Template Preparation Affects 16S rRNA High-Throughput Sequencing Analysis of Phyllosphere Microbial Communities

文献类型： 外文期刊

第一作者： Geng, Lili

作者： Geng, Lili;Zhang, Jie;Song, Fuping;Shu, Changlong;Tian, Xiaoyan;Duan, Jiangyan;Shi, Yu;Chu, Haiyan

作者机构：

关键词： phyllosphere;template;method;16S rRNA gene;amplicon sequencing

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：5.753； 五年影响因子：6.612 ）

ISSN： 1664-462X

年卷期： 2017 年 8 卷

页码：

收录情况： SCI

摘要： Phyllosphere microbial communities are highly diverse and have important ecological implications; in that context, bacterial identification based on 16S rRNA genes is an important research issue. In studies of phyllosphere microbial communities, microporous filtration and centrifugation are used to collect microorganism samples, but it is unclear which one has a better collection efficiency. In this study, we compared these two microorganism collection methods and investigated the effects of the DNA extraction process on the estimation of microbial community composition and organization. The following four treatments were examined: (A) filtration, resuspension, and direct PCR; (B) filtration, DNA isolation, and PCR; (C) centrifugation, resuspension, and direct PCR; (D) centrifugation, DNA isolation, and PCR. Our results showed that the percentage of chloroplast sequence contaminants was affected by the DNA extraction process. The bacterial compositions clearly differed between treatments A and C, suggesting that the collection method has an influence on the determination of community structure. Compared with treatments B and D, treatments A and C resulted in higher Shannon index values, indicating that the DNA extraction process might reduce the observed phyllosphere microbial alpha diversity. However, with respect to community structure, treatments B and D yielded very similar results, suggesting that the DNA extraction process erases the effect of the collection method. Our findings provide key information to ensure accurate estimates of diversity and community composition in studies of phyllosphere microorganisms.

分类号：

  • 相关文献

[1]Pathogen invasion indirectly changes the composition of soil microbiome via shifts in root exudation profile. Wei, Zhong,Wang, Xueqi,Wang, Xiaofang,Mei, Xinlan,Xu, Yangchun,Shen, Qirong,Jousset, Alexandre,Friman, Ville-Petri,Huang, Jianfeng,Jousset, Alexandre.

[2]Phyllosphere bacterial communities associated with the degradation of acetamiprid in Phaseolus vulgaris. Zhou, Yu,Xu, Junfeng,Wang, Wei,Chen, Xiaoyun,Qiao, Xiongwu,Zhou, Yu,Li, Wenjun,Zhou, Yu,Li, Wenjun. 2011

[3]Profile of the culturable microbiome capable of producing acyl-homoserine lactone in the tobacco phyllosphere. Lv, Di,Ma, Anzhou,Bai, Zhihui,Qi, Hongyan,Zhuang, Guoqiang,Tang, Xuanming.

[4]The impacts of cypermethrin pesticide application on the non-target microbial community of the pepper plant phyllosphere. Zhang, Baoguo,Bai, Zhihui,Tang, Ling,Zhuang, Guoqiang,Hoefel, Daniel,Wang, Xiaoyi,Li, Baoju,Li, Zuming.

[5]Multivariate analysis linkage of phyllospheric microbial community of transgenic cotton from SGK321 to Cry1Ac: A temporal expression dynamics. Pan, Jiangang,Cui, Mengmeng,Hu, Qing,Ma, Anzhou,Bai, Zhihui,Qi, Hongyan,Pan, Jiangang,Zhang, Hongxun,Guo, Hongguang,Pan, Jiangang,Yang, Dianlin. 2012

[6]Effect of cypermethrin insecticide on the microbial community in cucumber phyllosphere. Zhang Baoguo,Zhang Hongxun,Tang Ling,Yang Jianzhou,Zhuang Guoqiang,Bai Zhihui,Jin Bo,Bai Zhihui,Zhang Baoguo,Zhang Hongxun,Li Baoju.

