Archive BacDiveID:10.13145/bacdive506.20230509.8.1

Strain identifier

BacDive ID: 506

Type strain:

Species: Ornatilinea apprima

Strain Designation: P3M-1

Strain history: <- O. A. Podosocorskaya, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; P3M-1 <- O. A. Podosokorskaya {2009}

NCBI tax ID(s): 1134406 (species)

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

General

@ref: 17386

BacDive-ID: 506

DSM-Number: 23815

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative

description: Ornatilinea apprima P3M-1 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from microbial mat in a wooden bath filled with hot water from a 2775 m-deep well.

NCBI tax id

NCBI tax id: 1134406
Matching level: species

strain history

@ref: 17386
history: <- O. A. Podosocorskaya, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; P3M-1 <- O. A. Podosokorskaya {2009}

doi: 10.13145/bacdive506.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/chloroflexota
domain: Bacteria
phylum: Chloroflexota
class: Anaerolineae
order: Anaerolineales
family: Anaerolineaceae
genus: Ornatilinea
species: Ornatilinea apprima
full scientific name: Ornatilinea apprima Podosokorskaya et al. 2013

@ref: 17386

domain: Bacteria

phylum: Chloroflexi

class: Anaerolineae

order: Anaerolineales

family: Anaerolineaceae

genus: Ornatilinea

species: Ornatilinea apprima

full scientific name: Ornatilinea apprima Podosokorskaya et al. 2013

strain designation: P3M-1

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	motility	cell shape
30646	negative	200 µm	0.5 µm	no
26977	negative		0.3-0.7 µm		filament-shaped

pigmentation

@ref: 30646
production: no

Culture and growth conditions

culture medium

@ref: 17386
name: ANAEROLINEA MEDIUM (DSMZ Medium 1004)
growth: yes
link: https://mediadive.dsmz.de/medium/1004
composition: Name: ANAEROLINEA MEDIUM (DSMZ Medium 1004; with strain-specific modifications) Composition: NaHCO3 2.49252 g/l Yeast extract 2.29312 g/l Cellobiose 1.99402 g/l NH4Cl 0.538385 g/l Na2S x 9 H2O 0.249252 g/l L-Cysteine HCl x H2O 0.249252 g/l MgCl2 x 6 H2O 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l KH2PO4 0.139581 g/l Na2-EDTA x 2 H2O 0.00518445 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 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 (DL)-alpha-Lipoic acid 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 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
17386	positive	growth	42	thermophilic
30646	positive	growth	20-50
30646	positive	optimum	43.5	thermophilic
26977	positive	optimum	42-45	thermophilic
26977	positive	growth	20-50

culture pH

@ref	ability	type	pH	PH range
30646	positive	growth	6.5-9	alkaliphile
30646	positive	optimum	7.75
26977	positive	growth	6.5-9.0
26977	positive	optimum	7.5-8.0

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance
17386	anaerobe
30646	anaerobe
26977	obligate anaerobe

spore formation

@ref	spore formation
30646	no
26977	no

halophily

@ref	salt	growth	tested relation	concentration
30646	NaCl	positive	growth	0-2 %
30646	NaCl	positive	optimum	1 %
26977	NaCl	positive	growth	0-2 %(w/v)
26977	NaCl	positive	optimum	0.1 %(w/v)

observation

@ref: 26977
observation: doubling time of 6h

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
30646	17057	cellobiose	+	carbon source
30646	17234	glucose	+	carbon source
30646	17306	maltose	+	carbon source
30646	17992	sucrose	+	carbon source
30646	18222	xylose	+	carbon source
26977	30089	acetate	-	growth
26977		amorphous iron (iii) oxide	-	electron acceptor
26977	22599	arabinose	-	growth
26977		beef extract	+	growth
26977		casein hydrolysate	+	growth
26977	17057	cellobiose	+	growth
26977	62968	cellulose	+	growth
26977	17029	chitin	-	growth
26977	33403	elemental sulfur	-	electron acceptor
26977	16236	ethanol	-	growth
26977	28757	fructose	-	growth
26977	28260	galactose	-	growth
26977	17234	glucose	+	growth
26977	17754	glycerol	-	growth
26977	24996	lactate	-	growth
26977	17306	maltose	+	growth
26977	17632	nitrate	-	electron acceptor
26977	17309	pectin	-	growth
26977		peptone	-	growth
26977	15361	pyruvate	-	growth
26977	28017	starch	-	growth
26977	17992	sucrose	+	growth
26977	16189	sulfate	-	electron acceptor
26977	17359	sulfite	-	electron acceptor
26977	16094	thiosulfate	-	electron acceptor
26977	37166	xylan	-	growth
26977	18222	xylose	+	growth
26977		yeast extract (0.01 %, w/v)	+	required for growth

