酞酸酯污染农田土壤生物修复研究进展

酞酸酯是目前世界上产量最大、应用面积最广的人工合成有机物,作为塑化剂被广泛应用于塑料制品中。近年来发现酞酸酯是一类典型的环境内分泌干扰物。随着生活中塑料制品日益增多,尤其是农用薄膜和有机肥的大量使用,农田土壤中酞酸酯污染日益加剧,酞酸酯污染土壤的修复逐渐引起国内外学者的广泛关注。生物修复具有价格低廉、效果良好和环境友好等特点,尤其适合于大面积污染农田土壤修复。从植物修复、微生物修复、植物微生物联合修复和动物修复等方面综述了国内外酞酸酯污染土壤生物修复的研究现状,并从高效修复植物筛选及机理探讨、实际污染土壤的降解菌修复研究、高效降解菌群的构建和作用机制等方面对该领域的研究进行了展望,以期为酞酸酯污染土壤的修复研究提供借鉴并拓展新的思路。     

In-Situ Bioremediation of DDTs and PAH Contaminated Aging Farmland Soil Using Blood Meal

The use of blood meal was studied for in-site bioremediation of contaminated farmland soil. The combination of blood meal and indigenous microorganisms helped to in-site remediate the combined contaminated aging farmland soil of DDTs and PAH in Shenyang, China. The concentration of DDTs and PAHs was 47.94 ± 0.63 μg/kg and 690.10 ± 5.16 μg/kg, respectively. Biostimulation using blood meal or glucose promoted the bioremediation rate of DDTs and PAHs. Compared to glucose, blood meal was a longer term repair additive of DDTs and PAHs, and the remediation result was more efficient and durable. In the blood meal treatment, plowing the soil once every 7 days could increase the soil enzyme activities and bacterial populations, and it could significantly promote the remediation rates of DDTs (P < 0.05) and more evidently promote the remediation rates of PAHs. The DDTs and PAHs remediation rates increased from 32.18% and 20.17% to 43.41% and 26.09%, respectively, in soil treated with blood meal and plowed weekly after the five month remediation. This study provides an highly efficient in-site farmland soil bioremediation technology that could have practical utility.     

Kinetics of Polycyclic Aromatic Hydrocarbon (PAH) Degradation in Long-term Polluted Soils during Bioremediation

Bioremediation experiments with ten different soil samples from former industrial sites which were long-term polluted with polycyclic aromatic hydrocarbons (PAHs) were carried out using outdoor pot trials. The degradation of 15 PAHs according to the US EPA was investigated for 168 weeks through repeated soil sampling and determination of the total PAH concentration. On average, degradation was largest for acenaphthene (88%; 63 to 99%) and smallest for anthracene (22%; no significant degradation to 89%). For most of the PAH single substances, degradation kinetics were characterised by a first initial phase of fast degradation. In a subsequent second phase, degradation diminished and residual PAH concentrations were approached within 168 weeks, resulting in a similar PAH pattern in the ten soil samples. Degradation kinetics was calculated through the selection of the appropriate differential rate equation from a set of seven equations. Kinetics of PAH degradation was best fitted by single and two coupled first order exponential equations with median R2 of 0.71 (0.01 to 1.00). Degradation rate constants of the rapid phase (k ₁) ranged from 0.05×10⁻² week⁻¹ for benzo[k]fluoranthene to 18.3 week⁻¹ for naphthalene and for the subsequent slow degradation phase (k ₂) they ranged from 0.01×10⁻² week⁻¹ for benzo[a]anthracene to 2.3×10⁻² week⁻¹ for fluoranthene. Degradation was governed by desorption and diffusion processes of different rates, while microbial activity did not influence the kinetics. Median disappearance times (DT₅₀) ranged from 6.1 weeks for naphthalene to 522 weeks for benzo[k]fluoranthene. With the exception of the 6-ring PAHs dibenzo[ah]anthracene and indeno[1,2,3-cd]pyrene, this sequence followed the PAHs’ degree of condensation. The total initial PAH concentration and the residual concentration were correlated with R2 of 0.69, with larger initial PAH concentrations leading to larger residual concentrations and degradation rates.     

