Collimonas arenae (DSM 21398, CCUG 54727, LMG 23964)

Name: Collimonas arenae (DSM 21398, CCUG 54727, LMG 23964)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11310

Type strain

Culture col. no. DSM 21398 CCUG 54727 LMG 23964 NCCB 100031 TER Ter10 2 more

NCBI tax ID(s) 279058

Special Collections DSMZ CCUG Literature strains UCCCB

History <- W. de Boer, Centre for Terrestrial Ecology, Heteren de Boer W, Centre for Terrestrial Ecology

Links

Collimonas arenae DSM 21398 is a mesophilic prokaryote that was isolated from Acidic dune grassland soil.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 111266

LMG 23964,DSM 21398,NCCB 100031,CCUG 54727

@ref 20215

Last LPSN update 2026-02-09 11:20:31

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Oxalobacteraceae

Genus Collimonas

Species Collimonas arenae

Full scientific name Collimonas arenae Höppener-Ogawa et al. 2008

Morphology

Pigmentation

32359

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15676	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l NaCl 5.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15676	positive	growth	28	mesophilic
32359	positive	growth	20	psychrophilic
67772	positive	optimum	28	mesophilic

Physiology and metabolism

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32359	22599 ChEBI	arabinose	+	carbon source
32359	35391 ChEBI	aspartate	+	carbon source
32359	15740 ChEBI	formate	+	carbon source
32359	33984 ChEBI	fucose	+	carbon source
32359	24175 ChEBI	galacturonate	+	carbon source
32359	24265 ChEBI	gluconate	+	carbon source
32359	17754 ChEBI	glycerol	+	carbon source
32359	17596 ChEBI	inosine	+	carbon source
32359	18403 ChEBI	L-arabitol	+	carbon source
32359	37684 ChEBI	mannose	+	carbon source
32359	17268 ChEBI	myo-inositol	+	carbon source
32359	17272 ChEBI	propionate	+	carbon source
32359	30031 ChEBI	succinate	+	carbon source
32359	16704 ChEBI	uridine	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32359	catalase	+	1.11.1.6
32359	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Grassland
#Environmental	#Terrestrial	#Soil
#Condition	#Acidic	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Sampling date
15676	Acidic dune grassland soil	Terschelling	Netherlands	NLD	Europe
60295	(Semi-)natural grasslands		Netherlands	NLD	Europe
67772	(Semi-)Natural grassland		Netherlands	NLD	Europe	1994

Taxonmaps

69479

Global distribution of 16S sequence AY281146 (>99% sequence identity) for Collimonas arenae from Microbeatlas

Aquatic Samples	142
Soil Samples	190
Animal Samples	65
Plant Samples	23
Total Samples	420

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15676	1	Risk group (German classification) According to TRBA 466
67772	1

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
67772	ASM158416v1 assembly for Collimonas arenae Ter10	complete	GCA_001584165	2687453510	279058	93.52

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Collimonas arenae strain NCCB 100031 16S ribosomal RNA gene, partial sequence	AF530049	481		279058
15676	Collimonas arenae strain NCCB 100031 16S ribosomal RNA gene, partial sequence	AY281146	1453		279058

GC content

32359

GC-content (mol%)59

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Collimonas antrihumi sp. nov., isolated from a natural cave and emended description of the genus Collimonas.	Lee SD	Int J Syst Evol Microbiol	10.1099/ijsem.0.002855	2018
Phylogeny	Glaciimonas immobilis gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from alpine glacier cryoconite.	Zhang DC, Redzic M, Schinner F, Margesin R	Int J Syst Evol Microbiol	10.1099/ijs.0.028001-0	2010
Phylogeny	Collimonas arenae sp. nov. and Collimonas pratensis sp. nov., isolated from (semi-)natural grassland soils.	Hoppener-Ogawa S, de Boer W, Leveau JH, van Veen JA, de Brandt E, Vanlaere E, Sutton H, Dare DJ, Vandamme P	Int J Syst Evol Microbiol	10.1099/ijs.0.65375-0	2008

References

#15676	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21398
#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 )
#28588	IJSEM 414 2008 ( DOI 10.1099/ijs.0.65375-0 , PubMed 18218941 )
#32359	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 #28588
#60295	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54727
#67772	The University of Coimbra Bacteria Culture Collection (UCCCB) ; Curators of the UCCCB;
#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 .
#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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Collimonas arenae (DSM 21398, CCUG 54727, LMG 23964)

Name and taxonomic classification

Morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

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_001584165

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

BacDive

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