Annals of Microbiology

, Volume 69, Issue 8, pp 867–870 | Cite as

Thaumarchaeota affiliated with Soil Crenarchaeotic Group are prevalent in the alkaline soil of an alpine grassland in northwestern China

  • Keqiang ShaoEmail author
  • Xingyu Jiang
  • Yang Hu
  • Xiangming Tang
  • Guang Gao
Short Communication



Thaumarchaeota are key players within the global nitrogen cycle. Investigations of the Thaumarchaeota communities are important for an integrated understanding of nitrogen nutrient cycle in soil ecosystems. Therefore, the objective of this study was to examine the presence and diversity of Thaumarchaeota within an alkaline soil in the Bayinbuluke alpine grassland, China.


The community DNAs were directly extracted from soil samples, collected on 15 July 2014, and paired-end V5–V6 amplicons of the 16S rRNA gene were sequenced by Illumina Miseq. Sequencing reads were processed using the Quantitative Insights Into Microbial Ecology (QIIME) v. 1.8.0 pipeline. After quality control, the validated sequence reads were classified into different operational taxonomic units (OTUs) based on a 97% identity level, using the Uclust algorithm to generate stable OTUs. The longest sequence in each cluster was chosen to be the representative sequence, and sequences were annotated using the Silva rRNA database project.


In the analyzed grassland soil, Thaumarchaeota had a relative abundance of 3.65 to 51.07% of the microbial community (mean = 20.20%), representing the most dominant phylum. The thaumarchaeal community was dominated by the Soil Crenarchaeotic Group (SCG, 34.55 to 99.82%, mean = 95.10%), with specifically low fraction of the ammonia-oxidizing genus Candidatus Nitrososphaera (2.83 to 30.37%, mean = 13.10%) and remaining unclassified genus.


Our results show Thaumarchaeota affiliated with SCG were prevalent in the alkaline soil of this grassland.


Alkaline soil, Illumina amplicon sequencing, Thaumarchaeota Soil Crenarchaeotic Group Candidatus Nitrososphaera 



We thank staff at the Institute of Lake Bosten, of the Environmental Protection Bureau of Bayingolin Mongolia Autonomous Prefecture, for help with sample collection. We are grateful to the editor and anonymous reviewers for their constructive comments and helpful suggestions.


This study was funded by the “One-Three-Five” Strategic Planning of Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences (Grant No. NIGLAS2017GH05), the National Natural Science Foundation of China (Grant No. 41790423) and the Special Environmental Research Funds for Public Welfare of the State Environmental Protection Administration (Grant No. 201309041).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Research involving human participants and/or animals

This article does not contain any studies with human participants or animals.

Informed consent

A statement regarding informed consent is not applicable for this study.

Supplementary material

13213_2019_1492_MOESM1_ESM.docx (111 kb)
ESM 1 (DOCX 111 kb)


  1. Bik HM, Porazinska DL, Creer S et al (2012) Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evo 27(4):233–243CrossRefGoogle Scholar
  2. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) Uchime improves sensitivity and speed of chimera detection. Bioinformatics 27(16):2194–2200CrossRefGoogle Scholar
  3. He GX, Li KH, Liu XJ, Gong YM, Hu YK (2014) Fluxes of methane, carbon dioxide and nitrous oxide in an alpine wetland and an alpine grassland of the Tianshan Mountains, China. J Arid Land 6(6):717–724CrossRefGoogle Scholar
  4. He JZ, Hu HW, Zhang LM (2012) Current insights into the autotrophic thaumarchaeal ammonia oxidation in acidic soils. Soil Biol Biochem 55(6):146–154CrossRefGoogle Scholar
  5. He Y, Caporaso JG, Jiang XT, Sheng HF, Huse SM, Rideout JR, Edgar RC, Kopylova E, Walters WA, Knight R, Zhou HW (2015) Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity. Microbiome 3(1):20CrossRefGoogle Scholar
  6. Lehtovirta LE, Prosser JI, Nicol GW (2009) Soil pH regulates the abundance and diversity of Group1.1c Crenarchaeota. FEMS Microbiol Ecol 70(3):367–376CrossRefGoogle Scholar
  7. Levicnik-Höfferle S, Nicol GW, Ausec L, Mulec I, Prosser JI (2012) Stimulation of thaumarchaeal ammonia oxidation by ammonia derived from organic nitrogen but not inorganic nitrogen. FEMS Microbiol Ecol 80(1):114–123CrossRefGoogle Scholar
  8. Ochsenreiter T, Selezi D, Quaiser A, Bonchosmolovskaya L, Schleper C (2003) Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. Environ Microbiol 5(9):787–797CrossRefGoogle Scholar
  9. Rughöft S, Herrmann M, Lazar CS, Cesarz S, Levick SR, Trumbore SE, Küsel K (2016) Community composition and abundance of bacterial, archaeal, and nitrifying populations in savanna soils on contrasting bedrock material in Kruger National Park, South Africa. Front Microbiol 7:1638Google Scholar
  10. Schneider D, Engelhaupt M, Allen K, Kurniawan S, Krashevska V, Heinemann M, Nacke H, Wijayanti M, Meryandini A, Corre MD, Scheu S, Daniel R (2015) Impact of lowland rainforest transformation on diversity and composition of soil prokaryotic communities in Sumatra (Indonesia). Front Microbiol 6:1339CrossRefGoogle Scholar
  11. Shen JP, Zhang LM, Zhu YG, Zhang JB, He JZ (2008) Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. Environ Microbiol 10(6):1601–1611CrossRefGoogle Scholar
  12. Sigunga DO, Janssen BH, Oenema O (2002) Ammonia volatilization from vertisols. Eur J Soil Sci 53(2):195–202CrossRefGoogle Scholar
  13. Spang A, Poehlein A, Offre P, Zumbrägel S, Haider S, Rychlik N, Nowka B, Schmeisser C, Lebedeva EV, Rattei T, Böhm C, Schmid M, Galushko A, Hatzenpichler R, Weinmaier T, Daniel R, Schleper C, Spieck E, Streit W, Wagner M (2012) The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations. Environ Microbiol 14(12):3122–3145CrossRefGoogle Scholar
  14. Stahl DA, dela Torre JR (2012) Physiology and diversity of ammonia-oxidizing archaea. Annu Rev Microbiol 66(66):83–101CrossRefGoogle Scholar
  15. Su P, Lou J, Brookes PC, Luo Y, He Y, Xu JM (2017) Taxon-specific responses of soil microbial communities to different soil priming effects induced by addition of plant residues and their biochars. J Soils Sediments 17(3):674–684CrossRefGoogle Scholar
  16. Tago K, Okubo T, Shimomura Y, Kikuchi Y, Hori T, Nagayama A, Hayatsu M (2015) Environmental factors shaping the community structure of ammonia-oxidizing bacteria and archaea in sugarcane field soil. Microbes Environ 30(1):21–28CrossRefGoogle Scholar
  17. Zinger L, Gobet A, Pommier T (2012) Two decades of describing the unseen majority of aquatic microbial diversity. Mol Ecol 21(8):1878–1896CrossRefGoogle Scholar

Copyright information

© Università degli studi di Milano 2019

Authors and Affiliations

  • Keqiang Shao
    • 1
    Email author
  • Xingyu Jiang
    • 1
  • Yang Hu
    • 1
  • Xiangming Tang
    • 1
  • Guang Gao
    • 1
  1. 1.Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of SciencesNanjingChina

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