Aromatic Hydrocarbon-degrading Bacteria Research Articles

Acidovorax benzenivorans sp. nov., a novel aromatic hydrocarbon-degrading bacterium isolated from a xylene-degrading enrichment culture.

A Gram-stain-negative strain, designated as D2M1T was isolated from xylene-degrading enrichment culture and characterized using a polyphasic approach to determine its taxonomic position. The 16S rRNA gene sequence analysis revealed that strain D2M1T belongs to the genus Acidovorax, with the highest 16S rRNA gene similarity to Acidovorax delafieldii DSM 64T (99.93 %), followed by Acidovorax radicis DSM 23535T (98.77 %) and Acidovorax kalamii MTCC 12652T (98.76 %). The draft genome sequence of strain D2M1T is 5.49 Mb long, and the G+C content of the genome is 64.2 mol%. Orthologous average nucleotide identity and digital DNA-DNA hybridization relatedness values between strain D2M1T and its closest relatives were below the threshold values for species demarcation confirming that strain D2M1T is distinctly separated from its closest relatives. The whole genome analysis of the strain revealed a phenol degradation gene cluster, encoding a multicomponent phenol hydroxylase (mPH) together with a complete meta-cleavage pathway including an I.2.C-type catechol 2,3-dioxygenase (C23O) gene. The strain was able to degrade benzene and ethylbenzene as sole sources of carbon and energy under aerobic and microaerobic conditions. Cells were facultatively aerobic rods and motile with a single polar flagellum. The predominant fatty acids (>10 % of the total) of strain D2M1T were summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c). The major ubiquinone of strain D2M1T was Q8, while the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on polyphasic data, it is concluded that strain D2M1T represents a novel species of the genus Acidovorax, for which the name of Acidovorax benzenivorans sp. nov. is proposed. The type strain of the species is strain D2M1T (=DSM 115238T=NCAIM B.02679T).

Responses of a polycyclic aromatic hydrocarbon-degrading bacterium, Paraburkholderia fungorum JT-M8, to Cd (II) under P-limited oligotrophic conditions

For the bioremediation of mixed-contamination sites, studies on polycyclic aromatic hydrocarbon (PAH) degradation or Cd (II) tolerance in bacteria are commonly implemented in nutrient-rich media. In contrast, in the field, inocula usually encounter harsh oligotrophic habitats. In this study, the environmental strain Paraburkholderia fungorum JT-M8 was used to explore the overlooked Cd (II) defense mechanism during PAH dissipation under P-limited oligotrophic condition. The results showed that the growth and PAH degradation ability of JT-M8 under Cd (II) stress were correlated with phosphate contents and exhibited self-regulating properties. Phosphates mainly affected the Cd (II) content in solution, while the cellular distribution of Cd (II) depended on Cd (II) levels; Cd (II) was mainly located in the cytoplasm when exposed to less Cd (II), and vice versa. The unique Cd (II) detoxification pathways could be classified into three aspects: (i) Cd (II) ionic equilibrium and dose–response effects regulated by environmental matrices (phosphate contents); (ii) bacterial physiological self-regulation, e.g., cell surface-binding, protein secretion and active transport systems; and (iii) specific adaptive responses (flagellum aggregation). This study emphasizes the importance of considering culture conditions when assessing the metal tolerance and provides new insight into the bacterial detoxification process of complex PAH-Cd (II) pollutants.

Nitrogen transfer and cross-feeding between Azotobacter chroococcum and Paracoccus aminovorans promotes pyrene degradation

