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

Bahram, M., Lehtovirta-Morley, L., Mikryukov, V., Sveen, T. R., Grant, A., Pent, M., Hildebrand, F., Labouyrie, M., Köninger, J., Tedersoo, L., Jones, A., Panagos, P. and Orgiazzi, A. (2026) Intensive land use enhances soil ammonia-oxidising archaea at a continental scale. Soil Biology and Biochemistry, 213. ISSN 0038-0717

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Abstract

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.

Item Type:	Article
Additional Information:	Data availability: Archaeal 16S rRNA gene sequences and shotgun metagenomics sequence data have been deposited in the Sequence Read Archive (SRA) database under BioProject ID PRJNA1118194 and PRJNA1032917, respectively. Metadata for soil properties measured in LUCAS 2018 survey are available on the European Soil Data Centre (ESDAC; https://esdac.jrc.ec.europa.eu/content/soil-biodiversity-dna-eukaryotes). Funding: This work was supported by the Swedish Research Councils Formas (Grant, 2020–00807) and Vetenskapsrådet (2021–03724).
Uncontrolled Keywords:	nitrous oxide,land-use change,soil ecology,nitrification,microbial communities
Faculty \ School:	Faculty of Science > School of Biological Sciences University of East Anglia Research Groups/Centres > Theme - ClimateUEA Faculty of Science > School of Environmental Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Environmental Biology Faculty of Science > Research Groups > Centre for Ocean and Atmospheric Sciences
Depositing User:	LivePure Connector
Date Deposited:	03 Nov 2025 14:31
Last Modified:	03 Nov 2025 14:31
URI:	https://ueaeprints.uea.ac.uk/id/eprint/100876
DOI:	10.1016/j.soilbio.2025.110024

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