Haloalkane and haloacid dehalogenases from aerobic bacterial isolates indigenous to contaminated sites in Africa demonstrate diverse substrate specificities

Determination of 19 chlorophenols in fish by QuEChERS-gas chromatography-mass spectrometry

大量含氯农药、次氯酸消毒水以及水产品杀虫剂和杀菌剂的广泛使用,使鱼类容易受到氯酚类化合物的污染,因而建立鱼肉中氯酚类化合物的检测方法十分重要。建立了QuEChERS结合气相色谱-质谱法同时检测鱼肉中19种氯酚类化合物的分析方法。19种氯酚类化合物选用DB-5MS毛细管色谱柱(30 m×0.25 mm×0.25 μm),载气流速1 mL/min进行分离,可以得到很好的峰形。前处理采用改良的QuEChERS方法,通过对提取剂的种类和剂量、净化剂的种类和剂量,以及衍生条件中的衍生温度、衍生时间和衍生剂用量等进行优化,确定最优的前处理方法。选择10 mL乙酸乙酯作为提取剂,500 mg的C₁₈作为净化剂,加入3 g氯化钠和5 g无水硫酸镁,过0.22 μm的有机滤膜,加入50 μL的硅烷化衍生剂在45 ℃条件下衍生30 min,用EI源测定,选择离子监测模式,以外标法定量。19种氯酚类化合物在0.4~10 μg/L范围内具有良好的线性关系,相关系数R²大于0.998,方法定量限为0.04~0.16 μg/kg。空白基质不同加标水平的回收率为70.6%~115.0%,相对标准偏差为2.6%~10.5%。将建立的方法应用于实际样品的检测分析,结果显示,各种鱼肉中均有不同程度的氯酚类化合物检出,其中,黄花鱼检出的氯酚类化合物总量最大,为8.74 μg/kg;其次为鲫鱼7.59 μg/kg;米鱼的检出量最少,为1.59 μg/kg。所建立的方法简化了样品的前处理步骤,操作简单,方法灵敏度高、重复性好,可满足鱼肉中19种氯酚类化合物的高通量检测要求,能显著提高氯酚类化合物的检测效率。

Direct aerobic oxidation (DAO) of chlorinated aliphatic hydrocarbons: A review of key DAO bacteria, biometabolic pathways and in-situ bioremediation potential

Contamination of aquifers and vadose zones with chlorinated aliphatic hydrocarbons (CAH) is a world-wide issue. Unlike other reactions, direct aerobic oxidation (DAO) of CAHs does not require growth substrates and avoids the generation of toxic by-products. Here, we critically review the current understanding of chlorinated aliphatic hydrocarbons-DAO and its application in bioreactors and at the field scale. According to reports on chlorinated aliphatic hydrocarbons-DAO bacteria, isolates mainly consisted of Methylobacterium and Proteobacterium. Chlorinated aliphatic hydrocarbons-DAO bacteria are characterized by tolerance to a high concentration of CAHs and highly efficient removal of CAHs. Trans-1,2-dichloroethylene (t-DCE) is easily transformed biomass for bacteria, followed by 1,2-dichloroethane (1,2-DCA), dichloromethane (DCM), vinyl chloride (VC) and cis-1,2-dichloroethylene (c-DCE). Significant differences in the maximum specific growth rates were observed with different CAHs and biometabolic pathways for DCM, 1,2-DCA, VC and c-DCE degradation have been successfully parsed. Detection of the functional genes etnC and etnE is useful for the determination of active VC DAO bacteria. Additionally, DAO bacteria have been successfully applied to CAHs in new types of bioreactors with satisfactory results. To the best of the authors' knowledge, only one study on DAO-CAHs was conducted in-situ and resulted in 99% CAH removal. Lastly, we put forward future development prospect of chlorinated aliphatic hydrocarbons-DAO.

Streptomyces sp. is a powerful biotechnological tool for the biodegradation of HCH isomers: biochemical and molecular basis

