High pH-enhanced soil nitrification was associated with ammonia-oxidizing bacteria rather than archaea in acidic soils

Jing Che, Xue Qiang Zhao, Xue Zhou, Zhong Jun Jia, Ren Fang Shen

Research output: Contribution to journalArticle

33 Citations (Scopus)

Abstract

The integrated effects of environmental factors on soil nitrification are largely unknown. Here, we performed a microcosm experiment to investigate the interactive effects of pH and NH4+ on nitrification activity in two acidic soils with different land use patterns (Anhui soil, a forest soil; Jiangxi soil, a brush land soil). Both soils were incubated under native pH and CaCO3-manipulated pH in the presence or absence of added ammonium for 60 days. The addition of CaCO3 alone did not change the nitrification activity of either soil. Ammonium addition stimulated nitrification in Anhui soil, but not in Jiangxi soil, and this stimulation was more pronounced with increased CaCO3. The ammonia monooxygenase (amoA) gene copy number of both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) was much higher in Anhui soil than in Jiangxi soil. The amoA gene copy number of AOB in Anhui soil was more highly upregulated under CaCO3+NH4+ than NH4+ during incubation. In Anhui soil, changes in the denaturing gradient gel electrophoresis (DGGE) fingerprint patterns of bacterial amoA genes were parallel to changes in the amoA gene copy number of AOB. In Jiangxi soil, DGGE could not be performed because the PCR for bacterial DGGE did not yield any products, while quantitative PCR revealed that the amoA gene copy number of AOB changed during incubation. These results suggest that AOB plays an important role in CaCO3-enhanced nitrification of Anhui soil with ammonium addition. The low nitrification rates of Jiangxi soil regardless of CaCO3 with or without NH4+ supply may be ascribed to the lower activity of both AOB and AOA, especially AOA.

Original languageEnglish
Pages (from-to)21-29
Number of pages9
JournalApplied Soil Ecology
Volume85
DOIs
Publication statusPublished - Sep 3 2014
Externally publishedYes

Fingerprint

Nitrification
Archaea
Ammonia
nitrification
acid soils
ammonia
Soil
Bacteria
bacterium
bacteria
China
soil
gene dosage
Gene Dosage
Denaturing Gradient Gel Electrophoresis
denaturing gradient gel electrophoresis
gene
Ammonium Compounds
electrokinesis
ammonium

Keywords

  • Ammonium
  • AmoA
  • CaCO
  • Denaturing gradient gel electrophoresis
  • Soil pH

ASJC Scopus subject areas

  • Soil Science
  • Ecology
  • Agricultural and Biological Sciences (miscellaneous)

Cite this

High pH-enhanced soil nitrification was associated with ammonia-oxidizing bacteria rather than archaea in acidic soils. / Che, Jing; Zhao, Xue Qiang; Zhou, Xue; Jia, Zhong Jun; Shen, Ren Fang.

In: Applied Soil Ecology, Vol. 85, 03.09.2014, p. 21-29.

Research output: Contribution to journalArticle

Che, Jing ; Zhao, Xue Qiang ; Zhou, Xue ; Jia, Zhong Jun ; Shen, Ren Fang. / High pH-enhanced soil nitrification was associated with ammonia-oxidizing bacteria rather than archaea in acidic soils. In: Applied Soil Ecology. 2014 ; Vol. 85. pp. 21-29.
@article{69379cda8ac94e369c7b483b9c4c7170,
title = "High pH-enhanced soil nitrification was associated with ammonia-oxidizing bacteria rather than archaea in acidic soils",
abstract = "The integrated effects of environmental factors on soil nitrification are largely unknown. Here, we performed a microcosm experiment to investigate the interactive effects of pH and NH4+ on nitrification activity in two acidic soils with different land use patterns (Anhui soil, a forest soil; Jiangxi soil, a brush land soil). Both soils were incubated under native pH and CaCO3-manipulated pH in the presence or absence of added ammonium for 60 days. The addition of CaCO3 alone did not change the nitrification activity of either soil. Ammonium addition stimulated nitrification in Anhui soil, but not in Jiangxi soil, and this stimulation was more pronounced with increased CaCO3. The ammonia monooxygenase (amoA) gene copy number of both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) was much higher in Anhui soil than in Jiangxi soil. The amoA gene copy number of AOB in Anhui soil was more highly upregulated under CaCO3+NH4+ than NH4+ during incubation. In Anhui soil, changes in the denaturing gradient gel electrophoresis (DGGE) fingerprint patterns of bacterial amoA genes were parallel to changes in the amoA gene copy number of AOB. In Jiangxi soil, DGGE could not be performed because the PCR for bacterial DGGE did not yield any products, while quantitative PCR revealed that the amoA gene copy number of AOB changed during incubation. These results suggest that AOB plays an important role in CaCO3-enhanced nitrification of Anhui soil with ammonium addition. The low nitrification rates of Jiangxi soil regardless of CaCO3 with or without NH4+ supply may be ascribed to the lower activity of both AOB and AOA, especially AOA.",
keywords = "Ammonium, AmoA, CaCO, Denaturing gradient gel electrophoresis, Soil pH",
author = "Jing Che and Zhao, {Xue Qiang} and Xue Zhou and Jia, {Zhong Jun} and Shen, {Ren Fang}",
year = "2014",
month = "9",
day = "3",
doi = "10.1016/j.apsoil.2014.09.003",
language = "English",
volume = "85",
pages = "21--29",
journal = "Applied Soil Ecology",
issn = "0929-1393",
publisher = "Elsevier",

