蔬菜根际土壤微生物多样性及拮抗菌调控研究
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摘要
本文采用了变性梯度凝胶电泳（DGGE）技术和16S rDNA基因文库分析相结合的方法，对辽宁大连地区罹患辣椒疫病和黄瓜枯萎病的植株与健康植株根际土壤样品的细菌种群多样性进行了研究，并初步揭示了根际细菌种群结构与土传病害发病情况之间的关系；本文以大量的放线菌资源作为研究对象，筛选了2组拮抗放线菌组合，优化了其发酵条件，并对其施入土壤后对黄瓜枯萎病的生防效果以及对土壤样品细菌种群多样性的影响进行了分析。主要研究结果如下：
1.研究了罹患辣椒疫病植株和健康植株根际土壤样品中细菌种群多样性。
分别对种植前、接菌前、接菌后发病、接菌后健康以及未接菌5种辣椒根际土壤样品进行了PCR-DGGE和16S rDNA基因文库分析。根据PCR-DGGE电泳结果，这5个样品中细菌的16S rDNA片段经变性梯度凝胶电泳可以分离出38~49条清晰可见的条带，各个样品中的条带间存在着一定的差异。其中，条带最多的是接菌后健康的样品，表明抗病植株根际土壤中优势微生物种群多于患病植株根际土壤中的优势微生物。
构建16S rDNA克隆文库，分析结果表明，接菌后健康植株根际土壤和患病植株根际土壤文库分别得到了89和52个阳性克隆子，分别属于67和44个OUT。这两个文库中的细菌共包括11个门类，较优势的是变形细菌门、酸杆菌门、拟杆菌门。在这两个文库中，健康植株根际土壤样品克隆文库中的细菌种群多样性高于患病植株根际土壤样品，其中Sphingomonas属细菌的克隆子数目明显多于患病植株样品。
2.分析了罹患黄瓜枯萎病和健康植株根际土壤细菌种群多样性及酮基合酶编码基因（KS）多样性。
根据PCR-DGGE电泳结果，种植前、接菌前、接菌后发病、接菌后健康以及未接菌5个样品中细菌的16S rDNA片段经变性梯度凝胶电泳后，可以分离出15~24条清晰可见的条带，接菌后健康黄瓜根际土壤样品条带数量最多。对DGGE凝胶中部分共有条带和特异性条带进行回收、克隆及测序后发现，所获得的10条序列主要归属于变形菌门、拟杆菌门、厚壁菌门、酸杆菌门、芽单胞菌门以及放线菌门，厚壁菌门为优势菌群。在健康植株根际土壤样品中的特有条带分属于拟杆菌门和厚壁菌门。
构建16S rDNA克隆文库分析了健康黄瓜和患病黄瓜根际土壤微生物种群多样性，共得到199个阳性克隆子，其中健康黄瓜根际土壤样品118个克隆子，发病黄瓜根际土壤样品81个克隆子。其归属门类与辣椒根际土壤样品结果相似，健康植株样品细菌多样性高于患病样品，且Sphingomonas属细菌的克隆子数目明显高于患病样品文库。
在此基础上，同时以KS特异性引物构建了健康黄瓜根际土壤和患病黄瓜根际土壤样品中的KS基因文库，分别从健康黄瓜根际土壤和患病黄瓜根际土壤样品中获得80个和102个KS基因片段，分析了I型聚酮合酶功能基因（KS基因）序列多样性，根据KS基因的系统发育树的聚类分析，结果形成了7个明显的分支，其中来自于健康植株根际土壤样品的部分KS基因单独构成一个分支，且比对结果显示与来源于链霉菌属（Streptomyces）的KS基因亲缘关系最近。
3.优化了拮抗放线菌菌株组合的发酵条件。
采用菌饼法从26株具有抑菌活性的放线菌菌株中筛选出4株抑菌活性较好，且彼此之间不相互抑制的菌株，并根据拮抗靶标的不同设计了2个组合，分别为ACT-1、ACT-2。在此基础上，分别通过单因素和正交实验优化了发酵培养基配方，明确了最佳发酵条件。ACT-1的最佳发酵条件为：高青-17、YH91和YH23最佳接种比例为3:3:2，培养基初始pH值为自然，培养温度为25℃，装液量为250mL三角瓶装液50mL，最佳接种量为3%，最佳转速为180r/min，培养5d。ACT-2的最佳发酵条件为：高青-17、YH91、YH23和YH6的最佳接种比例为3:1:3:2，培养基初始pH值为自然，培养温度为25℃，装液量为250mL三角瓶装液50mL，最佳接种量为3%，最佳转速为200r/min，培养5d。在优化后的发酵条件下，2个组合发酵液的抑菌活性比优化前提高了14.03%和15.10%。
4.测定了生防菌剂组合对黄瓜枯萎病的防治效果及对黄瓜根际土壤细菌种群影响。
测定了2个组合对黄瓜枯萎病的防治效果。结果发现，这2个生防菌剂组合对黄瓜枯萎病防效较好。在此基础上，采用PCR-DGGE分析了施入2个生防菌剂组合后发病、不发病及对照发病、不发病共6个样品的根际土壤细菌多样性。结果显示，样品间细菌种群结构相似，但施入生防菌剂组合的样品中细菌种类和数量发生了变化，说明根际土壤微生物的种群结构发生了改变，尤其是发病和未发病的样品的DGGE条带之间的差异更为明显，说明生防菌剂组合的施入对植株是否发病具有影响作用。
Bacterial community structure and diversity of rhizosphere soil in infected plants pepperphytophthora blight and cucumber Fusarium wilt in Dalian of Liaoning were studied, usingboth the16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) and the16S rDNAgene clone library. And the relationship between the rhizosphere bacterial communitystructure and soil-borne disease was initially revealed. The co-operative and synergisticcombination ACT-1and ACT-2were screening from a large number of actinomyces strains,and the fermentation condition was optimized. Furthermore, the control efficiency and theeffect on the diversity of bacterial community after applying the biological agents wereanalysed. The results were as follows:
