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.     

油污土中降解柴油细菌的分离鉴定及降解能力研究

从所采集柴油污染土壤样品中富集、分离得到柴油降解优势菌株,命名为B-3和B-4.根据其生理生化性质及16S rDNA序列比对分析,确定2株菌分别属于Tetrathiobacter kashmirensis、假单胞菌属(Pseudomonas sp.).由于实验中,B-3的生长曲线较特殊,故以B-3和典型石油烃降解菌假单...     

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.     

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.     

Isolation and characterization of mesotrione-degrading Bacillus sp. from soil

Dissipation kinetics of mesotrione, a new triketone herbicide, sprayed on soil from Limagne (Puy-de-Dôme, France) showed that the soil microflora were able to biotransform it.Bacteria from this soil were cultured in mineral salt solution supplemented with mesotrione as sole source of carbon for the isolation of mesotrione-degrading bacteria. The bacterial community structure of the enrichment cultures was analyzed by temporal temperature gradient gel electrophoresis (TTGE). The TTGE fingerprints revealed that mesotrione had an impact on bacterial community structure only at its highest concentrations and showed mesotrione-sensitive and mesotrione-adapted strains. Two adapted strains, identified as Bacillus sp. and Arthrobacter sp., were isolated by colony hybridization methods.Biodegradation assays showed that only the Bacillus sp. strain was able to completely and rapidly biotransform mesotrione. Among several metabolites formed, 2-amino-4-methylsulfonylbenzoic acid (AMBA) accumulated in the medium. Although sulcotrione has a chemical structure closely resembling that of mesotrione, the isolates were unable to degrade it.     

Bioremediation of oil-contaminated soil using Candida catenulata and food waste

Even though petroleum-degrading microorganisms are widely distributed in soil and water, they may not be present in sufficient numbers to achieve contaminant remediation. In such cases, it may be useful to inoculate the polluted area with highly effective petroleum-degrading microbial strains to augment the exiting ones. In order to identify a microbial strain for bioaugmentation of oil-contaminated soil, we isolated a microbial strain with high emulsification and petroleum hydrocarbon degradation efficiency of diesel fuel in culture. The efficacy of the isolated microbial strain, identified as Candida catenulata CM1, was further evaluated during composting of a mixture containing 23% food waste and 77% diesel-contaminated soil including 2% (w/w) diesel. After 13 days of composting, 84% of the initial petroleum hydrocarbon was degraded in composting mixes containing a powdered form of CM1 (CM1-solid), compared with 48% of removal ratio in control reactor without inoculum. This finding suggests that CM1 is a viable microbial strain for bioremediation of oil-contaminated soil with food waste through composting processes.     

Isolation of mesotrione-degrading bacteria from aquatic environments in Brazil

Mesotrione is a benzoylcyclohexane-1,3-dione herbicide that inhibits 4-hydroxyphenyl pyruvate dioxygenase in target plants. Although it has been used since 2000, only a limited number of degrading microorganisms have been reported. Mesotrione-degrading bacteria were selected among strains isolated from Brazilian aquatic environments, located near corn fields treated with this herbicide. Pantoea ananatis was found to rapidly and completely degrade mesotrione. Mesotrione did not serve as a sole C, N, or S source for growth of P. ananatis, and mesotrione catabolism required glucose supplementation to minimal media. LC-MS/MS analyses indicated that mesotrione degradation produced intermediates other than 2-amino-4-methylsulfonyl benzoic acid or 4-methylsulfonyl-2-nitrobenzoic acid, two metabolites previously identified in a mesotrione-degrading Bacillus strain. Since P. ananatis rapidly degraded mesotrione, this strain might be useful for bioremediation purposes.     

