Biodegradation Of Phenanthrene In Soil Research Articles

A multi-omics approach to unravelling the coupling mechanism of nitrogen metabolism and phenanthrene biodegradation in soil amended with biochar

The presence of polycyclic aromatic hydrocarbons (PAHs) in soil negatively affects the environment and the degradation of these contaminants is influenced by nitrogen metabolism. However, the mechanisms underlying the interrelationships between the functional genes involved in nitrogen metabolism and phenanthrene (PHE) biodegradation, as well as the effects of biochar on these mechanisms, require further study. Therefore, this study utilised metabolomic and metagenomic analysis to investigate primary nitrogen processes, associated functional soil enzymes and functional genes, and differential soil metabolites in PHE-contaminated soil with and without biochar amendment over a 45-day incubation period. Results showed that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification were the dominant nitrogen metabolism processes in PHE-contaminated soil. The addition of biochar enhanced nitrogen modules, exhibiting discernible temporal fluctuations in denitrification and DNRA proportions. Co-occurrence networks and correlation heatmap analysis revealed potential interactions among functional genes and enzymes responsible for PHE biodegradation and nitrogen metabolism. Notably, enzymes associated with denitrification and DNRA displayed significant positive correlation with enzymes involved in downstream phenanthrene degradation. Of particular interest was stronger correlation observed with the addition of biochar. However, biochar amendment inhibited the 9-phenanthrol degradation pathway, resulting in elevated levels of glutathione (GSH) in response to environmental stress. These findings provide new insights into the interactions between nitrogen metabolism and PHE biodegradation in soil and highlight the dual effects of biochar on these processes.

Biodegradation of Phenanthrene Polluted Soil through Native Strains in the Darkhouvin Oil Field

As a resistant and toxic polycyclic aromatic hydrocarbon (PAHs), phenanthrene is largely distributed in aquatic and terrestrial environments with adverse biological consequences. Mineralization of this toxic component via bioremediation has been vastly studied in recent years and might lead to new hope in the economic clean-up of this contaminant. The aim of this study was the isolation and identification of phenanthrene degrading bacteria from petroleum polluted environments and the assessment of their growth kinetics. Soil samples were collected from the oil-polluted sites of Darkhouvin oilfield, Iran. Bacterial isolates capable of degrading phenanthrene were characterized genetically and morphologically. Optimal level of environmental parameters including pH, time, temperature, nitrogen and phosphate source, and phenanthrene concentration were determined using Taguchi method. The results showed that different bacterial genera were isolated in which Bacillus mojavensis and Lysinibacillus sphaericus were identified as phenanthrene degrading isolates. Isolated strains showed hemolytic activity and deceased surface tension values. The optimal condition was determined as 45 °C, pH 7, nitrate 1 µg/mL, sodium phosphate 0.3 µg/mL, and on the fifth day of culturing for B. mojavensis, which showed prominent activity in phenanthrene biodegradation. In this study, the ability of native strains on the biodegradation of phenanthrene in soil was investigated. The findings suggest that isolated biosurfactant generating bacteria could biodegrade phenanthrene in optimum conditions.

Biochar prepared from Fe‐rich sludge as suitable microbial carriers for facilitating biodegradation of phenanthrene in soil

AbstractBACKGROUNDConverting waste biomass to biochar by pyrolysis is increasingly recognized as an effective waste regeneration method and could be applied in contaminated soil bioremediation. In this work, we compared the properties of three biochars (FB300, FB500 and FB700) derived from iron (Fe)‐rich sludge (FS) at 300, 500 and 700 °C, and selected FB500 as microbial carrier to evaluate its function in facilitating phenanthrene (PHE) biodegradation in soil.RESULTSIncreasing pyrolysis temperature induced a positive relationship with the ash content, pH and pore size of biochars, but a negative relationship with the yield and surface area of the biochars. FB300 and FB500 maintained more organic matter than FB700, whereas, FB500 and FB700 had greater aromatic constituents and more crystal structures than FB300. Besides, FB500 showed the strongest stability and unique magnetic properties. Thus, FB500 was selected as microbial carrier in facilitating PHE biodegradation in soil. The degradation results indicated that FB500 with bacteria immobilization played a significant role in PHE degradation; its PHE removal rate of 58.15 ± 4.90% was much higher than that of 38.73 ± 3.98% for free bacteria treatment on the first day of degradation.CONCLUSIONFe‐rich sludge can be efficiently converted into biochar that in turn can serve as microbial carrier for PHE biodegradation in contaminated soil. FB500 with bacteria immobilization was proven to promote PHE degradation. Pyrolyzing Fe‐rich sludge to biochar is a promising method for remediation of PAH‐contaminated soil. © 2021 Society of Chemical Industry (SCI).

