Intensive land use enhances soil ammonia-oxidising archaea at a continental scale

Archaea are an important group of soil organisms that play key roles in carbon and nitrogen cycling, particularly in nitrification (ammonia oxidation) and methanogenesis. However, there are knowledge gaps regarding their importance in ecosystem processes relative to other microbial groups and how they may be impacted by land-use and environmental changes. Here, by carrying out a continental-scale sample collection and utilising archaea-specific primers for metabarcoding and shotgun metagenomics, we aimed to decipher the structure and function of archaeal communities across various land-use types in Europe. Metagenomic data reveal that land-use intensification increases the relative abundance of archaea, whereas bacteria and eukaryotes show no increase. Alongside this, ammonia oxidising archaea (AOA) increase as a proportion of the total metabarcoding reads, from 1% of archaea in coniferous woodland to >90% in croplands. Functional gene profiles reveal that land-use intensification shifts archaeal communities from adaptive metabolic pathways in forests to specialised, ammonia-oxidising microbes in fertiliser-enriched cropland soils. Our data suggest that land-use intensification may shift archaeal communities toward greater dependence on external nitrogen inputs, with potential consequences for soil fertility and greenhouse gas emissions. • Land-use intensification significantly increases the relative abundance of soil archaea across Europe. • Soil pH structures archaeal communities but also modulates their roles in nitrogen cycling. • Croplands exhibit a multiple-fold increase in ammonia-oxidising archaea (AOA) compared to coniferous woodlands. • Cropland soils show AOA-dominated archaeal communities, suggesting reduced resilience to environmental stress.