Background: Haloquadratum walsbyi dominates saturated thalassic lakes worldwide where they can constitute upto 80-90% of the total prokaryotic community. Despite the abundance of the enigmatic square-flattened cells, only7 isolates are currently known with 2 genomes fully sequenced and annotated due to difficulties to grow themunder laboratory conditions. We have performed a transcriptomic analysis of one of these isolates, the Spanishstrain HBSQ001 in order to investigate gene transcription under light and dark conditions.Results: Despite a potential advantage for light as additional source of energy, no significant differences werefound between light and dark expressed genes. Constitutive high gene expression was observed in genesencoding surface glycoproteins, light mediated proton pumping by bacteriorhodopsin, several nutrient uptakesystems, buoyancy and storage of excess carbon. Two low expressed regions of the genome were characterized bya lower codon adaptation index, low GC content and high incidence of hypothetical genes.Conclusions: Under the extant cultivation conditions, the square hyperhalophile devoted most of its transcriptometowards processes maintaining cell integrity and exploiting solar energy. Surface glycoproteins are essential formaintaining the large surface to volume ratio that facilitates light and organic nutrient harvesting whereas constitutiveexpression of bacteriorhodopsin warrants an immediate source of energy when light becomes available.
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