醚磺隆降解菌的分离鉴定、基因组学分析及其降解特性研究
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摘要
磺酰脲类除草剂是一类高效、低毒、高选择性的新型除草剂,被广泛应用于水稻、玉米、小麦、大豆等田间杂草的防控,其用量也呈逐年增加的趋势。然而其微量的环境残留就会对后茬敏感作物产生严重的药害,引起作物减产,甚至绝收,并且造成了大量“癌症田”,给农业生产造成了巨大的经济损失,如何清除其在环境中的残留已成为当今的热点问题。以微生物代谢活动为核心的微生物修复技术,因其具有能耗低、效率高、环境友好等优点,逐渐成为治理环境污染的重要手段之一。
本文从规模化工程沼液样品中分离得到多株能以醚磺隆(cinosulfuron)为唯一氮源进行生长的降解菌株,其中菌株LAM0713和LAM0618降解效率最高。菌株16S rRNA基因的序列对比分析结果表明,LAM0713和LAM0618均归属于库特氏属(Kurthia),且与现有Kurthia属有效发表菌株的16S rRNA基因序列最高位相似性分别为97.1%和96.9%,初步判断二者为Kurthia属的疑似新种。
对疑似新种菌株LAM0713和LAM0618进行了系统分类学研究。利用表型特征分析、生理生化指标测定、重要细胞化学组分分析、16S rRNA基因序列系统进化分析、基因组DNA G+C mol%含量测定等手段,完成了菌株的多相分类鉴定工作,结果表明,LAM0713和LAM0618两菌株的16S rRNA基因序列相似性为100%,DNA-DNA杂交率为85.3±1.4%,多项分类鉴定结果表明,两株菌属于库特氏属(Kurthia)的一个新种,为缅怀我国著名土壤微生物学家陈华癸院士,该新种被命名为Kurthia huakuii sp. nov.,其模式菌株为LAM0618T(=ACCC06121T=JCM19187T)。
采用Illumina Hiseq2000测序平台测定了Kurthia huakuii的全基因组序列(GenBank登录号AYTB00000000)。样品共产出755Mb数据。基于测序数据组装得到菌株Kurthia huakuii的基因组大小为3,585,165bp,GC含量39.91%,共25个scaffold,56个contig。基因组组分分析后发现,Kurthia huakuii的基因组含有3,560个编码序列(CDs),总长度为3,050,526bp,平均长度857bp,占基因组全长的85.09%。含有112个tRNA,33个rRNA。共有2242个功能基因的功能得到了预测,被注释到21个COG簇中。KEGG数据库分析工得到138个代谢图,其中45个与异源物质代谢有关,约有169个CDs参与其中。Kurthia huakuii的全基因组序列的分析将有助于降解基因鉴定,为进一步阐明磺酰脲类除草剂的代谢途径与机理奠定基础。这是迄今为止首次关于磺酰脲类除草剂降解菌株基因组测序的报道。
利用Kurhia huakuii全基因组信息分析的结果,从菌株LAM0713中克隆得到了一个新的酯酶基因Sue,该基因全长831bp,在GenBank中的登陆号为KJ702613。sue基因与目前已发表的磺酰脲类除草剂降解酶基因的同源性较低,且具有典型的水解酶超家族特征。利用成功构建的pET32a-sue重组质粒,在37℃培养时经过1mmol／LIPTG的诱导,成功实现了重组SUE蛋白的高水平表达,获得了一条约32kDa的特异性条带,其对醚磺隆的降解试验表明,SUE蛋白15mmin内对50mg/L浓度的醚磺隆的降解率达43.2%。运用在线数据库和生物信息学软件初步分析了SUE蛋白的信号肽和夸膜区并推测了一级、二级和三级结构,分析结果表明SUE蛋白可能为新的可降解醚磺隆的酯酶。
利用单因素试验,并结合响应面法对高效醚磺隆降解菌株Kurhia huakuiiLAM0713的最适降解条件进行了研究,结果表明：该菌株在GSM液体培养基中的最适降解条件为31.8℃和pH6.9。在最适条件下,LAM0713在5d时间里,对50mg/L醚磺隆的降解率达到92.4%。菌株LAM0713可耐受并降解高达400mg/L的醚磺隆,同时对苯磺隆(Tribenuron methyl),胺苯磺隆(ethametsulfuron methyl),玉嘧磺隆(rimsulfuron),氯磺隆(chlorsulfuron)和苄嘧磺隆(bensulfuron methyl)均有较好的降解效果。运用高效液相色谱质谱联用技术(HPLC-MS)检测菌株LAM0713降解醚磺隆时产生的中间代谢产物,获得了5种中间代谢产物,根据醚磺隆分子结构特征,推断了LAM0713降解醚磺隆的可能代谢途径,LAM0713对醚磺隆的降解主要以磺酰脲桥的水解为主。土壤模拟降解实验结果表明,菌株LAM0713在15d内对50mg/kg浓度的醚磺隆的降解率达到79.7%。
As a new kind of herbicide, sulfonylurea herbicides characterized by high efficiency and selectivity, and have been widely used for weed control in cultivation of many crops, however, the residue of the herbicides can serious damage subsequent rotation of sulfonylurea-sensitive crops, which can result in serious agricultural loss and even the formation of "cancel field", destroy the ecological balance, thus, great concern and interest have been raised regarding elimination of the herbicide residues in soil. Because of its low energy consumption, high efficiency and environmental friendliness, microbiological remediation technique has been regarded as one of the most important way to eliminate the herbicides and pesticides pollution.
