, and can be exploited for engineered remediation processes.

Advenella mandrilli sp. nov., a bacterium isolated from the faeces of Mandrillus sphinx

A novel Gram-negative strain WQ 585^T, isolated from the faeces of mandrills (Mandrillus sphinx) collected at Yunnan Wild Animal Park, Yunnan province, China, was subjected to a polyphasic taxonomic study. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belongs to the genus Advenella, sharing 98.5% and 98.2% sequence similarity with the type strain Advenella alkanexedens LAM0050^T and Advenella faeciporci M-07^T, respectively. The predominant ubiquinone was Q-8. The major cellular fatty acids (> 10%) were C_16:0, C_17:0 cyclo and Summed Feature 2. The G + C content of the genomic DNA of strain WQ 585^T was 49.0%. The whole genome average nucleotide identity (gANI) values of strain WQ 585^T with strain A. alkanexedens LAM0050^T and A. faeciporci M-07^T were 86.7% and 86.7%, and the digital DNA-DNA hybridization values of strain WQ 585^T with strain A. alkanexedens LAM0050^T and A. faeciporci M-07^T were 64.5% and 62.5%, respectively. Growth occurred at 10-45 °C (optimally at 20-30 °C), pH 6.0-9.0 (optimally at pH 7.0), and 0-5% (w/v) NaCl (optimally at 0.5-2.0%). On the basis of the taxonomic evidence, a novel species, Advenella mandrilli sp. nov., is proposed. The type strain is WQ 585^T (= KCTC 82396 ^T = CCTCC AA 2020028 ^T).

Rhizobacteria Communities of Phytoremediation Plant Species in Petroleum Hydrocarbon Contaminated Soil of the Sudd Ecosystem, South Sudan

The Sudd wetland is one of the oil-rich regions of South Sudan where environmental pollution resulting from oil extraction activities has been unprecedented. Although phytoremediation is the most feasible technique, its efficacy reduces at high TPH concentration in soil. This has made rhizoremediation the most preferred approach. Rhizoremediation involves use of a combination of phytoremediation and biostimulation. The process is catalyzed by the action of rhizobacteria. Therefore, the objective of this study is to characterize rhizobacteria communities prevalent in phytoremediation species growing in hydrocarbon-contaminated soils biostimulated with cattle manure. The treatments studied were plant species only (T1), plant species and hydrocarbons (T2), plant species and manure (T3), and plant species, manure, and hydrocarbons (T4). The rhizobacteria communities were determined using pyrosequencing of 16S rRNA. In the treatment with phytoremediation species, hydrocarbons 75 g · kg-1soil, and cattle manure 5 g · kg-1soil (T4), there was a significant increase (p < 0.05) in rhizobacteria abundance with the highest ASV observed in H. rufa (4980) and the lowest in S. arundinaceum (3955). In the same treatment, bacteria community diversity was high in H. rufa (Chao1, 10310) and the least in S. arundinaceum (Chao 1, 8260) with Proteobacteria, Firmicutes, and Actinobacteria as the dominant phyla. Similarly, in contaminated soil treated with cattle manure, there was a significant increase (p < 0.05) in abundance of rhizobacteria genera with Pseudomonas dominating across phytoremediation species. H. rufa was dominated by Bacillus, Fusibacter, and Rhodococcus; G. barbadense was mainly associated with Luteimonas and Mycobacterium, and T. diversifolia was inhabited by Bacillus and Luteimonas. The rhizosphere of O. longistaminata was dominated by Bacillus, Fusibacter, and Luteimonas, while S. arundinaceum was largely inhabited by Sphingomonas. These rhizobacteria genera ought to be applied in the Sudd region for bioremediation.

