The adaptation of two similar soils to pyrene catabolism

Shifts of the new functional marker gene (pahE) of polycyclic aromatic hydrocarbons (PAHs) degrading bacterial population and its relationship with PAHs biodegradation

Identification of polycyclic aromatic hydrocarbons (PAHs) degrading bacterial populations and understanding their responses to PAHs are crucial for the designing of appropriate bioremediation strategies. In this study, the responses of PAHs-degrading bacterial populations to different PAHs were studied in terms of the compositions and abundance variations of their new functional marker gene (pahE) by gene-targeted metagenomic and qPCR analysis. Overall, PAHs species significantly affected the composition and abundance of pahE gene within the PAHs-degrading bacteria in each treatment and different pahE of PAHs-degrading bacteria involved in the different stages of PAHs degradation. Noted that new pahE genotypes were also discovered in all PAHs treatment groups, indicating that some potential new PAHs-degrading bacterial genera were also involved in PAHs degradation. Besides, all three PAH removal rates were significantly positively related with pahE gene abundances (R² = 0.908 ~ 0.922, p < 0.01), demonstrating that pahE could be a good indicator of PAHs degradation activity or potential. This is the first study focusing on the dynamic changes of the pahE gene within PAHs-degrading bacterial community during the degradation of PAHs in mangrove sediment, providing novel insights into the use of pahE gene as the functional marker to indicate PAH degradation.

Global distribution of oxygenated polycyclic aromatic hydrocarbons in mineral topsoils

Hazardous oxygenated polycyclic aromatic hydrocarbons (OPAHs) originate from combustion (primary sources) or postemission conversion of polycyclic aromatic hydrocarbons (PAHs) (secondary sources). We evaluated the global distribution of up to 15 OPAHs in 195 mineral topsoils from 33 study sites (covering 52° N-47° S, 71° W-118 °E) to identify indications of primary or secondary sources of OPAHs. The sums of the (frequently measured 7 and 15) OPAH concentrations correlated with those of the Σ16EPA-PAHs. The relationship of the Σ16EPA-PAH concentrations with the Σ7OPAH/Σ16EPA-PAH concentration ratios (a measure of the variable OPAH sources) could be described by a power function with a negative exponent <1, leveling off at a Σ16EPA-PAH concentration of approximately 400 ng g^-1 . We suggest that below this value, secondary sources contributed more to the OPAH burden in soil than above this value, where primary sources dominated the OPAH mixture. This was supported by a negative correlation of the Σ16EPA-PAH concentrations with the contribution of the more readily biologically produced highly polar OPAHs (log octanol-water partition coefficient <3) to the Σ7OPAH concentrations. We identified mean annual precipitation (Spearman ρ = .33, p < .001, n = 143) and clay concentrations (ρ = .55, p < .001, n = 33) as important drivers of the Σ7OPAH/Σ16EPA-PAH concentration ratios. Our results indicate that at low PAH contamination levels, secondary sources contribute considerably and to a variable extent to total OPAH concentrations, whereas at Σ16EPA-PAH contamination levels >400 ng g^-1 , there was a nearly constant Σ7OPAH/Σ16EPA-PAH ratio (0.08 ± 0.005 [SE], n = 80) determined by their combustion sources.

Impact of digestate and its fractions on mineralization of 14C-phenanthrene in aged soil

The impact of whole digestate (WD) and its fractions (solid [SD] and liquid [LD]) on ¹⁴C-phenanthrene mineralization in soil over 90 d contact time was investigated. The ¹⁴C-phenanthrene spiked soil was aged for 1, 30, 60 and 90 d. Analysis of water-soluble nitrogen, phosphorus, total (organic and inorganic) carbon, and quantitative bacterial count were conducted at each time point to assess their impact on mineralization of ¹⁴C-phenanthrene in soils. Indigenous catabolic activity (total extents, maximum rates and lag phases) of ¹⁴C-phenanthrene mineralization were measured using respirometric soil slurry assay. The soil amended with WD outperformed the SD and LD fractions as well as showed a shorter lag phase, higher rate and extent of mineralization throughout the study. The digestates improved (P < 0.05) the microbial population and nutritive content of the soil. However, findings showed that spiking soil with phenanthrene generally reduced the growth of microbial populations from 1 to 90 d and gave a lower nutritive content in comparison with the non-spiked soil. Also, soil fertility and bacteria count were major factors driving ¹⁴C-phenanthrene mineralization. Particularly, the non-phenanthrene degraders positively influenced the cumulative mineralization of ¹⁴C-phenanthrene after 60 d incubation. Therefore, the digestates (residue from anaerobic digestion) especially WD, which enhanced ¹⁴C-phenanthrene mineralization of the soil without minimal basal salts medium nor additional degraders should be further exploited for sustainable bioremediation of PAHs contaminated soil.

Indigenous 14C-phenanthrene biodegradation in "pristine" woodland and grassland soils from Norway and the United Kingdom

In this study, the indigenous microbial mineralisation of ¹⁴C-phenanthrene in seven background soils (four from Norwegian woodland and three from the UK (two grasslands and one woodland)) was investigated. ∑PAHs ranged from 16.39 to 285.54 ng g^-1 dw soil. Lag phases (time before ¹⁴C-phenanthrene mineralisation reached 5%) were longer in all of the Norwegian soils and correlated positively with TOC, but negatively with ∑PAHs and phenanthrene degraders for all soils. ¹⁴C-phenanthrene mineralisation in the soils varied due to physicochemical properties. The results show that indigenous microorganisms can adapt to ¹⁴C-phenanthrene mineralisation following diffuse PAH contamination. Considering the potential of soil as a secondary PAH source, these findings highlight the important role of indigenous microflora in the processing of PAHs in the environment.

