Land Use Management Shifts in Agricultural Small Water Bodies Drive Microbial Mediated Greenhouse Gas Mitigation via Substrate Environment Coordination

ABSTRACT Abundant water resources in rice cultivation areas foster ecological symbiosis through small water bodies; however, these systems are also potential hotspots for greenhouse gas (GHG) emissions. Driven by economic incentives, these aquatic systems have transitioned from natural states to extensive aquaculture and subsequently to intensive, complicating the quantification of emission dynamics and underlying mechanisms. We conducted an annual GHG flux monitoring and metagenomic analysis across four agricultural water systems in Hubei, China. These waterbodies cover both traditional and aquaculture‐oriented types: traditional paddy field ditches (PD), crayfish ditches (CD, converted from PD in 2017), crayfish aquaculture ponds (CP, converted from CD in 2020), and fish aquaculture ponds (FP, converted from PD in 2008). Our findings reveal that all systems acted as net GHG sources, but their global warming potential (GWP) varied over 15‐fold (636–10,049 kg CO 2 ‐eq ha −1 y −1 ), driven by substrate properties and environmental gradients. CD exhibited the highest GWP, where metagenomics revealed carbon input elevated methanogenic gene abundance by 2.15‐fold compared to PD, establishing methane (CH 4 ; contributing 79.9% of the GWP) as the primary contributor. In contrast, continuous aeration in FP suppressed CH 4 emissions but induced substantial nitrous oxide (N 2 O) release through nitrate accumulation. Both denitrification and nitrification pathways contributed substantially to N 2 O production in FP, leading to the second‐highest GWP. Notably, the meticulous cultivation of aquatic plants, aimed at augmenting oxygen release and nitrogen uptake in CP, unexpectedly not only reduced CH 4 emissions but also transformed the system into a sink for both CO 2 and N 2 O through coordinated microbial community restructuring and substrate properties. This transition was accompanied by reduced gene abundances associated with nitrification, denitrification, and TCA cycle pathways, ultimately achieving the lowest GWP among the four systems. In summary, our study elucidates novel insights into the limiting factors governing GHG emissions under land‐use transitions in agricultural small water bodies, while providing actionable strategies for climate change mitigation.