Enhanced Production of Biosurfactant from Bacillus subtilis Strain Al-Dhabi-130 under Solid-State Fermentation Using Date Molasses from Saudi Arabia for Bioremediation of Crude-Oil-Contaminated Soils

Crude oil and its derivatives are the most important pollutants in natural environments. Bioremediation of crude oil using bacteria has emerged as a green cleanup approach in recent years. In this study, biosurfactant-producing Bacillus subtilis strain Al-Dhabi-130 was isolated from the marine soil sediment. This organism was cultured in solid-state fermentation using agro-residues to produce cost-effective biosurfactants for the bioremediation of crude-oil contaminated environments. Date molasses improved biosurfactant production and were used for further optimization studies. The traditional “one-variable-at-a-time approach”, “two-level full factorial designs”, and a response surface methodology were used to optimize the concentrations of date molasses and nutrient supplements for surfactant production. The optimum bioprocess conditions were 79.3% (v/w) moisture, 34 h incubation period, and 8.3% (v/v) glucose in date molasses. To validate the quadratic model, the production of biosurfactant was performed in triplicate experiments, with yields of 74 mg/g substrate. These findings support the applications of date molasses for the production of biosurfactants by B. subtilis strain Al-Dhabi-130. Analytical experiments revealed that the bacterial strain degraded various aromatic hydrocarbons and n-alkanes within two weeks of culture with 1% crude oil. The crude biosurfactant produced by the B. subtilis strain Al-Dhabi-130 desorbed 89% of applied crude oil from the soil sample. To conclude, biosurfactant-producing bacterial strains can increase emulsification of crude oil and support the degradation of crude oil.

Whole genome sequence of Serratia marcescens 39_H1, a potential hydrolytic and acidogenic strain

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Serratia marcescens 39_H1 could enhance the hydrolysis of lignocellulosic biomass.

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Serratia marcescens 39_H1 is a plant growth promoting organism.

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Genome analysis showed diverse potential biotechnological application of organism.

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This is an original report on the hydrolytic and acidogenic attributes ofSerratia marcescens 39_H1 for biogas production.

Here, we report a high quality annotated draft genome of Serratia marcescens 39_H1, a Gram-negative facultative anaerobe that was isolated from an anaerobic digester. The strain exhibited hydrolytic/acidogenic properties by significantly improving methane production when used as a single isolate inoculum during anaerobic digestion of water hyacinth and cow dung. The total genome size of the isolate was 5,106,712 bp which corresponds to an N50 of 267,528 and G + C content of 59.7 %. Genome annotation with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) predicted a total of 4,908 genes of which 4,755 were protein coding genes; there were no plasmids detected. A number of genes associated with hydrolytic/acidogenic activities as well as other metabolic activities were identified and discussed.

The Role of Dactylis Glomerata and Diesel Oil in the Formation of Microbiome and Soil Enzyme Activity

The global demand for petroleum contributes to a significant increase in soil pollution with petroleum-based products that pose a severe risk not only to humans but also to plants and the soil microbiome. The increasing pollution of the natural environment urges the search for effective remediation methods. Considering the above, the objective of this study was to determine the usability of Dactylis glomerata for the degradation of hydrocarbons contained in diesel oil (DO), as well as the effects of both the plant tested and DO on the biochemical functionality and changes in the soil microbiome. The experiment was conducted in a greenhouse with non-polluted soil as well as soil polluted with DO and phytoremediated with Dactylis glomerata. Soil pollution with DO increased the numbers of microorganisms and soil enzymes and decreased the value of the ecophysiological diversity index of microorganisms. Besides, it contributed to changes in the bacterial structure at all taxonomic levels. DO was found to increase the abundance of Proteobacteria and to decrease that of Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes and Firmicutes. In the non-polluted soil, the core microbiome was represented by Kaistobacter and Rhodoplanes, whereas in the DO-polluted soil, it was represented by Parvibaculum and Rhodococcus. In soil sown with Dactylis glomerata, gasoline fraction (C₆–C₁₂) degradation was higher by 17%; mineral oil (C₁₂–C₃₅), by 9%; benzene, by 31%; anthracene, by 12%; chrysene, by 38%; benzo(a)anthracene, by 19%; benzo(a)pyrene, by 17%; benzo(b)fluoranthene, by 15%; and benzo(k)fluoranthene, by 18% than in non-sowed soil. To conclude, Dactylis glomerata proved useful in degrading DO hydrocarbons and, therefore, may be recommended for the phytoremediation of soils polluted with petroleum-based products. It has been shown that the microbiological, biochemical and chemical tests are fast and sensitive in the diagnosis of soil contamination with petroleum products, and a combination of all these tests gives a reliable assessment of the state of soils.

