Abstract
We report here the main characteristics of ‘Halomonas saudii’ strain Saudii DR2 (CSUR P2512), a new species of the Halomonas genus that was isolated from a rhizosphere of Halocnemum strobilaceum in April 2015.
Keywords: Culturomics, ‘Halomonas saudii’ sp. nov., Halocnemum strobilaceum, New species, Saudi Arabia
As a part of a wider culturomics [1] and metagenomics study [2] in Saudi Arabia, we isolated a new bacterium, strain Saudii DR2, from a rhizosphere of Halocnemum strobilaceum in April 2015. No identification was obtained for the strain Saudii DR2 using systematic matrix-assisted desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) screening on a MicroFlex spectrometer (Bruker Daltonics, Bremen, Germany). The strain Saudii DR2 was cultured in a homemade liquid medium [3] incubated for 2 days in an aerobic atmosphere at 37°C. Optimal growth for this strain was obtained at 37°C at pH 7; strain Saudii DR2 is halotolerant and tolerates NaCl concentration up to 20%. Saudii DR2 is a Gram-negative bacterium, is motile non–spore forming and does not exhibit catalase or oxidase activities. The growing colonies on our homemade culture medium were orange, circular, entire, smooth and convex, with a diameter of 1.0 to 2.0 mm.
The complete 16S rRNA gene was sequenced using fD1-rP2 primers as previously described and a 3130-XL sequencer (Applied Biosciences, Saint Aubin, France) [4]. The strain Saudii DR2 exhibited a 98.3% sequence similarity with Halomonas xianhensis (GenBank accession no. NR116016.1), which was the phylogenetically closest species with standing in nomenclature (Fig. 1). Consequently, it putatively classifies the strain Saudii DR2 as a new member of the genus Halomonas within the family Halomonadaceae in the phylum Proteobacteria. H. xianhensis was first described by Zhao et al. [5] in 2012 as an aerobic, Gram-negative, short rod-shaped, moderately halophilic bacterium. So far, the genus Halomonas includes more than 80 species with validly published names [6]. Strain Saudii DR2 exhibited a 16S rRNA gene sequence divergence of >1.3% with H. xianhensis, the closest related species with standing in nomenclature, which classifies it as a new representative of the Halomonas genus isolated from H. strobilaceum. As a result, we propose the creation of ‘Halomonas saudii’ sp. nov., and the strain Saudii DR2 as the type strain.
Fig. 1.
Phylogenetic tree highlighting position of ‘Halomonas saudii’ (in red) relative to other phylogenetically closest members of Halomonas genus. Number at node is percentage of bootstrap value obtained by repeating analysis 500 times to generate majority consensus tree. Only values >95% were displayed. Scale bar represents 2% nucleotide sequence divergence.
MALDI-TOF MS spectrum accession number
The MALDI-TOF MS spectrum of Saudii DR2 is available online (http://www.mediterranee-infection.com/article.php?laref=256&titre=urms-database).
Nucleotide sequence accession number
The 16S rRNA gene sequence of the strain Saudii DR2 was deposited in GenBank under accession number LT 558840.1.
Deposit in a culture collection
Strain Saudii DR2 was deposited in the Collection de Souches de l'Unité des Rickettsies (CSUR, WDCM 875) under number P2512.
Acknowledgements
This project was funded by the National Plan for Science, Technology and Innovation (MAARIFAH), King Abdulaziz City for Science and Technology, Kingdom of Saudi Arabia (award 12BIO2724-03). The authors also acknowledge with thanks the members of the Science and Technology Unit, King Abdulaziz University, for technical support.
Conflict of Interest
None declared.
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