Biotechnology Institute, School of Environment and Chemical Engineering, Dalian Jiaotong University, Dalian, China.
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, China.
J Basic Microbiol. 2018 Jun;58(6):501-512. doi: 10.1002/jobm.201700663. Epub 2018 Apr 20.
In the present study, the shotgun high throughput metagenomic sequencing was implemented to globally capture the features of Taxus rhizosphere microbiome. Total reads could be assigned to 6925 species belonging to 113 bacteria phyla and 301 species of nine fungi phyla. For archaea and virus, 263 and 134 species were for the first time identified, respectively. More than 720,000 Unigenes were identified by clean reads assembly. The top five assigned phyla were Actinobacteria (363,941 Unigenes), Proteobacteria (182,053), Acidobacteria (44,527), Ascomycota (fungi; 18,267), and Chloroflexi (15,539). KEGG analysis predicted numerous functional genes; 7101 Unigenes belong to "Xenobiotics biodegradation and metabolism." A total of 12,040 Unigenes involved in defense mechanisms (e.g., xenobiotic metabolism) were annotated by eggNOG. Talaromyces addition could influence not only the diversity and structure of microbial communities of Taxus rhizosphere, but also the relative abundance of functional genes, including metabolic genes, antibiotic resistant genes, and genes involved in pathogen-host interaction, bacterial virulence, and bacterial secretion system. The structure and function of rhizosphere microbiome could be sensitive to non-native microbe addition, which could impact on the pollutant degradation. This study, complementary to the amplicon sequencing, more objectively reflects the native microbiome of Taxus rhizosphere and its response to environmental pressure, and lays a foundation for potential combination of phytoremediation and bioaugmentation.
在本研究中，采用高通量 shotgun 宏基因组测序技术，全面捕获红豆杉根际微生物组的特征。总reads 可分为 6925 个物种，隶属于 113 个细菌门和 301 个真菌门。首次鉴定出古菌和病毒分别为 263 种和 134 种。通过清洁reads 组装，鉴定出超过 720000 个 Unigenes。前五个分类群是放线菌（363941 个 Unigenes）、变形菌（182053 个）、酸杆菌（44527 个）、子囊菌（真菌；18267 个）和绿弯菌（15539 个）。KEGG 分析预测了大量功能基因；7101 个 Unigenes 属于“外来物质生物降解与代谢”。共有 12040 个 Unigenes参与防御机制（如外来物质代谢），通过 eggNOG 注释。塔宾曲霉的添加不仅可以影响红豆杉根际微生物群落的多样性和结构，还可以影响功能基因的相对丰度，包括代谢基因、抗生素抗性基因以及与病原体-宿主相互作用、细菌毒力和细菌分泌系统相关的基因。根际微生物组的结构和功能对非本地微生物的添加非常敏感，这可能会影响污染物的降解。本研究与扩增子测序相辅相成，更客观地反映了红豆杉根际的天然微生物组及其对环境压力的响应，为植物修复和生物强化的潜在结合奠定了基础。
