中文题名: | 细菌降解杀菌剂异菌脲及其代谢产物 3,5-二氯苯胺的机制研究 |
姓名: | |
学号: | 2019216021 |
保密级别: | 公开 |
论文语种: | chi |
学科代码: | 071005 |
学科名称: | 理学 - 生物学 - 微生物学 |
学生类型: | 博士 |
学位: | 理学博士 |
学校: | 南京农业大学 |
院系: | |
专业: | |
研究方向: | 环境微生物学 |
第一导师姓名: | |
第一导师单位: | |
完成日期: | 2023-03-30 |
答辩日期: | 2023-05-21 |
外文题名: | Mechanisms of Bacterial Degradation of The Fungicide Iprodione and Its Metabolite 3,5-Dichloroaniline |
中文关键词: | |
外文关键词: | Iprodione ; Degradation mechanism ; Gene cloning ; Enzymatic properties ; Anaerobic degradation of 3 ; 5-DCA |
中文摘要: |
异菌脲(Iprodione)是二甲酰亚胺类杀菌剂的代表性品种之一,由于其广泛的使用,在环境中常检测到异菌脲的残留,给人类健康和生态环境带来了潜在的风险。微生物作为消除环境中污染物的主力军,其在异菌脲降解方面发挥着重要作用。目前,国内外有关异菌脲微生物降解方面的研究主要集中于降解菌株的分离和代谢途径的鉴定,而相关的降解基因只报道了来自菌株Paenarthrobacter sp. YJN-5的异菌脲水解酶基因ipaH。微生物降解异菌脲的分子机制仍未完全阐明。目前报道的异菌脲降解菌株都通过相同的途径,即连续三步的水解反应将其转化为最终产物3,5-二氯苯胺(3,5-DCA),该产物与其母体化合物相比具有更高的毒性,且更难以被降解。而关于3,5-DCA降解方面的研究也仅限于一些降解菌株的分离,其代谢产物和代谢途径的研究鲜有报道。因此,异菌脲及其代谢产物3,5-DCA的微生物降解机制还未完全阐明。 菌株Paenarthrobacter sp. YJN-5是本实验室前期分离的异菌脲降解菌,它具有典型的异菌脲降解途径,本实验室已经克隆了其负责起始降解步骤的异菌脲水解酶基因ipaH(AEM e01150-18),但后续的异菌脲降解基因仍未揭示。我们继续通过富集传代培养分离到一株异菌脲降解菌Paenarthrobacter sp. YJN-D,它和YJN-5具有相同的异菌脲代谢途径。在本研究中仍然以菌株YJN-5为研究对象,通过比较两株异菌脲降解菌株基因组的方法克隆了菌株YJN-5中负责异菌脲降解第二和第三步的基因ddaH和duaH,并表征了DdaH和DuaH的酶学特性,从基因及酶学水平上解析了菌株YJN-5代谢异菌脲的机制。由于菌株YJN-5只能将异菌脲降解成3,5-DCA。为此,我们设计厌氧反应器,成功驯化了厌氧降解3,5-DCA的活性污泥,进而研究了活性污泥对3,5-DCA的降解特性、降解途径和群落结构变化。主要得到了以下研究结果: 1、异菌脲降解菌的分离鉴定及其降解特性研究 使用富集培养的方法,从葡萄园的土壤中分离到一株异菌脲降解菌株YJN-D,基于该菌的形态和16S rRNA基因序列相似性分析,将其初步鉴定为Paenarthrobacter sp.。菌株YJN-D降解异菌脲的最适温度和pH分别为30-35°C和pH7.0-8.0,而且该菌株能够利用异菌脲为唯一碳源生长,该菌株和本实验室前期报道的菌株Paenarthrobacter sp. YJN-5同属,而且具有相同的异菌脲代谢途径。我们已经克隆了YJN-5负责起始降解步骤的异菌脲水解酶基因ipaH。因此,通过比较基因组的手段来寻找和克隆菌株YJN-5中参与异菌脲降解的其它基因。 2、菌株YJN-5中异菌脲降解相关基因(ddaH和duaH)的功能鉴定 异菌脲降解菌株YJN-5和YJN-D基因组比对分析:对菌株YJN-D和YJN-5的基因组测序和分析显示,菌株YJN-5基因组大小为5,331,418 bp,含有一条染色体和四个质粒,共编码5129个基因;菌株YJN-D基因组大小为4,479,271 bp,含有一条染色体和三个质粒,共编码4217个基因。这两个基因组中相似性大于90%的基因一共有1304个,只有29个基因位于质粒上。通过对这29个保守基因进行注释分析及功能验证,成功找到三个保守的基因,其中一个是已经报道的异菌脲水解酶基因ipaH(大小为1410 bp)分别位于菌株YJN-5质粒1上和菌株YJN-D的质粒3上(两者相似性为98.03%);一个是N-(3,5-二氯苯基)-2,4-二氧代咪唑烷水解基因ddaH(大小为840 bp)分别位于菌株YJN-5质粒3上和菌株YJN-D的质粒2上(两者相似性为98.93%),与Swissport数据库中的肽聚糖脱乙酰酶(B5ZA76)具有34.06%的相似性;一个是N-[[(3,5-二氯苯基)氨基]羰基]甘氨酸水解基因duaH(大小为1227 bp)分别位于菌株YJN-5质粒2上和菌株YJN-D的染色体上(两者相似性为92.18%),与Swissport数据库中的耐热羧肽酶1(P80092)具有36.83%的相似性。鉴于ipaH的功能已经被本课题组鉴定,后续将鉴定ddaH和duaH的功能。 水解酶DdaH负责N-(3,5-二氯苯基)-2,4-二氧代咪唑烷的水解生成N-[[(3,5-二氯苯基)氨基]羰基]甘氨酸:将ddaH基因在大肠杆菌表达系统中进行异源表达、纯化并研究DdaH的酶学特性,结果显示DdaH水解N-(3,5-二氯苯基)-2,4-二氧代咪唑烷的最适温度为60°C,最适pH为7.5;它的活性不受EDTA浓度的影响,Zn2+和Ni2+(10 mM)能够显著促进DdaH的酶活。10 mM的Cu2+和Hg2+完全抑制其酶活。DdaH对N-(3,5-二氯苯基)-2,4-二氧代咪唑烷的Km、Vmax和kcat值分别为6.58 ± 0.34 µM, 0.31 ± 0.04 μmol s-1 mg-1和10.70 ± 1.32 s-1,其催化效率kcat/Km为1.63 μM-1 s-1与菌株YJN-D中的DdaH催化效率(1.61 μM-1 s-1)没有显著性差异。系统发育进化树分析表明DdaH属于CE4_HpPgdA家族中的新成员,同样具有该家族保守的催化基序DDHHH。基因插入失活和回补实验证明了ddaH是菌株YJN-5中负责N-(3,5-二氯苯基)-2,4-二氧代咪唑烷降解的唯一基因。 水解酶DuaH负责N-[[(3,5-二氯苯基)氨基]羰基]甘氨酸的水解生成3,5-DCA:对基因duaH进行异源表达、纯化并研究DuaH酶学特性,结果表明该酶最适反应温度为40°C,最适pH为7.5。Zn2+和Co2+(10 mM)能够显著增强DuaH的酶活力。