Name: Opitutus terrae PB90-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11301

Type strain:

Species: Opitutus terrae

Strain Designation: PB90-1

Culture col. no.: DSM 11246, JCM 15787

Strain history: DSM 11246 <-- K.-J. Chin PB90-1.

NCBI tax ID(s): 452637 (strain), 107709 (species)

SI-ID 49055

DSM 11246, JCM 15787

Other strains from Opitutus terrae

O. terrae ACB90, DSM 11249

Section

Opitutus terrae PB90-1 is an anaerobe, mesophilic bacterium that was isolated from anoxic rice paddy soil.

anaerobe
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	*Verrucomicrobiota*
	Class	*Opitutia*
	Order	*Opitutales*
	Family	*Opitutaceae*
	Genus	*Opitutus*
	Species	**Opitutus terrae**
	Full Scientific Name (LPSN)	Opitutus terrae Chin et al. 2001

Information on morphological and physiological properties Morphology

[Ref.: #4257]

Incubation period

8-14 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4257]

Culture medium

OPITUTUS MEDIUM (DSMZ Medium 295)

[Ref.: #4257]

Culture medium growth

[Ref.: #4257]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4257]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4257]			growth	28 °C
[Ref.: #67770]			growth	28 °C

[Ref.: #4257]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #4257]

Oxygen tolerance

anaerobe

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	glycogen biosynthesis	100	4 of 4
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	pyrimidine metabolism	86.67	39 of 45
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	purine metabolism	85.11	80 of 94
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	degradation of pentoses	71.43	20 of 28
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	ascorbate metabolism	59.09	13 of 22
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	oxidative phosphorylation	53.85	49 of 91
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ppGpp biosynthesis	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	degradation of sugar acids	48	12 of 25
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	vitamin B1 metabolism	38.46	5 of 13
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	vitamin B12 metabolism	26.47	9 of 34
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	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.: #4257]	Sample type/isolated from	anoxic rice paddy soil
[Ref.: #4257]	Geographic location (country and/or sea, region)	Vercelli
[Ref.: #4257]	Country	Italy
[Ref.: #4257]	Country ISO 3 Code	ITA
[Ref.: #4257]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Anoxic rice paddy soil sample
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Condition	#Anoxic (anaerobic)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ229235 (>99% sequence identity) for Opitutus terrae subclade from Microbeatlas

Aquatic Samples	3265
Soil Samples	1953
Animal Samples	289
Plant Samples	181
Total Samples	5688

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

[Ref.: #4257]

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.: #4257]	Opitutus terrae 16S rRNA gene, strain PB90-1	AJ229235	1480	ENA	452637 tax ID
[Ref.: #20218]	Opitutus terrae 16S rRNA gene (partial), 23S rRNA gene, tRNA-Ala gene, tRNA-Ile gene, ITS1 and ITS2, strain DSM 11246	AJ966884	3576	ENA	107709 tax ID	*
[Ref.: #20218]	Opitutus sp. VeGlc2 16S rRNA gene (partial), 23S rRNA gene, tRNA-Ala gene, tRNA-Ile gene, ITS1 and ITS2, strain DSM 11246	AJ966885	3908	ENA	134634 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Opitutus terrae PB90-1	GCA_000019965	complete	GenBank	452637 tax ID	*
[Ref.: #66792]	Opitutus terrae PB90-1	452637.7	complete	PATRIC	452637 tax ID	*
[Ref.: #66792]	Opitutus terrae PB90-1	641522643	complete	JGI IMG/M	452637 tax ID	*

[Ref.: #4257]	GC-content	65.3 mol%	sequence analysis
[Ref.: #4257]	GC-content	74 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	73.7 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 Diaspora project based on: Opitutus terrae PB90-1 PB90-1 NCBI: GCA_000019965.1
[Ref.: #69480]	motile	yes	73.765	no
[Ref.: #69480]	flagellated	no	79.209	no
[Ref.: #69480]	gram-positive	no	98.773	no
[Ref.: #69480]	anaerobic	no	74.27	yes
[Ref.: #69480]	aerobic	no	66.842	yes
[Ref.: #69480]	halophile	no	88.391	no
[Ref.: #69480]	spore-forming	no	95.721	no
[Ref.: #69480]	thermophile	no	95.099	yes
[Ref.: #69480]	glucose-util	yes	90.137	no
[Ref.: #69480]	glucose-ferment	no	75.857	no

Availability in culture collections External links

[Ref.: #4257]

Culture collection no.