1. Bacterial community structure and diversity of rhizosphere soil in infected plantspepper phytophthora blight were studied. There are five rhizosphere soil samples, includingpre-planting soil, pre-inoculation soil, rhizosphere soil from diseased pepper, healthy pepperand not inoculated as a control. They were analysed by DGGE and the16S rDNA gene clonelibrary. A total of38to49bands were separated from five samples, respectively, and there aresome differences among each sample. Among them, the healthy pepper rhizosphere soil hasthe most DNA bands. It indicates that the dominant bacterial community in healthy pepperrhizosphere soil sample was more than that in the infected pepper rhizosphere soil sample.
Based on the analysis of16S rDNA gene clone library, a total of89clones and52cloneswere sequenced from healthy pepper rhizosphere soil and diseased pepper rhizosphere soilsample respectively. The bacterial community in the two samples displayed a highlydiversified composition including members from11bacterial phylum and some unclassifiedsequences. Proteobacteria, Acidobacteria and Bacteroidetes were the rather dominant groups.
The bacterial community in the infected pepper rhizosphere soil sample was slightly lessdiversity than those in the healthy pepper rhizosphere soil sample, and the clone number thatwere most affiliated with Sphingomonas sp. in the health soil sample was more than diseasedsoil sample.
2. Bacterial community structure and diversity of type I ketosynthase of rhizosphere soil in infected cucumber Fusarium wilt and healthy cucumber were studied.
There are five rhizosphere soil samples, including pre-planting soil, pre-inoculation soil,rhizosphere soil from diseased cucumber, healthy cucumber and not inoculated as a control.They were analysed by DGGE and the16S rDNA gene clone library. A total of15to24bandswere separated from five samples, respectively, and there are some differences among eachsample. The results of nucleotide sequence analysis for the dominant bands demonstrated thatthe major phylogenetic groups identified by DGGE belong to Proteobacteria, Bacteroidetes,Firmicutes, Acidobacteria, Gemmatimonadetes and Actinobacteria. Firmicutes was dominantphylum. Bacteroidetes and Firmicutes were the unique phylum in the healthy cucumberrhizosphere soil.
Based on the analysis of16S rDNA gene clone library, a total of118clones and81clones were sequenced from healthy cucumber rhizosphere soil and diseased cucumberrhizosphere soil sample respectively. The bacterial communities in these two samplesdisplayed a highly similarity with the pepper samples. The bacterial community in theinfected cucumber rhizosphere soil sample was slightly less diversity than those in the healthycucumber rhizosphere soil sample, and the clone number that were most affiliated withSphingomonas sp. in the health soil sample was more than diseased soil sample.
