Molecular characterization of polycyclic aromatic hydrocarbon (PAH)-degrading methanogenic communities

Previous research demonstrated that methanogenic cultures enriched from Baltimore Harbor (Baltimore, MD) sediments were able to degrade naphthalene and phenanthrene. In this report, the degradation activity was maintained through a sequential transfer without adding additional sediments and the established polycyclic aromatic hydrocarbon (PAH)-degrading methanogenic communities were characterized via comparative sequence analysis of clone libraries of 16S rRNA genes amplified using bacteria-specific and Archaea-specific primers. The phylogenetic analysis indicated that the addition of PAHs clearly shifted the structure of the methanogenic community and resulted in an increase in populations of species previously found in other hydrocarbon-degrading communities. Of particular interest is the fact that the dominant microbial population of the naphthalene cultures was different from that of the phenanthrene cultures, suggesting that different species are involved in the degradation. Finally, this information may lead to the identification and isolation of methanogenic populations that can degrade PAHs.     

Degradation of polycyclic aromatic hydrocarbons by an immobilized mixed bacterial culture

The mixed bacterial culture MK1 was capable of degrading a wide spectrum of aromatic compounds both as free and as immobilized cells. By offering anthracene oil or a defined mixture of phenol, naphthalene, phenanthrene, anthracene and pyrene (in concentrations of 0.1–0.2 mm, respectively) as sources of carbon and energy, a specific degradation pattern correlating with the condensation degree was observed. Regarding the defined mixture of aromatic hydrocarbons, complete metabolism was reached for phenol (0.1 mm) after 1 day, for naphthalene (0.1 mm) after 2 days and for phenanthrene (0.1 mm) after 15 days of cultivation. The conversion of anthracene (0.1 mm) and pyrene (0.1 mm) resulted in minimal residual concentrations, analogous to fluoranthene and pyrene of the anthracene oil (0.1%). Maximal total degradation for the tricyclic compounds dibenzofurane, fluorene, dibenzothiophene, phenanthrene and anthracene of the anthracene oil (0.1%) occurred after 5 days. In general, a significant metabolisation of the tetracyclic aromatic hydrocarbons fluoranthene and pyrene was observed after the degradation of phenol, naphthalene and most of the tricyclic compounds. Doubling the start concentrations of the polycyclic aromatic hydrocarbons effected higher degradation rates. Cell growth occurred simultaneously with the conversion of phenol, naphthalene and the tricyclic compounds. The immobilized cells showed stable growth and, compared to freely suspended cells, the same degradation sequence as well as an equivalent degradation potential — even in a model soil system. Correspondence to: I. Wiesel     

多环芳烃降解菌的筛选、鉴定及降解特性

【目的】多环芳烃(PAHs)是一类普遍存在于环境中且具有高毒性的持久性有机污染物,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。研究拟从供试菌株中筛选多环芳烃高效降解菌,并分析其降解特性,为多环芳烃污染环境的微生物修复提供资源保障和科学依据。【方法】采用平板法从25株供试菌株中筛选出以菲和芘为唯一碳源和能源的高效降解菌,经16S rRNA基因序列进行初步鉴定,通过单因素实验法分析其在液体培养基中的降解特性。【结果】筛选出的3株多环芳烃高效降解菌SL-1、02173和02830经16S rRNA基因序列分析,02173和02830分别与假单胞菌属中的Pseudomonas alcaliphila和Pseudomonas corrugate同源性最近,SL-1为本课题组发表新类群Rhizobium petrolearium的模式菌株;降解实验表明,菌株SL-1 3 d内对单一多环芳烃菲(100 mg/L)和芘(50 mg/L)的降解率分别达到100%和48%,5 d后能够降解74%的芘;而其3 d内对混合PAHs中菲和芘的降解率分别为75.89%和81.98%。菌株02173和02830 3 d内对混合多环芳烃中萘(200 mg/L)、芴(50 mg/L)、菲(100 mg/L)和芘(50 mg/L)的降解率均分别超过97%。【结论】筛选出的3株PAHs降解菌SL-1、02173和02830不仅可以高效降解低分子量PAHs,还对高分子量PAHs具有很好的降解潜力。研究表明,由于共代谢作用低分子量多环芳烃可促进高分子量多环芳烃的降解,而此时低分子量多环芳烃的降解将受到抑制。     

