Abstract
We report here the main characteristics of ‘Pseudomonas saudimassiliensis’ strain 12M76_airT (CSUR P1220), a new species of the Pseudomonas genus that was isolated from air samples in the city environment of Makkah, Saudi Arabia, during the pilgrim period of Hajj 2012.
Keywords: Air isolates, culturomics, new species, ‘Pseudomonas saudimassiliensis’ sp. nov., Saudi Arabia
As part of a wider culturomics [1] and metagenomics study [2] in Saudi Arabia we isolated a new bacterium named strain 12M76_airT from air samples in the urban environment of Makkah, Saudi Arabia, during the pilgrim period of Hajj 2012. For each air sample, a volume of 1000 L was collected with an FCC-IV biological air sampler (AES Laboratories, Combourg, France) mounted with a nutrient agar plate containing the antifungal agent amphotericin (Majed Al-Buqami Co. BMC, Riyadh, Saudi Arabia) according to the manufacturer’s instructions. No identification was obtained for strain 12M76_airT using our systematic matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) screening on a MicroFlex spectrometer (Bruker Daltonics, Bremen, Germany) [3]. Strain 12M76_airT was cultured in 5% sheep-blood-enriched Columbia agar (bioMérieux, Marcy l'Étoile, France) for 2 days in an aerobic atmosphere at 37°C. On Columbia agar colonies were opaque, round with grey colour and an average size of 1 mm in diameter. Growth of the strain 12M76_airT was observed in both aerobic and anaerobic conditions. No growth was observed at pH values of 5.0 and 6.0, whereas growth occurred at alkaline pH with an optimum at pH ≥10. Strain 12M76_airT is a Gram-negative, rod-shaped, motile, catalase- and oxidase-positive bacterium. Cells from fresh colonies grown on agar exhibit a mean diameter of 0.56 μm and a mean length of 1.22 μm in electron microscopy.
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]. Strain 20_BNT exhibited a 98.5% sequence similarity with Pseudomonas bauzanensis (NR117232.1), which was the phylogenetically closest species with standing nomenclature (Fig. 1). Consequently, it putatively classifies the strain 12M76_airT as a new member of the genus Pseudomonas within the family Pseudomonadaceae in the phylum Proteobacteria. The genus Pseudomonas was first created in 1894 by Migula and an emended description of the genus Pseudomonas was proposed by Yang et al. in 2013 [5]. To date, more than 200 species have been described (http://www.bacterio.cict.fr/c/pseudomonas.html). Members of the genus Pseudomonas are mostly environmental bacteria widely distributed in soil, water and air [6].
Fig. 1.
Phylogenetic tree highlighting the position of ‘Pseudomonas saudimassiliensis’ relative to other phylogenetically closest members of the Pseudomonas genus. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 500 times to generate a majority consensus tree. Only values >95% are displayed. The scale bar represents a 0.5% nucleotide sequence divergence.
Strain 12M76_airT exhibited a 16S rRNA gene sequence divergence >1.3% with P. bauzanensis, the most closely related species with standing in nomenclature, which classifies it as a new representative of the Pseudomonas genus isolated from air samples from the city environment of Makkah, Saudi Arabia, during the pilgrim period of Hajj 2012. As a result, we propose the creation of ‘Pseudomonas saudimassiliensis’ sp. nov., and the strain 12M76_airT as the type strain.
MALDI-TOF MS spectrum accession number. The MALDI-TOF MS spectrum of ‘Pseudomonas saudimassiliensis’ strain 12M76_airT 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 12M76_airT was deposited in GenBank under Accession number LM997413.
Deposit in a culture collection. Strain 12M76_airT was deposited in the Collection de Souches de l’Unité des Rickettsies (CSUR, WDCM 875) under number P1220.
Transparency declaration
The authors have no conflicts of interest to declare.
Acknowledgements
This work was funded by the Deanship of Scientific Research (DSR), King Abdulaziz University, under grant No. (1-141/1433 HiCi). The authors, therefore, acknowledge technical and financial support of KAU.
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