Isolation of pyrene degrading Achromobacter xylooxidans and characterization of metabolic product

Sources of Polycyclic Aromatic Hydrocarbons in Fecal Pellets of a Marphysa Species (Annelida: Eunicidae) in the Yoro Tidal Flat, Japan

The fecal pellets of Marphysa sp. E sensu Abe et al. (2019) (Annelida, Eunicidae) living in the Yoro tidal flat (Ichihara, Chiba, Japan) contain high levels of polycyclic aromatic hydrocarbons (PAHs), and the concentrations rapidly decrease over time. To investigate the origin of the high-concentration PAHs in the fecal pellets and food sources of the worms, the PAH concentrations, carbon and nitrogen stable isotope ratios (δ13C and δ15N), total organic carbon, and total nitrogen for two types of sediment (sands and reduced muds), fecal pellets, and the body of the worms were determined. The PAH concentrations and chemical properties of the fecal pellets were similar to those of the reduced muds (20-30 cm sediment depth). The δ13C, δ15N, and C/N values of reduced muds were the same as the typical values of terrestrial C3 plants, suggesting that reduced muds were derived from terrestrial plants. These data indicated that the worms selectively take up reduced muds containing high levels of PAHs. The δ13C and δ15N values of the worm bodies indicated that the worms did not use the organic carbon derived from terrestrial C3 plants as primary nutrition. Taking into consideration their selective uptake of reduced muds, excretion, and subsequent rapid decrease of PAHs in the fecal pellets, the worms could contribute to the remediation of chemical pollutants in the tidal flat sediments.

Cell surface hydrophobicity and petroleum hydrocarbon degradation by biofilm-forming marine bacterium Pseudomonas furukawaii PPS-19 under different physicochemical stressors

Biofilm-forming marine bacterium Pseudomonas furukawaii PPS-19 showed strong hydrophobicity under different physicochemical stressors, such as pH and salinity. Strong aggregation of P. furukawaii PPS-19 was observed at hydrophobic interfaces of n-dodecane and crude oil, while uptake of pyrene resulted in blue fluorescence of the bacterium. Changes in biofilm microcolonies were observed under different physicochemical stressors with maximum biofilm thickness of 15.15 µm and 15.77 µm at pH 7% and 1% salinity, respectively. Relative expression analysis of alkB2 gene revealed the maximum expression in n-dodecane (10.5 fold) at pH 7 (1 fold) and 1% salinity (8.3 fold). During the degradation process, a significant drop in surface tension resulted in increased emulsification activity. P. furukawaii PPS-19 showed the respective n-dodecane and pyrene degradation of 94.3% and 81.5% at pH 7% and 94.5% and 83% at 1% salinity. A significant positive correlation was obtained between cell surface hydrophobicity (CSH), biofilm formation, and PHs degradation (P < 0.05) under all the physicochemical stressors, with the highest value at pH 7% and 1% salinity. Analysis of metabolites indicated that mono-terminal oxidation and multiple pathways were followed for n-dodecane and pyrene biodegradation, respectively. Thus, P. furukawaii PPS-19 is an efficient hydrocarbonoclastic bacterium that may be exploited for large-scale oil pollution abatement.

Folin-Ciocalteu assay as a rapid colourimetric screening method for evaluating PAH degradation abilities of heterotrophic bacteria

Bioremediation using microbes is an eco-friendly approach being explored for reclaiming PAH-contaminated areas. However, isolation and screening of potential bacteria to degrade PAHs are very laborious and cumbersome. To alleviate this issue, we describe a rapid method for screening the bacterial cultures for their ability to degrade PAHs using Folin-Ciocalteu (FC) assay. Six hundred bacterial isolates were tested for their ability to degrade PAH using FC assay. The cultures capable of degrading PAH show blue colouration, resulting from the reaction of FC reagent with phenolic intermediates generated during PAH degradation. Out of the 600 cultures screened, 64 showed an ability to degrade PAH. This study provides a very easy, rapid, less laborious, and sensitive method to screen a large number of bacterial cultures for their ability to degrade PAH.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03549-4.

