Genome Analysis of Acinetobacter lwoffii Strains Isolated from Permafrost Soils Aged from 15 Thousand to 1.8 Million Years Revealed Their Close Relationships with Present-Day Environmental and Clinical Isolates

SIMPLE SUMMARY: Arctic ecosystems are an extreme habitat characterized by a negative average annual temperature and the presence of permafrost that occupies about 25% of the land. Permafrost can retain viable microorganisms for several million years and therefore it is a source of unique “ancient” microbes. Acinetobacter lwoffii are aerobic chemoorganotrophic bacteria widespread in a variety of natural and artificial environments, and have been reported as hospital pathogens associated with nosocomial infections. Here, we carried out a genome-wide analysis of five strains of A. lwoffii isolated from permafrost aged from 15 thousand to 1.8 million years. Surprisingly, we did not reveal genetic determinants that distinguish them from modern clinical and environmental A. lwoffii isolates. On the phylogenetic tree permafrost strains do not form a separate cluster, but are related to various clinical isolates. The genomes of clinical and permafrost strains contain similar mobile elements and prophages, which indicates an intense horizontal gene transfer. Like clinical isolates, permafrost strains harbored antibiotic resistance genes, although plasmids from the modern strains are enriched with antibiotic resistance genes compared to permafrost ones. The obtained results indicate that thawing of permafrost caused by global warming could release new potentially pathogenic strains of Acinetobacter into the modern biosphere. ABSTRACT: Microbial life can be supported at subzero temperatures in permafrost up to several million years old. Genome analysis of strains isolated from permafrost provides a unique opportunity to study microorganisms that have not previously come into contact with the human population. Acinetobacter lwoffii is a typical soil bacterium that has been increasingly reported as hospital pathogens associated with bacteremia. In order to identify the specific genetic characteristics of ancient permafrost-conserved strains of A. lwoffii and their differences from present-day clinical isolates, we carried out a genome-wide analysis of five strains of A. lwoffii isolated from permafrost aged from 15 thousand to 1.8 million years. Surprisingly, we did not identify chromosomal genetic determinants that distinguish permafrost strains from clinical A. lwoffii isolates and strains from other natural habitats. Phylogenetic analysis based on whole genome sequences showed that permafrost strains do not form a separate cluster and some of them are most closely related to clinical isolates. The genomes of clinical and permafrost strains contain similar mobile elements and prophages, which indicates an intense horizontal transfer of genetic material. Comparison of plasmids of modern and permafrost strains showed that plasmids from the modern strains are enriched with antibiotic resistance genes, while the content of genes for resistance to heavy metals and arsenic is nearly the same. The thawing of permafrost caused by global warming could release new potentially pathogenic strains of Acinetobacter.