Whole genome shotgun sequencing of POPs degrading bacterial community dwelling tannery effluents and petrol contaminated soil

The present study involved identification of genes which are present in the genome of native bacteria to make them effective tools for bioremediation of persistent organic pollutants (POPs). During this study, forty-one POPs (naphthalene, toluene and petrol) metabolizing bacteria were isolated from tannery effluents and petrol contaminated soil samples by successive enrichment culturing. The taxonomic diversity and gene repertoire conferring POPs degradation ability to the isolated bacterial community were studied through whole genome shotgun sequencing of DNA consortium. The DNA consortium contained equimolar concentration of DNA extracted from each bacterial isolate using organic method. To add a double layer of confirmation the established DNA consortium was subjected to 16S rRNA metagenome sequencing and whole genome shotgun sequencing analysis. Biodiversity analysis revealed that the consortium was composed of phyla Firmicutes (80 %), Proteobacteria (12 %) and Actinobacteria (5%). Genera found included Bacillus (45 %), Burkholderia (25 %), Brevibacillus (9%) and Geobacillus (4%). Functional profiling of consortium helped us to identify genes associated with degradation pathways of a variety of organic compounds including toluene, naphthalene, caprolactam, benzoate, aminobenzoate, xylene, 4-hydroxyphenyl acetic acid, biphenyl, anthracene, aminobenzoate, chlorocyclohexane, chlorobenzene, n-phenylalkanoic acid, phenylpropanoid, salicylate, gentisate, central meta cleavage of aromatic compounds, cinnamic acid, catechol and procatechuate branch of β-ketoadipate pathway, phenyl-acetyl CoA and homogentisate catabolic pathway. The information thus generated has ensured not only biodegradation potential but also revealed many possible future applications of the isolated bacteria.

Use of hydrocarbons sludge as a substrate for the production of biosurfactants by Pseudomonas aeruginosa ATCC 27853

The purpose of this study was to elucidate the capacity of a Pseudomonas aeruginosa strain to metabolize hydrocarbons sludge in the production of biosurfactants to fight against environmental threats. The performance of the treatment consisted in monitoring the inductive metabolism of the strain during 48 h at a temperature of 37 °C which constitutes an opportunity of treatment of various hydrocarbons contained in crude oil and spilled in the ecosystem to prevent pollution and damage. The results showed that a treatment rate of 96,8% and an emulsification index of 71.8% were obtained corresponding to a phosphate buffer concentration of 30 mmol/L. The main role of the biosurfactants produced was to emulsify the medium and to absorb the oils contained in the hydrocarbons sludge. This allowed to stabilize hydrocarbon oils and favored the inductive metabolism of P. aeruginosa. Furthermore, physicochemical and Fourier transform infrared spectroscopy (FTIR) analysis showed that the produced biosurfactants were of rhamnolipid type. They showed promising surfactant properties, such as a strong reduction in the surface tension of water from 72 to 40.52 mN/m, a high reactivity in the culture medium at pH 7, a high osmotolerance up to 150 g/L of salt, and a critical micellar concentration of 21 mg/L.

