Robiginitomaculum antarcticum | Type strain | DSM 21748, IMCC 3195, KCCM 42687, NBRC 103098 | BacDiveID:6224

Strain identifier

BacDive ID: 6224

Type strain:

Species: Robiginitomaculum antarcticum

Culture col. no.: DSM 21748, IMCC 3195, KCCM 42687, NBRC 103098

Strain history: <- NBRC <- K. Lee, Inha University, Incheon, Korea

NCBI tax ID(s): 1123059 (strain), 437507 (species)

SI-ID 400578

DSM 21748

Section

Robiginitomaculum antarcticum DSM 21748 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from surface seawater.

Gram-negative
rod-shaped
aerobe
psychrophilic
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	*Caulobacterales*
	Family	*Hyphomonadaceae*
	Genus	*Robiginitomaculum*
	Species	**Robiginitomaculum antarcticum**
	Full Scientific Name (LPSN)	Robiginitomaculum antarcticum Lee et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32295]	Gram stain	negative
[Ref.: #32295]	Cell length	2.9 µm
[Ref.: #32295]	Cell width	0.7 µm
[Ref.: #32295]	Cell shape	rod-shaped
[Ref.: #32295]	Motility	no

[Ref.: #69480]	Gram stain	negative Confidence in %99.999

Pigment production

yes

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #15911]			growth	20 °C
[Ref.: #32295]			growth	03-25 °C
[Ref.: #32295]			optimum	20 °C

[Ref.: #15911]	Temperature range	psychrophilic
[Ref.: #32295]	Temperature range	psychrophilic

	pH	Kind of pH		pH
[Ref.: #32295]			optimum	7
[Ref.: #32295]			growth	05-10

Information on physiology and metabolism Physiology and metabolism

Oxygen tolerance

aerobe

[Ref.: #32295]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32295]		NaCl		growth	0.5-5.0	%
[Ref.: #32295]		NaCl		optimum	2.25	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32295]		alanine ChEBI	+	carbon source
[Ref.: #32295]		asparagine ChEBI	+	carbon source
[Ref.: #32295]		esculin ChEBI	+	hydrolysis
[Ref.: #32295]		galactose ChEBI	+	carbon source
[Ref.: #32295]		gluconate ChEBI	+	carbon source
[Ref.: #32295]		glutamate ChEBI	+	carbon source
[Ref.: #32295]		glycerol ChEBI	+	carbon source
[Ref.: #32295]		myo-inositol ChEBI	+	carbon source
[Ref.: #32295]		nitrate ChEBI	+	reduction
[Ref.: #32295]		ornithine ChEBI	+	carbon source
[Ref.: #32295]		proline ChEBI	+	carbon source
[Ref.: #32295]		quinate ChEBI	+	carbon source
[Ref.: #32295]		serine ChEBI	+	carbon source
[Ref.: #32295]		trehalose ChEBI	+	carbon source
[Ref.: #32295]		tween 40 ChEBI	+	carbon source
[Ref.: #32295]		tween 80 ChEBI	+	carbon source
		Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #32295]		alkaline phosphatase	+	3.1.3.1
[Ref.: #32295]		catalase	+	1.11.1.6

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

[Ref.: #15911]	Sample type/isolated from	surface seawater
[Ref.: #15911]	Geographic location (country and/or sea, region)	Maxwell Bay, King George Island, West Antarctica
[Ref.: #15911]	Continent	Australia and Oceania
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Surface water

What are isolation sources categories?

Global distribution of 16S sequence AB681940 (>99% sequence identity) for Robiginitomaculum antarcticum subclade from Microbeatlas

Aquatic Samples	2081
Soil Samples	72
Animal Samples	124
Plant Samples	18
Total Samples	2295

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

Biosafety level

1

Risk group (German classification)
According to TRBA 466

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.: #15911]	Robiginitomaculum antarcticum strain IMCC3195 16S ribosomal RNA gene, partial sequence	EF495229	1415	ENA	437507 tax ID
[Ref.: #20218]	Robiginitomaculum antarcticum gene for 16S rRNA, partial sequence, strain: NBRC 103098	AB681940	1404	ENA	437507 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Robiginitomaculum antarcticum DSM 21748	GCA_000365025	scaffold	GenBank	1123059 tax ID	*
[Ref.: #66792]	Robiginitomaculum antarcticum DSM 21748	1123059.3	wgs	PATRIC	1123059 tax ID	*
[Ref.: #66792]	Robiginitomaculum antarcticum DSM 21748	2522125083	draft	JGI IMG/M	1123059 tax ID	*

GC-content

60.3 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Robiginitomaculum antarcticum DSM 21748 DSM 21748 NCBI: GCA_000365025.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Robiginitomaculum antarcticum DSM 21748 DSM 21748 NCBI: GCA_000365025.1
[Ref.: #69480]	motile	no	77.076	yes
[Ref.: #69480]	flagellated	no	96.682	no
[Ref.: #69480]	gram-positive	no	98.908	yes
[Ref.: #69480]	anaerobic	no	99.191	yes
[Ref.: #69480]	aerobic	yes	91.739	yes
[Ref.: #69480]	halophile	no	65.793	no
[Ref.: #69480]	spore-forming	no	97.958	yes
[Ref.: #69480]	glucose-util	yes	80.589	no
[Ref.: #69480]	thermophile	no	97.973	no
[Ref.: #69480]	glucose-ferment	no	92.808	no

Availability in culture collections External links

Culture collection no.

DSM 21748, IMCC 3195, KCCM 42687, NBRC 103098

SI-ID 400578

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Robiginitomaculum antarcticum gen. nov., sp. nov., a member of the family Hyphomonadaceae, from Antarctic seawater.	Lee K, Lee HK, Choi TH, Cho JC	Int J Syst Evol Microbiol	10.1099/ijs.0.65274-0	2007	*

References

#15911

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21748

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#32295

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28535 (see below)

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#75703

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID400578.1 )

#28535

IJSEM 2595 2007 ( DOI 10.1099/ijs.0.65274-0 , PubMed 17978224 )

* These data were automatically processed and therefore are not curated

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