Rhizobium aggregatum (DSM 1111, ATCC 43293, IFAM 1003)

Name: Rhizobium aggregatum (DSM 1111, ATCC 43293, IFAM 1003)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13623

Type strain

Strain Designation 161A

Culture col. no. DSM 1111 ATCC 43293 IFAM 1003 161A

NCBI tax ID(s) 1368425 34013

Special Collections DSMZ

Links

Rhizobium aggregatum 161A is a mesophilic prokaryote that was isolated from surface lake water.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 379771

ATCC 43293,DSM 1111,NCIMB 12290,VKM B-2061,LMG 23059

@ref 20215

Last LPSN update 2025-12-16 09:50:08

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Rhizobiaceae

Genus Rhizobium

Species Rhizobium aggregatum

Full scientific name Rhizobium aggregatum (Hirsch and Müller 1986) Kaur et al. 2011

Synonyms (2)

Blastobacter aggregatus
Peteryoungia aggregata

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	98.8

Colony morphology

560

Incubation period1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
560	RHIZOBIUM MEDIUM (DSMZ Medium 98)		Medium recipe at MediaDive	Name: RHIZOBIUM MEDIUM (DSMZ Medium 98) Composition: air-dried garden soil 80.0 g/l Agar 15.0 g/l Mannitol 10.0 g/l Yeast extract 1.0 g/l Na2CO3 0.2 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
560	positive	growth	25	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	92.5

Spore formation

@ref	Spore formation	Confidence
125439		98.7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	+	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
560	-	-	-	-	+	+	-	+	+	+	+	+	+	+	-	-	-	-	-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Surface water

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
560	surface lake water	Schleswig-Holstein, Höftsee	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence X73041 (>99% sequence identity) for Rhizobium aggregatum from Microbeatlas

Aquatic Samples	94
Soil Samples	61
Animal Samples	60
Plant Samples	20
Total Samples	235

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
560	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	Rhizobium aggregatum DSM 1111	complete			2738541329	1368425	91.66
124043	ASM3081443v1 assembly for Peteryoungia aggregata LMG 23059 DSM 1111	contig	GCA_030814435	1368425.4	2926661365	1368425	72.66

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
560	Blastobacter aggregatus 16S rRNA gene, strain IFAM 1003	X73041	1414		1368425

GC content

@ref	GC-content (mol%)	Method
560	62.7	thermal denaturation, midpoint method (Tm)
560	60.4	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhizobium aggregatum DSM 1111
IMG: 2738541329

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.70	no
125439	motility	BacteriaNetⓘ	yes	73.60	no
125439	gram_stain	BacteriaNetⓘ	negative	98.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	92.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhizobium rosettiformans sp. nov., isolated from a hexachlorocyclohexane dump site, and reclassification of Blastobacter aggregatus Hirsch and Muller 1986 as Rhizobium aggregatum comb. nov.	Kaur J, Verma M, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.017491-0	2010

References

#560	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1111
#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 )
#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) .
#68369	Automatically annotated from API 20NE .
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Rhizobium aggregatum (DSM 1111, ATCC 43293, IFAM 1003)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_030814435

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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