Agriculture alters protein evolution of nitrogen cycling genes in soil bacteria at a global scale

Humans are the world’s greatest evolutionary force. Yet, our impacts on the evolution of Earth’s microbiomes and their biogeochemical processes remain poorly understood. Notably, the overlooked potential for the intensive use of agricultural fertiliser to drive evolutionary changes in soil nutrient cycling genes warrants urgent attention. Here, analysing >2,500 soil metagenomes from across the globe, we identify increased rates of diversifying positive selection on genes involved in the reduction of nitrate (a key component of nitrogen fertilisers) in agricultural, but not natural land systems. Altered selection on genes encoding the respiratory nitrate reductase were specific to Burkholderiales, a major group of denitrifying bacteria. We provide evidence that agriculture is driving evolution of protein regions implicated in substrate access to the enzyme’s active site, possibly resulting in increased rates of nitrate reduction. We hypothesise that increasing substrate turnover would be evolutionarily advantageous under excess nitrate availability, ultimately enhancing growth rates despite potential enzymatic trade-offs. As Burkholderiales are dominant denitrifiers globally, such evolutionary consequences of agriculture on this lineage could have cascading ecological impacts. These findings indicate that anthropogenic selection can alter protein-level evolution of vital microbial biogeochemical processes.