Responses of phenanthrene degradation to the changes in bioavailability and microbial community structure in soils amended with biochars pyrolyzed at low and high temperatures

This study investigated the impact of wheat straw biochars pyrolyzed at temperatures of 100–700 ℃ (BC100-BC700) on biodegradation of phenanthrene in soils. During a 42-day experiment, biochar amendment reduced the biodegradation ratio of phenanthrene in soils by no change-77.0%. The biodegradation ratio decreased with the increase of pyrolysis temperature from 100 to 400 ℃ and then increased with the increase of pyrolysis temperature from 400 to 700 ℃, exhibiting a U-shape. Meanwhile, desorbing fraction of phenanthrene extracted by n-butanol declined with increasing pyrolysis temperature. Biochar-derived dissolved organic carbon (DOC) obviously influenced the soil DOC contents which were negatively correlated with the total relative abundances of dominant polycyclic aromatic hydrocarbon (PAH)-degraders. These results indicated that in soils amended with biochars pyrolyzed at low temperatures (i.e. 100–400 ℃), both the reduced bioavailability of phenanthrene and the reduced PAH-degrader abundance resulted in decreasing phenanthrene degradation with pyrolysis temperature. In soils amended with biochars pyrolyzed at high temperatures (i.e. 500–700 ℃; HT-biochars), two possible reasons contribute to increasing phenanthrene degradation with pyrolysis temperature: (1) high sorbed-phenanthrene concentration due to large specific surface area and high aromaticity of the biochars, and (2) the increased dominant PAH-degrader abundance for the removal of sorbed-phenanthrene due to the impact of HT-biochars on soil properties (mainly on DOC content).

Both artificial root exudates and natural Koelreuteria paniculata exudates modify bacterial community structure and enhance phenanthrene biodegradation in contaminated soils

Polycyclic aromatic hydrocarbons (PAHs) are environmental pollutants that represent a serious threat to the health of humans and ecosystems. The effects of plant root and artificial root exudates (ARE) on the biodegradation of phenanthrene (PHE) and their impact on soil bacterial community structure was the focus of this work using four treatments for 180 days. Treatments included; control treatment (CK), low concentration of ARE (AREL), high concentration of ARE (AREH), and planting Koelreuteria paniculata saplings (KOE). The diversity and composition of soil bacterial community were analyzed using high-throughput sequencing. The results showed that KOE treatments had the most significant effect on the biodegradation of PHE compared to controls. ARE treatments had the similar effects on the biodegradation of PHE in soil with high efficiency in AREH than AREL. Both KOE and ARE treatments reduced diversity of bacterial community but increased the abundance of PAHs degrading bacterial populations within representative phyla, including Proteobacteria and Firmicutes. During the study, the total bacterial OTUs showed the number of unique genus types initially increased, then lowered in the later stages of the incubation process. Specific bacterial populations enriched by the treatments and supported by the exudates seemed to determine the biodegradation of PHE and not the overall bacterial diversity.

Impact of organic amendments on the development of 14C-phenanthrene catabolism in soil

This study investigated the impact of spent brewery grains and spent mushroom compost on the development of phenanthrene biodegradation in soil. Two aspects were considered: (i) the influence of increasing waste-to-soil ratios (1:10, 1:5, 1:2, 1:1 & 2:1) and (ii) the impact of soil-PAH contact time (1–100 d). Biodegradation was quantified by measuring changes in the lag phase, the fastest rates and extents of mineralization of 14C-phenanthrene, as well as changes in the number of total heterotrophic and phenanthrene degrading bacteria and fungi. The amendment of smaller amounts of the wastes (1:10 & 1:5) resulted in greatest levels of biodegradation. Microbial numbers increased in all of the amended soils but phenanthrene-degrading numbers in most amended soils did not correlate with the rates and extents of 14C-phenanthrene mineralization. This investigation highlighted the value of waste organic materials as nutrient sources to stimulate microbial degradation of contaminants in soil.

