Archive BacDiveID:10.13145/bacdive17640.20230509.8.1

Strain identifier

BacDive ID: 17640

Type strain:

Species: Balnearium lithotrophicum

Strain Designation: 17S

Strain history: K. Takai 17S.

NCBI tax ID(s): 223788 (species)

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

General

@ref: 6353

BacDive-ID: 17640

DSM-Number: 16304

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, motile, rod-shaped

description: Balnearium lithotrophicum 17S is an anaerobe, spore-forming, thermophilic bacterium that was isolated from deep-sea hydrothermal vent, 1385 m depth.

NCBI tax id

NCBI tax id: 223788
Matching level: species

strain history

@ref	history
6353	<- JCM <- K. Takai; 17S
67770	K. Takai 17S.

doi: 10.13145/bacdive17640.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/aquificota
domain: Bacteria
phylum: Aquificota
class: Aquificia
order: Desulfurobacteriales
family: Desulfurobacteriaceae
genus: Balnearium
species: Balnearium lithotrophicum
full scientific name: Balnearium lithotrophicum Takai et al. 2003

@ref: 6353

domain: Bacteria

phylum: Aquificae

class: Aquificae

order: Aquificales

family: Desulfurobacteriaceae

genus: Balnearium

species: Balnearium lithotrophicum

full scientific name: Balnearium lithotrophicum Takai et al. 2003

strain designation: 17S

type strain: yes

Morphology

cell morphology

@ref	cell length	cell width	cell shape	motility	confidence	gram stain
29984	1.5-3.5 µm	0.7-1 µm	rod-shaped	yes
69480				yes	92.823
69480					100	negative

Culture and growth conditions

culture medium

@ref: 6353
name: DESULFUROBACTERIUM CRINIFEX MEDIUM (DSMZ Medium 829c)
growth: yes
link: https://mediadive.dsmz.de/medium/829c
composition: Name: DESULFUROBACTERIUM CRINIFEX MEDIUM (DSMZ Medium 829c) Composition: Sea Salt 29.6736 g/l Sulfur 9.8912 g/l MES [2-(N-morpholino) ethane sulfonic acid] 1.92878 g/l NH4Cl 0.98912 g/l Na2S x 9 H2O 0.49456 g/l Na2CO3 0.49456 g/l KH2PO4 0.346192 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l CoSO4 x 7 H2O 0.00178042 g/l ZnSO4 x 7 H2O 0.00178042 g/l FeSO4 x 7 H2O 0.00098912 g/l CaCl2 x 2 H2O 0.00098912 g/l Sodium resazurin 0.00049456 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l CuSO4 x 5 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Biotin 1.97824e-05 g/l Folic acid 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range	confidence
6353	positive	growth	70	thermophilic
29984	positive	growth	35-65
29984	positive	optimum	55	thermophilic
67770	positive	growth	70	thermophilic
69480				thermophilic	99.999

culture pH

@ref	ability	type	pH
29984	positive	growth	4.9-7.2
29984	positive	optimum	5.9

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
6353	anaerobe
29984	anaerobe
69480	anaerobe	99.998

spore formation

@ref	spore formation	confidence
69481	yes	98
69480	no	99.896

halophily

@ref	salt	growth	tested relation	concentration
29984	NaCl	positive	growth	1.6-5.6 %
29984	NaCl	positive	optimum	3.2 %

metabolite production

@ref: 29984
Chebi-ID: 16136
metabolite: hydrogen sulfide
production: yes

enzymes

@ref: 29984
value: cytochrome oxidase
activity: +
ec: 1.9.3.1

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent	latitude	longitude
6353	deep-sea hydrothermal vent, 1385 m depth	Suiyo Seamount in the Izu-Bonin Arc	Japan	JPN	Asia	28.5667	140.633
67770	Deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc		Japan	JPN	Asia

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine
#Condition	#Thermophilic (>45°C)

taxonmaps

@ref: 69479
File name: preview.99_44500.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_243;96_20471;97_25467;98_32290;99_44500&stattab=map
Last taxonomy: Balnearium lithotrophicum subclade
16S sequence: AB105049
Sequence Identity:
Total samples: 30
aquatic counts: 30

Safety information

risk assessment

@ref: 6353
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 6353
description: Balnearium lithotrophicum rrn gene for 16S rRNA, partial sequence
accession: AB105049
length: 1481
database: ena
NCBI tax ID: 223788

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Balnearium lithotrophicum DSM 16304	GCA_900182585	scaffold	ncbi	223788
66792	Balnearium lithotrophicum strain DSM 16304	223788.3	wgs	patric	223788
66792	Balnearium lithotrophicum DSM 16304	2724679708	draft	img	223788

GC content

@ref	GC-content	method
6353	34.6
67770	34.6	high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	98	no
motile	yes	86.834	yes
flagellated	no	92.136	no
gram-positive	no	99.445	no
anaerobic	yes	98.548	no
aerobic	no	98.677	yes
halophile	no	82.801	no
spore-forming	no	95.558	no
thermophile	yes	100	yes
glucose-util	no	59.358	no
glucose-ferment	no	79.927	no

External links

@ref: 6353

culture collection no.: DSM 16304, ATCC BAA 736, JCM 11970

straininfo link

@ref: 86632
straininfo: 127982

literature

topic: Phylogeny
Pubmed-ID: 14657128
title: Balnearium lithotrophicum gen. nov., sp. nov., a novel thermophilic, strictly anaerobic, hydrogen-oxidizing chemolithoautotroph isolated from a black smoker chimney in the Suiyo Seamount hydrothermal system.
authors: Takai K, Nakagawa S, Sako Y, Horikoshi K
journal: Int J Syst Evol Microbiol
DOI: 10.1099/ijs.0.02773-0
year: 2003
mesh: Bacteria/*classification/genetics/growth & development/isolation & purification, Hot Temperature, Japan, Microscopy, Electron, Molecular Sequence Data, *Phylogeny, *Smoke
topic2: Stress

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
6353	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16304)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-16304
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
29984	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	26351	28776041
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)
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
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
86632	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID127982.1	StrainInfo: A central database for resolving microbial strain identifiers