Kocuria indica sp. nov., isolated from a sediment sample

Abstract

An actinobacterial strain was isolated from a sediment sample from Chorao Island, in Goa province, India, and subjected to a taxonomic investigation. The isolate, designated NIO-1021 T , was a Gram-stain positive, aerobic, non-motile and coccoid. Strain NIO-1021 T was identified as a member of the genus Kocuria by a polyphasic approach. Strain NIO-1021 T could be differentiated from other members of the genus Kocuria on the basis of physiology and 16S rRNA gene sequence analysis. The 16S rRNA gene sequence similarity of strain NIO-1021 T to the most closely related species, Kocuria marina KCTC 9943 T , was 98.6 % with 19 nt differences). Furthermore, DNA-DNA hybridization analysis revealed that the novel strain had lower relatedness with the type strains of other members of the genus Kocuria. The strain formed a monophyletic clade with K. marina with 100 % bootstrap values. The major phospholipids were phosphatidylglycerol, diphosphatidylglycerol and two unidentified lipids. The predominant menaquinone was MK-7(H 2 ). The major fatty acids were anteiso-C 15 : 0 , iso-C 16 : 0 and anteiso-C 17 : 0 . The DNA G+C content of strain NIO-1021 T was 60.5 mol%. Chemotaxonomic and phylogenetic properties of the strain were consistent with its classification as representing a member of the genus Kocuria. On the basis of phenotypic, chemotypic and molecular characteristics, strain NIO-1021 T is considered to represent a novel species of the genus Kocuria, for which the name Kocuria indica sp. nov. is proposed, with strain NIO-1021 T (5NCIM 5455 T 5DSM 25126 T 5CCTCC AA 209050 T ) as the type strain.The genus Kocuria was first proposed by Stackebrandt et al. (1995) on the basis of a detailed phylogenetic and chemotaxonomic analysis of the genus Micrococcus (Stackebrandt et al., 1995). This led further to the description of the genera Dermacoccus, Kocuria, Kytococcus and Nesterenkonia. The genus Kocuria embraced three species formerly classified as members of the genus Micrococcus, i.e. Kocuria rosea (Micrococcus roseus; Flügge 1886), Kocuria varians (Micrococcus varians; Migula, 1900) and Kocuria kristinae (Micrococcus kristinae; Kloos et al., 1974). Based upon 16S rRNA gene sequence similarities the genus Kocuria represents one of the deepest lineages in the family Stackebrandt et al., 1995). The third clade includes only Kocuria palustris (Kovács et al., 1999). The last clade appears to be the deepest lineage in the family and comprises Kocuria atrinae (Park et al., 2010b) During an investigation exploring actinobacterial diversity in the marine environment of Chorao Island of Goa province, India, a coccoid actinobacterial strain was isolated and was subjected to a polyphasic investigation to determine its taxonomic position.Strain NIO-1021 T was isolated from a marine sediment sample taken from Chorao Island. After primary isolation and purification on marine agar 2216 (Difco) at 28 u C for 2 weeks, the purified strain was subcultured on the same medium and stored as slants at 4 u C and as 20 % (v/v) glycerol suspension...

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

“…The description is as before (Dastager et al, 2014c ) with the following modification. The G+C content of the type-strain genome is 68.9%, its approximate size 2.88 Mbp, its GenBank deposit SAMN06296028 .…”

Comparative Genomics Provides Insights Into the Marine Adaptation in Sponge-Derived Kocuriaflava S43

“…The genome sequences of K. flava HO-9041 from inland air, Kocuria sp. SM24M-10 from the mucus of the coral Mussismilia hispida ( Palermo et al, 2016 ), K. indica DSM 25126 from a marine sediment sample ( Dastager et al, 2014 ), K. rhizophila P7-4 from the intestine of the fish Siganus doliatus ( Kim et al, 2011 ) and K. rhizophila DC2201 from a soil sample ( Takarada et al, 2008 ) were downloaded from NCBI 3 and served as the reference genomes for subsequent analysis. Genome alignment of K. flava S43 and K. flava HO-9041 was carried out using MAUVE software ( Darling et al, 2010 ).…”

Kocuria dechangensis sp. nov., an actinobacterium isolated from saline and alkaline soils

“…The genus Kocuria was established by Stackebrandt et al (1995) by taxonomic dissection of the genus Micrococcus , and was clearly separated from Micrococcus and Micrococcus -related taxa on the basis of phylogenetic analyses using 16S rRNA gene sequences. At the time of writing (November 2014), the genus Kocuria , contains 19 species with validly published names including Kocuria kristinae , Kocuria rosea and Kocuria varians (Stackebrandt et al , 1995), Kocuria erythromyxa (Rainey et al , 1997; later reclassified as a later synonym of K. rosea ), Kocuria palustris , Kocuria rhizophila (Kovács et al , 1999), Kocuria polaris (Reddy et al , 2003), Kocuria marina (Kim et al , 2004), Kocuria carniphila (Tvrzová et al , 2005), Kocuria aegyptia (Li et al , 2006), Kocuria himachalensis (Mayilraj et al , 2006), Kocuria flava , Kocuria turfanensis (Zhou et al , 2008), Kocuria halotolerans (Tang et al , 2009), Kocuria atrinae (Park et al , 2010a), Kocuria koreensis (Park et al , 2010b), Kocuria gwangalliensis (Seo et al , 2009), Kocuria salsicia (Yun et al , 2011) and Kocuria indica (Dastager et al , 2014). During our study on the microbial diversity and taxonomy of the halotolerant and halophilic bacteria from saline and alkaline soils in the Songnen Plain (Pan et al , 2012), an actinobacterium, designated NEAU-ST5-33 T , was shown to share a 16S rRNA gene sequence similarity of 98.8 % with K. polaris CMS 76or T and K. rosea DMS 20447 T , suggesting that strain NEAU-ST5-33 T may represent a novel taxon.…”