Metagenomic exploration of halophile microbial communities of salina de Ambargasta in northern Argentina

Abstract

Salinas de Ambargasta (SA) is a salt flat located in northern Argentinawith an extension of 4700 km2 and is part of Cuenca Saliniana, one of thelargest saline complexes in the world. The Ambargasta region experiences asemi-arid climate with hot, rainy summers and cold, dry winters. These climaticconditions, together with its unique geomorphological and sedimentological characteristics,make SA an interesting location to explore its halophile adapted microbialcommunity. In this study, we analyzed the microbial diversity in two distinctareas of the eastern zone of SA: vegetated areas (VA) and non-vegetated areas(NVA). Shotgun metagenomic sequencing was performed on environmental DNAextracted from each area. A total of 78,324,438 paired-end reads were generatedfor the VA sample, with a GC content of 64.26%, and 73,257,256 paired-end readsfor the NVA sample, with a GC content of 61.98%, using Illumina technology.Trimmomatic (version 0.39) was employed for quality control and adapterremoval. Functional and taxonomic profiles of the microbiome were obtainedthrough the direct analysis of raw metagenomic reads and from assembled readsobtained with MegaHit (version 1.2.9). Further metagenome processing for rawreads was carried out through MetaPhlAn and HUMAnN, and for assembled reads,Semibin, Checkm, and GTDBtk were used to obtain Metagenome Assembled Genomes(MAGs). For MAGs metabolic estimation, Anvio´s metabolism suite of programs wasused. The metagenomic data provided a comprehensive taxonomic characterizationof both SA areas. Both areas were dominated by Bacteria, with some differencesin taxa abundance distribution. Proteobacteria was the dominant phylum in bothVA and NVA, but with distinct secondary phyla: NVA was enriched in Firmicutesand Bacteroidetes, whereas VA lacked Firmicutes and exhibited a higherabundance of Euryarchaeota, which was exclusive to VA. At the family level,Halanaerobiaceae and Halomonadaceae were predominant in NVA, while VA wascharacterized by the presence of Halomonadaceae and Saccharospirillaceae. Genesessential for survival in extreme environments were identified as Ars genes(arsC, arsR, arsD) involved in arsenic resistance, and uvr and recA genescritical for DNA repair under UV radiation, particularly significant in highsolar incidence environments like SA. From VA, eleven high-quality MAGs wererecovered. In contrast, from NVA, 28 MAGs were recovered. From these MAGs, onlytwelve were classified to the genus level, pointing to unusual microorganismsat these locations. To our knowledge, this is the first metagenomicinvestigation of the microbial communities of Salinas de Ambargasta. Thefindings highlight the diversity and functional potential of theseextremophilic communities, laying the groundwork for future research aimed atunderstanding the ecological roles and adaptations in one of the largest salineenvironments of northern Argentina.