Several bacteria capable of degrading sulfonylurea herbicides were isolated from biogas slurry samples and two of them which had a high efficiency and widest range of substrate degradation were named as LAM0713and LAM0618. Both of them were found to be able to utilized cinosulfuron as sole nitrogen source for growth. The analysis of16S rRNA gene sequence revealed that both of the two strains LAM0713and LAM0618were Kurthia like strain, and with the similarity of97.1%and96.9%to the most closely realted strains, respectively. Based on the chemotaxonomy analysis, phenotypic and biochemical characteristics, major cellular chemical composition,16S rRNA gene and G+C mol%, strain LAM0713and LAM0618were identified as a novel species of the genus Kurthia, for which their sequence similarity was100%and the DNA-DNA hybridization value of two strains was85.3±1.4%. The novel strain LAM0618was classified as the type strain, for which the name of Kurthia huakuii sp. nov., was porposed and in honour of the Chinese microbiologist Hua-Kui Chen for his contributions to soil microbiology in China. The type strain is LAM0618T (=ACCC06121T=JCM19187T).
The genome of Kurthia huakuii was sequenced by using Illumina Hiseq2000platform with a whole-genome shotgun (WGS) strategy (GenBank accession number: AYTB00O00000), and755M draft data was generated. All clean reads of3,585,165bp were assembled into56contigs and25scaffolds using the SOAPdenovo v.2.04. The genome G+C content was39.91%, and it contains3560coding sequences (CDSs),112tRNA genes and33rRNA genes. The total length of coding sequences (CDs) was3,050,526bp, the average length was857bp, and representing85.09%of the full length genome. A total of2242protein-coding genes were assigned with predicted function and have been categorized into21COG groups. Based on the KEGG database analysis,138metabolic maps have got and45of them were related to xenobiotic metabolism, about169CDs involved. The analysis of Kurthia huakuii genome sequence will contribute to the identification of degrade gene, and lay the foundation for further elucidate the metabolic pathways of sulfonylurea herbicides and mechanism. This is the first report on the genome sequencing of sulfonylurea herbicides degradation strain.
Based on the analysis results of Kurhia huakuii genome, a new esterase gene Sue was cloned from LAM0713. The gene G+C content is37.67%, and the Genbank accession number is KJ702613with831bp full-length. Compared with those have been published sulfonylurea herbicides degrading enzyme gene, sue gene has low similarity and has the typical characteristics of suprefamily of hydrolase. Online darabases and bioinformatics software were used to analysis the signal peptide and transmembrane regions, and used to duce the primary, secondary, tertiary structure of protein SUE, showed that the protein may be a new esterase to biodegrade cinosulfuron. The recombinant protein SUE was successfully expressed at a high level after incubated the recombinant plasmid pET32a-sue at37℃with induction via lmmol/L IPTG, shown that it was a32kDa specific bands. And cinosulfuron degradation revealed that protein SUE could efficiently degrade43.2%of cinosulfuron in15min.
Single factor experiments and response surface methodology were used to optimize the parameters that significantly affected cinosulfuron biodegradation by Kurthia huakuii LAM0713and their interactions. The results suggested that the optimal degrading condition in GSM fluid medium were of31.8℃and pH6.9, respectively. Strain LAM0713could efficiently degrade92.4%of initially supplemented50mg/L cinosulfuron under the optimum conditions within5days, and could endure high concentration of cinosulfuron and grew well in GSM containing400mg/L of cinosulfuron. Strain LAM0713was also found to be highly efficient in degrading tribenuron methyl, rimsulfuron, chlorsulfuron and bensulfuron methyl. Five intermediates formed during cinosulfuron degradation were detected by high performance liquid chromatography mass spectrometry (HPLC-MS), and a metabolic pathway for cinosulfuron degradation was proposed via cleavage of the sulfonylurea bridge. The results of soil simulated degradation show that the strain LAM0713could efficiently degrade79.7%of initially supplemented50mg/kg cinosulfuron within15d.
