, Volume 23, Issue 6, pp 747–757 | Cite as

Comparative evaluation of three archaeal primer pairs for exploring archaeal communities in deep-sea sediments and permafrost soils

  • Shiping WeiEmail author
  • Hongpeng Cui
  • Yuchen Zhang
  • Xin Su
  • Hailiang Dong
  • Fang Chen
  • Youhai Zhu
Original Paper


16S rRNA gene profiling is a powerful method for characterizing microbial communities; however, no universal primer pair can target all bacteria and archaea, resulting in different primer pairs which may impact the diversity profile obtained. Here, we evaluated three pairs of high-throughput sequencing primers for characterizing archaeal communities from deep-sea sediments and permafrost soils. The results show that primer pair Arch519/Arch915 (V4–V5 regions) produced the highest alpha diversity estimates, followed by Arch349f/Arch806r (V3–V4 regions) and A751f/AU1204r (V5–V7 regions) in both sample types. The archaeal taxonomic compositions and the relative abundance estimates of archaeal communities are influenced by the primer pairs. Beta diversity of the archaeal community detected by the three primer pairs reveals that primer pairs Arch349f/Arch806r and Arch519f/Arch915r are biased toward detection of Halobacteriales, Methanobacteriales and MBG-E/Hydrothermarchaeota, whereas the primer pairs Arch519f/Arch915r and A751f/UA1204r are biased to detect MBG-B/Lokiarchaeota, and the primers pairs Arch349f/Arch806r and A751f/UA1204r are biased to detect Methanomicrobiales and Methanosarcinales. The data suggest that the alpha and beta diversities of archaeal communities as well as the community compositions are influenced by the primer pair choice. This finding provides researchers with valuable experimental insight for selection of appropriate archaeal primer pairs to characterize archaeal communities.


High-throughput sequencing Archaeal primers Archaeal communities Deep-sea sediment Permafrost soil 



This research was supported by Funds of Oil and Gas Survey, China Geological Survey (GZH201400308). We thank Dr. Fei Liu at the Institute of Microbiology, Chinese Academy of Sciences for calculating and analyzing the archaeal beta diversity. We also thank James Hurley at the Virginia Polytechnic Institute and State University for making a critical reading and revision of this paper.

Supplementary material

792_2019_1128_MOESM1_ESM.docx (76 kb)
Supplementary file1 (DOCX 75 kb)


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Copyright information

© Springer Japan KK, part of Springer Nature 2019

Authors and Affiliations

  • Shiping Wei
    • 1
    • 2
    Email author
  • Hongpeng Cui
    • 2
  • Yuchen Zhang
    • 2
  • Xin Su
    • 2
  • Hailiang Dong
    • 1
  • Fang Chen
    • 3
  • Youhai Zhu
    • 4
  1. 1.State Key Laboratory of Biogeology and Environmental GeologyChina University of GeosciencesBeijingChina
  2. 2.School of Marine SciencesChina University of GeosciencesBeijingChina
  3. 3.Guangzhou Marine Geological SurveyGuangdongChina
  4. 4.Oil and Gas Survey, China Geological SurveyBeijingChina

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