微生物分子生态学技术在石油污染土壤修复中的应用研究
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摘要
本文首先简要回顾了国内外石油污染耕地生物修复技术及其实际应用现状，重点介绍了微生物分子生态学技术在揭示土壤修复过程中土壤微生物种类、数量以及功能基因的变化等方面的研究进展，展望了该技术在生物修复过程的设计、实施以及效果评估方面的应用前景。
研究了接种阴沟肠杆菌（E. cloacae）的石油污染土壤的生物强化修复过程，PCR-DGGE分析结果显示阴沟肠杆菌可在污染土壤中稳定存在，在接种微生物的同时添加麦秸可显著增加土壤微生物群落的种类和数量；所获得的真菌和细菌的数量最多，分别达到5.5×10~3和4.6×10~7；土壤脱氢酶活最高，达到0.79；石油烃的降解率也最高，处理56d后的石油烃降解率达到56%。微生态分析结果还显示了不同的修复操作所获得的土壤微生态组成上的差异。
采用基因文库法分析对比了污染耕地、修复耕地和正常耕地的细菌和真核生物的基因类型和组成。结果显示正常耕地细菌和真核生物的基因类型分别为122个和34个，细菌优势菌门是变形杆菌门、酸杆菌门和拟杆菌门；真核生物优势门是节肢动物门、真菌未知、双核真菌门和丝足虫门。石油污染导致土壤细菌和真菌基因类型分别减少到96个和21个，优势细菌菌门分布和真核生物门组成也发生明显变化。经过生物修复后，耕地的基因类型分别恢复到115个和30个，优势细菌菌门分布和真核生物门种类也恢复到正常耕地的水平。
以氮循环过程中固氮、硝化以及氨化作用的特征基因，即nifH、narG和amoA为例，考察了生物修复过程的土壤生物功能性变化。对于nifH而言，正常耕地共发现25个基因型，而污染耕地仅存在15个基因型，修复后耕地的基因型数量恢复到21个，聚类分析表明三种土壤均分为6个类群，包括放线菌亚纲、α、γ、β和δ变形杆菌亚纲和未确定亚纲，但组成比例存在差异。类似的情形也出现在amoA和narG基因，后者则会因石油污染而消失。修复后的基因类型则达到甚至超过了正常耕地水平，在优势菌株和比例组成上与正常耕地相似，表明修复耕地的功能基因恢复到了正常耕地的水平。
This dissertation started with an overview of the recent advancement ofbioremediation techniques and their applications in the remediation ofpetroleum-contaminated soil. The application of molecular biological techniques toprobe the microbial ecological changes in terms of composition and quantity of bothmicrobial community and functional genes was highlighted. The prospects of thesetechniques as enabling tools in the design, implementation and assessment ofbioremediation practice were discussed.
The variation of microbial society occurred to a bioaugmentation of petroleumcontaminated soil using Enterobacter cloacae as an inoculant was monitored bydenaturing gradient gel electrophoresis (DGGE) of16S rDNA of the bacteria. It wasshown that the addition of wheat straw in the augmentation enhanced the growth ofbacterium and fungi in comparison to that obtained with solely inoculant. A maximumconcentration of4.6×10~7and5.5×10~3, for bacterial and fungal species respectively, wasobtained in case of adding wheat straw, which also resulted in a highest dehydrogenaseactivity (0.79) and degradation rate (56%in56d). The remediated soil with differenttreatment presented different bacterial composition, as shown by PCR-DGGE.
The variations in the microbial ecological system of remediated soil (R) andpetroleum contaminated soil (P) based on comparison with soil that has not beencontaminated (N) was profiled using a cloning library of taxonomic genes (16S rDNAfor bacterium and18S rDNA for eukaryotes). The genotype number of prokaryote andeukaryote found in the N soil was122and34, respectively. Proteobacterial,Acidobacteria, Bacteroidetes, and Arthropoda were the predominant bacterial phylum,while Incertae seids, Dikarya and Cercozoa accounted for predominant ones ineukaryotic composition. The contamination with crude oil led to a reduction ofgenotype number to96(bacteria) and21(fungi), respectively, and, moreover, analteration in composition and proportion of both bacterial and eukaryotic phylum in theP soil. The R soil, as treated using a microbial consortium of Enterobacter cloacae andCunninghamella echinulata as inoculant, gave a genotype number of115(bacteria) and30(fungi), and moreover, a more close distribution of predominant bacterial andeukaryotic phylum with reference to the N soil. The restoration of microbial ecology, as indicated by aforementioned results, confirmed the effectiveness of the remediationpractice.
The change of soil function due to the bioagumentation using a microbialconsortium of Enterobacter cloacae and Cunninghamella echinulata as inoculant wasevaluated using three genes encoding the key enzyme in nitrogen fixation, nitrificationand ammoniation as target genes, i.e., nifH, amoA and narG. For nifH gene, while thepetroleum contamination led to a reduction of genotype number in the P soil from25to15, the R soil presented a genotype number of21, being close to that of the N soil.Moreover, the cluster analysis showed the existence of six subclasses in the three soilsample, which was Actinbacteridae, α-，γ-，β-, δ-Proteobacteria and unclassified group,though the relative density of each subclass varied, particularly that of the contaminatedsoil. Similar results were found for amoA and narG gene, the latter was absent in the Psoil, a direct evidence of the imperfection of soil nitrogen cycle due to petroleumcontamination. The remedation restored the above mentioned genotype and gaveenhanced narG gene diversity with reference to the normal soil. These confirmed theremediation of the soil in terms of functional genes. The results obtained by the presentstudy provided a microbial ecological insight that can be used to aid the design andimplementation of bioaugmentation.