On the base of these results, the KS gene library was constructed by the specific primersof KS.80and102clones were obtained from the healthy cucumber rhizosphere soil sampleand diseased cucumber rhizosphere soil sample, respectively. According to the phylogeneticanalysis of KS amino acid (AA) sequences indicate that the KS genes in the rhizosphere soilsamples were clustered into diverse seven clades. Some KS AA sequences come form oneclade, and this clade was peculiar to healthy cucumber rhizosphere soil sample, moreover,these KS genes showed high homology with that from Streptomyces by Blast program.
3. Optimization of fermentation conditions of antagonistic actinomycetes combination.
Four antagonistic strains were screened from26strains with fungus cake method andthere have no interference among the four strains. According to the different target pathogens,2antagonistic actinomycetes combinations were designed, that is ACT-1and ACT-2. Theeffect of single factor on fermentation conditions of ACT-1and ACT-2and orthogonal experiment was studied. It was demonstrated that the optimum fermentation conditions ofACT-1were as follows: the proportion of GAOQING-17, YH91and YH23was3:3:2, pH wasnatura1, inoculum volume was3%, respectively. The ACT-1was cultured in50ml of culturemedium in250ml shaking flasks with rotation speed180r/min at25℃for5d. The optimumfermentation conditions of ACT-2were as follows: the proportion of GAOQING-17, YH91,YH23and YH6was3:1:3:2, pH was natura1, inoculum volume was3%, respectively. TheACT-2was cultured in50ml of culture medium in250ml shaking flasks with rotation speed180r/min at25℃for5d. The antimicrobial activity of ACT-1and ACT-2increased14.03%and15.10%after the optimization fermented the condition.
4. Control efficiencies to cucumber Fusarium wilt of antagonistic actinomycetescombination and the effect on cucumber rhizosphere soil bacterial community weredetermined.
The results of control effect to cucumber Fusarium wilt of antagonistic actinomycetescombination of ACT-1and ACT-2showed better control efficiencies. Furthermore, thediversity of these samples after appling ACT-1and ACT-2(including diseased cucumberrhizosphere soil sample, healthy sample), control sample (including diseased cucumberrhizosphere soil sample, healthy sample) were analysed by PCR-DGGE. The results showedthat the bacterial community is similarity among samples. The bacterial species and quantityhave change after applying ACT-1and ACT-2. So, it indicates that the rhizosphere soilmicroorganisms community was changed by antagonistic actinomycetes combination. Inparticular, there is obvious difference between the diseased sample and the healthy sample. Italso declares that antagonistic actinomycetes combination effect cucumber whether or notdisease.
1.研究了罹患辣椒疫病植株和健康植株根际土壤样品中细菌种群多样性。
分别对种植前、接菌前、接菌后发病、接菌后健康以及未接菌5种辣椒根际土壤样品进行了PCR-DGGE和16S rDNA基因文库分析。根据PCR-DGGE电泳结果，这5个样品中细菌的16S rDNA片段经变性梯度凝胶电泳可以分离出38~49条清晰可见的条带，各个样品中的条带间存在着一定的差异。其中，条带最多的是接菌后健康的样品，表明抗病植株根际土壤中优势微生物种群多于患病植株根际土壤中的优势微生物。
构建16S rDNA克隆文库，分析结果表明，接菌后健康植株根际土壤和患病植株根际土壤文库分别得到了89和52个阳性克隆子，分别属于67和44个OUT。这两个文库中的细菌共包括11个门类，较优势的是变形细菌门、酸杆菌门、拟杆菌门。在这两个文库中，健康植株根际土壤样品克隆文库中的细菌种群多样性高于患病植株根际土壤样品，其中Sphingomonas属细菌的克隆子数目明显多于患病植株样品。
