Name: Microvirga ossetica V5/3M
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133326

Type strain:

Species: Microvirga ossetica

Strain Designation: V5/3M

Culture col. no.: LMG 29787, RCAM 02728

NCBI tax ID(s): 1882682 (species)

Section

Microvirga ossetica V5/3M is a Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from root nodules of Vicia alpestris plants.

colony-forming
Gram-negative
rod-shaped
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	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Methylobacteriaceae*
	Genus	*Microvirga*
	Species	**Microvirga ossetica**
	Full Scientific Name (LPSN)	Microvirga ossetica Safronova et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #25156]	Gram stain	negative
[Ref.: #25156]	Cell length	1.0-1.7 µm
[Ref.: #25156]	Cell width	0.6-1.0 µm
[Ref.: #25156]	Cell shape	rod-shaped
[Ref.: #25156]	Motility	no

[Ref.: #69480]	Gram stain	negative Confidence in %99.985

[Ref.: #25156]	Colony size	1 mm
[Ref.: #25156]	Colony color	transparent
[Ref.: #25156]	Colony shape	circular
[Ref.: #25156]	Cultivation medium used	modified yeast extract mannitol agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25156]

Culture medium

modified yeast extract mannitol agar

[Ref.: #25156]

Culture medium growth

[Ref.: #25156]

Culture medium composition

expand / minimize

	pH	Kind of pH		pH
[Ref.: #25156]			growth	6
[Ref.: #25156]		no	growth	5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.96

	Salt		Salt conc.
[Ref.: #25156]	NaCl	growth	1	%(w/v)
[Ref.: #25156]	NaCl	growth	2	%(w/v)
[Ref.: #25156]	NaCl	growth	4	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25156]	(-)-quinic acid ChEBI	-	assimilation
[Ref.: #25156]	(S)-lactate ChEBI	-	assimilation
[Ref.: #25156]	2-oxobutanoate ChEBI	-	assimilation
[Ref.: #25156]	2-oxoglutarate ChEBI	-	assimilation
[Ref.: #25156]	3-hydroxybutyrate ChEBI	+	assimilation
[Ref.: #25156]	3-O-methyl-D-glucose ChEBI	+	assimilation
[Ref.: #25156]	acetate ChEBI	+	assimilation
[Ref.: #25156]	acetoacetate ChEBI	+	assimilation
[Ref.: #25156]	alpha-lactose ChEBI	-	assimilation
[Ref.: #25156]	aspartate ChEBI	-	assimilation
[Ref.: #25156]	bromosuccinate ChEBI	+	assimilation
[Ref.: #25156]	cellobiose ChEBI	+	assimilation
[Ref.: #25156]	citrate ChEBI	-	assimilation
[Ref.: #25156]	D-arabitol ChEBI	-	assimilation
[Ref.: #25156]	D-fructose ChEBI	+	assimilation
[Ref.: #25156]	D-fructose 6-phosphate ChEBI	+	assimilation
[Ref.: #25156]	D-fucose ChEBI	+	assimilation
[Ref.: #25156]	D-galactose ChEBI	+	assimilation
[Ref.: #25156]	D-galacturonic acid ChEBI	+	assimilation
[Ref.: #25156]	D-glucarate ChEBI	-	assimilation
[Ref.: #25156]	D-gluconate ChEBI	-	assimilation
[Ref.: #25156]	D-glucose ChEBI	+	assimilation
[Ref.: #25156]	D-glucuronate ChEBI	+	assimilation
[Ref.: #25156]	D-malate ChEBI	-	assimilation
[Ref.: #25156]	D-mannitol ChEBI	-	assimilation
[Ref.: #25156]	D-mannose ChEBI	+	assimilation
[Ref.: #25156]	D-sorbitol ChEBI	+	assimilation
[Ref.: #25156]	dextrin ChEBI	-	assimilation
[Ref.: #25156]	formate ChEBI	-	assimilation
[Ref.: #25156]	galactarate ChEBI	-	assimilation
[Ref.: #25156]	gelatin ChEBI	-	assimilation
[Ref.: #25156]	gentiobiose ChEBI	+	assimilation
[Ref.: #25156]	glucuronamide ChEBI	+	assimilation
[Ref.: #25156]	glycerol ChEBI	-	assimilation
[Ref.: #25156]	inosine ChEBI	+	assimilation
[Ref.: #25156]	L-alanine ChEBI	-	assimilation
[Ref.: #25156]	L-arginine ChEBI	-	assimilation
[Ref.: #25156]	L-galactonic acid gamma-lactone ChEBI	+	assimilation
[Ref.: #25156]	L-glutamate ChEBI	-	assimilation
[Ref.: #25156]	L-histidine ChEBI	-	assimilation
[Ref.: #25156]	L-malate ChEBI	+	assimilation
[Ref.: #25156]	L-rhamnose ChEBI	+	assimilation
[Ref.: #25156]	maltose ChEBI	-	assimilation
[Ref.: #25156]	melibiose ChEBI	+	assimilation
[Ref.: #25156]	nitrate ChEBI	+	reduction
[Ref.: #25156]	pectin ChEBI	-	assimilation
[Ref.: #25156]	propionate ChEBI	-	assimilation
[Ref.: #25156]	raffinose ChEBI	-	assimilation
[Ref.: #25156]	serine ChEBI	-	assimilation
[Ref.: #25156]	stachyose ChEBI	+	assimilation
[Ref.: #25156]	sucrose ChEBI	-	assimilation
[Ref.: #25156]	trehalose ChEBI	+	assimilation
[Ref.: #25156]	turanose ChEBI	+	assimilation
[Ref.: #25156]	urea ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #25156]		catalase	+	1.11.1.6
[Ref.: #25156]		urease	+	3.5.1.5

