Nevskia ramosa (DSM 11499, Soe1)

Name: Nevskia ramosa (DSM 11499, Soe1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17659

Type strain

Strain Designation Soe1

Culture col. no. DSM 11499 Soe1

NCBI tax ID(s) 1122603 64002

Special Collections DSMZ

History <- H. Cypionka <- H. Stürmeyer, Soe1

Links

Nevskia ramosa Soe1 is a bacterium that was isolated from freshwater lake, neuston layer.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 101381

DSM 11499

@ref 20215

Last LPSN update 2026-02-09 11:22:16

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Nevskiales

Family Nevskiaceae

Genus Nevskia

Species Nevskia ramosa

Full scientific name Nevskia ramosa Famintzin 1892 (Approved Lists 1980)

BacDive ID	Other strains from **Nevskia ramosa** (2)	Type strain
17660	N. ramosa OL1, DSM 11500
146715	N. ramosa CCUG 32012

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.726
125439	negative	98.8

Multimedia

@ref:	66793
multimedia content:	EM_DSM_11499_1.jpg
multimedia.multimedia content:	EM_DSM_11499_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_11499_2.jpg
multimedia.multimedia content:	EM_DSM_11499_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_11499_3.jpg
multimedia.multimedia content:	EM_DSM_11499_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_11499_4.jpg
multimedia.multimedia content:	EM_DSM_11499_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_11537_1.jpg
multimedia.multimedia content:	EM_DSM_11537_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_11625_2.jpg
multimedia.multimedia content:	EM_DSM_11625_2.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
4390	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
4390	NEVSKIA MEDIUM (DSMZ Medium 828)		Medium recipe at MediaDive	Name: NEVSKIA MEDIUM (DSMZ Medium 828) Composition: Potassium phosphate buffer 64.35 g/l Agar 15.0 g/l Na-lactate 0.56 g/l MgSO4 x 7 H2O 0.05 g/l CaCl2 x 2 H2O 0.014 g/l Nitrilotriacetic acid 0.0064 g/l HCl 0.00125 g/l FeCl2 x 4 H2O 0.001 g/l Pyridoxine hydrochloride 0.00015 g/l Thiamine-HCl x 2 H2O 0.0001 g/l Nicotinic acid 0.0001 g/l CoCl2 x 6 H2O 9.5e-05 g/l Calcium pantothenate 5e-05 g/l MnCl2 x 4 H2O 5e-05 g/l Vitamin B12 5e-05 g/l p-Aminobenzoic acid 4e-05 g/l ZnCl2 3.5e-05 g/l Na2MoO4 x 2 H2O 1.8e-05 g/l NiCl2 x 6 H2O 1.2e-05 g/l D-(+)-biotin 1e-05 g/l H3BO3 3e-06 g/l CuCl2 x 2 H2O 1e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
4390	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.9

Spore formation

@ref	Spore formation	Confidence
125438		92.833
125439		97.3

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	cytochrome oxidase	+	1.9.3.1	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
4390	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
4390	freshwater lake, neuston layer	Soelkensee	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence AJ001010 (>99% sequence identity) for Nevskia ramosa from Microbeatlas

Aquatic Samples	1059
Soil Samples	473
Animal Samples	624
Plant Samples	56
Total Samples	2212

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4390	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	ASM42064v1 assembly for Nevskia ramosa DSM 11499	contig	GCA_000420645	1122603.18	2523231050	1122603	75.66

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4390	Nevskia ramosa 16S ribosomal RNA (strain Soe1)	AJ001010	1394		64002

GC content

@ref	GC-content (mol%)	Method
4390	67.8	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nevskia ramosa DSM 11499
NCBI: GCA_000420645

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.90	no
125439	gram_stain	BacteriaNetⓘ	negative	98.80	no
125439	motility	BacteriaNetⓘ	yes	75.70	no
125439	spore_formation	BacteriaNetⓘ	no	97.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nevskia ramosa DSM 11499
PATRIC: 1122603.18

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.73	no
125438	anaerobic	anaerobicⓘ	no	95.12	no
125438	spore-forming	spore-formingⓘ	no	92.83	no
125438	aerobic	aerobicⓘ	yes	88.03	no
125438	thermophilic	thermophileⓘ	no	96.36	yes
125438	flagellated	motile2+ⓘ	yes	69.17	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Evidence for novel polycyclic aromatic hydrocarbon degradation pathways in culturable marine isolates.	Walton JL, Buchan A.	Microbiol Spectr	10.1128/spectrum.03409-23	2024
	Bubble biofilm: Bacterial colonization of air-air interface.	Sjoberg S, Stairs C, Allard B, Hallberg R, Homa F, Martin T, Ettema TJG, Dupraz C.	Biofilm	10.1016/j.bioflm.2020.100030	2020
Proteome	Proteotyping Environmental Microorganisms by Phylopeptidomics: Case Study Screening Water from a Radioactive Material Storage Pool.	Hayoun K, Pible O, Petit P, Allain F, Jouffret V, Culotta K, Rivasseau C, Armengaud J, Alpha-Bazin B.	Microorganisms	10.3390/microorganisms8101525	2020
	Microbiomes in a manganese oxide producing ecosystem in the Ytterby mine, Sweden: impact on metal mobility.	Sjoberg S, Stairs CW, Allard B, Homa F, Martin T, Sjoberg V, Ettema TJG, Dupraz C.	FEMS Microbiol Ecol	10.1093/femsec/fiaa169	2020
Metabolism	Improved fatty aldehyde and wax ester production by overexpression of fatty acyl-CoA reductases.	Lehtinen T, Efimova E, Santala S, Santala V.	Microb Cell Fact	10.1186/s12934-018-0869-z	2018
	Production of alkanes from CO₂ by engineered bacteria.	Lehtinen T, Virtanen H, Santala S, Santala V.	Biotechnol Biofuels	10.1186/s13068-018-1229-2	2018
Phylogeny	Nevskia terrae sp. nov., isolated from soil.	Kim SJ, Weon HY, Kim YS, Park IC, Son JA, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.021238-0	2010
Phylogeny	Panacagrimonas perspica gen. nov., sp. nov., a novel member of Gammaproteobacteria isolated from soil of a ginseng field.	Im WT, Liu QM, Yang JE, Kim MS, Kim SY, Lee ST, Yi TH	J Microbiol	10.1007/s12275-010-0067-0	2010

References

#4390	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11499
#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) .
#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 )
#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 .
#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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Nevskia ramosa (DSM 11499, Soe1)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

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_000420645

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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