Linking 16S rRNA Gene Classification to <i>amoA</i> Gene Taxonomy Reveals Environmental Distribution of Ammonia-Oxidizing Archaeal Clades in Peatland Soils

Abstract

A highly resolved taxonomy for ammonia-oxidizing archaea (AOA) based on the alpha subunit of ammonia monooxygenase (<i>amoA</i>) was recently established, which uncovered novel environmental patterns of AOA, challenging previous generalizations. However, many microbiome studies target the 16S rRNA gene as a marker; thus, the usage of this novel taxonomy is currently limited. Here, we exploited the phylogenetic congruence of archaeal <i>amoA</i> and 16S rRNA genes to link 16S rRNA gene classification to the novel <i>amoA</i> taxonomy. We screened publicly available archaeal genomes and contigs for the co-occurring <i>amoA</i> and 16S rRNA genes and constructed a 16S rRNA gene database with the corresponding <i>amoA</i> clade taxonomy. Phylogenetic trees of both marker genes confirmed congruence, enabling the identification of clades. We validated this approach with 16S rRNA gene amplicon data from peatland soils. We succeeded in linking 16S rRNA gene amplicon sequence variants belonging to the class <i>Nitrososphaeria</i> to seven different AOA (<i>amoA</i>) clades, including two of the most frequently detected clades (<i>Nitrososphaerales</i> γ and δ clades) for which no pure culture is currently available. Water status significantly impacted the distribution of the AOA clades as well as the whole AOA community structure, which was correlated with pH, nitrate, and ammonium, consistent with previous clade predictions. Our study emphasizes the need to distinguish among AOA clades with distinct ecophysiologies and environmental preferences, for a better understanding of the ecology of the globally abundant AOA. <b>IMPORTANCE</b> The recently established phylogeny of <i>amoA</i> provides a finer resolution than previous studies, allowing clustering of AOA beyond the order level and thus revealing novel clades. While the 16S rRNA gene is mostly appreciated in microbiome studies, this novel phylogeny is in limited use. Here, we provide an alternative path to identifying AOA with this novel and highly resolved <i>amoA</i> taxonomy by using 16S rRNA gene sequencing data. We constructed a 16S rRNA gene database with the associated <i>amoA</i> clade taxonomy based on their phylogenetic congruence. With this database, we were able to assign 16S rRNA gene amplicons from peatland soils to different AOA clades, with a level of resolution provided previously only by <i>amoA</i> phylogeny. As 16S rRNA gene amplicon sequencing is still widely employed in microbiome studies, our database may have a broad application for interpreting the ecology of globally abundant AOA.