Skip to main content
SpringerLink
Log in

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

  • Original Paper
  • Published:
Extremophiles Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Bahram M, Anslan S, Hildebrand F, Bork P, Tedersoo L (2018) Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment. Environ Microbiol Rep 9999(9999) na–na

  • Bai R, Wang JT, Deng Y, He JZ, Feng K, Zhang LM (2017) Microbial community and functional structure significantly varied among distinct types of paddy soils but responded differently along gradients of soil depth layers. Front Microbiol 8:945

    Article  PubMed  PubMed Central  Google Scholar 

  • Baker GC, Smith JJ, Cowan DA (2003) Review and re-analysis of domain-specific 16S primers. J Microbiol Meth 55:541–555

    Article  CAS  Google Scholar 

  • Bartram AK, Lynch MDJ, Stearns JC, Moreno-Hagelsieb G, Meufeld JD (2011) Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end Illumina reads. Appl Environ Microbiol 77:3846–3852

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bell TAS, Prithiviraj B, Wahlent BD, Fields MW, Peyton BM (2016) A lipid-accumulating alga maintains growth in outdoor, alkaliphilic raceway pond with mixed microbial communities. Frontiers in microbiology 6:1480.

    Article  Google Scholar 

  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chakravorty S, Helb D, Burday M, Connell N, Alland D (2007) A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbial Meth 69:330–339

    Article  CAS  Google Scholar 

  • Claesson MJ, Wang Q, O’Sullivan O, Greene-Diniz R, Cole JR, Ross RP, O’Toole PW (2010) Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res 38:e200

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Coolen MJL, Hopmans EC, Rijpstra WIC, Muyzer G, Schouten S, Volkman JK, Damsté JSS (2004) Evolution of the methane cycle in ace lake (Antarctica) during the Holocene: response of methanogens and methanotrophs to environmental change. Org Geochem 35(1151):1167

    Google Scholar 

  • Cui H, Su X, Chen F, Wei S, Chen S, Wang J (2016) Vertical distribution of archaeal communities in cold seep sediments from the Jiulong methane reef area in the South China Sea. Biosci J 32:1059–1068

    Article  Google Scholar 

  • De León KB, Gerlach R, Peyton BM, Fields MY (2013) Archaeal and bacterial communities in three alkaline hot springs in Heart Lake Geyser Basin. Yellowstone Natl Park 4:330

    Google Scholar 

  • Ding J, Zhang Y, Wang H, Jian H, Leng H, Xiao X (2017) Microbial community structure of deep-sea hydrothermal vents on the ultraslow spreading Southwest Indian Ridge. Front Microbiol 8:1012

    Article  PubMed  PubMed Central  Google Scholar 

  • Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL et al (2012) Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci USA 109:21390–21395

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fischer MA, Güllert S, Neulinger SC, Streit WR, Schmitz RA (2016) Evaluation of 16S rRNA gene primer pairs for monitoring microbial community structures showed high reproducibility within and low comparability between datasets generated with multiple archaeal and bacterial primer pairs. Front Microbiol 7:1297

    Article  PubMed  PubMed Central  Google Scholar 

  • Fredriksson NJ, Hermansson M, Wilén BM (2013) The Choice of PCR primers has great impact on assessments of bacterial community diversity and dynamics in a wastewater treatment plant. PLoS One 8:e76431

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Galand PE, Lucas S, Fagervold SK, Peru E, Pruski AM, Vétion G et al (2016) Disturbance increases microbial community diversity and production in marine sediments. Front Microbiol 7:1950

    Article  PubMed  PubMed Central  Google Scholar 

  • Gantner S, Andersson AF, Alonso-Sáez L, Bertilsson S (2011) Novel primers for 16S rRNA-based archaeal community analyses in environmental samples. J Microbiol Meth 84:12–18

    Article  CAS  Google Scholar 

  • Genderjahn S, Alawi M, Mangelsdorf K, Horn F, Wagner D (2018) Desiccation- and saline-tolerant bacteria and archaea in Kalahari Pan sediments. Front Microbiol 9:2082

    Article  PubMed  PubMed Central  Google Scholar 

  • Ghyselinck J, Pfeiffer S, Heylen K, Sessitsch A, De Vos P (2013) The effect of primer choice and short read sequences on the outcome of 16S rRNA gene based diversity studies. PLoS One 8:e71360

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Head IM, Saunders JR, Pickup RW (1998) Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microb Ecol 35:1–21

    Article  CAS  PubMed  Google Scholar 

  • Herfort L, Kim JH, Coolen MJL, Abbas B, Schouten S, Herndl G, Damsté JSS (2009) Diversity of archaea and detection of crenarchaeotal amoA genes in the rivers Rhine and Têt. Aquat Microb Ecol 55:189–201