本文从规模化工程沼液样品中分离得到多株能以醚磺隆(cinosulfuron)为唯一氮源进行生长的降解菌株,其中菌株LAM0713和LAM0618降解效率最高。菌株16S rRNA基因的序列对比分析结果表明,LAM0713和LAM0618均归属于库特氏属(Kurthia),且与现有Kurthia属有效发表菌株的16S rRNA基因序列最高位相似性分别为97.1%和96.9%,初步判断二者为Kurthia属的疑似新种。
对疑似新种菌株LAM0713和LAM0618进行了系统分类学研究。利用表型特征分析、生理生化指标测定、重要细胞化学组分分析、16S rRNA基因序列系统进化分析、基因组DNA G+C mol%含量测定等手段,完成了菌株的多相分类鉴定工作,结果表明,LAM0713和LAM0618两菌株的16S rRNA基因序列相似性为100%,DNA-DNA杂交率为85.3±1.4%,多项分类鉴定结果表明,两株菌属于库特氏属(Kurthia)的一个新种,为缅怀我国著名土壤微生物学家陈华癸院士,该新种被命名为Kurthia huakuii sp. nov.,其模式菌株为LAM0618T(=ACCC06121T=JCM19187T)。
采用Illumina Hiseq2000测序平台测定了Kurthia huakuii的全基因组序列(GenBank登录号AYTB00000000)。样品共产出755Mb数据。基于测序数据组装得到菌株Kurthia huakuii的基因组大小为3,585,165bp,GC含量39.91%,共25个scaffold,56个contig。基因组组分分析后发现,Kurthia huakuii的基因组含有3,560个编码序列(CDs),总长度为3,050,526bp,平均长度857bp,占基因组全长的85.09%。含有112个tRNA,33个rRNA。共有2242个功能基因的功能得到了预测,被注释到21个COG簇中。KEGG数据库分析工得到138个代谢图,其中45个与异源物质代谢有关,约有169个CDs参与其中。Kurthia huakuii的全基因组序列的分析将有助于降解基因鉴定,为进一步阐明磺酰脲类除草剂的代谢途径与机理奠定基础。这是迄今为止首次关于磺酰脲类除草剂降解菌株基因组测序的报道。
利用Kurhia huakuii全基因组信息分析的结果,从菌株LAM0713中克隆得到了一个新的酯酶基因Sue,该基因全长831bp,在GenBank中的登陆号为KJ702613。sue基因与目前已发表的磺酰脲类除草剂降解酶基因的同源性较低,且具有典型的水解酶超家族特征。利用成功构建的pET32a-sue重组质粒,在37℃培养时经过1mmol／LIPTG的诱导,成功实现了重组SUE蛋白的高水平表达,获得了一条约32kDa的特异性条带,其对醚磺隆的降解试验表明,SUE蛋白15mmin内对50mg/L浓度的醚磺隆的降解率达43.2%。运用在线数据库和生物信息学软件初步分析了SUE蛋白的信号肽和夸膜区并推测了一级、二级和三级结构,分析结果表明SUE蛋白可能为新的可降解醚磺隆的酯酶。
利用单因素试验,并结合响应面法对高效醚磺隆降解菌株Kurhia huakuiiLAM0713的最适降解条件进行了研究,结果表明：该菌株在GSM液体培养基中的最适降解条件为31.8℃和pH6.9。在最适条件下,LAM0713在5d时间里,对50mg/L醚磺隆的降解率达到92.4%。菌株LAM0713可耐受并降解高达400mg/L的醚磺隆,同时对苯磺隆(Tribenuron methyl),胺苯磺隆(ethametsulfuron methyl),玉嘧磺隆(rimsulfuron),氯磺隆(chlorsulfuron)和苄嘧磺隆(bensulfuron methyl)均有较好的降解效果。运用高效液相色谱质谱联用技术(HPLC-MS)检测菌株LAM0713降解醚磺隆时产生的中间代谢产物,获得了5种中间代谢产物,根据醚磺隆分子结构特征,推断了LAM0713降解醚磺隆的可能代谢途径,LAM0713对醚磺隆的降解主要以磺酰脲桥的水解为主。土壤模拟降解实验结果表明,菌株LAM0713在15d内对50mg/kg浓度的醚磺隆的降解率达到79.7%。
As a new kind of herbicide, sulfonylurea herbicides characterized by high efficiency and selectivity, and have been widely used for weed control in cultivation of many crops, however, the residue of the herbicides can serious damage subsequent rotation of sulfonylurea-sensitive crops, which can result in serious agricultural loss and even the formation of "cancel field", destroy the ecological balance, thus, great concern and interest have been raised regarding elimination of the herbicide residues in soil. Because of its low energy consumption, high efficiency and environmental friendliness, microbiological remediation technique has been regarded as one of the most important way to eliminate the herbicides and pesticides pollution.