菌株YJN-D中DuaH对N-[[(3,5-二氯苯基)氨基]羰基]甘氨酸的Km、Vmax和kcat值分别为5.67 ± 1.25 µM, 12.14 ± 0.64 μmol s-1 mg-1和523.29 ± 0.24 s-1,其催化效率kcat/Km为92.29 μM-1 s-1是菌株YJN-D中的DuaH催化效率(11.83 μM-1 s-1)的9倍。系统发育进化树分析表明DuaH属于M20 Peptidase Aminoacylase 1家族中的新成员,同样具有该家族保守的催化基序CHEHH。插入失活和回补实验证明了duaH是负责N-[[(3,5-二氯苯基)氨基]羰基]甘氨酸降解的唯一基因。 3、3,5-DCA厌氧降解活性污泥的降解特性及相关微生物分析 3,5-DCA厌氧降解活性污泥的降解特性:利用连续流动式厌氧反应器成功富集驯化出了能够高效降解3,5-DCA的活性污泥,和起始污泥相比,经62d富集后的活性污泥对3,5-DCA的降解能力提高了74倍。其降解3,5-DCA的最适温度和pH分别为30°C和pH7.0。厌氧活性污泥对其他二氯苯胺类化合物的降解速率为:3,5-DCA > 2,4-DCA > 3,4-DCA > 2,6-DCA > 2,5-DCA 或2,3-DCA。该厌氧活性污泥可以对二氯苯胺类化合物进行间位和邻位还原脱氯,不能进行对位还原脱氯。对3,5-DCA厌氧降解产物的鉴定发现,活性污泥先3,5-DCA还原脱氯生成3-氯苯胺(3-CA),后者可以进一步开环降解,也检测到了很少量的苯胺生成以及一些3,5-DCA、3-CA和苯胺等化合物的甲酰化、乙酰化和丙酰化的相关产物。 活性污泥富集驯化期间微生物群落结构研究:在活性污泥富集驯化期间,3,5-DCA的加入改变了活性污泥中微生物群落结构,细菌的多样性和丰富度均降低。富集驯化至62 d,属于OHRB (Organohalide-respiring bacteria)的三个门(Firmicutes、Chloroflexi和Proteobacteria)的微生物总量占据着相当大的比例(71.39%)。在属水平,脱卤杆菌(Dehalobacter)、Anaerolineaceae_uncultured、Smithella、Denitratisoma和鞘脂菌属(Sphingobium)的细菌的相对丰度逐渐升高,同时结合环境因子关联分析以及Network网络分析,发现脱卤杆菌(Dehalobacter)、Anaerolineaceae_uncultured、Smithella、Denitratisoma和鞘脂菌属(Sphingobium)与进水的流速和厌氧活性污泥对3,5-DCA的厌氧降解能力两个环境因子呈正相关,表明了这些属的微生物可能直接或者间接参与了厌氧反应器中3,5-DCA的降解。另外我们使用特异性引物来扩增活性污泥中Dehalobacter的16S rRNA,测序结果表明活性污泥中只含有一种Dehalobacter,将其命名为DH-1,对其进行系统发育树分析发现Dehalobacter sp. DH-1与已报道的2,4,6-三氯苯酚厌氧降解菌株Dehalobacter sp. TCP1具有最高的相似性(99.21%)。 |
外文摘要: |
Iprodione is one of the representatives of dicarboxamide fungicides, and due to its widespread use, residues of iprodione are often detected in the environment, posing potential risks to human health and the ecological environment. Microorganisms, as the main force in eliminating pollutants from the environment, play an important role in the degradation of iprodione. Up to now, the microbial degradation of iprodione has been focused on the isolation of degradation strains and the identification of metabolic pathways, while the related degradation gene was reported only for the iprodione hydrolase gene ipaH (AEM e01150-18) from strain Paenarthrobacter sp. YJN-5. The microbial metabolic mechanism of iprodione has not been fully elucidated. At present, the currently reported iprodione-degrading strains all convert it to the end product 3,5-dichloroaniline (3,5-DCA) via the same pathway of a sequential three-step hydrolysis reaction, 3,5-DCA is more toxic and more difficult to be degraded than its parent compound. Studies on the degradation of 3,5-DCA have been limited to the isolation of some degradation strains, and few studies on its metabolites and metabolic pathways have been reported. Therefore, the microbial degradation mechanism of iprodione and its metabolites 3,5-DCA has not been fully elucidated. Paenarthrobacter sp. YJN-5, an iprodione-degrading strain with a typical degradation pathway, was isolated in our laboratory. We have cloned its iprodione hydrolase gene ipaH (AEMe01150-18), which is responsible for the initial degradation step, while the subsequent iprodione degradation gene has not been