The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria

Graeme W Nicol, Sven Leininger, Christa Schleper, James I Prosser

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983 Citations (Scopus)


Autotrophic ammonia oxidation occurs in acid soils, even though laboratory cultures of isolated ammonia oxidizing bacteria fail to grow below neutral pH. To investigate whether archaea possessing ammonia monooxygenase genes were responsible for autotrophic nitrification in acid soils, the community structure and phylogeny of ammonia oxidizing bacteria and archaea were determined across a soil pH gradient (4.9-7.5) by amplifying 16S rRNA and amoA genes followed by denaturing gradient gel electrophoresis (DGGE) and sequence analysis. The structure of both communities changed with soil pH, with distinct populations in acid and neutral soils. Phylogenetic reconstructions of crenarchaeal 16S rRNA and amoA genes confirmed selection of distinct lineages within the pH gradient and high similarity in phylogenies indicated a high level of congruence between 16S rRNA and amoA genes. The abundance of archaeal and bacterial amoA gene copies and mRNA transcripts contrasted across the pH gradient. Archaeal amoA gene and transcript abundance decreased with increasing soil pH, while bacterial amoA gene abundance was generally lower and transcripts increased with increasing pH. Short-term activity was investigated by DGGE analysis of gene transcripts in microcosms containing acidic or neutral soil or mixed soil with pH readjusted to that of native soils. Although mixed soil microcosms contained identical archaeal ammonia oxidizer communities, those adapted to acidic or neutral pH ranges showed greater relative activity at their native soil pH. Findings indicate that different bacterial and archaeal ammonia oxidizer phylotypes are selected in soils of different pH and that these differences in community structure and abundances are reflected in different contributions to ammonia oxidizer activity. They also suggest that both groups of ammonia oxidizers have distinct physiological characteristics and ecological niches, with consequences for nitrification in acid soils.
Original languageEnglish
Pages (from-to)2966-2978
Number of pages13
JournalEnvironmental Microbiology
Issue number11
Early online date14 Aug 2008
Publication statusPublished - Nov 2008


  • Ammonia
  • Archaeal Proteins
  • Bacteria
  • Bacterial Physiological Phenomena
  • Bacterial Proteins
  • Biodiversity
  • Cluster Analysis
  • Crenarchaeota
  • DNA Fingerprinting
  • Electrophoresis, Polyacrylamide Gel
  • Hydrogen-Ion Concentration
  • Molecular Sequence Data
  • Nitrites
  • Nucleic Acid Denaturation
  • Oxidation-Reduction
  • Oxidoreductases
  • RNA, Archaeal
  • RNA, Bacterial
  • RNA, Ribosomal, 16S
  • Sequence Analysis, DNA
  • Soil Microbiology
  • Transcription, Genetic


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