Adaptive Genomic Features of Raoultella ornithinolytica LAM1 from the Geothermal Site of Los Azufres Reveal Potential for Heavy-Metal Bioremediation.

Raoultella ornithinolytica strain LAM1, a facultative anaerobe isolated from a metal-rich geothermal pond in Los Azufres, Mexico, grew in sodium arsenate concentrations up to 1500 ppm (7.215 mM/L). Whole-genome sequencing yielded a 6.01-Mbp draft genome across 104 contigs, encoding 5744 predicted genes annotated using Prokka and NCBI PGAP. Among these, 99 genes were associated with resistance to arsenic, mercury, copper, zinc, cobalt, cadmium, nickel, and lead. We identified a complete ars operon (arsR-arsB-arsC-arsA-arsD) with three arsC paralogs; mer operon genes (four merA copies, merR); zntA-zntR; copA-cueO-cusA; and the metal homeostasis system nikABCDE-nikR. Functional classification assigned 27.9% of resistance genes to zinc, 20.9% to nickel, 18.6% to copper, and 16.3% to arsenic. Cluster of orthologous genes (COG) annotation revealed enrichment in ABC-type permeases (COG0601/1173/0444), metal ion efflux systems (COG1566), and redox enzymes. Growth on CHROMagar™ ESBL medium indicated β-lactamase activity. Comparative analysis with 508 publicly available R. ornithinolytica genomes confirmed conservation of core resistance operons and identified adaptations in sulfur metabolism (dsrB). These results support R. ornithinolytica strain LAM1's survival in metal-contaminated geothermal environments and indicate potential for bioremediation applications.