[7]Study and Practice on Farmer-Participate-to-Experience-Type Agricultural Extension Method. Cao, Cheng-Zhong,Luo, Chang-Shou,Zhang, Jun-Feng,Zou, Guo-Yuan,Zuo, Qiang,Wu, Zhong-Zhi,Wang, Rui. 2014

[8]Estimating the Contribution of New Seed Cultivars to Increases in Crop Yields: A Case Study for Corn. Qian, Jiarong,Zhao, Zhijun. 2017

[9]A High-Throughput Standard PCR-Based Genotyping Method for Determining Transgene Zygosity in Segregating Plant Populations. Geng, Lige,Deng, Dewayne D.,Wubben, Martin J.,Jenkins, Johnie N.,McCarty, Jack C., Jr.,Abdurakhmonov, Ibrokhim. 2017

[10]Analysis of genetic structure and relationship among nine indigenous Chinese chicken populations by the Structure program. Li, H. F.,Han, W.,Zhu, Y. F.,Shu, J. T.,Zhang, X. Y.,Chen, K. W..

[11]Estimating wheat grain protein content from ground-based hyperspectral data using an improved detecting method. Lu, YL,Li, SK,Xie, RZ,Gao, SJ,Wang, KR,Wang, G,Xiao, CH. 2005

[12]Visual assessment of soil structure: Evaluation of methodologies on sites in Canada, China and Germany Part I: Comparing visual methods and linking them with soil physical data and grain yield of cereals. Mueller, Lothar,Schindler, Uwe,Kay, Bev D.,Hu, Chunsheng,Li, Yong,Behrendt, Axel,Shepherd, T. Graham,Ball, Bruce C.. 2009

[13]Highly sensitive method for the quantification of trans-linolenic acid isomers in trilinolenin of edible oils using an ionic liquid capillary column. Guo, Qin,Jiang, Fan,Jin, Jing,Li, Qingpeng,Wang, Feng,Wang, Qiang,Ha, Yiming. 2017

[14]A novel zoonotic Anaplasma species is prevalent in small ruminants: potential public health implications. Yang, Jifei,Liu, Zhijie,Niu, Qingli,Liu, Junlong,Han, Rong,Guan, Guiquan,Hassan, Muhammad Adeel,Liu, Guangyuan,Luo, Jianxun,Yin, Hong,Yin, Hong. 2017

[15]First molecular survey and identification of Anaplasma spp. in white yaks (Bos grunniens) in China. Yang, Jifei,Liu, Zhijie,Niu, Qingli,Liu, Junlong,Guan, Guiquan,Xie, Jingying,Luo, Jianxun,Yin, Hong,Wang, Shuqing,Wang, Shufang,Yin, Hong. 2016

[16]Streptomyces tritici sp nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.). Shi, Linlin,Li, Wenchao,Wang, Jiabin,Wang, Han,Tian, Yuanyuan,Xiang, Wensheng,Wang, Xiangjing,Xiang, Wensheng. 2018

[17]Paenibacillus thermophilus sp nov., a novel bacterium isolated from a sediment of hot spring in Fujian province, China. Zhou, Yu,Gao, Sheng,Yang, Ling-Ling,He, Jie,Zhang, Yun-Jiao,Tang, Shu-Kun,Li, Wen-Jun,Gao, Sheng,Yang, Ling-Ling,He, Jie,Zhang, Yun-Jiao,Tang, Shu-Kun,Li, Wen-Jun,Wei, Da-Qiao,Huang, Xing,Li, Wen-Jun. 2012

[18]Deep sequencing reveals high bacterial diversity and phylogenetic novelty in pit mud from Luzhou Laojiao cellars for Chinese strong-flavor Baijiu. Tang, Yu-Ming,Guo, Xiao-Jiao,Tian, Xin-Hui,Liu, Ying,Yao, Wan-Chun,Ren, Dao-Qun,Liu, Mao-Ke,Zhao, Ke,Zhang, Xiao-Ping,Deng, Bo. 2017

[19]Molecular survey and characterization of a novel Anaplasma species closely related to Anaplasma capra in ticks, northwestern China. Yang, Jifei,Liu, Zhijie,Niu, Qingli,Liu, Junlong,Han, Rong,Liu, Guangyuan,Luo, Jianxun,Yin, Hong,Yin, Hong,Shi, Yaoxu. 2016

[20]Illumina-based analysis of bacterial diversity related to halophytes Salicornia europaea and Sueada aralocaspica. Sh, Ying-wu,Lou, Kai,Li, Chun,Wang, Lei,Zhao, Zhen-yong,Zhao, Shuai,Tian, Chang-yan. 2015

作者其他论文 更多>>

微信小程序