Nitrogen is a limiting nutrient for degraders function in hydrocarbon-contaminated environments. Biological nitrogen fixation by diazotrophs is a natural solution for supplying bioavailable nitrogen. Here, we determined whether the diazotroph Azotobacter chroococcum HN can provide nitrogen to the polycyclic aromatic hydrocarbon-degrading bacterium Paracoccus aminovorans HPD-2 and further explored the synergistic interactions that facilitate pyrene degradation in nitrogen-deprived environments. We found that A. chroococcum HN and P. aminovorans HPD-2 grew and degraded pyrene more quickly in co-culture than in monoculture. Surface-enhanced Raman spectroscopy combined with 15N stable isotope probing (SERS − 15N SIP) demonstrated that A. chroococcum HN provided nitrogen to P. aminovorans HPD-2. Metabolite analysis and feeding experiments confirmed that cross-feeding occurred between A. chroococcum HN and P. aminovorans HPD-2 during pyrene degradation. Transcriptomic and metabolomic analyses further revealed that co-culture significantly upregulated key pathways such as nitrogen fixation, aromatic compound degradation, protein export, and the TCA cycle in A. chroococcum HN and quorum sensing, aromatic compound degradation and ABC transporters in P. aminovorans HPD-2. Phenotypic and fluorescence in situ hybridization (FISH) assays demonstrated that A. chroococcum HN produced large amounts of biofilm and was located at the bottom of the biofilm in co-culture, whereas P. aminovorans HPD-2 attached to the surface layer and formed a bridge-like structure with A. chroococcum HN. This study demonstrates that distinct syntrophic interactions occur between A. chroococcum HN and P. aminovorans HPD-2 and provides support for their combined use in organic pollutant degradation in nitrogen-deprived environments.

A highly effective polycyclic aromatic hydrocarbon-degrading bacterium, Paracoccus sp. HPD-2, shows opposite remediation potential in two soil types

Bioaugmentation is an efficient and eco-friendly strategy for the bioremediation of polycyclic aromatic hydrocarbons (PAHs). Since the degrading abilities of soils can greatly alter the abilities of PAH-degrading bacteria, illustrating the potential and mechanism of highly efficient degrading bacteria in different soil environments is of great importance for bioremediation. A PAH-degrading bacterium, Paracoccus aminovorans HPD-2, and two soil types, red and paddy soils, with distinct PAH-degrading abilities, were selected for this study. A soil microcosm experiment was performed by adding pyrene (PYR) and benzo[a]pyrene (B[a]P). Illumina sequencing was used to examine bacterial community structure. The results showed that inoculation with HPD-2 significantly elevated PYR and B[a]P degradation rates by 44.7% and 30.7%, respectively, in the red soil, while it only improved the degradation rates by 1.9% and 11%, respectively, in the paddy soil. To investigate the underlying mechanism, the fate of strain HPD-2 and the response of the indigenous bacterial communities were determined. Strain HPD-2 occupied certain niches in both soils, and the addition of the bacterium changed the native community structure more noticeably in the red soil than in the paddy soil. The addition of PAHs and strain HPD-2 significantly changed the abundances of 7 phyla among the 15 detected phyla in the red soil. In the paddy soil, 5 of the 12 dominant phyla were significantly affected by PAHs and the inoculation of HPD-2, while 6 new phyla were detected in the low-abundance phyla (< 0.1%). The abundances of Massilia, Burkholderia , and Rhodococcus genera with PAH degradation efficiency were significantly increased by the inoculation of HPD-2 in the red soil during 42 d of incubation. Meanwhile, in the paddy soil, the most dominant effective genus, Massilia , was reduced by HPD-2 inoculation. This research revealed the remediation ability and inherent mechanism of the highly effective PAH-degrading strain HPD-2 in two different soil types, which would provide a theoretical basis for the application of degrading bacteria in different soils.

Pinisolibacter aquiterrae sp. nov., a novel aromatic hydrocarbon-degrading bacterium isolated from benzene-, and xylene-degrading enrichment cultures, and emended description of the genus Pinisolibacter.

Two Gram-reaction-negative strains, designated as B13T and MA2-2, were isolated from two different aromatic hydrocarbon-degrading enrichment cultures and characterized using a polyphasic approach to determine their taxonomic position. The two strains had identical 16S rRNA gene sequences and were most closely related to Pinisolibacter ravus E9T (97.36 %) and Siculibacillus lacustris SA-279T (96.33 %). Cells were facultatively aerobic rods and motile with a single polar flagellum. The strains were able to degrade ethylbenzene as sole source of carbon and energy. The assembled genome of strain B13T had a total length of 4.91 Mb and the DNA G+C content was 68.8 mol%. The predominant fatty acids (>5 % of the total) of strains B13T and MA2-2 were C18 : 1 ω7c/C18 : 1 ω6c, C16 : 1 ω7c/C16 : 1 ω6c and C16 : 0. The major ubiquinone of strain B13T was Q10, while the major polar lipids were phosphatidyl-N-methylethanolamine, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and a phospholipid. Based on phenotypic characteristics and phylogenetic data, it is concluded that strains B13T and MA2-2 are members of the genus Pinisolibacter and represent a novel species for which the name Pinisolibacter aquiterrae sp. nov. is proposed. The type strain of the species is strain B13T (=LMG 32346T=NCAIM B.02665T).

Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants

BackgroundBiosurfactants are naturally derived products that play a similar role to synthetic dispersants in oil spill response but are easily biodegradable and less toxic. Using a combination of analytical chemistry, 16S rRNA amplicon sequencing and simulation-based approaches, this study investigated the microbial community dynamics, ecological drivers, functional diversity and robustness, and oil biodegradation potential of a northeast Atlantic marine microbial community to crude oil when exposed to rhamnolipid or synthetic dispersant Finasol OSR52.ResultsPsychrophilic Colwellia and Oleispira dominated the community in both the rhamnolipid and Finasol OSR52 treatments initially but later community structure across treatments diverged significantly: Rhodobacteraceae and Vibrio dominated the Finasol-amended treatment, whereas Colwellia, Oleispira, and later Cycloclasticus and Alcanivorax, dominated the rhamnolipid-amended treatment. Key aromatic hydrocarbon-degrading bacteria, like Cycloclasticus, was not observed in the Finasol treatment but it was abundant in the oil-only and rhamnolipid-amended treatments. Overall, Finasol had a significant negative impact on the community diversity, weakened the taxa-functional robustness of the community, and caused a stronger environmental filtering, more so than oil-only and rhamnolipid-amended oil treatments. Rhamnolipid-amended and oil-only treatments had the highest functional diversity, however, the overall oil biodegradation was greater in the Finasol treatment, but aromatic biodegradation was highest in the rhamnolipid treatment.ConclusionOverall, the natural marine microbial community in the northeast Atlantic responded differently to crude oil dispersed with either synthetic or biogenic surfactants over time, but oil degradation was more enhanced by the synthetic dispersant. Collectively, our results advance the understanding of how rhamnolipid biosurfactants and synthetic dispersant Finasol affect the natural marine microbial community in the FSC, supporting their potential application in oil spills.43fSDwbdHYX3Ei4X1BHK1YVideo abstract

Functionalization of the model asphaltene 1-dodecylnaphthalene by Pseudomonas aeruginosa KK6 through subterminal metabolism

Asphaltenic compounds in heavy oils may be biologically functionalized in the contexts of oil upgrading and in mitigating contamination however there are knowledge gaps in regard to the mechanisms of asphaltene functionalization by microorganisms. Due to the challenges of studying asphaltene functionalization, model asphaltene compounds comprised of polyaromatic centers and long alkyl chains may be utilized. In this work, a soil bacterium identified as Pseudomonas aeruginosa KK6 was characterized and it was found to extensively biotransform the water insoluble polycyclic n-alkylaromatic model asphaltene, 1-dodecylnaphthalene (1-DDN). Gas chromatography was utilized to quantify 1-DDN transformation and liquid chromatography with UV detection coupled to electrospray ionization tandem mass spectrometry (LC-UV/ESI-MS/MS) was used to analyze transformation products. An unusual transformation product profile occurred that showed that varying alkyl chain length compounds that differed by one methylene unit each were detected attached to their polycyclic aromatic chromophores. CID product ion scan analyses revealed that 1-DDN was transformed into oxidized, alkyl chain-shortened, reduced molecular weight 1-naphthyl-alkanoic acids and 1-naphthyl-alkanals and results interpretation supported that these compounds were produced through subterminal oxidation mechanisms by strain KK6. Based upon the results, biotransformation pathways that described the biological functionalization of a model asphaltene compound were constructed. On its own or in conjunction with polycyclic aromatic hydrocarbon-degrading bacteria, this strain may be applied to upgrading heavy oil.

Co-treatment of an oily sludge and aged contaminated soil: permanganate oxidation followed by bioremediation

