Using RNA-Sequencing Data to Examine Tissue-Specific Garlic Microbiomes

Garlic (Allium sativum) is a perennial bulbous plant. Due to its clonal propagation, various diseases threaten the yield and quality of garlic. In this study, we conducted in silico analysis to identify microorganisms, bacteria, fungi, and viruses in six different tissues using garlic RNA-sequencing data. The number of identified microbial species was the highest in inflorescences, followed by flowers and bulb cloves. With the Kraken2 tool, 57% of identified microbial reads were assigned to bacteria and 41% were assigned to viruses. Fungi only made up 1% of microbial reads. At the species level, Streptomyces lividans was the most dominant bacteria while Fusarium pseudograminearum was the most abundant fungi. Several allexiviruses were identified. Of them, the most abundant virus was garlic virus C followed by shallot virus X. We obtained a total of 14 viral genome sequences for four allexiviruses. As we expected, the microbial community varied depending on the tissue types, although there was a dominant microorganism in each tissue. In addition, we found that Kraken2 was a very powerful and efficient tool for the bacteria using RNA-sequencing data with some limitations for virome study.     

基于宏基因组学研究污水生物处理系统微生物暗物质

活性污泥和微生物生物膜是污水生物处理系统的主要菌群存在形式,利用微生物的不同代谢途径可实现水中污染物的转化和降解.微生物群落结构直接影响污染物生物转化速度和末端产物的类型,而全面了解微生物群落结构和功能可为污水生物处理的定向调控提供微生物学依据.由于绝大多数微生物未获得纯培养,因此,揭示生物处理系统中的微生物暗物质成为重要的挑战.核酸测序技术和生物信息学的快速发展推动了环境微生物学和微生物生态研究.近年来,基于高通量核酸测序的宏组学技术为研究未培养微生物和未知基因资源提供了重要工具.宏基因组学和宏转录组学技术可以研究特定环境下未培养微生物的生理功能和代谢,揭示生态条件变化下微生物的环境适应和代谢调控机制.目前,基于宏组学研究微生物暗物质,已经获得了一些突破传统认识的物质循环新机理.本文回顾了核酸测序技术的发展,综述了近年宏基因组学和宏转录组学在污水生物脱氮、强化生物除磷及微生物电化学技术微生物学研究的进展,对多组学在污水处理微生物学研究的前景和面临的主要挑战进行分析.