Chloropicrin fumigation alters the soil phosphorus and the composition of the encoding alkaline phosphatase PhoD gene microbial community

The transformation of phosphorus (P) compounds in soil depends largely on soil microbial communities and is sensitive to agricultural practices. However, the effects of soil fumigation on soil P, and microbes involved in P transformation, are unknown. Our results showed that chloropicrin (CP) fumigation significantly increased the available-P, Leached-P and active-P fractionation (inorganic P extracted from H₂O, NaHCO₃ and NaOH) in Shangdong and Miyun soils in the early stages of culture, while soil alkaline phosphatase (ALP) activity and phoD gene abundance decreased significantly. Leached-P in fumigated soil was positively correlated with increased active-P fractionation, indicating that it was an important source of soil Leached-P after fumigation. The changes in P-fractionation, Leached-P and ALP after fumigation were also significantly correlated with the composition of the microbial communities. CP fumigation briefly stimulated an increase in the abundance and diversity of phoD-harboring microbial communities and promoted the mineralization process of soil P. PICRUSt metagenomic analysis showed an increase in the relative abundance of microorganisms with involved in carbohydrate/lipid transport and metabolism functions after fumigation. These results suggest CP fumigation altered soil P transformation and phoD-harboring microbes that might lead to an increased risk of P enrichment in waterways.

Isolation and Characterization of Biosurfactant-Producing Bacteria From Oil Well Batteries With Antimicrobial Activities Against Food-Borne and Plant Pathogens

Microbial biosurfactants, produced by fungi, yeast, and bacteria, are surface-active compounds with emulsifying properties that have a number of known activities, including the solubilization of microbial biofilms. In an on-going survey to uncover new or enhanced antimicrobial metabolite-producing microbes from harsh environments, such as oil-rich niches, 123 bacterial strains were isolated from three oil batteries in the region of Chauvin, Alberta, and characterized by 16S rRNA gene sequencing. Based on their nucleotide sequences, the strains are associated with 3 phyla (Actinobacteria, Proteobacteria and Firmicutes), as well as 17 other discrete genera that shared high homology with known sequences, with the majority of these strains identified to the species level. The most prevalent strains associated with the three oil wells belonged to the Bacillus genus. Thirty-four of the 123 strains were identified as biosurfactant-producers, among which Bacillus methylotrophicus strain OB9 exhibited the highest biosurfactant activity based on multiple screening methods and a comparative analysis with the commercially available biosurfactant, Tween 20. B. methylotrophicus OB9 was selected for further antimicrobial analysis and addition of live cultures of B. methylotrophicus OB9 (or partially purified biosurfactant fractions thereof) were highly effective on biofilm disruption in agar diffusion assays against several Gram-negative food-borne bacteria and plant pathogens. Upon co-culturing with B. methylotrophicus OB9, the number of either Salmonella enterica subsp. enterica Newport SL1 or Xanthomonas campestris B07.007 cells significantly decreased after 6 h and were not retrieved from co-cultures following 12 h exposure. These results also translated to studies on plants, where bacterized tomato seedlings with OB9 significantly protected the tomato leaves from Salmonella enterica Newport SL1 contamination, as evidenced by a 40% reduction of log10 CFU of Salmonella/mg leaf tissue compared to non-bacterized tomato leaves. When B. methylotrophicus 0B9 was used for bacterized lettuce, the growth of X. campestris B07.007, the causal agent of bacterial leaf spot of lettuce, was completely inhibited. While limited, these studies are noteworthy as they demonstrate the inhibition spectrum of B. methylotrophicus 0B9 against both human and plant pathogens; thereby making this bacterium attractive for agricultural and food safety applications in a climate where microbial-biofilm persistence is an increasing problem.

Microbial diversity changes and enrichment of potential petroleum hydrocarbon degraders in crude oil-, diesel-, and gasoline-contaminated soil