Different phenanthrene degraders between free-cell mediated and biochar-immobilization assisted soil bioaugmentation as identified by RNA-based stable isotope probing (RNA-SIP)

Bioaugmentation (BA) is an effective approach to remove polycyclic aromatic hydrocarbons (PAHs) from contaminated soils, and biochar is frequently used to enhance PAH degradation performance. In this study, phenanthrene (PHE) degradation behavior and active degraders in a petroleum-contaminated soil were investigated and compared between free-cell mediated and biochar-immobilization assisted bioaugmentation. Biochar-immobilization assisted bioaugmentation (BA-IPB) introduced PHE degraders immobilized on biochar and effectively promoted PHE degradation, achieving higher PHE removal efficiencies within 24 h (~58 %) than free-cell mediated bioaugmentation (BA-FPB, ~39 %). Soil microbial community structure significantly changed in both BA-FPB and BA-IPB treatments. Through RNA-stable isotope probing (SIP), 14 and 11 bacterial lineages responsible for in situ PHE degradation were identified in BA-FPB and BA-IPB treatments, respectively. ASV_17 in BA-FPB treatment was Rhodococcus in the exogenous bacterial mixture; in contrast, none of exogenous bacteria were involved in PHE degradation in BA-IPB treatment. Methylobacterium (ASV_186), Xanthomonas (ASV_41), Kroppenstedtia (ASV_205), Scopulibacillus (ASV_243), Bautia (ASV_356), and Lactobacillus (ASV_376) were identified as PHE degraders for the first time. Our findings expanded the knowledge of the active PHE degraders and underlying mechanisms in bioaugmentation process, and suggested biochar-immobilization assisted bioaugmentation as a promising strategy for the bioremediation of PAH contaminated soils.

The metabolism of pyrene by a novel Altererythrobacter sp. with in-situ co-substrates: A mechanistic analysis based on pathway, genomics, and enzyme activity

Using co-substrates to enhance the metabolic activity of microbes is an effective way for high-molecular-weight polycyclic aromatic hydrocarbons removal in petroleum-contaminated environments. However, the long degradation period and exhausting substrates limit the enhancement of metabolic activity. In this study, Altererythrobacter sp. N1 was screened from petroleum-contaminated soil in Shengli Oilfield, China, which could utilize pyrene as the sole carbon source and energy source. Saturated aromatic fractions and crude oils were used as in-situ co-substrates to enhance pyrene degradation. Enzyme activity was influenced by the different co-substrates. The highest degradation rate (75.98%) was achieved when crude oil was used as the substrate because strain N1 could utilize saturated and aromatic hydrocarbons from crude oil simultaneously to enhance the degrading enzyme activity. Moreover, the phthalate pathway was dominant, while the salicylate pathway was secondary. Furthermore, the Rieske-type aromatic cyclo-dioxygenase gene was annotated in the Altererythrobacter sp. N1 genome for the first time. Therefore, the co-metabolism of pyrene was sustained to achieve a long degradation period without the addition of exogenous substrates. This study is valuable as a potential method for the biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons.

Fate of PAHs in treated wastewater reused as irrigation water: Environmental risks in water-soil-ryegrass multimedia system

The main aim of this study was to determine the fate, bio-metabolism and environmental risk of low-ring and high-ring polycyclic aromatic hydrocarbons (PAHs) in a water-soil-ryegrass multi-media system, under long-term irrigation condition with micro-polluted treated wastewater. Field experiments were carried out to simulate garden irrigation using treated wastewater containing typical representative low-ring naphthalene (Nap) and high-ring benzo[a]pyrene (BaP). The results showed that BaP's vertical attenuation rate and adsorption accumulation rate were 1.7 and 1.2 times higher than Nap's, respectively. The adsorption, biodegradation, and the rhizosphere effect were responsible for 40.7%, 28.4%, 21.6%, and 30.5%, 36.6%, 17.7%, respectively, of the attenuation of BaP and Nap. The major metabolic pathways of Nap and BaP are hydroxylation, ring opening cleavage, and decarboxylation, with the metabolic chain of BaP being longer than that of Nap due to more ring cleaving reactions. Pseudomonas, Mycobacterium, and Sphingomonas were the functional microorganisms with PAHs degradation capacity that were positively correlated with PAHs degradation, particularly in the rhizosphere. After ten years of irrigation with treated wastewater, the prediction of environmental risk revealed that there were few potential risks. Thus, the results of this feasibility study demonstrated that using treated wastewater for garden irrigation was a relatively safe and effective strategy.

