暗黑鳃金龟幼虫肠道微生物分子多态性及纤维素降解菌多样性研究
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摘要
从生态学和进化角度来说,肠道微生物对宿主昆虫有着非常重要的作用。然而,肠道微生物种类和群落组成是否会随着宿主昆虫栖息地环境的变化而变化,目前鲜有报道,是值得深入研究的问题。本文研究了不同地理种群暗黑鳃金龟幼虫后肠肠道细菌群落组成和多样性,以及环境因子对肠道细菌群落组成和多样性的影响。同时,采用好氧培养技术,从暗黑鳃金龟幼虫后肠内分离了具有纤维素酶产生能力的菌株,并从中克隆了纤维素酶基因,研究了肠道细菌对蛴螬的生理功能方面的作用。
1.构建了10个不同地理种群暗黑鳃金龟幼虫肠道细菌的16S rRNA基因克隆文库,并通过变性梯度凝胶电泳(Denaturing Gradient Gel Electrophoresis, DGGE)分析归类克隆子,挑取不同DGGE斑型(band type)对应的克隆子测序。结果表明幼虫肠道细菌可归为205个操作分类单元(Operational Taxonomic Units, OTUs),分别属于厚壁菌门(Firmicutes),变形菌门(Proteobacteria),拟杆菌门(Bacteroidetes),放线菌门(Actinobacteria)和梭杆菌门(Fusobacteria).
比较不同地理种群暗黑鳃金龟幼虫肠道细菌群落及组成,可以发现以下几个特征：(1)厚壁菌门和变形菌门细菌为肠道细菌优势细菌类群。厚壁菌门中的梭菌纲细菌广泛存在于所有10个地理种群蛴螬肠道内,且为肠道细菌绝对优势菌群。β-变形菌纲,γ-变形菌纲和ε-变形菌纲的细菌也广泛存在于10个地理种群样本蛴螬肠道内,只不过与梭菌纲细菌相比,所占比例较小。拟杆菌门,放线菌门和梭杆菌门细菌的分布则非常不均匀,在有些种群的蛴螬肠道内有分布,有些种群肠道内则没有。(2)有6种OTUs代表的细菌遗传型为所有地理种群的蛴螬所共有,在10个种群蛴螬肠道细菌克隆文库内都有发现。其余的细菌遗传型在地理种群样本肠道内则呈不均匀分布：很多细菌遗传型只存在特定的地理种群蛴螬肠道内,在其他种群的蛴螬肠道内没有分布。(3)不同种群蛴螬肠道细菌群落多样性存在很大差异：天津种群肠道细菌种类数最少,为38.8,而福建种群肠道细菌丰富度最高,细菌种类数为86.5。∫-LIBSHUFF分析发现绝大部分种群肠道细菌克隆文库组成之间存显著性差异。(4)相关分析(Spearman nonparametric correlation test)和冗余分析(Redundancy discriminate analysis, RDA)结果显示,不同地理种群蛴螬肠道细菌群落组成和多样性方面的差异,与宿主昆虫栖息地环境条件密切相关。宿主昆虫栖息的土壤理化条件(如土壤pH,土壤有机质含量和土壤全氮量),以及栖息地的气候条件(年平均温度,一月份最低温和年降雨量)等环境因子,都可以显著影响蛴螬肠道细菌多样性和群落组成。
2.从暗黑鳃金龟幼虫后肠内分离到207株纤维素降解菌。通过核糖体DNA扩增片段限制性内切酶分析(Amplifed Ribosomal DNA Restriction Analysis, ARDRA)分型后,结合代表菌株16S rDNA测序比对结果和生理生化试验结果,所有这些纤维素降解菌可以归为21种不同的细菌,分布在4个不同的门：变形菌门,放线菌门,厚壁菌门和拟杆菌门,其中,变形菌门细菌为纤维素降解菌中最优势的细菌类群。假单胞菌属Pseudomonas,纤维菌属Cellulosimicrobium,苍白杆菌属Ochrobactrum,根瘤菌属Rhizobium和微杆菌属Microbacterium为最主要的属。而属于芽孢杆菌属Bacillus,发酵成对杆菌属Dyadobacter, Siphonobacter属,副球菌属Paracoccus, Kaistia属,德沃斯氏菌属Devosia, Labrys属,剑菌属Ensifer,贪食菌属Variovorax, Shinella属,柠檬酸杆菌属Citrobacter和寡养食单胞菌属Stenotrophomonas的细菌也被分离得到,只不过所占比例较小。此外,在本研究中,有一些种类的细菌,如Siphonobacter aquaeclarae,芬氏纤维微菌Cellulosimicrobium funkei, Paracoccus sulfuroxidans,弗氏柠檬酸杆菌Citrobacter freundii和硝化还原假单胞菌Pseudomonas nitroreducens都是首次被报道具有纤维素降解活性。
3.本研究使用兼并引物同源克隆并结合染色体步移的方法,从1株暗黑鳃金龟肠道内的纤维素降解菌Rhizobium radiobacter基因组内成功获得2个纤维素酶编码基因。其中1个基因为GH3家族的纤维素酶基因(暂命名celⅢ), Blast结果显示,celⅢ与来自Grosmannia clavigera kw1407的beta-glucosidase的相似性为60%。另1个基因属于GH8家族的纤维素酶基因(暂命名celⅧ),而BlastX结果显示,celⅧ编码的蛋白与来自Agrobacterium sp. ATCC31749的endoglucanase (ZP_08530463)的相似性为87%。我们的研究结果显示暗黑鳃金龟肠道内丰富多样的微生物是一个资源宝库,可以从中分离发现许多新的纤维素(半纤维素)降解菌,克隆新的纤维素(半纤维素)酶基因,并最终应用于生物能源生产。