This study investigated the impacts of crude oil, diesel, and gasoline on the diversity of indigenous microbial communities as well as culturable microorganisms in the studied soil. Oil contamination led to shifts in the diversity of the soil's microbial communities, regardless of the contaminant applied. Unpolluted soils were more diverse and evenly distributed than contaminated samples. The domain Bacteria accounted for 65.15% of the whole microbial community. The bacterial phylum Proteobacteria dominated in all samples, followed by Actinobacteria and Acidobacteria. Pseudomonas with 28.15% of reads dominated in Proteobacteria, while Rhodococcus (3.07%) dominated in Actinobacteria, and Blastocatella (2.53%) dominated in Acidobacteria. The dominant fungal phyla across all samples were Ascomycota dominated by Penicillium (50.48% of sequences), and Zygomycota dominated by Mortierella (16.87%). Sequences similar to the archaeal phyla, Euryarchaeota and Thaumarchaeota, were also detected. The number of culturable microorganisms increased following the contamination and was higher in contaminated samples than in clean samples. Oil contamination also resulted in the enrichment of oil-degrading strains. Two bacteria, Serratia marcescens strain PL and Raoultella ornithinolytica PS, which were isolated from crude oil-contaminated soil, exhibited strong crude oil degradation ability. Strain PL was the most efficient strain and degraded 75.10% of crude oil, while strain PL degraded 65.48%, after 20 days of incubation. However, the mixed culture of the two strains was more effective than single strain and could achieve up to 96.83% of crude oil degradation, with a complete abatement of straight-chain hydrocarbons (from C12 to C25), and more than 91% removal of highly branched hydrocarbons, phytane and pristane, which are known to be more recalcitrant to biodegradation. Strains PS and PL are two newly isolated crude oil degraders that are not among the most prominent crude oil-degrading strains referenced in the literature. Therefore, their high degradation capacity makes them perfect candidates for the bioremediation of petroleum hydrocarbon contaminated environments.

The applicability of gene sequencing and MALDI-TOF to identify less common gram-negative rods (Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium) from environmental isolates

Our aim was to identify less common non-fermenting gram-negative rods during the bioremediation process. Five genera were found: Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium, for a total of 15 isolates. Therefore, we evaluated the applicability of four methods currently available for bacteria identification: (1) conventional biochemical methods, (2) the VITEK^®-2 system, (3) MALDI-TOF mass spectrometry and (4) 16S rRNA gene sequencing. The biochemical methods and the VITEK^®-2 system were reliable only for the Sphingobacterium isolate and solely at the genus level. Both MALDI-TOF mass spectrometry platforms (Bruker and VITEK^® MS) did not achieve reliable identification results for any of these genera. 16S rRNA gene sequencing identified eight isolates to the species level but not to the subspecies level, when applicable. The remaining seven isolates were reliably identified through 16S rRNA gene sequencing to the genus level only. Our findings suggest that the detection and identification of less common genera (and species) that appeared at certain moments during the bioremediation process can be a challenge to microbiologists considering the most used techniques. In addition, more studies are required to confirm our results.

Diversity and degradative capabilities of bacteria and fungi isolated from oil-contaminated and hydrocarbon-polluted soils in Kazakhstan

Bacteria and fungi were isolated from eight different soil samples from different regions in Kazakhstan contaminated with oil or salt or aromatic compounds. For the isolation of the organisms, we used, on the one hand, typical hydrocarbons such as the well utilizable aliphatic alkane tetradecane, the hardly degradable multiple-branched alkane pristane, and the biaromatic compound biphenyl as enrichment substrates. On the other hand, we also used oxygenated derivatives of alicyclic and monoaromatic hydrocarbons, such as cyclohexanone and p-tert-amylphenol, which are known as problematic pollutants. Seventy-nine bacterial and fungal strains were isolated, and 32 of them that were clearly able to metabolize some of these substrates, as tested by HPLC-UV/Vis and GC-MS analyses, were characterized taxonomically by DNA sequencing. Sixty-two percent of the 32 isolated strains from 14 different genera belong to well-described hydrocarbon degraders like some Rhodococci as well as Acinetobacter, Pseudomonas, Fusarium, Candida, and Yarrowia species. However, species of the bacterial genus Curtobacterium, the yeast genera Lodderomyces and Pseudozyma, as well as the filamentous fungal genera Purpureocillium and Sarocladium, which have rarely been described as hydrocarbon degrading, were isolated and shown to be efficient tetradecane degraders, mostly via monoterminal oxidation. Pristane was exclusively degraded by Rhodococcus isolates. Candida parapsilosis, Fusarium oxysporum, Fusarium solani, and Rhodotorula mucilaginosa degraded cyclohexanone, and in doing so accumulate ε-caprolactone or hexanedioic acid as metabolites. Biphenyl was transformed by Pseudomonas/Stenotrophomonas isolates. When p-tert-amylphenol was used as growth substrate, none of the isolated strains were able to use it.

