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ABSTRACT
Background: Permafrost preserves a variety of viable ancient microorganisms. Some of them can be cultivated after being kept at subzero temperatures for thousands or even millions of years.
Objective: To cultivate bacterial strains from permafrost.
Design: We isolated and cultivated two bacterial strains from permafrost that was obtained at Mammoth Mountain in Siberia and attributed to the Middle Miocene. Bacterial genomic DNA was sequenced with 40-60× coverage and high-quality contigs were assembled. The first strain was assigned to Staphylococcus warneri species (designated MMP1) and the second one to Staphylococcus hominis species (designated MMP2), based on the classification of 16S ribosomal RNA genes and genomic sequences.
Results: Genomic sequence analysis revealed the close relation of the isolated ancient bacteria to the modern bacteria of this species. Moreover, several genes associated with resistance to different groups of antibiotics were found in the S. hominis MMP2 genome.
Conclusions: These findings supports a hypothesis that antibiotic resistance has an ancient origin. The enrichment of cultivated bacterial communities with ancient permafrost strains is essential for the analysis of bacterial evolution and antibiotic resistance.
ARTICLE HISTORY
Received 4 January 2017
Accepted 14 June 2017
KEYWORDS
Permafrost; genome sequence; evolution; antibiotic resistance; microbial physiology; biofilm; Staphylococcus
Introduction
Psychrotrophs and psychrophiles are microorganisms that can survive or even thrive in cold places [1,2]. Investigations of glacier ice at the Vostok station in the Antarctic [3] and surface snow from the South Pole [4] revealed that bacteria, fungi, diatoms, and other microorganisms were probably trapped in the snow and remained in the ice for thousands of years. Microbial activity was also found in ice sediments of perennial and permanent lake ice [5,6] and in the Antarctic Sea [7,8]. Anaerobic microorganisms were isolated from glacier samples in the Arctic [9,10] and Greenland [11].
Permafrost (permafrost soil) is soil that stays at 5-10°C below zero for 2 years or longer. Most of the permafrost is located in lands close to the North and South Poles. However, some permafrost exists at much lower latitudes. A thin active layer of the soil above the permafrost usually thaws during the summer. The thickness ofthis active layer varies depending on season and location, but is typically 0.6-4.0 m. In the northern Lena and Yana River basins in Siberia...