soil amoA and nxrB amplicon sequencing
amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions
Amplicon sequencing of archaeal amoA, bacterial amoA, Nitrospira nxrB, Nitrobacter nxrB in 16 soils from Namibia, Costa Rica, Austria, and Greenland and from one wastewater treatment plant.
Ammonia-oxidizing archaea (AOA) play a crucial role in nitrification and many studies exploit their amoA genes as marker for their diversity and abundance. We present an archaeal amoA consensus phylogeny based on all publicly available sequences (status June 2010) and provide evidence for the diversification of AOA into four previously recognized and one newly identified major clusters. These clusters, for which we suggest a new nomenclature, harbored 83 AOA species-level OTU (using an inferred species threshold of 85% amoA identity). 454 pyrosequencing of amoA amplicons from 16 soils sampled in Austria, Costa Rica, Greenland, and Namibia revealed that only 2% of the retrieved sequences had no database representative on the species-level and represented 30–37 additional species-level OTUs. With the exception of an acidic soil from which mostly sequences of the Nitrosotalea cluster were retrieved, all soils were dominated by amoA sequences from the Nitrososphaera cluster (also called group I.1b), showing that the previously reported AOA from the Nitrosopumilus cluster (also called group I.1a) are absent or represent minor populations in soils. AOA richness estimates on the species level ranged from 8–83 co-existing AOAs per soil. Presence/absence of amoA OTUs (97% identity level) correlated with geographic location, indicating that besides contemporary environmental conditions also dispersal limitation across different continents and/or historical environmental conditions might influence AOA biogeography in soils.