Genomic adaptation of Pseudomonas strains to acidity and antibiotics in hydrothermal vents at Kolumbo submarine volcano, Greece

Although the rise of antibiotic and multidrug resistant bacteria is one of the biggest current threats to human health, our understanding of the mechanisms involved in antibiotic resistance selection remains scarce. We performed whole genome sequencing of 21 Pseudomonas strains, previously isolated from an active submarine volcano of Greece, the Kolumbo volcano. Our goal was to identify the genetic basis of the enhanced co-tolerance to antibiotics and acidity of these Pseudomonas strains. Pangenome analysis identified 10,908 Gene Clusters (GCs). It revealed that the numbers of phage-related GCs and sigma factors, which both provide the mechanisms of adaptation to environmental stressors, were much higher in the high tolerant Pseudomonas strains compared to the rest ones. All identified GCs of these strains were associated with antimicrobial and multidrug resistance. The present study provides strong evidence that the CO2-rich seawater of the volcano associated with low pH might be a reservoir of microorganisms carrying multidrug efflux-mediated systems and pumps. We, therefore, suggest further studies of other extreme environments (or ecosystems) and their associated physicochemical parameters (or factors) in the rise of antibiotic resistance.

Automated summary

This study conducted whole genome sequencing of 21 Pseudomonas strains isolated from the Kolumbo volcano in Greece, revealing an enhanced co-tolerance to antibiotics and acidity in these strains. The analysis identified a high number of phage-related GCs and sigma factors in the tolerant Pseudomonas strains, suggesting a possible reservoir of multidrug efflux-mediated systems and pumps in CO2-rich seawater with low pH. Further studies on extreme environments and their associated physicochemical parameters are recommended to understand the rise of antibiotic resistance.