The bioremediation of an oily sludge (321 ± 30 mg of polycyclic aromatic hydrocarbons/kgDRY SLUDGE and 13420 ± 1300 mg of aliphatic hydrocarbons/kgDRY SLUDGE) by mixture with contaminated soil (23 ± 2 mg of polycyclic aromatic hydrocarbons/kgDRY SOIL and 98 ± 10 mg of aliphatic hydrocarbons/kgDRY SOIL) was studied. Furthermore, the effect of oxidative pretreatments (persulfate and permanganate) on the performance of the global process was examined.The treatments reached contamination levels lower than the original residues, indicating the presence of synergic processes between a highly contaminated sludge and soil with a selected hydrocarbon-degrading community.Pretreatment with permanganate significantly improved biodegradation, possibly due to the increase in bioavailability and biodegradability of petroleum hydrocarbons. Two months of incubation was enough to reach the complete elimination of polycyclic aromatic hydrocarbons and 92% elimination of aliphatic hydrocarbons. Monitoring using five parameters (concentration of total petroleum hydrocarbons, total cultivable heterotrophic bacteria count, lipase and dehydrogenase activities, and polycyclic aromatic hydrocarbon-degrading bacteria count) as an approach for a preliminary scanning of the effectiveness of a treatment is proposed based on principal components analysis.

Isolasi Bakteri Pendegradasi Minyak Mentah dan Polisiklik Aromatik Hidrokarbon dari Sedimen Mangrove Bintan

&lt;strong&gt;Isolation of Crude Oil and Polycyclic Aromatic Hydrocarbon-Degrading Bacteria from Mangrove Sediments in Bintan.&lt;/strong&gt; Bintan is known for its extensive mangrove areas, but it is prone to pollution from oil spills due to it is close to the international shipping lane. Indigenous bacteria plays important roles in bioremediation of oil spills in the natural environment. This research aims to explore indigenous bacteria from Bintan’s mangrove sediments which may have ability to degrade crude oil and polycyclic aromatic hydrocarbon (PAH). The mangrove sediment samples were taken in March 2018 from the sediments near four different mangrove plant species, i.e. &lt;em&gt;Rhizophora apiculata, Xylocarpus granatum, Ceriops tagal &lt;/em&gt;and &lt;em&gt;Lumnitzera littorea&lt;/em&gt;. Isolation of oil degrading bacteria was carried out using enrichment media supplemented with crude oil ALCO. A total of 45 strains of oil degrading bacteria were successfully isolated from the sediment samples. By using sublimation method, 13 bacterial isolates showed the ability to degrade various PAHs, including phenanthrene, acenaphthene, dibenzothiophene and fluorene. Sequencing analysis of 16s rRNA genes confirmed that the 13 isolated bacteria belong to the genera &lt;em&gt;Rhodococcus, Bacillus&lt;/em&gt;, &lt;em&gt;Sphingopyxis&lt;/em&gt;, &lt;em&gt;Rhizobium&lt;/em&gt;, &lt;em&gt;Mycobacterium&lt;/em&gt;, and &lt;em&gt;Gordonia&lt;/em&gt;

Colonization of polycyclic aromatic hydrocarbon-degrading bacteria on roots reduces the risk of PAH contamination in vegetables

This is a primary investigation on the mitigation of polycyclic aromatic hydrocarbon (phenanthrene as a model PAH) contamination in vegetables including water spinach (Ipomoea aquatica Forsk), pakchoi (Brassica campestris) and Chinese cabbage (Brassica chinensis) using a gfp-labeled PAH-degrading bacterium (RS1-gfp). Effective root colonization led to dense RS1-gfp populations inhabiting the rhizosphere and endosphere of the vegetables, which subsequently led to a reduction in phenanthrene accumulation and risk in vegetables. When compared with the controls without RS1-gfp, the amount of phenanthrene accumulation due to strain RS1-gfp colonization reduced by up to ~93.7% in roots and ~75.2% in shoots of vegetables, respectively. The estimated incremental lifetime cancer risk (ILCR) for adults due to phenanthrene in vegetables was reduced by 24.6%–48% through RS1-gfp inoculation. The proposed method was developed to circumvent the risk of phenanthrene contamination in vegetables by inoculating PAH-degrading bacteria. The findings provide an in-depth understanding of PAH detoxification in agricultural plants grown on contaminated sites by exploiting bacteria like RS1-gfp, which portray both rhizo- and endophytic lifestyles.

Genomic and Physiological Traits of the Marine Bacterium Alcaligenes aquatilis QD168 Isolated From Quintero Bay, Central Chile, Reveal a Robust Adaptive Response to Environmental Stressors.

