Description of Domibacillus indicus sp. nov., isolated from ocean sediments and emended description of the genus Domibacillus

Abstract

). The genomic DNA G+C content was 37.4 mol% and the strain showed 37.7 % DNA-DNA relatedness to D. robiginosus DSM 25058 T . The major fatty acids were anteiso-C 15 : 0 , C 16 : 0 , iso-C 15 : 0 and iso-C 16 : 0 and MK-6 was the predominant quinone. The polar lipid profile of strain SD111T consisted of unidentified phospholipids (PL1 and PL2), phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG). The cell wall contained mesodiaminopimelic acid and the peptidoglycan was of A1c type. Glucose and ribose were detected as major cell-wall sugars. Results from polyphasic studies indicated that SD111 T represents a novel species of the genus Domibacillus for which the name Domibacillus indicus sp. nov. is proposed. The type strain is SD111 T (5MCC 2255 T 5DSM 28032 T ).The genus Domibacillus was described by Seiler et al. (2013) to incorporate a strain of a bacterium that formed red-pigmented colonies isolated from a pharmaceutical clean room in eastern Germany based on its morphological, chemotaxonomic and phylogenetic differences from closely related members of the genera Bacillus, Jeotgalibacillus and Planococcus. Taxonomically Domibacillus belongs to the phylum Firmicutes, class Bacilli, order Bacillales and family Bacillaceae (Parte, 2014). At the time of writing only a single species (Domibacillus robiginosus) with a validly published name is included in the genus Domibacillus. Members of the genus Domibacillus are Gram-stain-positive, spore-forming, oxidative, motile and strictly aerobic rods. The presence of MK-6 as the dominant quinone is one of the characteristic features of the genus. The cell-wall peptidoglycan is of A1c type, with meso-diaminopimelic acid, and glucose and ribose are dominant cell-wall sugars. Based on differences in phylogenetic, chemotaxonomic and phenetic characteristics between a novel strain, SD111 T , and D. robiginosus DSM 25058 T , in current study we propose that strain SD111T represents a novel species of the genus Domibacillus. Strain SD111T was isolated from a sediment sample collected from Lakshadweep, India, using seawater agar (HiMedia) after 72 h of incubation at 30 u C. Purity of the culture was checked by restreaking several times on the same medium, microscopic observation and 16S rRNA gene sequencing. Glycerol (20 % w/v) stocks of pure culture were preserved in liquid nitrogen at the Microbial Culture Collection (MCC), National Centre for Cell Science (Pune, India) for further study. For SSU rRNA gene sequencing, genomic DNA was extracted using a standard phenol/ chloroform method (Marmur 1961) and the 16S rRNA gene sequence was amplified using the 27F (AGAGTTTGATC-MTGGCTCAG) and 1492R (GGTTACCTTGTTACGAC-TT) eubacterial primers (Lane, 1991). The PCR product was purified using a Rapid Tip kit from Diffinity Genomics and DNA sequencing was carried out using an ABI PRISM Big Dye Terminator v3.1 Cycle Sequencing kit on a 3730xl Genetic Analyzer (Applied Biosystems). The sequence data were edited with the ChromasPro software as discussed by Prakash et al. (2014). A cont...

Microbial composition in seasonal time series of free tropospheric air and precipitation reveals community separation

“…? oxidation , Domibacillus (Firmicutes), a gram-positive, spore-forming, aerobic, nonmotile, rod-shaped organism isolated from deep-sea sediment (Sun and Sun 2016), ocean sediment (Sharma et al 2014), mangrove sediment soil and macroalgae (Verma et al 2017) and GP1 (Acidobacteria), found in alpine grassland on the Tibetian Plateau (Yuan et al 2014). Winter samples were more characterized by extremophile but omnipresent bacteria like Bifidobacterium (Actinobacteria) that can withstand a high range of pH (from 8 to 2) (Charteris et al 1998), Vulcaniibacterium, a thermotolerant Gammaproteobacteria isolated from a geothermally heated soil (Yu et al 2013), and Polaribacter (Bacteriodetes), which has been found in several arctic habitats (Cuthbertson et al 2017;Harding et al 2011;Collins et al 2010).…”

Insights into Diversity and Imputed Metabolic Potential of Bacterial Communities in the Continental Shelf of Agatti Island

“…This bacterium showed 97.6% 16S rRNA gene sequence similarity with the only other species reported, i.e. Domibacillus robiginosus strain WS 4628 T , in genus Domibacillus [31]. We were also able to isolate the bacterium Sulfitobacter dubius at the depth of 20 meters.…”

“…Additionally, the bacterium Alteromonas macleodii isolated from sediment samples is known to be widespread in the tropical environments as an opportunistic copiotroph harboring the Na + /H + antiporters to survive in high salinity environments [29,30]. We also found a novel bacterium Domibacillus indicus , which was isolated from the depth of 5 meters [31]. This bacterium showed 97.6% 16S rRNA gene sequence similarity with the only other species reported, i.e.…”

Natrialba swarupiae sp. nov., a halophilic archaeon isolated from a hypersaline lake in India

“…The extraction of genomic DNA of strain ESP3B_9 T was carried out as described previously [12]. Archaeal primer pair 21F (5′-TCCGGTTGATCCYGCCGG-3′) and 1492R (5′-GGTTACCTTGTTACGACTT-3′) [13] was used for 16S rRNA gene amplification by PCR.…”