Biodegradation kinetics of select polycyclic aromatic hydrocarbon (PAH) mixtures by Sphingomonas paucimobilis EPA505

Deciphering Toxic Pollutants Breakdown Potential in Microbial Community of Chumathang Hot Spring, Ladakh, India via Shotgun Metagenome Sequencing

Persistent Organic Pollutants (POPs) have been in focus of research due to their massive contamination of environment and bio-accumulation. Bioremediation and high-throughput research have gained momentum to curb the harmful effects of POPs. The present research has explored the microbial diversity of Chumathang Hot Spring, Ladakh, India, through Illumina metagenomic HiSeq 4000 sequencing platform and their potential to degrade persistent pollutants, especially xenobiotics. Taxonomic characterization based on raw metagenomic data illuminated the abundance of members of Pseudomonadota and Actinomyceota. The re-construction of the microbial genomes from assembled contigs and scaffolds using de novo assembler metaSPAdes and their further annotation through contig alignment with available reference genomes elucidated the landscape of the hot spring's microbes. The predominantly occupied key genera reported were Pannonibacter and Novosphingobium. Comparative genomic analysis established evolutionary relationships and functional diversities among hot spring microbial communities. The function annotation through MG-RAST has revealed their metabolic versatility of degrading a wide array of xenobiotic compounds, including caprolactam, dioxin, chlorobenzene, benzoate, and. Further, the hydroxylating dioxygenase (Saro_3901) was identified as a pivotal component in the aromatic degradation pathways, showcasing extensive metabolic interconnectivity. Interestingly, protein interaction network analysis identified hub genes like Saro_1233 (protocatechuate 4,5-dioxygenase alpha subunit), while Saro_3057 (amidase) was noted for its critical role in network communication and control. The resilience of thermal ecosystems, evidenced by robust enzymatic activity and degradation capability among organisms with < 95% genetic similarity, underscores their potential for industrial and bioremediation exploration, emphasizing the importance of preserving and studying biodiverse habitats.

Bacterial benz(a)anthracene catabolic networks in contaminated soils and their modulation by other co-occurring HMW-PAHs

Polycyclic aromatic hydrocarbons (PAHs) are major environmental pollutants in a number of point source contaminated sites, where they are found embedded in complex mixtures containing different polyaromatic compounds. The application of bioremediation technologies is often constrained by unpredictable end-point concentrations enriched in recalcitrant high molecular weight (HMW)-PAHs. The aim of this study was to elucidate the microbial populations and potential interactions involved in the biodegradation of benz(a)anthracene (BaA) in PAH-contaminated soils. The combination of DNA stable isotope probing (DNA-SIP) and shotgun metagenomics of ¹³C-labeled DNA identified a member of the recently described genus Immundisolibacter as the key BaA-degrading population. Analysis of the corresponding metagenome assembled genome (MAG) revealed a highly conserved and unique genetic organization in this genus, including novel aromatic ring-hydroxylating dioxygenases (RHD). The influence of other HMW-PAHs on BaA degradation was ascertained in soil microcosms spiked with BaA and fluoranthene (FT), pyrene (PY) or chrysene (CHY) in binary mixtures. The co-occurrence of PAHs resulted in a significant delay in the removal of PAHs that were more resistant to biodegradation, and this delay was associated with relevant microbial interactions. Members of Immundisolibacter, associated with the biodegradation of BaA and CHY, were outcompeted by Sphingobium and Mycobacterium, triggered by the presence of FT and PY, respectively. Our findings highlight that interacting microbial populations modulate the fate of PAHs during the biodegradation of contaminant mixtures in soils.

Biodegradation of chemicals tested in mixtures and individually: mixture effects on biodegradation kinetics and microbial composition

Biodegradation in the aquatic environment occurs in the presence of many chemicals, while standard simulation biodegradation tests are conducted with single chemicals. This study aimed to investigate the effect of the presence of additional chemicals on (1) biodegradation kinetics of individual chemicals and (2) the microbial composition in test systems. Parallel mixture and single substance experiments were conducted for 9 chemicals (phenethyl benzoate, oxacycloheptadec-10-en-2-one, α-ionone, methyl 2-naphthyl ether, decan-5-olide, octan-2-one, 2'-acetonaphthanone, methyl N-methylanthranilate, (+)-menthone) using inoculum from a Danish stream. Biotic and abiotic test systems were incubated at 12 °C for 1-30 days. Primary biodegradation kinetics were then determined from biotic/abiotic peak area ratios using SPME GC/MS analysis. The effect of the mixture on biodegradation varied with test chemical and was more pronounced for chemicals with lag-phases above 14 days: two chemicals degraded in the mixture but not when tested alone (i.e., positive mixture effect), and two degraded when tested alone but not in the mixture (i.e., negative mixture effect). Microbial composition (16S rRNA gene amplicon sequencing) was highly affected by 14 days incubation and the presence of the mixture (significant carbon source), but less by single chemicals (low carbon source). Growth on chemical mixtures resulted in consistent proliferation of Pseudomonas and Malikia, while specific chemicals increased the abundance of putative degraders belonging to Novosphingobium and Zoogloea. The chemical and microbiological results support (1) that simulation biodegradation kinetics should be determined in mixtures at low environmentally relevant concentrations and (2) that degradation times beyond some weeks are associated with more uncertainty.

