Halophilic archaea cultivated from surface sterilized middle-late eocene rock salt are polyploid

Salla T Jaakkola; Karolin Zerulla; Qinggong Guo; Ying Liu; Hongling Ma; Chunhe Yang; Dennis H Bamford; Xiangdong Chen; Jörg Soppa; Hanna M Oksanen

doi:10.1371/journal.pone.0110533

Halophilic archaea cultivated from surface sterilized middle-late eocene rock salt are polyploid

PLoS One. 2014 Oct 22;9(10):e110533. doi: 10.1371/journal.pone.0110533. eCollection 2014.

Authors

Affiliations

¹ Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki, Finland.
² Institute for Molecular Biology, Goethe-University Frankfurt am Main, Frankfurt am Main, Germany.
³ State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China.
⁴ Institute of Rock and Soil Mechanics, The Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
Biological Evolution
China
DNA, Archaeal / genetics*
Genome, Archaeal*
Geologic Sediments / microbiology
Halobacteriaceae / classification
Halobacteriaceae / genetics*
Halobacteriaceae / isolation & purification
Molecular Sequence Data
Phylogeny
Polyploidy*
RNA, Ribosomal, 16S / genetics*
Salts

Substances

DNA, Archaeal
RNA, Ribosomal, 16S
Salts

Associated data

GENBANK/KJ917623
GENBANK/KJ917624
GENBANK/KJ917625
GENBANK/KJ917626
GENBANK/KJ917627
GENBANK/KJ917628
GENBANK/KJ917629
GENBANK/KJ917630

Grants and funding

This study was supported by Academy Professor (Academy of Finland; http://www.aka.fi) funding grants 255342 and 256518 (to DHB), the German Research Council (DFG; http://www.dfg.de) with the project So264/16 (to JS), and by grants from the National Basic Research Program of China (973 Program) no. 2011CB808800 (http://www.973.gov.cn/Default_3.aspx), Ministry of Science and Technology of the People's Republic of China (to XC). STJ is a University of Helsinki fellow of the Integrative Life Science Doctoral Program (ILS; http://www.finbionet.fi/ils/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.