Increased methane concentration alters soil prokaryotic community structure along an artificial pH gradient

  • Petr HeděnecEmail author
  • Roey Angel
  • Qiang Lin
  • Junpeng Rui
  • Xiangzhen Li
Original Article


Global climate change may have a large impact on increased emission rates of carbon dioxide and methane to total greenhouse gas emissions from terrestrial wetlands. Methane consumption by soil microbiota in alpine wet meadows serves as a biofilter for the methane produced in the waterlogged soil below. Altered pH regimes change microbial community composition and structure by exerting selection pressure on soil microorganisms with different ecological strategies and thus affect greenhouse gas emissions resulting from the metabolic activity of soil microorganisms. However, responses of prokaryotic communities to artificial pH shift under elevated methane concentration remain unclear. In this study, we assessed diversity and relative abundance of soil prokaryotes in an alpine meadow under elevated methane concentration along an artificial pH gradient using laboratory incubation experiments. We established an incubation experiment treated with artificial pH gradient (pH 4.5–8.5). After 3 months of incubation, 300 ml of methane at a concentration of 20,000 ppm was added to stimulate potential methanothrophs in topsoil. Sequencing of 16S rRNA gene indicated increasing of relative abundances of Crenarchaeota, Chloroflexi, Bacteroidetes, and Planctomycetes in soil after addition of methane, while the relative abundances of Actinobacteria and Gemmatimonadetes did not significant change before and after methane treatment. Results of phylogenetic relatedness of soil prokaryotes showed that microbial community is mostly shaped by deterministic factors. Species indicator analysis revealed distinct OTUs among various pH and methane treatments. Network analysis revealed distinct co-occurrence patterns of soil prokaryotic community before and after methane addition, and different correlation patterns among various prokaryotic taxa. Linear regression model revealed significant decrease of methane oxidation along elevated pH gradient. Soil pH constituted a strong environmental filter in species assembly of soil prokaryotic community. Methane oxidation rates decreased significantly with elevated pH. The interactive effects of elevated methane concentration and pH are therefore promising topic for future research.


Elevated methane oxidation Soil prokaryotes pH gradient Methanotrophs 



We thank Ondřej Mudrák for helpful advice with the statistical analysis and Adrienne Godschalx for help with English grammar and spelling.


The work was supported by the National Natural Science Foundation of China (41771293, 31670503, 41630751), Key Laboratory of Sichuan Province (KLCAS-2017-3), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB15010303), 13th five-year information plan of Chinese Academy of Sciences (XXH13503-03-106), and Ministry of Education, Youth and Sports of the Czech Republic - MEYS (projects LM2015075, EF16_013/0001782).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Research involving human participants and/or animals

No human or animal participants were involved in this study.

Informed consent

Informed consent rules were not applicable to this research because no human participants were involved.

Supplementary material

13213_2018_1421_MOESM1_ESM.docx (22 kb)
ESM 1 (DOCX 22 kb)


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Copyright information

© Università degli studi di Milano 2019

Authors and Affiliations

  1. 1.Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and EnvironmentFujian Agriculture and Forestry UniversityFuzhouChina
  2. 2.Institute for Environmental Studies and SoWa Research Infrastructure, Faculty of ScienceCharles University in PraguePrague 2Czech Republic
  3. 3.Laboratory of Soil BiodiversityUniversity of NeuchâtelNeuchâtelSwitzerland
  4. 4.SoWa Research Infrastructure and Institute of Soil Biology, Biology Centre of the Czech Academy of SciencesČeské BudějoviceCzech Republic

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