Abatement of binary gaseous chlorinated VOC by biotrickling filter: Performance, interactions, and microbial community

The treatment of waste-gas containing chlorinated volatile organic compounds (CVOCs) has become a difficult issue in current air pollution control. Biotrickling filters (BTFs) have been recognized to be applicable for the treatment of CVOCs, but research on the biodegradation of binary gaseous CVOCs is rare. Herein, a BTF inoculated with Methylobacterium (M.) rhodesianum H13, Starkeya sp. T-2 and activated sludge was established to investigate the biodegradation of the gaseous dichloromethane (DCM) and 1,2-dichloroethane (1,2-DCE) and their interactions implicated. The bioaugmented BTF showed a faster startup (13 days), better removal efficiencies of DCM (80%) and 1,2-DCE (72%), and superior mineralization (65.9%) than that inoculated with activated sludge alone. The ECs of DCM and 1,2-DCE were positively related with the inlet load when the total inlet load was <50 g m^-3 h^-1. However, inlet loads higher than 50 g m^-3 h^-1 led to dramatic drop of the RE of DCM and 1,2-DCE due to the limitation of the degradation capacity of microorganisms and the toxic effect of high-concentration substrates. Besides, BTF could stand a lower shock load of 400 mg m^-3, while higher shock loads would deteriorate the RE of DCM and 1,2-DCE. And BTF showed better impact resistance toward DCM than 1,2-DCE, probably because the 1,2-DCE biodegrading bacteria was more sensitive to the concentration change. For the same reason, the removal recovery of DCM after starvation was quicker than 1,2-DCE. Kinetic interactions were quantified by the EC-SKIP model, results of which revealed that DCM cast negative effect on 1,2-DCE biodegradation, while 1,2-DCE could promote DCM biodegradation. Moreover, both the results of real-time PCR and high-throughput sequencing showed M. rhodesianum H13 had stronger competitiveness and adaptability than Starkeya sp. T-2. The survived M. rhodesianum H13 and Starkeya sp. T-2 after starvation robustly demonstrated the success of bioaugmentation as well as its great potential of engineering application.

Identification of New Dioxygenases Able to Recognize Polycyclic Aromatic Hydrocarbons with High Aromaticity

Polycyclic aromatic hydrocarbons (PAHs), products from the incomplete combustion of crude oil, are pollutants present in nature. Ring hydroxylating dioxygenase enzymes are able to catalyze polycyclic aromatic hydrocarbons in the biodegradation process with a high degree of stereo-, regio-, and enantiospecificity. In this work, we present the first approximation of the binding modes of 9 PAHs with high aromaticity in the catalytic sites of biphenyl or naphthalene dioxygenases from four microorganisms usually used in bio-remediation processes: Sphingobium yanoikuyae, Rhodococcus jostii RHA1, Pseudomonas sp. C18, and Paraburkholderia xenovorans. Molecular modeling studies of two biphenyl dioxygenases from Sphingobium yanoikuyae and Paraburkholderia xenovorans showed good binding affinity for PAHs with 2–4 benzene rings (fluoranthene, pyrene, and chrysene), and both enzymes had a similar amount of substrate binding. Molecular docking studies using naphthalene dioxygenase from Pseudomonas sp. C18 showed that the enzyme is able to accommodate PAHs with high aromaticity (benzo(a)pyrene, indeno(1,2,3-cd)pyrene), with good docking scores. This study provides important insight into the utility of naphthalene dioxygenases in the degradation of HAPs with high aromaticity.

Genomic Characterization of Potential Plant Growth-Promoting Features of Sphingomonas Strains Isolated from the International Space Station

In an ongoing microbial tracking investigation of the International Space Station (ISS), several Sphingomonas strains were isolated. Based on the 16S rRNA gene sequence, phylogenetic analysis identified the ISS strains as Sphingomonas sanguinis (n = 2) and one strain isolated from the Kennedy Space Center cleanroom (used to assemble various Mars mission spacecraft components) as Sphingomonas paucimobilis. Metagenomic sequence analyses of different ISS locations identified 23 Sphingomonas species. An abundance of shotgun metagenomic reads were detected for S. sanguinis in the location from where the ISS strains were isolated. A complete metagenome-assembled genome was generated from the shotgun reads metagenome, and its comparison with the whole-genome sequences (WGS) of the ISS S. sanguinis isolates revealed that they were highly similar. In addition to the phylogeny, the WGS of these Sphingomonas strains were compared with the WGS of the type strains to elucidate genes that can potentially aid in plant growth promotion. Furthermore, the WGS comparison of these strains with the well-characterized Sphingomonas sp. LK11, an arid desert strain, identified several genes responsible for the production of phytohormones and for stress tolerance. Production of one of the phytohormones, indole-3-acetic acid, was further confirmed in the ISS strains using liquid chromatography-mass spectrometry. Pathways associated with phosphate uptake, metabolism, and solubilization in soil were conserved across all the S. sanguinis and S. paucimobilis strains tested. Furthermore, genes thought to promote plant resistance to abiotic stress, including heat/cold shock response, heavy metal resistance, and oxidative and osmotic stress resistance, appear to be present in these space-related S. sanguinis and S. paucimobilis strains. Characterizing these biotechnologically important microorganisms found on the ISS and harnessing their key features will aid in the development of self-sustainable long-term space missions in the future. IMPORTANCESphingomonas is ubiquitous in nature, including the anthropogenically contaminated extreme environments. Members of the Sphingomonas genus have been identified as potential candidates for space biomining beyond earth. This study describes the isolation and identification of Sphingomonas members from the ISS, which are capable of producing the phytohormone indole-3-acetic acid. Microbial production of phytohormones will help future in situ studies, grow plants beyond low earth orbit, and establish self-sustainable life support systems. Beyond phytohormone production, stable genomic elements of abiotic stress resistance, heavy metal resistance, and oxidative and osmotic stress resistance were identified, rendering the ISS Sphingomonas isolate a strong candidate for biotechnology-related applications.

