Transcriptome analysis of Haloquadratum walsbyi: vanity is but the surface

Abstract

Background Haloquadratum walsbyi dominates saturated thalassic lakes worldwide where they can constitute up to 80-90% of the total prokaryotic community. Despite the abundance of the enigmatic square-flattened cells, only 7 isolates are currently known with 2 genomes fully sequenced and annotated due to difficulties to grow them under laboratory conditions. We have performed a transcriptomic analysis of one of these isolates, the Spanish strain HBSQ001 in order to investigate gene transcription under light and dark conditions.ResultsDespite a potential advantage for light as additional source of energy, no significant differences were found between light and dark expressed genes. Constitutive high gene expression was observed in genes encoding surface glycoproteins, light mediated proton pumping by bacteriorhodopsin, several nutrient uptake systems, buoyancy and storage of excess carbon. Two low expressed regions of the genome were characterized by a lower codon adaptation index, low GC content and high incidence of hypothetical genes.ConclusionsUnder the extant cultivation conditions, the square hyperhalophile devoted most of its transcriptome towards processes maintaining cell integrity and exploiting solar energy. Surface glycoproteins are essential for maintaining the large surface to volume ratio that facilitates light and organic nutrient harvesting whereas constitutive expression of bacteriorhodopsin warrants an immediate source of energy when light becomes available.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3892-2) contains supplementary material, which is available to authorized users.

Halobacterium salinarum and Haloferax volcanii Comparative Transcriptomics Reveals Conserved Transcriptional Processing Sites

“…J7-2 and Haloquadratum walsbyi . H. walsbyi , a hyperhalophilic organism isolated from a brine pool in Egypt [ 41 ], was probed under different illumination conditions by regular RNA-seq [ 42 ]. This experiment revealed a coverage signal peak around an equivalent position inside kef1 (HQ_RS10745 locus , D = 71) ( Figure S3b ).…”

Prokaryotic Communities in the Thalassohaline Tuz Lake, Deep Zone, and Kayacik, Kaldirim and Yavsan Salterns (Turkey) Assessed by 16S rRNA Amplicon Sequencing

“…In the present study, we determined a lower diversity of extremely halophilic archaea in the Deep Zone ( Table 2 and Figure 3 ), which contained higher Na + and Cl − concentrations compared to the other sampling sites ( Table S1 ). Haloquadratum is considered the most hyperhalophilic organism known and dominates NaCl supersaturated thalassic lakes where the other halophilic archaea are eliminated by the uninhabitable conditions [ 72 ]. Moreover, the concentration of NaCl in the crystallizer ponds due to evaporation of the saline water finally results in the precipitation of sodium chloride (halite); consequently, a MgCl 2 rich brine is produced.…”

Ubiquitousness of Haloferax and Carotenoid Producing Genes in Arabian Sea Coastal Biosystems of India

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