Molecular Characterization of a Bacterial Consortium Enriched from an Oilfield that Degrades Phenanthrene

Characterization of functional and phylogenetic genes was carried out on a bacterial consortium, enriched from a water treatment system of an oilfield, that could use phenanthrene as the sole carbon source. The mixed culture degraded 130 mg phenanthrene l⁻¹ in 16 days, which is significantly faster than previously reported pure cultures. The existence of catabolic genes (nahAc, C23O) in the mixed culture was quantitated by most probable number PCR. The plasmid encoding phenanthrene catabolic genes increased relative to the chromosome genes. Heterogeneous bacteria were present according to both PCR denaturing gradient gel electrophoresis and cloning methods, suggesting the possible existence of cooperation between different biochemical PAH-transforming pathways. Revisions requested 15 December 2005; Revisions received 23 January 2006     

Increase in d-tagatose Production Rate by Site-directed Mutagenesis of l-arabinose Isomerase from Geobacillus thermodenitrificans

Among single-site mutations of l-arabinose isomerase derived from Geobacillus thermodenitrificans, two mutants were produced having the lowest and highest activities of d-tagatose production. Site-directed mutagenesis at these sites showed that the aromatic ring at amino acid 164 and the size of amino acid 475 were important for d-tagatose production. Among double-site mutations, one mutant converted d-galactose into d-tagatose with a yield of 58% whereas the wild type gave 46% d-tagatose conversion after 300 min at 65 °C. Received 31 August 2005; Revisions requested 27 September 2005; Revisions received 8 November 2005; Accepted 8 November 2005     

Both Cycloclasticus spp. and Pseudomonas spp. as PAH-degrading bacteria in the Seine estuary (France)

Like other highly urbanized and industrialized estuaries, the Seine estuary (France) has, for decades, received high inputs of polycyclic aromatic hydrocarbons (PAHs). In order to estimate the bioremediation potentials and to identify the bacterial species involved in hydrocarbon degradation, we used microcosms containing seawater from the Seine estuary supplemented with either naphthalene, phenanthrene, fluorene or pyrene. In the microcosms enriched with naphthalene or phenanthrene, hydrocarbon biodegradation was significant within 9 weeks (43% or 46%, respectively), as shown by analyses in GC-MS. In similar microcosms incubated also with naphthalene or phenanthrene, analysis of the 16S rRNA gene sequences (DNA and cDNA) with denaturing gradient gel electrophoresis and clone libraries indicated that the PAH-degrading communities were dominated by Cycloclasticus spp., confirming their universal key role in degradation of low-molecular-weight PAHs in marine environments. However, in contrast to previous studies, we found that Pseudomonas spp. also degraded naphthalene and phenanthrene in seawater; this occurred only after 21 days, as was confirmed by real-time PCR. Although this genus has been abundantly described in the literature as a good PAH-degrading bacterial group in soil or in sediment, to our knowledge, this is the first evidence of a significant fitness in PAH degradation in seawater.     