Photodegradation of modified petroleum impregnated bentonite mulch under the effects of solar radiation simulating the outdoor condition

The objectives of this study were investigating the photodegradation of the polycyclic aromatic hydrocarbons (PAHs) in modified petroleum impregnated bentonite mulch through solar radiation, determining PAHs' translocation in the soils that underlay the mulch and finding a solution to prevent the uncontrolled release of petroleum into the environment. For this research, various formulated mulches were prepared: mulch no. 1 was a mixture of 5:1 sandy soil: natural bentonite + petroleum; mulch no. 2 composed a mixture of 5:1 sandy soil: modified bentonite + natural bentonite + petroleum; and mulch no. 3 composed a mixture of 5:1:0.5 ratio of sandy soil: natural bentonite: modified bentonite mixed with petroleum at a ratio of 1:1. PAHs in surface mulches and subsurface sandy soil were monitored over 5, 20, 40 and 80 days. The results demonstrated that PAHs undergo numerous changes over time because of sunlight. Photodegradation is the most dominant process for low molecular weight (LMW) PAHs (≤ 3 fused aromatic rings) and high molecular weight (HMW) PAHs (≥ 4 fused aromatic rings). HMW PAHs could be sequestrated strongly within the soil particles because of their higher aromaticity and lower polarity; they were more resilient in the soil matrices than LMW PAHs. Mulch no. 2 retained more PAHs compounds (p > 95%) than mulch nos. 1 and 3, which could be attributed to the retention of numerous PAHs in its interlayers, preventing its movement into the underlying soil, environment and atmosphere.

Biodegradation of di-(2-ethylhexyl) phthalate by novel Rhodococcus sp. PFS1 strain isolated from paddy field soil

Di-(2-ethylhexyl)-phthalate (DEHP) is the phthalate ester frequently utilized as a plasticizer, commonly found in cosmetics, packaging materials; moreover, it has carcinogenic and mutagenic effects on humans. In the current study, we isolated the soil bacterium Rhodococcus sp. PFS1 and to assess its DEHP degradation ability in various environmental conditions. The strain PFS1 was isolated from paddy field soil and identified by the 16S rRNA sequencing analyses. The strain PFS1 was examined for its biodegradation ability of DEHP at various pH, temperature, salt concentration, glucose concentration, and high and low concentrations of DEHP. Moreover, the biodegradation of DEHP at a contaminated soil environment by strain PFS1 was assessed. Further, the metabolic pathway of DEHP degradation by PFS1 was analyzed by HPLC-MS analysis. The results showed that the strain PFS1 effectively degraded the DEHP at neutral pH and temperature 30 °C; moreover, expressed excellent DEHP degradation at the high salt concentration (up to 50 g/L). The strain PFS1 was efficiently degraded the different tested phthalate esters (PAEs) up to 90%, significantly removed the DEHP contamination in soil along with native organisms which are present in soil up to 94.66%; nevertheless, the PFS1 alone degraded the DEHP up to 87.665% in sterilized soil. According to HPLC-MS analysis, DEHP was degraded into phthalate (PA) by PFS1 strain via mono(2-ethylehxyl) phthalate (MEHP); then PA was utilized for cell growth. These results suggest that Rhodococcus sp. PFS1 has excellent potential to degrade DEHP at various environmental conditions especially in contaminated paddy field soil.

Influencing mechanisms of siderite and magnetite, on naphthalene biodegradation: Insights from degradability and mineral surface structure

Biodegradation is the most economical and efficient process for remediating polycyclic aromatic hydrocarbons (PAHs) such as naphthalene (Nap). Soil composition is pivotal in controlling PAH migration and transformation. Iron minerals such as siderite and magnetite are the primary components of soil and sediment and play key roles in organic pollutant biodegradation. However, it is unclear whether siderite and magnetite promote or inhibit Nap biodegradation. The effects of siderite and magnetite on Nap biodegradation were investigated through batch experiments in this study. The results indicated that siderite increased Nap biodegradation efficiency by 7.87%, whereas magnetite inhibited Nap biodegradation efficiency by 3.54%. In the presence of siderite, Nap-degrading bacteria with acid-producing effects promoted siderite dissolution via metabolic activity, resulting in an increased Fe (II) concentration in solution which accelerated the iron reduction process and promoted Nap biodegradation. In addition, the presence of iron minerals altered the genus-level community structure. Anaerobic sulfate-reducing bacteria such as Desulfosporosinus occurred in the presence of siderite, indicating that sulfate reduction occurred in advance under the influence of siderite. In the presence of magnetite, Fe (III) in iron minerals were converted to Fe (II), and under the mediation of microorganisms, Fe (II) combined with carbonate to form secondary minerals (e.g., siderite). Secondary minerals were attached to the surface of magnetite, which inhibited magnetite dissolution and reduced the efficiency of Fe (III) utilization by microorganisms. Furthermore, as the reaction proceeds, acid-producing microorganisms promoted magnetite further dissolution, resulting in a longer duration of the Fe (III) reduction process. Bacteria utilizing sulfuric acid as the terminal electron acceptor consumed organic matter more rapidly than those using iron as the terminal electron acceptor. Therefore, magnetite inhibited Nap degradation. These observations enhance our understanding of the interaction mechanisms of iron minerals, organic pollutants, and degrading bacteria during the biodegradation process.

