Rich mobilomes and a conserved adaptive core in bacteria from an intensifying Mexican soda lake

Abstract

The haloalkaline maar lake at Rincón de Parangueo, in central Mexico’s volcanic belt, is a doubly extreme habitat where high salinity and high alkalinity co-occur. Unlike the long-lived soda lakes that dominate the literature, it is a young system undergoing rapid desiccation, its salinity and pH intensifying over decades. Its microbes have been surveyed only by 16S amplicons, with no genome or mobilome reported from the site, and the wider soda-lake mobilome is known almost entirely from host-unlinked, short-read viromes. Using long-read sequencing, we recovered high-quality genomes for six isolates that dereplicate to three independent, bona fide haloalkaliphilic lineages spanning two distant families (Halomonadaceae, Bacillaceae). Each lineage’s closest relative is not its type strain but an isolate from another distant extreme habitat, including two other Mexican hypersaline systems. All three are aerobic, facultatively fermentative heterotrophs that meet high pH and salinity with the canonical toolkit — multisubunit Mrp/Mnh Na+/H+ antiporters and a “salt-out” compatible-solute strategy — whose distribution tracks phylogeny, with only complementary lineage-specific elaboration. In contrast, the isolates carry an unexpectedly rich and apparently active mobilome: a novel plasmid, multiple intact prophages, and multiple other mobile genetic elements alongside an above-average antiviral defense arsenal, including an 89-spacer CRISPR array. Horizontal transfer is thus likely active at Rincón de Parangueo but is not the vehicle of haloalkaliphily. Intensifying extremes like this one are tractable natural laboratories for dissecting how inherited toolkits and recent innovation shape microbial survival at the limits of life.