Alcaligenes aquatilis QD168 is a marine, aromatic hydrocarbon-degrading bacterium, isolated from an oil-polluted sediment of Quintero Bay, an industrial-coastal zone that has been chronically impacted by diverse pollutants. The aims of this study were to characterize the phylogenomic positions of Alcaligenes spp. and to characterize the genetic determinants and the physiological response of A. aquatilis QD168 to model environmental stressors (benzene, oxidizing agents, and salt). Phylogenomic analyses, using 35 housekeeping genes, clustered A. aquatilis QD168 with four other strains of Alcaligenes spp. (A. aquatilis BU33N, A. faecalis JQ135, A. faecalis UBA3227, and A. faecalis UBA7629). Genomic sequence analyses of A. aquatilis QD168 with 25 Alcaligenes spp., using ANIb, indicated that A. aquatilis BU33N is the closest related strain, with 96.8% ANIb similarity. Strain QD168 harbors 95 genes encoding proteins of seven central catabolic pathways, as well as sixteen peripheral catabolic pathways/reactions for aromatic compounds. A. aquatilis QD168 was able to grow on 3-hydroxybenzoate, 4-hydroxybenzoate, benzoate, benzene, 3-hydroxycinnamate, cinnamate, anthranilate, benzamide, 4-aminobenzoate, nicotinate, toluene, biphenyl and tryptophan, as sole carbon or nitrogen source. Benzene degradation was further analyzed by growth, metabolite identification and gene expression analyses. Benzene strongly induced the expression of the genes encoding phenol hydroxylase (dmpP) and catechol 1,2-dioxygenase (catA). Additionally, 30 genes encoding transcriptional regulators, scavenging enzymes, oxidative damage repair systems and isozymes involved in oxidative stress response were identified. Oxidative stress response of strain QD168 to hydrogen peroxide and paraquat was characterized, demonstrating that A. aquatilis QD168 is notably more resistant to paraquat than to H2O2. Genetic determinants (47 genes) for osmoprotective responses were identified, correlating with observed high halotolerance by strain QD168. The physiological adaptation of A. aquatilis QD168 to environmental stressors such as pollutants, oxidative stress and salinity may be exploited for bioremediation of oil-polluted saline sites.

Cave Drip Water-Related Samples as a Natural Environment for Aromatic Hydrocarbon-Degrading Bacteria.

Restricted contact with the external environment has allowed the development of microbial communities adapted to the oligotrophy of caves. However, nutrients can be transported to caves by drip water and affect the microbial communities inside the cave. To evaluate the influence of aromatic compounds carried by drip water on the microbial community, two limestone caves were selected in Brazil. Drip-water-saturated and unsaturated sediment, and dripping water itself, were collected from each cave and bacterial 16S rDNA amplicon sequencing and denaturing gradient gel electrophoresis (DGGE) of naphthalene dioxygenase (ndo) genes were performed. Energy-dispersive X-ray spectroscopy (EDX) and atomic absorption spectroscopy (AAS) were performed to evaluate inorganic nutrients, and GC was performed to estimate aromatic compounds in the samples. The high frequency of Sphingomonadaceae in drip water samples indicates the presence of aromatic hydrocarbon-degrading bacteria. This finding was consistent with the detection of naphthalene and acenaphthene and the presence of ndo genes in drip-water-related samples. The aromatic compounds, aromatic hydrocarbon-degrading bacteria and 16S rDNA sequencing indicate that aromatic compounds may be one of the sources of energy and carbon to the system and the drip-water-associated bacterial community contains several potentially aromatic hydrocarbon-degrading bacteria. To the best of our knowledge, this is the first work to present compelling evidence for the presence of aromatic hydrocarbon-degrading bacteria in cave drip water.

Assembling a genome for novel nitrogen-fixing bacteria with capabilities for utilization of aromatic hydrocarbons

Metagenome from refinery wastewater treatment plant running under nitrogen stress was analyzed for mining of novel aromatic hydrocarbon-degrading bacteria. The sequence data were assembled using metaspade followed by binning using the Metabat tool to assemble genome; where coverage and depth were calculated using bowtie and samtools. The analysis picked a novel genome belonging to family Bradyrhizobiaceae, identified based on 16S rDNA gene which was supported by CheckM and Kraken analysis. Using RAST, the assembled genome showed the capabilities for nitrogen fixation with the utilization of multiple hydrocarbon substrates with 14 different types of oxygenases as mapped by Minpath. An additional genetic feature like genes for stress and resistance towards heavy metals and antibiotic suggested that the genome has gone through the rigorous process of adaptation. If such bacteria could be cultivated then it will open the broad window of bioremediation strategies under nitrogen stress environment.

