1. Long-term mowing can cause morphological stuntedness of plants, thus reducing grassland productivity and exacerbating grassland degradation. Although plant microbiomes can enhance plant resistance against disturbance, considerable uncertainty exists regarding how mowing and mowing-induced plant trait plasticity affect plant microbiomes in natural grasslands.

2. Here we examined the responses of leaf/root-associated bacterial (LAB/RAB) communities of 11 dominant herbaceous perennials (six replicates per species) to a 17-year mowing treatment in a temperate grassland. We also measured leaf/root physiological and morphological traits, and analysed the relationships among mowing practice, bacterial community structures and leaf/root trait parameters.

3. We found that both leaf and root functional traits showed interspecific variations (variations across different plant species), while only the leaf traits exhibited intraspecific variation (treatment-induced variations within plant species) between the treatments. Similarly, the LAB community structure was more sensitive to mowing but less influenced by host species identity, compared to the RAB community. The RAB community structure was primarily shaped by host species identity, while mowing was a secondary influencing factor.

4. The different patterns of LAB and RAB communities in response to mowing could be specifically explained by the inter/intraspecific variations of the related leaf and root traits. The LAB community was strongly correlated with the leaf traits which exhibited mowing-induced plasticity (intraspecific variation), with the correlations with nitrogen resorption efficiency and above-ground dry weight being the greatest. The root traits were important indicators of bacterial community structure in the root compartment across the hosts, rather than between the treatments. Root tissue density showed the strongest interspecific variation, and was identified as an overwhelming driver of the RAB community. The shifts in LAB/RAB communities under mowing were largely attributed to the increased proportions of Actinobacteria. The high mowing sensitivity of the LAB community was associated with the enrichment of soil-derived Actinobacteria in leaves under mowing. Actinobacteria were also the main keystone taxa in the bacterial community networks under mowing.

5. Our results demonstrate that the magnitude of plant-associated microbial community response to long-term mowing is plant compartment and trait variation dependent, and advance our understanding of the leaf/root microbiome-trait relationships in complex plant communities.