Identification and characterization of PAH-degrading endophytes isolated from plants growing around a sludge dam

This study involved the isolation of bacteria endophytes with PAH-degrading ability from plants growing around a sludge dam. A total of 19 distinct isolates that were morphologically identified were isolated from 4 species of plant with a follow-up confirmatory identification using the molecular technique. Polymerase chain reaction (PCR) of the 16S rRNA gene with specific primers (16S-27F PCR and 16S-1491R PCR) was carried out. The sequence of the PCR products was carried out, compared with similar nucleotides available in GenBank. Results of the phylogenetic analysis of the isolates indicated their belonging to 4 different clades including Proteobacteria, Actinobacteria, Cyanobacteria, and Firmicutes. These were related to the genera Bacillus, Pseudomonas, Terribacillus, Virgibacillus, Stenotrophomonas, Paenibacillus, Brevibacterium, Geobacillus, Acinetobacter. From the result, Pseudomonas demonstrated a high incidence in the plants sampled. The in-vitro degradation study and the presence of dioxygenase genes indicated that these lists of endophytes are able to use the list of PAHs tested as their source of food and energy leading to their breakdown. This means that the bacterial endophytes contributed to the remediation of petroleum hydrocarbons in planta, a situation that may have been phytotoxic to plant alone. Therefore, these bacteria endophytes could be potential organisms for enhanced phytoremediation of PAHs.

Molecular and Microbiological Insights on the Enrichment Procedures for the Isolation of Petroleum Degrading Bacteria and Fungi

Autochthonous bioaugmentation, by exploiting the indigenous microorganisms of the contaminated environment to be treated, can represent a successful bioremediation strategy. In this perspective, we have assessed by molecular methods the evolution of bacterial and fungal communities during the selective enrichment on different pollutants of a soil strongly polluted by mixtures of aliphatic and polycyclic hydrocarbons. Three consecutive enrichments were carried out on soil samples from different soil depths (0-1, 1-2, 2-3 m), and analyzed at each step by means of high-throughput sequencing of bacterial and fungal amplicons biomarkers. At the end of the enrichments, bacterial and fungal contaminants degrading strains were isolated and identified in order to (i) compare the composition of enriched communities by culture-dependent and culture-independent molecular methods and to (ii) obtain a collection of hydrocarbon degrading microorganisms potentially exploitable for soil bioremediation. Molecular results highlighted that for both bacteria and fungi the pollutant had a partial shaping effect on the enriched communities, with paraffin creating distinct enriched bacterial community from oil, and polycyclic aromatic hydrocarbons generally overlapping; interestingly neither the soil depth or the enrichment step had significant effects on the composition of the final enriched communities. Molecular analyses well-agreed with culture-dependent analyses in terms of most abundant microbial genera. A total of 95 bacterial and 94 fungal strains were isolated after selective enrichment procedure on different pollutants. On the whole, isolated bacteria where manly ascribed to Pseudomonas genus followed by Sphingobacterium, Bacillus, Stenothrophomonas, Achromobacter, and Serratia. As for fungi, Fusarium was the most abundant genus followed by Trichoderma and Aspergillus. The species comprising more isolates, such as Pseudomonas putida, Achromobacter xylosoxidans and Ochromobactrum anthropi for bacteria, Fusarium oxysporum and Fusarium solani for fungi, were also the dominant OTUs assessed in Illumina.

