Silicate fertilizer mitigates methane emissions from rice paddies by enriching Burkholderia to modulate microbial interactions

Methane emissions from rice paddies are a major source of greenhouse gases, and silicate fertilizer (SF) derived from blast furnace slag has emerged as an environmentally friendly amendment that reduces methane release. SF modifies the soil redox environment by supplying electron acceptors such as iron, but the microbial mechanisms underlying methane mitigation remain unclear. Here, we combined metagenomic profiling, microbial isolation, and greenhouse experiments to show that SF consistently enriched Burkholderia vietnamiensis together with the methanotrophs in the rice rhizosphere. Inoculation of B. vietnamiensis strain HU01 alone reproduced the methane-suppressing effect of SF and increased methanotroph abundance. Cell-free culture supernatants of HU01 stimulated the growth of Methylococcus geothermalis and Methylocystis parvus through secreted, low-molecular-weight, heat-stable metabolites. Although metabolic modeling predicted primary metabolites such as L-glutamate and cobalamin as candidate cross-feeding factors, LC-MS/MS analysis of the highly active fractions indicated that the robust bioactivity was primarily driven by a chemically complex metabolite mixture rather than these ubiquitous single compounds. These results provide direct evidence that enrichment of a single heterotrophic species can enhance methane oxidation by stimulating methanotroph activity through metabolite exchange. B. vietnamiensis HU01 represents a promising microbial resource for methane mitigation and illustrates how targeted heterotroph-methanotroph interactions can be leveraged for climate-smart rice cultivation.