Paraburkholderia aromaticivorans sp. nov., an aromatic hydrocarbon-degrading bacterium, isolated from gasoline-contaminated soil.

A Gram-stain-negative, facultatively aerobic, aromatic hydrocarbon-degrading bacterium, designated strain BN5T, was isolated from gasoline-contaminated soil. Cells were motile and slightly curved rods with a single flagellum showing catalase and oxidase activities. Growth was observed at 20-37 °C (optimum, 25-30 °C), pH 3-7 (optimum, pH 5-6) and 0-2 % NaCl (optimum, 0 %). Ubiquinone-8 was the predominant respiratory quinone. The major fatty acids were C16 : 0, cyclo-C19 : 0ω8c and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phosphoamino lipid, three unidentified amino lipids and eight unidentified lipids were the identified polar lipids. The DNA G+C content was 62.93 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BN5T formed a phylogenic lineage with members of the genus Paraburkholderia and showed the highest 16S rRNA gene sequence similarities to Paraburkholderia phytofirmans PsJNT (99.4 %), Paraburkholderia dipogonis DL7T (98.8 %) and Paraburkholderia insulsa PNG-AprilT (98.8 %). The average nucleotide identity and in silico DNA-DNA hybridization (DDH) values between strain BN5T and P. phytofirmans PsJNT were 88.5 and 36.5 %, respectively. The DDH values for strain BN5T with P. dipogonis LMG 28415T and P. insulsa DSM 28142T were 41.0±4.9 % (reciprocal, 33.0±4.3 %) and 47.1±6.6 % (reciprocal, 51.7±5.4 %), respectively. Based on its physiological, chemotaxonomic and phylogenetic features, we conclude that strain BN5T is a novel species of the genus Paraburkholderia, for which the name Paraburkholderia aromaticivorans sp. nov. is proposed. The type strain is BN5T (=KACC 19419T=JCM 32303T).

Comments on “Influence of thermally modified palygorskite on the viability of polycyclic aromatic hydrocarbon-degrading bacteria” by B. Biswas, B. Sarkar, and R. Naidy Applied Clay Science 134 (2016) 153–160, DOI 10.1016/j.clay.2016.07.003

Comments on “Influence of thermally modified palygorskite on the viability of polycyclic aromatic hydrocarbon-degrading bacteria” by B. Biswas, B. Sarkar, and R. Naidy Applied Clay Science 134 (2016) 153–160, DOI 10.1016/j.clay.2016.07.003

Isolation and characterization of polycyclic aromatic hydrocarbon-degrading bacteria with tolerance to hypoxic environments

ABSTRACTHypoxic conditions are considerably different from aerobic and anaerobic conditions, and they are widely distributed in natural environments. Many pollutants, including polycyclic aromatic hydrocarbons (PAHs), tend to accumulate in hypoxic environments. However, PAH biodegradation under hypoxic conditions is poorly understood compared with that under obligate aerobic and obligate anaerobic conditions. In the present study, PAH-degrading bacteria were enriched, and their biodegradation rates were tested using a hypoxic station with an 8% oxygen concentration. PAH-degrading bacteria collected from sediments in low-oxygen environments were enriched using phenanthrene (Phe) or pyrene (Pyr) as the sole carbon and energy source. Individual bacterial colonies showing the ability to degrade Phe or Pyr were isolated and identified by 16S rDNA gene sequencing. Morphological and physiological characterizations of the isolated bacterial colonies were performed. The isolated bacteria were observed by scanning electron microscopy (SEM) and were identified as Pseudomonas sp., Klebsiella sp., Bacillus sp., and Comamonas sp. Phylogenetic tree of the isolated PAH-degrading bacteria was also constructed. The biodegradation ability of these bacteria was tested at an initial Phe or Pyr concentration of 50 mg L−1. The biodegradation kinetics were best fit by a first-order rate model and presented regression coefficients (r2) that varied from 0.7728 to 0.9725 (P < 0.05). The half-lives of the PAHs varied from 2.99 to 3.65 d for Phe and increased to 60.3–82.5 d for Pyr. These half-lives were much shorter than those observed under anaerobic conditions but were similar to those observed under aerobic conditions.

Microbial Transformation of Multiwalled Carbon Nanotubes by Mycobacterium vanbaalenii PYR-1.