revealed, we continued to isolate iprodione-degrading bacteria by serial enrichment culture. Paenarthrobacter sp. YJN-D that shares the same iprodione metabolic pathway as strain YJN-5 was isolated. In the present study, strain YJN-5 was still used as the object of study, the genes responsible for the second (ddaH) and third (duaH) steps of iprodione degradation in strain YJN-5 were cloned by comparing the genomes of the two iprodione-degrading strains and and characterized DdaH and DuaH enzymatic properties. The mechanism of iprodione metabolism in strain YJN-5 was analyzed from the level of gene and enzyme. Because strain YJN-5 can only degrade iprodione into 3,5-DCA. For this reason, we designed an anaerobic reactor and successfully accumulated the activated sludge of the anaerobic degradation of 3,5-DCA, and then studied the degradation characteristics, degradation pathway and community structure changes of 3,5-DCA by activated sludge. The main results are as follows: 1、Isolation and identification of iprodione-degrading bacteria and its degradation characteristics. A strain YJN-D with high degradation efficiency of iprodione was isolated from the soil of vineyard by the traditional enrichment method. Based on the analysis of its morphology and 16S rRNA gene sequence similarity analysis, it was preliminarily identified as Paenarthrobacter sp. The optimum temperature and pH for the degradation of iprodione by strain YJN-D were 30-35°C and pH7.0-8.0, respectively. Strain YJN-D can grow with iprodione as the sole carbon source. This strain belongs to the same genus as the strain Paenarthrobacter sp.YJN-5 previously reported in our laboratory and has the same metabolic pathway of iprodione. We have cloned iprodione hydrolase gene ipaH from strain YJN-5. Therefore, the other genes involved in the degradation of iprodione were searched and cloned by comparing genomes. 2、Functional identification of genes (ddaH and duaH) involved in the degradation of iprodione in strain YJN-5 Genomic alignment analysis of iprodione-degrading strains YJN-D and YJN-5: After sequencing and comparing the genomes of strains YJN-5 and YJN-D, it was found that the genome of strain YJN-5 was 5,331,418 bp, containing one chromosome and four plasmids, encoding 5129 genes, while the genome of strain YJN-D was 4,479,271 bp, containing one chromosome and three plasmids, encoding 4217 genes. There are 1304 genes with more than 90% similarity in these two genomes, while only 29 genes are on their plasmids. Through annotation analysis and functional verification of the 29 conserved genes, three conserved genes were successfully found, one of which is that the reported iprodione hydrolase gene ipaH (1410 bp) is located on strain YJN-5-plasmid 1 and strain YJN-D-plasmid 3, respectively (the similarity is 98.03%). One is N-(3-dichlorophenyl)-2-dioximidazolidine hydrolase gene ddaH (840 bp) located on strain YJN-5-plasmid 3 and YJN-D-plasmid 2 respectively (the similarity is 98.93%). It shares 34.06% identity with peptidoglycan deacetylase (B5ZA76) in Swissport database. One is that (3,5-dichlorophenylurea)acetic acid hydrolase gene duaH (1227 bp) is located on strain YJN-5-plasmid 2 and strain YJN-D-chromosome respectively (the similarity is 92.18%). It shares 36.83% identity with thermostable carboxypeptidase 1 (P80092) in Swissport database. Since the function of ipaH has been identified, the function of ddaH and duaH will be identified later. The hydrolase DdaH is responsible for the hydrolysis of N-(3,5-dichlorophenyl)-2,4-dioxoimidazolidine to (3,5-dichlorophenylurea)acetic acid: We used the Escherichia coli expression system to heterologously express and purify the ddaH gene and then studied the enzymatic properties of DdaH. The optimum temperature of DdaH hydrolysis of N-(3,5-dichlorophenyl)-2,4-dioxoimidazolidine was 60°C, and the optimum pH was 7.5. Its activity was not affected by EDTA, 10 mM of Zn2+ and Ni2+ could significantly promote the enzyme activity of DdaH. 10 mM of Cu2+ and Hg2+ completely inhibited the enzyme activity. The Km, Vmax and kcat values of DdaH to N-(3,5-dichlorophenyl)-2,4-dioxoimidazolidine were, 6.58 ± 0.34 µM, 0.31 ± 0.04 μmol s-1 mg-1 and 10.70 ± 1.32 s-1, respectively. The catalytic efficiency of kcat/Km was 1.63 μM-1 s-1, which no significant difference with that of DdaH (1.61 μM-1 s-1) in strain YJN-D. Phylogenetic tree analysis showed that DdaH belonged to the CE4_HpPgdA family. Amino acid alignment analysis showed that DdaH also had the conserved catalytic motif DDHHH of this family. The ddaH gene inactivation and complementation experiment proved that it was the only gene responsible for the degradation of N-(3,5-dichlorophenyl)-2,4-dioxoimidazolidine in strain YJN-5. The hydrolase DuaH is responsible for the hydrolysis of (3,5-dichlorophenylurea)acetic acid to 3,5-DCA: We used the Escherichia coli expression system to heterologously express and purify the duaH gene and then studied the enzymatic properties of DuaH. The optimum reaction temperature and pH of DuaH were 40°C and 7.5, respectively. 10mM of Zn2+ and Co2+ could significantly enhance the enzyme activity of DuaH. The Km, Vmax and kcat values of DuaH to (3,5-dichlorophenylurea)acetic acid in strain YJN-5 were 5.67 ± 1.25 µM, 12.14 ± 0.64 μmol s-1 mg-1 and 523.29 ± 0.24 s-1, respectively. Its catalytic efficiency kcat/Km was 92.29 μM-1 s-1, which was 9 times of DuaH catalytic efficiency (11.83 μM-1 s-1) in strain YJN-D. Phylogenetic tree analysis showed that DuaH belonged to the M20 Peptidase Aminoacylase 1 family. Amino acid alignment analysis showed that DuaH also had the conserved catalytic motif CHEHH of this family. The duaH gene inactivation and complementation experiment proved that it was the only gene responsible for the degradation of (3,5-dichlorophenylurea)acetic acid in strain YJN-5. 