Bacterivorous nematodes are important grazers in the soil micro‐food web. Their trophic regulation shapes the composition and ecosystem services of the soil microbiome, but the underlying population dynamics of bacteria and archaea are poorly understood. We followed soil respiration and 221 dominant bacterial and archaeal 16S rRNA gene amplicon sequencing variants (ASVs) in response to top‐down control by a common bacterivorou...

Summary Ammonia released during organic matter mineralization is converted during nitrification to nitrate. We followed spatiotemporal dynamics of the nitrifying microbial community in deep oligotrophic Lake Constance. Depth‐dependent decrease of total ammonium (0.01–0.84 μM) indicated the hypolimnion as the major place of nitrification with 15 N‐isotope dilution measurements indicating a threefold daily turnover of hypolimnet...

Summary Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus ( Ca . N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca . Nitrosotalea s...

Summary Genes encoding dissimilatory sulfite reductase ( DsrAB ) are commonly used as diagnostic markers in ecological studies of sulfite‐ and sulfate‐reducing microorganisms. Here, we developed new high‐coverage primer sets for generation of reductive bacterial‐type dsrA and dsrB polymerase chain reaction ( PCR ) products for highly parallel amplicon sequencing and a bioinformatics workflow for processing and taxonomic classi...

Summary N itrospira are the most widespread and diverse known nitrite‐oxidizing bacteria and key nitrifiers in natural and engineered ecosystems. Nevertheless, their ecophysiology and environmental distribution are understudied because of the recalcitrance of N itrospira to cultivation and the lack of a molecular functional marker, which would allow the detection of N itrospira in the environment. Here we introduce nxrB , the...

Summary Ammonia‐oxidizing archaea (AOA) play an important 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 clusters and one newly identified major cluster. These clusters, for w...

Summary Reductive acetogenesis is an important metabolic process in the hindgut of wood‐feeding termites. We analysed diversity and expression profiles of the bacterial fhs gene, a marker gene encoding a key enzyme of reductive acetogenesis, formyl tetrahydrofolate synthetase (FTHFS), to identify the active homoacetogenic populations in representatives of three different termite families. Clone libraries of polymerase chain re...