接种功能内生细菌Diaphorobacter sp.Phe15减少蔬菜亚细胞菲积累的体外试验研究

[目的]土壤中的多环芳烃(polycyclic aromatic hydrocarbons, PAHs)可被蔬菜根系吸收并在可食部分积累进而通过食物链威胁人群健康。接种功能内生细菌能有效减低蔬菜中PAHs的积累,而关于其对蔬菜亚细胞组分中PAHs积累的影响却鲜有报道。[方法]采用体外实验,研究了接种具有菲降解功能的菌株Diaphorobacter sp. Phe15对空心菜茎叶亚细胞组分中菲积累的影响及PAHs代谢相关酶活性的响应。[结果]接种Phe15可以可加速空心菜茎叶亚细胞中菲的降解,显著削减空心菜亚细胞组分中菲的含量,接菌后空心菜亚细胞组分中菲降解率达90%以上。此外,接种功能菌Phe15可以影响空心菜亚细胞组分中PAHs代谢相关酶系的活性,空心菜亚细胞水平POD、PPO、C230活性整体得到提高,且酶系活性与空心菜体内菲积累呈负相关关系。[结论]接种具有菲降解功能的菌株Phe15增加了空心菜亚细胞水平PAHs代谢相关酶系活性,进而降低空心菜体内菲的积累,研究结果为利用功能内生细菌削减蔬菜中多环芳烃污染提供了一定的参考和理论依据。     

Enhanced Degradation of a Mixture of Polycyclic Aromatic Hydrocarbons by a Defined Microbial Consortium in a Two-Phase Partitioning Bioreactor

Biological treatment methods are effective at destroying polycyclic aromatic hydrocarbons (PAHs), and some of the highest rates of PAH degradation have been achieved using two-phase-partitioning bioreactors (TPPBs). TPPBs consist of a cell-containing aqueous phase and a biocompatible and immiscible organic phase that partitions toxic and/or recalcitrant substrates to the cells based on their metabolic demand and on maintaining the thermodynamic equilibrium of the system. In this study, the degradation of a 5-component mixture of high and low molecular weight PAHs by a defined microbial consortium of Sphingomonas aromaticivorans B0695 and Sphingomonas paucimobilis EPA505 in a TPPB was examined. The extremely low aqueous solubilities of the high molecular weight (HMW) PAHs significantly reduce their bioavailability to cells, not only in the environment, but in TPPBs as well. That is, in the two-phase system, the originally selected solvent, dodecane, was found to sequester the HMW PAHs from the cells in the aqueous phase due to the inherent high solubility of the hydrophobic compounds in this solvent. To circumvent this limitation, the initial PAH concentrations in dodecane were increased to sufficient levels in the aqueous phase to support degradation: LMW PAHs (naphthalene, phenanthrene) and fluoranthene were degraded completely in 8 h, while the HMW PAHs, pyrene and benzo[a]pyrene, were degraded by 64% and 11%, at rates of 42.9 mg l⁻¹ d⁻¹ and 7.5 mg l⁻¹ d⁻¹, respectively. Silicone oil has superior PAH partitioning abilities compared to dodecane for the HMW PAHs, and was used to improve the extent of degradation for the PAH mixture. Although silicone oil increased the bioavailability of the HMW PAHs and greater extents of biodegradation were observed, the rates of degradation were lower than that obtained in the TPPB employing dodecane.     

Microbial degradation of high and low molecular weight polyaromatic hydrocarbons in a two-phase partitioning bioreactor by two strains of Sphingomonas sp.

A mixture of six polyaromatic hydrocarbons (naphthalene, phenanthrene, fluoranthene, pyrene, chyrysene and benzo[a]pyrene), varying in size from 2 to 5 rings, was dissolved in dodecane, and used as the delivery phase of a partitioning bioreactor. Two species of Sphingomonas were then used individually, and as a consortium, to determine which of the PAHs were degraded. Only low molecular weight PAHs (naphthalene, phenanthrene and fluoranthene) were degraded by the individual strains, but the consortium degraded all substrates either to completion or near completion.     

