Comparative Genomic Analysis of Metal-Tolerant Bacteria Reveals Significant Differences in Metal Adaptation Strategies

Metal-tolerant bacteria have been commercially used in wastewater treatment, bio-fertilizer and soil remediation etc. However, their action mechanisms have not yet been well understood. We screened metal-tolerant bacteria isolated from the rhizosphere soil samples with metal-enriched media containing Cu, Fe or Mn, sequenced and compared the genomes, and analyzed their metal adaptation strategies at genomic levels to better understand their mechanisms of actions. Totally 32 metal-tolerant isolates were identified and classified into 12 genera based on phylogenetic analysis. The determination of MTC and effect of metal ions on the isolates indicated that Serratia marcescens X1, Mammaliicoccus sciuri X26 and Rummeliibacillus pycnus X33 showed the significant differences in metal tolerance to Cu, Fe and Mn with other isolates. They have quite different genomic features to adapt various metal ions. S. marcescens X1 possesses abundant genes required for Cu, Fe and Mn homeostasis. M. sciuri X26 has a number of genes involved in Mn and Zn homeostasis but with no genes responsible for Cu and Ca transport. R. pycnus X33 is rich in Fe, Zn and Mg transport systems but poor in Cu and Mn transport systems. It is thus inferred that the combined use of them would compensate their differences and enhance their ability in accumulating a wider range of heavy metals for promoting their applications in wastewater treatment, soil remediation and organic fertilizer etc. IMPORTANCEMetal-tolerant bacteria have wide applications in environment, agriculture and ecology, but their action strategies have not yet been well understood. We isolated 32 metal-tolerant bacteria from the rhizosphere soil samples. Among them, S. marcescens X1, M. sciuri X26 and R. pycnus X33 showed the significant differences in metal tolerance to Cu, Fe and Mn with other isolates. Comparative genomic analysis revealed that they have abundant and different genomic features to adapt various metal ions. It is thus inferred that the combined use of them would compensate their differences and enhance their ability in accumulating heavy metal ions widening their applications in industry, agriculture and ecology.