Simazine degradation in bioaugmented soil: urea impact and response of ammonia-oxidizing bacteria and other soil bacterial communities

The objective of this study was to investigate the impact of exogenous urea nitrogen on ammonia-oxidizing bacteria (AOB) and other soil bacterial communities in soil bioaugmented for simazine remediation. The previously isolated simazine-degrading Arthrobacter sp. strain SD1 was used to degrade the herbicide. The effect of urea on the simazine degradation capacity of the soil bioaugmented with Arthrobacter strain SD1 was assessed using quantitative PCR targeting the s-triazine-degrading trzN and atzC genes. Structures of bacterial and AOB communities were characterized using terminal restriction fragment length polymorphism. Urea fertilizer could affect simazine biodegradation and decreased the proportion of its trzN and atzC genes in soil augmented with Arthrobacter strain SD1. Bioaugmentation process could significantly alter the structures of both bacterial and AOB communities, which were strongly affected by urea amendment, depending on the dosage. This study could provide some new insights towards s-triazine bioremediation and microbial ecology in a bioaugmented system. However, further studies are necessary in order to elucidate the impact of different types and levels of nitrogen sources on s-triazine-degraders and bacterial and AOB communities in bioaugmented soil.     

Atrazine biodegradation by Arthrobacter strain DAT1: effect of glucose supplementation and change of the soil microbial community

The objective of this study was to investigate the impact of glucose supplementation on the soil microbiota inoculated with the atrazine-degrading Arthrobacter strain DAT1. Soil microcosms with different treatments were constructed for biodegradation tests. The impact of glucose supplementation on atrazine degradation capacity of the strain DAT1 and the strain’s survival and growth were assessed. The densities of the 16S rRNA gene and the atrazine-metabolic trzN gene were determined using quantitative PCR. The growth of the strain DAT1 and the bacterial community structure were characterized using terminal restriction fragment length polymorphism. Glucose supplementation could affect atrazine degradation by the strain DAT1 and the strain’s trzN gene density and growth. The density of the16S rRNA gene decreased during the incubation period. Glucose supplementation could alter the bacterial community structure during the bioaugmentation process. Glucose supplementation could promote the growth of the autochthonous soil degraders that harbored novel functional genes transforming atrazine. Further study will be necessary in order to elucidate the impact of exogenous carbon on autochthonous and inoculated degraders. This study could add some new insights on atrazine bioremediation.     

Combined bioremediation of atrazine-contaminated soil by <Emphasis Type="Italic">Pennisetum</Emphasis> and <Emphasis Type="Italic">Arthrobacter</Emphasis> sp. strain DNS10

Strain DNS10 was isolated from the black soil collected from the northeast of China which had been cultivated with atrazine as the sole nitrogen source. Pennisetum is a common plant in Heilongjiang Province of China. The main objective of this paper was to evaluate the efficiency of plant–microbe joint interactions (Arthrobacter sp. DNS10 + Pennisetum) in atrazine degradation compared with single-strain and single-plant effects. Plant–microbe joint interactions degraded 98.10 % of the atrazine, while single strain and single plant only degraded 87.38 and 66.71 % after a 30-day experimental period, respectively. The results indicated that plant–microbe joint interactions had a better degradation effect. Meanwhile, we found that plant–microbe joint interactions showed a higher microbial diversity. The results of microbial diversity illustrated that the positive effects of cropping could improve soil microbial growth and activity. In addition, we planted atrazine-sensitive plants (soybean) in the soil after repair. The results showed that soybean growth in soil previously treated with the plant–microbe joint interactions treatment was better compared with other treatments after 20 days of growth. This was further proved that the soil is more conducive for crop cultivation. Hence, plant–microbe joint interactions are considered to be a potential tool in the remediation of atrazine-contaminated soil.     