Rhizosphere effect is stronger than PAH concentration on shaping spatial bacterial assemblages along centimetre-scale depth gradients

At centimetre scale, soil bacterial assemblages are shaped by both abiotic (edaphic characteristics and pollutants) and biotic parameters. In a rhizobox experiment carried out on planted industrial soil contaminated with polycyclic aromatic hydrocarbons (PAHs), we previously showed that pollution was distributed randomly with hot and cold spots. Therefore, in the present study, we investigated the effect of this patchy PAH distribution on the bacterial community assemblage and compared it with that of root depth gradients found in the rhizosphere of either alfalfa or ryegrass. Sequencing of 16S rRNA amplicons revealed a higher bacterial diversity in ryegrass rhizosphere and enrichment in specific taxa by the 2 plant species. Indeed, Bacteroidetes, Firmicutes, and Gammaproteobacteria were globally favored in alfalfa, whereas Acidimicrobiia, Chloroflexi, Alpha-, and Betaproteobacteria were globally favored in ryegrass rhizosphere. The presence of alfalfa created depth gradients of root biomass, carbohydrate, and pH, and actually shaped the bacterial assemblage, favoring Actinobacteria near the surface and Gemmatimonadetes and Proteobacteria at greater depths. Contrarily, the bacterial assemblage was homogeneous all along depths of the ryegrass root system. With both plant species, the PAH content and random distribution had no significant effect on bacterial assemblage. Globally, at centimeter scale, bacterial community assemblages were mostly shaped by soil physical and chemical depth gradients induced by root growth but not by patchy PAH content.

Bioavailability of five hydrophobic organic compounds to earthworms from sterile and non-sterile artificial soils

Bioaccumulation factors (BAFs) of organic pollutants to soil biota, often required by risk assessment, are mostly obtained in non-sterile laboratory-contaminated artificial soils. However, microbial degradation has been indicated by many authors to influence the fate of hydrophobic organic compounds (HOCs) in soils. A question arises if the microbial community of peat which is used for artificial soil preparation affects the measured values of BAFs. In this study the effect of soil microorganisms on bioavailability of HOCs was studied and a portion of each soil was sterilized by gamma irradiation. Results indicated that the sterilization process significantly affected the fate of polycyclic aromatic hydrocarbons (PAHs; phenanthrene and pyrene) and increased bioavailability of these compounds to earthworms with BAFs several times higher in the sterile soils compared to their non-sterile variants. This suggests that sterilization of soils can be used as the "worst-case scenario" for laboratory tests of toxicity or bioaccumulation of biodegradable HOCs such as PAHs. It represents a situation of limited microbial degradation resulting in higher bioavailable fractions to other organisms (e.g. invertebrates). This may be the case in soils where microbial communities face stresses caused by contamination or land management. The bioavailability of chlorinated HOCs (lindane, 4,4'-DDT and PCB 153) was not affected by sterilization, as their BAFs were similar in the sterile and non-sterile soils during the experiment.

Residual hydrophobic organic contaminants in soil: Are they a barrier to risk-based approaches for managing contaminated land?

Risk-based approaches to managing contaminated land, rather than approaches based on complete contaminant removal, have gained acceptance as they are likely to be more feasible and cost effective. Risk-based approaches aim to minimise risks of exposure of a specified contaminant to humans. However, adopting a risk-based approach over alternative overly-conservative approaches requires that associated uncertainties in decision making are understood and minimised. Irrespective of the nature of contaminants, a critical uncertainty is whether there are potential risks associated with exposure to the residual contaminant fractions in soil to humans and other ecological receptors, and how they should be considered in the risk assessment process. This review focusing on hydrophobic organic contaminants (HOCs), especially polycyclic aromatic hydrocarbons (PAHs), suggests that there is significant uncertainty on the residual fractions of contaminants from risk perspectives. This is because very few studies have focused on understanding the desorption behaviour of HOCs, with few or no studies considering the influence of exposure-specific factors. In particular, it is not clear whether the exposure of soil-associated HOCs to gastrointestinal fluids and enzyme processes release bound residues. Although, in vitro models have been used to predict PAH bioaccessibility, and chemical extractions have been used to determine residual fractions in various soils, there are still doubts about what is actually being measured. Therefore it is not certain which bioaccessibility method currently represents the best choice, or provides the best estimate, of in vivo PAH bioavailability. It is suggested that the fate and behaviour of HOCs in a wide range of soils, and that consider exposure-specific scenarios, be investigated. Exposure-specific scenarios are important for validation purposes, which may be useful for the development of standardised methods and procedures for HOC bioaccessibility determinations. Research is needed to propose the most appropriate testing methods and for assessing potential risks posed by residual fractions of HOCs. Such investigations may be useful for minimising uncertainties associated with a risk-based approach, so that consideration may then be given to its adoption on a global scale. This review critically appraises existing information on the bioavailability of HOC residues in soil to establish whether there may be risks from highly sequestered contaminant residues.

Metal/metalloid elements and polycyclic aromatic hydrocarbon in various biochars: The effect of feedstock, temperature, minerals, and properties

Fourteen metal/metalloid elements and sixteen polycyclic aromatic hydrocarbons (PAHs) within biochars were quantified to investigate how heat treatment temperatures (HTTs) and feedstocks affect their concentration and composition. Concentrations and composition of metals/metalloids were strongly dependent upon feedstocks rather than HTTs. HTTs significantly affected concentrations and composition of PAHs. The highest concentration of PAHs was observed for plant residue-derived biochars (PLABs) produced at 450 °C and the opposite result was for animal waste-derived bichars. High mineral content was responsible for depolymerization of organic matter (OM), which facilitated high production of PAHs. High HTTs pyrolysis or combustion PAHs (COMB) of PLABs possibly blocks their micropores derived from other components within OM and leads to a decline of CO2-surface areas (CO2-SAs). Concentration of ∑COMB or individual PAH was affected by biochar properties, including composition and contents of functional groups, ash content, and CO2-SAs. PLABs produced at 600 °C were recommended for low toxicity.

