Robiginitomaculum antarcticum (DSM 21748, IMCC 3195, KCCM 42687)

Name: Robiginitomaculum antarcticum (DSM 21748, IMCC 3195, KCCM 42687)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6224

Type strain

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

NCBI tax ID(s) 1123059 437507

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

Gram-negative rod-shaped aerobe psychrophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 400578

NBRC 103098,DSM 21748

@ref 20215

Last LPSN update 2025-12-16 09:48:16

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Caulobacterales

Family Hyphomonadaceae

Genus Robiginitomaculum

Species Robiginitomaculum antarcticum

Full scientific name Robiginitomaculum antarcticum Lee et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
32295	negative	2.9 µm	0.7 µm	rod-shaped
125438	negative
125439	negative

Pigmentation

32295

Productionyes

Multimedia

@ref:	66793
multimedia content:	EM_DSM_21748_1.jpg
multimedia.multimedia content:	EM_DSM_21748_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_21748_2.jpg
multimedia.multimedia content:	EM_DSM_21748_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_21748_3.jpg
multimedia.multimedia content:	EM_DSM_21748_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_21748_4.jpg
multimedia.multimedia content:	EM_DSM_21748_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_21748_5.jpg
multimedia.multimedia content:	EM_DSM_21748_5.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15911	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15911	positive	growth	20	psychrophilic
32295	positive	growth	03-25
32295	positive	optimum	20	psychrophilic

Culture pH

@ref	Ability	Type	PH
32295	positive	optimum	7
32295	positive	growth	05-10

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
32295	aerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation
32295
125438
125439

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32295	NaCl	positive	growth	0.5-5.0 %
32295	NaCl	positive	optimum	2.25 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32295	16449 ChEBI	alanine	+	carbon source
32295	22653 ChEBI	asparagine	+	carbon source
32295	4853 ChEBI	esculin	+	hydrolysis
32295	28260 ChEBI	galactose	+	carbon source
32295	24265 ChEBI	gluconate	+	carbon source
32295	29987 ChEBI	glutamate	+	carbon source
32295	17754 ChEBI	glycerol	+	carbon source
32295	17268 ChEBI	myo-inositol	+	carbon source
32295	17632 ChEBI	nitrate	+	reduction
32295	18257 ChEBI	ornithine	+	carbon source
32295	26271 ChEBI	proline	+	carbon source
32295	26490 ChEBI	quinate	+	carbon source
32295	17822 ChEBI	serine	+	carbon source
32295	27082 ChEBI	trehalose	+	carbon source
32295	53423 ChEBI	tween 40	+	carbon source
32295	53426 ChEBI	tween 80	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32295	alkaline phosphatase	+	3.1.3.1
32295	catalase	+	1.11.1.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Surface water

Isolation

@ref	Sample type	Geographic location	Continent
15911	surface seawater	Maxwell Bay, King George Island, West Antarctica	Australia and Oceania

Taxonmaps

69479

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15911	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM36502v1 assembly for Robiginitomaculum antarcticum DSM 21748	scaffold	GCA_000365025	1123059.3	2522125083	1123059	77.81

Genome browser: GCA_000365025

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Robiginitomaculum antarcticum gene for 16S rRNA, partial sequence, strain: NBRC 103098	AB681940	1404		437507
15911	Robiginitomaculum antarcticum strain IMCC3195 16S ribosomal RNA gene, partial sequence	EF495229	1415		437507

GC content

15911

GC-content (mol%)60.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Robiginitomaculum antarcticum DSM 21748
NCBI: GCA_000365025

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.80	no
125439	motility	BacteriaNetⓘ	yes	62.40	no
125439	gram_stain	BacteriaNetⓘ	negative	99.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Robiginitomaculum antarcticum DSM 21748 DSM 21748
NCBI: GCA_000365025.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.80	yes
125438	anaerobic	anaerobicⓘ	no	95.93	no
125438	aerobic	aerobicⓘ	yes	86.18	yes
125438	spore-forming	spore-formingⓘ	no	92.74	yes
125438	thermophilic	thermophileⓘ	no	97.06	no
125438	flagellated	motile2+ⓘ	no	73.25	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Unlocking Survival Mechanisms for Metal and Oxidative Stress in the Extremely Acidophilic, Halotolerant Acidihalobacter Genus.	Khaleque HN, Fathollazadeh H, Gonzalez C, Shafique R, Kaksonen AH, Holmes DS, Watkin ELJ.	Genes (Basel)	10.3390/genes11121392	2020
	AmiP from hyperthermophilic Thermus parvatiensis prophage is a thermoactive and ultrathermostable peptidoglycan lytic amidase.	Jasilionis A, Plotka M, Wang L, Dorawa S, Lange J, Watzlawick H, van den Bergh T, Vroling B, Altenbuchner J, Kaczorowska AK, Pohl E, Kaczorowski T, Nordberg Karlsson E, Freitag-Pohl S.	Protein Sci	10.1002/pro.4585	2023
Genetics	Probiotic Potential and Safety Assessment of Type Strains of Weissella and Periweissella Species.	Fanelli F, Montemurro M, Verni M, Garbetta A, Bavaro AR, Chieffi D, Cho GS, Franz CMAP, Rizzello CG, Fusco V.	Microbiol Spectr	10.1128/spectrum.03047-22	2023
Enzymology	Cloning, characterization, and expression of cDNA encoding a lipase from Kurtzmanomyces sp. I-11.	Kakugawa K, Shobayashi M, Suzuki O, Miyakawa T.	Biosci Biotechnol Biochem	10.1271/bbb.66.1328	2002
	Genomic Insights into the Distribution and Phylogeny of Glycopeptide Resistance Determinants within the Actinobacteria Phylum.	Andreo-Vidal A, Binda E, Fedorenko V, Marinelli F, Yushchuk O.	Antibiotics (Basel)	10.3390/antibiotics10121533	2021
Metabolism	Structural basis for conductance through TRIC cation channels.	Su M, Gao F, Yuan Q, Mao Y, Li DL, Guo Y, Yang C, Wang XH, Bruni R, Kloss B, Zhao H, Zeng Y, Zhang FB, Marks AR, Hendrickson WA, Chen YH.	Nat Commun	10.1038/ncomms15103	2017
Metabolism	The coprophilous mushroom Coprinus radians secretes a haloperoxidase that catalyzes aromatic peroxygenation.	Anh DH, Ullrich R, Benndorf D, Svatos A, Muck A, Hofrichter M.	Appl Environ Microbiol	10.1128/aem.00026-07	2007
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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Robiginitomaculum antarcticum (DSM 21748, IMCC 3195, KCCM 42687)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000365025

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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