High-quality draft genome sequence of Kocuria marina SO9-6, an actinobacterium isolated from a copper mine

Castro, Daniel Bedo Assumpção; Pereira, Letícia Bianca; Silva, Marcus Vinícius M. e; Silva, Bárbara Pereira da; Palermo, Bruna Rafaella Zanardi; Carlos, Camila; Belgini, Daiane R.B.; Limache, Elmer Erasmo G.; Lacerda, Gileno V.; Nery, Mariana B.P.; Gomes, Milene Barbosa; Souza, Salatiel S. de; Silva, Thiago M. da; Rodrigues, Viviane Drumond; Paulino, Luciana Campos; Vicentini, Renato; Ferraz, Lúcio Fábio Caldas; Ottoboni, Laura Maria Mariscal

doi:10.1016/j.gdata.2015.05.006

Cited by 5 publications

(3 citation statements)

References 18 publications

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“…The distribution and abundance of the MAGs in six Kocuria representatives were shown in Table 4 . Besides four marine isolates, two strains from hyperosmotic environments, i.e., K. polaris CD08-4 from a celiac disease patient and K. marina SO9-6 from a copper iron sulfide mineral ( Castro et al, 2015 ), were also included. Apparently, the MAGs were distributed in all or the majority of the analyzed Kocuria isolates though their abundance sometimes varied as the species, indicating that the Kocuria isolates possessed common genetic basis for marine adaptation.…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2018

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Sponge-derived actinomycetes represent a significant component of marine actinomycetes. Members of the genus Kocuria are distributed in various habitats such as soil, rhizosphere, clinical specimens, marine sediments, and sponges, however, to date, little is known about the mechanism of their environmental adaptation. Kocuria flava S43 was isolated from a coastal sponge. Phylogenetic analysis revealed that it was closely related to the terrestrial airborne K. flava HO-9041. In this study, to gain insights into the marine adaptation in K. flava S43 we sequenced the draft genome for K. flava S43 by third generation sequencing (TGS) and compared it with those of K. flava HO-9041 and some other Kocuria relatives. Comparative genomics and phylogenetic analyses revealed that K. flava S43 might adapt to the marine environment mainly by increasing the number of the genes linked to potassium homeostasis, resistance to heavy metals and phosphate metabolism, and acquiring the genes associated with electron transport and the genes encoding ATP-binding cassette (ABC) transporter, aquaporin, and thiol/disulfide interchange protein. Notably, gene acquisition was probably a primary mechanism of environmental adaptation in K. flava S43. Furthermore, this study also indicated that the Kocuria isolates from various marine and hyperosmotic environments possessed common genetic basis for environmental adaptation.

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Section: Resultsmentioning

confidence: 99%

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

et al. 2018

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“…So far, it comprises the species Kocuria rosea , Kocuria varians , Kocuria kristinae [1] , Kocuria rhizophila , Kocuria palustris [2] , Kocuria polaris [3] , Kocuria marina [4] , Kocuria atrinae [5] , Kocuria koreensis [6] , Kocuria gwangalliensis [7] , Kocuria himachalensis [8] , Kocuria aegyptia [9] , Kocuria flava , Kocuria turfanensis [10] , Kocuria salsicia [11] , Kocuria halotolerans [12] , Kocuria carniphila [13] , Kocuria sediminis [14] , and Kocuria assamensis [15] . Members of the Kocuria genus can be found in soil, mammal skin, the rhizosphere, clinical samples, and several other ecological niches, such as the Antarctic cyanobacterial mat [3] , marine sediment [4] , fermented food [5] , [6] , seawater [7] , and sulfide ore [16] . Although isolated from various sources, the size of the Kocuria genus is relatively small among the Actinomycetes , which suggests that each species of Kocuria is highly adapted to its ecological niche [8] , [9] .…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

Draft genome sequence of Kocuria sp. SM24M-10 isolated from coral mucus

et al. 2016

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Here, we describe the genomic features of the Actinobacteria Kocuria sp. SM24M-10 isolated from mucus of the Brazilian endemic coral Mussismilia hispida. The sequences are available under accession number LDNX01000000 (http://www.ncbi.nlm.nih.gov/nuccore/LDNX00000000). The genomic analysis revealed interesting information about the adaptation of bacteria to the marine environment (such as genes involved in osmotic and oxidative stress) and to the nutrient-rich environment provided by the coral mucus.

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“…(Bala et al, 2012) providing another evidence to the reliable identification of the strain DDK6. Genome sequences of members of Kocuria genus such as K. marina SO9-6 (Castro et al, 2015) and K. rhizophila strain TPW45 (Tan et al, 2016) revealed the existence of many gene clusters involved in catabolic pathways of carbohydrate. The ability of the strain DDK6 to grow using a wide range of different biochemical compounds.…”

Section: Biochemical Characterization Using the Api50ch Strip Kitmentioning

confidence: 99%

Degradation of diesel-oil by a newly isolated Kocuria sediminis DDK6

Khalifa¹

2017

Afr. J. Microbiol. Res.

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A bacterial strain named DDK6 was isolated from diesel-contaminated soil from a petrol station in Al-Hofuf city, after enrichment on diesel oil. The strain DDK6 formed a reddish-pink colony with a 2 to 3 mm diameter after two days of incubation at 30°C. Cells were Gram-positive coccoid and formed no endospores. Phenotypic identification by the automated bacterial system, Vitek compact II, identified the DDK6 as Kocuria sp. at 95% probability level. The 16s rRNA gene sequencing analysis confirmed the identity of the strain as K. sedimins at an identity level of 99.15%. Results of Gas chromatographymass spectrometry (GC-MS) revealed that the DDK6 degraded the C14-C19 compounds in diesel. In addition, the DDK6 strain consumed the majority (68%) of the carbon sources tested, including monosaccharides, disaccharides, polysaccharides, and sugar alcohols as noticed by biochemical characterization using the API 50CH. The cultural, biochemical, and molecular characteristics were in general agreement with the strain identification. The results confirmed the metabolic versatility of the strain DDK6, in addition to its ability to degrade diesel oil, thereby providing ecological and environmental merits for its application in bioremediation of hydrocarbon pollutants.

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High-quality draft genome sequence of Kocuria marina SO9-6, an actinobacterium isolated from a copper mine

Cited by 5 publications

References 18 publications

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

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

Draft genome sequence of Kocuria sp. SM24M-10 isolated from coral mucus

Degradation of diesel-oil by a newly isolated Kocuria sediminis DDK6

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