Unraveling the rate-limiting step in microorganisms mediate denitrification and phosphorus absorption transport processes in a highly regulated river lake system

River lake ecosystems are indispensable hubs for water transfers and flow regulation engineering, which have frequented and complex artificial hydrological regulation processes, and is tend to unstable water quality. Microorganisms usually affect these systems by driving nutrient cycling process. Thus, understanding the key biochemical rate limiting steps under highly regulated conditions was critical for water quality stability of river lake ecosystems. This study investigated how the key microorganisms and genes involving the nitrogen and phosphorus cycling contributed to the stability of water by combining 16S rRNA and metagenomic sequencing using Dongping river lake system as the case study. The results showed that nitrogen and phosphorus concentrations were significantly lower in lake zones than in river inflow and outflow zones (p < 0.05).