The impact of carbon nanomaterials on the development of phenanthrene catabolism in soil

This study investigates the impact of different types of carbon nanomaterials (CNMs) namely C60, multi-walled carbon nanotubes (MWCNTs) and fullerene soot on the catabolism of (14)C-phenanthrene in soil by indigenous microorganisms. Different concentrations (0%, 0.01%, 0.1% and 1%) of the different CNMs were blended with soil spiked with 50 mg kg(-1) of (12)C-phenanthrene, and aged for 1, 25, 50 and 100 days. An increase in the concentration of MWCNT- and FS-amended soils showed a significant difference (P = 0.014) in the lag phase, maximum rates and overall extent of (14)C-phenanthrene mineralisation. Microbial cell numbers did not show an obvious trend, but it was observed that control soils had the highest population of heterotrophic and phenanthrene degrading bacteria at all time points.

Experimental design approach to the optimization of PAHs bioremediation from artificially contaminated soil: application of variables screening development

BACKGROUND

The effectiveness of bioremediation systems for PAH-contaminated soil may be constrained by physicochemical properties of contaminants and environmental factors. Information on what is the most effective factor in bioremediation process is essential in the decision of what stimulations can be taken to assist the biodegradation efficacy.

METHODS

In this study, four factors of surfactant (Tween 80), humic acid (HA), salinity and nutrients in a 2(4) full factorial design were screened in bioremediation of phenanthrene contaminated soil by using a consortium of bacteria.

RESULTS

Between the employed levels of the factors only salinity had not significant effect. Optimal concentrations of surfactant, HA and nutrient were obtained by a response surface design. For phenanthrene biodegradation, a central composite face centred design (CCFD) showed that nutrient, surfactant and HA concentrations had highly significant, significant and insignificant effects, respectively. The best conditions with 87.1% phenanthrene biodegradation were 150 mg HA/Kg soil, 12.68 μg/L surfactant, and nutrients as K2HPO4, 0.8; KH2PO4, 0.2 and KNO3, 1 g/L. A high similarity was between the model prediction and experimental results.

CONCLUSIONS

This study showed that nutrient with 81.27% efficiency could be considered as the most effective factor for practical implications of bioremediation process for PAHs contaminated soil cleanup strategies.

Potential impact of soil microbial heterogeneity on the persistence of hydrocarbons in contaminated subsurface soils

In situ bioremediation is potentially a cost effective treatment strategy for subsurface soils contaminated with petroleum hydrocarbons, however, limited information is available regarding the impact of soil spatial heterogeneity on bioremediation efficacy. In this study, we assessed issues associated with hydrocarbon biodegradation and soil spatial heterogeneity (samples designated as FTF 1, 5 and 8) from a site in which in situ bioremediation was proposed for hydrocarbon removal. Test pit activities showed similarities in FTF soil profiles with elevated hydrocarbon concentrations detected in all soils at 2 m below ground surface. However, PCR-DGGE-based cluster analysis showed that the bacterial community in FTF 5 (at 2 m) was substantially different (53% dissimilar) and 2-3 fold more diverse than communities in FTF 1 and 8 (with 80% similarity). When hydrocarbon degrading potential was assessed, differences were observed in the extent of (14)C-benzene mineralisation under aerobic conditions with FTF 5 exhibiting the highest hydrocarbon removal potential compared to FTF 1 and 8. Further analysis indicated that the FTF 5 microbial community was substantially different from other FTF samples and dominated by putative hydrocarbon degraders belonging to Pseudomonads, Xanthomonads and Enterobacteria. However, hydrocarbon removal in FTF 5 under anaerobic conditions with nitrate and sulphate electron acceptors was limited suggesting that aerobic conditions were crucial for hydrocarbon removal. This study highlights the importance of assessing available microbial capacity prior to bioremediation and shows that the site's spatial heterogeneity can adversely affect the success of in situ bioremediation unless area-specific optimizations are performed.

Short-term effect of aniline on soil microbial activity: a combined study by isothermal microcalorimetry, glucose analysis, and enzyme assay techniques

The accidents of aniline spill and explosion happened almost every year in China, whereas the toxic effect of aniline on soil microbial activity remained largely unexplored. In this study, isothermal microcalorimetric technique, glucose analysis, and soil enzyme assay techniques were employed to investigate the toxic effect of aniline on microbial activity in Chinese soil for the first time. Soil samples were treated with aniline from 0 to 2.5 mg/g soil to tie in with the fact of aniline spill. Results from microcalorimetric analysis showed that the introduction of aniline had a significant adverse effect on soil microbial activity at the exposure concentrations ≥0.4 mg/g soil (p < 0.05) and ≥0.8 mg/g soil (p < 0.01), and the activity was totally inhibited when the concentration increased to 2.5 mg/g soil. The glucose analysis indicated that aniline significantly decreased the soil microbial respiratory activity at the concentrations ≥0.8 mg/g soil (p < 0.05) and ≥1.5 mg/g soil (p < 0.01). Soil enzyme activities for β-glucosidase, urease, acid-phosphatase, and dehydrogenase revealed that aniline had a significant effect (p < 0.05) on the nutrient cycling of C, N, and P as well as the oxidative capacity of soil microorganisms, respectively. All of these results showed an intensively toxic effect of aniline on soil microbial activity. The proposed methods can provide toxicological information of aniline to soil microbes from the metabolic and biochemical point of views which are consistent with and correlated to each other.

Impact of Zn and Cu on the development of phenanthrene catabolism in soil

Mixtures of polycyclic aromatic hydrocarbons (PAHs) and heavy metals are of major concern in contaminated soil. Biodegradation of PAHs in metal-contaminated soils is complicated because metals are toxic and cannot be degraded by biological processes. This investigation considered the effects of Zn and Cu (50, 100, 500 and 1,000 mg/kg) on (14)C-phenanthrene biodegradation in soil over 60-day contact time. The presence of Zn at all concentrations and low concentrations of Cu (50 and 100 mg/kg) had no significant effect (p > 0.05) on the development of phenanthrene catabolism; however, at higher Cu concentrations, the development of phenanthrene catabolism and bacterial cell numbers were significantly reduced (p < 0.05). This suggests that Cu is more toxic than Zn to soil microbial PAH catabolic activity. Metal/PAH-contaminated soils represent one of the most difficult remedial challenges and insights into PAH biodegradation in the presence of metals is necessary in order to assess the potential for bioremediation.

