Effect of pyrene on denitrification activity and abundance and composition of denitrifying community in an agricultural soil

Toxicity of pyrene on the denitrifiers was studied by spiking an agricultural soil with pyrene to a series of concentrations (0-500 mg kg⁻¹) followed by dose-response and dynamic incubation experiments. Results showed a positive correlation between potential denitrification activity and copy numbers of denitrifying functional genes (nirK, nirS and nosZ), and were both negatively correlated with pyrene concentrations. Based on the comparison of EC₅₀ values, denitrifiers harboring nirK, nirS or nosZ gene were more sensitive than denitrification activity, and denitrifiers harboring nirS gene were more sensitive than that harboring nirK or nosZ genes. Seven days after spiking with EC₅₀ concentration of pyrene, denitrifiers diversity decreased and community composition changed in comparison with the control. Phylogenetic analyses of three genes showed that the addition of pyrene increased the proportion of Bradyrhizobiaceae, Rhodospirillales, Burkholderiales and Pseudomonadales. Some species belonging to these groups were reported to be able to degrade PAHs.     

菌源对多环芳烃降解菌的筛选及降解性能的影响

高效降解菌的筛选对利用生物修复技术有效去除环境中的多环芳烃具有重要意义。分别以石油污染土壤和焦化废水活性污泥为菌源,分离出芘降解菌和混合PAHs(菲、荧蒽和芘)降解菌共14株并对其降解性能进行对比研究。结果表明,筛选得到的菌株分别属于9个菌属,其中2种菌源共有的菌属为Mycobacterium sp.、Ralstonia sp.和Shinella sp.。芘和PAHs的高效降解菌(CP16和CM32)均属于分支杆菌属(Mycobacterium),来源于焦化废水活性污泥;菌株CP16对芘(50mg/L)的7 d降解率为74.99%,CM32对PAHs(菲50 mg/L、荧蒽和芘各10 mg/L)的7 d降解率为100%。因此,以焦化废水活性污泥为菌源更有利于获得高效的多环芳烃降解菌。     

Fungal degradation of an acetolactate synthase (ALS) inhibitor pyrazosulfuron-ethyl in soil

Owing to reported phytotoxicity of some sulfonylurea class of herbicides in number of sensitive crops and higher persistence in soil, present study was conducted to isolate and identify pyrazosulfuron-ethyl degrading fungi from soil of rice field. Penicillium chrysogenum and Aspergillus niger, were isolated and identified from rhizospere soil of rice field, as potent pyrazosulfuron-ethyl degrading fungi. Degradation of pyrazosulfuron-ethyl by P. chrysogenum and A. niger, yielded transformation products/metabolites which were identified and characterized by LC/MS/MS. The rate of dissipation of pyrazosulfuron-ethyl was found higher in soil of rice field and soil inoculated with P. chrysogenum. This showed important route of degradation of pyrazosulfuron-ethyl by microbes apart from chemical degradation.     

Influence of flooding and metal immobilising soil amendments on availability of metals for willows and earthworms in calcareous dredged sediment-derived soils

Soil amendments previously shown to be effective in reducing metal bioavailability and/or mobility in calcareous metal-polluted soils were tested on a calcareous dredged sediment-derived soil with 26 mg Cd/kg dry soil, 2200 mg Cr/kg dry soil, 220 mg Pb/kg dry soil, and 3000 mg Zn/kg dry soil. The amendments were 5% modified aluminosilicate (AS), 10% w/w lignin, 1% w/w diammonium phosphate (DAP, (NH₄)₂HPO₄), 1% w/w MnO, and 5% w/w CaSO₄. In an additional treatment, the contaminated soil was submerged. Endpoints were metal uptake in Salix cinerea and Lumbricus terrestris, and effect on oxidation-reduction potential (ORP) in submerged soils. Results illustrated that the selected soil amendments were not effective in reducing ecological risk to vegetation or soil inhabiting invertebrates, as metal uptake in willows and earthworms did not significantly decrease following their application. Flooding the polluted soil resulted in metal uptake in S. cinerea comparable with concentrations for an uncontaminated soil.     