Isolation and identification of a yeast strain capable of degrading four and five ring aromatic hydrocarbons

A yeast strain AEH was isolated from oil contaminated soil and identified by analysis of 18S and 26S ribosomal DNA sequences asPichia anomala. Strain AEH was capable of degrading naphthalene, phenanthrene and chrysene, singly, and benzo(a)pyrene in combination. The yeast degraded 5.36 mg naphthalene l^?1 within 2 days, and 5.04 mg phenanthrene l^?1 and 1.54 mg chrysene 1^?1 within 10 days. When a mixture of the four polycyclic aromatic hydrocarbons (PAHs) was treated at a concentration between 2.98 mg l^?1 and 6.89 mg l^?1, degradation rates were delayed for naphthalene and phenanthrene (3.79 mg l^?1 and, 4.20 mg l^?1 within 10 days, respectively), but enhanced for chrysene and benzo(a)pyrene (3.37 mg l^?1 and, 1.91 mg l^?1 within 10 days, respectively). In a binary system, all of the other 3 PAHs could be utilized as the carbon source for the cometabolic degradation of benzo(a)pyrene with naphthale ne as the best one.     

Bacterial degradation of low concentrations of phenanthrene and inhibition by naphthalene

Phenanthrene-degrading bacteria were isolated from enrichment cultures of soils contaminated with creosote and jet fuel. The isolates from the creosote enrichments were classified by fatty acid methyl ester profiles as Acidovorax delafieldii and Sphingomonas paucimobilis; the bacterium from the jet fuel-contaminated soil was not identified and was designated strain JFD 11. All three isolates used phenanthrene as a sole carbon and energy source, and two of the isolates used fluoranthene as a sole carbon and energy source. Anthracene and fluorene were cometabolized by all three strains, but pyrene was not transformed. Naphthalene inhibited all of the strains, and 28-h cultures of A. delafieldii were inhibited by naphthalene concentrations as low as 5 ppm. Short-term degradation experiments were undertaken with center-well flasks and concentrations of phenanthrene ranging from 1.2 to 12.0 m. Since initial degradation rates were not a function of phenanthrene concentration, it was inferred that the half-saturation constants were less than the lowest phenanthrene concentration tested. Correspondence to: C.E. Cemiglia.     

乳白耙齿菌F17对单一和复合多环芳烃的降解差异解析

[目的] 针对菲、蒽、荧蒽多环芳烃（PAHs）污染物,利用乳白耙齿菌F17,研究单一和复合PAHs污染物的生物降解规律。[方法] 采用气相色谱-质谱法（GC-MS）分析降解过程中PAHs的浓度,并采用准一级反应动力学模型对降解结果进行拟合。[结果] 对于单一PAHs,第15天时菲、蒽、荧蒽的降解率由高到低依次为菲（97.8%） > 蒽（89.3%） > 荧蒽（81.5%）。菲、蒽和荧蒽的降解过程具有准一级反应动力学特征,菲的生物降解速率最快,其次是蒽,荧蒽的降解速率最慢。与单一PAHs的降解相比,在复合PAHs的降解过程中,乳白耙齿菌F17的生长和锰过氧化物酶的合成均表现出不同的特征。此外,水溶性极可能是复合污染物降解的重要控制因子,三者水溶性为：菲 > 荧蒽 > 蒽。因此,在菲或荧蒽加入条件下,微生物能优先降解这些污染物,抑制了污染物蒽的降解;同时,蒽或菲的存在对荧蒽的降解也有抑制作用;然而外源加入水溶性较差的蒽和荧蒽,则对菲的生物降解无显著影响。[结论] 复合PAHs的生物降解主要表现为相互竞争的特点,通过GC-MS分析了PAHs的生物降解途径。     

Aluminium Chloride Enhances Colchicine Production in Root Cultures of Gloriosa superba

Root cultures of Gloriosa superba were treated with 5 mm methyl jasmonate and 125 μm AlCl₃ which enhanced the intracellular colchicine content of the roots by 50-fold and 63-fold, respectively. Ten millimolar of CaCl₂ and 1 mm CdCl₂ enhanced biomass significantly (7- to 8.6-fold, respectively) while maximum release of colchicine into the medium was obtained with 10 mm CdCl₂. Casein hydrolysate, yeast extract and silver nitrate had no significant effect on growth and colchicine accumulation in root cultures. Revisions requested 2 November 2005; Revisions received 9 January 2006     