Growth kinetics of Pseudomonas aeruginosa RS1 on fluorene and dibenzothiophene, concomitant degradation kinetics and uptake mechanism

The current study illustrates the growth kinetics of an efficient PAH and heterocyclic PAH degrading bacterial strain, Pseudomonas aeruginosa RS1 on fluorene (FLU) and dibenzothiophene (DBT) over the concentration 25-500 mg L-1 and their concomitant degradation kinetics. The specific growth rate (µ) was found to lie within the range of 0.32-0.57 day-1 for FLU and 0.24-0.45 day-1 for DBT. The specific substrate utilization rate (q) of FLU and DBT over the log growth phase was between 0.01 and 0.14 mg FLU mg VSS-1 day-1 for FLU and between 0.01 and 0.18 mg DBT mg VSS-1 day-1 for DBT, respectively. The µ and q values varied within a narrow range for both FLU and DBT and they did not follow any specific trend. Dissolution together with direct interfacial uptake was the possible uptake mechanism for both FLU and DBT. The q values over the log growth phase depicts the specific substrate transformation rates. Kirby-Bauer disc diffusion studies performed using an E. coli strain indicated accumulation of some toxic intermediates of FLU and DBT during their degradation. Decrease in TOC and toxicity towards the end of the degradation experiments indicates further utilization of the intermediates.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02742-7.

Enhancement of Toxic Efficacy of Alkylated Polycyclic Aromatic Hydrocarbons Transformed by Sphingobium quisquiliarum

Alkylated polycyclic aromatic hydrocarbons (PAHs) are abundant in crude oils and refined petroleum products and are considered as major contributors to the toxicity of spilled oils. In this study, the microbial degradation of model (alkylated) PAHs (i.e., phenanthrene, 3-methylphenanthrene, 3,6-dimethylphenanthrene (36DMPhe), pyrene, and 1-methylpyrene (1MP)) by the bacterium Sphingobium quisquiliarum EPA505, a known degrader of PAHs, was studied. To evaluate the toxic potential of the metabolic products, reaction mixtures containing metabolites of 36DMPhe and 1MP were fractionated by high-performance liquid chromatography, and their effects on the luminescence inhibition of Aliivibrio fischeri were evaluated. Although the luminescence inhibition of 36DMPhe and 1MP at their solubility levels was not observed, inhibition was observed in their metabolite fractions at the solubility limit of their parent molecule. This indicates that initial biotransformation increases the toxicity of alkylated PAHs because of the increased solubility and/or inherent toxicity of metabolites. Qualitative analysis of the metabolite fractions suggested that mono-oxidation of the methyl group is the main metabolic pathway of 36DMPhe and 1MP.

Comprehensive Genome Analysis on the Novel Species Sphingomonas panacis DCY99T Reveals Insights into Iron Tolerance of Ginseng

Plant growth-promoting rhizobacteria play vital roles not only in plant growth, but also in reducing biotic/abiotic stress. Sphingomonas panacis DCY99T is isolated from soil and root of Panax ginseng with rusty root disease, characterized by raised reddish-brown root and this is seriously affects ginseng cultivation. To investigate the relationship between 159 sequenced Sphingomonas strains, pan-genome analysis was carried out, which suggested genomic diversity of the Sphingomonas genus. Comparative analysis of S. panacis DCY99T with Sphingomonas sp. LK11 revealed plant growth-promoting potential of S. panacis DCY99T through indole acetic acid production, phosphate solubilizing, and antifungal abilities. Detailed genomic analysis has shown that S. panacis DCY99T contain various heavy metals resistance genes in its genome and the plasmid. Functional analysis with Sphingomonas paucimobilis EPA505 predicted that S. panacis DCY99T possess genes for degradation of polyaromatic hydrocarbon and phenolic compounds in rusty-ginseng root. Interestingly, when primed ginseng with S. panacis DCY99T during high concentration of iron exposure, iron stress of ginseng was suppressed. In order to detect S. panacis DCY99T in soil, biomarker was designed using spt gene. This study brings new insights into the role of S. panacis DCY99T as a microbial inoculant to protect ginseng plants against rusty root disease.

Mixture Effects on Biodegradation Kinetics of Hydrocarbons in Surface Water: Increasing Concentrations Inhibited Degradation whereas Multiple Substrates Did Not

Most biodegradation tests are conducted using single chemicals at high concentrations, although these chemicals are present in the environment as mixtures at low concentrations. A partitioning-based platform was recently developed for biodegradation testing of composed mixtures of hydrophobic chemicals at ng/L to μg/L concentrations. We used this platform to study the concentration and mixture effect on biodegradation kinetics. Biodegradation tests were conducted in 20 mL vials using environmental water samples as inocula. Passive dosing was applied (1) to vary initial test concentrations of individual test compounds and (2) to vary the number of mixture components between 1 and 16. Automated solid-phase microextraction coupled to gas chromatography-mass spectrometry was used to measure substrate depletion relative to abiotic controls. The number of mixture components had no or only a limited effect on the biodegradation half times for three compounds when tested at environmentally relevant concentrations. In contrast, longer lag phases and half lives were observed for single compounds when tested at higher concentrations that approached aqueous solubility. The obtained results support that simultaneous testing of multiple chemicals at low concentrations can accelerate the generation of biodegradation kinetic data, which are more environmentally relevant compared with data from tests conducted with single chemicals at much higher concentrations.

Development of mixed bacterial cultures DAK11 capable for degrading mixture of polycyclic aromatic hydrocarbons (PAHs)

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous and persistent pollutants having mutagenic and carcinogenic properties. Microbial metabolism is an alternative approach for removal of PAHs from polluted environment. Mixed bacterial cultures DAK11 capable for degrading mixture of PAHs was developed from long term polluted marine sediments. DAK11 was able to degrade 500 mg/L of mixture of four PAHs and their degradation efficiency was enhanced by supplementing commercially available NPK fertilizer (0.1%, w/v). Anionic surfactant SDS has enhanced the degradation of PAHs, but DAK11 growth was inhibited in presence of cationic surfactant CTAB. Heavy metals have decreased the rate of degradation, while it was completely inhibited in the presence of Zn²⁺ and CrO₄^2- (1mM). DAK11 was able to degrade PAHs in the presence of mono-aromatic hydrocarbons, lubricant oil and diesel. Lower molecular weight aromatic and aliphatic compounds were identified using GC-MS during metabolism of mixture of PHAs.

