Effects of graphene oxide on PCR amplification for microbial community survey

BMC Microbiology

article

Li, Shuzhen¹  Wang, Zhujun¹  Wang, Yuanyuan⁴  Song, Maoyong⁴  Lu, Guangxin⁵  Dang, Ning⁵  Yin, Huaqun⁶  Qu, Yuanyuan²  Deng, Ye¹ 

[1] CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences;Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technolog;College of Resources and Environment, University of Chinese Academy of Sciences;State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences;College of Agriculture and Animal Husbandry, Qinghai University;School of Minerals Processing and Bioengineering, Central South University

关键词: Oxidized graphene;    Bacteria;    Fungi;    Chimera;    Community composition;   

DOI  :  10.1186/s12866-020-01965-7

学科分类：放射科、核医学、医学影像

来源: BioMed Central

【 摘 要 】

Graphene oxide (GO) has been suggested as an efficient assistant additive to eliminate non-specific amplification of the polymerase chain reaction (PCR). Although many studies have focused on exploring its molecular mechanism, the practice of GO on the quantitation of microbial community has not been implemented yet. In this study, GO was added in PCR system to explore the changes on removing typical amplification errors, such as chimera and mismatches on two kinds of mock communities (an evenly mixed and a staggered mock communities) and environmental samples. High-throughput sequencing of bacterial and fungal communities, based on 16S rRNA genes and internal transcribed spacers (ITS) respectively, showed that GO could significantly increase large segmental error (chimeric sequence) in PCR procedure while had no specific effect on point error (mismatched sequence). Besides, GO reduced the α-diversity of community, and changed the composition of fungal community more obviously than bacterial community. Our study provides the first quantitative data on microbial community level to prove the negative effect of GO, and also indicates that there may be a more complex interaction between GO and comprehensive DNA fragments in PCR process.

【 授权许可】

CC BY|CC0