Comparative analysis of 16S rRNA and amoA Genes from archaea selected with organic and inorganic amendments in enrichment culture

Mouzhong Xu, Jon Schnorr, Brandon Keibler, Holly M. Simon

Research output: Contribution to journalArticlepeer-review

28 Scopus citations

Abstract

We took advantage of a plant-root enrichment culture system to characterize mesophilic soil archaea selected through the use of organic and inorganic amendments. Comparative analysis of 16S rRNA and amoA genes indicated that specific archaeal clades were selected under different conditions. Three amoA sequence clades were identified, while for a fourth group, identified by 16S rRNA gene analysis alone and referred to as the "root" clade, we detected no corresponding amoA gene. The amoA-containing archaea were present in media with either organic or inorganic amendments, whereas archaea representing the root clade were present only when organic amendment was used. Analysis of amoA gene abundance and expression, together with nitrificationcoupled growth assays, indicated potential growth by autotrophic ammonia oxidation for members of two group 1.1b clades. Increased abundance of one of these clades, however, also occurred upon the addition of organic amendment. Finally, although amoA-containing group 1.1a archaea were present in enrichments, we detected neither expression of amoA genes nor evidence for nitrification-coupled growth of these organisms. These data support a model of a diverse metabolic community in mesophilic soil archaea that is just beginning to be characterized.

Original languageEnglish (US)
Pages (from-to)2137-2146
Number of pages10
JournalApplied and Environmental Microbiology
Volume78
Issue number7
DOIs
StatePublished - Apr 2012

ASJC Scopus subject areas

  • Biotechnology
  • Food Science
  • Applied Microbiology and Biotechnology
  • Ecology

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