Bioaugmentation of PAH-Contaminated Soils With Novel Specific Degrader Strains Isolated From a Contaminated Industrial Site. Effect of Hydroxypropyl-β-Cyclodextrin as PAH Bioavailability Enhancer

A PAHs-contaminated industrial soil was analyzed using PCR amplification of the gene 16S ribosomal RNA for the detection and identification of different isolated bacterial strains potentially capable of degrading PAHs. Novel degrader strains were isolated and identified as Achromobacter xylosoxidans 2BC8 and Stenotrophomonas maltophilia JR62, which were able to degrade PYR in solution, achieving a mineralization rate of about 1% day^-1. A. xylosoxidans was also able to mineralize PYR in slurry systems using three selected soils, and the total extent of mineralization (once a plateau was reached) increased 4.5, 21, and 57.5% for soils LT, TM and CR, respectively, regarding the mineralization observed in the absence of the bacterial degrader. Soil TM contaminated with PYR was aged for 80 days and total extent of mineralization was reduced (from 46 to 35% after 180 days), and the acclimation period increased (from 49 to 79 days). Hydroxypropyl-ß-cyclodextrin (HPBCD) was used as a bioavailability enhancer of PYR in this aged soil, provoking a significant decrease in the acclimation period (from 79 to 54 days) due to an increase in PYR bioavailable fraction just from the beginning of the assay. However, a similar global extension of mineralization was obtained. A. xylosoxidans was then added together with HPBCD to this aged TM soil contaminated with PYR, and the total extent of mineralization decreased to 25% after 180 days, possibly due to the competitive effect of endogenous microbiota and the higher concentration of PYR in the soil solution provoked by the addition of HPBCD, which could have a toxic effect on the A. xylosoxidans strain.

Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches

The present study describes the behavior of a natural phenanthrene-degrading consortium (CON), a synthetic consortium (constructed with isolated strains from CON) and an isolated strain form CON (Sphingobium sp. AM) in phenanthrene cultures to understand the interactions among the microorganisms present in the natural consortium during phenanthrene degradation as a sole carbon and energy source in liquid cultures. In the contaminant degradation assay, the defined consortium not only achieved a major phenanthrene degradation percentage (> 95%) but also showed a more efficient elimination of the intermediate metabolite. The opposite behavior occurred in the CON culture where the lowest phenanthrene degradation and the highest HNA accumulation were observed, which suggests the presence of positive and also negative interaction in CON. To consider the uncultured bacteria present in CON, a metagenomic library was constructed with total CON DNA. One of the resulting scaffolds (S1P3) was affiliated with the Betaproteobacteria class and resulted in a significant similarity with a genome fragment from Burkholderia sp. HB1 chromosome 1. A complete gene cluster, which is related to one of the lower pathways (meta-cleavage of catechol) involved in PAH degradation (ORF 31-43), mobile genetic elements and associated proteins, was found. These results suggest the presence of at least one other microorganism in CON besides Sphingobium sp. AM, which is capable of degrading PAH through the meta-cleavage pathway. Burkholderiales order was further found, along with Sphingomonadales order, by a metaproteomic approach, which indicated that both orders were metabolically active in CON. Our results show the presence of negative interactions between bacterial populations found in a natural consortium selected by enrichment techniques; moreover, the synthetic syntrophic processing chain with only one microorganism with the capability of degrading phenanthrene was more efficient in contaminant and intermediate metabolite degradation than a generalist strain (Sphingobium sp. AM).

Effects of root exudates on gel-beads/reeds combination remediation of high molecular weight polycyclic aromatic hydrocarbons

Changes in root exudates, including low molecular weight organic acids (LMWOAs), amino acids and sugars, in rhizosphere soils during the gel-beads/reeds combination remediation for high molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) and the degree of the effects on HMW-PAH biodegradation were evaluated in this study. The results showed that the gel-beads/reeds combination remediation notably increased the removal rates of pyrene, benzo(a)pyrene and indeno(1,2,3-cd)pyrene (65.0-68.9%, 60.0-68.5% and 85.2-85.9%, respectively). During the removal of HMW-PAHs, the LMWOAs, particularly maleic acid, enhanced the biodegradation of HMW-PAHs. Arginine and trehalose monitored in reed root exudates promoted the growth of plants and microorganisms and then improved the removal of HMW-PAHs, especially pyrene. However, the contribution of reed root exudates on degradation of 5- and 6-ring PAHs was minor. These results indicated that the utilization of root exudates was certainly not the only important trait for the removal of HMW-PAHs.