Optimisation of XAD extraction methodology for the assessment of biodegradation potential of 14C-phenanthrene in soil

Abstract This study investigated the use of a hydrophobic resin, amberlite XAD, as a tool for assessing the biodegradation potential of 14C-phenanthrene in soil. The method was optimised in terms of soil/XAD ratio, shaking, extraction time and eluting solvent. The most effective method was then tested on selected XADs, and the performance compared with cyclodextrin (HP- β -CD) and dichloromethane (DCM) extractions suitability to predict phenanthrene biodegradation in soil over 100 d. Results showed that the optimum conditions for the XAD extraction technique are a 2:1 soil/XAD ratio, 100 rpm mixing for 22 h and elution using a DCM:methanol solution (1:1). Mineralisation of 14C-phenanthrene was accurately predicted by HP- β -CD ( r 2 = 0 . 990 , slope = 0.953, intercept = 1.374) and XAD-4 extractions ( r 2 = 0 . 989 , slope = 0.820, intercept = 6.567), while DCM overestimated the bioaccessibility of 14C-phenanthrene ( r 2 = 0 . 999 , slope = 1.328, intercept = − 49 . 507 ). This investigation showed that XAD extraction can be considered a suitable non-exhaustive technique for estimating biodegradability of phenanthrene in soil.

The effective migration of Massilia sp. WF1 by Phanerochaete chrysosporium and its phenanthrene biodegradation in soil

Pollutant-degrading bacteria migrated by fungi may enhance the contacts between microorganisms and pollutants and improve the bioremediation efficiency of persistent organic pollutants in soil. Here, the migration of phenanthrene (PHE)-degrading bacteria Massilia sp. WF1 and Mycobacterium sp. WY10 by the hydrophobic fungi Phanerochaete chrysosporium (P. chrysosporium) and its effects on the PHE biodegradation in soil were investigated. Migration of the hydrophilic bacterium WF1 was better than that of the hydrophobic bacterium WY10 by P. chrysosporium mycelia since strain WF1 possesses flagellum and the type III secretion system. The interaction energy change of P. chrysosporium-WF1 was lower, but the interaction forces (van der Waals attractions, capillary forces, and cross-linking effects) were stronger than those of P. chrysosporium-WY10. Thus, the adhesive attraction between strain WF1 and P. chrysosporium was stronger, and consequently, strain WF1 was migrated by P. chrysosporium to a greater extent than WY10. The corresponding migration mechanism was inferred to be a bacterial ‘passive’ method: bacteria adhered to mycelia before they migrated with the growing mycelia. Moreover, migrated strain WF1 via P. chrysosporium showed effective PHE biodegradation in soil. Fungus-mediated migration of pollutant-degrading bacteria may play an important role in the bioremediation of pollutants in soil.

Effects of plant species identity, diversity and soil fertility on biodegradation of phenanthrene in soil

The work presented in this paper investigated the effects of plant species composition, species diversity and soil fertility on biodegradation of 14C-phenanthrene in soil. The two soils used were of contrasting fertility, taken from long term unfertilised and fertilised grassland, showing differences in total nitrogen content (%N). Plant communities consisted of six different plant species: two grasses, two forbs, and two legume species, and ranged in species richness from 1 to 6. The degradation of 14C-phenanthrene was evaluated by measuring indigenous catabolic activity following the addition of the contaminant to soil using respirometry. Soil fertility was a driving factor in all aspects of 14C-phenanthrene degradation; lag phase, maximum rates and total extents of 14C-phenanthrene mineralisation were higher in improved soils compared to unimproved soils. Plant identity had a significant effect on the lag phase and extents of mineralisation. Soil fertility was the major influence also on abundance of microbial communities.

Influence of Activated Charcoal on Desorption Kinetics and Biodegradation of Phenanthrene in Soil

The observed strong sorption of polycyclic aromatic hydrocarbons (PAHs) to black carbon (BC) presents potential implications for PAH bioaccessibility in soils. The effects of BC on the desorption kinetics and mineralization of phenanthrene in four soils was investigated after 1, 25, 50, and 100 d soil-PAH contact time, using sequential hydroxypropyl-β-cyclodextrin (HPCD) extractions in soils amended with 0, 0.1, 1, and 5% (dry wt. soil) activated charcoal (AC, a form of BC). The rapidly (%F(rap)) and slowly (%F(slow)) desorbing phenanthrene fractions and their rate constants were determined using a first-order two-compartment (biphasic) desorption model. A minimum 7.8-fold decrease in %F(rap) occurred when AC was increased from 0 to 5%, with a corresponding increase in %F(slow). Desorption rate constants followed the progression k(rap) (% h(-1)) > k(slow) (% h(-1)) and were in the order of 10(-1) to 10(-2) and 10(-3) to 10(-4), respectively. Linear regressions between %F(rap) and the fractions degraded by a phenanthrene-degrading inoculum (%F(min)) indicated that slopes did not approximate 1 at concentrations greater than 0% AC; %F(min) often exceeded %F(rap), indicating a fraction of sorbed phenanthrene (%F(slow)) remained microbially accessible. Therefore, HPCD-desorption kinetics alone may not be an adequate basis for the prediction of the bioaccessibility of PAHs to microorganisms or bioremediation potential in AC-amended soils.