Assessing impediments to hydrocarbon biodegradation in weathered contaminated soils

In this study, impediments to hydrocarbon biodegradation in contaminated soils were assessed using chemical and molecular methodologies. Two long-term hydrocarbon contaminated soils were utilised which were similar in physico-chemical properties but differed in the extent of hydrocarbon (C10-C40) contamination (S1: 16.5 g kg(-1); S2: 68.9 g kg(-1)). Under enhanced natural attenuation (ENA) conditions, hydrocarbon biodegradation was observed in S1 microcosms (26.4% reduction in C10-C40 hydrocarbons), however, ENA was unable to stimulate degradation in S2. Although eubacterial communities (PCR-DGGE analysis) were similar for both soils, the alkB bacterial community was less diverse in S2 presumably due to impacts associated with elevated hydrocarbons. When hydrocarbon bioaccessibility was assessed using HP-β-CD extraction, large residual concentrations remained in the soil following the extraction procedure. However, when linear regression models were used to predict the endpoints of hydrocarbon degradation, there was no significant difference (P>0.05) between HP-β-CD predicted and microcosm measured biodegradation endpoints. This data suggested that the lack of hydrocarbon degradation in S2 resulted primarily from limited hydrocarbon bioavailability.

Impact of bacterial and fungal processes on 14C-hexadecane mineralisation in weathered hydrocarbon contaminated soil

In this study, the impact of bacterial and fungal processes on (14)C-hexadecane mineralisation was investigated in weathered hydrocarbon contaminated soil. The extent of (14)C-hexadecane mineralisation varied depending on the bioremediation strategy employed. Under enhanced natural attenuation conditions, (14)C-hexadecane mineralisation after 98 days was 8.5 ± 3.7% compared to <1.2% without nitrogen and phosphorus additions. (14)C-hexadecane mineralisation was further enhanced through Tween 80 amendments (28.9 ± 2.4%) which also promoted the growth of a Phanerochaete chyrsosporium fungal mat. Although fungal growth in weathered hydrocarbon contaminated soil could be promoted through supplementing additional carbon sources (Tween 80, sawdust, compost, pea straw), fungal (14)C-hexadecane mineralisation was negligible when sodium azide was added to soil microcosms to inhibit bacterial activity. In contrast, when fungal activity was inhibited through nystatin additions, (14)C-hexadecane mineralisation ranged from 6.5 ± 0.2 to 35.8 ± 3.8% after 98 days depending on the supplied amendment. Bacteria inhibition with sodium azide resulted in a reduction in bacterial diversity (33-37%) compared to microcosms supplemented with nystatin or microcosms without inhibitory supplements. However, alkB bacterial groups were undetected in sodium azide supplemented microcosms, highlighting the important role of this bacterial group in (14)C-hexadecane mineralisation.

A comparison of POPs bioaccumulation in Eisenia fetida in natural and artificial soils and the effects of aging

The close relationship between soil organic matter and the bioavailability of POPs in soils suggests the possibility of using it for the extrapolation between different soils. The aim of this study was to prove that TOC content is not a single factor affecting the bioavailability of POPs and that TOC based extrapolation might be incorrect, especially when comparing natural and artificial soils. Three natural soils with increasing TOC and three artificial soils with TOC comparable to these natural soils were spiked with phenanthrene, pyrene, lindane, p,p'-DDT, and PCB 153 and studied after 0, 14, 28, and 56 days. At each sampling point, total soil concentration and bioaccumulation in earthworms Eisenia fetida were measured. The results showed different behavior and bioavailability of POPs in natural and artificial soils and apparent effects of aging on these differences. Hence, direct TOC based extrapolation between various soils seems to be limited.

The formation of bound residues of diazinon in four UK soils: implications for risk assessment

The behaviour of diazinon in the soil determines the likelihood of further pollution incidents, particularly leaching to water. The most significant processes in the control of the fate of diazinon in the soil are microbial degradation and the formation of bound residues. Soils from four sites in the UK were amended with diazinon and its (14)C labelled analogue and incubated for 100 days. After 0, 10, 21, 50 and 100 days, the formation of bound residues was assessed by solvent extraction, and the microbial degradation of diazinon by mineralisation assay. In microbially active soils, diazinon is degraded rapidly, reducing the risk of future pollution incidents. However, where there was limited mineralisation there was also significantly lower formation of bound residues, which may lead to water pollution via leaching. The formation of bound residues was dependent on extraction type. Acetonitrile extraction identified bound residues in all soils, with the bound residue fraction increasing with increasing incubation time.

Mineralisation of target hydrocarbons in three contaminated soils from former refinery facilities

This study investigated the microbial degradation of (14)C-labelled hexadecane, octacosane, phenanthrene and pyrene and considered how degradation might be optimised in three genuinely hydrocarbon-contaminated soils from former petroleum refinery sites. Hydrocarbon mineralisation by the indigenous microbial community was monitored over 23 d. Hydrocarbon mineralisation enhancement by nutrient amendment (biostimulation), hydrocarbon degrader addition (bioaugmentation) and combined nutrient and degrader amendment, was also explored. The ability of indigenous soil microflora to mineralise (14)C-target hydrocarbons was appreciable; ≥ 16% mineralised in all soils. Generally, addition of nutrients or degraders increased the rates and extents of mineralisation of (14)C-hydrocarbons. However, the addition of nutrients and degraders in combination had a negative effect upon (14)C-octacosane mineralisation and resulted in lower extents of mineralisation in the three soils. In general, the rates and extents of mineralisation will be dependent upon treatment type, nature of the contamination and adaptation of the ingenious microbial community.