}

TY - JOUR

T1 - High pH-enhanced soil nitrification was associated with ammonia-oxidizing bacteria rather than archaea in acidic soils

AU - Che, Jing

AU - Zhao, Xue Qiang

AU - Zhou, Xue

AU - Jia, Zhong Jun

AU - Shen, Ren Fang

PY - 2014/9/3

Y1 - 2014/9/3

N2 - The integrated effects of environmental factors on soil nitrification are largely unknown. Here, we performed a microcosm experiment to investigate the interactive effects of pH and NH4+ on nitrification activity in two acidic soils with different land use patterns (Anhui soil, a forest soil; Jiangxi soil, a brush land soil). Both soils were incubated under native pH and CaCO3-manipulated pH in the presence or absence of added ammonium for 60 days. The addition of CaCO3 alone did not change the nitrification activity of either soil. Ammonium addition stimulated nitrification in Anhui soil, but not in Jiangxi soil, and this stimulation was more pronounced with increased CaCO3. The ammonia monooxygenase (amoA) gene copy number of both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) was much higher in Anhui soil than in Jiangxi soil. The amoA gene copy number of AOB in Anhui soil was more highly upregulated under CaCO3+NH4+ than NH4+ during incubation. In Anhui soil, changes in the denaturing gradient gel electrophoresis (DGGE) fingerprint patterns of bacterial amoA genes were parallel to changes in the amoA gene copy number of AOB. In Jiangxi soil, DGGE could not be performed because the PCR for bacterial DGGE did not yield any products, while quantitative PCR revealed that the amoA gene copy number of AOB changed during incubation. These results suggest that AOB plays an important role in CaCO3-enhanced nitrification of Anhui soil with ammonium addition. The low nitrification rates of Jiangxi soil regardless of CaCO3 with or without NH4+ supply may be ascribed to the lower activity of both AOB and AOA, especially AOA.

AB - The integrated effects of environmental factors on soil nitrification are largely unknown. Here, we performed a microcosm experiment to investigate the interactive effects of pH and NH4+ on nitrification activity in two acidic soils with different land use patterns (Anhui soil, a forest soil; Jiangxi soil, a brush land soil). Both soils were incubated under native pH and CaCO3-manipulated pH in the presence or absence of added ammonium for 60 days. The addition of CaCO3 alone did not change the nitrification activity of either soil. Ammonium addition stimulated nitrification in Anhui soil, but not in Jiangxi soil, and this stimulation was more pronounced with increased CaCO3. The ammonia monooxygenase (amoA) gene copy number of both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) was much higher in Anhui soil than in Jiangxi soil. The amoA gene copy number of AOB in Anhui soil was more highly upregulated under CaCO3+NH4+ than NH4+ during incubation. In Anhui soil, changes in the denaturing gradient gel electrophoresis (DGGE) fingerprint patterns of bacterial amoA genes were parallel to changes in the amoA gene copy number of AOB. In Jiangxi soil, DGGE could not be performed because the PCR for bacterial DGGE did not yield any products, while quantitative PCR revealed that the amoA gene copy number of AOB changed during incubation. These results suggest that AOB plays an important role in CaCO3-enhanced nitrification of Anhui soil with ammonium addition. The low nitrification rates of Jiangxi soil regardless of CaCO3 with or without NH4+ supply may be ascribed to the lower activity of both AOB and AOA, especially AOA.

KW - Ammonium

KW - AmoA

KW - CaCO

KW - Denaturing gradient gel electrophoresis

KW - Soil pH

UR - http://www.scopus.com/inward/record.url?scp=84907270523&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84907270523&partnerID=8YFLogxK

U2 - 10.1016/j.apsoil.2014.09.003

DO - 10.1016/j.apsoil.2014.09.003

M3 - Article

VL - 85

SP - 21

EP - 29

JO - Applied Soil Ecology

JF - Applied Soil Ecology

SN - 0929-1393

ER -