Journal of Soils and Sediments

, Volume 19, Issue 3, pp 1416–1426 | Cite as

The relative contribution of nitrifiers to autotrophic nitrification across a pH-gradient in a vegetable cropped soil

  • Yaying Li
  • Ruijiao Xi
  • Weijin Wang
  • Huaiying YaoEmail author
Soils, Sec 5 • Soil and Landscape Ecology • Research Article



Microbial nitrification plays an important role in nitrogen cycling in ecosystems. Nitrification is performed by ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) including complete ammonia oxidizers. However, the relative importance of nitrifiers in autotrophic nitrification in relation to soil pH is still unclear.

Materials and methods

Combining DNA-based stable isotope probing (SIP) and molecular biological techniques, we investigated the abundance, structure, and activity of AOA, AOB, and NOB along a pH-gradient (3.97–7.04) in a vegetable cropped soil.

Results and discussion

We found that AOA abundance outnumbered AOB abundance and had a significantly negative relationship with soil pH. The abundances of NOB Nitrospira 16S rRNA, nxrB gene, and Nitrobacter nxrA gene were affected by soil pH. Incubation of soil with 13CO2 and DNA-SIP analysis demonstrated that significant 13CO2 assimilation by AOA rather than by AOB occurred in the acidic soils, whereas the labeled 13C level of AOA was much less in the neutral soil than in the acidic soils. There was no evidence of 13CO2 assimilation by NOB except for Nitrobacter with NxrB gene at pH 3.97. Phylogenetic analysis of AOA amoA gene in the 13C- and 12C-labeled treatments showed that the active AOA mainly belonged to Nitrososphaera in the acidic soils.


These results suggested that the main performer of nitrification was AOA in the acidic soils, but both AOA and AOB participated in nitrification in the neutral soil with low nitrification activity. NOB Nitrospira and Nitrobacter did not grow in the soils with pH 4.82–7.04 and other populations of NOB were probably involved in nitrite oxidation in the vegetable cropped soil.


Nitrifiers Soil pH Stable isotope probing Vegetable soil 


Funding information

This work was supported by the National Key R & D Program of China (2017YFD0200102, 2016YFC0502704), the National Natural Science Foundation of China (41525002, 41471206), the Strategic Priority Research Program of Chinese Academy of Sciences (XDB15020301), the Program of Key Laboratory of Urban Environment and Health (KLUEH-C-201701), and Ningbo Municipal Science and Technology Bureau (2015C10031).

Supplementary material

11368_2018_2109_MOESM1_ESM.docx (546 kb)
ESM 1 (DOCX 546 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Yaying Li
    • 1
    • 2
  • Ruijiao Xi
    • 1
    • 2
    • 3
  • Weijin Wang
    • 4
  • Huaiying Yao
    • 1
    • 2
    • 5
    Email author
  1. 1.Key Laboratory of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenPeople’s Republic of China
  2. 2.Ningbo Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station—NUEORSChinese Academy of SciencesNingboPeople’s Republic of China
  3. 3.University of Chinese Academy of SciencesBeijingPeople’s Republic of China
  4. 4.Department of ScienceInformation Technology and InnovationBrisbaneAustralia
  5. 5.Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological EngineeringWuhan Institute of TechnologyWuhanPeople’s Republic of China

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