Exploring archaeal adaptations and ecosystem roles in tropical soda lake sediments

• Fifteen archaeal MAGs were recovered from tropical soda lake sediments. • Eutrophic turbid (ET) and clear-vegetated oligotrophic (CVO) lakes harbor the highest archaeal diversity. • Methanogenic taxa dominate Eutrophic turbid (ET) lakes, correlating positively with methane emissions. • MAGS encode adaptive traits for tolerance to higher levels of salinity, alkalinity, and arsenic. Archaea are recognized for their physiological versatility and ecological significance, which allow them to thrive in extreme environments such as hot springs and saline or hypersaline soda lakes. While several studies have documented their presence in habitats traditionally considered inhospitable, the extent of archaeal diversity in tropical regions remains largely unexplored. In this study, we investigated the archaeal diversity across six soda lake sediments in the Pantanal wetlands of Brazil, including eutrophic, oligotrophic, and clear-vegetated oligotrophic lakes, using a Metagenome-assembled genome (MAG) approach. We recovered 15 archaeal MAGs representing the most prevalent archaeal phyla in these lakes, including Methanobacteriota, Halobacteriota, Thermoplasmatota, Thermoproteota, and the rare phylum Asgardarchaeota. The prevalence of methanogenic taxa and the diversity of methanogenic gene pathways were positively correlated with prior methane measurements in these ecosystems, underscoring the contribution of sediment archaea to greenhouse gas emissions. Furthermore, identified pathways for nitrogen, sulfur, and phosphorus cycling corroborate the importance of archaea in the biogeochemical processes of lake sediments. Genomic evidence of adaptation to extreme conditions characterized by high pH, salinity, and arsenic levels included arsenic-resistance operons, genes responsible for the antioxidant carotenoid pigment bacterioruberin, various ion transport systems, and transporters for compatible solutes such as ectoine and trehalose. Additionally, the identification of biosynthetic gene clusters for incompletely characterized secondary metabolites reveals significant untapped potential for biotechnological applications. Collectively, these findings identify the sediments of tropical soda lakes as reservoirs of archaeal diversity and highlight their role in ecosystem functioning.