The extractability and mineralisation of cypermethrin aged in four UK soils

Cypermethrin is a widely used insecticide that has caused concern due to its toxicity in the aquatic environment. As with all land applied pesticides, the most significant source of water pollution is from the soil, either due to leaching or washoff. The behaviour of cypermethrin in the soil controls the likelihood of future pollution incidents, with two of the most significant processes being the formation of bound residues and microbial degradation. The formation of bound residues and mineralisation was measured in four organically managed soils from the UK. The formation of bound residues was measured using three different extraction solutions, 0.01 M CaCl₂, 0.05 M HPCD and acetonitrile. Biodegradation was assessed by measurement of mineralisation of cypermethrin to CO₂. The formation of bound residues varied according to extraction method, soil type and length of ageing. In two of the four soils studied, acetonitrile extractability decreased from 100% initially to 12-14% following 100 d ageing. The extent of mineralisation increased after 10-21 d ageing, reaching 33% of remaining activity in one soil, however following 100 d ageing the extent of mineralisation was significantly reduced in three out of the four soils. As with the formation of bound residues, mineralisation was impacted by soil type and length of ageing.

Biodegradation of PAHs in soil: Influence of chemical structure, concentration and multiple amendment

The influence of PAH chemical structure and concentration, added in either single (75 or 300 mg kg(-1)) or multiple (2 × 75, 2 × 150 or 4 × 75 mg kg(-1)) applications as single- or multiple-contaminant systems, on the development of PAH biodegradation in a pristine soil was investigated. Development in microbial catabolic ability was assessed at 0, 28, 56 and 84 d by monitoring (14)C-naphthalene, (14)C-phenanthrene and (14)C-pyrene mineralisation over 14 d in respirometric assays. The presence of other contaminants influenced the ability of the indigenous microflora to mineralise structurally different contaminants over time. (14)C-Naphthalene mineralisation was inhibited by the presence of other contaminants; whereas the presence of naphthalene significantly enhanced rates of mineralisation in multiple-contaminant systems containing (14)C-phenanthrene and (14)C-pyrene. Generally, increasing the number of contaminant applications has implications for catabolic activity of soil microbes. It is suggested the toxic nature of PAHs retarded mineralisation at increased contaminant concentrations.

Dynamic changes in functional gene copy numbers and microbial communities during degradation of pyrene in soils

This study investigates the dynamics of pyrene degradation rates, microbial communities, and functional gene copy numbers during the incubation of pyrene-spiked soils. Spiking pyrene to the soil was found to have negligible effects on the bacterial community present. Our results demonstrated that there was a significant difference in nidA gene copy numbers between sampling dates in QZ soil. Mycobacterium 16S rDNA clone libraries showed that more than 90% mycobacteria detected were closely related to fast-growing PAH-degrading Mycobacterium in pyrene-spiked soil, while other sequences related to slow-growing Mycobacterium were only detected in the control soil. It is suggested that nidA gene copy number and fast-growing PAH-degrading Mycobacterium could be used as indicators to predict pyrene contamination and its degradation activity in soils.

Soil type-dependent responses to phenanthrene as revealed by determining the diversity and abundance of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase genes by using a novel PCR detection system

A novel PCR primer system that targets a wide range of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD(alpha)) genes of both Gram-positive and Gram-negative bacteria was developed and used to study their abundance and diversity in two different soils in response to phenanthrene spiking. The specificities and target ranges of the primers predicted in silico were confirmed experimentally by cloning and sequencing of PAH-RHD(alpha) gene amplicons from soil DNA. Cloning and sequencing showed the dominance of phnAc genes in the contaminated Luvisol. In contrast, high diversity of PAH-RHD(alpha) genes of Gram-positive and Gram-negative bacteria was observed in the phenanthrene-spiked Cambisol. Quantitative real-time PCR based on the same primers revealed that 63 days after phenanthrene spiking, PAH-RHD(alpha) genes were 1 order of magnitude more abundant in the Luvisol than in the Cambisol, while they were not detected in both control soils. In conclusion, sequence analysis of the amplicons obtained confirmed the specificity of the novel primer system and revealed a soil type-dependent response of PAH-RHD(alpha) gene-carrying soil bacteria to phenanthrene spiking.

Impact of activated charcoal on the mineralisation of 14C-phenanthrene in soils

The development of phenanthrene catabolism in four soils amended with varying concentrations of activated charcoal (AC) (0%, 0.1%, 1% and 5%), a type of black carbon, was investigated. Mineralisation of (14)C-phenanthrene was monitored after 1, 25, 50 and 100 d soil-PAH contact time; lag phases, rates and extents of mineralisation of the (14)C-phenanthrene to (14)CO(2) were determined. At concentrations >0.1% AC rates and extents of mineralisation were reduced by more than 99%. This revealed that the presence of >0.1% AC in soils may substantially diminish the rate at which the catabolic activity of indigenous soil microflora develops in contaminated soil. Soil C, which had the highest organic carbon (OC) content, consistently exhibited the highest extents of degradation. It is suggested that, in accordance with other researchers, OC may have blocked available phenanthrene sorption sites. This enhanced phenanthrene availability ultimately facilitated a greater level of catabolic activity within this soil. Such results reflect the complex nature of interactions between soil, biota and contaminants and their influence on the degradation of contaminants in the environment.

Biogenic volatile organic compounds as a potential stimulator for organic contaminant degradation by soil microorganisms

The effects of monoterpenes on the degradation of (14)C-2,4-dichlorophenol (DCP) were investigated in soils collected from areas surrounding monoterpene and non-monoterpene-emitting vegetation. Indigenous microorganisms degraded (14)C-2,4-DCP to (14)CO(2), after 1d contact time. Degradation was enhanced by prior exposure of the soils to 2,4-DCP for 32 d, increasing extents of mineralisation up to 60%. Monoterpene amendments further enhanced 2,4-DCP degradation, but only following pre-exposure to both 2,4-DCP and monoterpene, with total 2,4-DCP mineralisation extents of up to 71%. Degradation was greatest at the higher monoterpene concentrations (> or = 1 microg kg(-1)). Total mineralisation extents were similar between concentrations, but higher than the control and the 0.1 microg kg(-1) amendment, indicating that increases in monoterpene concentration has a diminishing enhancing effect. We suggest that monoterpenes can stimulate the biodegradation of 2,4-DCP by indigenous soil microorganisms and that monoterpene amendment in soils is an effective strategy for removing organic contaminants.

