Diversity and distribution of the lanthanome in aerobic methane-oxidising bacteria

Background Lanthanides (Ln) play essential roles in the metabolism of methanotrophs, catalysing key reactions in the methane oxidation pathway. However, the diversity, distribution, and ecological roles of Ln-dependent proteins (the lanthanome) in aerobic methane-oxidising bacteria (MOB) remain underexplored. This study investigates the lanthanome using genome, plasmid, and proteome data, as well as metatranscriptome data from methane-rich lake sediments. Results Comparative genomic analysis of a custom database of 179 MOB genomes revealed the presence of various methanol dehydrogenase (MDH) isoforms, including xoxF variants, distributed across Proteobacteria and Verrucomicrobia phyla. Using Methylosinus trichosporium OB3b as a model, we measured methane oxidation rates in response to CeCl₃ and ore containing a mixture of lanthanides. Using proteomics, we uncovered differential protein expression in response to Ln. Despite differences in adaptation times, methane oxidation rates were consistent across treatments, indicating similar overall metabolic efficiencies after Ln acclimatisation. The genomic analysis uncovered several Ln-binding proteins, including the TonB-dependent receptors (LanA and LutH-like), as well as Lanmodulin and LanPepsy, with unique phylogenetic patterns. Metatranscriptomic analysis confirmed the expression of lanthanome, particularly in Proteobacteria, with xoxF5 as the dominant MDH variant in MOB genomes. The discovery of Ln-binding proteins in plasmids suggests horizontal gene transfer, highlighting the adaptive mechanisms of MOB to Ln availability and their ecological role in methane cycling. Conclusion This work expands our understanding of Ln-dependent methane oxidation in MOB, highlighting their metabolic flexibility and ecological significance in methane cycling. The findings suggest potential applications for Ln-dependent processes in biotechnology, particularly in methane capture and bio-utilization, as well as lanthanide recovery from geological sources.