Metagenome Analysis Reveals a Response of the Antibiotic Resistome to Mars-like Extraterrestrial Conditions

Abstract

The spread of antibiotic resistance is becoming a serious global health concern. Numerous studies have been done to investigate the dynamics of antibiotic resistance genes (ARGs) in both indoor and outdoor environments. Nonetheless, few studies are available about the dynamics of the antibiotic resistome (total content of ARGs in the microbial cultures or communities) under stress in outer space environments. In this study, we aimed to experimentally investigate the dynamics of ARGs and metal resistance genes (MRGs) in Kombucha Mutualistic Community (KMC) samples exposed to Mars-like conditions simulated during the BIOMEX experiment outside the International Space Station with analysis of the metagenomics data previously produced. Thus, we compared them with those of the respective non-exposed KMC samples. The antibiotic resistome responded to the Mars-like conditions by enriching its diversity with ARGs after exposure, which were not found in non-exposed samples (i.e., tet and van genes against tetracycline and vancomycin, respectively). Furthermore, ARGs and MRGs were correlated; therefore, their co-selection could be assumed as a mechanism for maintaining antibiotic resistance in Mars-like environments. Overall, these results highlight the high plasticity of the antibiotic resistome in response to extraterrestrial conditions and in the absence of anthropogenic stresses.

Keywords: Antimicrobial resistance; Extraterrestrial environment; Kombucha multimicrobial community; Metal resistance.

FIG. 1.

Resistance class composition. Composition of the samples according to (a) antibiotic or (b) metal resistance classes. The relative abundances of specific resistance classes (against antibiotics or metals) were expressed as percentage for each sample.

FIG. 2.

Richness of resistance genes. Boxplot of the richness of (a) ARGs and (b) MRGs. The thick horizontal line represents the median, the box represents 50% of the values, the whiskers extend to the highest and lowest value within the 1.5 interquartile range.

FIG. 3.

Total relative abundances of resistance genes. Boxplot of the total relative abundances of (a) ARGs and (b) MRGs. The thick horizontal line represents the median, the box represents 50% of the values, the whiskers extend to the highest and lowest value within the 1.5 interquartile range.

FIG. 4.

Co-occurrence network. For network construction, elements with a significant and strong correlation (rho >0.8 and p < 0.01) were chosen. Node size is proportional to the number of edges. ARGs are indicated in blue, MRGs in red. Different colors were used for the modules in the network (Supplementary Table S7). In green: module A; in light blue: module B; in yellow: module C; in gray: modules with less than 6.5% of network nodes.