Name: Microterricola viridarii KV-677
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7499

Type strain:

Species: Microterricola viridarii

Strain Designation: KV-677

Culture col. no.: DSM 21772, NBRC 102123, NRRL B-24538, JCM 15926

Strain history: NRRL B-24538 <-- S. ?mura KV-677.

NCBI tax ID(s): 412690 (species)

SI-ID 400982

DSM 21772

Section

Microterricola viridarii KV-677 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from park soil.

Gram-positive
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Microterricola*
	Species	**Microterricola viridarii**
	Full Scientific Name (LPSN)	Microterricola viridarii Matsumoto et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32171]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #32171]	Cell length	0.9 µm

[Ref.: #32171]	Cell width	0.45 µm

[Ref.: #32171]	Cell shape	rod-shaped

[Ref.: #32171]	Motility	yes

[Ref.: #32171]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15938]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #15938]

Culture medium growth

[Ref.: #15938]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15938]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15938]	growth	28 °C
[Ref.: #32171]	growth	10-38 °C
[Ref.: #32171]	optimum	22.5 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #15938]	Temperature range	mesophilic
[Ref.: #32171]	Temperature range	psychrophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32171]			growth	06-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32171]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.993

[Ref.: #67770]

Observation

quinones: MK-12 (69%), MK-11 (21%), MK-13 (10%)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32171]	arabinose ChEBI	+	carbon source
[Ref.: #32171]	glycerol ChEBI	+	carbon source
[Ref.: #32171]	glycogen ChEBI	+	carbon source
[Ref.: #32171]	maltose ChEBI	+	carbon source
[Ref.: #32171]	ribose ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #32171]		acid phosphatase	+	3.1.3.2
[Ref.: #32171]		catalase	+	1.11.1.6

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	pyrimidine metabolism	84.44	38 of 45
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	purine metabolism	77.66	73 of 94
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[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]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	degradation of sugar acids	72	18 of 25
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	70	7 of 10
[Ref.: #66794]	phenol degradation	70	14 of 20
[Ref.: #66794]	isoprenoid biosynthesis	69.23	18 of 26
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	degradation of pentoses	64.29	18 of 28
[Ref.: #66794]	oxidative phosphorylation	61.54	56 of 91
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	ascorbate metabolism	59.09	13 of 22
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	55.56	5 of 9
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	53.85	7 of 13
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	carotenoid biosynthesis	50	11 of 22
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	vitamin B1 metabolism	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	glutathione metabolism	35.71	5 of 14
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	daunorubicin biosynthesis	22.22	2 of 9
		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.: #15938]	Sample type/isolated from	park soil
[Ref.: #15938]	Geographic location (country and/or sea, region)	Tokyo
[Ref.: #15938]	Country	Japan
[Ref.: #15938]	Country ISO 3 Code	JPN
[Ref.: #15938]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Arisugawa Park, Tokyo
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB282862 (>99% sequence identity) for Microterricola from Microbeatlas

Aquatic Samples	3680
Soil Samples	6929
Animal Samples	3725
Plant Samples	3868
Total Samples	18202

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

[Ref.: #15938]

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.: #15938]	Microterricola viridarii gene for 16S rRNA, partial sequence	AB282862	1442	ENA	412690 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Microterricola viridarii DSM 21772	GCA_900104895	chromosome	GenBank	412690 tax ID	*
[Ref.: #66792]	Microterricola viridarii strain DSM 21772	412690.4	complete	PATRIC	412690 tax ID	*
[Ref.: #66792]	Microterricola viridarii DSM 21772	2634166341	draft	JGI IMG/M	412690 tax ID	*

[Ref.: #15938]	GC-content	70 mol%
[Ref.: #67770]	GC-content	70 mol%	high performance liquid chromatography (HPLC)

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: Microterricola viridarii strain DSM 21772 PATRIC: 412690.6
[Ref.: #69481]	spore-forming	no	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Microterricola viridarii strain DSM 21772 PATRIC: 412690.4
[Ref.: #69480]	gram-positive	yes	89.811	yes
[Ref.: #69480]	anaerobic	no	99.139	yes
[Ref.: #69480]	halophile	no	88.859	no
[Ref.: #69480]	spore-forming	no	91.905	no
[Ref.: #69480]	glucose-util	yes	84.812	no
[Ref.: #69480]	aerobic	yes	92.617	yes
[Ref.: #69480]	flagellated	no	90.727	no
[Ref.: #69480]	thermophile	no	99.488	yes
[Ref.: #69480]	motile	yes	77.861	yes
[Ref.: #69480]	glucose-ferment	no	79.572	no

Availability in culture collections External links

[Ref.: #15938]

Culture collection no.

DSM 21772, NBRC 102123, NRRL B-24538, JCM 15926

[Ref.: #76945]

SI-ID 400982

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Reclassification of Phycicola gilvus (Lee et al. 2008) and Leifsonia pindariensis (Reddy et al. 2008) as Microterricola gilva comb. nov. and Microterricola pindariensis comb. nov. and emended description of the genus Microterricola.	Dhotre DP, Rajabal V, Sharma A, Kulkarni GJ, Prakash O, Vemuluri VR, Joseph N, Rahi P, Shouche YS	Int J Syst Evol Microbiol	10.1099/ijsem.0.002019	2017	*
Phylogeny	Amnibacterium kyonggiense gen. nov., sp. nov., a new member of the family Microbacteriaceae.	Kim SJ, Lee SS	Int J Syst Evol Microbiol	10.1099/ijs.0.018788-0	2010	*
Phylogeny	Microterricola viridarii gen. nov., sp. nov., a new member of the family Microbacteriaceae.	Matsumoto A, Yamada M, Omura S, Takahashi Y	Int J Syst Evol Microbiol	10.1099/ijs.0.65070-0	2008	*

References

#15938

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21772

#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 )

#32171

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 #28413 (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) .

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

#76945

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-ID400982.1 )

#28413

IJSEM 1019 2008 ( DOI 10.1099/ijs.0.65070-0 , PubMed 18398212 )

* These data were automatically processed and therefore are not curated

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Microterricola viridarii strain DSM 21772

Microterricola viridarii strain DSM 21772

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