Degrader density determines spatial variability of 2,6-dichlorobenzamide mineralisation in soil

The metabolite 2,6-dichlorobenzamide (BAM) is a frequent groundwater pollutant produced during degradation of the herbicide 2,6-dichlorobenzonitrile (dichlobenile). Spatial variability of BAM mineralisation is uncharacterized in surface soil, however, and factors controlling the heterogeneity remain unknown. We addressed these issues by sample-to-sample comparisons of BAM mineralisation rates and a range of soil characteristics at spatial scales ranging from meters to centimetres. For mineralisation assays nano-molar concentrations of labelled BAM were added to determine mineralisation rates under realistic conditions. We found a significant variability of BAM mineralisation which increased with decreasing spatial scale. BAM mineralisation rates were correlated to the density of BAM-degrading bacteria but not to water content, TOC, NH₄⁺, NO₃⁻, or pH. The genus Aminobacter, which contains the only BAM degraders known, was detected in MPN samples of BAM degraders by a specific PCR assay targeting the 16S rRNA gene, confirming a role of Aminobacter in BAM mineralisation.     

The exposition of a calcareous Mediterranean soil to toxic concentrations of Cr, Cd and Pb produces changes in the microbiota mainly related to differential metal bioavailability

The involvement of the bacterial community of an agricultural Mediterranean calcareous soil in relation to several heavy metals has been studied in microcosms under controlled laboratory conditions. Soil samples were artificially polluted with Cr(VI), Cd(II) and Pb(II) at concentrations ranging from 0.1 to 5000 mg kg⁻¹ and incubated along 28 d. The lowest concentrations with significant effects in soil respirometry were 10 mg kg⁻¹ Cr and 1000 mg kg⁻¹ Cd and Pb. However, only treatments showing more than 40% inhibition of respirometric activity led to significant changes in bacterial composition, as indicated by PCR-DGGE analyses. Presumable Cr- and Cd-resistant bacteria were detected in polluted microcosms, but development of the microbiota was severely impaired at the highest amendments of both metals. Results also showed that bioavailability is an important factor determining the impact of the heavy metals assayed, and even an inverted potential toxicity ranking could be achieved if their soluble fraction is considered instead of the total concentration. Moreover, multiresistant bacteria were isolated from Cr-polluted soil microcosms, some of them showing the capacity to reduce Cr(VI) concentrations between 26% and 84% of the initial value. Potentially useful strains for bioremediation were related to Arthrobacter crystallopoietes, Stenotrophomonas maltophilia and several species of Bacillus.     

Comparative bioremediation potential of four rhizospheric microbial species against lindane

Four microbial species (Kocuria rhizophila, Microbacterium resistens, Staphylococcus equorum and Staphylococcus cohnii subspecies urealyticus) were isolated from the rhizospheric zone of selected plants growing in a lindane contaminated environment and acclimatized in lindane spiked media (5-100 μg mL⁻¹). The isolated species were inoculated with soil containing 5, 50 and 100 mg kg⁻¹ of lindane and incubated at room temperature. Soil samples were collected periodically to evaluate the microbial dissipation kinetics, dissipation rate, residual lindane concentration and microbial biomass carbon (MBC). There was a marked difference (p < 0.05) in the MBC content and lindane dissipation rate of microbial isolates cultured in three different lindane concentrations. Further, the dissipation rate tended to decrease with increasing lindane concentrations. After 45 d, the residual lindane concentrations in three different spiked soils were reduced to 0%, 41% and 33%, respectively. Among the four species, S. cohnii subspecies urealyticus exhibited maximum dissipation (41.65 mg kg⁻¹) and can be exploited for the in situ remediation of low to medium level lindane contaminated soils.     

The rhizosphere and PAH amendment mediate impacts on functional and structural bacterial diversity in sandy peat soil

To reveal the degradation capacity of bacteria in PAH polluted soil and rhizosphere we combined bacterial extradiol ring-cleavage dioxygenase and 16S rRNA analysis in Betula pubescens rhizoremediation. Characterisation of the functional bacterial community by RFLP revealed novel environmental dioxygenases, and their putative hosts were studied by 16S rRNA amplification. Plant rhizosphere and PAH amendment effects were detected by the RFLP/T-RFLP analysis. Functional species richness increased in the birch rhizosphere and PAH amendment impacted the compositional diversity of the dioxygenases and the structural 16S rRNA community. A shift from an Acidobacteria and Verrucomicrobia dominated to an Alpha- and Betaproteobacteria dominated community structure was detected in polluted soil. Clone sequence analysis indicated catabolic significance of Burkholderia in PAH polluted soil. These results advance our understanding of rhizoremediation and unveil the extent of uncharacterized functional bacteria to benefit bioremediation by facilitating the development of the molecular tool box to monitor bacterial populations in biodegradation.     

