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Cited by 225Soil Carbon and Nitrogen DynamicsWastewater Treatment and Nitrogen RemovalMicrobial Community Ecology and Physiology

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Differential contributions of ammonia oxidizers and nitrite oxidizers to nitrification in four paddy soils

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Wang, Baozhan, Zhao, Jun, Guo, Zhiying, Ma, Jing, Xu, Hua, Jia, Zhongjun·2015·The ISME Journal
DOI 10.1038/ismej.2014.194PMC PMC4409153
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Abstract

Rice paddy fields are characterized by regular flooding and nitrogen fertilization, but the functional importance of aerobic ammonia oxidizers and nitrite oxidizers under unique agricultural management is poorly understood. In this study, we report the differential contributions of ammonia-oxidizing archaea (AOA), bacteria (AOB) and nitrite-oxidizing bacteria (NOB) to nitrification in four paddy soils from different geographic regions (Zi-Yang (ZY), Jiang-Du (JD), Lei-Zhou (LZ) and Jia-Xing (JX)) that are representative of the rice ecosystems in China. In urea-amended microcosms, nitrification activity varied greatly with 11.9, 9.46, 3.03 and 1.43 μg NO3−-N g−1 dry weight of soil per day in the ZY, JD, LZ and JX soils, respectively, over the course of a 56-day incubation period. Real-time quantitative PCR of amoA genes and pyrosequencing of 16S rRNA genes revealed significant increases in the AOA population to various extents, suggesting that their relative contributions to ammonia oxidation activity decreased from ZY to JD to LZ. The opposite trend was observed for AOB, and the JX soil stimulated only the AOB populations. DNA-based stable-isotope probing further demonstrated that active AOA numerically outcompeted their bacterial counterparts by 37.0-, 10.5- and 1.91-fold in 13C-DNA from ZY, JD and LZ soils, respectively, whereas AOB, but not AOA, were labeled in the JX soil during active nitrification. NOB were labeled to a much greater extent than AOA and AOB, and the addition of acetylene completely abolished the assimilation of 13CO2 by nitrifying populations. Phylogenetic analysis suggested that archaeal ammonia oxidation was predominantly catalyzed by soil fosmid 29i4-related AOA within the soil group 1.1b lineage. Nitrosospira cluster 3-like AOB performed most bacterial ammonia oxidation in the ZY, LZ and JX soils, whereas the majority of the 13C-AOB in the JD soil was affiliated with the Nitrosomona communis lineage. The 13C-NOB was overwhelmingly dominated by Nitrospira rather than Nitrobacter. A significant correlation was observed between the active AOA/AOB ratio and the soil oxidation capacity, implying a greater advantage of AOA over AOB under microaerophilic conditions. These results suggest the important roles of soil physiochemical properties in determining the activities of ammonia oxidizers and nitrite oxidizers.

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Metadata

Authors
Wang, B., Zhao, J., Guo, Z., Ma, J., Xu, H., & Jia, Z.
Affiliations
Chinese Academy of Sciences (CN)
Corresponding author
Jia, Zhongjun
ORCID
Venue
The ISME Journal
Publisher
Oxford University Press (OUP)
Published
2014-10-10
Volume
9
Issue
5
Pages
1062-1075
ISSN
  • 1751-7362 (ISSN-L)
  • 1751-7370
DOI
10.1038/ismej.2014.194
PMC
PMC4409153
OpenAlex
W2054606614
Cited by
225
References
1
Citations by year
2026: 14 · 2025: 13 · 2024: 21 · 2023: 16 · 2022: 24 · 2021: 30 · 2020: 26 · 2019: 26 · 2018: 27 · 2017: 17 · 2016: 8 · 2015: 3
FWCI
12.27
Type
journal article
Language
en
Open access
Licence
Locations
  • The ISME Journal (publishedVersion, cc-by-nc-sa)
  • PubMed Central (publishedVersion, cc-by-nc-sa)
  • PubMed (publishedVersion)
Funders
  • National Natural Science Foundation of China (XDB15040000, 41101227, 41090281)
  • Chinese Academy of Sciences (XDB15040000)
  • Government of Jiangsu Province
Topics
  • Life Sciences › Agricultural and Biological Sciences › Soil Science › Soil Carbon and Nitrogen Dynamics
  • Physical Sciences › Environmental Science › Pollution › Wastewater Treatment and Nitrogen Removal
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords
nitrification, ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, paddy soil, paddy fields, amoA gene, stable isotope probing, Nitrososphaera, Nitrosomonas, Nitrospira, Nitrobacter, nitrogen cycling
MeSH terms
Agriculture, Ammonia, Archaea, Bacteria, China, Nitrites, Nitrogen, Oxidation-Reduction, Phylogeny, Oryza, RNA, Ribosomal, 16S, Soil, Soil Microbiology, Ecosystem, Betaproteobacteria, Nitrification

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