研究了接种阴沟肠杆菌（E. cloacae）的石油污染土壤的生物强化修复过程，PCR-DGGE分析结果显示阴沟肠杆菌可在污染土壤中稳定存在，在接种微生物的同时添加麦秸可显著增加土壤微生物群落的种类和数量；所获得的真菌和细菌的数量最多，分别达到5.5×10~3和4.6×10~7；土壤脱氢酶活最高，达到0.79；石油烃的降解率也最高，处理56d后的石油烃降解率达到56%。微生态分析结果还显示了不同的修复操作所获得的土壤微生态组成上的差异。
采用基因文库法分析对比了污染耕地、修复耕地和正常耕地的细菌和真核生物的基因类型和组成。结果显示正常耕地细菌和真核生物的基因类型分别为122个和34个，细菌优势菌门是变形杆菌门、酸杆菌门和拟杆菌门；真核生物优势门是节肢动物门、真菌未知、双核真菌门和丝足虫门。石油污染导致土壤细菌和真菌基因类型分别减少到96个和21个，优势细菌菌门分布和真核生物门组成也发生明显变化。经过生物修复后，耕地的基因类型分别恢复到115个和30个，优势细菌菌门分布和真核生物门种类也恢复到正常耕地的水平。
以氮循环过程中固氮、硝化以及氨化作用的特征基因，即nifH、narG和amoA为例，考察了生物修复过程的土壤生物功能性变化。对于nifH而言，正常耕地共发现25个基因型，而污染耕地仅存在15个基因型，修复后耕地的基因型数量恢复到21个，聚类分析表明三种土壤均分为6个类群，包括放线菌亚纲、α、γ、β和δ变形杆菌亚纲和未确定亚纲，但组成比例存在差异。类似的情形也出现在amoA和narG基因，后者则会因石油污染而消失。修复后的基因类型则达到甚至超过了正常耕地水平，在优势菌株和比例组成上与正常耕地相似，表明修复耕地的功能基因恢复到了正常耕地的水平。
This dissertation started with an overview of the recent advancement ofbioremediation techniques and their applications in the remediation ofpetroleum-contaminated soil. The application of molecular biological techniques toprobe the microbial ecological changes in terms of composition and quantity of bothmicrobial community and functional genes was highlighted. The prospects of thesetechniques as enabling tools in the design, implementation and assessment ofbioremediation practice were discussed.
The variation of microbial society occurred to a bioaugmentation of petroleumcontaminated soil using Enterobacter cloacae as an inoculant was monitored bydenaturing gradient gel electrophoresis (DGGE) of16S rDNA of the bacteria. It wasshown that the addition of wheat straw in the augmentation enhanced the growth ofbacterium and fungi in comparison to that obtained with solely inoculant. A maximumconcentration of4.6×10~7and5.5×10~3, for bacterial and fungal species respectively, wasobtained in case of adding wheat straw, which also resulted in a highest dehydrogenaseactivity (0.79) and degradation rate (56%in56d). The remediated soil with differenttreatment presented different bacterial composition, as shown by PCR-DGGE.
The variations in the microbial ecological system of remediated soil (R) andpetroleum contaminated soil (P) based on comparison with soil that has not beencontaminated (N) was profiled using a cloning library of taxonomic genes (16S rDNAfor bacterium and18S rDNA for eukaryotes). The genotype number of prokaryote andeukaryote found in the N soil was122and34, respectively. Proteobacterial,Acidobacteria, Bacteroidetes, and Arthropoda were the predominant bacterial phylum,while Incertae seids, Dikarya and Cercozoa accounted for predominant ones ineukaryotic composition. The contamination with crude oil led to a reduction ofgenotype number to96(bacteria) and21(fungi), respectively, and, moreover, analteration in composition and proportion of both bacterial and eukaryotic phylum in theP soil. The R soil, as treated using a microbial consortium of Enterobacter cloacae andCunninghamella echinulata as inoculant, gave a genotype number of115(bacteria) and30(fungi), and moreover, a more close distribution of predominant bacterial andeukaryotic phylum with reference to the N soil. The restoration of microbial ecology, as indicated by aforementioned results, confirmed the effectiveness of the remediationpractice.
The change of soil function due to the bioagumentation using a microbialconsortium of Enterobacter cloacae and Cunninghamella echinulata as inoculant wasevaluated using three genes encoding the key enzyme in nitrogen fixation, nitrificationand ammoniation as target genes, i.e., nifH, amoA and narG. For nifH gene, while thepetroleum contamination led to a reduction of genotype number in the P soil from25to15, the R soil presented a genotype number of21, being close to that of the N soil.Moreover, the cluster analysis showed the existence of six subclasses in the three soilsample, which was Actinbacteridae, α-，γ-，β-, δ-Proteobacteria and unclassified group,though the relative density of each subclass varied, particularly that of the contaminatedsoil. Similar results were found for amoA and narG gene, the latter was absent in the Psoil, a direct evidence of the imperfection of soil nitrogen cycle due to petroleumcontamination. The remedation restored the above mentioned genotype and gaveenhanced narG gene diversity with reference to the normal soil. These confirmed theremediation of the soil in terms of functional genes. The results obtained by the presentstudy provided a microbial ecological insight that can be used to aid the design andimplementation of bioaugmentation.
引文
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