Fate and behaviour of phenanthrene in the natural and artificial soils

OECD artificial soil has been used routinely as a standardized substrate for soil toxicity tests. However, can be the fate, behaviour and effects of contaminants in artificial soil extrapolated to natural soils? The aim of our study was to verify this hypothesis by comparing the loss, extraction, and bioavailability of phenanthrene in three artificial and three natural soils of comparable organic carbon content. Soils were spiked with 14C-phenanthrene and total 14C-activity change, the fractions extracted by dichloromethane, 70% ethanol, and hydroxypropyl-beta-cyclodextrin, the fraction mineralized by Pseudomonas sp., and taken up by Enchytraeus albidus were measured after 1, 14, 42, and 84 d aging. The loss, extraction, biodegradation and uptake were several times lower in the artificial than natural soils and these differences increased with increasing soil-phenanthrene contact time. These results imply that artificial soil should be used cautiously for the prediction of fate and behaviour in natural soils.

Development of phenanthrene catabolism in natural and artificial soils

The characteristics of natural soils often vary from those of artificial soil (e.g. OECD), which may lead to substantial differences in the bioavailability of test substances. The aim of this investigation was to characterise the development of phenanthrene catabolism in both natural and artificial soils with varying total organic carbon (TOC) content after 1, 14, 42 and 84 d soil-phenanthrene contact time. Indigenous catabolic activity was measured via the addition of 14C-phenanthrene using the respirometric soil slurry assay. Notably, the lag phases, fastest rates and total extents of 14C-phenanthrene degradation were relatively comparable in soils with similar TOC content after 1 d contact time. However, natural soils generally exhibited significantly shorter lag phases, faster rates and higher extents of mineralisation, than their artificial counterparts after 42 and 84 d contact time. Such findings suggest that the extrapolation of results from artificial soils to real/natural soils may not be straightforward.

Impact of black carbon in the extraction and mineralization of phenanthrene in soil

During the past century, increased biomass burning and fossil fuel consumption have drastically increased the input of black carbon (BC) into the environment, and that has been shown to influence the behavior of organic contaminants in soil. A study was conducted to investigate the effects of BC on the relationship between aqueous hydroxypropyl-beta-cyclodextrin (HPCD) extraction and microbial mineralization (bioaccessibility) of 14C-phenanthrene (10 mg kg(-1)) in four soils amended with 0, 0.1, 0.5, 1, 2.5, and 5% (% dry wt soil) activated charcoal, a type of BC. Mineralisation was monitored over 20 d incubation, within respirometric assays, using an inoculum containing a phenanthrene-degrading pseudomonad and compared to HPCD extraction (24 h) using 50 mM aqueous solution; analyses were conducted after 1, 25, 50, and 100 d soil-phenanthrene contact time. Statistical analyses revealed that for each soil the addition of BC led to significant (P < 0.001) reductions in both HPCD extractability and microbial mineralization. Linear correlations for BC concentrations of 0% (r2 = 0.95; slope = 0.89) and 0.1% (r2 = 0.67; slope = 0.95) revealed a highly significant (P < 0.01) relationship between HPCD extractability and total mineralization (20 d), indicating a direct prediction of phenanthrene bioaccessibility by HPCD. However, in soils amended with 0.5, 1, 2.5, and 5% BC exhibited r2 values ranging 0.51-0.13 and slopes of 2.19-12.73. This study has shown that BC strongly sorbs phenanthrene causing reductions in extractability and, to a lesser extent, bioaccessibility to degrading microorganisms.

Study of pyrene biodegradation capacity in two types of solid media

Removal of pyrene, a representative PAH, was studied using laboratory tests in two different types of solid media: an organic matter collected on the surface of a vertical flow constructed wetland (VFCW) and a formulated clay silicate sand (inorganic matter). The aim of this study was to evaluate the capacity of pyrene biodegradation in these media in order to use them for treating run-off water. The sorption process, the kinetics of pyrene biodegradation and the influence of selected bacteria were also investigated. The sorption process was evaluated by adsorption isotherms and desorption kinetics using a batch equilibration method. The adsorption coefficient values of 28.8 and 2.1 for the organic and the inorganic matter respectively, confirmed the relationship of adsorption with organic carbon content. A small proportion of the sorbed pyrene was available for desorption (8% and 15% for the organic and the inorganic matter, respectively), indicating that sorption was partially irreversible, with the presence of hysteresis. For the formulated clay silicate sand inoculated with a specific bacteria (Mycobacterium sp.6PY1), selected for its ability to degrade PAHs, pyrene removal was complete in 32 days. With the organic matter, these values ranged from 40% to 95% for the different experiments, following a lag time of 3 weeks before observation of a significant degradation. Indigenous bacterial species in the organic medium had the metabolic capacity to degrade pyrene, and microbial populations pre-exposed to the PAH degraded pyrene faster than similar unexposed populations. Three metabolites of pyrene degradation by Mycobacterium were found. They accumulated in both organic and inorganic matter, indicating that the enzymes catalyzing them have slow kinetics.

Diffuse PAH contamination of surface soils: environmental occurrence, bioavailability, and microbial degradation

The purpose of this review is to recognize the scientific and environmental importance of diffuse pollution with polycyclic aromatic hydrocarbons (PAHs). Diffuse PAH pollution of surface soil is characterized by large area extents, low PAH concentrations, and the lack of point sources. Urban and pristine topsoils receive a continuous input of pyrogenic PAHs, which induces a microbial potential for PAH degradation. The significance of this potential in relation to black carbon particles, PAH bioaccessibility, microbial PAH degradation, and the fate of diffuse PAHs in soil is discussed. Finally, the state-of-the-art methods for future investigations of the microbial degradation of diffuse PAH pollution are reviewed.

