Thaumarchaeal ammonia oxidation in an acidic forest peat soil is not influenced by ammonium amendment

Nejc Stopnisek, Cécile Gubry-Rangin, Spela Höfferle, Graeme W Nicol, Ines Mandic-Mulec, James I Prosser

Research output: Contribution to journalArticle

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Abstract

Both bacteria and thaumarchaea contribute to ammonia oxidation, the first step in nitrification. The abundance of putative ammonia oxidizers is estimated by quantification of the functional gene amoA, which encodes ammonia monooxygenase subunit A. In soil, thaumarchaeal amoA genes often outnumber the equivalent bacterial genes. Ecophysiological studies indicate that thaumarchaeal ammonia oxidizers may have a selective advantage at low ammonia concentrations, with potential adaptation to soils in which mineralization is the major source of ammonia. To test this hypothesis, thaumarchaeal and bacterial ammonia oxidizers were investigated during nitrification in microcosms containing an organic, acidic forest peat soil (pH 4.1) with a low ammonium concentration but high potential for ammonia release during mineralization. Net nitrification rates were high but were not influenced by addition of ammonium. Bacterial amoA genes could not be detected, presumably because of low abundance of bacterial ammonia oxidizers. Phylogenetic analysis of thaumarchaeal 16S rRNA gene sequences indicated that dominant populations belonged to group 1.1c, 1.3, and "deep peat" lineages, while known amo-containing lineages (groups 1.1a and 1.1b) comprised only a small proportion of the total community. Growth of thaumarchaeal ammonia oxidizers was indicated by increased abundance of amoA genes during nitrification but was unaffected by addition of ammonium. Similarly, denaturing gradient gel electrophoresis analysis of amoA gene transcripts demonstrated small temporal changes in thaumarchaeal ammonia oxidizer communities but no effect of ammonium amendment. Thaumarchaea therefore appeared to dominate ammonia oxidation in this soil and oxidized ammonia arising from mineralization of organic matter rather than added inorganic nitrogen.
Original languageEnglish
Pages (from-to)7626-7634
Number of pages9
JournalApplied and Environmental Microbiology
Volume76
Issue number22
Early online date1 Oct 2010
DOIs
Publication statusPublished - Nov 2010

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peat soils
peat soil
Ammonium Compounds
Ammonia
forest soils
forest soil
ammonia
Soil
ammonium
oxidation
oxidants
Nitrification
nitrification
gene
Bacterial Genes
mineralization
genes
Genes
Forests
soil

Keywords

  • archaea
  • bacteria
  • cluster analysis
  • DNA, archaeal
  • DNA, bacterial
  • DNA, ribosomal
  • molecular sequence data
  • nitrification
  • oxidation-reduction
  • oxidoreductases
  • phylogeny
  • quaternary ammonium compounds
  • RNA, ribosomal, 16S
  • sequence analysis, DNA
  • soil
  • soil microbiology
  • trees

Cite this

Thaumarchaeal ammonia oxidation in an acidic forest peat soil is not influenced by ammonium amendment. / Stopnisek, Nejc; Gubry-Rangin, Cécile; Höfferle, Spela; Nicol, Graeme W; Mandic-Mulec, Ines; Prosser, James I.

In: Applied and Environmental Microbiology, Vol. 76, No. 22, 11.2010, p. 7626-7634.

Research output: Contribution to journalArticle

Stopnisek, Nejc ; Gubry-Rangin, Cécile ; Höfferle, Spela ; Nicol, Graeme W ; Mandic-Mulec, Ines ; Prosser, James I. / Thaumarchaeal ammonia oxidation in an acidic forest peat soil is not influenced by ammonium amendment. In: Applied and Environmental Microbiology. 2010 ; Vol. 76, No. 22. pp. 7626-7634.
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abstract = "Both bacteria and thaumarchaea contribute to ammonia oxidation, the first step in nitrification. The abundance of putative ammonia oxidizers is estimated by quantification of the functional gene amoA, which encodes ammonia monooxygenase subunit A. In soil, thaumarchaeal amoA genes often outnumber the equivalent bacterial genes. Ecophysiological studies indicate that thaumarchaeal ammonia oxidizers may have a selective advantage at low ammonia concentrations, with potential adaptation to soils in which mineralization is the major source of ammonia. To test this hypothesis, thaumarchaeal and bacterial ammonia oxidizers were investigated during nitrification in microcosms containing an organic, acidic forest peat soil (pH 4.1) with a low ammonium concentration but high potential for ammonia release during mineralization. Net nitrification rates were high but were not influenced by addition of ammonium. Bacterial amoA genes could not be detected, presumably because of low abundance of bacterial ammonia oxidizers. Phylogenetic analysis of thaumarchaeal 16S rRNA gene sequences indicated that dominant populations belonged to group 1.1c, 1.3, and {"}deep peat{"} lineages, while known amo-containing lineages (groups 1.1a and 1.1b) comprised only a small proportion of the total community. Growth of thaumarchaeal ammonia oxidizers was indicated by increased abundance of amoA genes during nitrification but was unaffected by addition of ammonium. Similarly, denaturing gradient gel electrophoresis analysis of amoA gene transcripts demonstrated small temporal changes in thaumarchaeal ammonia oxidizer communities but no effect of ammonium amendment. Thaumarchaea therefore appeared to dominate ammonia oxidation in this soil and oxidized ammonia arising from mineralization of organic matter rather than added inorganic nitrogen.",
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T1 - Thaumarchaeal ammonia oxidation in an acidic forest peat soil is not influenced by ammonium amendment