Biodegradation of pyrene by pseudomonas sp. JPN2 and its initial degrading mechanism study by combining the catabolic nahAc gene and structure-based analyses

In this study, a pyrene-degrading bacterial strain Pseudomonas sp. JPN2 was isolated from crude oil in Dagang Oilfield, China. The degrading percent of the strain JPN2 to pyrene was increased with the extension of culture time and achieved a maximum of 82.88% after 25 d culture. Meanwhile, four metabolites 4,5-dihydroxy-4,5-dihydropyrene, 4-phenanthrol, 1-hydroxy-2-naphthoic acid and phthalate were detected in the culture solution by GC-MS analysis. In addition, DNA fragments of nahAc gene, encoding α subunit of naphthalene dioxygenase, were amplified by PCR program and sequenced. As a result, it was presumed that the initial cleavage of the aromatic rings on pyrene was occurred at C₄ and C₅ positions and formed the intermediate 4,5-dihydroxy-4,5-dihydropyrene. This issue had been verified by the interaction analysis between pyrene and the active site of naphthalene dioxygenase in the strain JPN2 by molecular docking. Meanwhile, the differences of the amino acid residues in the active sites of template and target enzymes may be a factor leading to the different biological activity between the strain JPN2 and the other bacteria from the genus Pseudomonas. Additionally, the microcalorimetry analysis displayed that the strain JPN2 had high tolerance for pyrene, and the effect could be negligible under the experimental concentration (100 mg L^-1). Consequently, the strain JPN2 was considered as an excellent candidate for the further bioremediation study of pyrene and the other aromatic contaminants.

Application of cinder gel-beads/reeds combination strategy for bioremediation of pyrene- and indeno(1,2,3-cd)pyrene-contaminated estuarine wetlands

Pseudomonas putida PYR1 and Acinetobacter baumannii INP1 isolated from Liaohe estuarine wetlands were entrapped in cinder beads to make cinder gel-beads. They were combined with reeds for bioremediation of pyrene- and indeno(1,2,3-cd)pyrene-contaminated estuarine wetlands. The results showed that the removal percentages of pyrene and indeno(1,2,3-cd)pyrene (69.2 and 89.8 % respectively) in 40 days using cinder gel-beads/reeds were obviously higher than those using cinder gel-beads(52.6 and 70.0 %) and reeds (33.5 and 78.6 %) alone, about four times those of the control (13.8 and 31.1 %). The removal efficiency of pyrene was in the order cinder gel-beads/reeds > cinder gel-beads > reeds > control, which was different from cinder gel-beads/reeds > reeds > cinder gel-beads > control of indeno(1,2,3-cd)pyrene. This result indicated that the functional mechanism to remove indeno(1,2,3-cd)pyrene with six benzene rings was different from that of pyrene. The synergistic effect of reeds and cinder gel-beads for indeno(1,2,3-cd)pyrene removal was weaker than that of pyrene. But the absorption and transformation of reeds with high efficiency were beneficial to indeno(1,2,3-cd)pyrene removal from wetlands. Additionally, microbial analysis with high-throughput sequencing presented that Gammaproteobacteria were dominant PAH-degrading groups in bioremediation with immobilized bacteria. This strategy can serve as a model system for the removal of more complex or structurally related organic compounds from contaminated sites.

Enhanced biodegradation of pyrene and indeno(1,2,3-cd)pyrene using bacteria immobilized in cinder beads in estuarine wetlands

Two strains (Pseudomonas taiwanensis PYR1 and Acinetobacter baumannii INP1) were isolated from PAH-contaminated Liaohe estuarine wetland using enrichment. The cells of PYR1 and INP1 were immobilized in cinder beads for pyrene and indeno(1,2,3-cd)pyrene biodegradation in wetland. Biodegradation of pyrene and indeno(1,2,3-cd)pyrene in soils from wetland was carried out in pots using free cells as well as those immobilized in cinder beads to ascertain the role of bioaugmentation. Supported by the cinder beads, the immobilized cells degraded 70.7% and 80.9% of pyrene and indeno(1,2,3-cd)pyrene respectively after 30 days. While the free cells degraded only 58.2% and 55.3%. Additionally, microbial analysis with high-throughput sequencing revealed the changes of microbial communities in soil without and with cinder beads immobilized with strains. The result indicated that Gammaproteobacteria were dominant PAH-degrading groups during bioaugmentation. This effective approach can be used to treat other PAH-contaminated wetlands by immobilizing different species of bacteria in cinder beads.

