不同环境中纤维素降解菌群多样性差异分析

Differential Analysis of Diversity in Cellulose-decomposing Bacterial Communities from Diverse Environments

【目的】纤维素是地球上最丰富的有机聚合物,被视为有潜质的能源生物质。迄今为止,纤维素降解机制依然未被完全解析。通过对不同环境来源的纤维素降解菌群16S rDNA序列数据进行了生物信息学分析,以揭示纤维素降解菌群之间的共性和差异,鉴定核心功能菌,为开发有利用价值的纤维素降解菌和探索纤维素降解机制提供理论依据。【方法】应用SRA Toolkit软件下载NCBI SRA数据库中的16S rDNA基因扩增子测序数据,包括牛瘤胃、牛粪堆肥、森林土壤3个来自于不同纤维素降解环境样本组以及以家犬粪便为对照组的共102个样本的数据。应用FLASH、UCHIME、USEARCH、RDP classifier、mothur、QIIME、Metastats和LEfSe等软件对这些数据进行生物多样性差异比较分析。【结果】Alpha多样性分析显示牛粪堆肥的菌群多样性显著高于其他环境,Beta多样性分析显示不同环境中纤维素降解菌群结构存在很大的差异。所有菌群中共检测到55个门和1936个属。森林土壤中的变形菌门(Proteobacteria)、牛瘤胃和牛粪堆肥环境中的厚壁菌门(Firmicutes)以及牛粪堆肥中的放线菌门(Actinobacteria)均分别显著高于其他环境,而牛粪堆肥中的拟杆菌门(Bacteroidetes)和森林土壤中的Firmicutes均分别显著低于其他环境,表明不同环境下执行纤维素降解功能的菌群存在着显著差异。相对丰度、LEfSe分析以及之前报道的文献等证据表明,牛瘤胃环境中可作为生物标志物的纤维素降解菌包括毛螺菌科(Lachnospiraceae)、普雷沃氏菌属(Prevotella)、月形单胞菌目(Selenomonadales)和解琥珀酸菌属(Succiniclasticum);牛粪堆肥中包括放线菌纲(Actinobacteria)、芽孢杆菌目(Bacillales)和嗜盐菌属(Halocella);森林土壤中则包括甲型变形菌纲(Alphaproteobacteria)、假单胞菌属(Pseudomonas)、黄杆菌科(Flavobacteriaceae)、伯克氏菌科(Burkholderiaceae)和假噬纤维菌属(Pseudarcicella)。这进一步揭示了不同环境中纤维素降解细菌群落的特异性,同时意味着不同环境间纤维素降解机制也可能不同。【结论】不同环境来源的纤维素降解菌群多样性和结构存在极大的差异;牛瘤胃、牛粪堆肥、森林土壤中具有环境特异性的纤维素降解菌分类单元分别有4,3和5个。

[Objective]Cellulose is the most abundant organic polymer on earth,and is regarded as a potential energy source.To date,the detailed mechanism of cellulose degradation by bacteria is still unclear.In this study,a series of 16S rDNA gene sequence data of cellulose-decomposing bacterial communities from different environmental sources were analyzed to reveal the commonness and differences of biodiversity and identify of the key functional bacteria,which will lay a foundation for developing the useful cellulosedecomposing bacteria and analyzing their biological function.[Method]The 16S rDNA gene amplicon sequencing data of 102 samples which came from 3 different cellulose-decomposing environments including bovine rumen,cow dung compost and forest soil and a control environment from Canis familiaris feces were downloaded from NCBI SRA database using the SRA Toolkit software,and were further analyzed by using a combination of the bioinformatics tools,such as FLASH,UCHIME,USEARCH,RDP classifier,mothur,QIIME,Metastats and LEfSe[.Result]Alpha diversity analysis showed that the diversity of the cow dung compost group was significantly higher than that of the others.Beta diversity analysis showed great differences in microbiomes composition between cellulose-decomposing bacterial communities from different environments.Overall,55 phyla and 1936 genera were observed in all the samples.Proteobacteria from forest soil,Firmicutes from bovine rumen and cow dung compost,and Actinobacteria from cow dung compost had significantly higher relative abundance than that from other environments respectively,and the Bacteroidetes from cow dung compost and the Firmicutes from forest soil were significantly lower than those from other environments respectively.These results indicated that there might be significant differences in microbial communities that performed the major function from different environments.According to the evidences from relative abundance of taxon,LEfSe analysis and previous studies,several putative cellulolytic biomarkers for each environment were identified.These biomarkers included Lachnospiraceae,Prevotella,Succiniclasticum,Selenomonadales,and Succiniclasticum from bovine rumen,Actinobacteria,Bacillus and Halocella from cow dung compost,and Alphaproteobacteria,Pseudomonas,Flavobacteriaceae,Burkholderiaceae and Pseudarcicella from forest soil,which further revealed the specificity of cellulose-decomposing bacteria communities from different sources and the diverse cellulosedecomposing mechanism.[Conclusion]Biodiversity and composition showed great differences between cellulose-decomposing bacterial communities from different environments,and 4,3 and 5 taxa of cellulosedecomposing bacteria with environmental specificity were identified in bovine rumen,cow manure compost and forest soil,respectively.