Microbial characterization and hydrocarbon biodegradation potential of natural bilge waste microflora

Shipping operations produce oily wastes that must be managed properly to avoid environmental pollution. The aim of this study was to characterize microorganisms occurring in ship bilge wastes placed in open lagoons and, particularly, to assess their potential to degrade polycyclic aromatic hydrocarbons (PAHs). A first-order kinetic was suitable for describing hydrocarbon biodegradation after 17 days of treatment. The calculated rate constants were 0.0668 and 0.0513 day^–1 with a corresponding half-life of 10.3 and 13.5 days for the aliphatic and aromatic hydrocarbon fractions, respectively. At day 17, PAH removal percentages were: acenaphtylene 100, fluorene 95.2, phenanthrene 93.6, anthracene 70.3, and pyrene 71.5. Methyl phenanthrene removals were lower than that of their parent compound (3-methyl phenanthrene 83.6, 2-methyl phenanthrene 80.8, 1-methyl phenanthrene 77.3, 9-methyl phenanthrene 75.1, and 2,7-dimethyl phenanthrene 76.6). Neither pure cultures nor the microbial community from these wastes showed extracellular biosurfactant production suggesting that the addition of an exogenously produced biosurfactant may be important in enhancing hydrocarbon bioavailability and biodegradation. DNA analysis of bilge waste samples revealed a ubiquitous distribution of the nahAc genotype in the dump pools. Although almost all of the isolates grew on naphthalene as sole carbon source, only some of them yielded nahAc amplification under the experimental conditions used. The variety of PAHs in bilge wastes could support bacteria with multiple degradation pathways and a diversity of catabolic genes divergent from the classical nah-like type.     

Suspension culture of gametophytes of transgenic kelp in a photobioreactor

Transgenic Laminaria japonica gametophytes producing a recombinant tissue-type plasminogen activator (rtPA) protein, which is an effective third-generation thrombolytic agent for acute myocardial infarction (AMI), were cultured in an illuminated bubble column bioreactor. A maximum final dry cell weight of 1120 mg l⁻¹ was obtained in batch culture with an initial dry cell weight of 126 mg l⁻¹ and with aeration rate of 1.2 l air min⁻¹ l⁻¹ culture, nitrate at 1.5 mM and phosphate at 0.17 mM. The yield of rtPA was 56 μg g⁻¹ dry cell wt. This is the first report regarding cultivation of a transgenic macroalga in a bioreactor.Revisions requested 27 January 2005 and 14 April 2005; Revisions received 6 April 2005 and 17 May 2005     

Reduction of Cr(VI) by a Bacillus sp.

A Bacillus sp. RE was resistant to chromium and reduced Cr(VI) without accumulating chromium inside the cell. When Cr(VI) was 10 and 40 μg ml⁻¹, >95% of the total Cr(VI) was reduced in 24 and 72 h of growth, respectively, whereas at 80 μg Cr(VI) ml⁻¹ only 50% of Cr(VI) was reduced. However growth was not affected; the cell mass was 0.7–0.8 mg ml⁻¹ in all cases. The cell-free extract showed Cr(VI) reducing enzyme activity which was enhanced (>5 fold) by NADH and NADPH. Like whole cells the enzyme also reduced Cr(VI) with decreasing efficiency on increasing Cr(VI) concentration. The enzyme activity was optimal at pH 6.0 and 30 °C. The enzyme was stable up to 30 °C and from pH 5.5 to 8, but from pH 4 to 5 the enzyme was severely destabilized. Its K_m and V_max were 14 μm and 3.8 nmol min⁻¹ mg⁻¹ respectively. The enzyme activity was enhanced by Cu²⁺ and Ni²⁺ and inhibited by Hg²⁺. Received 21 September 2005; Revisions requested 5 October 2005; Revisions received 16 November 2005; Accepted 16 November 2005     