Gut microbiota has diverse ecological and evolutionary effects on their hosts. However, the ways in which it responds to environmental heterogeneity remain poorly understood. In this study, we surveyed intestinal microbiota of Holotrichia parallela larvae that from different geographic regions, and examined how environmental factors account for the variation of gut community composition between natural population. Furthermoer, by applying aerobic cultivation conditions we isolated and identified cellulose-degrading bacteria from the gut of H. parallela and cloned genes fragments encoding cellulose, to evaluate the nutritional contributions of gut microbiota to scarabs.
1. Bacterial16S rRNA gene clone libraries were constructed and clones were subsequently screened by Denaturing Gradient Gel Electrophoresis (DGGE) and sequenced. The result showed that the bacterial16S rRNA gene sequences grouped into205OTUs, and identified as Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria and Fusobacteria sequences.
After comparing microbial community richness and composition among these host populations, several feature of the gut microbiota can be found:(1). One prominent feature of the gut microbiota of H. parallela larvae was the high prevalence of Firmicutes and Proteobacteria sequences. Sequences affiliated with Firmicutes (mainly Clostridia) were detectable in all of the natural populations, and they were the most prominent group in the hindgut microbiota of the ten populations. Sequences related to Beta-, Gamma-and Deltaproteobacteria were also present in all natural populations, although at relatively low proportions. However, bacteria belonging to other phyla (Bacteroidetes, Actinobacteria, and Fusobacteria) were unevenly distributed across the host populations. Bacteria belonging some phyla were only detected in several population but absent from other natural populations.(2). Six OTUs were shared between the ten natural populations, and the remaining OTUs were unevenly spread across the host populations, with many appearing in only1host population among the ten sampled.(3). Species richness also varied across the host locations. The bacterial community from the TJ population (38.8) possessed the least species richness, while the FJ (86.5) population had the highest species richness. The∫-LIBSHUFF analysis also showed that most of the ten clone libraries were significantly different from each other.(4) Spearman nonparametric correlation test and redundancy discriminate analysis(RDA) showed that the bacterial diversity (Chaol estimator) and community structure variation that we observed can be explained by soil pH, organic carbon and total nitrogen, and the climate factors (e.g., mean annual temperature, January low temperature, mean annual precipitation) of the locations where the populations were sampled.
