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Nitrosospira cluster 3-like bacterial ammonia oxidizers and Nitrospira-like nitrite oxidizers dominate nitrification activity in acidic terrace paddy soils

Nitrosospira cluster 3-like bacterial ammonia oxidizers and Nitrospira-like nitrite oxidizers dominate nitrification activity in acidic terrace paddy soils
Nitrosospira cluster 3-like bacterial ammonia oxidizers and Nitrospira-like nitrite oxidizers dominate nitrification activity in acidic terrace paddy soils

The isolation of acid-adapted ammonia-oxidizing bacteria (AOB) has suggested the functional importance of AOB in acidic soils. However, there is, currently, no convincing evidence that links AOB activity to nitrification in acidic paddy soils. Here we demonstrated the incorporation of 13CO2 into the genomes of ammonia-oxidizing archaea (AOA), AOB and nitrite-oxidizing bacteria (NOB) following urea application by using stable isotope probing (SIP) in three acidic terrace paddy soils with altitudes of 200 m (E200), 600 m (E600) and 1100 m (E1100), respectively. Nitrification activity increased from E200 to E600 and then to E1100, accompanied with significant growth of AOB over the 56-day incubation, while the abundance of archaeal amoA gene declined significantly in all soils after incubation. DNA-SIP demonstrated that active AOB outnumbered AOA and were much more heavily labeled than AOA and NOB, implying their more significant contributions to nitrification in these soils. Phylogenetic analysis indicated that Nitrosospira cluster 3-like AOB predominantly catalyzed bacterial ammonia oxidation. 13C-labeled NOB was dominated by Nitrospira moscoviensis in E1100, while in E200 and E600, Nitrospira marina and Nitrospira japonica were as prevalent as Nitrospira moscoviensis, respectively. Canonical correlation analysis and the Mantel test indicated the importance of soil physiochemical properties (e.g., pH, available phosphorus (AP) and soil oxidation capacity (OXC)) in determining the composition of the active nitrifying populations. These results suggest a greater functional importance of AOB in ammonia oxidation in the tested acidic paddy soils and the existence of a broader ecological niche for AOB than previously considered.

Acidic paddy soil, Bacterial ammonia oxidation, DNA stable isotope probing, Nitrosospira cluster 3-like AOB, Nitrospira-like nitrite oxidizers
0038-0717
229-237
Zhang, Qian
5768ab4e-5e98-4a28-bf41-56a8abb54c64
Li, Yong
54918a50-109d-48f2-be51-93a669fa1aec
He, Yan
885a7e1a-8e77-4bee-8628-ddc4aa470197
Liu, Haiyang
da7ce0fd-b090-4ba2-b37e-44832a0a95ca
Dumont, Marc G.
afd9f08f-bdbb-4cee-b792-1a7f000ee511
Brookes, Philip C.
937c55a8-e2ba-4ca6-bcd6-31f5591263b0
Xu, Jianming
0f86411b-4727-4737-ba01-6fd64aac2c5d
Zhang, Qian
5768ab4e-5e98-4a28-bf41-56a8abb54c64
Li, Yong
54918a50-109d-48f2-be51-93a669fa1aec
He, Yan
885a7e1a-8e77-4bee-8628-ddc4aa470197
Liu, Haiyang
da7ce0fd-b090-4ba2-b37e-44832a0a95ca
Dumont, Marc G.
afd9f08f-bdbb-4cee-b792-1a7f000ee511
Brookes, Philip C.
937c55a8-e2ba-4ca6-bcd6-31f5591263b0
Xu, Jianming
0f86411b-4727-4737-ba01-6fd64aac2c5d

Zhang, Qian, Li, Yong, He, Yan, Liu, Haiyang, Dumont, Marc G., Brookes, Philip C. and Xu, Jianming (2019) Nitrosospira cluster 3-like bacterial ammonia oxidizers and Nitrospira-like nitrite oxidizers dominate nitrification activity in acidic terrace paddy soils. Soil Biology and Biochemistry, 131, 229-237. (doi:10.1016/j.soilbio.2019.01.006).

Record type: Article

Abstract

The isolation of acid-adapted ammonia-oxidizing bacteria (AOB) has suggested the functional importance of AOB in acidic soils. However, there is, currently, no convincing evidence that links AOB activity to nitrification in acidic paddy soils. Here we demonstrated the incorporation of 13CO2 into the genomes of ammonia-oxidizing archaea (AOA), AOB and nitrite-oxidizing bacteria (NOB) following urea application by using stable isotope probing (SIP) in three acidic terrace paddy soils with altitudes of 200 m (E200), 600 m (E600) and 1100 m (E1100), respectively. Nitrification activity increased from E200 to E600 and then to E1100, accompanied with significant growth of AOB over the 56-day incubation, while the abundance of archaeal amoA gene declined significantly in all soils after incubation. DNA-SIP demonstrated that active AOB outnumbered AOA and were much more heavily labeled than AOA and NOB, implying their more significant contributions to nitrification in these soils. Phylogenetic analysis indicated that Nitrosospira cluster 3-like AOB predominantly catalyzed bacterial ammonia oxidation. 13C-labeled NOB was dominated by Nitrospira moscoviensis in E1100, while in E200 and E600, Nitrospira marina and Nitrospira japonica were as prevalent as Nitrospira moscoviensis, respectively. Canonical correlation analysis and the Mantel test indicated the importance of soil physiochemical properties (e.g., pH, available phosphorus (AP) and soil oxidation capacity (OXC)) in determining the composition of the active nitrifying populations. These results suggest a greater functional importance of AOB in ammonia oxidation in the tested acidic paddy soils and the existence of a broader ecological niche for AOB than previously considered.

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Zhang_et_al_accepted - Accepted Manuscript
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Accepted/In Press date: 9 January 2019
e-pub ahead of print date: 14 January 2019
Published date: 1 April 2019
Keywords: Acidic paddy soil, Bacterial ammonia oxidation, DNA stable isotope probing, Nitrosospira cluster 3-like AOB, Nitrospira-like nitrite oxidizers

Identifiers

Local EPrints ID: 428453
URI: http://eprints.soton.ac.uk/id/eprint/428453
ISSN: 0038-0717
PURE UUID: a860c932-8fd2-4b25-975c-9c2e0865b82e
ORCID for Marc G. Dumont: ORCID iD orcid.org/0000-0002-7347-8668

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Date deposited: 27 Feb 2019 17:30
Last modified: 07 Oct 2020 06:44

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Contributors

Author: Qian Zhang
Author: Yong Li
Author: Yan He
Author: Haiyang Liu
Author: Marc G. Dumont ORCID iD
Author: Philip C. Brookes
Author: Jianming Xu

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