Paddy fields, as the largest anthropogenic wetlands on Earth, face a high risk of micronutrient loss through surface runoff and leaching due to their frequent irrigation-drainage cycles, as well as removal with crop harvest. While micronutrient’s losses largely impede biological nitrogen fixation (BNF) in soils, agricultural practices that retain micronutrients and thus increase BNF in paddy soils remain underexplored. Using a long-term (40 years) field experiment, we showed that manure and straw inputs substantially increased the content and bioavailability of micronutrients, including molybdenum (Mo) and vanadium (V), compared to the soil without fertilization or with mineral fertilization only. The total content and bioavailability of Mo and V had a strong correlation with microbial necromass and short-range ordered minerals. Metagenomic sequencing analysis further indicated that the content and bioavailability of micronutrients were strongly correlated with the abundance of the key N-fixing genera (i.e., Azospirillum and Bradyrhizobium). Unexpectedly, structural equation modeling (SEM) identified that microbial necromass exerted the strongest control on N-fixing genera, highlighting an underappreciated role of microbial necromass as a reservoir of micronutrients. Based on micronutrient’s bioavailability and metagenomic sequencing, we conclude that micronutrients are the key factor for BNF in paddy soils, offering significant implications for managing BNF in paddy soils.
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