2. Applying aerobic cultivation conditions,207strains of aerobic and facultatively anaerobic cellulolytic bacteria ifrom the gut of H. parallela larvae. These bacterial isolates were assigned to21genotypes by amplified ribosomal DNA restriction analysis (ARDRA). A partial16S rDNA sequence analysis and standard biochemical and physiological tests were used for the assignment of the21representative isolates. Our results show that the cellulolytic bacterial community is dominated by the Proteobacteria (70.05%), followed by the Actinobacteria (24.15%), the Firmicutes (4.35%), and the Bacteroidetes (1.45%). Pseudomonas, Ochrobactrum, Rhizobium, Cellulosimicrobium, and Microbacterium were the predominant groups, but members of Bacillus, Dyadobacter, Siphonobacter, Paracoccus, Kaistia, Devosia, Labrys, Ensifer, Variovorax, Shinella, Citrobacter, and Stenotrophomonas were also found. Furthermore, some cellulolytic bacteria, such as Siphonobacter aquaeclarae, Cellulosimicrobium funkei, Paracoccus sulfuroxidans, Citrobacter freundii, and Pseudomonas nitroreducens are reported to be cellulolytic for the first time in this study.
3. Using the homologous cloning strategy with degenerate primers and chromosome walking techniques, two genes fragments encoding cellulase were cloned from one bacterial strain Rhizobium radiobacter isolated from the gut of H. parallela larvae. One gene is glycosyl hydrolase family (GH)3family, and temporarily called celⅢ. Sequence analysis showed that the celⅢ encoded products shared sixty percent similarity to the beta-glucosidase from Grosmannia clavigera kw1407. The other gene is glycosyl hydrolase family (GH)8family, and temporarily called celⅧ. Sequence analysis showed that the celⅢencoded products shared sixty percent similarity to the endoglucanase from Agrobacterium sp. ATCC31749. The presented results suggests scarab larvae have potential to assist the bio-fuel industry by providing new sources of (hemi)cellulolytic bacteria and bacterial (hemi)cellulolytic enzymes.
1.构建了10个不同地理种群暗黑鳃金龟幼虫肠道细菌的16S rRNA基因克隆文库,并通过变性梯度凝胶电泳(Denaturing Gradient Gel Electrophoresis, DGGE)分析归类克隆子,挑取不同DGGE斑型(band type)对应的克隆子测序。结果表明幼虫肠道细菌可归为205个操作分类单元(Operational Taxonomic Units, OTUs),分别属于厚壁菌门(Firmicutes),变形菌门(Proteobacteria),拟杆菌门(Bacteroidetes),放线菌门(Actinobacteria)和梭杆菌门(Fusobacteria).
