Halophilic Archaea Cultivated from Surface Sterilized Middle-Late Eocene Rock Salt Are Polyploid

Abstract

Live bacteria and archaea have been isolated from several rock salt deposits of up to hundreds of millions of years of age from all around the world. A key factor affecting their longevity is the ability to keep their genomic DNA intact, for which efficient repair mechanisms are needed. Polyploid microbes are known to have an increased resistance towards mutations and DNA damage, and it has been suggested that microbes from deeply buried rock salt would carry several copies of their genomes. Here, cultivable halophilic microbes were isolated from a surface sterilized middle-late Eocene (38–41 million years ago) rock salt sample, drilled from the depth of 800 m at Yunying salt mine, China. Eight unique isolates were obtained, which represented two haloarchaeal genera, Halobacterium and Halolamina. We used real-time PCR to show that our isolates are polyploid, with genome copy numbers of 11–14 genomes per cell in exponential growth phase. The ploidy level was slightly downregulated in stationary growth phase, but the cells still had an average genome copy number of 6–8. The polyploidy of halophilic archaea living in ancient rock salt might be a factor explaining how these organisms are able to overcome the challenge of prolonged survival during their entombment.

Polyploidy in Archaea and Bacteria: About Desiccation Resistance, Giant Cell Size, Long-Term Survival, Enforcement by a Eukaryotic Host and Additional Aspects

“…The maintenance energy could originate from dead and lysed cells that were originally also entrapped in the same liquid inclusion. Recently, the chromosome copy numbers have been determined from three clones that have been freshly isolated from an ancient halite, and indeed, all three were found to be polyploid [Jakkola et al, 2014].…”

The complete genome of a viable archaeum isolated from 123‐million‐year‐old rock salt

“…These small coccoid cells might be archaeal resting cells. In addition, Halobacterium cells isolated from middle to late Eocene halite grew as tiny, clustered cocci instead of rods typical of Halobacterium species (Jaakkola et al ., ). It seems that archaea in general deploy a range of survival methods despite not being able to sporulate: desiccated cells of Methanosarcina barkeri have an enhanced tolerance towards high temperatures, radiation and oxygen (Anderson et al ., ), and Methanosarcina soligelidi , an isolate from Siberian permafrost, has remarkable resistance towards desiccation, freezing and thawing (Wagner et al ., ).…”

Patterns and Determinants of Halophilic Archaea (Class Halobacteria) Diversity in Tunisian Endorheic Salt Lakes and Sebkhet Systems

“…are encountered (12,14,(27)(28)(29)(30)(31)(32)(33), extrapolation of diversity and community structure studies to these atypical, nonhypersaline habitats is warranted. Such studies would expand our knowledge regarding overall diversity and ecological distribution within the Halobacteria and aid in deciphering the importance of various factors, e.g., salinity, physical characteristics, and geographical location, on shaping their diversity and community structure patterns.…”