Linking desorption kinetics to phenanthrene biodegradation in soil

The desorption of polycyclic aromatic hydrocarbons (PAHs) often exhibits a biphasic profile similar to that observed for biodegradation whereby an initial rapid phase of degradation or desorption is followed by a phase of much slower transformation or release. Most investigations to-date have utilised a polymeric sorbent, such as Tenax, to characterise desorption, which is methodologically unsuitable for the analysis of soil. In this study, desorption kinetics of 14C-phenanthrene were measured by consecutive extraction using aqueous solutions of hydroxypropyl-β-cyclodextrin (HPCD). The data indicate that the fraction extracted after 24 h generally approximated the linearly sorbed, rapidly desorbing fraction ( F rap), calculated using a three-compartment model. A good linear correlation between phenanthrene mineralised and F rap was observed ( r 2 = 0.89; gradient = 0.85; intercept = 8.20). Hence HPCD extraction (24 h) and first-order three-compartment modelling appear to provide an operationally straightforward tool for estimating mass-transfer limited biodegradation in soil.

Electronic nose and SPME techniques to monitor phenanthrene biodegradation in soil

Abstract Phenanthrene is a hydrophobic organic pollutant, composed of three-fused benzene rings belonging to polycyclic aromatic hydrocarbons (PAHs). PAHs are produced by incomplete combustion of organic matter due to natural events, i.e. fires, and anthropogenic actions, i.e. C-containing fuels combustion. The presence of PAHs in contaminated soils is usually detected by classical extraction techniques, such as solvent extractions through Soxhlet extractor. In this work two recently developed techniques (solid phase microextraction—SPME and electronic nose—EN) able to analyse the headspace of solid or liquid samples were used to monitor the possible degradation of phenanthrene in an artificially contaminated soil. The analysis by SPME showed a drastic decrease of phenanthrene content after 30 days of incubation (−92%) and different treatments with nutrient solutions and/or surfactant improve this rate up to 97%. Differently, the analysis of soil headspaces by EN, processed by principal component analysis (PCA), showed that contaminated and uncontaminated soil samples (controls) might be distinguished on a temporal scale. Furthermore, PCA showed that phenanthrene-contaminated soil samples produced chemical images, which were delayed relative to controls at the same period of incubation. The application of partial least square-discriminant analysis (PLS-DA) to chromatograms obtained by SPME pointed out the presence, in the headspace of phenanthrene-treated soils, of a series of possible indicators involved in phenanthrene degradation, which were completely absent in relative unpolluted controls. Results suggest that the two techniques do not necessarily represent mutually exclusive alternatives, but giving different information, they may be considered as complementary.

Enhanced desorption and biodegradation of phenanthrene in soil–water systems with the presence of anionic–nonionic mixed surfactants

The effects of anionic–nonionic mixed surfactants, sodium dodecyl sulfate (SDS) mixed with Triton X-100 (TX100), on the desorption and biodegradation of phenanthrene in soil–water system were investigated in an aim to improve the efficiency of surfactant bioremediation technology. Results indicated that the presence of SDS not only increased the solubilization of TX100 for phenanthrene, but also reduced the sorption of TX100 onto soils. As a result, the desorption efficiency of phenanthrene from the contaminated soil was greatly enhanced by mixed surfactant solutions compared with that by single TX100 solution and appeared to be positively related with the mole fraction of SDS in solution. Mixed surfactants with relatively smaller ratio promoted phenanthrene biodegradation, for example, the biodegradation percentage of phenanthrene in 1:9 SDS–TX100 mixed solutions was about 165% of that in the single TX100 solution at the same TX100 concentration of 1.6 mmol/L in 24 h. But the biodegradation was inhibited with larger ratio of SDS in the mixed solutions, which may be due to the preferential utilization of SDS by phenanthrene degraders. Thus, the selection of mixed surfactants should consider simultaneously the effects of SDS on desorption and biodegradation. The experimental results can be used to provide valuable information in designing the surfactant bioremediation technology for contaminated soils.

