Name: Roseomonas deserti M3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158692

Type strain:

Species: Roseomonas deserti

Strain Designation: M3

Culture col. no.: KEMB 2255-459, JCM 31275

Strain history: S.-S. Lee; KEMB, Kyonggi Univ., South Korea; M3.

NCBI tax ID(s): 1817963 (species)

Section

Roseomonas deserti M3 is a Gram-negative, rod-shaped bacterium that was isolated from crude oil contaminated desert sand.

Gram-negative
rod-shaped
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodospirillales*
	Family	*Acetobacteraceae*
	Genus	*Roseomonas*
	Species	**Roseomonas deserti**
	Full Scientific Name (LPSN)	Roseomonas deserti Subhash and Lee 2018

Synonym

Pseudoroseomonas deserti

Information on morphological and physiological properties Morphology

[Ref.: #65430]	Gram stain	negative

[Ref.: #65430]	Cell length	1.0-1.2 µm

[Ref.: #65430]	Cell width	0.6-0.8 µm

[Ref.: #65430]	Cell shape	rod-shaped

[Ref.: #65430]	Motility	no

[Ref.: #65430]	Colony color	dark pink
[Ref.: #65430]	Cultivation medium used	agar medium

[Ref.: #65430]	Pigment production	yes
[Ref.: #65430]	Pigment name	carotenoids

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65430]

Culture medium

agar medium

[Ref.: #65430]

Culture medium growth

		Temperature
[Ref.: #65430]	growth	13-42 °C
[Ref.: #65430]	optimum	30-35 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #65430]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #65430]			optimum	7.0-7.5
[Ref.: #65430]			growth	6.5-9

Information on physiology and metabolism Physiology and metabolism

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65430]		NaCl		growth	0-3.5	%(w/v)
[Ref.: #65430]		NaCl		optimum	0.5	%(w/v)

[Ref.: #65430]	Observation	diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified glycolipid are present as major polar lipids with minor amounts of an unidentified phospholipid, unidentified minolipids (AL1-3) and unide
[Ref.: #65430]	Observation	spermidine is the major polyamine
[Ref.: #67770]	Observation	quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65430]	ammonium ChEBI	+	carbon source
[Ref.: #65430]	aspartate ChEBI	-	assimilation
[Ref.: #65430]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #65430]	casein	+	hydrolysis
[Ref.: #65430]	cellobiose ChEBI	-	assimilation
[Ref.: #65430]	cellobiose ChEBI	-	builds acid from
[Ref.: #65430]	chitin ChEBI	-	hydrolysis
[Ref.: #65430]	D-alanine ChEBI	+	assimilation
[Ref.: #65430]	D-fructose ChEBI	-	assimilation
[Ref.: #65430]	D-fructose ChEBI	-	builds acid from
[Ref.: #65430]	D-galactose ChEBI	-	builds acid from
[Ref.: #65430]	D-galactose ChEBI	+	assimilation
[Ref.: #65430]	D-glucose ChEBI	-	builds acid from
[Ref.: #65430]	D-glucose ChEBI	+	assimilation
[Ref.: #65430]	D-mannitol ChEBI	-	assimilation
[Ref.: #65430]	D-ribose ChEBI	-	assimilation
[Ref.: #65430]	D-sorbitol ChEBI	+	assimilation
[Ref.: #65430]	esculin ChEBI	-	hydrolysis
[Ref.: #65430]	gelatin ChEBI	-	hydrolysis
[Ref.: #65430]	glutamate ChEBI	+	assimilation
[Ref.: #65430]	hexadecane ChEBI	-	assimilation
[Ref.: #65430]	L-arabinose ChEBI	-	builds acid from
[Ref.: #65430]	L-arabinose ChEBI	+	assimilation
[Ref.: #65430]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #65430]	L-rhamnose ChEBI	+	assimilation
[Ref.: #65430]	lactose ChEBI	+	assimilation
[Ref.: #65430]	maltose ChEBI	-	builds acid from
[Ref.: #65430]	maltose ChEBI	+	assimilation
[Ref.: #65430]	melibiose ChEBI	-	builds acid from
[Ref.: #65430]	methyl pyruvate ChEBI	+	assimilation
[Ref.: #65430]	nitrate ChEBI	-	reduction
[Ref.: #65430]	phenanthrene ChEBI	-	assimilation
[Ref.: #65430]	pyrene ChEBI	-	assimilation
[Ref.: #65430]	raffinose ChEBI	-	assimilation
[Ref.: #65430]	raffinose ChEBI	-	builds acid from
[Ref.: #65430]	starch ChEBI	-	hydrolysis
[Ref.: #65430]	sucrose ChEBI	-	builds acid from
[Ref.: #65430]	sucrose ChEBI	+	assimilation
[Ref.: #65430]	toluene ChEBI	-	assimilation
[Ref.: #65430]	trehalose ChEBI	-	assimilation
[Ref.: #65430]	tween 20 ChEBI	-	hydrolysis
[Ref.: #65430]	tween 80 ChEBI	-	hydrolysis
[Ref.: #65430]	urea ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration
[Ref.: #65430]	ampicillin ChEBI	yes	10	µg (disc)
[Ref.: #65430]	chloramphenicol ChEBI	yes	30	µg (disc)
[Ref.: #65430]	nalidixic acid ChEBI	yes	30	µg (disc)
[Ref.: #65430]	penicillin g ChEBI	yes	10	µg (disc)
[Ref.: #65430]	rifampicin ChEBI	yes	30	µg (disc)

