Metagenomic insights into nitrogen and phosphorus metabolisms of bacteria in lakes with distinct nutrient conditions

Nitrogen (N) and phosphorus (P) cycling are crucial for preserving ecosystem functioning in lakes, yet our comprehension of the dynamics of N/P cycling genes and microorganisms under diverse nutrient levels is still limited. Herein, we conducted a comprehensive investigation into the profiles of N/P cycling genes and bacteria across three lakes with distinct nutrient levels. We found that N and P cycling genes were most abundant in the high-nutrient lake, particularly those involved in ammonification, assimilatory nitrate reduction, P regulation, and P transportation. Bacteria responsible for mediating most N/P cycling processes (excluding nitrogen fixation and P regulation) were predominant in the high-nutrient lake and mainly affiliated with Cyanobacteria, Proteobacteria, Actinobacteriota, and Bacteroidota. Furthermore, a potential biogeochemical hotspot for the co-metabolism of N and P was identified in the high-nutrient lake, consolidated by the most intricate co-occurrence pattern between N and P cycling genes. More importantly, these versatile bacteria capable of N/P metabolisms, primarily influenced by total nitrogen, total phosphorus, Secchi depth, and total dissolved solids, played important roles in maintaining the stability of bacterial communities in lakes. These findings offer significant insights into microbial-mediated N and P biogeochemical cycling in lakes with varying nutrient conditions, improving our understanding of utilizing N/P co-metabolism microbes to regulate ecosystem function and service amid the challenges of global lake eutrophication.