Behavior of decabromodiphenyl ether (BDE-209) in soil: effects of rhizosphere and mycorrhizal colonization of ryegrass roots

A rhizobox experiment was conducted to investigate degradation of decabromodiphenyl ether (BDE-209) in the rhizosphere of ryegrass and the influence of root colonization with an arbuscular mycorrhizal (AM) fungus. BDE-209 dissipation in soil varied with its proximity to the roots and was enhanced by AM inoculation. A negative correlation (P < 0.001, R² = 0.66) was found between the residual BDE-209 concentration in soil and soil microbial biomass estimated as the total phospholipid fatty acids, suggesting a contribution of microbial degradation to BDE-209 dissipation. Twelve and twenty-four lower brominated PBDEs were detected in soil and plant samples, respectively, with a higher proportion of di- through hepta-BDE congeners in the plant tissues than in the soils, indicating the occurrence of BDE-209 debromination in the soil-plant system. AM inoculation increased the levels of lower brominated PBDEs in ryegrass. These results provide important information about the behavior of BDE-209 in the soil-plant system.     

Arbuscular mycorrhizal fungi enhance both absorption and stabilization of Cd by Alfred stonecrop (Sedum alfredii Hance) and perennial ryegrass (Lolium perenne L.) in a Cd-contaminated acidic soil

A greenhouse pot experiment was conducted to compare the phytoextraction efficiencies of Cd by hyper-accumulating Alfred stonecrop (Sedum alfredii Hance) and fast-growing perennial ryegrass (Lolium perenne L.) from a Cd-contaminated (1.6 mg kg⁻¹) acidic soil, and their responses to the inoculations of two arbuscular mycorrhizal (AM) fungal strains, Glomus caledonium 90036 (Gc) and Glomus mosseae M47V (Gm). Ryegrass and stonecrop were harvested after growing for 9 and 27 wk, respectively. Without AM fungal inoculation, the weekly Cd extraction by stonecrop (8.0 μg pot⁻¹) was 4.3 times higher than that by ryegrass (1.5 μg pot⁻¹). Both Gc and Gm significantly increased (P < 0.05) root mycorrhizal colonization rates, soil acid phosphatase activities, and available P concentrations, and thereby plant P absorptions (except for Gm-inoculated ryegrass), shoot biomasses, and Cd absorptions (except for Gm-inoculated stonecrop), while only Gc-inoculated stonecrop significantly accelerated (P < 0.05) the phytoextraction efficiency of Cd by 78%. In addition, both Gc and Gm significantly decreased (P < 0.05) phytoavailable Cd concentrations by 21–38% via elevating soil pH. The results suggested the potential application of hyper-accumulating Alfred stonecrop associated with AM fungi (notably Gc) for both extraction and stabilization of Cd in the in situ treatment of Cd-contaminated acidic soil.     

Hydrocarbon degradation, plant colonization and gene expression of alkane degradation genes by endophytic Enterobacter ludwigii strains

The genus Enterobacter comprises a range of beneficial plant-associated bacteria showing plant growth promotion. Enterobacter ludwigii belongs to the Enterobacter cloacae complex and has been reported to include human pathogens but also plant-associated strains with plant beneficial capacities. To assess the role of Enterobacter endophytes in hydrocarbon degradation, plant colonization, abundance and expression of CYP153 genes in different plant compartments, three plant species (Italian ryegrass, birdsfoot trefoil and alfalfa) were grown in sterile soil spiked with 1% diesel and inoculated with three endophytic E. ludwigii strains. Results showed that all strains were capable of hydrocarbon degradation and efficiently colonized the rhizosphere and plant interior. Two strains, ISI10-3 and BRI10-9, showed highest degradation rates of diesel fuel up to 68% and performed best in combination with Italian ryegrass and alfalfa. All strains expressed the CYP153 gene in all plant compartments, indicating an active role in degradation of diesel in association with plants.     

Response of bacterial pdo1, nah,and C12O genes to aged soil PAH pollution in a coke factory area

Soil pollution caused by polycyclic aromatic hydrocarbons (PAHs) is threatening human health and environmental safety. Investigating the relative prevalence of different PAH-degrading genes in PAH-polluted soils and searching for potential bioindicators reflecting the impact of PAH pollution on microbial communities are useful for microbial monitoring, risk evaluation, and potential bioremediation of soils polluted by PAHs. In this study, three functional genes, pdo1, nah, and C12O, which might be involved in the degradation of PAHs from a coke factory, were investigated by real-time quantitative PCR (qPCR) and clone library approaches. The results showed that the pdo1 and C12O genes were more abundant than the nah gene in the soils. There was a significantly positive relationship between the nah or pdo1 gene abundances and PAH content, while there was no correlation between C12O gene abundance and PAH content. Analyses of clone libraries showed that all the pdo1 sequences were grouped into Mycobacterium, while all the nah sequences were classified into three groups: Pseudomonas, Comamonas, and Polaromonas. These results indicated that the abundances of nah and pdo1 genes were positively influenced by levels of PAHs in soil and could be potential microbial indicators reflecting the impact of soil PAH pollution and that Mycobacteria were one of the most prevalent PAHs degraders in these PAH-polluted soils. Principal component analysis (PCA) and correlation analyses between microbial parameters and environmental factors revealed that total carbon (TC), total nitrogen (TN), and dissolved organic carbon (DOC) had positive effects on the abundances of all PAH-degrading genes. It suggests that increasing TC, TN, and DOC inputs could be a useful way to remediate PAH-polluted soils.     