Effect of Red Clay on Diesel Bioremediation and Soil Bacterial Community

Red clay is a type of soil, the red color of which results from the presence of iron oxide. It is considered an eco-friendly material, with many industrial, cosmetic, and architectural uses. A patented method was applied to red clay in order to change its chemical composition and mineral bioavailability. The resulting product was designated processed red clay. This study evaluates the novel use of red clay and processed red clay as biostimulation agents in diesel-contaminated soils. Diesel biodegradation was enhanced in the presence of red clay and processed red clay by 4.9- and 6.7-fold, respectively, and the number of culturable bacterial cells was correlated with the amount of diesel biodegradation. The growth of Acinetobacter oleivorans DR1, Pseudomonas putida KT2440, and Cupriavidus necator was promoted by both types of red clays. Culture-independent community analysis determined via barcoded pyrosequencing indicated that Nocardioidaceae, Xanthomonadaceae, Pseudomonadaceae, and Caulobacteraceae were enriched by diesel contamination. Bacterial strain isolation from naphthalene- and liquid paraffin-amended media was affiliated with enriched taxa based on 16S rRNA gene sequence identity. We suggest that the biostimulating mechanism of red clay and processed red clay is able to support bacterial growth without apparent selection for specific bacterial species.     

Impacts of Bioremediation Schemes on Bacterial Population in Naphthalene-Contaminated Marine Sediments

Microcosm experiments were conduced in which the surface of marine sediment was contaminated with naphthalene and subjected to either of three different bioremediation schemes, i.e., biostimulation (BS) by supplementing with slow-release nitrogen and phosphorus fertilizers, bioaugmentation (BA) by inoculating with Cycloclasticus sp. E2, an aromatics-degrading bacterium identified to play an important role for aromatic-hydrocarbon degradation in marine environments and combination (CB) of BS and BA. These three schemes were found to be similarly effective for removing naphthalene, while naphthalene disappearance in sediment without any treatment (WT) was slower than those in the treated sediments. Shifts in bacterial populations during and after bioremediation were analyzed by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments. It was found that the Cycloclasticus rRNA type occurred as the strongest bands in the course of naphthalene degradation. Clustering analysis of DGGE profiles showed that bacterial populations in the WT, BS and CB sediments differed consistently from those in the uncontaminated control, while the profile for the BA sediment was finally included in the cluster for uncontaminated control sediments after a 150-day treatment. The results suggest that bioaugmentation with ecologically competent pollutant-degrading bacteria is an ecologically promising bioremediation scheme.     

细菌RNA聚腺苷酸化修饰及其调控机制与生理作用

聚腺苷酸化 (polyadenylation) 是指在底物RNA的3′-端加上一段聚腺苷酸残基的转录后修饰作用。1971年,第一次发现真核生物mRNA的3′-端存在多聚腺苷酸 (poly (A)) 尾,它保护mRNA免受核酸外切酶攻击,且对于转录终止、mRNA运输及翻译都起到重要作用,学者们一度将该现象认为是真核细胞mRNA的特征之一。时至今日,细菌RNA聚腺苷酸化现象的发现引起了学术界的高度重视,大量的研究结果不仅证明了该种修饰在细菌中普遍存在,而且发现其在细菌RNA的加工、降解及质量监控中扮演重要的角色;然而,与真核生物不同的是,在原核生物中该修饰倾向于使RNA去稳定化,即加速RNA的降解。本文综述了近年来细菌中RNA聚腺苷酸化修饰及其调控机制与生理作用的研究进展。     

Virulence and Immunomodulatory Roles of Bacterial Outer Membrane Vesicles

Summary: Outer membrane (OM) vesicles are ubiquitously produced by Gram-negative bacteria during all stages of bacterial growth. OM vesicles are naturally secreted by both pathogenic and nonpathogenic bacteria. Strong experimental evidence exists to categorize OM vesicle production as a type of Gram-negative bacterial virulence factor. A growing body of data demonstrates an association of active virulence factors and toxins with vesicles, suggesting that they play a role in pathogenesis. One of the most popular and best-studied pathogenic functions for membrane vesicles is to serve as natural vehicles for the intercellular transport of virulence factors and other materials directly into host cells. The production of OM vesicles has been identified as an independent bacterial stress response pathway that is activated when bacteria encounter environmental stress, such as what might be experienced during the colonization of host tissues. Their detection in infected human tissues reinforces this theory. Various other virulence factors are also associated with OM vesicles, including adhesins and degradative enzymes. As a result, OM vesicles are heavily laden with pathogen-associated molecular patterns (PAMPs), virulence factors, and other OM components that can impact the course of infection by having toxigenic effects or by the activation of the innate immune response. However, infected hosts can also benefit from OM vesicle production by stimulating their ability to mount an effective defense. Vesicles display antigens and can elicit potent inflammatory and immune responses. In sum, OM vesicles are likely to play a significant role in the virulence of Gram-negative bacterial pathogens.     

