Long-Term Adaptation of Acidophilic Archaeal Ammonia Oxidisers Following Different Soil Fertilisation Histories

Jun Zhao; Baozhan  Wang; Xue  Zhou; Mohammad  Saiful Alam; Jianbo  Fan; Zhiying  Guo; Huimin  Zhang; Cecile Gubry-Rangin; Zhongjun  Jia

doi:10.1007/s00248-021-01763-2

Long-Term Adaptation of Acidophilic Archaeal Ammonia Oxidisers Following Different Soil Fertilisation Histories

Jun Zhao, Baozhan Wang, Xue Zhou, Mohammad Saiful Alam, Jianbo Fan, Zhiying Guo, Huimin Zhang, Cecile Gubry-Rangin^* (Corresponding Author), Zhongjun Jia^* (Corresponding Author)

^*Corresponding author for this work

Aberdeen Centre For Environmental Sustainability

Research output: Contribution to journal › Article › peer-review

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Abstract

Ammonia oxidising archaea (AOA) are ecologically important nitrifiers in acidic agricultural soils. Two AOA phylogenetic clades, belonging to order-level lineages of Nitrososphaerales (clade C11; also classified as NS-Gamma-2.3.2) and family-level lineage of Candidatus Nitrosotaleaceae (clade C14; NT-Alpha-1.1.1), usually dominate AOA population in low pH soils. This study aimed to investigate the effect of different fertilisation histories on community composition and activity of acidophilic AOA in soils. High-throughput sequencing of ammonia monooxygenase gene (amoA) was performed on six low pH agricultural plots originating from the same soil but amended with different types of fertilisers for over 20 years and nitrification rates in those soils were measured. In these fertilised acidic soils, nitrification was likely dominated by Nitrososphaerales AOA and ammonia-oxidising bacteria, while Ca. Nitrosotaleaceae AOA activity was non-significant. Within Nitrososphaerales AOA, community composition differed based on the fertilisation history, with Nitrososphaerales C11 only representing a low proportion of the community. This study revealed that long-term soil fertilisation selects for different acidophilic nitrifier communities, potentially through soil pH change or through direct effect of nitrogen, potassium and phosphorus. Comparative community composition among the differently fertilised soils also highlighted the existence of AOA phylotypes with different levels of stability to environmental changes, contributing to the understanding of high AOA diversity maintenance in terrestrial ecosystems

Original language	English
Pages (from-to)	424-435
Number of pages	12
Journal	Microbial Ecology
Volume	83
Early online date	10 May 2021
DOIs	https://doi.org/10.1007/s00248-021-01763-2
Publication status	Published - Feb 2022

Bibliographical note

Acknowledgements
We thank Prof Yuanqiu He (now deceased) at the State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences for his contribution to this study. In addition, we thank the staff of the Analysis Center at the Institute of Soil Science for technical support, including Ms Rong Huang and Mr Zuohao Ma for 454-pyrosequencing, Mr Ruhai Wang for the ammonia and nitrate and nitrite content assays, Mr Guoxing Lu for the SOM assay. We also thank Dr Jian Cui and Dr Xiaoli Liu for assistance in soil sampling in the fields.

Funding
This work was supported by the National Natural Science Foundation of China (41530857, 91751204 and 41977056). JZ was funded by a Natural Environment Research Council grant (NE/K016342/1) and CGR was supported by a Royal Society University Research Fellowship (URF150571).

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Cite this

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title = "Long-Term Adaptation of Acidophilic Archaeal Ammonia Oxidisers Following Different Soil Fertilisation Histories",

abstract = "Ammonia oxidising archaea (AOA) are ecologically important nitrifiers in acidic agricultural soils. Two AOA phylogenetic clades, belonging to order-level lineages of Nitrososphaerales (clade C11; also classified as NS-Gamma-2.3.2) and family-level lineage of Candidatus Nitrosotaleaceae (clade C14; NT-Alpha-1.1.1), usually dominate AOA population in low pH soils. This study aimed to investigate the effect of different fertilisation histories on community composition and activity of acidophilic AOA in soils. High-throughput sequencing of ammonia monooxygenase gene (amoA) was performed on six low pH agricultural plots originating from the same soil but amended with different types of fertilisers for over 20 years and nitrification rates in those soils were measured. In these fertilised acidic soils, nitrification was likely dominated by Nitrososphaerales AOA and ammonia-oxidising bacteria, while Ca. Nitrosotaleaceae AOA activity was non-significant. Within Nitrososphaerales AOA, community composition differed based on the fertilisation history, with Nitrososphaerales C11 only representing a low proportion of the community. This study revealed that long-term soil fertilisation selects for different acidophilic nitrifier communities, potentially through soil pH change or through direct effect of nitrogen, potassium and phosphorus. Comparative community composition among the differently fertilised soils also highlighted the existence of AOA phylotypes with different levels of stability to environmental changes, contributing to the understanding of high AOA diversity maintenance in terrestrial ecosystems",

author = "Jun Zhao and Baozhan Wang and Xue Zhou and {Saiful Alam}, Mohammad and Jianbo Fan and Zhiying Guo and Huimin Zhang and Cecile Gubry-Rangin and Zhongjun Jia",

note = "Acknowledgements We thank Prof Yuanqiu He (now deceased) at the State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences for his contribution to this study. In addition, we thank the staff of the Analysis Center at the Institute of Soil Science for technical support, including Ms Rong Huang and Mr Zuohao Ma for 454-pyrosequencing, Mr Ruhai Wang for the ammonia and nitrate and nitrite content assays, Mr Guoxing Lu for the SOM assay. We also thank Dr Jian Cui and Dr Xiaoli Liu for assistance in soil sampling in the fields. Funding This work was supported by the National Natural Science Foundation of China (41530857, 91751204 and 41977056). JZ was funded by a Natural Environment Research Council grant (NE/K016342/1) and CGR was supported by a Royal Society University Research Fellowship (URF150571).",