	Metabolite production	Metabolite	Production
[Ref.: #65430]		indole ChEBI	no
[Ref.: #65430]		sulfide ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #65430]	alkaline phosphatase	-	3.1.3.1
[Ref.: #65430]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #65430]	alpha-fucosidase	+	3.2.1.51
[Ref.: #65430]	alpha-glucosidase	+	3.2.1.20
[Ref.: #65430]	alpha-mannosidase	+	3.2.1.24
[Ref.: #65430]	arginine decarboxylase	-	4.1.1.19
[Ref.: #65430]	beta-galactosidase	+	3.2.1.23
[Ref.: #65430]	catalase	+	1.11.1.6
[Ref.: #65430]	cytochrome oxidase	+	1.9.3.1
[Ref.: #65430]	esterase (C 4)	+
[Ref.: #65430]	esterase Lipase (C 8)	+
[Ref.: #65430]	leucine arylamidase	+	3.4.11.1
[Ref.: #65430]	lysine decarboxylase	-	4.1.1.18
[Ref.: #65430]	trypsin	+	3.4.21.4
[Ref.: #65430]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #65430]

Fatty acid	Percentage
C18:1ω6c/C18:1ω7c	74.5
C16:0	8.5
C16:1ω6c/C16:1ω7c	6.7
C18:1-2OH	3.2
C16:1ω5c	3.2
C19:0cyclo-ω8c	2
C18:0	1
C18:1ω5c	1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	100	8 of 8
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	chorismate metabolism	100	9 of 9
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	91.67	11 of 12
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	glutathione metabolism	85.71	12 of 14
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	methionine metabolism	84.62	22 of 26
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	degradation of sugar acids	80	20 of 25
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	purine metabolism	77.66	73 of 94
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	degradation of pentoses	75	21 of 28
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	vitamin B12 metabolism	73.53	25 of 34
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	coenzyme M biosynthesis	70	7 of 10
[Ref.: #66794]	oxidative phosphorylation	69.23	63 of 91
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	3-phenylpropionate degradation	66.67	10 of 15
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	allantoin degradation	66.67	6 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	61.54	8 of 13
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	peptidoglycan biosynthesis	60	9 of 15
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	glycolysis	52.94	9 of 17
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	d-xylose degradation	45.45	5 of 11
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	carotenoid biosynthesis	40.91	9 of 22
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	elloramycin biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #65430]	Sample type/isolated from	crude oil contaminated desert sand
[Ref.: #65430]	Country	Kuwait
[Ref.: #65430]	Country ISO 3 Code	KWT
[Ref.: #65430]	Continent	Asia
[Ref.: #65430]	Enrichment culture	liquid medium
[Ref.: #65430]	Enrichment culture duration	5 days
[Ref.: #65430]	Enrichment culture temperature	30 ̊C

[Ref.: #67770]	Sample type/isolated from	Crude oil contaminated desert sand
[Ref.: #67770]	Country	Kuwait
[Ref.: #67770]	Country ISO 3 Code	KWT
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Desert
#Engineered	#Contamination	#Oil (Fuel)
#Environmental	#Terrestrial	#Sandy

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LT837512 (>99% sequence identity) for Roseomonas from Microbeatlas

Aquatic Samples
Soil Samples	6
Animal Samples	3
Plant Samples	2
Total Samples	11

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #65430]	16S rRNA gene sequence	LT837512		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudoroseomonas deserti M3	GCA_001982615	contig	GenBank	1817963 tax ID	*
[Ref.: #66792]	Roseomonas deserti M3	2791354997	draft	JGI IMG/M	1817963 tax ID	*

[Ref.: #65430]	GC-content	69-69.5 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	69.5 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #65430]

Culture collection no.

KEMB 2255-459, JCM 31275

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Roseomonas coralli sp. nov., a heavy metal resistant bacterium isolated from coral.	Li F, Huang Y, Hu W, Li Z, Wang Q, Huang S, Jiang F, Pan X	Int J Syst Evol Microbiol	10.1099/ijsem.0.004624	2021	*
Phylogeny	Roseomonas deserti sp. nov., isolated from crude oil contaminated desert sand.	Subhash Y, Lee SS	Int J Syst Evol Microbiol	10.1099/ijsem.0.002565	2018	*

References

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#65430

Y. Subhash, Sang-Seob Lee: Roseomonas deserti sp. nov., isolated from crude oil contaminated desert sand. IJSEM 68: 675 - 680 2018 ( DOI 10.1099/ijsem.0.002565 , PubMed 29388546 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

* These data were automatically processed and therefore are not curated

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