Archive BacDiveID:10.13145/bacdive3846.20230509.8.1

Strain identifier

BacDive ID: 3846

Type strain:

Species: Calditerrivibrio nitroreducens

Strain Designation: Yu37-1

Strain history: <- T. Iino; Yu37-1 {2005}

NCBI tax ID(s): 768670 (strain), 477976 (species)

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

General

@ref: 8246

BacDive-ID: 3846

DSM-Number: 19672

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

description: Calditerrivibrio nitroreducens Yu37-1 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from terrestrial hot spring.

NCBI tax id

NCBI tax id	Matching level
477976	species
768670	strain

strain history

@ref: 8246
history: <- T. Iino; Yu37-1 {2005}

doi: 10.13145/bacdive3846.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/deferribacterota
domain: Bacteria
phylum: Deferribacterota
class: Deferribacteres
order: Deferribacterales
family: Deferribacteraceae
genus: Calditerrivibrio
species: Calditerrivibrio nitroreducens
full scientific name: Calditerrivibrio nitroreducens Iino et al. 2008

@ref: 8246

domain: Bacteria

phylum: Deferribacteres

class: Deferribacteres

order: Deferribacterales

family: Deferribacteraceae

genus: Calditerrivibrio

species: Calditerrivibrio nitroreducens

full scientific name: Calditerrivibrio nitroreducens Iino et al. 2008

strain designation: Yu37-1

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
32572	negative	1.4-2 µm	0.4-0.5 µm	ovoid-shaped	yes
69480	negative					99.982

pigmentation

@ref: 32572
production: yes

multimedia

@ref: 66793
multimedia content: EM_DSM_19672_1.jpg
caption: electron microscopic image
intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@ref: 8246
name: CALDITERRIVIBRIO MEDIUM (DSMZ Medium 1112)
growth: yes
link: https://mediadive.dsmz.de/medium/1112
composition: Name: CALDITERRIVIBRIO MEDIUM (DSMZ Medium 1112) Composition: Na2CO3 0.997009 g/l NaNO3 0.847458 g/l Na-acetate 0.817547 g/l NH4Cl 0.538385 g/l Na2S x 9 H2O 0.498504 g/l MgCl2 x 6 H2O 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l KH2PO4 0.139581 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 (DL)-alpha-Lipoic acid 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 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	confidence
8246	positive	growth	55	thermophilic
32572	positive	growth	30-65
32572	positive	optimum	55	thermophilic
69480				thermophilic	99.999

culture pH

@ref	ability	type	pH
32572	positive	growth	5.5-8
32572	positive	optimum	7-7.5

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
8246	anaerobe
32572	anaerobe
69480	anaerobe	100

spore formation

@ref	spore formation	confidence
32572	no
69481	no	100
69480	no	99.082

halophily

@ref	salt	growth	tested relation	concentration
32572	NaCl	positive	growth	0-0.5 %
32572	NaCl	positive	optimum	0-0.5 %

observation

@ref: 32572
observation: aggregates in chains

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
32572	30089	acetate	+	carbon source
32572	24996	lactate	+	carbon source
32572	25115	malate	+	carbon source
32572	15361	pyruvate	+	carbon source
32572	30031	succinate	+	carbon source

Isolation, sampling and environmental information

isolation

@ref: 8246
sample type: terrestrial hot spring
geographic location: Nagano, Yumata
country: Japan
origin.country: JPN
continent: Asia

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Thermal spring
#Environmental	#Terrestrial
#Condition	#Thermophilic (>45°C)

taxonmaps

@ref: 69479
File name: preview.99_1404.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16333;96_813;97_947;98_1111;99_1404&stattab=map
Last taxonomy: Calditerrivibrio nitroreducens subclade
16S sequence: AB364234
Sequence Identity:
Total samples: 242
soil counts: 8
aquatic counts: 198
animal counts: 35
plant counts: 1

Safety information

risk assessment

@ref: 8246
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 8246
description: Calditerrivibrio nitroreducens gene for 16S rRNA, partial sequence
accession: AB364234
length: 1487
database: ena
NCBI tax ID: 768670

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Calditerrivibrio nitroreducens DSM 19672	GCA_000183405	complete	ncbi	768670
66792	Calditerrivibrio nitroreducens DSM 19672	768670.24	plasmid	patric	768670
66792	Calditerrivibrio nitroreducens DSM 19672	768670.3	complete	patric	768670
66792	Calditerrivibrio nitroreducens Yu37-1, DSM 19672	649633026	complete	img	768670

GC content

@ref	GC-content	method
8246	35.6	sequence analysis
32572	35.1

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	yes	90.436	yes
flagellated	no	79.32	no
gram-positive	no	99.502	yes
anaerobic	yes	100	no
aerobic	no	99.385	yes
halophile	no	91.607	yes
spore-forming	no	95.87	yes
thermophile	yes	98.993	yes
glucose-util	no	69.772	no
glucose-ferment	no	86.367	no

External links

@ref: 8246

culture collection no.: DSM 19672, NBRC 101217

straininfo link

@ref: 73356
straininfo: 400608

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	18599715	Calditerrivibrio nitroreducens gen. nov., sp. nov., a thermophilic, nitrate-reducing bacterium isolated from a terrestrial hot spring in Japan.	Iino T, Nakagawa T, Mori K, Harayama S, Suzuki K	Int J Syst Evol Microbiol	10.1099/ijs.0.65714-0	2008	Bacteria/classification/genetics/isolation & purification/ultrastructure, Hot Springs/microbiology, Japan, Microscopy, Electron, Transmission, Molecular Sequence Data, Nitrates/metabolism, RNA, Ribosomal, 16S/genetics, Species Specificity	Genetics
Genetics	21475587	Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1).	Pitluck S, Sikorski J, Zeytun A, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Liolios K, Pagani I, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Djao OD, Rohde M, Spring S, Goker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M	Stand Genomic Sci	10.4056/sigs.1523807	2011
Phylogeny	24053548	A thermophilic gram-negative nitrate-reducing bacterium, Calditerrivibrio nitroreducens, exhibiting electricity generation capability.	Fu Q, Kobayashi H, Kawaguchi H, Wakayama T, Maeda H, Sato K	Environ Sci Technol	10.1021/es402749f	2013	Bacteriological Techniques, Bioelectric Energy Sources/microbiology, Gram-Negative Bacteria/classification/genetics/physiology/ultrastructure, Nitrates/metabolism, Sewage/microbiology	Metabolism

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed	journal
8246	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19672)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-19672
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
32572	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	28787	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)
66793	Mukherjee et al.		10.1038/nbt.3886	GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life		28604660	35: 676-683 2017
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
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
73356	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID400608.1	StrainInfo: A central database for resolving microbial strain identifiers