Biodegradation of phenanthrene by the indigenous microbial biomass in a zinc amended soil

To study the effect of zinc on the biodegradation of phenanthrene by the microbial biomass in soil. Uncontaminated soil was amended with zinc and phenanthrene as single or co-contaminants, and microbial metabolic activity was measured using an intracellular dehydrogenase enzyme bioassay over 37 days. Contaminants were amended at optimum, action and double the action level specified in 'The New Dutch List' (Ministry of Housing, Spatial Planning and Environment, the Netherlands, 2000). Microbial activity in soils with zinc or phenanthrene alone indicated the presence of tolerant, albeit inhibited soil micro-organisms. A zinc concentration at the optimum level of 140 mg kg(-1) in the co-contaminated soil (phenanthrene at 40 mg kg(-1)) resulted in marginal stimulation of the rate of phenanthrene biodegradation. However, Zn2+ concentrations at the action and double the action level of zinc (720 and 1440 mg kg(-1)) inhibited phenanthrene degradation. Biodegradation of phenanthrene in soils co-contaminated with zinc at concentrations above the action value is impeded. Bioremediation efforts to remove polycyclic aromatic hydrocarbon in zinc co-contaminated soils are likely to be constrained.

Enhanced phenanthrene biodegradation in soil by slender oat root exudates and root debris.

To investigate the mechanisms by which slender oat (Avena barbata Pott ex Link) enhances phenanthrene biodegradation, we analyzed the impacts of root exudates and root debris on phenanthrene biodegradation and degrader community dynamics. Accelerated phenanthrene biodegradation rates occurred in soils amended with slender oat root exudates as well as combined root debris + root exudate as compared with unamended controls. Root exudates significantly enhanced phenanthrene biodegradation in rhizosphere soils, either by increasing contaminant bioavailability and/or increasing microbial population size and activity. A modified most probable number (MPN) method was used to determine quantitative shifts in heterotrophic and phenanthrene degrader communities. During the first 4 to 6 d of treatment, heterotrophic populations increased in all amended soils. Both root debris-amended and exudate-amended soil then maintained larger phenanthrene degrader populations than in control soils later in the experiment after much of the phenanthrene had been utilized. Thus, root amendments had a greater impact over time on phenanthrene degraders than heterotrophs resulting in selective maintenance of degrader populations in amended soils compared with controls.

Effect of organic matter and clays on the biodegradation of Phenanthrene in soils

Soil organic matter and clays represent an important hinderance for bioremediation technologies, as they may cause a retardation in the biological removal of hydrophobic pollutants. To overcome this limitation it is necessary to understand how these two soil constituents influence biodegradation. The results herein reported suggest that the bioavailability of phenanthrene in soils is affected not only by sorption to the organic matter or clays, but also by the interaction of phenanthrene with humic fractions-clay complexes.

Bacterial Transport and Phenanthrene Biodegradation in Soil and Aquifer Sand

AbstractRemediation of contaminated soil by inoculated bacteria requires movement of the bacteria to the site of contamination. Addition of a phenanthrene‐metabolizing Psudomonas sp. to the surface of 1.5‐cm columns of sterile or nonsterile soil or aquifer sand resulted in the rapid mineralization of phenanthrene present in the top 0.4 cm of sand or soil columns receiving intermittent or no water flow. However, the surface‐inoculated pseudomonad mineralized little of the substrate present in the bottom 0.4‐cm portion of nonsterile soil or aquifer sand that had been sterilized prior to inoculation, although mineralization occurred at the bottom of nonsterile aquifer sand. Little biodegradation was evident if the bacterium and the substrate were both at the bottom part of columns of soil and aquifer sand receiving intermittent flows of water, although rapid biodegradation occurred at this site in soil if the water flow was constant. Only ≈1% of the added cells passed through the soil after passage of ≈1.5 pore volumes of water, although ≈4% passed through the aquifer sand. We suggest that bacteria added to the soil surface or to aquifer solids for biodegradation may not be transported sufficiently to reach organic pollutants at sites distant from channels or macropores.

Enhanced mineralization of organic compounds in nonaqueous‐phase liquids

AbstractBiodegradation of phenanthrene, biphenyl, or di(2 ethylhexyl) phthalate initially present in a variety of nonaqueous phase liquids (NAPLs) was slow in samples of soil and aquifer solids The NAPLs were hexadecane, dibutyl phthalate, 2,2,4,4,6,8,8‐heptamethylnonane, cyclohexane, commercial oils, crude oil, creosote, and kerosene Slurrying the soil or aquifer solids markedly enhanced the rate and extent of mineralization of the test compounds initially in many of the NAPLs Both the low rate and the extent of mineralization of the three compounds initially in dibutyl phthalate in soil slurries and of di(2 ethylhexyl) phthalate in heptamethylnonane present in slurries of aquifer solids were increased by inoculation of acclimated microbial cultures Increasing the NAPL volume decreased phenanthrene biodegradation in soil, but the effect of larger NAPL volume could be alleviated by slurrying and inoculation The rate or extent of mineralization in aquifer slurries of di(2‐ethylhexyl) phthalate initially in some NAPLs was increased by addition of N and P, and inoculation further enhanced the degradation