The article delves into the role of molecular hydrogen (H2) in the microbial world, particularly focusing on its significance in cyanobacterial aggregates. Molecular hydrogen acted as an essential energy carrier in the primordial stages of Earth's development. Recent studies have shed light on the microbial capacity to utilize trace H2 for growth, impacting nitrogen cycling in anaerobic environments. Interspecies hydrogen transfer (IHT) between H2-producing microbes like cyanobacteria and hydrogenotrophic microbes presents a symbiotic metabolism pathway for nitrogen loss, previously overlooked in natural environments. The study conducted on engineered cyanobacterial aggregates showcased superior nitrogen removal rates without external electron donors, demonstrating the importance of H2 in driving nitrogen loss. The research suggests that hydrogenotrophic denitrifiers within cyanobacterial aggregates play a crucial role in hydrogenotrophic denitrification processes, influencing nitrogen cycling in eutrophic aquatic ecosystems. Metagenomic analysis of globally distributed cyanobacterial aggregates further confirms the universality of IHT-driven hydrogenotrophic denitrification, emphasizing its impact on the biogeochemical cycle.