Carbonaceous nanomaterials are widely used in industry and consumer products, but concerns have been raised regarding their release into the environment and subsequent impacts on ecosystems and human health. Although many efforts have been devoted to understanding the environmental fate of carbonaceous nanomaterials, information about their microbial transformation is still rare. In this study, we found that within 1 month a polycyclic aromatic hydrocarbon-degrading bacterium, Mycobacterium vanbaalenii PYR-1, was able to degrade both pristine and carboxyl-functionalized multiwalled carbon nanotubes (p-MWCNT and c-MWCNT), as demonstrated by consistent results from high resolution transmission electron microscopy, Raman spectroscopy, and confocal Raman microspectroscopy. Statistical analysis of Raman spectra identified a significant increase in the density of disordered or amorphous carbon in p-MWCNT and c-MWCNT after biodegradation. Microbial respiration further suggested potential mineralization of MWCNTs within about 1 month. All of our analyses consistently showed higher degradation or mineralization of c-MWCNT compared to p-MWCNT. These results highlight the potential of using bacteria in engineered systems to remove residual carbonaceous nanomaterials and reduce risk of human exposure and environmental impact. Meanwhile, our finding suggests possible transformation of carbonaceous nanomaterials by polycyclic aromatic hydrocarbon-degrading bacteria in the natural environment, which should be accounted for in predicting the environmental fate of these emerging contaminants and in nanotechnology risk regulation.

Draft genome of Nocardia farcinica TRH1, a linear and polycyclic aromatic hydrocarbon-degrading bacterium isolated from the coast of Trindade Island, Brazil

Here, we report the draft genome sequence and annotation of Nocardia farcinica TRH1, a petroleum hydrocarbons degrading Actinobacteria isolated from the coastal water of Trindade Island, Brazil.

Influence of thermally modified palygorskite on the viability of polycyclic aromatic hydrocarbon-degrading bacteria

Thermal activation of palygorskite is considered as a simple and cost-effective method for modifying its structural and surface properties, which can be congenial for the adsorptive removal of environmental contaminants. However, for a more efficient removal of organic contaminants like polycyclic aromatic hydrocarbons (PAH), clay-microbial synergy combining both adsorption and biodegradation is an emerging strategy. In this study, we investigated the compatibility of heat treated palygorskite products (100–900°C) with a PAH-degrading soil bacterium Burkholderia sartisoli. The mineralogical and physico-chemical properties were characterised in detail, and the bacterial adhesion to the substrate and their growth were observed in relation to these properties. The major variation in the cation exchange capacity (CEC), surface area, water content and the elemental dissolution in the aqueous medium occurred in the palygorskite products heated at extreme temperature (700–900°C). These changes significantly influenced the bacterial growth and attachment. The maximum viability was imparted by the palygorskite product obtained at 400°C. Dissolution of Al from products heated above 500°C also posed inhibitory effect on bacterial growth in the aqueous media. This study provided valuable information about the mechanisms of bacterial viability as affected by modified clay minerals, which is important for developing a novel clay-modulated-bioremediation technology.

Erratum to: Identification of inducible proteins in the phenanthrene degrader Sphingobium chungbukense DJ77 by 2-dimensional electrophoresis and liquid chromatography/tandem mass spectrometry

Sphingomonas chungbukensis DJ77 is a novel aromatic hydrocarbon-degrading bacterium capable of growing on phenanthrene as its sole source of carbon and energy. In this study, the protein expression profiles of S. chungbukensis DJ77 grown in the presence of phenanthrene were investigated by using two-dimensional gel electrophoresis (2-DE). Among 1000 protein spots visualized by 2-DE, the four proteins (i.e. 4-oxalocrotonate decarboxylase, 2-hydroxy-6-oxo-phenylhexa-2,4-dienoate hydrolase, glutathione S-transferase, and 2,3-dihydroxybiphenyl 1,2-dioxygenase) showing the significant upregulation by phenanthrene were identified by reversed-phase liquid chromatography–tandem mass spectrometry. Evidently, these proteins were involved in the metabolism of aromatic hydrocarbons. This can explain why S. chungbukensis DJ77 shows a significantly higher rate of phenanthrene consumption during the degradation process. The present analysis of proteomic responses and the detailed analysis results will be quite helpful to better understand the global physiology of S. chungbukensis DJ77, as proteome databases for various aromatic hydrocarbon-degrading strains have already been established.