Melatonin–nitrogen synergy reshapes paddy soil microbiomes and suppresses methane emissions in rice

Methane emission from rice paddies represents an extensive source of greenhouse gases, largely controlled by microbial activity in the soil. We investigated how melatonin, nitrogen, and a combination treatment affected soil methane emissions and microbial diversity in rice fields; wild-type rice plants were cultivated under six treatments: nitrogen1 and nitrogen2 alone, combined nitrogen1 + melatonin and nitrogen2 + melatonin treatments, melatonin, and control. Microbial diversity, community composition, and methane-cycling bacteria abundance were evaluated to identify the mechanisms through which methane emittance occurs. Melatonin-inclusive treatments significantly increased microbial diversity and changed community structures compared to the control and N-alone. Moreover, microbial richness (Chao1 index) increased by up to 45 % in melatonin-inclusive treatments, exhibiting the greatest diversity. Beta diversity analysis revealed discrete microbial community shifts, showing that nitrogen + melatonin combinations support stable, distinct microbiomes best suited for soil ecosystem functionality. Critically, these synergistic treatments enriched key methanotrophic genera (e.g., Methylocystis , Methylomonas , Methylocaldum ; η² > 0.58) and were associated with a 50 % reduction in methane emissions compared to the control. Differential abundance analysis and LEfSe demonstrated a selective enrichment of microbial families important for methane oxidation and nutrient cycling. However, nitrogen-alone treatments had moderate effects related to the synergism of the treatment of nitrogen and melatonin. Methane mitigation through enhanced methanotrophic activity was, notably, further supported by a significant increase in the abundance of the family Methylococcaceae. Thus, melatonin can be applied as a strategic soil amendment to increase microbial diversity and select functional taxa in methane oxidation while reducing methane emissions from rice production. • Melatonin treatments boosted microbial diversity up to 45 % in rice paddies. • Nitrogen + melatonin created distinct, stable soil microbiomes. • Methane emissions dropped by 50 % with melatonin application. • Melatonin enriched methanotrophs, notably the Methylococcaceae family. • LEfSe showed functional taxa for methane oxidation were selectively enriched.