Genome-based taxonomy and provirus identification in Halococcus from hypersaline environments

Halococcus species are widely distributed in hypersaline environments and possess unusual cell wall structures. However, their genomic diversity, antiviral defenses, and interactions with viruses remain poorly understood. Here, we sequenced and analyzed the genomes of seven Halococcus strains isolated from hypersaline habitats. Comparative analyses showed substantial variation in growth dynamics, genome size, and defense repertoires, revealing considerable differences among species within the genus. Growth analyses showed distinct behavior among closely related strains, with slow-growing isolates strongly associated with the presence of proviruses, suggesting a fitness cost of lysogeny. Genome-based metrics, including ANI and dDDH, indicated that five of the seven isolates represent four novel species candidates. Two divergent Caudoviricetes-like proviruses were identified. A CRISPR spacer-protospacer match in one strain suggests virus-host interactions and may indicate maintenance of lysogeny. The low sequence similarity of these proviruses to known archaeal viruses supports the existence of previously unrecognized viral lineages infecting Halococcus, providing new insights into the ecology and evolution of this genus in extreme saline environments.