Name: Microvirga lotononidis DSM 28906
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 131253

Type strain:

Species: Microvirga lotononidis

Culture col. no.: DSM 28906, HAMBI 3237, LMG 26455, WSM 3557, CB 1322

Strain history: <- HAMBI; HAMBI 3237 <- K. Lindström, HAMBI; LMG 26455 <- A. Willems, LMG; WSM3557 <- J.K. Ardley, Murdoch University, Australia; CB 1322 <- A. McInnes, CB <- W.C. Verboom

NCBI tax ID(s): 864069 (species)

SI-ID 377578

LMG 26455, HAMBI 3237

Special Collections

Section

Microvirga lotononidis DSM 28906 is an aerobe, Gram-negative, motile bacterium that was isolated from Lotononis angolensis, nitrogen-fixing nodule.

Gram-negative
motile
rod-shaped
aerobe
16S sequence
Bacteria

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 lotononidis**
	Full Scientific Name (LPSN)	Microvirga lotononidis Ardley et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30397]	Gram stain	negative

[Ref.: #30397]	Cell length	1.6 µm

[Ref.: #30397]	Cell width	0.45 µm

[Ref.: #30397]	Cell shape	rod-shaped

[Ref.: #30397]	Motility	yes

[Ref.: #30397]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22480]

Culture medium

MODIFIED YMA MEDIUM (HAMBI) (DSMZ Medium 1545)

[Ref.: #22480]

Culture medium growth

[Ref.: #22480]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22480]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #22480]	growth	28 °C
[Ref.: #30397]	growth	15-45 °C
[Ref.: #30397]	optimum	41 °C

	pH	Kind of pH		pH
[Ref.: #30397]			optimum	7.75
[Ref.: #30397]			growth	5.5-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30397]

Oxygen tolerance

aerobe

[Ref.: #30397]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30397]		NaCl		growth	0-2	%
[Ref.: #30397]		NaCl		optimum	0.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30397]	acetate ChEBI	+	carbon source
[Ref.: #30397]	arabinose ChEBI	+	carbon source
[Ref.: #30397]	cellobiose ChEBI	+	carbon source
[Ref.: #30397]	fructose ChEBI	+	carbon source
[Ref.: #30397]	glucose ChEBI	+	carbon source
[Ref.: #30397]	glutamate ChEBI	+	carbon source
[Ref.: #30397]	glycerol ChEBI	+	carbon source
[Ref.: #30397]	mannitol ChEBI	+	carbon source
[Ref.: #30397]	nitrate ChEBI	+	reduction
[Ref.: #30397]	succinate ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30397]		catalase	+	1.11.1.6
[Ref.: #30397]		urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	91.67	11 of 12
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	degradation of sugar acids	88	22 of 25
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	selenocysteine biosynthesis	83.33	5 of 6
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	lysine metabolism	76.19	32 of 42
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	histidine metabolism	75.86	22 of 29
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	arginine metabolism	75	18 of 24
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	degradation of hexoses	72.22	13 of 18
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	oxidative phosphorylation	71.43	65 of 91
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	degradation of pentoses	67.86	19 of 28
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	phenol degradation	55	11 of 20
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	d-xylose degradation	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	alginate 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.: #22480]	Sample type/isolated from	Lotononis angolensis, nitrogen-fixing nodule
[Ref.: #22480]	Geographic location (country and/or sea, region)	Chibala (Fort Jameson)
[Ref.: #22480]	Country	Zambia
[Ref.: #22480]	Country ISO 3 Code	ZMB
[Ref.: #22480]	Continent	Africa
* 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 HM362432 (>99% sequence identity) for Microvirga from Microbeatlas

Aquatic Samples	74
Soil Samples	307
Animal Samples	70
Plant Samples	24
Total Samples	475

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

[Ref.: #22480]

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.: #22480]	Dictyostelium discoideum strain QS38 anonymous locus 06_2763183 genomic sequence	HM362332	531	GenBank ENA	44689 tax ID
[Ref.: #30397]	Microvirga lotononidis strain WSM3557 16S ribosomal RNA gene, partial sequence	HM362432	1457	GenBank ENA	864069 tax ID
[Ref.: #124043]	Microvirga lotononidis partial 16S rRNA gene, strain HAMBI 3237	LT899968	1386	GenBank ENA	864069 tax ID	*

[Ref.: #30397]

GC-content

62.8-63 mol%

Availability in culture collections External links

[Ref.: #22480]

Culture collection no.

DSM 28906, HAMBI 3237, LMG 26455, WSM 3557, CB 1322

[Ref.: #89697]

SI-ID 377578

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Microvirga lupini sp. nov., Microvirga lotononidis sp. nov. and Microvirga zambiensis sp. nov. are alphaproteobacterial root-nodule bacteria that specifically nodulate and fix nitrogen with geographically and taxonomically separate legume hosts.	Ardley JK, Parker MA, De Meyer SE, Trengove RD, O'Hara GW, Reeve WG, Yates RJ, Dilworth MJ, Willems A, Howieson JG	Int J Syst Evol Microbiol	10.1099/ijs.0.035097-0	2011	*
Phylogeny	Microvirga calopogonii sp. nov., a novel alphaproteobacterium isolated from a root nodule of Calopogonium mucunoides in Southwest China.	Wang F, Yang L, Deng J, Liu X, Lu Y, Chen W, Wu J	Antonie Van Leeuwenhoek	10.1007/s10482-019-01285-5	2019	*
Genetics	Microvirga massiliensis sp. nov., the human commensal with the largest genome.	Caputo A, Lagier JC, Azza S, Robert C, Mouelhi D, Fournier PE, Raoult D	Microbiologyopen	10.1002/mbo3.329	2016	*
Genetics	Genome sequence of the Listia angolensis microsymbiont Microvirga lotononidis strain WSM3557(T.).	Reeve W, Ardley J, Tian R, De Meyer S, Terpolilli J, Melino V, Tiwari R, Yates R, O'Hara G, Howieson J, Ninawi M, Zhang X, Bruce D, Detter C, Tapia R, Han C, Wei CL, Huntemann M, Han J, Chen IM, Mavromatis K, Markowitz V, Szeto E, Ivanova N, Pagani I, Pati A, Goodwin L, Woyke T, Kyrpides N	Stand Genomic Sci	10.4056/sigs.4548266	2013	*

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 )

#22480

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28906

#30397

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 #26734 (see below)

#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 .

#89697

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-ID377578.1 )

#124043

Dr. Isabel Schober, Dr. Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

#26734

IJSEM 2579 2012 ( DOI 10.1099/ijs.0.035097-0 , PubMed 22199210 )

* These data were automatically processed and therefore are not curated

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