Archive BacDiveID:10.13145/bacdive5451.20240916.9.1

Strain identifier

BacDive ID: 5451

Type strain:

Species: Garciella nitratireducens

Strain history: <- B. Ollivier, IRD, Marseille; MET79 <- E. Miranda-Tello {2000}

NCBI tax ID(s): 1121911 (strain), 218205 (species)

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

General

@ref: 5713

BacDive-ID: 5451

DSM-Number: 15102

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming

description: Garciella nitratireducens DSM 15102 is an anaerobe, spore-forming bacterium that was isolated from separator tank.

NCBI tax id

NCBI tax id	Matching level
1121911	strain
218205	species

strain history

@ref: 5713
history: <- B. Ollivier, IRD, Marseille; MET79 <- E. Miranda-Tello {2000}

doi: 10.13145/bacdive5451.20240916.9.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Clostridia
order: Eubacteriales
family: Eubacteriaceae
genus: Garciella
species: Garciella nitratireducens
full scientific name: Garciella nitratireducens Miranda-Tello et al. 2003

@ref: 5713

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Garciella

species: Garciella nitratireducens

full scientific name: Garciella nitratireducens Miranda-Tello et al. 2003

type strain: yes

Culture and growth conditions

culture medium

@ref: 5713
name: DESULFOBACTER MEDIUM (DSMZ Medium 193)
growth: yes
link: https://mediadive.dsmz.de/medium/193
composition: Name: DESULFOBACTER MEDIUM (DSMZ Medium 193; with strain-specific modifications) Composition: NaCl 6.97906 g/l D-Glucose 3.48953 g/l Na2SO4 2.99102 g/l Na2CO3 1.49551 g/l MgCl2 x 6 H2O 1.29611 g/l Yeast extract 0.997009 g/l KCl 0.498505 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299102 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149552 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 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 (DL)-alpha-Lipoic acid 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 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 Biotin 1.99402e-05 g/l Folic acid 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: 5713
growth: positive
type: growth
temperature: 55

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
5713	anaerobe
69480	anaerobe	92.276

spore formation

@ref: 69481
spore formation: yes
confidence: 100

Isolation, sampling and environmental information

isolation

@ref: 5713
sample type: separator tank
geographic location: Gulf of Mexico, Tabasco, SAMIII oilfield
country: Mexico
origin.country: MEX
continent: North America

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Industrial	#Engineered product
#Engineered	#Industrial	#Oil reservoir

taxonmaps

@ref: 69479
File name: preview.99_11521.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1342;96_5799;97_6974;98_8629;99_11521&stattab=map
Last taxonomy: Garciella nitratireducens subclade
16S sequence: AY176772
Sequence Identity:
Total samples: 34
soil counts: 2
aquatic counts: 12
animal counts: 19
plant counts: 1

Safety information

risk assessment

@ref: 5713
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 5713
description: Garciaella petrolearia strain Met 79 16S ribosomal RNA gene, partial sequence
accession: AY176772
length: 1471
database: nuccore
NCBI tax ID: 218205

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Garciella nitratireducens DSM 15102	GCA_900167305	scaffold	ncbi	1121911
66792	Garciella nitratireducens DSM 15102 strain DSM 15102	1121911.3	wgs	patric	1121911
66792	Garciella nitratireducens DSM 15102	2568526006	draft	img	1121911

GC content

@ref: 5713
GC-content: 30.9
method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@ref	trait	model	description	prediction	confidence	training_data
69481	spore-forming	spore-forming	Ability to form endo- or exospores	yes	100	no
69480	gram-positive	gram-positive	Positive reaction to Gram-staining	yes	73.229	no
69480	anaerobic	anaerobic	Ability to grow under anoxygenic conditions (including facultative anaerobes)	yes	92.276	yes
69480	aerobic	aerobic	Ability to grow under oxygenic conditions (including facultative aerobes)	no	98.596	no
69480	spore-forming	spore-forming	Ability to form endo- or exospores	yes	62.989	no
69480	thermophilic	thermophile	Ability to grow at temperatures above or equal to 45°C	yes	60.666	yes
69480	flagellated	motile2+	Ability to perform flagellated movement	yes	71.422	no

External links

@ref: 5713

culture collection no.: DSM 15102, CIP 107615, MET 79

straininfo link

@ref: 74939
straininfo: 97650

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	13130040	Garciella nitratireducens gen. nov., sp. nov., an anaerobic, thermophilic, nitrate- and thiosulfate-reducing bacterium isolated from an oilfield separator in the Gulf of Mexico.	Miranda-Tello E, Fardeau ML, Sepulveda J, Fernandez L, Cayol JL, Thomas P, Ollivier B	Int J Syst Evol Microbiol	10.1099/ijs.0.02662-0	2003	Anaerobiosis, Base Composition, Base Sequence, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fuel Oils, Gram-Positive Rods/classification/genetics/isolation & purification/metabolism, Hot Temperature, Mexico, Microscopy, Electron, Scanning, Molecular Sequence Data, Nitrates/metabolism, Oxidation-Reduction, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Thiosulfates/metabolism, Water Microbiology	Metabolism
Phylogeny	28945534	Rhabdanaerobium thermarum gen. nov., sp. nov., a novel anaerobic bacterium isolated from a hot spring.	Liu L, Jiao JY, Salam N, Zhou EM, Fang BZ, Xian WD, Li MM, Ding YP, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.002335	2017	Bacterial Typing Techniques, Base Composition, China, Clostridiales/classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hot Springs/microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
5713	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15102)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-15102
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
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
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
74939	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID97650.1	StrainInfo: A central database for resolving microbial strain identifiers