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

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Abstract

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.

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Acknowledgements

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.

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Authors and Affiliations

  1. State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China

    Shiping Wei & Hailiang Dong

  2. School of Marine Sciences, China University of Geosciences, Beijing, 100083, China

    Shiping Wei, Hongpeng Cui, Yuchen Zhang & Xin Su

  3. Guangzhou Marine Geological Survey, Guangdong, 510760, China

    Fang Chen

  4. Oil and Gas Survey, China Geological Survey, Beijing, 100029, China

    Youhai Zhu

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  1. Shiping Wei
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  2. Hongpeng Cui
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Correspondence to Shiping Wei.

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Wei, S., Cui, H., Zhang, Y. et al. Comparative evaluation of three archaeal primer pairs for exploring archaeal communities in deep-sea sediments and permafrost soils. Extremophiles 23, 747–757 (2019). https://doi.org/10.1007/s00792-019-01128-1

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