Actinobacteria are well-known degraders of toxic materials that have the ability to tolerate and remove organochloride pesticides; thus, they are used for bioremediation. The biodegradation of organochlorines by actinobacteria has been demonstrated in pure and mixed cultures with the concomitant production of metabolic intermediates including γ-pentachlorocyclohexene (γ-PCCH); 1,3,4,6-tetrachloro-1,4-cyclohexadiene (1,4-TCDN); 1,2-dichlorobenzene (1,2-DCB), 1,3-dichlorobenzene (1,3-DCB), or 1,4-dichlorobenzene (1,4-DCB); 1,2,3-trichlorobenzene (1,2,3-TCB), 1,2,4-trichlorobenzene (1,2,4-TCB), or 1,3,5-trichlorobenzene (1,3,5-TCB); 1,3-DCB; and 1,2-DCB. Chromatography coupled to mass spectrometric detection, especially GC-MS, is typically used to determine HCH-isomer metabolites. The important enzymes involved in HCH isomer degradation metabolic pathways include hexachlorocyclohexane dehydrochlorinase (LinA), haloalkane dehalogenase (LinB), and alcohol dehydrogenase (LinC). The metabolic versatility of these enzymes is known. Advances have been made in the identification of actinobacterial haloalkane dehydrogenase, which is encoded by linB. This knowledge will permit future improvements in biodegradation processes using Actinobacteria. The enzymatic and genetic characterizations of the molecular mechanisms involved in these processes have not been fully elucidated, necessitating further studies. New advances in this area suggest promising results. The scope of this paper encompasses the following: (i) the aerobic degradation pathways of hexachlorocyclohexane (HCH) isomers; (ii) the important genes and enzymes involved in the metabolic pathways of HCH isomer degradation; and (iii) the identification and quantification of intermediate metabolites through gas chromatography coupled to mass spectrometry (GC-MS).

Draft Genome Sequence of the 1,2-Dichloroethane-Utilizing Micrococcus sp. Strain NDB3Y10, Isolated from an Australian Bore Well Producing Coal Seam Gas

Micrococcus luteus strain NDB3Y10, which utilizes 1,2-dichloroethane as a carbon source, was isolated from a bore well that produces coal seam gas. The draft genome size of the strain was 2.49 Mb with a G+C content of 72.97%. Genes involved in the metabolism of halogenated substrates, including halogenated hydrocarbons, were identified.

Isolation, characterization and identification of a Paracoccus sp. 2-haloacid-degrading bacterium from the marine sponge Hymeniacidon perlevis

A 2-haloacid dehalogenase-producing bacterium, designated DEH99, was isolated from the marine sponge Hymeniacidon perlevis using a modified enrichment medium and a pH indicator method. DEH99 could degrade only half of the racemic mixture 2-chloropropionic acid (2-CPA) in the medium. The dehalogenase of DEH99 was further determined to be a (S)-2-haloacid dehalogenase, which can degrade 2-CPA, 2-bromopropionic acid (2-BPA), and iodoacetic acid. The gene encoding the (S)-2-haloacid dehalogenase was partially sequenced and classified into the Group II family. The 2-haloacid dehalogenase showed the highest sequence similarity (77% with 21% query coverage) to the haloacid dehalogenase (dhlB) gene of Xanthobacter autotrophicus. A phylogenetic analysis of the 16S rDNA sequence demonstrated that the isolate DEH99 is a member of the genus Paracoccus. To our knowledge, this is the first report detailing the isolation of a strain of genus Paracoccus having 2-haloacid dehalogenase activity from marine sponges.

Aerobic biodegradation of dichloroethenes by indigenous bacteria isolated from contaminated sites in Africa

The widespread use of tetrachloroethene (PCE) and trichloroethene (TCE) as dry cleaning solvents and degreasing agents for military and industrial applications has resulted in significant environmental contamination worldwide. Anaerobic biotransformation of PCE and TCE through reductive dechlorination frequently lead to the accumulation of dichloroethenes (DCEs), thus limiting the use of reductive dechlorination for the biotransformation of the compounds. In this study, seven bacteria indigenous to contaminated sites in Africa were characterized for DCE degradation under aerobic conditions. The specific growth rate constants of the bacterial isolates ranged between 0.346-0.552 d(-1) and 0.461-0.667 d(-1) in cis-DCE and trans-DCE, respectively. Gas chromatographic analysis revealed that up to 75% of the compounds were degraded within seven days with the degradation rate constants ranging between 0.167 and 0.198 d(-1). The two compounds were also observed to be significantly degraded, simultaneously, rather than sequentially, when present as a mixture. Phylogenetic analysis of the 16S rRNA gene sequences of the bacterial isolates revealed their identity as well as their relation to other environmentally-important bacteria. The observed biodegradation of DCEs may contribute to PCE and TCE removal at the aerobic fringe of groundwater plumes undergoing reductive dechlorination in contaminated sites.