Assessment of bacterial communities and characterization of lead-resistant bacteria in the rhizosphere soils of metal-tolerant Chenopodium ambrosioides grown on lead-zinc mine tailings

Bacterial communities in the rhizosphere soils of metal tolerant and accumulating Chenopodium ambrosioides grown in highly and moderately lead-zinc mine tailings contaminated-soils as well as the adjacent soils with low metal contamination were characterized by using cultivation-independent and cultivation techniques. A total of 69, 73, and 83 bacterial operational taxonomic units (OTUs) having 84.8-100% similarity with the closest match in the database were detected among high, moderate, and low-contamination soil clone libraries, respectively. These OTUs had a Shannon diversity index value in the range of 4.06-4.30. There were 9, 10, and 14 bacterial genera specific to high, moderate, and low metal-contaminated soil clone libraries, respectively. Phylogenetic analysis showed that the Pb-resistant isolates belonged to 8 genera. Pseudomonas and Arthrobacter were predominant among the isolates. Most of the isolates (82-86%) produced indole acetic acid and siderophores. More strains from the highly metal-contaminated soil produced 1-aminocyclopropane-1-carboxylate deaminase than the strains from the moderately and lowly metal-contaminated soils. In experiments involving canola grown in quartz sand containing 200 mg kg⁻¹ of Pb, inoculation with the isolated Paenibacillusjamilae HTb8 and Pseudomonas sp. GTa5 was found to significantly increase the above-ground tissues dry weight (ranging from 19% to 36%) and Pb uptake (ranging from 30% to 40%) compared to the uninoculated control. These results show that C. ambrosioides harbor different metal-resistant bacterial communities in their rhizosphere soils and the isolates expressing plant growth promoting traits may be exploited for improving the phytoextraction efficiency of Pb-polluted environment.     

Influence of fly ash aided phytostabilisation of Pb, Cd and Zn highly contaminated soils on Lolium perenne and Trifolium repens metal transfer and physiological stress

Due to anthropogenic activities, large extends of soils are highly contaminated by Metal Trace Element (MTE). Aided phytostabilisation aims to establish a vegetation cover in order to promote in situ immobilisation of trace elements by combining the use of metal-tolerant plants and inexpensive mineral or organic soil amendments. Eight years after Coal Fly Ash (CFA) soil amendment, MTE bioavailability and uptake by two plants, Lolium perenne and Trifolium repens, were evaluated, as some biological markers reflecting physiological stress. Results showed that the two plant species under study were suitable to reduce the mobility and the availability of these elements. Moreover, the plant growth was better on CFA amended MTE-contaminated soils, and the plant sensitivity to MTE-induced physiological stress, as studied through photosynthetic pigment contents and oxidative damage was lower or similar. In conclusion, these results supported the usefulness of aided phytostabilisation of MTE-highly contaminated soils.     

Potential use of DNA adducts to detect mutagenic compounds in soil

In this study, three different soils with contrasting features, spiked with 300 mg benzo[a]pyrene (BaP)/kg dry soil, were incubated at 20 °C and 60% water holding capacity for 540 days. At different time points, BaP and DNA were extracted and quantified, and DNA adducts were quantified by ³²P-postlabelling. After 540 days incubation, 69.3, 81.6 and 83.2% of initial BaP added remained in Cruden Bay, Boyndie and Insch soils, respectively. Meanwhile, a significantly different amount of DNA-BaP adducts were found in the three soils exposed to BaP over time. The work demonstrates the concept that DNA adducts can be detected on DNA extracted from soil. Results suggest the technique is not able to directly reflect bioavailability of BaP transformation products. However, this new method provides a potential way to detect mutagenic compounds in contaminated soil and to assess the outcomes of soil remediation.     

