In river sediments, nitrate is a more preferable electron sink for microbial respiration than oxygen, for its good solubility and high redox potential. Nitrate amendment has been used to accelerate oxidation of pollutants but very few studies focused on microbial dynamics during bioremediation. Here we simulated a nitrate surge and monitored the microbial responses in a sulfide-rich river sediment. Original communities were found dominated by methanogens and syntrophic bacteria, yet nitrate input enriched two chemolithotrophic denitrifiersThiobacillus and Luteimonas , in spite of abundant organic carbons there. This led to simplified community composition, function and interactive networks. Similarly, serial dilutions of sediments found that Thiobacillus thiophilu s dominated 18/30 communities because of its simultaneous nitrate reduction and sulfide oxidation. Interestingly, syntrophic bacteria and archaea performing interspecies cross-feeding rather than the dominant denitrifiers were sustaining microbial interactions. Therefore, environment perturbations that inhibit native auxotrophs will very likely disrupt original microbial interactions.