Evaluation of different primers of the 18S rRNA gene to profile amoeba communities in environmental samples  

作　　者：Xiafei Zheng Zhili He Cheng Wang Qingyun Yan Longfei Shu 

机构地区：[1]Environmental Microbiomics Research Center,School of Environmental Science and Engineering,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai),Sun Yat-sen University,Guangzhou,510006,China [2]Ninghai Institute of Mariculture Breeding and Seed Industry,Zhejiang Wanli University,Ningbo,315100,China

出　　处：《Water Biology and Security》2022年第3期56-66,共11页水生生物与安全（英文）

基　　金：supported by the National Natural Science Foundation of China(31970384,41907021,21806044,92051120,31802350);the Fundamental Research Funds for the Central Universities Sun Yat-sen University(22lgqb22,19lgzd28);the Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)(311021006);the Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)(SML2021SP203);the Guangdong Natural Resources Department Contract(GDNRC[2021]62);Guangzhou Basic and Applied Basic Research Foundation(202102020257)。

摘　　要：Amoeboid protists,an assemblage of organisms belonging to different phylogenetic lineages,have drawn increasing attention due to their crucial ecological roles in various environments and their potential health risks.Currently,18S rRNA gene sequencing is widely applied for the detection of amoebae.However,it is not clear which is the best primer pair for 18S rRNA gene amplification in amoebae.This study compared the four most commonly used primer pairs for revealing the diversity,composition,core species,and community assembly processes of amoebae in water and sediments.We found that the choice of primers artificially influences the detection of community composition of amoebae.We also found that short-read fragments may lead to mismatches in taxonomy and were not suitable for phylogenetic analyses.In contrast,full-length primers could detect the highest number of amoeba lineages and annotate 80%of reads belonging to amoebae to known species.However,full-length primers did not detect as many amoeba species as V4 primers.Moreover,we showed that beta diversity and community assembly determination were largely unaffected by primer choice,but different primers could influence our interpretations of the ecological process underlying stochasticity and determinism.This study indicates that full-length read sequencing and V4 region Illumina sequencing are suitable for profiling amoeba diversity in the environment.

关 键 词：Amoeba community Diversity Drinking water safety METAGENOMICS 18S rRNA gene PROTIST 

分 类 号：Q78[生物学—分子生物学]