A rice rhizosphere-derived methanotrophic consortium enhances root growth and reduces methane intensity in flooded soil

초록

Methanotrophic bacteria are key regulators of methane oxidation in flooded soils and may provide functional benefits as rhizosphere bioinoculants. Here, we isolated two methanotrophic consortia, NCN8 and UCBe9, from rice rhizosphere and evaluated their effects on methane emissions, rice growth, and rhizosphere microbial communities under greenhouse pot conditions. Both consortia grew rapidly at 30 °C and carried nitrogenase genes, whereas only NCN8 showed robust growth in nitrogen-free medium with CH₄ as the sole carbon source, supporting a functional diazotrophic phenotype. Whole-genome sequencing of NCN8 revealed a Methylocystis – Methylophilus consortium, with the Methylocystis member representing a putative novel species-level lineage. In the first-year pot experiment, NCN8 and UCBe9 reduced cumulative CH₄ emissions by more than 15%, reduced methane intensity by 35%, and increased grain yield by approximately 30% (from 4.9 to 6.4 t ha−1) relative to the uninoculated control. In the second-year experiment, high-density (HIGH) NCN8 inoculation significantly reduced cumulative CH₄ emissions by 27%, whereas the 15% reduction under low-density (LOW) inoculation was not statistically significant; methane intensity was significantly reduced by 44% (LOW) and 50% (HIGH). Grain yield increased significantly under LOW inoculation (from 5.8 to 8.6 t ha−1), whereas the increase under HIGH inoculation (to 8.3 t ha−1) was not significant. Amplicon sequencing showed no major disruption of overall bacterial or archaeal diversity, although the relative abundance of the genus Methylocystis increased in inoculated rhizospheres. These results identify NCN8 as a promising methanotrophic–methylotrophic bioinoculant that links methane oxidation, putative nitrogen fixation, and rice root growth promotion in flooded soil. Field-scale validation across diverse soils and management regimes is required to confirm its agronomic robustness and environmental performance, as actual field-scale yield effects may be significantly more modest than these preliminary pot-scale findings. © 2026 The Authors.

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