Combined effects of nitrate levels and elevated CO₂ on structure and function of wheat root microbiome

Elevated CO₂ (eCO₂) stimulates plant growth and photosynthesis, which affect root deposition. Combined with nitrate supply, these lead to altered structure and function of the root microbiome. We studied the interactions between eCO₂ and nitrate supply at different levels, on wheat-root microbiome structure and function, with an emphasis on denitrifying communities. Wheat plants were grown in a greenhouse under ambient CO₂ (400 ppm) or eCO₂ (850 ppm). Total bacterial community was quantified using qPCR with universal 16S RNA gene primers, and denitrifying genes (nirK, nirS, nosZ) levels were quantified. In addition, total microbial community function and composition in roots were analyzed by shotgun sequencing (metagenome).

Nitrate fertigation had a significant impact on structure and function of root microbiome, while CO₂ level effect was less pronounced in both cases. With increase in CO₂ level, relative abundance of Parcubacteria and Opitutales have decreased while relative abundance of Cytophagales have increased. Members of those three groups are known to support anaerobic fermentative metabolisms and are capable of reducing nitrate. With increase in CO₂ level, relative abundance of genes in denitrification pathway in the metagenome has decreased at low and medium nitrate levels and has increased in high nitrate level. In addition, negative correlation was observed between denitrification pathway and oxidative phosphorylation. Genes related to type VI secretion system have decreased with eCO₂ at all nitrate treatments. These findings may suggest that the balance between aerobic and anaerobic conditions in wheat roots is disturbed by combined effect of eCO₂ and nitrate, resulting in shift of denitrifying community.