Estimation of decrease in cancer risk by biodegradation of PAHs content from an urban traffic soil

The role of preferential biodegradation in the reduction of cancer risk caused by polycyclic aromatic hydrocarbons (PAHs) has been studied. A consortium of microorganisms isolated from aged oil refinery exposed soil was used to degrade 13 PAHs content extracted from an urban traffic site soil. The biodegradation arranged in a batch process with a mineral salt broth, where PAHs were the sole carbon source. 70.46% biodegradation of the total PAHs occurred in an incubation period of 25 days. Sequential or preferential biodegradation took place as the lower molecular weight (LMW) PAHs were more prone to biodegradation than that of the higher molecular weight (HMW) PAHs. Microorganisms from the isolated consortia preferred the simpler carbon sources first. The relatively higher carcinogenicity of the HMW PAHs than that of the LMW PAHs leads to only 40.26% decrement in cancer risk. Initial cancer risk for children was 1.60E-05, which was decreased to 9.47E-06, whereas, for the adults, the risk decreased to 1.01E-05 from an initial value of 1.71E-05. The relative skin adherence factor for soil (AF) turned out to be the most influential parameter with 54.2% contributions to variance in total cancer risk followed by the exposure duration (ED) for children. For the adults, most contributions to the variance in total cancer risk were 58.5% by ED and followed by AF.

Soil properties and microbial ecology of a paddy field after repeated applications of domestic and industrial sewage sludges

The effects of repeated application of two types of sewage sludge, domestic and industrial (petrochemical, PSS) sludges, into paddy fields over a 5-year period on the soil properties and microbial ecology were studied and compared with conventional NPK fertilizer application. Soil organic matter and total nitrogen contents were significantly higher in the two sludge treatments than that in fertilized plots after 5 years. Soil concentrations of potentially toxic metals were low after 5 years of both sludge treatments, but the polycyclic aromatic hydrocarbons (PAHs) showed differences between the two sludge types. Concentrations of high-molecular-weight PAHs were significantly higher (p < 0.05) in the petrochemical sludge treatment than the domestic sludge treatment or the fertilizer control, although the total concentrations of 16 types of PAH in the petrochemical sludge treatment were only slightly higher than in the domestic sludge treatment and the control. The biological toxicity of soil dimethyl sulfoxide extracts from the petrochemical sludge treatment was also significantly higher (p < 0.05) than those from the fertilizer control and the domestic sludge treatment when evaluated using Photobacterium phosphoreum T3. Both types of sewage sludge increased soil microbial activity, but only the petrochemical sludge led to enrichment with specific PAH degraders such as Mycobacterium, Nocardioides, and Sphingomonas.

Biosurfactant-enhanced bioremediation of aged polycyclic aromatic hydrocarbons (PAHs) in creosote contaminated soil

The potential for biological treatment of an environment contaminated by complex petrochemical contaminants was evaluated using creosote contaminated soil in ex situ bio-slurry reactors. The efficacy of biosurfactant application and stimulation of in situ biosurfactant production was investigated. The biosurfactant produced was purified and characterised using Fourier transform infrared (FTIR) spectroscopy. Biosurfactant enhanced degradation of PAHs was 86.5% (with addition of biosurfactant) and 57% in controls with no biosurfactant and nutrient amendments after incubation for 45 days. A slight decrease in degradation rate observed in the simultaneous biosurfactant and nutrient, NH4NO3 and KH2PO4, supplemented microcosm can be attributed to preferential microbial consumption of the biosurfactant supplemented. The overall removal of PAHs was determined to be mass transport limited since the dissolution rate caused by the biosurfactant enhanced the bioavailability of the PAHs to the microorganisms. The consortium culture was predominated by the aromatic ring-cleaving species Bacillus stratosphericus, Bacillus subtilis, Bacillus megaterium, and Pseudomonas aeruginosa.

Polycyclic aromatic hydrocarbons (PAHs) biodegradation potential and diversity of microbial consortia enriched from tsunami sediments in Miyagi, Japan

The Great East Japan Earthquake caused tsunamis and resulted in widespread damage to human life and infrastructure. The disaster also resulted in contamination of the environment by chemicals such as polycyclic aromatic hydrocarbons (PAHs). This study was conducted to investigate the degradation potential and describe the PAH-degrading microbial communities from tsunami sediments in Miyagi, Japan. PAH-degrading bacteria were cultured by enrichment using PAH mixture or pyrene alone as carbon and energy sources. Among the ten consortia tested for PAH mixture, seven completely degraded fluorene and more than 95% of phenanthrene in 10 days, while only four consortia partially degraded pyrene. Six consortia partially degraded pyrene as a single substrate. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) revealed that each sample was dominated by unique microbial populations, regardless of sampling location. The consortia were dominated by known PAHs degraders including Sphingomonas, Pseudomonas, and Sphingobium; and previously unknown degraders such as Dokdonella and Luteimonas. A potentially novel and PAH-degrading Dokdonella was detected for the first time. PAH-ring hydroxylating dioxygenase (PAH-RHDα) gene was shown to be more effective than nidA in estimating pyrene-degrading bacteria in the enriched consortia. The consortia obtained in this study are potential candidates for remediation of PAHs contaminated soils.