Biodegradation of microcystins by aquatic Burkholderia sp. from a South Brazilian coastal lagoon

Biological degradation of cyanobacterial hepatotoxin microcystins in estuarine and coastal water samples from the Patos Lagoon estuarine system, a coastal lagoon situated at the southernmost region of Brazil, was observed. Samples of natural surface water were spiked with purified and semi-purified microcystins (MC-LR and [D-Leu(1)]MC-LR) and their concentrations were monitored by HPLC analysis. After 15 days, the toxins were no longer detectable and after 43 days less than 90% of the initial concentration added to the samples was detected by ELISA. The average degradation rates and the exponential decay rate constants from inside and outside of the estuary were similar. A microcystin degradative bacterium was isolated from the estuarine region. Partial sequence of the 16S rDNA showed a 96% homology with the Burkholderia genus. This genus belongs to the beta subdivision on proteobacteria. This is the first report showing the genus Burkholderia as a cyanobacterial toxin degrader.

Proteomic analysis of Burkholderia cepacia MBA4 in the degradation of monochloroacetate

Burkholderia cepacia MBA4 is a bacterium that degrades 2-haloacids by removing the halogen and subsequent metabolism of the product for energy. In this study, 2-DE, MS/MS, and N-terminal amino acid sequencing were used to investigate the protein expression profiles of MBA4 grown in a 2-haloacid (monochloroacetate, MCA) and in the corresponding metabolic product (glycolate). Glycolate was used as a control to eliminate the proteins induced by it. Five proteins were found to be up-regulated and five proteins were down-regulated in response to MCA. The differentially expressed proteins were examined, seven of them were identified by MS/MS and two of them were sequenced by Edman degradation. Our results definitely provide an insight for understanding the physiology of B. cepacia MBA4 in response to organohalide contaminated site.

Biodegradation of dibromoneopentyl glycol by a bacterial consortium

Dibromoneopentyl glycol (DBNPG) is a brominated flame retardant that is used as an additive during the manufacture of plastic polymers and as a chemical intermediate for other flame retardants. It is classified as not readily biodegradable and based on experimental studies in animals is believed to be a carcinogen. We have demonstrated, to the best of our knowledge for the first time, the complete biodegradation of DBNPG under aerobic conditions. Total organic carbon (TOC) analysis indicates the complete mineralization of DBNPG. DBNPG biodegradation was accompanied by the release of bromide into the medium, probably due to a biological debromination reaction by bacterial consortia. A denaturing gradient gel electrophoresis (DGGE) analysis of PCR amplified 16S rRNA gene was used, to characterize the bacterial consortia involved in DBNPG biodegradation. At least seven bacterial species were found to be involved in this process, among them species with similarity to strains that are known for their dehalogenating ability.

Isolation of novel bacteria able to degrade alpha-halocarboxylic acids by enrichment from environmental samples

In order to isolate novel bacteria able to degrade alpha-halocarboxylic acids a variety of culturing strategies were implemented. Eight pure cultures were obtained and were found to be associated with the Gram negative Proteobacteria and the Gram positive Bacillus and Enterococcus genera. Furthermore, several strains were obtained which were able to degrade the DL-halocarboxylic acids anaerobically. Molecular analysis of the pure cultures led us to conclude that they may possess novel enzymes involved in the biodegradation of the alpha-halocarboxylic acids. These results are the first for nearly 40 years to describe the isolation of Gram positive isolates on an alpha-halocarboxylic acid as the sole source of carbon and energy, which also show the ability to de-toxify the test substrate by releasing chloride.

Biostimulation and bioaugmentation enhances aerobic biodegradation of dichloroethenes

The accumulation of dichloroethenes (DCEs) as dominant products of microbial reductive dechlorination activity in soil and water represent a significant obstacle to the application of bioremediation as a remedial option for chloroethenes in many contaminated systems. In this study, the effects of biostimulation and/or bioaugmentation on the biodegradation of cis- and trans-DCE in soil and water samples collected from contaminated sites in South Africa were evaluated in order to determine the possible bioremediation option for these compounds in the contaminated sites. Results from this study indicate that cis- and trans-DCE were readily degraded to varying degrees by natural microbial populations in all the soil and water samples tested, with up to 44% of cis-DCE and 41% of trans-DCE degraded in the untreated soil and water samples in two weeks. The degradation rate constants ranged significantly (P<0.05) between 0.0938 and 0.560 wk(-1) and 0.182 and 0.401 wk(-1), for cis- and trans-DCE, respectively, for the various treatments employed. A combination of biostimulation and bioaugmentation significantly increased the biodegradation of both compounds within two weeks; 14% for cis-DCE and 18% for trans-DCE degradation, above those observed in untreated soil and water samples. These findings support the use of a combination of biostimulation and bioaugmentation for the efficient biodegradation of these compounds in contaminated soil and water. In addition, the results clearly demonstrate that while naturally occurring microorganisms are capable of aerobic biodegradation of cis- and trans-DCE, biotransformation may be affected by several factors, including isomer structure, soil type, and the amount of nutrients available in the water and soil.