Ancient saltern metagenomics: tracking changes in microbes and their viruses from the underground to the surface

Abstract

Microbial communities in hypersaline underground waters derive from ancient organisms trapped within the evaporitic salt crystals and are part of the poorly known subterranean biosphere. Here, we characterized the viral and prokaryotic assemblages present in the hypersaline springs that dissolve Triassic-Keuper evaporite rocks and feed the Añana Salt Valley (Araba/Alava, Basque Country, Spain). Four underground water samples (around 23% total salinity) with different levels of exposure to the open air were analysed by means of microscopy and metagenomics. Cells and viruses in the spring water had lower concentrations than what are normally found in hypersaline environments and seemed to be mostly inactive. Upon exposure to the open air, there was an increase in activity of both cells and viruses as well as a selection of phylotypes. The underground water was inhabited by a rich community harbouring a diverse set of genes coding for retinal binding proteins. A total of 35 viral contigs from 15 to 104 kb, representing partial or total viral genomes, were assembled and their evolutionary changes through the spring system were followed by SNP analysis and metagenomic island tracking. Overall, both the viral and the prokaryotic assemblages changed quickly upon exposure to the open air conditions.

Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species

“…At the gene level, 90.6% of pN/pS ratios were less than 0.4, much lower ( P < 0.0001) than those observed for viral assemblages present in underground saline waters from hypersaline springs 55 ( Figure 5a, Supplementary Figure 10 and Supplementary Table 13 ), indicating that most cold seep viral genes were under strong purifying selection. However, genes under positive selection were also detected in relation to viral DNA replication, recombination, repair and maturation ( Figure 5b ), including terL , polA and dnaB with abnormally high pN/pS values ( Supplementary Table 13 ).…”

“…(a) pN/pS ratio of viral genes from cold seeps (this study) and viral genes from an ancient saltern 55 . (b) Viral genes under positive selection in active and extinct cold seeps.…”

Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species

“…At the gene level, 90.6% of pN/pS ratios were less than 0.4, much lower ( p < 0.0001) than those observed for viral assemblages present in underground saline waters from hypersaline springs [ 64 ] (Fig. 5a , Supplementary Fig.…”

Water is a preservative of microbes

“…The oceans, populated by microbes, are for the most part nutrient‐depleted (Kelly et al ., 2021; Rech et al ., 2021) so they also act as a planetary‐scale repository for viable microorganisms. It is likely that climate change will lead to the large‐scale release of nutrients into aqueous environments (Feng et al ., 2020; Duerschlag et al ., 2021; Kluge et al ., 2021), lead to the emergence of new or old pathogens (Revich et al ., 2012), and in places may promote the dissolution of some ancient salt deposits in which preserved microbes (from past biospheres) are abundant (Ramos‐Barbero et al , 2021; Pedrós‐Alió, 2021). Episodes of climate change have occurred throughout the Earth’s geological history, driven by factors such as volcanic activity (Robock, 2000).…”