2.分析了罹患黄瓜枯萎病和健康植株根际土壤细菌种群多样性及酮基合酶编码基因（KS）多样性。
根据PCR-DGGE电泳结果，种植前、接菌前、接菌后发病、接菌后健康以及未接菌5个样品中细菌的16S rDNA片段经变性梯度凝胶电泳后，可以分离出15~24条清晰可见的条带，接菌后健康黄瓜根际土壤样品条带数量最多。对DGGE凝胶中部分共有条带和特异性条带进行回收、克隆及测序后发现，所获得的10条序列主要归属于变形菌门、拟杆菌门、厚壁菌门、酸杆菌门、芽单胞菌门以及放线菌门，厚壁菌门为优势菌群。在健康植株根际土壤样品中的特有条带分属于拟杆菌门和厚壁菌门。
构建16S rDNA克隆文库分析了健康黄瓜和患病黄瓜根际土壤微生物种群多样性，共得到199个阳性克隆子，其中健康黄瓜根际土壤样品118个克隆子，发病黄瓜根际土壤样品81个克隆子。其归属门类与辣椒根际土壤样品结果相似，健康植株样品细菌多样性高于患病样品，且Sphingomonas属细菌的克隆子数目明显高于患病样品文库。
在此基础上，同时以KS特异性引物构建了健康黄瓜根际土壤和患病黄瓜根际土壤样品中的KS基因文库，分别从健康黄瓜根际土壤和患病黄瓜根际土壤样品中获得80个和102个KS基因片段，分析了I型聚酮合酶功能基因（KS基因）序列多样性，根据KS基因的系统发育树的聚类分析，结果形成了7个明显的分支，其中来自于健康植株根际土壤样品的部分KS基因单独构成一个分支，且比对结果显示与来源于链霉菌属（Streptomyces）的KS基因亲缘关系最近。
3.优化了拮抗放线菌菌株组合的发酵条件。
采用菌饼法从26株具有抑菌活性的放线菌菌株中筛选出4株抑菌活性较好，且彼此之间不相互抑制的菌株，并根据拮抗靶标的不同设计了2个组合，分别为ACT-1、ACT-2。在此基础上，分别通过单因素和正交实验优化了发酵培养基配方，明确了最佳发酵条件。ACT-1的最佳发酵条件为：高青-17、YH91和YH23最佳接种比例为3:3:2，培养基初始pH值为自然，培养温度为25℃，装液量为250mL三角瓶装液50mL，最佳接种量为3%，最佳转速为180r/min，培养5d。ACT-2的最佳发酵条件为：高青-17、YH91、YH23和YH6的最佳接种比例为3:1:3:2，培养基初始pH值为自然，培养温度为25℃，装液量为250mL三角瓶装液50mL，最佳接种量为3%，最佳转速为200r/min，培养5d。在优化后的发酵条件下，2个组合发酵液的抑菌活性比优化前提高了14.03%和15.10%。
4.测定了生防菌剂组合对黄瓜枯萎病的防治效果及对黄瓜根际土壤细菌种群影响。
测定了2个组合对黄瓜枯萎病的防治效果。结果发现，这2个生防菌剂组合对黄瓜枯萎病防效较好。在此基础上，采用PCR-DGGE分析了施入2个生防菌剂组合后发病、不发病及对照发病、不发病共6个样品的根际土壤细菌多样性。结果显示，样品间细菌种群结构相似，但施入生防菌剂组合的样品中细菌种类和数量发生了变化，说明根际土壤微生物的种群结构发生了改变，尤其是发病和未发病的样品的DGGE条带之间的差异更为明显，说明生防菌剂组合的施入对植株是否发病具有影响作用。
Bacterial community structure and diversity of rhizosphere soil in infected plants pepperphytophthora blight and cucumber Fusarium wilt in Dalian of Liaoning were studied, usingboth the16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) and the16S rDNAgene clone library. And the relationship between the rhizosphere bacterial communitystructure and soil-borne disease was initially revealed. The co-operative and synergisticcombination ACT-1and ACT-2were screening from a large number of actinomyces strains,and the fermentation condition was optimized. Furthermore, the control efficiency and theeffect on the diversity of bacterial community after applying the biological agents wereanalysed. The results were as follows:
1. Bacterial community structure and diversity of rhizosphere soil in infected plantspepper phytophthora blight were studied. There are five rhizosphere soil samples, includingpre-planting soil, pre-inoculation soil, rhizosphere soil from diseased pepper, healthy pepperand not inoculated as a control. They were analysed by DGGE and the16S rDNA gene clonelibrary. A total of38to49bands were separated from five samples, respectively, and there aresome differences among each sample. Among them, the healthy pepper rhizosphere soil hasthe most DNA bands. It indicates that the dominant bacterial community in healthy pepperrhizosphere soil sample was more than that in the infected pepper rhizosphere soil sample.
Based on the analysis of16S rDNA gene clone library, a total of89clones and52cloneswere sequenced from healthy pepper rhizosphere soil and diseased pepper rhizosphere soilsample respectively. The bacterial community in the two samples displayed a highlydiversified composition including members from11bacterial phylum and some unclassifiedsequences. Proteobacteria, Acidobacteria and Bacteroidetes were the rather dominant groups.