Isolation and identification of Bacillus megaterium YB3 from an effluent contaminated site efficiently degrades pyrene

Industrial effluents contaminated sites may serve as repositories of ecologically adapted efficient pyrene degrading bacteria. In the present study, six bacterial isolates from industrial effluents were purified using serial enrichment technique and their pyrene degrading potential on pyrene supplemented mineral salt medium was assessed. 16S rRNA sequence analysis showed that they belong to four bacterial genera, namely Acinetobacter, Bacillus, Microbacterium, and Ochrobactrum. Among these isolates, Bacillus megaterium YB3 showed considerably good growth and was further evaluated for its pyrene-degrading efficiency. B. megaterium YB3 could degrade 72.44% of 500 mg L(-1) pyrene within 7 days. GC-MS analysis of ethyl acetate extracted fractions detected two relatively less toxic metabolic intermediates of the pyrene degradation pathway. B. megaterium YB3 also tested positive for catechol 1, 2-dioxygenase and aromatic-ring-hydroxylating dioxygenase indole-indigo conversion assays. Considering the ability and efficiency of B. megaterium YB3 to degrade high pyrene content, the strain can be used as a tool to develop bioremediation technologies for the effective biodegradation of pyrene and possibly other PAHs in the environment.

Biodegradation of pyrene by a Pseudomonas aeruginosa strain RS1 isolated from refinery sludge

High molecular weight (HMW) polynuclear aromatic hydrocarbons (PAHs) with more than three rings are inherently difficult to degrade. Degradation of HMW PAHs is primarily reported for actinomycetes, such as, Rhodococcus and Mycobacterium. This study reports pyrene degradation by a Pseudomonas aeruginosa strain isolated from tank bottom sludge in a refinery. High cell surface hydrophobicity induced during growth on pyrene facilitated its utilization as sole carbon source. Specific growth rate (μ) in the range of 0.03-0.085 h(-1) could be achieved over the concentration range 25-500 mg/L. The specific growth rate and specific pyrene utilization rate increased linearly with increase in total pyrene concentration. Although various degradation intermediates were identified in the aqueous phase, accumulation of total organic carbon (TOC) in the aqueous phase was only a small fraction of TOC equivalents of pyrene lost from the cultures. The degradation pathway appears to be similar to that reported for Mycobacterium sp. PYR-I.

Bioremediation assessment of diesel-biodiesel-contaminated soil using an alternative bioaugmentation strategy

This study investigated the effectiveness of successive bioaugmentation, conventional bioaugmentation, and biostimulation of biodegradation of B10 in soil. In addition, the structure of the soil microbial community was assessed by polymerase chain reaction-denaturing gradient gel electrophoresis. The consortium was inoculated on the initial and the 11th day of incubation for successive bioaugmentation and only on the initial day for bioaugmentation and conventional bioaugmentation. The experiment was conducted for 32 days. The microbial consortium was identified based on sequencing of 16S rRNA gene and consisted as Pseudomonas aeruginosa, Achromobacter xylosoxidans, and Ochrobactrum intermedium. Nutrient introduction (biostimulation) promoted a positive effect on microbial populations. The results indicate that the edaphic community structure and dynamics were different according to the treatments employed. CO2 evolution demonstrated no significant difference in soil microbial activity between biostimulation and bioaugmentation treatments. The total petroleum hydrocarbon (TPH) analysis indicated a biodegradation level of 35.7 and 32.2 % for the biostimulation and successive bioaugmentation treatments, respectively. Successive bioaugmentation displayed positive effects on biodegradation, with a substantial reduction in TPH levels.

Abilities and genes for PAH biodegradation of bacteria isolated from mangrove sediments from the central of Thailand

PAH-degrading bacteria, including Novosphingobium sp. PCY, Microbacterium sp. BPW, Ralstonia sp. BPH, Alcaligenes sp. SSK1B, and Achromobacter sp. SSK4, were isolated from mangrove sediments. These isolates degraded 50-76% of 100 mg/l phenanthrene within 2 weeks. Strains PCY and BPW also degraded pyrene at 98% and 71%, respectively. Furthermore, all of them probably produced biosurfactants in the presence of hydrocarbons. Interestingly, PCY has a versatility to degrade various PAHs. Molecular techniques and plasmid curing remarkably revealed the presence of the alpha subunit of pyrene dioxygenase gene (nidA), involving in its pyrene/phenanthrene degrading ability, located on megaplasmid of PCY which has never before been reported in sphingomonads. Moreover, genes encoding ferredoxin, reductase, extradiol dioxygenase (bphA3A4C) and exopolysaccharide biosynthetase, which may be involved in PAH degradation and biosurfactant production, were also found in PCY. Therefore, we conclude that these isolates, especially PCY, can be the candidates for use as inoculums in the bioremediation.