| Abstract | Methane (CH4) emissions from flooded rice cultivation are a major contributor to global climate change, accounting for approximately 18% of total agricultural CH4 emissions worldwide. The net methane flux from rice paddies is governed by the balance between methane production by methanogenic archaea under anaerobic conditions and methane oxidation by aerobic methanotrophs residing in the rice rhizosphere. The activity of methanotrophs is critically regulated by metal cofactors, particularly copper (Cu) for particulate methane monooxygenase (pMMO) and cerium (Ce) for the rare earth element dependent methanol dehydrogenase (XoxF-MDH). In parallel, synthetic microbial communities (SynComs) assembled from functionally complementary plant growth promoting (PGP) bacterial strains have demonstrated potential to simultaneously mitigate methane emissions and enhance rice productivity through metabolic division of labor.This study compared two scalable methane mitigation strategies in a pilot-scale greenhouse rice mesocosm experiment using century-cultivated paddy soils from Surin Province, Thailand, over a 100-day rice growth cycle (November 2025 to March 2026): (1) synergistic application of mixed metal micronutrients (Cu at 17 mg/kg soil and Ce at 50 mg/kg soil), and (2) a designed SynCom assembled from ten functionally selected PGP bacterial isolates from rice rhizosphere soils, including Azonexus, Hydrogenophaga, Thauera, Pseudomonas, and Methylocystis-associated strains. A continuous flooding control was maintained as the reference baseline. Methane flux was quantified using the closed-chamber method every ten days, and soil and water physicochemical parameters including nitrogen species and total organic carbon (TOC) were characterized at pre- and post-experiment time points.Results showed that all treatments followed the characteristic seasonal methane trajectory, with flux peaking during the reproductive phase (DAT 60-80) and declining through ripening. The SynCom treatment (MC) achieved a statistically significant reduction of 65.08% in seasonal methane flux relative to the control (p < 0.05), and near-complete methane depletion within 72 hours in closed-chamber incubation assays. In contrast, the metal micronutrient treatment (M) resulted in a statistically significant net increase of +181.92% in mean seasonal methane flux (p < 0.05), attributed to supraoptimal copper concentrations generating reactive oxygen species that impaired methanotroph community integrity and elevated the available carbon pool for methanogens. Correlation analysis revealed a stratified biogeochemical control structure: median methane flux was strongly correlated with soil nitrite (r = 1.0, p = 0.009), peak flux with water TKN (r = 0.999, p = 0.029), and cumulative flux with soil TOC (r = 0.9998, p = 0.013). For rice yield, the SynCom treatment increased grain dry weight by 108% above the control, while the metal treatment caused a marginal yield suppression of 4.36%.In conclusion, the SynCom-based biofertilizer strategy proved superior by simultaneously achieving significant methane mitigation and enhanced rice grain productivity, establishing it as a scientifically valid dual-benefit tool for climate-smart rice agriculture. The metal micronutrient strategy underscored the critical importance of precise dose calibration, as copper toxicity to methanotrophs at the applied levels outweighed the intended enzymatic benefits. These findings support the development of SynCom biofertilizers as a scalable, field deployable approach to converting rice cultivation systems into climate-resilient operations contributing to both greenhouse gas reduction and global food security goals. |