Development of microbial degradation of cypermethrin and diazinon in organically and conventionally managed soils

The behaviour of pesticides in the soil is a complex issue and is controlled by the physical, chemical and biological properties of the soil. The ability of microorganisms to degrade pesticides is not only controlled by the bioavailability of a chemical but also by their capacity to develop the ability to utilise available chemicals. The development of catabolism in the indigenous soil microflora of four organically and one conventionally managed soils was investigated for two pesticides: cypermethrin and diazinon. Soils were amended with cypermethrin and diazinon and aged for 0, 2, 4, 6, 8, and 14 weeks and, at each time point, mineralisation of freshly added 14C-cypermethrin or 14C-diazinon was measured by trapping 14CO2. In general, contact times between the soil and the pesticide resulted in a reduction in the lag phase (the period of time before mineralisation exceeded 5% of the added activity), followed by increases in the extent of mineralisation. Cypermethrin was mineralised significantly in all soils; whereas, diazinon was only appreciably mineralised in two of the soils, most notably in the organic soil from Redesdale. Statistical analysis showed pH and organic matter content of the soil had a significant effect on the extent of mineralisation (P< or = 0.05) of the cypermethrin in the soils.

Biodegradation of 2,4-dichlorophenol in the presence of volatile organic compounds in soils under different vegetation types

It has been suggested that monoterpenes emitted within the soil profile, either by roots or by decaying biomass, may enhance the biodegradation of organic pollutants. The aim of this study was to evaluate the effect of biogenic volatile organic compounds (VOCs) on the catabolism of 2,4-dichlorophenol in soils. Soils were collected from areas surrounding monoterpene (woodland) and nonmonoterpene (grassland)-emitting vegetation types. Soils were spiked with [UL-14C] 2,4-dichlorophenol at 10 mg kg(-1) and amended with alpha-pinene, p-cymene or a mix of monoterpenes (alpha-pinene, limonene and p-cymene in 1:1:1 ratio). The effects of monoterpene addition on the catabolism of [UL-14C] 2,4-dichlorophenol to 14CO2 by indigenous soil microbial communities were assessed in freshly spiked and 4-week-aged soils. It was found that aged woodland soils exhibited a higher level of [UL-14C] 2,4-dichlorophenol degradation, which was subsequently enhanced by the addition of monoterpenes (P<0.001), with the VOC mix and alpha-pinene amendments showing increased [UL-14C] 2,4-dichlorophenol catabolism. This study supports claims that the addition of biogenic VOCs to soils enhances the degradation of xenobiotic contaminants.

Distribution of the Mycobacterium community and polycyclic aromatic hydrocarbons (PAHs) among different size fractions of a long-term PAH-contaminated soil

Summary Mycobacterium is often isolated from polycyclic aromatic hydrocarbon (PAH)-contaminated soil as degraders of PAHs. In model systems, Mycobacterium shows attachment to the PAH substrate source, which is considered to be a particular adaptation to low bioavailability as it results into increased substrate flux to the degraders. To examine whether PAH-degrading Mycobacterium in real PAH-contaminated soils, in analogy with model systems, are preferentially associated with PAH-enriched soil particles, the distribution of PAHs, of the PAH-mineralizing capacity and of Mycobacterium over different fractions of a soil with an aged PAH contamination was investigated. The clay fraction contained the majority of the PAHs and showed immediate pyrene- and phenanthrene-mineralizing activity upon addition of (14)C-labelled pyrene or phenanthrene. In contrast, the sand and silt fractions showed a lag time of 15-26 h for phenanthrene and 3-6 days for pyrene mineralization. The maximum pyrene and phenanthrene mineralization rates of the clay fraction expressed per gram fraction were three to six times higher than those of the sand and silt fractions. Most-probable-number (MPN)-polymerase chain reaction demonstrated that Mycobacterium represented about 10% of the eubacteria in the clay fraction, while this was only about 0.1% in the sand and silt fractions, indicating accumulation of Mycobacterium in the PAH-enriched clay fraction. The Mycobacterium community composition in the clay fraction represented all dominant Mycobacterium populations of the bulk soil and included especially species related to Mycobacterium pyrenivorans, which was also recovered as one of the dominant species in the eubacterial communities of the bulk soil and the clay fraction. Moreover, Mycobacterium could be identified among the major culturable PAH-degrading populations in both the bulk soil and the clay fraction. The results demonstrate that PAH-degrading mycobacteria are mainly associated with the PAH-enriched clay fraction of the examined PAH-contaminated soil and hence, that also in the environmental setting of a PAH-contaminated soil, Mycobacterium might experience advantages connected to substrate source attachment.

The influence of single and multiple applications of pyrene on the evolution of pyrene catabolism in soil

The influence of pyrene added in a single application (0, 50, 100 and 200 mg kg(-1)) was investigated in multiple applications (1 x 50, 2 x 50 and 4 x 50 mg kg(-1)) on the evolution of catabolic activity in a pristine pasture soil. The microbial community's ability to degrade pyrene was assessed at 0, 4, 8 and 12 weeks by the mineralization of added 14C-pyrene. Significant mineralization (>5%) of added 14C-pyrene only occurred after 4 weeks soil-pyrene contact time in most of the pyrene-amended soils. Pyrene-amended soils showed statistically significantly shorter (P<0.05) lag times compared to the control soil after 8 and 12 weeks soil-pyrene contact time. Further, the rates of degradation increased in the presence of pyrene, peaking at 8 weeks. In terms of the overall extents of pyrene mineralization, there were statistically significant increases (P<0.05) between 4 and 8 weeks, with little difference between 8 and 12 weeks, with the general trend that an increase in pyrene concentration resulted in higher levels of mineralization. Increasing the concentration and number of pyrene additions can have a significant impact on the adaptation of the soil microflora to degrade pyrene over time.