Comparative metagenomics reveals different hydrocarbon degradative abilities from enriched oil-drilling waste

The oil drilling process generates large volumes of waste with inadequate treatments. Here, oil drilling waste (ODW) microbial communities demonstrate different hydrocarbon degradative abilities when exposed to distinct nutrient enrichments as revealed by comparative metagenomics. The ODW was enriched in Luria Broth (LBE) and Potato Dextrose (PDE) media to examine the structure and functional variations of microbial consortia. Two metagenomes were sequenced on Ion Torrent platform and analyzed using MG-RAST. The STAMP software was used to analyze statistically significant differences amongst different attributes of metagenomes. The microbial diversity presented in the different enrichments was distinct and heterogeneous. The metabolic pathways and enzymes were mainly related to the aerobic hydrocarbons degradation. Moreover, our results showed efficient biodegradation after 15 days of treatment for aliphatic hydrocarbons (C8-C33) and polycyclic aromatic hydrocarbons (PAHs), with a total of about 50.5% and 46.4% for LBE and 44.6% and 37.9% for PDE, respectively. The results obtained suggest the idea that the enzymatic apparatus have the potential to degrade petroleum compounds.

Coliform Bacteria for Bioremediation of Waste Hydrocarbons

Raw, domestic sewage of Kuwait City contained about 106 ml-1 colony forming units of Enterobacter hormaechei subsp. oharae (56.6%), Klebsiella spp. (36%), and Escherichia coli (7.4%), as characterized by their 16S rRNA-gene sequences. The isolated coliforms grew successfully on a mineral medium with crude oil vapor as a sole source of carbon and energy. Those strains also grew, albeit to different degrees, on individual n-alkanes with carbon chains between C9 and C36 and on the individual aromatic hydrocarbons, toluene, naphthalene, phenanthrene, and biphenyl as sole sources of carbon and energy. These results imply that coliforms, like other hydrocarbonoclastic microorganisms, oxidize hydrocarbons to the corresponding alcohols and then to aldehydes and fatty acids which are biodegraded by β-oxidation to acetyl CoA. The latter is a well-known key intermediate in cell material and energy production. E. coli cells grown in the presence of n-hexadecane (but not in its absence) exhibited typical intracellular hydrocarbon inclusions, as revealed by transmission electron microscopy. Raw sewage samples amended with crude oil, n-hexadecane, or phenanthrene lost these hydrocarbons gradually with time. Meanwhile, the numbers of total and individual coliforms, particularly Enterobacter, increased. It was concluded that coliform bacteria in domestic sewage, probably in other environmental materials too, are effective hydrocarbon-biodegrading microorganisms.

Isolation and Characterization of Phenanthrene Degrading Bacteria from Diesel Fuel-Contaminated Antarctic Soils

Antarctica is an attractive target for human exploration and scientific investigation, however the negative effects of human activity on this continent are long lasting and can have serious consequences on the native ecosystem. Various areas of Antarctica have been contaminated with diesel fuel, which contains harmful compounds such as heavy metals and polycyclic aromatic hydrocarbons (PAH). Bioremediation of PAHs by the activity of microorganisms is an ecological, economical, and safe decontamination approach. Since the introduction of foreign organisms into the Antarctica is prohibited, it is key to discover native bacteria that can be used for diesel bioremediation. By following the degradation of the PAH phenanthrene, we isolated 53 PAH metabolizing bacteria from diesel contaminated Antarctic soil samples, with three of these isolates exhibiting a high phenanthrene degrading capacity. In particular, the Sphingobium xenophagum D43FB isolate showed the highest phenanthrene degradation ability, generating up to 95% degradation of initial phenanthrene. D43FB can also degrade phenanthrene in the presence of its usual co-pollutant, the heavy metal cadmium, and showed the ability to grow using diesel-fuel as a sole carbon source. Microtiter plate assays and SEM analysis revealed that S. xenophagum D43FB exhibits the ability to form biofilms and can directly adhere to phenanthrene crystals. Genome sequencing analysis also revealed the presence of several genes involved in PAH degradation and heavy metal resistance in the D43FB genome. Altogether, these results demonstrate that S. xenophagum D43FB shows promising potential for its application in the bioremediation of diesel fuel contaminated-Antarctic ecosystems.