DSM 11246, JCM 15787

[Ref.: #80534]

SI-ID 49055

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nibricoccus aquaticus gen. nov., sp. nov., a new genus of the family Opitutaceae isolated from hyporheic freshwater.	Baek K, Song J, Cho JC, Chung EJ, Choi A	Int J Syst Evol Microbiol	10.1099/ijsem.0.003198	2018	*
Phylogeny	Oleiharenicola alkalitolerans gen. nov., sp. nov., a new member of the phylum Verrucomicrobia isolated from an oilsands tailings pond.	Rochman FF, Kim JJ, Rijpstra WIC, Sinninghe Damste JS, Schumann P, Verbeke TJ, Dunfield PF	Int J Syst Evol Microbiol	10.1099/ijsem.0.002624	2018	*
Genetics	Genome sequence of the verrucomicrobium Opitutus terrae PB90-1, an abundant inhabitant of rice paddy soil ecosystems.	van Passel MW, Kant R, Palva A, Copeland A, Lucas S, Lapidus A, Glavina del Rio T, Pitluck S, Goltsman E, Clum A, Sun H, Schmutz J, Larimer FW, Land ML, Hauser L, Kyrpides N, Mikhailova N, Richardson PP, Janssen PH, de Vos WM, Smidt H	J Bacteriol	10.1128/JB.00228-11	2011	*
Phylogeny	Puniceicoccus vermicola gen. nov., sp. nov., a novel marine bacterium, and description of Puniceicoccaceae fam. nov., Puniceicoccales ord. nov., Opitutaceae fam. nov., Opitutales ord. nov. and Opitutae classis nov. in the phylum 'Verrucomicrobia'.	Choo YJ, Lee K, Song J, Cho JC	Int J Syst Evol Microbiol	10.1099/ijs.0.64616-0	2007	*
Metabolism	Propionate formation by Opitutus terrae in pure culture and in mixed culture with a hydrogenotrophic methanogen and implications for carbon fluxes in anoxic rice paddy soil.	Chin KJ, Janssen PH	Appl Environ Microbiol	10.1128/AEM.68.4.2089-2092.2002	2002	*
Phylogeny	Opitutus terrae gen. nov., sp. nov., to accommodate novel strains of the division 'Verrucomicrobia' isolated from rice paddy soil.	Chin KJ, Liesack W, Janssen PH	Int J Syst Evol Microbiol	10.1099/00207713-51-6-1965	2001	*
Phylogeny	Horticoccus luteus gen. nov., sp. nov., A Novel Member of the Phylum Verrucomicrobia Isolated from a Dichlorodiphenyltrichloroethane (DDT)-Contaminated Orchard Soil.	Chung JH, Lee JY, Choi GH, Won M, Yeon J, Yoon Y, An SH, Kim DY, Park I, Kim YE, Ahn JH	Curr Microbiol	10.1007/s00284-022-03036-8	2022	*
	Three Novel Species with Peptidoglycan Cell Walls form the New Genus Lacunisphaera gen. nov. in the Family Opitutaceae of the Verrucomicrobial Subdivision 4.	Rast P, Glockner I, Boedeker C, Jeske O, Wiegand S, Reinhardt R, Schumann P, Rohde M, Spring S, Glockner FO, Jogler C, Jogler M	Front Microbiol	10.3389/fmicb.2017.00202	2017	*

References

#4257

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11246

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#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) .

#80534

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-ID49055.1 )

* These data were automatically processed and therefore are not curated

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Opitutus terrae PB90-1 PB90-1

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