Biodegradation of methyl red by Bacillus sp. strain UN2: decolorization capacity,metabolites characterization,and enzyme analysis

Azo dyes are recalcitrant and refractory pollutants that constitute a significant menace to the environment. The present study is focused on exploring the capability of Bacillus sp. strain UN2 for application in methyl red (MR) degradation. Effects of physicochemical parameters (pH of medium, temperature, initial concentration of dye, and composition of the medium) were studied in detail. The suitable pH and temperature range for MR degradation by strain UN2 were respectively 7.0–9.0 and 30–40 °C, and the optimal pH value and temperature were respectively 8.0 and 35 °C. Mg²⁺ and Mn²⁺ (1 mM) were found to significantly accelerate the MR removal rate, while the enhancement by either Fe³⁺ or Fe²⁺ was slight. Under the optimal degradation conditions, strain UN2 exhibited greater than 98 % degradation of the toxic azo dye MR (100 ppm) within 30 min. Analysis of samples from decolorized culture flasks confirmed biodegradation of MR into two prime metabolites: N,N′dimethyl-p-phenyle-nediamine and 2-aminobenzoic acid. A study of the enzymes responsible for the biodegradation of MR, in the control and cells obtained during (10 min) and after (30 min) degradation, showed a significant increase in the activities of azoreductase, laccase, and NADH-DCIP reductase. Furthermore, a phytotoxicity analysis demonstrated that the germination inhibition was almost eliminated for both the plants Triticum aestivum and Sorghum bicolor by MR metabolites at 100 mg/L concentration, yet the germination inhibition of parent dye was significant. Consequently, the high efficiency of MR degradation enables this strain to be a potential candidate for bioremediation of wastewater containing MR.     

Isolation of a novel Pseudomonas sp from soil that can efficiently degrade polyethylene succinate

Purpose

Polyethylene succinate (PES) is a biodegradable synthetic polymer and therefore widely used as a base material in plastic industry to circumvent the environmental problems related with the non-biodegradability of other polymers like polyethylene. Till date only few organisms have been reported to have the ability to degrade PES. Therefore for better management of PES-related environmental waste, the present study is targeted towards isolating mesophilic organism(s) capable of more efficient degradation of PES.

Results

Strain AKS2 was isolated from soil based on survival on a selection plate wherein PES was used as sole carbon source. Ribotyping and biochemical tests revealed that AKS2 is a new strain of Pseudomonas. Scanning electron and atomic force microscopic analysis of the PES films obtained after incubation with AKS2 confirmed PES-degradation ability of AKS2, wherein an alteration in surface topology was observed. The kinetics of PES weight loss showed that AKS2 degrades PES maximally during its logarithmic growth phase at a rate of 1.65?mg/day. This degradation is mediated by esterase activity and may also involve cell-surface hydrophobicity. It has also been observed that AKS2 is able to degrade PES considerably even in the presence of glucose, which is likely to increase the bioremediation potential of this isolate.

Conclusion

A new strain of Pseudomonas has been isolated from soil that is able to adhere to PES and degrade this polymer efficiently. This organism has the potential to be implemented as a useful tool for bioremediation of PES-derived materials.     

Sequential biodegradation of TNT,RDX and HMX in a mixture

We describe TNT's inhibition of RDX and HMX anaerobic degradation in contaminated soil containing indigenous microbial populations. Biodegradation of RDX or HMX alone was markedly faster than their degradation in a mixture with TNT, implying biodegradation inhibition by the latter. The delay caused by the presence of TNT continued even after its disappearance and was linked to the presence of its intermediate, tetranitroazoxytoluene. PCR–DGGE analysis of cultures derived from the soil indicated a clear reduction in microbial biomass and diversity with increasing TNT concentration. At high-TNT concentrations (30 and 90 mg/L), only a single band, related to Clostridium nitrophenolicum, was observed after 3 days of incubation. We propose that the mechanism of TNT inhibition involves a cytotoxic effect on the RDX- and HMX-degrading microbial population. TNT inhibition in the top active soil can therefore initiate rapid transport of RDX and HMX to the less active subsurface and groundwater.     

