Integrated transcriptomic and DNA methylomic analysis of Yarrowia lipolytica in response to La(III)/Ce(III) stress

Rare earth elements (REEs), as strategic resources, cause severe pollution and ecological degradation through chemical leaching processes. Bioremediation technology offers an efficient green alternative for REE recovery from wastewater. This study investigated Yarrowia lipolytica to elucidate its efficient adsorption mechanisms and stress adaptation towards La(III)/Ce(III). Phenotypic analysis revealed that the strain enhances adsorption capacity for La(III)/ Ce(III) by increasing specific surface area through dimorphic transition. Under optimal conditions, adsorption rates reached 84.33% for La(III) and 87.21% for Ce(III). Adsorption kinetics followed a pseudo-second-order model (indicating chemisorption dominance), and isotherms conformed to the Langmuir model (suggesting monolayer adsorption). FTIR and XPS analyses identified cell surface -OH groups as key active sites, directly capturing REE ions via complexation. Integrated transcriptomic and DNA methylomic analyses uncovered interaction mechanisms and stress responses: La(III) exposure inhibited glycolysis/TCA cycle genes while activating peroxisome pathways (antioxidant defense) and ABC transporters (ion efflux). Ce(III) exposure specifically suppressed amino acid metabolism (e.g., glutamate pathway). Whole-genome methylation levels decreased significantly with preferential methylation in CHH contexts. 10 (La(III)) and 4 (Ce(III)) were identified differentially expressed genes accompanied by altered methylation levels, demonstrating DNA methylation-mediated regulation of La(III)/Ce(III) resistance genes. This study lays a theoretical foundation for bioremediation of REE pollution.