Biodegradation of lignite by Rhizopus arrhizus: Degradation products, pathways, and genomics characterization

Lignite, as a low-rank coal, suffers from inefficient and highly polluting traditional utilization methods. There is an urgent need to develop clean technologies for their efficient conversion into high-value-added chemicals. Microbial degradation of low-rank coal is a promising green pathway, yet linking efficient degradation phenotypes to their genetic basis remains a challenge. This study addressed this by integrating the discovery of the highly efficient degrader Rhizopus arrhizus RA-01 with its complete genome analysis to elucidate the underlying biological degradation mechanisms and metabolic pathways. The results demonstrated that this strain achieved an oxidized lignite degradation rate of 71.6 ± 0.2% within 5 days. After 4 days of treatment with Rhizopus arrhizus RA-01, the lignite surface exhibited significant roughening and developed large fissures. Mechanism studies revealed that RA-01 disrupts the lignite molecular network by reducing the crystallinity of its carbon skeleton, particularly cleaving key reactive chemical bonds (such as OH-O hydrogen bonds, OH-π bonds, and ether linkages), and metabolically transforming N/O-containing functional groups. In the liquid phase fraction of the degradation products, various low-molecular-weight compounds were identified, including long-chain alkanes, amides, etc. Integrated metabolic analysis disclosed that RA-01 primarily degrades lignite macromolecules into small organic acids and carbon dioxide through the synergistic integration of multiple metabolic pathways, including hydrolysis/acidification, glycolysis, the TCA cycle, fatty acid metabolism, and benzoate degradation. This study provides the first elucidation of the efficient degradation mechanism of oxidized lignite by Rhizopus arrhizus, offering a theoretical basis for achieving high-value coal conversion via microbial and metabolic engineering strategies.