Bioaugmentation of polyethylene succinate-contaminated soil with Pseudomonas sp. AKS2 results in increased microbial activity and better polymer degradation

Pseudomonas sp. AKS2 isolated from soil degrades polyethylene succinate (PES) efficiently in the laboratory. However, this organism may not be able to degrade PES with similar efficiency in a natural habitat. Since in situ remediation is preferred for the effective removal of recalcitrant materials like plastic, in the current study, bioaugmentation potential of this organism was investigated. To investigate the potential of the AKS2 strain to bioaugment the PES-contaminated soil, a microcosm-based study was carried out wherein naturally attenuated, biostimulated, and AKS2-inoculated (bioaugmented) soil samples were examined for their ability to degrade PES. The results showed better degradation of PES by bioaugmented soil than other microcosms. Consistent with it, a higher number of PES-degrading organisms were found in the bioaugmented microcosm. The bioaugmented microcosm also exhibited a higher level of average well color development in BiOLOG ECO plate assay than the other two. The corresponding Shannon–Weaver index and Gini coefficient revealed a higher soil microbial diversity of bioaugmented microcosm than the others. This was further supported by community-level physiological profile of three different microcosms wherein we have observed better utilization of different carbon sources by bioaugmented microcosms. Collectively, these results demonstrate that bioaugmentation of PES-contaminated soil with AKS2 not only enhances polymer degradation but also increases microbial diversity. Bioaugmentation of soil with AKS2 enhances PES degradation without causing damage to soil ecology. Thus, Pseudomonas sp. AKS2 has the potential to be implemented as a useful tool for in situ bioremediation of PES.     

Use of reporter-gene based bacteria to quantify phenanthrene biodegradation and toxicity in soil

A phenanthrene-degrading bacterium, Sphingomonas paucimobilis EPA505 was used to construct two fluorescence-based reporter strains. Strain D harboring gfp gene was constructed to generate green fluorescence when the strain started to biodegrade phenanthrene. Strain S possessing gef gene was designed to die once phenanthrene biodegradation was initiated and thus to lose green fluorescence when visualized by a live/dead cell staining. Confocal laser scanning microscopic observation followed by image analysis demonstrates that the fluorescence intensity generated by strain D increased and the intensity by strain S decreased linearly at the phenanthrene concentration of up to 200 mg/L. Such quantitative increase and decrease of fluorescence intensity in strain D (i.e., from 1 to 11.90 ± 0.72) and strain S (from 1 to 0.40 ± 0.07) were also evident in the presence of Ottawa sand spiked with the phenanthrene up to 1000 mg/kg. The potential use of the reporter strains in quantitatively determining biodegradable or toxic phenanthrene was discussed.     

Novel enzymatic activity of cell free extract from thermophilic Geobacillus sp. UZO 3 catalyzes reductive cleavage of diaryl ether bonds of 2,7-dichlorodibenzo-p-dioxin

We characterized the ability of the cell free extract from polychlorinated dibenzo-p-dioxins degrading bacterium Geobacillus sp. UZO 3 to reduce even highly chlorinated dibenzo-p-dioxins such as octachlorodibenzo-p-dioxins in incineration fly ash. The degradation of 2,7-dichlorodibenzo-p-dioxin (2,7-DCDD) as a model dioxin catalyzed by the cell free extract from this strain implicates that the ether bonds of 2,7-DCDD molecule undergo reductive cleavage, since 4′,5-dichloro-2-hydroxydiphenyl ether and 4-chlorophenol were detected as intermediate products of 2,7-DCDD degradation.     

Biological degradation and microbial function effect of norfloxacin in a soil under different conditions

This paper investigated the degradation kinetics of norfloxacin in a soil, and its effects on soil respiration and nitrogen transformation under different conditions. Compared to the sterile control, the degradation rates of norfloxacin in the non-sterile soil were greatly enhanced, suggesting that microorganisms played a major role in the degradation. Accelerated degradation for norfloxacin in the soil was observed with decreasing concentrations (30 mg/kg to 5 mg/kg) with its half-life decreasing from 62 days to 31 days. Amending swine manure into the soil and increasing the soil moisture level enhanced the biological degradation of norfloxacin. No obvious inhibition of norfloxacin on soil respiration was observed in the soil, while only slight effect on nitrogen transformation was found. The results suggested that norfloxacin at the reported environmental concentrations (<100 mg/kg) would have little effect on microbial activity and functions in the soils.     

