Expanding genomic resources for heritage science: characterization of selected microbial isolates from salt-weathered...

On historic masonry and plaster, moisture-driven salt crystallization cycles impose mechanical stress and create niches for halophilic and halotolerant microbial communities. Halotolerant/halophilic microorganisms isolated from these man-made heritage environments are usually not as well characterized as those isolated from natural environments and represent a genetic and biotechnological potential that has not been thoroughly studied to date.

This study provides insights into the genomes of five selected halophilic and halotolerant microorganisms isolated from two salt-weathered heritage sites in Austria: the subterranean St. Virgil Chapel beneath St. Stephen's Cathedral (13th century) and the Charterhouse Mauerbach (14th century). Isolates displaying coloration under 10-20% NaCl were sequenced using Oxford Nanopore long-read technology, yielding complete genomes and plasmids. Functional annotation focused on metabolic, osmoregulatory and pigment biosynthesis pathways to elucidate adaptive strategies underpinning their persistence under extreme salinity.

Comparative genomic analyses revealed variations between the isolated strains with their respective references, as well as species-specific traits that have not been described in detail before and confirmed the presence of robust carotenoid pathways including bacterioruberin synthesis in Halococcus, mixed C40/C50 carotenoids in Nesterenkonia, and C30/C40 carotenoids in Halobacillus. Furthermore, two isolates, Marinobacter sp. 119-V2 and Modicisalibacter sp. 110-V3, likely represent novel taxa, indicating that salt-weathered heritage sites represent a specific environmental niche that selects for specific microbial colonizers.

By integrating cultivation, phenotypic characterization, and genomic analysis, this work advances beyond descriptive community surveys toward mechanistic understanding of microbial functions relevant to conservation science. Genome-informed insights into pigment biosynthesis and osmotic stress response help predict microbial behavior under environmental or treatment-induced salinity fluctuations, supporting the development of targeted, scientifically grounded preservation approaches for salt-affected cultural heritage.