Liming enhances the abundance and stability of nitrogen-cycling microbes: the buffering effect of long-term lime application

Akari Mitsuta; Késia Silva Lourenço; Jingjing Chang; Mart Ros; René Schils; Yoshitaka Uchida; Eiko Eurya Kuramae

doi:10.1007/s00374-025-01889-2

Liming enhances the abundance and stability of nitrogen-cycling microbes: the buffering effect of long-term lime application

Akari Mitsuta, Késia Silva Lourenço, Jingjing Chang, Mart Ros, René Schils, Yoshitaka Uchida, Eiko Eurya Kuramae^*

^*Corresponding author for this work

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

Abstract

Lime application (liming) has historically been used to ameliorate soil acidity in grasslands. Liming effectively improves soil pH, plant productivity, and soil physicochemical properties, but the long-term impact of acidity control by liming on key microbial nitrogen (N)-cycling genes in semi-natural grasslands is unknown. We investigated the effect of 65 years of liming on N-cycling processes in the limed and control plots of the Ossekampen long-term grassland experiment in the Netherlands. These plots have not received any other fertilizers for 65 years. Soil sampling and nitrous oxide (N₂O) emission measurements were conducted three times in spring and four times in summer, and quantitative real-time PCR was performed to determine the absolute abundances of N-cycling genes, including ammonia-oxidation (amoA-AOB, amoA-AOA, amoA-comammox), denitrification (nirS, nirK, nosZ), nitrate ammonification (nrfA), and N-fixation (nifH) genes. Long-term liming increased the absolute abundances of nitrifiers, denitrifiers, and nitrate ammonifiers. Soil N₂O emissions did not differ significantly between liming and control treatments. Additionally, liming had a buffering effect that maintained the population of N-cycling microbes against seasonal variations in abundance. Our results indicate that improving soil acidity through liming potentially facilitates microbial N-cycling processes without increasing N₂O emissions.

Original language	English
Pages (from-to)	761-772
Number of pages	12
Journal	Biology and Fertility of Soils
Volume	61
Issue number	4
Early online date	2025
DOIs	https://doi.org/10.1007/s00374-025-01889-2
Publication status	Published - May 2025

Bibliographical note

Publisher Copyright:
© The Author(s) 2025.

Funding

The first author was supported by JSPS KAKENHI (grant number 21J22147) and the JSPS Overseas Challenge Program for Young Researchers. The authors would like to acknowledge fundings from the Top Consortium for Knowledge and Innovation (project number TU 17008 TKI), and the Wageningen University Knowledge Base program: KB36 Biodiversity in a Nature Inclusive Society (project number KB36-004-014) - that is supported by finance from the Dutch Ministry of Agriculture, Nature and Food Quality. The authors thank Ji Li and Shuaimin Chen for their assistance with field sampling, and Agata S. Pijl for molecular laboratory technical assistance.

Funders	Funder number
Ministerie van Landbouw, Natuur en Voedselkwaliteit
Japan Society for the Promotion of Science	21J22147
Topconsortium voor Kennis en Innovatie	TU 17008 TKI
Nature Inclusive Society	KB36-004-014

Keywords

Denitrification
Grassland
Limestone
N-fixation
Nitrate ammonification
Nitrification
Nitrogen

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Cite this

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title = "Liming enhances the abundance and stability of nitrogen-cycling microbes: the buffering effect of long-term lime application",

abstract = "Lime application (liming) has historically been used to ameliorate soil acidity in grasslands. Liming effectively improves soil pH, plant productivity, and soil physicochemical properties, but the long-term impact of acidity control by liming on key microbial nitrogen (N)-cycling genes in semi-natural grasslands is unknown. We investigated the effect of 65 years of liming on N-cycling processes in the limed and control plots of the Ossekampen long-term grassland experiment in the Netherlands. These plots have not received any other fertilizers for 65 years. Soil sampling and nitrous oxide (N2O) emission measurements were conducted three times in spring and four times in summer, and quantitative real-time PCR was performed to determine the absolute abundances of N-cycling genes, including ammonia-oxidation (amoA-AOB, amoA-AOA, amoA-comammox), denitrification (nirS, nirK, nosZ), nitrate ammonification (nrfA), and N-fixation (nifH) genes. Long-term liming increased the absolute abundances of nitrifiers, denitrifiers, and nitrate ammonifiers. Soil N2O emissions did not differ significantly between liming and control treatments. Additionally, liming had a buffering effect that maintained the population of N-cycling microbes against seasonal variations in abundance. Our results indicate that improving soil acidity through liming potentially facilitates microbial N-cycling processes without increasing N2O emissions.",

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AU - Mitsuta, Akari

AU - Lourenço, Késia Silva

AU - Chang, Jingjing

AU - Ros, Mart

AU - Schils, René

AU - Uchida, Yoshitaka

AU - Kuramae, Eiko Eurya

N1 - Publisher Copyright: © The Author(s) 2025.

PY - 2025/5

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ER -

Liming enhances the abundance and stability of nitrogen-cycling microbes: the buffering effect of long-term lime application

Abstract

Bibliographical note

Funding

Keywords

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