# 'Halomonas saudii' sp. nov., a new bacterial species isolated from marine plant Halocnemum strobilaceum

F. Bibi, M. Yasir, S. A. Alvi, E. I. Azhar, A. A. K. Al-Ghamdi, A. M.

Abuzenadah, Didier Raoult, E. Angelakis

► To cite this version:

F. Bibi, M. Yasir, S. A. Alvi, E. I. Azhar, A. A. K. Al-Ghamdi, et al., 'Halomonas saudii' sp. nov., a new bacterial species isolated from marine plant Halocnemum strobilaceum. New Microbes and New Infections, 2017, 15, pp.42-43. 10.1016/j.nmni.2016.11.007. hal-01795930

HAL Id: hal-01795930

https://amu.hal.science/hal-01795930v1

Submitted on 3 Sep 2024

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# ‘Halomonas saudii’ sp. nov., a new bacterial species isolated from marine plant *Halocnemum strobilaceum*

F. Bibi¹, M. Yasir¹, S. A. Alvi¹, E. I. Azhar¹,², A. A. K. Al-Ghamdi², A. M. Abuzenadah³,⁴, D. Raoult⁵ and E. Angelakis⁵

1) Special Infectious Agents Unit, King Fahd Medical Research Center, 2) Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, 3) Center of Excellence in Genomic Medicine Research (CEGMR), 4) KACST Technology Innovation Center in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia and 5) Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, URMITE CNRS-IRD 198 UMR 6236, Aix-Marseille Université, Faculté de Médecine, Marseille, France

## 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.
© 2016 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases.

**Keywords:** Culturomics, *'Halomonas saudii'* sp. nov., *Halocnemum strobilaceum*, New species, Saudi Arabia

**Original Submission:** 6 October 2016; **Revised Submission:** 31 October 2016; **Accepted:** 9 November 2016

**Article published online:** 15 November 2016

**Corresponding author:** E. Angelakis, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, URMITE CNRS-IRD 198 UMR 6236, Aix Marseille Université, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille, France
**E-mail:** e.angelakis@hotmail.com

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 fDI-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.

## 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).
<figure><img src="image_2.png" /><figcaption>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.</figcaption></figure>

## 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.

## References

[1] Angelakis E, Raoult D. Methods for the discovery of emerging pathogens. Microb Pathog 2014;77:114-8.

[2] Angelakis E, Yasir M, Bachar D, Azhar El, Lagier JC, Bibi F, et al. Gut microbiome and dietary patterns in different Saudi populations and monkeys. Sci Rep 2016;6:32191.

[3] Khelaifia S, Croce O, Lagier JC, Robert C, Couderc C, Di Pinto F, et al. Noncontiguous finished genome sequence and description of *Virgibacillus massiliensis* sp. nov., a moderately halophilic bacterium isolated from human gut. New Microb New Infect 2015;8:78-88.

[4] Safont M, Angelakis E, Richet H, Lepidi H, Fournier PE, Drancourt M, et al. Bacterial lymphadenitis at a major referral hospital in France from 2008 to 2012. J Clin Microbiol 2014;52:1161-7.

[5] Zhao B, Wang H, Mao X, Li R, Zhang YJ, Tang S, et al. *Halomonas xianensis* sp. nov., a moderately halophilic bacterium isolated from a saline soil contaminated with crude oil. Int J Syst Evol Microbiol 2012;62:173-8.

[6] Seck EH, Fournier PE, Raoult D, Khelaifia S. 'Halomonas massiliensis' sp. nov., a new halotolerant bacterium isolated from the human gut. New Microb New Infect 2016;14:19-20.