Characterization of the mechanism of prolonged adaptation to osmotic stress of Jeotgalibacillus malaysiensis via genome and transcriptome sequencing analyses.

Amira Suriaty Yaakop,Robson Ee,Siew-Kim Lee,Kok-Gan Chan,Yan Lue Lim,Kian Mau Goh,Fazilah Abd Manan

doi:10.1038/srep33660

Abstract

Jeotgalibacillus malaysiensis, a moderate halophilic bacterium isolated from a pelagic area, can endure higher concentrations of sodium chloride (NaCl) than other Jeotgalibacillus type strains. In this study, we therefore chose to sequence and assemble the entire J. malaysiensis genome. This is the first report to provide a detailed analysis of the genomic features of J. malaysiensis, and to perform genetic comparisons between this microorganism and other halophiles. J. malaysiensis encodes a native megaplasmid (pJeoMA), which is greater than 600 kilobases in size, that is absent from other sequenced species of Jeotgalibacillus. Subsequently, RNA-Seq-based transcriptome analysis was utilised to examine adaptations of J. malaysiensis to osmotic stress. Specifically, the eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) and KEGG (Kyoto Encyclopaedia of Genes and Genomes) databases were used to elucidate the overall effects of osmotic stress on the organism. Generally, saline stress significantly affected carbohydrate, energy, and amino acid metabolism, as well as fatty acid biosynthesis. Our findings also indicate that J. malaysiensis adopted a combination of approaches, including the uptake or synthesis of osmoprotectants, for surviving salt stress. Among these, proline synthesis appeared to be the preferred method for withstanding prolonged osmotic stress in J. malaysiensis.

Highlights

IntroductionMany halophiles have been well characterized; Jeotgalibacillus remains one of the least-studied genera in terms of the number of published reports, as well as the total number of strains characterized
Comparative genomic analyses were performed between J. malaysiensis (JMA) and the halophilic microorganisms J. alimentarius (JAL)[13], J. campisalis (JCA)[14], J. soli (JSO)[15], Planococcus halocryophilus (PLA)[16], Salinibacter ruber (SRU)[2], Chromohalobacter salexigens (CHR)[17], Halobacillus halophilus (HAH)[18], and Dehalobacter restrictus (DEH)[19] (Table 1)
Phylogenetic tree analyses indicated that all Jeotgalibacillus spp. clustered together, but separately from other halophilic microorganisms

Summary

Introduction

Many halophiles have been well characterized; Jeotgalibacillus remains one of the least-studied genera in terms of the number of published reports, as well as the total number of strains characterized. Six species of Jeotgalibacillus have been identified: J. alimentarius[9], J. marinus[10], J. campisalis[10], J. salarius[10], J. soli[11], and the most recently characterized type strain, J. malaysiensis[12]. We analysed and compared the complete genome sequence of this microorganism, together with draft genomes of J. alimentarius, J. campisalis, and J. soli, to the published genomes of five halophilic bacteria and of one halophilic archaeon. We evaluated the transcriptomic responses of J. malaysiensis to osmotic stress via RNA sequencing (RNA-Seq) analysis of cells cultivated under low and high NaCl conditions

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