Mapping the microbial diversity and natural resistome of North Antarctica soils

Abstract

The rising of multi-resistant bacterial pathogens is currently one of the most critical threats to global health and requires urgent actions for its control and a better understanding of the origin, evolution, and spread of antibiotic resistance. It is of consensus that this must be faced under a one-health prism that includes the environment and non-human animals as possible sources and media for resistance amplification and evolution. In this regard, the resistome extension and diversity present in natural and remote environments remain largely unexplored. Moreover, little is known about the availability of antimicrobial resistance genes (ARGs) from these environments to be disseminated through horizontal transfer, potentially mediating the rise of new resistance mechanisms among clinically relevant pathogenic microorganisms. Furthermore, the impact of the anthropogenic intervention on the presence of antibiotic resistant bacteria and the underlying genes is still a matter of controversy. In this context, the Antarctic Peninsula soils are attractive remote environments to study, since their high microbial diversity, the presence of ice-covered soils sheltering ancestral microorganisms that are being exposed as cause of the global warming, and because it is one of the most transited routes between Antarctica and the rest of the world, thus permitting genetic and microbial carriage among those places. Also, it harbors both human bases and places without noticeable human intervention. In this work, we explored the culturable resistome of soils from different places of North Antarctica, including human bases and non-intervened areas. We identified bacterial isolates resistant to a wide array of antibiotics, harboring up to 10 simultaneous resistances, most of them belonging to the genus Pseudomonas. Genomic analyses of the two top resistant bacteria revealed a dominant presence of efflux pumps although an unexpectedly low abundance of known resistance genes, suggesting the presence of unidentified new mechanisms. Moreover, using 16S rRNA amplicon and metagenomic sequencing we explored the microbial diversity in the sampled soils and evaluated the presence and abundance of antimicrobial resistance genes. Proteobacteria, Bacteroidota, Acidobacteriota, and Verrucomicrobiota corresponded to the most abundant Phyla in most of the soils, while among the most abundant genera were Candidatus Udaeobacter, RB41, Polaromonas, and Ferruginibacter. A similarly high microbial diversity was observed when comparing humanized with non-intervened sites, although beta diversity analysis, as well as sequence composition analysis revealed significant clustering of non-intervened apart from humanized areas. We identified a variety of genes potentially involved in resistance to more than 15 drug classes in both short reads based analyses and ARGs detection among assembled contigs. Further, through performing hybrid assembly by combining short and long read sequence data we searched for resistance genes located inside possible mobile genetic elements and identified the source taxa. Polaromonas, Pseudomonas, Streptomyces, Variovorax, Bhurkolderia, and Gemmatimonas were the host taxa of most of the identified ARGs. Plasmid prediction among the assembled metagenomes led to the identification of a putative OXA-like beta-lactamase from Polaromonas spp. located inside a putative plasmid, which included all the key conserved residues for the activity of this kind of beta-lactamases. Taken together, this evidence indicates that resident North Antarctica soil microbial communities harbor a highly diverse natural resistome, part of which is located inside mobile genetic elements that could act disseminating these ARGs to other bacteria.

Bacterial Community Composition and Presence of Plasmids in the Endosphere- and Rhizosphere-Associated Microbiota of Sea Fig (Carpobrotus aequilaterus)

“…Over the last several decades, conjugative plasmid-mediated horizontal gene transfer (HGT) occurring between bacteria in the environment has acquired a high relevance in public health and environmental sciences [1][2][3][4]. Conjugative plasmids are mobile genetic elements (MGEs), self-replicative and auto-transferable, that usually carry genes involved in antimicrobial resistance, virulence, heavy-metal resistance, and degradation of compounds.…”