Meanwhile, the deeper evolutionary divergences observed with other species points to the long-term evolutionary isolation and specialization of lineages that have adapted to distinct ecological niches, like Haloarcula, Halococcoides and Halodesulfurarcheum genera. From a broader haloarchaeal evolution perspective, the clear separation of Halobacterium from other genera (like Haloferax, Haloarcula,) reinforces that haloarchaea have diversified into multiple lineages that, despite sharing extreme halophily, have long independent evolutionary histories​. Such insights can inform how haloarchaeal species may have radiated into different ecological niches, since some clusters consist of strains isolated from similar habitats (salt mines, salterns, etc.), indicating that geographic or environmental factors played a role in their divergence [100].

The close genetic relationships within Halobacterium clade suggest that recent evolutionary pressures have maintained high genetic similarity, likely due to similar environmental conditions and adaptive strategies. We propose that their evolutionary adaptations have been driven more by microenvironmental pressures not involving large-scale genetic changes within a relatively recent evolutionary timeframe, which might explain their close phylogenetic clustering. This highlights the importance of integrating phylogenetic, genomic, and ecological data to better understand microevolution in halophilic organisms.

We hypothesize that Halobacterium salinarum AD88, isolated from CCB, has acquired genetic adaptations absent in previously studied strains, given the distinct ecological pressures present in the Cuatro Cienegas Basin (CCB) and limited number of cultured H. salinarum strains

Recent studies have shown that a particular site at CCB harbors an extensive archaeal diversity. This site, named Archaean Domes (AD) given the microbial mats that form dome-like structures under wet conditions, is particularly rich in members of the Euryarchaeota phylum, which includes halophiles and methanogens, showing a relative abundance of approximately 14% over seven years

Overall, the genome of Halobacterium salinarum is highly dynamic and polyploid, typically possessing between 10 and 30 copies of its genome per cell [14, 15]. With an average genome size of ~2.0 Mbp and high G+C content (60%) [2, 16], Halobacterium sp. NRC-1, generally holds two 191 and 365 kbp-containing mega-plasmids, pNRC100 and pNRC200, respectively, which encode several genes essential for the organism’s survival in saline environments

easy culturing, and tractability

bacteriorhodopsin

Its sophisticated mechanisms for ion regulation, osmoregulation, and phototrophic growth exemplify versatility for stress resistance and energy acquisition

gram-negative

as essentially all of the genetically accessible archaeal organisms require unique culturing techniques that present real challenges