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

Abstract

Live microbes have been isolated from rock salt up to Permian age. Only obligatory cellular functions can be performed in halite-buried cells. Consequently, their genomic sequences are likely to remain virtually unchanged. However, the available sequence information from these organisms is scarce and consists of mainly ribosomal 16S sequences. Here, live archaea were isolated from early Cretaceous (∼ 123 million years old) halite from the depth of 2000 m in Qianjiang Depression, Hubei Province, China. The sample was radiologically dated and subjected to rigorous surface sterilization before microbe isolation. The isolates represented a single novel species of Halobacterium, for which we suggest the name Halobacterium hubeiense, type strain Hbt. hubeiense JI20-1. The species was closely related to a Permian (225-280 million years old) isolate, Halobacterium noricense, originating from Alpine rock salt. This study is the first one to publish the complete genome of an organism originating from surface-sterilized ancient halite. In the future, genomic data from halite-buried microbes can become a key factor in understanding the mechanisms by which these organisms are able to survive in harsh conditions deep underground or possibly on other celestial bodies.

Whole‐genome comparison between the type strain of Halobacterium salinarum (DSM 3754T) and the laboratory strains R1 and NRC‐1

“…The plasmids share a perfect duplication of 39,230 bp. The overall genomic arrangement of a highly GC‐rich chromosome with less GC‐rich plasmids that carry extensive duplications is similar to that found in other Halobacterium strains (Jaakkola et al, ; Lim et al, ; Ng et al, ; Pfeiffer, Schuster, et al, ) (see also Appendix 3).…”

“…For the chromosome, we adopted the convention of choosing a position close to a canonical replication origin. However, we used a biologically relevant variation that we have used previously for Natronomonas moolapensis (Dyall‐Smith et al, ) and Halobacterium hubeiense (Jaakkola et al, ). Most haloarchaeal genomes contain a canonical replication origin that is flanked on one side by a distinctive, highly conserved paralog of the Orc/Cdc6 family, and on the other side by a highly conserved but divergently transcribed three‐gene cluster ( oapABC ; oap: origin‐associated protein).…”

Computational Exploration of Putative LuxR Solos in Archaea and Their Functional Implications in Quorum Sensing

“…and drives various biogeochemical cycles like sulfur, nitrogen, and carbon. Most of the sequences are from halophilic (Enache et al, 2007) archaea followed by thermophilic (Jaakkola et al, 2016), piezophilic (Vannier et al, 2011), methanogenic (Borrel et al, 2013), alkaliphilic (Xu et al, 1999), ammonia oxidizing (Mosier et al, 2012), etc. More than 95% archaea are the inhabitant of aquatic (marine and fresh-water) ecosystem and rest belongs to terrestrial one.…”

“…More than 95% archaea are the inhabitant of aquatic (marine and fresh-water) ecosystem and rest belongs to terrestrial one. Oldest archaea with LuxR domain containing protein is isolated from stromatolites (∼3 billion years) and early cretaceous (∼123 million years) halite was Halococcus hamelinensis 100A6 (Goh et al, 2006) and Halobacterium hubeiense (Jaakkola et al, 2016), respectively.…”

How to Search for Life in Martian Chemical Sediments and Their Fluid and Solid Inclusions Using Petrographic and Spectroscopic Methods

“…Fish et al (2002) extracted ancient bacterial and archaeal DNA from 11-425 myr halites. Recently, the genome was reported for a Halobacterium noricense-related archaeum isolated from 123-million year-old halite (Jaakkola et al, 2016).…”