Complete genome sequence of Geodermatophilus obscurus type strain (G-20T)

Ivanova, Natalia; Sikorski, Johannes; Jando, Marlen; Munk, Christine; Lapidus, Alla; Rio, Tijana Glavina del; Copeland, Alex; Tice, Hope; Cheng, Jan‐Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun Juan; Jeffries, Cynthia D.; Meincke, Linda; Brettin, Thomas; Detter, John C.; Rohde, Manfred; Göker, Markus; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans Peter

doi:10.4056/sigs.711311

Cited by 53 publications

(38 citation statements)

References 37 publications

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“…Characteristics of proteogenomes Life in biotopes with low trophic resources has driven the three Geodermatophilaceae members toward medium-sized genomes (Ivanova et al, 2010;Chouaia et al, 2012;Normand et al, 2012) from 4.87 to 5.32 Mb (Figure 1 and Supplementary Table S1). The three plasmidless genomes had very high G+C% (72.95-74.1%).…”

Section: Resultsmentioning

confidence: 99%

“…To understand how Geodermatophilaceae adapt to stones and soil, here we present a proteogenome analysis and detailed comparison of B. saxobsidens (Bs) , M. marinus (Mm) (Normand et al, 2012) and G. obscurus (Go) (Ivanova et al, 2010). To get a close-up view of their physiology, we analyzed the proteome content of stationary-phase Bs, Mm and Go cells by a liquid chromatography-tandem mass spectrometry (MS/MS) shotgun approach and semi-quantification by spectral counting.…”

Section: Introductionmentioning

confidence: 99%

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Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes

Sghaier¹,

Hezbri²,

Ghodhbane‐Gtari³

et al. 2015

The ISME Journal

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The Geodermatophilaceae are unique model systems to study the ability to thrive on or within stones and their proteogenomes (referring to the whole protein arsenal encoded by the genome) could provide important insight into their adaptation mechanisms. Here we report the detailed comparative genome analysis of Blastococcus saxobsidens (Bs), Modestobacter marinus (Mm) and Geodermatophilus obscurus (Go) isolated respectively from the interior and the surface of calcarenite stones and from desert sandy soils. The genome-scale analysis of Bs, Mm and Go illustrates how adaptation to these niches can be achieved through various strategies including 'molecular tinkering/ opportunism' as shown by the high proportion of lost, duplicated or horizontally transferred genes and ORFans. Using high-throughput discovery proteomics, the three proteomes under unstressed conditions were analyzed, highlighting the most abundant biomarkers and the main protein factors. Proteomic data corroborated previously demonstrated stone-related ecological distribution. For instance, these data showed starvation-inducible, biofilm-related and DNA-protection proteins as signatures of the microbes associated with the interior, surface and outside of stones, respectively.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes

Sghaier¹,

Hezbri²,

Ghodhbane‐Gtari³

et al. 2015

The ISME Journal

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“…The genome of only one type strain, that of G. obscurus, has been sequenced (Ivanova et al, 2010). Moreover, three named subspecies have been identified: 'G.…”

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Geodermatophilus normandii sp. nov., isolated from Saharan desert sand

