Purpose <p>Denitrifying bacteria perform a crucial ecological process regulating nitrogen cycling and greenhouse gas emissions. However, the community assembly mechanisms of nitric oxide producing denitrifying bacteria, particularly abundant and rare communities, are poorly understood.</p> Materials and methods <p>In this study, <i>nirK</i>- and <i>nirS</i> marker genes were amplified following 16S rRNA sequencing, with the aim to identify the mechanisms shaping abundant and rare <i>nirK</i>- and <i>nirS</i>-type denitrifying bacteria in Taihu Lake sediments, particularly regarding the heterogeneity of a wide range of environmental factors.</p> Results <p>Taihu Lake sediment showed low-pollution levels of heavy metals, but with significant differences of high nutrient status. The phylogenetic diversity of <i>nirK</i>- and <i>nirS</i>-type denitrifying bacteria, and beta-diversity of abundant and rare communities were affected by a combined stressor of heavy metals and nutrients. Our results revealed that rare denitrifying bacteria had significantly higher homogeneity of dispersal than that of abundant taxa. We found heterogeneous selection was the main process governing both abundant and rare <i>nirK</i>-type denitrifying bacteria, while the abundant <i>nirS</i>-type denitrifying bacteria were mainly governed by the dispersal limitation. Complex network interactions between abundant and rare <i>nirK</i>- and <i>nirS</i>-type denitrifying bacteria were detected, further the Mantel test showed strong significant correlations between keystone denitrifying bacteria with environmental factors.</p> Conclusion <p>This study provides insights into the effects of nutrient pollution on denitrifying bacteria in lake sediment, and also enhances our understanding of community assembly mechanisms of abundant and rare <i>nirK</i>- and <i>nirS</i>-type denitrifying bacteria in lake ecosystems.</p>