Combined effects of DOM and biosurfactant enhanced biodegradation of polycylic armotic hydrocarbons (PAHs) in soil-water systems

This study systematically investigated the interactive effects of dissolved organic matter (DOM) and biosurfactant (rhamnolipid) on the biodegradation of phenanthrene (PHE) and pyrene (PYR) in soil-water systems. The degradations of two polycyclic aromatic hydrocarbons (PAHs) were fitted well with first order kinetic model and the degradation rates were in proportion to the concentration of biosurfactant. In addition, the degradation enhancement of PHE was higher than that of PYR. The addition of soil DOM itself at an environmental level would inhibit the biodegradation of PAHs. However, in the system with co-existence of DOM and biosurfactant, the degradation of PAHs was higher than that in only biosurfactant addition system, which may be attributed to the formation of DOM-biosurfactant complex micelles. Furthermore, under the combined conditions, the degradation of PAH increased with the biosurfactant concentration, and the soil DOM added system showed slightly higher degradation than the compost DOM added system, indicating that the chemical structure and composition of DOM would also affect the bioavailability of PAHs. The study result may broaden knowledge of biosurfactant enhanced bioremediation of PAHs contaminated soil and groundwater.

Biodegradation ability and catabolic genes of petroleum-degrading Sphingomonas koreensis strain ASU-06 isolated from Egyptian oily soil

Polycyclic aromatic hydrocarbons (PAHs) are serious pollutants and health hazards. In this study, 15 PAHs-degrading bacteria were isolated from Egyptian oily soil. Among them, one Gram-negative strain (ASU-06) was selected and biodegradation ability and initial catabolic genes of petroleum compounds were investigated. Comparison of 16S rRNA gene sequence of strain ASU-06 to published sequences in GenBank database as well as phylogenetic analysis identified ASU-06 as Sphingomonas koreensis. Strain ASU-06 degraded 100, 99, 98, and 92.7% of 100 mg/L naphthalene, phenanthrene, anthracene, and pyrene within 15 days, respectively. When these PAHs present in a mixed form, the enhancement phenomenon appeared, particularly in the degradation of pyrene, whereas the degradation rate was 98.6% within the period. This is the first report showing the degradation of different PAHs by this species. PCR experiments with specific primers for catabolic genes alkB, alkB1, nahAc, C12O, and C23O suggested that ASU-06 might possess genes for aliphatic and PAHs degradation, while PAH-RHDαGP gene was not detected. Production of biosurfactants and increasing cell-surface hydrophobicity were investigated. GC/MS analysis of intermediate metabolites of studied PAHs concluded that this strain utilized these compounds via two main pathways, and phthalate was the major constant product that appeared in each day of the degradation period.

Comparison of the substrate specificity of two ring-hydroxylating dioxygenases from Sphingomonas sp. VKM B-2434 to polycyclic aromatic hydrocarbons

The genes of two ring-hydroxylating dioxygenases (RHDs) of Sphingomonas sp. VKM B-2434 were cloned and expressed in Escherichia coli. The relative values of the RHD specificity constants were estimated for six polycyclic aromatic hydrocarbons (PAHs) based on the kinetics of PAH mixture conversion by the recombinant strains. The substrate specificity profiles of the enzymes were found to be very different. Dioxygenase ArhA was the most specific to acenaphthylene and showed a low specificity to fluoranthene. Dioxygenase PhnA was the most specific to anthracene and phenanthrene and showed a considerable specificity to fluoranthene. Knockout derivatives of Sphingomonas sp. VKM B-2434 lacking ArhA, PhnA, and both dioxygenases were constructed. PAH degradation by the single-knockout mutants was in agreement with the substrate specificity of the RHD remaining intact. Double-knockout mutant lacking both enzymes was unable to oxidize PAHs. A mutant form of dioxygenase ArhA with altered substrate specificity was described.

Complete sequencing of Novosphingobium sp. PP1Y reveals a biotechnologically meaningful metabolic pattern

Background

Novosphingobium sp. strain PP1Y is a marine α-proteobacterium adapted to grow at the water/fuel oil interface. It exploits the aromatic fraction of fuel oils as a carbon and energy source. PP1Y is able to grow on a wide range of mono-, poly- and heterocyclic aromatic hydrocarbons. Here, we report the complete functional annotation of the whole Novosphingobium genome.

Results

PP1Y genome analysis and its comparison with other Sphingomonadal genomes has yielded novel insights into the molecular basis of PP1Y’s phenotypic traits, such as its peculiar ability to encapsulate and degrade the aromatic fraction of fuel oils. In particular, we have identified and dissected several highly specialized metabolic pathways involved in: (i) aromatic hydrocarbon degradation; (ii) resistance to toxic compounds; and (iii) the quorum sensing mechanism.

Conclusions

In summary, the unraveling of the entire PP1Y genome sequence has provided important insight into PP1Y metabolism and, most importantly, has opened new perspectives about the possibility of its manipulation for bioremediation purposes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-384) contains supplementary material, which is available to authorized users.

Evaluation of the biodegradation of Alaska North Slope oil in microcosms using the biodegradation model BIOB

We present the details of a numerical model, BIOB that is capable of simulating the biodegradation of oil entrapped in the sediment. The model uses Monod kinetics to simulate the growth of bacteria in the presence of nutrients and the subsequent consumption of hydrocarbons. The model was used to simulate experimental results of Exxon Valdez oil biodegradation in laboratory columns (Venosa et al., 2010). In that study, samples were collected from three different islands: Eleanor Island (EL107), Knight Island (KN114A), and Smith Island (SM006B), and placed in laboratory microcosms for a duration of 168 days to investigate oil bioremediation through natural attenuation and nutrient amendment. The kinetic parameters of the BIOB model were estimated by fitting to the experimental data using a parameter estimation tool based on Genetic Algorithms (GA). The parameter values of EL107 and KN114A were similar whereas those of SM006B were different from the two other sites; in particular biomass growth at SM006B was four times slower than at the other two islands. Grain size analysis from each site revealed that the specific surface area per unit mass of sediment was considerably lower at SM006B, which suggest that the surface area of sediments is a key control parameter for microbial growth in sediments. Comparison of the BIOB results with exponential decay curves fitted to the data indicated that BIOB provided better fit for KN114A and SM006B in nutrient amended treatments, and for EL107 and KN114A in natural attenuation. In particular, BIOB was able to capture the initial slow biodegradation due to the lag phase in microbial growth. Sensitivity analyses revealed that oil biodegradation at all three locations were sensitive to nutrient concentration whereas SM006B was sensitive to initial biomass concentration due to its slow growth rate. Analyses were also performed to compare the half-lives of individual compounds with that of the overall polycyclic aromatic hydrocarbons (PAHs).