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doi = "10.1007/s00248-021-01763-2",

language = "English",

volume = "83",

pages = "424--435",

journal = "Microbial Ecology",

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TY - JOUR

T1 - Long-Term Adaptation of Acidophilic Archaeal Ammonia Oxidisers Following Different Soil Fertilisation Histories

AU - Zhao, Jun

AU - Wang, Baozhan

AU - Zhou, Xue

AU - Saiful Alam, Mohammad

AU - Fan, Jianbo

AU - Guo, Zhiying

AU - Zhang, Huimin

AU - Gubry-Rangin, Cecile

AU - Jia, Zhongjun

N1 - Acknowledgements We thank Prof Yuanqiu He (now deceased) at the State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences for his contribution to this study. In addition, we thank the staff of the Analysis Center at the Institute of Soil Science for technical support, including Ms Rong Huang and Mr Zuohao Ma for 454-pyrosequencing, Mr Ruhai Wang for the ammonia and nitrate and nitrite content assays, Mr Guoxing Lu for the SOM assay. We also thank Dr Jian Cui and Dr Xiaoli Liu for assistance in soil sampling in the fields. Funding This work was supported by the National Natural Science Foundation of China (41530857, 91751204 and 41977056). JZ was funded by a Natural Environment Research Council grant (NE/K016342/1) and CGR was supported by a Royal Society University Research Fellowship (URF150571).

PY - 2022/2

Y1 - 2022/2

N2 - Ammonia oxidising archaea (AOA) are ecologically important nitrifiers in acidic agricultural soils. Two AOA phylogenetic clades, belonging to order-level lineages of Nitrososphaerales (clade C11; also classified as NS-Gamma-2.3.2) and family-level lineage of Candidatus Nitrosotaleaceae (clade C14; NT-Alpha-1.1.1), usually dominate AOA population in low pH soils. This study aimed to investigate the effect of different fertilisation histories on community composition and activity of acidophilic AOA in soils. High-throughput sequencing of ammonia monooxygenase gene (amoA) was performed on six low pH agricultural plots originating from the same soil but amended with different types of fertilisers for over 20 years and nitrification rates in those soils were measured. In these fertilised acidic soils, nitrification was likely dominated by Nitrososphaerales AOA and ammonia-oxidising bacteria, while Ca. Nitrosotaleaceae AOA activity was non-significant. Within Nitrososphaerales AOA, community composition differed based on the fertilisation history, with Nitrososphaerales C11 only representing a low proportion of the community. This study revealed that long-term soil fertilisation selects for different acidophilic nitrifier communities, potentially through soil pH change or through direct effect of nitrogen, potassium and phosphorus. Comparative community composition among the differently fertilised soils also highlighted the existence of AOA phylotypes with different levels of stability to environmental changes, contributing to the understanding of high AOA diversity maintenance in terrestrial ecosystems

AB - Ammonia oxidising archaea (AOA) are ecologically important nitrifiers in acidic agricultural soils. Two AOA phylogenetic clades, belonging to order-level lineages of Nitrososphaerales (clade C11; also classified as NS-Gamma-2.3.2) and family-level lineage of Candidatus Nitrosotaleaceae (clade C14; NT-Alpha-1.1.1), usually dominate AOA population in low pH soils. This study aimed to investigate the effect of different fertilisation histories on community composition and activity of acidophilic AOA in soils. High-throughput sequencing of ammonia monooxygenase gene (amoA) was performed on six low pH agricultural plots originating from the same soil but amended with different types of fertilisers for over 20 years and nitrification rates in those soils were measured. In these fertilised acidic soils, nitrification was likely dominated by Nitrososphaerales AOA and ammonia-oxidising bacteria, while Ca. Nitrosotaleaceae AOA activity was non-significant. Within Nitrososphaerales AOA, community composition differed based on the fertilisation history, with Nitrososphaerales C11 only representing a low proportion of the community. This study revealed that long-term soil fertilisation selects for different acidophilic nitrifier communities, potentially through soil pH change or through direct effect of nitrogen, potassium and phosphorus. Comparative community composition among the differently fertilised soils also highlighted the existence of AOA phylotypes with different levels of stability to environmental changes, contributing to the understanding of high AOA diversity maintenance in terrestrial ecosystems

U2 - 10.1007/s00248-021-01763-2

DO - 10.1007/s00248-021-01763-2

M3 - Article

SN - 0095-3628

VL - 83

SP - 424

EP - 435

JO - Microbial Ecology

JF - Microbial Ecology

ER -

Long-Term Adaptation of Acidophilic Archaeal Ammonia Oxidisers Following Different Soil Fertilisation Histories

Abstract

Bibliographical note

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