Patricio Arros

Klebsiella pneumoniae is a critical Gram-negative pathogen that frequently acquires and traffics mobile genetic elements (MGEs) carrying virulence and antimicrobial resistance genes. While plasmids have been extensively studied, chromosomal MGEs, particularly genomic islands (GIs), and their contribution to K. pneumoniae evolution remain comparatively underexplored. GIs commonly integrate into tRNA and tmRNA genes (t(m)DNAs) and play key roles in pathogenesis across diverse bacterial phyla. However, progress in understanding these elements has been hindered by the absence of a systematic nomenclature for identifying and comparing equivalent t(m)DNA loci and by limited insight into the determinants governing integration site selection, even among identical tDNA copies within the chromosome. To address these limitations, we established the GMI-K70 collection, a curated dataset of 70 high-quality complete Klebsiella spp. genomes, annotated with their complete repertoire of chromosomal GIs and integration sites. Using a novel t(m)DNA nomenclature based on conserved genomic context, we achieved unambiguous differentiation of identical t(m)DNAs across chromosomes, enabling precise comparative synteny analyses for GI identification. In total, we identified 676 chromosomal MGEs (median 10 per genome), substantially exceeding the GI burden previously detected by automated approaches. Of these, 427 GIs were associated with 21 t(m)DNA loci, while 249 were integrated at 46 non-t(m)DNA sites located downstream of coding sequences or within intergenic regions. Notably, the icd gene emerged as a previously unrecognized integration hotspot, with a usage frequency comparable to reported t(m)DNA sites such as asn1C and phe1A . Genome-wide integrase gene detection mapped nearly all these genes within the predicted MGEs, supporting the completeness of GI identification. The GMI-K70 collection provides a gold-standard framework for benchmarking GI and prophage detection tools and offers a refined view of chromosomal MGE diversity and integration dynamics in Klebsiella . This resource establishes a foundation for future studies of genome evolution and the dissemination of virulence and antimicrobial resistance determinants in this critical priority pathogen.

Salar de Ascotán is a high-altitude arsenic-rich salt flat exposed to high ultraviolet radiation in the Atacama Desert, Chile. It hosts unique endemic flora and fauna and is an essential habitat for migratory birds, making it an important site for conservation and protection. However, there is limited information on the resident microbiota’s diversity, genomic features, metabolic potential, and molecular mechanisms that enable it to thrive in this extreme environment. We used long- and short-read metagenomics to investigate the microbial communities in Ascotán’s water, sediment, and soil. Bacteria predominated, mainly Pseudomonadota, Acidobacteriota, and Bacteroidota, with a remarkable diversity of archaea in the soil. Following hybrid assembly, we recovered high-quality bacterial (101) and archaeal (6) metagenome-assembled genomes (MAGs), including representatives of two putative novel families of Patescibacteria and Pseudomonadota and two novel orders from the archaeal classes Halobacteriota and Thermoplasmata. We found different metabolic capabilities across distinct lineages and a widespread presence of genes related to stress response, DNA repair, and resistance to arsenic and other metals. These results highlight the remarkable diversity and taxonomic novelty of the Salar de Ascotán microbiota and its rich functional repertoire, making it able to resist different harsh conditions. The highly complete MAGs described here could serve future studies and bioprospection efforts focused on salt flat extremophiles, and contribute to enriching databases with microbial genome data from underrepresented regions of our planet.