Comparison of selected non-exhaustive extraction techniques to assess PAH availability in dissimilar soils

Recently, it has become apparent that the use of total contaminant concentrations as a measure of potential contaminant exposure to plants or soil organisms is inappropriate and that bioavailability of contaminants is a better measure of potential exposure. In light of this, non-exhaustive extraction techniques are being investigated to assess their appropriateness in determining bioavailability. In this study, phenanthrene extractability using hydroxypropyl-beta-cyclodextrin (HPCD) and desorption kinetics using butan-1-ol (BuOH) were determined in three dissimilar spiked soils. The soils were extracted after 1 d, 40 d and 80 d of soil-compound contact time. The amount of phenanthrene extracted by HPCD was compared to the rapidly desorbed fraction removed by BuOH. Further experiments using the same soils and extraction methods to assess the relative extractability of phenanthrene, pyrene and benzo(a)pyrene were conducted. Overall, the extraction methods used in this study had different extraction efficiencies. Results suggest that as compound hydrophobicity increased, BuOH became a more exhaustive extractant with respect to HPCD, especially for soils with high clay and organic matter content. These results are important as they highlight differences between two contrasting non-exhaustive extraction techniques both of which have been suggested to be appropriate in the assessment of bioavailability.

PAH degradation capacity of soil microbial communities--does it depend on PAH exposure?

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous pollutants of the environment. But is their microbial degradation equally wide in distribution? We estimated the PAH degradation capacity of 13 soils ranging from pristine locations (total PAHs approximately 0.1 mg kg(-1)) to heavily polluted industrial sites (total PAHs approximately 400 mg kg(-1)). The size of the pyrene- and phenanthrene-degrading bacterial populations was determined by most probable number (MPN) enumeration. Densities of phenanthrene degraders reflected previous PAH exposure, whereas pyrene degraders were detected only in the most polluted soils. The potentials for phenanthrene and pyrene degradation were measured as the mineralization of (14)C-labeled spikes. The time to 10% mineralization of added (14)C phenanthrene and (14)C pyrene was inversely correlated with the PAH content of the soils. Substantial (14)C phenanthrene mineralization in all soils tested, including seven unpolluted soils, demonstrated that phenanthrene is not a suitable model compound for predicting PAH degradation in soils. (14)C pyrene was mineralized by all Danish soil samples tested, regardless of whether they were from contaminated sites or not, suggesting that in industrialized areas the background level of pyrene is sufficient to maintain pyrene degradation traits in the gene pool of soil microorganisms. In contrast, two pristine forest soils from northern Norway and Ghana mineralized little (14)C pyrene within the 140-day test period. Mineralization of phenanthrene and pyrene by all Danish soils suggests that soil microbial communities of inhabited areas possess a sufficiently high PAH degradation capacity to question the value of bioaugmentation with specific PAH degraders for bioremediation.

Influence of the carbon/nitrogen/phosphorus ratio on polycyclic aromatic hydrocarbon degradation by Mycobacterium and Sphingomonas in soil

Biodegradation of polycyclic aromatic hydrocarbons (PAHs) in the environment is often limited due to unfavorable nutrient conditions for the bacteria that use these PAHs as sole source of carbon and energy. Mycobacterium and Sphingomonas are 2 PAH-degrading specialists commonly present in PAH-polluted soil, but not much is known about their specific nutrient requirements. By adding different inorganic supplements of nitrogen (N) and phosphorus (P), affecting the overall carbon/nitrogen/phosphorus ratio of soil in soil slurry degradation tests, we investigated the impact of soil inorganic N and P nutrient conditions on PAH degradation by PAH-degrading Sphingomonas and Mycobacterium strains. The general theoretically calculated C/N/P ratio of 100/10/1 (expressed in moles) allowed rapid PAH metabolization by Sphingomonas and Mycobacterium strains without limitation. In addition, PAH-degradation rate and extent was not affected when ca. ten times lower concentrations of N and P were provided, indicating that Sphingomonas and Mycobacterium strains are capable of metabolizing PAHs under low nutrient conditions. Nor does PAH-degradation seem to be affected by excesses of N and P creating an imbalanced C/N/P ratio. However, supplements of N and P salts increased the salinity of soil slurry solutions and seriously limited or even completely blocked biodegradation.

The development of phenanthrene catabolism in soil amended with transformer oil

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental contaminants frequently associated with light non-aqueous-phase liquids (LNAPLs) in soil. Microbial degradation comprises a major loss process for PAHs in the environment. Various laboratory studies, using known degraders, have shown reduced or enhanced mineralisation of PAHs when dissolved in different LNAPLs. Effects due to the presence of LNAPLs on indigenous micro-organisms, however, are not fully understood. A pristine pasture soil was spiked with [14C]phenanthrene and transformer oil to 0, 0.01 and 0.1%, and incubated for 180 days. The catabolic potential of the soil towards phenanthrene was assessed periodically during ageing. The extent of the lag phase (prior to >5% mineralisation), maximum rates and overall extents of mineralisation observed during the course of a 14-day bioassay appeared to be dependent upon phenanthrene concentration, the presence of transformer oil, and soil-contaminant contact time. Putatively, transformer oil enhanced acclimation and facilitated the development of measurable catabolic activity towards phenanthrene in a previously uncontaminated pasture soil. Exact mechanisms for the observed enhancement, longer-term fate/degradation of the oil and residual phenanthrene, and effects of the presence of the oil on the indigenous microbes over extended time frames warrant further investigation.

Degradation of microcystin in sediments at oxic and anoxic, denitrifying conditions

The potent toxin microcystin is frequently released during cyanobacterial blooms in eutrophic waters and may impose a risk to human health, when surface water is used for drinking water. For removal of microcystin in surface waters, infiltration through sediment is commonly used. In the present study, mineralization of 14C-labelled microcystin (accumulation of 14CO(2)) and concentration changes (protein phosphatase inhibition assay) demonstrated that indigenous microorganisms in the sediment of a water recharge facility were capable of degrading microcystin. At oxic or microaerophilic (<2% O(2)) conditions, microcystin added to sediment slurries at 70 microg l(-1) was reduced to <20 microg l(-1) in 1-2 weeks, and less than 3 microg l(-1) after 7 weeks. At anoxic conditions (<0.3% O(2)) and with addition of nitrate, the degradation was significantly stimulated, reducing microcystin from 100 to <20 microg l(-1) within 1 day. The simultaneous production of N(2)O in the samples suggests that the microcystin degradation was coupled to dissimilative nitrate reduction (denitrification). Since aquifers and sediments beneath drinking water reservoirs often are anoxic, nitrate respiration may be an important process in removal and detoxification of microcystin.