The application of high-throughput sequencing technology to analysis of amoA phylogeny and environmental niche specialisation of terrestrial bacterial ammonia-oxidisers

Axel Aigle, James I. Prosser, Cécile Gubry-Rangin (Corresponding Author)

Research output: Contribution to journalArticle

Abstract

Characterisation of microbial communities increasingly involves use of high throughput sequencing methods (e.g. MiSeq Illumina) that amplify relatively short sequences of 16S rRNA or functional genes, the latter including ammonia monooxygenase subunit A (amoA), a key functional gene for ammonia oxidising bacteria (AOB) and archaea (AOA). The availability of these techniques, in combination with developments in phylogenetic methodology, provides the potential for better analysis of microbial niche specialisation. This study aimed to develop an approach for sequencing of bacterial and archaeal amoA genes amplified from soil using bioinformatics pipelines developed for general analysis of functional genes and employed sequence data to reassess phylogeny and niche specialisation in terrestrial bacterial ammonia oxidisers.
Original languageEnglish
Article number3
JournalEnvironmental Microbiome
Volume14
Early online date4 Jul 2019
DOIs
Publication statusE-pub ahead of print - 4 Jul 2019

Fingerprint

oxidants
niches
ammonia
phylogeny
genes
Archaea
bioinformatics
microbial communities
methodology
ribosomal RNA
ammonia monooxygenase
bacteria
soil

Keywords

  • nitrification
  • amoA
  • 16S rRNA
  • Archaea
  • bacteria
  • Illumina MiSeq
  • pH
  • Nitrification
  • Bacteria

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Genetics
  • Microbiology

Cite this

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title = "The application of high-throughput sequencing technology to analysis of amoA phylogeny and environmental niche specialisation of terrestrial bacterial ammonia-oxidisers",
abstract = "Characterisation of microbial communities increasingly involves use of high throughput sequencing methods (e.g. MiSeq Illumina) that amplify relatively short sequences of 16S rRNA or functional genes, the latter including ammonia monooxygenase subunit A (amoA), a key functional gene for ammonia oxidising bacteria (AOB) and archaea (AOA). The availability of these techniques, in combination with developments in phylogenetic methodology, provides the potential for better analysis of microbial niche specialisation. This study aimed to develop an approach for sequencing of bacterial and archaeal amoA genes amplified from soil using bioinformatics pipelines developed for general analysis of functional genes and employed sequence data to reassess phylogeny and niche specialisation in terrestrial bacterial ammonia oxidisers.",
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author = "Axel Aigle and Prosser, {James I.} and C{\'e}cile Gubry-Rangin",
note = "AA was supported by a Natural Environmental Research Council grant (NE/L006286/1) and CGR by a Royal Society University Research Fellowship (UF150571).",
year = "2019",
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T1 - The application of high-throughput sequencing technology to analysis of amoA phylogeny and environmental niche specialisation of terrestrial bacterial ammonia-oxidisers

AU - Aigle, Axel

AU - Prosser, James I.

AU - Gubry-Rangin, Cécile

N1 - AA was supported by a Natural Environmental Research Council grant (NE/L006286/1) and CGR by a Royal Society University Research Fellowship (UF150571).

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Y1 - 2019/7/4

N2 - Characterisation of microbial communities increasingly involves use of high throughput sequencing methods (e.g. MiSeq Illumina) that amplify relatively short sequences of 16S rRNA or functional genes, the latter including ammonia monooxygenase subunit A (amoA), a key functional gene for ammonia oxidising bacteria (AOB) and archaea (AOA). The availability of these techniques, in combination with developments in phylogenetic methodology, provides the potential for better analysis of microbial niche specialisation. This study aimed to develop an approach for sequencing of bacterial and archaeal amoA genes amplified from soil using bioinformatics pipelines developed for general analysis of functional genes and employed sequence data to reassess phylogeny and niche specialisation in terrestrial bacterial ammonia oxidisers.

AB - Characterisation of microbial communities increasingly involves use of high throughput sequencing methods (e.g. MiSeq Illumina) that amplify relatively short sequences of 16S rRNA or functional genes, the latter including ammonia monooxygenase subunit A (amoA), a key functional gene for ammonia oxidising bacteria (AOB) and archaea (AOA). The availability of these techniques, in combination with developments in phylogenetic methodology, provides the potential for better analysis of microbial niche specialisation. This study aimed to develop an approach for sequencing of bacterial and archaeal amoA genes amplified from soil using bioinformatics pipelines developed for general analysis of functional genes and employed sequence data to reassess phylogeny and niche specialisation in terrestrial bacterial ammonia oxidisers.

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KW - Archaea

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KW - pH

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KW - Bacteria

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