Robust Hydrocarbon Degradation and Dynamics of Bacterial Communities during Nutrient-Enhanced Oil Spill Bioremediation

Degradation of oil on beaches is, in general, limited by the supply of inorganic nutrients. In order to obtain a more systematic understanding of the effects of nutrient addition on oil spill bioremediation, beach sediment microcosms contaminated with oil were treated with different levels of inorganic nutrients. Oil biodegradation was assessed respirometrically and on the basis of changes in oil composition. Bacterial communities were compared by numerical analysis of denaturing gradient gel electrophoresis (DGGE) profiles of PCR-amplified 16S rRNA genes and cloning and sequencing of PCR-amplified 16S rRNA genes. Nutrient amendment over a wide range of concentrations significantly improved oil degradation, confirming that N and P limited degradation over the concentration range tested. However, the extent and rate of oil degradation were similar for all microcosms, indicating that, in this experiment, it was the addition of inorganic nutrients rather than the precise amount that was most important operationally. Very different microbial communities were selected in all of the microcosms. Similarities between DGGE profiles of replicate samples from a single microcosm were high (95% ± 5%), but similarities between DGGE profiles from replicate microcosms receiving the same level of inorganic nutrients (68% ± 5%) were not significantly higher than those between microcosms subjected to different nutrient amendments (63% ± 7%). Therefore, it is apparent that the different communities selected cannot be attributed to the level of inorganic nutrients present in different microcosms. Bioremediation treatments dramatically reduced the diversity of the bacterial community. The decrease in diversity could be accounted for by a strong selection for bacteria belonging to the alkane-degrading Alcanivorax/Fundibacter group. On the basis of Shannon-Weaver indices, rapid recovery of the bacterial community diversity to preoiling levels of diversity occurred. However, although the overall diversity was similar, there were considerable qualitative differences in the community structure before and after the bioremediation treatments.     

Cadmium Resistance Mechanism in Acidophilic and Alkalophilic Bacterial Isolates and their Application in Bioremediation of Metal-Contaminated Soil

Acidophilic and alkalophilic cadmium-resistant bacterial strains were isolated from the metal-contaminated soil of Panki thermal power plant, Kanpur, India, and two strains, namely SB21 (acidophilic) and SB20 (alkalophilic), were selected as representative strains on the basis of their high resistance to cadmium as compared to other strains. The phylogenetic analysis of the strains using 16s rDNA sequence revealed the strains to be Pseudomonas putida and Comamonas species strain, respectively. Furthermore, to determine the mechanism involved in cadmium resistance, a czc gene was amplified from the strains and sequenced. Homology of the sequences of the two strains, when compared with the available database using a BLASTn search, showed that the 650bp amplicons possess a partial czcA gene sequence. Moreover, the mechanism was confirmed by the results of atomic absorption spectroscopy and transmission electron microscopy studies, which supported the efflux mechanism in the alkalophilic strain SB20, but the acidophilic strain SB21 showed intracellular and periplasmic accumulation of metal in the cells in spite of the presence of the czcA gene, indicating the presence of multiple mechanisms of metal resistance in strain SB21.

Further, the strains were characterized functionally for their bioremediation potential in cadmium-contaminated soil under acidic and alkaline conditions by performing an in-situ greenhouse experiment using mungbean plants. A marked increase in agronomical parameters was observed under acidic conditions in the presence of strain SB21. Moreover, the concentration of metal decreased in both plants and soil in the presence of these bioinoculants; however, strain SB21 was found to be a better decontaminator than SB20 and thus can further be employed in bioremediation applications.     

The Limited Roles of Autocatalysis and Enantiomeric Cross-Inhibition in Achieving Homochirality in Dilute Systems

Origins of Life and Evolution of Biospheres - To understand the effects of fluctuations on achieving homochirality, we employ a Monte-Carlo method where autocatalysis and enantiomeric...     

Bacterial Community Dynamics and Polycyclic Aromatic Hydrocarbon Degradation during Bioremediation of Heavily Creosote-Contaminated Soil

