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Geodermatophilus obscurus

ABSTRACT: Soil bacterium

PROVIDER: PRJNA60927 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
		Other
	SRR017878.fastq.gz	Fastqsanger.gz
	SRR017879.fastq.gz	Fastqsanger.gz
	SRR017880.fastq.gz	Fastqsanger.gz
	SRR017881.fastq.gz	Fastqsanger.gz

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Geodermatophilus obscurus DSM 43160

Project description:Filamentous soil bacterium

| PRJNA29547 | ENA

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

Project description:Geodermatophilus obscurus Luedemann 1968 is the type species of the genus, which is the type genus of the family Geodermatophilaceae. G. obscurus is of interest as it has frequently been isolated from stressful environments such as rock varnish in deserts, and as it exhibits interesting phenotypes such as lytic capability of yeast cell walls, UV-C resistance, strong production of extracellular functional amyloid (FuBA) and manganese oxidation. This is the first completed genome sequence of the family Geodermatophilaceae. The 5,322,497 bp long genome with its 5,161 protein-coding and 58 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

| S-EPMC3035280 | biostudies-literature

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

Project description: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.

| S-EPMC4681853 | biostudies-literature

Geodermatophilus obscurus DSM43160 proteomics

Project description:This project contributes to the proteomic comparison of different bacteria. A whole proteome catalogue was obtained for Geodermatophilus obscurus DSM43160 grown in standard conditions.

2015-08-03 | PXD001520 | Pride

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

Project description:This project contributes to the proteomic comparison of different bacteria. A whole proteome catalogue was obtained for Modestobacter marinus grown in standard conditions.

2015-08-03 | PXD001518 | Pride

Geodermatophilus obscurus subsp. utahensis strain:DSM 43162

Project description:Geodermatophilus uthaensis DSM 43162

| PRJNA262337 | ENA

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

Project description:This project contributes to the proteomic comparison of different bacteria. A whole proteome catalogue was obtained for Modestobacter marinus grown in standard conditions.

| MSV000079300 | MassIVE

Lsr2 and its novel paralogue mediate the adjustment of Mycobacterium smegmatis to unfavorable environmental conditions

Project description:In this study, we analyze the role of Lsr2 as a transcription factor in M. smegmatis, a saprophytic bacterium whose natural habitat (soil and water) substantially differs from that of the obligatory mycobacterial pathogens. In summary, the combined RNA-seq and ChIP-seq data revealed that Lsr2 controls gene expression either directly by binding their promoter regions or indirectly through DNA loop formation.

2021-04-22 | GSE164708 | GEO

Transcription profiling of Sinorhizobium meliloti after exposure to elevated concentrations of the heavy metals cadmium and zinc to analyze stress responses

Project description:The stress response of the soil bacterium Sinorhizobium meliloti towards elevated concentrations of the heavy metals cadmium and zinc was analyzed via transcriptional profiling.

2008-03-15 | E-MTAB-13 | biostudies-arrayexpress

Geodermatophilus poikilotrophi sp. nov.: a multitolerant actinomycete isolated from dolomitic marble.

Project description:A novel Gram-reaction-positive, aerobic actinobacterium, tolerant to mitomycin C, heavy metals, metalloids, hydrogen peroxide, desiccation, and ionizing- and UV-radiation, designated G18T, was isolated from dolomitic marble collected from outcrops in Samara (Namibia). The growth range was 15-35°C, at pH 5.5-9.5 and in presence of 1% NaCl, forming greenish-black coloured colonies on GYM Streptomyces agar. Chemotaxonomic and molecular characteristics of the isolate matched those described for other representatives of the genus Geodermatophilus. The peptidoglycan contained meso-diaminopimelic acid as diagnostic diaminoacid. The main phospholipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, and small amount of diphosphatidylglycerol. MK-9(H4) was the dominant menaquinone and galactose was detected as diagnostic sugar. The major cellular fatty acids were branched-chain saturated acids iso-C16:0 and iso-C15:0 and the unsaturated C17:1 ?8c and C16:1 ?7c. The 16S rRNA gene showed 97.4-99.1% sequence identity with the other representatives of genus Geodermatophilus. Based on phenotypic results and 16S rRNA gene sequence analysis, strain G18T is proposed to represent a novel species, Geodermatophilus poikilotrophi. Type strain is G18T (=DSM 44209T=CCUG 63018T). The INSDC accession number is HF970583. The novel R software package lethal was used to compute the lethal doses with confidence intervals resulting from tolerance experiments.

| S-EPMC4119925 | biostudies-literature

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