Dual functionality of Peribacillus frigoritolerans in methane mitigation and rice immunity

• Peribacillus frigoritolerans mitigated methane emission via methanotroph enrichment. • In silico modelling revealed l -alanine as a determinant for methanotroph growth. • P. frigoritolerans elicited induced resistance against Xanthomonas oryzae. • P. frigoritolerans reduced both methane production and disease occurrence in rice . Methane released from rice paddy soils is a major contributor to anthropogenic greenhouse gas accumulation, which accelerates global warming. In paddy soils, anaerobic methanogenic archaea produce methane that is simultaneously oxidized by methanotrophic bacteria. The unoxidized methane is released into the atmosphere through aerenchyma channels of rice. Since controlling the abundance and activity of methanotrophs in soils remains technically challenging, we aimed to identify root-colonizing heterotrophic bacteria that increase the growth of methanotrophs to mitigate methane emission. The screening of 960 aerobic and 960 anaerobic heterotrophic bacteria depending on colony morphology identified Peribacillus frigoritolerans AE95 as a rhizobacterium promoting the growth of methanotroph in vitro and reducing methane emission by up to 66.8 % when applied to the rice root system in vivo . Genome-scale metabolic modelling predicted that l -alanine as a key growth-supporting metabolite secreted by P. frigoritolerans AE95, which was experimentally validated to enhance Methylococcus geothermalis and Methylocystis parvus proliferation. In addition to methane mitigation, P. frigoritolerans and l -alanine supplementation elicited rice innate immunity against a bacterial pathogen Xanthomonas oryzae pv. oryzae . Our findings indicate that the rhizosphere heterotroph P. frigoritolerans AE95 possesses dual functionality, contributing to both methane mitigation and the enhancement of plant immunity.