    Article  Google Scholar 

  • Hugoni M, Taib N, Debroas D, Domaizon I, Dufournel IJ, Bronner G et al (2013) Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters. Proc Natl Acad Sci USA 110:6004–6009

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jiao S, Xu Y, Zhang J, Lu Y (2019) Environmental filtering drives distinct continental atlases of soil archaea between dryland and wetland agricultural ecosystems. Microbiome 7:15

    Article  PubMed  PubMed Central  Google Scholar 

  • Jungbluth SP, Amend JP, Rappé (2017) Data descriptor: Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids. Sci Data 4:170037

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41:e1

    Article  CAS  PubMed  Google Scholar 

  • Kuang JL, Huang LN, Chen LX, Hua ZS, Li SJ, Hu M, Li JT, Shu WS (2012) Contemporary environmental variation determines microbial diversity patterns in acid mine drainage. ISME J 5:1038–1050

    Google Scholar 

  • Kubo K, Lloyd KG, Biddle JF, Amann R, Teske A, Knittel K (2012) Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diversity and widespread in marine sediments. ISME J 6:1949–1965

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lauer A, Sørensen KB, Teske A (2016) Phylogenetic characterization of marine benthic archaea in organic-poor sediments of the eastern equatorial pacific ocean (ODP site 1225). Microorganisms 4:32

    Article  PubMed Central  Google Scholar 

  • Lazarevic V, Whiteson K, Huse S, Hernandez D, Farinelli L, Osteras M, Schrenzel J, Francois P (2009) Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J Microbiol Meth 79:266–271

    Article  CAS  Google Scholar 

  • Liebner S, Ganzert L, Kiss A, Yang S, Wagner D, Svenning MM (2015) Shifts in methanogenic community composition and methane fluxes along the degradation of discontinuous permafrost. Front Microbiol 6:356

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R (2007) Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res 35:e120

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Liu X, Fan H, Ding X, Hong Z, Nei Y, Liu Z, Li G, Guo H (2014a) Analysis of the gut microbiota by high-throughput sequencing of the V5–V6 regions of the 16S rRNA gene in Donkey. Curr Microbiol 68:657–662

    Article  CAS  PubMed  Google Scholar 

  • Liu Y, Zhang J, Zhang X, Xie S (2014b) Depth-related changes of sediment ammonia-oxidizing microorganisms in a high-altitude freshwater wetland. Appl Microbiol Biotechnol 98:5697–5707

    Article  CAS  PubMed  Google Scholar 

  • Liu J, Yu Z, Yao Q, Sui Y, Shi Y, Chu H et al (2019) Biogeographic distribution patterns of the archaeal communities across the black soil zone of Northeast China. Front Microbiol 10:23

    Article  PubMed  PubMed Central  Google Scholar 

  • Mackelprang R, Waldrop MP, DeAngelis KM, David MM, Chavarria KL, Blazewicz SJ et al (2011) Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480:368–371

    Article  CAS  PubMed  Google Scholar 

  • Martínez-Porchas M, Villalpando-Canchola E, Vargas-Albores F (2016) Significant loss of sensitivity and specificity in the taxonomic classification occurs when short 16S rRNA gene sequences are used. Heliyon 2:e00170

    Article  PubMed  PubMed Central  Google Scholar 

  • McKay LJ, Hatzenpichler R, Inskeep WP, Fields MW (2017) Occurrence and expression of novel methyl-coenzyme M reductase gene (mcrA) variants in hot spring sediments. Sci Rep 7:7252

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Meng J, Xu J, Qin D, He Y, Xiao X, Wang F (2014) Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analysis. ISME J 8:650–659

    Article  CAS  PubMed  Google Scholar 

  • Mesa V, Gallego JLR, González-Gil R, Lauga B, Sánchez J, Méndez-Garcla C, Peláez AI (2017) Bacterial, archaeal, and eukaryotic diversity across distinct microhabitats in an acid mine drainage. Fron Microbiol 8:1756

    Article  Google Scholar 

  • Nunoura T, Takaki Y, Kazama H, Hirai M, Ashi J, Imachi H, Takai K (2012) Microbial diversity in deep-sea methane seep sediments presented by SSU rRNA gene tag sequencing. Microbes Environ 27:381–390

    Article  Google Scholar 

  • Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40:337–365

    Article  CAS  PubMed  Google Scholar 

  • Peiffer JA, Spor A, Koren O, Jin Z, Tringe SG, Fangl JL, Buckler ES, Ley RE (2013) Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci USA 110:6548–6553

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SSK, McCulle SL et al (2011) Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci USA 108(suppl l):4680–4687