Montero‐Calasanz

Göker

Pötter

et al. 2013

International Journal of Systematic and Evolutionary Microbiology

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A novel Gram-reaction-positive actinobacterial strain, designated CF5/3 T , was isolated from a sand sample obtained in the Sahara Desert, Chad. The greenish-black-pigmented isolate was aerobic and exhibited optimal growth from 25-40 6C at pH 6.0-10.0 with 0-1 % (w/v) NaCl. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Geodermatophilus. The DNA G+C content of the genome of the novel strain was 75.5 mol%. The peptidoglycan contained meso-diaminopimelic acid as diagnostic diamino acid. The main phospholipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol and a minor fraction of phosphatidylglycerol. MK-9(H 4 ) was the dominant menaquinone, and galactose was detected as a diagnostic sugar. The major cellular fatty acids were branched-chain saturated acids: iso-C 15 : 0 and iso-C 16 : 0 . Analysis of 16S rRNA gene sequences showed 95.6-98.8 % pairwise sequence identity with the members of the genus Geodermatophilus. Based on phenotypic and chemotaxonomic properties, as well as phylogenetic distinctiveness, the isolate represents a novel species, Geodermatophilus normandii, with the type strain CF5/3 T (5DSM 45417 T 5CCUG 62814 T 5MTCC 11412 T ).The family Geodermatophilaceae was originally proposed by Normand et al. (1996), but a formal description of the family name was only published a decade later (Normand, 2006). At the time of writing, the family comprises the genera Blastococcus, Modestobacter and Geodermatophilus (type genus). The genus Geodermatophilus was first proposed by Luedemann (1968) and the name was accepted in the Approved Lists of Bacterial Names by Skerman et al. (1980). Members of this genus are frequently isolated from arid soils (Urzì et al., 2001), although some have also been isolated from rhizosphere soil (Zhang et al., 2011; Jin et al., 2012). Nevertheless, this genus was for a long time poorly studied and sampled due to challenges in culturing (Urzì et al., 2004). Pelczar (1957). Exponentially growing bacterial cultures were observed with an optical microscope (AxioScope A1, Zeiss) with a 100-fold magnification and phase-contrast illumination. Micrographs of bacterial cells grown on GYM Streptomyces broth for 4 days were taken with a field-emission scanning electron microscope (Merlin, Zeiss). Gram reaction was performed using the KOH test as described by Gregersen (1978). Cell motility was observed on modified ISP2 (Shirling & Gottlieb, 1966) swarming agar (0.3 %, w/v) at pH 7.2 that contained (l 21 ) 4.0 g dextrin, 4.0 g yeast extract and 10.0 g malt extract. Oxidase activity was analysed using filter paper discs (Sartorius grade 388) soaked in a 1 % solution of N,N,N9,N9-tetramethyl-p-phenylenediamine (Sigma-Aldrich); a positive test was defined by the development of a blue-purple colour after applying biomass on the filter paper. Catalase activity was determined based on formation of bubbles following the addition of 3 % H 2 O 2 (1 drop). Growth rates were determined on pla...

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“…everesti' (Ishiguro & Fletcher, 1975;Normand & Benson, 2012), remained the only representatives of the genus in the literature. This has changed dramatically in the last 3 years, when technical limitations were overcome and not only the first genome of a strain from the genus was sequenced, that of G. obscurus G-20, by Ivanova et al (2010), but 12 novel species have been assigned to the genus (in date order of effective publication): Geodermatophilus ruber (Zhang et al, 2011), G. nigrescens (Nie et al, 2012), G. arenarius (Montero-Calasanz et al, 2012), G. siccatus (Montero-Calasanz et al, 2013a), G. saharensis (Montero-Calasanz et al, 2013b), G. tzadiensis (Montero-Calasanz et al, 2013c), G. telluris (MonteroCalasanz et al, 2013d), G. soli and G. terrae (Jin et al, 2013) (Montero-Calasanz et al, 2013f) and G. taihuensis (Qu et al, 2013). Recently, Geodermatophilus amargosae (MonteroCalasanz et al, 2014a, b) was described in detail to elevate 'G.…”

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confidence: 99%

Geodermatophilus brasiliensis sp. nov., isolated from Brazilian soil

Bertazzo

Montero‐Calasanz

Martínez‐García

et al. 2014

International Journal of Systematic and Evolutionary Microbiology

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A Gram-reaction-positive bacterial isolate, designated Tü 6233 T , with rudimentary, coral-pink vegetative mycelium that formed neither aerial mycelium nor spores, was isolated from a Brazilian soil sample. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Geodermatophilus. Cell-wall hydrolysates contained mesodiaminopimelic acid as the diagnostic diamino acid and galactose as the diagnostic sugar. The major fatty acids were iso-C 16 : 0 , iso-C 15 : 0 and C 17 : 1 v8c and the predominant menaquinone was MK-9(H 4 ). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol, an unknown glycophospholipid and an unknown phospholipid. The DNA G+C content of the strain was 75.4 mol%. The 16S rRNA gene sequence identity with members of the genus Geodermatophilus was 94.2-98.7 %. Based on phenotypic, chemotaxonomic and phylogenetic data, strain Tü 6233 T is proposed to represent a novel species, Geodermatophilus brasiliensis sp. nov., with the type strain Tü 6233 T (5DSM 44526 T 5CECT 8402 T ).

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Complete genome sequence of Geodermatophilus obscurus type strain (G-20T)

Cited by 53 publications

References 37 publications

Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes

Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes

Geodermatophilus normandii sp. nov., isolated from Saharan desert sand

Geodermatophilus brasiliensis sp. nov., isolated from Brazilian soil

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