Archaea have been shown to be ubiquitous among soil microbial communities. However, our knowledge on their diversity and spatial distribution in soil ecosystems is still limited. This study was conducted to investigate archaeal community changes along a forest soil depth profile in Unterehrendingen, Switzerland. From four consecutive soil depth layers, bulk soil DNA was extracted. Archaea-specific PCR amplification of small subunit ribosomal RNA genes (rDNA) was performed and combined with restriction fragment length polymorphism (RFLP) analysis with restriction endonuclease HaeIII [Bundt et al., Soil Biol. Biochem. 33 (2001) 729-738]. Significant changes of the RFLP fingerprints were reproducibly observed from the soil surface to 1 m depth. From the surface soil layer (0-9 cm) and the bottom soil layer (50-100 cm), libraries of PCR-amplified archaeal rDNA fragments were constructed. Screening of the libraries yielded various clones of different HaeIII RFLP types from the surface and the bottom soil layers, revealing shifts in major archaeal components along the soil depth profile. Clones of all RFLP types were sequenced and phylogenetically affiliated. These analyses revealed even more pronounced Archaea community shifts along the depth gradient. Several novel soil archaeal clusters were identified and some appeared predominantly associated to either the surface or the bottom soil layer. Euryarchaeal rDNA sequences, not yet reported from aerated soils, were found in the surface soil layer and were affiliated to the order Thermoplasmales and relatives. Novel crenarchaeal soil clusters were identified that included sequences only retrieved from the bottom soil layer. In this study, a this far unreported variety of archaeal groups was found in a forest soil ecosystem. The distinct depth-related community shift suggested the occurrence of different archaeal types that depend on environmental parameters that change along the soil depth profil
