Community profiling and quantification of putative autotrophic thaumarchaeal communities in environmental samples

Growth of thaumarchaea with ammonia as a sole energy source has been demonstrated but their mode(s) of carbon metabolism remain uncertain, with evidence for autotrophy, heterotrophy and mixotrophy. Understanding the role played by autotrophy in thaumarchaeal growth strategies has been hindered by the lack of an adequate marker gene and PCR primers. The aim of this study was to develop PCR-based approaches to determine the prevalence of autotrophy associated with thaumarchaea. Primer pairs were designed specifically targeting hcd genes, encoding putative 4-hydroxybutyryl-CoA dehydratase, a key functional enzyme in thaumarchaeal autotrophy. Phylogenetic analysis of hcd gene sequences amplified from soils and sediments indicated the existence of environment-specific sequence clusters and hcd abundance in soil was 10(5) -10(6)  g(-1) soil, as assessed by quantitative PCR. Abundance and diversity of hcd genes were also determined in soil microcosms incubated with and without acetylene, a known inhibitor of nitrification. Nitrification was accompanied by increases in hcd gene abundance and in the relative abundance of two bands in denaturing gradient gel electrophoresis profiles. Nitrification, growth and community changes were inhibited by acetylene and the findings are consistent with active autotrophic ammonia oxidation by archaea in soil.