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Journal of Soils and Sediments

, Volume 19, Issue 1, pp 23–37 | Cite as

Distributions and environmental drivers of archaea and bacteria in paddy soils

  • Chao-Lei Yuan
  • Li-Mei Zhang
  • Jun-Tao Wang
  • Hang-Wei Hu
  • Ju-Pei Shen
  • Peng Cao
  • Ji-Zheng HeEmail author
Soils, Sec 1 • Soil Organic Matter Dynamics and Nutrient Cycling • Research Article
  • 184 Downloads

Abstract

Purpose

The aim of this study is to investigate the abundance, diversity, and distribution of archaea and bacteria as affected by environment parameters in paddy soils, with focus on putative functional microbial groups related to redox processes. Because there is generally a high iron content in the soil, we also want to test a hypothesis that soil iron concentration significantly affects microbial diversity and distribution.

Materials and methods

Quantitative PCR and barcoded pyrosequencing of 16S ribosomal RNA genes were employed to investigate the abundance and community composition of archaeal and bacterial communities in 27 surface paddy soil samples. Pearson’s correlation, analysis of variance, partial least squares regression, principal coordinates analysis, and structural equation models were performed for the analyses of gene copy numbers, α-diversity, β-diversity, and relative abundances of archaea and bacteria and their relationships with environmental factors.

Results and discussion

Archaeal abundance was correlated greatest with temperature, but bacterial abundance was affected mainly by soil organic matter and total nitrogen content. Soil pH and concentrations of different ions were associated with archaeal and bacterial β-diversity. The relative abundances of Euryarchaeota and Thaumarchaeota were 61.3 and 13.1% of archaea and correlated with soil pH, which may affect the availability of substrates to methanogens and ammonia oxidizers. Dominant bacterial phyla were Proteobacteria (32.4%), Acidobacteria (17.8%), Bacteroidetes (9.3%), and Verrucomicrobia (6.0%). The relative abundances of putative bacterial reducers of nitrate, Fe(III), sulfate, and sulfur, and oxidizers of ammonia, nitrite, reduced sulfur, and C1 compounds had positive, negative, or non-significant correlations with the concentrations of their substrates. Soil iron concentration was correlated only with the distributions of some putative iron-reducing bacteria.

Conclusions

In paddy soils characterized by dynamic redox processes, archaea and bacteria differ in relationships of abundance, diversity, and distribution with environmental factors. Especially, the concentrations of electron donors or acceptors can explain the distributions of some but not all the putative functional microbial groups related to redox processes. Depending on pH range, soil pH has a strong impact on microbial ecology in paddy soils.

Keywords

Archaea Bacteria Distribution Putative functional groups Paddy soil 

Notes

Funding information

This work was financially supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB15020201), the National Natural Science Foundation of China (41601239), the China Postdoctoral Science Foundation (2016M600644), the “Pearl River Talents” Postdoctoral Program of Guangdong Province, the National Key Research and Development Program of China (2016YFD0800703), and the High-level Leading Talent Introduction Program of GDAS.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11368_2018_1997_MOESM1_ESM.docx (2.2 mb)
ESM 1 (DOCX 2.24 mb)

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Copyright information

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Authors and Affiliations

  1. 1.State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijingChina
  2. 2.Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and ManagementGuangdong Institute of Eco-environmental Science and TechnologyGuangzhouChina
  3. 3.Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleAustralia

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