比较不同地理种群暗黑鳃金龟幼虫肠道细菌群落及组成,可以发现以下几个特征：(1)厚壁菌门和变形菌门细菌为肠道细菌优势细菌类群。厚壁菌门中的梭菌纲细菌广泛存在于所有10个地理种群蛴螬肠道内,且为肠道细菌绝对优势菌群。β-变形菌纲,γ-变形菌纲和ε-变形菌纲的细菌也广泛存在于10个地理种群样本蛴螬肠道内,只不过与梭菌纲细菌相比,所占比例较小。拟杆菌门,放线菌门和梭杆菌门细菌的分布则非常不均匀,在有些种群的蛴螬肠道内有分布,有些种群肠道内则没有。(2)有6种OTUs代表的细菌遗传型为所有地理种群的蛴螬所共有,在10个种群蛴螬肠道细菌克隆文库内都有发现。其余的细菌遗传型在地理种群样本肠道内则呈不均匀分布：很多细菌遗传型只存在特定的地理种群蛴螬肠道内,在其他种群的蛴螬肠道内没有分布。(3)不同种群蛴螬肠道细菌群落多样性存在很大差异：天津种群肠道细菌种类数最少,为38.8,而福建种群肠道细菌丰富度最高,细菌种类数为86.5。∫-LIBSHUFF分析发现绝大部分种群肠道细菌克隆文库组成之间存显著性差异。(4)相关分析(Spearman nonparametric correlation test)和冗余分析(Redundancy discriminate analysis, RDA)结果显示,不同地理种群蛴螬肠道细菌群落组成和多样性方面的差异,与宿主昆虫栖息地环境条件密切相关。宿主昆虫栖息的土壤理化条件(如土壤pH,土壤有机质含量和土壤全氮量),以及栖息地的气候条件(年平均温度,一月份最低温和年降雨量)等环境因子,都可以显著影响蛴螬肠道细菌多样性和群落组成。
2.从暗黑鳃金龟幼虫后肠内分离到207株纤维素降解菌。通过核糖体DNA扩增片段限制性内切酶分析(Amplifed Ribosomal DNA Restriction Analysis, ARDRA)分型后,结合代表菌株16S rDNA测序比对结果和生理生化试验结果,所有这些纤维素降解菌可以归为21种不同的细菌,分布在4个不同的门：变形菌门,放线菌门,厚壁菌门和拟杆菌门,其中,变形菌门细菌为纤维素降解菌中最优势的细菌类群。假单胞菌属Pseudomonas,纤维菌属Cellulosimicrobium,苍白杆菌属Ochrobactrum,根瘤菌属Rhizobium和微杆菌属Microbacterium为最主要的属。而属于芽孢杆菌属Bacillus,发酵成对杆菌属Dyadobacter, Siphonobacter属,副球菌属Paracoccus, Kaistia属,德沃斯氏菌属Devosia, Labrys属,剑菌属Ensifer,贪食菌属Variovorax, Shinella属,柠檬酸杆菌属Citrobacter和寡养食单胞菌属Stenotrophomonas的细菌也被分离得到,只不过所占比例较小。此外,在本研究中,有一些种类的细菌,如Siphonobacter aquaeclarae,芬氏纤维微菌Cellulosimicrobium funkei, Paracoccus sulfuroxidans,弗氏柠檬酸杆菌Citrobacter freundii和硝化还原假单胞菌Pseudomonas nitroreducens都是首次被报道具有纤维素降解活性。
3.本研究使用兼并引物同源克隆并结合染色体步移的方法,从1株暗黑鳃金龟肠道内的纤维素降解菌Rhizobium radiobacter基因组内成功获得2个纤维素酶编码基因。其中1个基因为GH3家族的纤维素酶基因(暂命名celⅢ), Blast结果显示,celⅢ与来自Grosmannia clavigera kw1407的beta-glucosidase的相似性为60%。另1个基因属于GH8家族的纤维素酶基因(暂命名celⅧ),而BlastX结果显示,celⅧ编码的蛋白与来自Agrobacterium sp. ATCC31749的endoglucanase (ZP_08530463)的相似性为87%。我们的研究结果显示暗黑鳃金龟肠道内丰富多样的微生物是一个资源宝库,可以从中分离发现许多新的纤维素(半纤维素)降解菌,克隆新的纤维素(半纤维素)酶基因,并最终应用于生物能源生产。
Gut microbiota has diverse ecological and evolutionary effects on their hosts. However, the ways in which it responds to environmental heterogeneity remain poorly understood. In this study, we surveyed intestinal microbiota of Holotrichia parallela larvae that from different geographic regions, and examined how environmental factors account for the variation of gut community composition between natural population. Furthermoer, by applying aerobic cultivation conditions we isolated and identified cellulose-degrading bacteria from the gut of H. parallela and cloned genes fragments encoding cellulose, to evaluate the nutritional contributions of gut microbiota to scarabs.