Several bacteria capable of degrading sulfonylurea herbicides were isolated from biogas slurry samples and two of them which had a high efficiency and widest range of substrate degradation were named as LAM0713and LAM0618. Both of them were found to be able to utilized cinosulfuron as sole nitrogen source for growth. The analysis of16S rRNA gene sequence revealed that both of the two strains LAM0713and LAM0618were Kurthia like strain, and with the similarity of97.1%and96.9%to the most closely realted strains, respectively. Based on the chemotaxonomy analysis, phenotypic and biochemical characteristics, major cellular chemical composition,16S rRNA gene and G+C mol%, strain LAM0713and LAM0618were identified as a novel species of the genus Kurthia, for which their sequence similarity was100%and the DNA-DNA hybridization value of two strains was85.3±1.4%. The novel strain LAM0618was classified as the type strain, for which the name of Kurthia huakuii sp. nov., was porposed and in honour of the Chinese microbiologist Hua-Kui Chen for his contributions to soil microbiology in China. The type strain is LAM0618T (=ACCC06121T=JCM19187T).
The genome of Kurthia huakuii was sequenced by using Illumina Hiseq2000platform with a whole-genome shotgun (WGS) strategy (GenBank accession number: AYTB00O00000), and755M draft data was generated. All clean reads of3,585,165bp were assembled into56contigs and25scaffolds using the SOAPdenovo v.2.04. The genome G+C content was39.91%, and it contains3560coding sequences (CDSs),112tRNA genes and33rRNA genes. The total length of coding sequences (CDs) was3,050,526bp, the average length was857bp, and representing85.09%of the full length genome. A total of2242protein-coding genes were assigned with predicted function and have been categorized into21COG groups. Based on the KEGG database analysis,138metabolic maps have got and45of them were related to xenobiotic metabolism, about169CDs involved. The analysis of Kurthia huakuii genome sequence will contribute to the identification of degrade gene, and lay the foundation for further elucidate the metabolic pathways of sulfonylurea herbicides and mechanism. This is the first report on the genome sequencing of sulfonylurea herbicides degradation strain.
Based on the analysis results of Kurhia huakuii genome, a new esterase gene Sue was cloned from LAM0713. The gene G+C content is37.67%, and the Genbank accession number is KJ702613with831bp full-length. Compared with those have been published sulfonylurea herbicides degrading enzyme gene, sue gene has low similarity and has the typical characteristics of suprefamily of hydrolase. Online darabases and bioinformatics software were used to analysis the signal peptide and transmembrane regions, and used to duce the primary, secondary, tertiary structure of protein SUE, showed that the protein may be a new esterase to biodegrade cinosulfuron. The recombinant protein SUE was successfully expressed at a high level after incubated the recombinant plasmid pET32a-sue at37℃with induction via lmmol/L IPTG, shown that it was a32kDa specific bands. And cinosulfuron degradation revealed that protein SUE could efficiently degrade43.2%of cinosulfuron in15min.
Single factor experiments and response surface methodology were used to optimize the parameters that significantly affected cinosulfuron biodegradation by Kurthia huakuii LAM0713and their interactions. The results suggested that the optimal degrading condition in GSM fluid medium were of31.8℃and pH6.9, respectively. Strain LAM0713could efficiently degrade92.4%of initially supplemented50mg/L cinosulfuron under the optimum conditions within5days, and could endure high concentration of cinosulfuron and grew well in GSM containing400mg/L of cinosulfuron. Strain LAM0713was also found to be highly efficient in degrading tribenuron methyl, rimsulfuron, chlorsulfuron and bensulfuron methyl. Five intermediates formed during cinosulfuron degradation were detected by high performance liquid chromatography mass spectrometry (HPLC-MS), and a metabolic pathway for cinosulfuron degradation was proposed via cleavage of the sulfonylurea bridge. The results of soil simulated degradation show that the strain LAM0713could efficiently degrade79.7%of initially supplemented50mg/kg cinosulfuron within15d.
引文
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