Bacterial community dynamics and biodegradation processes were examined in a highly creosote-contaminated soil undergoing a range of laboratory-based bioremediation treatments. The dynamics of the eubacterial community, the number of heterotrophs and polycyclic aromatic hydrocarbon (PAH) degraders, and the total petroleum hydrocarbon (TPH) and PAH concentrations were monitored during the bioremediation process. TPH and PAHs were significantly degraded in all treatments (72 to 79% and 83 to 87%, respectively), and the biodegradation values were higher when nutrients were not added, especially for benzo(a)anthracene and chrysene. The moisture content and aeration were determined to be the key factors associated with PAH bioremediation. Neither biosurfactant addition, bioaugmentation, nor ferric octate addition led to differences in PAH or TPH biodegradation compared to biodegradation with nutrient treatment. All treatments resulted in a high first-order degradation rate during the first 45 days, which was markedly reduced after 90 days. A sharp increase in the size of the heterotrophic and PAH-degrading microbial populations was observed, which coincided with the highest rates of TPH and PAH biodegradation. At the end of the incubation period, PAH degraders were more prevalent in samples to which nutrients had not been added. Denaturing gradient gel electrophoresis analysis and principal-component analysis confirmed that there was a remarkable shift in the composition of the bacterial community due to both the biodegradation process and the addition of nutrients. At early stages of biodegradation, the α-Proteobacteria group (genera Sphingomonas and Azospirillum) was the dominant group in all treatments. At later stages, the γ-Proteobacteria group (genus Xanthomonas), the α-Proteobacteria group (genus Sphingomonas), and the Cytophaga-Flexibacter-Bacteroides group (Bacteroidetes) were the dominant groups in the nonnutrient treatment, while the γ-Proteobacteria group (genus Xathomonas), the β-Proteobacteria group (genera Alcaligenes and Achromobacter), and the α-Proteobacteria group (genus Sphingomonas) were the dominant groups in the nutrient treatment. This study shows that specific bacterial phylotypes are associated both with different phases of PAH degradation and with nutrient addition in a preadapted PAH-contaminated soil. Our findings also suggest that there are complex interactions between bacterial species and medium conditions that influence the biodegradation capacity of the microbial communities involved in bioremediation processes.     

细菌的信号转导系统及其在耐药中的作用

耐药菌的日益增多给临床治疗带来巨大的困难,揭示耐药机制成为遏制耐药菌的基本环节.细菌的信号系统是菌体之间信息交流的主要渠道,在调控细菌耐药性方面发挥重要的作用.本文梳理了细菌双组分系统、群体感应系统、第二信使、吲哚等细菌信号系统(分子)与细菌耐药性的关系,总结了各信号系统调控细菌耐药性的机制和途径,包括调控生物膜的形成...     

拟核结合蛋白与细菌基因的表达调控

拟核结合蛋白是细菌遗传物质组织和基因表达调控的关键. 细菌基因组压缩为致密的拟核必需有拟核结合蛋白的支撑. 拟核结合蛋白、DNA超螺旋和大分子簇在拟核的结构形成中起到重要作用,其中拟核结合蛋白最重要.拟核结合蛋白还影响细菌DNA的复制、重组、转录和修复等多个重要生理过程.作为全局调控因子,拟核结合蛋白是调控细菌适应环境变化所需基因表达的关键. 本文总结拟核结合蛋白的结构、功能和调控,特别是其在致病与非致病分枝杆菌中的差别,为寻找新药物靶标提供线索.     

Bacterial Communities Associated with Culex Mosquito Larvae and Two Emergent Aquatic Plants of Bioremediation Importance

Microbes are important for mosquito nutrition, growth, reproduction and control. In this study, we examined bacterial communities associated with larval mosquitoes and their habitats. Specifically, we characterized bacterial communities associated with late larval instars of the western encephalitis mosquito ( Culex tarsalis ), the submerged portions of two emergent macrophytes (California bulrush, Schoenoplectus californicus and alkali bulrush, Schoenoplectus maritimus ), and the associated water columns to investigate potential differential use of resources by mosquitoes in different wetland habitats. Using next-generation sequence data from 16S rRNA gene hypervariable regions, the alpha diversity of mosquito gut microbial communities did not differ between pond mesocosms containing distinct monotypic plants. Proteobacteria, dominated by the genus Thorsellia (Enterobacteriaceae), was the most abundant phylum recovered from C . tarsalis larvae. Approximately 49% of bacterial OTUs found in larval mosquitoes were identical to OTUs recovered from the water column and submerged portions of the two bulrushes. Plant and water samples were similar to one another, both being dominated by Actinobacteria, Bacteroidetes, Cyanobacteria , Proteobacteria and Verrucomicrobia phyla. Overall, the bacterial communities within C . tarsalis larvae were conserved and did not change across sampling dates and between two distinct plant habitats. Although Thorsellia spp. dominated mosquito gut communities, overlap of mosquito gut, plant and water-column OTUs likely reveal the effects of larval feeding. Future research will investigate the role of the key indicator groups of bacteria across the different developmental stages of this mosquito species.