Lumbricus terrestris L. activity increases the availability of metals and their accumulation in maize and barley

The effect of the earthworm Lumbricus terrestris L. on metal availability in two mining soils was assessed by means of chemical extraction methods and a pot experiment using crop plants. Results from single and sequential extractions showed that L. terrestris had a slight effect on metal fractionation in the studied soils: only metals bound to the soil organic matter were significantly increased in some cases. However, we found that L. terrestris significantly increased root, shoot and total Pb and Zn concentrations in maize and barley for the soil with the highest concentrations of total and available metals. Specifically, shoot Pb concentration was increased by a factor of 7.5 and 3.9 for maize and barley, respectively, while shoot Zn concentration was increased by a factor of 3.7 and 1.7 for maize and barley, respectively. Our results demonstrated that earthworm activity increases the bioavailability of metals in soils.     

Direct and indirect effects of ammonia, ammonium and nitrate on phosphatase activity and carbon fluxes from decomposing litter in peatland

Here we investigate the response of soils and litter to 5 years of experimental additions of ammonium (NH₄), nitrate (NO₃), and ammonia (NH₃) to an ombrotrophic peatland. We test the importance of direct (via soil) and indirect (via litter) effects on phosphatase activity and efflux of CO₂. We also determined how species representing different functional types responded to the nitrogen treatments. Our results demonstrate that additions of NO₃, NH₄ and NH₃ all stimulated phosphatase activity but the effects were dependent on species of litter and mechanism (direct or indirect). Deposition of NH₃ had no effect on efflux of CO₂ from Calluna vulgaris litter, despite it showing signs of stress in the field, whereas both NO₃ and NH₄ reduced CO₂ fluxes. Our results show that the collective impacts on peatlands of the three principal forms of nitrogen in atmospheric deposition are a result of differential effects and mechanisms on individual components.     

Plants' use of different nitrogen forms in response to crude oil contamination

In this study, we investigated Phragmites australis’ use of different forms of nitrogen (N) and associated soil N transformations in response to petroleum contamination. ¹⁵N tracer studies indicated that the total amount of inorganic and organic N assimilated by P. australis was low in petroleum-contaminated soil, while the rates of inorganic and organic N uptake on a per-unit-biomass basis were higher in petroleum-contaminated soil than those in un-contaminated soil. The percentage of organic N in total plant-assimilated N increased with petroleum concentration. In addition, high gross N immobilization and nitrification rates relative to gross N mineralization rate might reduce inorganic-N availability to the plants. Therefore, the enhanced rate of N uptake and increased importance of organic N in plant N assimilation might be of great significance to plants growing in petroleum-contaminated soils. Our results suggest that plants might regulate N capture under petroleum contamination.     

Belowground effects of enhanced tropospheric ozone and drought in a beech/spruce forest (Fagus sylvatica L./Picea abies [L.] Karst)

The effects of experimentally elevated O₃ on soil respiration rates, standing fine-root biomass, fine-root production and δ¹³C signature of newly produced fine roots were investigated in an adult European beech/Norway spruce forest in Germany during two subsequent years with contrasting rainfall patterns. During humid 2002, soil respiration rate was enhanced under elevated O₃ under beech and spruce, and was related to O₃-stimulated fine-root production only in beech. During dry 2003, the stimulating effect of O₃ on soil respiration rate vanished under spruce, which was correlated with decreased fine-root production in spruce under drought, irrespective of the O₃ regime. δ¹³C signature of newly formed fine-roots was consistent with the differing g_s of beech and spruce, and indicated stomatal limitation by O₃ in beech and by drought in spruce. Our study showed that drought can override the stimulating O₃ effects on fine-root dynamics and soil respiration in mature beech and spruce forests.     

Bioaugmentation of a 4-chloronitrobenzene contaminated soil with Pseudomonas putida ZWL73

The strain Pseudomonas putida ZWL73, which metabolizes 4-chloronitrobenzene (4CNB) by a partial-reductive pathway, was inoculated into lab-scale 4CNB-contaminated soil for bioaugmentation purposes in this study. The degradation of 4CNB was clearly stimulated, as indicated with the gradual accumulation of ammonium and chloride. Simultaneously, the diversity and quantity of cultivable heterotrophic bacteria decreased due to 4CNB contamination, while the quantity of 4CNB-resistant bacteria increased. During the bioaugmentation, denaturing gradient gel electrophoresis analysis showed the changes of diversity in dominant populations of intrinsic soil microbiota. The results showed that Alphaproteobacteria and Betaproteobacteria were not distinctly affected, but Actinobacteria were apparently stimulated. In addition, an interesting dynamic within Acidobacteria was observed, as well as an influence on ammonia-oxidizing bacteria population. These combined findings demonstrate that the removal of 4CNB in soils by inoculating strain ZWL73 is feasible, and that specific populations in soils rapidly changed in response to 4CNB contamination and subsequent bioaugmentation.