Archive BacDiveID:10.13145/bacdive11301.20230509.8.1

Strain identifier

BacDive ID: 11301

Type strain:

Species: Opitutus terrae

Strain Designation: PB90-1

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

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

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 4257

BacDive-ID: 11301

DSM-Number: 11246

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

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

NCBI tax id

NCBI tax id	Matching level
452637	strain
107709	species

strain history

@ref	history
4257	<- K.-J. Chin, Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, Germany; PB90-1 <- K.-J. Chin {1994}
67770	DSM 11246 <-- K.-J. Chin PB90-1.

doi: 10.13145/bacdive11301.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/verrucomicrobiota
domain: Bacteria
phylum: Verrucomicrobiota
class: Opitutia
order: Opitutales
family: Opitutaceae
genus: Opitutus
species: Opitutus terrae
full scientific name: Opitutus terrae Chin et al. 2001

@ref: 4257

domain: Bacteria

phylum: Verrucomicrobia

class: Opitutae

order: Opitutales

family: Opitutaceae

genus: Opitutus

species: Opitutus terrae

full scientific name: Opitutus terrae Chin et al. 2001 emend. Hahnke et al. 2016 emend. Tegtmeier et al. 2018

strain designation: PB90-1

type strain: yes

Morphology

colony morphology

@ref: 4257
incubation period: 8-14 days

Culture and growth conditions

culture medium

@ref: 4257
name: OPITUTUS MEDIUM (DSMZ Medium 295)
growth: yes
link: https://mediadive.dsmz.de/medium/295
composition: Name: OPITUTUS MEDIUM (DSMZ Medium 295) Composition: NaCl 0.997009 g/l Na2CO3 0.997009 g/l D-Glucose 0.997009 g/l NaNO3 0.797607 g/l KCl 0.498504 g/l MgCl2 x 6 H2O 0.398804 g/l L-Cysteine HCl x H2O 0.299103 g/l NH4Cl 0.249252 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
4257	positive	growth	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

oxygen tolerance

@ref: 4257
oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
4257	anoxic rice paddy soil	Vercelli	Italy	ITA	Europe
67770	Anoxic rice paddy soil sample

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Condition	#Anoxic (anaerobic)

taxonmaps

@ref: 69479
File name: preview.99_6944.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_382;96_3265;97_4004;98_5108;99_6944&stattab=map
Last taxonomy: Opitutus terrae subclade
16S sequence: AJ229235
Sequence Identity:
Total samples: 5688
soil counts: 1953
aquatic counts: 3265
animal counts: 289
plant counts: 181

Safety information

risk assessment

@ref: 4257
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
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
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
4257	Opitutus terrae 16S rRNA gene, strain PB90-1	AJ229235	1480	ena	452637

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Opitutus terrae PB90-1	GCA_000019965	complete	ncbi	452637
66792	Opitutus terrae PB90-1	452637.7	complete	patric	452637
66792	Opitutus terrae PB90-1	641522643	complete	img	452637

GC content

@ref	GC-content	method
4257	65.3	sequence analysis
4257	74	high performance liquid chromatography (HPLC)
67770	73.7	high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
motile	yes	73.765	no
flagellated	no	79.209	no
gram-positive	no	98.773	no
anaerobic	no	74.27	yes
aerobic	no	66.842	yes
halophile	no	88.391	no
spore-forming	no	95.721	no
thermophile	no	95.099	yes
glucose-util	yes	90.137	no
glucose-ferment	no	75.857	no

External links

@ref: 4257

culture collection no.: DSM 11246, JCM 15787

straininfo link

@ref: 80534
straininfo: 49055

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	11760935	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	Bacteria, Anaerobic/classification/genetics/isolation & purification/physiology, DNA, Ribosomal/genetics, Genes, rRNA, Molecular Sequence Data, Oryza, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology	Genetics
Metabolism	11916740	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	Anaerobiosis, Bacteria/growth & development/metabolism, Culture Media, Glucose/metabolism, Hydrogen/metabolism, Methanospirillum/growth & development/metabolism, Oryza, Pectins/metabolism, Propionates/metabolism, Soil Microbiology	Cultivation
Phylogeny	17329779	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	Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Gram-Negative Bacteria/classification/genetics/metabolism, Molecular Sequence Data, Polychaeta/microbiology, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology	Genetics
Genetics	21398538	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	Bacteria/classification/genetics, Ecosystem, Genome, Bacterial, Molecular Sequence Data, Oryza/physiology, Soil Microbiology	Phylogeny
	28243229	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
Phylogeny	29461179	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
Phylogeny	30575499	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	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/microbiology, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Verrucomicrobia/*classification/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry	Transcriptome
Phylogeny	36209171	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	Amino Acids, Bacterial Typing Techniques, DDT, DNA, Bacterial/genetics, Fatty Acids/chemistry, Insecticides, Phylogeny, Quinones, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride, Soil, Terpenes, Verrucomicrobia/genetics, Vitamin K 2/chemistry	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
4257	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11246)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-11246
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	Nucleic Acids Res. 49: D498-D508 2020	33211880
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
80534	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID49055.1	StrainInfo: A central database for resolving microbial strain identifiers