AU - Stopnisek, Nejc

AU - Gubry-Rangin, Cécile

AU - Höfferle, Spela

AU - Nicol, Graeme W

AU - Mandic-Mulec, Ines

AU - Prosser, James I

PY - 2010/11

Y1 - 2010/11

N2 - Both bacteria and thaumarchaea contribute to ammonia oxidation, the first step in nitrification. The abundance of putative ammonia oxidizers is estimated by quantification of the functional gene amoA, which encodes ammonia monooxygenase subunit A. In soil, thaumarchaeal amoA genes often outnumber the equivalent bacterial genes. Ecophysiological studies indicate that thaumarchaeal ammonia oxidizers may have a selective advantage at low ammonia concentrations, with potential adaptation to soils in which mineralization is the major source of ammonia. To test this hypothesis, thaumarchaeal and bacterial ammonia oxidizers were investigated during nitrification in microcosms containing an organic, acidic forest peat soil (pH 4.1) with a low ammonium concentration but high potential for ammonia release during mineralization. Net nitrification rates were high but were not influenced by addition of ammonium. Bacterial amoA genes could not be detected, presumably because of low abundance of bacterial ammonia oxidizers. Phylogenetic analysis of thaumarchaeal 16S rRNA gene sequences indicated that dominant populations belonged to group 1.1c, 1.3, and "deep peat" lineages, while known amo-containing lineages (groups 1.1a and 1.1b) comprised only a small proportion of the total community. Growth of thaumarchaeal ammonia oxidizers was indicated by increased abundance of amoA genes during nitrification but was unaffected by addition of ammonium. Similarly, denaturing gradient gel electrophoresis analysis of amoA gene transcripts demonstrated small temporal changes in thaumarchaeal ammonia oxidizer communities but no effect of ammonium amendment. Thaumarchaea therefore appeared to dominate ammonia oxidation in this soil and oxidized ammonia arising from mineralization of organic matter rather than added inorganic nitrogen.

AB - Both bacteria and thaumarchaea contribute to ammonia oxidation, the first step in nitrification. The abundance of putative ammonia oxidizers is estimated by quantification of the functional gene amoA, which encodes ammonia monooxygenase subunit A. In soil, thaumarchaeal amoA genes often outnumber the equivalent bacterial genes. Ecophysiological studies indicate that thaumarchaeal ammonia oxidizers may have a selective advantage at low ammonia concentrations, with potential adaptation to soils in which mineralization is the major source of ammonia. To test this hypothesis, thaumarchaeal and bacterial ammonia oxidizers were investigated during nitrification in microcosms containing an organic, acidic forest peat soil (pH 4.1) with a low ammonium concentration but high potential for ammonia release during mineralization. Net nitrification rates were high but were not influenced by addition of ammonium. Bacterial amoA genes could not be detected, presumably because of low abundance of bacterial ammonia oxidizers. Phylogenetic analysis of thaumarchaeal 16S rRNA gene sequences indicated that dominant populations belonged to group 1.1c, 1.3, and "deep peat" lineages, while known amo-containing lineages (groups 1.1a and 1.1b) comprised only a small proportion of the total community. Growth of thaumarchaeal ammonia oxidizers was indicated by increased abundance of amoA genes during nitrification but was unaffected by addition of ammonium. Similarly, denaturing gradient gel electrophoresis analysis of amoA gene transcripts demonstrated small temporal changes in thaumarchaeal ammonia oxidizer communities but no effect of ammonium amendment. Thaumarchaea therefore appeared to dominate ammonia oxidation in this soil and oxidized ammonia arising from mineralization of organic matter rather than added inorganic nitrogen.

KW - archaea

KW - bacteria

KW - cluster analysis

KW - DNA, archaeal

KW - DNA, bacterial

KW - DNA, ribosomal

KW - molecular sequence data

KW - nitrification

KW - oxidation-reduction

KW - oxidoreductases

KW - phylogeny

KW - quaternary ammonium compounds

KW - RNA, ribosomal, 16S

KW - sequence analysis, DNA

KW - soil

KW - soil microbiology

KW - trees

U2 - 10.1128/AEM.00595-10

DO - 10.1128/AEM.00595-10

M3 - Article

C2 - 20889787

VL - 76

SP - 7626

EP - 7634

JO - Applied and Environmental Microbiology

JF - Applied and Environmental Microbiology

SN - 0099-2240

IS - 22

ER -