First report on antibiotic resistance and antimicrobial activity of bacterial isolates from 13,000-year old cave ice core

Abstract

Despite the unique physiology and metabolic pathways of microbiomes from cold environments providing key evolutionary insights and promising leads for discovering new bioactive compounds, cultivable bacteria entrapped in perennial ice from caves remained a largely unexplored life system. In this context, we obtained and characterized bacterial strains from 13,000-years old ice core of Scarisoara Ice Cave, providing first isolates from perennial ice accumulated in caves since Late Glacial, and first culture-based evidences of bacterial resistome and antimicrobial compounds production. The 68 bacterial isolates belonged to 4 phyla, 34 genera and 56 species, with 17 strains representing putative new taxa. The Gram-negative cave bacteria (Proteobacteria and Bacteroidetes) were more resistant to the great majority of antibiotic classes than the Gram-positive ones (Actinobacteria, Firmicutes). More than 50% of the strains exhibited high resistance to 17 classes of antibiotics. Some of the isolates inhibited the growth of clinically important Gram-positive and Gram-negative resistant strains and revealed metabolic features with applicative potential. The current report on bacterial strains from millennia-old cave ice revealed promising candidates for studying the evolution of environmental resistome and for obtaining new active biomolecules for fighting the antibiotics crisis, and valuable cold-active biocatalysts.

Figure 1

Phyla and growth temperature distribution of cave ice bacterial isolates along Scarisoara ice core. (A) Number of phyla in ice core strata up to 13,000 years BP; (B) Growth temperature interval distribution of cave isolates belonging to Actinobacteria, Proteobacteria, Firmicutes and Bacteroidetes phyla.

Figure 2

Antimicrobial susceptibility of cave ice bacterial isolates. The percentage of susceptible under standard dose (green), and resistant (blue) strains to the 28 tested antibiotics was indicated for the strains belonging to phyla Actinobacteria (A), Firmicutes (B), Proteobacteria (C), and Bacteroidetes (D).

Figure 3

Impact of substrate age and climate during ice deposition on the antimicrobial susceptibility of bacterial isolates from Scarisoara Ice Cave. (A) Resistance profile of the cave ice chronosequence. (B) Antibiotic resistance (blue) and susceptibility at standard dose (green) to 28 antibiotics (Supplementary Table S3) of cave isolates from ice layers accumulated during Little Ice Age (LIA; 430–475 years BP), Medieval Warm Period (MWP; 953–1124 years BP) and Mid Holocene Warm Period (MHWP; 4751–5335 years BP) (Supplementary Table S2).