Geodermatophilus pulveris sp. nov., a gamma-radiation-resistant actinobacterium isolated from the Sahara desert

Abstract

A black-pigmented, aerobic actinobacterium, tolerant to ionizing radiation, designated BMG 825 T , was isolated from desert limestone dust in Tunisia. The strain grew within the temperature range 10-40 C, at pH 5.5-11.0 and in the presence of 2 % NaCl. The DNA G+C content was 75.7 mol%, and its cell-wall peptidoglycan contained meso-diaminopimelic acid. Sugars of whole-cell hydrolysates were galactose, glucose, and trace amounts of ribose and mannose. The predominant menaquinone was MK-9(H 4 ), and the major fatty acids were iso-C 16 : 0 and C 16 : 1 !7c. The polar lipid profile comprised phosphatidylcholine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine and an unspecified glycolipid. 16S rRNA gene sequence analysis revealed that the strain fell into the genus Geodermatophilus, showing the highest similarity with Geodermatophilus poikilotrophus DSM 44209 T (99.1 %). DNA-DNA hybridization results, phylogenetic distinctiveness and phenotypic properties supported the classification of this strain as a representative of a novel species of the genus Geodermatophilus, for which the name Geodermatophilus pulveris sp. nov. is proposed. The type strain is BMG 825 T (=CECT 9003 T =DSM 46839 T ).Twenty species are currently described within the genus Geodermatophilus (Hezbri et al., 2015a), and several of these actinobacteria have been reported to be highly resistant to stresses known to give rise to reactive oxygen species such as gamma-radiation, UV and desiccation (Gtari et al., 2012; Hezbri et al., 2015a, b, c). The genome (Ivanova et al., 2010) and recently published proteogenome of Geodermatophilus obscurus (Sghaier et al., 2016) provided a close-up view of mechanisms permitting adaptation to environmental stresses, which are mainly pigmentation, catalase production and repair of double-strand breaks through the non-homologous end joining pathway.Strain BMG 825 T was isolated during an investigation about the dust microbial population in grooves in limestone cliffs from the Tunisian part of the Grand Erg Oriental (English: 'Great Eastern Sand Sea') in the Sahara desert. The sample collected initially was serially diluted in 0.85 % saline solution. Aliquots of each serial dilution were then spread on Luedemann medium (DSMZ medium 877) (Luedemann, 1968) and R2A agar (DSMZ medium 830) (Reasoner et al., 1979), and incubated at 28 C for about 3 weeks. Thereafter, a dry, black colony designated BMG 825 T was isolated. The culture was sub-cultivated on Luedemann medium at 28 C for 7 days. Following purification, the organism was maintained in glycerol (35 %, w/v) stocks at À80 C for further investigations. Strain BMG 825 T was routinely grown on GYM Streptomyces medium (DSMZ medium 65) at 28 C for testing the physiological and biochemical properties, except where mentioned.

Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae

“…It is in accordance with patterns obtained for the closely related species investigated in this study ( Figures 3b–d ) and the phospholipid pattern revealed by Bertazzo et al (2014) for G. brasiliensis . The randomForest analysis detected the lack of phosphatidylcholine and the presence of glycophosphatidylinositol as excellently predictive of the prospective new genus, whereas the absence of phosphatidylglycerol was also observed in other Geodermatophilus species ( Bertazzo et al, 2014 ; Montero-Calasanz et al, 2014b , 2015 ; Hezbri et al, 2015a , b , c , 2016a ). The unambiguous presence of hydroxyphosphatidylethanolamine is a slightly less relevant taxonomic marker for the prospective new genus; among core Geodermatophilus it was only detected in the polar lipid profile of G. pulveris DSM 45839 T by Hezbri et al (2016a) .…”

“…The properties are as given in the species description by Hezbri et al (2016a) with the following modification. The genomic G+C content is 75.6%.…”

“…The number of Geodermatophilus isolates is expected to continue to raise in coming years, as indicated by metagenomics studies carried out in arid and hyper-arid habitats ( Neilson et al, 2012 ; Giongo et al, 2013 ). Species belonging to the genus are indeed mainly isolated from arid soils and characterized by tolerance against oxidative stress ( Gtari et al, 2012 ; Montero-Calasanz et al, 2013a , 2014 , 2015 ; Hezbri et al, 2015a , 2016a ) although some isolates from rhizospheric soils and lake sediments have also been classified within the genus.…”

Geodermatophilus chilensis sp. nov., from soil of the Yungay core-region of the Atacama Desert, Chile

“…Despite the recent surge in the number of Geodermatophilus species the genus remains underspeciated [18][19][20]. Geodermatophilus strains tend to be associated with soils, notably desert soils [1,16,[21][22][23][24][25][26][27][28][29][30] though there is evidence that they are more widely distributed in the environment [15,30,31].…”

“…Phenotypic properties that differentiate Geodermatophilus chilensis isolates. B12 T , B20 and B25 from closely related type-strains of the genus Geodermatophilus.Strains: 1, B12 T , B20 and B25 (data from this study); 2, G. africanus DSM 45422 T[58]; 3, G. obscurus DSM 43160 T (data from this study, unless indicated); 4, G. poikilotrophus DSM 44209 T[64,73]; 5, G. pulveris DSM 46829 T[79]; 6, G. ruber DSM 45317 T[55]; 7, G. sabuli DSM 46844 T[31]; 8, G. siccatus DSM 45419 T[29].…”