A new model for the biodegradation kinetics of oil droplets: application to the Deepwater Horizon oil spill in the Gulf of Mexico

Oil biodegradation by native bacteria is one of the most important natural processes that can attenuate the environmental impacts of marine oil spills. Existing models for oil biodegradation kinetics are mostly for dissolved oil. This work developed a new mathematical model for the biodegradation of oil droplets and applied the model to estimate the time scale for oil biodegradation under conditions relevant to the Deepwater Horizon oil spill in the Gulf of Mexico. In the model, oil is composed of droplets of various sizes following the gamma function distribution. Each oil droplet shrinks during the microbe-mediated degradation at the oil-water interface. Using our developed model, we find that the degradation of oil droplets typically goes through two stages. The first stage is characterized by microbial activity unlimited by oil-water interface with higher biodegradation rates than that of the dissolved oil. The second stage is governed by the availability of the oil-water interface, which results in much slower rates than that of soluble oil. As a result, compared to that of the dissolved oil, the degradation of oil droplets typically starts faster and then quickly slows down, ultimately reaching a smaller percentage of degraded oil in longer time. The availability of the water-oil interface plays a key role in determining the rates and extent of degradation. We find that several parameters control biodegradation rates, including size distribution of oil droplets, initial microbial concentrations, initial oil concentration and composition. Under conditions relevant to the Deepwater Horizon spill, we find that the size distribution of oil droplets (mean and coefficient of variance) is the most important parameter because it determines the availability of the oil-water interface. Smaller oil droplets with larger variance leads to faster and larger extent of degradation. The developed model will be useful for evaluating transport and fate of spilled oil, different remediation strategies, and risk assessment.

Dynamic passive dosing for studying the biotransformation of hydrophobic organic chemicals: microbial degradation as an example

Biotransformation plays a key role in hydrophobic organic compound (HOC) fate, and understanding kinetics as a function of (bio)availability is critical for elucidating persistence, accumulation, and toxicity. Biotransformation mainly occurs in an aqueous environment, posing technical challenges for producing kinetic data because of low HOC solubilities and sorptive losses. To overcome these, a new experimental approach based on passive dosing is presented. This avoids using cosolvent for introducing the HOC substrate, buffers substrate depletion so biotransformation is measured within a narrow and defined dissolved concentration range, and enables high compound turnover even at low concentrations to simplify end point measurement. As a case study, the biodegradation kinetics of two model HOCs by the bacterium Sphingomonas paucimobilis EPA505 were measured at defined dissolved concentrations ranging over 4 orders of magnitude, from 0.017 to 658 μg L(-1) for phenanthrene and from 0.006 to 90.0 μg L(-1) for fluoranthene. Both compounds had similar mineralization fluxes, and these increased by 2 orders of magnitude with increasing dissolved concentrations. First-order mineralization rate constants were also similar for both PAHs, but decreased by around 2 orders of magnitude with increasing dissolved concentrations. Dynamic passive dosing is a useful tool for measuring biotransformation kinetics at realistically low and defined dissolved HOC concentrations.

Naphthalene degradation by bacterial consortium (DV-AL) developed from Alang-Sosiya ship breaking yard, Gujarat, India

Naphthalene degrading bacterial consortium (DV-AL) was developed by enrichment culture technique from sediment collected from the Alang-Sosiya ship breaking yard, Gujarat, India. The 16S rRNA gene based molecular analyzes revealed that the bacterial consortium (DV-AL) consisted of four strains namely, Achromobacter sp. BAB239, Pseudomonas sp. DV-AL2, Enterobacter sp. BAB240 and Pseudomonas sp. BAB241. Consortium DV-AL was able to degrade 1000 ppm of naphthalene in Bushnell Haas medium (BHM) containing peptone (0.1%) as co-substrate with an initial pH of 8.0 at 37°C under shaking conditions (150 rpm) within 24h. Maximum growth rate and naphthalene degradation rate were found to be 0.0389 h(-1) and 80 mg h(-1), respectively. Consortium DV-AL was able to utilize other aromatic and aliphatic hydrocarbons such as benzene, phenol, carbazole, petroleum oil, diesel fuel, and phenanthrene and 2-methyl naphthalene as sole carbon source. Consortium DV-AL was also efficient to degrade naphthalene in the presence of other pollutants such as petroleum hydrocarbons and heavy metals.

Enhanced anoxic bioremediation of PAHs-contaminated sediment

In this study, the biodegradation of 16 polycyclic aromatic hydrocarbons (PAHs) in marine sediment was investigated under three different anoxic conditions, i.e. sulfate-only, nitrate-only and mixed nitrate/sulfate as electron acceptors. All two-, three- and four-ring PAHs showed significant biodegradation with the removal efficiencies ranging from 42% to 77%, while five- and six-ring PAHs showed little degradation. The results illustrated that two- to three-ring PAHs could be degraded at a rate of 4.01×10(-2)-6.42×10(-2) d(-1) under nitrate-reducing condition, faster than that of under sulfate-reducing condition. Biodegradation of two- and three-ring PAHs followed first-order model well with the rate constants of 1.62×10(-2)-6.42×10(-2) d(-1). The biodegradation of four ring PAHs followed the zero-order kinetic model with the rate constants of 1.26×10(-2)-2.22×10(-2) mg/kg/d. Molecular analysis indicated that nahAc gene increased by two orders of magnitude during the biodegradation and served as a good indicator of PAHs-degrading bacterial population and biodegradation process.