3. Degradation characteristics and microbial community structure analysis of anaerobic degradation of 3,5-DCA by activated sludge. Degradation characteristics of 3,5-DCA by anaerobic activated sludge: The activated sludge which can efficiently degrade 3,5-DCA was successfully enriched and acclimated by continuous flow anaerobic reactor. Compared with the initial sludge, the degradation ability of activated sludge enriched for 62 d was 74 times higher than that of activated sludge enriched for 0 d. The optimum temperature and pH of activated sludge for the degradation of 3,5-DCA were 30°C and pH 7.0, respectively. The dynamics of anaerobic degradation of dichloroaniline compounds by anaerobic activated sludge accorded with the first-order kinetics, and the degradation rate was as follows: 3,5-DCA > 2,4-DCA >3,4-DCA > 2,6-DCA > 2,3-DCA or 2,5-DCA. The anaerobic activated sludge can dechlorinate dichloroaniline compounds by meta-and ortho-reductive dechlorination. The identification of the anaerobic degradation products of 3,5-DCA showed that 3-chloroaniline (3-CA) was obtained by reductive dechlorination in activated sludge, which could be further oxidized and then degraded by ring opening, and a small amount of aniline was also detected. The related products of formylation, acetylation and propionylation of some compounds such as 3,5-DCA, 3-CA and aniline were also detected. Research on the microbial community structure during the enrichment and acclimation of anaerobic activated sludge: the microbial community structure in activated sludge was changed, and the diversity and richness of bacteria decreased during the enrichment and acclimation of activated sludge. After 62 d of enrichment and domestication, the total microorganisms of the three phylum (Firmicutes, Chloroflexi and Proteobacteria) belonging to OHRB (Organohalide-respiring bacteria) occupied a large proportion (71.39%). At the genus level, the relative abundance of Dehalobacter, Anaerolineaceae_uncultured, Smithella, Denitratisoma and Sphingobium increased gradually, while that of Clostridium sensu stricto1, Pseudomonas, Enterobacteriaceae_Unclassified and Formivibrio decreased gradually. At the same time, combined with the correlation analysis of environmental factors and network analysis, it was found that Dehalobacter, Anaerolineaceae_uncultured, Smithella, Denitratisoma and Sphingobium were positively correlated with the influent flow rate and the degradation ability of anaerobic activated sludge, indicating that these microorganisms may be involved in the degradation of 3,5-DCA in the anaerobic reactor. In addition, we used specific primers to amplify the 16S rRNA of Dehalobacter in activated sludge, it was found that there was only one kind of Dehalobacter in activated sludge, which was named DH-1. Phylogenetic tree analysis showed that Dehalobacter sp. DH-1 had the highest similarity with the reported strain Dehalobacter sp. TCP1 (99.21%). |
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中图分类号: | Q939 |
开放日期: | 2023-06-15 |