Name: Pseudorhodoferax soli TBEA3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 3030

Type strain:

Species: Pseudorhodoferax soli

Strain Designation: TBEA3

Culture col. no.: DSM 21634, LMG 24555

Strain history: <- N. Bruland, Univ. Münster, Inst. Mol. Microbiol. Biotechnol., Germany; TBEA3

NCBI tax ID(s): 545864 (species)

SI-ID 358705

LMG 24555, DSM 21634

Section

Pseudorhodoferax soli TBEA3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil sample.

Gram-negative
motile
rod-shaped
aerobe
mesophilic
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	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Pseudorhodoferax*
	Species	**Pseudorhodoferax soli**
	Full Scientific Name (LPSN)	Pseudorhodoferax soli Bruland et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #29123]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.99

[Ref.: #29123]	Cell length	1.95 µm

[Ref.: #29123]	Cell width	0.85 µm

[Ref.: #29123]	Cell shape	rod-shaped

[Ref.: #29123]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %96.151

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15850]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)

[Ref.: #15850]

Culture medium growth

[Ref.: #15850]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15850]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #15850]			growth	28 °C
[Ref.: #29123]			optimum	30 °C

[Ref.: #15850]	Temperature range	mesophilic
[Ref.: #29123]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29123]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.976

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29123]	acetate ChEBI	+	carbon source
[Ref.: #29123]	adipate ChEBI	+	carbon source
[Ref.: #29123]	arabinose ChEBI	+	carbon source
[Ref.: #29123]	fructose ChEBI	+	carbon source
[Ref.: #29123]	gluconate ChEBI	+	carbon source
[Ref.: #29123]	malate ChEBI	+	carbon source
[Ref.: #29123]	mannitol ChEBI	+	carbon source
[Ref.: #29123]	propionate ChEBI	+	carbon source
[Ref.: #29123]	succinate ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29123]		catalase	+	1.11.1.6
[Ref.: #29123]		cytochrome oxidase	+	1.9.3.1

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

[Ref.: #15850]	Sample type/isolated from	soil sample
[Ref.: #15850]	Geographic location (country and/or sea, region)	Marschacht near Hamburg
[Ref.: #15850]	Country	Germany
[Ref.: #15850]	Country ISO 3 Code	DEU
[Ref.: #15850]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU825700 (>99% sequence identity) for Pseudorhodoferax from Microbeatlas

Aquatic Samples	712
Soil Samples	76
Animal Samples	127
Plant Samples	19
Total Samples	934

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

[Ref.: #15850]

Biosafety level

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.: #15850]	Pseudorhodoferax soli strain TBEA3 16S ribosomal RNA gene, partial sequence	EU825700	1524	ENA	545864 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudorhodoferax soli DSM 21634	GCA_003337555	scaffold	GenBank	545864 tax ID	*
[Ref.: #66792]	Pseudorhodoferax soli strain DSM 21634	545864.3	wgs	PATRIC	545864 tax ID	*
[Ref.: #66792]	Pseudorhodoferax soli DSM 21634	2770939619	draft	JGI IMG/M	545864 tax ID	*

[Ref.: #15850]	GC-content	69.1 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29123]	GC-content	69.1 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: Pseudorhodoferax soli DSM 21634 NCBI: GCA_003337555.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudorhodoferax soli DSM 21634 NCBI: GCA_003337555.1
[Ref.: #69480]	motile	yes	88.738	yes
[Ref.: #69480]	flagellated	yes	57.217	no
[Ref.: #69480]	gram-positive	no	98.335	yes
[Ref.: #69480]	anaerobic	no	97.715	yes
[Ref.: #69480]	aerobic	yes	94.959	yes
[Ref.: #69480]	halophile	no	94.34	no
[Ref.: #69480]	spore-forming	no	95.563	no
[Ref.: #69480]	glucose-util	yes	61.338	no
[Ref.: #69480]	thermophile	no	99.411	yes
[Ref.: #69480]	glucose-ferment	no	89.473	no

Availability in culture collections External links

[Ref.: #15850]

Culture collection no.

DSM 21634, LMG 24555

[Ref.: #72550]

SI-ID 358705

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Comamonas humi sp. nov., isolated from soil.	Hatayama K	Int J Syst Evol Microbiol	10.1099/ijs.0.067439-0	2014	*
Phylogeny	Pseudorhodoferax aquiterrae sp. nov., isolated from groundwater.	Chen WM, Lin YS, Young CC, Sheu SY	Int J Syst Evol Microbiol	10.1099/ijs.0.039842-0	2012	*
Phylogeny	Pseudorhodoferax soli gen. nov., sp. nov. and Pseudorhodoferax caeni sp. nov., two members of the class Betaproteobacteria belonging to the family Comamonadaceae.	Bruland N, Bathe S, Willems A, Steinbuchel A	Int J Syst Evol Microbiol	10.1099/ijs.0.006791-0	2009	*

References

#15850

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21634

#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 )

#29123

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 #25549 (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) .

#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 )

#72550

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-ID358705.1 )

#25549

IJSEM 2702 2009 ( DOI 10.1099/ijs.0.006791-0 , PubMed 19625429 )

* These data were automatically processed and therefore are not curated

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Pseudorhodoferax soli DSM 21634

Pseudorhodoferax soli DSM 21634

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