    Article  CAS  PubMed  Google Scholar 

  • Schloss PD, Westcott SI, Ryabin T, Hall JR, Hartmann M, Hollister EB et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schloss PD, Jenior ML, Koumpouras CC, Westcott SL, Highlander SK (2016) Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system. PeerJ 4:e1869

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sinclair L, Osman OA, Bertilsson S, Eiler A (2015) Microbial community composition and diversity via 16S rRNA gene amplicons: evaluating the illumine platform. PLoS One 10:e0116955

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sollai M, Villanueva L, Hopmans E, Reichart GJ, Damsté JSS (2019) A combined lipidomic and 16S rRNA gene amplicon sequencing approach reveals archaeal sources of intact polar lipids in the stratified Black Sea water column. Geobiology 17:91–109

    Article  CAS  PubMed  Google Scholar 

  • Spang A, Saw JH, Jørgensen SL, Zarenba-Niedzwiedzka K, Martijin J, Lind AE et al (2015) Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521:173–179

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Spang A, Caceres EF, Ettema TJG (2017) Genomic exploration of the diversity ecology and evolution of the archaeal domain of life. Science 357:3883

    Article  CAS  Google Scholar 

  • Takahashi S, Tomita J, Nishioka K, Hisada T, Nishijima M (2014) Development of a prokaryotic universal primer for simultaneous analysis of bacteria and archaea using next-generation sequencing. PLoS One 9:e105592

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Takai K, Horikoshi K (1999) Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics 152:1285–1297

    CAS  PubMed  PubMed Central  Google Scholar 

  • Takai K, Horikoshi K (2000) Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes. Appl Environ Microbiol 66:5066–5072

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Teske A, Sørensen KB (2008) Uncultured archaea in deep marine subsurface sediments: have we caught them all? ISME J 2:3–18

    Article  CAS  PubMed  Google Scholar 

  • Thijs S, Beeck MOP, Beckers B, Truyens S, Stevens V, Van Hamme JD, Weyens N, Vangronseld J (2017) Comparative evaluation of four bacteria-specific primer pairs for 16S rRNA gene surveys. Front Microbiol 8:494

    Article  PubMed  PubMed Central  Google Scholar 

  • Vavourakis CD, Ghai R, Rodriguez-Valera F, Sorokin DY, Tringe SG, Hugenholtz P, Muyzer G (2016) Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines. Front Microbiol 7:211

    Article  PubMed  PubMed Central  Google Scholar 

  • Vetriani C, Jannasch HW, MacGregor BJ, Stahl DA, Reysenbach AL (1999) Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments. Appl Environ Microbiol 65:4375–4384

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Qian PY (2009) Conservative fragments in bacterial 16S rRNA genes and primers design for 16S ribosomal DNA amplicons in metagenomic studies. PLoS ONE 4:e7401

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wei S, Cui H, Zhu Y, Lu Z, Pang S, Zhang S, Dong H, Su X (2018) Shifts of archaeal and methanogenic communities in response to permafrost thaw results in rising methane emissions and soil property changes. Extremophiles 22:447–459

    Article  CAS  PubMed  Google Scholar 

  • Yang B, Wang Y, Qian PY (2016a) Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis. BMC Bioinformatics 17:135

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yang Y, Dai Y, Wu Z, Xie S, Liu Y (2016b) Temporal and spatial dynamics of archaeal communities in two freshwater lakes at different trophic status. Front Microbiol 7:451

    PubMed  PubMed Central  Google Scholar 

  • You NH, Ashlock-Savage KN, Elshahed MS (2012) Phylogenetic diversities and community structure of members of the extremely halophilic archaea (Order Halobacteriales) in multiple saline sediments habitats. Appl Environ Microbiol 78:1332–1344

    Article  CAS  Google Scholar 

  • Zhang J, Ding X, Guan R, Zhu C, Xu C, Zhu B et al (2018) Evaluation of different 16S rRNA gene V regions for exploring bacterial diversity in a eutrophic freshwater lake. Sci Total Environ 618:1254–1267

    Article  CAS  PubMed  Google Scholar 

  • Zheng W, Tsompana M, Ruscitto A, Sharma A, Genco R, Sun Y, Buck MJ (2015) An accurate and efficient experimental approach for characterization of the complex oral microbiota. Microbiome 3:48

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhou HW, Li DF, Tam NFY, Jiang XT, Zhang H, Sheng HF et al (2011) BIPES, a cost-effective high-throughput method for assessing microbial diversity. ISME J 5:741–749

    Article  CAS  PubMed  Google Scholar 

Download references

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.

Author information

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

Authors
  1. Shiping Wei
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hongpeng Cui
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yuchen Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xin Su
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hailiang Dong
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Fang Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Youhai Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Shiping Wei.

Additional information

Communicated by L. Huang.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 75 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00792-019-01128-1

Keywords

Search

Navigation