The marine isolate Novosphingobium sp. PP1Y shows specific adaptation to use the aromatic fraction of fuels as the sole carbon and energy source

Novosphingobium sp. PP1Y, isolated from a surface seawater sample collected from a closed bay in the harbour of Pozzuoli (Naples, Italy), uses fuels as its sole carbon and energy source. Like some other Sphingomonads, this strain can grow as either planktonic free cells or sessile-aggregated flocks. In addition, this strain was found to grow as biofilm on several types of solid and liquid hydrophobic surfaces including polystyrene, polypropylene and diesel oil. Strain PP1Y is not able to grow on pure alkanes or alkane mixtures but is able to grow on a surprisingly wide range of aromatic compounds including mono, bi, tri and tetracyclic aromatic hydrocarbons and heterocyclic compounds. During growth on diesel oil, the organic layer is emulsified resulting in the formation of small biofilm-coated drops, whereas during growth on aromatic hydrocarbons dissolved in paraffin the oil layer is emulsified but the drops are coated only if the mixtures contain selected aromatic compounds, like pyrene, propylbenzene, tetrahydronaphthalene and heterocyclic compounds. These peculiar characteristics suggest strain PP1Y has adapted to efficiently grow at the water/fuel interface using the aromatic fraction of fuels as the sole carbon and energy source.

Degradation of polycyclic aromatic hydrocarbons by the Chilean white-rot fungus Anthracophyllum discolor

The degradation of three- and four-ring polycyclic aromatic hydrocarbons (PAHs) in Kirk medium by Anthracophyllum discolor, a white-rot fungus isolated from the forest of southern Chile, was evaluated. In addition, the removal efficiency of three-, four- and five-ring PAHs in contaminated soil bioaugmented with A. discolor in the absence and presence of indigenous soil microorganisms was investigated. Production of lignin-degrading enzymes and PAH mineralization in the soil were also determined. A. discolor was able to degrade PAHs in Kirk medium with the highest removal occurring in a PAH mixture, suggesting synergistic effects between PAHs or possible cometabolism. A high removal capability for phenanthrene (62%), anthracene (73%), fluoranthene (54%), pyrene (60%) and benzo(a)pyrene (75%) was observed in autoclaved soil inoculated with A. discolor in the absence of indigenous microorganisms, associated with the production of manganese peroxidase (MnP). The metabolites found in the PAH degradation were anthraquinone, phthalic acid, 4-hydroxy-9-fluorenone, 9-fluorenone and 4,5-dihydropyrene. A. discolor was able to mineralize 9% of the phenanthrene. In non-autoclaved soil, the inoculation with A. discolor did not improve the removal efficiency of PAHs. Suitable conditions must be found to promote a successful fungal bioaugmentation in non-autoclaved soils.

Bacteria-mediated PAH degradation in soil and sediment

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the natural environment and easily accumulate in soil and sediment due to their low solubility and high hydrophobicity, rendering them less available for biological degradation. However, microbial degradation is a promising mechanism which is responsible for the ecological recovery of PAH-contaminated soil and sediment for removing these recalcitrant compounds compared with chemical degradation of PAHs. The goal of this review is to provide an outline of the current knowledge of biodegradation of PAHs in related aspects. Over 102 publications related to PAH biodegradation in soil and sediment are compiled, discussed, and analyzed. This review aims to discuss PAH degradation under various redox potential conditions, the factors affecting the biodegradation rates, degrading bacteria, the relevant genes in molecular monitoring methods, and some recent-year bioremediation field studies. The comprehensive understanding of the bioremediation kinetics and molecular means will be helpful for optimizing and monitoring the process, and overcoming its limitations in practical projects.

Biodegradation of pyrene in sand, silt and clay fractions of sediment

Microbial degradation is the dominant pathway for natural attenuation of PAHs in environmental compartments such as sediments, which in turn depends on the bioavailability of PAHs. The bioavailability of PAHs has seldom been studied at the sediment particle size scale. We evaluated biodegradation of pyrene by Mycobacterium vanbaalenii PYR-1 as a function of sediment particle sizes, and investigated the relationship between the rate of degradation on sand, silt and clay particles with their individual desorption kinetics measured with the Tenax extraction method. Regression analysis showed that the total organic carbon (TOC), black carbon (BC), and specific surface area (SSA) of the specific particle size fractions, instead of the particle size scale itself, were closely related (P < 0.01) with the mineralization rate. While the fraction in the rapid desorption pool (F_rapid) ranged from 0.11 to 0.38 for the whole sediments and different size groups, the fractions mineralized after 336-h incubation (0.52 to 0.72) greatly surpassed the F_rapid values, suggesting utilization of pyrene in the slow desorption pool (F_slow). A biodegradation model was modified by imbedding a two-phase desorption relationship describing sequential Tenax extractions. Model analysis showed that pyrene sorbed on silt and clay aggregates was directly utilized by the degrading bacteria. The enhanced bioavailability may be attributed to the higher chemical concentration, higher TOC or larger SSA in the silt and clay fractions, which appeared to overcome the reduced bioavailability of pyrene due to sorption, making pyrene on the silt and clay particles readily available to degrading microbes. This conjecture merits further investigation.