metabolite production

@ref	Chebi-ID	metabolite	production
26977	30089	acetate	yes
26977	16236	ethanol	yes
26977	15740	formate	yes
26977	24996	lactate	yes
26977	15361	pyruvate	no
26977	30031	succinate	no

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
17386	microbial mat in a wooden bath filled with hot water from a 2775 m-deep well	Tomsk region	Russia	RUS	Asia
26977	microbial mat that had formed in a wooden bath filled with hot water from a 2775 m deep well	Tomsk region in Siberia	Russia	RUS	Asia

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic
#Environmental	#Microbial community	#Microbial mat
#Condition	#Thermophilic (>45°C)
#Environmental	#Biofilm
#Engineered	#Built environment	#Water reservoir (Aquarium/pool)

taxonmaps

@ref: 69479
File name: preview.99_8125.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_693;96_3748;97_4608;98_5916;99_8125&stattab=map
Last taxonomy: Ornatilinea apprima subclade
16S sequence: JQ292916
Sequence Identity:
Total samples: 848
soil counts: 80
aquatic counts: 620
animal counts: 111
plant counts: 37

Safety information

risk assessment

@ref: 17386
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 26977
description: 16S rRNA
accession: JQ292916
database: nuccore

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Ornatilinea apprima P3M-1	GCA_001306115	contig	ncbi	1134406
66792	Ornatilinea apprima strain P3M-1	1134406.9	wgs	patric	1134406

GC content

@ref	GC-content	method
17386	55	sequence analysis
30646	55
26977	55	genome sequence analysis

Genome-based predictions

predictions

trait	prediction	confidence	training_data
motile	no	58.729	yes
flagellated	no	87.731	yes
gram-positive	no	94.527	yes
anaerobic	yes	94.498	yes
aerobic	no	95.074	yes
halophile	no	93.545	no
spore-forming	no	82.618	yes
thermophile	yes	98.908	yes
glucose-util	yes	84.984	yes
glucose-ferment	no	63.588	no

External links

@ref: 17386

culture collection no.: DSM 23815, VKM B-2669

straininfo link

@ref: 70185
straininfo: 405567

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	22328612	Ornatilinea apprima gen. nov., sp. nov., a cellulolytic representative of the class Anaerolineae.	Podosokorskaya OA, Bonch-Osmolovskaya EA, Novikov AA, Kolganova TV, Kublanov IV	Int J Syst Evol Microbiol	10.1099/ijs.0.041012-0	2012	Bacterial Typing Techniques, Base Composition, Cellulose/metabolism, Chloroflexi/classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fermentation, Hot Temperature, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, *Water Microbiology	Stress
Genetics	26586890	Draft Genome Sequence of Ornatilinea apprima P3M-1, an Anaerobic Member of the Chloroflexi Class Anaerolineae.	Hemp J, Ward LM, Pace LA, Fischer WW	Genome Announc	10.1128/genomeA.01353-15	2015
Phylogeny	26637817	Isolation and characterization of Flexilinea flocculi gen. nov., sp. nov., a filamentous, anaerobic bacterium belonging to the class Anaerolineae in the phylum Chloroflexi.	Sun L, Toyonaga M, Ohashi A, Matsuura N, Tourlousse DM, Meng XY, Tamaki H, Hanada S, Cruz R, Yamaguchi T, Sekiguchi Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.000822	2015

Reference

@id	authors	catalogue	doi/url	title	pubmed	ID_cross_reference	journal
17386	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23815)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-23815
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
26977			10.1099/ijs.0.041012-0		22328612
30646	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	28776041	26977
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	33211880		Nucleic Acids Res. 49: D498-D508 2020
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
70185	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID405567.1	StrainInfo: A central database for resolving microbial strain identifiers