1. Bacterial16S rRNA gene clone libraries were constructed and clones were subsequently screened by Denaturing Gradient Gel Electrophoresis (DGGE) and sequenced. The result showed that the bacterial16S rRNA gene sequences grouped into205OTUs, and identified as Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria and Fusobacteria sequences.
After comparing microbial community richness and composition among these host populations, several feature of the gut microbiota can be found:(1). One prominent feature of the gut microbiota of H. parallela larvae was the high prevalence of Firmicutes and Proteobacteria sequences. Sequences affiliated with Firmicutes (mainly Clostridia) were detectable in all of the natural populations, and they were the most prominent group in the hindgut microbiota of the ten populations. Sequences related to Beta-, Gamma-and Deltaproteobacteria were also present in all natural populations, although at relatively low proportions. However, bacteria belonging to other phyla (Bacteroidetes, Actinobacteria, and Fusobacteria) were unevenly distributed across the host populations. Bacteria belonging some phyla were only detected in several population but absent from other natural populations.(2). Six OTUs were shared between the ten natural populations, and the remaining OTUs were unevenly spread across the host populations, with many appearing in only1host population among the ten sampled.(3). Species richness also varied across the host locations. The bacterial community from the TJ population (38.8) possessed the least species richness, while the FJ (86.5) population had the highest species richness. The∫-LIBSHUFF analysis also showed that most of the ten clone libraries were significantly different from each other.(4) Spearman nonparametric correlation test and redundancy discriminate analysis(RDA) showed that the bacterial diversity (Chaol estimator) and community structure variation that we observed can be explained by soil pH, organic carbon and total nitrogen, and the climate factors (e.g., mean annual temperature, January low temperature, mean annual precipitation) of the locations where the populations were sampled.
2. Applying aerobic cultivation conditions,207strains of aerobic and facultatively anaerobic cellulolytic bacteria ifrom the gut of H. parallela larvae. These bacterial isolates were assigned to21genotypes by amplified ribosomal DNA restriction analysis (ARDRA). A partial16S rDNA sequence analysis and standard biochemical and physiological tests were used for the assignment of the21representative isolates. Our results show that the cellulolytic bacterial community is dominated by the Proteobacteria (70.05%), followed by the Actinobacteria (24.15%), the Firmicutes (4.35%), and the Bacteroidetes (1.45%). Pseudomonas, Ochrobactrum, Rhizobium, Cellulosimicrobium, and Microbacterium were the predominant groups, but members of Bacillus, Dyadobacter, Siphonobacter, Paracoccus, Kaistia, Devosia, Labrys, Ensifer, Variovorax, Shinella, Citrobacter, and Stenotrophomonas were also found. Furthermore, some cellulolytic bacteria, such as Siphonobacter aquaeclarae, Cellulosimicrobium funkei, Paracoccus sulfuroxidans, Citrobacter freundii, and Pseudomonas nitroreducens are reported to be cellulolytic for the first time in this study.
3. Using the homologous cloning strategy with degenerate primers and chromosome walking techniques, two genes fragments encoding cellulase were cloned from one bacterial strain Rhizobium radiobacter isolated from the gut of H. parallela larvae. One gene is glycosyl hydrolase family (GH)3family, and temporarily called celⅢ. Sequence analysis showed that the celⅢ encoded products shared sixty percent similarity to the beta-glucosidase from Grosmannia clavigera kw1407. The other gene is glycosyl hydrolase family (GH)8family, and temporarily called celⅧ. Sequence analysis showed that the celⅢencoded products shared sixty percent similarity to the endoglucanase from Agrobacterium sp. ATCC31749. The presented results suggests scarab larvae have potential to assist the bio-fuel industry by providing new sources of (hemi)cellulolytic bacteria and bacterial (hemi)cellulolytic enzymes.
引文
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