Brownification of freshwater promotes nitrogen-cycling microorganism growth following terrestrial material increase and ultraviolet radiation reduction.

Brownification is an increasingly concerning phenomenon faced by aquatic ecosystems in the changing environments, and the microbiome plays an irreplaceable role in material circulation and food web construction. Insight into the influence of brownification on microbial communities is crucial from an ecological standpoint. In this study, we simulated brownification using a the mesocosm system and explored the relationship between the characteristics of microbial communities and brownification using excitation-emission matrix (EEM) fluorescence spectroscopy and ultraviolet (UV) spectroscopy combined with high-throughput amplicon sequencing techniques. The results showed that brownification reduced the richness of the microbial community and selectively promoted the growth of nitrogen-cycling microorganisms, including hgcI_clade, Microbacteriaceae, and Limnohabitans. Brownification affected microbial communities by altering the carbon source composition and underwater spectrum intensity; UV, blue, violet, and cyan light were significantly (p < 0.05) correlated with microbial community richness, and random forest analysis revealed that UV, C1 (microbial humic-like), and C3 (terrestrial humic-like) were the major factors significantly influencing microbiome variation. We found that brownification affected microorganisms in shallow lakes, especially nitrogen cycling microorganisms, and propose that controlling terrestrial material export is an effective strategy for managing freshwater brownification.