基于吐温-80下2株功能菌协同降解多环芳烃的特性研究

【目的】研究恶臭假单胞菌B6-2和克雷伯氏菌CW-D3T构建的混合功能菌对多环芳烃的协同修复效能,并探究非离子表面活性剂吐温-80对混菌降解多环芳烃的影响,以期为芳烃化合物的生物修复提供技术参考和理论依据。【方法】通过生长曲线及平板菌落计数法反映混菌生长情况及比例,从而评估混菌降解体系的可行性;通过高效液相色谱法探究各体系以及不同吐温-80浓度下混培体系对多环芳烃的降解效能;最后通过烷烃吸附法测定细胞表面疏水性,以探究吐温-80对混合功能菌降解多环芳烃的影响机制。【结果】等比例混合的2株菌共培养生长状态优于纯培体系,对混合多环芳烃(菲、荧蒽、芘)的降解率分别为33.4%、30.1%、28.6%(7 d),相较于菌CW-D3T,分别提高了1.31倍、1.46倍、1.42倍。混培体系中加入500 mg/L的吐温-80对菲、荧蒽、芘的降解率分别为47.7%、43.2%、38.8%(7 d),相较于对照组各提高了1.55倍、1.38倍、1.31倍,而更高浓度的吐温-80无明显促进作用或轻微抑制。添加吐温-80使菌CW-D3T和混菌的表面疏水性提高,而菌B6-2表面疏水性降低。结合细菌生长量分析...     

Spatial distribution,size structure,and prey of Craspedacusta sowerbyi Lankester in a shallow New Zealand lake

Solar ultraviolet radiation both degrades and alters the quality of natural organic matter as well as organic pollutants in surface waters. Still, it is only recently that this indirect influence of photochemical processes on aquatic organisms (e.g. bacteria) has received attention. We experimentally studied the photochemical degradation of three PAHs; anthracene, phenanthrene and naphthalene, in water. Anthracene and phenanthrene were rapidly photodegraded (half-lives of 1 and 20.4 hours, respectively), while the photochemical half-life of naphthalene exceeded 100 hours. Hence photodegradation is most likely a less important removal mechanism for the latter compound. The influence of humic substance additions (0–25 mg C l^–1) on degradation rates was also assessed, and while photodegradation of anthracene was not affected by these additions, phenanthrene photodegradation slowed down considerably at the higher humic substance concentrations. These differential responses of anthracene and phenanthrene can at least partially be explained by differences in the spectral absorbance of the two compounds. In contrast, ionic strength did not have any appreciable effect on the estimated photodegradation rates of either compound. The influence of PAHs on growth of aquatic bacteria was assessed in dilution cultures with and without exposure to PAHs and simulated solar UV radiation. Separately, neither PAHs nor simulated solar UV radiation had any effect on bacterial growth. However, when combined, a marked inhibition of bacterial growth could be observed in water obtained from a clearwater lake. This could be due to the formation of toxic photodegradation products such as quinones (detected in our incubations) or other reactive species that affect bacteria negatively. Hence, in addition to influencing the fate and persistence of PAHs in aquatic systems, solar radiation and natural organic matter and regulate the toxicity of these compounds to indigenous micro-organisms.     

多环芳烃微生物降解基因的研究进展

多环芳烃(PAHs)是环境中普遍存在的一类有机污染物,微生物的降解是PAHs去除的主要途径。近年来,有关PAHs微生物降解途径和代谢产物的研究已有很多报道。小分子PAHs一般可以直接被微生物降解,而大分子PAHs则需要微生物以共代谢的方式降解。在过去20年中,微生物降解PAHs的基因相继被发现,各种基因在调控PAHs降解过程中的功能也越来越清晰。本文概述了PAHs微生物降解基因方面的研究进展,详细介绍了微生物对萘、菲的降解基因,最后对PAHs微生物降解基因的应用前景进行了展望。