The bacterial community in the infected pepper rhizosphere soil sample was slightly lessdiversity than those in the healthy pepper rhizosphere soil sample, and the clone number thatwere most affiliated with Sphingomonas sp. in the health soil sample was more than diseasedsoil sample.
2. Bacterial community structure and diversity of type I ketosynthase of rhizosphere soil in infected cucumber Fusarium wilt and healthy cucumber were studied.
There are five rhizosphere soil samples, including pre-planting soil, pre-inoculation soil,rhizosphere soil from diseased cucumber, healthy cucumber and not inoculated as a control.They were analysed by DGGE and the16S rDNA gene clone library. A total of15to24bandswere separated from five samples, respectively, and there are some differences among eachsample. The results of nucleotide sequence analysis for the dominant bands demonstrated thatthe major phylogenetic groups identified by DGGE belong to Proteobacteria, Bacteroidetes,Firmicutes, Acidobacteria, Gemmatimonadetes and Actinobacteria. Firmicutes was dominantphylum. Bacteroidetes and Firmicutes were the unique phylum in the healthy cucumberrhizosphere soil.
Based on the analysis of16S rDNA gene clone library, a total of118clones and81clones were sequenced from healthy cucumber rhizosphere soil and diseased cucumberrhizosphere soil sample respectively. The bacterial communities in these two samplesdisplayed a highly similarity with the pepper samples. The bacterial community in theinfected cucumber rhizosphere soil sample was slightly less diversity than those in the healthycucumber rhizosphere soil sample, and the clone number that were most affiliated withSphingomonas sp. in the health soil sample was more than diseased soil sample.
On the base of these results, the KS gene library was constructed by the specific primersof KS.80and102clones were obtained from the healthy cucumber rhizosphere soil sampleand diseased cucumber rhizosphere soil sample, respectively. According to the phylogeneticanalysis of KS amino acid (AA) sequences indicate that the KS genes in the rhizosphere soilsamples were clustered into diverse seven clades. Some KS AA sequences come form oneclade, and this clade was peculiar to healthy cucumber rhizosphere soil sample, moreover,these KS genes showed high homology with that from Streptomyces by Blast program.
3. Optimization of fermentation conditions of antagonistic actinomycetes combination.
Four antagonistic strains were screened from26strains with fungus cake method andthere have no interference among the four strains. According to the different target pathogens,2antagonistic actinomycetes combinations were designed, that is ACT-1and ACT-2. Theeffect of single factor on fermentation conditions of ACT-1and ACT-2and orthogonal experiment was studied. It was demonstrated that the optimum fermentation conditions ofACT-1were as follows: the proportion of GAOQING-17, YH91and YH23was3:3:2, pH wasnatura1, inoculum volume was3%, respectively. The ACT-1was cultured in50ml of culturemedium in250ml shaking flasks with rotation speed180r/min at25℃for5d. The optimumfermentation conditions of ACT-2were as follows: the proportion of GAOQING-17, YH91,YH23and YH6was3:1:3:2, pH was natura1, inoculum volume was3%, respectively. TheACT-2was cultured in50ml of culture medium in250ml shaking flasks with rotation speed180r/min at25℃for5d. The antimicrobial activity of ACT-1and ACT-2increased14.03%and15.10%after the optimization fermented the condition.
4. Control efficiencies to cucumber Fusarium wilt of antagonistic actinomycetescombination and the effect on cucumber rhizosphere soil bacterial community weredetermined.
The results of control effect to cucumber Fusarium wilt of antagonistic actinomycetescombination of ACT-1and ACT-2showed better control efficiencies. Furthermore, thediversity of these samples after appling ACT-1and ACT-2(including diseased cucumberrhizosphere soil sample, healthy sample), control sample (including diseased cucumberrhizosphere soil sample, healthy sample) were analysed by PCR-DGGE. The results showedthat the bacterial community is similarity among samples. The bacterial species and quantityhave change after applying ACT-1and ACT-2. So, it indicates that the rhizosphere soilmicroorganisms community was changed by antagonistic actinomycetes combination. Inparticular, there is obvious difference between the diseased sample and the healthy sample. Italso declares that antagonistic actinomycetes combination effect cucumber whether or notdisease.
引文
1.白震,何红波,张威等.2006.磷脂脂肪酸技术及其在土壤微生物研究中的应用.生态学报,26(7):2377-2394.
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