Comparative Analysis of 16S rRNA andamoAGenes from Archaea Selected with Organic and Inorganic Amendments in Enrichment Culture

Abstract

ABSTRACTWe 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 andamoAgenes indicated that specific archaeal clades were selected under different conditions. ThreeamoAsequence 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 correspondingamoAgene. TheamoA-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 ofamoAgene abundance and expression, together with nitrification-coupled 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, althoughamoA-containing group 1.1a archaea were present in enrichments, we detected neither expression ofamoAgenes 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.