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #25156]

Fatty acid	Percentage	ECL
C18:1ω7c	63
C16:1 iso I / C14:0 3OH	12.4	11
C16:0	7.1
Cyclo C19:0ω8c	4.2
C16:1ω7c / C15:0 iso 2OH	3.7
C18:0	1.9
10-Methyl C19:0	1.6
C17:0	1.1
C18:0 3OH	1.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ketogluconate metabolism	100	8 of 8
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	resorcinol degradation	100	2 of 2
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	lactate fermentation	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	degradation of sugar acids	96	24 of 25
[Ref.: #66794]	alanine metabolism	93.1	27 of 29
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	89.29	25 of 28
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	vitamin B12 metabolism	88.24	30 of 34
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	pyrimidine metabolism	84.44	38 of 45
[Ref.: #66794]	purine metabolism	84.04	79 of 94
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	creatinine degradation	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	tyrosine metabolism	78.57	11 of 14
[Ref.: #66794]	degradation of pentoses	78.57	22 of 28
[Ref.: #66794]	lysine metabolism	76.19	32 of 42
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	oxidative phosphorylation	74.73	68 of 91
[Ref.: #66794]	tryptophan metabolism	73.68	28 of 38
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	degradation of hexoses	72.22	13 of 18
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	androgen and estrogen metabolism	68.75	11 of 16
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	phenol degradation	65	13 of 20
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	ascorbate metabolism	59.09	13 of 22
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	58.82	10 of 17
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	vitamin B1 metabolism	53.85	7 of 13
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	grixazone biosynthesis	50	1 of 2
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	cholesterol biosynthesis	45.45	5 of 11
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
[Ref.: #66794]	carotenoid biosynthesis	36.36	8 of 22
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #25156]	Sample type/isolated from	root nodules of Vicia alpestris plants
[Ref.: #25156]	Geographic location (country and/or sea, region)	North Ossetia region (Caucasus)
[Ref.: #25156]	Country	Russia
[Ref.: #25156]	Country ISO 3 Code	RUS
[Ref.: #25156]	Continent	Europe
[Ref.: #25156]	Enrichment culture	yeast extract mannitol agar
[Ref.: #25156]	Enrichment culture composition	supplemented with 0.5 % succinate
[Ref.: #25156]	Enrichment culture duration	4-5 days
[Ref.: #25156]	Enrichment culture temperature	28 ̊C
[Ref.: #25156]	Isolation/enrichment procedure	surface-sterilized in 96 % ethanol for 1 min,rinsed, individually crushed in 100 µl sterile water
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root nodule

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KX576552 (>99% sequence identity) for Microvirga from Microbeatlas

Aquatic Samples	30
Soil Samples	579
Animal Samples	32
Plant Samples	137
Total Samples	778

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.: #25156]	Microvirga sp. strain V5/3M 16S ribosomal RNA gene, partial sequence	KX576552	1394	GenBank	1873136 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Microvirga ossetica V5/3m	GCA_002741015	complete	GenBank	1882682 tax ID	*
[Ref.: #66792]	Microvirga ossetica V5/3m	2775506901	complete	JGI IMG/M	1882682 tax ID	*

[Ref.: #25156]

GC-content

61.8 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: Microvirga ossetica V5/3M NCBI: GCA_002741015.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Microvirga ossetica V5/3M NCBI: GCA_002741015.1
[Ref.: #69480]	flagellated	no	80.494	no
[Ref.: #69480]	gram-positive	no	97.482	yes
[Ref.: #69480]	anaerobic	no	97.134	no
[Ref.: #69480]	aerobic	yes	90.753	no
[Ref.: #69480]	halophile	no	93.163	no
[Ref.: #69480]	spore-forming	no	93.714	no
[Ref.: #69480]	glucose-util	yes	89.009	yes
[Ref.: #69480]	thermophile	no	98.631	no
[Ref.: #69480]	motile	yes	78.965	no
[Ref.: #69480]	glucose-ferment	no	90.906	no

Availability in culture collections External links

[Ref.: #25156]

Culture collection no.

LMG 29787, RCAM 02728

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Microvirga ossetica sp. nov., a species of rhizobia isolated from root nodules of the legume species Vicia alpestris Steven.	Safronova VI, Kuznetsova IG, Sazanova AL, Belimov AA, Andronov EE, Chirak ER, Osledkin YS, Onishchuk OP, Kurchak ON, Shaposhnikov AI, Willems A, Tikhonovich IA	Int J Syst Evol Microbiol	10.1099/ijsem.0.001577	2017	*

References

#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 )

#25156

V. I. K. Safronova, I. G.,Sazanova, A. L.,Belimov, A. A.,Andronov, E. E.,Chirak, E. R.,Osledkin, Y. S.,Onishchuk, O. P.,Kurchak, O. N.,Shaposhnikov, A. I.,Willems, A.,Tikhonovich, I. A.: Microvirga ossetica sp. nov., a species of rhizobia isolated from root nodules of the legume species Vicia alpestris Steven. IJSEM 67: 94 - 100 2017 ( DOI 10.1099/ijsem.0.001577 , PubMed 27902217 )

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 )

* These data were automatically processed and therefore are not curated

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