Comparative genome analysis on intraspecific evolution and nitrogen fixation of Leptospirillum ferriphilum isolates

To reveal the intraspecific evolution of Leptospirillum ferriphilum isolates which thrived in industrial bioleaching ecosystems and acid mine drainages, genome sequences of L. ferriphilum YSK, L. ferriphilum DX and L. ferriphilum ZJ were determined to compare with complete genome of L. ferriphilum ML-04. The genome comparisons reveal that extensive intraspecific variation occurs in their genomes, and that the loss and insertion of novel gene blocks of probable phage origin may mostly contribute to heterogeneity of gene content among L. ferriphilum genomes. Surprisingly, a nif gene cluster is identified in L. ferriphilum YSK and L. ferriphilum ZJ genomes. Intensive analysis and further experiments indicate that the nif gene cluster in L. ferriphilum YSK inherits from ancestor rather than lateral gene transfer. Overall, results suggest that the population of L. ferriphilum undergoes frequent genetic recombination, resulting in many closely related genome types in recent evolution. The combinatorial processes profoundly shape their physiologies and provide the basis for adaptation to different niches.