Remote estimation of phycocyanin (PC) for inland waters coupled with YSI PC fluorescence probe

Nuisance cyanobacterial blooms degrade water resources through accelerated eutrophication, odor generation, and production of toxins that cause adverse effects on human health. Quick and effective methods for detecting cyanobacterial abundance in drinking water supplies are urgently needed to compliment conventional laboratory methods, which are costly and time consuming. Hyperspectral remote sensing can be an effective approach for rapid assessment of cyanobacterial blooms. Samples (n?=?250) were collected from five drinking water sources in central Indiana (CIN), USA, and South Australia (SA), which experience nuisance cyanobacterial blooms. In situ hyperspectral data were used to develop models by relating spectral signal with handheld fluorescence probe (YSI 6600 XLM-SV) measured phycocyanin (PC in cell/ml), a proxy pigment unique for indicating the presence of cyanobacteria. Three-band model (TBM), which is effective for chlorophyll-a estimates, was tuned to quantify cyanobacteria coupled with the PC probe measured cyanobacteria. As a comparison, two band model proposed by Simis et al. (Limnol Oceanogr, 50(11): 237–245, 2005; denoted as SM05) was paralleled to evaluate TBM model performance. Our observation revealed a high correlation between measured and estimated PC for SA dataset (R ²?=?0.96; range: 534–20,200 cell/ml) and CIN dataset (R ²?=?0.88; range: 1,300–44,500 cell/ml). The potential of this modeling approach for imagery data were assessed by simulated ESA/Centinel3/OLCI spectra, which also resulted in satisfactory performance with the TBM for both SA dataset (RMSE %?=?26.12) and CIN dataset (RMSE %?=?34.49). Close relationship between probe-measured PC and laboratory measured cyanobacteria biovolume was observed (R ²?=?0.93, p?<?0.0001) for the CIN dataset, indicating a stable performance for PC probe. Based on our observation, field spectroscopic measurement coupled with PC probe measurements can provide quantitative cyanobacterial bloom information from both relatively static and flowing inland waters. Hence, it has promising implications for water resource managers to obtain information for early warning detection of cyanobacterial blooms through the close association between probe measured PC values and cyanobacterial biovolume via remote sensing modeling.     

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.     

Characterization of hydrocarbon-degrading and biosurfactant-producing Pseudomonas sp. P-1 strain as a potential tool for bioremediation of petroleum-contaminated soil

The Pseudomonas sp. P-1 strain, isolated from heavily petroleum hydrocarbon-contaminated soil, was investigated for its capability to degrade hydrocarbons and produce a biosurfactant. The strain degraded crude oil, fractions A5 and P3 of crude oil, and hexadecane (27, 39, 27 and 13 % of hydrocarbons added to culture medium were degraded, respectively) but had no ability to degrade phenanthrene. Additionally, the presence of gene-encoding enzymes responsible for the degradation of alkanes and naphthalene in the genome of the P-1 strain was reported. Positive results of blood agar and methylene blue agar tests, as well as the presence of gene rhl, involved in the biosynthesis of rhamnolipid, confirmed the ability of P-1 for synthesis of glycolipid biosurfactant. ¹H and ¹³C nuclear magnetic resonance, Fourier transform infrared spectrum and mass spectrum analyses indicated that the extracted biosurfactant was affiliated with rhamnolipid. The results of this study indicate that the P-1 and/or biosurfactant produced by this strain have the potential to be used in bioremediation of hydrocarbon-contaminated soils.